diff --git a/.github/workflows/n2p2-ci.yaml b/.github/workflows/n2p2-ci.yaml index 337709a65e..2aee0b310b 100644 --- a/.github/workflows/n2p2-ci.yaml +++ b/.github/workflows/n2p2-ci.yaml @@ -23,10 +23,12 @@ jobs: sudo apt install openmpi-bin libopenmpi-dev # BLAS sudo apt install libblas3 libblas-dev + # OpenBLAS + sudo apt install libopenblas0 libopenblas-dev # Eigen library sudo apt install libeigen3-dev # GSL library - sudo apt install libgsl-dev + sudo apt install libgsl-dev libgslcblas0 # Tests # Boost Test for C++ testing diff --git a/AUTHORS.rst b/AUTHORS.rst index a5993dccc9..abd8aff1a0 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -12,3 +12,4 @@ Contributions are much appreciated and will be recorded here: * Polynomial symmetry functions (`libnnp/Sym(Fnc/Grp)(Base)Comp...`): Martin P. Bircher and Andreas Singraber * 4G-HDNNP training/prediction implementation in n2p2: Philipp Misof +* 4G-HDNNP prediction implementation in LAMMPS+n2p2: Emir Kocer diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 963447327b..d2866c52cd 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -9,7 +9,8 @@ Version 3.0.0 - 2024-1?-?? New features ^^^^^^^^^^^^ -* 4G-HDNNPs training/prediction in n2p2. +* 4G-HDNNPs training/prediction in n2p2 (Philipp Misof). +* 4G-HDNNPs prediction in LAMMPS+n2p2 (Emir Kocer). Version 2.3.0 - 2024-11-23 -------------------------- diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/AlAuMgO.data b/examples/interface-LAMMPS/AlAuMgO_4G/AlAuMgO.data new file mode 100644 index 0000000000..585f7d9fe7 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/AlAuMgO.data @@ -0,0 +1,122 @@ +MgO with Al/Au, first structure from input.data (wrapped into box) + +110 atoms + +4 atom types + +0.0 1.7097166001000002E+01 xlo xhi +0.0 1.7097166001000002E+01 ylo yhi +0.0 5.0000000000999997E+01 zlo zhi + +Atoms + +1 2 0.0 1.7077390207502003E+01 1.7033133769712002E+01 2.0026111118999999E+01 +2 1 0.0 2.8784590472999998E+00 2.8904829958000002E+00 2.0053576907000000E+01 +3 1 0.0 7.2652159692999999E-02 1.7080954778737002E+01 2.4043132172000000E+01 +4 2 0.0 2.8780260733000000E+00 2.8998185634999998E+00 2.4032640394000001E+01 +5 2 0.0 1.7040370588769001E+01 1.7074725410399001E+01 2.8111288945999998E+01 +6 1 0.0 2.8421666140000004E+00 2.8834652149000006E+00 2.8032859288999997E+01 +7 1 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1.1412436308000000E+01 1.1399368513000002E+01 4.0122450030000003E+01 +108 2 0.0 1.4206953179000001E+01 1.4201432515000002E+01 4.0151366428999999E+01 +109 4 0.0 2.7674441650000001E+00 3.2676547854000000E+00 1.5266538963000000E+01 +110 4 0.0 2.7884963172999999E+00 3.1844017731000003E+00 1.0716139441999999E+01 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/AlAuMgO.data-n2p2 b/examples/interface-LAMMPS/AlAuMgO_4G/AlAuMgO.data-n2p2 new file mode 100644 index 0000000000..009c935ce2 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/AlAuMgO.data-n2p2 @@ -0,0 +1,125 @@ +MgO with Al/Au, first structure from input.data (wrapped into box) + +110 atoms + +4 atom types + +#0.0 1.7097166001000002E+01 xlo xhi +#0.0 1.7097166001000002E+01 ylo yhi +#0.0 5.0000000000999997E+01 zlo zhi +-1.0 1.6097166001000002E+01 xlo xhi +-1.0 1.6097166001000002E+01 ylo yhi +-1.0 4.0000000000999997E+01 zlo zhi + +Atoms + +1 2 0.0 -1.9775793498e-02 -6.4032231288e-02 2.0026111119e+01 +2 1 0.0 2.8784590473e+00 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4.0173253651e+01 +84 2 0.0 1.4256298422e+01 2.8717039194e+00 4.0140854601e+01 +85 2 0.0 1.1393721861e+01 5.7236951244e+00 2.0010035088e+01 +86 1 0.0 1.4257639788e+01 8.4981605285e+00 1.9925047364e+01 +87 1 0.0 1.1373306754e+01 5.7232945403e+00 2.3983895820e+01 +88 2 0.0 1.4251016393e+01 8.5961130012e+00 2.4011062539e+01 +89 2 0.0 1.1392303111e+01 5.6922237034e+00 2.8086502355e+01 +90 1 0.0 1.4307995467e+01 8.5052796177e+00 2.8127594522e+01 +91 1 0.0 1.1467787838e+01 5.7303018143e+00 3.2140124452e+01 +92 2 0.0 1.4223684114e+01 8.5394621152e+00 3.2083417385e+01 +93 2 0.0 1.1398360231e+01 5.6984501048e+00 3.6109137659e+01 +94 1 0.0 1.4243599161e+01 8.4926708934e+00 3.6111924268e+01 +95 1 0.0 1.1387116342e+01 5.7224672938e+00 4.0150551843e+01 +96 2 0.0 1.4251826367e+01 8.5541300360e+00 4.0169736719e+01 +97 2 0.0 1.1397087406e+01 1.1432029951e+01 1.9991521329e+01 +98 1 0.0 1.4222100486e+01 1.4237423386e+01 1.9890837446e+01 +99 1 0.0 1.1397172085e+01 1.1362254484e+01 2.4106729256e+01 +100 2 0.0 1.4223050564e+01 1.4272733426e+01 2.4026767277e+01 +101 2 0.0 1.1412415162e+01 1.1398466358e+01 2.8036581274e+01 +102 1 0.0 1.4265352610e+01 1.4216093689e+01 2.8052093903e+01 +103 1 0.0 1.1401696599e+01 1.1369599225e+01 3.2083243398e+01 +104 2 0.0 1.4233083328e+01 1.4215807831e+01 3.2083725032e+01 +105 3 0.0 1.1446195847e+01 1.1455486685e+01 3.6062830566e+01 +106 1 0.0 1.4275939497e+01 1.4231407235e+01 3.6076973257e+01 +107 1 0.0 1.1412436308e+01 1.1399368513e+01 4.0122450030e+01 +108 2 0.0 1.4206953179e+01 1.4201432515e+01 4.0151366429e+01 +109 4 0.0 2.7674441650e+00 3.2676547854e+00 1.5266538963e+01 +110 4 0.0 2.7884963173e+00 3.1844017731e+00 1.0716139442e+01 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.008.data b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.008.data new file mode 100644 index 0000000000..73f58fb1d5 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.008.data @@ -0,0 +1 @@ + 12.9752105872 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.012.data b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.012.data new file mode 100644 index 0000000000..08edbd0457 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.012.data @@ -0,0 +1 @@ + 14.5786310784 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.013.data b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.013.data new file mode 100644 index 0000000000..2ef11b2fb7 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.013.data @@ -0,0 +1 @@ + 1.4392244883 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.079.data b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.079.data new file mode 100644 index 0000000000..68962ae7b3 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.079.data @@ -0,0 +1 @@ + 0.0175182304 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/input.nn b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/input.nn new file mode 100644 index 0000000000..3ec83d0c01 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/input.nn @@ -0,0 +1,391 @@ +## ############################################################# +### This is the input file for RuNNer +### ############################################################# +### General remarks: +### - commands can be switched off by using the # character at the BEGINNING of the line +### - the input file can be structured by blank lines and comment lines +### - the order of the keywords is arbitrary +### - if keywords are missing, default values will be used and written to runner.out +### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message + +### THIS INPUT.NN IS AN EXAMPLE, IT IS NOT A REALISTIC CASE +### It contains only a subset of all keywords + +######################################################################################################################## +### general keywords +######################################################################################################################## + +nnp_generation 4 +use_electrostatics +use_short_nn +use_short_forces +precondition_weights +#regularize_fit_param 1.e-4 +runner_mode 2 +epochs 100 +#epochs 25 + +number_of_elements 4 +elements Al O Mg Au + +initial_hardness O 1.0 +initial_hardness Mg 1.0 +initial_hardness Al 1.0 +initial_hardness Au 1.0 + +fixed_gausswidth Mg 4.289 +fixed_gausswidth O 2.872 +fixed_gausswidth Al 3.477 +fixed_gausswidth Au 3.288 + +screen_electrostatics 3.2 8.0 + +parallel_mode 1 +random_seed 12346 +random_number_type 5 + +remove_atom_energies +atom_energy O -75.29000258799172 +atom_energy Mg -200.61689378490792 +atom_energy Au -19684.765036573383 +atom_energy Al -243.09681374120558 + +energy_threshold 100.0d0 +bond_threshold 0.4d0 +ewald_prec 1.e-6 +# + +######################################################################################################################## +### NN structure of the short-range NN +######################################################################################################################## +global_hidden_layers_short 2 +global_nodes_short 15 15 +global_activation_short t t l +global_hidden_layers_electrostatic 2 +global_nodes_electrostatic 15 15 +global_activation_electrostatic t t l + +######################################################################################################################## +### symmetry function generation ( mode 1): +######################################################################################################################## +test_fraction 0.1 + +######################################################################################################################## +### symmetry function definitions (all modes): +######################################################################################################################## +cutoff_type 2 + +symfunction Mg 2 Mg 0.000000 0.000000 8.000000 +symfunction Mg 2 Mg 0.001000 0.000000 8.000000 +symfunction Mg 2 Mg 0.002000 0.000000 8.000000 +symfunction Mg 2 Mg 0.003000 0.000000 8.000000 +symfunction Mg 2 Mg 0.004000 0.000000 8.000000 +symfunction Mg 2 Mg 0.005000 0.000000 8.000000 + + +symfunction O 2 Mg 0.000000 0.000000 8.000000 +symfunction O 2 Mg 0.004000 0.000000 8.000000 +symfunction O 2 Mg 0.007000 0.000000 8.000000 +symfunction O 2 Mg 0.010000 0.000000 8.000000 +symfunction O 2 Mg 0.014000 0.000000 8.000000 +symfunction O 2 Mg 0.018000 0.000000 8.000000 + +symfunction Mg 2 O 0.000000 0.000000 8.000000 +symfunction Mg 2 O 0.004000 0.000000 8.000000 +symfunction Mg 2 O 0.007000 0.000000 8.000000 +symfunction Mg 2 O 0.010000 0.000000 8.000000 +symfunction Mg 2 O 0.014000 0.000000 8.000000 +symfunction Mg 2 O 0.018000 0.000000 8.000000 + +symfunction O 2 O 0.000000 0.000000 8.000000 +symfunction O 2 O 0.001000 0.000000 8.000000 +symfunction O 2 O 0.002000 0.000000 8.000000 +symfunction O 2 O 0.003000 0.000000 8.000000 +symfunction O 2 O 0.004000 0.000000 8.000000 +symfunction O 2 O 0.005000 0.000000 8.000000 + +symfunction Mg 2 Au 0.000000 0.000000 8.000000 +symfunction Mg 2 Au 0.001000 0.000000 8.000000 +symfunction Mg 2 Au 0.002000 0.000000 8.000000 +symfunction Mg 2 Au 0.003000 0.000000 8.000000 +symfunction Mg 2 Au 0.004000 0.000000 8.000000 +symfunction Mg 2 Au 0.005000 0.000000 8.000000 + +symfunction Au 2 Mg 0.000000 0.000000 8.000000 +symfunction Au 2 Mg 0.001000 0.000000 8.000000 +symfunction Au 2 Mg 0.002000 0.000000 8.000000 +symfunction Au 2 Mg 0.003000 0.000000 8.000000 +symfunction Au 2 Mg 0.004000 0.000000 8.000000 +symfunction Au 2 Mg 0.005000 0.000000 8.000000 + + +symfunction Au 2 O 0.000000 0.000000 8.000000 +symfunction Au 2 O 0.004000 0.000000 8.000000 +symfunction Au 2 O 0.008000 0.000000 8.000000 +symfunction Au 2 O 0.013000 0.000000 8.000000 +symfunction Au 2 O 0.018000 0.000000 8.000000 +symfunction Au 2 O 0.024000 0.000000 8.000000 + +symfunction O 2 Au 0.000000 0.000000 8.000000 +symfunction O 2 Au 0.004000 0.000000 8.000000 +symfunction O 2 Au 0.008000 0.000000 8.000000 +symfunction O 2 Au 0.013000 0.000000 8.000000 +symfunction O 2 Au 0.018000 0.000000 8.000000 +symfunction O 2 Au 0.024000 0.000000 8.000000 + +symfunction Au 2 Au 0.000000 0.000000 8.000000 +symfunction Au 2 Au 0.004000 0.000000 8.000000 +symfunction Au 2 Au 0.008000 0.000000 8.000000 +symfunction Au 2 Au 0.012000 0.000000 8.000000 +symfunction Au 2 Au 0.017000 0.000000 8.000000 +symfunction Au 2 Au 0.022000 0.000000 8.000000 + + +symfunction O 2 Al 0.000000 0.000000 8.000000 +symfunction O 2 Al 0.003000 0.000000 8.000000 +symfunction O 2 Al 0.005000 0.000000 8.000000 +symfunction O 2 Al 0.008000 0.000000 8.000000 +symfunction O 2 Al 0.011000 0.000000 8.000000 +symfunction O 2 Al 0.014000 0.000000 8.000000 + +symfunction Al 2 O 0.000000 0.000000 8.000000 +symfunction Al 2 O 0.003000 0.000000 8.000000 +symfunction Al 2 O 0.005000 0.000000 8.000000 +symfunction Al 2 O 0.008000 0.000000 8.000000 +symfunction Al 2 O 0.011000 0.000000 8.000000 +symfunction Al 2 O 0.014000 0.000000 8.000000 + +symfunction Al 2 Mg 0.000000 0.000000 8.000000 +symfunction Al 2 Mg 0.001000 0.000000 8.000000 +symfunction Al 2 Mg 0.002000 0.000000 8.000000 +symfunction Al 2 Mg 0.003000 0.000000 8.000000 +symfunction Al 2 Mg 0.004000 0.000000 8.000000 +symfunction Al 2 Mg 0.005000 0.000000 8.000000 + +symfunction Mg 2 Al 0.000000 0.000000 8.000000 +symfunction Mg 2 Al 0.001000 0.000000 8.000000 +symfunction Mg 2 Al 0.002000 0.000000 8.000000 +symfunction Mg 2 Al 0.003000 0.000000 8.000000 +symfunction Mg 2 Al 0.004000 0.000000 8.000000 +symfunction Mg 2 Al 0.005000 0.000000 8.000000 + +#symfunction Al 2 Al 0.000000 0.000000 8.000000 +#symfunction Al 2 Al 0.001000 0.000000 8.000000 +#symfunction Al 2 Al 0.002000 0.000000 8.000000 +#symfunction Al 2 Al 0.003000 0.000000 8.000000 +#symfunction Al 2 Al 0.004000 0.000000 8.000000 +#symfunction Al 2 Al 0.005000 0.000000 8.000000 + + +symfunction Mg 3 Mg Mg 0.0 1.0 1.0 8.0 +symfunction Mg 3 Mg Mg 0.0 1.0 2.0 8.0 +symfunction Mg 3 Mg Mg 0.0 1.0 4.0 8.0 +#symfunction Mg 3 Mg Mg 0.0 1.0 8.0 8.0 +symfunction Mg 3 Mg Mg 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 Mg Mg 0.0 -1.0 2.0 8.0 + +symfunction Mg 3 Mg O 0.0 1.0 1.0 8.0 +symfunction Mg 3 Mg O 0.0 1.0 2.0 8.0 +symfunction Mg 3 Mg O 0.0 1.0 4.0 8.0 +symfunction Mg 3 Mg O 0.0 1.0 8.0 8.0 +symfunction Mg 3 Mg O 0.0 -1.0 1.0 8.0 +symfunction Mg 3 Mg O 0.0 -1.0 2.0 8.0 +#symfunction Mg 3 Mg O 0.0 -1.0 4.0 8.0 +#symfunction Mg 3 Mg O 0.0 -1.0 8.0 8.0 + +#symfunction Mg 3 Mg Al 0.0 1.0 1.0 8.0 +#symfunction Mg 3 Mg Al 0.0 1.0 2.0 8.0 +#symfunction Mg 3 Mg Al 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 Mg Al 0.0 -1.0 2.0 8.0 + +#symfunction Mg 3 Mg Au 0.0 1.0 1.0 8.0 +#symfunction Mg 3 Mg Au 0.0 1.0 2.0 8.0 +#symfunction Mg 3 Mg Au 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 Mg Au 0.0 -1.0 2.0 8.0 + +symfunction Mg 3 O O 0.0 1.0 1.0 8.0 +symfunction Mg 3 O O 0.0 1.0 2.0 8.0 +symfunction Mg 3 O O 0.0 1.0 4.0 8.0 +#symfunction Mg 3 O O 0.0 1.0 8.0 8.0 +symfunction Mg 3 O O 0.0 -1.0 1.0 8.0 +symfunction Mg 3 O O 0.0 -1.0 2.0 8.0 +symfunction Mg 3 O O 0.0 -1.0 4.0 8.0 +#symfunction Mg 3 O O 0.0 -1.0 8.0 8.0 + +symfunction Mg 3 O Al 0.0 1.0 1.0 8.0 +symfunction Mg 3 O Al 0.0 1.0 2.0 8.0 +symfunction Mg 3 O Al 0.0 1.0 4.0 8.0 +symfunction Mg 3 O Al 0.0 1.0 8.0 8.0 +symfunction Mg 3 O Al 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 O Al 0.0 -1.0 2.0 8.0 + +symfunction Mg 3 O Au 0.0 1.0 1.0 8.0 +symfunction Mg 3 O Au 0.0 1.0 2.0 8.0 +symfunction Mg 3 O Au 0.0 1.0 4.0 8.0 +symfunction Mg 3 O Au 0.0 1.0 8.0 8.0 +symfunction Mg 3 O Au 0.0 -1.0 1.0 8.0 +symfunction Mg 3 O Au 0.0 -1.0 2.0 8.0 + +#symfunction Mg 3 Al Al 0.0 1.0 1.0 8.0 +#symfunction Mg 3 Al Al 0.0 1.0 2.0 8.0 + +#symfunction Mg 3 Au Au 0.0 1.0 1.0 8.0 +#symfunction Mg 3 Au Au 0.0 1.0 2.0 8.0 +#symfunction Mg 3 Au Au 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 Au Au 0.0 -1.0 2.0 8.0 + + + +symfunction O 3 Mg Mg 0.0 1.0 1.0 8.0 +symfunction O 3 Mg Mg 0.0 1.0 2.0 8.0 +symfunction O 3 Mg Mg 0.0 1.0 4.0 8.0 +#symfunction O 3 Mg Mg 0.0 1.0 8.0 8.0 +symfunction O 3 Mg Mg 0.0 -1.0 1.0 8.0 +symfunction O 3 Mg Mg 0.0 -1.0 2.0 8.0 +symfunction O 3 Mg Mg 0.0 -1.0 4.0 8.0 +#symfunction O 3 Mg Mg 0.0 -1.0 8.0 8.0 + +symfunction O 3 Mg O 0.0 1.0 1.0 8.0 +symfunction O 3 Mg O 0.0 1.0 2.0 8.0 +symfunction O 3 Mg O 0.0 1.0 4.0 8.0 +symfunction O 3 Mg O 0.0 1.0 8.0 8.0 +symfunction O 3 Mg O 0.0 -1.0 1.0 8.0 +symfunction O 3 Mg O 0.0 -1.0 2.0 8.0 +#symfunction O 3 Mg O 0.0 -1.0 4.0 8.0 +#symfunction O 3 Mg O 0.0 -1.0 8.0 8.0 + +symfunction O 3 Mg Al 0.0 1.0 1.0 8.0 +symfunction O 3 Mg Al 0.0 1.0 2.0 8.0 +symfunction O 3 Mg Al 0.0 1.0 4.0 8.0 +#symfunction O 3 Mg Al 0.0 1.0 8.0 8.0 +symfunction O 3 Mg Al 0.0 -1.0 1.0 8.0 +symfunction O 3 Mg Al 0.0 -1.0 2.0 8.0 +symfunction O 3 Mg Al 0.0 -1.0 4.0 8.0 +#symfunction O 3 Mg Al 0.0 -1.0 8.0 8.0 + +symfunction O 3 Mg Au 0.0 1.0 1.0 8.0 +symfunction O 3 Mg Au 0.0 1.0 2.0 8.0 +symfunction O 3 Mg Au 0.0 -1.0 1.0 8.0 +symfunction O 3 Mg Au 0.0 -1.0 2.0 8.0 + +symfunction O 3 O O 0.0 1.0 1.0 8.0 +symfunction O 3 O O 0.0 1.0 2.0 8.0 +symfunction O 3 O O 0.0 -1.0 1.0 8.0 + +symfunction O 3 O Al 0.0 1.0 1.0 8.0 +symfunction O 3 O Al 0.0 1.0 2.0 8.0 +symfunction O 3 O Al 0.0 -1.0 1.0 8.0 +symfunction O 3 O Al 0.0 -1.0 2.0 8.0 + +#symfunction O 3 O Au 0.0 1.0 1.0 8.0 + + + + +symfunction Al 3 Mg Mg 0.0 1.0 1.0 8.0 +#symfunction Al 3 Mg Mg 0.0 1.0 2.0 8.0 +#symfunction Al 3 Mg Mg 0.0 -1.0 1.0 8.0 +#symfunction Al 3 Mg Mg 0.0 -1.0 2.0 8.0 + +symfunction Al 3 Mg O 0.0 1.0 1.0 8.0 +symfunction Al 3 Mg O 0.0 1.0 2.0 8.0 +symfunction Al 3 Mg O 0.0 -1.0 1.0 8.0 +#symfunction Al 3 Mg O 0.0 -1.0 2.0 8.0 + +#symfunction Al 3 Mg Al 0.0 1.0 1.0 8.0 +#symfunction Al 3 Mg Al 0.0 1.0 2.0 8.0 +#symfunction Al 3 Mg Al 0.0 -1.0 1.0 8.0 +#symfunction Al 3 Mg Al 0.0 -1.0 2.0 8.0 + +symfunction Al 3 O O 0.0 1.0 1.0 8.0 +symfunction Al 3 O O 0.0 1.0 2.0 8.0 +symfunction Al 3 O O 0.0 -1.0 1.0 8.0 +symfunction Al 3 O O 0.0 -1.0 2.0 8.0 + +#symfunction Al 3 O Al 0.0 1.0 1.0 8.0 +#symfunction Al 3 O Al 0.0 1.0 2.0 8.0 +#symfunction Al 3 O Al 0.0 -1.0 1.0 8.0 +#symfunction Al 3 O Al 0.0 -1.0 2.0 8.0 + +#symfunction Al 3 Al Al 0.0 1.0 1.0 8.0 +#symfunction Al 3 Al Al 0.0 1.0 2.0 8.0 +#symfunction Al 3 Al Al 0.0 -1.0 1.0 8.0 +#symfunction Al 3 Al Al 0.0 -1.0 2.0 8.0 + + + +symfunction Au 3 Mg Mg 0.0 1.0 1.0 8.0 +symfunction Au 3 Mg Mg 0.0 1.0 2.0 8.0 +#symfunction Au 3 Mg Mg 0.0 -1.0 1.0 8.0 +#symfunction Au 3 Mg Mg 0.0 -1.0 2.0 8.0 + +symfunction Au 3 Mg O 0.0 1.0 1.0 8.0 +symfunction Au 3 Mg O 0.0 1.0 2.0 8.0 +symfunction Au 3 Mg O 0.0 -1.0 1.0 8.0 +symfunction Au 3 Mg O 0.0 -1.0 2.0 8.0 + +#symfunction Au 3 Mg Au 0.0 1.0 1.0 8.0 +#symfunction Au 3 Mg Au 0.0 1.0 2.0 8.0 +#symfunction Au 3 Mg Au 0.0 -1.0 1.0 8.0 +#symfunction Au 3 Mg Au 0.0 -1.0 2.0 8.0 + +symfunction Au 3 O O 0.0 1.0 1.0 8.0 +#symfunction Au 3 O O 0.0 1.0 2.0 8.0 +#symfunction Au 3 O O 0.0 -1.0 1.0 8.0 +#symfunction Au 3 O O 0.0 -1.0 2.0 8.0 + +#symfunction Au 3 O Au 0.0 1.0 1.0 8.0 +#symfunction Au 3 O Au 0.0 1.0 2.0 8.0 +symfunction Au 3 O Au 0.0 1.0 -1.0 8.0 +symfunction Au 3 O Au 0.0 1.0 -2.0 8.0 + +#symfunction Au 3 Au Au 0.0 1.0 1.0 8.0 +#symfunction Au 3 Au Au 0.0 1.0 2.0 8.0 +#symfunction Au 3 Au Au 0.0 -1.0 1.0 8.0 +#symfunction Au 3 Au Au 0.0 -1.0 2.0 8.0 + + + + +######################################################################################################################## +### fitting (mode 2):general inputs for short range AND short part: +######################################################################################################################## +points_in_memory 1000 +mix_all_points +scale_symmetry_functions +center_symmetry_functions +fitting_unit eV +######################################################################################################################## +### fitting options ( mode 2): short range part only: +######################################################################################################################## +optmode_short_energy 1 +optmode_short_force 1 +short_energy_error_threshold 0.8 +short_force_error_threshold 0.8 +kalman_lambda_short 0.98000 +kalman_lambda_charge 0.98000 +kalman_nue_short 0.99870 +kalman_nue_charge 0.99870 +#use_old_weights_short +#force_update_scaling -1.0d0 +#short_energy_group 1 +#short_energy_fraction 1.00 +#short_force_group 1 +short_force_fraction 0.025 +weights_min -1.0 +weights_max 1.0 +repeated_energy_update +nguyen_widrow_weights_short + + +######################################################################################################################## +### output options for mode 2 (fitting): +######################################################################################################################## +#write_trainpoints +#write_trainforces +######################################################################################################################## +### output options for mode 3 (prediction): +######################################################################################################################## +calculate_forces +#calculate_stress + diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/scaling.data b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/scaling.data new file mode 100644 index 0000000000..167efade92 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/scaling.data @@ -0,0 +1,152 @@ + 1 1 0.157132975 0.280279850 0.234169887 + 1 2 0.379295480 0.622179554 0.545652438 + 1 3 0.000000000 0.205184943 0.016565410 + 1 4 0.000000000 0.167300348 0.001157152 + 1 5 0.151966913 0.271484679 0.226693585 + 1 6 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index 0000000000..294c3d1fa0 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/input.data @@ -0,0 +1,122 @@ +MgO with Al/Au, first structure from input.data (wrapped into box) + +110 atoms + +4 atom types + +0.0 1.7097166001000002E+01 xlo xhi +0.0 1.7097166001000002E+01 ylo yhi +0.0 5.0000000000999997E+01 zlo zhi + +Atoms + +1 2 0.0 -1.9775793498e-02 -6.4032231288e-02 2.0026111119e+01 +2 1 0.0 2.8784590473e+00 2.8904829958e+00 2.0053576907e+01 +3 1 0.0 7.2652159693e-02 -1.6211222263e-02 2.4043132172e+01 +4 2 0.0 2.8780260733e+00 2.8998185635e+00 2.4032640394e+01 +5 2 0.0 -5.6795412231e-02 -2.2440590601e-02 2.8111288946e+01 +6 1 0.0 2.8421666140e+00 2.8834652149e+00 2.8032859289e+01 +7 1 0.0 6.5214500558e-02 -3.8745751143e-02 3.2113867333e+01 +8 2 0.0 2.8332198764e+00 2.7977822229e+00 3.2113907679e+01 +9 3 0.0 1.9864553928e-02 1.0486013922e-02 3.6088078099e+01 +10 1 0.0 2.7981764575e+00 2.8796998036e+00 3.6124511960e+01 +11 1 0.0 -8.4521774292e-03 -2.2604637714e-02 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2.7674441650e+00 3.2676547854e+00 1.5266538963e+01 +110 4 0.0 2.7884963173e+00 3.1844017731e+00 1.0716139442e+01 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/input.data.q b/examples/interface-LAMMPS/AlAuMgO_4G/input.data.q new file mode 100644 index 0000000000..9ad90f2ea3 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/input.data.q @@ -0,0 +1,122 @@ +MgO with Al/Au, first structure from input.data (wrapped into box) + +110 atoms + +4 atom types + +0.0 1.7097166001000002E+01 xlo xhi +0.0 1.7097166001000002E+01 ylo yhi +0.0 5.0000000000999997E+01 zlo zhi + +Atoms + +1 2 3.8291924061925653E-01 -1.9775793498e-02 -6.4032231288e-02 2.0026111119e+01 +2 1 -3.4428156299665341E-01 2.8784590473e+00 2.8904829958e+00 2.0053576907e+01 +3 1 -3.5086580292126851E-01 7.2652159693e-02 -1.6211222263e-02 2.4043132172e+01 +4 2 3.2433687005490347E-01 2.8780260733e+00 2.8998185635e+00 2.4032640394e+01 +5 2 3.3204727049820898E-01 -5.6795412231e-02 -2.2440590601e-02 2.8111288946e+01 +6 1 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5.7117658322e+00 1.1454697101e+01 3.2073160784e+01 +68 2 3.3480445647613249E-01 8.5246584175e+00 1.4270581047e+01 3.2102696917e+01 +69 2 3.2813653471690885E-01 5.7186666391e+00 1.1422359335e+01 3.6101213660e+01 +70 1 -3.1044009306062004E-01 8.5627598477e+00 1.4273198941e+01 3.6166519038e+01 +71 1 -4.0152383538759395E-01 5.7264381750e+00 1.1398781375e+01 4.0260042284e+01 +72 2 3.8461825101443542E-01 8.5102664156e+00 1.4232221424e+01 4.0091178051e+01 +73 2 4.0434089461753853E-01 1.1401532344e+01 4.5076087540e-02 2.0029059110e+01 +74 1 -4.0269081201368068E-01 1.4239757122e+01 2.8608573080e+00 1.9951038844e+01 +75 1 -3.4644736886291427E-01 1.1393443466e+01 -4.2770168300e-04 2.4001081706e+01 +76 2 3.3391498829207378E-01 1.4231685554e+01 2.8864018680e+00 2.4021645383e+01 +77 2 3.2637464521159698E-01 1.1402686003e+01 3.9371628390e-02 2.8113584925e+01 +78 1 -3.4526722283733730E-01 1.4244927525e+01 2.8375641675e+00 2.8036863637e+01 +79 1 -3.4317538266324116E-01 1.1395989211e+01 4.7920427509e-03 3.2086785538e+01 +80 2 3.3859570914612275E-01 1.4238799238e+01 2.8820363931e+00 3.2090336900e+01 +81 2 3.2717406973233076E-01 1.1420507253e+01 1.8697459157e-02 3.6120652572e+01 +82 1 -3.1199799110455384E-01 1.4268517750e+01 2.8561106375e+00 3.6168027133e+01 +83 1 -3.9787972466062677E-01 1.1414591957e+01 -8.2592458544e-02 4.0173253651e+01 +84 2 3.8944129327761023E-01 1.4256298422e+01 2.8717039194e+00 4.0140854601e+01 +85 2 4.0293056065045130E-01 1.1393721861e+01 5.7236951244e+00 2.0010035088e+01 +86 1 -4.0308428555845843E-01 1.4257639788e+01 8.4981605285e+00 1.9925047364e+01 +87 1 -3.4610510814460854E-01 1.1373306754e+01 5.7232945403e+00 2.3983895820e+01 +88 2 3.3563369794527187E-01 1.4251016393e+01 8.5961130012e+00 2.4011062539e+01 +89 2 3.3577567445494227E-01 1.1392303111e+01 5.6922237034e+00 2.8086502355e+01 +90 1 -3.4632024265923089E-01 1.4307995467e+01 8.5052796177e+00 2.8127594522e+01 +91 1 -3.4272129620502212E-01 1.1467787838e+01 5.7303018143e+00 3.2140124452e+01 +92 2 3.2658585338481128E-01 1.4223684114e+01 8.5394621152e+00 3.2083417385e+01 +93 2 3.2446795575973625E-01 1.1398360231e+01 5.6984501048e+00 3.6109137659e+01 +94 1 -3.1027087421689914E-01 1.4243599161e+01 8.4926708934e+00 3.6111924268e+01 +95 1 -4.0224397193198974E-01 1.1387116342e+01 5.7224672938e+00 4.0150551843e+01 +96 2 3.9141809039880648E-01 1.4251826367e+01 8.5541300360e+00 4.0169736719e+01 +97 2 4.1163259599154606E-01 1.1397087406e+01 1.1432029951e+01 1.9991521329e+01 +98 1 -3.9861261294319328E-01 1.4222100486e+01 1.4237423386e+01 1.9890837446e+01 +99 1 -3.4426097778309650E-01 1.1397172085e+01 1.1362254484e+01 2.4106729256e+01 +100 2 3.3507591789797203E-01 1.4223050564e+01 1.4272733426e+01 2.4026767277e+01 +101 2 3.2599946771409777E-01 1.1412415162e+01 1.1398466358e+01 2.8036581274e+01 +102 1 -3.4707768329649691E-01 1.4265352610e+01 1.4216093689e+01 2.8052093903e+01 +103 1 -3.0688777105113402E-01 1.1401696599e+01 1.1369599225e+01 3.2083243398e+01 +104 2 3.3018690623164043E-01 1.4233083328e+01 1.4215807831e+01 3.2083725032e+01 +105 3 4.0123726733194143E-01 1.1446195847e+01 1.1455486685e+01 3.6062830566e+01 +106 1 -2.8677889278053709E-01 1.4275939497e+01 1.4231407235e+01 3.6076973257e+01 +107 1 -3.5646759316313670E-01 1.1412436308e+01 1.1399368513e+01 4.0122450030e+01 +108 2 3.7555739662669552E-01 1.4206953179e+01 1.4201432515e+01 4.0151366429e+01 +109 4 3.6996649330713637E-02 2.7674441650e+00 3.2676547854e+00 1.5266538963e+01 +110 4 -1.4394128296917899E-01 2.7884963173e+00 3.1844017731e+00 1.0716139442e+01 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/md-external.lmp b/examples/interface-LAMMPS/AlAuMgO_4G/md-external.lmp new file mode 100644 index 0000000000..98c0e36816 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/md-external.lmp @@ -0,0 +1,53 @@ +############################################################################### +# MD simulation for MgO with Al/Au +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "AlAuMgO.data" +# Timesteps +variable numSteps equal 5 +variable dt equal 0.0005 +# NN +variable nnpCutoff equal 8.01 +variable nnpDir string "nnp-data" +# Masses +variable mass_O equal 15.9994 +variable mass_Mg equal 24.305 +variable mass_Al equal 26.981539 +variable mass_Au equal 196.96657 + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary p p p +atom_style atomic +read_data ${cfgFile} +mass 1 ${mass_O} +mass 2 ${mass_Mg} +mass 3 ${mass_Al} +mass 4 ${mass_Au} +timestep ${dt} +thermo 1 + +############################################################################### +# NN +############################################################################### +pair_style nnp/external "O Mg Al Au" dir ${nnpDir} command "RuNNer-gaussian.x" cflength 1.0 cfenergy 1.0 +#pair_style nnp/external "O Mg Al Au" dir ${nnpDir} command "nnp-predict 0" cflength 1.0 cfenergy 1.0 +pair_coeff * * ${nnpCutoff} + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve +#dump 1 all atom 1 traj.dump + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/md.lmp b/examples/interface-LAMMPS/AlAuMgO_4G/md.lmp new file mode 100644 index 0000000000..87d0dca561 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/md.lmp @@ -0,0 +1,60 @@ +############################################################################### +# MD simulation for MgO with Al/Au +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "input.data" +# Timesteps +variable numSteps equal 0 +variable dt equal 0.0005 +# NN +#variable hdnnpCutoff equal 8.01 +variable hdnnpCutoff equal 8.00000001 +variable hdnnpDir string "hdnnp-data" +# Masses +variable mass_O equal 15.9994 +variable mass_Mg equal 24.305 +variable mass_Al equal 26.981539 +variable mass_Au equal 196.96657 + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary p p p +atom_style charge +atom_modify map yes +read_data ${cfgFile} +mass 1 ${mass_O} +mass 2 ${mass_Mg} +mass 3 ${mass_Al} +mass 4 ${mass_Au} +timestep ${dt} +velocity all create 300.0 12345 +thermo 1 + +neighbor 0.0 bin +neigh_modify delay 10 # Seems this was the default previously (29Oct2020). + +############################################################################### +# NN +############################################################################### +pair_style hdnnp/4g dir ${hdnnpDir} showew yes showewsum 10 resetew no maxew 1000000 cflength 1.0 cfenergy 1.0 emap "1:O,2:Mg,3:Al,4:Au" +pair_coeff * * ${hdnnpCutoff} +kspace_style hdnnp ewald 1.0e-6 +fix 1 all hdnnp 1 1.0e-7 1.0e-1 1.0e-1 100 nnp nnp 1 + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve +#dump 1 all atom 1 traj.dump + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.008.data b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.008.data new file mode 100644 index 0000000000..73f58fb1d5 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.008.data @@ -0,0 +1 @@ + 12.9752105872 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.012.data b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.012.data new file mode 100644 index 0000000000..08edbd0457 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.012.data @@ -0,0 +1 @@ + 14.5786310784 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.013.data b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.013.data new file mode 100644 index 0000000000..2ef11b2fb7 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.013.data @@ -0,0 +1 @@ + 1.4392244883 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.079.data b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.079.data new file mode 100644 index 0000000000..68962ae7b3 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/hardness.079.data @@ -0,0 +1 @@ + 0.0175182304 diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/input.data b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/input.data new file mode 100644 index 0000000000..0f12ed1200 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/input.data @@ -0,0 +1,117 @@ +begin +lattice 1.7097166001e+01 0.0000000000e+00 0.0000000000e+00 +lattice 0.0000000000e+00 1.7097166001e+01 0.0000000000e+00 +lattice 0.0000000000e+00 0.0000000000e+00 5.0000000001e+01 +atom -1.9775793498e-02 -6.4032231288e-02 2.0026111119e+01 Mg 3.8788494400e-01 0.0 4.0412140453e-03 7.0265869263e-03 -8.4677419696e-03 +atom 2.8784590473e+00 2.8904829958e+00 2.0053576907e+01 O -3.5909487600e-01 0.0 -3.5357067955e-03 -4.5792491166e-03 9.7973038610e-04 +atom 7.2652159693e-02 -1.6211222263e-02 2.4043132172e+01 O -3.4594157600e-01 0.0 -9.9524052388e-03 8.2613919709e-04 9.0438549577e-03 +atom 2.8780260733e+00 2.8998185635e+00 2.4032640394e+01 Mg 3.2864151400e-01 0.0 -4.1635240288e-03 -8.3031064753e-03 -7.5802494690e-03 +atom -5.6795412231e-02 -2.2440590601e-02 2.8111288946e+01 Mg 3.4539947400e-01 0.0 8.7251795163e-03 -6.4186986345e-05 -2.4363991342e-02 +atom 2.8421666140e+00 2.8834652149e+00 2.8032859289e+01 O -3.4176807600e-01 0.0 -4.0428635156e-04 -4.3146904728e-03 1.5444027344e-02 +atom 6.5214500558e-02 -3.8745751143e-02 3.2113867333e+01 O -3.0785905600e-01 0.0 -8.7729091934e-03 1.9519751482e-03 1.9968874099e-02 +atom 2.8332198764e+00 2.7977822229e+00 3.2113907679e+01 Mg 3.3011505400e-01 0.0 2.2963600668e-03 5.3318657122e-03 -1.5343107719e-02 +atom 1.9864553928e-02 1.0486013922e-02 3.6088078099e+01 Al 3.9917245400e-01 0.0 6.7803750166e-05 -7.0094514898e-04 1.5053560097e-02 +atom 2.7981764575e+00 2.8796998036e+00 3.6124511960e+01 O -2.8949547600e-01 0.0 3.6273019714e-03 -2.8183589325e-03 -7.9325270091e-03 +atom -8.4521774292e-03 -2.2604637714e-02 4.0153894391e+01 O -3.6598870600e-01 0.0 -5.8418150328e-04 2.0246535621e-03 -2.5173725174e-02 +atom 2.8234702698e+00 2.8619477366e+00 4.0124676317e+01 Mg 3.7450518400e-01 0.0 1.3973418832e-03 7.8928841829e-05 1.5591933809e-02 +atom -1.3119630546e-02 5.6888413584e+00 2.0013899747e+01 Mg 3.5809711400e-01 0.0 1.0417032765e-03 1.3876195467e-03 -1.2083096942e-02 +atom 2.8848335277e+00 8.5308909417e+00 1.9989943256e+01 O -3.9844002600e-01 0.0 -3.7448860438e-03 5.0357737828e-03 5.7879501668e-03 +atom 1.8241298201e-02 5.6837552365e+00 2.4026099826e+01 O -3.4215310600e-01 0.0 -2.8868044844e-03 2.3195077530e-03 1.1176398239e-02 +atom 2.9361062157e+00 8.4795591997e+00 2.4082757439e+01 Mg 3.2952672400e-01 0.0 -7.9282995215e-03 7.7984136030e-03 -1.5464891041e-02 +atom 1.6188356579e-02 5.6698041265e+00 2.8051270020e+01 Mg 3.3684778400e-01 0.0 2.2916383144e-03 4.1861975500e-03 -8.6622492722e-03 +atom 2.8977599905e+00 8.5660735578e+00 2.8036115495e+01 O -3.4409367600e-01 0.0 -3.3334995364e-03 -5.1017646429e-03 1.4470957486e-02 +atom 9.8433937020e-04 5.6927154290e+00 3.2118501962e+01 O -3.4614451600e-01 0.0 9.1005095975e-04 -4.0730943899e-03 4.9154030300e-03 +atom 2.8073628502e+00 8.5498039808e+00 3.2128399704e+01 Mg 3.3498536400e-01 0.0 1.6059193804e-03 2.0542016438e-03 -1.6551022033e-02 +atom -5.0996334501e-02 5.7492786883e+00 3.6121753734e+01 Mg 3.1982162400e-01 0.0 2.0618641544e-03 -3.0958082828e-03 5.5585234542e-03 +atom 2.9059518581e+00 8.5723518134e+00 3.6118083754e+01 O -3.1404623600e-01 0.0 6.9455266915e-03 -1.4599515105e-02 -4.8605312468e-03 +atom 5.2199900983e-04 5.6455106974e+00 4.0180597258e+01 O -4.0522186600e-01 0.0 7.6228232308e-04 7.0096828995e-03 -8.2712198059e-03 +atom 2.8610732470e+00 8.5614353199e+00 4.0139419524e+01 Mg 3.8989854400e-01 0.0 -1.8149964341e-03 3.0632250705e-03 1.2872167566e-02 +atom -3.9339238487e-02 1.1415957378e+01 1.9959977720e+01 Mg 4.3559881400e-01 0.0 5.0407268883e-03 -4.9856774589e-03 7.3154652172e-04 +atom 2.9183726113e+00 1.4291678042e+01 1.9988445497e+01 O -3.9816017600e-01 0.0 -9.0864151516e-03 -6.5665931399e-03 2.3483399976e-03 +atom -2.1271587207e-02 1.1421205582e+01 2.4027048544e+01 O -3.4569412600e-01 0.0 -1.6480077969e-03 -2.5662981317e-03 8.0363346320e-03 +atom 2.9026486927e+00 1.4185336528e+01 2.4050086987e+01 Mg 3.2444578400e-01 0.0 -6.8689188539e-03 3.2051673130e-03 -1.0907852568e-02 +atom -5.1509735258e-02 1.1382810885e+01 2.8094293015e+01 Mg 3.3699468400e-01 0.0 1.0337570946e-02 -2.4454976218e-03 -1.5847585775e-02 +atom 2.9119668371e+00 1.4181088046e+01 2.8044752601e+01 O -3.4257456600e-01 0.0 -8.2941301304e-03 6.6795718730e-03 1.4777589094e-02 +atom 1.0413278368e-02 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1.5464750274e-02 +atom 1.1401696599e+01 1.1369599225e+01 3.2083243398e+01 O -3.0799256600e-01 0.0 -1.8796304720e-04 3.6748951931e-03 2.3090729543e-02 +atom 1.4233083328e+01 1.4215807831e+01 3.2083725032e+01 Mg 3.3553753400e-01 0.0 6.4488285943e-04 1.0481239340e-03 -1.1624902137e-02 +atom 1.1446195847e+01 1.1455486685e+01 3.6062830566e+01 Al 3.9603740400e-01 0.0 -3.7845126362e-03 -5.5501858565e-03 1.3573459514e-02 +atom 1.4275939497e+01 1.4231407235e+01 3.6076973257e+01 O -2.8918410600e-01 0.0 -2.8119721838e-03 5.1917246104e-04 -6.1571751814e-03 +atom 1.1412436308e+01 1.1399368513e+01 4.0122450030e+01 O -3.6358139600e-01 0.0 -8.7882158509e-04 -9.1956096436e-04 -2.2866358560e-02 +atom 1.4206953179e+01 1.4201432515e+01 4.0151366429e+01 Mg 3.7335335400e-01 0.0 3.7450445387e-03 5.1525057893e-03 1.4302349011e-02 +atom 2.7674441650e+00 3.2676547854e+00 1.5266538963e+01 Au -1.8129486000e-02 0.0 4.7752095368e-04 -2.2142671411e-03 5.1007575752e-02 +atom 2.7884963173e+00 3.1844017731e+00 1.0716139442e+01 Au -2.1088749600e-01 0.0 -3.8108279331e-05 1.9467681277e-04 -4.1132711694e-02 +energy -5.4395981012e+04 +charge 0.0000000000e+00 +end diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/input.nn b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/input.nn new file mode 100644 index 0000000000..3ec83d0c01 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/input.nn @@ -0,0 +1,391 @@ +## ############################################################# +### This is the input file for RuNNer +### ############################################################# +### General remarks: +### - commands can be switched off by using the # character at the BEGINNING of the line +### - the input file can be structured by blank lines and comment lines +### - the order of the keywords is arbitrary +### - if keywords are missing, default values will be used and written to runner.out +### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message + +### THIS INPUT.NN IS AN EXAMPLE, IT IS NOT A REALISTIC CASE +### It contains only a subset of all keywords + +######################################################################################################################## +### general keywords +######################################################################################################################## + +nnp_generation 4 +use_electrostatics +use_short_nn +use_short_forces +precondition_weights +#regularize_fit_param 1.e-4 +runner_mode 2 +epochs 100 +#epochs 25 + +number_of_elements 4 +elements Al O Mg Au + +initial_hardness O 1.0 +initial_hardness Mg 1.0 +initial_hardness Al 1.0 +initial_hardness Au 1.0 + +fixed_gausswidth Mg 4.289 +fixed_gausswidth O 2.872 +fixed_gausswidth Al 3.477 +fixed_gausswidth Au 3.288 + +screen_electrostatics 3.2 8.0 + +parallel_mode 1 +random_seed 12346 +random_number_type 5 + +remove_atom_energies +atom_energy O -75.29000258799172 +atom_energy Mg -200.61689378490792 +atom_energy Au -19684.765036573383 +atom_energy Al -243.09681374120558 + +energy_threshold 100.0d0 +bond_threshold 0.4d0 +ewald_prec 1.e-6 +# + +######################################################################################################################## +### NN structure of the short-range NN +######################################################################################################################## +global_hidden_layers_short 2 +global_nodes_short 15 15 +global_activation_short t t l +global_hidden_layers_electrostatic 2 +global_nodes_electrostatic 15 15 +global_activation_electrostatic t t l + +######################################################################################################################## +### symmetry function generation ( mode 1): +######################################################################################################################## +test_fraction 0.1 + +######################################################################################################################## +### symmetry function definitions (all modes): +######################################################################################################################## +cutoff_type 2 + +symfunction Mg 2 Mg 0.000000 0.000000 8.000000 +symfunction Mg 2 Mg 0.001000 0.000000 8.000000 +symfunction Mg 2 Mg 0.002000 0.000000 8.000000 +symfunction Mg 2 Mg 0.003000 0.000000 8.000000 +symfunction Mg 2 Mg 0.004000 0.000000 8.000000 +symfunction Mg 2 Mg 0.005000 0.000000 8.000000 + + +symfunction O 2 Mg 0.000000 0.000000 8.000000 +symfunction O 2 Mg 0.004000 0.000000 8.000000 +symfunction O 2 Mg 0.007000 0.000000 8.000000 +symfunction O 2 Mg 0.010000 0.000000 8.000000 +symfunction O 2 Mg 0.014000 0.000000 8.000000 +symfunction O 2 Mg 0.018000 0.000000 8.000000 + +symfunction Mg 2 O 0.000000 0.000000 8.000000 +symfunction Mg 2 O 0.004000 0.000000 8.000000 +symfunction Mg 2 O 0.007000 0.000000 8.000000 +symfunction Mg 2 O 0.010000 0.000000 8.000000 +symfunction Mg 2 O 0.014000 0.000000 8.000000 +symfunction Mg 2 O 0.018000 0.000000 8.000000 + +symfunction O 2 O 0.000000 0.000000 8.000000 +symfunction O 2 O 0.001000 0.000000 8.000000 +symfunction O 2 O 0.002000 0.000000 8.000000 +symfunction O 2 O 0.003000 0.000000 8.000000 +symfunction O 2 O 0.004000 0.000000 8.000000 +symfunction O 2 O 0.005000 0.000000 8.000000 + +symfunction Mg 2 Au 0.000000 0.000000 8.000000 +symfunction Mg 2 Au 0.001000 0.000000 8.000000 +symfunction Mg 2 Au 0.002000 0.000000 8.000000 +symfunction Mg 2 Au 0.003000 0.000000 8.000000 +symfunction Mg 2 Au 0.004000 0.000000 8.000000 +symfunction Mg 2 Au 0.005000 0.000000 8.000000 + +symfunction Au 2 Mg 0.000000 0.000000 8.000000 +symfunction Au 2 Mg 0.001000 0.000000 8.000000 +symfunction Au 2 Mg 0.002000 0.000000 8.000000 +symfunction Au 2 Mg 0.003000 0.000000 8.000000 +symfunction Au 2 Mg 0.004000 0.000000 8.000000 +symfunction Au 2 Mg 0.005000 0.000000 8.000000 + + +symfunction Au 2 O 0.000000 0.000000 8.000000 +symfunction Au 2 O 0.004000 0.000000 8.000000 +symfunction Au 2 O 0.008000 0.000000 8.000000 +symfunction Au 2 O 0.013000 0.000000 8.000000 +symfunction Au 2 O 0.018000 0.000000 8.000000 +symfunction Au 2 O 0.024000 0.000000 8.000000 + +symfunction O 2 Au 0.000000 0.000000 8.000000 +symfunction O 2 Au 0.004000 0.000000 8.000000 +symfunction O 2 Au 0.008000 0.000000 8.000000 +symfunction O 2 Au 0.013000 0.000000 8.000000 +symfunction O 2 Au 0.018000 0.000000 8.000000 +symfunction O 2 Au 0.024000 0.000000 8.000000 + +symfunction Au 2 Au 0.000000 0.000000 8.000000 +symfunction Au 2 Au 0.004000 0.000000 8.000000 +symfunction Au 2 Au 0.008000 0.000000 8.000000 +symfunction Au 2 Au 0.012000 0.000000 8.000000 +symfunction Au 2 Au 0.017000 0.000000 8.000000 +symfunction Au 2 Au 0.022000 0.000000 8.000000 + + +symfunction O 2 Al 0.000000 0.000000 8.000000 +symfunction O 2 Al 0.003000 0.000000 8.000000 +symfunction O 2 Al 0.005000 0.000000 8.000000 +symfunction O 2 Al 0.008000 0.000000 8.000000 +symfunction O 2 Al 0.011000 0.000000 8.000000 +symfunction O 2 Al 0.014000 0.000000 8.000000 + +symfunction Al 2 O 0.000000 0.000000 8.000000 +symfunction Al 2 O 0.003000 0.000000 8.000000 +symfunction Al 2 O 0.005000 0.000000 8.000000 +symfunction Al 2 O 0.008000 0.000000 8.000000 +symfunction Al 2 O 0.011000 0.000000 8.000000 +symfunction Al 2 O 0.014000 0.000000 8.000000 + +symfunction Al 2 Mg 0.000000 0.000000 8.000000 +symfunction Al 2 Mg 0.001000 0.000000 8.000000 +symfunction Al 2 Mg 0.002000 0.000000 8.000000 +symfunction Al 2 Mg 0.003000 0.000000 8.000000 +symfunction Al 2 Mg 0.004000 0.000000 8.000000 +symfunction Al 2 Mg 0.005000 0.000000 8.000000 + +symfunction Mg 2 Al 0.000000 0.000000 8.000000 +symfunction Mg 2 Al 0.001000 0.000000 8.000000 +symfunction Mg 2 Al 0.002000 0.000000 8.000000 +symfunction Mg 2 Al 0.003000 0.000000 8.000000 +symfunction Mg 2 Al 0.004000 0.000000 8.000000 +symfunction Mg 2 Al 0.005000 0.000000 8.000000 + +#symfunction Al 2 Al 0.000000 0.000000 8.000000 +#symfunction Al 2 Al 0.001000 0.000000 8.000000 +#symfunction Al 2 Al 0.002000 0.000000 8.000000 +#symfunction Al 2 Al 0.003000 0.000000 8.000000 +#symfunction Al 2 Al 0.004000 0.000000 8.000000 +#symfunction Al 2 Al 0.005000 0.000000 8.000000 + + +symfunction Mg 3 Mg Mg 0.0 1.0 1.0 8.0 +symfunction Mg 3 Mg Mg 0.0 1.0 2.0 8.0 +symfunction Mg 3 Mg Mg 0.0 1.0 4.0 8.0 +#symfunction Mg 3 Mg Mg 0.0 1.0 8.0 8.0 +symfunction Mg 3 Mg Mg 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 Mg Mg 0.0 -1.0 2.0 8.0 + +symfunction Mg 3 Mg O 0.0 1.0 1.0 8.0 +symfunction Mg 3 Mg O 0.0 1.0 2.0 8.0 +symfunction Mg 3 Mg O 0.0 1.0 4.0 8.0 +symfunction Mg 3 Mg O 0.0 1.0 8.0 8.0 +symfunction Mg 3 Mg O 0.0 -1.0 1.0 8.0 +symfunction Mg 3 Mg O 0.0 -1.0 2.0 8.0 +#symfunction Mg 3 Mg O 0.0 -1.0 4.0 8.0 +#symfunction Mg 3 Mg O 0.0 -1.0 8.0 8.0 + +#symfunction Mg 3 Mg Al 0.0 1.0 1.0 8.0 +#symfunction Mg 3 Mg Al 0.0 1.0 2.0 8.0 +#symfunction Mg 3 Mg Al 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 Mg Al 0.0 -1.0 2.0 8.0 + +#symfunction Mg 3 Mg Au 0.0 1.0 1.0 8.0 +#symfunction Mg 3 Mg Au 0.0 1.0 2.0 8.0 +#symfunction Mg 3 Mg Au 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 Mg Au 0.0 -1.0 2.0 8.0 + +symfunction Mg 3 O O 0.0 1.0 1.0 8.0 +symfunction Mg 3 O O 0.0 1.0 2.0 8.0 +symfunction Mg 3 O O 0.0 1.0 4.0 8.0 +#symfunction Mg 3 O O 0.0 1.0 8.0 8.0 +symfunction Mg 3 O O 0.0 -1.0 1.0 8.0 +symfunction Mg 3 O O 0.0 -1.0 2.0 8.0 +symfunction Mg 3 O O 0.0 -1.0 4.0 8.0 +#symfunction Mg 3 O O 0.0 -1.0 8.0 8.0 + +symfunction Mg 3 O Al 0.0 1.0 1.0 8.0 +symfunction Mg 3 O Al 0.0 1.0 2.0 8.0 +symfunction Mg 3 O Al 0.0 1.0 4.0 8.0 +symfunction Mg 3 O Al 0.0 1.0 8.0 8.0 +symfunction Mg 3 O Al 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 O Al 0.0 -1.0 2.0 8.0 + +symfunction Mg 3 O Au 0.0 1.0 1.0 8.0 +symfunction Mg 3 O Au 0.0 1.0 2.0 8.0 +symfunction Mg 3 O Au 0.0 1.0 4.0 8.0 +symfunction Mg 3 O Au 0.0 1.0 8.0 8.0 +symfunction Mg 3 O Au 0.0 -1.0 1.0 8.0 +symfunction Mg 3 O Au 0.0 -1.0 2.0 8.0 + +#symfunction Mg 3 Al Al 0.0 1.0 1.0 8.0 +#symfunction Mg 3 Al Al 0.0 1.0 2.0 8.0 + +#symfunction Mg 3 Au Au 0.0 1.0 1.0 8.0 +#symfunction Mg 3 Au Au 0.0 1.0 2.0 8.0 +#symfunction Mg 3 Au Au 0.0 -1.0 1.0 8.0 +#symfunction Mg 3 Au Au 0.0 -1.0 2.0 8.0 + + + +symfunction O 3 Mg Mg 0.0 1.0 1.0 8.0 +symfunction O 3 Mg Mg 0.0 1.0 2.0 8.0 +symfunction O 3 Mg Mg 0.0 1.0 4.0 8.0 +#symfunction O 3 Mg Mg 0.0 1.0 8.0 8.0 +symfunction O 3 Mg Mg 0.0 -1.0 1.0 8.0 +symfunction O 3 Mg Mg 0.0 -1.0 2.0 8.0 +symfunction O 3 Mg Mg 0.0 -1.0 4.0 8.0 +#symfunction O 3 Mg Mg 0.0 -1.0 8.0 8.0 + +symfunction O 3 Mg O 0.0 1.0 1.0 8.0 +symfunction O 3 Mg O 0.0 1.0 2.0 8.0 +symfunction O 3 Mg O 0.0 1.0 4.0 8.0 +symfunction O 3 Mg O 0.0 1.0 8.0 8.0 +symfunction O 3 Mg O 0.0 -1.0 1.0 8.0 +symfunction O 3 Mg O 0.0 -1.0 2.0 8.0 +#symfunction O 3 Mg O 0.0 -1.0 4.0 8.0 +#symfunction O 3 Mg O 0.0 -1.0 8.0 8.0 + +symfunction O 3 Mg Al 0.0 1.0 1.0 8.0 +symfunction O 3 Mg Al 0.0 1.0 2.0 8.0 +symfunction O 3 Mg Al 0.0 1.0 4.0 8.0 +#symfunction O 3 Mg Al 0.0 1.0 8.0 8.0 +symfunction O 3 Mg Al 0.0 -1.0 1.0 8.0 +symfunction O 3 Mg Al 0.0 -1.0 2.0 8.0 +symfunction O 3 Mg Al 0.0 -1.0 4.0 8.0 +#symfunction O 3 Mg Al 0.0 -1.0 8.0 8.0 + +symfunction O 3 Mg Au 0.0 1.0 1.0 8.0 +symfunction O 3 Mg Au 0.0 1.0 2.0 8.0 +symfunction O 3 Mg Au 0.0 -1.0 1.0 8.0 +symfunction O 3 Mg Au 0.0 -1.0 2.0 8.0 + +symfunction O 3 O O 0.0 1.0 1.0 8.0 +symfunction O 3 O O 0.0 1.0 2.0 8.0 +symfunction O 3 O O 0.0 -1.0 1.0 8.0 + +symfunction O 3 O Al 0.0 1.0 1.0 8.0 +symfunction O 3 O Al 0.0 1.0 2.0 8.0 +symfunction O 3 O Al 0.0 -1.0 1.0 8.0 +symfunction O 3 O Al 0.0 -1.0 2.0 8.0 + +#symfunction O 3 O Au 0.0 1.0 1.0 8.0 + + + + +symfunction Al 3 Mg Mg 0.0 1.0 1.0 8.0 +#symfunction Al 3 Mg Mg 0.0 1.0 2.0 8.0 +#symfunction Al 3 Mg Mg 0.0 -1.0 1.0 8.0 +#symfunction Al 3 Mg Mg 0.0 -1.0 2.0 8.0 + +symfunction Al 3 Mg O 0.0 1.0 1.0 8.0 +symfunction Al 3 Mg O 0.0 1.0 2.0 8.0 +symfunction Al 3 Mg O 0.0 -1.0 1.0 8.0 +#symfunction Al 3 Mg O 0.0 -1.0 2.0 8.0 + +#symfunction Al 3 Mg Al 0.0 1.0 1.0 8.0 +#symfunction Al 3 Mg Al 0.0 1.0 2.0 8.0 +#symfunction Al 3 Mg Al 0.0 -1.0 1.0 8.0 +#symfunction Al 3 Mg Al 0.0 -1.0 2.0 8.0 + +symfunction Al 3 O O 0.0 1.0 1.0 8.0 +symfunction Al 3 O O 0.0 1.0 2.0 8.0 +symfunction Al 3 O O 0.0 -1.0 1.0 8.0 +symfunction Al 3 O O 0.0 -1.0 2.0 8.0 + +#symfunction Al 3 O Al 0.0 1.0 1.0 8.0 +#symfunction Al 3 O Al 0.0 1.0 2.0 8.0 +#symfunction Al 3 O Al 0.0 -1.0 1.0 8.0 +#symfunction Al 3 O Al 0.0 -1.0 2.0 8.0 + +#symfunction Al 3 Al Al 0.0 1.0 1.0 8.0 +#symfunction Al 3 Al Al 0.0 1.0 2.0 8.0 +#symfunction Al 3 Al Al 0.0 -1.0 1.0 8.0 +#symfunction Al 3 Al Al 0.0 -1.0 2.0 8.0 + + + +symfunction Au 3 Mg Mg 0.0 1.0 1.0 8.0 +symfunction Au 3 Mg Mg 0.0 1.0 2.0 8.0 +#symfunction Au 3 Mg Mg 0.0 -1.0 1.0 8.0 +#symfunction Au 3 Mg Mg 0.0 -1.0 2.0 8.0 + +symfunction Au 3 Mg O 0.0 1.0 1.0 8.0 +symfunction Au 3 Mg O 0.0 1.0 2.0 8.0 +symfunction Au 3 Mg O 0.0 -1.0 1.0 8.0 +symfunction Au 3 Mg O 0.0 -1.0 2.0 8.0 + +#symfunction Au 3 Mg Au 0.0 1.0 1.0 8.0 +#symfunction Au 3 Mg Au 0.0 1.0 2.0 8.0 +#symfunction Au 3 Mg Au 0.0 -1.0 1.0 8.0 +#symfunction Au 3 Mg Au 0.0 -1.0 2.0 8.0 + +symfunction Au 3 O O 0.0 1.0 1.0 8.0 +#symfunction Au 3 O O 0.0 1.0 2.0 8.0 +#symfunction Au 3 O O 0.0 -1.0 1.0 8.0 +#symfunction Au 3 O O 0.0 -1.0 2.0 8.0 + +#symfunction Au 3 O Au 0.0 1.0 1.0 8.0 +#symfunction Au 3 O Au 0.0 1.0 2.0 8.0 +symfunction Au 3 O Au 0.0 1.0 -1.0 8.0 +symfunction Au 3 O Au 0.0 1.0 -2.0 8.0 + +#symfunction Au 3 Au Au 0.0 1.0 1.0 8.0 +#symfunction Au 3 Au Au 0.0 1.0 2.0 8.0 +#symfunction Au 3 Au Au 0.0 -1.0 1.0 8.0 +#symfunction Au 3 Au Au 0.0 -1.0 2.0 8.0 + + + + +######################################################################################################################## +### fitting (mode 2):general inputs for short range AND short part: +######################################################################################################################## +points_in_memory 1000 +mix_all_points +scale_symmetry_functions +center_symmetry_functions +fitting_unit eV +######################################################################################################################## +### fitting options ( mode 2): short range part only: +######################################################################################################################## +optmode_short_energy 1 +optmode_short_force 1 +short_energy_error_threshold 0.8 +short_force_error_threshold 0.8 +kalman_lambda_short 0.98000 +kalman_lambda_charge 0.98000 +kalman_nue_short 0.99870 +kalman_nue_charge 0.99870 +#use_old_weights_short +#force_update_scaling -1.0d0 +#short_energy_group 1 +#short_energy_fraction 1.00 +#short_force_group 1 +short_force_fraction 0.025 +weights_min -1.0 +weights_max 1.0 +repeated_energy_update +nguyen_widrow_weights_short + + +######################################################################################################################## +### output options for mode 2 (fitting): +######################################################################################################################## +#write_trainpoints +#write_trainforces +######################################################################################################################## +### output options for mode 3 (prediction): +######################################################################################################################## +calculate_forces +#calculate_stress + diff --git a/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/scaling.data b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/scaling.data new file mode 100644 index 0000000000..167efade92 --- /dev/null +++ b/examples/interface-LAMMPS/AlAuMgO_4G/nnp-predict/scaling.data @@ -0,0 +1,152 @@ + 1 1 0.157132975 0.280279850 0.234169887 + 1 2 0.379295480 0.622179554 0.545652438 + 1 3 0.000000000 0.205184943 0.016565410 + 1 4 0.000000000 0.167300348 0.001157152 + 1 5 0.151966913 0.271484679 0.226693585 + 1 6 0.146970813 0.262965553 0.219456059 + 1 7 0.142139079 0.254713806 0.212449681 + 1 8 0.000000000 0.195870161 0.015737764 + 1 9 0.137466301 0.246721045 0.205667064 + 1 10 0.353782761 0.582354440 0.509841176 + 1 11 0.000000000 0.161223776 0.001045601 + 1 12 0.132947244 0.238979140 0.199101062 + 1 13 0.000000000 0.189896965 0.015211084 + 1 14 0.335850555 0.554313578 0.484647540 + 1 15 0.000000000 0.181277733 0.014456530 + 1 16 0.000000000 0.155367918 0.000947149 + 1 17 0.318878593 0.527730187 0.460782520 + 1 18 0.000000000 0.173050590 0.013742142 + 1 19 0.000000000 0.148346286 0.000839806 + 1 20 0.297643309 0.494532513 0.430890275 + 1 21 0.000000000 0.165197661 0.013065428 + 1 22 0.277886581 0.463747515 0.403042058 + 1 23 0.000000000 0.141641990 0.000747240 + 1 24 0.000000000 0.133995570 0.000652336 + 1 25 0.000045839 0.000152977 0.000106156 + 1 26 0.000680557 0.001734569 0.001348253 + 1 27 0.000000000 0.000580779 0.000043631 + 1 28 0.000687759 0.003088959 0.002094644 + 1 29 0.000000000 0.001975434 0.000139623 + 1 30 0.000000000 0.002858460 0.000006888 + 1 31 0.000141138 0.000459099 0.000318440 + 1 32 0.003883787 0.009565828 0.007507740 + 1 33 0.000000000 0.003170549 0.000242247 + 1 34 0.000723568 0.003193167 0.002190205 + 1 35 0.000000000 0.002015297 0.000146458 + 1 36 0.000000000 0.002849448 0.000008773 + 1 37 0.000108434 0.000298716 0.000226841 + 1 38 0.000000000 0.000100115 0.000007401 + 1 39 0.000337708 0.001533218 0.001037438 + 1 40 0.000000000 0.000985795 0.000069101 + 1 41 0.000000000 0.001452136 0.000003254 + 1 42 0.000106418 0.000344381 0.000238835 + 1 43 0.003311665 0.008129974 0.006386328 + 1 44 0.000000000 0.002695024 0.000206016 + 1 45 0.000376278 0.001638804 0.001133000 + 1 46 0.000000000 0.001025445 0.000075936 + 1 47 0.000000000 0.001443125 0.000005139 + 1 48 0.000083248 0.000381693 0.000258183 + 1 49 0.000000000 0.000247525 0.000017187 + 1 50 0.002416132 0.005909800 0.004645819 + 1 51 0.000108377 0.000463908 0.000321719 + 1 52 0.000000000 0.000274278 0.000021729 + 1 53 0.001290479 0.003153152 0.002478974 + 2 1 0.465366967 0.622899345 0.561220975 + 2 2 0.119958755 0.278325877 0.225814452 + 2 3 0.000000000 0.052290984 0.007517999 + 2 4 0.000000000 0.082321041 0.001283464 + 2 5 0.116028951 0.269574643 0.218604882 + 2 6 0.000000000 0.050704245 0.007277988 + 2 7 0.000000000 0.080774026 0.001244257 + 2 8 0.112227916 0.261098625 0.211625571 + 2 9 0.000000000 0.049165662 0.007045642 + 2 10 0.000000000 0.079257371 0.001206277 + 2 11 0.108551431 0.252889168 0.204869161 + 2 12 0.000000000 0.047673774 0.006820716 + 2 13 0.000000000 0.077770417 0.001169485 + 2 14 0.434143302 0.583124772 0.524387947 + 2 15 0.104995412 0.244937885 0.198328532 + 2 16 0.000000000 0.046227162 0.006602973 + 2 17 0.000000000 0.076312525 0.001133843 + 2 18 0.101555912 0.237236656 0.191996789 + 2 19 0.000000000 0.044824453 0.006392183 + 2 20 0.000000000 0.074883070 0.001099315 + 2 21 0.412169183 0.555114045 0.498475487 + 2 22 0.391351992 0.528554985 0.473929551 + 2 23 0.365280511 0.495248302 0.443184422 + 2 24 0.341001583 0.464173404 0.414541640 + 2 25 0.001304697 0.003073521 0.002226260 + 2 26 0.000658301 0.001747757 0.001341772 + 2 27 0.000000000 0.000344142 0.000044915 + 2 28 0.000000000 0.000536511 0.000003397 + 2 29 0.000015937 0.000150219 0.000098274 + 2 30 0.001379442 0.003196463 0.002328076 + 2 31 0.003777691 0.009615500 0.007472434 + 2 32 0.000000000 0.001853922 0.000249329 + 2 33 0.000000000 0.001669339 0.000012712 + 2 34 0.000048632 0.000451042 0.000294796 + 2 35 0.000640789 0.001524318 0.001102595 + 2 36 0.000104063 0.000302504 0.000225688 + 2 37 0.000000000 0.000263424 0.000001016 + 2 38 0.000709709 0.001647260 0.001204412 + 2 39 0.003223454 0.008170246 0.006356350 + 2 40 0.000000000 0.001575067 0.000212033 + 2 41 0.000000000 0.001450386 0.000010331 + 2 42 0.000036630 0.000338360 0.000221102 + 2 43 0.000156394 0.000379666 0.000274392 + 2 44 0.000197865 0.000461980 0.000342083 + 2 45 0.002354467 0.005937258 0.004624037 + 2 46 0.000000000 0.001144834 0.000154222 + 2 47 0.000000000 0.001123811 0.000007188 + 2 48 0.000020441 0.000190427 0.000124392 + 2 49 0.001262549 0.003166018 0.002467335 + 2 50 0.000000000 0.000611201 0.000082309 + 2 51 0.000000000 0.000698347 0.000003778 + 3 1 0.577136243 0.616694005 0.597156670 + 3 2 0.250892044 0.277137801 0.263493918 + 3 3 0.242773609 0.268416021 0.255081906 + 3 4 0.234917966 0.259968821 0.246938538 + 3 5 0.547624822 0.586625275 0.567321361 + 3 6 0.227316605 0.251787552 0.239055233 + 3 7 0.219961293 0.243863841 0.231423681 + 3 8 0.528861449 0.567471623 0.548335377 + 3 9 0.212844062 0.236189575 0.224035841 + 3 10 0.502003814 0.540003438 0.521134901 + 3 11 0.476603541 0.513965831 0.495382352 + 3 12 0.452569426 0.489271173 0.470987896 + 3 13 0.002144387 0.002924649 0.002514975 + 3 14 0.001446412 0.001705750 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b/examples/interface-LAMMPS/H2O_4G/correct-input-data/water.data-h2o-36 new file mode 100644 index 0000000000..1732792245 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/correct-input-data/water.data-h2o-36 @@ -0,0 +1,52 @@ +Generated by RuNNerUC, original comment lines: 7.1142 + +36 atoms +2 atom types + +0.0 7.1141994570823028E+00 xlo xhi +0.0 7.1141994570823028E+00 ylo yhi +0.0 7.1141994570823028E+00 zlo zhi + +Masses + +1 1.0079 +2 15.9994 + +Atoms + + 1 2 0.0 5.4407725127692641E-01 3.6384185563505054E+00 4.4961925860710092E+00 + 2 1 0.0 1.0817027740264313E+00 3.5577846500107415E+00 5.3355115606411010E+00 + 3 1 0.0 1.0837528065326016E+00 4.1098074970750078E+00 3.7986666445490349E+00 + 4 2 0.0 5.9228924412533273E+00 2.6466268911619726E+00 1.2239688914990485E+00 + 5 1 0.0 5.3892796692767426E+00 2.4596400077893872E+00 3.9917001035611654E-01 + 6 1 0.0 6.3950052963992130E+00 3.5224871395184847E+00 1.1240808724238647E+00 + 7 2 0.0 4.1822746115542317E+00 1.5987872250691670E+00 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5.9487319907798231E+00 +719 1 0.0 1.3751504013703714E+01 1.7024861026994632E+01 6.2904809822292362E+00 +720 1 0.0 1.2981525033816267E+01 1.5630577022414558E+01 5.9302979968823131E+00 +721 2 0.0 1.1359190005058706E+00 1.2558577027686010E+01 7.1101410234993176E+00 +722 1 0.0 3.5555899997235835E-01 1.3145807039876059E+01 6.8952040054044383E+00 +723 1 0.0 1.8162910013391120E+00 1.2628075034683143E+01 6.3805759949640883E+00 +724 2 0.0 3.5445290001230596E+00 8.5273250024454565E+00 1.8525293026523997E+01 +725 1 0.0 3.7665219983245608E+00 9.0847430228224244E+00 1.7725290024099518E+01 +726 1 0.0 2.9047139978250716E+00 9.0248459837566148E+00 1.9111048026038070E+01 +727 2 0.0 8.3271649933125165E+00 8.9521479892612721E+00 1.3660203006110430E+01 +728 1 0.0 7.6144619848588890E+00 9.5921119919858899E+00 1.3372974031192378E+01 +729 1 0.0 8.0817569990266680E+00 8.0274249991575282E+00 1.3369236029226171E+01 +730 2 0.0 7.0541169795056353E+00 1.2759896040741253E+01 7.7163560088964864E+00 +731 1 0.0 6.2757520225578372E+00 1.2137500033412250E+01 7.7986369792980614E+00 +732 1 0.0 7.7045580030304386E+00 1.2393996036503349E+01 7.0507399822311427E+00 +733 2 0.0 8.8963959952705380E+00 1.7381622024420789E+01 1.7715538023701086E+01 +734 1 0.0 8.0837689836915398E+00 1.6830631025287371E+01 1.7525681026026820E+01 +735 1 0.0 9.2110289940315955E+00 1.7201396025484438E+01 1.8647485023550498E+01 +736 2 0.0 1.8084033023009905E+01 7.7934830049570438E+00 5.7936099892834161E+00 +737 1 0.0 1.8196518026159566E+01 8.0380109775449693E+00 6.7567049946445028E+00 +738 1 0.0 1.8978413023722357E+01 7.5921139846555858E+00 5.3941910010506460E+00 +739 2 0.0 1.0292320015272002E+01 6.6018300130690770E+00 4.8409750022588041E+00 +740 1 0.0 9.9592850378345581E+00 5.9887210128335280E+00 5.5573450129725597E+00 +741 1 0.0 1.0639971025964531E+01 6.0613879975444451E+00 4.0747749985288246E+00 +742 2 0.0 4.3431360013205831E+00 7.7445060138504740E+00 6.6885350107701065E+00 +743 1 0.0 3.6088989995048033E+00 7.0805139791206457E+00 6.5470769998127638E+00 +744 1 0.0 4.0253689981674574E+00 8.4670829927573532E+00 7.3024620131347318E+00 +745 2 0.0 1.6676560022644992E+01 2.7681690003668029E+00 1.2790233029263002E+01 +746 1 0.0 1.6578238024142120E+01 3.3823579983674126E+00 1.2007223007695710E+01 +747 1 0.0 1.5926019023405868E+01 2.9240269974002655E+00 1.3432414019903108E+01 +748 2 0.0 1.1136732002968680E+01 3.5561379997655074E+00 1.1993247014274450E+01 +749 1 0.0 1.0957697012592215E+01 4.4755559989364393E+00 1.2343414050923052E+01 +750 1 0.0 1.1953278048036951E+01 3.1844040020146558E+00 1.2434911012836686E+01 +751 2 0.0 8.5855710086203878E+00 1.4614609022249748E+01 1.2741560050462779E+01 +752 1 0.0 9.0922540053683285E+00 1.5424202022762016E+01 1.3037923047343277E+01 +753 1 0.0 7.9885930230704600E+00 1.4305517043331857E+01 1.3481884045414944E+01 +754 2 0.0 1.3833893042091290E+01 7.4024589897971689E+00 1.4331337028118599E+01 +755 1 0.0 1.4728634026328368E+01 7.0474870240943526E+00 1.4602323025037228E+01 +756 1 0.0 1.3842727020576451E+01 8.4012120192657793E+00 1.4380463035527114E+01 +757 2 0.0 9.0429799870945615E+00 2.6061570004870283E+00 5.2591879995194200E+00 +758 1 0.0 8.4684860002905502E+00 3.4182969996973940E+00 5.3610939829619317E+00 +759 1 0.0 9.7318690157238645E+00 2.7716050009000539E+00 4.5534550010431021E+00 +760 2 0.0 1.1964111046345371E+01 1.0484564009623561E+01 1.6277865022918416E+01 +761 1 0.0 1.2197761040562144E+01 9.5471629919558474E+00 1.6536264026628274E+01 +762 1 0.0 1.2587834018442697E+01 1.1120797048438851E+01 1.6731934025355613E+01 +763 2 0.0 1.2356654011764853E+01 2.3614500019576593E-01 8.4160419988663016E+00 +764 1 0.0 1.1824028049446891E+01 6.5078099871424921E-01 9.1538680128052050E+00 +765 1 0.0 1.1746962014600767E+01 1.9720474024499346E+01 7.6627299843413574E+00 +766 2 0.0 8.2954529907319063E+00 1.6941897026402810E+01 1.5046029023195610E+01 +767 1 0.0 9.2826590030845129E+00 1.6807709026565885E+01 1.5132158022088607E+01 +768 1 0.0 8.1045429992055418E+00 1.7505451025850366E+01 1.4242313017136258E+01 diff --git a/examples/interface-LAMMPS/H2O_4G/hdnnp-data/hardness.001.data b/examples/interface-LAMMPS/H2O_4G/hdnnp-data/hardness.001.data new file mode 100644 index 0000000000..eeccca8ba7 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/hdnnp-data/hardness.001.data @@ -0,0 +1 @@ + 12.5140142151 diff --git a/examples/interface-LAMMPS/H2O_4G/hdnnp-data/hardness.008.data b/examples/interface-LAMMPS/H2O_4G/hdnnp-data/hardness.008.data new file mode 100644 index 0000000000..2f8cbafd74 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/hdnnp-data/hardness.008.data @@ -0,0 +1 @@ + 9.0176209746 diff --git a/examples/interface-LAMMPS/H2O_4G/hdnnp-data/input.nn b/examples/interface-LAMMPS/H2O_4G/hdnnp-data/input.nn new file mode 100755 index 0000000000..cfc0fb07dd --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/hdnnp-data/input.nn @@ -0,0 +1,175 @@ +## ############################################################# +### This is the input file for RuNNer +### ############################################################# +### General remarks: +### - commands can be switched off by using the # character at the BEGINNING of the line +### - the input file can be structured by blank lines and comment lines +### - the order of the keywords is arbitrary +### - if keywords are missing, default values will be used and written to runner.out +### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message + +### THIS INPUT.NN IS AN EXAMPLE, IT IS NOT A REALISTIC CASE +### It contains only a subset of all keywords + +######################################################################################################################## +### general keywords +######################################################################################################################## +use_electrostatics +use_short_nn +nnp_gen 4 # nnp_type_gen --> nnp_gen +runner_mode 3 +parallel_mode 1 +number_of_elements 2 +elements H O +random_seed 10 +random_number_type 5 +remove_atom_energies +atom_energy H -0.458907306351869 +atom_energy O -74.94518524 +initial_hardness H 10.0 ## fixed_atomhardness--> initial_hardness +initial_hardness O 10.0 +fixed_gausswidth H 0.585815056466 +fixed_gausswidth O 1.379499971678 +energy_threshold 100.0d0 +bond_threshold 0.4d0 +ewald_prec 1.0e-4 # for optimal combination of ewald parameters +screen_electrostatics 4.8 8.0 +######################################################################################################################## +### NN structure of the electrostatic-range NN +######################################################################################################################## +global_hidden_layers_electrostatic 2 +global_nodes_electrostatic 15 15 +global_activation_electrostatic t t l +global_hidden_layers_short 2 +global_nodes_short 15 15 +global_activation_short t t l +## element_hidden_layers_electrostatic needs to take care !!! should check the output +######################################################################################################################## +### symmetry function generation ( mode 1): +######################################################################################################################## +test_fraction 0.1 + +######################################################################################################################## +### symmetry function definitions (all modes): +######################################################################################################################## +cutoff_type 2 + + +# radial H H +symfunction H 2 H 0.001 0.0 8.00 +symfunction H 2 H 0.01 0.0 8.00 +symfunction H 2 H 0.03 0.0 8.00 +symfunction H 2 H 0.06 0.0 8.00 +symfunction H 2 H 0.15 1.9 8.00 +symfunction H 2 H 0.30 1.9 8.00 +symfunction H 2 H 0.60 1.9 8.00 +symfunction H 2 H 1.50 1.9 8.00 + +# radial H O / O H +symfunction H 2 O 0.001 0.0 8.00 +symfunction H 2 O 0.01 0.0 8.00 +symfunction H 2 O 0.03 0.0 8.00 +symfunction H 2 O 0.06 0.0 8.00 +symfunction H 2 O 0.15 0.9 8.00 +symfunction H 2 O 0.30 0.9 8.00 +symfunction H 2 O 0.60 0.9 8.00 +symfunction H 2 O 1.50 0.9 8.00 + +symfunction O 2 H 0.001 0.0 8.00 +symfunction O 2 H 0.01 0.0 8.00 +symfunction O 2 H 0.03 0.0 8.00 +symfunction O 2 H 0.06 0.0 8.00 +symfunction O 2 H 0.15 0.9 8.00 +symfunction O 2 H 0.30 0.9 8.00 +symfunction O 2 H 0.60 0.9 8.00 +symfunction O 2 H 1.50 0.9 8.00 + +# radial O O +symfunction O 2 O 0.001 0.0 8.00 +symfunction O 2 O 0.01 0.0 8.00 +symfunction O 2 O 0.03 0.0 8.00 +symfunction O 2 O 0.06 0.0 8.00 +symfunction O 2 O 0.15 4.0 8.00 +symfunction O 2 O 0.30 4.0 8.00 +symfunction O 2 O 0.60 4.0 8.00 +symfunction O 2 O 1.50 4.0 8.00 + +# angular +symfunction H 3 O H 0.2 1.0 1.0 8.00000 + +symfunction O 3 H H 0.07 1.0 1.0 8.00000 +symfunction H 3 O H 0.07 1.0 1.0 8.00000 +symfunction O 3 H H 0.07 -1.0 1.0 8.00000 +symfunction H 3 O H 0.07 -1.0 1.0 8.00000 + +symfunction O 3 H H 0.03 1.0 1.0 8.00000 +symfunction H 3 O H 0.03 1.0 1.0 8.00000 +symfunction O 3 H H 0.03 -1.0 1.0 8.00000 +symfunction H 3 O H 0.03 -1.0 1.0 8.00000 + +symfunction O 3 H H 0.01 1.0 4.0 8.00000 +symfunction H 3 O H 0.01 1.0 4.0 8.00000 +symfunction O 3 H H 0.01 -1.0 4.0 8.00000 +symfunction H 3 O H 0.01 -1.0 4.0 8.00000 + +symfunction O 3 O H 0.03 1.0 1.0 8.00000 +symfunction O 3 O H 0.03 -1.0 1.0 8.00000 +symfunction O 3 O H 0.001 1.0 4.0 8.00000 +symfunction O 3 O H 0.001 -1.0 4.0 8.00000 + +symfunction H 3 O O 0.03 1.0 1.0 8.00000 +symfunction H 3 O O 0.03 -1.0 1.0 8.00000 +symfunction H 3 O O 0.001 1.0 4.0 8.00000 +symfunction H 3 O O 0.001 -1.0 4.0 8.00000 + +#symfunction O 3 O O 0.03 1.0 1.0 8.00000 +#symfunction O 3 O O 0.03 -1.0 1.0 8.00000 +#symfunction O 3 O O 0.001 1.0 4.0 8.00000 +#symfunction O 3 O O 0.001 -1.0 4.0 8.00000 + +######################################################################################################################## +### fitting (mode 2):general inputs for electrostatic range AND electrostatic part: +######################################################################################################################## +epochs 30 +points_in_memory 500 +mix_all_points +scale_symmetry_functions +center_symmetry_functions +fitting_unit eV +######################################################################################################################## +### fitting options ( mode 2): electrostatic range part only: +######################################################################################################################## +optmode_short_energy 1 +optmode_short_force 1 +short_energy_error_threshold 0.8 +short_force_error_threshold 0.8 +kalman_lambda_charge 0.98000 +kalman_nue_charge 0.99870 +kalman_lambda_short 0.98000 +kalman_nue_short 0.99870 +#use_old_weights_electrostatic +#force_update_scaling -1.0d0 +#electrostatic_energy_group 1 +#electrostatic_energy_fraction 1.00 +#electrostatic_force_group 1 + +#short_force_fraction 0.025 +#use_short_forces +weights_min -1.0 +weights_max 1.0 +#precondition_weights +#repeated_energy_update +#nguyen_widrow_weights_short +regularize_fit_param 0.00001 ## 4G cases L2 regularization +######################################################################################################################## +### output options for mode 2 (fitting): +######################################################################################################################## +#write_trainpoints +#write_trainforces +write_traincharges +######################################################################################################################## +### output options for mode 3 (prediction): +######################################################################################################################## +calculate_forces +#calculate_stress + diff --git a/examples/interface-LAMMPS/H2O_4G/hdnnp-data/scaling.data b/examples/interface-LAMMPS/H2O_4G/hdnnp-data/scaling.data new file mode 100644 index 0000000000..bf9ab69d26 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/hdnnp-data/scaling.data @@ -0,0 +1,54 @@ + 1 1 0.332976205 0.801624245 0.529022897 + 1 2 0.302337347 0.559557103 0.444982986 + 1 3 0.279156661 0.689216779 0.447398011 + 1 4 0.281666680 0.500530512 0.405813837 + 1 5 0.184597589 0.500915675 0.315606906 + 1 6 0.246938750 0.411905369 0.340350304 + 1 7 0.108144137 0.321581311 0.196758358 + 1 8 0.206524003 0.332910999 0.275222988 + 1 9 0.192266492 0.337437016 0.268862686 + 1 10 0.137888800 0.438702601 0.258407517 + 1 11 0.123155815 0.264414914 0.211036382 + 1 12 0.079044824 0.323909809 0.164714948 + 1 13 0.060252990 0.223808509 0.148947959 + 1 14 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-0.3577272526 + 0.0341348973 + 0.5814419788 + -0.2362748063 + 0.2740130803 + 0.2005358826 + -0.1874268796 + 0.7040305804 diff --git a/examples/interface-LAMMPS/H2O_4G/md.lmp b/examples/interface-LAMMPS/H2O_4G/md.lmp new file mode 100644 index 0000000000..66a05c3979 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/md.lmp @@ -0,0 +1,63 @@ +############################################################################### +# MD simulation for carbon chain +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "water.data" +# Timesteps +variable numSteps equal 10 +variable dt equal 0.0005 +# NN +#variable hdnnpCutoff equal 4.238709440998 #8.01 +variable hdnnpCutoff equal 4.23341767420363 #8.00000001 +variable hdnnpDir string "hdnnp-data" +# Masses +variable mass_H equal 1.00794 +variable mass_O equal 15.9994 + +# Conversions +variable c1 equal 1.8897261328 +variable c2 equal 0.0367493254 +#variable c1 equal 1.0 +#variable c2 equal 1.0 + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary p p p +atom_style charge +atom_modify map yes +read_data ${cfgFile} +mass 1 ${mass_H} +mass 2 ${mass_O} +timestep ${dt} +thermo 1 + +neighbor 0.0 bin +neigh_modify delay 10 # Seems this was the default previously (29Oct2020). + +############################################################################### +# NN +############################################################################### +pair_style hdnnp/4g dir ${hdnnpDir} showew no showewsum 10 resetew no maxew 1000000 cflength ${c1} cfenergy ${c2} emap "1:H,2:O" +pair_coeff * * ${hdnnpCutoff} +kspace_style hdnnp ewald 1.0e-6 +#fix 1 all hdnnp 1 1.0e-5 1.0e-4 1.0e-2 100 nnp +fix 1 all hdnnp 1 1.0e-7 1.0e-1 1.0e-1 100 nnp nnp 1 # No clue whether this is the right flag at the end. + + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve +#dump 1 all atom 1 traj.dump + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/interface-LAMMPS/H2O_4G/nnp-predict/hardness.001.data b/examples/interface-LAMMPS/H2O_4G/nnp-predict/hardness.001.data new file mode 100644 index 0000000000..eeccca8ba7 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/nnp-predict/hardness.001.data @@ -0,0 +1 @@ + 12.5140142151 diff --git a/examples/interface-LAMMPS/H2O_4G/nnp-predict/hardness.008.data b/examples/interface-LAMMPS/H2O_4G/nnp-predict/hardness.008.data new file mode 100644 index 0000000000..2f8cbafd74 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/nnp-predict/hardness.008.data @@ -0,0 +1 @@ + 9.0176209746 diff --git a/examples/interface-LAMMPS/H2O_4G/nnp-predict/input.data b/examples/interface-LAMMPS/H2O_4G/nnp-predict/input.data new file mode 100644 index 0000000000..e4d00ad8a1 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/nnp-predict/input.data @@ -0,0 +1,44 @@ +begin +comment Values for ['energy', 'charge', 'force of atom'] were set to default values +lattice 1.3443888628000000E+01 0.0000000000000000E+00 0.0000000000000000E+00 +lattice 0.0000000000000000E+00 1.3443888628000000E+01 0.0000000000000000E+00 +lattice 0.0000000000000000E+00 0.0000000000000000E+00 1.3443888628000000E+01 +atom 1.0281570000000000E+00 6.8756146279999992E+00 8.4965726279999991E+00 O -2.8256347534442394E-01 0.0000000000000000E+00 -2.9283692352115263E+00 -2.1942965040430695E-01 -7.8128583031086121E-02 +atom 2.0441220000000002E+00 6.7232386279999998E+00 1.0082655627999999E+01 H 1.2277837277223855E-01 0.0000000000000000E+00 1.9482823532380507E+00 3.1792184330776235E-01 2.2469585801699852E+00 +atom 2.0479959999999999E+00 7.7664106280000009E+00 7.1784396279999996E+00 H 1.2747526484297358E-01 0.0000000000000000E+00 8.9380603941331793E-01 2.7100055065674783E-01 -2.0117787682273802E-01 +atom 1.1192644628000000E+01 5.0014000000000003E+00 2.3129659999999999E+00 O -2.0320633594884582E-01 0.0000000000000000E+00 2.8271820248615240E+00 3.8199554621973880E-01 3.5845413797895835E+00 +atom 1.0184262628000001E+01 4.6480459999999999E+00 7.5432200000000005E-01 H 1.5077528010356028E-01 0.0000000000000000E+00 -1.1936480532254552E+00 -2.3140105928612867E-01 -2.3175789249624752E+00 +atom 1.2084808628000001E+01 6.6565360000000000E+00 2.1242049999999999E+00 H 1.0545961981723478E-01 0.0000000000000000E+00 -3.4603179700863103E+00 -1.3868476023525984E+00 -1.0545047365673061E+00 +atom 7.9033536279999996E+00 3.0212699999999999E+00 6.9125696280000009E+00 O -2.3518637803977813E-01 0.0000000000000000E+00 4.2372154470977669E-01 1.8073177424203288E-01 3.0951853714291844E-01 +atom 8.8537476279999989E+00 1.9672839999999998E+00 5.6648090000000000E+00 H 1.1004800576876206E-01 0.0000000000000000E+00 7.7840436378832478E-02 5.2958376699306908E-01 -2.2524862715071485E+00 +atom 7.7022636279999999E+00 2.0587849999999999E+00 8.5263396280000006E+00 H 1.2457842239861067E-01 0.0000000000000000E+00 -2.3265786214644388E-01 2.0210037813235607E-01 2.1477750389810897E+00 +atom 7.8743726279999988E+00 1.0387881627999999E+01 1.1051255628000000E+01 O -2.2058240732065956E-01 0.0000000000000000E+00 -3.4565727104575689E-01 2.5528939648646114E+00 -3.8700539207258222E+00 +atom 9.2086816279999990E+00 9.1761326279999995E+00 1.1619012628000000E+01 H 1.2797577200732241E-01 0.0000000000000000E+00 1.5078420052350747E-01 -2.1634546570493454E+00 1.1018383816958270E+00 +atom 8.1086836279999996E+00 1.0767815628000001E+01 9.2150046279999991E+00 H 1.1917909653994410E-01 0.0000000000000000E+00 -1.8331532626603048E-01 -1.1747870971878707E+00 6.7991269031499835E+00 +atom 3.8907250000000002E+00 8.2707826279999992E+00 1.8582870000000000E+00 O -2.6183165626861749E-01 0.0000000000000000E+00 7.0244269367983858E-01 -1.1111776866062637E+00 1.6022264684182443E+00 +atom 3.6563539999999999E+00 7.5442296280000001E+00 1.2963000000000000E-01 H 1.2478853272527493E-01 0.0000000000000000E+00 -9.2733544280998526E-01 1.2708147351939285E+00 -2.1037967614413642E+00 +atom 4.0430140000000003E+00 6.8683186279999999E+00 3.1156519999999999E+00 H 9.9154652510639180E-02 0.0000000000000000E+00 1.8655372292621097E-01 1.3721069236350780E+00 -8.0692036225339978E-02 +atom 4.7885530000000003E+00 1.2039224627999999E+01 6.5503749999999998E+00 O -2.7263628991795935E-01 0.0000000000000000E+00 -1.1292771081345108E+00 -9.0760280713822394E-01 -1.5762793800709740E-01 +atom 4.6924869999999999E+00 1.1124599999999998E-01 5.4261629999999998E+00 H 1.1434733344402727E-01 0.0000000000000000E+00 -9.8293571178456843E-02 1.0082309420963453E+00 -5.8307946025373902E-01 +atom 5.5979869999999998E+00 1.2520381627999999E+01 8.1887696280000011E+00 H 1.1263403257973484E-01 0.0000000000000000E+00 -5.8627648478079153E-01 3.6509413794346102E-01 -1.1572643025824929E-01 +atom 4.8991110000000004E+00 3.3909980000000002E+00 1.3105727628000000E+01 O -2.7372231339107428E-01 0.0000000000000000E+00 1.0579372843395085E+00 1.1643437983388070E+00 1.2704653330434790E+00 +atom 4.0105050000000002E+00 2.4129309999999999E+00 1.1754866627999998E+01 H 1.3658196132808181E-01 0.0000000000000000E+00 -2.7108633263781412E+00 -1.3756498865725824E+00 -1.9441844331785387E+00 +atom 3.6245479999999999E+00 4.2738459999999998E+00 7.4217699999999998E-01 H 9.0172983387061936E-02 0.0000000000000000E+00 -4.0507125991796944E-01 -1.6796036702909269E+00 -1.4731090864111782E-01 +atom 1.1298731628000001E+01 1.2691991628000000E+01 4.4432619999999998E+00 O -2.5637106920821656E-01 0.0000000000000000E+00 -2.8283675022934567E+00 1.2289852492197650E+00 4.1542682352061577E-01 +atom 1.1360284628000000E+01 1.3169730628000000E+01 6.2705669999999998E+00 H 1.1847178479117913E-01 0.0000000000000000E+00 1.1556735718984914E+00 -7.1030210772562219E-01 1.8949900190596836E+00 +atom 1.2995212628000001E+01 1.2061610628000000E+01 3.8995389999999999E+00 H 1.3767024849619425E-01 0.0000000000000000E+00 2.6903838305192367E+00 -9.4978647053313636E-01 -1.3294639818356677E+00 +atom 1.2764696627999999E+01 1.5378200000000000E-01 1.0125363628000001E+01 O -2.2955663167309948E-01 0.0000000000000000E+00 -1.6237528514361890E+00 -1.7798214425490955E+00 -1.0320891233855798E+00 +atom 1.1249884628000000E+01 1.2710340000000000E+00 9.9575596280000003E+00 H 1.3433991100513273E-01 0.0000000000000000E+00 5.0306812661490385E-01 6.4606072642904910E-02 1.2035900324044681E-01 +atom 8.4522900000000001E-01 1.2098420000000001E+00 1.0488610628000000E+01 H 1.3761295680984548E-01 0.0000000000000000E+00 2.3015420911979811E+00 1.6439986297320848E+00 8.3471087553758916E-01 +atom 8.8003156279999999E+00 8.1706076280000008E+00 6.1612819999999999E+00 O -2.3412971681479525E-01 0.0000000000000000E+00 4.7823813809165792E+00 4.5453029913715861E+00 -3.2129178691353069E+00 +atom 7.4882556279999992E+00 6.9694036280000002E+00 6.7989826280000001E+00 H 1.1415705913922836E-01 0.0000000000000000E+00 -5.1160186352989925E+00 -5.4134409660054734E+00 1.5484060579498757E+00 +atom 8.7161336279999979E+00 9.7785886279999996E+00 7.1504036279999994E+00 H 1.1034962117814637E-01 0.0000000000000000E+00 1.2454296150285611E+00 -3.2682486247550602E-01 -2.3874749634340637E+00 +atom 3.1354829999999998E+00 3.7303289999999998E+00 4.8504040000000002E+00 O -2.2006091505768430E-01 0.0000000000000000E+00 -1.2832754207323978E+00 -1.4767181813664836E+00 -1.6544059920266059E+00 +atom 2.5813579999999998E+00 2.1819250000000001E+00 3.9195639999999994E+00 H 1.3641844939732595E-01 0.0000000000000000E+00 -1.8176714669371274E+00 -3.7272692203761654E-01 -2.5341845334408836E-01 +atom 4.8735999999999997E+00 4.2146619999999997E+00 4.2887670000000000E+00 H 1.1534057032122745E-01 0.0000000000000000E+00 2.8905795806354817E+00 1.2490296651432349E+00 4.4489626141762684E-01 +atom 1.2696753628000000E+01 9.5005796279999988E+00 1.3316218628000000E+01 O -2.0590918634609703E-01 0.0000000000000000E+00 3.6313703894020638E-01 -2.9210646513595001E-01 7.7685508623495614E-01 +atom 1.2096099628000001E+01 8.3233416279999997E+00 1.2230289999999999E+00 H 1.0721155781927215E-01 0.0000000000000000E+00 2.1821057837216054E+00 -8.1494640847712330E-01 1.1342821157055141E-02 +atom 1.1423969628000000E+01 1.0874955628000000E+01 1.3066854628000000E+01 H 1.1823488614823414E-01 0.0000000000000000E+00 4.8731746833591910E-01 4.0378869734607514E+00 -3.3331890572564116E-01 +energy -9.1689613647168449E+02 +charge 1.2212453270876722E-15 +end diff --git a/examples/interface-LAMMPS/H2O_4G/nnp-predict/input.nn b/examples/interface-LAMMPS/H2O_4G/nnp-predict/input.nn new file mode 100755 index 0000000000..cfc0fb07dd --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/nnp-predict/input.nn @@ -0,0 +1,175 @@ +## ############################################################# +### This is the input file for RuNNer +### ############################################################# +### General remarks: +### - commands can be switched off by using the # character at the BEGINNING of the line +### - the input file can be structured by blank lines and comment lines +### - the order of the keywords is arbitrary +### - if keywords are missing, default values will be used and written to runner.out +### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message + +### THIS INPUT.NN IS AN EXAMPLE, IT IS NOT A REALISTIC CASE +### It contains only a subset of all keywords + +######################################################################################################################## +### general keywords +######################################################################################################################## +use_electrostatics +use_short_nn +nnp_gen 4 # nnp_type_gen --> nnp_gen +runner_mode 3 +parallel_mode 1 +number_of_elements 2 +elements H O +random_seed 10 +random_number_type 5 +remove_atom_energies +atom_energy H -0.458907306351869 +atom_energy O -74.94518524 +initial_hardness H 10.0 ## fixed_atomhardness--> initial_hardness +initial_hardness O 10.0 +fixed_gausswidth H 0.585815056466 +fixed_gausswidth O 1.379499971678 +energy_threshold 100.0d0 +bond_threshold 0.4d0 +ewald_prec 1.0e-4 # for optimal combination of ewald parameters +screen_electrostatics 4.8 8.0 +######################################################################################################################## +### NN structure of the electrostatic-range NN +######################################################################################################################## +global_hidden_layers_electrostatic 2 +global_nodes_electrostatic 15 15 +global_activation_electrostatic t t l +global_hidden_layers_short 2 +global_nodes_short 15 15 +global_activation_short t t l +## element_hidden_layers_electrostatic needs to take care !!! should check the output +######################################################################################################################## +### symmetry function generation ( mode 1): +######################################################################################################################## +test_fraction 0.1 + +######################################################################################################################## +### symmetry function definitions (all modes): +######################################################################################################################## +cutoff_type 2 + + +# radial H H +symfunction H 2 H 0.001 0.0 8.00 +symfunction H 2 H 0.01 0.0 8.00 +symfunction H 2 H 0.03 0.0 8.00 +symfunction H 2 H 0.06 0.0 8.00 +symfunction H 2 H 0.15 1.9 8.00 +symfunction H 2 H 0.30 1.9 8.00 +symfunction H 2 H 0.60 1.9 8.00 +symfunction H 2 H 1.50 1.9 8.00 + +# radial H O / O H +symfunction H 2 O 0.001 0.0 8.00 +symfunction H 2 O 0.01 0.0 8.00 +symfunction H 2 O 0.03 0.0 8.00 +symfunction H 2 O 0.06 0.0 8.00 +symfunction H 2 O 0.15 0.9 8.00 +symfunction H 2 O 0.30 0.9 8.00 +symfunction H 2 O 0.60 0.9 8.00 +symfunction H 2 O 1.50 0.9 8.00 + +symfunction O 2 H 0.001 0.0 8.00 +symfunction O 2 H 0.01 0.0 8.00 +symfunction O 2 H 0.03 0.0 8.00 +symfunction O 2 H 0.06 0.0 8.00 +symfunction O 2 H 0.15 0.9 8.00 +symfunction O 2 H 0.30 0.9 8.00 +symfunction O 2 H 0.60 0.9 8.00 +symfunction O 2 H 1.50 0.9 8.00 + +# radial O O +symfunction O 2 O 0.001 0.0 8.00 +symfunction O 2 O 0.01 0.0 8.00 +symfunction O 2 O 0.03 0.0 8.00 +symfunction O 2 O 0.06 0.0 8.00 +symfunction O 2 O 0.15 4.0 8.00 +symfunction O 2 O 0.30 4.0 8.00 +symfunction O 2 O 0.60 4.0 8.00 +symfunction O 2 O 1.50 4.0 8.00 + +# angular +symfunction H 3 O H 0.2 1.0 1.0 8.00000 + +symfunction O 3 H H 0.07 1.0 1.0 8.00000 +symfunction H 3 O H 0.07 1.0 1.0 8.00000 +symfunction O 3 H H 0.07 -1.0 1.0 8.00000 +symfunction H 3 O H 0.07 -1.0 1.0 8.00000 + +symfunction O 3 H H 0.03 1.0 1.0 8.00000 +symfunction H 3 O H 0.03 1.0 1.0 8.00000 +symfunction O 3 H H 0.03 -1.0 1.0 8.00000 +symfunction H 3 O H 0.03 -1.0 1.0 8.00000 + +symfunction O 3 H H 0.01 1.0 4.0 8.00000 +symfunction H 3 O H 0.01 1.0 4.0 8.00000 +symfunction O 3 H H 0.01 -1.0 4.0 8.00000 +symfunction H 3 O H 0.01 -1.0 4.0 8.00000 + +symfunction O 3 O H 0.03 1.0 1.0 8.00000 +symfunction O 3 O H 0.03 -1.0 1.0 8.00000 +symfunction O 3 O H 0.001 1.0 4.0 8.00000 +symfunction O 3 O H 0.001 -1.0 4.0 8.00000 + +symfunction H 3 O O 0.03 1.0 1.0 8.00000 +symfunction H 3 O O 0.03 -1.0 1.0 8.00000 +symfunction H 3 O O 0.001 1.0 4.0 8.00000 +symfunction H 3 O O 0.001 -1.0 4.0 8.00000 + +#symfunction O 3 O O 0.03 1.0 1.0 8.00000 +#symfunction O 3 O O 0.03 -1.0 1.0 8.00000 +#symfunction O 3 O O 0.001 1.0 4.0 8.00000 +#symfunction O 3 O O 0.001 -1.0 4.0 8.00000 + +######################################################################################################################## +### fitting (mode 2):general inputs for electrostatic range AND electrostatic part: +######################################################################################################################## +epochs 30 +points_in_memory 500 +mix_all_points +scale_symmetry_functions +center_symmetry_functions +fitting_unit eV +######################################################################################################################## +### fitting options ( mode 2): electrostatic range part only: +######################################################################################################################## +optmode_short_energy 1 +optmode_short_force 1 +short_energy_error_threshold 0.8 +short_force_error_threshold 0.8 +kalman_lambda_charge 0.98000 +kalman_nue_charge 0.99870 +kalman_lambda_short 0.98000 +kalman_nue_short 0.99870 +#use_old_weights_electrostatic +#force_update_scaling -1.0d0 +#electrostatic_energy_group 1 +#electrostatic_energy_fraction 1.00 +#electrostatic_force_group 1 + +#short_force_fraction 0.025 +#use_short_forces +weights_min -1.0 +weights_max 1.0 +#precondition_weights +#repeated_energy_update +#nguyen_widrow_weights_short +regularize_fit_param 0.00001 ## 4G cases L2 regularization +######################################################################################################################## +### output options for mode 2 (fitting): +######################################################################################################################## +#write_trainpoints +#write_trainforces +write_traincharges +######################################################################################################################## +### output options for mode 3 (prediction): +######################################################################################################################## +calculate_forces +#calculate_stress + diff --git a/examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-1np b/examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-1np new file mode 100644 index 0000000000..42530540a2 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-1np @@ -0,0 +1,12 @@ +begin +comment 7.1142 +comment Values for ['energy', 'charge', 'force of atom'] were set to default values +lattice 50.0 0.00 0.00 +lattice 0.00 50.0 0.00 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+charge 0.0 +end diff --git a/examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-angs-p b/examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-angs-p new file mode 100644 index 0000000000..964ce28a77 --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/nnp-predict/other-input-data/input.data-angs-p @@ -0,0 +1,43 @@ +begin +lattice 7.1142 0.0000 0.0000 +lattice 0.0000 7.1142 0.0000 +lattice 0.0000 0.0000 7.1142 +atom 0.544077 -3.475781 -2.618007 O 0.0 0.0 0.0 0.0 0.0 +atom 1.081703 -3.556415 -1.778688 H 0.0 0.0 0.0 0.0 0.0 +atom 1.083753 -3.004392 -3.315533 H 0.0 0.0 0.0 0.0 0.0 +atom -1.191307 2.646627 1.223969 O 0.0 0.0 0.0 0.0 0.0 +atom -1.724920 2.459640 0.399170 H 0.0 0.0 0.0 0.0 0.0 +atom -0.719194 3.522487 1.124081 H 0.0 0.0 0.0 0.0 0.0 +atom -2.931925 1.598787 -3.456225 O 0.0 0.0 0.0 0.0 0.0 +atom -2.428998 1.041042 2.997688 H 0.0 0.0 0.0 0.0 0.0 +atom -3.038337 1.089462 -2.602255 H 0.0 0.0 0.0 0.0 0.0 +atom -2.947261 -1.617169 -1.266127 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5.0274902077599082E+00 7.0466394028585562E+00 + 35 1 0.0 6.4009802362616730E+00 4.4045226890456011E+00 6.4719907227395035E-01 + 36 1 0.0 6.0453043590359563E+00 5.7547786630259594E+00 6.9146816574097389E+00 diff --git a/examples/interface-LAMMPS/H2O_4G/water.data.q b/examples/interface-LAMMPS/H2O_4G/water.data.q new file mode 100644 index 0000000000..75b023fb9b --- /dev/null +++ b/examples/interface-LAMMPS/H2O_4G/water.data.q @@ -0,0 +1,52 @@ +Generated by RuNNerUC, original comment lines: 7.1142 + +36 atoms +2 atom types + +0.0 7.1141994570823028E+00 xlo xhi +0.0 7.1141994570823028E+00 ylo yhi +0.0 7.1141994570823028E+00 zlo zhi + +Masses + +1 1.0079 +2 15.9994 + +Atoms + + 1 2 -2.8256347534442394E-01 5.4407725127692641E-01 3.6384185563505054E+00 4.4961925860710092E+00 + 2 1 1.2277837277223856E-01 1.0817027740264313E+00 3.5577846500107415E+00 5.3355115606411010E+00 + 3 1 1.2747526484297361E-01 1.0837528065326016E+00 4.1098074970750078E+00 3.7986666445490349E+00 + 4 2 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1.2478853272527497E-01 1.9348592034245695E+00 3.9922343756879437E+00 6.8597241552630556E-02 + 15 1 9.9154652510639193E-02 2.1394708629072521E+00 3.6345576794364582E+00 1.6487320283725717E+00 + 16 2 -2.7263628991795930E-01 2.5339931098401118E+00 6.3708832825217518E+00 3.4663091578748157E+00 + 17 1 1.1434733344402730E-01 2.4831571721174011E+00 5.8868847749471091E-02 2.8714017898244730E+00 + 18 1 1.1263403257973484E-01 2.9623271345173623E+00 6.6255006006868298E+00 4.3333102537280004E+00 + 19 2 -2.7372231339107417E-01 2.5924978836700570E+00 1.7944388560555977E+00 6.9352523630401910E+00 + 20 1 1.3658196132808181E-01 2.1222678410324201E+00 1.2768680911581454E+00 6.2204075098346969E+00 + 21 1 9.0172983387062006E-02 1.9180281931273930E+00 2.2616218963260346E+00 3.9274315315749969E-01 + 22 2 -2.5637106920821656E-01 5.9790312637835585E+00 6.7163127014570758E+00 2.3512729823005811E+00 + 23 1 1.1847178479117916E-01 6.0116037085053753E+00 6.9691212919231109E+00 3.3182411414869546E+00 + 24 1 1.3767024849619425E-01 6.8767703438302163E+00 6.3827294435137851E+00 2.0635471629013606E+00 + 25 2 -2.2955663167309948E-01 6.7547865304093548E+00 8.1377929495075468E-02 5.3581116608665873E+00 + 26 1 1.3433991100513271E-01 5.9531825446743918E+00 6.7260222417346471E-01 5.2693136085523262E+00 + 27 1 1.3761295680984550E-01 4.4727592285958784E-01 6.4022081242395790E-01 5.5503336943639905E+00 + 28 2 -2.3412971681479519E-01 4.6569264589470469E+00 4.3236993372651531E+00 3.2604100102435756E+00 + 29 1 1.1415705913922840E-01 3.9626142106129842E+00 3.6880495575692027E+00 3.5978666484999993E+00 + 30 1 1.1034962117814638E-01 4.6123792631715030E+00 5.1746062343494730E+00 3.7838306323283333E+00 + 31 2 -2.2006091505768430E-01 1.6592261415965956E+00 1.9740050874317887E+00 2.5667232493700953E+00 + 32 1 1.3641844939732600E-01 1.3659958208733727E+00 1.1546249809050639E+00 2.0741439365038556E+00 + 33 1 1.1534057032122748E-01 2.5789980439011053E+00 2.2303030724114246E+00 2.2695177494557641E+00 + 34 2 -2.0590918634609698E-01 6.7188326433244958E+00 5.0274902077599082E+00 7.0466394028585562E+00 + 35 1 1.0721155781927211E-01 6.4009802362616730E+00 4.4045226890456011E+00 6.4719907227395035E-01 + 36 1 1.1823488614823419E-01 6.0453043590359563E+00 5.7547786630259594E+00 6.9146816574097389E+00 diff --git a/examples/interface-LAMMPS/H2O_RPBE-D3/md.lmp b/examples/interface-LAMMPS/H2O_RPBE-D3/md.lmp index c64960a84c..565798f49b 100644 --- a/examples/interface-LAMMPS/H2O_RPBE-D3/md.lmp +++ b/examples/interface-LAMMPS/H2O_RPBE-D3/md.lmp @@ -33,6 +33,7 @@ thermo 1 ############################################################################### # HDNNP ############################################################################### +#pair_style hdnnp/4g emap "1:H,2:O" dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 pair_coeff * * H O diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/carbon-chain.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/carbon-chain.data new file mode 100644 index 0000000000..7a9aee1da2 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/carbon-chain.data @@ -0,0 +1,24 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 1.17284095486 -0.172504222684 -0.667448516865 +2 2 -1.1595434822 -0.350641000445 -0.467598107194 +3 2 3.72594054969 -0.0837975179097 -0.229777168673 +4 2 -3.69146983116 -0.334172643167 -0.21088223315 +5 2 6.07758586771 -0.166745226042 -0.145024035228 +6 2 -6.06809789367 -0.00253733508489 -0.0705357610724 +7 2 8.59164353464 -0.0806915075831 0.402236831619 +8 2 -8.60892564573 0.117192245354 0.0982851777904 +9 2 10.8705405815 0.51581338865 0.435826522093 +10 2 -10.8879581104 0.411807821319 0.694948565342 +11 1 12.661965991 1.19502446714 1.1691448209 +12 1 -12.9307322131 0.525058551796 0.728011456903 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/log.lammps b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/log.lammps new file mode 100644 index 0000000000..23da3e7f91 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/log.lammps @@ -0,0 +1,994 @@ +LAMMPS (29 Oct 2020) +############################################################################### +# MD simulation for carbon chain +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "carbon-chain.data" +# Timesteps +variable numSteps equal 5 +variable dt equal 0.0005 +# NN +variable nnpCutoff equal 8.01 +variable nnpDir string "nnp-data" +# Masses +variable mass_H equal 1.00794 +variable mass_C equal 12.0107 + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary s s s +atom_style atomic +read_data ${cfgFile} +read_data carbon-chain.data +Reading data file ... + orthogonal box = (-12.940000 -0.36 -0.67) to (12.670000 1.2000000 1.1700000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 12 atoms + read_data CPU = 0.000 seconds +mass 1 ${mass_H} +mass 1 1.00794 +mass 2 ${mass_C} +mass 2 12.0107 +timestep ${dt} +timestep 0.0005 +thermo 1 + +############################################################################### +# NN +############################################################################### +pair_style nnp dir ${nnpDir} showew no showewsum 10 resetew no maxew 100 cflength 1.0 cfenergy 1.0 emap "1:H,2:C" +pair_style nnp dir nnp-data showew no showewsum 10 resetew no maxew 100 cflength 1.0 cfenergy 1.0 emap "1:H,2:C" +pair_coeff * * ${nnpCutoff} +pair_coeff * * 8.01 + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve +#dump 1 all atom 1 traj.dump + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} +run 5 + +******************************************************************************* + +WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS! +------------------------------------------------------------------ + +n²p² version : v2.1.1-43-g417919d +------------------------------------------------------------ +Git branch : 4G-HDNNP-prediction +Git revision : 417919d7ff1bc727b4f9032afc6a574811f7a75b +Compile date/time : Feb 27 2021 23:33:56 +------------------------------------------------------------ + +Please cite the following papers when publishing results obtained with n²p²: +------------------------------------------------------------------------------- + * General citation for n²p² and the LAMMPS interface: + + Singraber, A.; Behler, J.; Dellago, C. + Library-Based LAMMPS Implementation of High-Dimensional + Neural Network Potentials. + J. Chem. Theory Comput. 2019 15 (3), 1827–1840. + https://doi.org/10.1021/acs.jctc.8b00770 +------------------------------------------------------------------------------- + * Additionally, if you use the NNP training features of n²p²: + + Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C. + Parallel Multistream Training of High-Dimensional Neural + Network Potentials. + J. Chem. Theory Comput. 2019, 15 (5), 3075–3092. + https://doi.org/10.1021/acs.jctc.8b01092 +------------------------------------------------------------------------------- + * Additionally, if polynomial symmetry functions are used: + + Bircher, M. P.; Singraber, A.; Dellago, C. + Improved Description of Atomic Environments Using Low-Cost + Polynomial Functions with Compact Support. + arXiv:2010.14414 [cond-mat, physics:physics] 2020. + https://arxiv.org/abs/2010.14414 +******************************************************************************* + +*** SETUP: SETTINGS FILE ****************************************************** + +Settings file name: nnp-data/input.nn +Read 185 lines. +WARNING: Unknown keyword "bond_threshold" at line 34. +WARNING: Unknown keyword "calculate_forces" at line 183. +WARNING: Unknown keyword "energy_threshold" at line 33. +WARNING: Unknown keyword "fitting_unit" at line 148. +WARNING: Unknown keyword "initial_hardness" at line 29. +WARNING: Unknown keyword "initial_hardness" at line 30. +WARNING: Unknown keyword "kalman_lambda_charge" at line 156. +WARNING: Unknown keyword "kalman_nue_charge" at line 157. +WARNING: Unknown keyword "mix_all_points" at line 145. +WARNING: Unknown keyword "optmode_short_energy" at line 152. +WARNING: Unknown keyword "optmode_short_force" at line 153. +WARNING: Unknown keyword "points_in_memory" at line 144. +WARNING: Unknown keyword "random_number_type" at line 25. +WARNING: Unknown keyword "regularize_fit_param" at line 173. +WARNING: Unknown keyword "remove_atom_energies" at line 26. +WARNING: Unknown keyword "runner_mode" at line 20. +WARNING: Unknown keyword "use_electrostatics" at line 17. +WARNING: Unknown keyword "use_short_nn" at line 18. +WARNING: 18 problems detected (0 critical). +Found 113 lines with keywords. +This settings file defines a NNP with electrostatics and +non-local charge transfer (4G-HDNNP). +******************************************************************************* + +*** SETUP: NORMALIZATION ****************************************************** + +Data set normalization is not used. +******************************************************************************* + +*** SETUP: ELEMENT MAP ******************************************************** + +Number of element strings found: 2 +Element 0: H ( 1) +Element 1: C ( 6) +******************************************************************************* + +*** SETUP: ELEMENTS *********************************************************** + +Number of elements is consistent: 2 +Atomic energy offsets per element: +Element 0: -4.58907306E-01 +Element 1: -3.77481119E+01 +Energy offsets are automatically subtracted from reference energies. +******************************************************************************* + +*** SETUP: ELECTROSTATICS ***************************************************** + +Atomic hardness file name format: nnp-data/hardness.%03zu.data +Atomic hardness for element H from file nnp-data/hardness.001.data: 8.89533120E-03 +Atomic hardness for element C from file nnp-data/hardness.006.data: 6.61189426E-02 + +Gaussian width of charge distribution per element: +Element 0: 5.85815056E-01 +Element 1: 1.37949997E+00 + +Ewald precision: 1.00000000E-06 + +Screening function information: +Inner radius : 4.80000000E+00 +Outer radius : 8.00000000E+00 +Transition region functional form: +x := (r - inner) / (outer - inner) +fs(x) := 1 - f(x) +CoreFunction::Type::COS (0): +f(x) := 1/2 * (cos(pi*x) + 1) +******************************************************************************* + +*** SETUP: CUTOFF FUNCTIONS *************************************************** + +Parameter alpha for inner cutoff: 0.000000 +Inner cutoff = Symmetry function cutoff * alpha +Equal cutoff function type for all symmetry functions: +CutoffFunction::CT_TANHU (2) +f(r) = tanh^3(1 - r/rc) +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTIONS ************************************************* + +Abbreviations: +-------------- +ind .... Symmetry function index. +ec ..... Central atom element. +tp ..... Symmetry function type. +sbtp ... Symmetry function subtype (e.g. cutoff type). +e1 ..... Neighbor 1 element. +e2 ..... Neighbor 2 element. +eta .... Gaussian width eta. +rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial. +angl.... Left cutoff angle for polynomial. +angr.... Right cutoff angle for polynomial. +la ..... Angle prefactor lambda. +zeta ... Angle term exponent zeta. +rc ..... Cutoff radius / right cutoff radius for polynomial. +a ...... Free parameter alpha (e.g. cutoff alpha). +ln ..... Line number in settings file. + +Short range atomic symmetry functions element H : +------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln +------------------------------------------------------------------------------------------------- + 1 H 2 ct2 H 0.000E+00 0.000E+00 8.000E+00 0.00 59 + 2 H 2 ct2 C 0.000E+00 0.000E+00 8.000E+00 0.00 74 + 3 H 2 ct2 H 6.000E-03 0.000E+00 8.000E+00 0.00 60 + 4 H 2 ct2 H 1.100E-02 0.000E+00 8.000E+00 0.00 61 + 5 H 2 ct2 C 1.300E-02 0.000E+00 8.000E+00 0.00 75 + 6 H 2 ct2 H 1.800E-02 0.000E+00 8.000E+00 0.00 62 + 7 H 2 ct2 H 2.600E-02 0.000E+00 8.000E+00 0.00 63 + 8 H 2 ct2 C 2.900E-02 0.000E+00 8.000E+00 0.00 76 + 9 H 2 ct2 H 3.500E-02 0.000E+00 8.000E+00 0.00 64 + 10 H 2 ct2 C 5.400E-02 0.000E+00 8.000E+00 0.00 77 + 11 H 2 ct2 C 9.300E-02 0.000E+00 8.000E+00 0.00 78 + 12 H 2 ct2 C 1.610E-01 0.000E+00 8.000E+00 0.00 79 + 13 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 134 + 14 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 125 + 15 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 130 + 16 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 121 + 17 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 135 + 18 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 126 + 19 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 131 + 20 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 122 + 21 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 132 + 22 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 123 + 23 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 133 + 24 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 124 +------------------------------------------------------------------------------------------------- +Short range atomic symmetry functions element C : +------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln +------------------------------------------------------------------------------------------------- + 1 C 2 ct2 H 0.000E+00 0.000E+00 8.000E+00 0.00 67 + 2 C 2 ct2 C 0.000E+00 0.000E+00 8.000E+00 0.00 82 + 3 C 2 ct2 C 1.000E-02 0.000E+00 8.000E+00 0.00 83 + 4 C 2 ct2 H 1.300E-02 0.000E+00 8.000E+00 0.00 68 + 5 C 2 ct2 C 2.300E-02 0.000E+00 8.000E+00 0.00 84 + 6 C 2 ct2 H 2.900E-02 0.000E+00 8.000E+00 0.00 69 + 7 C 2 ct2 C 4.100E-02 0.000E+00 8.000E+00 0.00 85 + 8 C 2 ct2 H 5.400E-02 0.000E+00 8.000E+00 0.00 70 + 9 C 2 ct2 C 6.500E-02 0.000E+00 8.000E+00 0.00 86 + 10 C 2 ct2 H 9.300E-02 0.000E+00 8.000E+00 0.00 71 + 11 C 2 ct2 C 1.030E-01 0.000E+00 8.000E+00 0.00 87 + 12 C 2 ct2 H 1.610E-01 0.000E+00 8.000E+00 0.00 72 + 13 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 106 + 14 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 115 + 15 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 97 + 16 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 102 + 17 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 111 + 18 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 93 + 19 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 107 + 20 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 116 + 21 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 98 + 22 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 103 + 23 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 112 + 24 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 94 + 25 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 108 + 26 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 117 + 27 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 99 + 28 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 104 + 29 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 113 + 30 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 95 + 31 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 109 + 32 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 118 + 33 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 100 + 34 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 105 + 35 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 114 + 36 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 96 +------------------------------------------------------------------------------------------------- +Minimum cutoff radius for element H: 8.000000 +Minimum cutoff radius for element C: 8.000000 +Maximum cutoff radius (global) : 8.000000 +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION MEMORY ******************************************* + +Symmetry function derivatives memory table for element H : +------------------------------------------------------------------------------- +Relevant symmetry functions for neighbors with element: +- H: 12 of 24 ( 50.0 %) +- C: 18 of 24 ( 75.0 %) +------------------------------------------------------------------------------- +Symmetry function derivatives memory table for element C : +------------------------------------------------------------------------------- +Relevant symmetry functions for neighbors with element: +- H: 22 of 36 ( 61.1 %) +- C: 22 of 36 ( 61.1 %) +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION CACHE ******************************************** + +Element H: in total 4 caches, used 15.00 times on average. +Element C: in total 4 caches, used 22.00 times on average. +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION GROUPS ******************************************* + +Abbreviations: +-------------- +ind .... Symmetry function index. +ec ..... Central atom element. +tp ..... Symmetry function type. +sbtp ... Symmetry function subtype (e.g. cutoff type). +e1 ..... Neighbor 1 element. +e2 ..... Neighbor 2 element. +eta .... Gaussian width eta. +rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial. +angl.... Left cutoff angle for polynomial. +angr.... Right cutoff angle for polynomial. +la ..... Angle prefactor lambda. +zeta ... Angle term exponent zeta. +rc ..... Cutoff radius / right cutoff radius for polynomial. +a ...... Free parameter alpha (e.g. cutoff alpha). +ln ..... Line number in settings file. +mi ..... Member index. +sfi .... Symmetry function index. +e ...... Recalculate exponential term. + +Short range atomic symmetry function groups element H : +---------------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e +---------------------------------------------------------------------------------------------------------- + 1 H 2 ct2 H * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 59 1 1 + - - - - - 6.000E-03 0.000E+00 - - 60 2 3 + - - - - - 1.100E-02 0.000E+00 - - 61 3 4 + - - - - - 1.800E-02 0.000E+00 - - 62 4 6 + - - - - - 2.600E-02 0.000E+00 - - 63 5 7 + - - - - - 3.500E-02 0.000E+00 - - 64 6 9 + 2 H 2 ct2 C * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 74 1 2 + - - - - - 1.300E-02 0.000E+00 - - 75 2 5 + - - - - - 2.900E-02 0.000E+00 - - 76 3 8 + - - - - - 5.400E-02 0.000E+00 - - 77 4 10 + - - - - - 9.300E-02 0.000E+00 - - 78 5 11 + - - - - - 1.610E-01 0.000E+00 - - 79 6 12 + 3 H 3 ct2 H C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 134 1 13 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 130 2 15 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 135 3 17 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 131 4 19 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 132 5 21 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 133 6 23 0 + 4 H 3 ct2 C C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 125 1 14 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 121 2 16 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 126 3 18 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 122 4 20 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 123 5 22 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 124 6 24 0 +---------------------------------------------------------------------------------------------------------- +Short range atomic symmetry function groups element C : +---------------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e +---------------------------------------------------------------------------------------------------------- + 1 C 2 ct2 H * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 67 1 1 + - - - - - 1.300E-02 0.000E+00 - - 68 2 4 + - - - - - 2.900E-02 0.000E+00 - - 69 3 6 + - - - - - 5.400E-02 0.000E+00 - - 70 4 8 + - - - - - 9.300E-02 0.000E+00 - - 71 5 10 + - - - - - 1.610E-01 0.000E+00 - - 72 6 12 + 2 C 2 ct2 C * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 82 1 2 + - - - - - 1.000E-02 0.000E+00 - - 83 2 3 + - - - - - 2.300E-02 0.000E+00 - - 84 3 5 + - - - - - 4.100E-02 0.000E+00 - - 85 4 7 + - - - - - 6.500E-02 0.000E+00 - - 86 5 9 + - - - - - 1.030E-01 0.000E+00 - - 87 6 11 + 3 C 3 ct2 H H * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 106 1 13 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 102 2 16 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 107 3 19 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 103 4 22 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 108 5 25 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 104 6 28 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 109 7 31 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 105 8 34 0 + 4 C 3 ct2 H C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 115 1 14 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 111 2 17 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 116 3 20 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 112 4 23 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 117 5 26 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 113 6 29 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 118 7 32 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 114 8 35 0 + 5 C 3 ct2 C C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 97 1 15 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 93 2 18 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 98 3 21 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 94 4 24 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 99 5 27 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 95 6 30 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 100 7 33 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 96 8 36 0 +---------------------------------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: NEURAL NETWORKS **************************************************** + +Normalize neurons (all elements): 0 +------------------------------------------------------------------------------- +Atomic electronegativity NN for element H : +Number of weights : 600 +Number of biases : 31 +Number of connections: 631 +Architecture 24 15 15 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G t t + 12 G t t + 13 G t t + 14 G t t + 15 G t t + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G +------------------------------------------------------------------------------- +Atomic electronegativity NN for element C : +Number of weights : 780 +Number of biases : 31 +Number of connections: 811 +Architecture 36 15 15 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G t t + 12 G t t + 13 G t t + 14 G t t + 15 G t t + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + 26 G + 27 G + 28 G + 29 G + 30 G + 31 G + 32 G + 33 G + 34 G + 35 G + 36 G +------------------------------------------------------------------------------- +Atomic short range NN for element H : +Number of weights : 360 +Number of biases : 21 +Number of connections: 381 +Architecture 25 10 10 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G + 12 G + 13 G + 14 G + 15 G + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G +------------------------------------------------------------------------------- +Atomic short range NN for element C : +Number of weights : 480 +Number of biases : 21 +Number of connections: 501 +Architecture 37 10 10 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G + 12 G + 13 G + 14 G + 15 G + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + 26 G + 27 G + 28 G + 29 G + 30 G + 31 G + 32 G + 33 G + 34 G + 35 G + 36 G + 37 G +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION SCALING ****************************************** + +Equal scaling type for all symmetry functions: +Scaling type::ST_SCALECENTER (3) +Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin) +WARNING: Keyword "scale_min_short" not found. + Default value for Smin = 0.0. +WARNING: Keyword "scale_max_short" not found. + Default value for Smax = 1.0. +Smin = 0.000000 +Smax = 1.000000 +Symmetry function scaling statistics from file: nnp-data/scaling.data +------------------------------------------------------------------------------- + +Abbreviations: +-------------- +ind ..... Symmetry function index. +min ..... Minimum symmetry function value. +max ..... Maximum symmetry function value. +mean .... Mean symmetry function value. +sigma ... Standard deviation of symmetry function values. +sf ...... Scaling factor for derivatives. +Smin .... Desired minimum scaled symmetry function value. +Smax .... Desired maximum scaled symmetry function value. +t ....... Scaling type. + +Scaling data for symmetry functions element H : +------------------------------------------------------------------------------- + ind min max mean sigma sf Smin Smax t +------------------------------------------------------------------------------- + 1 0.00E+00 1.68E-01 5.14E-02 0.00E+00 5.94E+00 0.00 1.00 3 + 2 3.04E-01 4.17E-01 3.46E-01 0.00E+00 8.85E+00 0.00 1.00 3 + 3 0.00E+00 1.59E-01 4.77E-02 0.00E+00 6.27E+00 0.00 1.00 3 + 4 0.00E+00 1.52E-01 4.48E-02 0.00E+00 6.56E+00 0.00 1.00 3 + 5 2.70E-01 3.77E-01 3.12E-01 0.00E+00 9.35E+00 0.00 1.00 3 + 6 0.00E+00 1.43E-01 4.10E-02 0.00E+00 7.00E+00 0.00 1.00 3 + 7 0.00E+00 1.33E-01 3.71E-02 0.00E+00 7.53E+00 0.00 1.00 3 + 8 2.36E-01 3.37E-01 2.78E-01 0.00E+00 9.97E+00 0.00 1.00 3 + 9 0.00E+00 1.22E-01 3.31E-02 0.00E+00 8.18E+00 0.00 1.00 3 + 10 1.94E-01 2.86E-01 2.36E-01 0.00E+00 1.09E+01 0.00 1.00 3 + 11 1.46E-01 2.31E-01 1.88E-01 0.00E+00 1.18E+01 0.00 1.00 3 + 12 9.43E-02 1.67E-01 1.33E-01 0.00E+00 1.37E+01 0.00 1.00 3 + 13 0.00E+00 3.94E-03 7.66E-04 0.00E+00 2.54E+02 0.00 1.00 3 + 14 0.00E+00 2.18E-03 3.95E-04 0.00E+00 4.59E+02 0.00 1.00 3 + 15 0.00E+00 2.26E-02 6.69E-03 0.00E+00 4.42E+01 0.00 1.00 3 + 16 6.80E-03 1.48E-02 9.85E-03 0.00E+00 1.25E+02 0.00 1.00 3 + 17 0.00E+00 7.54E-04 1.18E-04 0.00E+00 1.33E+03 0.00 1.00 3 + 18 0.00E+00 3.07E-04 3.12E-05 0.00E+00 3.26E+03 0.00 1.00 3 + 19 0.00E+00 2.02E-02 6.04E-03 0.00E+00 4.96E+01 0.00 1.00 3 + 20 6.45E-03 1.30E-02 9.49E-03 0.00E+00 1.53E+02 0.00 1.00 3 + 21 0.00E+00 1.67E-02 5.00E-03 0.00E+00 5.97E+01 0.00 1.00 3 + 22 5.80E-03 1.11E-02 8.84E-03 0.00E+00 1.88E+02 0.00 1.00 3 + 23 0.00E+00 1.27E-02 3.57E-03 0.00E+00 7.90E+01 0.00 1.00 3 + 24 4.42E-03 1.10E-02 7.82E-03 0.00E+00 1.51E+02 0.00 1.00 3 +------------------------------------------------------------------------------- +Scaling data for symmetry functions element C : +------------------------------------------------------------------------------- + ind min max mean sigma sf Smin Smax t +------------------------------------------------------------------------------- + 1 0.00E+00 5.28E-01 8.65E-02 0.00E+00 1.89E+00 0.00 1.00 3 + 2 2.44E-01 5.76E-01 4.78E-01 0.00E+00 3.00E+00 0.00 1.00 3 + 3 2.20E-01 5.27E-01 4.38E-01 0.00E+00 3.26E+00 0.00 1.00 3 + 4 0.00E+00 5.04E-01 7.81E-02 0.00E+00 1.99E+00 0.00 1.00 3 + 5 1.95E-01 4.73E-01 3.93E-01 0.00E+00 3.59E+00 0.00 1.00 3 + 6 0.00E+00 4.75E-01 6.95E-02 0.00E+00 2.11E+00 0.00 1.00 3 + 7 1.66E-01 4.12E-01 3.41E-01 0.00E+00 4.07E+00 0.00 1.00 3 + 8 0.00E+00 4.33E-01 5.90E-02 0.00E+00 2.31E+00 0.00 1.00 3 + 9 1.36E-01 3.48E-01 2.86E-01 0.00E+00 4.72E+00 0.00 1.00 3 + 10 0.00E+00 3.76E-01 4.70E-02 0.00E+00 2.66E+00 0.00 1.00 3 + 11 1.02E-01 2.73E-01 2.22E-01 0.00E+00 5.83E+00 0.00 1.00 3 + 12 0.00E+00 2.93E-01 3.33E-02 0.00E+00 3.41E+00 0.00 1.00 3 + 13 0.00E+00 1.53E-02 6.08E-04 0.00E+00 6.55E+01 0.00 1.00 3 + 14 0.00E+00 2.04E-02 2.32E-03 0.00E+00 4.91E+01 0.00 1.00 3 + 15 0.00E+00 6.66E-03 3.99E-03 0.00E+00 1.50E+02 0.00 1.00 3 + 16 0.00E+00 9.28E-03 3.24E-04 0.00E+00 1.08E+02 0.00 1.00 3 + 17 0.00E+00 2.50E-02 2.80E-03 0.00E+00 4.00E+01 0.00 1.00 3 + 18 3.52E-03 1.25E-02 8.03E-03 0.00E+00 1.11E+02 0.00 1.00 3 + 19 0.00E+00 1.19E-02 4.30E-04 0.00E+00 8.39E+01 0.00 1.00 3 + 20 0.00E+00 1.56E-02 2.02E-03 0.00E+00 6.43E+01 0.00 1.00 3 + 21 0.00E+00 6.52E-03 3.94E-03 0.00E+00 1.53E+02 0.00 1.00 3 + 22 0.00E+00 3.82E-03 1.46E-04 0.00E+00 2.62E+02 0.00 1.00 3 + 23 0.00E+00 2.34E-02 2.50E-03 0.00E+00 4.27E+01 0.00 1.00 3 + 24 3.51E-03 1.24E-02 7.98E-03 0.00E+00 1.12E+02 0.00 1.00 3 + 25 0.00E+00 8.68E-03 2.29E-04 0.00E+00 1.15E+02 0.00 1.00 3 + 26 0.00E+00 1.07E-02 1.70E-03 0.00E+00 9.33E+01 0.00 1.00 3 + 27 0.00E+00 6.38E-03 3.88E-03 0.00E+00 1.57E+02 0.00 1.00 3 + 28 0.00E+00 1.76E-03 6.00E-05 0.00E+00 5.69E+02 0.00 1.00 3 + 29 0.00E+00 2.11E-02 2.32E-03 0.00E+00 4.74E+01 0.00 1.00 3 + 30 3.50E-03 1.23E-02 7.95E-03 0.00E+00 1.13E+02 0.00 1.00 3 + 31 0.00E+00 4.70E-03 6.92E-05 0.00E+00 2.13E+02 0.00 1.00 3 + 32 0.00E+00 1.07E-02 1.36E-03 0.00E+00 9.34E+01 0.00 1.00 3 + 33 0.00E+00 6.34E-03 3.76E-03 0.00E+00 1.58E+02 0.00 1.00 3 + 34 0.00E+00 9.43E-04 2.30E-05 0.00E+00 1.06E+03 0.00 1.00 3 + 35 0.00E+00 1.71E-02 2.11E-03 0.00E+00 5.84E+01 0.00 1.00 3 + 36 3.48E-03 1.22E-02 7.88E-03 0.00E+00 1.15E+02 0.00 1.00 3 +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION STATISTICS *************************************** + +Equal symmetry function statistics for all elements. +Collect min/max/mean/sigma : 0 +Collect extrapolation warnings : 1 +Write extrapolation warnings immediately to stderr: 0 +Halt on any extrapolation warning : 0 +******************************************************************************* + +*** SETUP: NEURAL NETWORK WEIGHTS ********************************************* + +Electronegativity weight file name format: nnp-data/weightse.%03zu.data +Setting weights for element H from file: nnp-data/weightse.001.data +Setting weights for element C from file: nnp-data/weightse.006.data +Short range weight file name format: nnp-data/weights.%03zu.data +Setting weights for element H from file: nnp-data/weights.001.data +Setting weights for element C from file: nnp-data/weights.006.data +******************************************************************************* + +*** SETUP: LAMMPS INTERFACE *************************************************** + +Individual extrapolation warnings will not be shown. +Extrapolation warning summary will be shown every 10 timesteps. +The simulation will be stopped when 100 extrapolation warnings are exceeded. +Extrapolation warnings are accumulated over all time steps. +------------------------------------------------------------------------------- +CAUTION: If the LAMMPS unit system differs from the one used + during NN training, appropriate conversion factors + must be provided (see keywords cflength and cfenergy). + +Length unit conversion factor: 1.0000000000000000E+00 +Energy unit conversion factor: 1.0000000000000000E+00 + +Checking consistency of cutoff radii (in LAMMPS units): +LAMMPS Cutoff (via pair_coeff) : 8.010E+00 +Maximum symmetry function cutoff: 8.000E+00 +Cutoff radii are consistent. +------------------------------------------------------------------------------- +Element mapping string from LAMMPS to n2p2: "1:H,2:C" + +CAUTION: Please ensure that this mapping between LAMMPS + atom types and NNP elements is consistent: + +--------------------------- +LAMMPS type | NNP element +--------------------------- + 1 <-> H ( 1) + 2 <-> C ( 6) +--------------------------- + +NNP setup for LAMMPS completed. +******************************************************************************* +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.01 + ghost atom cutoff = 10.01 + binsize = 5.005, bins = 6 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair nnp, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:963) +Atom 0 ( C) chi: -1.46678106E-01 +Atom 1 ( C) chi: -1.62293124E-01 +Atom 2 ( H) chi: -2.28364821E-01 +Atom 3 ( C) chi: -1.49337351E-01 +Atom 4 ( C) chi: -1.48569008E-01 +Atom 5 ( C) chi: -1.50037876E-01 +Atom 6 ( C) chi: -1.49461645E-01 +Atom 7 ( C) chi: -1.49033407E-01 +Atom 8 ( C) chi: -1.48516909E-01 +Atom 9 ( C) chi: -1.46830562E-01 +Atom 10 ( C) chi: -1.60724572E-01 +Atom 11 ( H) chi: -2.25977980E-01 +Solve relative error: -NAN +Atom 0 ( C) q: -NAN +Atom 1 ( C) q: -NAN +Atom 2 ( H) q: -NAN +Atom 3 ( C) q: -NAN +Atom 4 ( C) q: -NAN +Atom 5 ( C) q: -NAN +Atom 6 ( C) q: -NAN +Atom 7 ( C) q: -NAN +Atom 8 ( C) q: -NAN +Atom 9 ( C) q: -NAN +Atom 10 ( C) q: -NAN +Atom 11 ( H) q: -NAN +Total charge: -NAN (ref: 0.00000000E+00) +Electrostatic energy: -NAN +Atom 0 ( C) energy: -NAN +Atom 1 ( C) energy: -NAN +Atom 2 ( H) energy: -NAN +Atom 3 ( C) energy: -NAN +Atom 4 ( C) energy: -NAN +Atom 5 ( C) energy: -NAN +Atom 6 ( C) energy: -NAN +Atom 7 ( C) energy: -NAN +Atom 8 ( C) energy: -NAN +Atom 9 ( C) energy: -NAN +Atom 10 ( C) energy: -NAN +Atom 11 ( H) energy: -NAN +### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000E+00 +Per MPI rank memory allocation (min/avg/max) = 3.063 | 3.063 | 3.063 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0 -nan 0 -nan 0 72.695271 +Atom 0 ( C) chi: -1.46678106E-01 +Atom 1 ( C) chi: -1.62293124E-01 +Atom 2 ( H) chi: -2.28364821E-01 +Atom 3 ( C) chi: -1.49337351E-01 +Atom 4 ( C) chi: -1.48569008E-01 +Atom 5 ( C) chi: -1.50037876E-01 +Atom 6 ( C) chi: -1.49461645E-01 +Atom 7 ( C) chi: -1.49033407E-01 +Atom 8 ( C) chi: -1.48516909E-01 +Atom 9 ( C) chi: -1.46830562E-01 +Atom 10 ( C) chi: -1.60724572E-01 +Atom 11 ( H) chi: -2.25977980E-01 +Solve relative error: -NAN +Atom 0 ( C) q: -NAN +Atom 1 ( C) q: -NAN +Atom 2 ( H) q: -NAN +Atom 3 ( C) q: -NAN +Atom 4 ( C) q: -NAN +Atom 5 ( C) q: -NAN +Atom 6 ( C) q: -NAN +Atom 7 ( C) q: -NAN +Atom 8 ( C) q: -NAN +Atom 9 ( C) q: -NAN +Atom 10 ( C) q: -NAN +Atom 11 ( H) q: -NAN +Total charge: -NAN (ref: 0.00000000E+00) +Electrostatic energy: -NAN +Atom 0 ( C) energy: -NAN +Atom 1 ( C) energy: -NAN +Atom 2 ( H) energy: -NAN +Atom 3 ( C) energy: -NAN +Atom 4 ( C) energy: -NAN +Atom 5 ( C) energy: -NAN +Atom 6 ( C) energy: -NAN +Atom 7 ( C) energy: -NAN +Atom 8 ( C) energy: -NAN +Atom 9 ( C) energy: -NAN +Atom 10 ( C) energy: -NAN +Atom 11 ( H) energy: -NAN + 1 0 -nan 0 -nan 0 72.695271 +Atom 0 ( C) chi: -1.46678106E-01 +Atom 1 ( C) chi: -1.62293124E-01 +Atom 2 ( H) chi: -2.28364821E-01 +Atom 3 ( C) chi: -1.49337351E-01 +Atom 4 ( C) chi: -1.48569008E-01 +Atom 5 ( C) chi: -1.50037876E-01 +Atom 6 ( C) chi: -1.49461645E-01 +Atom 7 ( C) chi: -1.49033407E-01 +Atom 8 ( C) chi: -1.48516909E-01 +Atom 9 ( C) chi: -1.46830562E-01 +Atom 10 ( C) chi: -1.60724572E-01 +Atom 11 ( H) chi: -2.25977980E-01 +Solve relative error: -NAN +Atom 0 ( C) q: -NAN +Atom 1 ( C) q: -NAN +Atom 2 ( H) q: -NAN +Atom 3 ( C) q: -NAN +Atom 4 ( C) q: -NAN +Atom 5 ( C) q: -NAN +Atom 6 ( C) q: -NAN +Atom 7 ( C) q: -NAN +Atom 8 ( C) q: -NAN +Atom 9 ( C) q: -NAN +Atom 10 ( C) q: -NAN +Atom 11 ( H) q: -NAN +Total charge: -NAN (ref: 0.00000000E+00) +Electrostatic energy: -NAN +Atom 0 ( C) energy: -NAN +Atom 1 ( C) energy: -NAN +Atom 2 ( H) energy: -NAN +Atom 3 ( C) energy: -NAN +Atom 4 ( C) energy: -NAN +Atom 5 ( C) energy: -NAN +Atom 6 ( C) energy: -NAN +Atom 7 ( C) energy: -NAN +Atom 8 ( C) energy: -NAN +Atom 9 ( C) energy: -NAN +Atom 10 ( C) energy: -NAN +Atom 11 ( H) energy: -NAN + 2 0 -nan 0 -nan 0 72.695271 +Atom 0 ( C) chi: -1.46678106E-01 +Atom 1 ( C) chi: -1.62293124E-01 +Atom 2 ( H) chi: -2.28364821E-01 +Atom 3 ( C) chi: -1.49337351E-01 +Atom 4 ( C) chi: -1.48569008E-01 +Atom 5 ( C) chi: -1.50037876E-01 +Atom 6 ( C) chi: -1.49461645E-01 +Atom 7 ( C) chi: -1.49033407E-01 +Atom 8 ( C) chi: -1.48516909E-01 +Atom 9 ( C) chi: -1.46830562E-01 +Atom 10 ( C) chi: -1.60724572E-01 +Atom 11 ( H) chi: -2.25977980E-01 +Solve relative error: -NAN +Atom 0 ( C) q: -NAN +Atom 1 ( C) q: -NAN +Atom 2 ( H) q: -NAN +Atom 3 ( C) q: -NAN +Atom 4 ( C) q: -NAN +Atom 5 ( C) q: -NAN +Atom 6 ( C) q: -NAN +Atom 7 ( C) q: -NAN +Atom 8 ( C) q: -NAN +Atom 9 ( C) q: -NAN +Atom 10 ( C) q: -NAN +Atom 11 ( H) q: -NAN +Total charge: -NAN (ref: 0.00000000E+00) +Electrostatic energy: -NAN +Atom 0 ( C) energy: -NAN +Atom 1 ( C) energy: -NAN +Atom 2 ( H) energy: -NAN +Atom 3 ( C) energy: -NAN +Atom 4 ( C) energy: -NAN +Atom 5 ( C) energy: -NAN +Atom 6 ( C) energy: -NAN +Atom 7 ( C) energy: -NAN +Atom 8 ( C) energy: -NAN +Atom 9 ( C) energy: -NAN +Atom 10 ( C) energy: -NAN +Atom 11 ( H) energy: -NAN + 3 0 -nan 0 -nan 0 72.695271 +Atom 0 ( C) chi: -1.46678106E-01 +Atom 1 ( C) chi: -1.62293124E-01 +Atom 2 ( H) chi: -2.28364821E-01 +Atom 3 ( C) chi: -1.49337351E-01 +Atom 4 ( C) chi: -1.48569008E-01 +Atom 5 ( C) chi: -1.50037876E-01 +Atom 6 ( C) chi: -1.49461645E-01 +Atom 7 ( C) chi: -1.49033407E-01 +Atom 8 ( C) chi: -1.48516909E-01 +Atom 9 ( C) chi: -1.46830562E-01 +Atom 10 ( C) chi: -1.60724572E-01 +Atom 11 ( H) chi: -2.25977980E-01 +Solve relative error: -NAN +Atom 0 ( C) q: -NAN +Atom 1 ( C) q: -NAN +Atom 2 ( H) q: -NAN +Atom 3 ( C) q: -NAN +Atom 4 ( C) q: -NAN +Atom 5 ( C) q: -NAN +Atom 6 ( C) q: -NAN +Atom 7 ( C) q: -NAN +Atom 8 ( C) q: -NAN +Atom 9 ( C) q: -NAN +Atom 10 ( C) q: -NAN +Atom 11 ( H) q: -NAN +Total charge: -NAN (ref: 0.00000000E+00) +Electrostatic energy: -NAN +Atom 0 ( C) energy: -NAN +Atom 1 ( C) energy: -NAN +Atom 2 ( H) energy: -NAN +Atom 3 ( C) energy: -NAN +Atom 4 ( C) energy: -NAN +Atom 5 ( C) energy: -NAN +Atom 6 ( C) energy: -NAN +Atom 7 ( C) energy: -NAN +Atom 8 ( C) energy: -NAN +Atom 9 ( C) energy: -NAN +Atom 10 ( C) energy: -NAN +Atom 11 ( H) energy: -NAN + 4 0 -nan 0 -nan 0 72.695271 +Atom 0 ( C) chi: -1.46678106E-01 +Atom 1 ( C) chi: -1.62293124E-01 +Atom 2 ( H) chi: -2.28364821E-01 +Atom 3 ( C) chi: -1.49337351E-01 +Atom 4 ( C) chi: -1.48569008E-01 +Atom 5 ( C) chi: -1.50037876E-01 +Atom 6 ( C) chi: -1.49461645E-01 +Atom 7 ( C) chi: -1.49033407E-01 +Atom 8 ( C) chi: -1.48516909E-01 +Atom 9 ( C) chi: -1.46830562E-01 +Atom 10 ( C) chi: -1.60724572E-01 +Atom 11 ( H) chi: -2.25977980E-01 +Solve relative error: -NAN +Atom 0 ( C) q: -NAN +Atom 1 ( C) q: -NAN +Atom 2 ( H) q: -NAN +Atom 3 ( C) q: -NAN +Atom 4 ( C) q: -NAN +Atom 5 ( C) q: -NAN +Atom 6 ( C) q: -NAN +Atom 7 ( C) q: -NAN +Atom 8 ( C) q: -NAN +Atom 9 ( C) q: -NAN +Atom 10 ( C) q: -NAN +Atom 11 ( H) q: -NAN +Total charge: -NAN (ref: 0.00000000E+00) +Electrostatic energy: -NAN +Atom 0 ( C) energy: -NAN +Atom 1 ( C) energy: -NAN +Atom 2 ( H) energy: -NAN +Atom 3 ( C) energy: -NAN +Atom 4 ( C) energy: -NAN +Atom 5 ( C) energy: -NAN +Atom 6 ( C) energy: -NAN +Atom 7 ( C) energy: -NAN +Atom 8 ( C) energy: -NAN +Atom 9 ( C) energy: -NAN +Atom 10 ( C) energy: -NAN +Atom 11 ( H) energy: -NAN + 5 0 -nan 0 -nan 0 72.695271 +Loop time of 0.00210395 on 1 procs for 5 steps with 12 atoms + +Performance: 102.664 ns/day, 0.234 hours/ns, 2376.482 timesteps/s +29.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0019988 | 0.0019988 | 0.0019988 | 0.0 | 95.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 4.048e-06 | 4.048e-06 | 4.048e-06 | 0.0 | 0.19 +Output | 7.6602e-05 | 7.6602e-05 | 7.6602e-05 | 0.0 | 3.64 +Modify | 6.668e-06 | 6.668e-06 | 6.668e-06 | 0.0 | 0.32 +Other | | 1.783e-05 | | | 0.85 + +Nlocal: 12.0000 ave 12 max 12 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 76.0000 ave 76 max 76 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 76 +Ave neighs/atom = 6.3333333 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/md-external.lmp b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/md-external.lmp new file mode 100644 index 0000000000..fba1715878 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/md-external.lmp @@ -0,0 +1,49 @@ +############################################################################### +# MD simulation for carbon chain +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "carbon-chain.data" +# Timesteps +variable numSteps equal 5 +variable dt equal 0.0005 +# NN +variable nnpCutoff equal 8.01 +variable nnpDir string "nnp-data" +# Masses +variable mass_H equal 1.00794 +variable mass_C equal 12.0107 + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary s s s +atom_style atomic +read_data ${cfgFile} +mass 1 ${mass_H} +mass 2 ${mass_C} +timestep ${dt} +thermo 1 + +############################################################################### +# NN +############################################################################### +pair_style nnp/external "H C" dir ${nnpDir} command "RuNNer-gaussian.x" cflength 1.0 cfenergy 1.0 +#pair_style nnp/external "H C" dir ${nnpDir} command "nnp-predict 0" cflength 1.0 cfenergy 1.0 +pair_coeff * * ${nnpCutoff} + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve +#dump 1 all atom 1 traj.dump + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/md.lmp b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/md.lmp new file mode 100644 index 0000000000..505292c365 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/md.lmp @@ -0,0 +1,48 @@ +############################################################################### +# MD simulation for carbon chain +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "carbon-chain.data" +# Timesteps +variable numSteps equal 5 +variable dt equal 0.0005 +# NN +variable nnpCutoff equal 8.01 +variable nnpDir string "nnp-data" +# Masses +variable mass_H equal 1.00794 +variable mass_C equal 12.0107 + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary s s s +atom_style atomic +read_data ${cfgFile} +mass 1 ${mass_H} +mass 2 ${mass_C} +timestep ${dt} +thermo 1 + +############################################################################### +# NN +############################################################################### +pair_style nnp dir ${nnpDir} showew no showewsum 10 resetew no maxew 100 cflength 1.0 cfenergy 1.0 emap "1:H,2:C" +pair_coeff * * ${nnpCutoff} + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve +#dump 1 all atom 1 traj.dump + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/hardness.001.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/hardness.001.data new file mode 100644 index 0000000000..60e1493e7c --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/hardness.001.data @@ -0,0 +1 @@ + 0.0088953312 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/hardness.006.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/hardness.006.data new file mode 100644 index 0000000000..e8464ac99e --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/hardness.006.data @@ -0,0 +1 @@ + 0.0661189426 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/input.nn b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/input.nn new file mode 100644 index 0000000000..a53e0fa164 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/input.nn @@ -0,0 +1,185 @@ +## ############################################################# +### This is the input file for RuNNer +### ############################################################# +### General remarks: +### - commands can be switched off by using the # character at the BEGINNING of the line +### - the input file can be structured by blank lines and comment lines +### - the order of the keywords is arbitrary +### - if keywords are missing, default values will be used and written to runner.out +### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message + +### THIS INPUT.NN IS AN EXAMPLE, IT IS NOT A REALISTIC CASE +### It contains only a subset of all keywords + +######################################################################################################################## +### general keywords +######################################################################################################################## +use_electrostatics +use_short_nn +nnp_gen 4 # nnp_type_gen --> nnp_gen +runner_mode 3 +parallel_mode 1 +number_of_elements 2 +elements C H +random_seed 10 +random_number_type 5 +remove_atom_energies +atom_energy H -0.458907306351869 +atom_energy C -37.748111931202914 +initial_hardness H 10.0 ## fixed_atomhardness--> initial_hardness +initial_hardness C 10.0 +fixed_gausswidth H 0.585815056466 +fixed_gausswidth C 1.379499971678 +energy_threshold 100.0d0 +bond_threshold 0.4d0 +ewald_prec 1.0e-6 # for optimal combination of ewald parameters +screen_electrostatics 4.8 8.0 +######################################################################################################################## +### NN structure of the electrostatic-range NN +######################################################################################################################## +global_hidden_layers_electrostatic 2 +global_nodes_electrostatic 15 15 +global_activation_electrostatic t t l +global_hidden_layers_short 2 +global_nodes_short 10 10 +global_activation_short t t l +## element_hidden_layers_electrostatic needs to take care !!! should check the output +######################################################################################################################## +### symmetry function generation ( mode 1): +######################################################################################################################## +test_fraction 0.1 + +######################################################################################################################## +### symmetry function definitions (all modes): +######################################################################################################################## +cutoff_type 2 + + +# radial H H +symfunction H 2 H 0.000000 0.000000 8.000000 +symfunction H 2 H 0.006000 0.000000 8.000000 +symfunction H 2 H 0.011000 0.000000 8.000000 +symfunction H 2 H 0.018000 0.000000 8.000000 +symfunction H 2 H 0.026000 0.000000 8.000000 +symfunction H 2 H 0.035000 0.000000 8.000000 + +#radial C H +symfunction C 2 H 0.000000 0.000000 8.000000 +symfunction C 2 H 0.013000 0.000000 8.000000 +symfunction C 2 H 0.029000 0.000000 8.000000 +symfunction C 2 H 0.054000 0.000000 8.000000 +symfunction C 2 H 0.093000 0.000000 8.000000 +symfunction C 2 H 0.161000 0.000000 8.000000 + +symfunction H 2 C 0.000000 0.000000 8.000000 +symfunction H 2 C 0.013000 0.000000 8.000000 +symfunction H 2 C 0.029000 0.000000 8.000000 +symfunction H 2 C 0.054000 0.000000 8.000000 +symfunction H 2 C 0.093000 0.000000 8.000000 +symfunction H 2 C 0.161000 0.000000 8.000000 + +# radial C C +symfunction C 2 C 0.000000 0.000000 8.000000 +symfunction C 2 C 0.010000 0.000000 8.000000 +symfunction C 2 C 0.023000 0.000000 8.000000 +symfunction C 2 C 0.041000 0.000000 8.000000 +symfunction C 2 C 0.065000 0.000000 8.000000 +symfunction C 2 C 0.103000 0.000000 8.000000 + + +# +# angular + +symfunction C 3 C C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction C 3 H H 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction C 3 C H 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + + +symfunction H 3 C C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 C C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 C C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction H 3 H C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 H C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 H C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + + +######################################################################################################################## +### fitting (mode 2):general inputs for electrostatic range AND electrostatic part: +######################################################################################################################## +epochs 10 +points_in_memory 500 +mix_all_points +scale_symmetry_functions +center_symmetry_functions +fitting_unit eV +######################################################################################################################## +### fitting options ( mode 2): electrostatic range part only: +######################################################################################################################## +optmode_short_energy 1 +optmode_short_force 1 +short_energy_error_threshold 0.8 +short_force_error_threshold 0.8 +kalman_lambda_charge 0.98000 +kalman_nue_charge 0.99870 +kalman_lambda_short 0.98000 +kalman_nue_short 0.99870 +#use_old_weights_electrostatic +#force_update_scaling -1.0d0 +#electrostatic_energy_group 1 +#electrostatic_energy_fraction 1.00 +#electrostatic_force_group 1 + +short_force_fraction 0.025 +use_short_forces +weights_min -1.0 +weights_max 1.0 +precondition_weights +repeated_energy_update +nguyen_widrow_weights_short +regularize_fit_param 0.00001 ## 4G cases L2 regularization +######################################################################################################################## +### output options for mode 2 (fitting): +######################################################################################################################## +write_trainpoints +write_trainforces +#write_traincharges +######################################################################################################################## +### output options for mode 3 (prediction): +######################################################################################################################## +calculate_forces +#calculate_stress + diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/scaling.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/scaling.data new file mode 100644 index 0000000000..58924a796e --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/lammps-nnp/nnp-data/scaling.data @@ -0,0 +1,61 @@ + 1 1 0.000000000 0.168474325 0.051436597 + 1 2 0.304058579 0.417104776 0.345915594 + 1 3 0.000000000 0.159465228 0.047693255 + 1 4 0.000000000 0.152326768 0.044784312 + 1 5 0.270367239 0.377289298 0.312242885 + 1 6 0.000000000 0.142866546 0.041009575 + 1 7 0.000000000 0.132772126 0.037086368 + 1 8 0.236241291 0.336573119 0.278003131 + 1 9 0.000000000 0.122265892 0.033122717 + 1 10 0.194043783 0.286076543 0.235857711 + 1 11 0.146413959 0.230979612 0.188000406 + 1 12 0.094328785 0.167444236 0.133300930 + 1 13 0.000000000 0.003940598 0.000766277 + 1 14 0.000000000 0.002179848 0.000395242 + 1 15 0.000000000 0.022615147 0.006688070 + 1 16 0.006799063 0.014786064 0.009854503 + 1 17 0.000000000 0.000754211 0.000118471 + 1 18 0.000000000 0.000307111 0.000031177 + 1 19 0.000000000 0.020171446 0.006040265 + 1 20 0.006447566 0.012997039 0.009490438 + 1 21 0.000000000 0.016749223 0.005002441 + 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b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/hardness.006.data new file mode 100644 index 0000000000..e8464ac99e --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/hardness.006.data @@ -0,0 +1 @@ + 0.0661189426 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/input.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/input.data new file mode 100644 index 0000000000..dc858aa5f1 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/input.data @@ -0,0 +1,16 @@ +begin +atom 1.17284095486 -0.172504222684 -0.667448516865 C -0.00802366916667 0.0 0.0347925826351 -0.00110373556182 0.0172205087376 +atom -1.1595434822 -0.350641000445 -0.467598107194 C -0.00855427916667 0.0 -0.0190916650141 0.00319122911054 0.00166842074686 +atom 3.72594054969 -0.0837975179097 -0.229777168673 C -0.00986190916667 0.0 -0.0218470438236 -0.00628540399811 -0.0170756379211 +atom -3.69146983116 -0.334172643167 -0.21088223315 C -0.0100583891667 0.0 -0.0301687534058 0.0106478678179 -0.00452518599678 +atom 6.07758586771 -0.166745226042 -0.145024035228 C -0.00672012916667 0.0 0.00266924762633 -0.00156314063781 0.0115961079544 +atom -6.06809789367 -0.00253733508489 -0.0705357610724 C -0.00417966916667 0.0 0.0380293993069 -0.012272279507 -0.00385017456324 +atom 8.59164353464 -0.0806915075831 0.402236831619 C -0.0283825591667 0.0 0.0114358510185 0.0168883247486 -0.0145042007862 +atom -8.60892564573 0.117192245354 0.0982851777904 C -0.0314335491667 0.0 -0.0313212312302 0.00897304604753 0.0196935694367 +atom 10.8705405815 0.51581338865 0.435826522093 C -0.0539909791667 0.0 -0.0207616703214 -0.00491358425534 0.014173822701 +atom -10.8879581104 0.411807821319 0.694948565342 C -0.0495567391667 0.0 0.0330796233985 -0.00720705271362 -0.0192967826535 +atom 12.661965991 1.19502446714 1.1691448209 H 0.104980830833 0.0 -0.00448104672571 -0.00638001418343 -0.00747636563225 +atom -12.9307322131 0.525058551796 0.728011456903 H 0.105781040833 0.0 0.00766470653545 2.474313253e-05 0.00237591797661 +energy -381.611525444 +charge -0.0 +end diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/input.nn b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/input.nn new file mode 100644 index 0000000000..a53e0fa164 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/input.nn @@ -0,0 +1,185 @@ +## ############################################################# +### This is the input file for RuNNer +### ############################################################# +### General remarks: +### - commands can be switched off by using the # character at the BEGINNING of the line +### - the input file can be structured by blank lines and comment lines +### - the order of the keywords is arbitrary +### - if keywords are missing, default values will be used and written to runner.out +### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message + +### THIS INPUT.NN IS AN EXAMPLE, IT IS NOT A REALISTIC CASE +### It contains only a subset of all keywords + +######################################################################################################################## +### general keywords +######################################################################################################################## +use_electrostatics +use_short_nn +nnp_gen 4 # nnp_type_gen --> nnp_gen +runner_mode 3 +parallel_mode 1 +number_of_elements 2 +elements C H +random_seed 10 +random_number_type 5 +remove_atom_energies +atom_energy H -0.458907306351869 +atom_energy C -37.748111931202914 +initial_hardness H 10.0 ## fixed_atomhardness--> initial_hardness +initial_hardness C 10.0 +fixed_gausswidth H 0.585815056466 +fixed_gausswidth C 1.379499971678 +energy_threshold 100.0d0 +bond_threshold 0.4d0 +ewald_prec 1.0e-6 # for optimal combination of ewald parameters +screen_electrostatics 4.8 8.0 +######################################################################################################################## +### NN structure of the electrostatic-range NN +######################################################################################################################## +global_hidden_layers_electrostatic 2 +global_nodes_electrostatic 15 15 +global_activation_electrostatic t t l +global_hidden_layers_short 2 +global_nodes_short 10 10 +global_activation_short t t l +## element_hidden_layers_electrostatic needs to take care !!! should check the output +######################################################################################################################## +### symmetry function generation ( mode 1): +######################################################################################################################## +test_fraction 0.1 + +######################################################################################################################## +### symmetry function definitions (all modes): +######################################################################################################################## +cutoff_type 2 + + +# radial H H +symfunction H 2 H 0.000000 0.000000 8.000000 +symfunction H 2 H 0.006000 0.000000 8.000000 +symfunction H 2 H 0.011000 0.000000 8.000000 +symfunction H 2 H 0.018000 0.000000 8.000000 +symfunction H 2 H 0.026000 0.000000 8.000000 +symfunction H 2 H 0.035000 0.000000 8.000000 + +#radial C H +symfunction C 2 H 0.000000 0.000000 8.000000 +symfunction C 2 H 0.013000 0.000000 8.000000 +symfunction C 2 H 0.029000 0.000000 8.000000 +symfunction C 2 H 0.054000 0.000000 8.000000 +symfunction C 2 H 0.093000 0.000000 8.000000 +symfunction C 2 H 0.161000 0.000000 8.000000 + +symfunction H 2 C 0.000000 0.000000 8.000000 +symfunction H 2 C 0.013000 0.000000 8.000000 +symfunction H 2 C 0.029000 0.000000 8.000000 +symfunction H 2 C 0.054000 0.000000 8.000000 +symfunction H 2 C 0.093000 0.000000 8.000000 +symfunction H 2 C 0.161000 0.000000 8.000000 + +# radial C C +symfunction C 2 C 0.000000 0.000000 8.000000 +symfunction C 2 C 0.010000 0.000000 8.000000 +symfunction C 2 C 0.023000 0.000000 8.000000 +symfunction C 2 C 0.041000 0.000000 8.000000 +symfunction C 2 C 0.065000 0.000000 8.000000 +symfunction C 2 C 0.103000 0.000000 8.000000 + + +# +# angular + +symfunction C 3 C C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction C 3 H H 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction C 3 C H 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + + +symfunction H 3 C C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 C C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 C C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction H 3 H C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 H C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 H C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + + +######################################################################################################################## +### fitting (mode 2):general inputs for electrostatic range AND electrostatic part: +######################################################################################################################## +epochs 10 +points_in_memory 500 +mix_all_points +scale_symmetry_functions +center_symmetry_functions +fitting_unit eV +######################################################################################################################## +### fitting options ( mode 2): electrostatic range part only: +######################################################################################################################## +optmode_short_energy 1 +optmode_short_force 1 +short_energy_error_threshold 0.8 +short_force_error_threshold 0.8 +kalman_lambda_charge 0.98000 +kalman_nue_charge 0.99870 +kalman_lambda_short 0.98000 +kalman_nue_short 0.99870 +#use_old_weights_electrostatic +#force_update_scaling -1.0d0 +#electrostatic_energy_group 1 +#electrostatic_energy_fraction 1.00 +#electrostatic_force_group 1 + +short_force_fraction 0.025 +use_short_forces +weights_min -1.0 +weights_max 1.0 +precondition_weights +repeated_energy_update +nguyen_widrow_weights_short +regularize_fit_param 0.00001 ## 4G cases L2 regularization +######################################################################################################################## +### output options for mode 2 (fitting): +######################################################################################################################## +write_trainpoints +write_trainforces +#write_traincharges +######################################################################################################################## +### output options for mode 3 (prediction): +######################################################################################################################## +calculate_forces +#calculate_stress + diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/scaling.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/scaling.data new file mode 100644 index 0000000000..58924a796e --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain/nnp-predict/scaling.data @@ -0,0 +1,61 @@ + 1 1 0.000000000 0.168474325 0.051436597 + 1 2 0.304058579 0.417104776 0.345915594 + 1 3 0.000000000 0.159465228 0.047693255 + 1 4 0.000000000 0.152326768 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0.1413029799 + -0.1893761626 + -3.7391061335 + 0.0036828432 + 0.3886376713 + -0.6562280624 + 0.1083763220 + -0.0391240429 + 0.2267509693 + -0.2058136409 + -0.1430979256 + 0.7009168993 + 0.4931955095 + 0.7863721995 + 0.2472528221 + -1.2495204718 + 0.6875830102 + 1.9466142831 + 0.1023390652 + -0.2558956548 + 0.2852365762 + 0.0029291118 + 0.9868865541 + 0.0403577509 + -0.1047418136 + -0.3488408483 + -0.9674470264 + 0.1494635568 + 0.2065713356 + 2.3167621560 + -0.4749087023 + 1.3388042843 + 2.6993169368 + 0.0429258126 + 0.0103415735 + 0.2764993198 + 0.6813767545 + -0.4331521111 + 0.2551211682 + -0.2364161739 + -0.3079983949 + 0.6467916994 + -1.5260399719 + 0.6265168530 + -0.8105200453 + -0.3736370520 + 0.3084884217 + -0.2992212659 + -0.0273815678 + 0.1049134175 + 0.2536801614 + -1.1511637867 + -0.9000689224 + 0.1443339389 + 0.0620394402 + 1.9992994309 + 0.7843928157 + 1.4391271323 + -0.3321939402 + -2.4382905743 + -1.6734428117 + -0.9249641999 + -1.3018867082 + 0.0152212636 + 0.3104785525 + -0.2492140028 + -0.8955123746 + 0.9869474327 + 0.0822669444 + -0.1830559445 + -1.1230333927 + -0.1385515232 + -0.3696105195 + 0.1082286260 + 0.1748680549 + -1.2177151081 + 0.1079492551 + -0.2859594318 + -0.3121904922 + 0.1034155480 + 0.1806808724 + -0.2580117886 + 0.3535325828 + 0.0229540981 + 0.3238516401 + -0.7821787424 + -0.5357628124 + 1.2345527437 + 1.8953010665 + 0.3961253271 + -0.4570288514 + 0.4972780485 + 1.5141288000 + 0.1366535654 + -0.0558186183 + 0.5826411377 + -0.1801513810 + 0.4953259346 + -0.0545313333 + -0.1340448904 + -0.1234905918 + -1.2417564423 + -0.8220806959 + 0.1234736475 + -0.3094409144 + 0.3831220587 + -0.1464400551 + -0.2343229869 + 0.0007787294 + -0.4790095880 + 0.6993700632 + -0.1998249300 + 0.2858428262 + -0.2110018462 + 0.1624702703 + 0.6789582127 + -0.4868270904 + -0.2768406958 + -0.7069002115 + -0.6879166506 + -2.0867370236 + -0.7994656137 + 0.1719842944 + -0.0000752220 + -0.0003613176 + -0.0029232214 + 0.0445647221 + 0.0222816566 + -0.0003398342 + 0.0003305899 + -0.0272082042 + -0.0176071818 + 0.0295840498 + 0.0939072748 + -0.0735707973 + 0.0340777246 + -0.0573394490 + -0.1135653336 + -0.1319696539 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data new file mode 100644 index 0000000000..6cf458b3bc --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data @@ -0,0 +1,24 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 0.0 1.17284095486 -0.172504222684 -0.667448516865 +2 2 0.0 -1.1595434822 -0.350641000445 -0.467598107194 +3 2 0.0 3.72594054969 -0.0837975179097 -0.229777168673 +4 2 0.0 -3.69146983116 -0.334172643167 -0.21088223315 +5 2 0.0 6.07758586771 -0.166745226042 -0.145024035228 +6 2 0.0 -6.06809789367 -0.00253733508489 -0.0705357610724 +7 2 0.0 8.59164353464 -0.0806915075831 0.402236831619 +8 2 0.0 -8.60892564573 0.117192245354 0.0982851777904 +9 2 0.0 10.8705405815 0.51581338865 0.435826522093 +10 2 0.0 -10.8879581104 0.411807821319 0.694948565342 +11 1 0.0 12.661965991 1.19502446714 1.1691448209 +12 1 0.0 -12.9307322131 0.525058551796 0.728011456903 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-eg b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-eg new file mode 100644 index 0000000000..fe9b3348b8 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-eg @@ -0,0 +1,24 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 -2.36E-03 1.1729073318400078 -1.7250595988097372E-01 -6.6741810230359422E-01 +2 2 -8.49E-03 -1.1595817453608341 -3.5063784106789647E-01 -4.6759951235815161E-01 +3 2 -1.05E-02 3.7259094240411681 -8.3808446129817402E-02 -2.2980808620118351E-01 +4 2 -7.14E-03 -3.6915315204094927 -3.3414993292840278E-01 -2.1088572536199013E-01 +5 2 8.15E-04 6.0775914248949645 -1.6674672212588620E-01 -1.4499820679122288E-01 +6 2 8.35E-04 -6.0680299107700124 -2.5620260955245030E-03 -7.0543207699589230E-02 +7 2 -2.85E-02 8.5916667587931013 -8.0658783933167305E-02 4.0220650606187225E-01 +8 2 -3.24E-02 -8.6089840636623833 0.11721101618520001 9.8323591084281514E-02 +9 2 -6.05E-02 10.870494591100982 5.1580223738887498E-01 4.3585444122535055E-01 +10 2 -5.61E-02 -10.887890663537627 4.1179249277052421E-01 6.9490967680382398E-01 +11 1 1.01E-01 12.661796981509699 1.1948282077976258 1.1689054257962741 +12 1 1.02E-01 -12.930485451086453 5.2506382642642058E-01 7.2809053422821779E-01 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-mod b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-mod new file mode 100644 index 0000000000..24c09512e6 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-mod @@ -0,0 +1,24 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 -2.35997196E-03 1.172907331840007 -1.7250595988097372E-01 -6.6741810230359422E-01 +2 2 -8.49071586E-03 -1.159581745360834 -3.5063784106789647E-01 -4.6759951235815161E-01 +3 2 -1.05341133E-02 3.725909424041168 -8.3808446129817402E-02 -2.2980808620118351E-01 +4 2 -7.15563490E-03 -3.691531520409492 -3.3414993292840278E-01 -2.1088572536199013E-01 +5 2 8.14623403E-04 6.077591424894964 -1.6674672212588620E-01 -1.4499820679122288E-01 +6 2 8.34327483E-04 -6.068029910770012 -2.5620260955245030E-03 -7.0543207699589230E-02 +7 2 -2.83459938E-02 8.591666758793101 -8.0658783933167305E-02 4.0220650606187225E-01 +8 2 -3.24586443E-02 -8.608984063662383 0.11721101618520001 9.8323591084281514E-02 +9 2 -6.06473430E-02 10.870494591100982 5.1580223738887498E-01 4.3585444122535055E-01 +10 2 -5.61417786E-02 -10.887890663537627 4.1179249277052421E-01 6.9490967680382398E-01 +11 1 1.01543794E-01 12.661796981509699 1.1948282077976258 1.1689054257962741 +12 1 1.02941451E-01 -12.930485451086453 5.2506382642642058E-01 7.2809053422821779E-01 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-n2p2 b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-n2p2 new file mode 100644 index 0000000000..6e4467a4fa --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-n2p2 @@ -0,0 +1,25 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 0.0 1.1729073318400078 -0.17250595988097372 -0.66741810230359422 +2 2 0.0 -1.1595817453608341 -0.35063784106789647 -0.46759951235815161 +3 2 0.0 3.7259094240411681 -0.083808446129817402 -0.22980808620118351 +4 2 0.0 -3.6915315204094927 -0.33414993292840278 -0.21088572536199013 +5 2 0.0 6.0775914248949645 -0.16674672212588620 -0.14499820679122288 +6 2 0.0 -6.0680299107700124 -0.0025620260955245030 -0.070543207699589230 +7 2 0.0 8.5916667587931013 -0.080658783933167305 0.40220650606187225 +8 2 0.0 -8.6089840636623833 0.11721101618520001 0.098323591084281514 +9 2 0.0 10.870494591100982 0.51580223738887498 0.43585444122535055 +10 2 0.0 -10.887890663537627 0.41179249277052421 0.69490967680382398 +11 1 0.0 12.661796981509699 1.1948282077976258 1.168905425796274 +12 1 0.0 -12.930485451086453 0.52506382642642058 0.72809053422821779 + diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-org b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-org new file mode 100644 index 0000000000..3ea43476f1 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-org @@ -0,0 +1,24 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 -2.35997196E-03 1.17284095486 -0.172504222684 -0.667448516865 +2 2 -8.49071586E-03 -1.1595434822 -0.350641000445 -0.467598107194 +3 2 -1.05341133E-02 3.72594054969 -0.0837975179097 -0.229777168673 +4 2 -7.15563490E-03 -3.69146983116 -0.334172643167 -0.21088223315 +5 2 8.14623403E-04 6.07758586771 -0.166745226042 -0.145024035228 +6 2 8.34327483E-04 -6.06809789367 -0.00253733508489 -0.0705357610724 +7 2 -2.83459938E-02 8.59164353464 -0.0806915075831 0.402236831619 +8 2 -3.24586443E-02 -8.60892564573 0.117192245354 0.0982851777904 +9 2 -6.06473430E-02 10.8705405815 0.51581338865 0.435826522093 +10 2 -5.61417786E-02 -10.8879581104 0.411807821319 0.694948565342 +11 1 1.01543794E-01 12.661965991 1.19502446714 1.1691448209 +12 1 1.02941451E-01 -12.9307322131 0.525058551796 0.728011456903 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-q0 b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-q0 new file mode 100644 index 0000000000..6cf458b3bc --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-q0 @@ -0,0 +1,24 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 0.0 1.17284095486 -0.172504222684 -0.667448516865 +2 2 0.0 -1.1595434822 -0.350641000445 -0.467598107194 +3 2 0.0 3.72594054969 -0.0837975179097 -0.229777168673 +4 2 0.0 -3.69146983116 -0.334172643167 -0.21088223315 +5 2 0.0 6.07758586771 -0.166745226042 -0.145024035228 +6 2 0.0 -6.06809789367 -0.00253733508489 -0.0705357610724 +7 2 0.0 8.59164353464 -0.0806915075831 0.402236831619 +8 2 0.0 -8.60892564573 0.117192245354 0.0982851777904 +9 2 0.0 10.8705405815 0.51581338865 0.435826522093 +10 2 0.0 -10.8879581104 0.411807821319 0.694948565342 +11 1 0.0 12.661965991 1.19502446714 1.1691448209 +12 1 0.0 -12.9307322131 0.525058551796 0.728011456903 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-sameq b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-sameq new file mode 100644 index 0000000000..c8b9d39be1 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbon-chain.data-sameq @@ -0,0 +1,24 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 -2.3599719595358937E-03 1.1729073318400078 -1.7250595988097372E-01 -6.6741810230359422E-01 +2 2 -8.4907158646713859E-03 -1.1595817453608341 -3.5063784106789647E-01 -4.6759951235815161E-01 +3 2 -1.0534113290044665E-02 3.7259094240411681 -8.3808446129817402E-02 -2.2980808620118351E-01 +4 2 -7.1556348953342435E-03 -3.6915315204094927 -3.3414993292840278E-01 -2.1088572536199013E-01 +5 2 8.1462340324302566E-04 6.0775914248949645 -1.6674672212588620E-01 -1.4499820679122288E-01 +6 2 8.3432748292313285E-04 -6.0680299107700124 -2.5620260955245030E-03 -7.0543207699589230E-02 +7 2 -2.8345993789409479E-02 8.5916667587931013 -8.0658783933167305E-02 4.0220650606187225E-01 +8 2 -3.2458644274754651E-02 -8.6089840636623833 0.11721101618520001 9.8323591084281514E-02 +9 2 -6.0647343034107404E-02 10.870494591100982 5.1580223738887498E-01 4.3585444122535055E-01 +10 2 -5.6141778584216068E-02 -10.887890663537627 4.1179249277052421E-01 6.9490967680382398E-01 +11 1 1.0154379417885089E-01 12.661796981509699 1.1948282077976258 1.1689054257962741 +12 1 1.0294145062705674E-01 -12.930485451086453 5.2506382642642058E-01 7.2809053422821779E-01 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbond-chain.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbond-chain.data new file mode 100644 index 0000000000..24c09512e6 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/carbond-chain.data @@ -0,0 +1,24 @@ +Carbon chain, first structure from input.data + +12 atoms + +2 atom types + + -12.94 12.67 xlo xhi + -0.36 1.20 ylo yhi + -0.67 1.17 zlo zhi + +Atoms + +1 2 -2.35997196E-03 1.172907331840007 -1.7250595988097372E-01 -6.6741810230359422E-01 +2 2 -8.49071586E-03 -1.159581745360834 -3.5063784106789647E-01 -4.6759951235815161E-01 +3 2 -1.05341133E-02 3.725909424041168 -8.3808446129817402E-02 -2.2980808620118351E-01 +4 2 -7.15563490E-03 -3.691531520409492 -3.3414993292840278E-01 -2.1088572536199013E-01 +5 2 8.14623403E-04 6.077591424894964 -1.6674672212588620E-01 -1.4499820679122288E-01 +6 2 8.34327483E-04 -6.068029910770012 -2.5620260955245030E-03 -7.0543207699589230E-02 +7 2 -2.83459938E-02 8.591666758793101 -8.0658783933167305E-02 4.0220650606187225E-01 +8 2 -3.24586443E-02 -8.608984063662383 0.11721101618520001 9.8323591084281514E-02 +9 2 -6.06473430E-02 10.870494591100982 5.1580223738887498E-01 4.3585444122535055E-01 +10 2 -5.61417786E-02 -10.887890663537627 4.1179249277052421E-01 6.9490967680382398E-01 +11 1 1.01543794E-01 12.661796981509699 1.1948282077976258 1.1689054257962741 +12 1 1.02941451E-01 -12.930485451086453 5.2506382642642058E-01 7.2809053422821779E-01 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/debug.out b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/debug.out new file mode 100644 index 0000000000..a06fa562bd --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/debug.out @@ -0,0 +1 @@ + 00000000000000000000 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/energy.out b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/energy.out new file mode 100644 index 0000000000..acd0246e87 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/energy.out @@ -0,0 +1,16 @@ +################################################################################ +# Energy comparison. +################################################################################ +# Col Name Description +################################################################################ +# 1 conf Configuration index (starting with 1). +# 2 natoms Number of atoms in configuration. +# 3 Eref Reference potential energy. +# 4 Ennp Potential energy predicted by NNP. +# 5 Ediff Difference in energy per atom between reference and NNP prediction. +# 6 E_offset Sum of atomic offset energies (included in column Ennp). +######################################################################################################################### +# 1 2 3 4 5 6 +# conf natoms Eref Ennp Ediff E_offset +######################################################################################################################### + 1 12 0.0000000000000000E+00 -3.8161081273904063E+02 3.1800901061586718E+01 -3.7839893392473289E+02 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/external.out b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/external.out new file mode 100644 index 0000000000..11c84b4ce9 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/external.out @@ -0,0 +1,497 @@ + ------------------------------------------------------------- + ---------------------- Welcome to the ----------------------- + RuNNer Neural Network Energy Representation - RuNNer + ---------- (c) 2008-2020 Prof. Dr. Joerg Behler ---------- + ---------- Georg-August-Universitaet Goettingen ---------- + ---------- Theoretische Chemie ---------- + ---------- Tammannstr. 6 ---------- + ---------- 37077 Goettingen, Germany ---------- + ------------------------------------------------------------- + ------------------------------------------------------------- + This program is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the + Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. + + You should have received a copy of the GNU General Public License along + with this program. If not, see http://www.gnu.org/licenses. + ------------------------------------------------------------- + ------------------------------------------------------------- + When using RuNNer, please cite the following papers: + J. Behler, Angew. Chem. Int. Ed. 56, 12828 (2017). + J. Behler, Int. J. Quant. Chem. 115, 1032 (2015). + ------------------------------------------------------------- + Whenever using high-dimensional NNPs irrespective of the Code please cite: + J. Behler and M. Parrinello, Phys. Rev. Lett. 98, 146401 (2007). + ------------------------------------------------------------- + The reference for the atom-centered symmetry functions is: + J. Behler, J. Chem. Phys. 134, 074106 (2011). + ------------------------------------------------------------- + For high-dimensional NNs including electrostatics: + N. Artrith, T. Morawietz, and J. Behler, Phys. Rev. B 83, 153101 (2011). + ------------------------------------------------------------- + ------------------------------------------------------------- + RuNNer has been written by Joerg Behler + + *** with contributions from some friends *** + + Tobias Morawietz - Nguyen Widrow weights and electrostatic screening + Jovan Jose Kochumannil Varghese - Pair symmetry functions and pair NNPs + Michael Gastegger and Philipp Marquetand - element decoupled Kalman filter + Andreas Singraber - more efficient symmetry function type 3 implementation + Sinja Klees and Mariana Rossi - some infrastructure for i-Pi compatibility + Emir Kocer - Symmetry function groups + Fenfei Wei and Emir Kocer - Hessian, frequencies and normal modes + Alexander Knoll - vdW corrections long ranged + ------------------------------------------------------------- + ------------------------------------------------------------- + General job information: + ------------------------------------------------------------- + Executing host : Emir-MacBook-Pro.loc + User name : emirkocer + Starting date : 8. 2.2021 + Starting time : 10 h 29 min + Working directory : + ------------------------------------------------------------- + ------------------------------------------------------------- + Serial run requested + ------------------------------------------------------------- + Reading control parameters from input.nn + ============================================================= + ------------------------------------------------------------- + ### WARNING ### use_atom_charges is switched on for electrostatic NN + WARNING: reducing points_in_memory to max_num_atoms 12 + ============================================================= + General input parameters: + ------------------------------------------------------------- + Short range NN is on + Electrostatic NN is off + vdW corrections switched off + ------------------------------------------------------------- + RuNNer nn_type_short 3 + RuNNer is started in mode for prediction (3) + debugging mode is F + parallelization mode 1 + enable detailed time measurement F + using symmetry function groups F + silent mode F + NN force check F + number of elements 2 + elements (sorted): + 1 H + 6 C + seed for random number generator 10 + random number generator type 5 + remove free atom reference energies T + remove vdw dispersion energy and forces F + shortest allowed bond in structure 0.400 + Cutoff_type for symmetry function is 2 + Cutoff_alpha for inner cutoff radius is 0.000 + ------------------------------------------------------------- + Short range NN specifications: + ------------------------------------------------------------- + global hidden layers short range NN 2 + global nodes hidden layers short NN 10 10 + global activation functions short ttl + ------------------------------------------------------------- + Electrostatic specifications: + ------------------------------------------------------------- + electrostatic_type (nn_type_elec) 0 + Ewald alpha 0.000 + Ewald cutoff 0.000 + Ewald kmax 0 + Screening electrostatics 4.800000 8.000000 + ------------------------------------------------------------- + Parameters for symmetry function generation: short range part: + ------------------------------------------------------------- + using forces for fitting T + using atomic energies for fitting F + ------------------------------------------------------------- + Options for prediction mode: + ------------------------------------------------------------- + rescale symmetry functions T + remove CMS from symmetry functions T + rescale atomic charges F + remove CMS from atomic charges F + Reading formatted files + calculation of analytic forces T + calculation of analytic Hessian F + calculation of analytic stress F + write symmetry functions F + prepare md F + ============================================================= + Element pairs: 3 , shortest distance (Bohr) + pair 2 H C 2.046 + pair 3 C C 2.348 + ============================================================= + => short range NN weights type 3 H 381 + => short range NN weights type 3 C 501 + => electrostatic NN weights H 631 + => electrostatic NN weights C 811 + ------------------------------------------------------------- + ------------------------------------------------------------- + Atomic reference energies read from input.nn: + H -0.45890731 + C -37.74811193 + ------------------------------------------------------------- + ------------------------------------------------- + Atomic short range NN for element: H + architecture 25 10 10 1 + ------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G + 12 G + 13 G + 14 G + 15 G + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + ------------------------------------------------- + Atomic short range NN for element: C + architecture 37 10 10 1 + ------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G + 12 G + 13 G + 14 G + 15 G + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + 26 G + 27 G + 28 G + 29 G + 30 G + 31 G + 32 G + 33 G + 34 G + 35 G + 36 G + 37 G + --------------------------------------------------- + Electrostatic NN for element: H + architecture 24 15 15 1 + --------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G t t + 12 G t t + 13 G t t + 14 G t t + 15 G t t + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + --------------------------------------------------- + Electrostatic NN for element: C + architecture 36 15 15 1 + --------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G t t + 12 G t t + 13 G t t + 14 G t t + 15 G t t + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + 26 G + 27 G + 28 G + 29 G + 30 G + 31 G + 32 G + 33 G + 34 G + 35 G + 36 G + ------------------------------------------------------------- + ------------------------------------------------------------- + short range atomic symmetry functions element H : + ------------------------------------------------------------- + 1 H 2 H 0.000 0.000 8.000 + 2 H 2 C 0.000 0.000 8.000 + 3 H 2 H 0.006 0.000 8.000 + 4 H 2 H 0.011 0.000 8.000 + 5 H 2 C 0.013 0.000 8.000 + 6 H 2 H 0.018 0.000 8.000 + 7 H 2 H 0.026 0.000 8.000 + 8 H 2 C 0.029 0.000 8.000 + 9 H 2 H 0.035 0.000 8.000 + 10 H 2 C 0.054 0.000 8.000 + 11 H 2 C 0.093 0.000 8.000 + 12 H 2 C 0.161 0.000 8.000 + 13 H 3 H C 0.000 -1.000 1.000 8.000 + 14 H 3 C C 0.000 -1.000 1.000 8.000 + 15 H 3 H C 0.000 1.000 1.000 8.000 + 16 H 3 C C 0.000 1.000 1.000 8.000 + 17 H 3 H C 0.000 -1.000 2.000 8.000 + 18 H 3 C C 0.000 -1.000 2.000 8.000 + 19 H 3 H C 0.000 1.000 2.000 8.000 + 20 H 3 C C 0.000 1.000 2.000 8.000 + 21 H 3 H C 0.000 1.000 4.000 8.000 + 22 H 3 C C 0.000 1.000 4.000 8.000 + 23 H 3 H C 0.000 1.000 8.000 8.000 + 24 H 3 C C 0.000 1.000 8.000 8.000 + ------------------------------------------------------------- + short range atomic symmetry functions element C : + ------------------------------------------------------------- + 1 C 2 H 0.000 0.000 8.000 + 2 C 2 C 0.000 0.000 8.000 + 3 C 2 C 0.010 0.000 8.000 + 4 C 2 H 0.013 0.000 8.000 + 5 C 2 C 0.023 0.000 8.000 + 6 C 2 H 0.029 0.000 8.000 + 7 C 2 C 0.041 0.000 8.000 + 8 C 2 H 0.054 0.000 8.000 + 9 C 2 C 0.065 0.000 8.000 + 10 C 2 H 0.093 0.000 8.000 + 11 C 2 C 0.103 0.000 8.000 + 12 C 2 H 0.161 0.000 8.000 + 13 C 3 H H 0.000 -1.000 1.000 8.000 + 14 C 3 H C 0.000 -1.000 1.000 8.000 + 15 C 3 C C 0.000 -1.000 1.000 8.000 + 16 C 3 H H 0.000 1.000 1.000 8.000 + 17 C 3 H C 0.000 1.000 1.000 8.000 + 18 C 3 C C 0.000 1.000 1.000 8.000 + 19 C 3 H H 0.000 -1.000 2.000 8.000 + 20 C 3 H C 0.000 -1.000 2.000 8.000 + 21 C 3 C C 0.000 -1.000 2.000 8.000 + 22 C 3 H H 0.000 1.000 2.000 8.000 + 23 C 3 H C 0.000 1.000 2.000 8.000 + 24 C 3 C C 0.000 1.000 2.000 8.000 + 25 C 3 H H 0.000 -1.000 4.000 8.000 + 26 C 3 H C 0.000 -1.000 4.000 8.000 + 27 C 3 C C 0.000 -1.000 4.000 8.000 + 28 C 3 H H 0.000 1.000 4.000 8.000 + 29 C 3 H C 0.000 1.000 4.000 8.000 + 30 C 3 C C 0.000 1.000 4.000 8.000 + 31 C 3 H H 0.000 -1.000 8.000 8.000 + 32 C 3 H C 0.000 -1.000 8.000 8.000 + 33 C 3 C C 0.000 -1.000 8.000 8.000 + 34 C 3 H H 0.000 1.000 8.000 8.000 + 35 C 3 H C 0.000 1.000 8.000 8.000 + 36 C 3 C C 0.000 1.000 8.000 8.000 + ------------------------------------------------------------- + Prediction Mode for all configurations + NNconfiguration: 1 Number of atoms: 12 + ------------------------------------------------------------- + begin + atom -8.608984064 0.117211016 0.098323591 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom -10.887890664 0.411792493 0.694909677 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom -12.930485451 0.525063826 0.728090534 H 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom -3.691531520 -0.334149933 -0.210885725 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom -6.068029911 -0.002562026 -0.070543208 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom 1.172907332 -0.172505960 -0.667418102 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom -1.159581745 -0.350637841 -0.467599512 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom 3.725909424 -0.083808446 -0.229808086 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom 6.077591425 -0.166746722 -0.144998207 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom 8.591666759 -0.080658784 0.402206506 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom 10.870494591 0.515802237 0.435854441 C 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + atom 12.661796982 1.194828208 1.168905426 H 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 + energy 0.00000000 + charge 0.00000000 + end + ------------------------------------------------------------- + ============================================================= + Short range symmetry function values for element H + Training set: min max average range + 1 0.00000000 0.16847433 0.05143660 0.16847433 + 2 0.30405858 0.41710478 0.34591559 0.11304620 + 3 0.00000000 0.15946523 0.04769325 0.15946523 + 4 0.00000000 0.15232677 0.04478431 0.15232677 + 5 0.27036724 0.37728930 0.31224289 0.10692206 + 6 0.00000000 0.14286655 0.04100957 0.14286655 + 7 0.00000000 0.13277213 0.03708637 0.13277213 + 8 0.23624129 0.33657312 0.27800313 0.10033183 + 9 0.00000000 0.12226589 0.03312272 0.12226589 + 10 0.19404378 0.28607654 0.23585771 0.09203276 + 11 0.14641396 0.23097961 0.18800041 0.08456565 + 12 0.09432878 0.16744424 0.13330093 0.07311545 + 13 0.00000000 0.00394060 0.00076628 0.00394060 + 14 0.00000000 0.00217985 0.00039524 0.00217985 + 15 0.00000000 0.02261515 0.00668807 0.02261515 + 16 0.00679906 0.01478606 0.00985450 0.00798700 + 17 0.00000000 0.00075421 0.00011847 0.00075421 + 18 0.00000000 0.00030711 0.00003118 0.00030711 + 19 0.00000000 0.02017145 0.00604027 0.02017145 + 20 0.00644757 0.01299704 0.00949044 0.00654947 + 21 0.00000000 0.01674922 0.00500244 0.01674922 + 22 0.00579909 0.01111309 0.00884495 0.00531401 + 23 0.00000000 0.01266231 0.00356524 0.01266231 + 24 0.00441798 0.01101955 0.00782196 0.00660157 + ============================================================= + Short range symmetry function values for element C + Training set: min max average range + 1 0.00000000 0.52808592 0.08649996 0.52808592 + 2 0.24355100 0.57639765 0.47819195 0.33284665 + 3 0.22048695 0.52746937 0.43763560 0.30698242 + 4 0.00000000 0.50353455 0.07807973 0.50353455 + 5 0.19509715 0.47330565 0.39251071 0.27820850 + 6 0.00000000 0.47487956 0.06951771 0.47487956 + 7 0.16625451 0.41178373 0.34093485 0.24552922 + 8 0.00000000 0.43333727 0.05897878 0.43333727 + 9 0.13622094 0.34796466 0.28640072 0.21174372 + 10 0.00000000 0.37567165 0.04701155 0.37567165 + 11 0.10158128 0.27309231 0.22197774 0.17151103 + 12 0.00000000 0.29287798 0.03333335 0.29287798 + 13 0.00000000 0.01526781 0.00060792 0.01526781 + 14 0.00000000 0.02036732 0.00232310 0.02036732 + 15 0.00000000 0.00665803 0.00399047 0.00665803 + 16 0.00000000 0.00928448 0.00032410 0.00928448 + 17 0.00000000 0.02498584 0.00280302 0.02498584 + 18 0.00352236 0.01252347 0.00802997 0.00900111 + 19 0.00000000 0.01192185 0.00042997 0.01192185 + 20 0.00000000 0.01555842 0.00202393 0.01555842 + 21 0.00000000 0.00651859 0.00394164 0.00651859 + 22 0.00000000 0.00382338 0.00014615 0.00382338 + 23 0.00000000 0.02344629 0.00250385 0.02344629 + 24 0.00351299 0.01243332 0.00798114 0.00892033 + 25 0.00000000 0.00867873 0.00022911 0.00867873 + 26 0.00000000 0.01071420 0.00169575 0.01071420 + 27 0.00000000 0.00638443 0.00387839 0.00638443 + 28 0.00000000 0.00175837 0.00006004 0.00175837 + 29 0.00000000 0.02109576 0.00231908 0.02109576 + 30 0.00350470 0.01233977 0.00794786 0.00883507 + 31 0.00000000 0.00469998 0.00006919 0.00469998 + 32 0.00000000 0.01070123 0.00135740 0.01070123 + 33 0.00000000 0.00633887 0.00375782 0.00633887 + 34 0.00000000 0.00094265 0.00002301 0.00094265 + 35 0.00000000 0.01713776 0.00211168 0.01713776 + 36 0.00347687 0.01215547 0.00788315 0.00867860 + ------------------------------------------------------------- + eshortmin from scaling.data: -0.2691374625 + eshortmax from scaling.data: -0.2381480047 + ------------------------------------------------------------- + ------------------------------------------------------------- + NN sum of free atom energies,short range and electrostatic energy for configuration 1 + NN sum of free atom energies 0.00000000 Ha + NN short range energy -381.61079700 Ha + NN electrostatic energy -0.00001574 Ha + NN vdw dispersion energy 0.00000000 Ha + NNenergy -381.61081274 Ha + ------------------------------------------------------------- + NN atomenergies with configuration 1 +NNatomenergy 1 C -37.952909 +NNatomenergy 2 C -37.919421 +NNatomenergy 3 H -0.880328 +NNatomenergy 4 C -38.022413 +NNatomenergy 5 C -38.018132 +NNatomenergy 6 C -38.020613 +NNatomenergy 7 C -38.009915 +NNatomenergy 8 C -38.018981 +NNatomenergy 9 C -38.012933 +NNatomenergy 10 C -37.952059 +NNatomenergy 11 C -37.922947 +NNatomenergy 12 H -0.880147 + ------------------------------------------------------------- + NNcharges for configuration 1 + NNcharge 1 -0.03245864 + NNcharge 2 -0.05614178 + NNcharge 3 0.10294145 + NNcharge 4 -0.00715563 + NNcharge 5 0.00083433 + NNcharge 6 -0.00235997 + NNcharge 7 -0.00849072 + NNcharge 8 -0.01053411 + NNcharge 9 0.00081462 + NNcharge 10 -0.02834599 + NNcharge 11 -0.06064734 + NNcharge 12 0.10154379 + ------------------------------------------------------------- + NN forces for the configuration 1 + NNforces 1 -0.03084848 0.00994372 0.02035300 Ha/Bohr + NNforces 2 0.03575321 -0.00812376 -0.02060840 Ha/Bohr + NNforces 3 0.00817873 0.00018015 0.00264405 Ha/Bohr + NNforces 4 -0.03267242 0.01204150 -0.00185729 Ha/Bohr + NNforces 5 0.03596400 -0.01308899 -0.00394444 Ha/Bohr + NNforces 6 0.03510320 -0.00092789 0.01613691 Ha/Bohr + NNforces 7 -0.02021497 0.00168076 -0.00075111 Ha/Bohr + NNforces 8 -0.01645840 -0.00579815 -0.01639606 Ha/Bohr + NNforces 9 0.00292959 -0.00079391 0.01370348 Ha/Bohr + NNforces 10 0.01224082 0.01734497 -0.01609327 Ha/Bohr + NNforces 11 -0.02441314 -0.00593162 0.01477905 Ha/Bohr + NNforces 12 -0.00556215 -0.00652678 -0.00796590 Ha/Bohr + ------------------------------------------------------------- + ------------------------------------------------------------- + extrapolation warnings for configuration 1 + extrapolation warnings (energy) 0 +extrapolation warnings (symmetry functions 0 + ------------------------------------------------------------- + Total runtime (s) : 0.014 + Total runtime (min): 0.000 + Total runtime (h) : 0.000 + Normal termination of RuNNer + ------------------------------------------------------------- diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/hardness.001.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/hardness.001.data new file mode 100644 index 0000000000..60e1493e7c --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/hardness.001.data @@ -0,0 +1 @@ + 0.0088953312 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/hardness.006.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/hardness.006.data new file mode 100644 index 0000000000..e8464ac99e --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/hardness.006.data @@ -0,0 +1 @@ + 0.0661189426 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.data new file mode 100644 index 0000000000..e85b80682b --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.data @@ -0,0 +1,17 @@ +begin +comment +atom -8.6089840636623833E+00 1.1721101618520001E-01 9.8323591084281514E-02 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom -1.0887890663537627E+01 4.1179249277052421E-01 6.9490967680382398E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom -1.2930485451086453E+01 5.2506382642642058E-01 7.2809053422821779E-01 H 0.0000000000000000E+00 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a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.data-org b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.data-org new file mode 100644 index 0000000000..e85b80682b --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.data-org @@ -0,0 +1,17 @@ +begin +comment +atom -8.6089840636623833E+00 1.1721101618520001E-01 9.8323591084281514E-02 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom -1.0887890663537627E+01 4.1179249277052421E-01 6.9490967680382398E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom -1.2930485451086453E+01 5.2506382642642058E-01 7.2809053422821779E-01 H 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom -3.6915315204094927E+00 -3.3414993292840278E-01 -2.1088572536199013E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom -6.0680299107700124E+00 -2.5620260955245030E-03 -7.0543207699589230E-02 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom 1.1729073318400078E+00 -1.7250595988097372E-01 -6.6741810230359422E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom -1.1595817453608341E+00 -3.5063784106789647E-01 -4.6759951235815161E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom 3.7259094240411681E+00 -8.3808446129817402E-02 -2.2980808620118351E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom 6.0775914248949645E+00 -1.6674672212588620E-01 -1.4499820679122288E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom 8.5916667587931013E+00 -8.0658783933167305E-02 4.0220650606187225E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom 1.0870494591100982E+01 5.1580223738887498E-01 4.3585444122535055E-01 C 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +atom 1.2661796981509699E+01 1.1948282077976258E+00 1.1689054257962741E+00 H 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 +energy 0.0000000000000000E+00 +charge 0.0000000000000000E+00 +end diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.nn b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.nn new file mode 100644 index 0000000000..a53e0fa164 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/input.nn @@ -0,0 +1,185 @@ +## ############################################################# +### This is the input file for RuNNer +### ############################################################# +### General remarks: +### - commands can be switched off by using the # character at the BEGINNING of the line +### - the input file can be structured by blank lines and comment lines +### - the order of the keywords is arbitrary +### - if keywords are missing, default values will be used and written to runner.out +### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message + +### THIS INPUT.NN IS AN EXAMPLE, IT IS NOT A REALISTIC CASE +### It contains only a subset of all keywords + +######################################################################################################################## +### general keywords +######################################################################################################################## +use_electrostatics +use_short_nn +nnp_gen 4 # nnp_type_gen --> nnp_gen +runner_mode 3 +parallel_mode 1 +number_of_elements 2 +elements C H +random_seed 10 +random_number_type 5 +remove_atom_energies +atom_energy H -0.458907306351869 +atom_energy C -37.748111931202914 +initial_hardness H 10.0 ## fixed_atomhardness--> initial_hardness +initial_hardness C 10.0 +fixed_gausswidth H 0.585815056466 +fixed_gausswidth C 1.379499971678 +energy_threshold 100.0d0 +bond_threshold 0.4d0 +ewald_prec 1.0e-6 # for optimal combination of ewald parameters +screen_electrostatics 4.8 8.0 +######################################################################################################################## +### NN structure of the electrostatic-range NN +######################################################################################################################## +global_hidden_layers_electrostatic 2 +global_nodes_electrostatic 15 15 +global_activation_electrostatic t t l +global_hidden_layers_short 2 +global_nodes_short 10 10 +global_activation_short t t l +## element_hidden_layers_electrostatic needs to take care !!! should check the output +######################################################################################################################## +### symmetry function generation ( mode 1): +######################################################################################################################## +test_fraction 0.1 + +######################################################################################################################## +### symmetry function definitions (all modes): +######################################################################################################################## +cutoff_type 2 + + +# radial H H +symfunction H 2 H 0.000000 0.000000 8.000000 +symfunction H 2 H 0.006000 0.000000 8.000000 +symfunction H 2 H 0.011000 0.000000 8.000000 +symfunction H 2 H 0.018000 0.000000 8.000000 +symfunction H 2 H 0.026000 0.000000 8.000000 +symfunction H 2 H 0.035000 0.000000 8.000000 + +#radial C H +symfunction C 2 H 0.000000 0.000000 8.000000 +symfunction C 2 H 0.013000 0.000000 8.000000 +symfunction C 2 H 0.029000 0.000000 8.000000 +symfunction C 2 H 0.054000 0.000000 8.000000 +symfunction C 2 H 0.093000 0.000000 8.000000 +symfunction C 2 H 0.161000 0.000000 8.000000 + +symfunction H 2 C 0.000000 0.000000 8.000000 +symfunction H 2 C 0.013000 0.000000 8.000000 +symfunction H 2 C 0.029000 0.000000 8.000000 +symfunction H 2 C 0.054000 0.000000 8.000000 +symfunction H 2 C 0.093000 0.000000 8.000000 +symfunction H 2 C 0.161000 0.000000 8.000000 + +# radial C C +symfunction C 2 C 0.000000 0.000000 8.000000 +symfunction C 2 C 0.010000 0.000000 8.000000 +symfunction C 2 C 0.023000 0.000000 8.000000 +symfunction C 2 C 0.041000 0.000000 8.000000 +symfunction C 2 C 0.065000 0.000000 8.000000 +symfunction C 2 C 0.103000 0.000000 8.000000 + + +# +# angular + +symfunction C 3 C C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction C 3 H H 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction C 3 C H 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + + +symfunction H 3 C C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 C C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 C C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction H 3 H C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 H C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 H C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + + +######################################################################################################################## +### fitting (mode 2):general inputs for electrostatic range AND electrostatic part: +######################################################################################################################## +epochs 10 +points_in_memory 500 +mix_all_points +scale_symmetry_functions +center_symmetry_functions +fitting_unit eV +######################################################################################################################## +### fitting options ( mode 2): electrostatic range part only: +######################################################################################################################## +optmode_short_energy 1 +optmode_short_force 1 +short_energy_error_threshold 0.8 +short_force_error_threshold 0.8 +kalman_lambda_charge 0.98000 +kalman_nue_charge 0.99870 +kalman_lambda_short 0.98000 +kalman_nue_short 0.99870 +#use_old_weights_electrostatic +#force_update_scaling -1.0d0 +#electrostatic_energy_group 1 +#electrostatic_energy_fraction 1.00 +#electrostatic_force_group 1 + +short_force_fraction 0.025 +use_short_forces +weights_min -1.0 +weights_max 1.0 +precondition_weights +repeated_energy_update +nguyen_widrow_weights_short +regularize_fit_param 0.00001 ## 4G cases L2 regularization +######################################################################################################################## +### output options for mode 2 (fitting): +######################################################################################################################## +write_trainpoints +write_trainforces +#write_traincharges +######################################################################################################################## +### output options for mode 3 (prediction): +######################################################################################################################## +calculate_forces +#calculate_stress + diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnatoms.out b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnatoms.out new file mode 100644 index 0000000000..ac2380f9d4 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnatoms.out @@ -0,0 +1,28 @@ +################################################################################ +# Energy contributions calculated from NNP. +################################################################################ +# Col Name Description +################################################################################ +# 1 conf Configuration index (starting with 1). +# 2 index Atom index (starting with 1). +# 3 Z Nuclear charge of atom. +# 4 Qref Reference atomic charge. +# 5 Qnnp NNP atomic charge. +# 6 Eref_atom Reference atomic energy contribution. +# 7 Ennp_atom Atomic energy contribution (physical units, no mean or offset energy added). +############################################################################################################################# +# 1 2 3 4 5 6 7 +# conf index Z Qref Qnnp Eref_atom Ennp_atom +############################################################################################################################# + 1 1 6 0.0000000000000000E+00 -3.2458644274754651E-02 0.0000000000000000E+00 -2.0479710438970580E-01 + 1 2 6 0.0000000000000000E+00 -5.6141778584216068E-02 0.0000000000000000E+00 -1.7130864053608713E-01 + 1 3 1 0.0000000000000000E+00 1.0294145062705674E-01 0.0000000000000000E+00 -4.2142060824865357E-01 + 1 4 6 0.0000000000000000E+00 -7.1556348953342435E-03 0.0000000000000000E+00 -2.7430064475745047E-01 + 1 5 6 0.0000000000000000E+00 8.3432748292313285E-04 0.0000000000000000E+00 -2.7002047650869254E-01 + 1 6 6 0.0000000000000000E+00 -2.3599719595358937E-03 0.0000000000000000E+00 -2.7250138971765969E-01 + 1 7 6 0.0000000000000000E+00 -8.4907158646713859E-03 0.0000000000000000E+00 -2.6180345487358536E-01 + 1 8 6 0.0000000000000000E+00 -1.0534113290044665E-02 0.0000000000000000E+00 -2.7086885868262611E-01 + 1 9 6 0.0000000000000000E+00 8.1462340324302566E-04 0.0000000000000000E+00 -2.6482089673470777E-01 + 1 10 6 0.0000000000000000E+00 -2.8345993789409479E-02 0.0000000000000000E+00 -2.0394673774174502E-01 + 1 11 6 0.0000000000000000E+00 -6.0647343034107404E-02 0.0000000000000000E+00 -1.7483492203211570E-01 + 1 12 1 0.0000000000000000E+00 1.0154379417885089E-01 0.0000000000000000E+00 -4.2123934102023231E-01 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnforces.out b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnforces.out new file mode 100644 index 0000000000..9427fb9928 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnforces.out @@ -0,0 +1,29 @@ +################################################################################ +# Atomic force comparison (ordered by atom index). +################################################################################ +# Col Name Description +################################################################################ +# 1 conf Configuration index (starting with 1). +# 2 index Atom index (starting with 1). +# 3 fxRef Reference force in x direction. +# 4 fyRef Reference force in y direction. +# 5 fzRef Reference force in z direction. +# 6 fx Force in x direction. +# 7 fy Force in y direction. +# 8 fz Force in z direction. +########################################################################################################################################################################### +# 1 2 3 4 5 6 7 8 +# conf index fxRef fyRef fzRef fx fy fz +########################################################################################################################################################################### + 1 1 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 -3.0848483621290768E-02 9.9437229539220684E-03 2.0352999337438824E-02 + 1 2 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 3.5753209472753004E-02 -8.1237628180204809E-03 -2.0608404213202990E-02 + 1 3 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 8.1787276673429710E-03 1.8014717534816583E-04 2.6440476603640309E-03 + 1 4 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 -3.2672415145898345E-02 1.2041500311444986E-02 -1.8572895160292656E-03 + 1 5 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 3.5963999960799249E-02 -1.3088993906111521E-02 -3.9444423243935513E-03 + 1 6 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 3.5103202289331878E-02 -9.2789354753794961E-04 1.6136905570554479E-02 + 1 7 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 -2.0214969739033205E-02 1.6807648404055854E-03 -7.5111141444395750E-04 + 1 8 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 -1.6458402959242311E-02 -5.7981475984617377E-03 -1.6396064514211335E-02 + 1 9 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 2.9295943813836588E-03 -7.9390824921095359E-04 1.3703484666740151E-02 + 1 10 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 1.2240824229741747E-02 1.7344969704443759E-02 -1.6093273578742517E-02 + 1 11 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 -2.4413138020654052E-02 -5.9316238120533807E-03 1.4779052720039060E-02 + 1 12 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 -5.5621485152346096E-03 -6.5267750541684114E-03 -7.9659043941128650E-03 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnp-predict.log b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnp-predict.log new file mode 100644 index 0000000000..9bd13a392a --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/nnp-predict.log @@ -0,0 +1,681 @@ + +******************************************************************************* + +WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS! +------------------------------------------------------------------ + +n²p² version : v2.1.1-62-g8827e5b +------------------------------------------------------------ +Git branch : 4G-HDNNP-prediction +Git revision : 8827e5b707e89d6fef99548e0a4d5d9571739766 +Compile date/time : Jun 23 2021 19:31:05 +------------------------------------------------------------ + +Please cite the following papers when publishing results obtained with n²p²: +------------------------------------------------------------------------------- + * General citation for n²p² and the LAMMPS interface: + + Singraber, A.; Behler, J.; Dellago, C. + Library-Based LAMMPS Implementation of High-Dimensional + Neural Network Potentials. + J. Chem. Theory Comput. 2019 15 (3), 1827–1840. + https://doi.org/10.1021/acs.jctc.8b00770 +------------------------------------------------------------------------------- + * Additionally, if you use the NNP training features of n²p²: + + Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C. + Parallel Multistream Training of High-Dimensional Neural + Network Potentials. + J. Chem. Theory Comput. 2019, 15 (5), 3075–3092. + https://doi.org/10.1021/acs.jctc.8b01092 +------------------------------------------------------------------------------- + * Additionally, if polynomial symmetry functions are used: + + Bircher, M. P.; Singraber, A.; Dellago, C. + Improved Description of Atomic Environments Using Low-Cost + Polynomial Functions with Compact Support. + arXiv:2010.14414 [cond-mat, physics:physics] 2020. + https://arxiv.org/abs/2010.14414 +******************************************************************************* + +*** SETUP: SETTINGS FILE ****************************************************** + +Settings file name: input.nn +Read 185 lines. +WARNING: Unknown keyword "bond_threshold" at line 34. +WARNING: Unknown keyword "calculate_forces" at line 183. +WARNING: Unknown keyword "energy_threshold" at line 33. +WARNING: Unknown keyword "fitting_unit" at line 148. +WARNING: Unknown keyword "kalman_lambda_charge" at line 156. +WARNING: Unknown keyword "kalman_nue_charge" at line 157. +WARNING: Unknown keyword "mix_all_points" at line 145. +WARNING: Unknown keyword "optmode_short_energy" at line 152. +WARNING: Unknown keyword "optmode_short_force" at line 153. +WARNING: Unknown keyword "points_in_memory" at line 144. +WARNING: Unknown keyword "random_number_type" at line 25. +WARNING: Unknown keyword "regularize_fit_param" at line 173. +WARNING: Unknown keyword "remove_atom_energies" at line 26. +WARNING: Unknown keyword "runner_mode" at line 20. +WARNING: Unknown keyword "use_electrostatics" at line 17. +WARNING: Unknown keyword "use_short_nn" at line 18. +WARNING: 16 problems detected (0 critical). +Found 113 lines with keywords. +This settings file defines a NNP with electrostatics and +non-local charge transfer (4G-HDNNP). +******************************************************************************* + +*** SETUP: NORMALIZATION ****************************************************** + +Data set normalization is not used. +******************************************************************************* + +*** SETUP: ELEMENT MAP ******************************************************** + +Number of element strings found: 2 +Element 0: H ( 1) +Element 1: C ( 6) +******************************************************************************* + +*** SETUP: ELEMENTS *********************************************************** + +Number of elements is consistent: 2 +Atomic energy offsets per element: +Element 0: -4.58907306E-01 +Element 1: -3.77481119E+01 +Energy offsets are automatically subtracted from reference energies. +******************************************************************************* + +*** SETUP: ELECTROSTATICS ***************************************************** + +Atomic hardness file name format: hardness.%03zu.data +Atomic hardness for element H from file hardness.001.data: 8.89533120E-03 +Atomic hardness for element C from file hardness.006.data: 6.61189426E-02 + +Gaussian width of charge distribution per element: +Element 0: 5.85815056E-01 +Element 1: 1.37949997E+00 + +Ewald precision: 1.00000000E-06 + +Screening function information: +Inner radius : 4.80000000E+00 +Outer radius : 8.00000000E+00 +Transition region functional form: +x := (r - inner) / (outer - inner) +fs(x) := 1 - f(x) +CoreFunction::Type::COS (0): +f(x) := 1/2 * (cos(pi*x) + 1) +******************************************************************************* + +*** SETUP: CUTOFF FUNCTIONS *************************************************** + +Parameter alpha for inner cutoff: 0.000000 +Inner cutoff = Symmetry function cutoff * alpha +Equal cutoff function type for all symmetry functions: +CutoffFunction::CT_TANHU (2) +f(r) = tanh^3(1 - r/rc) +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTIONS ************************************************* + +Abbreviations: +-------------- +ind .... Symmetry function index. +ec ..... Central atom element. +tp ..... Symmetry function type. +sbtp ... Symmetry function subtype (e.g. cutoff type). +e1 ..... Neighbor 1 element. +e2 ..... Neighbor 2 element. +eta .... Gaussian width eta. +rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial. +angl.... Left cutoff angle for polynomial. +angr.... Right cutoff angle for polynomial. +la ..... Angle prefactor lambda. +zeta ... Angle term exponent zeta. +rc ..... Cutoff radius / right cutoff radius for polynomial. +a ...... Free parameter alpha (e.g. cutoff alpha). +ln ..... Line number in settings file. + +Short range atomic symmetry functions element H : +------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln +------------------------------------------------------------------------------------------------- + 1 H 2 ct2 H 0.000E+00 0.000E+00 8.000E+00 0.00 59 + 2 H 2 ct2 C 0.000E+00 0.000E+00 8.000E+00 0.00 74 + 3 H 2 ct2 H 6.000E-03 0.000E+00 8.000E+00 0.00 60 + 4 H 2 ct2 H 1.100E-02 0.000E+00 8.000E+00 0.00 61 + 5 H 2 ct2 C 1.300E-02 0.000E+00 8.000E+00 0.00 75 + 6 H 2 ct2 H 1.800E-02 0.000E+00 8.000E+00 0.00 62 + 7 H 2 ct2 H 2.600E-02 0.000E+00 8.000E+00 0.00 63 + 8 H 2 ct2 C 2.900E-02 0.000E+00 8.000E+00 0.00 76 + 9 H 2 ct2 H 3.500E-02 0.000E+00 8.000E+00 0.00 64 + 10 H 2 ct2 C 5.400E-02 0.000E+00 8.000E+00 0.00 77 + 11 H 2 ct2 C 9.300E-02 0.000E+00 8.000E+00 0.00 78 + 12 H 2 ct2 C 1.610E-01 0.000E+00 8.000E+00 0.00 79 + 13 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 134 + 14 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 125 + 15 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 130 + 16 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 121 + 17 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 135 + 18 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 126 + 19 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 131 + 20 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 122 + 21 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 132 + 22 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 123 + 23 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 133 + 24 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 124 +------------------------------------------------------------------------------------------------- +Short range atomic symmetry functions element C : +------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln +------------------------------------------------------------------------------------------------- + 1 C 2 ct2 H 0.000E+00 0.000E+00 8.000E+00 0.00 67 + 2 C 2 ct2 C 0.000E+00 0.000E+00 8.000E+00 0.00 82 + 3 C 2 ct2 C 1.000E-02 0.000E+00 8.000E+00 0.00 83 + 4 C 2 ct2 H 1.300E-02 0.000E+00 8.000E+00 0.00 68 + 5 C 2 ct2 C 2.300E-02 0.000E+00 8.000E+00 0.00 84 + 6 C 2 ct2 H 2.900E-02 0.000E+00 8.000E+00 0.00 69 + 7 C 2 ct2 C 4.100E-02 0.000E+00 8.000E+00 0.00 85 + 8 C 2 ct2 H 5.400E-02 0.000E+00 8.000E+00 0.00 70 + 9 C 2 ct2 C 6.500E-02 0.000E+00 8.000E+00 0.00 86 + 10 C 2 ct2 H 9.300E-02 0.000E+00 8.000E+00 0.00 71 + 11 C 2 ct2 C 1.030E-01 0.000E+00 8.000E+00 0.00 87 + 12 C 2 ct2 H 1.610E-01 0.000E+00 8.000E+00 0.00 72 + 13 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 106 + 14 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 115 + 15 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 97 + 16 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 102 + 17 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 111 + 18 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 93 + 19 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 107 + 20 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 116 + 21 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 98 + 22 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 103 + 23 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 112 + 24 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 94 + 25 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 108 + 26 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 117 + 27 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 99 + 28 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 104 + 29 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 113 + 30 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 95 + 31 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 109 + 32 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 118 + 33 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 100 + 34 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 105 + 35 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 114 + 36 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 96 +------------------------------------------------------------------------------------------------- +Minimum cutoff radius for element H: 8.000000 +Minimum cutoff radius for element C: 8.000000 +Maximum cutoff radius (global) : 8.000000 +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION MEMORY ******************************************* + +Symmetry function derivatives memory table for element H : +------------------------------------------------------------------------------- +Relevant symmetry functions for neighbors with element: +- H: 12 of 24 ( 50.0 ) +- C: 18 of 24 ( 75.0 ) +------------------------------------------------------------------------------- +Symmetry function derivatives memory table for element C : +------------------------------------------------------------------------------- +Relevant symmetry functions for neighbors with element: +- H: 22 of 36 ( 61.1 ) +- C: 22 of 36 ( 61.1 ) +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION CACHE ******************************************** + +Element H: in total 4 caches, used 15.00 times on average. +Element C: in total 4 caches, used 22.00 times on average. +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION GROUPS ******************************************* + +Abbreviations: +-------------- +ind .... Symmetry function index. +ec ..... Central atom element. +tp ..... Symmetry function type. +sbtp ... Symmetry function subtype (e.g. cutoff type). +e1 ..... Neighbor 1 element. +e2 ..... Neighbor 2 element. +eta .... Gaussian width eta. +rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial. +angl.... Left cutoff angle for polynomial. +angr.... Right cutoff angle for polynomial. +la ..... Angle prefactor lambda. +zeta ... Angle term exponent zeta. +rc ..... Cutoff radius / right cutoff radius for polynomial. +a ...... Free parameter alpha (e.g. cutoff alpha). +ln ..... Line number in settings file. +mi ..... Member index. +sfi .... Symmetry function index. +e ...... Recalculate exponential term. + +Short range atomic symmetry function groups element H : +---------------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e +---------------------------------------------------------------------------------------------------------- + 1 H 2 ct2 H * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 59 1 1 + - - - - - 6.000E-03 0.000E+00 - - 60 2 3 + - - - - - 1.100E-02 0.000E+00 - - 61 3 4 + - - - - - 1.800E-02 0.000E+00 - - 62 4 6 + - - - - - 2.600E-02 0.000E+00 - - 63 5 7 + - - - - - 3.500E-02 0.000E+00 - - 64 6 9 + 2 H 2 ct2 C * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 74 1 2 + - - - - - 1.300E-02 0.000E+00 - - 75 2 5 + - - - - - 2.900E-02 0.000E+00 - - 76 3 8 + - - - - - 5.400E-02 0.000E+00 - - 77 4 10 + - - - - - 9.300E-02 0.000E+00 - - 78 5 11 + - - - - - 1.610E-01 0.000E+00 - - 79 6 12 + 3 H 3 ct2 H C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 134 1 13 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 130 2 15 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 135 3 17 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 131 4 19 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 132 5 21 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 133 6 23 0 + 4 H 3 ct2 C C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 125 1 14 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 121 2 16 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 126 3 18 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 122 4 20 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 123 5 22 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 124 6 24 0 +---------------------------------------------------------------------------------------------------------- +Short range atomic symmetry function groups element C : +---------------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e +---------------------------------------------------------------------------------------------------------- + 1 C 2 ct2 H * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 67 1 1 + - - - - - 1.300E-02 0.000E+00 - - 68 2 4 + - - - - - 2.900E-02 0.000E+00 - - 69 3 6 + - - - - - 5.400E-02 0.000E+00 - - 70 4 8 + - - - - - 9.300E-02 0.000E+00 - - 71 5 10 + - - - - - 1.610E-01 0.000E+00 - - 72 6 12 + 2 C 2 ct2 C * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 82 1 2 + - - - - - 1.000E-02 0.000E+00 - - 83 2 3 + - - - - - 2.300E-02 0.000E+00 - - 84 3 5 + - - - - - 4.100E-02 0.000E+00 - - 85 4 7 + - - - - - 6.500E-02 0.000E+00 - - 86 5 9 + - - - - - 1.030E-01 0.000E+00 - - 87 6 11 + 3 C 3 ct2 H H * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 106 1 13 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 102 2 16 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 107 3 19 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 103 4 22 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 108 5 25 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 104 6 28 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 109 7 31 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 105 8 34 0 + 4 C 3 ct2 H C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 115 1 14 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 111 2 17 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 116 3 20 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 112 4 23 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 117 5 26 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 113 6 29 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 118 7 32 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 114 8 35 0 + 5 C 3 ct2 C C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 97 1 15 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 93 2 18 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 98 3 21 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 94 4 24 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 99 5 27 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 95 6 30 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 100 7 33 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 96 8 36 0 +---------------------------------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: NEURAL NETWORKS **************************************************** + +Normalize neurons (all elements): 0 +------------------------------------------------------------------------------- +Atomic electronegativity NN for element H : +Number of weights : 600 +Number of biases : 31 +Number of connections: 631 +Architecture 24 15 15 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G t t + 12 G t t + 13 G t t + 14 G t t + 15 G t t + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G +------------------------------------------------------------------------------- +Atomic electronegativity NN for element C : +Number of weights : 780 +Number of biases : 31 +Number of connections: 811 +Architecture 36 15 15 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G t t + 12 G t t + 13 G t t + 14 G t t + 15 G t t + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + 26 G + 27 G + 28 G + 29 G + 30 G + 31 G + 32 G + 33 G + 34 G + 35 G + 36 G +------------------------------------------------------------------------------- +Atomic short range NN for element H : +Number of weights : 360 +Number of biases : 21 +Number of connections: 381 +Architecture 25 10 10 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G + 12 G + 13 G + 14 G + 15 G + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G +------------------------------------------------------------------------------- +Atomic short range NN for element C : +Number of weights : 480 +Number of biases : 21 +Number of connections: 501 +Architecture 37 10 10 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G + 12 G + 13 G + 14 G + 15 G + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + 26 G + 27 G + 28 G + 29 G + 30 G + 31 G + 32 G + 33 G + 34 G + 35 G + 36 G + 37 G +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION SCALING ****************************************** + +Equal scaling type for all symmetry functions: +Scaling type::ST_SCALECENTER (3) +Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin) +WARNING: Keyword "scale_min_short" not found. + Default value for Smin = 0.0. +WARNING: Keyword "scale_max_short" not found. + Default value for Smax = 1.0. +Smin = 0.000000 +Smax = 1.000000 +Symmetry function scaling statistics from file: scaling.data +------------------------------------------------------------------------------- + +Abbreviations: +-------------- +ind ..... Symmetry function index. +min ..... Minimum symmetry function value. +max ..... Maximum symmetry function value. +mean .... Mean symmetry function value. +sigma ... Standard deviation of symmetry function values. +sf ...... Scaling factor for derivatives. +Smin .... Desired minimum scaled symmetry function value. +Smax .... Desired maximum scaled symmetry function value. +t ....... Scaling type. + +Scaling data for symmetry functions element H : +------------------------------------------------------------------------------- + ind min max mean sigma sf Smin Smax t +------------------------------------------------------------------------------- + 1 0.00E+00 1.68E-01 5.14E-02 0.00E+00 5.94E+00 0.00 1.00 3 + 2 3.04E-01 4.17E-01 3.46E-01 0.00E+00 8.85E+00 0.00 1.00 3 + 3 0.00E+00 1.59E-01 4.77E-02 0.00E+00 6.27E+00 0.00 1.00 3 + 4 0.00E+00 1.52E-01 4.48E-02 0.00E+00 6.56E+00 0.00 1.00 3 + 5 2.70E-01 3.77E-01 3.12E-01 0.00E+00 9.35E+00 0.00 1.00 3 + 6 0.00E+00 1.43E-01 4.10E-02 0.00E+00 7.00E+00 0.00 1.00 3 + 7 0.00E+00 1.33E-01 3.71E-02 0.00E+00 7.53E+00 0.00 1.00 3 + 8 2.36E-01 3.37E-01 2.78E-01 0.00E+00 9.97E+00 0.00 1.00 3 + 9 0.00E+00 1.22E-01 3.31E-02 0.00E+00 8.18E+00 0.00 1.00 3 + 10 1.94E-01 2.86E-01 2.36E-01 0.00E+00 1.09E+01 0.00 1.00 3 + 11 1.46E-01 2.31E-01 1.88E-01 0.00E+00 1.18E+01 0.00 1.00 3 + 12 9.43E-02 1.67E-01 1.33E-01 0.00E+00 1.37E+01 0.00 1.00 3 + 13 0.00E+00 3.94E-03 7.66E-04 0.00E+00 2.54E+02 0.00 1.00 3 + 14 0.00E+00 2.18E-03 3.95E-04 0.00E+00 4.59E+02 0.00 1.00 3 + 15 0.00E+00 2.26E-02 6.69E-03 0.00E+00 4.42E+01 0.00 1.00 3 + 16 6.80E-03 1.48E-02 9.85E-03 0.00E+00 1.25E+02 0.00 1.00 3 + 17 0.00E+00 7.54E-04 1.18E-04 0.00E+00 1.33E+03 0.00 1.00 3 + 18 0.00E+00 3.07E-04 3.12E-05 0.00E+00 3.26E+03 0.00 1.00 3 + 19 0.00E+00 2.02E-02 6.04E-03 0.00E+00 4.96E+01 0.00 1.00 3 + 20 6.45E-03 1.30E-02 9.49E-03 0.00E+00 1.53E+02 0.00 1.00 3 + 21 0.00E+00 1.67E-02 5.00E-03 0.00E+00 5.97E+01 0.00 1.00 3 + 22 5.80E-03 1.11E-02 8.84E-03 0.00E+00 1.88E+02 0.00 1.00 3 + 23 0.00E+00 1.27E-02 3.57E-03 0.00E+00 7.90E+01 0.00 1.00 3 + 24 4.42E-03 1.10E-02 7.82E-03 0.00E+00 1.51E+02 0.00 1.00 3 +------------------------------------------------------------------------------- +Scaling data for symmetry functions element C : +------------------------------------------------------------------------------- + ind min max mean sigma sf Smin Smax t +------------------------------------------------------------------------------- + 1 0.00E+00 5.28E-01 8.65E-02 0.00E+00 1.89E+00 0.00 1.00 3 + 2 2.44E-01 5.76E-01 4.78E-01 0.00E+00 3.00E+00 0.00 1.00 3 + 3 2.20E-01 5.27E-01 4.38E-01 0.00E+00 3.26E+00 0.00 1.00 3 + 4 0.00E+00 5.04E-01 7.81E-02 0.00E+00 1.99E+00 0.00 1.00 3 + 5 1.95E-01 4.73E-01 3.93E-01 0.00E+00 3.59E+00 0.00 1.00 3 + 6 0.00E+00 4.75E-01 6.95E-02 0.00E+00 2.11E+00 0.00 1.00 3 + 7 1.66E-01 4.12E-01 3.41E-01 0.00E+00 4.07E+00 0.00 1.00 3 + 8 0.00E+00 4.33E-01 5.90E-02 0.00E+00 2.31E+00 0.00 1.00 3 + 9 1.36E-01 3.48E-01 2.86E-01 0.00E+00 4.72E+00 0.00 1.00 3 + 10 0.00E+00 3.76E-01 4.70E-02 0.00E+00 2.66E+00 0.00 1.00 3 + 11 1.02E-01 2.73E-01 2.22E-01 0.00E+00 5.83E+00 0.00 1.00 3 + 12 0.00E+00 2.93E-01 3.33E-02 0.00E+00 3.41E+00 0.00 1.00 3 + 13 0.00E+00 1.53E-02 6.08E-04 0.00E+00 6.55E+01 0.00 1.00 3 + 14 0.00E+00 2.04E-02 2.32E-03 0.00E+00 4.91E+01 0.00 1.00 3 + 15 0.00E+00 6.66E-03 3.99E-03 0.00E+00 1.50E+02 0.00 1.00 3 + 16 0.00E+00 9.28E-03 3.24E-04 0.00E+00 1.08E+02 0.00 1.00 3 + 17 0.00E+00 2.50E-02 2.80E-03 0.00E+00 4.00E+01 0.00 1.00 3 + 18 3.52E-03 1.25E-02 8.03E-03 0.00E+00 1.11E+02 0.00 1.00 3 + 19 0.00E+00 1.19E-02 4.30E-04 0.00E+00 8.39E+01 0.00 1.00 3 + 20 0.00E+00 1.56E-02 2.02E-03 0.00E+00 6.43E+01 0.00 1.00 3 + 21 0.00E+00 6.52E-03 3.94E-03 0.00E+00 1.53E+02 0.00 1.00 3 + 22 0.00E+00 3.82E-03 1.46E-04 0.00E+00 2.62E+02 0.00 1.00 3 + 23 0.00E+00 2.34E-02 2.50E-03 0.00E+00 4.27E+01 0.00 1.00 3 + 24 3.51E-03 1.24E-02 7.98E-03 0.00E+00 1.12E+02 0.00 1.00 3 + 25 0.00E+00 8.68E-03 2.29E-04 0.00E+00 1.15E+02 0.00 1.00 3 + 26 0.00E+00 1.07E-02 1.70E-03 0.00E+00 9.33E+01 0.00 1.00 3 + 27 0.00E+00 6.38E-03 3.88E-03 0.00E+00 1.57E+02 0.00 1.00 3 + 28 0.00E+00 1.76E-03 6.00E-05 0.00E+00 5.69E+02 0.00 1.00 3 + 29 0.00E+00 2.11E-02 2.32E-03 0.00E+00 4.74E+01 0.00 1.00 3 + 30 3.50E-03 1.23E-02 7.95E-03 0.00E+00 1.13E+02 0.00 1.00 3 + 31 0.00E+00 4.70E-03 6.92E-05 0.00E+00 2.13E+02 0.00 1.00 3 + 32 0.00E+00 1.07E-02 1.36E-03 0.00E+00 9.34E+01 0.00 1.00 3 + 33 0.00E+00 6.34E-03 3.76E-03 0.00E+00 1.58E+02 0.00 1.00 3 + 34 0.00E+00 9.43E-04 2.30E-05 0.00E+00 1.06E+03 0.00 1.00 3 + 35 0.00E+00 1.71E-02 2.11E-03 0.00E+00 5.84E+01 0.00 1.00 3 + 36 3.48E-03 1.22E-02 7.88E-03 0.00E+00 1.15E+02 0.00 1.00 3 +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: NEURAL NETWORK WEIGHTS ********************************************* + +Electronegativity weight file name format: weightse.%03zu.data +Setting weights for element H from file: weightse.001.data +Setting weights for element C from file: weightse.006.data +Short range weight file name format: weights.%03zu.data +Setting weights for element H from file: weights.001.data +Setting weights for element C from file: weights.006.data +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION STATISTICS *************************************** + +Equal symmetry function statistics for all elements. +Collect min/max/mean/sigma : 0 +Collect extrapolation warnings : 0 +Write extrapolation warnings immediately to stderr: 1 +Halt on any extrapolation warning : 0 +******************************************************************************* + +*** PREDICTION **************************************************************** + +Reading structure file... +Structure contains 12 atoms (2 elements). +Calculating NNP prediction... +Atom 0 ( C) chi: -1.46685182E-01 +Atom 1 ( C) chi: -1.62299217E-01 +Atom 2 ( H) chi: -2.28364737E-01 +Atom 3 ( C) chi: -1.49331912E-01 +Atom 4 ( C) chi: -1.48572339E-01 +Atom 5 ( C) chi: -1.50034638E-01 +Atom 6 ( C) chi: -1.49457838E-01 +Atom 7 ( C) chi: -1.49032144E-01 +Atom 8 ( C) chi: -1.48516264E-01 +Atom 9 ( C) chi: -1.46835351E-01 +Atom 10 ( C) chi: -1.60732085E-01 +Atom 11 ( H) chi: -2.25971939E-01 +Solve relative error: 4.19968408E-16 +Atom 0 ( C) q: -3.24586443E-02 +Atom 1 ( C) q: -5.61417786E-02 +Atom 2 ( H) q: 1.02941451E-01 +Atom 3 ( C) q: -7.15563490E-03 +Atom 4 ( C) q: 8.34327483E-04 +Atom 5 ( C) q: -2.35997196E-03 +Atom 6 ( C) q: -8.49071586E-03 +Atom 7 ( C) q: -1.05341133E-02 +Atom 8 ( C) q: 8.14623403E-04 +Atom 9 ( C) q: -2.83459938E-02 +Atom 10 ( C) q: -6.06473430E-02 +Atom 11 ( H) q: 1.01543794E-01 +Total charge: 1.38777878E-17 (ref: 0.00000000E+00) +Electrostatic energy: -1.57390645E-05 +Atom 0 ( C) energy: -2.04797104E-01 +Atom 1 ( C) energy: -1.71308641E-01 +Atom 2 ( H) energy: -4.21420608E-01 +Atom 3 ( C) energy: -2.74300645E-01 +Atom 4 ( C) energy: -2.70020477E-01 +Atom 5 ( C) energy: -2.72501390E-01 +Atom 6 ( C) energy: -2.61803455E-01 +Atom 7 ( C) energy: -2.70868859E-01 +Atom 8 ( C) energy: -2.64820897E-01 +Atom 9 ( C) energy: -2.03946738E-01 +Atom 10 ( C) energy: -1.74834922E-01 +Atom 11 ( H) energy: -4.21239341E-01 + +------------------------------------------------------------------------------- +NNP energy: -3.81610813E+02 + +NNP forces: + 1 C -3.08484836E-02 9.94372295E-03 2.03529993E-02 + 2 C 3.57532095E-02 -8.12376282E-03 -2.06084042E-02 + 3 H 8.17872767E-03 1.80147175E-04 2.64404766E-03 + 4 C -3.26724151E-02 1.20415003E-02 -1.85728952E-03 + 5 C 3.59640000E-02 -1.30889939E-02 -3.94444232E-03 + 6 C 3.51032023E-02 -9.27893548E-04 1.61369056E-02 + 7 C -2.02149697E-02 1.68076484E-03 -7.51111414E-04 + 8 C -1.64584030E-02 -5.79814760E-03 -1.63960645E-02 + 9 C 2.92959438E-03 -7.93908249E-04 1.37034847E-02 + 10 C 1.22408242E-02 1.73449697E-02 -1.60932736E-02 + 11 C -2.44131380E-02 -5.93162381E-03 1.47790527E-02 + 12 H -5.56214852E-03 -6.52677505E-03 -7.96590439E-03 +------------------------------------------------------------------------------- +Writing output files... + - energy.out + - nnatoms.out + - nnforces.out +Writing structure with NNP prediction to "output.data". +Finished. +******************************************************************************* diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/output.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/output.data new file mode 100644 index 0000000000..62d92c7fbe --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/output.data @@ -0,0 +1,17 @@ +begin +comment +atom -8.6089840636623833E+00 1.1721101618520001E-01 9.8323591084281514E-02 C -3.2458644274754651E-02 0.0000000000000000E+00 -3.0848483621290768E-02 9.9437229539220684E-03 2.0352999337438824E-02 +atom -1.0887890663537627E+01 4.1179249277052421E-01 6.9490967680382398E-01 C -5.6141778584216068E-02 0.0000000000000000E+00 3.5753209472753004E-02 -8.1237628180204809E-03 -2.0608404213202990E-02 +atom -1.2930485451086453E+01 5.2506382642642058E-01 7.2809053422821779E-01 H 1.0294145062705674E-01 0.0000000000000000E+00 8.1787276673429710E-03 1.8014717534816583E-04 2.6440476603640309E-03 +atom -3.6915315204094927E+00 -3.3414993292840278E-01 -2.1088572536199013E-01 C -7.1556348953342435E-03 0.0000000000000000E+00 -3.2672415145898345E-02 1.2041500311444986E-02 -1.8572895160292656E-03 +atom -6.0680299107700124E+00 -2.5620260955245030E-03 -7.0543207699589230E-02 C 8.3432748292313285E-04 0.0000000000000000E+00 3.5963999960799249E-02 -1.3088993906111521E-02 -3.9444423243935513E-03 +atom 1.1729073318400078E+00 -1.7250595988097372E-01 -6.6741810230359422E-01 C -2.3599719595358937E-03 0.0000000000000000E+00 3.5103202289331878E-02 -9.2789354753794961E-04 1.6136905570554479E-02 +atom -1.1595817453608341E+00 -3.5063784106789647E-01 -4.6759951235815161E-01 C -8.4907158646713859E-03 0.0000000000000000E+00 -2.0214969739033205E-02 1.6807648404055854E-03 -7.5111141444395750E-04 +atom 3.7259094240411681E+00 -8.3808446129817402E-02 -2.2980808620118351E-01 C -1.0534113290044665E-02 0.0000000000000000E+00 -1.6458402959242311E-02 -5.7981475984617377E-03 -1.6396064514211335E-02 +atom 6.0775914248949645E+00 -1.6674672212588620E-01 -1.4499820679122288E-01 C 8.1462340324302566E-04 0.0000000000000000E+00 2.9295943813836588E-03 -7.9390824921095359E-04 1.3703484666740151E-02 +atom 8.5916667587931013E+00 -8.0658783933167305E-02 4.0220650606187225E-01 C -2.8345993789409479E-02 0.0000000000000000E+00 1.2240824229741747E-02 1.7344969704443759E-02 -1.6093273578742517E-02 +atom 1.0870494591100982E+01 5.1580223738887498E-01 4.3585444122535055E-01 C -6.0647343034107404E-02 0.0000000000000000E+00 -2.4413138020654052E-02 -5.9316238120533807E-03 1.4779052720039060E-02 +atom 1.2661796981509699E+01 1.1948282077976258E+00 1.1689054257962741E+00 H 1.0154379417885089E-01 0.0000000000000000E+00 -5.5621485152346096E-03 -6.5267750541684114E-03 -7.9659043941128650E-03 +energy -3.8161081273904063E+02 +charge 1.3877787807814457E-17 +end diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/scaling.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/scaling.data new file mode 100644 index 0000000000..58924a796e --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/scaling.data @@ -0,0 +1,61 @@ + 1 1 0.000000000 0.168474325 0.051436597 + 1 2 0.304058579 0.417104776 0.345915594 + 1 3 0.000000000 0.159465228 0.047693255 + 1 4 0.000000000 0.152326768 0.044784312 + 1 5 0.270367239 0.377289298 0.312242885 + 1 6 0.000000000 0.142866546 0.041009575 + 1 7 0.000000000 0.132772126 0.037086368 + 1 8 0.236241291 0.336573119 0.278003131 + 1 9 0.000000000 0.122265892 0.033122717 + 1 10 0.194043783 0.286076543 0.235857711 + 1 11 0.146413959 0.230979612 0.188000406 + 1 12 0.094328785 0.167444236 0.133300930 + 1 13 0.000000000 0.003940598 0.000766277 + 1 14 0.000000000 0.002179848 0.000395242 + 1 15 0.000000000 0.022615147 0.006688070 + 1 16 0.006799063 0.014786064 0.009854503 + 1 17 0.000000000 0.000754211 0.000118471 + 1 18 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b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/structure.out new file mode 100644 index 0000000000..486b93f0f1 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/hdnnp-data/structure.out @@ -0,0 +1,5045 @@ +******************************** +STRUCTURE +******************************** +******************************** +ELEMENT MAP +******************************** +-------------------------------- +forwardMap [*] : 2 +-------------------------------- + C : 1 + H : 0 +-------------------------------- +-------------------------------- +reverseMap [*] : 2 +-------------------------------- + 0 : H + 1 : C +-------------------------------- +******************************** +index : 0 +isPeriodic : 0 +isTriclinic : 0 +hasNeighborList : 1 +hasSymmetryFunctions : 1 +hasSymmetryFunctionDerivatives : 1 +numAtoms : 12 +numElements : 2 +numElementsPresent : 2 +pbc : 0 0 0 +energy : -3.81650775E+02 +energyRef : 0.00000000E+00 +charge : 0.00000000E+00 +chargeRef : 0.00000000E+00 +volume : 0.00000000E+00 +sampleType : 0 +comment : +box[0] : 0.00000000E+00 0.00000000E+00 0.00000000E+00 +box[1] : 0.00000000E+00 0.00000000E+00 0.00000000E+00 +box[2] : 0.00000000E+00 0.00000000E+00 0.00000000E+00 +invbox[0] : 0.00000000E+00 0.00000000E+00 0.00000000E+00 +invbox[1] : 0.00000000E+00 0.00000000E+00 0.00000000E+00 +invbox[2] : 0.00000000E+00 0.00000000E+00 0.00000000E+00 +-------------------------------- +numAtomsPerElement [*] : 2 +-------------------------------- + 0 : 2 + 1 : 10 +-------------------------------- +-------------------------------- +atoms [*] : 12 +-------------------------------- + 0 : +******************************** +ATOM +******************************** +hasNeighborList : 1 +hasSymmetryFunctions : 1 +hasSymmetryFunctionDerivatives : 1 +useChargeNeuron : 1 +index : 0 +indexStructure : 0 +tag : 0 +element : 1 +numNeighbors : 5 +numNeighborsUnique : 6 +numSymmetryFunctions : 36 +energy : -2.08976560E-01 +chi : -1.46685182E-01 +charge : 1.88081199E-03 +chargeRef : 0.00000000E+00 +r : -8.60898406E+00 1.17211016E-01 9.83235911E-02 +f : 0.00000000E+00 0.00000000E+00 0.00000000E+00 +fRef : 0.00000000E+00 0.00000000E+00 0.00000000E+00 +-------------------------------- +neighborsUnique [*] : 6 +-------------------------------- + 0 : 0 + 1 : 1 + 2 : 2 + 3 : 3 + 4 : 4 + 5 : 6 +-------------------------------- +-------------------------------- +numNeighborsPerElement [*] : 2 +-------------------------------- + 0 : 1 + 1 : 4 +-------------------------------- +-------------------------------- +numSymmetryFunctionDeriv. [*] : 2 +-------------------------------- + 0 : 22 + 1 : 22 +-------------------------------- +-------------------------------- +cacheSizePerElement [*] : 2 +-------------------------------- + 0 : 2 + 1 : 2 +-------------------------------- +-------------------------------- +G [*] : 36 +-------------------------------- + 0 : -2.01493731E-02 + 1 : 3.61112008E-03 + 2 : 1.91118741E-02 + 3 : -3.77455842E-02 + 4 : 3.57463110E-02 + 5 : -5.49519508E-02 + 6 : 5.30333835E-02 + 7 : -7.41584313E-02 + 8 : 6.74711735E-02 + 9 : -9.13975395E-02 + 10 : 7.65579355E-02 + 11 : -1.02114008E-01 + 12 : -3.98169770E-02 + 13 : -1.09033744E-01 + 14 : 9.80651355E-02 + 15 : -3.49080250E-02 + 16 : 2.28057313E-01 + 17 : -3.94573815E-01 + 18 : -3.60654596E-02 + 19 : -1.25320463E-01 + 20 : 9.99259970E-02 + 21 : -3.82258330E-02 + 22 : 2.54587797E-01 + 23 : -3.98320053E-01 + 24 : -2.63986903E-02 + 25 : -1.51388080E-01 + 26 : 9.70714059E-02 + 27 : -3.41458088E-02 + 28 : 2.89064471E-01 + 29 : -3.98949759E-01 + 30 : 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-0.0573394490 + -0.1135653336 + -0.1319696539 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/md-external.lmp b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/md-external.lmp new file mode 100644 index 0000000000..62b189b324 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/md-external.lmp @@ -0,0 +1,49 @@ +############################################################################### +# MD simulation for carbon chain +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "carbon-chain.data" +# Timesteps +variable numSteps equal 5 +variable dt equal 0.0005 +# NN +variable nnpCutoff equal 8.01 +variable nnpDir string "nnp-data" +# Masses +variable mass_H equal 1.00794 +variable mass_O equal 15.9994 + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary s s s +atom_style atomic +read_data ${cfgFile} +mass 1 ${mass_H} +mass 2 ${mass_O} +timestep ${dt} +thermo 1 + +############################################################################### +# NN +############################################################################### +pair_style nnp/external "H C" dir ${nnpDir} command "/Users/emirkocer/CLionProjects/JonasRuNNer/build/RuNNer-gaussian.x" cflength 1.0 cfenergy 1.0 +#pair_style nnp/external "H C" dir ${nnpDir} command "nnp-predict 0" cflength 1.0 cfenergy 1.0 +pair_coeff * * ${nnpCutoff} + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve +#dump 1 all atom 1 traj.dump + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/md.lmp b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/md.lmp new file mode 100644 index 0000000000..835d94378a --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/lammps-nnp/md.lmp @@ -0,0 +1,51 @@ +############################################################################### +# MD simulation for carbon chain +############################################################################### + +############################################################################### +# VARIABLES +############################################################################### +clear +# Configuration files +variable cfgFile string "carbon-chain.data" +# Timesteps +variable numSteps equal 0 +variable dt equal 0.0005 +# NN +variable hdnnpCutoff equal 8.01 +variable hdnnpDir string "hdnnp-data" +# Masses +variable mass_H equal 1.00794 +variable mass_C equal 12.0107 + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary s s s +atom_style charge +atom_modify map yes +read_data ${cfgFile} +mass 1 ${mass_H} +mass 2 ${mass_C} +timestep ${dt} +thermo 1 + +############################################################################### +# NN +############################################################################### +pair_style hdnnp/4g dir ${hdnnpDir} showew no showewsum 10 resetew no maxew 100 cflength 1.0 cfenergy 1.0 emap "1:H,2:C" +pair_coeff * * ${hdnnpCutoff} +fix 1 all hdnnp 1 1.0e-8 1.0e-8 1.0e-2 100 nnp + + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve +#dump 1 all atom 1 traj.dump + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/energy.out b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/energy.out new file mode 100644 index 0000000000..bb6cd2aa00 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/energy.out @@ -0,0 +1,16 @@ +################################################################################ +# Energy comparison. +################################################################################ +# Col Name Description +################################################################################ +# 1 conf Configuration index (starting with 1). +# 2 natoms Number of atoms in configuration. +# 3 Eref Reference potential energy. +# 4 Ennp Potential energy predicted by NNP. +# 5 Ediff Difference in energy per atom between reference and NNP prediction. +# 6 E_offset Sum of atomic offset energies (included in column Ennp). +######################################################################################################################### +# 1 2 3 4 5 6 +# conf natoms Eref Ennp Ediff E_offset +######################################################################################################################### + 1 12 -3.8161152544399999E+02 -3.8161078713069378E+02 -6.1526108851239769E-05 -3.7839893392473289E+02 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/hardness.001.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/hardness.001.data new file mode 100644 index 0000000000..60e1493e7c --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/hardness.001.data @@ -0,0 +1 @@ + 0.0088953312 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/hardness.006.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/hardness.006.data new file mode 100644 index 0000000000..e8464ac99e --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/hardness.006.data @@ -0,0 +1 @@ + 0.0661189426 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/input.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/input.data new file mode 100644 index 0000000000..dc858aa5f1 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/input.data @@ -0,0 +1,16 @@ +begin +atom 1.17284095486 -0.172504222684 -0.667448516865 C -0.00802366916667 0.0 0.0347925826351 -0.00110373556182 0.0172205087376 +atom -1.1595434822 -0.350641000445 -0.467598107194 C -0.00855427916667 0.0 -0.0190916650141 0.00319122911054 0.00166842074686 +atom 3.72594054969 -0.0837975179097 -0.229777168673 C -0.00986190916667 0.0 -0.0218470438236 -0.00628540399811 -0.0170756379211 +atom -3.69146983116 -0.334172643167 -0.21088223315 C -0.0100583891667 0.0 -0.0301687534058 0.0106478678179 -0.00452518599678 +atom 6.07758586771 -0.166745226042 -0.145024035228 C -0.00672012916667 0.0 0.00266924762633 -0.00156314063781 0.0115961079544 +atom -6.06809789367 -0.00253733508489 -0.0705357610724 C -0.00417966916667 0.0 0.0380293993069 -0.012272279507 -0.00385017456324 +atom 8.59164353464 -0.0806915075831 0.402236831619 C -0.0283825591667 0.0 0.0114358510185 0.0168883247486 -0.0145042007862 +atom -8.60892564573 0.117192245354 0.0982851777904 C -0.0314335491667 0.0 -0.0313212312302 0.00897304604753 0.0196935694367 +atom 10.8705405815 0.51581338865 0.435826522093 C -0.0539909791667 0.0 -0.0207616703214 -0.00491358425534 0.014173822701 +atom -10.8879581104 0.411807821319 0.694948565342 C -0.0495567391667 0.0 0.0330796233985 -0.00720705271362 -0.0192967826535 +atom 12.661965991 1.19502446714 1.1691448209 H 0.104980830833 0.0 -0.00448104672571 -0.00638001418343 -0.00747636563225 +atom -12.9307322131 0.525058551796 0.728011456903 H 0.105781040833 0.0 0.00766470653545 2.474313253e-05 0.00237591797661 +energy -381.611525444 +charge -0.0 +end diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/input.nn b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/input.nn new file mode 100644 index 0000000000..a53e0fa164 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/input.nn @@ -0,0 +1,185 @@ +## ############################################################# +### This is the input file for RuNNer +### ############################################################# +### General remarks: +### - commands can be switched off by using the # character at the BEGINNING of the line +### - the input file can be structured by blank lines and comment lines +### - the order of the keywords is arbitrary +### - if keywords are missing, default values will be used and written to runner.out +### - if mandatory keywords or keyword options are missing, RuNNer will stop with an error message + +### THIS INPUT.NN IS AN EXAMPLE, IT IS NOT A REALISTIC CASE +### It contains only a subset of all keywords + +######################################################################################################################## +### general keywords +######################################################################################################################## +use_electrostatics +use_short_nn +nnp_gen 4 # nnp_type_gen --> nnp_gen +runner_mode 3 +parallel_mode 1 +number_of_elements 2 +elements C H +random_seed 10 +random_number_type 5 +remove_atom_energies +atom_energy H -0.458907306351869 +atom_energy C -37.748111931202914 +initial_hardness H 10.0 ## fixed_atomhardness--> initial_hardness +initial_hardness C 10.0 +fixed_gausswidth H 0.585815056466 +fixed_gausswidth C 1.379499971678 +energy_threshold 100.0d0 +bond_threshold 0.4d0 +ewald_prec 1.0e-6 # for optimal combination of ewald parameters +screen_electrostatics 4.8 8.0 +######################################################################################################################## +### NN structure of the electrostatic-range NN +######################################################################################################################## +global_hidden_layers_electrostatic 2 +global_nodes_electrostatic 15 15 +global_activation_electrostatic t t l +global_hidden_layers_short 2 +global_nodes_short 10 10 +global_activation_short t t l +## element_hidden_layers_electrostatic needs to take care !!! should check the output +######################################################################################################################## +### symmetry function generation ( mode 1): +######################################################################################################################## +test_fraction 0.1 + +######################################################################################################################## +### symmetry function definitions (all modes): +######################################################################################################################## +cutoff_type 2 + + +# radial H H +symfunction H 2 H 0.000000 0.000000 8.000000 +symfunction H 2 H 0.006000 0.000000 8.000000 +symfunction H 2 H 0.011000 0.000000 8.000000 +symfunction H 2 H 0.018000 0.000000 8.000000 +symfunction H 2 H 0.026000 0.000000 8.000000 +symfunction H 2 H 0.035000 0.000000 8.000000 + +#radial C H +symfunction C 2 H 0.000000 0.000000 8.000000 +symfunction C 2 H 0.013000 0.000000 8.000000 +symfunction C 2 H 0.029000 0.000000 8.000000 +symfunction C 2 H 0.054000 0.000000 8.000000 +symfunction C 2 H 0.093000 0.000000 8.000000 +symfunction C 2 H 0.161000 0.000000 8.000000 + +symfunction H 2 C 0.000000 0.000000 8.000000 +symfunction H 2 C 0.013000 0.000000 8.000000 +symfunction H 2 C 0.029000 0.000000 8.000000 +symfunction H 2 C 0.054000 0.000000 8.000000 +symfunction H 2 C 0.093000 0.000000 8.000000 +symfunction H 2 C 0.161000 0.000000 8.000000 + +# radial C C +symfunction C 2 C 0.000000 0.000000 8.000000 +symfunction C 2 C 0.010000 0.000000 8.000000 +symfunction C 2 C 0.023000 0.000000 8.000000 +symfunction C 2 C 0.041000 0.000000 8.000000 +symfunction C 2 C 0.065000 0.000000 8.000000 +symfunction C 2 C 0.103000 0.000000 8.000000 + + +# +# angular + +symfunction C 3 C C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction C 3 H H 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 H H 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction C 3 C H 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction C 3 C H 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + + +symfunction H 3 C C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 C C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 C C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 C C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + +symfunction H 3 H C 0.0 1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 -1.0 1.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +symfunction H 3 H C 0.0 -1.0 2.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 H C 0.0 -1.0 4.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff +#symfunction H 3 H C 0.0 -1.0 8.0 8.000000 ! central_atom type neighbor_atom1 neighbor_atom2 eta lambda zeta funccutoff + + +######################################################################################################################## +### fitting (mode 2):general inputs for electrostatic range AND electrostatic part: +######################################################################################################################## +epochs 10 +points_in_memory 500 +mix_all_points +scale_symmetry_functions +center_symmetry_functions +fitting_unit eV +######################################################################################################################## +### fitting options ( mode 2): electrostatic range part only: +######################################################################################################################## +optmode_short_energy 1 +optmode_short_force 1 +short_energy_error_threshold 0.8 +short_force_error_threshold 0.8 +kalman_lambda_charge 0.98000 +kalman_nue_charge 0.99870 +kalman_lambda_short 0.98000 +kalman_nue_short 0.99870 +#use_old_weights_electrostatic +#force_update_scaling -1.0d0 +#electrostatic_energy_group 1 +#electrostatic_energy_fraction 1.00 +#electrostatic_force_group 1 + +short_force_fraction 0.025 +use_short_forces +weights_min -1.0 +weights_max 1.0 +precondition_weights +repeated_energy_update +nguyen_widrow_weights_short +regularize_fit_param 0.00001 ## 4G cases L2 regularization +######################################################################################################################## +### output options for mode 2 (fitting): +######################################################################################################################## +write_trainpoints +write_trainforces +#write_traincharges +######################################################################################################################## +### output options for mode 3 (prediction): +######################################################################################################################## +calculate_forces +#calculate_stress + diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnatoms.out b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnatoms.out new file mode 100644 index 0000000000..6c3946383f --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnatoms.out @@ -0,0 +1,28 @@ +################################################################################ +# Energy contributions calculated from NNP. +################################################################################ +# Col Name Description +################################################################################ +# 1 conf Configuration index (starting with 1). +# 2 index Atom index (starting with 1). +# 3 Z Nuclear charge of atom. +# 4 Qref Reference atomic charge. +# 5 Qnnp NNP atomic charge. +# 6 Eref_atom Reference atomic energy contribution. +# 7 Ennp_atom Atomic energy contribution (physical units, no mean or offset energy added). +############################################################################################################################# +# 1 2 3 4 5 6 7 +# conf index Z Qref Qnnp Eref_atom Ennp_atom +############################################################################################################################# + 1 1 6 -8.0236691666699996E-03 -2.3524823684152795E-03 0.0000000000000000E+00 -2.7250515638214623E-01 + 1 2 6 -8.5542791666700004E-03 -8.4942086481964076E-03 0.0000000000000000E+00 -2.6177206845636780E-01 + 1 3 6 -9.8619091666699993E-03 -1.0537654209871102E-02 0.0000000000000000E+00 -2.7088006119054531E-01 + 1 4 6 -1.0058389166700000E-02 -7.1248303653208261E-03 0.0000000000000000E+00 -2.7432729767876585E-01 + 1 5 6 -6.7201291666699999E-03 8.2658839443283238E-04 0.0000000000000000E+00 -2.6480583491973142E-01 + 1 6 6 -4.1796691666700003E-03 8.1741828473709803E-04 0.0000000000000000E+00 -2.7001383025822279E-01 + 1 7 6 -2.8382559166699999E-02 -2.8351566345695845E-02 0.0000000000000000E+00 -2.0397182296237129E-01 + 1 8 6 -3.1433549166699999E-02 -3.2468734085716766E-02 0.0000000000000000E+00 -2.0480779326445372E-01 + 1 9 6 -5.3990979166700002E-02 -6.0669724234771107E-02 0.0000000000000000E+00 -1.7486001433553769E-01 + 1 10 6 -4.9556739166700003E-02 -5.6146955747858017E-02 0.0000000000000000E+00 -1.7132387729341647E-01 + 1 11 1 1.0498083083300000E-01 1.0155744000109204E-01 0.0000000000000000E+00 -4.2118982678316602E-01 + 1 12 1 1.0578104083300000E-01 1.0294470932558338E-01 0.0000000000000000E+00 -4.2137996820117252E-01 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnforces.out b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnforces.out new file mode 100644 index 0000000000..ee08c93ba9 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnforces.out @@ -0,0 +1,29 @@ +################################################################################ +# Atomic force comparison (ordered by atom index). +################################################################################ +# Col Name Description +################################################################################ +# 1 conf Configuration index (starting with 1). +# 2 index Atom index (starting with 1). +# 3 fxRef Reference force in x direction. +# 4 fyRef Reference force in y direction. +# 5 fzRef Reference force in z direction. +# 6 fx Force in x direction. +# 7 fy Force in y direction. +# 8 fz Force in z direction. +########################################################################################################################################################################### +# 1 2 3 4 5 6 7 8 +# conf index fxRef fyRef fzRef fx fy fz +########################################################################################################################################################################### + 1 1 3.4792582635100003E-02 -1.1037355618200000E-03 1.7220508737600001E-02 3.5244238802598936E-02 -9.2064728582576792E-04 1.6139279140426486E-02 + 1 2 -1.9091665014100000E-02 3.1912291105400002E-03 1.6684207468599999E-03 -2.0320505353455472E-02 1.6756423734835108E-03 -7.4457791136594144E-04 + 1 3 -2.1847043823600001E-02 -6.2854039981100002E-03 -1.7075637921100000E-02 -1.6527242561909055E-02 -5.7989817531996874E-03 -1.6407639020990412E-02 + 1 4 -3.0168753405800001E-02 1.0647867817900000E-02 -4.5251859967799998E-03 -3.2745976522587684E-02 1.2052512199310998E-02 -1.8522742363607386E-03 + 1 5 2.6692476263300000E-03 -1.5631406378100001E-03 1.1596107954400000E-02 2.9524805895551585E-03 -7.9386012929745281E-04 1.3705716946330639E-02 + 1 6 3.8029399306899997E-02 -1.2272279507000000E-02 -3.8501745632399998E-03 3.6094736091666753E-02 -1.3104246537253889E-02 -3.9527368127116212E-03 + 1 7 1.1435851018500000E-02 1.6888324748600001E-02 -1.4504200786199999E-02 1.2339197396340543E-02 1.7367830541731095E-02 -1.6091368599610911E-02 + 1 8 -3.1321231230200003E-02 8.9730460475299992E-03 1.9693569436700000E-02 -3.1026908616236346E-02 9.9635507686791063E-03 2.0389044528357523E-02 + 1 9 -2.0761670321400000E-02 -4.9135842553400004E-03 1.4173822701000000E-02 -2.4402146254685439E-02 -5.9144467478372100E-03 1.4821559975006723E-02 + 1 10 3.3079623398499999E-02 -7.2070527136200001E-03 -1.9296782653499999E-02 3.5796249466896496E-02 -8.1357128272733104E-03 -2.0640604603679190E-02 + 1 11 -4.4810467257099997E-03 -6.3800141834300002E-03 -7.4763656322500002E-03 -5.6665404254611345E-03 -6.5672357918272230E-03 -8.0097656828994248E-03 + 1 12 7.6647065354499997E-03 2.4743132529999999E-05 2.3759179766099999E-03 8.2624173872767118E-03 1.7559518930972563E-04 2.6433662774967082E-03 diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnp-predict.log b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnp-predict.log new file mode 100644 index 0000000000..e6a0c033d3 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/nnp-predict.log @@ -0,0 +1,681 @@ + +******************************************************************************* + +WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS! +------------------------------------------------------------------ + +n²p² version : v2.1.1-63-ga041104 +------------------------------------------------------------ +Git branch : 4G-HDNNP-prediction +Git revision : a0411041f93eed45b833a27b591c2b1c0bfc73dd +Compile date/time : Jul 28 2021 16:18:12 +------------------------------------------------------------ + +Please cite the following papers when publishing results obtained with n²p²: +------------------------------------------------------------------------------- + * General citation for n²p² and the LAMMPS interface: + + Singraber, A.; Behler, J.; Dellago, C. + Library-Based LAMMPS Implementation of High-Dimensional + Neural Network Potentials. + J. Chem. Theory Comput. 2019 15 (3), 1827–1840. + https://doi.org/10.1021/acs.jctc.8b00770 +------------------------------------------------------------------------------- + * Additionally, if you use the NNP training features of n²p²: + + Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C. + Parallel Multistream Training of High-Dimensional Neural + Network Potentials. + J. Chem. Theory Comput. 2019, 15 (5), 3075–3092. + https://doi.org/10.1021/acs.jctc.8b01092 +------------------------------------------------------------------------------- + * Additionally, if polynomial symmetry functions are used: + + Bircher, M. P.; Singraber, A.; Dellago, C. + Improved Description of Atomic Environments Using Low-Cost + Polynomial Functions with Compact Support. + arXiv:2010.14414 [cond-mat, physics:physics] 2020. + https://arxiv.org/abs/2010.14414 +******************************************************************************* + +*** SETUP: SETTINGS FILE ****************************************************** + +Settings file name: input.nn +Read 185 lines. +WARNING: Unknown keyword "bond_threshold" at line 34. +WARNING: Unknown keyword "calculate_forces" at line 183. +WARNING: Unknown keyword "energy_threshold" at line 33. +WARNING: Unknown keyword "fitting_unit" at line 148. +WARNING: Unknown keyword "kalman_lambda_charge" at line 156. +WARNING: Unknown keyword "kalman_nue_charge" at line 157. +WARNING: Unknown keyword "mix_all_points" at line 145. +WARNING: Unknown keyword "optmode_short_energy" at line 152. +WARNING: Unknown keyword "optmode_short_force" at line 153. +WARNING: Unknown keyword "points_in_memory" at line 144. +WARNING: Unknown keyword "random_number_type" at line 25. +WARNING: Unknown keyword "regularize_fit_param" at line 173. +WARNING: Unknown keyword "remove_atom_energies" at line 26. +WARNING: Unknown keyword "runner_mode" at line 20. +WARNING: Unknown keyword "use_electrostatics" at line 17. +WARNING: Unknown keyword "use_short_nn" at line 18. +WARNING: 16 problems detected (0 critical). +Found 113 lines with keywords. +This settings file defines a NNP with electrostatics and +non-local charge transfer (4G-HDNNP). +******************************************************************************* + +*** SETUP: NORMALIZATION ****************************************************** + +Data set normalization is not used. +******************************************************************************* + +*** SETUP: ELEMENT MAP ******************************************************** + +Number of element strings found: 2 +Element 0: H ( 1) +Element 1: C ( 6) +******************************************************************************* + +*** SETUP: ELEMENTS *********************************************************** + +Number of elements is consistent: 2 +Atomic energy offsets per element: +Element 0: -4.58907306E-01 +Element 1: -3.77481119E+01 +Energy offsets are automatically subtracted from reference energies. +******************************************************************************* + +*** SETUP: ELECTROSTATICS ***************************************************** + +Atomic hardness file name format: hardness.%03zu.data +Atomic hardness for element H from file hardness.001.data: 8.89533120E-03 +Atomic hardness for element C from file hardness.006.data: 6.61189426E-02 + +Gaussian width of charge distribution per element: +Element 0: 5.85815056E-01 +Element 1: 1.37949997E+00 + +Ewald precision: 1.00000000E-06 + +Screening function information: +Inner radius : 4.80000000E+00 +Outer radius : 8.00000000E+00 +Transition region functional form: +x := (r - inner) / (outer - inner) +fs(x) := 1 - f(x) +CoreFunction::Type::COS (0): +f(x) := 1/2 * (cos(pi*x) + 1) +******************************************************************************* + +*** SETUP: CUTOFF FUNCTIONS *************************************************** + +Parameter alpha for inner cutoff: 0.000000 +Inner cutoff = Symmetry function cutoff * alpha +Equal cutoff function type for all symmetry functions: +CutoffFunction::CT_TANHU (2) +f(r) = tanh^3(1 - r/rc) +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTIONS ************************************************* + +Abbreviations: +-------------- +ind .... Symmetry function index. +ec ..... Central atom element. +tp ..... Symmetry function type. +sbtp ... Symmetry function subtype (e.g. cutoff type). +e1 ..... Neighbor 1 element. +e2 ..... Neighbor 2 element. +eta .... Gaussian width eta. +rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial. +angl.... Left cutoff angle for polynomial. +angr.... Right cutoff angle for polynomial. +la ..... Angle prefactor lambda. +zeta ... Angle term exponent zeta. +rc ..... Cutoff radius / right cutoff radius for polynomial. +a ...... Free parameter alpha (e.g. cutoff alpha). +ln ..... Line number in settings file. + +Short range atomic symmetry functions element H : +------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln +------------------------------------------------------------------------------------------------- + 1 H 2 ct2 H 0.000E+00 0.000E+00 8.000E+00 0.00 59 + 2 H 2 ct2 C 0.000E+00 0.000E+00 8.000E+00 0.00 74 + 3 H 2 ct2 H 6.000E-03 0.000E+00 8.000E+00 0.00 60 + 4 H 2 ct2 H 1.100E-02 0.000E+00 8.000E+00 0.00 61 + 5 H 2 ct2 C 1.300E-02 0.000E+00 8.000E+00 0.00 75 + 6 H 2 ct2 H 1.800E-02 0.000E+00 8.000E+00 0.00 62 + 7 H 2 ct2 H 2.600E-02 0.000E+00 8.000E+00 0.00 63 + 8 H 2 ct2 C 2.900E-02 0.000E+00 8.000E+00 0.00 76 + 9 H 2 ct2 H 3.500E-02 0.000E+00 8.000E+00 0.00 64 + 10 H 2 ct2 C 5.400E-02 0.000E+00 8.000E+00 0.00 77 + 11 H 2 ct2 C 9.300E-02 0.000E+00 8.000E+00 0.00 78 + 12 H 2 ct2 C 1.610E-01 0.000E+00 8.000E+00 0.00 79 + 13 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 134 + 14 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 125 + 15 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 130 + 16 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 121 + 17 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 135 + 18 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 126 + 19 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 131 + 20 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 122 + 21 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 132 + 22 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 123 + 23 H 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 133 + 24 H 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 124 +------------------------------------------------------------------------------------------------- +Short range atomic symmetry functions element C : +------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln +------------------------------------------------------------------------------------------------- + 1 C 2 ct2 H 0.000E+00 0.000E+00 8.000E+00 0.00 67 + 2 C 2 ct2 C 0.000E+00 0.000E+00 8.000E+00 0.00 82 + 3 C 2 ct2 C 1.000E-02 0.000E+00 8.000E+00 0.00 83 + 4 C 2 ct2 H 1.300E-02 0.000E+00 8.000E+00 0.00 68 + 5 C 2 ct2 C 2.300E-02 0.000E+00 8.000E+00 0.00 84 + 6 C 2 ct2 H 2.900E-02 0.000E+00 8.000E+00 0.00 69 + 7 C 2 ct2 C 4.100E-02 0.000E+00 8.000E+00 0.00 85 + 8 C 2 ct2 H 5.400E-02 0.000E+00 8.000E+00 0.00 70 + 9 C 2 ct2 C 6.500E-02 0.000E+00 8.000E+00 0.00 86 + 10 C 2 ct2 H 9.300E-02 0.000E+00 8.000E+00 0.00 71 + 11 C 2 ct2 C 1.030E-01 0.000E+00 8.000E+00 0.00 87 + 12 C 2 ct2 H 1.610E-01 0.000E+00 8.000E+00 0.00 72 + 13 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 106 + 14 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 115 + 15 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 1.0 0.00 97 + 16 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 102 + 17 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 111 + 18 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 1.0 0.00 93 + 19 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 107 + 20 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 116 + 21 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 2.0 0.00 98 + 22 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 103 + 23 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 112 + 24 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 2.0 0.00 94 + 25 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 108 + 26 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 117 + 27 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 4.0 0.00 99 + 28 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 104 + 29 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 113 + 30 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 4.0 0.00 95 + 31 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 109 + 32 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 118 + 33 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 -1 8.0 0.00 100 + 34 C 3 ct2 H H 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 105 + 35 C 3 ct2 H C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 114 + 36 C 3 ct2 C C 0.000E+00 0.000E+00 8.000E+00 1 8.0 0.00 96 +------------------------------------------------------------------------------------------------- +Minimum cutoff radius for element H: 8.000000 +Minimum cutoff radius for element C: 8.000000 +Maximum cutoff radius (global) : 8.000000 +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION MEMORY ******************************************* + +Symmetry function derivatives memory table for element H : +------------------------------------------------------------------------------- +Relevant symmetry functions for neighbors with element: +- H: 12 of 24 ( 50.0 ) +- C: 18 of 24 ( 75.0 ) +------------------------------------------------------------------------------- +Symmetry function derivatives memory table for element C : +------------------------------------------------------------------------------- +Relevant symmetry functions for neighbors with element: +- H: 22 of 36 ( 61.1 ) +- C: 22 of 36 ( 61.1 ) +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION CACHE ******************************************** + +Element H: in total 4 caches, used 15.00 times on average. +Element C: in total 4 caches, used 22.00 times on average. +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION GROUPS ******************************************* + +Abbreviations: +-------------- +ind .... Symmetry function index. +ec ..... Central atom element. +tp ..... Symmetry function type. +sbtp ... Symmetry function subtype (e.g. cutoff type). +e1 ..... Neighbor 1 element. +e2 ..... Neighbor 2 element. +eta .... Gaussian width eta. +rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial. +angl.... Left cutoff angle for polynomial. +angr.... Right cutoff angle for polynomial. +la ..... Angle prefactor lambda. +zeta ... Angle term exponent zeta. +rc ..... Cutoff radius / right cutoff radius for polynomial. +a ...... Free parameter alpha (e.g. cutoff alpha). +ln ..... Line number in settings file. +mi ..... Member index. +sfi .... Symmetry function index. +e ...... Recalculate exponential term. + +Short range atomic symmetry function groups element H : +---------------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e +---------------------------------------------------------------------------------------------------------- + 1 H 2 ct2 H * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 59 1 1 + - - - - - 6.000E-03 0.000E+00 - - 60 2 3 + - - - - - 1.100E-02 0.000E+00 - - 61 3 4 + - - - - - 1.800E-02 0.000E+00 - - 62 4 6 + - - - - - 2.600E-02 0.000E+00 - - 63 5 7 + - - - - - 3.500E-02 0.000E+00 - - 64 6 9 + 2 H 2 ct2 C * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 74 1 2 + - - - - - 1.300E-02 0.000E+00 - - 75 2 5 + - - - - - 2.900E-02 0.000E+00 - - 76 3 8 + - - - - - 5.400E-02 0.000E+00 - - 77 4 10 + - - - - - 9.300E-02 0.000E+00 - - 78 5 11 + - - - - - 1.610E-01 0.000E+00 - - 79 6 12 + 3 H 3 ct2 H C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 134 1 13 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 130 2 15 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 135 3 17 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 131 4 19 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 132 5 21 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 133 6 23 0 + 4 H 3 ct2 C C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 125 1 14 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 121 2 16 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 126 3 18 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 122 4 20 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 123 5 22 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 124 6 24 0 +---------------------------------------------------------------------------------------------------------- +Short range atomic symmetry function groups element C : +---------------------------------------------------------------------------------------------------------- + ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e +---------------------------------------------------------------------------------------------------------- + 1 C 2 ct2 H * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 67 1 1 + - - - - - 1.300E-02 0.000E+00 - - 68 2 4 + - - - - - 2.900E-02 0.000E+00 - - 69 3 6 + - - - - - 5.400E-02 0.000E+00 - - 70 4 8 + - - - - - 9.300E-02 0.000E+00 - - 71 5 10 + - - - - - 1.610E-01 0.000E+00 - - 72 6 12 + 2 C 2 ct2 C * * 8.000E+00 0.00 * * * + - - - - - 0.000E+00 0.000E+00 - - 82 1 2 + - - - - - 1.000E-02 0.000E+00 - - 83 2 3 + - - - - - 2.300E-02 0.000E+00 - - 84 3 5 + - - - - - 4.100E-02 0.000E+00 - - 85 4 7 + - - - - - 6.500E-02 0.000E+00 - - 86 5 9 + - - - - - 1.030E-01 0.000E+00 - - 87 6 11 + 3 C 3 ct2 H H * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 106 1 13 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 102 2 16 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 107 3 19 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 103 4 22 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 108 5 25 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 104 6 28 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 109 7 31 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 105 8 34 0 + 4 C 3 ct2 H C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 115 1 14 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 111 2 17 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 116 3 20 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 112 4 23 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 117 5 26 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 113 6 29 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 118 7 32 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 114 8 35 0 + 5 C 3 ct2 C C * * 8.000E+00 * * 0.00 * * * * + - - - - - - 0.000E+00 0.000E+00 - -1 1.0 - 97 1 15 1 + - - - - - - 0.000E+00 0.000E+00 - 1 1.0 - 93 2 18 0 + - - - - - - 0.000E+00 0.000E+00 - -1 2.0 - 98 3 21 0 + - - - - - - 0.000E+00 0.000E+00 - 1 2.0 - 94 4 24 0 + - - - - - - 0.000E+00 0.000E+00 - -1 4.0 - 99 5 27 0 + - - - - - - 0.000E+00 0.000E+00 - 1 4.0 - 95 6 30 0 + - - - - - - 0.000E+00 0.000E+00 - -1 8.0 - 100 7 33 0 + - - - - - - 0.000E+00 0.000E+00 - 1 8.0 - 96 8 36 0 +---------------------------------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: NEURAL NETWORKS **************************************************** + +Normalize neurons (all elements): 0 +------------------------------------------------------------------------------- +Atomic electronegativity NN for element H : +Number of weights : 600 +Number of biases : 31 +Number of connections: 631 +Architecture 24 15 15 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G t t + 12 G t t + 13 G t t + 14 G t t + 15 G t t + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G +------------------------------------------------------------------------------- +Atomic electronegativity NN for element C : +Number of weights : 780 +Number of biases : 31 +Number of connections: 811 +Architecture 36 15 15 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G t t + 12 G t t + 13 G t t + 14 G t t + 15 G t t + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + 26 G + 27 G + 28 G + 29 G + 30 G + 31 G + 32 G + 33 G + 34 G + 35 G + 36 G +------------------------------------------------------------------------------- +Atomic short range NN for element H : +Number of weights : 360 +Number of biases : 21 +Number of connections: 381 +Architecture 25 10 10 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G + 12 G + 13 G + 14 G + 15 G + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G +------------------------------------------------------------------------------- +Atomic short range NN for element C : +Number of weights : 480 +Number of biases : 21 +Number of connections: 501 +Architecture 37 10 10 1 +------------------------------------------------------------------------------- + 1 G t t l + 2 G t t + 3 G t t + 4 G t t + 5 G t t + 6 G t t + 7 G t t + 8 G t t + 9 G t t + 10 G t t + 11 G + 12 G + 13 G + 14 G + 15 G + 16 G + 17 G + 18 G + 19 G + 20 G + 21 G + 22 G + 23 G + 24 G + 25 G + 26 G + 27 G + 28 G + 29 G + 30 G + 31 G + 32 G + 33 G + 34 G + 35 G + 36 G + 37 G +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION SCALING ****************************************** + +Equal scaling type for all symmetry functions: +Scaling type::ST_SCALECENTER (3) +Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin) +WARNING: Keyword "scale_min_short" not found. + Default value for Smin = 0.0. +WARNING: Keyword "scale_max_short" not found. + Default value for Smax = 1.0. +Smin = 0.000000 +Smax = 1.000000 +Symmetry function scaling statistics from file: scaling.data +------------------------------------------------------------------------------- + +Abbreviations: +-------------- +ind ..... Symmetry function index. +min ..... Minimum symmetry function value. +max ..... Maximum symmetry function value. +mean .... Mean symmetry function value. +sigma ... Standard deviation of symmetry function values. +sf ...... Scaling factor for derivatives. +Smin .... Desired minimum scaled symmetry function value. +Smax .... Desired maximum scaled symmetry function value. +t ....... Scaling type. + +Scaling data for symmetry functions element H : +------------------------------------------------------------------------------- + ind min max mean sigma sf Smin Smax t +------------------------------------------------------------------------------- + 1 0.00E+00 1.68E-01 5.14E-02 0.00E+00 5.94E+00 0.00 1.00 3 + 2 3.04E-01 4.17E-01 3.46E-01 0.00E+00 8.85E+00 0.00 1.00 3 + 3 0.00E+00 1.59E-01 4.77E-02 0.00E+00 6.27E+00 0.00 1.00 3 + 4 0.00E+00 1.52E-01 4.48E-02 0.00E+00 6.56E+00 0.00 1.00 3 + 5 2.70E-01 3.77E-01 3.12E-01 0.00E+00 9.35E+00 0.00 1.00 3 + 6 0.00E+00 1.43E-01 4.10E-02 0.00E+00 7.00E+00 0.00 1.00 3 + 7 0.00E+00 1.33E-01 3.71E-02 0.00E+00 7.53E+00 0.00 1.00 3 + 8 2.36E-01 3.37E-01 2.78E-01 0.00E+00 9.97E+00 0.00 1.00 3 + 9 0.00E+00 1.22E-01 3.31E-02 0.00E+00 8.18E+00 0.00 1.00 3 + 10 1.94E-01 2.86E-01 2.36E-01 0.00E+00 1.09E+01 0.00 1.00 3 + 11 1.46E-01 2.31E-01 1.88E-01 0.00E+00 1.18E+01 0.00 1.00 3 + 12 9.43E-02 1.67E-01 1.33E-01 0.00E+00 1.37E+01 0.00 1.00 3 + 13 0.00E+00 3.94E-03 7.66E-04 0.00E+00 2.54E+02 0.00 1.00 3 + 14 0.00E+00 2.18E-03 3.95E-04 0.00E+00 4.59E+02 0.00 1.00 3 + 15 0.00E+00 2.26E-02 6.69E-03 0.00E+00 4.42E+01 0.00 1.00 3 + 16 6.80E-03 1.48E-02 9.85E-03 0.00E+00 1.25E+02 0.00 1.00 3 + 17 0.00E+00 7.54E-04 1.18E-04 0.00E+00 1.33E+03 0.00 1.00 3 + 18 0.00E+00 3.07E-04 3.12E-05 0.00E+00 3.26E+03 0.00 1.00 3 + 19 0.00E+00 2.02E-02 6.04E-03 0.00E+00 4.96E+01 0.00 1.00 3 + 20 6.45E-03 1.30E-02 9.49E-03 0.00E+00 1.53E+02 0.00 1.00 3 + 21 0.00E+00 1.67E-02 5.00E-03 0.00E+00 5.97E+01 0.00 1.00 3 + 22 5.80E-03 1.11E-02 8.84E-03 0.00E+00 1.88E+02 0.00 1.00 3 + 23 0.00E+00 1.27E-02 3.57E-03 0.00E+00 7.90E+01 0.00 1.00 3 + 24 4.42E-03 1.10E-02 7.82E-03 0.00E+00 1.51E+02 0.00 1.00 3 +------------------------------------------------------------------------------- +Scaling data for symmetry functions element C : +------------------------------------------------------------------------------- + ind min max mean sigma sf Smin Smax t +------------------------------------------------------------------------------- + 1 0.00E+00 5.28E-01 8.65E-02 0.00E+00 1.89E+00 0.00 1.00 3 + 2 2.44E-01 5.76E-01 4.78E-01 0.00E+00 3.00E+00 0.00 1.00 3 + 3 2.20E-01 5.27E-01 4.38E-01 0.00E+00 3.26E+00 0.00 1.00 3 + 4 0.00E+00 5.04E-01 7.81E-02 0.00E+00 1.99E+00 0.00 1.00 3 + 5 1.95E-01 4.73E-01 3.93E-01 0.00E+00 3.59E+00 0.00 1.00 3 + 6 0.00E+00 4.75E-01 6.95E-02 0.00E+00 2.11E+00 0.00 1.00 3 + 7 1.66E-01 4.12E-01 3.41E-01 0.00E+00 4.07E+00 0.00 1.00 3 + 8 0.00E+00 4.33E-01 5.90E-02 0.00E+00 2.31E+00 0.00 1.00 3 + 9 1.36E-01 3.48E-01 2.86E-01 0.00E+00 4.72E+00 0.00 1.00 3 + 10 0.00E+00 3.76E-01 4.70E-02 0.00E+00 2.66E+00 0.00 1.00 3 + 11 1.02E-01 2.73E-01 2.22E-01 0.00E+00 5.83E+00 0.00 1.00 3 + 12 0.00E+00 2.93E-01 3.33E-02 0.00E+00 3.41E+00 0.00 1.00 3 + 13 0.00E+00 1.53E-02 6.08E-04 0.00E+00 6.55E+01 0.00 1.00 3 + 14 0.00E+00 2.04E-02 2.32E-03 0.00E+00 4.91E+01 0.00 1.00 3 + 15 0.00E+00 6.66E-03 3.99E-03 0.00E+00 1.50E+02 0.00 1.00 3 + 16 0.00E+00 9.28E-03 3.24E-04 0.00E+00 1.08E+02 0.00 1.00 3 + 17 0.00E+00 2.50E-02 2.80E-03 0.00E+00 4.00E+01 0.00 1.00 3 + 18 3.52E-03 1.25E-02 8.03E-03 0.00E+00 1.11E+02 0.00 1.00 3 + 19 0.00E+00 1.19E-02 4.30E-04 0.00E+00 8.39E+01 0.00 1.00 3 + 20 0.00E+00 1.56E-02 2.02E-03 0.00E+00 6.43E+01 0.00 1.00 3 + 21 0.00E+00 6.52E-03 3.94E-03 0.00E+00 1.53E+02 0.00 1.00 3 + 22 0.00E+00 3.82E-03 1.46E-04 0.00E+00 2.62E+02 0.00 1.00 3 + 23 0.00E+00 2.34E-02 2.50E-03 0.00E+00 4.27E+01 0.00 1.00 3 + 24 3.51E-03 1.24E-02 7.98E-03 0.00E+00 1.12E+02 0.00 1.00 3 + 25 0.00E+00 8.68E-03 2.29E-04 0.00E+00 1.15E+02 0.00 1.00 3 + 26 0.00E+00 1.07E-02 1.70E-03 0.00E+00 9.33E+01 0.00 1.00 3 + 27 0.00E+00 6.38E-03 3.88E-03 0.00E+00 1.57E+02 0.00 1.00 3 + 28 0.00E+00 1.76E-03 6.00E-05 0.00E+00 5.69E+02 0.00 1.00 3 + 29 0.00E+00 2.11E-02 2.32E-03 0.00E+00 4.74E+01 0.00 1.00 3 + 30 3.50E-03 1.23E-02 7.95E-03 0.00E+00 1.13E+02 0.00 1.00 3 + 31 0.00E+00 4.70E-03 6.92E-05 0.00E+00 2.13E+02 0.00 1.00 3 + 32 0.00E+00 1.07E-02 1.36E-03 0.00E+00 9.34E+01 0.00 1.00 3 + 33 0.00E+00 6.34E-03 3.76E-03 0.00E+00 1.58E+02 0.00 1.00 3 + 34 0.00E+00 9.43E-04 2.30E-05 0.00E+00 1.06E+03 0.00 1.00 3 + 35 0.00E+00 1.71E-02 2.11E-03 0.00E+00 5.84E+01 0.00 1.00 3 + 36 3.48E-03 1.22E-02 7.88E-03 0.00E+00 1.15E+02 0.00 1.00 3 +------------------------------------------------------------------------------- +******************************************************************************* + +*** SETUP: NEURAL NETWORK WEIGHTS ********************************************* + +Electronegativity weight file name format: weightse.%03zu.data +Setting weights for element H from file: weightse.001.data +Setting weights for element C from file: weightse.006.data +Short range weight file name format: weights.%03zu.data +Setting weights for element H from file: weights.001.data +Setting weights for element C from file: weights.006.data +******************************************************************************* + +*** SETUP: SYMMETRY FUNCTION STATISTICS *************************************** + +Equal symmetry function statistics for all elements. +Collect min/max/mean/sigma : 0 +Collect extrapolation warnings : 0 +Write extrapolation warnings immediately to stderr: 1 +Halt on any extrapolation warning : 0 +******************************************************************************* + +*** PREDICTION **************************************************************** + +Reading structure file... +Structure contains 12 atoms (2 elements). +Calculating NNP prediction... +Atom 0 ( C) chi: -1.50037876E-01 +Atom 1 ( C) chi: -1.49461645E-01 +Atom 2 ( C) chi: -1.49033407E-01 +Atom 3 ( C) chi: -1.49337351E-01 +Atom 4 ( C) chi: -1.48516909E-01 +Atom 5 ( C) chi: -1.48569008E-01 +Atom 6 ( C) chi: -1.46830562E-01 +Atom 7 ( C) chi: -1.46678106E-01 +Atom 8 ( C) chi: -1.60724572E-01 +Atom 9 ( C) chi: -1.62293124E-01 +Atom 10 ( H) chi: -2.25977980E-01 +Atom 11 ( H) chi: -2.28364821E-01 +Solve relative error: 2.46817332E-16 +Atom 0 ( C) q: -2.35248237E-03 +Atom 1 ( C) q: -8.49420865E-03 +Atom 2 ( C) q: -1.05376542E-02 +Atom 3 ( C) q: -7.12483037E-03 +Atom 4 ( C) q: 8.26588394E-04 +Atom 5 ( C) q: 8.17418285E-04 +Atom 6 ( C) q: -2.83515663E-02 +Atom 7 ( C) q: -3.24687341E-02 +Atom 8 ( C) q: -6.06697242E-02 +Atom 9 ( C) q: -5.61469557E-02 +Atom 10 ( H) q: 1.01557440E-01 +Atom 11 ( H) q: 1.02944709E-01 +Total charge: -1.38777878E-17 (ref: -0.00000000E+00) +Electrostatic energy: -1.56542350E-05 +Atom 0 ( C) energy: -2.72505156E-01 +Atom 1 ( C) energy: -2.61772068E-01 +Atom 2 ( C) energy: -2.70880061E-01 +Atom 3 ( C) energy: -2.74327298E-01 +Atom 4 ( C) energy: -2.64805835E-01 +Atom 5 ( C) energy: -2.70013830E-01 +Atom 6 ( C) energy: -2.03971823E-01 +Atom 7 ( C) energy: -2.04807793E-01 +Atom 8 ( C) energy: -1.74860014E-01 +Atom 9 ( C) energy: -1.71323877E-01 +Atom 10 ( H) energy: -4.21189827E-01 +Atom 11 ( H) energy: -4.21379968E-01 + +------------------------------------------------------------------------------- +NNP energy: -3.81610787E+02 + +NNP forces: + 1 C 3.52442388E-02 -9.20647286E-04 1.61392791E-02 + 2 C -2.03205054E-02 1.67564237E-03 -7.44577911E-04 + 3 C -1.65272426E-02 -5.79898175E-03 -1.64076390E-02 + 4 C -3.27459765E-02 1.20525122E-02 -1.85227424E-03 + 5 C 2.95248059E-03 -7.93860129E-04 1.37057169E-02 + 6 C 3.60947361E-02 -1.31042465E-02 -3.95273681E-03 + 7 C 1.23391974E-02 1.73678305E-02 -1.60913686E-02 + 8 C -3.10269086E-02 9.96355077E-03 2.03890445E-02 + 9 C -2.44021463E-02 -5.91444675E-03 1.48215600E-02 + 10 C 3.57962495E-02 -8.13571283E-03 -2.06406046E-02 + 11 H -5.66654043E-03 -6.56723579E-03 -8.00976568E-03 + 12 H 8.26241739E-03 1.75595189E-04 2.64336628E-03 +------------------------------------------------------------------------------- +Writing output files... + - energy.out + - nnatoms.out + - nnforces.out +Writing structure with NNP prediction to "output.data". +Finished. +******************************************************************************* diff --git a/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/output.data b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/output.data new file mode 100644 index 0000000000..48f119cc94 --- /dev/null +++ b/examples/interface-LAMMPS/TO_BE_CHECKED/carbon-chain2/nnp-predict/output.data @@ -0,0 +1,17 @@ +begin +comment +atom 1.1728409548600001E+00 -1.7250422268400001E-01 -6.6744851686499995E-01 C -2.3524823684152795E-03 0.0000000000000000E+00 3.5244238802598936E-02 -9.2064728582576792E-04 1.6139279140426486E-02 +atom -1.1595434821999999E+00 -3.5064100044500002E-01 -4.6759810719400002E-01 C -8.4942086481964076E-03 0.0000000000000000E+00 -2.0320505353455472E-02 1.6756423734835108E-03 -7.4457791136594144E-04 +atom 3.7259405496900002E+00 -8.3797517909699998E-02 -2.2977716867299999E-01 C -1.0537654209871102E-02 0.0000000000000000E+00 -1.6527242561909055E-02 -5.7989817531996874E-03 -1.6407639020990412E-02 +atom -3.6914698311600000E+00 -3.3417264316700002E-01 -2.1088223314999999E-01 C -7.1248303653208261E-03 0.0000000000000000E+00 -3.2745976522587684E-02 1.2052512199310998E-02 -1.8522742363607386E-03 +atom 6.0775858677099999E+00 -1.6674522604200001E-01 -1.4502403522800000E-01 C 8.2658839443283238E-04 0.0000000000000000E+00 2.9524805895551585E-03 -7.9386012929745281E-04 1.3705716946330639E-02 +atom -6.0680978936700001E+00 -2.5373350848899999E-03 -7.0535761072400005E-02 C 8.1741828473709803E-04 0.0000000000000000E+00 3.6094736091666753E-02 -1.3104246537253889E-02 -3.9527368127116212E-03 +atom 8.5916435346399993E+00 -8.0691507583099994E-02 4.0223683161899998E-01 C -2.8351566345695845E-02 0.0000000000000000E+00 1.2339197396340543E-02 1.7367830541731095E-02 -1.6091368599610911E-02 +atom -8.6089256457300003E+00 1.1719224535400000E-01 9.8285177790399997E-02 C -3.2468734085716766E-02 0.0000000000000000E+00 -3.1026908616236346E-02 9.9635507686791063E-03 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0000000000..d8222b03b1 --- /dev/null +++ b/src/interface/LAMMPS/src/ML-HDNNP/fix_hdnnp.cpp @@ -0,0 +1,779 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_hdnnp.h" +#include "pair_hdnnp_4g.h" +#include +#include +#include +#include +#include +#include "pair_hdnnp.h" +#include "kspace_hdnnp.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" // check for periodicity +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" +#include "force.h" +#include "group.h" +#include "pair.h" +#include "memory.h" +#include "error.h" +#include "utils.h" +#include //time + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace std::chrono; +using namespace nnp; + +#define EV_TO_KCAL_PER_MOL 14.4 +#define SQR(x) ((x)*(x)) +#define CUBE(x) ((x)*(x)*(x)) +#define MIN_NBRS 100 +#define SAFE_ZONE 1.2 +#define DANGER_ZONE 0.90 +#define MIN_CAP 50 + + +FixHDNNP::FixHDNNP(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + hdnnp (nullptr), + kspacehdnnp (nullptr), + list (nullptr), + pertype_option(nullptr), + hdnnpflag (0 ), + kspaceflag (0 ), + ngroup (0 ), + periodic (false ), + qRef (0.0 ), + Q (nullptr), + type_all (nullptr), + type_loc (nullptr), + qall (nullptr), + qall_loc (nullptr), + dEdQ_all (nullptr), + dEdQ_loc (nullptr), + xx (nullptr), + xy (nullptr), + xz (nullptr), + xx_loc (nullptr), + xy_loc (nullptr), + xz_loc (nullptr) + +{ + if (narg<9 || narg>11) error->all(FLERR,"Illegal fix hdnnp command"); + + nevery = utils::inumeric(FLERR,arg[3],false,lmp); + if (nevery <= 0) error->all(FLERR,"Illegal fix hdnnp command"); + + int len = strlen(arg[8]) + 1; + pertype_option = new char[len]; + strcpy(pertype_option,arg[8]); + + hdnnp = nullptr; + kspacehdnnp = nullptr; + hdnnp = (PairHDNNP4G *) force->pair_match("^hdnnp/4g",0); + kspacehdnnp = (KSpaceHDNNP *) force->kspace_match("^hdnnp",0); + + hdnnp->chi = nullptr; + hdnnp->hardness = nullptr; + hdnnp->sigmaSqrtPi = nullptr; + hdnnp->gammaSqrt2 = nullptr; + hdnnp->screening_info = nullptr; + + // User-defined minimization parameters used in pair_hdnnp as well + // TODO: read only on proc 0 and then Bcast ? + hdnnp->grad_tol = utils::numeric(FLERR,arg[4],false,lmp); //tolerance for gradient check + hdnnp->min_tol = utils::numeric(FLERR,arg[5],false,lmp); //tolerance + hdnnp->step = utils::numeric(FLERR,arg[6],false,lmp); //initial hdnnp->step size + hdnnp->maxit = utils::inumeric(FLERR,arg[7],false,lmp); //maximum number of iterations + hdnnp->minim_init_style = utils::inumeric(FLERR,arg[10],false,lmp); //initialization style + + // TODO: check these initializations and allocations + int natoms = atom->natoms; + + // TODO: these are not necessary in case of periodic systems + memory->create(xx,atom->natoms,"fix_hdnnp:xx"); + memory->create(xy,atom->natoms,"fix_hdnnp:xy"); + memory->create(xz,atom->natoms,"fix_hdnnp:xz"); + memory->create(xx_loc,atom->natoms,"fix_hdnnp:xx_loc"); + memory->create(xy_loc,atom->natoms,"fix_hdnnp:xy_loc"); + memory->create(xz_loc,atom->natoms,"fix_hdnnp:xz_loc"); + memory->create(type_loc,atom->natoms,"fix_hdnnp:type_loc"); + memory->create(type_all,atom->natoms,"fix_hdnnp:type_all"); + +} + +/* ---------------------------------------------------------------------- */ + +FixHDNNP::~FixHDNNP() +{ + if (copymode) return; + + delete[] pertype_option; + + memory->destroy(hdnnp->chi); + memory->destroy(hdnnp->hardness); + memory->destroy(hdnnp->sigmaSqrtPi); + memory->destroy(hdnnp->gammaSqrt2); + + memory->destroy(qall); + memory->destroy(qall_loc); + memory->destroy(dEdQ_loc); + memory->destroy(dEdQ_all); + + memory->destroy(xx); + memory->destroy(xy); + memory->destroy(xz); + memory->destroy(xx_loc); + memory->destroy(xy_loc); + memory->destroy(xz_loc); + memory->destroy(type_loc); + memory->destroy(type_all); + +} + +void FixHDNNP::post_constructor() +{ + pertype_parameters(pertype_option); + +} + +int FixHDNNP::setmask() +{ + int mask = 0; + mask |= PRE_FORCE; + mask |= PRE_FORCE_RESPA; + mask |= MIN_PRE_FORCE; + return mask; +} + +void FixHDNNP::init() +{ + if (!atom->q_flag) + error->all(FLERR,"Fix hdnnp requires atom attribute q"); + + ngroup = group->count(igroup); + if (ngroup == 0) error->all(FLERR,"Fix hdnnp group has no atoms"); + + // need a half neighbor list w/ Newton off and ghost neighbors + // built whenever re-neighboring occurs + + //int irequest = neighbor->request(this,instance_me); + //neighbor->requests[irequest]->pair = 0; + //neighbor->requests[irequest]->fix = 1; + //neighbor->requests[irequest]->newton = 2; + //neighbor->requests[irequest]->ghost = 1; + + isPeriodic(); + + //if (periodic) neighbor->add_request(this, NeighConst::REQ_DEFAULT); + //else neighbor->add_request(this, NeighConst::REQ_FULL); + neighbor->add_request(this, NeighConst::REQ_FULL | + NeighConst::REQ_GHOST | + NeighConst::REQ_NEWTON_OFF); + + // TODO : do we really need a full NL in periodic cases ? + //if (periodic) { // periodic : full neighborlist + // neighbor->requests[irequest]->half = 0; + // neighbor->requests[irequest]->full = 1; + //} + + allocate_QEq(); +} + +void FixHDNNP::pertype_parameters(char *arg) +{ + if (strcmp(arg,"hdnnp") == 0) { + hdnnpflag = 1; + Pair *pair = force->pair_match("hdnnp",0); + if (pair == NULL) error->all(FLERR,"No pair hdnnp for fix hdnnp"); + } +} + +// Allocate QEq arrays +void FixHDNNP::allocate_QEq() +{ + int ne = atom->ntypes; + memory->create(hdnnp->chi,atom->natoms,"qeq:hdnnp->chi"); + memory->create(hdnnp->hardness,ne,"qeq:hdnnp->hardness"); + memory->create(hdnnp->sigmaSqrtPi,ne,"qeq:hdnnp->sigmaSqrtPi"); + memory->create(hdnnp->gammaSqrt2,ne,ne,"qeq:hdnnp->gammaSqrt2"); + memory->create(hdnnp->screening_info,4,"qeq:screening"); + memory->create(qall,atom->natoms,"qeq:qall"); + memory->create(qall_loc,atom->natoms,"qeq:qall_loc"); + memory->create(dEdQ_loc,atom->natoms,"qeq:dEdQ_loc"); + memory->create(dEdQ_all,atom->natoms,"qeq:dEdQ_all"); + + // Initialization + for (int i =0; i < atom->natoms; i++){ + hdnnp->chi[i] = 0.0; + } + for (int i = 0; i < ne; i++){ + hdnnp->hardness[i] = 0.0; + hdnnp->sigmaSqrtPi[i] = 0.0; + for (int j = 0; j < ne; j++){ + hdnnp->gammaSqrt2[i][j] = 0.0; + } + } + for (int i = 0; i < 4; i++){ + hdnnp->screening_info[i] = 0.0; + } +} + +// Deallocate QEq arrays +void FixHDNNP::deallocate_QEq() { + + memory->destroy(hdnnp->chi); + memory->destroy(hdnnp->hardness); + memory->destroy(hdnnp->sigmaSqrtPi); + memory->destroy(hdnnp->gammaSqrt2); + memory->destroy(hdnnp->screening_info); + memory->destroy(qall); + memory->destroy(qall_loc); + memory->destroy(dEdQ_loc); + memory->destroy(dEdQ_all); + +} + +void FixHDNNP::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +void FixHDNNP::setup_pre_force(int vflag) +{ + pre_force(vflag); +} + +void FixHDNNP::min_setup_pre_force(int vflag) +{ + setup_pre_force(vflag); +} + +void FixHDNNP::min_pre_force(int vflag) +{ + pre_force(vflag); +} + +// Main calculation routine, runs before pair->compute at each timehdnnp->step +void FixHDNNP::pre_force(int /*vflag*/) { + + double *q = atom->q; + double Qtot_loc = 0.0; + int n = atom->nlocal; + int j,jmap; + + //deallocate_QEq(); + //allocate_QEq(); + + if(periodic) { + //force->kspace->setup(); + kspacehdnnp->ewald_sfexp(); + } + + // Calculate atomic electronegativities \Chi_i + calculate_electronegativities(); + + // Calculate the current total charge + for (int i = 0; i < n; i++) { + //std::cout << q[i] << '\n'; + Qtot_loc += q[i]; + } + MPI_Allreduce(&Qtot_loc,&qRef,1,MPI_DOUBLE,MPI_SUM,world); + + //TODO + calculate_erfc_terms(); + + std::chrono::steady_clock::time_point begin = std::chrono::steady_clock::now(); + // Minimize QEq energy and calculate atomic charges + calculate_QEqCharges(); + std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); + //std::cout << "iQEq time (s) = " << std::chrono::duration_cast(end - begin).count() / 1000000.0 << std::endl; + +} + +void FixHDNNP::calculate_electronegativities() +{ + // Run first set of atomic NNs + process_first_network(); + + // Read QEq arrays from n2p2 into LAMMPS + hdnnp->interface.getQEqParams(hdnnp->chi,hdnnp->hardness,hdnnp->sigmaSqrtPi,hdnnp->gammaSqrt2,qRef); + + // Read screening function information from n2p2 into LAMMPS + hdnnp->interface.getScreeningInfo(hdnnp->screening_info); //TODO: read function type +} + +// Runs interface.process for electronegativities +void FixHDNNP::process_first_network() +{ + if(hdnnp->interface.getNnpType() == InterfaceLammps::NNPType::HDNNP_4G) + { + // Set number of local atoms and add element. + hdnnp->interface.setLocalAtoms(atom->nlocal,atom->type); + + // Set tags of local atoms. + hdnnp->interface.setLocalTags(atom->tag); + + // Transfer local neighbor list to HDNNP interface. + hdnnp->transferNeighborList(); + + // Run the first NN for electronegativities + hdnnp->interface.process(); + } + else{ //TODO + error->all(FLERR,"This fix style can only be used with a 4G-HDNNP."); + } +} + +// This routine is called once. Complementary error function terms are calculated and stored +void FixHDNNP::calculate_erfc_terms() +{ + int i,j,jmap; + int nlocal = atom->nlocal; + int *tag = atom->tag; + int *type = atom->type; + + double **x = atom->x; + double eta; + + int maxnumneigh = 0; + // TODO is this already available in LAMMPS ? + for (int i = 0; i < nlocal; i++) + { + int nneigh = list->numneigh[i]; + if (nneigh > maxnumneigh) maxnumneigh = nneigh; + } + + //maxnumneigh = 100000; + // allocate and initialize + memory->create(hdnnp->erfc_val,nlocal+1,maxnumneigh+1,"fix_hdnnp:erfc_val"); + + for (int i = 0; i < nlocal; i++){ + for (int j = 0; j < maxnumneigh; j++) + hdnnp->erfc_val[i][j] = 0.0; + } + + if (periodic) + { + eta = 1 / kspacehdnnp->g_ewald; // LAMMPS truncation + double sqrt2eta = (sqrt(2.0) * eta); + for (i = 0; i < nlocal; i++) + { + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + jmap = atom->map(tag[j]); + double const dx = x[i][0] - x[j][0]; + double const dy = x[i][1] - x[j][1]; + double const dz = x[i][2] - x[j][2]; + double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * hdnnp->cflength; + hdnnp->erfc_val[i][jj] = (erfc(rij/sqrt2eta) - erfc(rij/hdnnp->gammaSqrt2[type[i]-1][type[jmap]-1])) / rij; + } + } + } +} + +// QEq energy function, $E_{QEq}$ +double FixHDNNP::QEq_f(const gsl_vector *v) +{ + int i,j,jmap; + int *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = atom->natoms; + + double **x = atom->x; + double *q = atom->q; + + double E_qeq_loc,E_qeq; + double E_elec_loc,E_scr_loc,E_scr; + double E_real,E_recip,E_self; // for periodic examples + double iiterm,ijterm; + + double eta; + + if(periodic) eta = 1 / kspacehdnnp->g_ewald; // LAMMPS truncation + + E_qeq = 0.0; + E_qeq_loc = 0.0; + E_scr = 0.0; + E_scr_loc = 0.0; + hdnnp->E_elec = 0.0; + + if (periodic) + { + double sqrt2eta = (sqrt(2.0) * eta); + E_recip = 0.0; + E_real = 0.0; + E_self = 0.0; + for (i = 0; i < nlocal; i++) // over local atoms + { + double const qi = gsl_vector_get(v, tag[i]-1); + double qi2 = qi * qi; + // Self term + E_self += qi2 * (1 / (2.0 * hdnnp->sigmaSqrtPi[type[i]-1]) - 1 / (sqrt(2.0 * M_PI) * eta)); + E_qeq_loc += hdnnp->chi[i] * qi + 0.5 * hdnnp->hardness[type[i]-1] * qi2; + E_scr -= qi2 / (2.0 * hdnnp->sigmaSqrtPi[type[i]-1]); // self screening term TODO:parallel ? + // Real Term + // TODO: we loop over the full neighbor list, could this be optimized ? + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + jmap = atom->map(tag[j]); + double const qj = gsl_vector_get(v, tag[j]-1); // mapping based on tags + double const dx = x[i][0] - x[j][0]; + double const dy = x[i][1] - x[j][1]; + double const dz = x[i][2] - x[j][2]; + double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * hdnnp->cflength; + //double erfcRij = (erfc(rij / sqrt2eta) - erfc(rij / hdnnp->gammaSqrt2[type[i]-1][type[jmap]-1])) / rij; + //double real = 0.5 * qi * qj * erfcRij; + double real = 0.5 * qi * qj * hdnnp->erfc_val[i][jj]; + E_real += real; + if (rij <= hdnnp->screening_info[2]) { + E_scr += 0.5 * qi * qj * + erf(rij/hdnnp->gammaSqrt2[type[i]-1][type[jmap]-1])*(hdnnp->screening_f(rij) - 1) / rij; + } + } + } + // Reciprocal Term + if (kspacehdnnp->ewaldflag) // Ewald Sum + { + // Calls the charge equilibration energy calculation routine in the KSpace base class + // Returns reciprocal energy + E_recip = kspacehdnnp->compute_ewald_eqeq(v); + } + else if (kspacehdnnp->pppmflag) // PPPM + { + //TODO: add contributions to Eqeq for PPPM style + kspacehdnnp->particle_map(); + kspacehdnnp->make_rho_qeq(v); // map my particle charge onto my local 3d density grid + E_recip = kspacehdnnp->compute_pppm_eqeq(); // TODO: WIP + } + hdnnp->E_elec = E_real + E_self; // do not add E_recip, it is already global + E_qeq_loc += hdnnp->E_elec; + }else + { + // first loop over local atoms + for (i = 0; i < nlocal; i++) { + double const qi = gsl_vector_get(v,tag[i]-1); + double qi2 = qi * qi; + // add i terms + iiterm = qi2 * (1 / (2.0 * hdnnp->sigmaSqrtPi[type[i]-1]) + (0.5 * hdnnp->hardness[type[i]-1])); + E_qeq_loc += iiterm + hdnnp->chi[i] * qi; + hdnnp->E_elec += iiterm; + E_scr -= iiterm; //TODO parallel ? + // Looping over all atoms (parallelization of necessary arrays has been done beforehand) + for (j = 0; j < nall; j++) { + double const qj = gsl_vector_get(v, j); + double const dx = xx[j] - x[i][0]; + double const dy = xy[j] - x[i][1]; + double const dz = xz[j] - x[i][2]; + double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * hdnnp->cflength; + if (rij != 0.0) //TODO check + { + ijterm = (erf(rij / hdnnp->gammaSqrt2[type[i]-1][type_all[j]-1]) / rij); + E_qeq_loc += 0.5 * ijterm * qi * qj; + hdnnp->E_elec += ijterm; + if(rij <= hdnnp->screening_info[2]) { + E_scr += ijterm * (hdnnp->screening_f(rij) - 1); + } + } + } + } + } + + //TODO: add communication steps for E_elec !!! + hdnnp->E_elec = hdnnp->E_elec + E_scr; // add screening energy + + MPI_Allreduce(&E_qeq_loc,&E_qeq,1,MPI_DOUBLE,MPI_SUM,world); // MPI_SUM of local QEQ contributions + + if (periodic) E_qeq += E_recip; // adding already all-reduced reciprocal part now + + //fprintf(stderr, "Erecip = %24.16E\n", E_recip); + return E_qeq; +} + +// QEq energy function - wrapper +double FixHDNNP::QEq_f_wrap(const gsl_vector *v, void *params) +{ + return static_cast(params)->QEq_f(v); +} + +// QEq energy gradient, $\partial E_{QEq} / \partial Q_i$ +void FixHDNNP::QEq_df(const gsl_vector *v, gsl_vector *dEdQ) +{ + int i,j,jmap; + int nlocal = atom->nlocal; + int nall = atom->natoms; + int *tag = atom->tag; + int *type = atom->type; + + double **x = atom->x; + double *q = atom->q; + + double grad; + double grad_sum_loc; + double grad_sum; + double grad_recip; // reciprocal space contribution to the gradient + double grad_i; + double jsum; //summation over neighbors & kspace respectively + double recip_sum; + + double eta; + + if (periodic) eta = 1 / kspacehdnnp->g_ewald; // LAMMPS truncation + + + grad_sum = 0.0; + grad_sum_loc = 0.0; + if (periodic) + { + double sqrt2eta = (sqrt(2.0) * eta); + for (i = 0; i < nlocal; i++) // over local atoms + { + double const qi = gsl_vector_get(v,tag[i]-1); + // Reciprocal contribution + if (kspacehdnnp->ewaldflag) + { + grad_recip = 0.0; + for (int k = 0; k < kspacehdnnp->kcount; k++) // over k-space + { + grad_recip += 2.0 * kspacehdnnp->kcoeff[k] * + (kspacehdnnp->sf_real[k] * kspacehdnnp->sfexp_rl[k][i] + + kspacehdnnp->sf_im[k] * kspacehdnnp->sfexp_im[k][i]); + } + } + else if (kspacehdnnp->pppmflag) + { + //TODO: calculate dEdQ_i for a given local atom i + grad_recip = kspacehdnnp->compute_pppm_dEdQ(i); + } + // Real contribution - over neighbors + jsum = 0.0; + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + double const qj = gsl_vector_get(v, tag[j]-1); + //jmap = atom->map(tag[j]); + //double const dx = x[i][0] - x[j][0]; + //double const dy = x[i][1] - x[j][1]; + //double const dz = x[i][2] - x[j][2]; + //double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * hdnnp->cflength; + //double erfcRij = (erfc(rij / sqrt2eta) - erfc(rij / hdnnp->gammaSqrt2[type[i]-1][type[jmap]-1])); + //jsum += qj * erfcRij / rij; + jsum += qj * hdnnp->erfc_val[i][jj]; + } + grad = jsum + grad_recip + hdnnp->chi[i] + hdnnp->hardness[type[i]-1]*qi + + qi * (1/(hdnnp->sigmaSqrtPi[type[i]-1])- 2/(eta * sqrt(2.0 * M_PI))); + grad_sum_loc += grad; + dEdQ_loc[tag[i]-1] = grad; // fill gradient array based on tags instead of local IDs + } + }else + { + // first loop over local atoms + for (i = 0; i < nlocal; i++) { // TODO: indices + double const qi = gsl_vector_get(v,tag[i]-1); + // second loop over 'all' atoms + jsum = 0.0; + // Looping over all atoms (parallelization of necessary arrays has been done beforehand) + for (j = 0; j < nall; j++) { + { + double const qj = gsl_vector_get(v, j); + double const dx = xx[j] - x[i][0]; + double const dy = xy[j] - x[i][1]; + double const dz = xz[j] - x[i][2]; + double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * hdnnp->cflength; + if (rij != 0.0) jsum += qj * erf(rij / hdnnp->gammaSqrt2[type[i]-1][type_all[j]-1]) / rij; + } + } + grad = hdnnp->chi[i] + hdnnp->hardness[type[i]-1]*qi + qi/(hdnnp->sigmaSqrtPi[type[i]-1]) + jsum; + grad_sum_loc += grad; + dEdQ_loc[tag[i]-1] = grad; + //gsl_vector_set(dEdQ,i,grad); + } + } + + MPI_Allreduce(dEdQ_loc,dEdQ_all,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&grad_sum_loc,&grad_sum,1,MPI_DOUBLE,MPI_SUM,world); + + // Gradient projection + for (i = 0; i < nall; i++){ + grad_i = dEdQ_all[i]; + gsl_vector_set(dEdQ,i,grad_i - (grad_sum)/nall); + } +} + +// QEq energy gradient - wrapper +void FixHDNNP::QEq_df_wrap(const gsl_vector *v, void *params, gsl_vector *df) +{ + static_cast(params)->QEq_df(v, df); +} + +// QEq f*df, $E_{QEq} * (\partial E_{QEq} / \partial Q_i)$ +void FixHDNNP::QEq_fdf(const gsl_vector *v, double *f, gsl_vector *df) +{ + *f = QEq_f(v); + QEq_df(v, df); +} + +// QEq f*df - wrapper +void FixHDNNP::QEq_fdf_wrap(const gsl_vector *v, void *params, double *E, gsl_vector *df) +{ + static_cast(params)->QEq_fdf(v, E, df); +} + +// Main minimization routine +void FixHDNNP::calculate_QEqCharges() +{ + size_t iter = 0; + int status; + int i,j; + int nsize; + int nlocal; + int *tag = atom->tag; + + double *q = atom->q; + double qsum_it; + double gradsum; + double qi; + double df,alpha; + + nsize = atom->natoms; // total number of atoms + nlocal = atom->nlocal; // total number of atoms + + gsl_vector *Q; // charge vector + QEq_minimizer.n = nsize; // it should be n_all in the future + QEq_minimizer.f = &QEq_f_wrap; // function pointer f(x) + QEq_minimizer.df = &QEq_df_wrap; // function pointer df(x) + QEq_minimizer.fdf = &QEq_fdf_wrap; + QEq_minimizer.params = this; + + //fprintf(stderr, "q[%d] = %24.16E\n", atom->tag[0], q[0]); + + // Allocation + //memory->create(qall,atom->natoms,"qeq:qall"); + //memory->create(qall_loc,atom->natoms,"qeq:qall_loc"); + //memory->create(dEdQ_loc,atom->natoms,"qeq:dEdQ_loc"); + //memory->create(dEdQ_all,atom->natoms,"qeq:dEdQ_all"); + + // Initialization + for (int i =0; i < atom->natoms; i++){ + qall[i] = 0.0; + qall_loc[i] = 0.0; + dEdQ_loc[i] = 0.0; + dEdQ_all[i] = 0.0; + } + + for (int i = 0; i < atom->nlocal; i++) { + qall_loc[tag[i] - 1] = q[i]; + } + + MPI_Allreduce(qall_loc,qall,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + + if (!periodic) // we need global position arrays in nonperiodic systems + { + // Initialize global arrays + for (int i = 0; i < atom->natoms; i++){ + type_loc[i] = 0; + xx_loc[i] = 0.0; + xy_loc[i] = 0.0; + xz_loc[i] = 0.0; + xx[i] = 0.0; + xy[i] = 0.0; + xz[i] = 0.0; + } + + // Create global sparse arrays here + for (int i = 0; i < atom->nlocal; i++){ + xx_loc[tag[i]-1] = atom->x[i][0]; + xy_loc[tag[i]-1] = atom->x[i][1]; + xz_loc[tag[i]-1] = atom->x[i][2]; + type_loc[tag[i]-1] = atom->type[i]; + } + MPI_Allreduce(xx_loc,xx,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(xy_loc,xy,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(xz_loc,xz,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(type_loc,type_all,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + } + + + // Set the initial guess vector + Q = gsl_vector_alloc(nsize); + for (i = 0; i < nsize; i++) + { + if (hdnnp->minim_init_style == 0) + { + gsl_vector_set(Q, i, 0.0); + }else if (hdnnp->minim_init_style == 1) + { + gsl_vector_set(Q, i, qall[i]); + }else + { + error->all(FLERR,"Invalid minimization style. Allowed values are 0 and 1."); + } + } + + //memory->destroy(qall); + //memory->destroy(qall_loc); + + // TODO: is bfgs2 standard ? + T = gsl_multimin_fdfminimizer_vector_bfgs2; + s = gsl_multimin_fdfminimizer_alloc(T, nsize); + gsl_multimin_fdfminimizer_set(s, &QEq_minimizer, Q, hdnnp->step, hdnnp->min_tol); // tol = 0 might be expensive ??? + do + { + //fprintf(stderr, "eqeq-iter %zu\n", iter); + iter++; + qsum_it = 0.0; + gradsum = 0.0; + status = gsl_multimin_fdfminimizer_iterate(s); + // Projection (enforcing constraints) + // TODO: could this be done more efficiently ? + for(i = 0; i < nsize; i++) { + qsum_it = qsum_it + gsl_vector_get(s->x, i); // total charge after the minimization hdnnp->step + } + for(i = 0; i < nsize; i++) { + qi = gsl_vector_get(s->x,i); + gsl_vector_set(s->x,i, qi - (qsum_it-qRef)/nsize); // charge projection + } + status = gsl_multimin_test_gradient(s->gradient, hdnnp->grad_tol); // check for convergence + + // TODO: dump also iteration time ? + //if (status == GSL_SUCCESS) printf ("Minimum charge distribution is found at iteration : %zu\n", iter); + } + while (status == GSL_CONTINUE && iter < hdnnp->maxit); + + // Read calculated atomic charges back into local arrays for further calculations + for (int i = 0; i < atom->nlocal; i++){ + q[i] = gsl_vector_get(s->x,tag[i]-1); + } + + // Deallocation + gsl_multimin_fdfminimizer_free(s); + gsl_vector_free(Q); + //memory->destroy(dEdQ_loc); + //memory->destroy(dEdQ_all); +} + +// Check if the system is periodic +void FixHDNNP::isPeriodic() +{ + if (domain->nonperiodic == 0) periodic = true; + else periodic = false; +} diff --git a/src/interface/LAMMPS/src/ML-HDNNP/fix_hdnnp.h b/src/interface/LAMMPS/src/ML-HDNNP/fix_hdnnp.h new file mode 100644 index 0000000000..3bc074e83c --- /dev/null +++ b/src/interface/LAMMPS/src/ML-HDNNP/fix_hdnnp.h @@ -0,0 +1,125 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +#ifdef FIX_CLASS + +FixStyle(hdnnp,FixHDNNP) + +#else + +#ifndef LMP_FIX_HDNNP_H +#define LMP_FIX_HDNNP_H + +#include +#include "fix.h" +#include "InterfaceLammps.h" + + +namespace LAMMPS_NS { + + class FixHDNNP : public Fix { + friend class PairHDNNP4G; + public: + FixHDNNP(class LAMMPS *, int, char **); + ~FixHDNNP(); + + int setmask(); + virtual void post_constructor(); + virtual void init(); + void init_list(int,class NeighList *); + void setup_pre_force(int); + virtual void pre_force(int); + + void min_setup_pre_force(int); + void min_pre_force(int); + + protected: + + class PairHDNNP4G *hdnnp; // interface to HDNNP pair_style + class KSpaceHDNNP *kspacehdnnp; // interface to HDNNP kspace_style + class NeighList *list; + char *pertype_option; + + int hdnnpflag; + int kspaceflag; // 0:Ewald Sum, 1:PPPM + int ngroup; + + bool periodic; // true if periodic + double qRef; // total reference charge of the system + double *Q; + + virtual void pertype_parameters(char*); + void isPeriodic(); // check for periodicity + void calculate_electronegativities(); // calculates electronegatives via running first set of NNs + void process_first_network(); // interfaces to n2p2 and runs first NN + void allocate_QEq(); // allocates QEq arrays + void deallocate_QEq(); // deallocates QEq arrays + + /// QEq energy minimization via gsl library + + gsl_multimin_function_fdf QEq_minimizer; // minimizer object + const gsl_multimin_fdfminimizer_type *T; + gsl_multimin_fdfminimizer *s; + + double QEq_f(const gsl_vector*); // f : QEq energy as a function of atomic charges + void QEq_df(const gsl_vector*, gsl_vector*); // df : Gradient of QEq energy with respect to atomic charges + void QEq_fdf(const gsl_vector*, double*, gsl_vector*); // f * df + + static double QEq_f_wrap(const gsl_vector*, void*); // wrapper of f + static void QEq_df_wrap(const gsl_vector*, void*, gsl_vector*); // wrapper of df + static void QEq_fdf_wrap(const gsl_vector*, void*, double*, gsl_vector*); // wrapper of f * df + + void calculate_QEqCharges(); // main function where minimization happens + + void calculate_erfc_terms(); // loops over neighbors of local atoms and calculates erfc terms + // these consume the most time. Storing them speeds up calculations + + /// Global storage + int *type_all,*type_loc; + double *qall,*qall_loc; + double *dEdQ_all,*dEdQ_loc; // gradient of the charge equilibration energy wrt charges + double *xx,*xy,*xz; // global positions (here only for nonperiodic case) + double *xx_loc,*xy_loc,*xz_loc; // sparse local positions (here only for nonperiodic case) + + + /* Matrix Approach (DEPRECATED and to be deleted) + int nevery,hdnnpflag; + int n, N, m_fill; + int n_cap, m_cap; + int pack_flag; + bigint ngroup; + int nprev; + double **Q_hist; + double *p, *q, *r, *d; + virtual int pack_forward_comm(int, int *, double *, int, int *); + virtual void unpack_forward_comm(int, int, double *); + virtual int pack_reverse_comm(int, int, double *); + virtual void unpack_reverse_comm(int, int *, double *); + virtual double memory_usage(); + virtual void grow_arrays(int); + virtual void copy_arrays(int, int, int); + virtual int pack_exchange(int, double *); + virtual int unpack_exchange(int, double *); + + virtual double parallel_norm( double*, int ); + virtual double parallel_dot( double*, double*, int ); + virtual double parallel_vector_acc( double*, int ); + + virtual void vector_sum(double*,double,double*,double,double*,int); + virtual void vector_add(double*, double, double*,int);*/ + + }; + +} + +#endif +#endif diff --git a/src/interface/LAMMPS/src/ML-HDNNP/kspace_hdnnp.cpp b/src/interface/LAMMPS/src/ML-HDNNP/kspace_hdnnp.cpp new file mode 100644 index 0000000000..fd338facb6 --- /dev/null +++ b/src/interface/LAMMPS/src/ML-HDNNP/kspace_hdnnp.cpp @@ -0,0 +1,2111 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "kspace_hdnnp.h" + +#include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fft3d_wrap.h" +#include "force.h" +#include "grid3d.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" +#include "remap_wrap.h" +#include "fix_hdnnp.h" +#include "pair_hdnnp_4g.h" + +#include +#include +#include + +using namespace LAMMPS_NS; +using namespace MathConst; +using namespace MathSpecial; +using namespace std; + +#define MAXORDER 7 +#define OFFSET 16384 +#define LARGE 10000.0 +#define SMALL 0.00001 +#define EPS_HOC 1.0e-7 + +enum{REVERSE_RHO}; +enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM}; + +#ifdef FFT_SINGLE +#define ZEROF 0.0f +#define ONEF 1.0f +#else +#define ZEROF 0.0 +#define ONEF 1.0 +#endif + +/* ---------------------------------------------------------------------- */ + +KSpaceHDNNP::KSpaceHDNNP(LAMMPS *lmp) : KSpace(lmp), + kxvecs(nullptr), kyvecs(nullptr), kzvecs(nullptr), kcoeff(nullptr), ug(nullptr), eg(nullptr), vg(nullptr), + ek(nullptr), sfexp_rl(nullptr), sfexp_im(nullptr), sf_real(nullptr), sf_im(nullptr), + sfexp_rl_all(nullptr),sfexp_im_all(nullptr), + cs(nullptr), sn(nullptr), factors(nullptr), + density_brick(nullptr), vdx_brick(nullptr), + vdy_brick(nullptr), vdz_brick(nullptr),u_brick(nullptr), v0_brick(nullptr), v1_brick(nullptr), + v2_brick(nullptr), v3_brick(nullptr),v4_brick(nullptr), v5_brick(nullptr), greensfn(nullptr), + fkx(nullptr), fky(nullptr), fkz(nullptr), density_fft(nullptr), work1(nullptr), + work2(nullptr), gf_b(nullptr), rho1d(nullptr), + rho_coeff(nullptr), drho1d(nullptr), drho_coeff(nullptr), + sf_precoeff1(nullptr), sf_precoeff2(nullptr), sf_precoeff3(nullptr), + sf_precoeff4(nullptr), sf_precoeff5(nullptr), sf_precoeff6(nullptr), + acons(nullptr), fft1(nullptr), fft2(nullptr), remap(nullptr), gc(nullptr), + gc_buf1(nullptr), gc_buf2(nullptr), part2grid(nullptr), boxlo(nullptr) +{ + hdnnp = nullptr; + hdnnp = (PairHDNNP4G *) force->pair_match("^hdnnp/4g",0); + + ewaldflag = pppmflag = 0; // TODO check + + eflag_global = 1; // calculate global energy + + //// EWALD + kewaldflag = 0; + kmax_created = 0; + + kmax = 0; + kxvecs = kyvecs = kzvecs = nullptr; + kcoeff = nullptr; + ug = nullptr; + eg = vg = nullptr; + ek = nullptr; + + sfexp_rl = sfexp_im = nullptr; + sf_im = sf_real = nullptr; + sfexp_rl_all = sfexp_im_all = nullptr; + cs = sn = nullptr; + + kcount = 0; + + //// PPPM + peratom_allocate_flag = 0; + //group_allocate_flag = 0; + + group_group_enable = 1; + triclinic = domain->triclinic; + + //TODO: add a flag-check for these initializations + nfactors = 3; + factors = new int[nfactors]; + factors[0] = 2; + factors[1] = 3; + factors[2] = 5; + + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); + + nfft_both = 0; + nxhi_in = nxlo_in = nxhi_out = nxlo_out = 0; + nyhi_in = nylo_in = nyhi_out = nylo_out = 0; + nzhi_in = nzlo_in = nzhi_out = nzlo_out = 0; + + density_brick = vdx_brick = vdy_brick = vdz_brick = nullptr; + vx_brick = vy_brick = vz_brick = nullptr; + density_fft = nullptr; + u_brick = nullptr; + v0_brick = v1_brick = v2_brick = v3_brick = v4_brick = v5_brick = nullptr; + greensfn = nullptr; + work1 = work2 = nullptr; + vg = nullptr; + fkx = fky = fkz = nullptr; + + sf_precoeff1 = sf_precoeff2 = sf_precoeff3 = + sf_precoeff4 = sf_precoeff5 = sf_precoeff6 = nullptr; + + gf_b = nullptr; + rho1d = rho_coeff = drho1d = drho_coeff = nullptr; + + fft1 = fft2 = nullptr; + remap = nullptr; + gc = nullptr; + gc_buf1 = gc_buf2 = nullptr; + + nmax = 0; + part2grid = nullptr; + + // define acons coefficients for estimation of kspace errors + // see JCP 109, pg 7698 for derivation of coefficients + // higher order coefficients may be computed if needed + + memory->create(acons,8,7,"pppm:acons"); + acons[1][0] = 2.0 / 3.0; + acons[2][0] = 1.0 / 50.0; + acons[2][1] = 5.0 / 294.0; + acons[3][0] = 1.0 / 588.0; + acons[3][1] = 7.0 / 1440.0; + acons[3][2] = 21.0 / 3872.0; + acons[4][0] = 1.0 / 4320.0; + acons[4][1] = 3.0 / 1936.0; + acons[4][2] = 7601.0 / 2271360.0; + acons[4][3] = 143.0 / 28800.0; + acons[5][0] = 1.0 / 23232.0; + acons[5][1] = 7601.0 / 13628160.0; + acons[5][2] = 143.0 / 69120.0; + acons[5][3] = 517231.0 / 106536960.0; + acons[5][4] = 106640677.0 / 11737571328.0; + acons[6][0] = 691.0 / 68140800.0; + acons[6][1] = 13.0 / 57600.0; + acons[6][2] = 47021.0 / 35512320.0; + acons[6][3] = 9694607.0 / 2095994880.0; + acons[6][4] = 733191589.0 / 59609088000.0; + acons[6][5] = 326190917.0 / 11700633600.0; + acons[7][0] = 1.0 / 345600.0; + acons[7][1] = 3617.0 / 35512320.0; + acons[7][2] = 745739.0 / 838397952.0; + acons[7][3] = 56399353.0 / 12773376000.0; + acons[7][4] = 25091609.0 / 1560084480.0; + acons[7][5] = 1755948832039.0 / 36229939200000.0; + acons[7][6] = 4887769399.0 / 37838389248.0; +} + +/* ---------------------------------------------------------------------- */ + +void KSpaceHDNNP::settings(int narg, char **arg) +{ + if (narg < 2) error->all(FLERR,"Illegal kspace_style hdnnp command"); // we have two params, not one (style + FP) + + if (strcmp(arg[0],"pppm") == 0) pppmflag = 1; + else if (strcmp(arg[0],"ewald") == 0) ewaldflag = 1; + else error->all(FLERR,"Illegal kspace_style hdnnp command"); + + accuracy_relative = fabs(utils::numeric(FLERR,arg[1],false,lmp)); +} + +/* ---------------------------------------------------------------------- + free all memory +------------------------------------------------------------------------- */ + +KSpaceHDNNP::~KSpaceHDNNP() +{ + if (pppmflag) + { + deallocate(); + if (copymode) return; + delete [] factors; + //if (peratom_allocate_flag) deallocate_peratom(); + //if (group_allocate_flag) deallocate_groups(); + memory->destroy(part2grid); + memory->destroy(acons); + } + else if (ewaldflag) + { + deallocate(); + //if (group_allocate_flag) deallocate_groups(); + memory->destroy(ek); + //memory->destroy(acons); + memory->destroy3d_offset(cs,-kmax_created); + memory->destroy3d_offset(sn,-kmax_created); + } +} + +/* ---------------------------------------------------------------------- + called once before run +------------------------------------------------------------------------- */ + +void KSpaceHDNNP::init() +{ + // Make initializations based on the selected k-space style + if (pppmflag) + { + if (me == 0) utils::logmesg(lmp,"PPPM initialization ...\n"); + + // TODO: add other error handlings in LAMMPS + + if (order < 2 || order > MAXORDER) + error->all(FLERR,fmt::format("PPPM order cannot be < 2 or > {}",MAXORDER)); + + // compute two charge force (?) + two_charge(); + + triclinic = domain->triclinic; + + // extract short-range Coulombic cutoff from pair style + cutoff = hdnnp->maxCutoffRadius; + + // compute qsum & qsqsum and warn if not charge-neutral + scale = 1.0; + qqrd2e = force->qqrd2e; + qsum_qsq(); + natoms_original = atom->natoms; + + if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute; + else accuracy = accuracy_relative * two_charge_force; + + // free all arrays previously allocated + deallocate(); + + //if (peratom_allocate_flag) deallocate_peratom(); + //if (group_allocate_flag) deallocate_groups(); + + Grid3d *gctmp = nullptr; + int iteration = 0; + + while (order >= minorder) { + if (iteration && me == 0) + error->warning(FLERR, "Reducing PPPM order b/c stencil extends " + "beyond nearest neighbor processor"); + + //compute_gf_denom(); //TODO: stagger ? + set_grid_global(); + set_grid_local(); + // overlap not allowed + + gctmp = new Grid3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, + nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, + nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out); + + int tmp1, tmp2; + gctmp->setup_comm(tmp1, tmp2); + if (gctmp->ghost_adjacent()) break; + delete gctmp; + + order--; + iteration++; + } + + if (order < minorder) error->all(FLERR,"PPPM order < minimum allowed order"); + if (!overlap_allowed && !gctmp->ghost_adjacent()) + error->all(FLERR,"PPPM grid stencil extends " + "beyond nearest neighbor processor"); + if (gctmp) delete gctmp; + + // adjust g_ewald TODO(kspace_modify) + if (!gewaldflag) adjust_gewald(); + + // calculate the final accuracy + double estimated_accuracy = final_accuracy(); + + // print stats + int ngrid_max,nfft_both_max; + MPI_Allreduce(&ngrid,&ngrid_max,1,MPI_INT,MPI_MAX,world); + MPI_Allreduce(&nfft_both,&nfft_both_max,1,MPI_INT,MPI_MAX,world); + + if (me == 0) { + std::string mesg = fmt::format(" G vector (1/distance) = {:.8g}\n",g_ewald); + mesg += fmt::format(" grid = {} {} {}\n",nx_pppm,ny_pppm,nz_pppm); + mesg += fmt::format(" stencil order = {}\n",order); + mesg += fmt::format(" estimated absolute RMS force accuracy = {:.8g}\n", + estimated_accuracy); + mesg += fmt::format(" estimated relative force accuracy = {:.8g}\n", + estimated_accuracy/two_charge_force); + mesg += " using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"; + mesg += fmt::format(" 3d grid and FFT values/proc = {} {}\n", + ngrid_max,nfft_both_max); + utils::logmesg(lmp,mesg); + } + + // allocate K-space dependent memory + // don't invoke allocate peratom() or group(), will be allocated when needed + allocate(); + + // pre-compute Green's function denomiator expansion + // pre-compute 1d charge distribution coefficients + // (differentiation_flag == 0) + compute_gf_denom(); + compute_rho_coeff(); + } + else if (ewaldflag) + { + if (comm->me == 0) utils::logmesg(lmp,"Ewald initialization ...\n"); + + // error check + //triclinic_check(); + if (domain->dimension == 2) + error->all(FLERR,"Cannot use Ewald with 2d simulation"); + if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); + if (slabflag == 0 && domain->nonperiodic > 0) + error->all(FLERR,"Cannot use non-periodic boundaries with Ewald"); + + //TODO: no slab yet + + // compute two charge force TODO:check + two_charge(); + + // extract short-range Coulombic cutoff from pair style + triclinic = domain->triclinic; + + // extract short-range Coulombic cutoff from pair style + cutoff = hdnnp->maxCutoffRadius; + + // compute qsum & qsqsum and warn if not charge-neutral TODO:check + scale = 1.0; + qqrd2e = force->qqrd2e; + qsum_qsq(); + natoms_original = atom->natoms; + + // Via the method in RuNNer (umgekehrt) + // LAMMPS uses a different methodology to calculate g_ewald + accuracy = accuracy_relative; + g_ewald = sqrt(-2.0 * log(accuracy)) / (cutoff*hdnnp->cflength); + + // setup Ewald coefficients + setup(); + } +} + +/* ---------------------------------------------------------------------- + adjust coeffs, called initially and whenever volume has changed +------------------------------------------------------------------------- */ + +void KSpaceHDNNP::setup() +{ + if (pppmflag) + { + // TODO: trcilinic & slab + // perform some checks to avoid illegal boundaries with read_data + + if (slabflag == 0 && domain->nonperiodic > 0) + error->all(FLERR,"Cannot use non-periodic boundaries with PPPM"); + if (slabflag) { + if (domain->xperiodic != 1 || domain->yperiodic != 1 || + domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) + error->all(FLERR,"Incorrect boundaries with slab PPPM"); + } + + int i,j,k,n; + double *prd; + + // volume-dependent factors + // adjust z dimension for 2d slab PPPM + // z dimension for 3d PPPM is zprd since slab_volfactor = 1.0 + + //triclinic = 0 TODO:check + + // WARNING: Immediately convert to HDNNP units! + // volume-dependent factors + prd = domain->prd; + double xprd = prd[0] * hdnnp->cflength; + double yprd = prd[1] * hdnnp->cflength; + double zprd = prd[2] * hdnnp->cflength; + volume = xprd * yprd * zprd; + + delxinv = nx_pppm/xprd; + delyinv = ny_pppm/yprd; + delzinv = nz_pppm/zprd; + + delvolinv = delxinv*delyinv*delzinv; + + double unitkx = (MY_2PI/xprd); + double unitky = (MY_2PI/yprd); + double unitkz = (MY_2PI/zprd); + + // fkx,fky,fkz for my FFT grid pts + + double per; + + for (i = nxlo_fft; i <= nxhi_fft; i++) { + per = i - nx_pppm*(2*i/nx_pppm); + fkx[i] = unitkx*per; + } + + for (i = nylo_fft; i <= nyhi_fft; i++) { + per = i - ny_pppm*(2*i/ny_pppm); + fky[i] = unitky*per; + } + + for (i = nzlo_fft; i <= nzhi_fft; i++) { + per = i - nz_pppm*(2*i/nz_pppm); + fkz[i] = unitkz*per; + } + + // virial coefficients TODO + + /*double sqk,vterm; + + n = 0; + for (k = nzlo_fft; k <= nzhi_fft; k++) { + for (j = nylo_fft; j <= nyhi_fft; j++) { + for (i = nxlo_fft; i <= nxhi_fft; i++) { + sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k]; + if (sqk == 0.0) { + vg[n][0] = 0.0; + vg[n][1] = 0.0; + vg[n][2] = 0.0; + vg[n][3] = 0.0; + vg[n][4] = 0.0; + vg[n][5] = 0.0; + } else { + vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald)); + vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i]; + vg[n][1] = 1.0 + vterm*fky[j]*fky[j]; + vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k]; + vg[n][3] = vterm*fkx[i]*fky[j]; + vg[n][4] = vterm*fkx[i]*fkz[k]; + vg[n][5] = vterm*fky[j]*fkz[k]; + } + n++; + } + } + }*/ + + compute_gf_ik(); // diff option 'ik' is selected + } + else if (ewaldflag) + { + // WARNING: Immediately convert to HDNNP units! + // volume-dependent factors + double const xprd = domain->xprd * hdnnp->cflength; + double const yprd = domain->yprd * hdnnp->cflength; + double const zprd = domain->zprd * hdnnp->cflength; + volume = xprd * yprd * zprd; + + //TODO: slab feature + + unitk[0] = 2.0*MY_PI/xprd; + unitk[1] = 2.0*MY_PI/yprd; + unitk[2] = 2.0*MY_PI/zprd; + + // Get k-space resolution via the method in RuNNer + ewald_recip_cutoff = sqrt(-2.0 * log(accuracy)) * g_ewald; + //ewald_real_cutoff = sqrt(-2.0 * log(accuracy)) / g_ewald; + ewald_real_cutoff = cutoff * hdnnp->cflength; // we skip the calculation + + //std::cout << "recip cut:" << ewald_recip_cutoff << '\n'; + //std::cout << "real cut: " << ewald_real_cutoff << '\n'; + //std::cout << "eta: " << 1 / g_ewald << '\n'; + + int kmax_old = kmax; + kxmax = kymax = kzmax = 1; + + ewald_pbc(ewald_recip_cutoff); // get kxmax, kymax and kzmax + gsqmx = ewald_recip_cutoff * ewald_recip_cutoff; + + kmax = MAX(kxmax,kymax); + kmax = MAX(kmax,kzmax); + kmax3d = 4*kmax*kmax*kmax + 6*kmax*kmax + 3*kmax; + + // size change ? + kxmax_orig = kxmax; + kymax_orig = kymax; + kzmax_orig = kzmax; + + //allocate(); + // if size has grown, reallocate k-dependent and nlocal-dependent arrays + if (kmax > kmax_old) { + deallocate(); + allocate(); + memory->destroy(ek); + memory->destroy3d_offset(cs,-kmax_created); + memory->destroy3d_offset(sn,-kmax_created); + nmax = atom->nmax; + memory->create(ek,nmax,3,"ewald:ek"); + memory->create3d_offset(cs,-kmax,kmax,3,nmax,"ewald:cs"); + memory->create3d_offset(sn,-kmax,kmax,3,nmax,"ewald:sn"); + kmax_created = kmax; + } + + // pre-compute Ewald coefficients and structure factor arrays + ewald_coeffs(); + //ewald_sfexp(); + } +} + +// compute RMS accuracy for a dimension TODO: do we need this ? +double KSpaceHDNNP::rms(int km, double prd, bigint natoms, double q2) +{ + + if (natoms == 0) natoms = 1; // avoid division by zero + double value = 2.0*q2*g_ewald/prd * + sqrt(1.0/(MY_PI*km*natoms)) * + exp(-MY_PI*MY_PI*km*km/(g_ewald*g_ewald*prd*prd)); + + return value; +} + +// Calculate Ewald coefficients +void KSpaceHDNNP::ewald_coeffs() +{ + int k,l,m; + double sqk,vterm; + double preu = 4.0*M_PI/volume; + double etasq; + + etasq = 1.0 / (g_ewald*g_ewald); // LAMMPS truncation (RuNNer truncations has been removed) + + kcount = 0; + + // (k,0,0), (0,l,0), (0,0,m) + + for (m = 1; m <= kmax; m++) { + sqk = (m*unitk[0]) * (m*unitk[0]); + if (sqk <= gsqmx) { + //fprintf(stderr, "sqk 1x = %24.16E, m %d\n", sqrt(sqk), m); + kxvecs[kcount] = m; + kyvecs[kcount] = 0; + kzvecs[kcount] = 0; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + } + sqk = (m*unitk[1]) * (m*unitk[1]); + if (sqk <= gsqmx) { + //fprintf(stderr, "sqk 1y = %24.16E, m %d\n", sqrt(sqk), m); + kxvecs[kcount] = 0; + kyvecs[kcount] = m; + kzvecs[kcount] = 0; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + } + sqk = (m*unitk[2]) * (m*unitk[2]); + if (sqk <= gsqmx) { + //fprintf(stderr, "sqk 1z = %24.16E, m %d\n", sqrt(sqk), m); + kxvecs[kcount] = 0; + kyvecs[kcount] = 0; + kzvecs[kcount] = m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + } + } + + // 1 = (k,l,0), 2 = (k,-l,0) + + for (k = 1; k <= kxmax; k++) { + for (l = 1; l <= kymax; l++) { + sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[1]*l) * (unitk[1]*l); + if (sqk <= gsqmx) { + //fprintf(stderr, "sqk 2 = %24.16E, k %d l %d\n", sqrt(sqk), k, l); + kxvecs[kcount] = k; + kyvecs[kcount] = l; + kzvecs[kcount] = 0; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + + //fprintf(stderr, "sqk 2 = %24.16E, k %d -l %d\n", sqrt(sqk), k, l); + kxvecs[kcount] = k; + kyvecs[kcount] = -l; + kzvecs[kcount] = 0; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++;; + } + } + } + + // 1 = (0,l,m), 2 = (0,l,-m) + + for (l = 1; l <= kymax; l++) { + for (m = 1; m <= kzmax; m++) { + sqk = (unitk[1]*l) * (unitk[1]*l) + (unitk[2]*m) * (unitk[2]*m); + if (sqk <= gsqmx) { + //fprintf(stderr, "sqk 3 = %24.16E, l %d m %d\n", sqrt(sqk), l, m); + kxvecs[kcount] = 0; + kyvecs[kcount] = l; + kzvecs[kcount] = m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + + //fprintf(stderr, "sqk 3 = %24.16E, l %d -m %d\n", sqrt(sqk), l, m); + kxvecs[kcount] = 0; + kyvecs[kcount] = l; + kzvecs[kcount] = -m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + } + } + } + + // 1 = (k,0,m), 2 = (k,0,-m) + + for (k = 1; k <= kxmax; k++) { + for (m = 1; m <= kzmax; m++) { + sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[2]*m) * (unitk[2]*m); + if (sqk <= gsqmx) { + //fprintf(stderr, "sqk 4 = %24.16E, k %d m %d\n", sqrt(sqk), k, m); + kxvecs[kcount] = k; + kyvecs[kcount] = 0; + kzvecs[kcount] = m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + + //fprintf(stderr, "sqk 4 = %24.16E, k %d -m %d\n", sqrt(sqk), k, m); + kxvecs[kcount] = k; + kyvecs[kcount] = 0; + kzvecs[kcount] = -m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + } + } + } + + // 1 = (k,l,m), 2 = (k,-l,m), 3 = (k,l,-m), 4 = (k,-l,-m) + + for (k = 1; k <= kxmax; k++) { + for (l = 1; l <= kymax; l++) { + for (m = 1; m <= kzmax; m++) { + sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[1]*l) * (unitk[1]*l) + + (unitk[2]*m) * (unitk[2]*m); + if (sqk <= gsqmx) { + //fprintf(stderr, "sqk 5 = %24.16E, k %d l %d m %d\n", sqrt(sqk), k, l, m); + kxvecs[kcount] = k; + kyvecs[kcount] = l; + kzvecs[kcount] = m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + + //fprintf(stderr, "sqk 5 = %24.16E, k %d -l %d m %d\n", sqrt(sqk), k, l, m); + kxvecs[kcount] = k; + kyvecs[kcount] = -l; + kzvecs[kcount] = m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + + //fprintf(stderr, "sqk 5 = %24.16E, k %d l %d -m %d\n", sqrt(sqk), k, l, m); + kxvecs[kcount] = k; + kyvecs[kcount] = l; + kzvecs[kcount] = -m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + + //fprintf(stderr, "sqk 5 = %24.16E, k %d -l %d -m %d\n", sqrt(sqk), k, l, m); + kxvecs[kcount] = k; + kyvecs[kcount] = -l; + kzvecs[kcount] = -m; + kcoeff[kcount] = preu*exp(-0.5*sqk*etasq)/sqk; + kcount++; + } + } + } + } +} + +// Calculate Ewald structure factors +void KSpaceHDNNP::ewald_sfexp() +{ + int i,k,l,m,n,ic; + double sqk,clpm,slpm; + + double **x = atom->x; + int nlocal = atom->nlocal; + double cflength; + + n = 0; + cflength = hdnnp->cflength; // RuNNer truncation (conversion required) + + // (k,0,0), (0,l,0), (0,0,m) + + for (ic = 0; ic < 3; ic++) { + sqk = unitk[ic]*unitk[ic]; + if (sqk <= gsqmx) { + for (i = 0; i < nlocal; i++) { + cs[0][ic][i] = 1.0; + sn[0][ic][i] = 0.0; + cs[1][ic][i] = cos(unitk[ic]*x[i][ic]*cflength); + sn[1][ic][i] = sin(unitk[ic]*x[i][ic]*cflength); + cs[-1][ic][i] = cs[1][ic][i]; + sn[-1][ic][i] = -sn[1][ic][i]; + sfexp_rl[n][i] = cs[1][ic][i]; + sfexp_im[n][i] = sn[1][ic][i]; + } + n++; + } + } + + for (m = 2; m <= kmax; m++) { + for (ic = 0; ic < 3; ic++) { + sqk = m*unitk[ic] * m*unitk[ic]; + if (sqk <= gsqmx) { + for (i = 0; i < nlocal; i++) { + cs[m][ic][i] = cs[m-1][ic][i]*cs[1][ic][i] - + sn[m-1][ic][i]*sn[1][ic][i]; + sn[m][ic][i] = sn[m-1][ic][i]*cs[1][ic][i] + + cs[m-1][ic][i]*sn[1][ic][i]; + cs[-m][ic][i] = cs[m][ic][i]; + sn[-m][ic][i] = -sn[m][ic][i]; + sfexp_rl[n][i] = cs[m][ic][i]; + sfexp_im[n][i] = sn[m][ic][i]; + } + n++; + } + } + } + + // 1 = (k,l,0), 2 = (k,-l,0) + + for (k = 1; k <= kxmax; k++) { + for (l = 1; l <= kymax; l++) { + sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]); + if (sqk <= gsqmx) { + for (i = 0; i < nlocal; i++) { + sfexp_rl[n][i] = (cs[k][0][i]*cs[l][1][i] - sn[k][0][i]*sn[l][1][i]); + sfexp_im[n][i] = (sn[k][0][i]*cs[l][1][i] + cs[k][0][i]*sn[l][1][i]); + } + n++; + for (i = 0; i < nlocal; i++) { + sfexp_rl[n][i] = (cs[k][0][i]*cs[l][1][i] + sn[k][0][i]*sn[l][1][i]); + sfexp_im[n][i] = (sn[k][0][i]*cs[l][1][i] - cs[k][0][i]*sn[l][1][i]); + } + n++; + } + } + } + + // 1 = (0,l,m), 2 = (0,l,-m) + + for (l = 1; l <= kymax; l++) { + for (m = 1; m <= kzmax; m++) { + sqk = (l*unitk[1] * l*unitk[1]) + (m*unitk[2] * m*unitk[2]); + if (sqk <= gsqmx) { + for (i = 0; i < nlocal; i++) { + sfexp_rl[n][i] = (cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]); + sfexp_im[n][i] = (sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]); + } + n++; + for (i = 0; i < nlocal; i++) { + sfexp_rl[n][i] = (cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]); + sfexp_im[n][i] = (sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]); + } + n++; + } + } + } + + // 1 = (k,0,m), 2 = (k,0,-m) + + for (k = 1; k <= kxmax; k++) { + for (m = 1; m <= kzmax; m++) { + sqk = (k*unitk[0] * k*unitk[0]) + (m*unitk[2] * m*unitk[2]); + if (sqk <= gsqmx) { + for (i = 0; i < nlocal; i++) { + sfexp_rl[n][i] = (cs[k][0][i]*cs[m][2][i] - sn[k][0][i]*sn[m][2][i]); + sfexp_im[n][i] = (sn[k][0][i]*cs[m][2][i] + cs[k][0][i]*sn[m][2][i]); + } + n++; + for (i = 0; i < nlocal; i++) { + sfexp_rl[n][i] = (cs[k][0][i]*cs[m][2][i] + sn[k][0][i]*sn[m][2][i]); + sfexp_im[n][i] = (sn[k][0][i]*cs[m][2][i] - cs[k][0][i]*sn[m][2][i]); + } + n++; + } + } + } + + // 1 = (k,l,m), 2 = (k,-l,m), 3 = (k,l,-m), 4 = (k,-l,-m) + + for (k = 1; k <= kxmax; k++) { + for (l = 1; l <= kymax; l++) { + for (m = 1; m <= kzmax; m++) { + sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]) + + (m*unitk[2] * m*unitk[2]); + if (sqk <= gsqmx) { + for (i = 0; i < nlocal; i++) { + clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; + slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; + sfexp_rl[n][i] = (cs[k][0][i]*clpm - sn[k][0][i]*slpm); + sfexp_im[n][i] = (sn[k][0][i]*clpm + cs[k][0][i]*slpm); + } + n++; + for (i = 0; i < nlocal; i++) { + clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; + slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; + sfexp_rl[n][i] = (cs[k][0][i]*clpm - sn[k][0][i]*slpm); + sfexp_im[n][i] = (sn[k][0][i]*clpm + cs[k][0][i]*slpm); + } + n++; + for (i = 0; i < nlocal; i++) { + clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; + slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; + sfexp_rl[n][i] = (cs[k][0][i]*clpm - sn[k][0][i]*slpm); + sfexp_im[n][i] = (sn[k][0][i]*clpm + cs[k][0][i]*slpm); + } + n++; + for (i = 0; i < nlocal; i++) { + clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; + slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; + sfexp_rl[n][i] = (cs[k][0][i]*clpm - sn[k][0][i]*slpm); + sfexp_im[n][i] = (sn[k][0][i]*clpm + cs[k][0][i]*slpm); + } + n++; + } + } + } + } + +} + +// Compute E_QEQ (recip) in PPPM TODO:WIP +double KSpaceHDNNP::compute_pppm_eqeq() +{ + + // all procs communicate density values from their ghost cells + // to fully sum contribution in their 3d bricks + // remap from 3d decomposition to FFT decomposition + + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); + brick2fft(); + + // compute potential V(r) on my FFT grid and + // portion of e_long on this proc's FFT grid + // return potentials 3d brick decomposition + + std::cout << energy << '\n'; + poisson(); + + std::cout << energy << '\n'; + exit(0); + + // all procs communicate E-field values + // to fill ghost cells surrounding their 3d bricks + // TODO check + // differentiation_flag == 0 + + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); + + // sum global energy across procs and add in volume-dependent term + + const double qscale = qqrd2e * scale; + + if (eflag_global) { + double energy_all; + MPI_Allreduce(&energy, &energy_all, 1, MPI_DOUBLE, MPI_SUM, world); + energy = energy_all; + + energy *= 0.5 * volume; + energy -= g_ewald * qsqsum / MY_PIS + + MY_PI2 * qsum * qsum / (g_ewald * g_ewald * volume); + energy *= qscale; + } + + std::cout << "here" << '\n'; + //std::cout << qscale << '\n'; + std::cout << MY_PIS << '\n'; + std::cout << MY_PI2 << '\n'; + //std::cout << qsum << '\n'; + //std::cout << g_ewald << '\n'; + //std::cout << energy << '\n'; + exit(0); + + return energy; +} + +// Returns dE_qeq/dQ_i in PPPM for a given local atom i (inx) +double KSpaceHDNNP::compute_pppm_dEdQ(int inx) +{ + int i,l,m,n,nx,ny,nz,mx,my,mz; + FFT_SCALAR dx,dy,dz,x0,y0,z0; + FFT_SCALAR dEdQx,dEdQy,dEdQz; + + // loop over my charges, interpolate dEdQ from nearby grid points + // (nx,ny,nz) = global coords of grid pt to "lower left" of charge + // (dx,dy,dz) = distance to "lower left" grid pt + // (mx,my,mz) = global coords of moving stencil pt + // ek = 3 components of E-field on particle + + double *q = atom->q; + double **x = atom->x; + double **f = atom->f; + + double dEdQ; + + int nlocal = atom->nlocal; + + nx = part2grid[inx][0]; + ny = part2grid[inx][1]; + nz = part2grid[inx][2]; + dx = nx + shiftone - (x[inx][0] - boxlo[0]) * delxinv; + dy = ny + shiftone - (x[inx][1] - boxlo[1]) * delyinv; + dz = nz + shiftone - (x[inx][2] - boxlo[2]) * delzinv; + + compute_rho1d(dx, dy, dz); + + dEdQx = dEdQy = dEdQz = ZEROF; + for (n = nlower; n <= nupper; n++) { + mz = n + nz; + z0 = rho1d[2][n]; + for (m = nlower; m <= nupper; m++) { + my = m + ny; + y0 = z0 * rho1d[1][m]; + for (l = nlower; l <= nupper; l++) { + mx = l + nx; + x0 = y0 * rho1d[0][l]; + dEdQx -= x0 * vx_brick[mz][my][mx]; + dEdQy -= x0 * vy_brick[mz][my][mx]; + dEdQz -= x0 * vz_brick[mz][my][mx]; + } + } + } + + dEdQ = sqrt(dEdQx*dEdQx + dEdQy*dEdQy + dEdQz*dEdQz); + + std::cout << dEdQ << '\n'; + + + /*for (i = 0; i < nlocal; i++) { + nx = part2grid[i][0]; + ny = part2grid[i][1]; + nz = part2grid[i][2]; + dx = nx + shiftone - (x[i][0] - boxlo[0]) * delxinv; + dy = ny + shiftone - (x[i][1] - boxlo[1]) * delyinv; + dz = nz + shiftone - (x[i][2] - boxlo[2]) * delzinv; + + compute_rho1d(dx, dy, dz); + + dEdQx = dEdQy = dEdQz = ZEROF; + for (n = nlower; n <= nupper; n++) { + mz = n + nz; + z0 = rho1d[2][n]; + for (m = nlower; m <= nupper; m++) { + my = m + ny; + y0 = z0 * rho1d[1][m]; + for (l = nlower; l <= nupper; l++) { + mx = l + nx; + x0 = y0 * rho1d[0][l]; + dEdQx -= x0 * vx_brick[mz][my][mx]; + dEdQy -= x0 * vy_brick[mz][my][mx]; + dEdQz -= x0 * vz_brick[mz][my][mx]; + } + } + } + }*/ + + return dEdQ; +} + +// Compute E_QEQ (recip) in Ewald +double KSpaceHDNNP::compute_ewald_eqeq(const gsl_vector *v) +{ + int i; + int nlocal = atom->nlocal; + int *tag = atom->tag; + double E_recip; + + + E_recip = 0.0; + for (int k = 0; k < kcount; k++) // over k-space + { + //fprintf(stderr, "kcoeff[%d] = %24.16E\n", k, hdnnp->kcoeff[k]); + double sf_real_loc = 0.0; + double sf_im_loc = 0.0; + sf_real[k] = 0.0; + sf_im[k] = 0.0; + // TODO: this loop over all atoms can be replaced by a MPIallreduce ? + for (i = 0; i < nlocal; i++) + { + double const qi = gsl_vector_get(v,tag[i]-1); + sf_real_loc += qi * sfexp_rl[k][i]; + sf_im_loc += qi * sfexp_im[k][i]; + } + //fprintf(stderr, "sfexp %d : %24.16E\n", k, hdnnp->kcoeff[k] * (pow(sf_real,2) + pow(sf_im,2))); + MPI_Allreduce(&(sf_real_loc),&(sf_real[k]),1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&(sf_im_loc),&(sf_im[k]),1,MPI_DOUBLE,MPI_SUM,world); + E_recip += kcoeff[k] * (pow(sf_real[k],2) + pow(sf_im[k],2)); + } + + return E_recip; +} + +// TODO: this is called after the force->pair->compute calculations in verlet.cpp +// therefore we cannot make use of it as it is +void KSpaceHDNNP::compute(int eflag, int vflag) +{ + // Carry out k-space computations based on the selected method + if (pppmflag) + { + + } + else if (ewaldflag) + { + + } +} + +void KSpaceHDNNP::allocate() +{ + // Make allocations based on the selected K-space method + if (pppmflag) + { + memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:density_brick"); + + memory->create(density_fft,nfft_both,"pppm:density_fft"); + memory->create(greensfn,nfft_both,"pppm:greensfn"); + memory->create(work1,2*nfft_both,"pppm:work1"); + memory->create(work2,2*nfft_both,"pppm:work2"); + //memory->create(vg,nfft_both,6,"pppm:vg"); // TODO virial + + // triclinic = 0 TODO: triclinic systems ? + memory->create1d_offset(fkx,nxlo_fft,nxhi_fft,"pppm:fkx"); + memory->create1d_offset(fky,nylo_fft,nyhi_fft,"pppm:fky"); + memory->create1d_offset(fkz,nzlo_fft,nzhi_fft,"pppm:fkz"); + + // differentiation_flag = 0 + /*memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vdx_brick"); + memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vdy_brick"); + memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vdz_brick");*/ + + memory->create3d_offset(vx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vx_brick"); + memory->create3d_offset(vy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vy_brick"); + memory->create3d_offset(vz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vz_brick"); + + // summation coeffs + order_allocated = order; + memory->create(gf_b,order,"pppm:gf_b"); + memory->create2d_offset(rho1d,3,-order/2,order/2,"pppm:rho1d"); + memory->create2d_offset(drho1d,3,-order/2,order/2,"pppm:drho1d"); + memory->create2d_offset(rho_coeff,order,(1-order)/2,order/2,"pppm:rho_coeff"); + memory->create2d_offset(drho_coeff,order,(1-order)/2,order/2, + "pppm:drho_coeff"); + + // create 2 FFTs and a Remap + // 1st FFT keeps data in FFT decomposition + // 2nd FFT returns data in 3d brick decomposition + // remap takes data from 3d brick to FFT decomposition + + int tmp; + + fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, + nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, + nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, + 0,0,&tmp,collective_flag); + + fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, + nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, + nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + 0,0,&tmp,collective_flag); + + remap = new Remap(lmp,world, + nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, + 1,0,0,FFT_PRECISION,collective_flag); + + // create ghost grid object for rho and electric field communication + // also create 2 bufs for ghost grid cell comm, passed to GridComm methods + + gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, + nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + + gc->setup_comm(ngc_buf1,ngc_buf2); + npergrid = 3; + + memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1"); + memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); + } + else if (ewaldflag) + { + + //kxvecs = new int[kmax3d]; + //kyvecs = new int[kmax3d]; + //kzvecs = new int[kmax3d]; + //kcoeff = new int[kmax3d]; + + //sf_real = new double[kmax3d]; + //sf_im = new double[kmax3d]; + + //for(int i = 0; i < kmax3d; ++i){ + // sfexp_rl[i] = new int[nloc]; + // sfexp_im[i] = new int[nloc]; + //} + + memory->create(kxvecs,kmax3d,"ewald:kxvecs"); + memory->create(kyvecs,kmax3d,"ewald:kyvecs"); + memory->create(kzvecs,kmax3d,"ewald:kzvecs"); + memory->create(kcoeff,kmax3d,"ewald:kcoeff"); + + memory->create(sfexp_rl,kmax3d,atom->natoms,"ewald:sfexp_rl"); + memory->create(sfexp_im,kmax3d,atom->natoms,"ewald:sfexp_im"); + memory->create(sf_real,kmax3d,"ewald:sf_rl"); + memory->create(sf_im,kmax3d,"ewald:sf_im"); + + //memory->create(eg,kmax3d,3,"ewald:eg"); + //memory->create(vg,kmax3d,6,"ewald:vg"); // TODO: might be required for pressure + + } +} + +void KSpaceHDNNP::deallocate() +{ + // Make deallocations based on the selected K-space method + if (pppmflag) + { + memory->destroy3d_offset(density_brick,nzlo_out,nylo_out,nxlo_out); + + // differentiation_flag = 0 + /*memory->destroy3d_offset(vdx_brick,nzlo_out,nylo_out,nxlo_out); + memory->destroy3d_offset(vdy_brick,nzlo_out,nylo_out,nxlo_out); + memory->destroy3d_offset(vdz_brick,nzlo_out,nylo_out,nxlo_out);*/ + + memory->destroy3d_offset(vx_brick,nzlo_out,nylo_out,nxlo_out); + memory->destroy3d_offset(vy_brick,nzlo_out,nylo_out,nxlo_out); + memory->destroy3d_offset(vz_brick,nzlo_out,nylo_out,nxlo_out); + + memory->destroy(density_fft); + memory->destroy(greensfn); + memory->destroy(work1); + memory->destroy(work2); + memory->destroy(vg); + + memory->destroy1d_offset(fkx,nxlo_fft); + memory->destroy1d_offset(fky,nylo_fft); + memory->destroy1d_offset(fkz,nzlo_fft); + + memory->destroy(gf_b); + + memory->destroy2d_offset(rho1d,-order_allocated/2); + memory->destroy2d_offset(drho1d,-order_allocated/2); + memory->destroy2d_offset(rho_coeff,(1-order_allocated)/2); + memory->destroy2d_offset(drho_coeff,(1-order_allocated)/2); + + delete fft1; + delete fft2; + delete remap; + delete gc; + memory->destroy(gc_buf1); + memory->destroy(gc_buf2); + } + else if (ewaldflag) + { + + //delete [] kxvecs; + //delete [] kyvecs; + //delete [] kzvecs; + //delete [] kcoeff; + //delete [] sf_real; + //delete [] sf_im; + + //for(int i = 0; i < kmax3d; ++i) { + // delete [] sfexp_rl[i]; + // delete [] sfexp_im[i]; + //} + //delete [] sfexp_rl; + //delete [] sfexp_im; + + memory->destroy(kxvecs); + memory->destroy(kyvecs); + memory->destroy(kzvecs); + memory->destroy(kcoeff); + + memory->destroy(sf_real); + memory->destroy(sf_im); + memory->destroy(sfexp_rl); + memory->destroy(sfexp_im); + + //memory->destroy(ek); + //memory->destroy3d_offset(cs,-kmax_created); + //memory->destroy3d_offset(sn,-kmax_created); + + //memory->destroy(eg); + //memory->destroy(vg); + } +} + +// Maps atoms to corresponding grid points +void KSpaceHDNNP::particle_map() +{ + int nx,ny,nz; + + double **x = atom->x; + int nlocal = atom->nlocal; + + int flag = 0; + + // if atom count has changed, update qsum and qsqsum + + if (atom->natoms != natoms_original) { + qsum_qsq(); + natoms_original = atom->natoms; + } + + // return if there are no charges + + if (qsqsum == 0.0) return; + + boxlo = domain->boxlo; //triclinic = 0 + + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) + error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); + + if (atom->nmax > nmax) { + memory->destroy(part2grid); + nmax = atom->nmax; + memory->create(part2grid,nmax,3,"kspacehdnnp:part2grid"); + } + + for (int i = 0; i < nlocal; i++) { + + // (nx,ny,nz) = global coords of grid pt to "lower left" of charge + // current particle coord can be outside global and local box + // add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1 + + nx = static_cast ((x[i][0]-boxlo[0])*delxinv+shift) - OFFSET; + ny = static_cast ((x[i][1]-boxlo[1])*delyinv+shift) - OFFSET; + nz = static_cast ((x[i][2]-boxlo[2])*delzinv+shift) - OFFSET; + + + // check that entire stencil around nx,ny,nz will fit in my 3d brick + + if (nx+nlower < nxlo_out || nx+nupper > nxhi_out || + ny+nlower < nylo_out || ny+nupper > nyhi_out || + nz+nlower < nzlo_out || nz+nupper > nzhi_out) + flag = 1; + } + if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM"); +} + +void KSpaceHDNNP::make_rho_qeq(const gsl_vector *v) +{ + int l,m,n,nx,ny,nz,mx,my,mz; + FFT_SCALAR dx,dy,dz,x0,y0,z0; + + int *tag = atom->tag; + + // clear 3d density array + + memset(&(density_brick[nzlo_out][nylo_out][nxlo_out]),0, + ngrid*sizeof(FFT_SCALAR)); + + // loop over my charges, add their contribution to nearby grid points + // (nx,ny,nz) = global coords of grid pt to "lower left" of charge + // (dx,dy,dz) = distance to "lower left" grid pt + // (mx,my,mz) = global coords of moving stencil pt + + double **x = atom->x; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + //TODO:conversion ? + nx = part2grid[i][0]; + ny = part2grid[i][1]; + nz = part2grid[i][2]; + dx = (nx+shiftone - (x[i][0]-boxlo[0])*delxinv) * hdnnp->cflength; + dy = (ny+shiftone - (x[i][1]-boxlo[1])*delyinv) * hdnnp->cflength; + dz = (nz+shiftone - (x[i][2]-boxlo[2])*delzinv) * hdnnp->cflength; + + compute_rho1d(dx,dy,dz); + + double const qi = gsl_vector_get(v, tag[i]-1); + + //z0 = delvolinv * q[i]; + z0 = delvolinv * qi; + for (n = nlower; n <= nupper; n++) { + mz = n+nz; + y0 = z0*rho1d[2][n]; + for (m = nlower; m <= nupper; m++) { + my = m+ny; + x0 = y0*rho1d[1][m]; + for (l = nlower; l <= nupper; l++) { + mx = l+nx; + density_brick[mz][my][mx] += x0*rho1d[0][l]; + } + } + } + } +} + +void KSpaceHDNNP::compute_rho1d(const FFT_SCALAR &dx, const FFT_SCALAR &dy, const FFT_SCALAR &dz) +{ + int k,l; + FFT_SCALAR r1,r2,r3; + + for (k = (1-order)/2; k <= order/2; k++) { + r1 = r2 = r3 = ZEROF; + std::cout << r1 << '\n'; + std::cout << r2 << '\n'; + for (l = order-1; l >= 0; l--) { + std::cout << l << '\n'; + r1 = rho_coeff[l][k] + r1*dx; + std::cout << "aaau" << '\n'; + exit(0); + r2 = rho_coeff[l][k] + r2*dy; + r3 = rho_coeff[l][k] + r3*dz; + } + rho1d[0][k] = r1; + rho1d[1][k] = r2; + rho1d[2][k] = r3; + } +} + +// Poission solver in PPPM +void KSpaceHDNNP::poisson() +{ + int i,j,k,n; + double eng; + + // transform charge density (r -> k) + + n = 0; + for (i = 0; i < nfft; i++) { + work1[n++] = density_fft[i]; + work1[n++] = ZEROF; + } + + fft1->compute(work1,work1,1); + + // global energy and virial contribution + + double scaleinv = 1.0/(nx_pppm*ny_pppm*nz_pppm); + double s2 = scaleinv*scaleinv; + + if (eflag_global || vflag_global) { + if (vflag_global) { + n = 0; + for (i = 0; i < nfft; i++) { + eng = s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]); + for (j = 0; j < 6; j++) virial[j] += eng*vg[i][j]; + if (eflag_global) energy += eng; + n += 2; + } + } else { + n = 0; + for (i = 0; i < nfft; i++) { + //std::cout << "Green" << greensfn[i] << '\n'; + //std::cout << "S2" << s2 << '\n'; + //std::cout << "Par" << (work1[n]*work1[n] + work1[n+1]*work1[n+1]) << '\n'; + energy += s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]); + n += 2; + } + } + } + + + // scale by 1/total-grid-pts to get rho(k) + // multiply by Green's function to get V(k) + + n = 0; + for (i = 0; i < nfft; i++) { + work1[n++] *= scaleinv * greensfn[i]; + work1[n++] *= scaleinv * greensfn[i]; + } + + // extra FFTs for per-atom energy/virial + //if (evflag_atom) poisson_peratom(); // TODO: do we need ? + + // compute V(r) in each of 3 dims by transformimg V(k) + // FFT leaves data in 3d brick decomposition + // copy it into inner portion of vx,vy,vz arrays + + // x direction + + n = 0; + for (k = nzlo_fft; k <= nzhi_fft; k++) + for (j = nylo_fft; j <= nyhi_fft; j++) + for (i = nxlo_fft; i <= nxhi_fft; i++) { + work2[n] = work1[n+1]; + work2[n+1] = work1[n]; + n += 2; + } + + fft2->compute(work2,work2,-1); + + n = 0; + for (k = nzlo_in; k <= nzhi_in; k++) + for (j = nylo_in; j <= nyhi_in; j++) + for (i = nxlo_in; i <= nxhi_in; i++) { + vx_brick[k][j][i] = work2[n]; + n += 2; + } + + // y direction + + n = 0; + for (k = nzlo_fft; k <= nzhi_fft; k++) + for (j = nylo_fft; j <= nyhi_fft; j++) + for (i = nxlo_fft; i <= nxhi_fft; i++) { + work2[n] = work1[n+1]; + work2[n+1] = work1[n]; + n += 2; + } + + fft2->compute(work2,work2,-1); + + n = 0; + for (k = nzlo_in; k <= nzhi_in; k++) + for (j = nylo_in; j <= nyhi_in; j++) + for (i = nxlo_in; i <= nxhi_in; i++) { + vy_brick[k][j][i] = work2[n]; + n += 2; + } + + // z direction gradient + + n = 0; + for (k = nzlo_fft; k <= nzhi_fft; k++) + for (j = nylo_fft; j <= nyhi_fft; j++) + for (i = nxlo_fft; i <= nxhi_fft; i++) { + work2[n] = work1[n+1]; + work2[n+1] = work1[n]; + n += 2; + } + + fft2->compute(work2,work2,-1); + + n = 0; + for (k = nzlo_in; k <= nzhi_in; k++) + for (j = nylo_in; j <= nyhi_in; j++) + for (i = nxlo_in; i <= nxhi_in; i++) { + vz_brick[k][j][i] = work2[n]; + n += 2; + } +} + +//remap density from 3d brick decomposition to FFT decomposition +void KSpaceHDNNP::brick2fft() +{ + int n,ix,iy,iz; + + // copy grabs inner portion of density from 3d brick + // remap could be done as pre-stage of FFT, + // but this works optimally on only double values, not complex values + + n = 0; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + density_fft[n++] = density_brick[iz][iy][ix]; + + remap->perform(density_fft,density_fft,work1); +} + +void KSpaceHDNNP::set_grid_local() +{ + // global indices of PPPM grid range from 0 to N-1 + // nlo_in,nhi_in = lower/upper limits of the 3d sub-brick of + // global PPPM grid that I own without ghost cells + // for slab PPPM, assign z grid as if it were not extended + // both non-tiled and tiled proc layouts use 0-1 fractional sumdomain info + + if (comm->layout != Comm::LAYOUT_TILED) { + nxlo_in = static_cast (comm->xsplit[comm->myloc[0]] * nx_pppm); + nxhi_in = static_cast (comm->xsplit[comm->myloc[0]+1] * nx_pppm) - 1; + + nylo_in = static_cast (comm->ysplit[comm->myloc[1]] * ny_pppm); + nyhi_in = static_cast (comm->ysplit[comm->myloc[1]+1] * ny_pppm) - 1; + + nzlo_in = static_cast (comm->zsplit[comm->myloc[2]] * nz_pppm); + nzhi_in = static_cast (comm->zsplit[comm->myloc[2]+1] * nz_pppm) - 1; + + } else { + nxlo_in = static_cast (comm->mysplit[0][0] * nx_pppm); + nxhi_in = static_cast (comm->mysplit[0][1] * nx_pppm) - 1; + + nylo_in = static_cast (comm->mysplit[1][0] * ny_pppm); + nyhi_in = static_cast (comm->mysplit[1][1] * ny_pppm) - 1; + + nzlo_in = static_cast (comm->mysplit[2][0] * nz_pppm); + nzhi_in = static_cast (comm->mysplit[2][1] * nz_pppm) - 1; + } + + + // nlower,nupper = stencil size for mapping particles to PPPM grid + //TODO: conversion ? + nlower = -(order-1)/2; + nupper = order/2; + + // shift values for particle <-> grid mapping + // add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1 + //TODO: conversion ? + if (order % 2) shift = OFFSET + 0.5; + else shift = OFFSET; + if (order % 2) shiftone = 0.0; + else shiftone = 0.5; + + // nlo_out,nhi_out = lower/upper limits of the 3d sub-brick of + // global PPPM grid that my particles can contribute charge to + // effectively nlo_in,nhi_in + ghost cells + // nlo,nhi = global coords of grid pt to "lower left" of smallest/largest + // position a particle in my box can be at + // dist[3] = particle position bound = subbox + skin/2.0 + qdist + // qdist = offset due to TIP4P fictitious charge + // convert to triclinic if necessary + // nlo_out,nhi_out = nlo,nhi + stencil size for particle mapping + // for slab PPPM, assign z grid as if it were not extended + + double *prd,*sublo,*subhi; + + // triclinic = 0, no slab + prd = domain->prd; + boxlo = domain->boxlo; + sublo = domain->sublo; + subhi = domain->subhi; + + // Unit conversions for n2p2 + boxlo[0] = boxlo[0] * hdnnp->cflength; + boxlo[1] = boxlo[1] * hdnnp->cflength; + boxlo[2] = boxlo[2] * hdnnp->cflength; + + sublo[0] = sublo[0] * hdnnp->cflength; + sublo[1] = sublo[1] * hdnnp->cflength; + sublo[2] = sublo[2] * hdnnp->cflength; + + subhi[0] = subhi[0] * hdnnp->cflength; + subhi[1] = subhi[1] * hdnnp->cflength; + subhi[2] = subhi[2] * hdnnp->cflength; + + double xprd = prd[0] * hdnnp->cflength; + double yprd = prd[1] * hdnnp->cflength; + double zprd = prd[2] * hdnnp->cflength; + + double dist[3] = {0.0,0.0,0.0}; + double cuthalf = 0.5*neighbor->skin * hdnnp->cflength; + dist[0] = dist[1] = dist[2] = cuthalf; + + int nlo,nhi; + nlo = nhi = 0; + + nlo = static_cast ((sublo[0]-dist[0]-boxlo[0]) * + nx_pppm/xprd + shift) - OFFSET; + nhi = static_cast ((subhi[0]+dist[0]-boxlo[0]) * + nx_pppm/xprd + shift) - OFFSET; + nxlo_out = nlo + nlower; + nxhi_out = nhi + nupper; + + nlo = static_cast ((sublo[1]-dist[1]-boxlo[1]) * + ny_pppm/yprd + shift) - OFFSET; + nhi = static_cast ((subhi[1]+dist[1]-boxlo[1]) * + ny_pppm/yprd + shift) - OFFSET; + nylo_out = nlo + nlower; + nyhi_out = nhi + nupper; + + nlo = static_cast ((sublo[2]-dist[2]-boxlo[2]) * + nz_pppm/zprd + shift) - OFFSET; + nhi = static_cast ((subhi[2]+dist[2]-boxlo[2]) * + nz_pppm/zprd + shift) - OFFSET; + nzlo_out = nlo + nlower; + nzhi_out = nhi + nupper; + + // x-pencil decomposition of FFT mesh + // global indices range from 0 to N-1 + // each proc owns entire x-dimension, clumps of columns in y,z dimensions + // npey_fft,npez_fft = # of procs in y,z dims + // if nprocs is small enough, proc can own 1 or more entire xy planes, + // else proc owns 2d sub-blocks of yz plane + // me_y,me_z = which proc (0-npe_fft-1) I am in y,z dimensions + // nlo_fft,nhi_fft = lower/upper limit of the section + // of the global FFT mesh that I own in x-pencil decomposition + + int npey_fft,npez_fft; + if (nz_pppm >= nprocs) { + npey_fft = 1; + npez_fft = nprocs; + } else procs2grid2d(nprocs,ny_pppm,nz_pppm,&npey_fft,&npez_fft); + + int me_y = me % npey_fft; + int me_z = me / npey_fft; + + nxlo_fft = 0; + nxhi_fft = nx_pppm - 1; + nylo_fft = me_y*ny_pppm/npey_fft; + nyhi_fft = (me_y+1)*ny_pppm/npey_fft - 1; + nzlo_fft = me_z*nz_pppm/npez_fft; + nzhi_fft = (me_z+1)*nz_pppm/npez_fft - 1; + + // ngrid = count of PPPM grid pts owned by this proc, including ghosts + + ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * + (nzhi_out-nzlo_out+1); + + // count of FFT grids pts owned by this proc, without ghosts + // nfft = FFT points in x-pencil FFT decomposition on this proc + // nfft_brick = FFT points in 3d brick-decomposition on this proc + // nfft_both = greater of 2 values + + nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) * + (nzhi_fft-nzlo_fft+1); + int nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * + (nzhi_in-nzlo_in+1); + nfft_both = MAX(nfft,nfft_brick); +} + +/* ---------------------------------------------------------------------- + set global size of PPPM grid = nx,ny,nz_pppm + used for charge accumulation, FFTs, and electric field interpolation +------------------------------------------------------------------------- */ +void KSpaceHDNNP::set_grid_global() +{ + // use xprd,yprd,zprd (even if triclinic, and then scale later) + // adjust z dimension for 2d slab PPPM + // 3d PPPM just uses zprd since slab_volfactor = 1.0 + + double xprd = domain->xprd * hdnnp->cflength; + double yprd = domain->yprd * hdnnp->cflength; + double zprd = domain->zprd * hdnnp->cflength; + //double zprd_slab = zprd*slab_volfactor; + + // make initial g_ewald estimate + // based on desired accuracy and real space cutoff + // fluid-occupied volume used to estimate real-space error + // zprd used rather than zprd_slab + + double h; + bigint natoms = atom->natoms; + + // TODO: check this, we can also use 'kspace_modify' to pick gewald + if (!gewaldflag) { + if (accuracy <= 0.0) + error->all(FLERR, "KSpace accuracy must be > 0"); + if (q2 == 0.0) + error->all(FLERR, "Must use kspace_modify gewald for uncharged system"); + g_ewald = accuracy * sqrt(natoms * cutoff * xprd * yprd * zprd) / (2.0 * q2); + if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15 * log(accuracy)) / cutoff; + else g_ewald = sqrt(-log(g_ewald)) / cutoff; + } + + // set optimal nx_pppm,ny_pppm,nz_pppm based on order and accuracy + // nz_pppm uses extended zprd_slab instead of zprd + // reduce it until accuracy target is met + + if (!gridflag) { // gridflag = 0 if there is no kspace_modify command + + // differentiation_flag = 0 & stagger_flag = 0 TODO + double err; + h_x = h_y = h_z = 1.0/g_ewald; + + nx_pppm = static_cast (xprd/h_x) + 1; + ny_pppm = static_cast (yprd/h_y) + 1; + nz_pppm = static_cast (zprd/h_z) + 1; + + err = estimate_ik_error(h_x,xprd,natoms); + while (err > accuracy) { + err = estimate_ik_error(h_x,xprd,natoms); + nx_pppm++; + h_x = xprd/nx_pppm; + } + + err = estimate_ik_error(h_y,yprd,natoms); + while (err > accuracy) { + err = estimate_ik_error(h_y,yprd,natoms); + ny_pppm++; + h_y = yprd/ny_pppm; + } + + err = estimate_ik_error(h_z,zprd,natoms); + while (err > accuracy) { + err = estimate_ik_error(h_z,zprd,natoms); + nz_pppm++; + h_z = zprd/nz_pppm; + } + } + + // boost grid size until it is factorable + + while (!factorable(nx_pppm)) nx_pppm++; + while (!factorable(ny_pppm)) ny_pppm++; + while (!factorable(nz_pppm)) nz_pppm++; + + // triclinic = 0 + h_x = xprd/nx_pppm; + h_y = yprd/ny_pppm; + h_z = zprd/nz_pppm; + + + if (nx_pppm >= OFFSET || ny_pppm >= OFFSET || nz_pppm >= OFFSET) + error->all(FLERR,"PPPM grid is too large"); +} + +void KSpaceHDNNP::compute_rho_coeff() +{ + int j,k,l,m; + FFT_SCALAR s; + + FFT_SCALAR **a; + memory->create2d_offset(a,order,-order,order,"pppm:a"); + + for (k = -order; k <= order; k++) + for (l = 0; l < order; l++) + a[l][k] = 0.0; + + a[0][0] = 1.0; + for (j = 1; j < order; j++) { + for (k = -j; k <= j; k += 2) { + s = 0.0; + for (l = 0; l < j; l++) { + a[l+1][k] = (a[l][k+1]-a[l][k-1]) / (l+1); +#ifdef FFT_SINGLE + s += powf(0.5,(float) l+1) * + (a[l][k-1] + powf(-1.0,(float) l) * a[l][k+1]) / (l+1); +#else + s += pow(0.5,(double) l+1) * + (a[l][k-1] + pow(-1.0,(double) l) * a[l][k+1]) / (l+1); +#endif + } + a[0][k] = s; + } + } + + m = (1-order)/2; + for (k = -(order-1); k < order; k += 2) { + for (l = 0; l < order; l++) + rho_coeff[l][m] = a[l][k]; + for (l = 1; l < order; l++) + drho_coeff[l-1][m] = l*a[l][k]; + m++; + } + + memory->destroy2d_offset(a,-order); +} + +// pre-compute modified (Hockney-Eastwood) Coulomb Green's function +void KSpaceHDNNP::compute_gf_ik() +{ + const double * const prd = domain->prd; + //TODO: conversion ? + const double xprd = prd[0] * hdnnp->cflength; + const double yprd = prd[1] * hdnnp->cflength; + const double zprd = prd[2] * hdnnp->cflength; + + const double unitkx = (MY_2PI/xprd); + const double unitky = (MY_2PI/yprd); + const double unitkz = (MY_2PI/zprd); + + double snx,sny,snz; + double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz; + double sum1,dot1,dot2; + double numerator,denominator; + double sqk; + + int k,l,m,n,nx,ny,nz,kper,lper,mper; + + const int nbx = static_cast ((g_ewald*xprd/(MY_PI*nx_pppm)) * + pow(-log(EPS_HOC),0.25)); + const int nby = static_cast ((g_ewald*yprd/(MY_PI*ny_pppm)) * + pow(-log(EPS_HOC),0.25)); + const int nbz = static_cast ((g_ewald*zprd/(MY_PI*nz_pppm)) * + pow(-log(EPS_HOC),0.25)); + const int twoorder = 2*order; + + n = 0; + for (m = nzlo_fft; m <= nzhi_fft; m++) { + mper = m - nz_pppm*(2*m/nz_pppm); + snz = square(sin(0.5*unitkz*mper*zprd/nz_pppm)); + + for (l = nylo_fft; l <= nyhi_fft; l++) { + lper = l - ny_pppm*(2*l/ny_pppm); + sny = square(sin(0.5*unitky*lper*yprd/ny_pppm)); + + for (k = nxlo_fft; k <= nxhi_fft; k++) { + kper = k - nx_pppm*(2*k/nx_pppm); + snx = square(sin(0.5*unitkx*kper*xprd/nx_pppm)); + + sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper); + + if (sqk != 0.0) { + numerator = 12.5663706/sqk; + denominator = gf_denom(snx,sny,snz); + sum1 = 0.0; + + for (nx = -nbx; nx <= nbx; nx++) { + qx = unitkx*(kper+nx_pppm*nx); + sx = exp(-0.25*square(qx/g_ewald)); + argx = 0.5*qx*xprd/nx_pppm; + wx = powsinxx(argx,twoorder); + + for (ny = -nby; ny <= nby; ny++) { + qy = unitky*(lper+ny_pppm*ny); + sy = exp(-0.25*square(qy/g_ewald)); + argy = 0.5*qy*yprd/ny_pppm; + wy = powsinxx(argy,twoorder); + + for (nz = -nbz; nz <= nbz; nz++) { + qz = unitkz*(mper+nz_pppm*nz); + sz = exp(-0.25*square(qz/g_ewald)); + argz = 0.5*qz*zprd/nz_pppm; + wz = powsinxx(argz,twoorder); + + dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz; + dot2 = qx*qx+qy*qy+qz*qz; + sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz; + } + } + } + greensfn[n++] = numerator*sum1/denominator; + } else greensfn[n++] = 0.0; + } + } + } +} + +/* ---------------------------------------------------------------------- + calculate the final estimate of the accuracy +------------------------------------------------------------------------- */ + +double KSpaceHDNNP::final_accuracy() +{ + double xprd = domain->xprd; + double yprd = domain->yprd; + double zprd = domain->zprd; + bigint natoms = atom->natoms; + if (natoms == 0) natoms = 1; // avoid division by zero + + double df_kspace = compute_df_kspace(); + double q2_over_sqrt = q2 / sqrt(natoms*cutoff*xprd*yprd*zprd); + double df_rspace = 2.0 * q2_over_sqrt * exp(-g_ewald*g_ewald*cutoff*cutoff); + double df_table = estimate_table_accuracy(q2_over_sqrt,df_rspace); + double estimated_accuracy = sqrt(df_kspace*df_kspace + df_rspace*df_rspace + + df_table*df_table); + + return estimated_accuracy; +} + +/* ---------------------------------------------------------------------- + compute estimated kspace force error +------------------------------------------------------------------------- */ + +double KSpaceHDNNP::compute_df_kspace() +{ + double xprd = domain->xprd; + double yprd = domain->yprd; + double zprd = domain->zprd; + bigint natoms = atom->natoms; + double df_kspace = 0.0; + + //differentiation_flag = 0 + double lprx = estimate_ik_error(h_x,xprd,natoms); + double lpry = estimate_ik_error(h_y,yprd,natoms); + double lprz = estimate_ik_error(h_z,zprd,natoms); + df_kspace = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0); + + return df_kspace; +} + +/* ---------------------------------------------------------------------- + estimate kspace force error for ik method +------------------------------------------------------------------------- */ + +double KSpaceHDNNP::estimate_ik_error(double h, double prd, bigint natoms) +{ + double sum = 0.0; + if (natoms == 0) return 0.0; + for (int m = 0; m < order; m++) + sum += acons[order][m] * pow(h*g_ewald,2.0*m); + double value = q2 * pow(h*g_ewald,(double)order) * + sqrt(g_ewald*prd*sqrt(MY_2PI)*sum/natoms) / (prd*prd); + + return value; +} + +void KSpaceHDNNP::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py) +{ + // loop thru all possible factorizations of nprocs + // surf = surface area of largest proc sub-domain + // innermost if test minimizes surface area and surface/volume ratio + + int bestsurf = 2 * (nx + ny); + int bestboxx = 0; + int bestboxy = 0; + + int boxx,boxy,surf,ipx,ipy; + + ipx = 1; + while (ipx <= nprocs) { + if (nprocs % ipx == 0) { + ipy = nprocs/ipx; + boxx = nx/ipx; + if (nx % ipx) boxx++; + boxy = ny/ipy; + if (ny % ipy) boxy++; + surf = boxx + boxy; + if (surf < bestsurf || + (surf == bestsurf && boxx*boxy > bestboxx*bestboxy)) { + bestsurf = surf; + bestboxx = boxx; + bestboxy = boxy; + *px = ipx; + *py = ipy; + } + } + ipx++; + } +} + +// pre-compute Green's function denominator expansion coeffs, Gamma(2n) +void KSpaceHDNNP::compute_gf_denom() +{ + int k,l,m; + + for (l = 1; l < order; l++) gf_b[l] = 0.0; + gf_b[0] = 1.0; + + for (m = 1; m < order; m++) { + for (l = m; l > 0; l--) + gf_b[l] = 4.0 * (gf_b[l]*(l-m)*(l-m-0.5)-gf_b[l-1]*(l-m-1)*(l-m-1)); + gf_b[0] = 4.0 * (gf_b[0]*(l-m)*(l-m-0.5)); + } + + bigint ifact = 1; + for (k = 1; k < 2*order; k++) ifact *= k; + double gaminv = 1.0/ifact; + for (l = 0; l < order; l++) gf_b[l] *= gaminv; +} + +int KSpaceHDNNP::factorable(int n) +{ + int i; + + while (n > 1) { + for (i = 0; i < nfactors; i++) { + if (n % factors[i] == 0) { + n /= factors[i]; + break; + } + } + if (i == nfactors) return 0; + } + + return 1; +} + +/* ---------------------------------------------------------------------- + adjust the g_ewald parameter to near its optimal value + using a Newton-Raphson solver +------------------------------------------------------------------------- */ + +void KSpaceHDNNP::adjust_gewald() +{ + double dx; + + for (int i = 0; i < LARGE; i++) { + dx = newton_raphson_f() / derivf(); + g_ewald -= dx; + if (fabs(newton_raphson_f()) < SMALL) return; + } + error->all(FLERR, "Could not compute g_ewald"); +} + +/* ---------------------------------------------------------------------- + calculate f(x) using Newton-Raphson solver +------------------------------------------------------------------------- */ + +double KSpaceHDNNP::newton_raphson_f() +{ + double xprd = domain->xprd; + double yprd = domain->yprd; + double zprd = domain->zprd; + bigint natoms = atom->natoms; + + double df_rspace = 2.0*q2*exp(-g_ewald*g_ewald*cutoff*cutoff) / + sqrt(natoms*cutoff*xprd*yprd*zprd); + + double df_kspace = compute_df_kspace(); + + return df_rspace - df_kspace; +} + +/* ---------------------------------------------------------------------- + calculate numerical derivative f'(x) using forward difference + [f(x + h) - f(x)] / h +------------------------------------------------------------------------- */ + +double KSpaceHDNNP::derivf() +{ + double h = 0.000001; //Derivative step-size + double df,f1,f2,g_ewald_old; + + f1 = newton_raphson_f(); + g_ewald_old = g_ewald; + g_ewald += h; + f2 = newton_raphson_f(); + g_ewald = g_ewald_old; + df = (f2 - f1)/h; + + return df; +} + +// Calculate Ewald eta param (original method in RuNNer - JACKSON_CATLOW) +void KSpaceHDNNP::calculate_ewald_eta(int mflag) +{ + ewald_eta = 1.0 / sqrt(2.0 * M_PI); + + //TODO: check + if (mflag == 0) ewald_eta *= pow(volume * volume / atom->natoms, 1.0 / 6.0); // regular Ewald eta + else ewald_eta *= pow(volume, 1.0 / 3.0); // matrix approach + +} + +// Calculate Ewald eta param (efficient method - KOLAFA_PARRAM) +void KSpaceHDNNP::calculate_ewald_eta_efficient() +{ + // Ratio of computing times for one real space and k space iteration. + double TrOverTk = 3.676; // TODO: should it be hardcoded ? + + // Unit Conversion (in KOLAFA-PERRAM method precision has unit of a force) TODO:check + double fourPiEps = 1.0; + + /*precision *= convEnergy / convLength; + ewaldMaxCharge *= convCharge; + fourPiEps = pow(convCharge, 2) / (convLength * convEnergy);*/ + + // Initial approximation + double eta0 = pow(1 / TrOverTk * pow(volume, 2) / pow(2 * M_PI, 3),1.0 / 6.0); + + // Selfconsistent calculation of eta + ewald_eta = eta0; + s_ewald = 0.0; // TODO: check + double relError = 1.0; + while (relError > 0.01) + { + // Calculates S + double y = accuracy * sqrt(ewald_eta / sqrt(2)) * fourPiEps; + y /= 2 * sqrt(atom->natoms * 1.0 / volume) * pow(ewald_max_charge, 2); + + double relYError = 1.0; + if (s_ewald <= 0.0) + s_ewald = 0.5; + double step = s_ewald; + while (abs(step) / s_ewald > 0.01 || relYError > 0.01) + { + step = 2 * s_ewald / (4 * pow(s_ewald,2) + 1); + step *= 1 - sqrt(s_ewald) * y / exp(-pow(s_ewald,2)); + if (s_ewald <= -step) + { + s_ewald /= 2; + step = 1.0; + } + else + s_ewald += step; + relYError = (exp(-pow(s_ewald,2)) / sqrt(s_ewald) - y) / y; + } + + double newEta = eta0 * pow((1 + 1 / (2 * pow(s_ewald, 2))), 1.0 / 6.0); + relError = abs(newEta - ewald_eta) / ewald_eta; + ewald_eta = newEta; + } + + ewald_eta = max(ewald_eta, ewald_max_sigma); +} + +// Generate k-space grid in Ewald Sum (RuNNer) +void KSpaceHDNNP::ewald_pbc(double rcut) +{ + double proja = fabs(unitk[0]); + double projb = fabs(unitk[1]); + double projc = fabs(unitk[2]); + kxmax = 0; + kymax = 0; + kzmax = 0; + while (kxmax * proja <= rcut) kxmax++; + while (kymax * projb <= rcut) kymax++; + while (kzmax * projc <= rcut) kzmax++; + + return; +} + + + diff --git a/src/interface/LAMMPS/src/ML-HDNNP/kspace_hdnnp.h b/src/interface/LAMMPS/src/ML-HDNNP/kspace_hdnnp.h new file mode 100644 index 0000000000..82a56e6e6e --- /dev/null +++ b/src/interface/LAMMPS/src/ML-HDNNP/kspace_hdnnp.h @@ -0,0 +1,270 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef KSPACE_CLASS + +KSpaceStyle(hdnnp,KSpaceHDNNP) + +#else + +#ifndef LMP_KSPACE_HDNNP_H +#define LMP_KSPACE_HDNNP_H + +#include +#include "kspace.h" +#include "grid3d.h" + +#if defined(FFT_FFTW3) +#define LMP_FFT_LIB "FFTW3" +#elif defined(FFT_MKL) +#define LMP_FFT_LIB "MKL FFT" +#elif defined(FFT_CUFFT) +#define LMP_FFT_LIB "cuFFT" +#else +#define LMP_FFT_LIB "KISS FFT" +#endif + +#ifdef FFT_SINGLE +typedef float FFT_SCALAR; +#define LMP_FFT_PREC "single" +#define MPI_FFT_SCALAR MPI_FLOAT +#else + +typedef double FFT_SCALAR; +#define LMP_FFT_PREC "double" +#define MPI_FFT_SCALAR MPI_DOUBLE +#endif + +#include "InterfaceLammps.h" + + +namespace LAMMPS_NS { + + class KSpaceHDNNP : public KSpace { + friend class PairHDNNP4G; + friend class FixHDNNP; + public: + KSpaceHDNNP(class LAMMPS *); + ~KSpaceHDNNP(); + + virtual void settings(int, char **); + virtual void init(); + virtual void setup(); + //virtual void setup_grid(); + virtual void compute(int, int); + //virtual int timing_1d(int, double &); + //virtual int timing_3d(int, double &); + //virtual double memory_usage(); + + protected: + + class PairHDNNP4G *hdnnp; // interface to HDNNP pair_style + + int ewaldflag,pppmflag; + + int triclinic; // domain settings, orthog or triclinic + + double cutoff; + double gsqmx; + + //// EWALD SUM + int kewaldflag; // O if no kspace_modify + + double unitk[3]; + int *kxvecs,*kyvecs,*kzvecs; + int kxmax_orig,kymax_orig,kzmax_orig,kmax_created; + int kxmax,kymax,kzmax,kmax,kmax3d; + int kcount; + + int ewald_truncation_method; // truncation method (RuNNer) + + double ewald_eta; + double s_ewald; + double ewald_recip_cutoff; + double ewald_real_cutoff; + + double ewald_max_charge; + double ewald_max_sigma; + + double *ug; + double **eg,**vg; + double **ek; + + double *kcoeff; + double **sfexp_rl,**sfexp_im; + double *sf_real, *sf_im; + double *sfexp_rl_all,*sfexp_im_all; // structure factors after communications ? + double ***cs,***sn; // cosine and sine grid + + void calculate_ewald_eta(int); + void calculate_ewald_eta_efficient(); + + void ewald_coeffs(); + void ewald_sfexp(); + + void ewald_pbc(double); // TODO: this is from RuNNer + + double rms(int, double, bigint, double); + + double compute_ewald_eqeq(const gsl_vector*); + + //// PPPM + + int me,nprocs; + int nfactors; + int *factors; + + double volume; + double delxinv,delyinv,delzinv,delvolinv; + double h_x,h_y,h_z; + double shift,shiftone; + int peratom_allocate_flag; + int nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in; + int nxlo_out,nylo_out,nzlo_out,nxhi_out,nyhi_out,nzhi_out; + int nxlo_ghost,nxhi_ghost,nylo_ghost,nyhi_ghost,nzlo_ghost,nzhi_ghost; + int nxlo_fft,nylo_fft,nzlo_fft,nxhi_fft,nyhi_fft,nzhi_fft; + int nlower,nupper; + int ngrid,nfft,nfft_both; + + FFT_SCALAR ***density_brick; + FFT_SCALAR ***vdx_brick,***vdy_brick,***vdz_brick; + FFT_SCALAR ***vx_brick,***vy_brick,***vz_brick; + FFT_SCALAR ***u_brick; + FFT_SCALAR ***v0_brick,***v1_brick,***v2_brick; + FFT_SCALAR ***v3_brick,***v4_brick,***v5_brick; + double *greensfn; + double *fkx,*fky,*fkz; + FFT_SCALAR *density_fft; + FFT_SCALAR *work1,*work2; + + double *gf_b; + FFT_SCALAR **rho1d,**rho_coeff,**drho1d,**drho_coeff; + double *sf_precoeff1, *sf_precoeff2, *sf_precoeff3; + double *sf_precoeff4, *sf_precoeff5, *sf_precoeff6; + double sf_coeff[6]; // coefficients for calculating ad self-forces + double **acons; + + // FFTs and grid communication + + class FFT3d *fft1,*fft2; + class Remap *remap; + class Grid3d *gc; + + FFT_SCALAR *gc_buf1,*gc_buf2; + int ngc_buf1,ngc_buf2,npergrid; + + int **part2grid; // storage for particle -> grid mapping + int nmax; + + double *boxlo; + + virtual void set_grid_global(); + void set_grid_local(); + void adjust_gewald(); + virtual double newton_raphson_f(); + double derivf(); + double final_accuracy(); + + virtual void allocate(); + //virtual void allocate_peratom(); + virtual void deallocate(); + //virtual void deallocate_peratom(); + + + int factorable(int); + double compute_df_kspace(); + double estimate_ik_error(double, double, bigint); + //virtual double compute_qopt(); + virtual void compute_gf_denom(); + virtual void compute_gf_ik(); + + + void make_rho_qeq(const gsl_vector*); // charge density (rho) / charge + virtual void particle_map(); + double compute_pppm_eqeq(); + double compute_pppm_dEdQ(int); + + //virtual void make_rho(); + + virtual void brick2fft(); + + virtual void poisson(); // Poisson solver for P3M (differentiation_flag == 0) + + /*void compute_sf_precoeff(); + + virtual void fieldforce(); + virtual void fieldforce_ik(); + virtual void fieldforce_ad(); + + virtual void poisson_peratom(); + virtual void fieldforce_peratom();*/ + void procs2grid2d(int,int,int,int *, int*); + void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &, const FFT_SCALAR &); + //void compute_drho1d(const FFT_SCALAR &, const FFT_SCALAR &,const FFT_SCALAR &); + void compute_rho_coeff(); + + + // grid communication + /* + virtual void pack_forward_grid(int, void *, int, int *); + virtual void unpack_forward_grid(int, void *, int, int *); + virtual void pack_reverse_grid(int, void *, int, int *); + virtual void unpack_reverse_grid(int, void *, int, int *); + + // triclinic + + void setup_triclinic(); + void compute_gf_ik_triclinic(); + void poisson_ik_triclinic(); + void poisson_groups_triclinic(); + + // group-group interactions + + virtual void allocate_groups(); + virtual void deallocate_groups(); + virtual void make_rho_groups(int, int, int); + virtual void poisson_groups(int); + virtual void slabcorr_groups(int,int,int);*/ + +/* ---------------------------------------------------------------------- + denominator for Hockney-Eastwood Green's function + of x,y,z = sin(kx*deltax/2), etc + + inf n-1 + S(n,k) = Sum W(k+pi*j)**2 = Sum b(l)*(z*z)**l + j=-inf l=0 + + = -(z*z)**n /(2n-1)! * (d/dx)**(2n-1) cot(x) at z = sin(x) + gf_b = denominator expansion coeffs +------------------------------------------------------------------------- */ + + inline double gf_denom(const double &x, const double &y, + const double &z) const { + double sx,sy,sz; + sz = sy = sx = 0.0; + for (int l = order-1; l >= 0; l--) { + sx = gf_b[l] + sx*x; + sy = gf_b[l] + sy*y; + sz = gf_b[l] + sz*z; + } + double s = sx*sy*sz; + return s*s; + }; + + + }; + +} + +#endif +#endif diff --git a/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_4g.cpp b/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_4g.cpp new file mode 100644 index 0000000000..5e86fea364 --- /dev/null +++ b/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_4g.cpp @@ -0,0 +1,1351 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + This file initially came from n2p2 (https://github.com/CompPhysVienna/n2p2) + Copyright (2018) Andreas Singraber (University of Vienna) + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Emir Kocer + Andreas Singraber +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include //exit(0); +#include +#include "pair_hdnnp_4g.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include "update.h" +#include "domain.h" //periodicity +#include "fix_hdnnp.h" +#include "kspace_hdnnp.h" +#include //time +#include + +using namespace LAMMPS_NS; +using namespace std::chrono; +using namespace nnp; +using namespace std; + +#define SQR(x) ((x)*(x)) + +/* ---------------------------------------------------------------------- */ + +PairHDNNP4G::PairHDNNP4G(LAMMPS *lmp) : Pair(lmp), + kspacehdnnp (nullptr), + periodic (false ), + showew (false ), + resetew (false ), + showewsum (0 ), + maxew (0 ), + numExtrapolationWarningsTotal (0 ), + numExtrapolationWarningsSummary(0 ), + cflength (0.0 ), + cfenergy (0.0 ), + maxCutoffRadius (0.0 ), + directory (nullptr), + emap (nullptr), + list (nullptr), + chi (nullptr), + hardness (nullptr), + sigmaSqrtPi (nullptr), + gammaSqrt2 (nullptr), + dEdQ (nullptr), + forceLambda (nullptr), + grad_tol (0.0 ), + min_tol (0.0 ), + step (0.0 ), + maxit (0 ), + minim_init_style (0 ), + T (nullptr), + s (nullptr), + E_elec (0.0 ), + kcoeff_sum (0.0 ), + type_all (nullptr), + type_loc (nullptr), + dEdLambda_loc (nullptr), + dEdLambda_all (nullptr), + qall_loc (nullptr), + qall (nullptr), + xx (nullptr), + xy (nullptr), + xz (nullptr), + xx_loc (nullptr), + xy_loc (nullptr), + xz_loc (nullptr), + forceLambda_loc (nullptr), + forceLambda_all (nullptr), + erfc_val (nullptr), + kcos (nullptr), + ksinx (nullptr), + ksiny (nullptr), + ksinz (nullptr), + screening_info (nullptr) +{ + + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairHDNNP4G::~PairHDNNP4G() +{ +} + +void PairHDNNP4G::compute(int eflag, int vflag) +{ + if(eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + + if (interface.getNnpType() == InterfaceLammps::NNPType::HDNNP_2G) + { + // Set number of local atoms and add element. + interface.setLocalAtoms(atom->nlocal,atom->type); + + // Set tags of local atoms. + interface.setLocalTags(atom->tag); + + // Transfer local neighbor list to NNP interface. + transferNeighborList(); + + // Compute symmetry functions, atomic neural networks and add up energy. + interface.process(); + + // Do all stuff related to extrapolation warnings. + if(showew == true || showewsum > 0 || maxew >= 0) { + handleExtrapolationWarnings(); + } + + // get short-range forces of local and ghost atoms. + interface.getForces(atom->f); + + } + else if (interface.getNnpType() == InterfaceLammps::NNPType::HDNNP_4G) + { + // Transfer charges into n2p2 before running second set of NNs + transferCharges(); + + // Add electrostatic energy contribution to the total energy before conversion TODO:check + interface.addElectrostaticEnergy(E_elec); + + // Run second set of NNs for the short range contributions + interface.process(); + + // Get short-range forces of local and ghost atoms. + interface.getForces(atom->f); + + // Initialize global arrays + for (int i =0; i < atom->natoms; i++){ + qall[i] = 0.0; + qall_loc[i] = 0.0; + dEdLambda_all[i] = 0.0; + dEdLambda_loc[i] = 0.0; + forceLambda[i] = 0.0; + dEdQ[i] = 0.0; + forceLambda_loc[i] = 0.0; + forceLambda_all[i] = 0.0; + xx_loc[i] = 0.0; + xy_loc[i] = 0.0; + xz_loc[i] = 0.0; + xx[i] = 0.0; + xy[i] = 0.0; + xz[i] = 0.0; + type_loc[i] = 0; + type_all[i] = 0; + } + + // Create global sparse arrays here + for (int i = 0; i < atom->nlocal; i++){ + qall_loc[atom->tag[i]-1] = atom->q[i]; // global charge vector on each proc + xx_loc[atom->tag[i]-1] = atom->x[i][0]; + xy_loc[atom->tag[i]-1] = atom->x[i][1]; + xz_loc[atom->tag[i]-1] = atom->x[i][2]; + type_loc[atom->tag[i]-1] = atom->type[i]; + } + + // Communicate atomic charges and positions + MPI_Allreduce(qall_loc,qall,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(type_loc,type_all,atom->natoms,MPI_INT,MPI_SUM,world); + MPI_Allreduce(xx_loc,xx,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(xy_loc,xy,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(xz_loc,xz,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + + //TODO: it did not work when they were in the constructor as they are in FixHDNNP, check + if (periodic){ + kspacehdnnp = nullptr; + kspacehdnnp = (KSpaceHDNNP *) force->kspace_match("^hdnnp",0); + } + + // Calculates and stores k-space terms for speedup + calculate_kspace_terms(); + + // Calculate dEelecdQ and add pEelecpr contribution to the total force vector + calculateElecDerivatives(dEdQ,atom->f); // TODO: calculate fElec separately ? + + // Read dEdG array from n2p2 + interface.getdEdQ(dEdQ); + + // Calculate lambda vector that is necessary for optimized force calculation + calculateForceLambda(); // TODO: lambdaElec & f_elec ? + + // Communicate forceLambda + for (int i = 0; i < atom->nlocal; i++){ + forceLambda_loc[atom->tag[i]-1] = forceLambda[i]; + } + for (int i = 0; i < atom->natoms; i++){ + forceLambda_all[i] = 0.0; + } + MPI_Allreduce(forceLambda_loc,forceLambda_all,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + + // Add electrostatic contributions and calculate final force vector + calculateElecForce(atom->f); + + // TODO check + memory->destroy(erfc_val); + + // Do all stuff related to extrapolation warnings. + if(showew == true || showewsum > 0 || maxew >= 0) { + handleExtrapolationWarnings(); + } + } + // Add energy contribution to total energy. + if (eflag_global) + ev_tally(0,0,atom->nlocal,1,interface.getEnergy(),0.0,0.0,0.0,0.0,0.0); + + // Add atomic energy if requested (CAUTION: no physical meaning!). + if (eflag_atom) + for (int i = 0; i < atom->nlocal; ++i) + eatom[i] = interface.getAtomicEnergy(i); + + // If virial needed calculate via F dot r. + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairHDNNP4G::settings(int narg, char **arg) +{ + int iarg = 0; + + if (narg == 0) error->all(FLERR,"Illegal pair_style command"); + + // default settings + int len = strlen("nnp/") + 1; + directory = new char[len]; + strcpy(directory,"nnp/"); + showew = true; + showewsum = 0; + maxew = 0; + resetew = false; + cflength = 1.0; + cfenergy = 1.0; + len = strlen("") + 1; + emap = new char[len]; + strcpy(emap,""); + numExtrapolationWarningsTotal = 0; + numExtrapolationWarningsSummary = 0; + + while(iarg < narg) { + // set NNP directory + if (strcmp(arg[iarg],"dir") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + delete[] directory; + len = strlen(arg[iarg+1]) + 2; + directory = new char[len]; + sprintf(directory, "%s/", arg[iarg+1]); + iarg += 2; + // element mapping + } else if (strcmp(arg[iarg],"emap") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + delete[] emap; + len = strlen(arg[iarg+1]) + 1; + emap = new char[len]; + sprintf(emap, "%s", arg[iarg+1]); + iarg += 2; + // show extrapolation warnings + } else if (strcmp(arg[iarg],"showew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + if (strcmp(arg[iarg+1],"yes") == 0) + showew = true; + else if (strcmp(arg[iarg+1],"no") == 0) + showew = false; + else + error->all(FLERR,"Illegal pair_style command"); + iarg += 2; + // show extrapolation warning summary + } else if (strcmp(arg[iarg],"showewsum") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + showewsum = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // maximum allowed extrapolation warnings + } else if (strcmp(arg[iarg],"maxew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + maxew = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // reset extrapolation warning counter + } else if (strcmp(arg[iarg],"resetew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + if (strcmp(arg[iarg+1],"yes") == 0) + resetew = true; + else if (strcmp(arg[iarg+1],"no") == 0) + resetew = false; + else + error->all(FLERR,"Illegal pair_style command"); + iarg += 2; + // length unit conversion factor + } else if (strcmp(arg[iarg],"cflength") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + cflength = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // energy unit conversion factor + } else if (strcmp(arg[iarg],"cfenergy") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + cfenergy = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + } else error->all(FLERR,"Illegal pair_style command"); + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairHDNNP4G::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients"); + + int ilo,ihi,jlo,jhi; + + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + maxCutoffRadius = utils::numeric(FLERR,arg[2],false,lmp); // this the cutoff specified via pair_coeff in the input + + // TODO: Check how this flag is set. + int count = 0; + for(int i=ilo; i<=ihi; i++) { + for(int j=MAX(jlo,i); j<=jhi; j++) { + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairHDNNP4G::init_style() +{ + //int irequest = neighbor->request((void *) this); + //neighbor->requests[irequest]->pair = 1; + //neighbor->requests[irequest]->half = 0; + //neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); + + // Return immediately if NNP setup is already completed. + if (interface.isInitialized()) return; + + // Activate screen and logfile output only for rank 0. + if (comm->me == 0) { + if (lmp->screen != NULL) + interface.log.registerCFilePointer(&(lmp->screen)); + if (lmp->logfile != NULL) + interface.log.registerCFilePointer(&(lmp->logfile)); + } + + ///TODO: add nnpType + // Initialize interface on all processors. + interface.initialize(directory, + emap, + showew, + resetew, + showewsum, + maxew, + cflength, + cfenergy, + maxCutoffRadius, + atom->ntypes, + comm->me); + // LAMMPS cutoff radius (given via pair_coeff) should not be smaller than + // maximum symmetry function cutoff radius. + if (maxCutoffRadius < interface.getMaxCutoffRadius()) + error->all(FLERR,"Inconsistent cutoff radius"); + + if (interface.getNnpType() == InterfaceLammps::NNPType::HDNNP_4G) + { + isPeriodic(); // check for periodicity here + } +} + +/* ---------------------------------------------------------------------- + init neighbor list(TODO: check this) +------------------------------------------------------------------------- */ + +void PairHDNNP4G::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairHDNNP4G::init_one(int i, int j) +{ + // TODO: Check how this actually works for different cutoffs. + return maxCutoffRadius; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairHDNNP4G::write_restart(FILE *fp) +{ + return; +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairHDNNP4G::read_restart(FILE *fp) +{ + return; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairHDNNP4G::write_restart_settings(FILE *fp) +{ + return; +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairHDNNP4G::read_restart_settings(FILE *fp) +{ + return; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairHDNNP4G::allocate() +{ + allocated = 1; + int n = atom->ntypes; + int natoms = atom->natoms; + int nlocal = atom->nlocal; + + + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + // TODO: add an if and initialize only for 4G + // Allocate and initialize 4G-related arrays + dEdQ = nullptr; + forceLambda = nullptr; + memory->create(dEdQ,natoms+1,"pair:dEdQ"); + memory->create(forceLambda,natoms+1,"pair:forceLambda"); + memory->create(dEdLambda_loc,natoms,"pair_nnp:dEdLambda_loc"); + memory->create(dEdLambda_all,natoms,"pair_nnp:dEdLambda_all"); + memory->create(qall_loc,natoms,"pair_nnp:qall_loc"); + memory->create(qall,natoms,"pair_nnp:qall"); + memory->create(type_loc,natoms,"pair_nnp:type_loc"); + memory->create(type_all,natoms,"pair_nnp:type_all"); + memory->create(xx,natoms,"pair_nnp:xx"); + memory->create(xy,natoms,"pair_nnp:xy"); + memory->create(xz,natoms,"pair_nnp:xz"); + memory->create(xx_loc,natoms,"pair_nnp:xx_loc"); + memory->create(xy_loc,natoms,"pair_nnp:xy_loc"); + memory->create(xz_loc,natoms,"pair_nnp:xz_loc"); + memory->create(forceLambda_loc,natoms,"pair_nnp:forceLambda_loc"); + memory->create(forceLambda_all,natoms,"pair_nnp:forceLambda_all"); + + /*memory->create(kcos,nlocal,natoms,"pair_nnp:kcos"); + memory->create(ksinx,nlocal,natoms,"pair_nnp:ksinx"); + memory->create(ksiny,nlocal,natoms,"pair_nnp:ksiny"); + memory->create(ksinz,nlocal,natoms,"pair_nnp:ksinz");*/ + + for (int i = 0; i < natoms+1; i++) + { + forceLambda[i] = 0.0; + dEdQ[i] = 0.0; + } + + /*for (int i = 0; i < nlocal; i++) + { + for (int j = 0; j < natoms; j++) + { + kcos[i][j] = 0.0; + ksinx[i][j] = 0.0; + ksiny[i][j] = 0.0; + ksinz[i][j] = 0.0; + } + }*/ + +} + +// Transfers neighbor lists to n2p2 +void PairHDNNP4G::transferNeighborList() +{ + // Transfer neighbor list to NNP. + double rc2 = maxCutoffRadius * maxCutoffRadius; + for (int ii = 0; ii < list->inum; ++ii) { + int i = list->ilist[ii]; + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + int j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + double dx = atom->x[i][0] - atom->x[j][0]; + double dy = atom->x[i][1] - atom->x[j][1]; + double dz = atom->x[i][2] - atom->x[j][2]; + double d2 = dx * dx + dy * dy + dz * dz; + if (d2 <= rc2) { + interface.addNeighbor(i,j,atom->tag[j],atom->type[j],dx,dy,dz,d2); + } + } + } +} + +void PairHDNNP4G::handleExtrapolationWarnings() +{ + // Get number of extrapolation warnings for local atoms. + // TODO: Is the conversion from std::size_t to long ok? + long numCurrentEW = (long)interface.getNumExtrapolationWarnings(); + + // Update (or set, resetew == true) total warnings counter. + if (resetew) numExtrapolationWarningsTotal = numCurrentEW; + else numExtrapolationWarningsTotal += numCurrentEW; + + // Update warnings summary counter. + if(showewsum > 0) { + numExtrapolationWarningsSummary += numCurrentEW; + } + + // If requested write extrapolation warnings. + // Requires communication of all symmetry functions statistics entries to + // rank 0. + if(showew > 0) { + // First collect an overview of extrapolation warnings per process. + long* numEWPerProc = NULL; + if(comm->me == 0) numEWPerProc = new long[comm->nprocs]; + MPI_Gather(&numCurrentEW, 1, MPI_LONG, numEWPerProc, 1, MPI_LONG, 0, world); + + if(comm->me == 0) { + for(int i=1;inprocs;i++) { + if(numEWPerProc[i] > 0) { + long bs = 0; + MPI_Status ms; + // Get buffer size. + MPI_Recv(&bs, 1, MPI_LONG, i, 0, world, &ms); + char* buf = new char[bs]; + // Receive buffer. + MPI_Recv(buf, bs, MPI_BYTE, i, 0, world, &ms); + interface.extractEWBuffer(buf, bs); + delete[] buf; + } + } + interface.writeExtrapolationWarnings(); + } + else if(numCurrentEW > 0) { + // Get desired buffer length for all extrapolation warning entries. + long bs = interface.getEWBufferSize(); + // Allocate and fill buffer. + char* buf = new char[bs]; + interface.fillEWBuffer(buf, bs); + // Send buffer size and buffer. + MPI_Send(&bs, 1, MPI_LONG, 0, 0, world); + MPI_Send(buf, bs, MPI_BYTE, 0, 0, world); + delete[] buf; + } + + if(comm->me == 0) delete[] numEWPerProc; + } + + // If requested gather number of warnings to display summary. + if(showewsum > 0 && update->ntimestep % showewsum == 0) { + long globalEW = 0; + // Communicate the sum over all processors to proc 0. + MPI_Reduce(&numExtrapolationWarningsSummary, + &globalEW, 1, MPI_LONG, MPI_SUM, 0, world); + // Write to screen or logfile. + if(comm->me == 0) { + if(screen) { + fprintf(screen, + "### NNP EW SUMMARY ### TS: %10ld EW %10ld EWPERSTEP %10.3e\n", + update->ntimestep, + globalEW, + double(globalEW) / showewsum); + } + if(logfile) { + fprintf(logfile, + "### NNP EW SUMMARY ### TS: %10ld EW %10ld EWPERSTEP %10.3e\n", + update->ntimestep, + globalEW, + double(globalEW) / showewsum); + } + } + // Reset summary counter. + numExtrapolationWarningsSummary = 0; + } + + // Stop if maximum number of extrapolation warnings is exceeded. + if (numExtrapolationWarningsTotal > maxew) { + error->one(FLERR,"Too many extrapolation warnings"); + } + + // Reset internal extrapolation warnings counters. + interface.clearExtrapolationWarnings(); +} + +// Write atomic charges into n2p2 +void PairHDNNP4G::transferCharges() +{ + for (int i = 0; i < atom->nlocal; ++i) { + interface.addCharge(i,atom->q[i]); + } +} + +// forceLambda function +double PairHDNNP4G::forceLambda_f(const gsl_vector *v) +{ + int i,j,jmap; + int *type = atom->type; + int nlocal = atom->nlocal; + int *tag = atom->tag; + int nall = atom->natoms; + + double **x = atom->x; + double E_real, E_recip, E_self; + double E_lambda,E_lambda_loc; + double iiterm,ijterm; + + double eta; + + if (periodic) eta = 1 / kspacehdnnp->g_ewald; // LAMMPS truncation + + E_lambda = 0.0; + E_lambda_loc = 0.0; + if (periodic) + { + double sqrt2eta = (sqrt(2.0) * eta); + E_recip = 0.0; + E_real = 0.0; + E_self = 0.0; + for (i = 0; i < nlocal; i++) // over local atoms + { + double const lambda_i = gsl_vector_get(v, tag[i]-1); + double lambda_i2 = lambda_i * lambda_i; + + // Self interactionsterm + E_self += lambda_i2 * (1 / (2.0 * sigmaSqrtPi[type[i]-1]) - 1 / (sqrt(2.0 * M_PI) * eta)); + E_lambda_loc += dEdQ[i] * lambda_i + 0.5 * hardness[type[i]-1] * lambda_i2; + + // Real space + // TODO: we loop over the full neighbor list, could this be optimized ? + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + double const lambda_j = gsl_vector_get(v, tag[j]-1); + //jmap = atom->map(tag[j]); + //double const dx = x[i][0] - x[j][0]; + //double const dy = x[i][1] - x[j][1]; + //double const dz = x[i][2] - x[j][2]; + //double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * cflength; + //double erfcRij = (erfc(rij / sqrt2eta) - erfc(rij / gammaSqrt2[type[i]-1][type[jmap]-1])) / rij; + //double real = 0.5 * lambda_i * lambda_j * erfcRij; + double real = 0.5 * lambda_i * lambda_j * erfc_val[i][jj]; + E_real += real; + } + } + // Reciprocal space + for (int k = 0; k < kspacehdnnp->kcount; k++) // over k-space + { + double sf_real_loc = 0.0; + double sf_im_loc = 0.0; + kspacehdnnp->sf_real[k] = 0.0; + kspacehdnnp->sf_im[k] = 0.0; + for (i = 0; i < nlocal; i++) //TODO: check + { + double const lambda_i = gsl_vector_get(v,tag[i]-1); + sf_real_loc += lambda_i * kspacehdnnp->sfexp_rl[k][i]; + sf_im_loc += lambda_i * kspacehdnnp->sfexp_im[k][i]; + } + MPI_Allreduce(&(sf_real_loc),&(kspacehdnnp->sf_real[k]),1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&(sf_im_loc),&(kspacehdnnp->sf_im[k]),1,MPI_DOUBLE,MPI_SUM,world); + E_recip += kspacehdnnp->kcoeff[k] * (pow(kspacehdnnp->sf_real[k],2) + pow(kspacehdnnp->sf_im[k],2)); + } + E_lambda_loc += E_real + E_self; + }else + { + // first loop over local atoms + for (i = 0; i < nlocal; i++) { + double const lambda_i = gsl_vector_get(v,i); + // add i terms here + iiterm = lambda_i * lambda_i / (2.0 * sigmaSqrtPi[type[i]-1]); + E_lambda += iiterm + dEdQ[i]*lambda_i + 0.5*hardness[type[i]-1]*lambda_i*lambda_i; + // second loop over 'all' atoms + for (j = i + 1; j < nall; j++) { + double const lambda_j = gsl_vector_get(v, j); + double const dx = x[j][0] - x[i][0]; + double const dy = x[j][1] - x[i][1]; + double const dz = x[j][2] - x[i][2]; + double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * cflength; + ijterm = lambda_i * lambda_j * (erf(rij / gammaSqrt2[type[i]-1][type[j]-1]) / rij); + E_lambda += ijterm; + } + } + } + + MPI_Allreduce(&E_lambda_loc,&E_lambda,1,MPI_DOUBLE,MPI_SUM,world); // MPI_SUM of local QEQ contributions + E_lambda += E_recip; // adding already all-reduced reciprocal part + + return E_lambda; +} + +// forceLambda function - wrapper +double PairHDNNP4G::forceLambda_f_wrap(const gsl_vector *v, void *params) +{ + return static_cast(params)->forceLambda_f(v); +} + +// forceLambda gradient +void PairHDNNP4G::forceLambda_df(const gsl_vector *v, gsl_vector *dEdLambda) +{ + int i,j,jmap; + int nlocal = atom->nlocal; + int nall = atom->natoms; + int *tag = atom->tag; + int *type = atom->type; + + double **x = atom->x; + double val; + double grad; + double grad_sum,grad_sum_loc,grad_i; + double local_sum; + + double eta; + + if (periodic) eta = 1 / kspacehdnnp->g_ewald; // LAMMPS truncation + + grad_sum = 0.0; + grad_sum_loc = 0.0; + if (periodic) + { + double sqrt2eta = (sqrt(2.0) * eta); + for (i = 0; i < nlocal; i++) // over local atoms + { + double const lambda_i = gsl_vector_get(v,tag[i]-1); + + // Reciprocal space + double ksum = 0.0; + for (int k = 0; k < kspacehdnnp->kcount; k++) // over k-space + { + ksum += 2.0 * kspacehdnnp->kcoeff[k] * + (kspacehdnnp->sf_real[k] * kspacehdnnp->sfexp_rl[k][i] + + kspacehdnnp->sf_im[k] * kspacehdnnp->sfexp_im[k][i]); + } + + // Real space + double jsum = 0.0; + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + double const lambda_j = gsl_vector_get(v, tag[j]-1); + //jmap = atom->map(tag[j]); + //double const dx = x[i][0] - x[j][0]; + //double const dy = x[i][1] - x[j][1]; + //double const dz = x[i][2] - x[j][2]; + //double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * cflength; + //double erfcRij = (erfc(rij / sqrt2eta) - erfc(rij / gammaSqrt2[type[i]-1][type[jmap]-1])); + //jsum += lambda_j * erfcRij / rij; + jsum += lambda_j * erfc_val[i][jj]; + } + grad = jsum + ksum + dEdQ[i] + hardness[type[i]-1]*lambda_i + + lambda_i * (1/(sigmaSqrtPi[type[i]-1])- 2/(eta * sqrt(2.0 * M_PI))); + grad_sum_loc += grad; + dEdLambda_loc[tag[i]-1] = grad; // fill gradient array based on tags instead of local IDs + } + }else + { + // first loop over local atoms + for (i = 0; i < nlocal; i++) { // TODO: indices + double const lambda_i = gsl_vector_get(v,i); + local_sum = 0.0; + // second loop over 'all' atoms + for (j = 0; j < nall; j++) { + if (j != i) { + double const lambda_j = gsl_vector_get(v, j); + double const dx = x[j][0] - x[i][0]; + double const dy = x[j][1] - x[i][1]; + double const dz = x[j][2] - x[i][2]; + double const rij = sqrt(SQR(dx) + SQR(dy) + SQR(dz)) * cflength; + local_sum += lambda_j * erf(rij / gammaSqrt2[type[i]-1][type[j]-1]) / rij; + } + } + val = dEdQ[i] + hardness[type[i]-1]*lambda_i + + lambda_i/(sigmaSqrtPi[type[i]-1]) + local_sum; + grad_sum = grad_sum + val; + gsl_vector_set(dEdLambda,i,val); + } + } + + MPI_Allreduce(dEdLambda_loc,dEdLambda_all,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&grad_sum_loc,&grad_sum,1,MPI_DOUBLE,MPI_SUM,world); + + // Gradient projection //TODO: communication ? + for (i = 0; i < nall; i++){ + grad_i = dEdLambda_all[i]; + gsl_vector_set(dEdLambda,i,grad_i - (grad_sum)/nall); + } + +} + +// forceLambda gradient - wrapper +void PairHDNNP4G::forceLambda_df_wrap(const gsl_vector *v, void *params, gsl_vector *df) +{ + static_cast(params)->forceLambda_df(v, df); +} + +// forceLambda f*df +void PairHDNNP4G::forceLambda_fdf(const gsl_vector *v, double *f, gsl_vector *df) +{ + *f = forceLambda_f(v); + forceLambda_df(v, df); +} + +// forceLambda f*df - wrapper +void PairHDNNP4G::forceLambda_fdf_wrap(const gsl_vector *v, void *params, double *f, gsl_vector *df) +{ + static_cast(params)->forceLambda_fdf(v, f, df); +} + +// Calculate forcelambda vector $\lambda_i$ that is required for optimized force calculation +void PairHDNNP4G::calculateForceLambda() +{ + size_t iter = 0; + int i,j; + int nsize,status; + int nlocal; + + double psum_it; + double gradsum; + double lambda_i; + + nsize = atom->natoms; // total number of atoms + nlocal = atom->nlocal; // total number of atoms + + gsl_vector *x; // charge vector in our case + + forceLambda_minimizer.n = nsize; + forceLambda_minimizer.f = &forceLambda_f_wrap; + forceLambda_minimizer.df = &forceLambda_df_wrap; + forceLambda_minimizer.fdf = &forceLambda_fdf_wrap; + forceLambda_minimizer.params = this; + + for (int i =0; i < atom->natoms; i++) { + dEdLambda_all[i] = 0.0; + dEdLambda_loc[i] = 0.0; + forceLambda_loc[i] = 0.0; + forceLambda_all[i] = 0.0; + } + + // Communicate forceLambda + for (int i = 0; i < atom->nlocal; i++){ + forceLambda_loc[atom->tag[i]-1] = forceLambda[i]; + } + MPI_Allreduce(forceLambda_loc,forceLambda_all,atom->natoms,MPI_DOUBLE,MPI_SUM,world); + + + // TODO : check + x = gsl_vector_alloc(nsize); + for (i = 0; i < nsize; i++) { + gsl_vector_set(x,i,forceLambda_all[i]); + } + + T = gsl_multimin_fdfminimizer_vector_bfgs2; + s = gsl_multimin_fdfminimizer_alloc(T, nsize); + + gsl_multimin_fdfminimizer_set(s, &forceLambda_minimizer, x, step, min_tol); // TODO would tol = 0 be expensive ?? + do + { + iter++; + psum_it = 0.0; + status = gsl_multimin_fdfminimizer_iterate(s); + + // Projection + for(i = 0; i < nsize; i++) { + psum_it = psum_it + gsl_vector_get(s->x, i); + } + for(i = 0; i < nsize; i++) { + lambda_i = gsl_vector_get(s->x,i); + gsl_vector_set(s->x,i, lambda_i - psum_it/nsize); // projection + } + + status = gsl_multimin_test_gradient(s->gradient, grad_tol); + + //if (status == GSL_SUCCESS) printf ("Minimum forceLambda is found at iteration: %zu\n",iter); + + } + while (status == GSL_CONTINUE && iter < maxit); + + // Read charges before deallocating x + for (i = 0; i < nlocal; i++) { + forceLambda[i] = gsl_vector_get(s->x,atom->tag[i]-1); + } + + gsl_multimin_fdfminimizer_free(s); + gsl_vector_free(x); +} + +void PairHDNNP4G::calculate_kspace_terms() +{ + int i,j,k; + int nlocal = atom->nlocal; + int nall = atom->natoms; + + double **x = atom->x; + double dx,dy,dz; + double kdum_cos,kdum_sinx,kdum_siny,kdum_sinz; + + // This term is used in dEdQ calculation and can be calculated beforehand + for (k = 0; k < kspacehdnnp->kcount; k++) + { + kcoeff_sum += 2 * kspacehdnnp->kcoeff[k]; + } + + for (i = 0; i < nlocal; i++) + { + for (j = 0; j < nall; j++) + { + kdum_cos = 0.0; + kdum_sinx = 0.0; + kdum_siny = 0.0; + kdum_sinz = 0.0; + + /*dx = x[i][0] - xx[j]; + dy = x[i][1] - xy[j]; + dz = x[i][2] - xz[j]; + + for (int k = 0; k < kspacehdnnp->kcount; k++) { + double kx = kspacehdnnp->kxvecs[k] * kspacehdnnp->unitk[0]; + double ky = kspacehdnnp->kyvecs[k] * kspacehdnnp->unitk[1]; + double kz = kspacehdnnp->kzvecs[k] * kspacehdnnp->unitk[2]; + double kdr = (dx * kx + dy * ky + dz * kz) * cflength; + + // Cos term + if (dx != 0.0) kdum_cos += 2.0 * kspacehdnnp->kcoeff[k] * cos(kdr); + + // Sin terms + double sinkdr = sin(kdr); + kdum_sinx -= 2.0 * kspacehdnnp->kcoeff[k] * sinkdr * kx; + kdum_siny -= 2.0 * kspacehdnnp->kcoeff[k] * sinkdr * ky; + kdum_sinz -= 2.0 * kspacehdnnp->kcoeff[k] * sinkdr * kz; + } + kcos[i][j] = kdum_cos; + ksinx[i][j] = kdum_sinx; + ksiny[i][j] = kdum_siny; + ksinz[i][j] = kdum_sinz;*/ + } + } +} + +// Calculate $dEelec/dQ_i$ and add one part of the $\partial Eelec/\partial Q_i$ contribution to the total force vector +void PairHDNNP4G::calculateElecDerivatives(double *dEelecdQ, double **f) +{ + int i,j,jmap; + int nlocal = atom->nlocal; + int nall = atom->natoms; + int *tag = atom->tag; + int *type = atom->type; + + double **x = atom->x; + double *q = atom->q; + double qi,qj; + double dx,dy,dz; + double rij,rij2,erfrij; + double gams2; + double sij,tij; + double fsrij,dfsrij; // corrections due to screening + + double eta; + + if (periodic) eta = 1 / kspacehdnnp->g_ewald; // LAMMPS truncation (RuNNer truncation has been removed) + + for (i = 0; i < nlocal; i++) + { + qi = q[i]; + if (periodic) + { + double sqrt2eta = (sqrt(2.0) * eta); + double ksum = 0.0; + for (j = 0; j < nall; j++) + { + double Aij = 0.0; + qj = qall[j]; + dx = x[i][0] - xx[j]; + dy = x[i][1] - xy[j]; + dz = x[i][2] - xz[j]; + // Reciprocal part + for (int k = 0; k < kspacehdnnp->kcount; k++) { + double kdr = (dx * kspacehdnnp->kxvecs[k] * kspacehdnnp->unitk[0] + + dy * kspacehdnnp->kyvecs[k] * kspacehdnnp->unitk[1] + + dz * kspacehdnnp->kzvecs[k] * kspacehdnnp->unitk[2]) * cflength; + if (dx != 0.0) Aij += 2.0 * kspacehdnnp->kcoeff[k] * cos(kdr); + } + dEelecdQ[i] += qj * Aij; + //dEelecdQ[i] += qj * kcos[i][j]; + } + // Add remaining k-space contributions here + dEelecdQ[i] += qi * (kcoeff_sum - 2 / (sqrt2eta * sqrt(M_PI))); + + // Real space + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + jmap = atom->map(tag[j]); + qj = qall[tag[j]-1]; + dx = x[i][0] - x[j][0]; + dy = x[i][1] - x[j][1]; + dz = x[i][2] - x[j][2]; + rij2 = SQR(dx) + SQR(dy) + SQR(dz); + rij = sqrt(rij2) * cflength; + + gams2 = gammaSqrt2[type[i]-1][type[jmap]-1]; + + //double Aij = (erfc(rij / sqrt2eta) - erfc(rij / gams2)) / rij; + double Aij = erfc_val[i][jj]; + + dEelecdQ[i] += qj * Aij; // Add Aij contribution regardless of screening + + if (rij < screening_info[2]) + { + erfrij = erf(rij / gams2); + fsrij = screening_f(rij); + dfsrij = screening_df(rij); + + sij = erfrij * (fsrij - 1) / rij; + + tij = (2 / (sqrt(M_PI)*gams2) * exp(- pow(rij / gams2,2)) * + (fsrij - 1) + erfrij*dfsrij - erfrij*(fsrij-1)/rij) / rij2; + + dEelecdQ[i] += qj * (sij); // Add sij contributions if inside screening cutoff + + f[i][0] -= 0.5 * (qi * qj * dx * tij) / cfenergy; + f[i][1] -= 0.5 * (qi * qj * dy * tij) / cfenergy; + f[i][2] -= 0.5 * (qi * qj * dz * tij) / cfenergy; + + f[j][0] += 0.5 * (qi * qj * dx * tij) / cfenergy; + f[j][1] += 0.5 * (qi * qj * dy * tij) / cfenergy; + f[j][2] += 0.5 * (qi * qj * dz * tij) / cfenergy; + } + } + }else + { + for (j = 0; j < nall; j++) + { + // Retrieve position, type and charge from global arrays + //TODO check + dx = x[i][0] - xx[j]; + dy = x[i][1] - xy[j]; + dz = x[i][2] - xz[j]; + qj = qall[j]; + rij2 = SQR(dx) + SQR(dy) + SQR(dz); + rij = sqrt(rij2) * cflength; + + if (rij != 0.0) + { + gams2 = gammaSqrt2[type[i]-1][type_all[j]-1]; + + erfrij = erf(rij / gams2); + fsrij = screening_f(rij); + dfsrij = screening_df(rij); + + sij = erfrij * (fsrij - 1) / rij; + tij = (2 / (sqrt(M_PI)*gams2) * exp(- pow(rij / gams2,2)) * + (fsrij - 1) + erfrij*dfsrij - erfrij*(fsrij-1)/rij) / rij2; + + dEelecdQ[i] += qj * ((erfrij/rij) + sij); + f[i][0] -= qi * qj * dx * tij; + f[i][1] -= qi * qj * dy * tij; + f[i][2] -= qi * qj * dz * tij; + } + } + } + } + kcoeff_sum = 0.0; // re-initialize to 0.0 here +} + +// Calculate electrostatic forces and add to atomic force vectors +// TODO: clean-up & non-periodic +void PairHDNNP4G::calculateElecForce(double **f) +{ + + int i,j,k; + int nlocal = atom->nlocal; + int nall = atom->natoms; + int *tag = atom->tag; + int *type = atom->type; + + double rij; + double qi,qj,qk; + double *q = atom->q; + double **x = atom->x; + double delr,gams2; + double dx,dy,dz; + + double eta; + + if (periodic) eta = 1 / kspacehdnnp->g_ewald; // LAMMPS truncation + + // lambda_i * dChidr contributions are added into the force vectors in n2p2 + interface.getForcesChi(forceLambda_all, atom->f); + + for (i = 0; i < nlocal; i++) { + qi = q[i]; + double lambdai = forceLambda[i]; + if (periodic) { + double sqrt2eta = (sqrt(2.0) * eta); + double dAdrx = 0.0; + double dAdry = 0.0; + double dAdrz = 0.0; + + // Real space + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + k = list->firstneigh[i][jj]; + k &= NEIGHMASK; + int jmap = atom->map(tag[k]); + qk = qall[tag[k]-1]; + double lambdak = forceLambda_all[tag[k]-1]; + dx = x[i][0] - x[k][0]; + dy = x[i][1] - x[k][1]; + dz = x[i][2] - x[k][2]; + double rij2 = SQR(dx) + SQR(dy) + SQR(dz); + rij = sqrt(rij2) * cflength; + + if (rij < kspacehdnnp->ewald_real_cutoff) { + gams2 = gammaSqrt2[type[i]- 1][type[jmap]-1]; + //delr = (2 / sqrt(M_PI) * (-exp(-pow(rij / sqrt2eta, 2)) + // / sqrt2eta + exp(-pow(rij / gams2, 2)) / gams2) + // - 1 / rij * (erfc(rij / sqrt2eta) - erfc(rij / gams2))) / rij2; + delr = (2 / sqrt(M_PI) * (-exp(-pow(rij / sqrt2eta, 2)) + / sqrt2eta + exp(-pow(rij / gams2, 2)) / gams2) + - erfc_val[i][jj]) / rij2; + dAdrx = dx * delr; + dAdry = dy * delr; + dAdrz = dz * delr; + + // Contributions to the local atom i + f[i][0] -= 0.5 * (lambdai * qk + lambdak * qi) * dAdrx / cfenergy; + f[i][1] -= 0.5 * (lambdai * qk + lambdak * qi) * dAdry / cfenergy; + f[i][2] -= 0.5 * (lambdai * qk + lambdak * qi) * dAdrz / cfenergy; + + // Contributions to the neighbors of the local atom i + f[k][0] += 0.5 * (lambdai * qk + lambdak * qi) * dAdrx / cfenergy; + f[k][1] += 0.5 * (lambdai * qk + lambdak * qi) * dAdry / cfenergy; + f[k][2] += 0.5 * (lambdai * qk + lambdak * qi) * dAdrz / cfenergy; + + // Contributions to the local atom i (pEelecpr) + f[i][0] -= (0.5 * qk * dAdrx * qi) / cfenergy; + f[i][1] -= (0.5 * qk * dAdry * qi) / cfenergy; + f[i][2] -= (0.5 * qk * dAdrz * qi) / cfenergy; + + f[k][0] += (0.5 * qk * dAdrx * qi) / cfenergy; + f[k][1] += (0.5 * qk * dAdry * qi) / cfenergy; + f[k][2] += (0.5 * qk * dAdrz * qi) / cfenergy; + } + } + // Reciprocal space + for (j = 0; j < nall; j++){ + qj = qall[j]; + double lambdaj = forceLambda_all[j]; + dx = x[i][0] - xx[j]; + dy = x[i][1] - xy[j]; + dz = x[i][2] - xz[j]; + double ksx = 0; + double ksy = 0; + double ksz = 0; + for (int kk = 0; kk < kspacehdnnp->kcount; kk++) { + double kx = kspacehdnnp->kxvecs[kk] * kspacehdnnp->unitk[0]; + double ky = kspacehdnnp->kyvecs[kk] * kspacehdnnp->unitk[1]; + double kz = kspacehdnnp->kzvecs[kk] * kspacehdnnp->unitk[2]; + double kdr = (dx * kx + dy * ky + dz * kz) * cflength; + ksx -= 2.0 * kspacehdnnp->kcoeff[kk] * sin(kdr) * kx; + ksy -= 2.0 * kspacehdnnp->kcoeff[kk] * sin(kdr) * ky; + ksz -= 2.0 * kspacehdnnp->kcoeff[kk] * sin(kdr) * kz; + } + dAdrx = ksx; + dAdry = ksy; + dAdrz = ksz; + //dAdrx = ksinx[i][j]; + //dAdry = ksiny[i][j]; + //dAdrz = ksinz[i][j]; + + // Contributions to the local atom i + f[i][0] -= (lambdai * qj + lambdaj * qi) * dAdrx * (cflength/cfenergy); + f[i][1] -= (lambdai * qj + lambdaj * qi) * dAdry * (cflength/cfenergy); + f[i][2] -= (lambdai * qj + lambdaj * qi) * dAdrz * (cflength/cfenergy); + + // pEelecpr + f[i][0] -= (qj * dAdrx * qi) * (cflength/cfenergy); + f[i][1] -= (qj * dAdry * qi) * (cflength/cfenergy); + f[i][2] -= (qj * dAdrz * qi) * (cflength/cfenergy); + + // Contributions to the neighbors of the local atom i + /*f[k][0] += (lambdai * qj + lambdaj * qi) * dAdrx * (cflength/cfenergy); + f[k][1] += (lambdai * qj + lambdaj * qi) * dAdry * (cflength/cfenergy); + f[k][2] += (lambdai * qj + lambdaj * qi) * dAdrz * (cflength/cfenergy);*/ + + /*f[k][0] += (qj * dAdrx * qi) * (cflength/cfenergy); + f[k][1] += (qj * dAdry * qi) * (cflength/cfenergy); + f[k][2] += (qj * dAdrz * qi) * (cflength/cfenergy);*/ + } + } else { + // Over all atoms in the system + for (j = 0; j < nall; j++) { + double jt0 = 0; + double jt1 = 0; + double jt2 = 0; + //qj = q[j]; + qj = qall[j]; + if (i == j) { + // We have to loop over all atoms once again to calculate dAdrQ terms + for (k = 0; k < nall; k++) { + //qk = q[k]; + qk = qall[k]; + //dx = x[i][0] - x[k][0]; + dx = x[i][0] - xx[k]; + //dy = x[i][1] - x[k][1]; + dy = x[i][1] - xy[k]; + //dz = x[i][2] - x[k][2]; + dz = x[i][2] - xz[k]; + double rij2 = SQR(dx) + SQR(dy) + SQR(dz); + rij = sqrt(rij2) * cflength; + + if (rij != 0.0) + { + //gams2 = gammaSqrt2[type[i]-1][type[k]-1]; + gams2 = gammaSqrt2[type[i]-1][type_all[k]-1]; + delr = (2 / (sqrt(M_PI) * gams2) * exp(-pow(rij / gams2, 2)) - erf(rij / gams2) / rij); + + jt0 += (dx / rij2) * delr * qk; + jt1 += (dy / rij2) * delr * qk; + jt2 += (dz / rij2) * delr * qk; + } + } + } else { + //TODO + //dx = x[i][0] - x[j][0]; + dx = x[i][0] - xx[j]; + //dy = x[i][1] - x[j][1]; + dy = x[i][1] - xy[j]; + //dz = x[i][2] - x[j][2]; + dz = x[i][2] - xz[j]; + double rij2 = SQR(dx) + SQR(dy) + SQR(dz); + rij = sqrt(rij2) * cflength; + + //gams2 = gammaSqrt2[type[i]-1][type[j]-1]; + gams2 = gammaSqrt2[type[i]-1][type_all[j]-1]; + delr = (2 / (sqrt(M_PI) * gams2) * exp(-pow(rij / gams2, 2)) - erf(rij / gams2) / rij); + + jt0 = (dx / rij2) * delr * qi; + jt1 = (dy / rij2) * delr * qi; + jt2 = (dz / rij2) * delr * qi; + } + f[i][0] -= (forceLambda_all[j] * (jt0) + 0.5 * qj * jt0) / cfenergy; + f[i][1] -= (forceLambda_all[j] * (jt1) + 0.5 * qj * jt1) / cfenergy; + f[i][2] -= (forceLambda_all[j] * (jt2) + 0.5 * qj * jt2) / cfenergy; + } + } + } +} + +// Calculate screening function +// TODO : add other function types +double PairHDNNP4G::screening_f(double r) +{ + double x; + + if (r >= screening_info[2]) return 1.0; + else if (r <= screening_info[1]) return 0.0; + else + { + x = (r-screening_info[1])*screening_info[3]; + return 1.0 - 0.5*(cos(M_PI*x)+1); + } +} + +// Calculate derivative of the screening function +// TODO : add other function types +double PairHDNNP4G::screening_df(double r) { + + double x; + + if (r >= screening_info[2] || r <= screening_info[1]) return 0.0; + else { + x = (r - screening_info[1]) * screening_info[3]; + return -screening_info[3] * (-M_PI_2 * sin(M_PI * x)); + } +} + +// Check for periodicity +void PairHDNNP4G::isPeriodic() +{ + if (domain->nonperiodic == 0) periodic = true; + else periodic = false; +} + + + + + + diff --git a/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_4g.h b/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_4g.h new file mode 100644 index 0000000000..6d381b881b --- /dev/null +++ b/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_4g.h @@ -0,0 +1,136 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + This file initially came from n2p2 (https://github.com/CompPhysVienna/n2p2) + Copyright (2018) Andreas Singraber (University of Vienna) + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Emir Kocer + Andreas Singraber +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(hdnnp/4g,PairHDNNP4G) +// clang-format on +#else + +#ifndef LMP_PAIR_HDNNP4G_H +#define LMP_PAIR_HDNNP4G_H + +#include "pair.h" +#include "InterfaceLammps.h" +#include + +namespace LAMMPS_NS { + +class PairHDNNP4G : public Pair { + friend class FixHDNNP; + friend class KSpaceHDNNP; + public: + + PairHDNNP4G(class LAMMPS *); + virtual ~PairHDNNP4G(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + virtual void init_style(); + virtual double init_one(int, int); + void init_list(int,class NeighList *); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + + +protected: + + class KSpaceHDNNP *kspacehdnnp; // interface to HDNNP kspace_style + + int me,nprocs; + bool periodic; + bool showew; + bool resetew; + int showewsum; + int maxew; + long numExtrapolationWarningsTotal; + long numExtrapolationWarningsSummary; + double cflength; + double cfenergy; + double maxCutoffRadius; + char* directory; + char* emap; + class NeighList *list; + + nnp::InterfaceLammps interface; + + double *chi,*hardness,*sigmaSqrtPi,**gammaSqrt2; // QEq arrays + double *dEdQ,*forceLambda; + double grad_tol,min_tol,step; // user-defined minimization parameters + int maxit; + int minim_init_style; // initialization style for the minimization algorithm, 0: from zero or 1: from the final step + + virtual void allocate(); + void transferNeighborList(); + void isPeriodic(); + + void transferCharges(); + void handleExtrapolationWarnings(); + + void deallocateQEq(); + + // Minimization Setup for Force Lambda + const gsl_multimin_fdfminimizer_type *T; + gsl_multimin_fdfminimizer *s; + + gsl_multimin_function_fdf forceLambda_minimizer; + + double forceLambda_f(const gsl_vector*); + void forceLambda_df(const gsl_vector*, gsl_vector*); + void forceLambda_fdf(const gsl_vector*, double*, gsl_vector*); + static double forceLambda_f_wrap(const gsl_vector*, void*); + static void forceLambda_df_wrap(const gsl_vector*, void*, gsl_vector*); + static void forceLambda_fdf_wrap(const gsl_vector*, void*, double*, gsl_vector*); + + double E_elec; + double kcoeff_sum; // used in dEdQ calculation + + int nmax; + + int *type_all,*type_loc; + double *dEdLambda_loc,*dEdLambda_all; + double *qall_loc,*qall; + double *xx,*xy,*xz; // global positions + double *xx_loc,*xy_loc,*xz_loc; // sparse local positions + double *forceLambda_loc,*forceLambda_all; + + double **erfc_val; + double **kcos,**ksinx,**ksiny,**ksinz; + + void calculateForceLambda(); + void calculateElecDerivatives(double*,double**); + void calculateElecForce(double**); + void calculate_kspace_terms(); + + + // Screening + double *screening_info; + double screening_f(double); + double screening_df(double); + +}; + +} + +#endif +#endif diff --git a/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_develop.cpp b/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_develop.cpp index 577bc87c39..37b206390c 100644 --- a/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_develop.cpp +++ b/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_develop.cpp @@ -78,7 +78,7 @@ void PairHDNNPDevelop::compute(int eflag, int vflag) transferNeighborList(maxCutoffRadiusNeighborList); // Compute symmetry functions, atomic neural networks and add up energy. - interface->process(); + interface->processDevelop(); // Do all stuff related to extrapolation warnings. if(showew == true || showewsum > 0 || maxew >= 0) { @@ -86,7 +86,7 @@ void PairHDNNPDevelop::compute(int eflag, int vflag) } // Calculate forces of local and ghost atoms. - interface->getForces(atom->f); + interface->getForcesDevelop(atom->f); // Transfer charges LAMMPS. Does nothing if nnpType != 4G. interface->getCharges(atom->q); diff --git a/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_external.cpp b/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_external.cpp index 573abfbee8..19881366a3 100644 --- a/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_external.cpp +++ b/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_external.cpp @@ -23,10 +23,10 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" #include "Atom.h" // nnp::Atom #include "utility.h" // nnp:: @@ -249,6 +249,7 @@ void PairHDNNPExternal::coeff(int narg, char **arg) if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients"); int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); diff --git a/src/interface/makefile b/src/interface/makefile index df5010f73e..252b4f5ee8 100644 --- a/src/interface/makefile +++ b/src/interface/makefile @@ -51,13 +51,13 @@ lammps-hdnnp: @sed -i.bak "s;^CC .*$$;CC = $(PROJECT_MPICC);" lammps-hdnnp/src/MAKE/Makefile.mpi @sed -i.bak "s;^CCFLAGS .*$$;CCFLAGS = $(PROJECT_CFLAGS) $(PROJECT_CFLAGS_MPI) -I$(PROJECT_EIGEN);" lammps-hdnnp/src/MAKE/Makefile.mpi @sed -i.bak "s;^LINK .*$$;LINK = $(PROJECT_MPICC);" lammps-hdnnp/src/MAKE/Makefile.mpi - @sed -i.bak "s;^LINKFLAGS .*$$;LINKFLAGS = $(PROJECT_CFLAGS) $(PROJECT_CFLAGS_MPI) $(PROJECT_LDFLAGS_BLAS);" lammps-hdnnp/src/MAKE/Makefile.mpi + @sed -i.bak "s;^LINKFLAGS .*$$;LINKFLAGS = $(PROJECT_CFLAGS) $(PROJECT_CFLAGS_MPI);" lammps-hdnnp/src/MAKE/Makefile.mpi if [ "$(MODE)" = "test" ]; then \ sed -i.bak "/^CCFLAGS =/ s;$$; $(LAMMPS_DEBUG) $(PROJECT_TEST);" lammps-hdnnp/src/MAKE/Makefile.mpi; \ sed -i.bak "/^LINKFLAGS =/ s;$$; $(LAMMPS_DEBUG) $(PROJECT_TEST);" lammps-hdnnp/src/MAKE/Makefile.mpi; \ fi @rm lammps-hdnnp/src/MAKE/Makefile.mpi.bak - cd lammps-hdnnp/src/ && $(MAKE) yes-ml-hdnnp && $(MAKE) yes-molecule && $(MAKE) mpi + cd lammps-hdnnp/src/ && $(MAKE) yes-ml-hdnnp && $(MAKE) yes-kspace && $(MAKE) yes-molecule && $(MAKE) mpi cp lammps-hdnnp/src/lmp_mpi $(PROJECT_BIN)/ clean-lammps-hdnnp: diff --git a/src/libnnp/Atom.cpp b/src/libnnp/Atom.cpp index ab6f023591..8a373e5cf5 100644 --- a/src/libnnp/Atom.cpp +++ b/src/libnnp/Atom.cpp @@ -383,7 +383,7 @@ Vec3D Atom::calculatePairForceShort(Neighbor const& neighbor, const *const tableFull) const { Vec3D pairForce{}; -#ifndef NNP_FULL_SFD_MEMORY +#ifndef N2P2_FULL_SFD_MEMORY if (!tableFull) throw runtime_error( "ERROR: tableFull must not be null pointer"); vector const& table = tableFull->at(neighbor.element); @@ -404,7 +404,7 @@ Vec3D Atom::calculateDChidr(size_t const atomIndexOfR, double const maxCutoffRadius, vector > const *const tableFull) const { -#ifndef NNP_FULL_SFD_MEMORY +#ifndef N2P2_FULL_SFD_MEMORY if (!tableFull) throw runtime_error( "ERROR: tableFull must not be null pointer"); #endif @@ -426,7 +426,7 @@ Vec3D Atom::calculateDChidr(size_t const atomIndexOfR, // atomIndexOfR must not be larger than ~max(int64_t)/2. if (n.tag == (int64_t)atomIndexOfR) { -#ifndef NNP_FULL_SFD_MEMORY +#ifndef N2P2_FULL_SFD_MEMORY vector const& table = tableFull->at(n.element); for (size_t k = 0; k < n.dGdr.size(); ++k) { diff --git a/src/libnnp/EwaldSetup.h b/src/libnnp/EwaldSetup.h index 7f6398655f..2687cc1e8d 100644 --- a/src/libnnp/EwaldSetup.h +++ b/src/libnnp/EwaldSetup.h @@ -43,6 +43,7 @@ class EwaldSetup { EWALDTruncMethod getTruncMethod() const {return truncMethod;}; double getMaxCharge() const {return GlobSett.maxCharge;}; double getPrecision() const {return GlobSett.precision;}; + double getMaxQSigma() const {return GlobSett.maxQSigma;}; /** Setter for maximum width of charges. * diff --git a/src/libnnp/Kspace.cpp b/src/libnnp/Kspace.cpp index a85b0e7f62..b024242880 100644 --- a/src/libnnp/Kspace.cpp +++ b/src/libnnp/Kspace.cpp @@ -57,26 +57,54 @@ void KspaceGrid::setup(Vec3D box[3], EwaldSetup& ewaldSetup) // Compute box copies required in each direction. calculatePbcCopies(kCut); - // Compute k-grid (only half sphere because of symmetry) - for (int i = 0; i <= n[0]; ++i) + double halfSphere = 1; // TODO + if (halfSphere) { - int sj = -n[1]; - if (i == 0) sj = 0; - for (int j = sj; j <= n[1]; ++j) + // Compute k-grid (only half sphere because of symmetry). + for (int i = 0; i <= n[0]; ++i) { - int sk = -n[2]; - if (i == 0 && j == 0) sk = 0; - for (int k = sk; k <= n[2]; ++k) + int sj = -n[1]; + if (i == 0) sj = 0; + for (int j = sj; j <= n[1]; ++j) { - if (i == 0 && j == 0 && k == 0) continue; - Vec3D kv = i * kbox[0] + j * kbox[1] + k * kbox[2]; - double knorm2 = kv.norm2(); - if (kv.norm2() < kCut * kCut) + int sk = -n[2]; + if (i == 0 && j == 0) sk = 0; + for (int k = sk; k <= n[2]; ++k) { - kvectors.push_back(kv); - kvectors.back().knorm2 = knorm2; // TODO: Really necessary? - kvectors.back().coeff = exp(-0.5 * eta * eta * knorm2) - * 2.0 * pre / knorm2; + if (i == 0 && j == 0 && k == 0) continue; + Vec3D kv = i * kbox[0] + j * kbox[1] + k * kbox[2]; + double knorm2 = kv.norm2(); + if (kv.norm2() < kCut * kCut) + { + //fprintf(stderr, "sqk = %24.16E\n", kv.norm()); + kvectors.push_back(kv); + kvectors.back().knorm2 = knorm2; // TODO: Necessary? + kvectors.back().coeff = exp(-0.5 * eta * eta * knorm2) + * 2.0 * pre / knorm2; + } + } + } + } + } + else + { + // Compute full k-grid. + for (int i = -n[0]; i <= n[0]; ++i) + { + for (int j = -n[1]; j <= n[1]; ++j) + { + for (int k = -n[2]; k <= n[2]; ++k) + { + if (i == 0 && j == 0 && k == 0) continue; + Vec3D kv = i * kbox[0] + j * kbox[1] + k * kbox[2]; + double knorm2 = kv.norm2(); + if (kv.norm2() < kCut * kCut) + { + kvectors.push_back(kv); + kvectors.back().knorm2 = knorm2; // TODO: Necessary? + kvectors.back().coeff = exp(-0.5 * eta * eta * knorm2) + * 2.0 * pre / knorm2; + } } } } diff --git a/src/libnnp/Kspace.h b/src/libnnp/Kspace.h index caccfd8113..a79961e834 100644 --- a/src/libnnp/Kspace.h +++ b/src/libnnp/Kspace.h @@ -23,7 +23,14 @@ namespace nnp { - +enum class KSPACESolver { + /// Solver 0: Ewald summation. + EWALD_SUM, + /// Solver 1: PPPM. + PPPM, + /// Solver 2: Ewald summation in LAMMPS. + EWALD_SUM_LAMMPS +}; class Kvector { public: @@ -43,6 +50,8 @@ class Kvector class KspaceGrid { public: + /// Method for calculating the reciprocal part. + KSPACESolver kspaceSolver; /// Ewald summation eta parameter. double eta; /// Cutoff in reciprocal space. diff --git a/src/libnnp/Mode.cpp b/src/libnnp/Mode.cpp index baaa1090d0..2f9bf1be24 100644 --- a/src/libnnp/Mode.cpp +++ b/src/libnnp/Mode.cpp @@ -48,7 +48,8 @@ Mode::Mode() : nnpType (NNPType::HDNNP_2G), convLength (1.0 ), convCharge (1.0 ), fourPiEps (1.0 ), - ewaldSetup {} + ewaldSetup {}, + kspaceGrid {} { } @@ -448,18 +449,40 @@ void Mode::setupElectrostatics(bool initialHardness, } log << "\n"; + // K-Space Solver + if (settings.keywordExists("kspace_solver")) + { + string kspace_solver_string = settings["kspace_solver"]; + if (kspace_solver_string == "ewald") + { + kspaceGrid.kspaceSolver = KSPACESolver::EWALD_SUM; + } + else if (kspace_solver_string == "pppm") + { + kspaceGrid.kspaceSolver = KSPACESolver::PPPM; + } + else if (kspace_solver_string == "ewald_lammps") + { + kspaceGrid.kspaceSolver = KSPACESolver::EWALD_SUM_LAMMPS; + } + } + else kspaceGrid.kspaceSolver = KSPACESolver::EWALD_SUM; + // Ewald truncation error method. if (settings.keywordExists("ewald_truncation_error_method")) { string truncation_method_string = - settings["ewald_truncation_error_method"]; + settings["ewald_truncation_error_method"]; if (truncation_method_string == "0") + { ewaldSetup.setTruncMethod(EWALDTruncMethod::JACKSON_CATLOW); - if (truncation_method_string == "1") + } + else if (truncation_method_string == "1") + { ewaldSetup.setTruncMethod(EWALDTruncMethod::KOLAFA_PERRAM); + } } - else - ewaldSetup.setTruncMethod(EWALDTruncMethod::JACKSON_CATLOW); + else ewaldSetup.setTruncMethod(EWALDTruncMethod::JACKSON_CATLOW); // Ewald precision. if (settings.keywordExists("ewald_prec")) @@ -467,8 +490,7 @@ void Mode::setupElectrostatics(bool initialHardness, vector args = split(settings["ewald_prec"]); ewaldSetup.readFromArgs(args); ewaldSetup.setMaxQSigma(maxQsigma); - if (normalize) - ewaldSetup.toNormalizedUnits(convEnergy, convLength); + if (normalize) ewaldSetup.toNormalizedUnits(convEnergy, convLength); } else if (ewaldSetup.getTruncMethod() == EWALDTruncMethod::KOLAFA_PERRAM) { @@ -480,8 +502,10 @@ void Mode::setupElectrostatics(bool initialHardness, log << strpr("Ewald precision: %16.8E\n", ewaldSetup.getPrecision()); if (ewaldSetup.getTruncMethod() == EWALDTruncMethod::KOLAFA_PERRAM) + { log << strpr("Ewald expected maximum charge: %16.8E\n", ewaldSetup.getMaxCharge()); + } log << "\n"; // 4 * pi * epsilon @@ -1682,7 +1706,8 @@ void Mode::calculateAtomicNeuralNetworks(Structure& structure, } } nn.getOutput(&(a.chi)); - //double chi = a.chi; + //log << strpr("Atom %5zu (%2s) chi: %24.16E\n", + // a.index, elementMap[a.element].c_str(), a.chi); if (normalize) a.chi = normalized("negativity", a.chi); } } @@ -1692,8 +1717,6 @@ void Mode::calculateAtomicNeuralNetworks(Structure& structure, { NeuralNetwork& nn = elements.at(a.element) .neuralNetworks.at(id); - // This line is probably obsolete - //nn.setInput(&((a.G).front())); // TODO: This part should simplify with improved NN class. for (size_t i = 0; i < a.G.size(); ++i) { @@ -1708,6 +1731,8 @@ void Mode::calculateAtomicNeuralNetworks(Structure& structure, nn.calculateDEdG(&((a.dEdG).front())); } nn.getOutput(&(a.energy)); + //log << strpr("Atom %5zu (%2s) energy: %24.16E\n", + // a.index, elementMap[a.element].c_str(), a.energy); } } } @@ -1760,6 +1785,13 @@ void Mode::chargeEquilibration( Structure& structure, VectorXd hardness(numElements); MatrixXd gammaSqrt2(numElements, numElements); VectorXd sigmaSqrtPi(numElements); + // In case of natural units and no normalization + double fourPiEps = 1; + // In case of natural units but with normalization. Other units currently + // not supported. + if (normalize) fourPiEps = pow(convCharge, 2) / (convLength * convEnergy); + + fourPiEps = 1; for (size_t i = 0; i < numElements; ++i) { @@ -1787,16 +1819,12 @@ void Mode::chargeEquilibration( Structure& structure, { s.calculateDAdrQ(ewaldSetup, gammaSqrt2, fourPiEps, erfcBuf); s.calculateElectrostaticEnergyDerivatives(hardness, - gammaSqrt2, - sigmaSqrtPi, - screeningFunction, - fourPiEps); + gammaSqrt2, + sigmaSqrtPi, + screeningFunction, + fourPiEps); } - //for (auto const& a : structure.atoms) - //{ - // //structure.charge += a.charge; - //} return; } @@ -1834,14 +1862,14 @@ void Mode::calculateCharge(Structure& structure) const for (vector::iterator it = structure.atoms.begin(); it != structure.atoms.end(); ++it) { + //log << strpr("Atom %5zu (%2s) q: %24.16E\n", + // it->index, elementMap[it->element].c_str(), it->charge); structure.charge += it->charge; } - //cout << "---------------------\n"; - //cout << strpr("Total charge: %24.16E\n", structure.charge); - //cout << strpr("Reference charge: %24.16E\n", structure.chargeRef); - - //throw runtime_error("ERROR: Here ends code for 4G-HDNNPs\n"); + //log << "---------------------\n"; + //log << strpr("Total charge: %24.16E\n", structure.charge); + //log << strpr("Reference charge: %24.16E\n", structure.chargeRef); return; } @@ -1860,8 +1888,7 @@ void Mode::calculateForces(Structure& structure) const { #pragma omp for #endif - for (size_t i = 0; i < structure.atoms.size(); ++i) - { + for (size_t i = 0; i < structure.atoms.size(); ++i) { // Set pointer to atom. Atom &ai = structure.atoms.at(i); @@ -1882,21 +1909,20 @@ void Mode::calculateForces(Structure& structure) const // images of the central atom (happens when cutoff radii larger than // cell vector lengths are used, but this is already considered in the // self-interaction). - for (vector::const_iterator it = - ai.neighborsUnique.begin() + 1; + for (vector::const_iterator it = ai.neighborsUnique.begin() + 1; it != ai.neighborsUnique.end(); ++it) { // Define shortcut for atom j (aj). Atom &aj = structure.atoms.at(*it); #ifndef N2P2_FULL_SFD_MEMORY - vector > const& tableFull + vector> const& tableFull = elements.at(aj.element).getSymmetryFunctionTable(); #endif // Loop over atom j's neighbors (n), atom i should be one of them. // TODO: Could implement maxCutoffRadiusSymFunc for each element and // use this instead of maxCutoffRadius. size_t const numNeighbors = - aj.getStoredMinNumNeighbors(maxCutoffRadius); + aj.getStoredMinNumNeighbors(maxCutoffRadius); for (size_t k = 0; k < numNeighbors; ++k) { Atom::Neighbor const &n = aj.neighbors[k]; // If atom j's neighbor is atom i add force contributions. @@ -1933,7 +1959,7 @@ void Mode::calculateForces(Structure& structure) const { Atom const &aj = s.atoms.at(j); -#ifndef NNP_FULL_SFD_MEMORY +#ifndef N2P2_FULL_SFD_MEMORY vector > const &tableFull = elements.at(aj.element).getSymmetryFunctionTable(); Vec3D dChidr = aj.calculateDChidr(ai.index, @@ -1945,15 +1971,6 @@ void Mode::calculateForces(Structure& structure) const #endif ai.f -= lambdaTotal(j) * (ai.dAdrQ[j] + dChidr); ai.fElec -= lambdaElec(j) * (ai.dAdrQ[j] + dChidr); - - /* - loopFile << "i: " << ai.index << ", j: " << j << endl - << "ai.f: " << ai.f[0] << " " << ai.f[1] << " " << ai.f[2] << endl - << "lambda: " << lambdaTotal(j) << endl - << "dChidr: " << dChidr[0] << " " << dChidr[1] << " " << dChidr[2] << endl - << "dAdrQ: " << ai.dAdrQ[j][0] << " " << ai.dAdrQ[j][1] << " " << ai.dAdrQ[j][2] << endl - << endl; - */ } } } @@ -1967,20 +1984,19 @@ void Mode::calculateForces(Structure& structure) const void Mode::evaluateNNP(Structure& structure, bool useForces, bool useDEdG) { useDEdG = (useForces || useDEdG); - if (nnpType == NNPType::HDNNP_4G) { + if (nnpType == NNPType::HDNNP_4G) + { structure.calculateMaxCutoffRadiusOverall( - ewaldSetup, - screeningFunction.getOuter(), - maxCutoffRadius); - structure.calculateNeighborList(maxCutoffRadius, - cutoffs); - + ewaldSetup, + screeningFunction.getOuter(), + maxCutoffRadius); + structure.calculateNeighborList(maxCutoffRadius, cutoffs); } // TODO: For the moment sort neighbors only for 4G-HDNNPs (breaks some // CI tests because of small numeric changes). else structure.calculateNeighborList(maxCutoffRadius, false); -#ifdef NNP_NO_SF_GROUPS +#ifdef N2P2_NO_SF_GROUPS calculateSymmetryFunctions(structure, true); #else calculateSymmetryFunctionGroups(structure, useForces); diff --git a/src/libnnp/Mode.h b/src/libnnp/Mode.h index cb349a5579..30d2584d29 100644 --- a/src/libnnp/Mode.h +++ b/src/libnnp/Mode.h @@ -22,6 +22,7 @@ #include "ElementMap.h" #include "ErfcBuf.h" #include "EwaldSetup.h" +#include "Kspace.h" #include "Log.h" #include "ScreeningFunction.h" #include "Settings.h" @@ -509,6 +510,36 @@ class Mode * @return Charge unit conversion factor. */ double getConvCharge() const; + /** Getter for Mode::ewaldSetup.precision. + * + * @return Ewald precision in 4G-HDNNPs. + * + */ + double getEwaldPrecision() const; + /** Getter for Mode::ewaldSetup.maxCharge. + * + * @return Ewald max charge if specified in 4G-HDNNPs. + * + */ + double getEwaldMaxCharge() const; + /** Getter for Mode::ewaldSetup.maxQsigma. + * + * @return Ewald max sigma parameter in 4G-HDNNPs. + * + */ + double getEwaldMaxSigma() const; + /** Getter for Mode::ewaldSetup.truncMethod. + * + * @return Ewald truncation method in 4G-HDNNPs. + * + */ + EWALDTruncMethod getEwaldTruncationMethod() const; + /** Getter for Mode::kspaceSolver. + * + * @return K-space solver to be used in 4G-HDNNPs. + * + */ + KSPACESolver kspaceSolver() const; /** Getter for Mode::maxCutoffRadius. * * @return Maximum cutoff radius of all symmetry functions. @@ -523,6 +554,11 @@ class Mode * The number of elements is determined by setupElements(). */ std::size_t getNumElements() const; + /** Getter for Mode::screeningFunction. + * + * @return Copy of screening function instance. + */ + ScreeningFunction getScreeningFunction() const; /** Get number of symmetry functions per element. * * @return Vector with number of symmetry functions for each element. @@ -639,6 +675,7 @@ class Mode double convCharge; double fourPiEps; EwaldSetup ewaldSetup; + KspaceGrid kspaceGrid; settings::Settings settings; SymFnc::ScalingType scalingType; CutoffFunction::CutoffType cutoffType; @@ -700,6 +737,31 @@ inline std::size_t Mode::getNumElements() const return numElements; } +inline double Mode::getEwaldPrecision() const +{ + return ewaldSetup.getPrecision(); +} + +inline double Mode::getEwaldMaxCharge() const +{ + return ewaldSetup.getMaxCharge(); +} + +inline double Mode::getEwaldMaxSigma() const +{ + return ewaldSetup.getMaxQSigma(); +} + +inline EWALDTruncMethod Mode::getEwaldTruncationMethod() const +{ + return ewaldSetup.getTruncMethod(); +} + +inline KSPACESolver Mode::kspaceSolver() const +{ + return kspaceGrid.kspaceSolver; +} + inline bool Mode::useNormalization() const { return normalize; diff --git a/src/libnnp/Prediction.cpp b/src/libnnp/Prediction.cpp index 07ca701e36..6ffb6a878f 100644 --- a/src/libnnp/Prediction.cpp +++ b/src/libnnp/Prediction.cpp @@ -15,7 +15,9 @@ // along with this program. If not, see . #include "Prediction.h" +#include "Stopwatch.h" #include // std::ifstream +#include #include // std::map #include // std::runtime_error #include "utility.h" diff --git a/src/libnnp/Settings.cpp b/src/libnnp/Settings.cpp index 6efee6380b..aee75af796 100644 --- a/src/libnnp/Settings.cpp +++ b/src/libnnp/Settings.cpp @@ -64,6 +64,7 @@ map> const createKnownKeywordsMap() m["nnp_type" ] = ""; m["fixed_gausswidth" ] = ""; m["ewald_truncation_error_method" ] = ""; + m["kspace_solver" ] = ""; m["ewald_prec" ] = ""; m["screen_electrostatics" ] = ""; m["four_pi_epsilon" ] = ""; @@ -72,7 +73,7 @@ map> const createKnownKeywordsMap() m["random_seed" ] = ""; m["test_fraction" ] = ""; m["epochs" ] = ""; - m["normalize_data_set" ] = ""; + m["normalize_data_set" ] = ""; m["use_short_forces" ] = ""; m["rmse_threshold" ] = ""; m["rmse_threshold_energy" ] = ""; @@ -84,7 +85,7 @@ map> const createKnownKeywordsMap() m["rmse_threshold_trials_charge" ] = ""; m["energy_fraction" ] = ""; m["force_fraction" ] = ""; - m["force_energy_ratio" ] = ""; + m["force_energy_ratio" ] = ""; m["charge_fraction" ] = ""; m["use_old_weights_short" ] = ""; m["use_old_weights_charge" ] = ""; diff --git a/src/libnnp/Structure.cpp b/src/libnnp/Structure.cpp index 0845beb539..fbde68c41a 100644 --- a/src/libnnp/Structure.cpp +++ b/src/libnnp/Structure.cpp @@ -294,7 +294,6 @@ void Structure::calculateNeighborList( if (isPeriodic) { calculatePbcCopies(cutoffRadius, pbc); - // Use square of cutoffRadius (faster). cutoffRadius *= cutoffRadius; @@ -625,6 +624,7 @@ double Structure::calculateElectrostaticEnergy( KspaceGrid grid; grid.setup(box, ewaldSetup); double const rcutReal = ewaldSetup.params.rCut; + //fprintf(stderr, "CAUTION: rcutReal = %f\n", rcutReal); double const sqrt2eta = sqrt(2.0) * ewaldSetup.params.eta; #ifdef _OPENMP @@ -660,9 +660,7 @@ double Structure::calculateElectrostaticEnergy( A(i, j) += (erfcSqrt2Eta - erfcGammaSqrt2) / (rij * fourPiEps); } - // reciprocal part - //for (size_t j = i + 1; j < numAtoms; ++j) for (size_t j = i; j < numAtoms; ++j) { Atom const &aj = atoms.at(j); @@ -688,8 +686,7 @@ double Structure::calculateElectrostaticEnergy( Atom const &ai = atoms.at(i); size_t const ei = ai.element; - A(i, i) = hardness(ei) - + 1.0 / (sigmaSqrtPi(ei) * fourPiEps); + A(i, i) = hardness(ei) + 1.0 / (sigmaSqrtPi(ei) * fourPiEps); hardnessJ(i) = hardness(ei); b(i) = -ai.chi; for (size_t j = i + 1; j < numAtoms; ++j) @@ -841,11 +838,10 @@ double Structure::calculateScreeningEnergy( } -void Structure::calculateDAdrQ( - EwaldSetup& ewaldSetup, - MatrixXd gammaSqrt2, - double const fourPiEps, - ErfcBuf& erfcBuf) +void Structure::calculateDAdrQ(EwaldSetup& ewaldSetup, + MatrixXd gammaSqrt2, + double const fourPiEps, + ErfcBuf& erfcBuf) { #ifdef _OPENMP @@ -1109,7 +1105,6 @@ void Structure::calculateElectrostaticEnergyDerivatives( double const Qj = aj.charge; ai.pEelecpr += 0.5 * Qj * ai.dAdrQ[j]; - // Diagonal terms contain self-interaction --> screened if (i != j) ai.dEelecdQ += Qj * A(i,j); else if (isPeriodic) @@ -1127,6 +1122,7 @@ void Structure::calculateElectrostaticEnergyDerivatives( Atom& aj = atoms.at(j); if (j < i) continue; double const rij = ajN.d; + if (rij >= rcutScreen) break; size_t const ej = aj.element; diff --git a/src/libnnp/Structure.h b/src/libnnp/Structure.h index a69392c2d3..e73dfdbb36 100644 --- a/src/libnnp/Structure.h +++ b/src/libnnp/Structure.h @@ -174,7 +174,7 @@ struct Structure * interaction. * @param[in] maxCutoffRadius maximal cut-off of symmetry functions. */ - void calculateMaxCutoffRadiusOverall( + void calculateMaxCutoffRadiusOverall( EwaldSetup& ewaldSetup, double rcutScreen, double maxCutoffRadius); @@ -186,8 +186,8 @@ struct Structure * */ void calculateNeighborList( - double cutoffRadius, - bool sortByDistance = false); + double cutoffRadius, + bool sortByDistance = false); /** Calculate neighbor list for all atoms and setup neighbor cut-off map. * * @param[in] cutoffRadius Atoms are neighbors if there distance is smaller @@ -197,9 +197,9 @@ struct Structure * @return Maximum of {maxCutoffRadius, rcutScreen, rCut}. */ void calculateNeighborList( - double cutoffRadius, - std::vector< - std::vector>& cutoffs); + double cutoffRadius, + std::vector< + std::vector>& cutoffs); /** Sort all neighbor lists of this structure with respect to the distance. */ void sortNeighborList(); diff --git a/src/libnnpif/LAMMPS/InterfaceLammps.cpp b/src/libnnpif/LAMMPS/InterfaceLammps.cpp index aa1072a1b5..80f6963dfd 100644 --- a/src/libnnpif/LAMMPS/InterfaceLammps.cpp +++ b/src/libnnpif/LAMMPS/InterfaceLammps.cpp @@ -43,8 +43,8 @@ InterfaceLammps::InterfaceLammps() : myRank (0 ), showewsum (0 ), maxew (0 ), cflength (1.0 ), - cfenergy (1.0 ) - + cfenergy (1.0 ), + isElecDone (false) { } @@ -440,7 +440,6 @@ void InterfaceLammps::addNeighbor(int i, return; } - void InterfaceLammps::finalizeNeighborList() { if (nnpType == NNPType::HDNNP_4G) @@ -458,9 +457,49 @@ void InterfaceLammps::finalizeNeighborList() structure.setupNeighborCutoffMap(cutoffs); } + return; +} + +void InterfaceLammps::process() //TODO : add comments +{ +#ifdef N2P2_NO_SF_GROUPS + calculateSymmetryFunctions(structure, true); +#else + calculateSymmetryFunctionGroups(structure, true); +#endif + if (nnpType == NNPType::HDNNP_2G) + { + calculateAtomicNeuralNetworks(structure, true); + calculateEnergy(structure); + if (normalize) + { + structure.energy = physicalEnergy(structure, false); + } + addEnergyOffset(structure, false); + } + else if (nnpType == NNPType::HDNNP_4G) + { + if (!isElecDone) + { + calculateAtomicNeuralNetworks(structure, true, "elec"); + isElecDone = true; + } else + { + calculateAtomicNeuralNetworks(structure, true, "short"); + isElecDone = false; + calculateEnergy(structure); + if (normalize) + { + structure.energy = physicalEnergy(structure, false); + } + addEnergyOffset(structure, false); + } + } + + return; } -void InterfaceLammps::process() +void InterfaceLammps::processDevelop() { #ifdef N2P2_NO_SF_GROUPS calculateSymmetryFunctions(structure, true); @@ -530,7 +569,177 @@ double InterfaceLammps::getAtomicEnergy(int index) const } } -void InterfaceLammps::getForces(double* const* const& atomF) const +void InterfaceLammps::getQEqParams(double* const& atomChi, double* const& atomJ, + double* const& sigmaSqrtPi, double *const *const& gammaSqrt2, double& qRef) const +{ + for (size_t i = 0; i < structure.atoms.size(); ++i) { + Atom const& a = structure.atoms.at(i); + size_t const ia = a.index; + atomChi[ia] = a.chi; + } + + for (size_t i = 0; i < numElements; ++i) + { + double const iSigma = elements.at(i).getQsigma(); + atomJ[i] = elements.at(i).getHardness(); + sigmaSqrtPi[i] = sqrt(M_PI) * iSigma; + for (size_t j = 0; j < numElements; j++) + { + double const jSigma = elements.at(j).getQsigma(); + gammaSqrt2[i][j] = sqrt(2.0 * (iSigma * iSigma + jSigma * jSigma)); + } + } + qRef = structure.chargeRef; +} + +void InterfaceLammps::getdEdQ(double* const& dEtotdQ) const +{ + Atom const* ai = NULL; + for (size_t i = 0; i < structure.atoms.size(); ++i) + { + ai = &(structure.atoms.at(i)); + size_t const ia = ai->index; + dEtotdQ[ia] += ai->dEdG.back(); + } +} + +void InterfaceLammps::getdChidxyz(int ind, + double *const &dChidx, double *const &dChidy, double *const &dChidz) const +{ + Atom const &ai = structure.atoms.at(ind); + + for (size_t j = 0; j < structure.numAtoms; ++j) { + Atom const &aj = structure.atoms.at(j); +#ifndef NNP_FULL_SFD_MEMORY + vector > const &tableFull + = elements.at(aj.element).getSymmetryFunctionTable(); +#endif + Vec3D dChi; + // need to add this case because the loop over the neighbors + // does not include the contribution dChi_i/dr_i. + if (ai.index == j) { + for (size_t k = 0; k < aj.numSymmetryFunctions; ++k) { + dChi += aj.dChidG.at(k) * aj.dGdr.at(k); + } + } + + for (auto const &n : aj.neighbors) { + if (n.d > maxCutoffRadius) break; + if (n.index == ai.index) { +#ifndef NNP_FULL_SFD_MEMORY + vector const &table = tableFull.at(n.element); + for (size_t k = 0; k < n.dGdr.size(); ++k) { + dChi += aj.dChidG.at(table.at(k)) * n.dGdr.at(k); + } +#else + for (size_t k = 0; k < aj.numSymmetryFunctions; ++k) + { + dChi += aj.dChidG.at(k) * n.dGdr.at(k); + } +#endif + } + } + dChidx[j] = dChi[0]; + dChidy[j] = dChi[1]; + dChidz[j] = dChi[2]; + } +} + +void InterfaceLammps::addCharge(int index, double Q) +{ + Atom& a = structure.atoms.at(index); + a.charge = Q; + //log << strpr("Atom %5zu (%2s) q: %24.16E\n", + // a.tag, elementMap[a.element].c_str(), a.charge); +} + +void InterfaceLammps::getScreeningInfo(double* const& screenInfo) const +{ + screenInfo[0] = (double) screeningFunction.getCoreFunctionType(); //TODO: this does not work atm + screenInfo[1] = screeningFunction.getInner(); + screenInfo[2] = screeningFunction.getOuter(); + screenInfo[3] = 1.0 / (screenInfo[2] - screenInfo[1]); // scale +} + +double InterfaceLammps::getEwaldPrec() const +{ + return Mode::getEwaldPrecision(); +} + +void InterfaceLammps::setElecDone() +{ + if (isElecDone) isElecDone = false; +} + +void InterfaceLammps::addElectrostaticEnergy(double eElec) +{ + structure.energyElec = eElec; +} + +void InterfaceLammps::getForces(double* const* const& atomF) const { + double const cfforce = cflength / cfenergy; + double convForce = 1.0; + if (normalize) { + convForce = convLength / convEnergy; + } + + // Loop over all local atoms. Neural network and Symmetry function + // derivatives are saved in the dEdG arrays of atoms and dGdr arrays of + // atoms and their neighbors. These are now summed up to the force + // contributions of local and ghost atoms. + Atom const *a = NULL; + + for (size_t i = 0; i < structure.atoms.size(); ++i) { + // Set pointer to atom. + a = &(structure.atoms.at(i)); + +#ifndef NNP_FULL_SFD_MEMORY + vector > const &tableFull + = elements.at(a->element).getSymmetryFunctionTable(); +#endif + // Loop over all neighbor atoms. Some are local, some are ghost atoms. + for (vector::const_iterator n = a->neighbors.begin(); + n != a->neighbors.end(); ++n) { + // Temporarily save the neighbor index. Note: this is the index for + // the LAMMPS force array. + size_t const in = n->index; + // Now loop over all symmetry functions and add force contributions + // (local + ghost atoms). +#ifndef NNP_FULL_SFD_MEMORY + vector const &table = tableFull.at(n->element); + for (size_t s = 0; s < n->dGdr.size(); ++s) + { + double const dEdG = a->dEdG[table.at(s)] * cfforce * convForce; +#else + for (size_t s = 0; s < a->numSymmetryFunctions; ++s) + { + double const dEdG = a->dEdG[s] * cfforce * convForce; +#endif + double const *const dGdr = n->dGdr[s].r; + atomF[in][0] -= dEdG * dGdr[0]; + atomF[in][1] -= dEdG * dGdr[1]; + atomF[in][2] -= dEdG * dGdr[2]; + } + } + // Temporarily save the atom index. Note: this is the index for + // the LAMMPS force array. + size_t const ia = a->index; + // Loop over all symmetry functions and add force contributions (local + // atoms). + for (size_t s = 0; s < a->numSymmetryFunctions; ++s) + { + double const dEdG = a->dEdG[s] * cfforce * convForce; + double const *const dGdr = a->dGdr[s].r; + atomF[ia][0] -= dEdG * dGdr[0]; + atomF[ia][1] -= dEdG * dGdr[1]; + atomF[ia][2] -= dEdG * dGdr[2]; + } + } + + return; +} + +void InterfaceLammps::getForcesDevelop(double* const* const& atomF) const { double const cfforce = cflength / cfenergy; double convForce = 1.0; @@ -620,6 +829,77 @@ void InterfaceLammps::getForces(double* const* const& atomF) const return; } +void InterfaceLammps::getForcesChi(double const* const& lambda, + double* const* const& atomF) const { + double const cfforce = cflength / cfenergy; + double convForce = 1.0; + if (normalize) { + convForce = convLength / convEnergy; + } + + // Loop over all local atoms. Neural network and Symmetry function + // derivatives are saved in the dEdG arrays of atoms and dGdr arrays of + // atoms and their neighbors. These are now summed up to the force + // contributions of local and ghost atoms. + Atom const *a = NULL; + + for (size_t i = 0; i < structure.atoms.size(); ++i) { + // Set pointer to atom. + a = &(structure.atoms.at(i)); + + // Temporarily save the atom index. Note: this is the index for + // the LAMMPS force array. + size_t const ia = a->index; + // Also save tag - 1 which is the correct position in lambda array. + size_t const ta = a->tag - 1; + +#ifndef NNP_FULL_SFD_MEMORY + vector > const &tableFull + = elements.at(a->element).getSymmetryFunctionTable(); +#endif + // Loop over all neighbor atoms. Some are local, some are ghost atoms. + for (vector::const_iterator n = a->neighbors.begin(); + n != a->neighbors.end(); ++n) { + // Temporarily save the neighbor index. Note: this is the index for + // the LAMMPS force array. + size_t const in = n->index; + // Also save tag - 1 which is the correct position in lambda array. + size_t const tn = n->tag - 1; + //std::cout << "Chi : " << a->chi << '\t' << "nei :" << n->index << '\n'; + // Now loop over all symmetry functions and add force contributions + // (local + ghost atoms). +#ifndef NNP_FULL_SFD_MEMORY + vector const &table = tableFull.at(n->element); + for (size_t s = 0; s < n->dGdr.size(); ++s) + { + double const dChidG = a->dChidG[table.at(s)] + * cfforce * convForce; +#else + for (size_t s = 0; s < a->numSymmetryFunctions; ++s) + { + double const dChidG = a->dChidG[s] * cfforce * convForce; +#endif + double const *const dGdr = n->dGdr[s].r; + atomF[in][0] -= lambda[ta] * dChidG * dGdr[0]; + atomF[in][1] -= lambda[ta] * dChidG * dGdr[1]; + atomF[in][2] -= lambda[ta] * dChidG * dGdr[2]; + } + } + // Loop over all symmetry functions and add force contributions (local + // atoms). + for (size_t s = 0; s < a->numSymmetryFunctions; ++s) + { + double const dChidG = a->dChidG[s] * cfforce * convForce; + double const *const dGdr = a->dGdr[s].r; + atomF[ia][0] -= lambda[ta] * dChidG * dGdr[0]; + atomF[ia][1] -= lambda[ta] * dChidG * dGdr[1]; + atomF[ia][2] -= lambda[ta] * dChidG * dGdr[2]; + } + } + + return; +} + void InterfaceLammps::getCharges(double* const& atomQ) const { if (nnpType != NNPType::HDNNP_4G) return; @@ -633,6 +913,8 @@ void InterfaceLammps::getCharges(double* const& atomQ) const { atomQ[i] = s.atoms[i].charge; } + + return; } long InterfaceLammps::getEWBufferSize() const diff --git a/src/libnnpif/LAMMPS/InterfaceLammps.h b/src/libnnpif/LAMMPS/InterfaceLammps.h index 691e031b35..30e64fd9f2 100644 --- a/src/libnnpif/LAMMPS/InterfaceLammps.h +++ b/src/libnnpif/LAMMPS/InterfaceLammps.h @@ -23,6 +23,7 @@ #include // std::size_t #include // int64_t #include // std::string +#include // std::vector namespace nnp { @@ -137,6 +138,10 @@ class InterfaceLammps : public Mode * energy contributions. */ void process(); + /** Calculate symmetry functions, atomic neural networks and sum of local + * energy contributions (development version for "hdnnp/develop" pair style). + */ + void processDevelop(); /** Return sum of local energy contributions. * * @return Sum of local energy contributions. @@ -151,11 +156,29 @@ class InterfaceLammps : public Mode * @attention These atomic contributions are not physical! */ double getAtomicEnergy(int index) const; + /** Adds electrostatic energy contribution to the total structure energy + * + * @param[in] electrostatic energy (calculated in LAMMPS). + * + */ + void addElectrostaticEnergy(double energy); /** Calculate forces and add to LAMMPS atomic force arrays. * * @param[in,out] atomF LAMMPS force array for local and ghost atoms. */ void getForces(double* const* const& atomF) const; + /** Calculate forces and add to LAMMPS atomic force arrays (development version for + * "hdnnp/develop" pair style). + * + * @param[in,out] atomF LAMMPS force array for local and ghost atoms. + */ + void getForcesDevelop(double* const* const& atomF) const; + /** Calculate chi-term for forces and add to LAMMPS atomic force arrays. + * + * @param[in,out] atomF LAMMPS force array for local and ghost atoms. + */ + void getForcesChi(double const* const& lambda, + double* const* const& atomF) const; /** Transfer charges (in units of e) to LAMMPS atomic charge vector. Call * after getAtomicEnergy(). * @@ -172,8 +195,13 @@ class InterfaceLammps : public Mode * @return Largest cutoff of all symmetry functions. */ double getMaxCutoffRadius() const; + /** Get Ewald precision parameter. + * + * @return Ewald precision parameter. + */ + double getEwaldPrec() const; /** Get largest cutoff including structure specific cutoff and screening - * cutoff + * cutoff. * * @return Largest cutoff of all symmetry functions and structure specific * cutoff and screening cutoff. @@ -202,6 +230,46 @@ class InterfaceLammps : public Mode /** Clear extrapolation warnings storage. */ void clearExtrapolationWarnings(); + /** Read atomic charges from LAMMPS into n2p2. + */ + void addCharge(int index, double Q); + /** Write QEq arrays from n2p2 to LAMMPS. + * + * @param[in] atomChi Electronegativities. + * @param[in] atomJ Atomic hardness. + * @param[in] atomSigma Gaussian width. + * @param[in] qRef Reference charge of the structure. + */ + void getQEqParams(double* const& atomChi, + double* const& atomJ, + double* const& sigmaSqrtPi, + double *const *const& gammaSqrt2, + double& qRef) const; + /** Write the derivative of total energy with respect to atomic charges + * from n2p2 into LAMMPS. + * + * @param[in] dEtotdQ Derivative of the total energy w.r.t. atomic charge. + */ + void getdEdQ(double* const& dEtotdQ) const; + /** Read screening function information from n2p2 into LAMMPS. + * + * @param[in] rScreen Array that contains screening radii. + */ + void getScreeningInfo(double* const& rScreen) const; + /** Transfer spatial derivatives of atomic electronegativities. + * + * @param[in] tag Atom of interest + * @param dChidx + * @param dChidy + * @param dChidz + */ + void getdChidxyz(int tag, + double* const& dChidx, + double* const& dChidy, + double* const& dChidz) const; + /** Set isElecDone true after running the first NN in 4G-HDNNPs. + */ + void setElecDone(); /** Write current structure to file in units used in training data. * * @param fileName File name of the output structure file. @@ -247,6 +315,8 @@ class InterfaceLammps : public Mode std::map mapElementToType; /// Structure containing local atoms. Structure structure; + /// True if first NN is calculated + bool isElecDone; }; ////////////////////////////////// diff --git a/src/libnnpif/makefile b/src/libnnpif/makefile index 00ad1b5077..f01b0a0453 100644 --- a/src/libnnpif/makefile +++ b/src/libnnpif/makefile @@ -110,6 +110,7 @@ lammps-prep: lammps-mf lammps-cmake lammps-mf: cp LAMMPS/Makefile.lammps $(PROJECT_LIB)/Makefile.lammps-extra @sed -i.bak -E "s,(hdnnp_SYSINC =).*,\1 $(LAMMPS_OPTIONS)," $(PROJECT_LIB)/Makefile.lammps-extra + @sed -i.bak -E "s,(hdnnp_SYSLIB =.*),\1 $(PROJECT_LDFLAGS_BLAS)," $(PROJECT_LIB)/Makefile.lammps-extra @rm $(PROJECT_LIB)/Makefile.lammps-extra.bak lammps-cmake: diff --git a/src/makefile.gnu b/src/makefile.gnu index 7de5e87063..ba32ddfe25 100644 --- a/src/makefile.gnu +++ b/src/makefile.gnu @@ -6,7 +6,10 @@ # Enter here paths to GSL or EIGEN if they are not in your standard include # path. DO NOT completely remove the entry, leave at least "./". PROJECT_GSL=./ +#PROJECT_GSL=${HOME}/local/src/gsl-2.8/build/include PROJECT_EIGEN=/usr/include/eigen3/ +#PROJECT_EIGEN=${HOME}/local/src/eigen/ +PROJECT_BOOST=${BOOST_ROOT} ############################################################################### # COMPILERS AND FLAGS @@ -21,7 +24,7 @@ PROJECT_TEST=--coverage -fno-default-inline -fno-inline -fno-inline-small-functi PROJECT_AR=ar PROJECT_ARFLAGS=-rcsv PROJECT_CFLAGS_BLAS= -PROJECT_LDFLAGS_BLAS=-lblas -lgsl -lgslcblas +PROJECT_LDFLAGS_BLAS=-lopenblas -lgsl -lgslcblas ############################################################################### # COMPILE-TIME OPTIONS diff --git a/test/cpp/makefile b/test/cpp/makefile index 39908d5e46..c406d28571 100644 --- a/test/cpp/makefile +++ b/test/cpp/makefile @@ -34,10 +34,10 @@ OPTIONS+=$(PROJECT_OPTIONS) DEBUG=$(PROJECT_DEBUG) $(PROJECT_TEST) # Extra include paths for compiling. -INCLUDES=-I./ -I$(PROJECT_DIR)/src/libnnp -I$(PROJECT_DIR)/src/libnnptrain -I$(PROJECT_EIGEN) +INCLUDES=-I./ -I$(PROJECT_DIR)/src/libnnp -I$(PROJECT_DIR)/src/libnnptrain -I$(PROJECT_EIGEN) -I$(PROJECT_BOOST)/include # Extra flags for linking. -LDFLAGS=$(PROJECT_LIB)/libnnp.a $(PROJECT_LIB)/libnnptrain.a $(PROJECT_LDFLAGS_BLAS) -lboost_system -lboost_unit_test_framework -lboost_filesystem -lpthread +LDFLAGS=$(PROJECT_LIB)/libnnp.a $(PROJECT_LIB)/libnnptrain.a $(PROJECT_LDFLAGS_BLAS) -L$(PROJECT_BOOST)/lib -lboost_system -lboost_unit_test_framework -lboost_filesystem -lpthread ###############################################################################