4G-HDNNP Prediction and LAMMPS interface

.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

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

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
 --------------------------

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 0.0   6.5214500558000016E-02   1.7058420249857001E+01   3.2113867333000002E+01
+8 2 0.0   2.8332198764000003E+00   2.7977822229000000E+00   3.2113907679000000E+01
+9 3 0.0   1.9864553928000000E-02   1.0486013922000000E-02   3.6088078099000001E+01
+10 1 0.0  2.7981764574999999E+00   2.8796998035999999E+00   3.6124511960000000E+01
+11 1 0.0  1.7088713823570803E+01   1.7074561363286001E+01   4.0153894391000001E+01
+12 2 0.0  2.8234702698000000E+00   2.8619477365999999E+00   4.0124676317000002E+01
+13 2 0.0  1.7084046370454001E+01   5.6888413584000004E+00   2.0013899747000000E+01
+14 1 0.0  2.8848335277000001E+00   8.5308909416999992E+00   1.9989943256000000E+01
+15 1 0.0  1.8241298201000001E-02   5.6837552365000006E+00   2.4026099825999999E+01
+16 2 0.0  2.9361062157000006E+00   8.4795591997000006E+00   2.4082757439000002E+01
+17 2 0.0  1.6188356579000002E-02   5.6698041264999999E+00   2.8051270020000000E+01
+18 1 0.0  2.8977599905000000E+00   8.5660735577999993E+00   2.8036115495000001E+01
+19 1 0.0  9.8433937020000009E-04   5.6927154290000006E+00   3.2118501962000003E+01
+20 2 0.0  2.8073628502000005E+00   8.5498039808000019E+00   3.2128399704000003E+01
+21 2 0.0  1.7046169666499001E+01   5.7492786883000013E+00   3.6121753734000002E+01
+22 1 0.0  2.9059518581000003E+00   8.5723518133999992E+00   3.6118083753999997E+01
+23 1 0.0  5.2199900982999997E-04   5.6455106974000007E+00   4.0180597257999999E+01
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+25 2 0.0  1.7057826762513002E+01   1.1415957378000000E+01   1.9959977720000001E+01
+26 1 0.0  2.9183726113000006E+00   1.4291678041999999E+01   1.9988445497000001E+01
+27 1 0.0  1.7075894413793002E+01   1.1421205582000002E+01   2.4027048543999999E+01
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+29 2 0.0  1.7045656265742000E+01   1.1382810885000000E+01   2.8094293014999998E+01
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+38 1 0.0  8.5193853072000003E+00   2.8764031199000000E+00   1.9994398985000000E+01
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+42 1 0.0  8.5205746819000012E+00   2.8135749087000006E+00   2.8097702553000001E+01
+43 1 0.0  5.7090540565000003E+00   1.6821528168000002E-02   3.2068389906000000E+01
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+45 2 0.0  5.7491607504999998E+00   2.6551802873000005E-02   3.6161801185000002E+01
+46 1 0.0  8.5696933089999998E+00   2.8243981820000004E+00   3.6095548903999997E+01
+47 1 0.0  5.6004605746999996E+00   1.7058153326061003E+01   4.0102869652999999E+01
+48 2 0.0  8.5839177868000025E+00   2.8525893410000003E+00   4.0129186941000000E+01
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+50 1 0.0  8.5832999976000011E+00   8.5656793231999995E+00   1.9987182838999999E+01
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+53 2 0.0  5.7493104546000007E+00   5.6905967816000000E+00   2.8035716479000001E+01
+54 1 0.0  8.5305642648000024E+00   8.5336383575999992E+00   2.8041326564999999E+01
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+56 2 0.0  8.5337005863000002E+00   8.5466174492999993E+00   3.2081751156999999E+01
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+60 2 0.0  8.5592887233999999E+00   8.5947597306000016E+00   4.0146193152000002E+01
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+62 1 0.0  8.5029228270000008E+00   1.4343324046000001E+01   2.0023014406000001E+01
+63 1 0.0  5.6720512753000012E+00   1.1358988262000000E+01   2.4060251955999998E+01
+64 2 0.0  8.5254411798000014E+00   1.4231011829000000E+01   2.4012346344000001E+01
+65 2 0.0  5.7426630599999999E+00   1.1378874679999999E+01   2.8023933603000000E+01
+66 1 0.0  8.6362523685000010E+00   1.4255022857000000E+01   2.8036097202000001E+01
+67 1 0.0  5.7117658322000002E+00   1.1454697101000001E+01   3.2073160784000002E+01
+68 2 0.0  8.5246584174999995E+00   1.4270581047000002E+01   3.2102696917000003E+01
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+71 1 0.0  5.7264381750000002E+00   1.1398781375000002E+01   4.0260042284000001E+01
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+89 2 0.0  1.1392303111000002E+01   5.6922237034000007E+00   2.8086502354999997E+01
+90 1 0.0  1.4307995467000000E+01   8.5052796176999994E+00   2.8127594521999999E+01
+91 1 0.0  1.1467787838000001E+01   5.7303018143000006E+00   3.2140124452000002E+01
+92 2 0.0  1.4223684114000001E+01   8.5394621151999992E+00   3.2083417384999997E+01
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+97 2 0.0  1.1397087406000001E+01   1.1432029951000001E+01   1.9991521328999998E+01
+98 1 0.0  1.4222100486000002E+01   1.4237423386000001E+01   1.9890837445999999E+01
+99 1 0.0  1.1397172084999999E+01   1.1362254483999999E+01   2.4106729256000001E+01
+100 2 0.0 1.4223050564000001E+01   1.4272733426000002E+01   2.4026767277000001E+01
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+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

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  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  4.0153894391e+01
+12 2 0.0  2.8234702698e+00  2.8619477366e+00  4.0124676317e+01 
+13 2 0.0 -1.3119630546e-02  5.6888413584e+00  2.0013899747e+01
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+21 2 0.0 -5.0996334501e-02  5.7492786883e+00  3.6121753734e+01 
+22 1 0.0  2.9059518581e+00  8.5723518134e+00  3.6118083754e+01 
+23 1 0.0  5.2199900983e-04  5.6455106974e+00  4.0180597258e+01 
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+31 1 0.0  1.0413278368e-02  1.1323763827e+01  3.2100372838e+01 
+32 2 0.0  2.7888050607e+00  1.4200832470e+01  3.2081624640e+01 
+33 2 0.0 -5.2366574815e-03  1.1380297134e+01  3.6148026784e+01 
+34 1 0.0  2.8964801357e+00  1.4225437477e+01  3.6102833042e+01 
+35 1 0.0 -4.8130810704e-02  1.1455866520e+01  4.0155035313e+01 
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+40 2 0.0  8.5444746323e+00  2.8328648158e+00  2.4073209126e+01 
+41 2 0.0  5.6374929679e+00  8.9788629595e-03  2.8040190972e+01 
+42 1 0.0  8.5205746819e+00  2.8135749087e+00  2.8097702553e+01 
+43 1 0.0  5.7090540565e+00  1.6821528168e-02  3.2068389906e+01 
+44 2 0.0  8.5099907612e+00  2.8387661466e+00  3.2089405586e+01 
+45 2 0.0  5.7491607505e+00  2.6551802873e-02  3.6161801185e+01 
+46 1 0.0  8.5696933090e+00  2.8243981820e+00  3.6095548904e+01 
+47 1 0.0  5.6004605747e+00 -3.9012674939e-02  4.0102869653e+01 
+48 2 0.0  8.5839177868e+00  2.8525893410e+00  4.0129186941e+01 
+49 2 0.0  5.6735244868e+00  5.6849201959e+00  1.9979804725e+01 
+50 1 0.0  8.5832999976e+00  8.5656793232e+00  1.9987182839e+01 
+51 1 0.0  5.7075209596e+00  5.6897493150e+00  2.4036549652e+01 
+52 2 0.0  8.6020291474e+00  8.5486919149e+00  2.3965788409e+01 
+53 2 0.0  5.7493104546e+00  5.6905967816e+00  2.8035716479e+01 
+54 1 0.0  8.5305642648e+00  8.5336383576e+00  2.8041326565e+01 
+55 1 0.0  5.6467260935e+00  5.6755829275e+00  3.2090861072e+01 
+56 2 0.0  8.5337005863e+00  8.5466174493e+00  3.2081751157e+01 
+57 3 0.0  5.6610188849e+00  5.6993559450e+00  3.6064080941e+01 
+58 1 0.0  8.5010303798e+00  8.5362875267e+00  3.6131963187e+01 
+59 1 0.0  5.6984002350e+00  5.7462274801e+00  4.0178786901e+01 
+60 2 0.0  8.5592887234e+00  8.5947597306e+00  4.0146193152e+01 
+61 2 0.0  5.6032739042e+00  1.1399683984e+01  1.9913916443e+01 
+62 1 0.0  8.5029228270e+00  1.4343324046e+01  2.0023014406e+01 
+63 1 0.0  5.6720512753e+00  1.1358988262e+01  2.4060251956e+01 
+64 2 0.0  8.5254411798e+00  1.4231011829e+01  2.4012346344e+01 
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examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.008.data

@@ -0,0 +1 @@
+     12.9752105872

examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.012.data

@@ -0,0 +1 @@
+     14.5786310784

examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.013.data

@@ -0,0 +1 @@
+      1.4392244883

examples/interface-LAMMPS/AlAuMgO_4G/hdnnp-data/hardness.079.data

@@ -0,0 +1 @@
+      0.0175182304