Simulation hangs indefinitely after PPPM initialization with pppm/dplr + deepmd and Drude oscillators #5093
Unanswered
Ziyang-You
asked this question in
Q&A
Replies: 1 comment
-
|
有人知道这是什么原因吗? |
Beta Was this translation helpful? Give feedback.
0 replies
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Uh oh!
There was an error while loading. Please reload this page.
-
variable NSTEPS equal 202000000
variable DT equal 0.0005 #ps
variable BETA equal 0.1
variable KMESH equal 2
variable THERMO_FREQ equal 1000
variable DUMP_FREQ equal 2000
variable TEMP equal 330.000000
variable PRES equal 1.000000
variable TAU_T equal 0.100000
variable TAU_P equal 0.500000 该变量用于fix npt命令中的压力阻尼参数（damping parameter for pressure），单位为皮秒（ps），表示Nosé-Hoover气压计的弛豫时间常数，用于控制压力波动，这里为0.5 ps。
dimension 3
units metal
atom_style full
boundary p p p # xy 周期（界面无限大），z 非周期（slab + 真空），论文用 slab 几何
read_data system.data
Reading data file ...
orthogonal box = (-0.05 -0.03 -0.031) to (30.687 34.07 99.647)
2 by 4 by 8 MPI processor grid
reading atoms ...
6948 atoms
scanning bonds ...
1 = max bonds/atom
orthogonal box = (-0.05 -0.03 -0.031) to (30.687 34.07 99.647)
2 by 4 by 8 MPI processor grid
reading bonds ...
1206 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.336 seconds
read_data CPU = 1.253 seconds
write_data init.data
System init for write_data ...
WARNING: Bonds are defined but no bond style is set (src/force.cpp:197)
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (src/force.cpp:199)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
the neighbor list between real (1) and its corresponding virtual
type (3) should be excluded
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no exclude type 2 6 exclude type 4 7 exclude type 5 8
groups of real and virtual atoms
group real_atom type 1 2 3 4 5
5742 atoms in group real_atom
group virtual_atom type 6 7 8
1206 atoms in group virtual_atom
DPLR 势：短程 DP 模型 + 长程 Deep Wannier 模型
pair_style deepmd /hpc2hdd/home/ziyangyou/DPLR/50A/model.pb
Summary of lammps deepmd module ...
长程静电：pppm/dplr（你已经成功编译进 LAMMPS）
kspace_style pppm/dplr 1.0e-5 # 精度
kspace_modify gewald ${BETA} diff ik mesh ${KMESH} ${KMESH} ${KMESH}
kspace_modify gewald 0.1 diff ik mesh ${KMESH} ${KMESH} ${KMESH}
kspace_modify gewald 0.1 diff ik mesh 2 ${KMESH} ${KMESH}
kspace_modify gewald 0.1 diff ik mesh 2 2 ${KMESH}
kspace_modify gewald 0.1 diff ik mesh 2 2 2
外加 D-field（可变
variable efield_z equal 0.30
fix 0 all dplr model model.pb type_associate 2 6 bond_type 1 type_associate 4 7 bond_type 2 type_associate 5 8 bond_type 3 efield 0.0 0.0 0.30 # x=0, y=0, z=0.30
fix_modify 0 virial yes # include virial for pressure
Temperature and pressure from real atoms only (virtual WC excluded)
compute real_temp real_atom temp
compute real_press all pressure real_temp
NVT from real atoms
fix 1 real_atom nvt temp 330.0 330.0 100.0
fix_modify 1 temp real_temp
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1399)
timestep 0.0005 # 单位是ps，0.5 fs
输出（让温度显示正确的 real_temp）
thermo ${THERMO_FREQ}
thermo 1000
thermo_style custom step ke pe etotal enthalpy temp press vol lx ly lz pxx pyy pzz
thermo_modify temp real_temp press real_press
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)
dump 1 real_atom custom ${DUMP_FREQ} system.dump id type x y z vx vy vz${THERMO_FREQ} "$ (step) $(pe) $ (ke) $(etotal) $ (enthalpy) $(c_real_temp) $ (c_real_press) $(vol) $ (c_real_press[1]) $(c_real_press[2]) $ (c_real_press[3])" append thermo.out screen no title "# step pe ke etotal enthalpy temp press vol pxx pyy pzz"$(pe) $ (ke) $(etotal) $ (enthalpy) $(c_real_temp) $ (c_real_press) $(vol) $ (c_real_press[1]) $(c_real_press[2]) $ (c_real_press[3])" append thermo.out screen no title "# step pe ke etotal enthalpy temp press vol pxx pyy pzz"
dump 1 real_atom custom 2000 system.dump id type x y z vx vy vz
fix thermo_print all print
fix thermo_print all print 1000 "$(step)
velocity real_atom create ${TEMP} 23456784
velocity real_atom create 330 23456784
velocity real_atom zero linear
先跑 1 ns 测试体系是否稳定（论文正式轨迹 13 ns）
run 2000000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
@Article{Wang_ComputPhysCommun_2018_v228_p178,
author = {Wang, Han and Zhang, Linfeng and Han, Jiequn and E, Weinan},
doi = {10.1016/j.cpc.2018.03.016},
url = {https://doi.org/10.1016/j.cpc.2018.03.016},
year = 2018,
month = {jul},
publisher = {Elsevier {BV}},
volume = 228,
journal = {Comput. Phys. Commun.},
title = {{DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics}},
pages = {178--184}
}
@Article{Zeng_JChemPhys_2023_v159_p054801,
title = {{DeePMD-kit v2: A software package for deep potential models}},
author = {Jinzhe Zeng and Duo Zhang and Denghui Lu and Pinghui Mo and Zeyu Li
and Yixiao Chen and Mari{'a}n Rynik and Li'ang Huang and Ziyao Li and
Shaochen Shi and Yingze Wang and Haotian Ye and Ping Tuo and Jiabin
Yang and Ye Ding and Yifan Li and Davide Tisi and Qiyu Zeng and Han
Bao and Yu Xia and Jiameng Huang and Koki Muraoka and Yibo Wang and
Junhan Chang and Fengbo Yuan and Sigbj{\o}rn L{\o}land Bore and Chun
Cai and Yinnian Lin and Bo Wang and Jiayan Xu and Jia-Xin Zhu and
Chenxing Luo and Yuzhi Zhang and Rhys E A Goodall and Wenshuo Liang
and Anurag Kumar Singh and Sikai Yao and Jingchao Zhang and Renata
Wentzcovitch and Jiequn Han and Jie Liu and Weile Jia and Darrin M
York and Weinan E and Roberto Car and Linfeng Zhang and Han Wang},
journal = {J. Chem. Phys.},
volume = 159,
issue = 5,
year = 2023,
pages = 054801,
doi = {10.1063/5.0155600},
}
@Article{Zeng_JChemTheoryComput_2025_v21_p4375,
author = {Jinzhe Zeng and Duo Zhang and Anyang Peng and Xiangyu Zhang and Sensen
He and Yan Wang and Xinzijian Liu and Hangrui Bi and Yifan Li and Chun
Cai and Chengqian Zhang and Yiming Du and Jia-Xin Zhu and Pinghui Mo
and Zhengtao Huang and Qiyu Zeng and Shaochen Shi and Xuejian Qin and
Zhaoxi Yu and Chenxing Luo and Ye Ding and Yun-Pei Liu and Ruosong Shi
and Zhenyu Wang and Sigbj{\o}rn L{\o}land Bore and Junhan Chang and
Zhe Deng and Zhaohan Ding and Siyuan Han and Wanrun Jiang and Guolin
Ke and Zhaoqing Liu and Denghui Lu and Koki Muraoka and Hananeh Oliaei
and Anurag Kumar Singh and Haohui Que and Weihong Xu and Zhangmancang
Xu and Yong-Bin Zhuang and Jiayu Dai and Timothy J. Giese and Weile
Jia and Ben Xu and Darrin M. York and Linfeng Zhang and Han Wang},
title = {{DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning
Potentials}},
journal = {J. Chem. Theory Comput.},
year = 2025,
volume = 21,
number = 9,
pages = {4375--4385},
doi = {10.1021/acs.jctc.5c00340},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 11520 (src/kspace.cpp:327)
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.1
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 1714022.1
estimated relative force accuracy = 119032.25
using double precision FFTW3
3d grid and FFT values/proc = 216 2
WARNING: Interaction between types 1 and 6 is set with deepmd, but will be ignored.
Deepmd model has only 5 types, it only computes the mulitbody interaction of types: 1-5. (/home/conda/feedstock_root/build_artifacts/deepmd-kit_1762351187144/work/source/lmp/pair_base.cpp:446)
WARNING: Interaction between types 1 and 7 is set with deepmd, but will be ignored.
Deepmd model has only 5 types, it only computes the mulitbody interaction of types: 1-5. (/home/conda/feedstock_root/build_artifacts/deepmd-kit_1762351187144/work/source/lmp/pair_base.cpp:446)
WARNING: Interact 我的DPLR会直接卡住，请问这是什么原因。我尝试了缩小结构，还是会卡住。
Beta Was this translation helpful? Give feedback.
All reactions