How to run lammps with hybrid LJ interaction and DP potential

[Nana-bai]

When I use the nffc.pd model ( 5 atomic types ) hybrid with lj potential, the simulation can be carried out. When using the myc.pb model ( 3 atomic types ), the simulation will appear "core dump "and exit, the total atomic type of the simulation system is 5.


LAMMPS (29 Sep 2021 - Update 3)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Loading plugin: deepmd pair style v2.0 by Han Wang
Loading plugin: compute deeptensor/atom v2.0 by Han Wang
Loading plugin: fix dplr v2.0 by Han Wang
units metal
dimension 3
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style harmonic

#read_data NaCaCl-SiO2.data

read_restart lj.restart
Reading restart file ...
restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
WARNING: Restart file used different # of processors: 32 vs. 1 (src/read_restart.cpp:658)
restoring atom style full from restart
orthogonal box = (-2.5152592 -2.5152592 -2.5152592) to (72.515259 72.515259 72.515259)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut/coul/long from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
10522 atoms
466 bonds
842 angles
1124 dihedrals
22 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_restart CPU = 0.009 seconds

region fixed sphere 34.2761 37.7968 34.2943 3

mass 1 23.000000
mass 2 40.000000
mass 3 35.500000
mass 4 15.999430 #O
mass 5 28.085500 #Si

#############
pair_style hybrid/overlay lj/cut/coul/long 9.0 deepmd myc.pb
Summary of lammps deepmd module ...

Info of deepmd-kit:
installed to: /home/ps/anaconda/envs/deepmd
source: v2.0.3-1-g96e623d5
source branch: HEAD
source commit: 96e623d5
source commit at: 2021-11-09 17:54:01 -0500
surpport model ver.:1.0
build float prec: double
build with tf inc: /home/ps/anaconda/envs/deepmd/include;/home/ps/anaconda/envs/deepmd/include
build with tf lib: /home/ps/anaconda/envs/deepmd/lib/libtensorflow_cc.so;/home/ps/anaconda/envs/deepmd/lib/libtensorflow_framework.so
set tf intra_op_parallelism_threads: 0
set tf inter_op_parallelism_threads: 0
Info of lammps module:
use deepmd-kit at: /home/ps/anaconda/envs/deepmd
source: v2.0.3-1-g96e623d5
source branch: HEAD
source commit: 96e623d5
source commit at: 2021-11-09 17:54:01 -0500
build float prec: double
build with tf inc: /home/ps/anaconda/envs/deepmd/include;/home/ps/anaconda/envs/deepmd/include
build with tf lib: /home/ps/anaconda/envs/deepmd/lib/libtensorflow_cc.so;/home/ps/anaconda/envs/deepmd/lib/libtensorflow_framework.so
2023-03-15 16:22:00.377638: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-03-15 16:22:00.395970: I tensorflow/core/common_runtime/process_util.cc:146] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.
Info of model(s):
using 1 model(s): myc.pb
rcut in model: 9
ntypes in model: 3

pair_coeff * * deepmd myc.pb #na-na
WARNING: Interaction between types 0 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 0 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 1 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 1 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 2 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 2 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 3 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 3 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 4 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 4 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)
WARNING: Interaction between types 5 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)

pair_coeff 1 4 lj/cut/coul/long 0.01527718 2.4875 #o-na
pair_coeff 2 4 lj/cut/coul/long 0.01474814 2.7628 #o-ca
pair_coeff 3 4 lj/cut/coul/long 0.01453565 3.48 #o-cl

pair_coeff 1 5 lj/cut/coul/long 0.006399 3.084 #si-na
pair_coeff 2 5 lj/cut/coul/long 0.00617505 3.3593 #si-ca
pair_coeff 3 5 lj/cut/coul/long 0.00608832 4.0765 #si-cl

pair_coeff 4 4 lj/cut/coul/long 0.009891 2.86 #o-o
pair_coeff 4 5 lj/cut/coul/long 0.004143 3.4565 #o-si
pair_coeff 5 5 lj/cut/coul/long 0.001735 4.053 #si-si

kspace_style pppm 1.0e-5

neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes

#----------Region--------------------
group fixed region fixed
8 atoms in group fixed
group SiO2 type 3 4
4819 atoms in group SiO2
group Na type 1
3647 atoms in group Na
group Ca type 2
1925 atoms in group Ca
group Cl type 3
4559 atoms in group Cl
group L type 1 2 3
10131 atoms in group L
group shell subtract SiO2 fixed
4814 atoms in group shell

##----------------initialize-----------------------
thermo 1000
thermo_style custom step temp density pe ke etotal press vol

velocity all create 1200 23452342 rot yes dist gaussian mom yes
minimize 1.0e-4 1.0e-5 1000 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

• USER-DEEPMD package:
  The log file lists these citations in BibTeX format.

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
WARNING: System is not charge neutral, net charge = 2519.5932 (src/kspace.cpp:325)
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
G vector (1/distance) = 0.34163479
grid = 75 75 75
stencil order = 5
estimated absolute RMS force accuracy = 0.00018814002
estimated relative force accuracy = 1.3065601e-05
using double precision FFTW3
3d grid and FFT values/proc = 551368 421875
WARNING: Interaction between types 1 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Interaction between types 1 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Interaction between types 2 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Interaction between types 2 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Interaction between types 3 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Interaction between types 3 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Interaction between types 4 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Interaction between types 4 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Interaction between types 5 and 5 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:1015)
WARNING: Impropers are defined but no improper style is set (src/force.cpp:206)
Unused restart file global fix info:
fix style: nvt, fix ID: 1
fix style: npt, fix ID: 2
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 14 14 14
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair deepmd, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(3) neighbor class addition, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Setting up cg style minimization ...
Unit style : metal
Current step : 100000
Segmentation fault (core dumped)

[wanghan-iapcm]

The deepmd correctly ignores the interaction between type 0-2 with 3-5, you may see the warning

WARNING: Interaction between types 0 and 4 is set with deepmd, but will be ignored.
Deepmd model has only 3 types, it only computes the mulitbody interaction of types: 1-3. (/home/conda/feedstock_root/build_artifacts/libdeepmd_1638098235911/work/source/lmp/pair_deepmd.cpp:984)

From the provided information I do not see why the seg fault happens.

[njzjz]

A bug was fixed in #1727. It looks like your version is too old.

[Nana-bai]

However, I can 't use conda to upgrade deepkit to 2.1.2 or higher, the display error is glibc version 2.31, please ask glibc version downgrade will affect other programs, glibc version must be 2.17 version ?

[njzjz]

lammps-dp was renamed to lammps in recent versions.

[Nana-bai]

Ask, I upgraded to deepkit2.2.1, is deepmd unable to use hybrid deepmd lj command ?

#############
pair_style hybrid deepmd 5yc.pb lj/cut/coul/long 9.0
DeePMD-kit WARNING: Environmental variable TF_INTRA_OP_PARALLELISM_THREADS is not set. Tune TF_INTRA_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable TF_INTER_OP_PARALLELISM_THREADS is not set. Tune TF_INTER_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable OMP_NUM_THREADS is not set. Tune OMP_NUM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
Summary of lammps deepmd module ...

Info of deepmd-kit:
installed to: /home/ps/anaconda/envs/deepmd
source: v2.2.1
source branch: HEAD
source commit: 3ac8c4c
source commit at: 2023-03-16 12:33:24 +0800
surpport model ver.:1.1
build variant: cpu
build with tf inc: /home/ps/anaconda/envs/deepmd/include;/home/ps/anaconda/envs/deepmd/include
build with tf lib: /home/ps/anaconda/envs/deepmd/lib/libtensorflow_cc.so
set tf intra_op_parallelism_threads: 0
set tf inter_op_parallelism_threads: 0
Info of lammps module:
use deepmd-kit at: /home/ps/anaconda/envs/deepmdDeePMD-kit WARNING: Environmental variable TF_INTRA_OP_PARALLELISM_THREADS is not set. Tune TF_INTRA_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable TF_INTER_OP_PARALLELISM_THREADS is not set. Tune TF_INTER_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable OMP_NUM_THREADS is not set. Tune OMP_NUM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
2023-03-17 15:55:42.117379: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-03-17 15:55:42.139464: I tensorflow/core/common_runtime/process_util.cc:146] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.
2023-03-17 15:55:43.737495: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:354] MLIR V1 optimization pass is not enabled
Info of model(s):
using 1 model(s): 5yc.pb
rcut in model: 9
ntypes in model: 5

pair_coeff * * #na-na
ERROR: Incorrect args for pair coefficients (src/pair_hybrid.cpp:472)
Last command: pair_coeff * * #na-na

[njzjz]

This error is reported by LAMMPS itself. It looks that the correct command is pair_coeff * * deepmd. You might first read LAMMPS documentation carefully.