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Merge pull request #4181 from gplummer317/ctip

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Charge Transfer Interatomic Potential (CTIP) pair style and qeq fix
This commit is contained in:
Axel Kohlmeyer
2024-10-02 19:26:09 -04:00
committed by GitHub
parent 5322b172bd d33ecd6bbf
commit 8a7572fd5a
25 changed files with 21550 additions and 32 deletions
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examples/streitz/NiO.ctip Symbolic link
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../../potentials/NiO.ctip

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examples/streitz/NiO.eam.fs Symbolic link
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../../potentials/NiO.eam.fs

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examples/streitz/data.ctip Normal file
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examples/streitz/in.ctip Normal file
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#CTIP potential for NiO
#Contributing author: Gabriel Plummer (NASA)
#Initialize
units metal
atom_style charge
dimension 3
boundary p p p
#Create Structure
read_data data.ctip
#Define Charges
group type1 type 1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
#Define Potential
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
pair_coeff * * eam/fs NiO.eam.fs Ni O
pair_coeff * * coul/ctip NiO.ctip Ni O
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
#Setup
timestep 0.001
thermo 100
thermo_style custom step temp pe lx ly lz pxx pyy pzz c_q1 c_q2
#Minimization
fix relax all box/relax iso 0
minimize 1e-10 1e-10 100000 100000
unfix relax
#Dynamics
reset_timestep 0
variable T equal 1000
variable rnd equal round(random(0,999,${T}))
velocity all create ${T} ${rnd} mom yes rot yes
fix npt all npt temp ${T} ${T} 0.1 iso 0 0 1
run 1000

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examples/streitz/log.11Sep24.ctip.g++.1 Normal file
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-269-g5a12c762f3-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
#CTIP potential for NiO
#Contributing author: Gabriel Plummer (NASA)
#Initialize
units metal
atom_style charge
dimension 3
boundary p p p
#Create Structure
read_data data.ctip
Reading data file ...
orthogonal box = (0 0 0) to (24.719478 24.719478 24.719478)
1 by 1 by 1 MPI processor grid
reading atoms ...
1728 atoms
read_data CPU = 0.004 seconds
#Define Charges
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
864 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
#Define Potential
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
pair_coeff * * eam/fs NiO.eam.fs Ni O
Reading eam/fs potential file NiO.eam.fs with DATE: 2024-04-29
pair_coeff * * coul/ctip NiO.ctip Ni O
Reading coul/ctip potential file NiO.ctip with DATE: 2024-09-11
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
#Setup
timestep 0.001
thermo 100
thermo_style custom step temp pe lx ly lz pxx pyy pzz c_q1 c_q2
#Minimization
fix relax all box/relax iso 0
minimize 1e-10 1e-10 100000 100000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@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}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair eam/fs, perpetual, trim from (2)
attributes: half, newton on, cut 8
pair build: trim
stencil: none
bin: none
(2) pair coul/ctip, perpetual, half/full from (3)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(3) fix qeq/ctip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies
(src/min.cpp:219)
Per MPI rank memory allocation (min/avg/max) = 55.22 | 55.22 | 55.22 Mbytes
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
0 0 -9633.183 24.719478 24.719478 24.719478 -1491.273 -1491.273 -1491.273 1.2374666 -1.2374666
6 0 -9633.1929 24.707505 24.707505 24.707505 0.0050470506 0.0050470504 0.0050470502 1.2410908 -1.2410908
Loop time of 1.04745 on 1 procs for 6 steps with 1728 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-9633.18301850704 -9633.19294329023 -9633.19294333485
Force two-norm initial, final = 42.177998 0.00014264694
Force max component initial, final = 42.177998 0.00014260857
Final line search alpha, max atom move = 0.0079490417 1.1336014e-06
Iterations, force evaluations = 6 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.3534 | 0.3534 | 0.3534 | 0.0 | 33.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0004205 | 0.0004205 | 0.0004205 | 0.0 | 0.04
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.69216 | 0.69216 | 0.69216 | 0.0 | 66.08
Other | | 0.001461 | | | 0.14
Nlocal: 1728 ave 1728 max 1728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13897 ave 13897 max 13897 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 216000 ave 216000 max 216000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.34317e+06 ave 2.34317e+06 max 2.34317e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2343168
Ave neighs/atom = 1356
Neighbor list builds = 0
Dangerous builds = 0
unfix relax
#Dynamics
reset_timestep 0
variable T equal 1000
variable rnd equal round(random(0,999,${T}))
variable rnd equal round(random(0,999,1000))
velocity all create ${T} ${rnd} mom yes rot yes
velocity all create 1000 ${rnd} mom yes rot yes
velocity all create 1000 233 mom yes rot yes
fix npt all npt temp ${T} ${T} 0.1 iso 0 0 1
fix npt all npt temp 1000 ${T} 0.1 iso 0 0 1
fix npt all npt temp 1000 1000 0.1 iso 0 0 1
run 1000
Per MPI rank memory allocation (min/avg/max) = 54.35 | 54.35 | 54.35 Mbytes
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
0 1000 -9633.1929 24.707505 24.707505 24.707505 15934.991 15754.787 15735.602 1.2410908 -1.2410908
100 600.77874 -9528.0602 24.816519 24.816519 24.816519 -16709.313 -15443.072 -17750.832 1.2181988 -1.2181988
200 578.84295 -9490.9794 24.812627 24.812627 24.812627 -5879.8769 -4851.4601 -6722.107 1.2254363 -1.2254363
300 694.7973 -9478.5512 24.764285 24.764285 24.764285 14639.415 13827.989 13766.766 1.2372201 -1.2372201
400 803.93731 -9462.2542 24.866629 24.866629 24.866629 -4644.2854 -6017.2884 -7744.2567 1.2086229 -1.2086229
500 893.70492 -9441.0072 24.891756 24.891756 24.891756 -5784.2232 -8219.1644 -4187.392 1.2001224 -1.2001224
600 947.21728 -9416.7532 24.863623 24.863623 24.863623 11265.076 12952.469 11331.883 1.2115124 -1.2115124
700 1040.4874 -9409.8397 24.933859 24.933859 24.933859 -6570.5927 -8532.7457 -3284.7317 1.1902794 -1.1902794
800 1037.9366 -9398.4828 24.935138 24.935138 24.935138 -4681.8676 -2576.4998 -7160.562 1.1880324 -1.1880324
900 1049.4211 -9411.115 24.899733 24.899733 24.899733 3250.2695 8121.9271 5945.0542 1.2024086 -1.2024086
1000 964.18789 -9412.4405 24.926442 24.926442 24.926442 -7652.603 -5142.9259 -8351.8835 1.1908935 -1.1908935
Loop time of 183.932 on 1 procs for 1000 steps with 1728 atoms
Performance: 0.470 ns/day, 51.092 hours/ns, 5.437 timesteps/s, 9.395 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 37.347 | 37.347 | 37.347 | 0.0 | 20.30
Neigh | 0.22667 | 0.22667 | 0.22667 | 0.0 | 0.12
Comm | 0.052514 | 0.052514 | 0.052514 | 0.0 | 0.03
Output | 0.00053967 | 0.00053967 | 0.00053967 | 0.0 | 0.00
Modify | 146.29 | 146.29 | 146.29 | 0.0 | 79.53
Other | | 0.01552 | | | 0.01
Nlocal: 1728 ave 1728 max 1728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13901 ave 13901 max 13901 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 210388 ave 210388 max 210388 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.23448e+06 ave 2.23448e+06 max 2.23448e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2234476
Ave neighs/atom = 1293.0995
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:03:05

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examples/streitz/log.11Sep24.ctip.g++.4 Normal file
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-269-g5a12c762f3-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
#CTIP potential for NiO
#Contributing author: Gabriel Plummer (NASA)
#Initialize
units metal
atom_style charge
dimension 3
boundary p p p
#Create Structure
read_data data.ctip
Reading data file ...
orthogonal box = (0 0 0) to (24.719478 24.719478 24.719478)
1 by 2 by 2 MPI processor grid
reading atoms ...
1728 atoms
read_data CPU = 0.007 seconds
#Define Charges
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
864 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
#Define Potential
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
pair_coeff * * eam/fs NiO.eam.fs Ni O
Reading eam/fs potential file NiO.eam.fs with DATE: 2024-04-29
pair_coeff * * coul/ctip NiO.ctip Ni O
Reading coul/ctip potential file NiO.ctip with DATE: 2024-09-11
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
#Setup
timestep 0.001
thermo 100
thermo_style custom step temp pe lx ly lz pxx pyy pzz c_q1 c_q2
#Minimization
fix relax all box/relax iso 0
minimize 1e-10 1e-10 100000 100000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@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}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair eam/fs, perpetual, trim from (2)
attributes: half, newton on, cut 8
pair build: trim
stencil: none
bin: none
(2) pair coul/ctip, perpetual, half/full from (3)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(3) fix qeq/ctip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies
(src/min.cpp:219)
Per MPI rank memory allocation (min/avg/max) = 19.71 | 19.71 | 19.71 Mbytes
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
0 0 -9633.183 24.719478 24.719478 24.719478 -1491.273 -1491.273 -1491.273 1.2374666 -1.2374666
6 0 -9633.1929 24.707505 24.707505 24.707505 0.0050498849 0.0050498856 0.0050498855 1.2410908 -1.2410908
Loop time of 0.288818 on 4 procs for 6 steps with 1728 atoms
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-9633.18301849946 -9633.19294329957 -9633.19294333066
Force two-norm initial, final = 42.177998 0.00014286398
Force max component initial, final = 42.177998 0.00014268867
Final line search alpha, max atom move = 0.0079490643 1.1342414e-06
Iterations, force evaluations = 6 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.09401 | 0.095886 | 0.097631 | 0.4 | 33.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0024298 | 0.004185 | 0.0060676 | 2.1 | 1.45
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.18779 | 0.1878 | 0.18781 | 0.0 | 65.02
Other | | 0.000945 | | | 0.33
Nlocal: 432 ave 432 max 432 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 8593 ave 8593 max 8593 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 54000 ave 54000 max 54000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 585792 ave 585792 max 585792 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2343168
Ave neighs/atom = 1356
Neighbor list builds = 0
Dangerous builds = 0
unfix relax
#Dynamics
reset_timestep 0
variable T equal 1000
variable rnd equal round(random(0,999,${T}))
variable rnd equal round(random(0,999,1000))
velocity all create ${T} ${rnd} mom yes rot yes
velocity all create 1000 ${rnd} mom yes rot yes
velocity all create 1000 233 mom yes rot yes
fix npt all npt temp ${T} ${T} 0.1 iso 0 0 1
fix npt all npt temp 1000 ${T} 0.1 iso 0 0 1
fix npt all npt temp 1000 1000 0.1 iso 0 0 1
run 1000
Per MPI rank memory allocation (min/avg/max) = 18.83 | 18.83 | 18.83 Mbytes
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
0 1000 -9633.1929 24.707505 24.707505 24.707505 15934.991 15754.787 15735.602 1.2410908 -1.2410908
100 600.77874 -9528.0602 24.816519 24.816519 24.816519 -16709.313 -15443.072 -17750.832 1.2181988 -1.2181988
200 578.84295 -9490.9794 24.812627 24.812627 24.812627 -5879.8769 -4851.4601 -6722.107 1.2254363 -1.2254363
300 694.7973 -9478.5512 24.764285 24.764285 24.764285 14639.415 13827.989 13766.766 1.2372201 -1.2372201
400 803.93731 -9462.2542 24.866629 24.866629 24.866629 -4644.2853 -6017.2884 -7744.2567 1.2086229 -1.2086229
500 893.70492 -9441.0072 24.891756 24.891756 24.891756 -5784.2232 -8219.1644 -4187.392 1.2001224 -1.2001224
600 947.21728 -9416.7532 24.863623 24.863623 24.863623 11265.076 12952.469 11331.883 1.2115124 -1.2115124
700 1040.4874 -9409.8397 24.933859 24.933859 24.933859 -6570.5926 -8532.7456 -3284.7317 1.1902794 -1.1902794
800 1037.9366 -9398.4828 24.935138 24.935138 24.935138 -4681.8675 -2576.5001 -7160.5622 1.1880324 -1.1880324
900 1049.4211 -9411.115 24.899733 24.899733 24.899733 3250.2695 8121.9274 5945.0541 1.2024086 -1.2024086
1000 964.18789 -9412.4405 24.926442 24.926442 24.926442 -7652.603 -5142.926 -8351.8839 1.1908935 -1.1908935
Loop time of 63.5378 on 4 procs for 1000 steps with 1728 atoms
Performance: 1.360 ns/day, 17.649 hours/ns, 15.739 timesteps/s, 27.196 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.737 | 12.782 | 12.839 | 1.1 | 20.12
Neigh | 0.082989 | 0.083627 | 0.084898 | 0.3 | 0.13
Comm | 0.39773 | 0.45431 | 0.49896 | 5.5 | 0.72
Output | 0.00038299 | 0.0004067 | 0.00047658 | 0.0 | 0.00
Modify | 50.207 | 50.207 | 50.208 | 0.0 | 79.02
Other | | 0.01047 | | | 0.02
Nlocal: 432 ave 446 max 421 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 8594.5 ave 8608 max 8579 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 52597 ave 54466 max 51209 min
Histogram: 1 0 1 0 1 0 0 0 0 1
FullNghs: 558619 ave 576961 max 544134 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 2234476
Ave neighs/atom = 1293.0995
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:01:04