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Merge branch 'develop' into mdr-rebase2

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This commit is contained in:
Joel Clemmer
2025-01-17 12:17:20 -07:00
committed by GitHub
parent 769b0b9211 ffa4765b15
commit 72784262b1
1096 changed files with 97368 additions and 35091 deletions
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1
examples/COUPLE/plugin/liblammpsplugin.c
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@ -117,6 +117,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(set_string_variable);
ADDSYM(set_internal_variable);
ADDSYM(variable_info);
ADDSYM(eval);
ADDSYM(gather_atoms);
ADDSYM(gather_atoms_concat);

1
examples/COUPLE/plugin/liblammpsplugin.h
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@ -163,6 +163,7 @@ struct _liblammpsplugin {
int (*set_string_variable)(void *, const char *, const char *);
int (*set_internal_variable)(void *, const char *, double);
int (*variable_info)(void *, int, char *, int);
double (*eval)(void *, const char *);
void (*gather_atoms)(void *, const char *, int, int, void *);
void (*gather_atoms_concat)(void *, const char *, int, int, void *);

50
examples/LEPTON/in.efield-lepton Normal file
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@ -0,0 +1,50 @@
# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
units lj
atom_style hybrid sphere dipole
dimension 3
boundary s s s
region box block -2 2 -2 2 -2 2
create_box 1 box
create_atoms 1 random 100 12345 NULL
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
set group all diameter 0.1
set group all dipole/random 98934 0.01
pair_style none
comm_modify cutoff 3.0
velocity all create 0.0 87287 mom yes rot yes
fix 1 all nve/sphere update dipole
###############################################################################################################
## Yukawa potential
#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
## Gradually increasing uniform field
#variable E equal ramp(0,1)
#fix 2 all efield/lepton "-v_E*(x+y+z)"
## Linear gradient field
fix 2 all efield/lepton "-1/6*x^3" step 1e-6
fix_modify 2 energy yes
###############################################################################################################
timestep 1e-3
compute erot all erotate/sphere
variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
thermo_style custom step temp ke c_erot pe v_etotal
thermo 500
thermo_modify norm no
#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
run 10000

115
examples/LEPTON/log.13Jan25.efield-lepton.g++.1 Normal file
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@ -0,0 +1,115 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-283-g742c869534-modified)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
units lj
atom_style hybrid sphere dipole
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132)
dimension 3
boundary s s s
region box block -2 2 -2 2 -2 2
create_box 1 box
Created orthogonal box = (-2 -2 -2) to (2 2 2)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 100 12345 NULL
Created 100 atoms
using lattice units in orthogonal box = (-2.0004 -2.0004 -2.0004) to (2.0004 2.0004 2.0004)
create_atoms CPU = 0.000 seconds
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
Setting atom values ...
100 settings made for mass
set group all diameter 0.1
Setting atom values ...
100 settings made for diameter
set group all dipole/random 98934 0.01
Setting atom values ...
100 settings made for dipole/random
pair_style none
comm_modify cutoff 3.0
velocity all create 0.0 87287 mom yes rot yes
fix 1 all nve/sphere update dipole
###############################################################################################################
## Yukawa potential
#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
## Gradually increasing uniform field
#variable E equal ramp(0,1)
#fix 2 all efield/lepton "-v_E*(x+y+z)"
## Linear gradient field
fix 2 all efield/lepton "-1/6*x^3" step 1e-6
fix_modify 2 energy yes
###############################################################################################################
timestep 1e-3
compute erot all erotate/sphere
variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
thermo_style custom step temp ke c_erot pe v_etotal
thermo 500
thermo_modify norm no
#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
run 10000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2442)
Per MPI rank memory allocation (min/avg/max) = 4.273 | 4.273 | 4.273 Mbytes
Step Temp KinEng c_erot PotEng v_etotal
0 0 0 0 0.036419797 0.036419797
500 3.7159175e-06 0.00055181374 0.44262618 -0.40675701 0.036420985
1000 1.2808438e-05 0.0019020531 0.24499116 -0.21047295 0.036420259
1500 2.8343769e-05 0.0042090498 0.26504485 -0.2328336 0.036420307
2000 4.8796894e-05 0.0072463388 0.30953526 -0.28036098 0.036420618
2500 7.8933715e-05 0.011721657 0.2015076 -0.17680909 0.036420173
3000 0.00011381678 0.016901791 0.31002163 -0.29050294 0.036420476
3500 0.00015650339 0.023240753 0.27837968 -0.26520001 0.036420418
4000 0.00020429109 0.030337227 0.26201101 -0.25592795 0.036420289
4500 0.00026362339 0.039148074 0.29769952 -0.3004271 0.036420499
5000 0.00033328941 0.049493478 0.21642442 -0.22949776 0.036420131
5500 0.00040914224 0.060757622 0.28422322 -0.30856047 0.036420377
6000 0.00049425119 0.073396302 0.31767 -0.35464572 0.03642058
6500 0.00058508892 0.086885704 0.29079532 -0.34126075 0.036420276
7000 0.00069845073 0.10371993 0.25776048 -0.32506015 0.036420262
7500 0.0008215656 0.12200249 0.27033777 -0.35591972 0.036420539
8000 0.00095528125 0.14185927 0.33943527 -0.44487406 0.036420479
8500 0.0011052502 0.16412965 0.26727165 -0.39498109 0.036420218
9000 0.0012738298 0.18916373 0.31082058 -0.46356382 0.036420485
9500 0.001464197 0.21743325 0.25669856 -0.43771158 0.036420224
10000 0.0016627654 0.24692067 0.36273185 -0.57323194 0.036420578
Loop time of 0.84714 on 1 procs for 10000 steps with 100 atoms
Performance: 1019901.911 tau/day, 11804.420 timesteps/s, 1.180 Matom-step/s
62.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 9.21e-07 | 9.21e-07 | 9.21e-07 | 0.0 | 0.00
Comm | 0.00094138 | 0.00094138 | 0.00094138 | 0.0 | 0.11
Output | 0.0001983 | 0.0001983 | 0.0001983 | 0.0 | 0.02
Modify | 0.84105 | 0.84105 | 0.84105 | 0.0 | 99.28
Other | | 0.004946 | | | 0.58
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:00:00

115
examples/LEPTON/log.13Jan25.efield-lepton.g++.4 Normal file
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@ -0,0 +1,115 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-283-g742c869534-modified)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
units lj
atom_style hybrid sphere dipole
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132)
dimension 3
boundary s s s
region box block -2 2 -2 2 -2 2
create_box 1 box
Created orthogonal box = (-2 -2 -2) to (2 2 2)
1 by 2 by 2 MPI processor grid
create_atoms 1 random 100 12345 NULL
Created 100 atoms
using lattice units in orthogonal box = (-2.0004 -2.0004 -2.0004) to (2.0004 2.0004 2.0004)
create_atoms CPU = 0.000 seconds
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
Setting atom values ...
100 settings made for mass
set group all diameter 0.1
Setting atom values ...
100 settings made for diameter
set group all dipole/random 98934 0.01
Setting atom values ...
100 settings made for dipole/random
pair_style none
comm_modify cutoff 3.0
velocity all create 0.0 87287 mom yes rot yes
fix 1 all nve/sphere update dipole
###############################################################################################################
## Yukawa potential
#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
## Gradually increasing uniform field
#variable E equal ramp(0,1)
#fix 2 all efield/lepton "-v_E*(x+y+z)"
## Linear gradient field
fix 2 all efield/lepton "-1/6*x^3" step 1e-6
fix_modify 2 energy yes
###############################################################################################################
timestep 1e-3
compute erot all erotate/sphere
variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
thermo_style custom step temp ke c_erot pe v_etotal
thermo 500
thermo_modify norm no
#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
run 10000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2442)
Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes
Step Temp KinEng c_erot PotEng v_etotal
0 0 0 0 0.036419797 0.036419797
500 3.7159175e-06 0.00055181374 0.44262618 -0.40675701 0.036420985
1000 1.2808438e-05 0.0019020531 0.24499116 -0.21047295 0.036420259
1500 2.8343769e-05 0.0042090498 0.26504485 -0.2328336 0.036420307
2000 4.8796894e-05 0.0072463388 0.30953526 -0.28036098 0.036420618
2500 7.8933715e-05 0.011721657 0.2015076 -0.17680909 0.036420173
3000 0.00011381678 0.016901791 0.31002163 -0.29050294 0.036420476
3500 0.00015650339 0.023240753 0.27837968 -0.26520001 0.036420418
4000 0.00020429109 0.030337227 0.26201101 -0.25592795 0.036420289
4500 0.00026362339 0.039148074 0.29769952 -0.3004271 0.036420499
5000 0.00033328941 0.049493478 0.21642442 -0.22949776 0.036420131
5500 0.00040914224 0.060757622 0.28422322 -0.30856047 0.036420377
6000 0.00049425119 0.073396302 0.31767 -0.35464572 0.03642058
6500 0.00058508892 0.086885704 0.29079532 -0.34126075 0.036420276
7000 0.00069845073 0.10371993 0.25776048 -0.32506015 0.036420262
7500 0.0008215656 0.12200249 0.27033777 -0.35591972 0.036420539
8000 0.00095528125 0.14185927 0.33943527 -0.44487406 0.036420479
8500 0.0011052502 0.16412965 0.26727165 -0.39498109 0.036420218
9000 0.0012738298 0.18916373 0.31082058 -0.46356382 0.036420485
9500 0.001464197 0.21743325 0.25669856 -0.43771158 0.036420224
10000 0.0016627654 0.24692067 0.36273185 -0.57323194 0.036420578
Loop time of 0.985035 on 4 procs for 10000 steps with 100 atoms
Performance: 877125.838 tau/day, 10151.919 timesteps/s, 1.015 Matom-step/s
67.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 7.22e-07 | 8.9125e-07 | 1.031e-06 | 0.0 | 0.00
Comm | 0.09818 | 0.1024 | 0.10798 | 1.1 | 10.40
Output | 0.00021634 | 0.00028668 | 0.00044312 | 0.0 | 0.03
Modify | 0.773 | 0.81845 | 0.84055 | 3.0 | 83.09
Other | | 0.06389 | | | 6.49
Nlocal: 25 ave 30 max 23 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 75 ave 77 max 70 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:00:00

6
examples/PACKAGES/dispersion/README Normal file
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@ -0,0 +1,6 @@
To run these examples, one needs to compile LAMMPS with the ML-PACE (-DPKG_ML-PACE=ON) and the EXTRA-PAIR packages (-DPKG_EXTRA-PAIR=ON).
These examples show how to combine a short-ranged ML potential with a dispersion correction scheme. Here we combine a general-purpose ACE potential for carbon (10.1021/acs.jctc.2c01149), with two different dispersion correction schemes:
- D2 (a pure two-body potential, here tabulated)
- D3 (a many-body potential, implemented in LAMMPS).

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examples/PACKAGES/dispersion/in.d2 Normal file
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@ -0,0 +1,36 @@
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 region box
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace table linear 10000
pair_coeff * * pace potential_files/c_ace.yace C
pair_coeff * * table potential_files/d2.table D2 9.0
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair table
# calculate the e/atom for each pair style individually
variable dUpace equal c_c1/atoms
variable dUd2 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_dUpace v_dUd2
thermo 10
run 100

36
examples/PACKAGES/dispersion/in.d3 Normal file
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@ -0,0 +1,36 @@
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 region box
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace dispersion/d3 bj pbe 16.0 16.0
pair_coeff * * pace potential_files/c_ace.yace C
pair_coeff * * dispersion/d3 C
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair dispersion/d3
# calculate the e/atom for each pair style individually
variable Upace equal c_c1/atoms
variable Ud3 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_Upace v_Ud3
thermo 10
run 100

122
examples/PACKAGES/dispersion/log.20Dec2024.d2.g++.1 Normal file
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@ -0,0 +1,122 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-125-g095d33dafb)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace table linear 10000
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * table potential_files/d2.table D2 9.0
Reading pair table potential file potential_files/d2.table with DATE: 2021-12-16
WARNING: 8063 of 20000 force values in table D2 are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
WARNING: 2386 of 20000 distance values in table 1e-06 with relative error
WARNING: over D2 to re-computed values (src/pair_table.cpp:474)
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair table
# calculate the e/atom for each pair style individually
variable dUpace equal c_c1/atoms
variable dUd2 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_dUpace v_dUd2
thermo 10
run 100
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 = 9 9 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.735 | 3.735 | 3.735 Mbytes
Step Temp PotEng Press TotEng v_dUpace v_dUd2
0 200 -262.26589 -9971.6713 -236.43971 -0.2577066 -0.0045592958
10 198.01563 -261.95164 -9936.5218 -236.38171 -0.25738489 -0.004566747
20 199.80384 -261.06484 -9826.0969 -235.26399 -0.25647577 -0.0045890709
30 200.79867 -259.7549 -9655.8924 -233.82559 -0.25512792 -0.0046269853
40 194.7303 -258.36397 -9450.9508 -233.21827 -0.25368377 -0.004680203
50 197.08802 -257.40377 -9200.5727 -231.95362 -0.25265301 -0.0047507608
60 204.21755 -257.66495 -8919.2309 -231.29416 -0.25282305 -0.0048419012
70 216.81983 -260.19034 -8702.5441 -232.19221 -0.25523198 -0.0049583602
80 242.71952 -266.40641 -8617.9868 -235.06383 -0.26129243 -0.0051139831
90 294.45869 -279.46195 -8724.2954 -241.43824 -0.27411961 -0.0053423377
100 400.44323 -307.29577 -9070.6387 -255.58618 -0.30165815 -0.0056376175
Loop time of 2.66184 on 1 procs for 100 steps with 1000 atoms
Performance: 3.246 ns/day, 7.394 hours/ns, 37.568 timesteps/s, 37.568 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6584 | 2.6584 | 2.6584 | 0.0 | 99.87
Neigh | 0.0012861 | 0.0012861 | 0.0012861 | 0.0 | 0.05
Comm | 0.00064617 | 0.00064617 | 0.00064617 | 0.0 | 0.02
Output | 0.00024173 | 0.00024173 | 0.00024173 | 0.0 | 0.01
Modify | 0.00099328 | 0.00099328 | 0.00099328 | 0.0 | 0.04
Other | | 0.0002431 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2375 ave 2375 max 2375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 26027 ave 26027 max 26027 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 17736 ave 17736 max 17736 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 26027
Ave neighs/atom = 26.027
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:02

122
examples/PACKAGES/dispersion/log.20Dec2024.d2.g++.4 Normal file
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-125-g095d33dafb)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace table linear 10000
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * table potential_files/d2.table D2 9.0
Reading pair table potential file potential_files/d2.table with DATE: 2021-12-16
WARNING: 8063 of 20000 force values in table D2 are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
WARNING: 2386 of 20000 distance values in table 1e-06 with relative error
WARNING: over D2 to re-computed values (src/pair_table.cpp:474)
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair table
# calculate the e/atom for each pair style individually
variable dUpace equal c_c1/atoms
variable dUd2 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_dUpace v_dUd2
thermo 10
run 100
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 = 9 9 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.655 | 3.655 | 3.655 Mbytes
Step Temp PotEng Press TotEng v_dUpace v_dUd2
0 200 -262.26589 -9971.6713 -236.43971 -0.2577066 -0.0045592958
10 198.00622 -261.95011 -9934.5046 -236.38139 -0.25738304 -0.0045670733
20 199.81545 -261.06219 -9818.4051 -235.25985 -0.25647183 -0.0045903655
30 200.85902 -259.76256 -9639.9086 -233.82546 -0.25513263 -0.0046299265
40 195.00229 -258.4153 -9425.3772 -233.23448 -0.25372979 -0.0046855071
50 198.00573 -257.57066 -9164.7658 -232.00201 -0.25281159 -0.0047590772
60 206.26759 -258.09159 -8877.0162 -231.45607 -0.25323684 -0.0048547477
70 219.81939 -261.10607 -8668.5789 -232.7206 -0.25612771 -0.0049783595
80 250.27428 -268.27862 -8601.1343 -235.96048 -0.2631332 -0.0051454143
90 308.88167 -283.24793 -8745.8792 -243.36177 -0.27785093 -0.0053969977
100 427.60692 -315.05776 -9147.2389 -259.8405 -0.30933434 -0.0057234269
Loop time of 0.69628 on 4 procs for 100 steps with 1000 atoms
Performance: 12.409 ns/day, 1.934 hours/ns, 143.620 timesteps/s, 143.620 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 | 0.67839 | 0.68307 | 0.69054 | 0.6 | 98.10
Neigh | 0.00034181 | 0.00034811 | 0.00036188 | 0.0 | 0.05
Comm | 0.0045334 | 0.012031 | 0.016704 | 4.4 | 1.73
Output | 0.00015123 | 0.00017175 | 0.0002318 | 0.0 | 0.02
Modify | 0.00041346 | 0.00043062 | 0.00044327 | 0.0 | 0.06
Other | | 0.0002301 | | | 0.03
Nlocal: 250 ave 261 max 246 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 1250 ave 1254 max 1239 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 6501 ave 6778 max 6320 min
Histogram: 1 0 2 0 0 0 0 0 0 1
FullNghs: 4421.5 ave 4595 max 4332 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 26004
Ave neighs/atom = 26.004
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-125-g095d33dafb)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace dispersion/d3 bj pbe 16.0 16.0
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * dispersion/d3 C
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair dispersion/d3
# calculate the e/atom for each pair style individually
variable Upace equal c_c1/atoms
variable Ud3 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_Upace v_Ud3
thermo 10
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair dispersion/d3, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.225 | 4.225 | 4.225 Mbytes
Step Temp PotEng Press TotEng v_Upace v_Ud3
0 200 -269.22784 -10163.81 -243.40166 -0.2577066 -0.011521241
10 198.05578 -268.91992 -10128.61 -243.34481 -0.25738487 -0.01153505
20 199.85092 -268.05146 -10018.116 -242.24454 -0.25647561 -0.011575851
30 201.10902 -266.77119 -9847.2946 -240.80181 -0.2551274 -0.011643795
40 195.0686 -265.42225 -9641.6992 -240.23287 -0.25368339 -0.011738855
50 197.63706 -264.51951 -9390.1455 -238.99847 -0.25265765 -0.011861864
60 205.01072 -264.86268 -9107.4427 -238.38947 -0.25284579 -0.012016888
70 217.51797 -267.50863 -8890.9916 -239.42034 -0.25529813 -0.012210496
80 244.30754 -273.91051 -8806.154 -242.36286 -0.26145652 -0.01245399
90 296.72041 -287.2518 -8913.8963 -248.93603 -0.27448382 -0.012767981
100 404.07337 -315.6103 -9266.1292 -263.43195 -0.3024416 -0.013168694
Loop time of 4.52709 on 1 procs for 100 steps with 1000 atoms
Performance: 1.909 ns/day, 12.575 hours/ns, 22.089 timesteps/s, 22.089 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.5223 | 4.5223 | 4.5223 | 0.0 | 99.89
Neigh | 0.0023631 | 0.0023631 | 0.0023631 | 0.0 | 0.05
Comm | 0.00088624 | 0.00088624 | 0.00088624 | 0.0 | 0.02
Output | 0.00027759 | 0.00027759 | 0.00027759 | 0.0 | 0.01
Modify | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 0.02
Other | | 0.0002737 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3913 ave 3913 max 3913 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 116409 ave 116409 max 116409 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 17748 ave 17748 max 17748 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 116409
Ave neighs/atom = 116.409
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-125-g095d33dafb)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace dispersion/d3 bj pbe 16.0 16.0
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * dispersion/d3 C
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair dispersion/d3
# calculate the e/atom for each pair style individually
variable Upace equal c_c1/atoms
variable Ud3 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_Upace v_Ud3
thermo 10
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair dispersion/d3, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.732 | 3.732 | 3.732 Mbytes
Step Temp PotEng Press TotEng v_Upace v_Ud3
0 200 -269.22784 -10163.81 -243.40166 -0.2577066 -0.011521241
10 198.04813 -268.91867 -10126.59 -243.34454 -0.25738301 -0.011535654
20 199.86491 -268.04994 -10010.421 -242.24121 -0.25647167 -0.011578276
30 201.18317 -266.78129 -9831.2837 -240.80233 -0.25513213 -0.011649162
40 195.35281 -265.47802 -9616.0833 -240.25194 -0.2537296 -0.011748422
50 198.56247 -264.69401 -9354.3017 -239.05347 -0.25281709 -0.011876925
60 207.17238 -265.30194 -9065.1196 -238.54959 -0.25326251 -0.012039431
70 221.05245 -268.44583 -8856.3622 -239.90114 -0.25620278 -0.012243053
80 252.00942 -275.82142 -8789.4126 -243.27922 -0.26332044 -0.012500977
90 311.21153 -291.09334 -8935.4036 -250.90632 -0.27825852 -0.012834817
100 431.24438 -323.45003 -9344.1963 -267.76306 -0.31019084 -0.013259185
Loop time of 1.20684 on 4 procs for 100 steps with 1000 atoms
Performance: 7.159 ns/day, 3.352 hours/ns, 82.861 timesteps/s, 82.861 katom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2007 | 1.2019 | 1.2029 | 0.1 | 99.60
Neigh | 0.00060541 | 0.00062493 | 0.00064411 | 0.0 | 0.05
Comm | 0.0024344 | 0.0033552 | 0.0045996 | 1.4 | 0.28
Output | 0.00016956 | 0.00017999 | 0.00021054 | 0.0 | 0.01
Modify | 0.00046946 | 0.00048235 | 0.00049796 | 0.0 | 0.04
Other | | 0.0002449 | | | 0.02
Nlocal: 250 ave 261 max 246 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 2198 ave 2202 max 2187 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 29023.2 ave 29681 max 27646 min
Histogram: 1 0 0 0 0 0 0 1 0 2
FullNghs: 4421 ave 4595 max 4331 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 116093
Ave neighs/atom = 116.093
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01

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"""
For use with 'in.deca-ala-solv_imd_v3'.
Tested with imdclient v0.1.4 and MDAnalysis v2.8.0
"""
from imdclient.IMD import IMDReader
import MDAnalysis as mda
u = mda.Universe('data.deca-ala-solv', "imd://localhost:5678", topology_format='DATA')
for ts in u.trajectory:
print(ts.time)
print(ts.velocities)

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#
units real
neighbor 2.5 bin
neigh_modify delay 1 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
special_bonds charmm
read_data data.deca-ala-solv
group peptide id <= 103
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
thermo 100
thermo_style multi
timestep 2.0
kspace_style pppm 1e-5
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
# IMD setup. Client code available in 'deca-ala-solv_imd_v3.py'
fix comm all imd 5678 unwrap on trate 10 version 3 time on box on coordinates on velocities on forces off
run 5000000

1
examples/README
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@ -112,6 +112,7 @@ snap: examples for using several bundled SNAP potentials
srd: stochastic rotation dynamics (SRD) particles as solvent
steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
streitz: Streitz-Mintmire potential for Al2O3
stress_vcm: removing binned rigid body motion from binned stress profile
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
template: examples for using atom_style template and comparing to atom style molecular
tersoff: regression test input for Tersoff variants

4
examples/bpm/pour/in.bpm.pour
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@ -13,9 +13,9 @@ region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in
region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in
pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1
bond_style bpm/rotational
bond_style bpm/rotational break no smooth no
pair_coeff 1 1
bond_coeff 1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002
bond_coeff 1 1.0 0.2 0.01 0.01 0.0 0.0 0.0 0.0 0.2 0.04 0.002 0.002
compute nbond all nbond/atom
compute tbond all reduce sum c_nbond

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examples/comb/README
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@ -20,5 +20,3 @@ Examples:
4. in.comb.Cu2O.elastic: Cu2O crystal, qeq on, minimizes, then calculates
elastic constants
5. in.comb.HfO2: HfO2 polymorphs: Monoclinic HfO2 NVT @ 300K
6. in.comb.CuaS: Metallic Cu and amorphous silica interface, qeq on,
five step NVE run

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README stress_vcm
=================
Contents:
- in.stress_vcm: Example script showing how to remove binned
velocities of center of mass (VCM) from stress calculations.
- stress_comparison.19Nov24.png: Plot shows the stress
calculated in bars on the y axis for each positional bin on
the x axis. Plotted are three different time steps from
stress profiles with and without the VCM removed. Plot
generated using Python.
- stress_xx.19Nov24.out: Output file generated by fix ave/time.
- log.19Nov24.stress_vcm.g++.1: LAMMPS log file with 1 proc.
- log.19Nov24.stress_vcm.g++.4: LAMMPS log file with 4 procs.
Notes:
- Running this script as-is will generate two files. A log
file with thermodynamic data and a stress_xx.out file
containing the binned stress profile with the VCM removed.
- To generate the binned stress profile without removing the
VCM then the compute stress/atom command at step three
needs the last keyword "ch_temp_vcm" to be replaced with
"NULL".
- Uncommenting the line under "Atom dump" will generate an
all atom dump file every 50 time steps containing atom ID,
type, and xyz coordinates.
- Uncommenting the lines under "Image dumps" will generate
.jpg image files every 250 timesteps.
- Uncommenting lines under "Movie dump" will generate a .avi
movie file showing timesteps every 125 timesteps.

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# Removing Binned Velocities of Center of Mass (VCM) from Stress
# This example shows how to remove rigid body motion from
# binned stress calculations. This uses a combination of commands
# from compute chunk/atom, compute temp/chunk, compute
# stress/atom and fix ave/time. We'll show how these commands
# work in the context of a shockwave experiment on a cube of
# atoms. To shock the cube, a rectangular region of atoms is
# frozen, moved into the cube with a constant velocity along the
# x direction, and then unfrozen. As the shockwave begins
# propagating, the body of the cube also moves along the x
# direction. To better understand the stress dynamics of the
# cube we remove the velocity component belonging to the overall
# motion of each bin.
units metal
boundary p p p
atom_style atomic
lattice fcc 5.3589
processors 1 * *
# Defining regions for box and atoms.
# In this experiment an elongated simulation cell is
# defined in the x direction to allow for non-periodic
# motion of the atoms.
region box1 block -3 24 0 12 0 12 units lattice
region box2 block 0 12 0 12 0 12 units lattice
# Creating box and atoms
create_box 1 box1
create_atoms 1 region box2
mass 1 40.00
# Adding energy to the system
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.04 3.405
# Begin time integration
timestep 2e-3
fix fix_nve all nve
thermo 100
run 500
#--------------------------------------#
# Chunk, Stress, and VCM removal steps #
#--------------------------------------#
# 1. Create 20 equispaced bins sliced along the x direction.
# -"units reduced" normalizes the distance from 0.0 to 1.0
variable nbins index 20
variable fraction equal 1.0/v_nbins
variable volfrac equal 1/(vol*${fraction})
compute ch_id all chunk/atom bin/1d x lower ${fraction} units reduced
# 2. Calculate temperature bins with VCM aka COM velocities removed.
compute ch_temp_vcm all temp/chunk ch_id com yes
# 3. Compute per atom stress with VCM removed via temp-ID.
# -The velocities from specified temp-ID are used to compute stress.
# -Stress/atom units are pressure*volume! Optionally handled next step.
compute atom_stress_vcm all stress/atom ch_temp_vcm
# 4. Divide out bin volume from xx stress component.
variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
# 5. Sum the per atom stresses in each bin.
compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
# 6. Average and output to file.
# -The average output is every 100 steps with samples collected 20 times with 5 step intervals.
fix ave_stress_vcm all ave/time 5 20 100 c_ch_stress_vcm mode vector file stress_xx.out
#--------------------------------------#
# Piston compressing along x direction
region piston block -1 1 INF INF INF INF units lattice
group piston region piston
fix fix_piston piston move linear 5 0 0 units box # strain rate ~ 8e10 1/s
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve
# Atom dump
# dump atom_dump all atom 50 dump.vcm
# # Image dumps
# dump 2 all image 250 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
# dump_modify 2 pad 1
# # Movie dump
# dump 3 all movie 125 movie.avi type type &
# axes yes 0.8 0.02 view 60 -30
# dump_modify 3 pad 1
run 500
unfix fix_piston
run 1500

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LAMMPS (19 Nov 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Removing Binned Velocities of Center of Mass (VCM) from Stress
# This example shows how to remove rigid body motion from
# binned stress calculations. This uses a combination of commands
# from compute chunk/atom, compute temp/chunk, compute
# stress/atom and fix ave/time. We'll show how these commands
# work in the context of a shockwave experiment on a cube of
# atoms. To shock the cube, a rectangular region of atoms is
# frozen, moved into the cube with a constant velocity along the
# x direction, and then unfrozen. As the shockwave begins
# propagating, the body of the cube also moves along the x
# direction. To better understand the stress dynamics of the
# cube we remove the velocity component belonging to the overall
# motion of each bin.
units metal
boundary p p p
atom_style atomic
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
processors 1 * *
# Defining regions for box and atoms.
# In this experiment an elongated simulation cell is
# defined in the x direction to allow for non-periodic
# motion of the atoms.
region box1 block -3 24 0 12 0 12 units lattice
region box2 block 0 12 0 12 0 12 units lattice
# Creating box and atoms
create_box 1 box1
Created orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box2
Created 7200 atoms
using lattice units in orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
create_atoms CPU = 0.002 seconds
mass 1 40.00
# Adding energy to the system
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.04 3.405
# Begin time integration
timestep 2e-3
fix fix_nve all nve
thermo 100
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 25 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.721 | 5.721 | 5.721 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -2252.7567 0 -1694.4304 -974.62456
100 284.72172 -1977.4291 0 -1712.483 2453.7429
200 304.44519 -1994.7937 0 -1711.4941 1822.2699
300 304.28012 -1993.2958 0 -1710.1498 1498.3794
400 296.76492 -1985.1364 0 -1708.9836 1259.9474
500 295.00895 -1982.4224 0 -1707.9036 964.9526
Loop time of 3.01696 on 1 procs for 500 steps with 7200 atoms
Performance: 28.638 ns/day, 0.838 hours/ns, 165.730 timesteps/s, 1.193 Matom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8439 | 2.8439 | 2.8439 | 0.0 | 94.26
Neigh | 0.11212 | 0.11212 | 0.11212 | 0.0 | 3.72
Comm | 0.015585 | 0.015585 | 0.015585 | 0.0 | 0.52
Output | 0.003747 | 0.003747 | 0.003747 | 0.0 | 0.12
Modify | 0.026097 | 0.026097 | 0.026097 | 0.0 | 0.87
Other | | 0.01551 | | | 0.51
Nlocal: 7200 ave 7200 max 7200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6410 ave 6410 max 6410 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 615095 ave 615095 max 615095 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 615095
Ave neighs/atom = 85.429861
Neighbor list builds = 9
Dangerous builds = 0
#------------------------------------#
# Chunk, Stress, and VCM removal steps
#------------------------------------#
# 1. Create 20 equispaced bins sliced along the x direction.
# "units reduced" normalizes the distance from 0 to 1
variable nbins index 20
variable fraction equal 1.0/v_nbins
variable volfrac equal 1/(vol*${fraction})
variable volfrac equal 1/(vol*0.05)
compute ch_id all chunk/atom bin/1d x lower ${fraction} units reduced
compute ch_id all chunk/atom bin/1d x lower 0.05 units reduced
# 2. Calculate temperature bins with VCM aka COM velocities removed.
compute ch_temp_vcm all temp/chunk ch_id com yes
# 3. Compute per atom stress with VCM removed via temp-ID.
# The velocities from specified temp-ID are used to compute stress
# Stress/atom units are pressure*volume! Optionally handled next step.
compute atom_stress_vcm all stress/atom ch_temp_vcm
# 4. Divide out bin volume from xx stress component.
variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
variable stress atom -(c_atom_stress_vcm[1])/(vol*0.05)
# 5. Sum the per atom stresses in each bin.
compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
# 6. Average and output to file.
# The average output is every 100 steps with samples collected 20 times with 5 step intervals
# fix ave_stress_vcm all ave/time 5 20 100 c_ch_stress_vcm mode vector file stress_xx.out
#------------------------------------#
# Piston compressing along x direction
region piston block -1 1 INF INF INF INF units lattice
group piston region piston
863 atoms in group piston
fix fix_piston piston move linear 5 0 0 units box # strain rate ~ 8e10 1/s
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve
# Atom dump
# dump atom_dump all atom 50 dump.vcm
# # Image dumps
# dump 2 all image 250 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
# dump_modify 2 pad 1
# # Movie dump
# dump 3 all movie 125 movie.avi type type # axes yes 0.8 0.02 view 60 -30
# dump_modify 3 pad 1
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: One or more atoms are time integrated more than once (src/modify.cpp:296)
Per MPI rank memory allocation (min/avg/max) = 6.975 | 6.975 | 6.975 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
500 295.00895 274.51875 -1982.4224 144.6903 64.3068 64.3068 631.89976 1127.2965 1135.6616 -1707.9036
600 357.38902 332.56613 -1951.3422 144.6903 64.3068 64.3068 2236.6706 2003.2726 1943.6815 -1618.7761
700 420.30268 391.11005 -1911.8178 144.6903 64.3068 64.3068 3761.5011 3065.4699 3140.3169 -1520.7077
800 484.96279 451.27911 -1875.379 144.6903 64.3068 64.3068 5362.254 4174.4201 4166.0818 -1424.0999
900 587.78954 546.96391 -1871.217 144.6903 64.3068 64.3068 6481.4714 4875.705 4676.6083 -1324.2531
1000 684.07997 636.56636 -1868.1639 144.6903 64.3068 64.3068 7734.6158 5271.3524 5272.1276 -1231.5975
Loop time of 3.09383 on 1 procs for 500 steps with 7200 atoms
Performance: 27.927 ns/day, 0.859 hours/ns, 161.612 timesteps/s, 1.164 Matom-step/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8485 | 2.8485 | 2.8485 | 0.0 | 92.07
Neigh | 0.18767 | 0.18767 | 0.18767 | 0.0 | 6.07
Comm | 0.011533 | 0.011533 | 0.011533 | 0.0 | 0.37
Output | 0.003323 | 0.003323 | 0.003323 | 0.0 | 0.11
Modify | 0.031777 | 0.031777 | 0.031777 | 0.0 | 1.03
Other | | 0.01107 | | | 0.36
Nlocal: 7200 ave 7200 max 7200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6409 ave 6409 max 6409 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 646408 ave 646408 max 646408 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 646408
Ave neighs/atom = 89.778889
Neighbor list builds = 15
Dangerous builds = 0
unfix fix_piston
run 1500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.6 | 6.6 | 6.6 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
1000 684.07997 636.56636 -1868.1639 144.6903 64.3068 64.3068 7734.6158 5271.3524 5272.1276 -1231.5975
1100 710.19886 660.87113 -1894.0485 144.6903 64.3068 64.3068 8048.3485 5396.6668 5376.5956 -1233.1774
1200 717.16487 667.35331 -1901.3849 144.6903 64.3068 64.3068 8009.7984 5634.5121 5349.4113 -1234.0316
1300 710.26037 660.92837 -1894.9802 144.6903 64.3068 64.3068 8063.4125 5572.1245 5530.174 -1234.0519
1400 715.93921 666.21278 -1898.8885 144.6903 64.3068 64.3068 7752.0927 5293.5463 5322.2312 -1232.6757
1500 748.85411 696.84154 -1926.4891 144.6903 64.3068 64.3068 6030.5428 4076.8886 4012.7653 -1229.6475
1600 767.98982 714.64815 -1939.8556 144.6903 64.3068 64.3068 4200.3475 2532.5711 2530.5518 -1225.2075
1700 757.22042 704.62675 -1925.553 144.6903 64.3068 64.3068 2686.7843 1482.2796 1505.8073 -1220.9262
1800 727.30327 676.78754 -1894.6635 144.6903 64.3068 64.3068 1764.2793 781.37451 801.18668 -1217.8759
1900 688.82146 640.97853 -1856.5007 144.6903 64.3068 64.3068 1022.805 417.32394 359.74951 -1215.5221
2000 655.91228 610.35509 -1823.954 144.6903 64.3068 64.3068 551.98825 -20.148643 -56.976652 -1213.5989
2100 620.22468 577.14622 -1789.1761 144.6903 64.3068 64.3068 264.05975 -266.8323 -314.45533 -1212.0299
2200 589.13325 548.21428 -1758.9252 144.6903 64.3068 64.3068 41.369707 -533.503 -525.69401 -1210.7109
2300 563.20394 524.08593 -1733.6036 144.6903 64.3068 64.3068 -220.99189 -810.90513 -774.65084 -1209.5176
2400 540.44236 502.90528 -1711.3384 144.6903 64.3068 64.3068 -358.01508 -962.31635 -977.3253 -1208.4332
2500 523.5718 487.20648 -1694.7088 144.6903 64.3068 64.3068 -521.87444 -1152.8386 -1231.7615 -1207.5023
Loop time of 9.34327 on 1 procs for 1500 steps with 7200 atoms
Performance: 27.742 ns/day, 0.865 hours/ns, 160.543 timesteps/s, 1.156 Matom-step/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.4692 | 8.4692 | 8.4692 | 0.0 | 90.65
Neigh | 0.7512 | 0.7512 | 0.7512 | 0.0 | 8.04
Comm | 0.031189 | 0.031189 | 0.031189 | 0.0 | 0.33
Output | 0.010584 | 0.010584 | 0.010584 | 0.0 | 0.11
Modify | 0.053052 | 0.053052 | 0.053052 | 0.0 | 0.57
Other | | 0.02803 | | | 0.30
Nlocal: 7200 ave 7200 max 7200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6380 ave 6380 max 6380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 515773 ave 515773 max 515773 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 515773
Ave neighs/atom = 71.635139
Neighbor list builds = 57
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (19 Nov 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Removing Binned Velocities of Center of Mass (VCM) from Stress
# This example shows how to remove rigid body motion from
# binned stress calculations. This uses a combination of commands
# from compute chunk/atom, compute temp/chunk, compute
# stress/atom and fix ave/time. We'll show how these commands
# work in the context of a shockwave experiment on a cube of
# atoms. To shock the cube, a rectangular region of atoms is
# frozen, moved into the cube with a constant velocity along the
# x direction, and then unfrozen. As the shockwave begins
# propagating, the body of the cube also moves along the x
# direction. To better understand the stress dynamics of the
# cube we remove the velocity component belonging to the overall
# motion of each bin.
units metal
boundary p p p
atom_style atomic
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
processors 1 * *
# Defining regions for box and atoms.
# In this experiment an elongated simulation cell is
# defined in the x direction to allow for non-periodic
# motion of the atoms.
region box1 block -3 24 0 12 0 12 units lattice
region box2 block 0 12 0 12 0 12 units lattice
# Creating box and atoms
create_box 1 box1
Created orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box2
Created 7200 atoms
using lattice units in orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
create_atoms CPU = 0.001 seconds
mass 1 40.00
# Adding energy to the system
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.04 3.405
# Begin time integration
timestep 2e-3
fix fix_nve all nve
thermo 100
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 25 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/opt, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.662 | 3.662 | 3.662 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -2252.7567 0 -1694.4304 -974.62456
100 284.1896 -1976.961 0 -1712.5101 2462.6396
200 308.58965 -1998.6349 0 -1711.4787 1789.0033
300 300.55093 -1989.9838 0 -1710.308 1545.8576
400 297.91491 -1986.2519 0 -1709.029 1247.7121
500 294.66041 -1982.1097 0 -1707.9153 961.03073
Loop time of 0.942408 on 4 procs for 500 steps with 7200 atoms
Performance: 91.680 ns/day, 0.262 hours/ns, 530.556 timesteps/s, 3.820 Matom-step/s
82.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.61287 | 0.63781 | 0.65858 | 2.1 | 67.68
Neigh | 0.030246 | 0.031529 | 0.034546 | 1.0 | 3.35
Comm | 0.23074 | 0.25145 | 0.27819 | 3.7 | 26.68
Output | 0.000282 | 0.0003735 | 0.000463 | 0.0 | 0.04
Modify | 0.005566 | 0.0057635 | 0.005989 | 0.2 | 0.61
Other | | 0.01548 | | | 1.64
Nlocal: 1800 ave 1814 max 1787 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 3713.5 ave 3727 max 3699 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 153532 ave 154995 max 152312 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 614128
Ave neighs/atom = 85.295556
Neighbor list builds = 9
Dangerous builds = 0
#------------------------------------#
# Chunk, Stress, and VCM removal steps
#------------------------------------#
# 1. Create 20 equispaced bins sliced along the x direction.
# "units reduced" normalizes the distance from 0 to 1
variable nbins index 20
variable fraction equal 1.0/v_nbins
variable volfrac equal 1/(vol*${fraction})
variable volfrac equal 1/(vol*0.05)
compute ch_id all chunk/atom bin/1d x lower ${fraction} units reduced
compute ch_id all chunk/atom bin/1d x lower 0.05 units reduced
# 2. Calculate temperature bins with VCM aka COM velocities removed.
compute ch_temp_vcm all temp/chunk ch_id com yes
# 3. Compute per atom stress with VCM removed via temp-ID.
# The velocities from specified temp-ID are used to compute stress
# Stress/atom units are pressure*volume! Optionally handled next step.
compute atom_stress_vcm all stress/atom ch_temp_vcm
# 4. Divide out bin volume from xx stress component.
variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
variable stress atom -(c_atom_stress_vcm[1])/(vol*0.05)
# 5. Sum the per atom stresses in each bin.
compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
# 6. Average and output to file.
# The average output is every 100 steps with samples collected 20 times with 5 step intervals
# fix ave_stress_vcm all ave/time 5 20 100 c_ch_stress_vcm mode vector file stress_xx.out
#------------------------------------#
# Piston compressing along x direction
region piston block -1 1 INF INF INF INF units lattice
group piston region piston
864 atoms in group piston
fix fix_piston piston move linear 5 0 0 units box # strain rate ~ 8e10 1/s
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve
# Atom dump
# dump atom_dump all atom 50 dump.vcm
# # Image dumps
# dump 2 all image 250 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
# dump_modify 2 pad 1
# # Movie dump
# dump 3 all movie 125 movie.avi type type # axes yes 0.8 0.02 view 60 -30
# dump_modify 3 pad 1
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: One or more atoms are time integrated more than once (src/modify.cpp:296)
Per MPI rank memory allocation (min/avg/max) = 4.916 | 4.916 | 4.916 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
500 294.66041 274.19441 -1982.1097 144.6903 64.3068 64.3068 645.25795 1119.5337 1118.3006 -1707.9153
600 357.88641 333.02897 -1951.8158 144.6903 64.3068 64.3068 2176.0343 1929.2787 1981.8479 -1618.7869
700 418.41159 389.3503 -1912.8337 144.6903 64.3068 64.3068 3702.2875 3043.7607 3081.1607 -1523.4834
800 483.71102 450.11428 -1875.7955 144.6903 64.3068 64.3068 5254.3875 4190.9789 4158.3561 -1425.6813
900 586.0893 545.38176 -1870.9313 144.6903 64.3068 64.3068 6509.1439 4756.2216 4724.7086 -1325.5495
1000 686.32946 638.65962 -1874.811 144.6903 64.3068 64.3068 7515.1606 5193.049 5261.8688 -1236.1514
Loop time of 0.656417 on 4 procs for 500 steps with 7200 atoms
Performance: 131.624 ns/day, 0.182 hours/ns, 761.711 timesteps/s, 5.484 Matom-step/s
92.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.51672 | 0.52334 | 0.53259 | 0.8 | 79.73
Neigh | 0.045091 | 0.045915 | 0.047402 | 0.4 | 6.99
Comm | 0.060735 | 0.071794 | 0.079302 | 2.6 | 10.94
Output | 0.000208 | 0.000389 | 0.000926 | 0.0 | 0.06
Modify | 0.006007 | 0.0061595 | 0.00626 | 0.1 | 0.94
Other | | 0.008815 | | | 1.34
Nlocal: 1800 ave 1811 max 1785 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 3713.25 ave 3727 max 3702 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 161477 ave 162958 max 159732 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 645909
Ave neighs/atom = 89.709583
Neighbor list builds = 15
Dangerous builds = 0
unfix fix_piston
run 1500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.541 | 4.541 | 4.541 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
1000 686.32946 638.65962 -1874.811 144.6903 64.3068 64.3068 7515.1606 5193.049 5261.8688 -1236.1514
1100 709.7333 660.43791 -1898.2844 144.6903 64.3068 64.3068 7932.8638 5334.6171 5364.5335 -1237.8465
1200 713.27253 663.73132 -1902.4588 144.6903 64.3068 64.3068 7957.2574 5500.6231 5538.0516 -1238.7275
1300 705.44796 656.45022 -1895.1575 144.6903 64.3068 64.3068 7996.7265 5584.6233 5538.2494 -1238.7072
1400 711.86463 662.42121 -1899.8416 144.6903 64.3068 64.3068 7674.2462 5292.4915 5294.5366 -1237.4204
1500 742.18946 690.63979 -1924.9562 144.6903 64.3068 64.3068 6047.915 4056.6156 4014.4446 -1234.3164
1600 762.81764 709.83522 -1939.8563 144.6903 64.3068 64.3068 4185.5873 2530.0572 2576.1943 -1230.0211
1700 754.40428 702.00621 -1927.7337 144.6903 64.3068 64.3068 2662.7604 1509.1985 1484.7252 -1225.7275
1800 721.03504 670.95468 -1893.5556 144.6903 64.3068 64.3068 1765.8783 835.89765 861.9432 -1222.6009
1900 689.64162 641.74172 -1861.8886 144.6903 64.3068 64.3068 941.58148 312.93205 409.79901 -1220.1469
2000 650.79664 605.59477 -1823.9889 144.6903 64.3068 64.3068 543.39234 28.48735 80.396505 -1218.3941
2100 616.04072 573.25286 -1790.1764 144.6903 64.3068 64.3068 308.16444 -235.20997 -248.22531 -1216.9235
2200 587.18712 546.40333 -1761.8878 144.6903 64.3068 64.3068 37.044801 -476.50396 -470.83059 -1215.4845
2300 562.84178 523.74892 -1738.2239 144.6903 64.3068 64.3068 -139.28348 -711.17273 -730.80877 -1214.475
2400 540.48362 502.94367 -1716.3529 144.6903 64.3068 64.3068 -320.98222 -951.2066 -943.93966 -1213.4093
2500 519.80431 483.70067 -1696.1896 144.6903 64.3068 64.3068 -471.61317 -1088.8457 -1131.5396 -1212.4889
Loop time of 1.97213 on 4 procs for 1500 steps with 7200 atoms
Performance: 131.431 ns/day, 0.183 hours/ns, 760.598 timesteps/s, 5.476 Matom-step/s
95.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5455 | 1.5599 | 1.5723 | 0.8 | 79.10
Neigh | 0.16844 | 0.1704 | 0.17237 | 0.4 | 8.64
Comm | 0.19002 | 0.2047 | 0.22068 | 2.4 | 10.38
Output | 0.000525 | 0.0006785 | 0.001077 | 0.0 | 0.03
Modify | 0.012434 | 0.012601 | 0.012777 | 0.1 | 0.64
Other | | 0.02388 | | | 1.21
Nlocal: 1800 ave 1833 max 1776 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 3702 ave 3732 max 3674 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 129380 ave 132578 max 127003 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 517520
Ave neighs/atom = 71.877778
Neighbor list builds = 54
Dangerous builds = 0
Total wall time: 0:00:03

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# Time-averaged data for fix ave_stress_vcm
# TimeStep Number-of-rows
# Row c_ch_stress_vcm
600 20
1 0
2 -142.965
3 2142.79
4 12968.3
5 -336.7
6 2638.09
7 4214.83
8 3187.61
9 -488.891
10 -49.3553
11 151.373
12 -317.663
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
700 20
1 0
2 -14.3195
3 -1238.9
4 30664.3
5 18805.2
6 498.562
7 930.874
8 660.655
9 -266.903
10 -317.877
11 -386.989
12 -304.697
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
800 20
1 0
2 0
3 -1656.7
4 30424.3
5 37003.5
6 15562.5
7 -2441.9
8 -1766.09
9 272.718
10 -664.774
11 -72.6933
12 -469.765
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
900 20
1 0
2 0
3 -1567.21
4 24987.6
5 38068.9
6 31595
7 8864.94
8 -3423.99
9 -753.063
10 125.21
11 -50.4895
12 -172.14
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
1000 20
1 0
2 0
3 -893.168
4 15591.6
5 32690.6
6 30183
7 27172
8 9459.75
9 -1416.35
10 -432.731
11 444.323
12 -424.357
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
1100 20
1 0
2 0
3 -601.805
4 8890.79
5 23345.1
6 28529.2
7 29111.9
8 25846.2
9 7451.83
10 -1624.2
11 320.704
12 -50.9865
13 -5.50481
14 0
15 0
16 0
17 0
18 0
19 0
20 0
1200 20
1 0
2 0
3 1435.39
4 8818.29
5 7129.61
6 20281.7
7 28026.1
8 28327.7
9 26918.6
10 8277.12
11 -249.644
12 -171.806
13 -7.19065
14 0
15 0
16 0
17 0
18 0
19 0
20 0
1300 20
1 0
2 0
3 -718.118
4 3021.9
5 9010.51
6 9500.87
7 19432.8
8 27254.3
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