Merge branch 'develop' into sync_verlet
This commit is contained in:
jtclemm
@ -118,6 +118,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(set_internal_variable);
|
||||
ADDSYM(variable_info);
|
||||
ADDSYM(eval);
|
||||
ADDSYM(clearstep_compute);
|
||||
ADDSYM(addstep_compute);
|
||||
ADDSYM(addstep_compute_all);
|
||||
|
||||
ADDSYM(gather_atoms);
|
||||
ADDSYM(gather_atoms_concat);
|
||||
|
||||
@ -164,6 +164,9 @@ struct _liblammpsplugin {
|
||||
int (*set_internal_variable)(void *, const char *, double);
|
||||
int (*variable_info)(void *, int, char *, int);
|
||||
double (*eval)(void *, const char *);
|
||||
void (*clearstep_compute)(void *);
|
||||
void (*addstep_compute)(void *, void *);
|
||||
void (*addstep_compute_all)(void *, void *);
|
||||
|
||||
void (*gather_atoms)(void *, const char *, int, int, void *);
|
||||
void (*gather_atoms_concat)(void *, const char *, int, int, void *);
|
||||
|
||||
@ -21,6 +21,7 @@
|
||||
|
||||
#include <mpi.h>
|
||||
|
||||
#include <errno.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
@ -63,7 +64,7 @@ int main(int narg, char **arg)
|
||||
nprocs_lammps = atoi(arg[1]);
|
||||
if (nprocs_lammps > nprocs) {
|
||||
if (me == 0)
|
||||
printf("ERROR: LAMMPS cannot use more procs than available\n");
|
||||
printf("ERROR: LAMMPS cannot use more procs than available: %d\n", nprocs);
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
|
||||
@ -76,7 +77,7 @@ int main(int narg, char **arg)
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[2],"r");
|
||||
if (fp == NULL) {
|
||||
printf("ERROR: Could not open LAMMPS input script\n");
|
||||
printf("ERROR: Could not open LAMMPS input script %s: %s\n", arg[2], strerror(errno));
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
@ -87,9 +88,10 @@ int main(int narg, char **arg)
|
||||
all LAMMPS procs call lammps_command() on the line */
|
||||
|
||||
if (lammps == 1) {
|
||||
errno = 0;
|
||||
plugin = liblammpsplugin_load(arg[3]);
|
||||
if (plugin == NULL) {
|
||||
if (me == 0) printf("ERROR: Could not load shared LAMMPS library\n");
|
||||
if (me == 0) printf("ERROR: Could not load shared LAMMPS library file %s: %s\n", arg[3], strerror(errno));
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
/* must match the plugin ABI version */
|
||||
|
||||
50
examples/LEPTON/in.efield-lepton
Normal file
50
examples/LEPTON/in.efield-lepton
Normal file
@ -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
115
examples/LEPTON/log.13Jan25.efield-lepton.g++.1
Normal file
@ -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
115
examples/LEPTON/log.13Jan25.efield-lepton.g++.4
Normal file
@ -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
6
examples/PACKAGES/dispersion/README
Normal file
@ -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).
|
||||
|
||||
36
examples/PACKAGES/dispersion/in.d2
Normal file
36
examples/PACKAGES/dispersion/in.d2
Normal file
@ -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
36
examples/PACKAGES/dispersion/in.d3
Normal file
@ -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
122
examples/PACKAGES/dispersion/log.20Dec2024.d2.g++.1
Normal file
@ -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
122
examples/PACKAGES/dispersion/log.20Dec2024.d2.g++.4
Normal file
@ -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 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
|
||||
117
examples/PACKAGES/dispersion/log.20Dec2024.d3.g++.1
Normal file
117
examples/PACKAGES/dispersion/log.20Dec2024.d3.g++.1
Normal file
@ -0,0 +1,117 @@
|
||||
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
|
||||
117
examples/PACKAGES/dispersion/log.20Dec2024.d3.g++.4
Normal file
117
examples/PACKAGES/dispersion/log.20Dec2024.d3.g++.4
Normal file
@ -0,0 +1,117 @@
|
||||
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
|
||||
484
examples/PACKAGES/dispersion/potential_files/c_ace.yace
Normal file
484
examples/PACKAGES/dispersion/potential_files/c_ace.yace
Normal file
File diff suppressed because one or more lines are too long
20005
examples/PACKAGES/dispersion/potential_files/d2.table
Normal file
20005
examples/PACKAGES/dispersion/potential_files/d2.table
Normal file
File diff suppressed because it is too large
Load Diff
@ -16,7 +16,7 @@ comm_modify vel yes
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_style custom step pe temp etotal press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# Minimization
|
||||
@ -36,7 +36,7 @@ undump 2
|
||||
#velocity all create 300.0 4928459 dist uniform
|
||||
|
||||
# NVE
|
||||
timestep 0.001
|
||||
timestep 0.0001
|
||||
|
||||
fix 1 all nve/eff
|
||||
dump 1 all xyz 1000 ${sname}.nve.xyz
|
||||
|
||||
@ -0,0 +1,367 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index adamantane_ionized
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.adamantane_ionized
|
||||
Reading data file ...
|
||||
orthogonal box = (-50 -50 -50) to (50 50 50)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
101 atoms
|
||||
read_data CPU = 0.038 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp etotal press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# Minimization
|
||||
min_style cg
|
||||
dump 1 all xyz 500 ${sname}.min.xyz
|
||||
dump 1 all xyz 500 adamantane_ionized.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
dump 2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-5 10000 100000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 5.222 | 5.222 | 5.222 Mbytes
|
||||
Step PotEng Temp TotEng Press
|
||||
0 -320.50186 0 -320.50186 -45590269
|
||||
571 -324.30072 0 -324.30072 21193099
|
||||
Loop time of 2.61846 on 1 procs for 571 steps with 101 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
-320.501859657303 -324.30071870307 -324.30071870307
|
||||
Force two-norm initial, final = 2.8135352 2.2777398
|
||||
Force max component initial, final = 1.7194878 2.093044
|
||||
Final line search alpha, max atom move = 2.2781994e-09 4.7683716e-09
|
||||
Iterations, force evaluations = 571 5621
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.602 | 2.602 | 2.602 | 0.0 | 99.37
|
||||
Neigh | 2.5097e-05 | 2.5097e-05 | 2.5097e-05 | 0.0 | 0.00
|
||||
Comm | 0.00046417 | 0.00046417 | 0.00046417 | 0.0 | 0.02
|
||||
Output | 0.00029579 | 0.00029579 | 0.00029579 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0157 | | | 0.60
|
||||
|
||||
Nlocal: 101 ave 101 max 101 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: 5050 ave 5050 max 5050 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5050
|
||||
Ave neighs/atom = 50
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
#restart timestep
|
||||
|
||||
# set velocities for nve
|
||||
#velocity all create 300.0 4928459 dist uniform
|
||||
|
||||
# NVE
|
||||
timestep 0.0001
|
||||
|
||||
fix 1 all nve/eff
|
||||
dump 1 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 1 all xyz 1000 adamantane_ionized.nve.xyz
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
dump 2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
|
||||
|
||||
run 200000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.097 | 4.097 Mbytes
|
||||
Step PotEng Temp TotEng Press
|
||||
571 -324.30072 0 -324.30072 21193099
|
||||
1000 -324.00833 75606.318 -315.02966 1.9184325e+08
|
||||
2000 -322.45879 62558.11 -315.02966 1.4564261e+08
|
||||
3000 -322.01495 58820.681 -315.02966 1.3051251e+08
|
||||
4000 -321.3178 52950.225 -315.02966 75989118
|
||||
5000 -320.89488 49388.959 -315.02966 55413771
|
||||
6000 -320.97564 50069.086 -315.02966 67105302
|
||||
7000 -320.9772 50082.172 -315.02966 90728737
|
||||
8000 -320.76927 48331.305 -315.02966 1.1054849e+08
|
||||
9000 -320.40821 45290.936 -315.02966 1.1325434e+08
|
||||
10000 -320.10216 42713.788 -315.02966 1.0766253e+08
|
||||
11000 -320.00263 41875.679 -315.02966 1.0831982e+08
|
||||
12000 -319.92006 41180.36 -315.02966 1.0888686e+08
|
||||
13000 -319.85913 40667.331 -315.02966 1.0763265e+08
|
||||
14000 -319.86056 40679.317 -315.02966 1.1159571e+08
|
||||
15000 -319.79071 40091.129 -315.02966 1.1261281e+08
|
||||
16000 -319.7393 39658.231 -315.02966 1.0983394e+08
|
||||
17000 -319.74963 39745.211 -315.02966 1.12573e+08
|
||||
18000 -319.70347 39356.518 -315.02966 1.1249278e+08
|
||||
19000 -319.68924 39236.684 -315.02966 1.084432e+08
|
||||
20000 -319.74747 39727.04 -315.02966 1.109151e+08
|
||||
21000 -319.76264 39854.793 -315.02966 1.0990745e+08
|
||||
22000 -319.7997 40166.86 -315.02966 1.0446598e+08
|
||||
23000 -319.91061 41100.771 -315.02966 1.0605289e+08
|
||||
24000 -319.98762 41749.299 -315.02966 1.0312843e+08
|
||||
25000 -320.06842 42429.669 -315.02966 96790253
|
||||
26000 -320.2321 43807.92 -315.02966 98941422
|
||||
27000 -320.43008 45475.083 -315.02966 99172853
|
||||
28000 -320.75368 48199.998 -315.02966 1.0304506e+08
|
||||
29000 -321.43727 53956.239 -315.02966 1.2359013e+08
|
||||
30000 -322.86003 65936.838 -315.02966 1.6426506e+08
|
||||
31000 -325.85698 91173.108 -315.02966 2.3460809e+08
|
||||
32000 -323.96663 75255.122 -315.02967 1.4386254e+08
|
||||
33000 -324.31173 78161.078 -315.02966 1.9611146e+08
|
||||
34000 -321.81048 57098.954 -315.02966 1.3183304e+08
|
||||
35000 -321.11553 51247.011 -315.02966 1.1860383e+08
|
||||
36000 -320.7006 47753.061 -315.02966 1.0988072e+08
|
||||
37000 -320.42875 45463.834 -315.02966 1.0486186e+08
|
||||
38000 -320.37522 45013.139 -315.02966 1.0667734e+08
|
||||
39000 -320.16625 43253.419 -315.02966 1.0141734e+08
|
||||
40000 -320.09034 42614.247 -315.02966 1.0082579e+08
|
||||
41000 -320.21558 43668.822 -315.02966 1.0548768e+08
|
||||
42000 -320.19431 43489.747 -315.02966 1.0242614e+08
|
||||
43000 -320.35932 44879.232 -315.02966 1.0646487e+08
|
||||
44000 -320.67457 47533.878 -315.02966 1.1366565e+08
|
||||
45000 -320.83512 48885.757 -315.02966 1.111537e+08
|
||||
46000 -321.16647 51675.946 -315.02966 1.1302624e+08
|
||||
47000 -321.38122 53484.331 -315.02966 1.0507686e+08
|
||||
48000 -321.06774 50844.617 -315.02966 74672082
|
||||
49000 -322.49756 62884.615 -315.02966 1.044115e+08
|
||||
50000 -325.97731 92186.422 -315.02966 2.2498335e+08
|
||||
51000 -320.66106 47420.072 -315.02966 34605338
|
||||
52000 -323.2278 69033.706 -315.02966 1.4817693e+08
|
||||
53000 -322.82489 65640.939 -315.02966 1.6065307e+08
|
||||
54000 -321.95574 58322.133 -315.02966 1.3860454e+08
|
||||
55000 -321.41375 53758.198 -315.02966 1.1831887e+08
|
||||
56000 -320.82121 48768.626 -315.02966 97374067
|
||||
57000 -320.39876 45211.333 -315.02966 85881342
|
||||
58000 -320.26394 44076.088 -315.02966 80873235
|
||||
59000 -320.06828 42428.515 -315.02966 75885502
|
||||
60000 -320.12912 42940.809 -315.02966 83005858
|
||||
61000 -320.34086 44723.765 -315.02966 90748569
|
||||
62000 -320.3942 45172.977 -315.02966 93992240
|
||||
63000 -320.63122 47168.811 -315.02966 1.0726441e+08
|
||||
64000 -320.86235 49115.084 -315.02966 1.1515294e+08
|
||||
65000 -320.95075 49859.439 -315.02966 1.1705259e+08
|
||||
66000 -321.28995 52715.744 -315.02966 1.3144493e+08
|
||||
67000 -321.69035 56087.363 -315.02966 1.4188253e+08
|
||||
68000 -322.28755 61116.149 -315.02966 1.5220904e+08
|
||||
69000 -323.31574 69774.213 -315.02966 1.5914511e+08
|
||||
70000 -322.98352 66976.685 -315.02966 1.0382488e+08
|
||||
71000 -323.42006 70652.696 -315.02966 1.1257889e+08
|
||||
72000 -322.38839 61965.354 -315.02966 1.213394e+08
|
||||
73000 -321.62733 55556.719 -315.02966 1.2062207e+08
|
||||
74000 -321.10333 51144.304 -315.02966 1.0628135e+08
|
||||
75000 -320.84916 49004.001 -315.02966 1.0188029e+08
|
||||
76000 -320.51651 46202.858 -315.02966 94118114
|
||||
77000 -320.47427 45847.17 -315.02966 91437540
|
||||
78000 -320.52773 46297.312 -315.02966 95165197
|
||||
79000 -320.43972 45556.265 -315.02966 95366722
|
||||
80000 -320.58645 46791.792 -315.02966 1.0182068e+08
|
||||
81000 -320.75509 48211.862 -315.02966 1.0907204e+08
|
||||
82000 -320.77091 48345.056 -315.02966 1.1257336e+08
|
||||
83000 -321.02219 50461.057 -315.02966 1.2376776e+08
|
||||
84000 -321.20064 51963.656 -315.02966 1.2909546e+08
|
||||
85000 -321.2856 52679.138 -315.02966 1.3104703e+08
|
||||
86000 -321.67229 55935.33 -315.02966 1.4072532e+08
|
||||
87000 -322.11917 59698.307 -315.02966 1.4404812e+08
|
||||
88000 -324.23523 77516.896 -315.02966 1.9731217e+08
|
||||
89000 -320.62579 47123.095 -315.02966 75893884
|
||||
90000 -324.35107 78492.385 -315.02966 2.1044355e+08
|
||||
91000 -322.47803 62720.127 -315.02966 1.5538903e+08
|
||||
92000 -321.71623 56305.3 -315.02966 1.3227964e+08
|
||||
93000 -321.22259 52148.564 -315.02966 1.1511464e+08
|
||||
94000 -320.89326 49375.312 -315.02966 1.0320494e+08
|
||||
95000 -320.60652 46960.796 -315.02966 93163389
|
||||
96000 -320.42504 45432.671 -315.02966 82638699
|
||||
97000 -320.35025 44802.889 -315.02966 77728012
|
||||
98000 -320.38016 45054.714 -315.02966 76753988
|
||||
99000 -320.64823 47312.019 -315.02966 79089183
|
||||
100000 -321.20665 52014.291 -315.02966 90654215
|
||||
101000 -322.45176 62498.949 -315.02966 1.1671692e+08
|
||||
102000 -325.27551 86276.757 -315.02966 1.7450838e+08
|
||||
103000 -324.86597 82828.164 -315.02967 1.5358223e+08
|
||||
104000 -323.50288 71350.092 -315.02966 1.3914499e+08
|
||||
105000 -321.83206 57280.642 -315.02966 1.1374062e+08
|
||||
106000 -321.23029 52213.369 -315.02966 1.0154377e+08
|
||||
107000 -320.79552 48552.352 -315.02966 93581739
|
||||
108000 -320.85374 49042.571 -315.02966 1.0230141e+08
|
||||
109000 -320.711 47840.638 -315.02966 98035102
|
||||
110000 -320.92927 49678.547 -315.02966 1.0291687e+08
|
||||
111000 -321.37088 53397.184 -315.02966 1.161465e+08
|
||||
112000 -321.64623 55715.825 -315.02966 1.2178973e+08
|
||||
113000 -323.29623 69609.916 -315.02966 1.5738912e+08
|
||||
114000 -326.43458 96036.881 -315.02966 2.2117147e+08
|
||||
115000 -326.29249 94840.366 -315.02967 2.1727072e+08
|
||||
116000 -323.49398 71275.138 -315.02966 1.6236371e+08
|
||||
117000 -321.69956 56164.918 -315.02966 1.2248665e+08
|
||||
118000 -321.03061 50531.902 -315.02966 1.114646e+08
|
||||
119000 -320.58664 46793.421 -315.02966 1.0201646e+08
|
||||
120000 -320.31068 44469.633 -315.02966 92788900
|
||||
121000 -320.33764 44696.673 -315.02966 96573809
|
||||
122000 -320.29533 44340.406 -315.02966 96276795
|
||||
123000 -320.48178 45910.447 -315.02966 96702563
|
||||
124000 -320.99926 50267.91 -315.02966 1.1042709e+08
|
||||
125000 -321.72882 56411.316 -315.02966 1.2653574e+08
|
||||
126000 -323.76935 73593.887 -315.02966 1.6411768e+08
|
||||
127000 -323.84136 74200.288 -315.02967 1.2684596e+08
|
||||
128000 -325.27771 86295.322 -315.02966 1.7908195e+08
|
||||
129000 -322.44151 62412.6 -315.02966 1.2334056e+08
|
||||
130000 -321.33424 53088.672 -315.02966 1.0110915e+08
|
||||
131000 -320.74694 48143.276 -315.02966 87343006
|
||||
132000 -320.58456 46775.879 -315.02966 84619630
|
||||
133000 -320.42884 45464.64 -315.02966 80256772
|
||||
134000 -320.41844 45377.068 -315.02966 79998095
|
||||
135000 -320.67167 47509.417 -315.02966 88059739
|
||||
136000 -320.94223 49787.695 -315.02966 94538899
|
||||
137000 -321.61703 55469.964 -315.02966 1.1016475e+08
|
||||
138000 -323.12933 68204.503 -315.02966 1.4202379e+08
|
||||
139000 -326.08028 93053.485 -315.02966 1.894649e+08
|
||||
140000 -326.22688 94287.865 -315.02967 1.9082785e+08
|
||||
141000 -323.43485 70777.215 -315.02966 1.4698731e+08
|
||||
142000 -321.79035 56929.435 -315.02966 1.1785802e+08
|
||||
143000 -321.17113 51715.2 -315.02966 1.0630317e+08
|
||||
144000 -320.72407 47950.681 -315.02966 94302254
|
||||
145000 -320.53771 46381.4 -315.02966 89962864
|
||||
146000 -320.57538 46698.572 -315.02966 90769921
|
||||
147000 -320.65873 47400.459 -315.02966 88297290
|
||||
148000 -321.05389 50727.942 -315.02966 95860956
|
||||
149000 -321.86647 57570.413 -315.02966 1.1210695e+08
|
||||
150000 -323.71338 73122.627 -315.02966 1.4277977e+08
|
||||
151000 -325.52965 88416.746 -315.02967 1.7216009e+08
|
||||
152000 -325.82817 90930.57 -315.02966 1.8312663e+08
|
||||
153000 -322.5891 63655.44 -315.02966 1.2089115e+08
|
||||
154000 -321.32957 53049.334 -315.02966 96494848
|
||||
155000 -320.66612 47462.65 -315.02966 81236441
|
||||
156000 -320.47196 45827.713 -315.02966 78679995
|
||||
157000 -320.33169 44646.581 -315.02966 75407967
|
||||
158000 -320.42358 45420.371 -315.02966 76161171
|
||||
159000 -320.79103 48514.483 -315.02966 84173108
|
||||
160000 -321.27968 52629.281 -315.02966 92130817
|
||||
161000 -322.50401 62938.95 -315.02966 1.138272e+08
|
||||
162000 -325.40267 87347.575 -315.02966 1.6576028e+08
|
||||
163000 -323.59983 72166.432 -315.02967 1.1072655e+08
|
||||
164000 -324.04378 75904.823 -315.02966 1.4709858e+08
|
||||
165000 -322.01605 58829.972 -315.02966 1.0400742e+08
|
||||
166000 -321.15747 51600.213 -315.02966 82397014
|
||||
167000 -320.8409 48934.422 -315.02966 73988066
|
||||
168000 -320.58861 46810.029 -315.02966 64925698
|
||||
169000 -320.54312 46426.959 -315.02966 61942158
|
||||
170000 -320.68604 47630.438 -315.02966 64309567
|
||||
171000 -320.77008 48338.134 -315.02966 63324927
|
||||
172000 -321.08474 50987.727 -315.02966 69721832
|
||||
173000 -321.6134 55439.431 -315.02966 80485473
|
||||
174000 -322.41904 62223.44 -315.02966 94329801
|
||||
175000 -324.95819 83604.705 -315.02966 1.5681125e+08
|
||||
176000 -321.71907 56329.278 -315.02966 45217519
|
||||
177000 -324.24577 77605.673 -315.02966 1.5164385e+08
|
||||
178000 -322.34082 61564.766 -315.02966 1.0677988e+08
|
||||
179000 -321.3229 52993.228 -315.02966 80528491
|
||||
180000 -320.91614 49567.992 -315.02966 70928167
|
||||
181000 -320.79771 48570.793 -315.02966 70105356
|
||||
182000 -320.43289 45498.72 -315.02966 62263793
|
||||
183000 -320.59821 46890.81 -315.02966 67986358
|
||||
184000 -320.64879 47316.739 -315.02966 70175355
|
||||
185000 -320.52287 46256.459 -315.02966 68704646
|
||||
186000 -320.94252 49790.187 -315.02966 81368769
|
||||
187000 -321.10174 51130.914 -315.02966 84251825
|
||||
188000 -321.38014 53475.167 -315.02966 91376642
|
||||
189000 -322.14722 59934.547 -315.02966 1.1198813e+08
|
||||
190000 -322.9004 66276.794 -315.02966 1.2823518e+08
|
||||
191000 -323.63455 72458.807 -315.02966 1.6144592e+08
|
||||
192000 -324.3348 78355.338 -315.02966 1.5544396e+08
|
||||
193000 -321.63344 55608.185 -315.02966 85813641
|
||||
194000 -323.54261 71684.651 -315.02966 1.4340251e+08
|
||||
195000 -323.1577 68443.449 -315.02966 1.5089288e+08
|
||||
196000 -322.90055 66278.083 -315.02966 1.4392954e+08
|
||||
197000 -322.45751 62547.374 -315.02966 1.2607137e+08
|
||||
198000 -322.18257 60232.201 -315.02966 1.137101e+08
|
||||
199000 -322.24297 60740.76 -315.02966 1.0950975e+08
|
||||
200000 -322.47749 62715.575 -315.02966 1.070732e+08
|
||||
200571 -323.24897 69211.97 -315.02966 1.1694375e+08
|
||||
Loop time of 86.0986 on 1 procs for 200000 steps with 101 atoms
|
||||
|
||||
Performance: 20070.020 fs/day, 0.001 hours/fs, 2322.919 timesteps/s, 234.615 katom-step/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 85.691 | 85.691 | 85.691 | 0.0 | 99.53
|
||||
Neigh | 0.0010104 | 0.0010104 | 0.0010104 | 0.0 | 0.00
|
||||
Comm | 0.016762 | 0.016762 | 0.016762 | 0.0 | 0.02
|
||||
Output | 0.061098 | 0.061098 | 0.061098 | 0.0 | 0.07
|
||||
Modify | 0.22948 | 0.22948 | 0.22948 | 0.0 | 0.27
|
||||
Other | | 0.09905 | | | 0.12
|
||||
|
||||
Nlocal: 101 ave 101 max 101 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: 5050 ave 5050 max 5050 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5050
|
||||
Ave neighs/atom = 50
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
Total wall time: 0:01:28
|
||||
@ -0,0 +1,367 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index adamantane_ionized
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.adamantane_ionized
|
||||
Reading data file ...
|
||||
orthogonal box = (-50 -50 -50) to (50 50 50)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
101 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp etotal press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# Minimization
|
||||
min_style cg
|
||||
dump 1 all xyz 500 ${sname}.min.xyz
|
||||
dump 1 all xyz 500 adamantane_ionized.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
dump 2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-5 10000 100000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 5.253 | 5.253 | 5.253 Mbytes
|
||||
Step PotEng Temp TotEng Press
|
||||
0 -320.50186 0 -320.50186 -45590269
|
||||
493 -324.31743 0 -324.31743 20971271
|
||||
Loop time of 0.883439 on 4 procs for 493 steps with 101 atoms
|
||||
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
-320.501859657306 -324.317430790588 -324.317430790588
|
||||
Force two-norm initial, final = 2.8135352 1.2148731
|
||||
Force max component initial, final = 1.7194878 1.1232786
|
||||
Final line search alpha, max atom move = 4.245048e-09 4.7683716e-09
|
||||
Iterations, force evaluations = 493 3804
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24614 | 0.45831 | 0.84299 | 34.7 | 51.88
|
||||
Neigh | 1.1159e-05 | 1.2751e-05 | 1.5479e-05 | 0.0 | 0.00
|
||||
Comm | 0.019423 | 0.40607 | 0.62032 | 37.1 | 45.97
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01905 | | | 2.16
|
||||
|
||||
Nlocal: 25.25 ave 30 max 17 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 75.75 ave 84 max 71 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 1262.5 ave 2394 max 663 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 5050
|
||||
Ave neighs/atom = 50
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
#restart timestep
|
||||
|
||||
# set velocities for nve
|
||||
#velocity all create 300.0 4928459 dist uniform
|
||||
|
||||
# NVE
|
||||
timestep 0.0001
|
||||
|
||||
fix 1 all nve/eff
|
||||
dump 1 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 1 all xyz 1000 adamantane_ionized.nve.xyz
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
dump 2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
|
||||
#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
|
||||
|
||||
run 200000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.128 | 4.128 | 4.128 Mbytes
|
||||
Step PotEng Temp TotEng Press
|
||||
493 -324.31743 0 -324.31743 20971271
|
||||
1000 -324.2963 3994.2535 -323.82196 29875505
|
||||
2000 -324.14448 2715.8412 -323.82196 24005899
|
||||
3000 -323.9446 1032.7299 -323.82196 16224812
|
||||
4000 -323.83425 103.47941 -323.82196 11886177
|
||||
5000 -323.87559 451.59681 -323.82196 13395168
|
||||
6000 -324.05446 1957.8271 -323.82196 20034811
|
||||
7000 -324.24814 3588.7467 -323.82196 28092249
|
||||
8000 -324.3149 4150.7958 -323.82197 31632418
|
||||
9000 -324.25366 3635.1689 -323.82196 27760974
|
||||
10000 -324.05069 1926.0777 -323.82196 19436396
|
||||
11000 -323.88484 529.46541 -323.82196 13264080
|
||||
12000 -323.86286 344.37477 -323.82196 12741952
|
||||
13000 -324.00393 1532.3029 -323.82196 17720089
|
||||
14000 -324.20987 3266.4109 -323.82196 25528615
|
||||
15000 -324.34308 4388.1934 -323.82196 30700580
|
||||
16000 -324.30475 4065.4216 -323.82196 29168176
|
||||
17000 -324.12375 2541.2612 -323.82196 21928164
|
||||
18000 -323.93619 961.92262 -323.82196 14363951
|
||||
19000 -323.87105 413.39974 -323.82196 11446320
|
||||
20000 -323.9713 1257.5055 -323.82196 15118972
|
||||
21000 -324.16564 2894.0212 -323.82196 22749979
|
||||
22000 -324.32073 4199.9228 -323.82196 29044099
|
||||
23000 -324.34614 4413.8921 -323.82196 29514541
|
||||
24000 -324.20431 3219.6717 -323.82196 23595226
|
||||
25000 -324.01211 1601.1964 -323.82196 15812197
|
||||
26000 -323.90577 705.76969 -323.82196 11992491
|
||||
27000 -323.95668 1134.4631 -323.82196 14679820
|
||||
28000 -324.12645 2564.0146 -323.82196 21299092
|
||||
29000 -324.29158 3954.5234 -323.82196 28120074
|
||||
30000 -324.32731 4255.3405 -323.82196 31311574
|
||||
31000 -324.27771 3837.6901 -323.82196 28270491
|
||||
32000 -324.09259 2278.8862 -323.82196 21338356
|
||||
33000 -323.95465 1117.2898 -323.82196 15833338
|
||||
34000 -323.95469 1117.6477 -323.82196 16034624
|
||||
35000 -324.08796 2239.9037 -323.82196 22076527
|
||||
36000 -324.26866 3761.5323 -323.82196 29147703
|
||||
37000 -324.3502 4448.1533 -323.82196 33380564
|
||||
38000 -324.29459 3979.8076 -323.82196 31533851
|
||||
39000 -324.1694 2925.6774 -323.82196 25161011
|
||||
40000 -324.01365 1614.1815 -323.82196 19145060
|
||||
41000 -323.97015 1247.8234 -323.82196 16994462
|
||||
42000 -324.04755 1899.62 -323.82196 19654332
|
||||
43000 -324.22071 3357.7354 -323.82196 25666317
|
||||
44000 -324.35528 4490.9023 -323.82196 30318540
|
||||
45000 -324.35807 4514.3651 -323.82196 30645986
|
||||
46000 -324.24462 3559.0921 -323.82196 25690532
|
||||
47000 -324.09319 2283.909 -323.82196 18529309
|
||||
48000 -324.00266 1521.597 -323.82196 14177383
|
||||
49000 -324.04261 1858.0104 -323.82196 15780869
|
||||
50000 -324.19619 3151.2862 -323.82196 21070555
|
||||
51000 -324.32727 4255.0227 -323.82196 26451705
|
||||
52000 -324.3917 4797.6094 -323.82196 28066000
|
||||
53000 -324.30169 4039.6086 -323.82196 24214730
|
||||
54000 -324.14884 2752.5491 -323.82196 17848175
|
||||
55000 -324.02946 1747.258 -323.82196 13686029
|
||||
56000 -324.05031 1922.825 -323.82196 14113758
|
||||
57000 -324.16944 2925.9624 -323.82196 18723794
|
||||
58000 -324.30745 4088.1772 -323.82196 24387592
|
||||
59000 -324.36463 4569.6324 -323.82196 27059420
|
||||
60000 -324.32147 4206.1707 -323.82196 25012812
|
||||
61000 -324.18133 3026.1579 -323.82196 19500659
|
||||
62000 -324.07027 2090.9001 -323.82196 14626096
|
||||
63000 -324.04536 1881.129 -323.82196 13606034
|
||||
64000 -324.14417 2713.2333 -323.82196 17524492
|
||||
65000 -324.28817 3925.7771 -323.82196 23261363
|
||||
66000 -324.37816 4683.5409 -323.82196 26852878
|
||||
67000 -324.34311 4388.4452 -323.82196 25854003
|
||||
68000 -324.24346 3549.2763 -323.82196 20818195
|
||||
69000 -324.1067 2397.6992 -323.82196 15550338
|
||||
70000 -324.05471 1959.908 -323.82196 13178617
|
||||
71000 -324.12382 2541.8769 -323.82196 15655087
|
||||
72000 -324.25986 3687.3615 -323.82196 20831733
|
||||
73000 -324.37345 4643.9165 -323.82196 25082640
|
||||
74000 -324.38407 4733.3013 -323.82196 25377064
|
||||
75000 -324.28752 3920.3485 -323.82196 21185087
|
||||
76000 -324.14479 2718.409 -323.82196 15093238
|
||||
77000 -324.06273 2027.4447 -323.82196 11357895
|
||||
78000 -324.1027 2363.9918 -323.82196 12682184
|
||||
79000 -324.24431 3556.4784 -323.82196 17923460
|
||||
80000 -324.37329 4642.461 -323.82197 22977159
|
||||
81000 -324.40875 4941.1418 -323.82196 24175202
|
||||
82000 -324.33677 4334.993 -323.82196 20418362
|
||||
83000 -324.18471 3054.6117 -323.82196 14173787
|
||||
84000 -324.08262 2194.902 -323.82196 10107358
|
||||
85000 -324.07536 2133.7765 -323.82196 9748952.1
|
||||
86000 -324.18707 3074.432 -323.82196 13462472
|
||||
87000 -324.32091 4201.5211 -323.82196 19096674
|
||||
88000 -324.44557 5251.2038 -323.82196 22573960
|
||||
89000 -324.39988 4866.4678 -323.82196 21348490
|
||||
90000 -324.25685 3662.0864 -323.82196 15903121
|
||||
91000 -324.0755 2135.0001 -323.82196 10233161
|
||||
92000 -324.06354 2034.2765 -323.82196 7509452
|
||||
93000 -324.15185 2777.9236 -323.82196 9750370.3
|
||||
94000 -324.30478 4065.6146 -323.82196 15561885
|
||||
95000 -324.42696 5094.5186 -323.82196 20667693
|
||||
96000 -324.44094 5212.1846 -323.82196 21153174
|
||||
97000 -324.33283 4301.8232 -323.82196 16435314
|
||||
98000 -324.1883 3084.8099 -323.82196 10336860
|
||||
99000 -324.09656 2312.304 -323.82196 6808669.9
|
||||
100000 -324.13298 2619.0245 -323.82196 7675912.4
|
||||
101000 -324.25984 3687.2237 -323.82196 11868042
|
||||
102000 -324.40322 4894.6055 -323.82196 17007266
|
||||
103000 -324.44333 5232.3546 -323.82196 19025190
|
||||
104000 -324.39727 4844.4421 -323.82196 15980570
|
||||
105000 -324.25 3604.3886 -323.82196 9668044.1
|
||||
106000 -324.08507 2215.5839 -323.82196 4405958.8
|
||||
107000 -324.11835 2495.8211 -323.82196 3436936.2
|
||||
108000 -324.21008 3268.2404 -323.82196 6028268.3
|
||||
109000 -324.34118 4372.1743 -323.82196 10939013
|
||||
110000 -324.40282 4891.1987 -323.82196 14333667
|
||||
111000 -324.45353 5318.1927 -323.82196 13380345
|
||||
112000 -324.33795 4344.9374 -323.82196 7923709.9
|
||||
113000 -324.19654 3154.2192 -323.82196 1970263.7
|
||||
114000 -324.12867 2582.7343 -323.82196 -1481413.1
|
||||
115000 -324.17132 2941.8126 -323.82196 -290956.43
|
||||
116000 -324.33613 4329.6247 -323.82196 5245770.9
|
||||
117000 -324.41548 4997.8222 -323.82196 10354303
|
||||
118000 -324.48518 5584.7558 -323.82196 11795673
|
||||
119000 -324.41046 4955.5092 -323.82196 8031391.3
|
||||
120000 -324.24749 3583.2536 -323.82196 1845177.6
|
||||
121000 -324.14124 2688.5331 -323.82196 -2784584.1
|
||||
122000 -324.14467 2717.4458 -323.82196 -2261498.4
|
||||
123000 -324.28472 3896.7771 -323.82196 3080452.1
|
||||
124000 -324.43687 5177.9121 -323.82196 9819540.9
|
||||
125000 -324.51452 5831.8132 -323.82196 13180239
|
||||
126000 -324.47691 5515.0823 -323.82196 11018721
|
||||
127000 -324.31812 4178.0163 -323.82196 4976672.9
|
||||
128000 -324.16884 2920.9366 -323.82196 -186371.44
|
||||
129000 -324.13025 2596.0395 -323.82196 -1883126.3
|
||||
130000 -324.22275 3374.922 -323.82196 1526423.1
|
||||
131000 -324.41343 4980.5335 -323.82196 8415685
|
||||
132000 -324.45089 5296.046 -323.82196 13250300
|
||||
133000 -324.51148 5806.2229 -323.82196 12827560
|
||||
134000 -324.39463 4822.239 -323.82196 7049805.8
|
||||
135000 -324.20254 3204.6979 -323.82196 -187723.51
|
||||
136000 -324.1379 2660.4388 -323.82196 -3970679.9
|
||||
137000 -324.18473 3054.7443 -323.82196 -2351010.9
|
||||
138000 -324.35172 4460.9406 -323.82196 3024494.5
|
||||
139000 -324.48743 5603.6722 -323.82196 8652609.2
|
||||
140000 -324.53668 6018.4343 -323.82196 9612584.9
|
||||
141000 -324.43638 5173.8016 -323.82196 4805500.8
|
||||
142000 -324.28353 3886.746 -323.82196 -2740880.4
|
||||
143000 -324.14169 2692.2995 -323.82196 -8310197.6
|
||||
144000 -324.13063 2599.1788 -323.82196 -9603391.1
|
||||
145000 -324.27459 3811.4423 -323.82196 -5690559.8
|
||||
146000 -324.4342 5155.4519 -323.82196 431484.28
|
||||
147000 -324.55834 6200.7798 -323.82196 4166801.6
|
||||
148000 -324.51567 5841.5105 -323.82196 2299540.9
|
||||
149000 -324.34424 4397.967 -323.82196 -4487220.6
|
||||
150000 -324.20348 3212.6032 -323.82196 -10852097
|
||||
151000 -324.13211 2611.6979 -323.82196 -12942852
|
||||
152000 -324.20634 3236.7635 -323.82196 -10732036
|
||||
153000 -324.35827 4516.0788 -323.82196 -4665668.3
|
||||
154000 -324.5074 5771.8121 -323.82196 1703175.2
|
||||
155000 -324.51881 5867.9505 -323.82196 2959605.5
|
||||
156000 -324.44762 5268.4581 -323.82196 -1706620
|
||||
157000 -324.25179 3619.4025 -323.82196 -8511782.3
|
||||
158000 -324.13478 2634.1695 -323.82196 -11767435
|
||||
159000 -324.17085 2937.9043 -323.82196 -10356431
|
||||
160000 -324.28946 3936.6179 -323.82196 -5252437.9
|
||||
161000 -324.47596 5507.0864 -323.82196 1737812.2
|
||||
162000 -324.52686 5935.7476 -323.82196 5782720.9
|
||||
163000 -324.5121 5811.4236 -323.82196 4273238.8
|
||||
164000 -324.35265 4468.7315 -323.82196 -1590319.8
|
||||
165000 -324.19582 3148.1193 -323.82196 -6770200.2
|
||||
166000 -324.15306 2788.0507 -323.82196 -8385908.5
|
||||
167000 -324.24186 3535.8588 -323.82196 -4776412.5
|
||||
168000 -324.4 4867.4913 -323.82196 2207883.7
|
||||
169000 -324.52732 5939.6216 -323.82196 7770368.9
|
||||
170000 -324.53787 6028.4604 -323.82196 8163057.7
|
||||
171000 -324.42167 5049.9129 -323.82196 2893037
|
||||
172000 -324.25784 3670.3642 -323.82196 -4020286
|
||||
173000 -324.16815 2915.1362 -323.82196 -7461767.8
|
||||
174000 -324.21774 3332.737 -323.82196 -5214520.3
|
||||
175000 -324.37502 4657.1185 -323.82196 -81968.156
|
||||
176000 -324.5128 5817.2882 -323.82196 5130806.8
|
||||
177000 -324.4983 5695.2281 -323.82196 6394017.7
|
||||
178000 -324.47309 5482.9629 -323.82196 2466372.3
|
||||
179000 -324.31526 4153.8777 -323.82196 -4378953.5
|
||||
180000 -324.2046 3222.0434 -323.82196 -9221400.9
|
||||
181000 -324.21978 3349.8648 -323.82196 -9338327.2
|
||||
182000 -324.33867 4351.0162 -323.82196 -5586765.2
|
||||
183000 -324.44483 5244.9523 -323.82196 -706564.21
|
||||
184000 -324.54787 6112.6128 -323.82196 1971109.1
|
||||
185000 -324.49436 5662.0508 -323.82196 -1239.0449
|
||||
186000 -324.38425 4734.8404 -323.82196 -5595239.9
|
||||
187000 -324.25734 3666.1954 -323.82196 -10793981
|
||||
188000 -324.21303 3293.0496 -323.82196 -11574584
|
||||
189000 -324.28662 3912.7067 -323.82196 -8579023.4
|
||||
190000 -324.4316 5133.5815 -323.82196 -2888022.8
|
||||
191000 -324.51735 5855.6722 -323.82196 1558206.4
|
||||
192000 -324.55207 6147.9783 -323.82196 1897782.9
|
||||
193000 -324.43491 5161.4381 -323.82196 -1998628.2
|
||||
194000 -324.28751 3920.2514 -323.82196 -6841627.4
|
||||
195000 -324.24114 3529.7564 -323.82196 -8565471.5
|
||||
196000 -324.30158 4038.6851 -323.82196 -5634096.8
|
||||
197000 -324.44261 5226.2386 -323.82196 443851.89
|
||||
198000 -324.53354 5991.9831 -323.82196 5993350.1
|
||||
199000 -324.5697 6296.4193 -323.82196 7393255.8
|
||||
200000 -324.46863 5445.3485 -323.82196 4272906.2
|
||||
200493 -324.39372 4814.6196 -323.82196 1812660.2
|
||||
Loop time of 42.6156 on 4 procs for 200000 steps with 101 atoms
|
||||
|
||||
Performance: 40548.540 fs/day, 0.001 hours/fs, 4693.118 timesteps/s, 474.005 katom-step/s
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.576 | 22.615 | 40.956 | 235.7 | 53.07
|
||||
Neigh | 1.9114e-05 | 2.3629e-05 | 2.5892e-05 | 0.0 | 0.00
|
||||
Comm | 0.99241 | 19.433 | 30.581 | 255.9 | 45.60
|
||||
Output | 0.03344 | 0.035732 | 0.037864 | 0.8 | 0.08
|
||||
Modify | 0.066393 | 0.082377 | 0.09318 | 3.4 | 0.19
|
||||
Other | | 0.4486 | | | 1.05
|
||||
|
||||
Nlocal: 25.25 ave 31 max 21 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 75.75 ave 80 max 70 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 1262.5 ave 2143 max 476 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 5050
|
||||
Ave neighs/atom = 50
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
Total wall time: 0:00:43
|
||||
@ -0,0 +1,90 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index Be-solid
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Be-solid
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (64.288 63.628618 63.225)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
20160 atoms
|
||||
read_data CPU = 0.060 seconds
|
||||
|
||||
pair_style eff/cut 31.6125
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neigh_modify one 10000 page 100000
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
dump 1 all custom 1 Be-solid.spe.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
|
||||
fix 1 all nve/eff
|
||||
|
||||
run 0
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 33.6125
|
||||
ghost atom cutoff = 33.6125
|
||||
binsize = 16.80625, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 152.2 | 157 | 161.7 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press
|
||||
0 -49308.807 -49308.807 0 0 1.7906684e+11
|
||||
Loop time of 2.49575e-06 on 4 procs for 0 steps with 20160 atoms
|
||||
|
||||
140.2% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.496e-06 | | |100.00
|
||||
|
||||
Nlocal: 5040 ave 5040 max 5040 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 97370 ave 97370 max 97370 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3.11643e+07 ave 3.241e+07 max 2.99372e+07 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1.2465734e+08
|
||||
Ave neighs/atom = 6183.4
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
118
examples/PACKAGES/eff/ECP/SiC/bulk/log.01Feb25.SiC.g++.4
Normal file
118
examples/PACKAGES/eff/ECP/SiC/bulk/log.01Feb25.SiC.g++.4
Normal file
@ -0,0 +1,118 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index SiC
|
||||
variable nstep equal 100
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.SiC
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (41.1 41.1 41.1)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
5000 atoms
|
||||
read_data CPU = 0.016 seconds
|
||||
|
||||
pair_style eff/cut 20.0 limit/eradius pressure/evirials ecp 1 Si 2 C
|
||||
pair_coeff * *
|
||||
pair_coeff 1 s 0.320852 2.283269 0.814857
|
||||
pair_coeff 2 p 22.721015 0.728733 1.103199 17.695345 6.693621
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neigh_modify one 4000 page 40000
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable ecoul equal c_energies[3]
|
||||
variable erres equal c_energies[4]
|
||||
variable etotalnew equal c_energies[1]+c_energies[2]+c_energies[3]+c_energies[4]
|
||||
|
||||
thermo ${nstep}
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_etotalnew v_eke v_epauli v_ecoul v_erres
|
||||
thermo_modify format float %16.8f
|
||||
thermo_modify lost warn norm yes flush yes
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz ${nstep} ${sname}.min.xyz
|
||||
dump 1 all xyz 100 ${sname}.min.xyz
|
||||
dump 1 all xyz 100 SiC.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom ${nstep} ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
dump 2 all custom 100 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
dump 2 all custom 100 SiC.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
dump 3 all custom ${nstep} ${sname}.data.restart id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all custom 100 ${sname}.data.restart id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all custom 100 SiC.data.restart id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic
|
||||
minimize 0 1e-8 100000 1000000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 4000, page size: 40000
|
||||
master list distance cutoff = 22
|
||||
ghost atom cutoff = 22
|
||||
binsize = 11, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 20.12 | 20.7 | 21.34 Mbytes
|
||||
Step TotEng PotEng KinEng v_etotalnew v_eke v_epauli v_ecoul v_erres
|
||||
0 -0.61266585 -0.61266585 0.00000000 -3063.32924433 2666.66666667 2055.59661323 -7785.59252422 0.00000000
|
||||
27 -0.87995767 -0.87995767 0.00000000 -4399.78836066 2569.46885777 446.25650389 -7415.51372232 0.00000000
|
||||
Loop time of 7.78522 on 4 procs for 27 steps with 5000 atoms
|
||||
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.612665848866385 -0.879957672127075 -0.879957672129693
|
||||
Force two-norm initial, final = 254.76567 6.2598998e-09
|
||||
Force max component initial, final = 2.9077051 3.4450958e-10
|
||||
Final line search alpha, max atom move = 1 3.4450958e-10
|
||||
Iterations, force evaluations = 27 37
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.976 | 7.3573 | 7.6627 | 10.1 | 94.50
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.11037 | 0.41578 | 0.79718 | 42.4 | 5.34
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0121 | | | 0.16
|
||||
|
||||
Nlocal: 1250 ave 1250 max 1250 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 25192 ave 25192 max 25192 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.9985e+06 ave 2.14947e+06 max 1.84582e+06 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 7994000
|
||||
Ave neighs/atom = 1598.8
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:08
|
||||
11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.ang.g++.4
Normal file
11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.ang.g++.4
Normal file
@ -0,0 +1,11 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index SiH4.ang
|
||||
log ${sname}.log
|
||||
log SiH4.ang.log
|
||||
11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.g++.4
Normal file
11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.g++.4
Normal file
@ -0,0 +1,11 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index SiH4
|
||||
log ${sname}.log
|
||||
log SiH4.log
|
||||
95
examples/PACKAGES/eff/H/log.01Feb25.h_atom.spe.ang.g++.4
Normal file
95
examples/PACKAGES/eff/H/log.01Feb25.h_atom.spe.ang.g++.4
Normal file
@ -0,0 +1,95 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h_atom.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h_atom.ang
|
||||
Reading data file ...
|
||||
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 0.529177249
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
timestep 0.0001
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
run 0
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 1 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 = 2.5291772
|
||||
ghost atom cutoff = 2.5291772
|
||||
binsize = 1.2645886, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.35 | 4.35 | 4.35 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 367.03102 367.03102 0 1882.5288 389.88475 -1905.3825 0 0 29191582 29191582
|
||||
Loop time of 2.124e-06 on 4 procs for 0 steps with 4 atoms
|
||||
|
||||
70.6% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.124e-06 | | |100.00
|
||||
|
||||
Nlocal: 1 ave 4 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 549 ave 550 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 121.5 ave 486 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 486
|
||||
Ave neighs/atom = 121.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
94
examples/PACKAGES/eff/H/log.01Feb25.h_atom.spe.bohr.g++.4
Normal file
94
examples/PACKAGES/eff/H/log.01Feb25.h_atom.spe.bohr.g++.4
Normal file
@ -0,0 +1,94 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h_atom.bohr
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h_atom.bohr
|
||||
Reading data file ...
|
||||
orthogonal box = (-1 -1 -1) to (1 1 1)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style eff/cut 1.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
run 0
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 1 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 = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.301 | 4.301 | 4.301 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -0.095769122 -0.095769122 0 1.5 0 -1.5957691 0 0 0 0
|
||||
Loop time of 2.4135e-06 on 4 procs for 0 steps with 2 atoms
|
||||
|
||||
0.0% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.414e-06 | | |100.00
|
||||
|
||||
Nlocal: 0.5 ave 2 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 159.5 ave 160 max 158 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 9.25 ave 37 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 37
|
||||
Ave neighs/atom = 18.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
381
examples/PACKAGES/eff/H2/log.01Feb25.h2.g++.4
Normal file
381
examples/PACKAGES/eff/H2/log.01Feb25.h2.g++.4
Normal file
@ -0,0 +1,381 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h2
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h2
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (12.895936 12.895936 12.895936)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style eff/cut 6.447968 pressure/evirials
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
min_style cg
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-6 1000 2000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 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 = 8.447968
|
||||
ghost atom cutoff = 8.447968
|
||||
binsize = 4.223984, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 5.473 | 5.473 | 5.473 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -25.681592 0 -25.681592 4.1596728e+10
|
||||
43 0 -29.402735 0 -29.402735 5.8094784e+10
|
||||
Loop time of 0.00763171 on 4 procs for 43 steps with 128 atoms
|
||||
|
||||
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-25.6815917951629 -29.4027346945036 -29.4027347455099
|
||||
Force two-norm initial, final = 0.90233034 1.9851971e-07
|
||||
Force max component initial, final = 0.10428109 2.0171202e-08
|
||||
Final line search alpha, max atom move = 1 2.0171202e-08
|
||||
Iterations, force evaluations = 43 49
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0027162 | 0.0036134 | 0.0039713 | 0.9 | 47.35
|
||||
Neigh | 4.3664e-05 | 4.9777e-05 | 5.6567e-05 | 0.0 | 0.65
|
||||
Comm | 0.0030668 | 0.0034209 | 0.004339 | 0.9 | 44.82
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0005477 | | | 7.18
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 928 ave 928 max 928 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2416 ave 2579 max 2253 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 9664
|
||||
Ave neighs/atom = 75.5
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
region part block INF 2.0 INF 2.0 INF 5.0 units box
|
||||
group sub id < 32
|
||||
31 atoms in group sub
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
compute regionT sub temp/region/eff part
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp press v_press c_regionT
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
#velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 3 all temp/rescale/eff 10 0.0 300.0 0.02 1.0
|
||||
fix 1 all nve/eff
|
||||
|
||||
run 10000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.723 | 4.723 | 4.723 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press v_press c_regionT
|
||||
43 -29.402735 -29.402735 0 0 5.8094784e+10 5.8094784e+10 0
|
||||
100 -29.402222 -29.402734 0.00051174152 1.71 5.811788e+10 5.8115522e+10 0.84298014
|
||||
200 -29.401297 -29.402706 0.0014095337 4.71 5.8200069e+10 5.8193571e+10 2.2642129
|
||||
300 -29.400299 -29.402606 0.0023073258 7.71 5.8313355e+10 5.8302716e+10 3.5188104
|
||||
400 -29.399185 -29.40239 0.003205118 10.71 5.8450303e+10 5.8435537e+10 4.4975076
|
||||
500 -29.397917 -29.40202 0.0041029101 13.71 5.8606915e+10 5.8588085e+10 5.0938111
|
||||
600 -29.396468 -29.401468 0.0050007023 16.71 5.8780191e+10 5.8757458e+10 5.214099
|
||||
700 -29.394823 -29.400721 0.0058984944 19.71 5.8967293e+10 5.8940983e+10 4.7987742
|
||||
800 -29.392986 -29.399782 0.0067962866 22.71 5.9165038e+10 5.9135736e+10 3.8586623
|
||||
900 -29.390985 -29.398679 0.0076940787 25.71 5.936952e+10 5.9338162e+10 2.5267164
|
||||
1000 -29.388873 -29.397465 0.0085918709 28.71 5.9575808e+10 5.9543743e+10 1.1129096
|
||||
1100 -29.386732 -29.396221 0.009489663 31.71 5.9777799e+10 5.9746754e+10 0.12904766
|
||||
1200 -29.38466 -29.395047 0.010387455 34.71 5.9968346e+10 5.9940231e+10 0.23254239
|
||||
1300 -29.382761 -29.394047 0.011285247 37.71 6.0139768e+10 6.0116306e+10 2.0555958
|
||||
1400 -29.381123 -29.393306 0.012183039 40.71 6.0284712e+10 6.0267009e+10 5.9623931
|
||||
1500 -29.379789 -29.39287 0.013080832 43.71 6.0397168e+10 6.0385416e+10 11.867131
|
||||
1600 -29.378749 -29.392728 0.013978624 46.71 6.0473266e+10 6.0466731e+10 19.241519
|
||||
1700 -29.377937 -29.392813 0.014876416 49.71 6.051158e+10 6.0508871e+10 27.309028
|
||||
1800 -29.377239 -29.393013 0.015774208 52.71 6.0512895e+10 6.0512343e+10 35.292057
|
||||
1900 -29.376517 -29.393189 0.016672 55.71 6.0479626e+10 6.0479611e+10 42.576307
|
||||
2000 -29.375623 -29.393193 0.017569792 58.71 6.0415141e+10 6.0414287e+10 48.751559
|
||||
2100 -29.374415 -29.392882 0.018467585 61.71 6.0323201e+10 6.0320436e+10 53.567423
|
||||
2200 -29.372763 -29.392128 0.019365377 64.71 6.0207563e+10 6.0202104e+10 56.859803
|
||||
2300 -29.370562 -29.390825 0.020263169 67.71 6.0071772e+10 6.0063077e+10 58.484447
|
||||
2400 -29.367733 -29.388894 0.021160961 70.71 5.9919081e+10 5.9906793e+10 58.272649
|
||||
2500 -29.36423 -29.386289 0.022058753 73.71 5.9752468e+10 5.9736389e+10 56.015194
|
||||
2600 -29.360049 -29.383005 0.022956545 76.71 5.9574736e+10 5.9554816e+10 51.483979
|
||||
2700 -29.355237 -29.379092 0.023854337 79.71 5.9388664e+10 5.9365044e+10 44.512157
|
||||
2800 -29.349911 -29.374664 0.02475213 82.71 5.9197231e+10 5.9170319e+10 35.165882
|
||||
2900 -29.344268 -29.369918 0.025649922 85.71 5.9003898e+10 5.8974484e+10 24.034217
|
||||
3000 -29.338593 -29.365141 0.026547714 88.71 5.8812903e+10 5.8782274e+10 12.596437
|
||||
3100 -29.333256 -29.360702 0.027445506 91.71 5.8629493e+10 5.8599437e+10 3.4545231
|
||||
3200 -29.328661 -29.357004 0.028343298 94.71 5.8459894e+10 5.8432478e+10 0.016534267
|
||||
3300 -29.325167 -29.354408 0.02924109 97.71 5.8310843e+10 5.828792e+10 5.3243002
|
||||
3400 -29.322991 -29.35313 0.030138882 100.71 5.8188646e+10 5.8171288e+10 20.462635
|
||||
3500 -29.322131 -29.353168 0.031036675 103.71 5.8098076e+10 5.8086277e+10 43.783703
|
||||
3600 -29.322365 -29.3543 0.031934467 106.71 5.8041579e+10 5.8034437e+10 71.730426
|
||||
3700 -29.323314 -29.356147 0.032832259 109.71 5.8019147e+10 5.8015336e+10 100.55288
|
||||
3800 -29.32453 -29.35826 0.033730051 112.71 5.8028749e+10 5.8026989e+10 127.58755
|
||||
3900 -29.325571 -29.360199 0.034627843 115.71 5.8067003e+10 5.8066317e+10 151.55747
|
||||
4000 -29.326051 -29.361577 0.035525635 118.71 5.8129753e+10 5.8129529e+10 172.22883
|
||||
4100 -29.325653 -29.362076 0.036423427 121.71 5.8212438e+10 5.8212365e+10 189.92431
|
||||
4200 -29.324129 -29.36145 0.03732122 124.71 5.8310227e+10 5.8310175e+10 205.15122
|
||||
4300 -29.321298 -29.359517 0.038219012 127.71 5.8417974e+10 5.8417851e+10 218.38021
|
||||
4400 -29.317038 -29.356155 0.039116804 130.71 5.853006e+10 5.8529625e+10 229.92521
|
||||
4500 -29.311285 -29.3513 0.040014596 133.71 5.8640135e+10 5.8638756e+10 239.8628
|
||||
4600 -29.304036 -29.344948 0.040912388 136.71 5.8740796e+10 5.8737084e+10 247.94642
|
||||
4700 -29.295358 -29.337168 0.04181018 139.71 5.8823225e+10 5.8814498e+10 253.48762
|
||||
4800 -29.285407 -29.328115 0.042707973 142.71 5.8876834e+10 5.8858342e+10 255.20199
|
||||
4900 -29.274456 -29.318062 0.043605765 145.71 5.8889029e+10 5.8852994e+10 251.07158
|
||||
5000 -29.262921 -29.307424 0.044503557 148.71 5.8845331e+10 5.8780052e+10 238.3896
|
||||
5100 -29.251383 -29.296784 0.045401349 151.71 5.8730207e+10 5.8619991e+10 214.32208
|
||||
5200 -29.240581 -29.286881 0.046299141 154.71 5.8529067e+10 5.8356259e+10 177.37505
|
||||
5300 -29.231338 -29.278535 0.047196933 157.71 5.8231557e+10 5.7981728e+10 129.63824
|
||||
5400 -29.2244 -29.272495 0.048094725 160.71 5.783545e+10 5.7504658e+10 78.320218
|
||||
5500 -29.220236 -29.269228 0.048992518 163.71 5.734924e+10 5.6948969e+10 34.221251
|
||||
5600 -29.218882 -29.268773 0.04989031 166.71 5.6791455e+10 5.6346643e+10 6.9175951
|
||||
5700 -29.219941 -29.270729 0.050788102 169.71 5.6186504e+10 5.5727327e+10 0.29716744
|
||||
5800 -29.222711 -29.274397 0.051685894 172.71 5.5559255e+10 5.5112403e+10 12.070047
|
||||
5900 -29.226384 -29.278968 0.052583686 175.71 5.4930986e+10 5.4515116e+10 36.620819
|
||||
6000 -29.230194 -29.283676 0.053481478 178.71 5.4317798e+10 5.394343e+10 68.124786
|
||||
6100 -29.233502 -29.287881 0.05437927 181.71 5.373093e+10 5.3402599e+10 102.15151
|
||||
6200 -29.235817 -29.291094 0.055277063 184.71 5.317797e+10 5.2896659e+10 135.88236
|
||||
6300 -29.236796 -29.29297 0.056174855 187.71 5.266419e+10 5.2429163e+10 167.68481
|
||||
6400 -29.236229 -29.293302 0.057072647 190.71 5.2193678e+10 5.2003557e+10 196.5624
|
||||
6500 -29.234036 -29.292006 0.057970439 193.71 5.1770207e+10 5.1623395e+10 221.67578
|
||||
6600 -29.230262 -29.28913 0.058868231 196.71 5.1397868e+10 5.1292425e+10 241.95867
|
||||
6700 -29.225101 -29.284867 0.059766023 199.71 5.1081526e+10 5.1014513e+10 255.81687
|
||||
6800 -29.218918 -29.279582 0.060663816 202.71 5.0827088e+10 5.0793357e+10 260.95381
|
||||
6900 -29.212279 -29.27384 0.061561608 205.71 5.0641515e+10 5.0632006e+10 254.493
|
||||
7000 -29.20597 -29.26843 0.0624594 208.71 5.0532428e+10 5.0532428e+10 233.71509
|
||||
7100 -29.200973 -29.264331 0.063357192 211.71 5.0507114e+10 5.0495687e+10 197.6792
|
||||
7200 -29.198346 -29.262601 0.064254984 214.71 5.0570894e+10 5.0523214e+10 149.34022
|
||||
7300 -29.199011 -29.264163 0.065152776 217.71 5.0725246e+10 5.061858e+10 96.508036
|
||||
7400 -29.203489 -29.26954 0.066050568 220.71 5.0966567e+10 5.0787531e+10 49.67303
|
||||
7500 -29.211725 -29.278674 0.066948361 223.71 5.1286493e+10 5.103478e+10 17.246635
|
||||
7600 -29.223104 -29.29095 0.067846153 226.71 5.167383e+10 5.1359868e+10 1.9485991
|
||||
7700 -29.236642 -29.305386 0.068743945 229.71 5.2117092e+10 5.1756034e+10 1.0837556
|
||||
7800 -29.251244 -29.320885 0.069641737 232.71 5.2606457e+10 5.2212741e+10 9.4375813
|
||||
7900 -29.265892 -29.336432 0.070539529 235.71 5.3134616e+10 5.2719209e+10 21.964752
|
||||
8000 -29.279741 -29.351178 0.071437321 238.71 5.3696722e+10 5.3266678e+10 34.999087
|
||||
8100 -29.292137 -29.364472 0.072335113 241.71 5.4289899e+10 5.3849048e+10 46.31642
|
||||
8200 -29.3026 -29.375833 0.073232906 244.71 5.4912636e+10 5.4462542e+10 54.747327
|
||||
8300 -29.310798 -29.384928 0.074130698 247.71 5.5564256e+10 5.510506e+10 59.766256
|
||||
8400 -29.316514 -29.391542 0.07502849 250.71 5.6244467e+10 5.5775533e+10 61.201976
|
||||
8500 -29.319632 -29.395559 0.075926282 253.71 5.6952997e+10 5.6473403e+10 59.079366
|
||||
8600 -29.32013 -29.396954 0.076824074 256.71 5.7689238e+10 5.719821e+10 53.567555
|
||||
8700 -29.318072 -29.395794 0.077721866 259.71 5.845187e+10 5.7949231e+10 45.014327
|
||||
8800 -29.313622 -29.392241 0.078619658 262.71 5.923839e+10 5.8725125e+10 34.059265
|
||||
8900 -29.307054 -29.386572 0.079517451 265.71 6.0044529e+10 5.9523495e+10 21.822776
|
||||
9000 -29.298773 -29.379188 0.080415243 268.71 6.0863509e+10 6.0340317e+10 10.151211
|
||||
9100 -29.289324 -29.370637 0.081313035 271.71 6.1685216e+10 6.1169112e+10 1.8420489
|
||||
9200 -29.279397 -29.361608 0.082210827 274.71 6.2495436e+10 6.1999812e+10 0.66834686
|
||||
9300 -29.269795 -29.352904 0.083108619 277.71 6.3275527e+10 6.2817393e+10 10.912705
|
||||
9400 -29.261351 -29.345358 0.084006411 280.71 6.400305e+10 6.3600785e+10 36.169722
|
||||
9500 -29.254801 -29.339705 0.084904204 283.71 6.4653796e+10 6.4323113e+10 77.605603
|
||||
9600 -29.250616 -29.336418 0.085801996 286.71 6.520517e+10 6.4954574e+10 132.59334
|
||||
9700 -29.248872 -29.335572 0.086699788 289.71 6.5640092e+10 6.5468097e+10 194.91905
|
||||
9800 -29.249212 -29.33681 0.08759758 292.71 6.59499e+10 6.5845645e+10 256.81628
|
||||
9900 -29.250911 -29.339406 0.088495372 295.71 6.6135085e+10 6.6081884e+10 311.59173
|
||||
10000 -29.253024 -29.342417 0.089393164 298.71 6.6203807e+10 6.6183517e+10 355.23319
|
||||
10043 -29.253759 -29.343588 0.089828702 300.16536 6.6201159e+10 6.6189815e+10 370.38327
|
||||
Loop time of 1.04131 on 4 procs for 10000 steps with 128 atoms
|
||||
|
||||
Performance: 829720.937 fs/day, 0.000 hours/fs, 9603.252 timesteps/s, 1.229 Matom-step/s
|
||||
90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.43097 | 0.51117 | 0.59532 | 10.4 | 49.09
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.40178 | 0.48688 | 0.56619 | 10.6 | 46.76
|
||||
Output | 0.0046624 | 0.0047434 | 0.0049664 | 0.2 | 0.46
|
||||
Modify | 0.0074002 | 0.007613 | 0.0078044 | 0.2 | 0.73
|
||||
Other | | 0.0309 | | | 2.97
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 928 ave 928 max 928 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2480 ave 2645 max 2315 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 9920
|
||||
Ave neighs/atom = 77.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix 3
|
||||
|
||||
#compute 1 all property/atom spin eradius
|
||||
#fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0 drag 0.5
|
||||
#dump 1 all custom 100 dump.file id type q c_1[1] c_1[2] x y z
|
||||
|
||||
#fix 1 all nve/eff
|
||||
|
||||
run 10000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press v_press c_regionT
|
||||
10043 -29.253759 -29.343588 0.089828702 300.16536 6.6201159e+10 6.6189815e+10 370.38327
|
||||
10100 -29.253759 -29.344838 0.091079452 304.34478 6.6176296e+10 6.6172538e+10 389.80019
|
||||
10200 -29.253759 -29.345711 0.091951632 307.2592 6.6052925e+10 6.6052773e+10 409.04715
|
||||
10300 -29.253759 -29.344222 0.09046268 302.28382 6.5835973e+10 6.5829924e+10 406.94188
|
||||
10400 -29.253759 -29.339884 0.086124587 287.78795 6.5537696e+10 6.5519727e+10 382.65817
|
||||
10500 -29.253759 -29.33263 0.078870586 263.54848 6.5173326e+10 6.5140691e+10 337.96709
|
||||
10600 -29.253759 -29.32285 0.069091456 230.87122 6.476052e+10 6.4713236e+10 277.25232
|
||||
10700 -29.253759 -29.311365 0.057605907 192.4919 6.4318542e+10 6.4258684e+10 207.17514
|
||||
10800 -29.253759 -29.299325 0.045566125 152.26061 6.3867235e+10 6.379814e+10 136.00177
|
||||
10900 -29.253759 -29.288069 0.034309769 114.64714 6.3425834e+10 6.3351345e+10 72.65992
|
||||
11000 -29.253759 -29.278938 0.025178778 84.135657 6.3011735e+10 6.2935563e+10 25.640652
|
||||
11100 -29.253759 -29.273091 0.01933168 64.597401 6.2639343e+10 6.2564598e+10 1.8969587
|
||||
11200 -29.253759 -29.271337 0.01757805 58.737592 6.2319122e+10 6.224804e+10 5.9017765
|
||||
11300 -29.253759 -29.27402 0.02026083 67.702184 6.2056961e+10 6.1990807e+10 39.010867
|
||||
11400 -29.253759 -29.280964 0.02720461 90.905038 6.1853928e+10 6.1793041e+10 99.231156
|
||||
11500 -29.253759 -29.291496 0.037737065 126.09956 6.1706426e+10 6.1650353e+10 181.43067
|
||||
11600 -29.253759 -29.304538 0.050778773 169.67883 6.1606742e+10 6.1554398e+10 277.95525
|
||||
11700 -29.253759 -29.318745 0.064985916 217.15243 6.1543891e+10 6.1493702e+10 379.55439
|
||||
11800 -29.253759 -29.332682 0.078922995 263.72361 6.1504653e+10 6.1454647e+10 476.47604
|
||||
11900 -29.253759 -29.344999 0.091239641 304.88006 6.1474696e+10 6.1422513e+10 559.5746
|
||||
12000 -29.253759 -29.354586 0.10082711 336.91689 6.1439645e+10 6.1382484e+10 621.28769
|
||||
12100 -29.253759 -29.360694 0.10693515 357.32707 6.1386022e+10 6.1320551e+10 656.36975
|
||||
12200 -29.253759 -29.362996 0.10923714 365.01925 6.1301987e+10 6.1224243e+10 662.31507
|
||||
12300 -29.253759 -29.361599 0.10783979 360.34996 6.1177837e+10 6.1083188e+10 639.45046
|
||||
12400 -29.253759 -29.357 0.10324072 344.98202 6.1006282e+10 6.0889481e+10 590.72007
|
||||
12500 -29.253759 -29.350003 0.096243698 321.60127 6.0782503e+10 6.0637874e+10 521.21754
|
||||
12600 -29.253759 -29.341604 0.087845122 293.53717 6.0504033e+10 6.032581e+10 437.54122
|
||||
12700 -29.253759 -29.332866 0.079107181 264.33907 6.017052e+10 5.995332e+10 347.0566
|
||||
12800 -29.253759 -29.324792 0.071033241 237.35975 5.9783407e+10 5.9522812e+10 257.14865
|
||||
12900 -29.253759 -29.318218 0.064459023 215.3918 5.9345591e+10 5.9038771e+10 174.53724
|
||||
13000 -29.253759 -29.313729 0.059970255 200.39245 5.8861097e+10 5.8507403e+10 104.71393
|
||||
13100 -29.253759 -29.311613 0.057853612 193.31962 5.8334792e+10 5.7936245e+10 51.540581
|
||||
13200 -29.253759 -29.311843 0.05808372 194.08853 5.777218e+10 5.7333762e+10 17.031706
|
||||
13300 -29.253759 -29.314104 0.060345047 201.64482 5.7179263e+10 5.6708972e+10 1.3240561
|
||||
13400 -29.253759 -29.317843 0.064084089 214.13895 5.6562484e+10 5.6071106e+10 2.82093
|
||||
13500 -29.253759 -29.322344 0.068584649 229.17771 5.5928737e+10 5.542933e+10 18.484961
|
||||
13600 -29.253759 -29.326816 0.073057273 244.12312 5.528542e+10 5.4792545e+10 44.242832
|
||||
13700 -29.253759 -29.330492 0.076733214 256.40639 5.4640519e+10 5.4169259e+10 75.458518
|
||||
13800 -29.253759 -29.332712 0.07895342 263.82528 5.4002682e+10 5.3567542e+10 107.42845
|
||||
13900 -29.253759 -29.333003 0.079244028 264.79635 5.3381274e+10 5.2995036e+10 135.85235
|
||||
14000 -29.253759 -29.33113 0.077371384 258.53885 5.2786371e+10 5.2459011e+10 157.23725
|
||||
14100 -29.253759 -29.327131 0.073371666 245.17367 5.2228695e+10 5.196645e+10 169.19917
|
||||
14200 -29.253759 -29.321311 0.06755247 225.72865 5.1719461e+10 5.1524114e+10 170.63669
|
||||
14300 -29.253759 -29.314225 0.060466227 202.04975 5.1270133e+10 5.1138601e+10 161.76275
|
||||
14400 -29.253759 -29.306617 0.052857773 176.62587 5.089211e+10 5.0816349e+10 143.99448
|
||||
14500 -29.253759 -29.29935 0.045590774 152.34297 5.059633e+10 5.0563589e+10 119.71531
|
||||
14600 -29.253759 -29.293319 0.039559773 132.1902 5.0392837e+10 5.0386251e+10 91.93698
|
||||
14700 -29.253759 -29.289355 0.035596197 118.94579 5.029032e+10 5.0289808e+10 63.900552
|
||||
14800 -29.253759 -29.288137 0.034377629 114.8739 5.029568e+10 5.0279104e+10 38.66315
|
||||
14900 -29.253759 -29.290109 0.036349691 121.46361 5.0413636e+10 5.0358148e+10 18.71998
|
||||
15000 -29.253759 -29.295428 0.041669069 139.23847 5.0646422e+10 5.0529927e+10 5.7077538
|
||||
15100 -29.253759 -29.303933 0.050174363 167.65917 5.099359e+10 5.079623e+10 0.22655448
|
||||
15200 -29.253759 -29.315148 0.061388837 205.13268 5.1451944e+10 5.1157502e+10 1.802684
|
||||
15300 -29.253759 -29.328315 0.074555888 249.13079 5.2015605e+10 5.1612742e+10 8.997261
|
||||
15400 -29.253759 -29.342464 0.088704628 296.40923 5.2676201e+10 5.2159429e+10 19.646426
|
||||
15500 -29.253759 -29.356499 0.10273965 343.30769 5.3423173e+10 5.2793473e+10 31.201748
|
||||
15600 -29.253759 -29.369305 0.11554633 386.10162 5.4244166e+10 5.3509204e+10 41.12616
|
||||
15700 -29.253759 -29.37986 0.1261011 421.37071 5.5125447e+10 5.429932e+10 47.293231
|
||||
15800 -29.253759 -29.387334 0.13357524 446.34577 5.6052334e+10 5.5154866e+10 48.336756
|
||||
15900 -29.253759 -29.39118 0.13742108 459.19674 5.7009617e+10 5.6065206e+10 43.903332
|
||||
16000 -29.253759 -29.39119 0.13743084 459.22936 5.798194e+10 5.7018034e+10 34.771959
|
||||
16100 -29.253759 -29.38752 0.13376082 446.96588 5.8954112e+10 5.7999411e+10 22.820321
|
||||
16200 -29.253759 -29.380676 0.12691686 424.09659 5.9911355e+10 5.8993881e+10 10.835339
|
||||
16300 -29.253759 -29.37146 0.11770099 393.30145 6.083948e+10 5.9984681e+10 2.1841693
|
||||
16400 -29.253759 -29.360882 0.10712336 357.956 6.1725019e+10 6.095406e+10 0.37905177
|
||||
16500 -29.253759 -29.350047 0.096287961 321.74918 6.255531e+10 6.1883732e+10 8.5837627
|
||||
16600 -29.253759 -29.340023 0.086263871 288.25337 6.3318582e+10 6.2755451e+10 29.119377
|
||||
16700 -29.253759 -29.331716 0.077957034 260.49582 6.4004055e+10 6.3551677e+10 63.031437
|
||||
16800 -29.253759 -29.325757 0.071998194 240.58417 6.460208e+10 6.4256316e+10 109.77858
|
||||
16900 -29.253759 -29.322421 0.06866219 229.43681 6.5104343e+10 6.4855474e+10 167.09379
|
||||
17000 -29.253759 -29.32159 0.067830842 226.65884 6.5504142e+10 6.5338169e+10 231.05378
|
||||
17100 -29.253759 -29.322766 0.06900694 230.58881 6.5796723e+10 6.5696949e+10 296.37046
|
||||
17200 -29.253759 -29.325139 0.071380489 238.52009 6.5979662e+10 6.5928378e+10 356.89258
|
||||
17300 -29.253759 -29.3277 0.073941262 247.07699 6.6053264e+10 6.6033329e+10 406.27733
|
||||
17400 -29.253759 -29.329384 0.075624794 252.70257 6.6020907e+10 6.6017081e+10 438.765
|
||||
17500 -29.253759 -29.329232 0.075473164 252.19589 6.5889298e+10 6.5889197e+10 449.9672
|
||||
17600 -29.253759 -29.326547 0.072788435 243.22479 6.5668557e+10 6.566317e+10 437.56505
|
||||
17700 -29.253759 -29.321015 0.067255999 224.73798 6.537209e+10 6.5355863e+10 401.81223
|
||||
17800 -29.253759 -29.312777 0.059017856 197.20998 6.5016192e+10 6.4986737e+10 345.75083
|
||||
17900 -29.253759 -29.302441 0.048681923 162.67214 6.461938e+10 6.4576898e+10 275.07707
|
||||
18000 -29.253759 -29.291021 0.037262252 124.51296 6.4201459e+10 6.4148001e+10 197.63846
|
||||
18100 -29.253759 -29.279814 0.026055453 87.065095 6.3782375e+10 6.3721066e+10 122.59764
|
||||
18200 -29.253759 -29.270228 0.016469061 55.031873 6.3380961e+10 6.3315275e+10 59.354773
|
||||
18300 -29.253759 -29.263585 0.009826229 32.834645 6.3013664e+10 6.2946844e+10 16.367993
|
||||
18400 -29.253759 -29.260935 0.0071761426 23.9793 6.2693422e+10 6.2628079e+10 0.04021999
|
||||
18500 -29.253759 -29.262899 0.0091396789 30.540517 6.2428791e+10 6.2366686e+10 13.840884
|
||||
18600 -29.253759 -29.269574 0.01581463 52.84507 6.2223448e+10 6.2165441e+10 57.800802
|
||||
18700 -29.253759 -29.280514 0.026755117 89.403044 6.2076104e+10 6.2022224e+10 128.46082
|
||||
18800 -29.253759 -29.294786 0.041027472 137.09456 6.1980858e+10 6.1930427e+10 219.28144
|
||||
18900 -29.253759 -29.311091 0.057332365 191.57786 6.1927902e+10 6.1879682e+10 321.44654
|
||||
19000 -29.253759 -29.327932 0.074172828 247.85078 6.1904521e+10 6.1856811e+10 424.935
|
||||
19100 -29.253759 -29.343801 0.090041852 300.87761 6.1896231e+10 6.1846902e+10 519.70032
|
||||
19200 -29.253759 -29.357361 0.10360217 346.18982 6.1887942e+10 6.1834406e+10 596.79434
|
||||
19300 -29.253759 -29.367593 0.11383425 380.38063 6.1865031e+10 6.1804149e+10 649.29447
|
||||
19400 -29.253759 -29.373894 0.12013535 401.43594 6.1814231e+10 6.1742208e+10 672.93539
|
||||
19500 -29.253759 -29.37612 0.12236075 408.87221 6.1724294e+10 6.1636603e+10 666.39687
|
||||
19600 -29.253759 -29.374566 0.12080701 403.68034 6.1586396e+10 6.1477781e+10 631.24827
|
||||
19700 -29.253759 -29.369903 0.11614425 388.09956 6.1394308e+10 6.1258917e+10 571.59167
|
||||
19800 -29.253759 -29.363069 0.10931013 365.26317 6.1144351e+10 6.0976023e+10 493.47418
|
||||
19900 -29.253759 -29.35514 0.10138144 338.76918 6.0835203e+10 6.0627905e+10 404.15587
|
||||
20000 -29.253759 -29.347199 0.093439728 312.23172 6.0467587e+10 6.0215993e+10 311.32317
|
||||
20043 -29.253759 -29.344026 0.090267282 301.63089 6.0292085e+10 6.002012e+10 272.18496
|
||||
Loop time of 1.02899 on 4 procs for 10000 steps with 128 atoms
|
||||
|
||||
Performance: 839654.865 fs/day, 0.000 hours/fs, 9718.228 timesteps/s, 1.244 Matom-step/s
|
||||
91.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.42341 | 0.50618 | 0.59534 | 10.4 | 49.19
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.39233 | 0.48231 | 0.56438 | 10.7 | 46.87
|
||||
Output | 0.0047128 | 0.0048033 | 0.0050386 | 0.2 | 0.47
|
||||
Modify | 0.0052563 | 0.0055253 | 0.0058241 | 0.3 | 0.54
|
||||
Other | | 0.03018 | | | 2.93
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 928 ave 928 max 928 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2416 ave 2582 max 2250 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 9664
|
||||
Ave neighs/atom = 75.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.npt.g++.4
Normal file
161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.npt.g++.4
Normal file
@ -0,0 +1,161 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h2bulk
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h2bulk
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
13718 atoms
|
||||
read_data CPU = 0.048 seconds
|
||||
|
||||
pair_style eff/cut 30.627847
|
||||
pair_coeff * *
|
||||
|
||||
neigh_modify one 20000 page 200000
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step pe temp press vol
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# structure minimization
|
||||
dump 1 all xyz 1 ${sname}.min.xyz
|
||||
dump 1 all xyz 1 h2bulk.min.xyz
|
||||
min_style cg
|
||||
minimize 0 1.0e-4 1 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 20000, page size: 200000
|
||||
master list distance cutoff = 32.627847
|
||||
ghost atom cutoff = 32.627847
|
||||
binsize = 16.313924, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 87.11 | 93.61 | 100.1 Mbytes
|
||||
Step PotEng Temp Press Volume
|
||||
0 -2871.4801 0 2.8596879e+10 229847.29
|
||||
1 -2872.8077 0 2.8046824e+10 229847.29
|
||||
Loop time of 1.02378 on 4 procs for 1 steps with 13718 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-2871.48013813359 -2871.48013813359 -2872.8076730722
|
||||
Force two-norm initial, final = 5.4264823 5.0563616
|
||||
Force max component initial, final = 0.21424475 0.19518835
|
||||
Final line search alpha, max atom move = 0.046675588 0.0091105311
|
||||
Iterations, force evaluations = 1 1
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.7704 | 0.89228 | 1.0165 | 11.0 | 87.16
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0028288 | 0.12705 | 0.24891 | 29.2 | 12.41
|
||||
Output | 0.0037898 | 0.0038794 | 0.0039584 | 0.1 | 0.38
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0005774 | | | 0.06
|
||||
|
||||
Nlocal: 3429.5 ave 3800 max 3078 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 65600.5 ave 67122 max 64060 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 59740807
|
||||
Ave neighs/atom = 4354.9211
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
undump 1
|
||||
|
||||
# create initial velocities according to temp, w/out e radial dof
|
||||
velocity all create 20000.0 4928459 rot yes dist gaussian
|
||||
|
||||
# npt
|
||||
fix 1 all npt/eff temp 20000.0 20000.0 1.0 iso 1e9 1e9 1.0
|
||||
variable density equal 11.2058851*mass(all)
|
||||
thermo_style custom step pe temp press vol v_density
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
|
||||
thermo_modify temp effTemp
|
||||
|
||||
dump 2 all xyz 10000 ${sname}.npt.xyz
|
||||
dump 2 all xyz 10000 h2bulk.npt.xyz
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
dump 3 all custom 10000 h2bulk.npt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
|
||||
thermo 1
|
||||
run 10
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.61 | 86.11 | 92.6 Mbytes
|
||||
Step PotEng Temp Press Volume v_density
|
||||
1 -2872.8077 40002.916 1.392533e+11 229847.29 154332.61
|
||||
2 -2872.8075 40002.808 1.3925254e+11 229847.72 154332.61
|
||||
3 -2872.8072 40002.493 1.3925022e+11 229849.01 154332.61
|
||||
4 -2872.8068 40001.97 1.3924633e+11 229851.15 154332.61
|
||||
5 -2872.8064 40001.241 1.3924088e+11 229854.15 154332.61
|
||||
6 -2872.8058 40000.304 1.3923386e+11 229858.01 154332.61
|
||||
7 -2872.8052 39999.161 1.3922528e+11 229862.72 154332.61
|
||||
8 -2872.8045 39997.81 1.3921514e+11 229868.29 154332.61
|
||||
9 -2872.8037 39996.253 1.3920343e+11 229874.72 154332.61
|
||||
10 -2872.8028 39994.488 1.3919016e+11 229882.01 154332.61
|
||||
11 -2872.8018 39992.517 1.3917533e+11 229890.15 154332.61
|
||||
Loop time of 10.5538 on 4 procs for 10 steps with 13718 atoms
|
||||
|
||||
Performance: 81.866 fs/day, 0.293 hours/fs, 0.948 timesteps/s, 12.998 katom-step/s
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.6596 | 9.2995 | 10.519 | 24.8 | 88.12
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.029706 | 1.2492 | 1.8893 | 67.7 | 11.84
|
||||
Output | 0.00056676 | 0.00059312 | 0.00063847 | 0.0 | 0.01
|
||||
Modify | 0.0017284 | 0.0019179 | 0.0020891 | 0.4 | 0.02
|
||||
Other | | 0.002503 | | | 0.02
|
||||
|
||||
Nlocal: 3429.5 ave 3800 max 3078 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 65600.5 ave 67122 max 64060 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 1.49356e+07 ave 1.64691e+07 max 1.33702e+07 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 59742327
|
||||
Ave neighs/atom = 4355.0319
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
undump 2
|
||||
undump 3
|
||||
Total wall time: 0:00:14
|
||||
161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.ang.g++.4
Normal file
161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.ang.g++.4
Normal file
@ -0,0 +1,161 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h2bulk.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h2bulk.ang
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (32.41512 32.41512 32.41512)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
13718 atoms
|
||||
read_data CPU = 0.039 seconds
|
||||
|
||||
pair_style eff/cut 16.207559818252903 limit/eradius pressure/evirials
|
||||
pair_coeff * *
|
||||
|
||||
neigh_modify one 10000 page 100000
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable ecoul equal c_energies[3]
|
||||
variable erres equal c_energies[4]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
|
||||
thermo_modify temp effTemp press effPress flush yes
|
||||
|
||||
# structure minimization
|
||||
min_style cg
|
||||
minimize 0 1.0e-4 10 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 18.20756
|
||||
ghost atom cutoff = 18.20756
|
||||
binsize = 9.1037799, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 99.9 | 106.9 | 113.6 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
|
||||
0 -1801882.2 -1801882.2 0 1941449.2 111650.99 -3854982.4 0 169191.44 169191.44 0
|
||||
10 -1812982.2 -1812982.2 0 2023531 93131.746 -3929644.9 0 204251.79 204251.79 0
|
||||
Loop time of 11.8971 on 4 procs for 10 steps with 13718 atoms
|
||||
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max force evaluations
|
||||
Energy initial, next-to-last, final =
|
||||
-1801882.20439777 -1811783.39715666 -1812982.21160594
|
||||
Force two-norm initial, final = 4976.0965 945.50616
|
||||
Force max component initial, final = 134.44103 23.528388
|
||||
Final line search alpha, max atom move = 0.0010624281 0.024997221
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.9682 | 10.823 | 11.655 | 22.1 | 90.97
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.23254 | 1.0651 | 1.9201 | 70.3 | 8.95
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.009102 | | | 0.08
|
||||
|
||||
Nlocal: 3429.5 ave 3800 max 3078 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 75372.5 ave 75724 max 75002 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 1.74322e+07 ave 1.91106e+07 max 1.57195e+07 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 69728955
|
||||
Ave neighs/atom = 5083.0263
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
timestep 0.001
|
||||
|
||||
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
# nve
|
||||
fix 1 all nve/eff
|
||||
#fix 2 all imd 8888 trate 1 unwrap on nowait on
|
||||
|
||||
compute peatom all pe/atom
|
||||
compute keatom all ke/atom/eff
|
||||
|
||||
dump 2 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 2 all xyz 1000 h2bulk.ang.nve.xyz
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||
dump 3 all custom 1000 h2bulk.ang.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||
|
||||
run 10
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 101 | 105.7 | 110.5 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
|
||||
10 -995226.78 -1812982.2 817755.43 2023531 93131.746 -3929644.9 0 1301774.2 1301774.2 40002.916
|
||||
20 -995226.78 -1812951.8 817725.06 2023530.9 93136.224 -3929618.9 0 1301757.1 1301757.1 40001.431
|
||||
Loop time of 9.29954 on 4 procs for 10 steps with 13718 atoms
|
||||
|
||||
Performance: 0.000 ns/day, 258320.521 hours/ns, 1.075 timesteps/s, 14.751 katom-step/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.5126 | 8.8333 | 9.1491 | 9.5 | 94.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.14252 | 0.45853 | 0.77938 | 41.7 | 4.93
|
||||
Output | 0.0046943 | 0.0047097 | 0.0047198 | 0.0 | 0.05
|
||||
Modify | 0.00051144 | 0.00055804 | 0.00059726 | 0.0 | 0.01
|
||||
Other | | 0.002462 | | | 0.03
|
||||
|
||||
Nlocal: 3429.5 ave 3610 max 3249 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 75372.5 ave 75553 max 75192 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 1.74471e+07 ave 1.82017e+07 max 1.66315e+07 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 69788395
|
||||
Ave neighs/atom = 5087.3593
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
#unfix 2
|
||||
undump 2
|
||||
undump 3
|
||||
Total wall time: 0:00:24
|
||||
150
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.g++.4
Normal file
150
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.g++.4
Normal file
@ -0,0 +1,150 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h2bulk
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h2bulk
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
13718 atoms
|
||||
read_data CPU = 0.036 seconds
|
||||
|
||||
pair_style eff/cut 30.627847
|
||||
pair_coeff * *
|
||||
|
||||
neigh_modify one 10000 page 100000
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# structure minimization
|
||||
min_style cg
|
||||
minimize 0 1.0e-4 10 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 32.627847
|
||||
ghost atom cutoff = 32.627847
|
||||
binsize = 16.313924, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 86.33 | 92.54 | 98.55 Mbytes
|
||||
Step PotEng Temp Press
|
||||
0 -2871.4801 0 2.8596879e+10
|
||||
10 -2882.3401 0 2.1869586e+10
|
||||
Loop time of 11.6123 on 4 procs for 10 steps with 13718 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max force evaluations
|
||||
Energy initial, next-to-last, final =
|
||||
-2871.48013813359 -2881.24844591398 -2882.34005034714
|
||||
Force two-norm initial, final = 5.4264823 1.3218657
|
||||
Force max component initial, final = 0.21424475 0.025681865
|
||||
Final line search alpha, max atom move = 0.4402147 0.011305535
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.2083 | 10.221 | 11.528 | 31.2 | 88.02
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.07895 | 1.3856 | 2.3982 | 84.8 | 11.93
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.005564 | | | 0.05
|
||||
|
||||
Nlocal: 3429.5 ave 3800 max 3078 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 65600.5 ave 67122 max 64060 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 59740807
|
||||
Ave neighs/atom = 4354.9211
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
timestep 0.001
|
||||
|
||||
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
# nve
|
||||
fix 1 all nve/eff
|
||||
#fix 2 all imd 8888 trate 1 unwrap on nowait on
|
||||
|
||||
compute peatom all pe/atom
|
||||
compute keatom all ke/atom/eff
|
||||
|
||||
dump 2 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 2 all xyz 1000 h2bulk.nve.xyz
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||
dump 3 all custom 1000 h2bulk.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||
|
||||
run 10
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 82.52 | 87.21 | 91.69 Mbytes
|
||||
Step PotEng Temp Press
|
||||
10 -2882.3401 40002.916 1.3307606e+11
|
||||
20 -2882.2908 40001.405 1.3306905e+11
|
||||
Loop time of 9.25154 on 4 procs for 10 steps with 13718 atoms
|
||||
|
||||
Performance: 93.390 fs/day, 0.257 hours/fs, 1.081 timesteps/s, 14.828 katom-step/s
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.2948 | 8.675 | 8.9946 | 10.1 | 93.77
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.2531 | 0.57292 | 0.9531 | 39.5 | 6.19
|
||||
Output | 3.7757e-05 | 5.7819e-05 | 7.5679e-05 | 0.0 | 0.00
|
||||
Modify | 0.0005098 | 0.0005357 | 0.00055895 | 0.0 | 0.01
|
||||
Other | | 0.002988 | | | 0.03
|
||||
|
||||
Nlocal: 3429.5 ave 3610 max 3249 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 65600.5 ave 66951 max 64250 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 1.49409e+07 ave 1.56765e+07 max 1.41457e+07 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 59763523
|
||||
Ave neighs/atom = 4356.577
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
#unfix 2
|
||||
undump 2
|
||||
undump 3
|
||||
Total wall time: 0:00:23
|
||||
@ -0,0 +1,111 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index Li-dendritic
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Li-dendritic
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (100.224 100.224 100.224)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3456 atoms
|
||||
read_data CPU = 0.023 seconds
|
||||
#read_restart ${sname}.min.restart2
|
||||
|
||||
pair_style eff/cut 50.112
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 1 all custom 10 Li-dendritic.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 2 all xyz 10 ${sname}.min.xyz
|
||||
dump 2 all xyz 10 Li-dendritic.min.xyz
|
||||
|
||||
restart 10 ${sname}.nve.restart1 ${sname}.nve.restart2
|
||||
restart 10 Li-dendritic.nve.restart1 ${sname}.nve.restart2
|
||||
restart 10 Li-dendritic.nve.restart1 Li-dendritic.nve.restart2
|
||||
|
||||
#min_style cg
|
||||
#min_modify line quadratic dmax 2.0
|
||||
#minimize 0.0 1.0e-5 10000 100000
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all nve/eff
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 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 = 52.112
|
||||
ghost atom cutoff = 52.112
|
||||
binsize = 26.056, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 11.4 | 11.59 | 11.78 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press
|
||||
0 -5167.408 -5172.3316 4.9236061 1201.0429 -1.5761339e+09
|
||||
10 -5167.408 -5172.3292 4.9211748 1200.4498 -1.5762759e+09
|
||||
20 -5167.408 -5172.3219 4.9139105 1198.6778 -1.5767007e+09
|
||||
30 -5167.408 -5172.3099 4.9019017 1195.7484 -1.5774041e+09
|
||||
40 -5167.408 -5172.2933 4.885295 1191.6974 -1.5783794e+09
|
||||
50 -5167.408 -5172.2723 4.8642936 1186.5744 -1.5796171e+09
|
||||
60 -5167.408 -5172.2471 4.839155 1180.4422 -1.5811053e+09
|
||||
70 -5167.408 -5172.2182 4.8101883 1173.3762 -1.5828297e+09
|
||||
80 -5167.408 -5172.1857 4.7777514 1165.4637 -1.5847737e+09
|
||||
90 -5167.408 -5172.1502 4.7422469 1156.8029 -1.5869184e+09
|
||||
100 -5167.408 -5172.1121 4.7041183 1147.502 -1.5892434e+09
|
||||
Loop time of 9.14099 on 4 procs for 100 steps with 3456 atoms
|
||||
|
||||
Performance: 945.193 fs/day, 0.025 hours/fs, 10.940 timesteps/s, 37.808 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.0683 | 7.7216 | 8.7585 | 22.7 | 84.47
|
||||
Neigh | 0.24686 | 0.25299 | 0.2618 | 1.2 | 2.77
|
||||
Comm | 0.079533 | 1.1252 | 1.784 | 60.0 | 12.31
|
||||
Output | 0.035036 | 0.03505 | 0.03506 | 0.0 | 0.38
|
||||
Modify | 0.0014139 | 0.0014999 | 0.0015446 | 0.1 | 0.02
|
||||
Other | | 0.004642 | | | 0.05
|
||||
|
||||
Nlocal: 864 ave 888 max 851 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 17185 ave 17198 max 17161 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 890568 ave 965810 max 799750 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 3562272
|
||||
Ave neighs/atom = 1030.75
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:09
|
||||
@ -0,0 +1,178 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index Li-dendritic
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Li-dendritic
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (100.224 100.224 100.224)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3456 atoms
|
||||
read_data CPU = 0.016 seconds
|
||||
#read_restart ${sname}.min.restart
|
||||
|
||||
pair_style eff/cut 50.112
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
print "Starting minimizer"
|
||||
Starting minimizer
|
||||
min_style cg
|
||||
|
||||
compute 1 all property/atom spin eradius
|
||||
#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2]
|
||||
#dump 2 all xyz 100 ${sname}.min.xyz
|
||||
min_modify line quadratic dmax 0.05
|
||||
minimize 0 1.0e-7 100 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 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 = 52.112
|
||||
ghost atom cutoff = 52.112
|
||||
binsize = 26.056, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 14.88 | 15.07 | 15.26 Mbytes
|
||||
Step PotEng Temp Press
|
||||
0 -5172.3316 0 -1.6720594e+09
|
||||
10 -5199.5494 0 -1.6721099e+09
|
||||
20 -5220.9343 0 -1.6720299e+09
|
||||
30 -5238.4037 0 -1.6694987e+09
|
||||
40 -5252.5928 0 -1.6515154e+09
|
||||
50 -5263.7845 0 -1.5851579e+09
|
||||
60 -5271.8051 0 -1.4304709e+09
|
||||
70 -5275.1692 0 -1.2764647e+09
|
||||
80 -5276.9804 0 -1.1135845e+09
|
||||
87 -5277.5186 0 -1.0157231e+09
|
||||
Loop time of 9.1237 on 4 procs for 87 steps with 3456 atoms
|
||||
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max force evaluations
|
||||
Energy initial, next-to-last, final =
|
||||
-5172.33158699748 -5277.50851484438 -5277.51857905665
|
||||
Force two-norm initial, final = 10.47944 0.61719987
|
||||
Force max component initial, final = 0.33333431 0.020508985
|
||||
Final line search alpha, max atom move = 0.48148149 0.0098746969
|
||||
Iterations, force evaluations = 87 101
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.2296 | 8.0451 | 8.9943 | 23.5 | 88.18
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.11943 | 1.0682 | 1.8834 | 64.3 | 11.71
|
||||
Output | 0.00021247 | 0.00022521 | 0.00026234 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01011 | | | 0.11
|
||||
|
||||
Nlocal: 864 ave 864 max 864 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17185 ave 17185 max 17185 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 890568 ave 968400 max 812736 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 3562272
|
||||
Ave neighs/atom = 1030.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart ${sname}.min.restart
|
||||
write_restart Li-dendritic.min.restart
|
||||
System init for write_restart ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
# NVT
|
||||
reset_timestep 0
|
||||
timestep 0.005
|
||||
|
||||
print "Starting nvt"
|
||||
Starting nvt
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
dump 1 all custom 100 Li-dendritic.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
dump 2 all xyz 100 Li-dendritic.nvt.xyz
|
||||
restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
|
||||
restart 100 Li-dendritic.nvt.restart1 ${sname}.nvt.restart2
|
||||
restart 100 Li-dendritic.nvt.restart1 Li-dendritic.nvt.restart2
|
||||
|
||||
run 100
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.9 | 12.09 | 12.28 Mbytes
|
||||
Step PotEng Temp Press
|
||||
0 -5277.5186 0 -1.0157231e+09
|
||||
10 -5277.5187 0.028803274 -1.0157155e+09
|
||||
20 -5277.519 0.12372272 -1.0156917e+09
|
||||
30 -5277.5195 0.29618333 -1.0156507e+09
|
||||
40 -5277.5201 0.55263617 -1.0155924e+09
|
||||
50 -5277.5206 0.8932531 -1.0155176e+09
|
||||
60 -5277.521 1.3127021 -1.015428e+09
|
||||
70 -5277.5211 1.8037418 -1.0153251e+09
|
||||
80 -5277.5208 2.3644081 -1.0152094e+09
|
||||
90 -5277.52 3.0093875 -1.0150781e+09
|
||||
100 -5277.5187 3.7858675 -1.0149239e+09
|
||||
Loop time of 8.47644 on 4 procs for 100 steps with 3456 atoms
|
||||
|
||||
Performance: 5096.477 fs/day, 0.005 hours/fs, 11.797 timesteps/s, 40.772 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 | 6.8234 | 7.537 | 8.2853 | 24.1 | 88.92
|
||||
Neigh | 0.023585 | 0.024246 | 0.024867 | 0.4 | 0.29
|
||||
Comm | 0.15595 | 0.90456 | 1.6184 | 69.6 | 10.67
|
||||
Output | 0.0032476 | 0.0032612 | 0.0032984 | 0.0 | 0.04
|
||||
Modify | 0.0036078 | 0.0037554 | 0.0039448 | 0.2 | 0.04
|
||||
Other | | 0.003634 | | | 0.04
|
||||
|
||||
Nlocal: 864 ave 881 max 834 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 17185 ave 17215 max 17168 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Neighs: 890568 ave 976912 max 789323 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 3562272
|
||||
Ave neighs/atom = 1030.75
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
Total wall time: 0:00:17
|
||||
155
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.ang.g++.4
Normal file
155
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.ang.g++.4
Normal file
@ -0,0 +1,155 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index Li.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
dielectric 1.0
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Li.ang
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (22.098442 22.098442 22.098442)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2000 atoms
|
||||
read_data CPU = 0.014 seconds
|
||||
#read_restart ${sname}.min.restart
|
||||
|
||||
pair_style eff/cut 11.049221 limit/eradius pressure/evirials
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neigh_modify one 2000 page 20000
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable ecoul equal c_energies[3]
|
||||
variable erres equal c_energies[4]
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
|
||||
thermo_modify temp effTemp press effPress flush yes
|
||||
|
||||
#min_style cg
|
||||
#minimize 0 1e-6 100 1000
|
||||
#write_restart ${sname}.min.restart
|
||||
|
||||
timestep 0.005
|
||||
|
||||
velocity all create 10.0 4928459 rot yes mom yes dist gaussian
|
||||
fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
|
||||
#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
|
||||
fix 1 all nve/eff
|
||||
|
||||
run 200
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 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: 20000
|
||||
master list distance cutoff = 13.049221
|
||||
ghost atom cutoff = 13.049221
|
||||
binsize = 6.5246105, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 6.772 | 6.887 | 7.001 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
|
||||
0 -1934872.7 -1934932.3 59.586393 1973239.1 9338.8528 -3917510.2 0 119790.47 119790.47 40.06012
|
||||
100 -1932300.8 -1934539.4 2238.5734 1864086.1 9857.8379 -3808483.3 0 -100104.15 -105089 1505
|
||||
200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
|
||||
Loop time of 6.61662 on 4 procs for 200 steps with 2000 atoms
|
||||
|
||||
Performance: 0.013 ns/day, 1837.949 hours/ns, 30.227 timesteps/s, 60.454 katom-step/s
|
||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.572 | 5.9389 | 6.2372 | 9.8 | 89.76
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.37051 | 0.66886 | 1.0359 | 29.2 | 10.11
|
||||
Output | 0.00076947 | 0.00078111 | 0.00081552 | 0.0 | 0.01
|
||||
Modify | 0.0035517 | 0.0038042 | 0.0040517 | 0.4 | 0.06
|
||||
Other | | 0.004249 | | | 0.06
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10252 ave 10252 max 10252 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 424625 ave 448237 max 400021 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1698500
|
||||
Ave neighs/atom = 849.25
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix 0
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt/eff temp 3000.0 3000.0 100.0
|
||||
compute 1 all property/atom spin eradius ervel
|
||||
dump 1 all custom 500 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
|
||||
dump 1 all custom 500 Li.ang.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
|
||||
|
||||
run 500
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.522 | 7.656 | 7.751 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
|
||||
200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
|
||||
300 -1929902.8 -1934223.4 4320.5724 2031898.3 11427.685 -3977549.4 0 268725.75 262717.84 2904.7345
|
||||
400 -1929360.3 -1935088.8 5728.4403 1850892.1 13473.172 -3799454 0 -105609.57 -118457.31 3851.2485
|
||||
500 -1929066.1 -1935648.1 6581.9291 1901305.5 14887.365 -3851840.9 0 7045.2102 -9644.887 4425.0518
|
||||
600 -1929593.6 -1934406.5 4812.986 2003446.8 16194.971 -3954048.4 0 221662.39 211620.13 3235.7857
|
||||
700 -1930061.3 -1933572.3 3510.9499 1811788.7 18436.004 -3763797 0 -182749.21 -186750.23 2360.4227
|
||||
Loop time of 16.6082 on 4 procs for 500 steps with 2000 atoms
|
||||
|
||||
Performance: 0.013 ns/day, 1845.351 hours/ns, 30.106 timesteps/s, 60.211 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 12.79 | 14.632 | 16.232 | 32.8 | 88.10
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.35155 | 1.9504 | 3.7924 | 89.8 | 11.74
|
||||
Output | 0.0034195 | 0.0035878 | 0.0038027 | 0.3 | 0.02
|
||||
Modify | 0.01108 | 0.011237 | 0.0114 | 0.1 | 0.07
|
||||
Other | | 0.01046 | | | 0.06
|
||||
|
||||
Nlocal: 500 ave 520 max 480 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 10252 ave 10272 max 10232 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 426287 ave 457559 max 396571 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1705148
|
||||
Ave neighs/atom = 852.574
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:23
|
||||
166
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.bohr.g++.4
Normal file
166
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.bohr.g++.4
Normal file
@ -0,0 +1,166 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index Li.bohr
|
||||
|
||||
units electron
|
||||
newton off
|
||||
boundary p p p
|
||||
dielectric 1.0
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Li.bohr
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (41.76 41.76 41.76)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2000 atoms
|
||||
read_data CPU = 0.006 seconds
|
||||
|
||||
pair_style eff/cut 20.88 limit/eradius pressure/evirials
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neigh_modify one 2000 page 20000
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain press v_press temp
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
min_style cg
|
||||
minimize 0 1e-6 100 200
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 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: 20000
|
||||
master list distance cutoff = 22.88
|
||||
ghost atom cutoff = 22.88
|
||||
binsize = 11.44, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/atomonly/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.51 | 9.51 | 9.51 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
|
||||
0 -3083.509 -3083.509 0 3144.5578 14.882406 -6242.9492 0 1.2112606e+10 1.2112606e+10 0
|
||||
10 -3085.4657 -3085.4657 0 3062.6201 21.113244 -6169.199 0 1.797769e+09 1.797769e+09 0
|
||||
20 -3085.9152 -3085.9152 0 3063.3218 21.843788 -6171.0808 0 1.9306772e+09 1.9306772e+09 0
|
||||
30 -3086.103 -3086.103 0 3065.4937 21.7953 -6173.392 0 2.1693045e+09 2.1693045e+09 0
|
||||
40 -3086.2065 -3086.2065 0 3062.3955 22.002457 -6170.6045 0 1.7527596e+09 1.7527596e+09 0
|
||||
50 -3086.2558 -3086.2558 0 3059.7162 22.165243 -6168.1372 0 1.4005967e+09 1.4005967e+09 0
|
||||
60 -3086.2823 -3086.2823 0 3061.7509 22.016476 -6170.0497 0 1.6419693e+09 1.6419693e+09 0
|
||||
70 -3086.3068 -3086.3068 0 3063.1496 22.125331 -6171.5817 0 1.8371954e+09 1.8371954e+09 0
|
||||
80 -3086.3286 -3086.3286 0 3063.4058 22.112083 -6171.8465 0 1.8595352e+09 1.8595352e+09 0
|
||||
90 -3086.342 -3086.342 0 3062.6876 22.145517 -6171.1752 0 1.761838e+09 1.761838e+09 0
|
||||
100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
|
||||
Loop time of 9.51021 on 4 procs for 100 steps with 2000 atoms
|
||||
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-3083.5089570212 -3086.34842671529 -3086.34926128553
|
||||
Force two-norm initial, final = 3.4238461 0.15353209
|
||||
Force max component initial, final = 0.15119069 0.017560878
|
||||
Final line search alpha, max atom move = 0.75419179 0.01324427
|
||||
Iterations, force evaluations = 100 191
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.8842 | 9.0722 | 9.2808 | 5.4 | 95.39
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.04463 | 0.04473 | 0.04481 | 0.0 | 0.47
|
||||
Output | 0.00071317 | 0.00073223 | 0.0007793 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.3926 | | | 4.13
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10252 ave 10252 max 10252 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 648158 ave 648158 max 648158 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2592632
|
||||
Ave neighs/atom = 1296.316
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5
|
||||
|
||||
fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
|
||||
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 100 ${sname}.spe.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 1 all custom 100 Li.bohr.spe.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
|
||||
run 100
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.76 | 8.76 | 8.76 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
|
||||
100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
|
||||
110 -3085.709 -3086.35 0.64098668 3062.5195 22.168933 -6171.0384 0 1.9130428e+09 1.8610249e+09 270.41729
|
||||
120 -3084.995 -3086.3497 1.3546418 3064.69 22.151949 -6173.1916 0 2.3968054e+09 2.2869572e+09 571.49172
|
||||
130 -3084.2774 -3086.3449 2.0675114 3067.5683 22.125927 -6176.0391 0 2.9762332e+09 2.8088108e+09 872.23471
|
||||
140 -3083.5543 -3086.3327 2.7783319 3071.0091 22.090343 -6179.4321 0 3.6318905e+09 3.4073653e+09 1172.1133
|
||||
150 -3082.8209 -3086.3101 3.4891918 3074.9323 22.044189 -6183.2866 0 4.3538347e+09 4.0726292e+09 1472.0085
|
||||
160 -3082.0735 -3086.274 4.2005492 3079.2855 21.986186 -6187.5458 0 5.1353281e+09 4.7979569e+09 1772.1135
|
||||
170 -3081.3099 -3086.2215 4.911672 3084.0302 21.914874 -6192.1667 0 5.9710184e+09 5.5781934e+09 2072.1196
|
||||
180 -3080.5276 -3086.1495 5.6218934 3089.1358 21.828679 -6197.1139 0 6.8564778e+09 6.4091119e+09 2371.7454
|
||||
190 -3079.7237 -3086.0546 6.330928 3094.5768 21.725972 -6202.3574 0 7.787914e+09 7.2871001e+09 2670.8705
|
||||
200 -3078.895 -3085.9337 7.0387107 3100.3318 21.605131 -6207.8707 0 8.7619059e+09 8.2089091e+09 2969.4675
|
||||
Loop time of 5.34836 on 4 procs for 100 steps with 2000 atoms
|
||||
|
||||
Performance: 1615.450 fs/day, 0.015 hours/fs, 18.697 timesteps/s, 37.395 katom-step/s
|
||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.8621 | 5.065 | 5.2272 | 5.9 | 94.70
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.02486 | 0.025085 | 0.025316 | 0.1 | 0.47
|
||||
Output | 0.0016755 | 0.0018282 | 0.0019368 | 0.2 | 0.03
|
||||
Modify | 0.092978 | 0.25534 | 0.4584 | 26.2 | 4.77
|
||||
Other | | 0.00111 | | | 0.02
|
||||
|
||||
Nlocal: 500 ave 518 max 484 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 10252 ave 10268 max 10234 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 621113 ave 642857 max 604509 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2484453
|
||||
Ave neighs/atom = 1242.2265
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:15
|
||||
1165
examples/PACKAGES/eff/fixed-core/C2H6/log.01Feb25.C2H6fc.ang.g++.4
Normal file
1165
examples/PACKAGES/eff/fixed-core/C2H6/log.01Feb25.C2H6fc.ang.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,158 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# Created 2010-12-13
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index C2H6fc.bohr
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.C2H6fc.bohr
|
||||
Reading data file ...
|
||||
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
22 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 1000.0
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 10 ${sname}.min.xyz
|
||||
dump 1 all xyz 10 C2H6fc.bohr.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
dump 2 all custom 10 C2H6fc.bohr.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
dump 3 all custom 10 data.${sname}.restart id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all custom 10 data.C2H6fc.bohr.restart id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic
|
||||
minimize 0 1e-6 1000 2000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 6.129 | 6.129 | 6.129 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -67.202286 -67.202286 0 65.187662 2.0185521 -134.4085 0 0 15.150502 15.150502
|
||||
48 -67.202342 -67.202342 0 65.186464 2.0145106 -134.40332 0 0 -0.00017005462 -0.00017005462
|
||||
Loop time of 0.00261219 on 4 procs for 48 steps with 22 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-67.202286382145 -67.2023415752272 -67.2023415752273
|
||||
Force two-norm initial, final = 0.0096326869 5.0767445e-07
|
||||
Force max component initial, final = 0.0062811481 1.588169e-07
|
||||
Final line search alpha, max atom move = 1 1.588169e-07
|
||||
Iterations, force evaluations = 48 94
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00010749 | 0.00066682 | 0.0010722 | 0.0 | 25.53
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0005904 | 0.0010031 | 0.0015945 | 1.2 | 38.40
|
||||
Output | 0.00029404 | 0.00030533 | 0.0003226 | 0.0 | 11.69
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0006369 | | | 24.38
|
||||
|
||||
Nlocal: 5.5 ave 6 max 5 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 16.5 ave 17 max 16 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 57.75 ave 92 max 13 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 231
|
||||
Ave neighs/atom = 10.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
undump 3
|
||||
|
||||
fix 1 all nvt/eff temp 1 2000 1.0
|
||||
dump 2 all custom 10 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
dump 2 all custom 10 C2H6fc.bohr.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
|
||||
run 10000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.738 | 5.738 | 5.738 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
48 -67.202342 -67.202342 0 65.186464 2.0145106 -134.40332 0 0 -0.00017005463 -0.00017005463
|
||||
10048 -67.202342 -67.202342 1.2683664e-08 65.186455 2.0144921 -134.40329 0 0.00038144568 -0.070540027 -0.070540735
|
||||
Loop time of 0.194625 on 4 procs for 10000 steps with 22 atoms
|
||||
|
||||
Performance: 4439300.953 fs/day, 0.000 hours/fs, 51380.798 timesteps/s, 1.130 Matom-step/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0161 | 0.064789 | 0.10999 | 14.0 | 33.29
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.031236 | 0.07675 | 0.12576 | 13.2 | 39.43
|
||||
Output | 0.01923 | 0.021471 | 0.025663 | 1.7 | 11.03
|
||||
Modify | 0.011945 | 0.014438 | 0.017136 | 1.6 | 7.42
|
||||
Other | | 0.01718 | | | 8.83
|
||||
|
||||
Nlocal: 5.5 ave 7 max 4 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 16.5 ave 18 max 15 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 57.75 ave 98 max 16 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 231
|
||||
Ave neighs/atom = 10.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
40165
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.ang.g++.4
Normal file
40165
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.ang.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
4166
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.bohr.g++.4
Normal file
4166
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.bohr.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,100 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Created 2010-11-28
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index CH4fc.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.CH4fc.ang
|
||||
Reading data file ...
|
||||
orthogonal box = (-529.17725 -529.17725 -529.17725) to (529.17725 529.17725 529.17725)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
13 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 1000.0 limit/eradius pressure/evirials
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
timestep 0.0001
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
run 0
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 3 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 = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 4.387 | 4.387 | 4.387 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -17700.537 -17700.537 0 20676.282 6270.6707 -44647.489 0 0 0.21737096 0.21737096
|
||||
Loop time of 2.41775e-06 on 4 procs for 0 steps with 13 atoms
|
||||
|
||||
113.7% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.418e-06 | | |100.00
|
||||
|
||||
Nlocal: 3.25 ave 4 max 3 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 152.75 ave 153 max 152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 19.5 ave 33 max 6 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 78
|
||||
Ave neighs/atom = 6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,99 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Created 2010-11-28
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index CH4fc.bohr
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.CH4fc.bohr
|
||||
Reading data file ...
|
||||
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
13 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 1000.0 limit/eradius pressure/evirials
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
run 0
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 3 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 = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/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) = 4.388 | 4.388 | 4.388 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -28.207572 -28.207572 0 32.949786 9.9929585 -71.150317 0 0 22025.158 22025.158
|
||||
Loop time of 2.353e-06 on 4 procs for 0 steps with 13 atoms
|
||||
|
||||
53.1% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.353e-06 | | |100.00
|
||||
|
||||
Nlocal: 3.25 ave 4 max 3 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 152.75 ave 153 max 152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 19.5 ave 31 max 10 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 78
|
||||
Ave neighs/atom = 6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -32,7 +32,7 @@ fix 1 all nvt temp 0.7 0.7 0.2
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 2 all recenter NULL NULL 15 units lattice
|
||||
compute p1 all stress/cartesian z 0.5
|
||||
compute p1 all stress/cartesian z 0.5 NULL 0
|
||||
fix 3 all ave/time 100 1 100 c_p1[*] file flat.out mode vector
|
||||
|
||||
thermo 50
|
||||
|
||||
149
examples/granular/in.tableting.200
Normal file
149
examples/granular/in.tableting.200
Normal file
@ -0,0 +1,149 @@
|
||||
##################################### SIMULATION SETTINGS ###################################################
|
||||
|
||||
atom_style sphere 1
|
||||
atom_modify map array
|
||||
comm_modify vel yes
|
||||
units si
|
||||
newton off
|
||||
neighbor 1.0e-3 bin
|
||||
neigh_modify every 10 delay 60 check no
|
||||
timestep 4e-6
|
||||
#processors 2 2 1
|
||||
|
||||
############################## SIMULATION BOUNDING BOX AND INSERT PARTICLES #################################
|
||||
|
||||
boundary f f f
|
||||
read_data spheres200.data
|
||||
|
||||
#################################### ADD DIE AND ATOM PARAMETERIZATION ######################################
|
||||
|
||||
variable atomRadius equal 0.44e-3*1.25
|
||||
variable atomDiameter equal 2*${atomRadius}
|
||||
variable atomDensity equal 1560
|
||||
variable atomMassAvg equal ${atomDensity}*4.0/3.0*PI*${atomRadius}^3.0
|
||||
variable dieRadius equal 4e-3
|
||||
variable dieHeight equal 1e-2
|
||||
|
||||
############################## PARTICLE MATERIAL PROPERTIES AND FORCE MODEL ##################################
|
||||
|
||||
pair_style granular
|
||||
|
||||
# mdr = E, nu, Y, gamma, psi_b, CoR
|
||||
variable YoungsModulus equal 5e6
|
||||
variable YieldStress equal 1.9e5
|
||||
variable PoissonsRatio equal 0.4
|
||||
variable SurfaceEnergy equal 2
|
||||
variable SurfaceEnergyWall equal 0.0
|
||||
variable CoR equal 0.5
|
||||
variable psi_b equal 0.5
|
||||
|
||||
# linear_history = k_t, x_gammat, mu_s
|
||||
variable kt equal 2/7*${YoungsModulus}*${atomRadius}
|
||||
variable kt_wall equal 2/7*${YoungsModulus}*${atomRadius}
|
||||
variable xgammat equal 0.0
|
||||
variable mu_s equal 0.7
|
||||
variable mu_s_wall equal 0.1
|
||||
|
||||
# sds = mu_roll, k_roll, gamma_roll
|
||||
variable mu_roll equal 0.6
|
||||
variable k_roll equal 2.25*${mu_roll}*${mu_roll}*${YoungsModulus}*${atomRadius}
|
||||
variable gamma_roll equal 0.0
|
||||
|
||||
pair_coeff * * mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${CoR} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll} damping none
|
||||
|
||||
######################################### ADD DIE AND PUNCH WALLS ############################################
|
||||
|
||||
variable disp_upper equal 0.0
|
||||
variable disp_lower equal 0.0
|
||||
|
||||
variable wall_contact_string string "granular mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergyWall} ${psi_b} ${CoR} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll} damping none"
|
||||
|
||||
variable dieHeight2 equal 2*${dieHeight}
|
||||
|
||||
region lowerPunch plane 0 0 0 0 0 1 side in units box move NULL NULL v_disp_lower units box
|
||||
region upperPunch plane 0 0 ${dieHeight} 0 0 -1 side in move NULL NULL v_disp_upper units box
|
||||
region die cylinder z 0 0 ${dieRadius} 0 ${dieHeight2} side in units box
|
||||
|
||||
fix lowerPunch all wall/gran/region ${wall_contact_string} region lowerPunch contacts
|
||||
fix upperPunch all wall/gran/region ${wall_contact_string} region upperPunch contacts
|
||||
fix die all wall/gran/region ${wall_contact_string} region die contacts
|
||||
|
||||
compute avgUpperPunchForce all reduce sum f_upperPunch[4]
|
||||
variable avgUpperPunchForce equal c_avgUpperPunchForce
|
||||
compute avgLowerPunchForce all reduce sum f_lowerPunch[4]
|
||||
variable avgLowerPunchForce equal c_avgLowerPunchForce
|
||||
|
||||
fix printFD all print 1 "${disp_upper} ${avgUpperPunchForce} ${avgLowerPunchForce}" file punch_force_disp_tableting200.csv screen no
|
||||
|
||||
##################################### INTEGRATION AND GRAVITY #################################################
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix grav all gravity 9.81 vector 0 0 -1
|
||||
|
||||
########################################### SCREEN OUTPUT ####################################################
|
||||
|
||||
compute 1 all erotate/sphere
|
||||
thermo_style custom dt step atoms ke vol v_disp_upper
|
||||
thermo 100
|
||||
thermo_modify lost ignore norm no
|
||||
|
||||
##################################### SET UP DUMP OUTPUTS ####################################################
|
||||
|
||||
compute ke all ke/atom
|
||||
variable output_rate equal round(1e-3/dt)
|
||||
|
||||
run 0
|
||||
|
||||
compute sigmaxx all property/atom d_sigmaxx
|
||||
compute sigmayy all property/atom d_sigmayy
|
||||
compute sigmazz all property/atom d_sigmazz
|
||||
compute Velas all property/atom d_Velas
|
||||
|
||||
compute sigmaxx_ave all reduce ave c_sigmaxx
|
||||
compute sigmayy_ave all reduce ave c_sigmayy
|
||||
compute sigmazz_ave all reduce ave c_sigmazz
|
||||
compute Velas_sum all reduce sum c_Velas
|
||||
|
||||
variable sxx_ave equal c_sigmaxx_ave
|
||||
variable syy_ave equal c_sigmayy_ave
|
||||
variable szz_ave equal c_sigmazz_ave
|
||||
variable Vparticles equal c_Velas_sum
|
||||
|
||||
fix log all print 1 "${sxx_ave} ${syy_ave} ${szz_ave} ${Vparticles}" file average_normal_stresses_tableting200.csv screen no
|
||||
dump dumpParticles all custom ${output_rate} tableting200.dump id type mass diameter x y z vx vy vz fx fy fz c_ke c_sigmaxx c_sigmayy c_sigmazz
|
||||
#dump dumpParticlesVTK all vtk ${output_rate} post/particles_*.vtk id x y z fx fy fz vx vy vz c_ke radius c_sigmaxx c_sigmayy c_sigmazz
|
||||
|
||||
############################################## RUN SIMULATION #################################################
|
||||
|
||||
variable upper_punch_stroke equal 0.6733*${dieHeight}
|
||||
variable vel_upper equal 0.25
|
||||
|
||||
variable settling_steps equal round(0.02/dt)
|
||||
variable compression_steps equal 2*round(${upper_punch_stroke}/${vel_upper}/dt)
|
||||
variable ejection_steps equal ${compression_steps}
|
||||
variable free_float_steps equal round(0.02/dt)
|
||||
|
||||
##### SETTLING #####
|
||||
|
||||
run ${settling_steps}
|
||||
|
||||
##### Compression & Release #####
|
||||
|
||||
variable punch_frequency equal PI/2/(dt*${compression_steps}/2)
|
||||
variable disp_upper equal -${upper_punch_stroke}*sin(${punch_frequency}*elapsed*dt)
|
||||
variable short_release equal round(${compression_steps}*1.0)
|
||||
run ${short_release}
|
||||
|
||||
##### EJECTION #####
|
||||
|
||||
variable punch_frequency equal PI/2/(dt*${ejection_steps})
|
||||
variable disp_lower equal ${dieHeight}*sin(${punch_frequency}*elapsed*dt)
|
||||
variable disp_upper equal 0.9*v_disp_lower
|
||||
run ${ejection_steps}
|
||||
|
||||
##### FREE FLOAT #####
|
||||
|
||||
variable disp_lower equal ${dieHeight}
|
||||
variable disp_upper equal ${dieHeight}*0.9
|
||||
variable max_disp equal ${dieRadius}*0.75
|
||||
run ${free_float_steps}
|
||||
109
examples/granular/in.triaxial.compaction.12
Normal file
109
examples/granular/in.triaxial.compaction.12
Normal file
@ -0,0 +1,109 @@
|
||||
############################### SIMULATION SETTINGS ###################################################
|
||||
|
||||
atom_style sphere 1
|
||||
atom_modify map array
|
||||
comm_modify vel yes
|
||||
units si
|
||||
newton off
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 0
|
||||
timestep 1e-6
|
||||
|
||||
##################### SIMULATION BOUNDING BOX, INSERT PARTICLES, AND INTEGRATION #######################
|
||||
|
||||
boundary f f f
|
||||
read_data spheres12.data
|
||||
fix integr all nve/sphere
|
||||
|
||||
# create pair group for contact area outputs
|
||||
group particles_1_12 id 1 12
|
||||
|
||||
########################### PARTICLE MATERIAL PROPERTIES AND FORCE MODEL ###############################
|
||||
|
||||
variable atomRadius equal 0.5
|
||||
|
||||
pair_style granular
|
||||
|
||||
# mdr = E, nu, Y, gamma, psi_b, CoR
|
||||
variable YoungsModulus equal 1e9
|
||||
variable PoissonsRatio equal 0.3
|
||||
variable YieldStress equal 50e6
|
||||
variable SurfaceEnergy equal 0.0
|
||||
variable psi_b equal 0.5
|
||||
variable CoR equal 0.5
|
||||
|
||||
# linear_history = k_t, x_gamma,t, mu_s
|
||||
variable kt equal 2/7*${YoungsModulus}*${atomRadius}
|
||||
variable xgammat equal 0.0
|
||||
variable mu_s equal 0.5
|
||||
|
||||
pair_coeff * * mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${CoR} tangential linear_history ${kt} ${xgammat} ${mu_s} damping none
|
||||
|
||||
######################################### ADD IN PLANES ################################################
|
||||
|
||||
variable boxWidth equal 3
|
||||
variable halfBoxWidth equal ${boxWidth}/2
|
||||
|
||||
variable plane_disp equal 0.0
|
||||
variable plane_disp_neg equal 0.0
|
||||
|
||||
region plane_yz_pos plane ${halfBoxWidth} 0 0 -1 0 0 side in move v_plane_disp_neg NULL NULL units box
|
||||
region plane_yz_neg plane -${halfBoxWidth} 0 0 1 0 0 side in move v_plane_disp NULL NULL units box
|
||||
region plane_xz_pos plane 0 ${halfBoxWidth} 0 0 -1 0 side in move NULL v_plane_disp_neg NULL units box
|
||||
region plane_xz_neg plane 0 -${halfBoxWidth} 0 0 1 0 side in move NULL v_plane_disp NULL units box
|
||||
region plane_xy_pos plane 0 0 ${halfBoxWidth} 0 0 -1 side in move NULL NULL v_plane_disp_neg units box
|
||||
region plane_xy_neg plane 0 0 -${halfBoxWidth} 0 0 1 side in move NULL NULL v_plane_disp units box
|
||||
|
||||
variable wall_contact_string string "granular mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${CoR} tangential linear_history ${kt} ${xgammat} ${mu_s} damping none"
|
||||
|
||||
fix plane_yz_pos all wall/gran/region ${wall_contact_string} region plane_yz_pos contacts
|
||||
fix plane_yz_neg all wall/gran/region ${wall_contact_string} region plane_yz_neg contacts
|
||||
fix plane_xz_pos all wall/gran/region ${wall_contact_string} region plane_xz_pos contacts
|
||||
fix plane_xz_neg all wall/gran/region ${wall_contact_string} region plane_xz_neg contacts
|
||||
fix plane_xy_pos all wall/gran/region ${wall_contact_string} region plane_xy_pos contacts
|
||||
fix plane_xy_neg all wall/gran/region ${wall_contact_string} region plane_xy_neg contacts
|
||||
|
||||
compute plane_xy_neg_force all reduce sum f_plane_xy_neg[4]
|
||||
variable plane_xy_neg_force equal c_plane_xy_neg_force
|
||||
|
||||
compute plane_xz_neg_force all reduce sum f_plane_xz_neg[3]
|
||||
variable plane_xz_neg_force equal c_plane_xz_neg_force
|
||||
|
||||
compute plane_yz_neg_force all reduce sum f_plane_yz_neg[2]
|
||||
variable plane_yz_neg_force equal c_plane_yz_neg_force
|
||||
|
||||
fix print1 all print 1 "${plane_disp} ${plane_xy_neg_force} ${plane_xz_neg_force} ${plane_yz_neg_force}" file force_disp_triaxial12.csv screen no
|
||||
|
||||
######################################## SCREEN OUTPUT ####################################################
|
||||
|
||||
compute 1 all erotate/sphere
|
||||
thermo_style custom dt step atoms ke c_1 vol
|
||||
thermo 100
|
||||
thermo_modify lost ignore norm no
|
||||
|
||||
##################################### DEFINE WALL MOVEMENT #################################################
|
||||
|
||||
variable disp_max equal 0.499
|
||||
variable ddisp equal 0.00001
|
||||
variable compression_steps equal round(${disp_max}/${ddisp})
|
||||
variable output_rate equal round(${compression_steps}/100)
|
||||
|
||||
##################################### SET UP DUMP OUTPUTS ####################################################
|
||||
|
||||
dump dumpParticles all custom ${output_rate} triaxial_compaction_12.dump id type mass x y z vx vy vz fx fy fz radius
|
||||
#dump dmp all vtk ${output_rate} post/triaxial12particles_*.vtk id type mass x y z vx vy vz fx fy fz radius
|
||||
|
||||
#################################### COMPRESS THE PARTICLES ##################################################
|
||||
|
||||
run 0
|
||||
|
||||
# print out contact area evolution for particles 1 and 12
|
||||
compute Ac_1_12 particles_1_12 pair/local p13 cutoff radius
|
||||
compute Ac_1_12_sum particles_1_12 reduce sum c_Ac_1_12 inputs local
|
||||
variable Ac_1_12 equal c_Ac_1_12_sum
|
||||
fix logArea all print 100 "${plane_disp} ${Ac_1_12}" file pair_1_12_contact_area_triaxial12.csv screen no
|
||||
|
||||
variable plane_disp equal ${ddisp}*elapsed
|
||||
variable plane_disp_neg equal -${ddisp}*elapsed
|
||||
|
||||
run ${compression_steps}
|
||||
23
examples/granular/spheres12.data
Normal file
23
examples/granular/spheres12.data
Normal file
@ -0,0 +1,23 @@
|
||||
#LAMMPS data file created by matlab.
|
||||
12 atoms
|
||||
|
||||
1 atom types
|
||||
|
||||
-10.0000000000 10.0000000000 xlo xhi
|
||||
-10.0000000000 10.0000000000 ylo yhi
|
||||
-10.0000000000 10.0000000000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.8000000000 1000.0000000000 0.0717535226 -0.2092222842 0.3662146798
|
||||
2 1 1.2000000000 1000.0000000000 -0.8233763986 -0.7426114800 -0.8263932264
|
||||
3 1 0.8000000000 1000.0000000000 -1.0685863278 -0.4494609702 0.2196698078
|
||||
4 1 0.8000000000 1000.0000000000 0.5829432471 -1.0098803839 -0.7607543861
|
||||
5 1 0.8000000000 1000.0000000000 -0.8658471132 0.6951192569 0.0107556658
|
||||
6 1 1.2000000000 1000.0000000000 0.3966456126 0.7215053869 -0.7540113087
|
||||
7 1 1.2000000000 1000.0000000000 0.7316242921 0.8996483982 0.6751483031
|
||||
8 1 1.0000000000 1000.0000000000 0.6267527768 -0.8419367233 0.6964197101
|
||||
9 1 0.8000000000 1000.0000000000 -0.0409043189 -0.1452314035 -1.0102948313
|
||||
10 1 0.8000000000 1000.0000000000 -0.9495107709 0.6760151650 -0.9220534482
|
||||
11 1 1.0000000000 1000.0000000000 -0.7488486472 0.2188003421 0.7892021020
|
||||
12 1 1.2000000000 1000.0000000000 0.8968590780 -0.2350366437 -0.2006719701
|
||||
211
examples/granular/spheres200.data
Normal file
211
examples/granular/spheres200.data
Normal file
@ -0,0 +1,211 @@
|
||||
#LAMMPS data file created by matlab.
|
||||
200 atoms
|
||||
|
||||
1 atom types
|
||||
|
||||
-0.005000 0.005000 xlo xhi
|
||||
-0.005000 0.005000 ylo yhi
|
||||
-0.001000 0.020000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.001206 1560.000000 -0.000938 0.000556 0.000883
|
||||
2 1 0.000953 1560.000000 -0.002626 -0.000145 0.002778
|
||||
3 1 0.001035 1560.000000 -0.000434 0.000172 0.008458
|
||||
4 1 0.001225 1560.000000 -0.003126 -0.000604 0.004986
|
||||
5 1 0.001119 1560.000000 0.000772 0.002972 0.002568
|
||||
6 1 0.001243 1560.000000 -0.000363 0.001184 0.004927
|
||||
7 1 0.001173 1560.000000 0.000218 0.000243 0.005475
|
||||
8 1 0.000937 1560.000000 0.000033 0.000029 0.003141
|
||||
9 1 0.001055 1560.000000 -0.001660 0.001975 0.008611
|
||||
10 1 0.000938 1560.000000 -0.001818 0.002352 0.002534
|
||||
11 1 0.000990 1560.000000 0.001592 0.000435 0.004416
|
||||
12 1 0.000927 1560.000000 -0.001659 -0.000004 0.005901
|
||||
13 1 0.001272 1560.000000 0.002972 0.000553 0.007291
|
||||
14 1 0.001226 1560.000000 0.002090 0.000983 0.001406
|
||||
15 1 0.000957 1560.000000 0.002241 -0.001608 0.001304
|
||||
16 1 0.001020 1560.000000 -0.001944 0.001290 0.002030
|
||||
17 1 0.001289 1560.000000 -0.002256 -0.001173 0.003474
|
||||
18 1 0.000998 1560.000000 0.000771 0.002127 0.000906
|
||||
19 1 0.000927 1560.000000 0.000186 0.000567 0.001207
|
||||
20 1 0.001095 1560.000000 -0.000937 -0.003179 0.008173
|
||||
21 1 0.001006 1560.000000 -0.001736 0.000751 0.004618
|
||||
22 1 0.001037 1560.000000 0.000784 0.001844 0.002380
|
||||
23 1 0.001297 1560.000000 0.000234 -0.001597 0.008560
|
||||
24 1 0.001017 1560.000000 0.002454 -0.000505 0.001171
|
||||
25 1 0.001110 1560.000000 -0.000803 -0.000415 0.003714
|
||||
26 1 0.001192 1560.000000 0.002283 0.000648 0.003048
|
||||
27 1 0.000992 1560.000000 -0.000065 -0.000545 0.007062
|
||||
28 1 0.001116 1560.000000 0.002174 -0.001463 0.005830
|
||||
29 1 0.001258 1560.000000 0.001602 0.001853 0.007246
|
||||
30 1 0.001055 1560.000000 -0.001535 -0.002770 0.007196
|
||||
31 1 0.000958 1560.000000 -0.000438 -0.000260 0.004709
|
||||
32 1 0.001188 1560.000000 0.000339 -0.000355 0.009171
|
||||
33 1 0.001166 1560.000000 0.002513 -0.001215 0.004434
|
||||
34 1 0.000907 1560.000000 0.001905 -0.000373 0.004921
|
||||
35 1 0.001245 1560.000000 -0.000091 -0.002620 0.004150
|
||||
36 1 0.001302 1560.000000 0.003292 0.000184 0.005377
|
||||
37 1 0.001305 1560.000000 0.002099 0.001261 0.008939
|
||||
38 1 0.000988 1560.000000 0.003274 0.000136 0.003667
|
||||
39 1 0.000892 1560.000000 0.001798 -0.002104 0.008610
|
||||
40 1 0.001247 1560.000000 -0.003058 -0.000575 0.000948
|
||||
41 1 0.000900 1560.000000 -0.000258 -0.000469 0.001478
|
||||
42 1 0.000945 1560.000000 -0.001434 -0.001711 0.004610
|
||||
43 1 0.000977 1560.000000 -0.001410 0.002808 0.004963
|
||||
44 1 0.000930 1560.000000 -0.002110 -0.001362 0.006749
|
||||
45 1 0.000931 1560.000000 0.001256 -0.000876 0.000844
|
||||
46 1 0.000901 1560.000000 0.000899 -0.001189 0.005316
|
||||
47 1 0.000940 1560.000000 -0.002189 -0.000047 0.007240
|
||||
48 1 0.001217 1560.000000 -0.000108 -0.001333 0.002257
|
||||
49 1 0.001088 1560.000000 0.001364 -0.000594 0.002789
|
||||
50 1 0.001143 1560.000000 -0.000311 -0.001425 0.006092
|
||||
51 1 0.001054 1560.000000 0.002262 0.002312 0.004315
|
||||
52 1 0.001016 1560.000000 -0.000724 0.000741 0.003295
|
||||
53 1 0.001051 1560.000000 0.000527 -0.001987 0.003307
|
||||
54 1 0.000905 1560.000000 0.000827 0.001457 0.005868
|
||||
55 1 0.001195 1560.000000 -0.001176 -0.000645 0.000798
|
||||
56 1 0.001253 1560.000000 0.002583 -0.001847 0.003310
|
||||
57 1 0.000982 1560.000000 0.001551 -0.002803 0.005076
|
||||
58 1 0.000945 1560.000000 -0.000481 0.000354 0.007220
|
||||
59 1 0.001040 1560.000000 -0.002736 0.001076 0.008769
|
||||
60 1 0.000917 1560.000000 0.000826 -0.001887 0.006449
|
||||
61 1 0.000914 1560.000000 -0.001171 -0.001592 0.007266
|
||||
62 1 0.000959 1560.000000 0.000834 -0.002671 0.007105
|
||||
63 1 0.000990 1560.000000 -0.000251 -0.001327 0.004339
|
||||
64 1 0.001220 1560.000000 0.001384 0.002896 0.005874
|
||||
65 1 0.000949 1560.000000 -0.001340 -0.000608 0.007496
|
||||
66 1 0.001306 1560.000000 0.002187 0.002068 0.002629
|
||||
67 1 0.001206 1560.000000 0.000148 0.001506 0.008517
|
||||
68 1 0.001123 1560.000000 0.001288 -0.000303 0.006613
|
||||
69 1 0.001151 1560.000000 -0.000876 0.001549 0.001740
|
||||
70 1 0.001315 1560.000000 -0.001902 -0.002590 0.001344
|
||||
71 1 0.000927 1560.000000 0.002285 -0.000866 0.006900
|
||||
72 1 0.001279 1560.000000 -0.000165 0.002689 0.007449
|
||||
73 1 0.000910 1560.000000 0.001009 0.001054 0.005049
|
||||
74 1 0.001148 1560.000000 -0.002229 -0.001285 0.008736
|
||||
75 1 0.001067 1560.000000 -0.000261 -0.002945 0.002157
|
||||
76 1 0.000993 1560.000000 -0.001641 0.002272 0.007601
|
||||
77 1 0.001228 1560.000000 0.001939 -0.000214 0.008903
|
||||
78 1 0.001076 1560.000000 0.000767 0.001172 0.003556
|
||||
79 1 0.001105 1560.000000 -0.000561 0.002493 0.004214
|
||||
80 1 0.001195 1560.000000 0.002694 -0.000817 0.007949
|
||||
81 1 0.001239 1560.000000 -0.000968 -0.003145 0.006096
|
||||
82 1 0.001083 1560.000000 -0.000808 0.001813 0.006396
|
||||
83 1 0.000923 1560.000000 0.000632 -0.001437 0.001310
|
||||
84 1 0.000981 1560.000000 -0.001842 0.002774 0.006508
|
||||
85 1 0.000998 1560.000000 -0.002775 0.001616 0.001453
|
||||
86 1 0.000979 1560.000000 -0.002520 0.001715 0.007741
|
||||
87 1 0.001002 1560.000000 -0.001465 -0.001931 0.006048
|
||||
88 1 0.000958 1560.000000 0.003264 0.000707 0.001189
|
||||
89 1 0.001052 1560.000000 -0.001314 -0.000701 0.002721
|
||||
90 1 0.001096 1560.000000 0.001154 0.002129 0.004403
|
||||
91 1 0.001104 1560.000000 0.002118 0.001977 0.000794
|
||||
92 1 0.001263 1560.000000 -0.001499 -0.002764 0.003441
|
||||
93 1 0.001086 1560.000000 -0.001096 0.002514 0.001154
|
||||
94 1 0.000895 1560.000000 0.001130 0.000029 0.001045
|
||||
95 1 0.000964 1560.000000 0.000905 -0.003200 0.000542
|
||||
96 1 0.000898 1560.000000 -0.000868 0.003148 0.008306
|
||||
97 1 0.000907 1560.000000 -0.001406 0.001144 0.007862
|
||||
98 1 0.001176 1560.000000 0.001246 -0.001074 0.004327
|
||||
99 1 0.001148 1560.000000 0.001512 -0.002739 0.003346
|
||||
100 1 0.000922 1560.000000 0.001470 -0.000036 0.007695
|
||||
101 1 0.001031 1560.000000 -0.002751 0.000928 0.004124
|
||||
102 1 0.001030 1560.000000 -0.000177 -0.002370 0.005374
|
||||
103 1 0.000915 1560.000000 0.000824 0.000521 0.007070
|
||||
104 1 0.001085 1560.000000 -0.002281 -0.000023 0.009123
|
||||
105 1 0.001004 1560.000000 -0.000167 0.002610 0.008905
|
||||
106 1 0.001060 1560.000000 -0.000389 -0.002220 0.007688
|
||||
107 1 0.000920 1560.000000 -0.000483 0.003231 0.006505
|
||||
108 1 0.001122 1560.000000 0.001781 -0.001547 0.002237
|
||||
109 1 0.001172 1560.000000 -0.002650 0.000830 0.005429
|
||||
110 1 0.001137 1560.000000 -0.000030 -0.003246 0.001024
|
||||
111 1 0.001315 1560.000000 0.001470 -0.001735 0.007580
|
||||
112 1 0.001245 1560.000000 0.000481 -0.003067 0.006025
|
||||
113 1 0.000904 1560.000000 0.000632 -0.000184 0.002010
|
||||
114 1 0.000883 1560.000000 -0.001828 0.002191 0.003819
|
||||
115 1 0.000974 1560.000000 0.002167 0.001616 0.006226
|
||||
116 1 0.001150 1560.000000 0.000871 -0.002731 0.002136
|
||||
117 1 0.001312 1560.000000 -0.000326 -0.001971 0.001000
|
||||
118 1 0.000914 1560.000000 0.001020 0.000810 0.002086
|
||||
119 1 0.001136 1560.000000 -0.000101 -0.003277 0.007246
|
||||
120 1 0.000991 1560.000000 -0.001944 0.000576 0.003215
|
||||
121 1 0.001216 1560.000000 -0.000913 -0.001165 0.008857
|
||||
122 1 0.001045 1560.000000 -0.003110 0.001062 0.002973
|
||||
123 1 0.000918 1560.000000 0.000348 0.000365 0.004046
|
||||
124 1 0.001279 1560.000000 -0.000884 0.003087 0.002268
|
||||
125 1 0.001065 1560.000000 -0.002238 0.001309 0.006452
|
||||
126 1 0.001012 1560.000000 -0.002059 -0.001354 0.001935
|
||||
127 1 0.001142 1560.000000 -0.003011 0.000567 0.001739
|
||||
128 1 0.000921 1560.000000 0.001764 0.002804 0.008177
|
||||
129 1 0.001151 1560.000000 -0.003105 -0.000384 0.006602
|
||||
130 1 0.000967 1560.000000 0.000932 0.000588 0.008823
|
||||
131 1 0.000908 1560.000000 -0.001873 -0.001947 0.007825
|
||||
132 1 0.000923 1560.000000 -0.002993 0.000883 0.007425
|
||||
133 1 0.001171 1560.000000 0.003310 -0.000405 0.006558
|
||||
134 1 0.000977 1560.000000 -0.000098 -0.000180 0.000492
|
||||
135 1 0.000938 1560.000000 -0.000706 -0.000129 0.006085
|
||||
136 1 0.001008 1560.000000 -0.000256 0.002333 0.000550
|
||||
137 1 0.001073 1560.000000 0.000534 -0.000055 0.008080
|
||||
138 1 0.000890 1560.000000 0.000351 0.001695 0.007195
|
||||
139 1 0.000973 1560.000000 0.002593 0.001907 0.005394
|
||||
140 1 0.001176 1560.000000 -0.001862 -0.000534 0.004494
|
||||
141 1 0.001306 1560.000000 -0.000951 0.001053 0.009299
|
||||
142 1 0.001103 1560.000000 -0.001937 -0.002711 0.008485
|
||||
143 1 0.001262 1560.000000 -0.002947 -0.001470 0.007682
|
||||
144 1 0.000914 1560.000000 0.002047 0.000811 0.005504
|
||||
145 1 0.000954 1560.000000 0.001935 -0.002349 0.006632
|
||||
146 1 0.001003 1560.000000 0.000766 -0.002635 0.008483
|
||||
147 1 0.001137 1560.000000 0.000102 0.003195 0.004922
|
||||
148 1 0.001006 1560.000000 -0.001982 0.001014 0.000685
|
||||
149 1 0.001255 1560.000000 -0.000718 0.001939 0.003056
|
||||
150 1 0.001057 1560.000000 -0.001189 -0.001717 0.003045
|
||||
151 1 0.001228 1560.000000 0.001581 0.002926 0.003510
|
||||
152 1 0.001052 1560.000000 -0.002172 0.001949 0.004831
|
||||
153 1 0.000979 1560.000000 -0.001817 0.000291 0.002048
|
||||
154 1 0.001286 1560.000000 -0.002647 -0.001839 0.004620
|
||||
155 1 0.001085 1560.000000 -0.000081 0.000850 0.002139
|
||||
156 1 0.000990 1560.000000 -0.000081 0.002105 0.005587
|
||||
157 1 0.001043 1560.000000 0.001636 -0.000112 0.001860
|
||||
158 1 0.001309 1560.000000 0.003216 -0.000851 0.002791
|
||||
159 1 0.000913 1560.000000 0.000608 0.003148 0.006565
|
||||
160 1 0.000919 1560.000000 0.000536 -0.003106 0.003249
|
||||
161 1 0.000943 1560.000000 0.003145 -0.000528 0.008915
|
||||
162 1 0.000993 1560.000000 -0.002811 -0.000099 0.008110
|
||||
163 1 0.001125 1560.000000 0.001415 -0.002271 0.000643
|
||||
164 1 0.000919 1560.000000 -0.001406 0.000223 0.006781
|
||||
165 1 0.001040 1560.000000 0.000690 0.003193 0.008329
|
||||
166 1 0.001055 1560.000000 0.001075 0.002584 0.009093
|
||||
167 1 0.001176 1560.000000 0.000851 0.003176 0.000591
|
||||
168 1 0.001003 1560.000000 -0.001462 0.001511 0.005544
|
||||
169 1 0.001126 1560.000000 -0.000077 0.003324 0.001347
|
||||
170 1 0.001068 1560.000000 0.003110 0.000810 0.008495
|
||||
171 1 0.001011 1560.000000 -0.001661 0.000117 0.008201
|
||||
172 1 0.001066 1560.000000 -0.000359 -0.003279 0.009094
|
||||
173 1 0.001303 1560.000000 0.003066 0.001188 0.004082
|
||||
174 1 0.000983 1560.000000 0.000354 0.002261 0.003558
|
||||
175 1 0.001137 1560.000000 0.002860 -0.001571 0.009180
|
||||
176 1 0.001070 1560.000000 0.001246 -0.001279 0.009104
|
||||
177 1 0.000886 1560.000000 0.002271 -0.000316 0.003675
|
||||
178 1 0.000983 1560.000000 -0.001987 -0.002490 0.005377
|
||||
179 1 0.000939 1560.000000 0.000601 -0.000861 0.003477
|
||||
180 1 0.001177 1560.000000 0.001522 0.002902 0.001690
|
||||
181 1 0.001036 1560.000000 -0.001200 -0.002874 0.004750
|
||||
182 1 0.000898 1560.000000 -0.001705 -0.001140 0.005503
|
||||
183 1 0.001315 1560.000000 0.002732 0.001766 0.007885
|
||||
184 1 0.001318 1560.000000 -0.002909 -0.001610 0.005936
|
||||
185 1 0.001218 1560.000000 0.003213 0.000884 0.002316
|
||||
186 1 0.001234 1560.000000 -0.002394 -0.002298 0.002575
|
||||
187 1 0.001160 1560.000000 -0.003313 -0.000065 0.003625
|
||||
188 1 0.001022 1560.000000 -0.003096 -0.001048 0.002151
|
||||
189 1 0.000966 1560.000000 0.001891 -0.002093 0.004404
|
||||
190 1 0.001048 1560.000000 -0.002367 0.002338 0.000697
|
||||
191 1 0.000995 1560.000000 -0.001204 -0.001912 0.002030
|
||||
192 1 0.001136 1560.000000 -0.001152 -0.002402 0.009223
|
||||
193 1 0.001083 1560.000000 -0.002588 -0.001768 0.000753
|
||||
194 1 0.000946 1560.000000 -0.001338 -0.000741 0.006527
|
||||
195 1 0.000943 1560.000000 -0.000073 0.003254 0.003663
|
||||
196 1 0.001059 1560.000000 0.000087 0.000958 0.006388
|
||||
197 1 0.001131 1560.000000 0.001030 0.001019 0.000752
|
||||
198 1 0.001257 1560.000000 -0.001365 0.002946 0.009266
|
||||
199 1 0.000891 1560.000000 -0.000445 -0.000273 0.002382
|
||||
200 1 0.001055 1560.000000 0.001781 0.000748 0.006583
|
||||
@ -1,30 +1,30 @@
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
read_data data.meam
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
#dump 2 all image 10 image.*.jpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
#dump 3 all movie 10 movie.mpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
run 100
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
# Big colloid particles and small LJ particles
|
||||
# Binary granular system
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
@ -13,7 +12,7 @@ Reading data file ...
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
@ -70,7 +69,7 @@ Neighbor list info ...
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
@ -111,20 +110,20 @@ Per MPI rank memory allocation (min/avg/max) = 16.3 | 16.3 | 16.3 Mbytes
|
||||
2800 481.73908 -10082.193 0 -9932.852 -27.838881
|
||||
2900 487.56555 -10082.752 0 -9931.6045 1772.2131
|
||||
3000 510.30601 -10091.368 0 -9933.1706 1273.0501
|
||||
Loop time of 5.35022 on 1 procs for 3000 steps with 105 atoms
|
||||
Loop time of 3.73297 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 12.112 ns/day, 1.982 hours/ns, 560.725 timesteps/s, 58.876 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 17.359 ns/day, 1.383 hours/ns, 803.649 timesteps/s, 84.383 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 | 4.7927 | 4.7927 | 4.7927 | 0.0 | 89.58
|
||||
Neigh | 0.15169 | 0.15169 | 0.15169 | 0.0 | 2.84
|
||||
Comm | 0.011036 | 0.011036 | 0.011036 | 0.0 | 0.21
|
||||
Output | 0.00080628 | 0.00080628 | 0.00080628 | 0.0 | 0.02
|
||||
Modify | 0.3906 | 0.3906 | 0.3906 | 0.0 | 7.30
|
||||
Other | | 0.003436 | | | 0.06
|
||||
Pair | 3.323 | 3.323 | 3.323 | 0.0 | 89.02
|
||||
Neigh | 0.098934 | 0.098934 | 0.098934 | 0.0 | 2.65
|
||||
Comm | 0.0060071 | 0.0060071 | 0.0060071 | 0.0 | 0.16
|
||||
Output | 0.00048946 | 0.00048946 | 0.00048946 | 0.0 | 0.01
|
||||
Modify | 0.30295 | 0.30295 | 0.30295 | 0.0 | 8.12
|
||||
Other | | 0.001559 | | | 0.04
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -137,4 +136,4 @@ Total # of neighbors = 3065
|
||||
Ave neighs/atom = 29.190476
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:05
|
||||
Total wall time: 0:00:03
|
||||
139
examples/reaxff/RDX/log.1Feb25.RDX.g++.4
Normal file
139
examples/reaxff/RDX/log.1Feb25.RDX.g++.4
Normal file
@ -0,0 +1,139 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.78 | 11.56 | 12.26 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10197.932 0 -10197.932 38.347492
|
||||
100 47.478568 -10176.425 0 -10161.706 633.00869
|
||||
200 166.95267 -10181.513 0 -10129.757 -27.201454
|
||||
300 142.53607 -10148.039 0 -10103.852 5120.6542
|
||||
400 322.68532 -10178.868 0 -10078.834 2342.957
|
||||
500 193.81485 -10117.984 0 -10057.901 8412.6921
|
||||
600 300.27212 -10134.473 0 -10041.388 -2801.7705
|
||||
700 272.6339 -10110.146 0 -10025.628 10749.262
|
||||
800 339.99701 -10114.123 0 -10008.723 5123.3071
|
||||
900 231.65605 -10068.587 0 -9996.7728 5306.5428
|
||||
1000 329.93457 -10088.778 0 -9986.4964 3190.7822
|
||||
1100 376.61097 -10092.399 0 -9975.6475 2921.8154
|
||||
1200 361.98407 -10076.598 0 -9964.3813 3613.8142
|
||||
1300 358.66787 -10069.369 0 -9958.1801 4341.836
|
||||
1400 470.15712 -10098.554 0 -9952.8032 -146.37541
|
||||
1500 509.64688 -10106.577 0 -9948.5846 2355.8342
|
||||
1600 417.94216 -10075.288 0 -9945.7246 1758.8486
|
||||
1700 453.28944 -10084.351 0 -9943.8294 -570.98573
|
||||
1800 472.90567 -10087.824 0 -9941.2211 1541.9022
|
||||
1900 507.19643 -10096.443 0 -9939.2104 -441.97035
|
||||
2000 443.66882 -10076.87 0 -9939.3312 -131.88097
|
||||
2100 485.44927 -10088.414 0 -9937.9225 -632.00796
|
||||
2200 507.55973 -10095.16 0 -9937.8139 1222.9997
|
||||
2300 496.62243 -10089.722 0 -9935.7672 42.209939
|
||||
2400 455.56537 -10077.338 0 -9936.1111 1335.7712
|
||||
2500 512.89536 -10094.239 0 -9935.2396 -593.65834
|
||||
2600 440.18205 -10070.5 0 -9934.0422 613.18152
|
||||
2700 501.65067 -10088.403 0 -9932.8889 430.74811
|
||||
2800 485.3846 -10083.269 0 -9932.7982 715.15642
|
||||
2900 489.47747 -10083.355 0 -9931.6151 1845.1781
|
||||
3000 501.34719 -10088.58 0 -9933.1605 2209.09
|
||||
Loop time of 1.90582 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 34.001 ns/day, 0.706 hours/ns, 1574.129 timesteps/s, 165.284 katom-step/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3982 | 1.4628 | 1.4959 | 3.2 | 76.75
|
||||
Neigh | 0.048259 | 0.056611 | 0.066179 | 2.7 | 2.97
|
||||
Comm | 0.059452 | 0.092743 | 0.15695 | 12.5 | 4.87
|
||||
Output | 0.00028355 | 0.00033432 | 0.00048015 | 0.0 | 0.02
|
||||
Modify | 0.28239 | 0.29189 | 0.30051 | 1.2 | 15.32
|
||||
Other | | 0.001446 | | | 0.08
|
||||
|
||||
Nlocal: 26.25 ave 46 max 8 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 399.5 ave 512 max 288 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1011.75 ave 1820 max 420 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4047
|
||||
Ave neighs/atom = 38.542857
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:01
|
||||
@ -1,140 +0,0 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.78 | 11.56 | 12.26 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10197.932 0 -10197.932 38.347492
|
||||
100 47.47852 -10176.425 0 -10161.706 632.97359
|
||||
200 166.95287 -10181.513 0 -10129.757 -27.146803
|
||||
300 142.53582 -10148.039 0 -10103.852 5120.6397
|
||||
400 322.68523 -10178.868 0 -10078.834 2342.7187
|
||||
500 193.81484 -10117.984 0 -10057.901 8412.4559
|
||||
600 300.27165 -10134.473 0 -10041.388 -2801.9143
|
||||
700 272.63408 -10110.146 0 -10025.629 10749.2
|
||||
800 339.99669 -10114.123 0 -10008.723 5123.2489
|
||||
900 231.65632 -10068.587 0 -9996.7729 5306.0392
|
||||
1000 329.93324 -10088.777 0 -9986.4967 3190.4707
|
||||
1100 376.60924 -10092.398 0 -9975.6478 2920.8475
|
||||
1200 361.98231 -10076.598 0 -9964.3816 3612.0573
|
||||
1300 358.6599 -10069.366 0 -9958.1803 4341.9871
|
||||
1400 470.14856 -10098.552 0 -9952.8036 -146.9069
|
||||
1500 509.6454 -10106.577 0 -9948.5847 2355.4022
|
||||
1600 417.9276 -10075.284 0 -9945.7249 1749.565
|
||||
1700 453.25817 -10084.343 0 -9943.8306 -570.48011
|
||||
1800 472.9517 -10087.84 0 -9941.2226 1532.6424
|
||||
1900 507.14171 -10096.428 0 -9939.212 -404.84948
|
||||
2000 443.62843 -10076.86 0 -9939.3329 -132.17302
|
||||
2100 485.441 -10088.414 0 -9937.925 -609.75758
|
||||
2200 507.23914 -10095.067 0 -9937.8209 1288.5372
|
||||
2300 499.64956 -10090.665 0 -9935.7719 149.06622
|
||||
2400 457.97848 -10078.107 0 -9936.1317 2065.2075
|
||||
2500 510.58254 -10093.537 0 -9935.2543 -559.75965
|
||||
2600 440.97503 -10070.865 0 -9934.1605 1164.1078
|
||||
2700 500.4945 -10088.165 0 -9933.0096 1051.9016
|
||||
2800 485.77814 -10083.543 0 -9932.9498 294.64404
|
||||
2900 487.73983 -10082.939 0 -9931.7373 2208.263
|
||||
3000 504.69717 -10089.803 0 -9933.3447 1723.6386
|
||||
Loop time of 2.81192 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 23.045 ns/day, 1.041 hours/ns, 1066.887 timesteps/s, 112.023 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0513 | 2.1567 | 2.2232 | 4.3 | 76.70
|
||||
Neigh | 0.072125 | 0.087048 | 0.10214 | 3.7 | 3.10
|
||||
Comm | 0.086792 | 0.15326 | 0.25749 | 16.2 | 5.45
|
||||
Output | 0.00058533 | 0.00064027 | 0.00080207 | 0.0 | 0.02
|
||||
Modify | 0.39587 | 0.41124 | 0.42647 | 1.7 | 14.62
|
||||
Other | | 0.003062 | | | 0.11
|
||||
|
||||
Nlocal: 26.25 ave 46 max 8 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 399.5 ave 512 max 288 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1011.25 ave 1819 max 420 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4045
|
||||
Ave neighs/atom = 38.52381
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
144
examples/reaxff/log.1Feb25.reaxff.rdx-shielded.g++.1
Normal file
144
examples/reaxff/log.1Feb25.reaxff.rdx-shielded.g++.1
Normal file
@ -0,0 +1,144 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
Reading data file ...
|
||||
orthogonal box = (35 35 35) to (48 48 48)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.rdx
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all atom 10 dump.reaxff.rdx
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/shielded, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.86 | 13.86 | 13.86 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79932 0 168.88397 12
|
||||
10 1288.6114 -1989.6644 -1912.8422 -19456.349 -2734.6769 -15.607218 0.20177961 0 54.629555 3.1252297 -77.7067 0 14.933901 -5.810854 843.92074 -180.43322 0 107.75935 8
|
||||
20 538.95852 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.9078343 0.077926704 0 81.610044 0.22951937 -57.557105 0 30.331203 -10.178049 878.99016 -159.69263 0 89.316862 7
|
||||
30 463.09515 -1933.5765 -1905.9685 -33255.499 -2749.8591 -8.0154635 0.02762867 0 81.627413 0.1197239 -50.262272 0 20.82032 -9.632703 851.88721 -149.49497 0 79.205707 8
|
||||
40 885.49689 -1958.9125 -1906.1226 -4814.6325 -2795.644 9.1505916 0.13747481 0 70.948074 0.24360544 -57.862695 0 19.076518 -11.14121 873.73893 -159.9939 0 92.434061 11
|
||||
50 861.16008 -1954.4602 -1903.1211 -1896.648 -2784.8451 3.8269988 0.1579331 0 79.851597 3.349208 -78.066133 0 32.628942 -7.9565363 872.8186 -190.98572 0 114.76001 10
|
||||
60 1167.7831 -1971.8435 -1902.2247 -3482.927 -2705.8639 -17.121541 0.22749081 0 44.507721 7.8559737 -74.789039 0 16.2565 -4.6046718 835.8307 -188.33687 0 114.19412 10
|
||||
70 1439.9897 -1989.3024 -1903.4557 23845.83 -2890.7894 31.958658 0.26671716 0 85.758318 3.1804201 -71.002959 0 24.35723 -10.31128 905.86819 -175.38505 0 106.79678 10
|
||||
80 502.39931 -1930.7551 -1900.804 -20356.375 -2703.8109 -18.66274 0.1128617 0 99.80351 2.0329611 -76.171312 0 19.236815 -6.2786426 826.47424 -166.03148 0 92.539616 9
|
||||
90 749.08601 -1946.984 -1902.3264 17798.716 -2863.7585 42.068606 0.24338046 0 96.181674 0.96183581 -69.955564 0 24.615514 -11.582742 903.68878 -190.13822 0 120.69121 11
|
||||
100 1109.6946 -1968.588 -1902.4322 -4490.4001 -2755.899 -7.1224954 0.21757676 0 61.805955 7.0825894 -75.645488 0 20.115437 -6.2372635 863.56481 -198.56946 0 122.09935 10
|
||||
Loop time of 0.0692709 on 1 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 124.728 ns/day, 0.192 hours/ns, 1443.607 timesteps/s, 30.316 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 | 0.060491 | 0.060491 | 0.060491 | 0.0 | 87.33
|
||||
Neigh | 0.0031331 | 0.0031331 | 0.0031331 | 0.0 | 4.52
|
||||
Comm | 0.00016256 | 0.00016256 | 0.00016256 | 0.0 | 0.23
|
||||
Output | 0.00014098 | 0.00014098 | 0.00014098 | 0.0 | 0.20
|
||||
Modify | 0.0052841 | 0.0052841 | 0.0052841 | 0.0 | 7.63
|
||||
Other | | 5.873e-05 | | | 0.08
|
||||
|
||||
Nlocal: 21 ave 21 max 21 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 546 ave 546 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1096 ave 1096 max 1096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1306 ave 1306 max 1306 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1306
|
||||
Ave neighs/atom = 62.190476
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
144
examples/reaxff/log.1Feb25.reaxff.rdx-shielded.g++.4
Normal file
144
examples/reaxff/log.1Feb25.reaxff.rdx-shielded.g++.4
Normal file
@ -0,0 +1,144 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
Reading data file ...
|
||||
orthogonal box = (35 35 35) to (48 48 48)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.rdx
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all atom 10 dump.reaxff.rdx
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/shielded, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.856 | 11.02 | 12.23 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79963 0 168.88428 12
|
||||
10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
|
||||
20 538.95831 -1942.7037 -1910.5731 -10725.628 -2803.7395 7.9078316 0.077926725 0 81.610046 0.22951948 -57.55711 0 30.331206 -10.178049 878.99011 -159.68964 0 89.313879 6
|
||||
30 463.09528 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.015479 0.027628772 0 81.627413 0.11972402 -50.262283 0 20.82031 -9.6327014 851.88714 -149.49498 0 79.205717 8
|
||||
40 885.49492 -1958.9125 -1906.1227 -4814.6646 -2795.6439 9.1506063 0.13747482 0 70.948055 0.2436053 -57.862686 0 19.076515 -11.141211 873.73888 -159.99391 0 92.434067 11
|
||||
50 861.15982 -1954.4602 -1903.1212 -1896.7209 -2784.845 3.8269674 0.15793308 0 79.851587 3.3492059 -78.06613 0 32.628933 -7.9565341 872.81849 -190.9857 0 114.75999 10
|
||||
60 1167.7827 -1971.8436 -1902.2248 -3482.8501 -2705.8641 -17.121497 0.22749093 0 44.507698 7.8559911 -74.78902 0 16.256511 -4.6046743 835.83081 -188.33692 0 114.19416 10
|
||||
70 1439.9904 -1989.3026 -1903.4558 23846.02 -2890.7894 31.95863 0.26671716 0 85.758232 3.1804311 -71.002978 0 24.357223 -10.311272 905.86809 -175.38506 0 106.79678 10
|
||||
80 502.39774 -1930.7552 -1900.8041 -20356.27 -2703.8119 -18.66246 0.11286127 0 99.803504 2.0329528 -76.171312 0 19.236983 -6.278675 826.47474 -166.03143 0 92.539573 9
|
||||
90 749.07673 -1946.984 -1902.3269 17798.497 -2863.7581 42.06868 0.24338043 0 96.181508 0.9618341 -69.955454 0 24.615416 -11.582759 903.68853 -190.13817 0 120.69116 11
|
||||
100 1109.6909 -1968.5881 -1902.4325 -4490.3603 -2755.8994 -7.1223998 0.21757662 0 61.805909 7.0826145 -75.645472 0 20.115466 -6.2372802 863.565 -198.56948 0 122.09938 10
|
||||
Loop time of 0.0643048 on 4 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 134.360 ns/day, 0.179 hours/ns, 1555.095 timesteps/s, 32.657 katom-step/s
|
||||
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.023311 | 0.03235 | 0.044316 | 4.2 | 50.31
|
||||
Neigh | 0.0013612 | 0.0019412 | 0.002633 | 1.0 | 3.02
|
||||
Comm | 0.0010934 | 0.013057 | 0.022095 | 6.7 | 20.31
|
||||
Output | 0.00014529 | 0.00015387 | 0.00016787 | 0.0 | 0.24
|
||||
Modify | 0.016042 | 0.016754 | 0.017353 | 0.4 | 26.05
|
||||
Other | | 4.816e-05 | | | 0.07
|
||||
|
||||
Nlocal: 5.25 ave 15 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 355.5 ave 432 max 282 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 298.75 ave 822 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
FullNghs: 326.5 ave 927 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1306
|
||||
Ave neighs/atom = 62.190476
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
154
examples/reaxff/log.1Feb25.reaxff.rdx.g++.1
Normal file
154
examples/reaxff/log.1Feb25.reaxff.rdx.g++.1
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
Reading data file ...
|
||||
orthogonal box = (35 35 35) to (48 48 48)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.rdx
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all atom 10 dump.reaxff.rdx
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.36 | 13.36 | 13.36 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79947 0 168.88412 12
|
||||
10 1288.6115 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629555 3.1252295 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43321 0 107.75934 8
|
||||
20 538.95838 -1942.7037 -1910.5731 -10725.629 -2803.7395 7.9078326 0.07792674 0 81.610044 0.22951951 -57.557111 0 30.331206 -10.178049 878.99011 -159.6897 0 89.31394 6.5
|
||||
30 463.09527 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.0154824 0.027628758 0 81.627415 0.11972401 -50.262282 0 20.82031 -9.6327011 851.88713 -149.49499 0 79.205722 8
|
||||
40 885.49524 -1958.9125 -1906.1227 -4814.6579 -2795.6439 9.1505958 0.13747478 0 70.948066 0.24360531 -57.862686 0 19.076518 -11.141211 873.73887 -159.9939 0 92.434064 11
|
||||
50 861.1608 -1954.4602 -1903.121 -1896.6931 -2784.8449 3.8269759 0.15793298 0 79.851634 3.349206 -78.06613 0 32.628956 -7.9565349 872.81845 -190.98568 0 114.75998 10
|
||||
60 1167.7834 -1971.8435 -1902.2247 -3482.8529 -2705.8639 -17.121541 0.2274908 0 44.507704 7.8559998 -74.789016 0 16.256511 -4.60467 835.83072 -188.33689 0 114.19413 10
|
||||
70 1439.9911 -1989.3024 -1903.4556 23845.704 -2890.7894 31.958692 0.2667172 0 85.758357 3.1804062 -71.002958 0 24.3572 -10.311286 905.86808 -175.385 0 106.79674 10
|
||||
80 502.3988 -1930.755 -1900.8039 -20356.389 -2703.8108 -18.662751 0.11286169 0 99.803574 2.032954 -76.171326 0 19.236814 -6.2786428 826.47419 -166.03149 0 92.539626 9
|
||||
90 749.08532 -1946.9839 -1902.3263 17798.667 -2863.7584 42.06871 0.24338047 0 96.181692 0.96182992 -69.955524 0 24.615455 -11.582756 903.68873 -190.13825 0 120.69125 11
|
||||
100 1109.6964 -1968.5879 -1902.432 -4490.4599 -2755.8982 -7.1227208 0.21757669 0 61.806042 7.082597 -75.645484 0 20.115271 -6.2372452 863.56435 -198.56945 0 122.09933 10.5
|
||||
Loop time of 0.0666662 on 1 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 129.601 ns/day, 0.185 hours/ns, 1500.011 timesteps/s, 31.500 katom-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 | 0.060081 | 0.060081 | 0.060081 | 0.0 | 90.12
|
||||
Neigh | 0.0029204 | 0.0029204 | 0.0029204 | 0.0 | 4.38
|
||||
Comm | 0.000161 | 0.000161 | 0.000161 | 0.0 | 0.24
|
||||
Output | 0.00014497 | 0.00014497 | 0.00014497 | 0.0 | 0.22
|
||||
Modify | 0.0033107 | 0.0033107 | 0.0033107 | 0.0 | 4.97
|
||||
Other | | 4.861e-05 | | | 0.07
|
||||
|
||||
Nlocal: 21 ave 21 max 21 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 546 ave 546 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1096 ave 1096 max 1096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1096
|
||||
Ave neighs/atom = 52.190476
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
154
examples/reaxff/log.1Feb25.reaxff.rdx.g++.4
Normal file
154
examples/reaxff/log.1Feb25.reaxff.rdx.g++.4
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
Reading data file ...
|
||||
orthogonal box = (35 35 35) to (48 48 48)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.rdx
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all atom 10 dump.reaxff.rdx
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.353 | 10.52 | 11.73 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -1884.3081 -1884.3081 27186.182 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79916 0 168.88381 12.5
|
||||
10 1288.6116 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.60722 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
|
||||
20 538.95827 -1942.7037 -1910.5731 -10725.675 -2803.7395 7.9078297 0.077926636 0 81.610054 0.22951925 -57.557099 0 30.331205 -10.178049 878.99014 -159.69256 0 89.316794 7
|
||||
30 463.09513 -1933.5765 -1905.9686 -33255.526 -2749.8591 -8.0154533 0.027628873 0 81.62739 0.11972403 -50.262284 0 20.820312 -9.6327039 851.88722 -149.49494 0 79.205672 8
|
||||
40 885.49116 -1958.9126 -1906.123 -4814.6959 -2795.6441 9.1506835 0.13747507 0 70.947963 0.24360514 -57.862673 0 19.076493 -11.141218 873.73898 -159.99394 0 92.434099 11
|
||||
50 861.1691 -1954.4598 -1903.1202 -1896.8779 -2784.8448 3.8270203 0.1579326 0 79.851903 3.3492208 -78.066129 0 32.629013 -7.9565355 872.81826 -190.98566 0 114.75994 10
|
||||
60 1167.7861 -1971.8427 -1902.2238 -3482.6559 -2705.8627 -17.121772 0.22749069 0 44.507644 7.8561147 -74.788923 0 16.256476 -4.6046327 835.83036 -188.33691 0 114.19412 10
|
||||
70 1440.0001 -1989.3024 -1903.4551 23845.322 -2890.7895 31.958913 0.26671723 0 85.758826 3.1803176 -71.002871 0 24.357078 -10.311326 905.8676 -175.38455 0 106.79634 10
|
||||
80 502.39424 -1930.7541 -1900.8033 -20356.365 -2703.8112 -18.662536 0.11285996 0 99.804396 2.032884 -76.171335 0 19.237003 -6.2786875 826.47433 -166.03121 0 92.539366 9
|
||||
90 749.08858 -1946.9836 -1902.3258 17798.514 -2863.7575 42.068829 0.24338073 0 96.181699 0.9618465 -69.955421 0 24.615236 -11.582776 903.6881 -190.13852 0 120.69151 11
|
||||
100 1109.7005 -1968.5871 -1902.431 -4490.1423 -2755.8949 -7.1235131 0.21757701 0 61.80622 7.0827961 -75.645322 0 20.114715 -6.2371564 863.56266 -198.56982 0 122.09964 10.5
|
||||
Loop time of 0.0666879 on 4 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 129.559 ns/day, 0.185 hours/ns, 1499.522 timesteps/s, 31.490 katom-step/s
|
||||
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.023807 | 0.033573 | 0.04688 | 4.6 | 50.34
|
||||
Neigh | 0.0013829 | 0.001879 | 0.0024761 | 0.9 | 2.82
|
||||
Comm | 0.0015767 | 0.014898 | 0.024673 | 6.9 | 22.34
|
||||
Output | 0.00015887 | 0.00016828 | 0.00018839 | 0.0 | 0.25
|
||||
Modify | 0.015511 | 0.01612 | 0.016628 | 0.3 | 24.17
|
||||
Other | | 4.966e-05 | | | 0.07
|
||||
|
||||
Nlocal: 5.25 ave 15 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 355.5 ave 432 max 282 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 298.75 ave 822 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1195
|
||||
Ave neighs/atom = 56.904762
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
143
examples/reaxff/log.1Feb25.reaxff.tatb-shielded.g++.1
Normal file
143
examples/reaxff/log.1Feb25.reaxff.tatb-shielded.g++.1
Normal file
@ -0,0 +1,143 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
|
||||
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.tatb
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
|
||||
fix 4 all reaxff/bonds 5 bonds.reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 3 all reaxff/species 1 5 5 species.tatb
|
||||
|
||||
run 25
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 5 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/shielded, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 141.8 | 141.8 | 141.8 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -44760.998 -44760.998 7827.7813 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6412 0 6391.0292 31
|
||||
5 0.61603967 -44761.698 -44760.994 8934.6348 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.191 0 6388.6671 9
|
||||
10 2.3525554 -44763.227 -44760.541 12288.592 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9738 0 6381.7115 10
|
||||
15 4.9013248 -44766.36 -44760.764 17716.966 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2495 0 6370.4158 11
|
||||
20 7.8294647 -44769.686 -44760.747 25205.601 -61089.006 490.21315 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.498 0 6355.2493 10
|
||||
25 10.697903 -44772.904 -44760.691 34232.795 -61069.308 490.25888 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3636 0 6336.8444 8
|
||||
Loop time of 1.38877 on 1 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.097 ns/day, 246.892 hours/ns, 18.002 timesteps/s, 6.913 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 | 0.84541 | 0.84541 | 0.84541 | 0.0 | 60.87
|
||||
Neigh | 0.18596 | 0.18596 | 0.18596 | 0.0 | 13.39
|
||||
Comm | 0.00085484 | 0.00085484 | 0.00085484 | 0.0 | 0.06
|
||||
Output | 0.00015065 | 0.00015065 | 0.00015065 | 0.0 | 0.01
|
||||
Modify | 0.35629 | 0.35629 | 0.35629 | 0.0 | 25.66
|
||||
Other | | 0.0001081 | | | 0.01
|
||||
|
||||
Nlocal: 384 ave 384 max 384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7559 ave 7559 max 7559 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 286828 ave 286828 max 286828 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 336304 ave 336304 max 336304 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 336304
|
||||
Ave neighs/atom = 875.79167
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:01
|
||||
143
examples/reaxff/log.1Feb25.reaxff.tatb-shielded.g++.4
Normal file
143
examples/reaxff/log.1Feb25.reaxff.tatb-shielded.g++.4
Normal file
@ -0,0 +1,143 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
|
||||
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.tatb
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
|
||||
fix 4 all reaxff/bonds 5 bonds.reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 3 all reaxff/species 1 5 5 species.tatb
|
||||
|
||||
run 25
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 5 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/shielded, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 95.02 | 95.02 | 95.02 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -44760.998 -44760.998 7827.7867 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277 31
|
||||
5 0.61603966 -44761.698 -44760.994 8934.6345 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9
|
||||
10 2.3525551 -44763.227 -44760.541 12288.585 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.7139 10
|
||||
15 4.9013353 -44766.36 -44760.764 17716.927 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2618 0 6370.428 9
|
||||
20 7.8294728 -44769.686 -44760.747 25205.533 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.5246 0 6355.2758 9
|
||||
25 10.697909 -44772.904 -44760.691 34232.903 -61069.308 490.25887 4.7163736 0 1570.7397 20.181346 -251.91376 -1582.3261 253.82253 -653.53184 18791.975 -8684.3314 0 6336.8122 9
|
||||
Loop time of 0.788795 on 4 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.171 ns/day, 140.230 hours/ns, 31.694 timesteps/s, 12.170 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.56139 | 0.56526 | 0.56947 | 0.5 | 71.66
|
||||
Neigh | 0.10336 | 0.10367 | 0.10413 | 0.1 | 13.14
|
||||
Comm | 0.0032435 | 0.0074406 | 0.011341 | 4.5 | 0.94
|
||||
Output | 0.00018108 | 0.0012272 | 0.0015806 | 1.7 | 0.16
|
||||
Modify | 0.11024 | 0.11106 | 0.11251 | 0.3 | 14.08
|
||||
Other | | 0.0001416 | | | 0.02
|
||||
|
||||
Nlocal: 96 ave 96 max 96 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5118 ave 5118 max 5118 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 79754 ave 79754 max 79754 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 84076 ave 84076 max 84076 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 336304
|
||||
Ave neighs/atom = 875.79167
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
159
examples/reaxff/log.1Feb25.reaxff.tatb.g++.1
Normal file
159
examples/reaxff/log.1Feb25.reaxff.tatb.g++.1
Normal file
@ -0,0 +1,159 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
|
||||
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.tatb
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
|
||||
fix 4 all reaxff/bonds 5 bonds.reaxff
|
||||
compute bonds all reaxff/atom bonds yes
|
||||
variable nqeq equal f_2
|
||||
|
||||
# dumps out the local bond information
|
||||
dump 1 all local 5 bonds_local.reaxff c_bonds[1] c_bonds[2] c_bonds[3]
|
||||
|
||||
# dumps out the peratom bond information
|
||||
dump 2 all custom 5 bonds_atom.reaxff id type q c_bonds[*]
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 3 all reaxff/species 1 5 5 species.tatb
|
||||
|
||||
run 25
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 5 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 148.7 | 148.7 | 148.7 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -44760.998 -44760.998 7827.7886 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6392 0 6391.0272 31.5
|
||||
5 0.61603945 -44761.698 -44760.994 8934.6263 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1931 0 6388.6691 10.5
|
||||
10 2.3525551 -44763.227 -44760.541 12288.607 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9689 0 6381.7066 8.5
|
||||
15 4.9013324 -44766.36 -44760.764 17716.909 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56848 -1566.3829 252.95174 -654.96611 18835.777 -8719.2637 0 6370.4299 9
|
||||
20 7.8294652 -44769.686 -44760.747 25205.631 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4897 0 6355.241 10
|
||||
25 10.697902 -44772.904 -44760.691 34232.78 -61069.308 490.25885 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.364 0 6336.8448 10
|
||||
Loop time of 1.24712 on 1 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.108 ns/day, 221.710 hours/ns, 20.046 timesteps/s, 7.698 katom-step/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.87392 | 0.87392 | 0.87392 | 0.0 | 70.07
|
||||
Neigh | 0.1672 | 0.1672 | 0.1672 | 0.0 | 13.41
|
||||
Comm | 0.0010267 | 0.0010267 | 0.0010267 | 0.0 | 0.08
|
||||
Output | 0.0031358 | 0.0031358 | 0.0031358 | 0.0 | 0.25
|
||||
Modify | 0.20171 | 0.20171 | 0.20171 | 0.0 | 16.17
|
||||
Other | | 0.0001369 | | | 0.01
|
||||
|
||||
Nlocal: 384 ave 384 max 384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7559 ave 7559 max 7559 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 286828 ave 286828 max 286828 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 286828
|
||||
Ave neighs/atom = 746.94792
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:01
|
||||
159
examples/reaxff/log.1Feb25.reaxff.tatb.g++.4
Normal file
159
examples/reaxff/log.1Feb25.reaxff.tatb.g++.4
Normal file
@ -0,0 +1,159 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
|
||||
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.tatb
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
|
||||
fix 4 all reaxff/bonds 5 bonds.reaxff
|
||||
compute bonds all reaxff/atom bonds yes
|
||||
variable nqeq equal f_2
|
||||
|
||||
# dumps out the local bond information
|
||||
dump 1 all local 5 bonds_local.reaxff c_bonds[1] c_bonds[2] c_bonds[3]
|
||||
|
||||
# dumps out the peratom bond information
|
||||
dump 2 all custom 5 bonds_atom.reaxff id type q c_bonds[*]
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 3 all reaxff/species 1 5 5 species.tatb
|
||||
|
||||
run 25
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 5 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 99.8 | 99.8 | 99.8 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277 31
|
||||
5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666 8.5
|
||||
10 2.352554 -44763.227 -44760.541 12288.582 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.7139 10
|
||||
15 4.9013231 -44766.36 -44760.764 17716.979 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2473 0 6370.4136 7
|
||||
20 7.8294566 -44769.686 -44760.747 25205.638 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4803 0 6355.2315 8.5
|
||||
25 10.6979 -44772.904 -44760.691 34232.844 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3433 0 6336.8241 9.5
|
||||
Loop time of 0.771261 on 4 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.175 ns/day, 137.113 hours/ns, 32.414 timesteps/s, 12.447 katom-step/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.56965 | 0.57597 | 0.58104 | 0.5 | 74.68
|
||||
Neigh | 0.097254 | 0.097483 | 0.097832 | 0.1 | 12.64
|
||||
Comm | 0.003347 | 0.0083916 | 0.014749 | 4.5 | 1.09
|
||||
Output | 0.00131 | 0.0022935 | 0.0026708 | 1.2 | 0.30
|
||||
Modify | 0.086284 | 0.086988 | 0.088382 | 0.3 | 11.28
|
||||
Other | | 0.0001324 | | | 0.02
|
||||
|
||||
Nlocal: 96 ave 96 max 96 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5118 ave 5118 max 5118 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 79754 ave 79754 max 79754 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 319016
|
||||
Ave neighs/atom = 830.77083
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
@ -1,144 +0,0 @@
|
||||
LAMMPS (2 Jul 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
Reading data file ...
|
||||
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.rdx
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all atom 10 dump.reaxff.rdx
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/shielded, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.86 | 13.86 | 13.86 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79932 0 168.88397 12
|
||||
10 1288.6114 -1989.6644 -1912.8422 -19456.349 -2734.6769 -15.607218 0.20177961 0 54.629555 3.1252297 -77.7067 0 14.933901 -5.810854 843.92074 -180.43322 0 107.75935 8
|
||||
20 538.95852 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.9078343 0.077926704 0 81.610044 0.22951937 -57.557105 0 30.331203 -10.178049 878.99016 -159.69263 0 89.316862 7
|
||||
30 463.09515 -1933.5765 -1905.9685 -33255.499 -2749.8591 -8.0154635 0.02762867 0 81.627413 0.1197239 -50.262272 0 20.82032 -9.632703 851.88721 -149.49497 0 79.205707 8
|
||||
40 885.49689 -1958.9125 -1906.1226 -4814.6325 -2795.644 9.1505916 0.13747481 0 70.948074 0.24360544 -57.862695 0 19.076518 -11.14121 873.73893 -159.9939 0 92.434061 11
|
||||
50 861.16008 -1954.4602 -1903.1211 -1896.648 -2784.8451 3.8269988 0.1579331 0 79.851597 3.349208 -78.066133 0 32.628942 -7.9565363 872.8186 -190.98572 0 114.76001 10
|
||||
60 1167.7831 -1971.8435 -1902.2247 -3482.927 -2705.8639 -17.121541 0.22749081 0 44.507721 7.8559737 -74.789039 0 16.2565 -4.6046718 835.8307 -188.33687 0 114.19412 10
|
||||
70 1439.9897 -1989.3024 -1903.4557 23845.83 -2890.7894 31.958658 0.26671716 0 85.758318 3.1804201 -71.002959 0 24.35723 -10.31128 905.86819 -175.38505 0 106.79678 10
|
||||
80 502.39931 -1930.7551 -1900.804 -20356.375 -2703.8109 -18.66274 0.1128617 0 99.80351 2.0329611 -76.171312 0 19.236815 -6.2786426 826.47424 -166.03148 0 92.539616 9
|
||||
90 749.08601 -1946.984 -1902.3264 17798.716 -2863.7585 42.068606 0.24338046 0 96.181674 0.96183581 -69.955564 0 24.615514 -11.582742 903.68878 -190.13822 0 120.69121 11
|
||||
100 1109.6946 -1968.588 -1902.4322 -4490.4001 -2755.899 -7.1224954 0.21757676 0 61.805955 7.0825894 -75.645488 0 20.115437 -6.2372635 863.56481 -198.56946 0 122.09935 10
|
||||
Loop time of 0.23792 on 1 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 36.315 ns/day, 0.661 hours/ns, 420.310 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.21046 | 0.21046 | 0.21046 | 0.0 | 88.46
|
||||
Neigh | 0.010947 | 0.010947 | 0.010947 | 0.0 | 4.60
|
||||
Comm | 0.00060345 | 0.00060345 | 0.00060345 | 0.0 | 0.25
|
||||
Output | 0.00071705 | 0.00071705 | 0.00071705 | 0.0 | 0.30
|
||||
Modify | 0.014873 | 0.014873 | 0.014873 | 0.0 | 6.25
|
||||
Other | | 0.0003213 | | | 0.14
|
||||
|
||||
Nlocal: 21.0000 ave 21 max 21 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 546.000 ave 546 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1096.00 ave 1096 max 1096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1306.00 ave 1306 max 1306 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1306
|
||||
Ave neighs/atom = 62.190476
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
@ -1,144 +0,0 @@
|
||||
LAMMPS (2 Jul 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
Reading data file ...
|
||||
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.rdx
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all atom 10 dump.reaxff.rdx
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/shielded, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.856 | 11.02 | 12.23 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79963 0 168.88428 12
|
||||
10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
|
||||
20 538.95831 -1942.7037 -1910.5731 -10725.628 -2803.7395 7.9078316 0.077926725 0 81.610046 0.22951948 -57.55711 0 30.331206 -10.178049 878.99011 -159.68964 0 89.313879 6
|
||||
30 463.09528 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.015479 0.027628772 0 81.627413 0.11972402 -50.262283 0 20.82031 -9.6327014 851.88714 -149.49498 0 79.205717 8
|
||||
40 885.49492 -1958.9125 -1906.1227 -4814.6646 -2795.6439 9.1506063 0.13747482 0 70.948055 0.2436053 -57.862686 0 19.076515 -11.141211 873.73888 -159.99391 0 92.434067 11
|
||||
50 861.15982 -1954.4602 -1903.1212 -1896.7209 -2784.845 3.8269674 0.15793308 0 79.851587 3.3492059 -78.06613 0 32.628933 -7.9565341 872.81849 -190.9857 0 114.75999 10
|
||||
60 1167.7827 -1971.8436 -1902.2248 -3482.8501 -2705.8641 -17.121497 0.22749093 0 44.507698 7.8559911 -74.78902 0 16.256511 -4.6046743 835.83081 -188.33692 0 114.19416 10
|
||||
70 1439.9904 -1989.3026 -1903.4558 23846.02 -2890.7894 31.95863 0.26671716 0 85.758232 3.1804311 -71.002978 0 24.357223 -10.311272 905.86809 -175.38506 0 106.79678 10
|
||||
80 502.39774 -1930.7552 -1900.8041 -20356.27 -2703.8119 -18.66246 0.11286127 0 99.803504 2.0329528 -76.171312 0 19.236983 -6.278675 826.47474 -166.03143 0 92.539573 9
|
||||
90 749.07673 -1946.984 -1902.3269 17798.497 -2863.7581 42.06868 0.24338043 0 96.181508 0.9618341 -69.955454 0 24.615416 -11.582759 903.68853 -190.13817 0 120.69116 11
|
||||
100 1109.6909 -1968.5881 -1902.4325 -4490.3603 -2755.8994 -7.1223998 0.21757662 0 61.805909 7.0826145 -75.645472 0 20.115466 -6.2372802 863.565 -198.56948 0 122.09938 10
|
||||
Loop time of 0.427646 on 4 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 20.204 ns/day, 1.188 hours/ns, 233.838 timesteps/s
|
||||
88.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1373 | 0.20047 | 0.27938 | 11.8 | 46.88
|
||||
Neigh | 0.0067 | 0.009334 | 0.01249 | 2.1 | 2.18
|
||||
Comm | 0.057132 | 0.13685 | 0.19972 | 14.4 | 32.00
|
||||
Output | 0.00078935 | 0.0013884 | 0.0031266 | 2.7 | 0.32
|
||||
Modify | 0.075213 | 0.079164 | 0.082556 | 0.9 | 18.51
|
||||
Other | | 0.0004359 | | | 0.10
|
||||
|
||||
Nlocal: 5.25000 ave 15 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 355.500 ave 432 max 282 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 298.750 ave 822 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
FullNghs: 326.500 ave 927 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1306
|
||||
Ave neighs/atom = 62.190476
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
@ -1,154 +0,0 @@
|
||||
LAMMPS (2 Jul 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
Reading data file ...
|
||||
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.rdx
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all atom 10 dump.reaxff.rdx
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.36 | 13.36 | 13.36 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
|
||||
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
|
||||
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
|
||||
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
|
||||
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
|
||||
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
|
||||
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
|
||||
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
|
||||
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
|
||||
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
|
||||
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
|
||||
Loop time of 0.231802 on 1 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 37.273 ns/day, 0.644 hours/ns, 431.402 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20857 | 0.20857 | 0.20857 | 0.0 | 89.98
|
||||
Neigh | 0.010489 | 0.010489 | 0.010489 | 0.0 | 4.52
|
||||
Comm | 0.00059632 | 0.00059632 | 0.00059632 | 0.0 | 0.26
|
||||
Output | 0.00067498 | 0.00067498 | 0.00067498 | 0.0 | 0.29
|
||||
Modify | 0.011161 | 0.011161 | 0.011161 | 0.0 | 4.82
|
||||
Other | | 0.000307 | | | 0.13
|
||||
|
||||
Nlocal: 21.0000 ave 21 max 21 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 546.000 ave 546 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1096.00 ave 1096 max 1096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1096
|
||||
Ave neighs/atom = 52.190476
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
@ -1,154 +0,0 @@
|
||||
LAMMPS (2 Jul 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
Reading data file ...
|
||||
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.rdx
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all atom 10 dump.reaxff.rdx
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.353 | 10.52 | 11.73 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418 12
|
||||
10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252292 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
|
||||
20 538.95847 -1942.7037 -1910.5731 -10725.668 -2803.7395 7.9078328 0.077926688 0 81.610045 0.22951933 -57.557103 0 30.331203 -10.178049 878.99015 -159.69262 0 89.316856 7
|
||||
30 463.09521 -1933.5765 -1905.9685 -33255.503 -2749.8591 -8.0154614 0.027628708 0 81.627408 0.11972393 -50.262275 0 20.820319 -9.6327031 851.88721 -149.49497 0 79.205707 8
|
||||
40 885.49559 -1958.9126 -1906.1227 -4814.661 -2795.644 9.1506103 0.13747486 0 70.948058 0.24360549 -57.862693 0 19.076514 -11.141211 873.73894 -159.9939 0 92.434063 11
|
||||
50 861.16222 -1954.4601 -1903.1209 -1896.7328 -2784.8449 3.8269573 0.15793301 0 79.851661 3.3492101 -78.066131 0 32.628939 -7.9565311 872.81847 -190.9857 0 114.75999 10
|
||||
60 1167.7838 -1971.8434 -1902.2246 -3482.8253 -2705.8639 -17.121553 0.22749078 0 44.507707 7.8560156 -74.789002 0 16.256509 -4.6046674 835.83076 -188.33689 0 114.19413 10
|
||||
70 1439.9922 -1989.3024 -1903.4556 23845.682 -2890.7894 31.958742 0.26671722 0 85.758402 3.1803955 -71.002937 0 24.357176 -10.311293 905.86805 -175.38494 0 106.79668 10
|
||||
80 502.39847 -1930.7549 -1900.8038 -20356.357 -2703.8111 -18.662668 0.11286141 0 99.803668 2.0329484 -76.17132 0 19.236866 -6.2786536 826.47435 -166.03145 0 92.539587 9
|
||||
90 749.0857 -1946.984 -1902.3263 17798.657 -2863.7584 42.068704 0.24338054 0 96.181666 0.96183837 -69.955527 0 24.615445 -11.58275 903.68864 -190.13828 0 120.69127 11
|
||||
100 1109.695 -1968.5879 -1902.4321 -4490.3441 -2755.8984 -7.1226574 0.21757683 0 61.806014 7.0826278 -75.645456 0 20.115306 -6.2372466 863.56451 -198.56953 0 122.09941 10.5
|
||||
Loop time of 0.371707 on 4 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 23.244 ns/day, 1.033 hours/ns, 269.029 timesteps/s
|
||||
91.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.13518 | 0.19123 | 0.24947 | 9.7 | 51.45
|
||||
Neigh | 0.0073075 | 0.0096968 | 0.012228 | 1.8 | 2.61
|
||||
Comm | 0.034511 | 0.093329 | 0.14912 | 14.0 | 25.11
|
||||
Output | 0.00081416 | 0.0011345 | 0.0019655 | 1.4 | 0.31
|
||||
Modify | 0.073177 | 0.075449 | 0.078618 | 0.7 | 20.30
|
||||
Other | | 0.0008711 | | | 0.23
|
||||
|
||||
Nlocal: 5.25000 ave 15 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 355.500 ave 432 max 282 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 298.750 ave 822 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1195
|
||||
Ave neighs/atom = 56.904762
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
@ -1,142 +0,0 @@
|
||||
LAMMPS (2 Jul 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
Reading data file ...
|
||||
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.tatb
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
|
||||
fix 4 all reaxff/bonds 5 bonds.reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 3 all reaxff/species 1 5 5 species.tatb
|
||||
|
||||
run 25
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/shielded, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 141.3 | 141.3 | 141.3 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275 31
|
||||
5 0.61603968 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665 8
|
||||
10 2.3525543 -44763.227 -44760.541 12288.589 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714 10
|
||||
15 4.9013256 -44766.36 -44760.764 17716.957 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2536 0 6370.4198 9
|
||||
20 7.8294699 -44769.686 -44760.747 25205.552 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5055 0 6355.2567 8
|
||||
25 10.697916 -44772.904 -44760.691 34232.955 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.308 0 6336.7889 7
|
||||
Loop time of 3.31728 on 1 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.041 ns/day, 589.738 hours/ns, 7.536 timesteps/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 | 1.9321 | 1.9321 | 1.9321 | 0.0 | 58.24
|
||||
Neigh | 0.6452 | 0.6452 | 0.6452 | 0.0 | 19.45
|
||||
Comm | 0.0020122 | 0.0020122 | 0.0020122 | 0.0 | 0.06
|
||||
Output | 0.00030173 | 0.00030173 | 0.00030173 | 0.0 | 0.01
|
||||
Modify | 0.73726 | 0.73726 | 0.73726 | 0.0 | 22.22
|
||||
Other | | 0.0003829 | | | 0.01
|
||||
|
||||
Nlocal: 384.000 ave 384 max 384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7559.00 ave 7559 max 7559 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 286828.0 ave 286828 max 286828 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 336304.0 ave 336304 max 336304 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 336304
|
||||
Ave neighs/atom = 875.79167
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:03
|
||||
@ -1,142 +0,0 @@
|
||||
LAMMPS (2 Jul 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
Reading data file ...
|
||||
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.tatb
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
|
||||
fix 4 all reaxff/bonds 5 bonds.reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 3 all reaxff/species 1 5 5 species.tatb
|
||||
|
||||
run 25
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/shielded, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 94.50 | 94.50 | 94.50 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -44760.998 -44760.998 7827.7865 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0278 31
|
||||
5 0.61603964 -44761.698 -44760.994 8934.6344 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9
|
||||
10 2.3525559 -44763.227 -44760.541 12288.611 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9712 0 6381.7089 11
|
||||
15 4.9013319 -44766.36 -44760.764 17716.965 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2514 0 6370.4176 9
|
||||
20 7.8294706 -44769.686 -44760.747 25205.511 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5196 0 6355.2708 7
|
||||
25 10.69792 -44772.904 -44760.691 34232.831 -61069.308 490.25885 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.353 0 6336.8339 11
|
||||
Loop time of 2.66226 on 4 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.051 ns/day, 473.290 hours/ns, 9.391 timesteps/s
|
||||
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7311 | 1.7619 | 1.794 | 2.0 | 66.18
|
||||
Neigh | 0.46483 | 0.46901 | 0.47348 | 0.5 | 17.62
|
||||
Comm | 0.039253 | 0.073989 | 0.10705 | 10.7 | 2.78
|
||||
Output | 0.0012206 | 0.0080282 | 0.010299 | 4.4 | 0.30
|
||||
Modify | 0.34359 | 0.3488 | 0.36264 | 1.4 | 13.10
|
||||
Other | | 0.0005529 | | | 0.02
|
||||
|
||||
Nlocal: 96.0000 ave 96 max 96 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5118.00 ave 5118 max 5118 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 79754.0 ave 79754 max 79754 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 84076.0 ave 84076 max 84076 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 336304
|
||||
Ave neighs/atom = 875.79167
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:03
|
||||
@ -1,151 +0,0 @@
|
||||
LAMMPS (2 Jul 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
Reading data file ...
|
||||
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
read_data CPU = 0.008 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.tatb
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
|
||||
fix 4 all reaxff/bonds 5 bonds.reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 3 all reaxff/species 1 5 5 species.tatb
|
||||
|
||||
run 25
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 148.1 | 148.1 | 148.1 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -44760.998 -44760.998 7827.7878 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274 31.5
|
||||
5 0.61603968 -44761.698 -44760.994 8934.6346 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9
|
||||
10 2.3525552 -44763.227 -44760.541 12288.581 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9765 0 6381.7142 10.5
|
||||
15 4.9013309 -44766.36 -44760.764 17716.918 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2622 0 6370.4284 9.5
|
||||
20 7.829469 -44769.686 -44760.747 25205.568 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.5126 0 6355.2639 8
|
||||
25 10.697899 -44772.904 -44760.691 34232.788 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3619 0 6336.8427 11
|
||||
Loop time of 2.91659 on 1 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.046 ns/day, 518.504 hours/ns, 8.572 timesteps/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 | 1.9139 | 1.9139 | 1.9139 | 0.0 | 65.62
|
||||
Neigh | 0.5948 | 0.5948 | 0.5948 | 0.0 | 20.39
|
||||
Comm | 0.0020205 | 0.0020205 | 0.0020205 | 0.0 | 0.07
|
||||
Output | 0.00031287 | 0.00031287 | 0.00031287 | 0.0 | 0.01
|
||||
Modify | 0.40513 | 0.40513 | 0.40513 | 0.0 | 13.89
|
||||
Other | | 0.0003856 | | | 0.01
|
||||
|
||||
Nlocal: 384.000 ave 384 max 384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7559.00 ave 7559 max 7559 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 286828.0 ave 286828 max 286828 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 286828
|
||||
Ave neighs/atom = 746.94792
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:03
|
||||
@ -1,151 +0,0 @@
|
||||
LAMMPS (2 Jul 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
Reading data file ...
|
||||
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_style reaxff control.reax_c.tatb
|
||||
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
|
||||
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
|
||||
fix 4 all reaxff/bonds 5 bonds.reaxff
|
||||
variable nqeq equal f_2
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 3 all reaxff/species 1 5 5 species.tatb
|
||||
|
||||
run 25
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 99.27 | 99.27 | 99.27 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
|
||||
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277 31
|
||||
5 0.61603941 -44761.698 -44760.994 8934.6279 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691 10
|
||||
10 2.352555 -44763.227 -44760.541 12288.61 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9686 0 6381.7064 9
|
||||
15 4.9013339 -44766.36 -44760.764 17716.995 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2413 0 6370.4076 10.5
|
||||
20 7.8294636 -44769.686 -44760.747 25205.611 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4966 0 6355.2478 10
|
||||
25 10.6979 -44772.904 -44760.691 34232.798 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3574 0 6336.8382 10.5
|
||||
Loop time of 2.53633 on 4 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.053 ns/day, 450.902 hours/ns, 9.857 timesteps/s
|
||||
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7343 | 1.7637 | 1.815 | 2.4 | 69.54
|
||||
Neigh | 0.44441 | 0.44869 | 0.45403 | 0.6 | 17.69
|
||||
Comm | 0.025287 | 0.074702 | 0.10592 | 11.9 | 2.95
|
||||
Output | 0.0016916 | 0.0080527 | 0.010178 | 4.1 | 0.32
|
||||
Modify | 0.23126 | 0.24065 | 0.25706 | 2.1 | 9.49
|
||||
Other | | 0.000566 | | | 0.02
|
||||
|
||||
Nlocal: 96.0000 ave 96 max 96 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5118.00 ave 5118 max 5118 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 79754.0 ave 79754 max 79754 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 319016
|
||||
Ave neighs/atom = 830.77083
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
@ -1,124 +0,0 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.013 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * acks2_ff.water O H
|
||||
Reading potential file acks2_ff.water with DATE: 2021-09-21
|
||||
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix acks2/reaxff command:
|
||||
|
||||
@Article{O'Hearn2020,
|
||||
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
|
||||
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
|
||||
journal = {SIAM J. Sci. Comput.},
|
||||
year = 2020,
|
||||
volume = 42,
|
||||
pages = {1--22}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix acks2/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 271.9 | 273.6 | 275.1 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 1572.3807 1 29915.273
|
||||
10 300.6152 8252.4834 1 29915.273
|
||||
20 294.73868 2502.5661 1 29915.273
|
||||
Loop time of 11.1133 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.078 ns/day, 308.702 hours/ns, 1.800 timesteps/s
|
||||
92.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.3609 | 4.7715 | 5.4812 | 19.5 | 42.94
|
||||
Neigh | 0.15797 | 0.17176 | 0.19405 | 3.5 | 1.55
|
||||
Comm | 0.21014 | 0.922 | 1.3353 | 44.6 | 8.30
|
||||
Output | 8.815e-05 | 0.0002 | 0.00030501 | 0.0 | 0.00
|
||||
Modify | 5.2267 | 5.2468 | 5.2584 | 0.5 | 47.21
|
||||
Other | | 0.001074 | | | 0.01
|
||||
|
||||
Nlocal: 750.000 ave 760 max 735 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 6231.50 ave 6255 max 6192 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 277006.0 ave 280567 max 271394 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1108026
|
||||
Ave neighs/atom = 369.34200
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:12
|
||||
@ -1,128 +0,0 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p s
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
3000 atoms
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 1.0
|
||||
fix 4 all wall/reflect zlo EDGE zhi EDGE
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 332.3 | 332.3 | 332.3 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 25015.837 0.99996859 29916.212
|
||||
10 348.83356 31131.298 0.99964273 29925.965
|
||||
20 414.67243 27564.999 0.99979791 29921.32
|
||||
Loop time of 15.4107 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.056 ns/day, 428.074 hours/ns, 1.298 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.413 | 11.413 | 11.413 | 0.0 | 74.06
|
||||
Neigh | 0.57486 | 0.57486 | 0.57486 | 0.0 | 3.73
|
||||
Comm | 0.0019709 | 0.0019709 | 0.0019709 | 0.0 | 0.01
|
||||
Output | 0.00013211 | 0.00013211 | 0.00013211 | 0.0 | 0.00
|
||||
Modify | 3.4192 | 3.4192 | 3.4192 | 0.0 | 22.19
|
||||
Other | | 0.001104 | | | 0.01
|
||||
|
||||
Nlocal: 3000.00 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5439.00 ave 5439 max 5439 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 786591.0 ave 786591 max 786591 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 786591
|
||||
Ave neighs/atom = 262.19700
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:16
|
||||
@ -1,128 +0,0 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p s
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
3000 atoms
|
||||
read_data CPU = 0.017 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 1.0
|
||||
fix 4 all wall/reflect zlo EDGE zhi EDGE
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 188.9 | 189.5 | 190.1 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 25015.837 0.99996859 29916.212
|
||||
10 348.83356 31131.298 0.99964273 29925.965
|
||||
20 414.67243 27564.999 0.99979791 29921.32
|
||||
Loop time of 5.71549 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.151 ns/day, 158.764 hours/ns, 3.499 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.6678 | 3.8126 | 4.1402 | 9.8 | 66.71
|
||||
Neigh | 0.31449 | 0.34639 | 0.38898 | 5.5 | 6.06
|
||||
Comm | 0.032125 | 0.35935 | 0.50408 | 31.9 | 6.29
|
||||
Output | 7.643e-05 | 0.00015959 | 0.00039876 | 0.0 | 0.00
|
||||
Modify | 1.1534 | 1.1959 | 1.2283 | 3.0 | 20.92
|
||||
Other | | 0.001099 | | | 0.02
|
||||
|
||||
Nlocal: 750.000 ave 757 max 738 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 4219.00 ave 4232 max 4198 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 230549.0 ave 233374 max 225849 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 922196
|
||||
Ave neighs/atom = 307.39867
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
@ -1,123 +0,0 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 780.33989 1 29915.273
|
||||
10 301.29205 5433.7415 1 29915.273
|
||||
20 297.90652 1572.6111 1 29915.273
|
||||
Loop time of 17.5765 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.049 ns/day, 488.237 hours/ns, 1.138 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.806 | 13.806 | 13.806 | 0.0 | 78.55
|
||||
Neigh | 0.34211 | 0.34211 | 0.34211 | 0.0 | 1.95
|
||||
Comm | 0.0028155 | 0.0028155 | 0.0028155 | 0.0 | 0.02
|
||||
Output | 0.00012279 | 0.00012279 | 0.00012279 | 0.0 | 0.00
|
||||
Modify | 3.4248 | 3.4248 | 3.4248 | 0.0 | 19.49
|
||||
Other | | 0.001008 | | | 0.01
|
||||
|
||||
Nlocal: 3000.00 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11077.0 ave 11077 max 11077 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 971826.0 ave 971826 max 971826 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 971826
|
||||
Ave neighs/atom = 323.94200
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:18
|
||||
@ -1,123 +0,0 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command:
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 780.34006 1 29915.273
|
||||
10 301.29205 5433.7414 1 29915.273
|
||||
20 297.90652 1572.6111 1 29915.273
|
||||
Loop time of 6.79573 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.127 ns/day, 188.770 hours/ns, 2.943 timesteps/s
|
||||
93.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.4827 | 4.6649 | 4.866 | 6.6 | 68.64
|
||||
Neigh | 0.16329 | 0.17253 | 0.18074 | 1.6 | 2.54
|
||||
Comm | 0.44871 | 0.64804 | 0.82827 | 17.5 | 9.54
|
||||
Output | 9.9269e-05 | 0.00013061 | 0.00022048 | 0.0 | 0.00
|
||||
Modify | 1.3028 | 1.3091 | 1.3201 | 0.6 | 19.26
|
||||
Other | | 0.001043 | | | 0.02
|
||||
|
||||
Nlocal: 750.000 ave 759 max 735 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 6230.50 ave 6256 max 6190 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 277008.0 ave 280943 max 271394 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1108032
|
||||
Ave neighs/atom = 369.34400
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p s
|
||||
@ -7,14 +8,12 @@ atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (src/read_data.cpp:1548)
|
||||
3000 atoms
|
||||
read_data CPU = 0.010 seconds
|
||||
read_data CPU = 0.008 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
@ -24,8 +23,8 @@ replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0.0012889577) to (31.043046 31.043046 31.045309)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
@ -33,7 +32,7 @@ Replicating atoms ...
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * acks2_ff.water O H
|
||||
Reading potential file acks2_ff.water with DATE: 2021-09-21
|
||||
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
@ -42,7 +41,7 @@ velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 1.0
|
||||
fix 4 all wall/reflect zlo EDGE zhi EDGE
|
||||
fix 4 all wall/reflect zlo EDGE zhi EDGE
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
@ -54,32 +53,34 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix acks2/reaxff command:
|
||||
- fix acks2/reaxff command: doi:10.1137/18M1224684
|
||||
|
||||
@Article{O'Hearn2020,
|
||||
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
|
||||
author = {K. A. {O'Hearn} and A. Alperen and H. M. Aktulga},
|
||||
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
|
||||
journal = {SIAM J. Sci. Comput.},
|
||||
journal = {SIAM J.\ Sci.\ Comput.},
|
||||
year = 2020,
|
||||
volume = 42,
|
||||
number = 1,
|
||||
pages = {1--22}
|
||||
}
|
||||
|
||||
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
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
@ -87,43 +88,43 @@ Neighbor list info ...
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix acks2/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 361.2 | 361.2 | 361.2 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 -20762.954 0.99996859 29916.212
|
||||
10 396.27588 -18423.747 1.0000143 29914.844
|
||||
20 518.59361 -10010.691 1.0000209 29914.647
|
||||
Loop time of 29.8896 on 1 procs for 20 steps with 3000 atoms
|
||||
Step Temp Press Density Volume
|
||||
0 300 -20760.354 0.99996859 29916.212
|
||||
10 396.27605 -18422.111 1.0000144 29914.843
|
||||
20 518.59317 -10012.424 1.0000209 29914.649
|
||||
Loop time of 10.4397 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.029 ns/day, 830.268 hours/ns, 0.669 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.083 ns/day, 289.992 hours/ns, 1.916 timesteps/s, 5.747 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 | 11.611 | 11.611 | 11.611 | 0.0 | 38.85
|
||||
Neigh | 0.6729 | 0.6729 | 0.6729 | 0.0 | 2.25
|
||||
Comm | 0.0020791 | 0.0020791 | 0.0020791 | 0.0 | 0.01
|
||||
Output | 0.00015777 | 0.00015777 | 0.00015777 | 0.0 | 0.00
|
||||
Modify | 17.602 | 17.602 | 17.602 | 0.0 | 58.89
|
||||
Other | | 0.001149 | | | 0.00
|
||||
Pair | 1.9062 | 1.9062 | 1.9062 | 0.0 | 18.26
|
||||
Neigh | 0.16536 | 0.16536 | 0.16536 | 0.0 | 1.58
|
||||
Comm | 0.00083949 | 0.00083949 | 0.00083949 | 0.0 | 0.01
|
||||
Output | 7.5785e-05 | 7.5785e-05 | 7.5785e-05 | 0.0 | 0.00
|
||||
Modify | 8.3669 | 8.3669 | 8.3669 | 0.0 | 80.14
|
||||
Other | | 0.0003943 | | | 0.00
|
||||
|
||||
Nlocal: 3000.00 ave 3000 max 3000 min
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5438.00 ave 5438 max 5438 min
|
||||
Nghost: 5438 ave 5438 max 5438 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 787357.0 ave 787357 max 787357 min
|
||||
Neighs: 787355 ave 787355 max 787355 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 787357
|
||||
Ave neighs/atom = 262.45233
|
||||
Total # of neighbors = 787355
|
||||
Ave neighs/atom = 262.45167
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:32
|
||||
Total wall time: 0:00:11
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p s
|
||||
@ -7,14 +8,12 @@ atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (src/read_data.cpp:1548)
|
||||
3000 atoms
|
||||
read_data CPU = 0.011 seconds
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
@ -24,8 +23,8 @@ replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0.0012889577) to (31.043046 31.043046 31.045309)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
@ -33,7 +32,7 @@ Replicating atoms ...
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * acks2_ff.water O H
|
||||
Reading potential file acks2_ff.water with DATE: 2021-09-21
|
||||
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
@ -42,7 +41,7 @@ velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 1.0
|
||||
fix 4 all wall/reflect zlo EDGE zhi EDGE
|
||||
fix 4 all wall/reflect zlo EDGE zhi EDGE
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
@ -54,32 +53,34 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix acks2/reaxff command:
|
||||
- fix acks2/reaxff command: doi:10.1137/18M1224684
|
||||
|
||||
@Article{O'Hearn2020,
|
||||
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
|
||||
author = {K. A. {O'Hearn} and A. Alperen and H. M. Aktulga},
|
||||
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
|
||||
journal = {SIAM J. Sci. Comput.},
|
||||
journal = {SIAM J.\ Sci.\ Comput.},
|
||||
year = 2020,
|
||||
volume = 42,
|
||||
number = 1,
|
||||
pages = {1--22}
|
||||
}
|
||||
|
||||
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
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
@ -87,43 +88,43 @@ Neighbor list info ...
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix acks2/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 198.5 | 199.3 | 199.9 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 -20761.724 0.99996859 29916.212
|
||||
10 396.27588 -18420.441 1.0000144 29914.843
|
||||
20 518.59146 -10012.622 1.0000207 29914.652
|
||||
Loop time of 11.3556 on 4 procs for 20 steps with 3000 atoms
|
||||
Step Temp Press Density Volume
|
||||
0 300 -20760.178 0.99996859 29916.212
|
||||
10 396.27472 -18425.294 1.0000143 29914.845
|
||||
20 518.59015 -10012.352 1.0000209 29914.647
|
||||
Loop time of 3.14386 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.076 ns/day, 315.433 hours/ns, 1.761 timesteps/s
|
||||
94.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.275 ns/day, 87.329 hours/ns, 6.362 timesteps/s, 19.085 katom-step/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.7511 | 3.8123 | 3.9245 | 3.4 | 33.57
|
||||
Neigh | 0.36492 | 0.3767 | 0.39023 | 1.5 | 3.32
|
||||
Comm | 0.12022 | 0.23202 | 0.29307 | 13.8 | 2.04
|
||||
Output | 8.0451e-05 | 0.00017452 | 0.00045489 | 0.0 | 0.00
|
||||
Modify | 6.9172 | 6.9312 | 6.9431 | 0.4 | 61.04
|
||||
Other | | 0.003189 | | | 0.03
|
||||
Pair | 0.66121 | 0.66884 | 0.68146 | 1.0 | 21.27
|
||||
Neigh | 0.095801 | 0.09707 | 0.098006 | 0.3 | 3.09
|
||||
Comm | 0.0018538 | 0.014557 | 0.022268 | 6.8 | 0.46
|
||||
Output | 3.5758e-05 | 4.0192e-05 | 5.2801e-05 | 0.0 | 0.00
|
||||
Modify | 2.3621 | 2.3631 | 2.3644 | 0.1 | 75.17
|
||||
Other | | 0.0002583 | | | 0.01
|
||||
|
||||
Nlocal: 750.000 ave 758 max 737 min
|
||||
Nlocal: 750 ave 758 max 737 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4219.50 ave 4233 max 4198 min
|
||||
Nghost: 4219.5 ave 4233 max 4198 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 230733.0 ave 233431 max 225531 min
|
||||
Neighs: 230733 ave 233430 max 225532 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
|
||||
Total # of neighbors = 922931
|
||||
Ave neighs/atom = 307.64367
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:12
|
||||
Total wall time: 0:00:03
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p p
|
||||
@ -7,11 +8,11 @@ atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.010 seconds
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
@ -21,8 +22,8 @@ replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
@ -30,7 +31,7 @@ Replicating atoms ...
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * acks2_ff.water O H
|
||||
Reading potential file acks2_ff.water with DATE: 2021-09-21
|
||||
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
@ -49,32 +50,34 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command:
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
|
||||
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix acks2/reaxff command:
|
||||
- fix acks2/reaxff command: doi:10.1137/18M1224684
|
||||
|
||||
@Article{O'Hearn2020,
|
||||
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
|
||||
author = {K. A. {O'Hearn} and A. Alperen and H. M. Aktulga},
|
||||
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
|
||||
journal = {SIAM J. Sci. Comput.},
|
||||
journal = {SIAM J.\ Sci.\ Comput.},
|
||||
year = 2020,
|
||||
volume = 42,
|
||||
number = 1,
|
||||
pages = {1--22}
|
||||
}
|
||||
|
||||
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
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
@ -82,43 +85,43 @@ Neighbor list info ...
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix acks2/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 574.5 | 574.5 | 574.5 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 1572.3474 1 29915.273
|
||||
10 300.61522 8252.7686 1 29915.273
|
||||
20 294.7387 2502.6624 1 29915.273
|
||||
Loop time of 25.9579 on 1 procs for 20 steps with 3000 atoms
|
||||
Step Temp Press Density Volume
|
||||
0 300 1572.375 1 29915.273
|
||||
10 300.61529 8252.5531 1 29915.273
|
||||
20 294.73872 2502.6392 1 29915.273
|
||||
Loop time of 8.11777 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.033 ns/day, 721.052 hours/ns, 0.770 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.106 ns/day, 225.494 hours/ns, 2.464 timesteps/s, 7.391 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 | 14.081 | 14.081 | 14.081 | 0.0 | 54.24
|
||||
Neigh | 0.34284 | 0.34284 | 0.34284 | 0.0 | 1.32
|
||||
Comm | 0.0027799 | 0.0027799 | 0.0027799 | 0.0 | 0.01
|
||||
Output | 0.00012876 | 0.00012876 | 0.00012876 | 0.0 | 0.00
|
||||
Modify | 11.53 | 11.53 | 11.53 | 0.0 | 44.42
|
||||
Other | | 0.001007 | | | 0.00
|
||||
Pair | 2.5199 | 2.5199 | 2.5199 | 0.0 | 31.04
|
||||
Neigh | 0.084903 | 0.084903 | 0.084903 | 0.0 | 1.05
|
||||
Comm | 0.00099846 | 0.00099846 | 0.00099846 | 0.0 | 0.01
|
||||
Output | 8.0735e-05 | 8.0735e-05 | 8.0735e-05 | 0.0 | 0.00
|
||||
Modify | 5.5116 | 5.5116 | 5.5116 | 0.0 | 67.90
|
||||
Other | | 0.0002721 | | | 0.00
|
||||
|
||||
Nlocal: 3000.00 ave 3000 max 3000 min
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11077.0 ave 11077 max 11077 min
|
||||
Nghost: 11077 ave 11077 max 11077 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 971815.0 ave 971815 max 971815 min
|
||||
Neighs: 971815 ave 971815 max 971815 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 971815
|
||||
Ave neighs/atom = 323.93833
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:27
|
||||
Total wall time: 0:00:08
|
||||
127
examples/reaxff/water/log.1Feb25.water.acks2.g++.4
Normal file
127
examples/reaxff/water/log.1Feb25.water.acks2.g++.4
Normal file
@ -0,0 +1,127 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.008 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * acks2_ff.water O H
|
||||
Reading potential file acks2_ff.water with DATE: 2021-09-21
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix acks2/reaxff command: doi:10.1137/18M1224684
|
||||
|
||||
@Article{O'Hearn2020,
|
||||
author = {K. A. {O'Hearn} and A. Alperen and H. M. Aktulga},
|
||||
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
|
||||
journal = {SIAM J.\ Sci.\ Comput.},
|
||||
year = 2020,
|
||||
volume = 42,
|
||||
number = 1,
|
||||
pages = {1--22}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix acks2/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 271.9 | 273.6 | 275.1 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 1572.3706 1 29915.273
|
||||
10 300.61525 8252.6882 1 29915.273
|
||||
20 294.7387 2502.7174 1 29915.273
|
||||
Loop time of 2.53362 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.341 ns/day, 70.378 hours/ns, 7.894 timesteps/s, 23.682 katom-step/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.8583 | 0.87474 | 0.88456 | 1.1 | 34.53
|
||||
Neigh | 0.041176 | 0.041568 | 0.041796 | 0.1 | 1.64
|
||||
Comm | 0.0025543 | 0.012388 | 0.028859 | 9.1 | 0.49
|
||||
Output | 3.4346e-05 | 3.8911e-05 | 5.1678e-05 | 0.0 | 0.00
|
||||
Modify | 1.6044 | 1.6047 | 1.6051 | 0.0 | 63.34
|
||||
Other | | 0.0001809 | | | 0.01
|
||||
|
||||
Nlocal: 750 ave 760 max 735 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 6231.5 ave 6255 max 6192 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 277006 ave 280567 max 271394 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1108026
|
||||
Ave neighs/atom = 369.342
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
1
examples/reaxff/water/log.1Feb25.water.gtpie.field.g++.1
Normal file
1
examples/reaxff/water/log.1Feb25.water.gtpie.field.g++.1
Normal file
@ -0,0 +1 @@
|
||||
ERROR: Cannot open input script in.water.gtpie.field: No such file or directory (src/lammps.cpp:565)
|
||||
128
examples/reaxff/water/log.1Feb25.water.qeq.field.g++.1
Normal file
128
examples/reaxff/water/log.1Feb25.water.qeq.field.g++.1
Normal file
@ -0,0 +1,128 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p s
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (src/read_data.cpp:1548)
|
||||
3000 atoms
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0.0012889577) to (31.043046 31.043046 31.045309)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.000 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 1.0
|
||||
fix 4 all wall/reflect zlo EDGE zhi EDGE
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 332.3 | 332.3 | 332.3 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 25015.837 0.99996859 29916.212
|
||||
10 348.83356 31131.298 0.99964273 29925.965
|
||||
20 414.67243 27564.999 0.99979791 29921.32
|
||||
Loop time of 3.50891 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.246 ns/day, 97.470 hours/ns, 5.700 timesteps/s, 17.099 katom-step/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0529 | 2.0529 | 2.0529 | 0.0 | 58.51
|
||||
Neigh | 0.14819 | 0.14819 | 0.14819 | 0.0 | 4.22
|
||||
Comm | 0.00068525 | 0.00068525 | 0.00068525 | 0.0 | 0.02
|
||||
Output | 7.7489e-05 | 7.7489e-05 | 7.7489e-05 | 0.0 | 0.00
|
||||
Modify | 1.3066 | 1.3066 | 1.3066 | 0.0 | 37.24
|
||||
Other | | 0.0004355 | | | 0.01
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5439 ave 5439 max 5439 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 786591 ave 786591 max 786591 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 786591
|
||||
Ave neighs/atom = 262.197
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
128
examples/reaxff/water/log.1Feb25.water.qeq.field.g++.4
Normal file
128
examples/reaxff/water/log.1Feb25.water.qeq.field.g++.4
Normal file
@ -0,0 +1,128 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p s
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (src/read_data.cpp:1548)
|
||||
3000 atoms
|
||||
read_data CPU = 0.008 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0.0012889577) to (31.043046 31.043046 31.045309)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 1.0
|
||||
fix 4 all wall/reflect zlo EDGE zhi EDGE
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 188.9 | 189.5 | 190.1 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 25015.837 0.99996859 29916.212
|
||||
10 348.83356 31131.298 0.99964273 29925.965
|
||||
20 414.67243 27564.999 0.99979791 29921.32
|
||||
Loop time of 1.25077 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.691 ns/day, 34.744 hours/ns, 15.990 timesteps/s, 47.971 katom-step/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.76221 | 0.7759 | 0.78605 | 1.2 | 62.03
|
||||
Neigh | 0.083557 | 0.08496 | 0.086573 | 0.4 | 6.79
|
||||
Comm | 0.0090777 | 0.019109 | 0.032959 | 7.4 | 1.53
|
||||
Output | 3.8563e-05 | 4.1662e-05 | 5.0627e-05 | 0.0 | 0.00
|
||||
Modify | 0.36853 | 0.37036 | 0.37195 | 0.2 | 29.61
|
||||
Other | | 0.0003959 | | | 0.03
|
||||
|
||||
Nlocal: 750 ave 757 max 738 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 4219 ave 4232 max 4198 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 230549 ave 233374 max 225849 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 922196
|
||||
Ave neighs/atom = 307.39867
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
125
examples/reaxff/water/log.1Feb25.water.qeq.g++.1
Normal file
125
examples/reaxff/water/log.1Feb25.water.qeq.g++.1
Normal file
@ -0,0 +1,125 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 780.33989 1 29915.273
|
||||
10 301.29205 5433.7414 1 29915.273
|
||||
20 297.90652 1572.6111 1 29915.273
|
||||
Loop time of 3.64687 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.237 ns/day, 101.302 hours/ns, 5.484 timesteps/s, 16.452 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 | 2.3756 | 2.3756 | 2.3756 | 0.0 | 65.14
|
||||
Neigh | 0.086129 | 0.086129 | 0.086129 | 0.0 | 2.36
|
||||
Comm | 0.00090825 | 0.00090825 | 0.00090825 | 0.0 | 0.02
|
||||
Output | 7.3411e-05 | 7.3411e-05 | 7.3411e-05 | 0.0 | 0.00
|
||||
Modify | 1.1839 | 1.1839 | 1.1839 | 0.0 | 32.46
|
||||
Other | | 0.0002483 | | | 0.01
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11077 ave 11077 max 11077 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 971826 ave 971826 max 971826 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 971826
|
||||
Ave neighs/atom = 323.942
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
125
examples/reaxff/water/log.1Feb25.water.qeq.g++.4
Normal file
125
examples/reaxff/water/log.1Feb25.water.qeq.g++.4
Normal file
@ -0,0 +1,125 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
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 = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 780.34006 1 29915.273
|
||||
10 301.29205 5433.7414 1 29915.273
|
||||
20 297.90652 1572.6111 1 29915.273
|
||||
Loop time of 1.21853 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.709 ns/day, 33.848 hours/ns, 16.413 timesteps/s, 49.240 katom-step/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.81943 | 0.83131 | 0.84443 | 1.2 | 68.22
|
||||
Neigh | 0.040127 | 0.040506 | 0.040961 | 0.2 | 3.32
|
||||
Comm | 0.0025704 | 0.015716 | 0.027606 | 8.9 | 1.29
|
||||
Output | 3.3504e-05 | 3.7908e-05 | 5.1038e-05 | 0.0 | 0.00
|
||||
Modify | 0.33037 | 0.33079 | 0.33116 | 0.1 | 27.15
|
||||
Other | | 0.0001712 | | | 0.01
|
||||
|
||||
Nlocal: 750 ave 759 max 735 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 6230.5 ave 6256 max 6190 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 277008 ave 280943 max 271394 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1108032
|
||||
Ave neighs/atom = 369.344
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-76-g3f232caf9b)
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QTPIE Water
|
||||
|
||||
@ -12,7 +12,7 @@ Reading data file ...
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.056 seconds
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
@ -50,18 +50,6 @@ 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}
|
||||
}
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
@ -98,20 +86,20 @@ Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes
|
||||
0 300 10137.041 1 29915.273
|
||||
10 296.09128 3564.7969 1 29915.273
|
||||
20 293.04308 10299.201 1 29915.273
|
||||
Loop time of 10.7863 on 1 procs for 20 steps with 3000 atoms
|
||||
Loop time of 5.72124 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.080 ns/day, 299.620 hours/ns, 1.854 timesteps/s, 5.563 katom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.151 ns/day, 158.923 hours/ns, 3.496 timesteps/s, 10.487 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 | 4.7275 | 4.7275 | 4.7275 | 0.0 | 43.83
|
||||
Neigh | 0.17533 | 0.17533 | 0.17533 | 0.0 | 1.63
|
||||
Comm | 0.0017376 | 0.0017376 | 0.0017376 | 0.0 | 0.02
|
||||
Output | 8.2065e-05 | 8.2065e-05 | 8.2065e-05 | 0.0 | 0.00
|
||||
Modify | 5.8812 | 5.8812 | 5.8812 | 0.0 | 54.52
|
||||
Other | | 0.0005226 | | | 0.00
|
||||
Pair | 2.4349 | 2.4349 | 2.4349 | 0.0 | 42.56
|
||||
Neigh | 0.087463 | 0.087463 | 0.087463 | 0.0 | 1.53
|
||||
Comm | 0.0008652 | 0.0008652 | 0.0008652 | 0.0 | 0.02
|
||||
Output | 7.2618e-05 | 7.2618e-05 | 7.2618e-05 | 0.0 | 0.00
|
||||
Modify | 3.1977 | 3.1977 | 3.1977 | 0.0 | 55.89
|
||||
Other | | 0.0002686 | | | 0.00
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -124,4 +112,4 @@ Total # of neighbors = 971775
|
||||
Ave neighs/atom = 323.925
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:12
|
||||
Total wall time: 0:00:06
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-76-g3f232caf9b)
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QTPIE Water
|
||||
|
||||
@ -12,7 +12,7 @@ Reading data file ...
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.053 seconds
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
@ -50,18 +50,6 @@ 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}
|
||||
}
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
@ -98,20 +86,20 @@ Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
|
||||
0 300 10137.041 1 29915.273
|
||||
10 296.09128 3564.7969 1 29915.273
|
||||
20 293.04308 10299.201 1 29915.273
|
||||
Loop time of 3.14492 on 4 procs for 20 steps with 3000 atoms
|
||||
Loop time of 1.608 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.275 ns/day, 87.359 hours/ns, 6.359 timesteps/s, 19.078 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.537 ns/day, 44.667 hours/ns, 12.438 timesteps/s, 37.313 katom-step/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6557 | 1.6847 | 1.7281 | 2.1 | 53.57
|
||||
Neigh | 0.086503 | 0.086968 | 0.087627 | 0.2 | 2.77
|
||||
Comm | 0.003309 | 0.046699 | 0.075729 | 12.4 | 1.48
|
||||
Output | 5.0156e-05 | 5.483e-05 | 6.8111e-05 | 0.0 | 0.00
|
||||
Modify | 1.3254 | 1.3261 | 1.3266 | 0.0 | 42.16
|
||||
Other | | 0.0004552 | | | 0.01
|
||||
Pair | 0.87233 | 0.88282 | 0.89373 | 1.1 | 54.90
|
||||
Neigh | 0.041191 | 0.041319 | 0.041633 | 0.1 | 2.57
|
||||
Comm | 0.0054984 | 0.016437 | 0.026941 | 7.8 | 1.02
|
||||
Output | 3.5678e-05 | 3.9736e-05 | 5.1198e-05 | 0.0 | 0.00
|
||||
Modify | 0.66686 | 0.6672 | 0.66733 | 0.0 | 41.49
|
||||
Other | | 0.0001861 | | | 0.01
|
||||
|
||||
Nlocal: 750 ave 760 max 735 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
@ -124,4 +112,4 @@ Total # of neighbors = 1107981
|
||||
Ave neighs/atom = 369.327
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
Total wall time: 0:00:01
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-76-g3f232caf9b)
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QTPIE Water
|
||||
|
||||
@ -12,7 +12,7 @@ Reading data file ...
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.055 seconds
|
||||
read_data CPU = 0.008 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
@ -49,18 +49,6 @@ 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}
|
||||
}
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
@ -97,20 +85,20 @@ Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes
|
||||
0 300 10138.375 1 29915.273
|
||||
10 295.97879 3575.2769 1 29915.273
|
||||
20 292.76583 10309.128 1 29915.273
|
||||
Loop time of 10.8138 on 1 procs for 20 steps with 3000 atoms
|
||||
Loop time of 5.70229 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.080 ns/day, 300.383 hours/ns, 1.849 timesteps/s, 5.548 katom-step/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.152 ns/day, 158.397 hours/ns, 3.507 timesteps/s, 10.522 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 | 4.7177 | 4.7177 | 4.7177 | 0.0 | 43.63
|
||||
Neigh | 0.17607 | 0.17607 | 0.17607 | 0.0 | 1.63
|
||||
Comm | 0.0017295 | 0.0017295 | 0.0017295 | 0.0 | 0.02
|
||||
Output | 8.5431e-05 | 8.5431e-05 | 8.5431e-05 | 0.0 | 0.00
|
||||
Modify | 5.9177 | 5.9177 | 5.9177 | 0.0 | 54.72
|
||||
Other | | 0.0004911 | | | 0.00
|
||||
Pair | 2.4269 | 2.4269 | 2.4269 | 0.0 | 42.56
|
||||
Neigh | 0.084723 | 0.084723 | 0.084723 | 0.0 | 1.49
|
||||
Comm | 0.00093159 | 0.00093159 | 0.00093159 | 0.0 | 0.02
|
||||
Output | 7.4061e-05 | 7.4061e-05 | 7.4061e-05 | 0.0 | 0.00
|
||||
Modify | 3.1894 | 3.1894 | 3.1894 | 0.0 | 55.93
|
||||
Other | | 0.0002537 | | | 0.00
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -123,4 +111,4 @@ Total # of neighbors = 971830
|
||||
Ave neighs/atom = 323.94333
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:12
|
||||
Total wall time: 0:00:06
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-76-g3f232caf9b)
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QTPIE Water
|
||||
|
||||
@ -12,7 +12,7 @@ Reading data file ...
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.053 seconds
|
||||
read_data CPU = 0.008 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
@ -49,18 +49,6 @@ 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}
|
||||
}
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
@ -97,20 +85,20 @@ Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
|
||||
0 300 10138.375 1 29915.273
|
||||
10 295.97879 3575.2769 1 29915.273
|
||||
20 292.76583 10309.128 1 29915.273
|
||||
Loop time of 3.13598 on 4 procs for 20 steps with 3000 atoms
|
||||
Loop time of 1.53381 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.276 ns/day, 87.111 hours/ns, 6.378 timesteps/s, 19.133 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.563 ns/day, 42.606 hours/ns, 13.039 timesteps/s, 39.118 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6622 | 1.695 | 1.7252 | 2.2 | 54.05
|
||||
Neigh | 0.086543 | 0.087117 | 0.087848 | 0.2 | 2.78
|
||||
Comm | 0.0048192 | 0.035002 | 0.067754 | 15.4 | 1.12
|
||||
Output | 4.8033e-05 | 5.3375e-05 | 6.6893e-05 | 0.0 | 0.00
|
||||
Modify | 1.3176 | 1.3183 | 1.3189 | 0.0 | 42.04
|
||||
Other | | 0.0004753 | | | 0.02
|
||||
Pair | 0.8105 | 0.82543 | 0.84031 | 1.4 | 53.82
|
||||
Neigh | 0.041129 | 0.041436 | 0.041966 | 0.2 | 2.70
|
||||
Comm | 0.0019875 | 0.016866 | 0.031795 | 9.9 | 1.10
|
||||
Output | 3.2672e-05 | 3.6427e-05 | 4.734e-05 | 0.0 | 0.00
|
||||
Modify | 0.64934 | 0.64987 | 0.65017 | 0.0 | 42.37
|
||||
Other | | 0.0001691 | | | 0.01
|
||||
|
||||
Nlocal: 750 ave 760 max 735 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
@ -123,4 +111,4 @@ Total # of neighbors = 1108044
|
||||
Ave neighs/atom = 369.348
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
Total wall time: 0:00:01
|
||||
@ -9,5 +9,11 @@ in.snap.Mo_Chen # SNAP linear Mo potential
|
||||
in.snap.compute # SNAP compute for training a linear model
|
||||
in.snap.compute.quadratic # SNAP compute for training a quadratic model
|
||||
in.snap.scale.Ni_Zuo_JCPA2020 # SNAP linear Ni potential with thermodynamic integration (fix adapt scale)
|
||||
in.C_SNAP # SNAP carbon potential
|
||||
|
||||
compute_snap_dgrad.py # SNAP compute with dgradflag (dBi/dRj) for training a non-linear model
|
||||
|
||||
in.snap.grid # SNAP descriptors on a grid
|
||||
in.snap.grid.triclinic # SNAP descriptors on a grid, triclinic
|
||||
in.gaussian.grid # Gaussian descriptors on a grid
|
||||
|
||||
|
||||
68
examples/snap/in.gaussian.grid
Normal file
68
examples/snap/in.gaussian.grid
Normal file
@ -0,0 +1,68 @@
|
||||
# Demonstrate calculation of Gaussian descriptors on a grid
|
||||
# for a cell with two atoms of type 1 and type 2.
|
||||
# The output in dump.glocal shows that for grid points
|
||||
# sitting on an atom of type 1 or 2:
|
||||
# val1 = 1.0/(0.1355*sqrt(2.0*pi))**3 = 25.5219
|
||||
# val2 = 1.0/(0.2 *sqrt(2.0*pi))**3 = 7.93670
|
||||
# These values are extracted to the log file
|
||||
#
|
||||
|
||||
variable nrep index 1
|
||||
variable a index 3.316
|
||||
variable ngrid index 2
|
||||
|
||||
units metal
|
||||
atom_modify map hash
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable ny equal ${nrep}
|
||||
variable nz equal ${nrep}
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice custom $a &
|
||||
a1 1 0 0 &
|
||||
a2 0 1 0 &
|
||||
a3 0 0 1 &
|
||||
basis 0 0 0 &
|
||||
basis 0.5 0.5 0.5 &
|
||||
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
create_box 2 box
|
||||
create_atoms 1 box basis 1 1 basis 2 2
|
||||
|
||||
mass * 180.88
|
||||
|
||||
# define atom compute and grid compute
|
||||
|
||||
variable rcutfac equal 4.67637
|
||||
variable radelem1 equal 0.5
|
||||
variable radelem2 equal 0.5
|
||||
variable sigmaelem1 equal 0.1355
|
||||
variable sigmaelem2 equal 0.2
|
||||
variable gaussian_options string &
|
||||
"${rcutfac} ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}"
|
||||
|
||||
# build zero potential to force ghost atom creation
|
||||
|
||||
pair_style zero ${rcutfac}
|
||||
pair_coeff * *
|
||||
|
||||
# define atom and grid computes
|
||||
|
||||
compute mygridlocal all gaussian/grid/local grid ${ngrid} ${ngrid} ${ngrid} &
|
||||
${gaussian_options}
|
||||
|
||||
# define output
|
||||
|
||||
dump 1 all local 1000 dump.glocal c_mygridlocal[*]
|
||||
dump 2 all custom 1000 dump.gatom id x y z
|
||||
compute val1 all reduce max c_mygridlocal[7] inputs local
|
||||
compute val2 all reduce max c_mygridlocal[8] inputs local
|
||||
thermo_style custom step c_val1 c_val2
|
||||
|
||||
# run
|
||||
|
||||
run 0
|
||||
@ -47,7 +47,6 @@ lattice custom $a &
|
||||
basis 0.0 0.0 0.5 &
|
||||
spacing 1 1 1
|
||||
|
||||
box tilt large
|
||||
region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
129
examples/snap/log.10Dec24.gaussian.grid.g++.1
Normal file
129
examples/snap/log.10Dec24.gaussian.grid.g++.1
Normal file
@ -0,0 +1,129 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-59-g16e0a7788a)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate calculation of Gaussian descriptors on a grid
|
||||
# for a cell with two atoms of type 1 and type 2.
|
||||
# The output in dump.glocal shows that for grid points
|
||||
# sitting on an atom of type 1 or 2:
|
||||
# val1 = 1.0/(0.1355*sqrt(2.0*pi))**3 = 25.5219
|
||||
# val2 = 1.0/(0.2 *sqrt(2.0*pi))**3 = 7.93670
|
||||
# These values are extracted to the log file
|
||||
#
|
||||
|
||||
variable nrep index 1
|
||||
variable a index 3.316
|
||||
variable ngrid index 2
|
||||
|
||||
units metal
|
||||
atom_modify map hash
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
|
||||
lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2
|
||||
Created 2 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
# define atom compute and grid compute
|
||||
|
||||
variable rcutfac equal 4.67637
|
||||
variable radelem1 equal 0.5
|
||||
variable radelem2 equal 0.5
|
||||
variable sigmaelem1 equal 0.1355
|
||||
variable sigmaelem2 equal 0.2
|
||||
variable gaussian_options string "${rcutfac} ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}"
|
||||
4.67637 ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}
|
||||
4.67637 0.5 ${radelem2} ${sigmaelem1} ${sigmaelem2}
|
||||
4.67637 0.5 0.5 ${sigmaelem1} ${sigmaelem2}
|
||||
4.67637 0.5 0.5 0.1355 ${sigmaelem2}
|
||||
4.67637 0.5 0.5 0.1355 0.2
|
||||
|
||||
# build zero potential to force ghost atom creation
|
||||
|
||||
pair_style zero ${rcutfac}
|
||||
pair_style zero 4.67637
|
||||
pair_coeff * *
|
||||
|
||||
# define atom and grid computes
|
||||
|
||||
compute mygridlocal all gaussian/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${gaussian_options}
|
||||
compute mygridlocal all gaussian/grid/local grid 2 ${ngrid} ${ngrid} ${gaussian_options}
|
||||
compute mygridlocal all gaussian/grid/local grid 2 2 ${ngrid} ${gaussian_options}
|
||||
compute mygridlocal all gaussian/grid/local grid 2 2 2 ${gaussian_options}
|
||||
compute mygridlocal all gaussian/grid/local grid 2 2 2 4.67637 0.5 0.5 0.1355 0.2
|
||||
|
||||
# define output
|
||||
|
||||
dump 1 all local 1000 dump.glocal c_mygridlocal[*]
|
||||
dump 2 all custom 1000 dump.gatom id x y z
|
||||
compute val1 all reduce max c_mygridlocal[7] inputs local
|
||||
compute val2 all reduce max c_mygridlocal[8] inputs local
|
||||
thermo_style custom step c_val1 c_val2
|
||||
|
||||
# run
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 1 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 = 6.67637
|
||||
ghost atom cutoff = 6.67637
|
||||
binsize = 3.338185, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, 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) = 3.492 | 3.492 | 3.492 Mbytes
|
||||
Step c_val1 c_val2
|
||||
0 25.521859 7.9367045
|
||||
Loop time of 1.088e-06 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
183.8% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.088e-06 | | |100.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 339 ave 339 max 339 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 64 ave 64 max 64 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 64
|
||||
Ave neighs/atom = 32
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
130
examples/snap/log.10Dec24.gaussian.grid.g++.4
Normal file
130
examples/snap/log.10Dec24.gaussian.grid.g++.4
Normal file
@ -0,0 +1,130 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-59-g16e0a7788a)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate calculation of Gaussian descriptors on a grid
|
||||
# for a cell with two atoms of type 1 and type 2.
|
||||
# The output in dump.glocal shows that for grid points
|
||||
# sitting on an atom of type 1 or 2:
|
||||
# val1 = 1.0/(0.1355*sqrt(2.0*pi))**3 = 25.5219
|
||||
# val2 = 1.0/(0.2 *sqrt(2.0*pi))**3 = 7.93670
|
||||
# These values are extracted to the log file
|
||||
#
|
||||
|
||||
variable nrep index 1
|
||||
variable a index 3.316
|
||||
variable ngrid index 2
|
||||
|
||||
units metal
|
||||
atom_modify map hash
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
|
||||
lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2
|
||||
Created 2 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
# define atom compute and grid compute
|
||||
|
||||
variable rcutfac equal 4.67637
|
||||
variable radelem1 equal 0.5
|
||||
variable radelem2 equal 0.5
|
||||
variable sigmaelem1 equal 0.1355
|
||||
variable sigmaelem2 equal 0.2
|
||||
variable gaussian_options string "${rcutfac} ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}"
|
||||
4.67637 ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}
|
||||
4.67637 0.5 ${radelem2} ${sigmaelem1} ${sigmaelem2}
|
||||
4.67637 0.5 0.5 ${sigmaelem1} ${sigmaelem2}
|
||||
4.67637 0.5 0.5 0.1355 ${sigmaelem2}
|
||||
4.67637 0.5 0.5 0.1355 0.2
|
||||
|
||||
# build zero potential to force ghost atom creation
|
||||
|
||||
pair_style zero ${rcutfac}
|
||||
pair_style zero 4.67637
|
||||
pair_coeff * *
|
||||
|
||||
# define atom and grid computes
|
||||
|
||||
compute mygridlocal all gaussian/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${gaussian_options}
|
||||
compute mygridlocal all gaussian/grid/local grid 2 ${ngrid} ${ngrid} ${gaussian_options}
|
||||
compute mygridlocal all gaussian/grid/local grid 2 2 ${ngrid} ${gaussian_options}
|
||||
compute mygridlocal all gaussian/grid/local grid 2 2 2 ${gaussian_options}
|
||||
compute mygridlocal all gaussian/grid/local grid 2 2 2 4.67637 0.5 0.5 0.1355 0.2
|
||||
|
||||
# define output
|
||||
|
||||
dump 1 all local 1000 dump.glocal c_mygridlocal[*]
|
||||
dump 2 all custom 1000 dump.gatom id x y z
|
||||
compute val1 all reduce max c_mygridlocal[7] inputs local
|
||||
compute val2 all reduce max c_mygridlocal[8] inputs local
|
||||
thermo_style custom step c_val1 c_val2
|
||||
|
||||
# run
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 1 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 = 6.67637
|
||||
ghost atom cutoff = 6.67637
|
||||
binsize = 3.338185, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.522 | 3.523 | 3.524 Mbytes
|
||||
Step c_val1 c_val2
|
||||
0 25.521859 7.9367045
|
||||
Loop time of 2.238e-06 on 4 procs for 0 steps with 2 atoms
|
||||
|
||||
89.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.238e-06 | | |100.00
|
||||
|
||||
Nlocal: 0.5 ave 1 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 274.5 ave 275 max 274 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 16 ave 40 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 64
|
||||
Ave neighs/atom = 32
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
Reference in New Issue
Block a user