Merge branch 'develop' into bond/react-molmap_option
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,5 @@
|
||||
LAMMPS (15 Sep 2022)
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# flat membrane demo
|
||||
variable r0 equal 0.97
|
||||
@ -46,7 +47,7 @@ set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
1920 settings made for mass
|
||||
|
||||
set type 1 shape 1 1 1
|
||||
set type 1 shape 1 0.99 0.99
|
||||
Setting atom values ...
|
||||
1920 settings made for shape
|
||||
|
||||
@ -99,7 +100,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 10 steps, check = yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.6
|
||||
ghost atom cutoff = 3.6
|
||||
@ -113,47 +114,47 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
|
||||
Step Temp Press Pxx Pyy
|
||||
0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
||||
200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
|
||||
400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
|
||||
600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
|
||||
800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
|
||||
1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
|
||||
1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
|
||||
1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
|
||||
1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
|
||||
1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
|
||||
2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
|
||||
2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
|
||||
2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
|
||||
2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
|
||||
2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
|
||||
3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
|
||||
Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
|
||||
200 0.20906916 -0.0010610794 -0.0011895359 -0.00198968
|
||||
400 0.21907691 -0.00068750897 -0.0013175111 -0.00072355516
|
||||
600 0.22648739 -0.00057306694 -0.000831971 -0.00096776143
|
||||
800 0.2368957 -0.00028517767 -0.00050638195 -0.00052670236
|
||||
1000 0.22735705 -0.00032638104 -0.00037959812 -0.00071879257
|
||||
1200 0.22910882 -0.00019457758 -0.00024451315 -0.00027807764
|
||||
1400 0.22754022 -0.00033048317 -0.00010053263 -0.00075173132
|
||||
1600 0.22503496 -7.593954e-05 5.2989168e-05 -0.00022521685
|
||||
1800 0.22673577 -0.00017917699 1.0176667e-05 -0.00047893102
|
||||
2000 0.22480858 9.318318e-05 0.00031024343 1.2738253e-05
|
||||
2200 0.22387294 -6.9083174e-05 -4.6170865e-05 4.6682009e-05
|
||||
2400 0.22686231 0.00022776785 0.00028204391 0.00030116273
|
||||
2600 0.23055637 8.2778175e-05 0.00027137529 4.2254076e-05
|
||||
2800 0.23126717 0.00044863024 0.00071654709 0.00057652233
|
||||
3000 0.22234736 0.00031577792 0.00051797227 0.00039087282
|
||||
Loop time of 7.17991 on 1 procs for 3000 steps with 1920 atoms
|
||||
|
||||
Performance: 383058.431 tau/day, 443.355 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 361007.348 tau/day, 417.833 timesteps/s, 802.239 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 | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67
|
||||
Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27
|
||||
Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51
|
||||
Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01
|
||||
Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22
|
||||
Other | | 0.02181 | | | 0.32
|
||||
Pair | 6.2257 | 6.2257 | 6.2257 | 0.0 | 86.71
|
||||
Neigh | 0.11392 | 0.11392 | 0.11392 | 0.0 | 1.59
|
||||
Comm | 0.036614 | 0.036614 | 0.036614 | 0.0 | 0.51
|
||||
Output | 0.00052672 | 0.00052672 | 0.00052672 | 0.0 | 0.01
|
||||
Modify | 0.78577 | 0.78577 | 0.78577 | 0.0 | 10.94
|
||||
Other | | 0.01743 | | | 0.24
|
||||
|
||||
Nlocal: 1920 ave 1920 max 1920 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 772 ave 772 max 772 min
|
||||
Nghost: 771 ave 771 max 771 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 46804 ave 46804 max 46804 min
|
||||
Neighs: 46750 ave 46750 max 46750 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46804
|
||||
Ave neighs/atom = 24.377083
|
||||
Neighbor list builds = 99
|
||||
Total # of neighbors = 46750
|
||||
Ave neighs/atom = 24.348958
|
||||
Neighbor list builds = 98
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
Total wall time: 0:00:07
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (15 Sep 2022)
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# flat membrane demo
|
||||
variable r0 equal 0.97
|
||||
@ -46,7 +47,7 @@ set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
1920 settings made for mass
|
||||
|
||||
set type 1 shape 1 1 1
|
||||
set type 1 shape 1 0.99 0.99
|
||||
Setting atom values ...
|
||||
1920 settings made for shape
|
||||
|
||||
@ -99,7 +100,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 10 steps, check = yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.6
|
||||
ghost atom cutoff = 3.6
|
||||
@ -113,47 +114,47 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
|
||||
Step Temp Press Pxx Pyy
|
||||
0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
||||
200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502
|
||||
400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093
|
||||
600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609
|
||||
800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294
|
||||
1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572
|
||||
1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505
|
||||
1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05
|
||||
1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754
|
||||
1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05
|
||||
2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213
|
||||
2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05
|
||||
2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05
|
||||
2600 0.23085675 0.00014029405 0.00017983536 0.00017895001
|
||||
2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243
|
||||
3000 0.23421357 0.00023505702 0.00020752013 0.00053567111
|
||||
Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
|
||||
200 0.21866566 -0.0011213114 -0.0017540296 -0.0017008786
|
||||
400 0.22409469 -0.00055137604 -0.00050366017 -0.0012846672
|
||||
600 0.21623646 -0.0004808564 -0.00063496522 -0.00071617302
|
||||
800 0.22248339 -0.00066333806 -0.00093812145 -0.00099410261
|
||||
1000 0.22367907 -0.0003439459 -0.00076259578 -0.00013354375
|
||||
1200 0.23276206 8.5764334e-06 -0.00036165178 0.00038543803
|
||||
1400 0.23129049 -5.1997966e-06 -0.00040514787 0.00017093646
|
||||
1600 0.22074564 -0.0001604642 -0.00053959031 9.0463391e-05
|
||||
1800 0.2276062 -0.00015655254 -0.00042925633 5.4938379e-05
|
||||
2000 0.22469391 -3.6198836e-05 -1.8538296e-06 -0.00010464749
|
||||
2200 0.22737515 -1.8967356e-05 0.0001341006 -0.00022739894
|
||||
2400 0.22607533 0.00014650382 -2.4871789e-05 0.00058296255
|
||||
2600 0.24044743 0.00045066449 0.00049153595 0.00078042437
|
||||
2800 0.23346628 0.00017994019 -5.0897724e-05 0.00046011801
|
||||
3000 0.22427206 0.00040437022 0.00049580531 0.00046259202
|
||||
Loop time of 5.04539 on 4 procs for 3000 steps with 1920 atoms
|
||||
|
||||
Performance: 553164.568 tau/day, 640.237 timesteps/s
|
||||
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 513736.789 tau/day, 594.603 timesteps/s, 1.142 Matom-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 | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21
|
||||
Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54
|
||||
Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28
|
||||
Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50
|
||||
Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57
|
||||
Other | | 2.338 | | | 49.90
|
||||
Pair | 4.1163 | 4.2634 | 4.4004 | 6.5 | 84.50
|
||||
Neigh | 0.00088605 | 0.032793 | 0.083516 | 19.1 | 0.65
|
||||
Comm | 0.006704 | 0.20003 | 0.40672 | 42.5 | 3.96
|
||||
Output | 0.00033812 | 0.0012192 | 0.0020905 | 2.3 | 0.02
|
||||
Modify | 0.00035967 | 0.20167 | 0.42535 | 45.0 | 4.00
|
||||
Other | | 0.3462 | | | 6.86
|
||||
|
||||
Nlocal: 480 ave 1011 max 0 min
|
||||
Nlocal: 480 ave 1052 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 860 ave 1771 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 11697.8 ave 30095 max 0 min
|
||||
Nghost: 854.5 ave 1801 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 11684.2 ave 31145 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 46791
|
||||
Ave neighs/atom = 24.370313
|
||||
Neighbor list builds = 99
|
||||
Total # of neighbors = 46737
|
||||
Ave neighs/atom = 24.342188
|
||||
Neighbor list builds = 98
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:04
|
||||
Total wall time: 0:00:05
|
||||
@ -1,5 +1,5 @@
|
||||
# FENE beadspring benchmark
|
||||
|
||||
variable t index 1.0
|
||||
units lj
|
||||
atom_style bond
|
||||
special_bonds fene
|
||||
|
||||
@ -117,6 +117,10 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(set_string_variable);
|
||||
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);
|
||||
@ -200,6 +204,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(has_error);
|
||||
ADDSYM(get_last_error_message);
|
||||
}
|
||||
ADDSYM(set_show_error);
|
||||
|
||||
ADDSYM(python_api_version);
|
||||
return lmp;
|
||||
|
||||
@ -24,7 +24,7 @@
|
||||
* Follow the behavior of regular LAMMPS compilation and assume
|
||||
* -DLAMMPS_SMALLBIG when no define is set.
|
||||
*/
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#define LAMMPS_SMALLBIG
|
||||
#endif
|
||||
|
||||
@ -100,8 +100,6 @@ extern "C" {
|
||||
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
|
||||
#elif defined(LAMMPS_SMALLSMALL)
|
||||
typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
|
||||
#else
|
||||
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
|
||||
#endif
|
||||
@ -111,6 +109,7 @@ struct _liblammpsplugin {
|
||||
int abiversion;
|
||||
int has_exceptions;
|
||||
void *handle;
|
||||
|
||||
#if defined(LAMMPS_LIB_MPI)
|
||||
void *(*open)(int, char **, MPI_Comm, void **);
|
||||
#else
|
||||
@ -163,6 +162,10 @@ struct _liblammpsplugin {
|
||||
int (*set_string_variable)(void *, const char *, const char *);
|
||||
int (*set_internal_variable)(void *, const char *, double);
|
||||
int (*variable_info)(void *, int, char *, int);
|
||||
double (*eval)(void *, const char *);
|
||||
void (*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 *);
|
||||
@ -185,7 +188,7 @@ struct _liblammpsplugin {
|
||||
* the ifdef ensures they are compatible with rest of LAMMPS
|
||||
* caller must match to how LAMMPS library is built */
|
||||
|
||||
#ifndef LAMMPS_BIGBIG
|
||||
#if !defined(LAMMPS_BIGBIG)
|
||||
int (*create_atoms)(void *, int, int *, int *, double *, double *, int *, int);
|
||||
#else
|
||||
int (*create_atoms)(void *, int, int64_t *, int *, double *, double *, int64_t *, int);
|
||||
@ -253,6 +256,7 @@ struct _liblammpsplugin {
|
||||
|
||||
int (*has_error)(void *);
|
||||
int (*get_last_error_message)(void *, char *, int);
|
||||
int (*set_show_error)(void *, const int);
|
||||
|
||||
int (*python_api_version)();
|
||||
};
|
||||
|
||||
@ -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
|
||||
1
examples/PACKAGES/atc/elastic/Au_u3.eam
Symbolic link
1
examples/PACKAGES/atc/elastic/Au_u3.eam
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/Au_u3.eam
|
||||
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
@ -15,12 +15,12 @@ Masses
|
||||
|
||||
PairIJ Coeffs # dpd/coul/slater/long
|
||||
|
||||
1 1 78 4.5 yes 1
|
||||
1 2 78 4.5 yes 1
|
||||
1 3 78 4.5 yes 1
|
||||
2 2 78 4.5 no 1
|
||||
2 3 78 4.5 no 1
|
||||
3 3 78 4.5 no 1
|
||||
1 1 78 4.5 no 1
|
||||
1 2 78 4.5 no 1
|
||||
1 3 78 4.5 no 1
|
||||
2 2 78 4.5 yes 1
|
||||
2 3 78 4.5 yes 1
|
||||
3 3 78 4.5 yes 1
|
||||
|
||||
Atoms # full
|
||||
|
||||
|
||||
@ -10,49 +10,47 @@ variable cut_coul equal 2.0
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
|
||||
unfix 1
|
||||
run 1000
|
||||
|
||||
|
||||
@ -1,147 +0,0 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Ionic Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable cut_DPD equal 1.0
|
||||
variable seed equal 165412
|
||||
variable lambda equal 0.25
|
||||
variable cut_coul equal 2.0
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
375 atoms
|
||||
reading velocities ...
|
||||
375 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 1.4828454
|
||||
grid = 20 20 20
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||
estimated relative force accuracy = 7.7240141e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 24389 8000
|
||||
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 = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/coul/slater/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
|
||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||
0 0.9849949 69.271905 125 4673.0443 0 -30.365103 4642.6792 552.58214 646.76798 65.851035
|
||||
100 1.0614027 69.794624 125 4659.0139 0 -31.906319 4627.1075 595.44692 612.94396 60.338653
|
||||
200 0.9422517 68.721098 125 4687.8862 0 -33.81531 4654.0709 528.6032 620.25627 62.726994
|
||||
300 0.8956649 69.323482 125 4721.0824 0 -33.854275 4687.2281 502.46801 670.22699 73.087908
|
||||
400 0.99584547 69.670416 125 4713.9086 0 -30.783633 4683.125 558.66931 607.65881 59.224652
|
||||
500 1.0565931 69.497816 125 4701.2584 0 -26.80545 4674.4529 592.74873 646.18907 71.398122
|
||||
600 1.0071523 70.26222 125 4659.2061 0 -29.98909 4629.217 565.01243 630.00244 58.264115
|
||||
700 1.0507355 67.920078 125 4695.255 0 -32.649209 4662.6058 589.46259 651.80459 70.573524
|
||||
800 0.98561942 68.279591 125 4745.7603 0 -28.98491 4716.7754 552.9325 627.14371 67.196483
|
||||
900 0.96470105 70.742864 125 4706.3605 0 -30.271633 4676.0889 541.19729 644.43036 79.474998
|
||||
1000 1.0204819 70.164419 125 4654.6077 0 -27.797433 4626.8103 572.49035 624.19728 71.825307
|
||||
Loop time of 2.10153 on 1 procs for 1000 steps with 375 atoms
|
||||
|
||||
Performance: 411128.483 tau/day, 475.843 timesteps/s, 178.441 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1779 | 1.1779 | 1.1779 | 0.0 | 56.05
|
||||
Bond | 6.507e-05 | 6.507e-05 | 6.507e-05 | 0.0 | 0.00
|
||||
Kspace | 0.74636 | 0.74636 | 0.74636 | 0.0 | 35.51
|
||||
Neigh | 0.12903 | 0.12903 | 0.12903 | 0.0 | 6.14
|
||||
Comm | 0.039726 | 0.039726 | 0.039726 | 0.0 | 1.89
|
||||
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 0.01
|
||||
Modify | 0.0037596 | 0.0037596 | 0.0037596 | 0.0 | 0.18
|
||||
Other | | 0.004451 | | | 0.21
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3613 ave 3613 max 3613 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 62354 ave 62354 max 62354 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 62354
|
||||
Ave neighs/atom = 166.27733
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 65
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
|
||||
Total wall time: 0:00:02
|
||||
@ -1,147 +0,0 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Ionic Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable cut_DPD equal 1.0
|
||||
variable seed equal 165412
|
||||
variable lambda equal 0.25
|
||||
variable cut_coul equal 2.0
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
375 atoms
|
||||
reading velocities ...
|
||||
375 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 1.4828454
|
||||
grid = 20 20 20
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||
estimated relative force accuracy = 7.7240141e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10469 2000
|
||||
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 = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/coul/slater/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
|
||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||
0 0.9849949 69.076433 125 4673.0443 0 -30.365103 4642.6792 552.58214 613.18374 70.700582
|
||||
100 0.95374867 69.110009 125 4681.1097 0 -31.260804 4649.8489 535.053 629.95109 62.05418
|
||||
200 1.0076152 69.824904 125 4670.7458 0 -28.382203 4642.3636 565.27213 656.8501 72.049813
|
||||
300 1.0014752 69.666331 125 4696.454 0 -26.943577 4669.5105 561.8276 631.49861 74.737274
|
||||
400 0.98863876 69.731774 125 4700.7552 0 -23.816077 4676.9391 554.62634 637.74742 68.928573
|
||||
500 0.95782852 68.588075 125 4698.588 0 -29.249543 4669.3385 537.3418 646.31897 68.800569
|
||||
600 0.97443232 70.864079 125 4674.8821 0 -26.415644 4648.4664 546.65653 606.50755 78.664429
|
||||
700 0.98783988 68.908299 125 4692.5536 0 -28.092022 4664.4616 554.17817 638.98401 69.691814
|
||||
800 0.98000145 69.83977 125 4706.6365 0 -29.648365 4676.9881 549.78082 626.84362 73.133934
|
||||
900 1.0526251 69.466078 125 4671.9648 0 -30.941117 4641.0237 590.52269 618.1049 62.333546
|
||||
1000 0.98340746 69.527121 125 4728.2894 0 -31.869907 4696.4195 551.69159 630.14208 61.392611
|
||||
Loop time of 0.928543 on 4 procs for 1000 steps with 375 atoms
|
||||
|
||||
Performance: 930490.137 tau/day, 1076.956 timesteps/s, 403.859 katom-step/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.30761 | 0.34974 | 0.38864 | 4.9 | 37.67
|
||||
Bond | 8.4633e-05 | 9.0539e-05 | 9.9184e-05 | 0.0 | 0.01
|
||||
Kspace | 0.39038 | 0.42976 | 0.47215 | 4.4 | 46.28
|
||||
Neigh | 0.033986 | 0.035576 | 0.036791 | 0.5 | 3.83
|
||||
Comm | 0.10247 | 0.10324 | 0.10481 | 0.3 | 11.12
|
||||
Output | 0.00024145 | 0.00027404 | 0.00036867 | 0.0 | 0.03
|
||||
Modify | 0.0022402 | 0.0025068 | 0.0026343 | 0.3 | 0.27
|
||||
Other | | 0.007356 | | | 0.79
|
||||
|
||||
Nlocal: 93.75 ave 96 max 93 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 2289.75 ave 2317 max 2271 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 15590.2 ave 16765 max 14540 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 62361
|
||||
Ave neighs/atom = 166.296
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 64
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Ionic Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable cut_DPD equal 1.0
|
||||
variable seed equal 165412
|
||||
variable lambda equal 0.25
|
||||
variable cut_coul equal 2.0
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
375 atoms
|
||||
reading velocities ...
|
||||
375 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 1.4828454
|
||||
grid = 20 20 20
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||
estimated relative force accuracy = 7.7240141e-05
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 24389 8000
|
||||
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 = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/coul/slater/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
|
||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||
0 0.9849949 69.242343 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 646.89929 65.851035
|
||||
100 1.023885 69.716134 125 4676.9465 -4.9878506 -34.092864 4637.8658 574.39949 663.35845 94.350026
|
||||
200 1.0286646 69.674249 125 4636.201 -4.6314926 -33.406897 4598.1626 577.08087 614.52805 62.295431
|
||||
300 0.9745797 69.689534 125 4679.9157 -4.3964184 -30.560567 4644.9588 546.73921 603.46282 60.56253
|
||||
400 0.99487931 69.17085 125 4678.0362 -4.9518269 -34.446596 4638.6378 558.12729 656.99738 88.090014
|
||||
500 0.97732377 69.551562 125 4684.3709 -5.0851581 -33.863212 4645.4226 548.27864 647.12533 75.851935
|
||||
600 0.95396337 68.358297 125 4706.824 -4.269168 -33.634096 4668.9207 535.17345 604.31276 63.41042
|
||||
700 0.99397324 68.365109 125 4669.1062 -4.700146 -35.014001 4629.3921 557.61899 633.29262 74.300913
|
||||
800 1.0157864 69.263686 125 4664.1398 -4.0142381 -34.372669 4625.7529 569.85616 595.81462 67.046561
|
||||
900 0.9925779 70.008922 125 4652.3023 -2.7845751 -33.095293 4616.4224 556.8362 620.13154 82.785317
|
||||
1000 0.97336501 68.973657 125 4688.8002 -5.5239266 -36.42345 4646.8529 546.05777 625.66451 64.948859
|
||||
Loop time of 0.755094 on 1 procs for 1000 steps with 375 atoms
|
||||
|
||||
Performance: 1144228.093 tau/day, 1324.338 timesteps/s, 496.627 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 | 0.14421 | 0.14421 | 0.14421 | 0.0 | 19.10
|
||||
Bond | 3.8885e-05 | 3.8885e-05 | 3.8885e-05 | 0.0 | 0.01
|
||||
Kspace | 0.53292 | 0.53292 | 0.53292 | 0.0 | 70.58
|
||||
Neigh | 0.056741 | 0.056741 | 0.056741 | 0.0 | 7.51
|
||||
Comm | 0.017676 | 0.017676 | 0.017676 | 0.0 | 2.34
|
||||
Output | 0.00024925 | 0.00024925 | 0.00024925 | 0.0 | 0.03
|
||||
Modify | 0.0016688 | 0.0016688 | 0.0016688 | 0.0 | 0.22
|
||||
Other | | 0.001588 | | | 0.21
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3570 ave 3570 max 3570 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19729 ave 19729 max 19729 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19729
|
||||
Ave neighs/atom = 52.610667
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 66
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Ionic Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable cut_DPD equal 1.0
|
||||
variable seed equal 165412
|
||||
variable lambda equal 0.25
|
||||
variable cut_coul equal 2.0
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
375 atoms
|
||||
reading velocities ...
|
||||
375 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 1.4828454
|
||||
grid = 20 20 20
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||
estimated relative force accuracy = 7.7240141e-05
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 10469 2000
|
||||
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 = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/coul/slater/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
|
||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||
0 0.9849949 69.04687 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 613.14254 70.700582
|
||||
100 1.0206537 69.308834 125 4676.3153 -4.5693306 -33.647673 4638.0983 572.58672 630.70953 76.020236
|
||||
200 0.99990746 68.572978 125 4707.1556 -3.4977853 -33.275671 4670.3821 560.94809 633.00167 77.040049
|
||||
300 0.91055241 69.390592 125 4685.5268 -2.9764038 -29.986737 4652.5637 510.8199 614.61006 62.799933
|
||||
400 1.0080135 69.442971 125 4677.3078 -4.8740989 -32.908722 4639.525 565.49557 649.20121 61.033612
|
||||
500 0.99500653 68.275189 125 4718.6774 -4.2475783 -35.206868 4679.223 558.19867 657.3073 74.738502
|
||||
600 1.052925 70.601712 125 4703.6749 -2.8511316 -34.085418 4666.7383 590.69094 641.70441 59.043346
|
||||
700 0.96467445 69.502018 125 4720.4257 -4.3345734 -34.310005 4681.7811 541.18237 656.24965 72.433637
|
||||
800 1.0657358 70.960958 125 4685.5637 -5.8903418 -35.207202 4644.4661 597.87781 595.54446 61.462159
|
||||
900 1.0273388 68.735518 125 4693.5106 -2.4175829 -28.602387 4662.4906 576.33707 598.80294 71.747886
|
||||
1000 0.9702835 69.885576 125 4701.4385 -3.6513555 -29.487331 4668.2999 544.32904 666.55262 73.231425
|
||||
Loop time of 0.270344 on 4 procs for 1000 steps with 375 atoms
|
||||
|
||||
Performance: 3195929.791 tau/day, 3698.993 timesteps/s, 1.387 Matom-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 | 0.031268 | 0.035485 | 0.039491 | 1.6 | 13.13
|
||||
Bond | 3.3378e-05 | 3.4848e-05 | 3.5667e-05 | 0.0 | 0.01
|
||||
Kspace | 0.18632 | 0.19083 | 0.19556 | 0.8 | 70.59
|
||||
Neigh | 0.012413 | 0.012991 | 0.013598 | 0.4 | 4.81
|
||||
Comm | 0.028195 | 0.028407 | 0.028626 | 0.1 | 10.51
|
||||
Output | 0.00013369 | 0.00015738 | 0.00022498 | 0.0 | 0.06
|
||||
Modify | 0.00055373 | 0.00059062 | 0.00068807 | 0.0 | 0.22
|
||||
Other | | 0.001846 | | | 0.68
|
||||
|
||||
Nlocal: 93.75 ave 95 max 92 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Nghost: 2286 ave 2307 max 2269 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Neighs: 4945 ave 5443 max 4513 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19780
|
||||
Ave neighs/atom = 52.746667
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 66
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -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
|
||||
13
examples/PACKAGES/imd/deca-ala-solv_imd_v3.py
Normal file
13
examples/PACKAGES/imd/deca-ala-solv_imd_v3.py
Normal file
@ -0,0 +1,13 @@
|
||||
"""
|
||||
For use with 'in.deca-ala-solv_imd_v3'.
|
||||
|
||||
Tested with imdclient v0.1.4 and MDAnalysis v2.8.0
|
||||
"""
|
||||
from imdclient.IMD import IMDReader
|
||||
import MDAnalysis as mda
|
||||
|
||||
u = mda.Universe('data.deca-ala-solv', "imd://localhost:5678", topology_format='DATA')
|
||||
|
||||
for ts in u.trajectory:
|
||||
print(ts.time)
|
||||
print(ts.velocities)
|
||||
31
examples/PACKAGES/imd/in.deca-ala-solv_imd_v3
Normal file
31
examples/PACKAGES/imd/in.deca-ala-solv_imd_v3
Normal file
@ -0,0 +1,31 @@
|
||||
#
|
||||
units real
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 1 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 8 10
|
||||
pair_modify mix arithmetic
|
||||
special_bonds charmm
|
||||
read_data data.deca-ala-solv
|
||||
|
||||
|
||||
group peptide id <= 103
|
||||
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
kspace_style pppm 1e-5
|
||||
|
||||
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
|
||||
|
||||
# IMD setup. Client code available in 'deca-ala-solv_imd_v3.py'
|
||||
fix comm all imd 5678 unwrap on trate 10 version 3 time on box on coordinates on velocities on forces off
|
||||
|
||||
run 5000000
|
||||
@ -9,7 +9,7 @@ read_data pafipath.4.data fix pa NULL PafiPath
|
||||
|
||||
## EAM potential
|
||||
pair_style eam/fs
|
||||
pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe
|
||||
pair_coeff * * Fe_mm.eam.fs Fe
|
||||
|
||||
mass * 55.85
|
||||
thermo 100
|
||||
|
||||
11
examples/PACKAGES/pimd_bosonic/README
Normal file
11
examples/PACKAGES/pimd_bosonic/README
Normal file
@ -0,0 +1,11 @@
|
||||
This directory contains example input files for the pimd/nvt/bosonic and pimd/langevin/bosonic fix commands.
|
||||
The demonstrated system is that of 3 non-interacting bosons in a harmonic trap.
|
||||
The input files initiate a simulation of 100 steps using 4 beads. The expected output log files are included.
|
||||
|
||||
The input files can be edited to provide a physically meaningful output, by extending the simulations to a few nanoseconds
|
||||
and increasing the number of beads (32 beads should be enough).
|
||||
The total energy can be computed by summing the potential energy and either the virial or primitive kinetic energy estimator, and averaging over time.
|
||||
Notice that for pimd/langevin/bosonic the summed value of either kinetic estimator is printed across all log files.
|
||||
It should be taken from a single log file, with all files providing the same output.
|
||||
For pimd/nvt/bosonic, one has to sum over the output of all log files. For the potential energy, summing over log files is required for both fix commands.
|
||||
The obtained energy should be compared to the analytical value of 0.00058031 Hartree.
|
||||
57
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp
Normal file
57
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp
Normal file
@ -0,0 +1,57 @@
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
|
||||
|
||||
# Outputs
|
||||
variable prim_kinetic equal f_pimdb[5]
|
||||
variable virial equal f_pimdb[6]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
@ -0,0 +1,2 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Running on 4 partitions of processors
|
||||
@ -0,0 +1,238 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Processor partition = 0
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188891 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
|
||||
|
||||
# Outputs
|
||||
variable prim_kinetic equal f_pimdb[5]
|
||||
variable virial equal f_pimdb[6]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
Initializing PI Langevin equation thermostat...
|
||||
Bead ID | omega | tau | c1 | c2
|
||||
0 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
|
||||
1 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
|
||||
2 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
|
||||
3 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
|
||||
PILE_L thermostat successfully initialized!
|
||||
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 1.3661449e-08 0.0009918329
|
||||
1 1.3158398e-09 1.8742641e-09 0.00099182267
|
||||
2 5.0818396e-09 7.1801177e-09 0.00099180053
|
||||
3 1.2446727e-08 1.4372388e-08 0.00099176038
|
||||
4 2.1754941e-08 3.1274072e-08 0.00099170266
|
||||
5 3.2927703e-08 5.2470231e-08 0.00099162511
|
||||
6 4.7293056e-08 7.2301291e-08 0.00099153
|
||||
7 6.526455e-08 9.5440683e-08 0.00099141194
|
||||
8 8.6974168e-08 1.1669162e-07 0.00099127168
|
||||
9 1.1249595e-07 1.3551097e-07 0.00099109846
|
||||
10 1.4190482e-07 1.6050328e-07 0.00099089759
|
||||
11 1.7313555e-07 1.8645705e-07 0.0009906735
|
||||
12 2.0672874e-07 2.1181418e-07 0.00099042271
|
||||
13 2.4042615e-07 2.4218941e-07 0.00099012073
|
||||
14 2.7524432e-07 2.7507982e-07 0.00098977876
|
||||
15 3.1513375e-07 3.1771012e-07 0.00098940169
|
||||
16 3.6161087e-07 3.6075963e-07 0.00098900826
|
||||
17 4.0813191e-07 4.0059005e-07 0.00098859985
|
||||
18 4.5194598e-07 4.3883585e-07 0.00098817535
|
||||
19 4.9898075e-07 4.8036287e-07 0.00098770764
|
||||
20 5.5458728e-07 5.2362451e-07 0.00098721266
|
||||
21 6.1220768e-07 5.7705077e-07 0.00098670407
|
||||
22 6.6573849e-07 6.3271105e-07 0.00098617081
|
||||
23 7.2475089e-07 6.9382916e-07 0.00098557406
|
||||
24 7.804837e-07 7.5979853e-07 0.0009849612
|
||||
25 8.3194987e-07 8.232213e-07 0.00098434971
|
||||
26 8.8723792e-07 8.9901705e-07 0.0009836645
|
||||
27 9.3837241e-07 9.7033126e-07 0.0009830068
|
||||
28 9.897077e-07 1.0444697e-06 0.00098229311
|
||||
29 1.043431e-06 1.1208219e-06 0.00098150213
|
||||
30 1.0900368e-06 1.1899315e-06 0.00098077686
|
||||
31 1.1303314e-06 1.2560026e-06 0.00098003518
|
||||
32 1.1725968e-06 1.3287355e-06 0.00097921099
|
||||
33 1.2081344e-06 1.399856e-06 0.0009784037
|
||||
34 1.2449387e-06 1.4769272e-06 0.00097754491
|
||||
35 1.2852285e-06 1.5642459e-06 0.00097667479
|
||||
36 1.3234189e-06 1.6571388e-06 0.00097572641
|
||||
37 1.3666391e-06 1.7603492e-06 0.00097475881
|
||||
38 1.4102743e-06 1.8666516e-06 0.00097373763
|
||||
39 1.454172e-06 1.9696572e-06 0.0009727081
|
||||
40 1.5031422e-06 2.0910539e-06 0.00097155807
|
||||
41 1.5538491e-06 2.2198868e-06 0.00097030871
|
||||
42 1.6079193e-06 2.3576614e-06 0.00096896762
|
||||
43 1.6637051e-06 2.496284e-06 0.00096760456
|
||||
44 1.7189714e-06 2.637657e-06 0.00096619083
|
||||
45 1.7656688e-06 2.795845e-06 0.00096470693
|
||||
46 1.8092153e-06 2.9727162e-06 0.00096303835
|
||||
47 1.8415769e-06 3.1451673e-06 0.00096140406
|
||||
48 1.8664597e-06 3.3241907e-06 0.00095971129
|
||||
49 1.8940033e-06 3.5094834e-06 0.00095790964
|
||||
50 1.9211844e-06 3.7049195e-06 0.00095603039
|
||||
51 1.9533838e-06 3.9139587e-06 0.0009540918
|
||||
52 1.9833776e-06 4.1289537e-06 0.0009520767
|
||||
53 2.0106231e-06 4.3481079e-06 0.00095003676
|
||||
54 2.0429292e-06 4.5702968e-06 0.00094802906
|
||||
55 2.0747842e-06 4.7928135e-06 0.00094600351
|
||||
56 2.1043981e-06 5.0253448e-06 0.0009438419
|
||||
57 2.1474343e-06 5.2569331e-06 0.00094169256
|
||||
58 2.2115003e-06 5.4997767e-06 0.00093948055
|
||||
59 2.2773037e-06 5.7547729e-06 0.00093714003
|
||||
60 2.3402972e-06 6.0074589e-06 0.00093480857
|
||||
61 2.4107157e-06 6.2647899e-06 0.00093244785
|
||||
62 2.4953095e-06 6.5384938e-06 0.00092998209
|
||||
63 2.58923e-06 6.8124372e-06 0.00092751453
|
||||
64 2.682021e-06 7.0913777e-06 0.00092505171
|
||||
65 2.7538688e-06 7.3773956e-06 0.00092256944
|
||||
66 2.8444661e-06 7.6811232e-06 0.00091984092
|
||||
67 2.9532286e-06 7.9951107e-06 0.0009170037
|
||||
68 3.0551339e-06 8.3096758e-06 0.00091414977
|
||||
69 3.1625164e-06 8.6232285e-06 0.00091137219
|
||||
70 3.2717759e-06 8.9388929e-06 0.00090857909
|
||||
71 3.3924986e-06 9.2524846e-06 0.00090583473
|
||||
72 3.5236727e-06 9.5688611e-06 0.00090308342
|
||||
73 3.6440162e-06 9.8873586e-06 0.00090026584
|
||||
74 3.7692169e-06 1.0203245e-05 0.00089755256
|
||||
75 3.8946044e-06 1.0523755e-05 0.00089485804
|
||||
76 4.0498738e-06 1.0848398e-05 0.00089217189
|
||||
77 4.2099346e-06 1.1164286e-05 0.00088956967
|
||||
78 4.3589564e-06 1.1466652e-05 0.00088700311
|
||||
79 4.5069481e-06 1.177381e-05 0.00088439373
|
||||
80 4.6635354e-06 1.2059606e-05 0.00088199635
|
||||
81 4.8398269e-06 1.233837e-05 0.0008797438
|
||||
82 5.0191539e-06 1.261531e-05 0.00087745162
|
||||
83 5.205285e-06 1.2899972e-05 0.00087506863
|
||||
84 5.3708116e-06 1.3160246e-05 0.00087288444
|
||||
85 5.5534416e-06 1.3438712e-05 0.00087052617
|
||||
86 5.7613e-06 1.372546e-05 0.00086818634
|
||||
87 5.9645662e-06 1.4017631e-05 0.00086572407
|
||||
88 6.1830289e-06 1.4328439e-05 0.000862992
|
||||
89 6.423646e-06 1.4640964e-05 0.00086017364
|
||||
90 6.688219e-06 1.4978644e-05 0.0008570595
|
||||
91 6.9305603e-06 1.5307214e-05 0.00085411601
|
||||
92 7.1857573e-06 1.5649328e-05 0.00085112325
|
||||
93 7.4653538e-06 1.6015833e-05 0.0008479391
|
||||
94 7.8132911e-06 1.6393131e-05 0.00084474237
|
||||
95 8.1540941e-06 1.674573e-05 0.00084165639
|
||||
96 8.4943231e-06 1.7094435e-05 0.00083858996
|
||||
97 8.8504733e-06 1.7451741e-05 0.00083536142
|
||||
98 9.2042324e-06 1.780703e-05 0.00083221292
|
||||
99 9.5058078e-06 1.8141862e-05 0.00082913227
|
||||
100 9.8087647e-06 1.8457846e-05 0.00082619877
|
||||
Loop time of 0.00116399 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 3711359336.904 fs/day, 0.000 hours/fs, 85911.096 timesteps/s, 257.733 katom-step/s
|
||||
89.8% 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 | 1.292e-06 | 1.292e-06 | 1.292e-06 | 0.0 | 0.11
|
||||
Comm | 1.2305e-05 | 1.2305e-05 | 1.2305e-05 | 0.0 | 1.06
|
||||
Output | 0.00018105 | 0.00018105 | 0.00018105 | 0.0 | 15.55
|
||||
Modify | 0.00090255 | 0.00090255 | 0.00090255 | 0.0 | 77.54
|
||||
Other | | 6.68e-05 | | | 5.74
|
||||
|
||||
Nlocal: 3 ave 3 max 3 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 = 33
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,230 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Processor partition = 1
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188892 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
|
||||
|
||||
# Outputs
|
||||
variable prim_kinetic equal f_pimdb[5]
|
||||
variable virial equal f_pimdb[6]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 1.3661449e-08 0.0009918329
|
||||
1 7.3810761e-10 1.8742641e-09 0.00099182267
|
||||
2 3.0654593e-09 7.1801177e-09 0.00099180053
|
||||
3 6.4534507e-09 1.4372388e-08 0.00099176038
|
||||
4 1.1681892e-08 3.1274072e-08 0.00099170266
|
||||
5 1.8404818e-08 5.2470231e-08 0.00099162511
|
||||
6 2.6171374e-08 7.2301291e-08 0.00099153
|
||||
7 3.5990441e-08 9.5440683e-08 0.00099141194
|
||||
8 4.9770229e-08 1.1669162e-07 0.00099127168
|
||||
9 6.6159035e-08 1.3551097e-07 0.00099109846
|
||||
10 8.7281867e-08 1.6050328e-07 0.00099089759
|
||||
11 1.1505206e-07 1.8645705e-07 0.0009906735
|
||||
12 1.4564491e-07 2.1181418e-07 0.00099042271
|
||||
13 1.8674942e-07 2.4218941e-07 0.00099012073
|
||||
14 2.3275077e-07 2.7507982e-07 0.00098977876
|
||||
15 2.833552e-07 3.1771012e-07 0.00098940169
|
||||
16 3.3078875e-07 3.6075963e-07 0.00098900826
|
||||
17 3.7783787e-07 4.0059005e-07 0.00098859985
|
||||
18 4.3007763e-07 4.3883585e-07 0.00098817535
|
||||
19 4.8592613e-07 4.8036287e-07 0.00098770764
|
||||
20 5.4429898e-07 5.2362451e-07 0.00098721266
|
||||
21 6.0140068e-07 5.7705077e-07 0.00098670407
|
||||
22 6.6036274e-07 6.3271105e-07 0.00098617081
|
||||
23 7.3748601e-07 6.9382916e-07 0.00098557406
|
||||
24 8.1086859e-07 7.5979853e-07 0.0009849612
|
||||
25 8.8638234e-07 8.232213e-07 0.00098434971
|
||||
26 9.8252709e-07 8.9901705e-07 0.0009836645
|
||||
27 1.0768657e-06 9.7033126e-07 0.0009830068
|
||||
28 1.1810654e-06 1.0444697e-06 0.00098229311
|
||||
29 1.2964318e-06 1.1208219e-06 0.00098150213
|
||||
30 1.4097624e-06 1.1899315e-06 0.00098077686
|
||||
31 1.5368367e-06 1.2560026e-06 0.00098003518
|
||||
32 1.6777082e-06 1.3287355e-06 0.00097921099
|
||||
33 1.8186759e-06 1.399856e-06 0.0009784037
|
||||
34 1.9730383e-06 1.4769272e-06 0.00097754491
|
||||
35 2.1285065e-06 1.5642459e-06 0.00097667479
|
||||
36 2.2809575e-06 1.6571388e-06 0.00097572641
|
||||
37 2.4393024e-06 1.7603492e-06 0.00097475881
|
||||
38 2.6212592e-06 1.8666516e-06 0.00097373763
|
||||
39 2.8115312e-06 1.9696572e-06 0.0009727081
|
||||
40 3.0115212e-06 2.0910539e-06 0.00097155807
|
||||
41 3.2325069e-06 2.2198868e-06 0.00097030871
|
||||
42 3.4582526e-06 2.3576614e-06 0.00096896762
|
||||
43 3.6838101e-06 2.496284e-06 0.00096760456
|
||||
44 3.9267475e-06 2.637657e-06 0.00096619083
|
||||
45 4.1942569e-06 2.795845e-06 0.00096470693
|
||||
46 4.4694976e-06 2.9727162e-06 0.00096303835
|
||||
47 4.7570486e-06 3.1451673e-06 0.00096140406
|
||||
48 5.0917213e-06 3.3241907e-06 0.00095971129
|
||||
49 5.4581889e-06 3.5094834e-06 0.00095790964
|
||||
50 5.8607381e-06 3.7049195e-06 0.00095603039
|
||||
51 6.2673583e-06 3.9139587e-06 0.0009540918
|
||||
52 6.6764632e-06 4.1289537e-06 0.0009520767
|
||||
53 7.0828028e-06 4.3481079e-06 0.00095003676
|
||||
54 7.4858144e-06 4.5702968e-06 0.00094802906
|
||||
55 7.8711706e-06 4.7928135e-06 0.00094600351
|
||||
56 8.2756726e-06 5.0253448e-06 0.0009438419
|
||||
57 8.6667628e-06 5.2569331e-06 0.00094169256
|
||||
58 9.0585083e-06 5.4997767e-06 0.00093948055
|
||||
59 9.4634766e-06 5.7547729e-06 0.00093714003
|
||||
60 9.8696653e-06 6.0074589e-06 0.00093480857
|
||||
61 1.0308345e-05 6.2647899e-06 0.00093244785
|
||||
62 1.0757919e-05 6.5384938e-06 0.00092998209
|
||||
63 1.1183568e-05 6.8124372e-06 0.00092751453
|
||||
64 1.1585073e-05 7.0913777e-06 0.00092505171
|
||||
65 1.1993605e-05 7.3773956e-06 0.00092256944
|
||||
66 1.2382612e-05 7.6811232e-06 0.00091984092
|
||||
67 1.2768116e-05 7.9951107e-06 0.0009170037
|
||||
68 1.3181941e-05 8.3096758e-06 0.00091414977
|
||||
69 1.3605472e-05 8.6232285e-06 0.00091137219
|
||||
70 1.4027012e-05 8.9388929e-06 0.00090857909
|
||||
71 1.4471706e-05 9.2524846e-06 0.00090583473
|
||||
72 1.4896833e-05 9.5688611e-06 0.00090308342
|
||||
73 1.5345003e-05 9.8873586e-06 0.00090026584
|
||||
74 1.5779905e-05 1.0203245e-05 0.00089755256
|
||||
75 1.6189898e-05 1.0523755e-05 0.00089485804
|
||||
76 1.6654778e-05 1.0848398e-05 0.00089217189
|
||||
77 1.7131363e-05 1.1164286e-05 0.00088956967
|
||||
78 1.7572176e-05 1.1466652e-05 0.00088700311
|
||||
79 1.8000817e-05 1.177381e-05 0.00088439373
|
||||
80 1.838117e-05 1.2059606e-05 0.00088199635
|
||||
81 1.8762432e-05 1.233837e-05 0.0008797438
|
||||
82 1.9099052e-05 1.261531e-05 0.00087745162
|
||||
83 1.9507863e-05 1.2899972e-05 0.00087506863
|
||||
84 1.9885648e-05 1.3160246e-05 0.00087288444
|
||||
85 2.0266439e-05 1.3438712e-05 0.00087052617
|
||||
86 2.0612316e-05 1.372546e-05 0.00086818634
|
||||
87 2.0959061e-05 1.4017631e-05 0.00086572407
|
||||
88 2.13065e-05 1.4328439e-05 0.000862992
|
||||
89 2.1634898e-05 1.4640964e-05 0.00086017364
|
||||
90 2.2023174e-05 1.4978644e-05 0.0008570595
|
||||
91 2.2431573e-05 1.5307214e-05 0.00085411601
|
||||
92 2.2872283e-05 1.5649328e-05 0.00085112325
|
||||
93 2.338476e-05 1.6015833e-05 0.0008479391
|
||||
94 2.3912199e-05 1.6393131e-05 0.00084474237
|
||||
95 2.437725e-05 1.674573e-05 0.00084165639
|
||||
96 2.4828999e-05 1.7094435e-05 0.00083858996
|
||||
97 2.5286762e-05 1.7451741e-05 0.00083536142
|
||||
98 2.5769956e-05 1.780703e-05 0.00083221292
|
||||
99 2.624134e-05 1.8141862e-05 0.00082913227
|
||||
100 2.6731735e-05 1.8457846e-05 0.00082619877
|
||||
Loop time of 0.0011782 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 3666606971.137 fs/day, 0.000 hours/fs, 84875.161 timesteps/s, 254.625 katom-step/s
|
||||
88.4% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.773e-06 | 1.773e-06 | 1.773e-06 | 0.0 | 0.15
|
||||
Comm | 1.4979e-05 | 1.4979e-05 | 1.4979e-05 | 0.0 | 1.27
|
||||
Output | 0.00021888 | 0.00021888 | 0.00021888 | 0.0 | 18.58
|
||||
Modify | 0.00086503 | 0.00086503 | 0.00086503 | 0.0 | 73.42
|
||||
Other | | 7.754e-05 | | | 6.58
|
||||
|
||||
Nlocal: 3 ave 3 max 3 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 = 44
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,230 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Processor partition = 2
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188893 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
|
||||
|
||||
# Outputs
|
||||
variable prim_kinetic equal f_pimdb[5]
|
||||
variable virial equal f_pimdb[6]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 1.3661449e-08 0.0009918329
|
||||
1 8.3480048e-10 1.8742641e-09 0.00099182267
|
||||
2 2.8201389e-09 7.1801177e-09 0.00099180053
|
||||
3 7.3605781e-09 1.4372388e-08 0.00099176038
|
||||
4 1.4967393e-08 3.1274072e-08 0.00099170266
|
||||
5 2.4978087e-08 5.2470231e-08 0.00099162511
|
||||
6 3.5908849e-08 7.2301291e-08 0.00099153
|
||||
7 4.8226614e-08 9.5440683e-08 0.00099141194
|
||||
8 6.3621045e-08 1.1669162e-07 0.00099127168
|
||||
9 8.0119736e-08 1.3551097e-07 0.00099109846
|
||||
10 9.7965614e-08 1.6050328e-07 0.00099089759
|
||||
11 1.1538858e-07 1.8645705e-07 0.0009906735
|
||||
12 1.365443e-07 2.1181418e-07 0.00099042271
|
||||
13 1.5920175e-07 2.4218941e-07 0.00099012073
|
||||
14 1.8252589e-07 2.7507982e-07 0.00098977876
|
||||
15 2.0858909e-07 3.1771012e-07 0.00098940169
|
||||
16 2.3676046e-07 3.6075963e-07 0.00098900826
|
||||
17 2.689757e-07 4.0059005e-07 0.00098859985
|
||||
18 3.0022172e-07 4.3883585e-07 0.00098817535
|
||||
19 3.3127637e-07 4.8036287e-07 0.00098770764
|
||||
20 3.6044366e-07 5.2362451e-07 0.00098721266
|
||||
21 3.8484646e-07 5.7705077e-07 0.00098670407
|
||||
22 4.1435067e-07 6.3271105e-07 0.00098617081
|
||||
23 4.4508994e-07 6.9382916e-07 0.00098557406
|
||||
24 4.7879333e-07 7.5979853e-07 0.0009849612
|
||||
25 5.0918223e-07 8.232213e-07 0.00098434971
|
||||
26 5.4733661e-07 8.9901705e-07 0.0009836645
|
||||
27 5.7932115e-07 9.7033126e-07 0.0009830068
|
||||
28 6.1775401e-07 1.0444697e-06 0.00098229311
|
||||
29 6.6883535e-07 1.1208219e-06 0.00098150213
|
||||
30 7.0943445e-07 1.1899315e-06 0.00098077686
|
||||
31 7.4477897e-07 1.2560026e-06 0.00098003518
|
||||
32 7.8183156e-07 1.3287355e-06 0.00097921099
|
||||
33 8.1987667e-07 1.399856e-06 0.0009784037
|
||||
34 8.5514962e-07 1.4769272e-06 0.00097754491
|
||||
35 8.9607784e-07 1.5642459e-06 0.00097667479
|
||||
36 9.4986753e-07 1.6571388e-06 0.00097572641
|
||||
37 1.0024729e-06 1.7603492e-06 0.00097475881
|
||||
38 1.0526731e-06 1.8666516e-06 0.00097373763
|
||||
39 1.103419e-06 1.9696572e-06 0.0009727081
|
||||
40 1.1640352e-06 2.0910539e-06 0.00097155807
|
||||
41 1.2292837e-06 2.2198868e-06 0.00097030871
|
||||
42 1.3024454e-06 2.3576614e-06 0.00096896762
|
||||
43 1.3788736e-06 2.496284e-06 0.00096760456
|
||||
44 1.4503248e-06 2.637657e-06 0.00096619083
|
||||
45 1.5334106e-06 2.795845e-06 0.00096470693
|
||||
46 1.6246777e-06 2.9727162e-06 0.00096303835
|
||||
47 1.715884e-06 3.1451673e-06 0.00096140406
|
||||
48 1.8096683e-06 3.3241907e-06 0.00095971129
|
||||
49 1.916714e-06 3.5094834e-06 0.00095790964
|
||||
50 2.0374848e-06 3.7049195e-06 0.00095603039
|
||||
51 2.1747488e-06 3.9139587e-06 0.0009540918
|
||||
52 2.3236882e-06 4.1289537e-06 0.0009520767
|
||||
53 2.4790586e-06 4.3481079e-06 0.00095003676
|
||||
54 2.6478101e-06 4.5702968e-06 0.00094802906
|
||||
55 2.8275135e-06 4.7928135e-06 0.00094600351
|
||||
56 3.0338638e-06 5.0253448e-06 0.0009438419
|
||||
57 3.2428318e-06 5.2569331e-06 0.00094169256
|
||||
58 3.4414566e-06 5.4997767e-06 0.00093948055
|
||||
59 3.6324968e-06 5.7547729e-06 0.00093714003
|
||||
60 3.8269172e-06 6.0074589e-06 0.00093480857
|
||||
61 4.0183315e-06 6.2647899e-06 0.00093244785
|
||||
62 4.2263009e-06 6.5384938e-06 0.00092998209
|
||||
63 4.4382735e-06 6.8124372e-06 0.00092751453
|
||||
64 4.6488232e-06 7.0913777e-06 0.00092505171
|
||||
65 4.8707403e-06 7.3773956e-06 0.00092256944
|
||||
66 5.1178339e-06 7.6811232e-06 0.00091984092
|
||||
67 5.377713e-06 7.9951107e-06 0.0009170037
|
||||
68 5.63843e-06 8.3096758e-06 0.00091414977
|
||||
69 5.8975743e-06 8.6232285e-06 0.00091137219
|
||||
70 6.168921e-06 8.9388929e-06 0.00090857909
|
||||
71 6.4488238e-06 9.2524846e-06 0.00090583473
|
||||
72 6.7115203e-06 9.5688611e-06 0.00090308342
|
||||
73 6.995134e-06 9.8873586e-06 0.00090026584
|
||||
74 7.284199e-06 1.0203245e-05 0.00089755256
|
||||
75 7.6029528e-06 1.0523755e-05 0.00089485804
|
||||
76 7.9431391e-06 1.0848398e-05 0.00089217189
|
||||
77 8.2768015e-06 1.1164286e-05 0.00088956967
|
||||
78 8.6058917e-06 1.1466652e-05 0.00088700311
|
||||
79 8.9683477e-06 1.177381e-05 0.00088439373
|
||||
80 9.3324487e-06 1.2059606e-05 0.00088199635
|
||||
81 9.6876036e-06 1.233837e-05 0.0008797438
|
||||
82 1.0061754e-05 1.261531e-05 0.00087745162
|
||||
83 1.0457019e-05 1.2899972e-05 0.00087506863
|
||||
84 1.0866064e-05 1.3160246e-05 0.00087288444
|
||||
85 1.1298832e-05 1.3438712e-05 0.00087052617
|
||||
86 1.1762526e-05 1.372546e-05 0.00086818634
|
||||
87 1.2264941e-05 1.4017631e-05 0.00086572407
|
||||
88 1.2784125e-05 1.4328439e-05 0.000862992
|
||||
89 1.332533e-05 1.4640964e-05 0.00086017364
|
||||
90 1.3897966e-05 1.4978644e-05 0.0008570595
|
||||
91 1.4473024e-05 1.5307214e-05 0.00085411601
|
||||
92 1.5067033e-05 1.5649328e-05 0.00085112325
|
||||
93 1.5677943e-05 1.6015833e-05 0.0008479391
|
||||
94 1.6254294e-05 1.6393131e-05 0.00084474237
|
||||
95 1.6791089e-05 1.674573e-05 0.00084165639
|
||||
96 1.7362795e-05 1.7094435e-05 0.00083858996
|
||||
97 1.7961498e-05 1.7451741e-05 0.00083536142
|
||||
98 1.8568337e-05 1.780703e-05 0.00083221292
|
||||
99 1.9188379e-05 1.8141862e-05 0.00082913227
|
||||
100 1.9789011e-05 1.8457846e-05 0.00082619877
|
||||
Loop time of 0.00116163 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 3718915419.639 fs/day, 0.000 hours/fs, 86086.005 timesteps/s, 258.258 katom-step/s
|
||||
89.6% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.582e-06 | 1.582e-06 | 1.582e-06 | 0.0 | 0.14
|
||||
Comm | 1.3306e-05 | 1.3306e-05 | 1.3306e-05 | 0.0 | 1.15
|
||||
Output | 0.00017996 | 0.00017996 | 0.00017996 | 0.0 | 15.49
|
||||
Modify | 0.00090771 | 0.00090771 | 0.00090771 | 0.0 | 78.14
|
||||
Other | | 5.907e-05 | | | 5.09
|
||||
|
||||
Nlocal: 3 ave 3 max 3 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 = 41
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,230 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Processor partition = 3
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188894 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
|
||||
fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
|
||||
|
||||
# Outputs
|
||||
variable prim_kinetic equal f_pimdb[5]
|
||||
variable virial equal f_pimdb[6]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 1.3661449e-08 0.0009918329
|
||||
1 8.448696e-10 1.8742641e-09 0.00099182267
|
||||
2 3.5286528e-09 7.1801177e-09 0.00099180053
|
||||
3 8.2936659e-09 1.4372388e-08 0.00099176038
|
||||
4 1.4586045e-08 3.1274072e-08 0.00099170266
|
||||
5 2.4161875e-08 5.2470231e-08 0.00099162511
|
||||
6 3.8801085e-08 7.2301291e-08 0.00099153
|
||||
7 5.9758384e-08 9.5440683e-08 0.00099141194
|
||||
8 8.5838823e-08 1.1669162e-07 0.00099127168
|
||||
9 1.1684437e-07 1.3551097e-07 0.00099109846
|
||||
10 1.4954974e-07 1.6050328e-07 0.00099089759
|
||||
11 1.8686687e-07 1.8645705e-07 0.0009906735
|
||||
12 2.2747543e-07 2.1181418e-07 0.00099042271
|
||||
13 2.807392e-07 2.4218941e-07 0.00099012073
|
||||
14 3.3827867e-07 2.7507982e-07 0.00098977876
|
||||
15 3.9918359e-07 3.1771012e-07 0.00098940169
|
||||
16 4.6034561e-07 3.6075963e-07 0.00098900826
|
||||
17 5.2315136e-07 4.0059005e-07 0.00098859985
|
||||
18 5.8457073e-07 4.3883585e-07 0.00098817535
|
||||
19 6.5273892e-07 4.8036287e-07 0.00098770764
|
||||
20 7.2150647e-07 5.2362451e-07 0.00098721266
|
||||
21 8.0596691e-07 5.7705077e-07 0.00098670407
|
||||
22 8.946994e-07 6.3271105e-07 0.00098617081
|
||||
23 9.9120142e-07 6.9382916e-07 0.00098557406
|
||||
24 1.09722e-06 7.5979853e-07 0.0009849612
|
||||
25 1.2053692e-06 8.232213e-07 0.00098434971
|
||||
26 1.3196547e-06 8.9901705e-07 0.0009836645
|
||||
27 1.4380033e-06 9.7033126e-07 0.0009830068
|
||||
28 1.5700587e-06 1.0444697e-06 0.00098229311
|
||||
29 1.7089133e-06 1.1208219e-06 0.00098150213
|
||||
30 1.839944e-06 1.1899315e-06 0.00098077686
|
||||
31 1.9718088e-06 1.2560026e-06 0.00098003518
|
||||
32 2.1244847e-06 1.3287355e-06 0.00097921099
|
||||
33 2.2823018e-06 1.399856e-06 0.0009784037
|
||||
34 2.4607034e-06 1.4769272e-06 0.00097754491
|
||||
35 2.6410061e-06 1.5642459e-06 0.00097667479
|
||||
36 2.8395019e-06 1.6571388e-06 0.00097572641
|
||||
37 3.0476467e-06 1.7603492e-06 0.00097475881
|
||||
38 3.2661567e-06 1.8666516e-06 0.00097373763
|
||||
39 3.4857766e-06 1.9696572e-06 0.0009727081
|
||||
40 3.7310241e-06 2.0910539e-06 0.00097155807
|
||||
41 3.9947356e-06 2.2198868e-06 0.00097030871
|
||||
42 4.2722057e-06 2.3576614e-06 0.00096896762
|
||||
43 4.5444932e-06 2.496284e-06 0.00096760456
|
||||
44 4.8307956e-06 2.637657e-06 0.00096619083
|
||||
45 5.1356773e-06 2.795845e-06 0.00096470693
|
||||
46 5.4835294e-06 2.9727162e-06 0.00096303835
|
||||
47 5.8235502e-06 3.1451673e-06 0.00096140406
|
||||
48 6.1541132e-06 3.3241907e-06 0.00095971129
|
||||
49 6.4796693e-06 3.5094834e-06 0.00095790964
|
||||
50 6.8009213e-06 3.7049195e-06 0.00095603039
|
||||
51 7.1253629e-06 3.9139587e-06 0.0009540918
|
||||
52 7.4712081e-06 4.1289537e-06 0.0009520767
|
||||
53 7.8322309e-06 4.3481079e-06 0.00095003676
|
||||
54 8.1941694e-06 4.5702968e-06 0.00094802906
|
||||
55 8.579188e-06 4.7928135e-06 0.00094600351
|
||||
56 8.9656493e-06 5.0253448e-06 0.0009438419
|
||||
57 9.351102e-06 5.2569331e-06 0.00094169256
|
||||
58 9.7645407e-06 5.4997767e-06 0.00093948055
|
||||
59 1.0230434e-05 5.7547729e-06 0.00093714003
|
||||
60 1.0724041e-05 6.0074589e-06 0.00093480857
|
||||
61 1.1207453e-05 6.2647899e-06 0.00093244785
|
||||
62 1.171285e-05 6.5384938e-06 0.00092998209
|
||||
63 1.221299e-05 6.8124372e-06 0.00092751453
|
||||
64 1.2743686e-05 7.0913777e-06 0.00092505171
|
||||
65 1.3295725e-05 7.3773956e-06 0.00092256944
|
||||
66 1.3906023e-05 7.6811232e-06 0.00091984092
|
||||
67 1.4511348e-05 7.9951107e-06 0.0009170037
|
||||
68 1.5116776e-05 8.3096758e-06 0.00091414977
|
||||
69 1.571005e-05 8.6232285e-06 0.00091137219
|
||||
70 1.6297136e-05 8.9388929e-06 0.00090857909
|
||||
71 1.6849099e-05 9.2524846e-06 0.00090583473
|
||||
72 1.7417168e-05 9.5688611e-06 0.00090308342
|
||||
73 1.7971613e-05 9.8873586e-06 0.00090026584
|
||||
74 1.8509472e-05 1.0203245e-05 0.00089755256
|
||||
75 1.9047825e-05 1.0523755e-05 0.00089485804
|
||||
76 1.9510646e-05 1.0848398e-05 0.00089217189
|
||||
77 1.9903304e-05 1.1164286e-05 0.00088956967
|
||||
78 2.0300948e-05 1.1466652e-05 0.00088700311
|
||||
79 2.0696905e-05 1.177381e-05 0.00088439373
|
||||
80 2.1058218e-05 1.2059606e-05 0.00088199635
|
||||
81 2.139726e-05 1.233837e-05 0.0008797438
|
||||
82 2.1755155e-05 1.261531e-05 0.00087745162
|
||||
83 2.2051018e-05 1.2899972e-05 0.00087506863
|
||||
84 2.2294567e-05 1.3160246e-05 0.00087288444
|
||||
85 2.2559076e-05 1.3438712e-05 0.00087052617
|
||||
86 2.2815918e-05 1.372546e-05 0.00086818634
|
||||
87 2.3062616e-05 1.4017631e-05 0.00086572407
|
||||
88 2.3324206e-05 1.4328439e-05 0.000862992
|
||||
89 2.3559323e-05 1.4640964e-05 0.00086017364
|
||||
90 2.3792776e-05 1.4978644e-05 0.0008570595
|
||||
91 2.3990667e-05 1.5307214e-05 0.00085411601
|
||||
92 2.4198637e-05 1.5649328e-05 0.00085112325
|
||||
93 2.4419398e-05 1.6015833e-05 0.0008479391
|
||||
94 2.4625252e-05 1.6393131e-05 0.00084474237
|
||||
95 2.4816363e-05 1.674573e-05 0.00084165639
|
||||
96 2.4982897e-05 1.7094435e-05 0.00083858996
|
||||
97 2.5153682e-05 1.7451741e-05 0.00083536142
|
||||
98 2.5288512e-05 1.780703e-05 0.00083221292
|
||||
99 2.5384836e-05 1.8141862e-05 0.00082913227
|
||||
100 2.5401412e-05 1.8457846e-05 0.00082619877
|
||||
Loop time of 0.00116067 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 3721997782.310 fs/day, 0.000 hours/fs, 86157.356 timesteps/s, 258.472 katom-step/s
|
||||
88.3% 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 | 1.441e-06 | 1.441e-06 | 1.441e-06 | 0.0 | 0.12
|
||||
Comm | 1.2111e-05 | 1.2111e-05 | 1.2111e-05 | 0.0 | 1.04
|
||||
Output | 0.00018148 | 0.00018148 | 0.00018148 | 0.0 | 15.64
|
||||
Modify | 0.0009054 | 0.0009054 | 0.0009054 | 0.0 | 78.01
|
||||
Other | | 6.023e-05 | | | 5.19
|
||||
|
||||
Nlocal: 3 ave 3 max 3 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 = 42
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1 @@
|
||||
mpirun -np $NBEADS $LMP -in in.lmp -partition ${NBEADS}x1
|
||||
60
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp
Normal file
60
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp
Normal file
@ -0,0 +1,60 @@
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
@ -0,0 +1,2 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Running on 4 partitions of processors
|
||||
@ -0,0 +1,237 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Processor partition = 0
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188891 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.2139311e-05 (kcal/mol/A^2)
|
||||
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 0 0.00024794798
|
||||
1 8.5849317e-10 4.5664581e-10 0.00024794215
|
||||
2 3.4338094e-09 1.3424585e-09 0.00024793325
|
||||
3 7.7255501e-09 2.6573351e-09 0.00024792129
|
||||
4 1.3733112e-08 4.4011211e-09 0.00024790626
|
||||
5 2.1455686e-08 6.5736113e-09 0.00024788818
|
||||
6 3.0892259e-08 9.1745487e-09 0.00024786704
|
||||
7 4.2041614e-08 1.2203626e-08 0.00024784285
|
||||
8 5.4902328e-08 1.5660483e-08 0.0002478156
|
||||
9 6.9472776e-08 1.9544712e-08 0.00024778532
|
||||
10 8.5751128e-08 2.385585e-08 0.00024775199
|
||||
11 1.0373535e-07 2.8593386e-08 0.00024771564
|
||||
12 1.234232e-07 3.3756758e-08 0.00024767626
|
||||
13 1.4481225e-07 3.9345352e-08 0.00024763386
|
||||
14 1.6789985e-07 4.5358504e-08 0.00024758844
|
||||
15 1.9268316e-07 5.1795501e-08 0.00024754003
|
||||
16 2.1915914e-07 5.8655576e-08 0.00024748862
|
||||
17 2.4732452e-07 6.5937915e-08 0.00024743423
|
||||
18 2.7717588e-07 7.3641654e-08 0.00024737686
|
||||
19 3.0870956e-07 8.1765876e-08 0.00024731653
|
||||
20 3.4192172e-07 9.0309618e-08 0.00024725324
|
||||
21 3.7680831e-07 9.9271863e-08 0.00024718701
|
||||
22 4.1336509e-07 1.0865155e-07 0.00024711785
|
||||
23 4.5158762e-07 1.1844756e-07 0.00024704578
|
||||
24 4.9147126e-07 1.2865874e-07 0.0002469708
|
||||
25 5.3301119e-07 1.3928387e-07 0.00024689293
|
||||
26 5.7620236e-07 1.5032169e-07 0.00024681218
|
||||
27 6.2103957e-07 1.6177089e-07 0.00024672857
|
||||
28 6.675174e-07 1.7363012e-07 0.00024664212
|
||||
29 7.1563024e-07 1.8589798e-07 0.00024655283
|
||||
30 7.6537229e-07 1.9857299e-07 0.00024646073
|
||||
31 8.1673756e-07 2.1165368e-07 0.00024636584
|
||||
32 8.6971988e-07 2.2513849e-07 0.00024626816
|
||||
33 9.2431288e-07 2.3902582e-07 0.00024616772
|
||||
34 9.8051001e-07 2.5331402e-07 0.00024606453
|
||||
35 1.0383045e-06 2.6800143e-07 0.00024595862
|
||||
36 1.0976895e-06 2.8308629e-07 0.00024585001
|
||||
37 1.1586578e-06 2.9856682e-07 0.0002457387
|
||||
38 1.2212021e-06 3.1444121e-07 0.00024562473
|
||||
39 1.2853151e-06 3.3070757e-07 0.00024550812
|
||||
40 1.350989e-06 3.4736399e-07 0.00024538888
|
||||
41 1.4182159e-06 3.644085e-07 0.00024526703
|
||||
42 1.4869879e-06 3.8183911e-07 0.00024514261
|
||||
43 1.5572969e-06 3.9965375e-07 0.00024501562
|
||||
44 1.6291343e-06 4.1785034e-07 0.0002448861
|
||||
45 1.7024917e-06 4.3642673e-07 0.00024475406
|
||||
46 1.7773604e-06 4.5538075e-07 0.00024461954
|
||||
47 1.8537315e-06 4.7471016e-07 0.00024448255
|
||||
48 1.9315959e-06 4.9441271e-07 0.00024434312
|
||||
49 2.0109445e-06 5.1448608e-07 0.00024420127
|
||||
50 2.0917677e-06 5.3492792e-07 0.00024405703
|
||||
51 2.1740562e-06 5.5573584e-07 0.00024391043
|
||||
52 2.2578001e-06 5.769074e-07 0.00024376149
|
||||
53 2.3429895e-06 5.9844014e-07 0.00024361023
|
||||
54 2.4296146e-06 6.2033154e-07 0.00024345669
|
||||
55 2.5176649e-06 6.4257904e-07 0.00024330088
|
||||
56 2.6071302e-06 6.6518005e-07 0.00024314285
|
||||
57 2.6980001e-06 6.8813194e-07 0.00024298261
|
||||
58 2.7902637e-06 7.1143203e-07 0.0002428202
|
||||
59 2.8839103e-06 7.3507763e-07 0.00024265563
|
||||
60 2.9789289e-06 7.5906598e-07 0.00024248895
|
||||
61 3.0753084e-06 7.833943e-07 0.00024232018
|
||||
62 3.1730376e-06 8.0805977e-07 0.00024214934
|
||||
63 3.2721049e-06 8.3305953e-07 0.00024197647
|
||||
64 3.372499e-06 8.5839069e-07 0.00024180161
|
||||
65 3.474208e-06 8.8405032e-07 0.00024162477
|
||||
66 3.5772201e-06 9.1003545e-07 0.00024144598
|
||||
67 3.6815235e-06 9.3634309e-07 0.00024126529
|
||||
68 3.7871058e-06 9.6297021e-07 0.00024108272
|
||||
69 3.893955e-06 9.8991374e-07 0.0002408983
|
||||
70 4.0020586e-06 1.0171706e-06 0.00024071206
|
||||
71 4.1114041e-06 1.0447376e-06 0.00024052403
|
||||
72 4.2219789e-06 1.0726116e-06 0.00024033425
|
||||
73 4.3337702e-06 1.1007895e-06 0.00024014274
|
||||
74 4.4467651e-06 1.1292679e-06 0.00023994955
|
||||
75 4.5609507e-06 1.1580437e-06 0.0002397547
|
||||
76 4.6763137e-06 1.1871136e-06 0.00023955822
|
||||
77 4.792841e-06 1.2164741e-06 0.00023936014
|
||||
78 4.9105191e-06 1.2461221e-06 0.00023916051
|
||||
79 5.0293346e-06 1.276054e-06 0.00023895935
|
||||
80 5.149274e-06 1.3062666e-06 0.00023875669
|
||||
81 5.2703234e-06 1.3367563e-06 0.00023855257
|
||||
82 5.392469e-06 1.3675198e-06 0.00023834703
|
||||
83 5.515697e-06 1.3985535e-06 0.00023814009
|
||||
84 5.6399934e-06 1.4298539e-06 0.00023793178
|
||||
85 5.7653439e-06 1.4614174e-06 0.00023772215
|
||||
86 5.8917344e-06 1.4932406e-06 0.00023751123
|
||||
87 6.0191505e-06 1.5253199e-06 0.00023729904
|
||||
88 6.1475779e-06 1.5576515e-06 0.00023708563
|
||||
89 6.277002e-06 1.590232e-06 0.00023687102
|
||||
90 6.4074081e-06 1.6230576e-06 0.00023665526
|
||||
91 6.5387817e-06 1.6561246e-06 0.00023643837
|
||||
92 6.6711079e-06 1.6894294e-06 0.00023622039
|
||||
93 6.8043718e-06 1.7229682e-06 0.00023600135
|
||||
94 6.9385585e-06 1.7567372e-06 0.00023578129
|
||||
95 7.0736529e-06 1.7907328e-06 0.00023556024
|
||||
96 7.2096401e-06 1.8249512e-06 0.00023533824
|
||||
97 7.3465046e-06 1.8593885e-06 0.00023511531
|
||||
98 7.4842314e-06 1.8940408e-06 0.0002348915
|
||||
99 7.622805e-06 1.9289045e-06 0.00023466684
|
||||
100 7.76221e-06 1.9639756e-06 0.00023444136
|
||||
Loop time of 0.00193128 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 2236858456.568 fs/day, 0.000 hours/fs, 51779.131 timesteps/s, 155.337 katom-step/s
|
||||
36.5% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.454e-06 | 1.454e-06 | 1.454e-06 | 0.0 | 0.08
|
||||
Comm | 2.3033e-05 | 2.3033e-05 | 2.3033e-05 | 0.0 | 1.19
|
||||
Output | 0.00030824 | 0.00030824 | 0.00030824 | 0.0 | 15.96
|
||||
Modify | 0.001541 | 0.001541 | 0.001541 | 0.0 | 79.79
|
||||
Other | | 5.754e-05 | | | 2.98
|
||||
|
||||
Nlocal: 3 ave 3 max 3 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 = 24
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,235 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Processor partition = 1
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188892 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 0 0.00024796164
|
||||
1 8.5850843e-10 5.313724e-10 0.00024796083
|
||||
2 3.4339027e-09 1.4919466e-09 0.00024795841
|
||||
3 7.7257901e-09 2.8816048e-09 0.00024795438
|
||||
4 1.3733516e-08 4.7001635e-09 0.00024794873
|
||||
5 2.1456164e-08 6.9473741e-09 0.00024794148
|
||||
6 3.0892555e-08 9.6229225e-09 0.00024793261
|
||||
7 4.2041252e-08 1.2726429e-08 0.00024792214
|
||||
8 5.4900553e-08 1.6257449e-08 0.00024791006
|
||||
9 6.9468499e-08 2.0215473e-08 0.00024789638
|
||||
10 8.5742867e-08 2.4599926e-08 0.0002478811
|
||||
11 1.0372118e-07 2.9410168e-08 0.00024786422
|
||||
12 1.2340069e-07 3.4645495e-08 0.00024784576
|
||||
13 1.447784e-07 4.0305136e-08 0.0002478257
|
||||
14 1.6785106e-07 4.6388259e-08 0.00024780406
|
||||
15 1.9261515e-07 5.2893965e-08 0.00024778084
|
||||
16 2.190669e-07 5.9821291e-08 0.00024775605
|
||||
17 2.4720228e-07 6.7169211e-08 0.00024772969
|
||||
18 2.7701701e-07 7.4936635e-08 0.00024770176
|
||||
19 3.0850655e-07 8.312241e-08 0.00024767228
|
||||
20 3.416661e-07 9.1725317e-08 0.00024764125
|
||||
21 3.7649064e-07 1.0074408e-07 0.00024760868
|
||||
22 4.1297485e-07 1.1017735e-07 0.00024757457
|
||||
23 4.511132e-07 1.2002372e-07 0.00024753893
|
||||
24 4.9089989e-07 1.3028173e-07 0.00024750177
|
||||
25 5.3232887e-07 1.4094984e-07 0.0002474631
|
||||
26 5.7539386e-07 1.5202647e-07 0.00024742293
|
||||
27 6.2008832e-07 1.6350996e-07 0.00024738126
|
||||
28 6.6640547e-07 1.7539859e-07 0.00024733811
|
||||
29 7.1433828e-07 1.876906e-07 0.00024729348
|
||||
30 7.6387949e-07 2.0038414e-07 0.00024724738
|
||||
31 8.150216e-07 2.1347732e-07 0.00024719983
|
||||
32 8.6775685e-07 2.2696818e-07 0.00024715084
|
||||
33 9.2207727e-07 2.4085472e-07 0.0002471004
|
||||
34 9.7797464e-07 2.5513485e-07 0.00024704855
|
||||
35 1.0354405e-06 2.6980645e-07 0.00024699528
|
||||
36 1.0944662e-06 2.8486732e-07 0.00024694061
|
||||
37 1.1550427e-06 3.0031522e-07 0.00024688456
|
||||
38 1.2171611e-06 3.1614785e-07 0.00024682713
|
||||
39 1.2808118e-06 3.3236283e-07 0.00024676833
|
||||
40 1.3459853e-06 3.4895776e-07 0.00024670818
|
||||
41 1.4126717e-06 3.6593016e-07 0.0002466467
|
||||
42 1.4808611e-06 3.832775e-07 0.0002465839
|
||||
43 1.5505431e-06 4.009972e-07 0.00024651978
|
||||
44 1.6217074e-06 4.1908663e-07 0.00024645437
|
||||
45 1.6943431e-06 4.3754308e-07 0.00024638767
|
||||
46 1.7684394e-06 4.5636381e-07 0.00024631971
|
||||
47 1.8439852e-06 4.7554603e-07 0.0002462505
|
||||
48 1.9209691e-06 4.9508689e-07 0.00024618005
|
||||
49 1.9993796e-06 5.1498348e-07 0.00024610839
|
||||
50 2.079205e-06 5.3523286e-07 0.00024603551
|
||||
51 2.1604333e-06 5.5583202e-07 0.00024596145
|
||||
52 2.2430524e-06 5.7677791e-07 0.00024588621
|
||||
53 2.32705e-06 5.9806742e-07 0.00024580981
|
||||
54 2.4124135e-06 6.1969741e-07 0.00024573228
|
||||
55 2.4991302e-06 6.4166468e-07 0.00024565362
|
||||
56 2.5871872e-06 6.6396597e-07 0.00024557386
|
||||
57 2.6765714e-06 6.8659801e-07 0.00024549301
|
||||
58 2.7672695e-06 7.0955745e-07 0.00024541108
|
||||
59 2.859268e-06 7.328409e-07 0.00024532811
|
||||
60 2.9525533e-06 7.5644494e-07 0.00024524409
|
||||
61 3.0471115e-06 7.8036609e-07 0.00024515907
|
||||
62 3.1429287e-06 8.0460083e-07 0.00024507304
|
||||
63 3.2399907e-06 8.2914562e-07 0.00024498603
|
||||
64 3.3382831e-06 8.5399683e-07 0.00024489807
|
||||
65 3.4377915e-06 8.7915084e-07 0.00024480916
|
||||
66 3.5385011e-06 9.0460395e-07 0.00024471933
|
||||
67 3.6403972e-06 9.3035245e-07 0.0002446286
|
||||
68 3.7434648e-06 9.5639257e-07 0.00024453698
|
||||
69 3.8476886e-06 9.8272051e-07 0.0002444445
|
||||
70 3.9530535e-06 1.0093324e-06 0.00024435118
|
||||
71 4.0595439e-06 1.0362244e-06 0.00024425703
|
||||
72 4.1671443e-06 1.0633926e-06 0.00024416208
|
||||
73 4.275839e-06 1.0908331e-06 0.00024406635
|
||||
74 4.3856121e-06 1.1185418e-06 0.00024396985
|
||||
75 4.4964475e-06 1.1465147e-06 0.00024387262
|
||||
76 4.6083292e-06 1.1747478e-06 0.00024377466
|
||||
77 4.7212408e-06 1.2032371e-06 0.00024367601
|
||||
78 4.835166e-06 1.2319783e-06 0.00024357668
|
||||
79 4.9500883e-06 1.2609674e-06 0.00024347669
|
||||
80 5.0659909e-06 1.2902001e-06 0.00024337607
|
||||
81 5.1828572e-06 1.3196723e-06 0.00024327483
|
||||
82 5.3006702e-06 1.3493797e-06 0.000243173
|
||||
83 5.419413e-06 1.379318e-06 0.0002430706
|
||||
84 5.5390685e-06 1.4094831e-06 0.00024296765
|
||||
85 5.6596194e-06 1.4398705e-06 0.00024286417
|
||||
86 5.7810485e-06 1.4704759e-06 0.00024276019
|
||||
87 5.9033384e-06 1.501295e-06 0.00024265573
|
||||
88 6.0264715e-06 1.5323234e-06 0.00024255081
|
||||
89 6.1504303e-06 1.5635565e-06 0.00024244545
|
||||
90 6.275197e-06 1.5949902e-06 0.00024233967
|
||||
91 6.400754e-06 1.6266197e-06 0.0002422335
|
||||
92 6.5270834e-06 1.6584408e-06 0.00024212696
|
||||
93 6.6541672e-06 1.6904488e-06 0.00024202007
|
||||
94 6.7819875e-06 1.7226394e-06 0.00024191285
|
||||
95 6.9105262e-06 1.7550078e-06 0.00024180534
|
||||
96 7.0397651e-06 1.7875497e-06 0.00024169754
|
||||
97 7.169686e-06 1.8202604e-06 0.00024158948
|
||||
98 7.3002707e-06 1.8531354e-06 0.00024148118
|
||||
99 7.4315008e-06 1.88617e-06 0.00024137268
|
||||
100 7.563358e-06 1.9193596e-06 0.00024126398
|
||||
Loop time of 0.00190888 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 2263110719.025 fs/day, 0.000 hours/fs, 52386.822 timesteps/s, 157.160 katom-step/s
|
||||
0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 2.774e-06 | 2.774e-06 | 2.774e-06 | 0.0 | 0.15
|
||||
Comm | 2.3215e-05 | 2.3215e-05 | 2.3215e-05 | 0.0 | 1.22
|
||||
Output | 0.00042246 | 0.00042246 | 0.00042246 | 0.0 | 22.13
|
||||
Modify | 0.0013744 | 0.0013744 | 0.0013744 | 0.0 | 72.00
|
||||
Other | | 8.601e-05 | | | 4.51
|
||||
|
||||
Nlocal: 3 ave 3 max 3 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 = 23
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,235 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Processor partition = 2
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188893 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 0 0.00024796164
|
||||
1 8.5850845e-10 -3.6831179e-10 0.0002479594
|
||||
2 3.4338783e-09 -3.0736303e-10 0.00024795267
|
||||
3 7.7256433e-09 1.8277487e-10 0.00024794145
|
||||
4 1.3733026e-08 1.1019528e-09 0.00024792576
|
||||
5 2.145494e-08 2.449944e-09 0.00024790558
|
||||
6 3.0889985e-08 4.226444e-09 0.00024788093
|
||||
7 4.2036455e-08 6.4310711e-09 0.00024785181
|
||||
8 5.4892332e-08 9.0633658e-09 0.00024781823
|
||||
9 6.9455288e-08 1.2122792e-08 0.00024778019
|
||||
10 8.572269e-08 1.5608734e-08 0.0002477377
|
||||
11 1.0369159e-07 1.9520504e-08 0.00024769077
|
||||
12 1.2335875e-07 2.3857331e-08 0.00024763941
|
||||
13 1.4472059e-07 2.8618373e-08 0.00024758363
|
||||
14 1.6777327e-07 3.3802708e-08 0.00024752344
|
||||
15 1.9251262e-07 3.940934e-08 0.00024745886
|
||||
16 2.1893415e-07 4.5437194e-08 0.00024738989
|
||||
17 2.4703311e-07 5.1885122e-08 0.00024731656
|
||||
18 2.768044e-07 5.8751899e-08 0.00024723887
|
||||
19 3.0824267e-07 6.6036227e-08 0.00024715685
|
||||
20 3.4134222e-07 7.3736729e-08 0.00024707051
|
||||
21 3.7609709e-07 8.1851958e-08 0.00024697986
|
||||
22 4.1250102e-07 9.0380389e-08 0.00024688494
|
||||
23 4.5054742e-07 9.9320426e-08 0.00024678575
|
||||
24 4.9022945e-07 1.086704e-07 0.00024668231
|
||||
25 5.3153996e-07 1.1842856e-07 0.00024657466
|
||||
26 5.744715e-07 1.285931e-07 0.00024646281
|
||||
27 6.1901635e-07 1.3916212e-07 0.00024634678
|
||||
28 6.6516648e-07 1.5013367e-07 0.0002462266
|
||||
29 7.1291361e-07 1.6150571e-07 0.00024610229
|
||||
30 7.6224914e-07 1.7327614e-07 0.00024597388
|
||||
31 8.1316422e-07 1.8544279e-07 0.0002458414
|
||||
32 8.6564969e-07 1.9800342e-07 0.00024570487
|
||||
33 9.1969614e-07 2.109557e-07 0.00024556432
|
||||
34 9.7529388e-07 2.2429727e-07 0.00024541978
|
||||
35 1.0324329e-06 2.3802567e-07 0.00024527128
|
||||
36 1.0911031e-06 2.5213838e-07 0.00024511886
|
||||
37 1.1512938e-06 2.6663282e-07 0.00024496253
|
||||
38 1.2129943e-06 2.8150634e-07 0.00024480234
|
||||
39 1.2761936e-06 2.9675622e-07 0.00024463831
|
||||
40 1.3408803e-06 3.1237968e-07 0.00024447049
|
||||
41 1.407043e-06 3.2837388e-07 0.0002442989
|
||||
42 1.4746698e-06 3.447359e-07 0.00024412359
|
||||
43 1.5437487e-06 3.6146277e-07 0.00024394458
|
||||
44 1.6142674e-06 3.7855146e-07 0.00024376192
|
||||
45 1.6862132e-06 3.9599886e-07 0.00024357564
|
||||
46 1.7595735e-06 4.1380182e-07 0.00024338577
|
||||
47 1.8343351e-06 4.3195711e-07 0.00024319237
|
||||
48 1.9104848e-06 4.5046147e-07 0.00024299547
|
||||
49 1.9880091e-06 4.6931154e-07 0.00024279511
|
||||
50 2.0668943e-06 4.8850394e-07 0.00024259132
|
||||
51 2.1471263e-06 5.0803521e-07 0.00024238416
|
||||
52 2.228691e-06 5.2790184e-07 0.00024217367
|
||||
53 2.311574e-06 5.4810027e-07 0.00024195988
|
||||
54 2.3957606e-06 5.6862687e-07 0.00024174285
|
||||
55 2.481236e-06 5.8947797e-07 0.00024152261
|
||||
56 2.5679851e-06 6.1064984e-07 0.00024129922
|
||||
57 2.6559926e-06 6.3213871e-07 0.00024107271
|
||||
58 2.7452431e-06 6.5394073e-07 0.00024084313
|
||||
59 2.8357209e-06 6.7605203e-07 0.00024061054
|
||||
60 2.9274101e-06 6.9846868e-07 0.00024037498
|
||||
61 3.0202947e-06 7.2118669e-07 0.00024013649
|
||||
62 3.1143583e-06 7.4420204e-07 0.00023989513
|
||||
63 3.2095846e-06 7.6751065e-07 0.00023965094
|
||||
64 3.3059569e-06 7.911084e-07 0.00023940398
|
||||
65 3.4034585e-06 8.1499113e-07 0.00023915429
|
||||
66 3.5020722e-06 8.3915461e-07 0.00023890193
|
||||
67 3.601781e-06 8.6359461e-07 0.00023864694
|
||||
68 3.7025676e-06 8.8830681e-07 0.00023838939
|
||||
69 3.8044144e-06 9.132869e-07 0.00023812931
|
||||
70 3.9073038e-06 9.3853048e-07 0.00023786677
|
||||
71 4.0112181e-06 9.6403314e-07 0.00023760182
|
||||
72 4.1161392e-06 9.8979043e-07 0.00023733451
|
||||
73 4.2220491e-06 1.0157978e-06 0.0002370649
|
||||
74 4.3289295e-06 1.0420509e-06 0.00023679303
|
||||
75 4.4367621e-06 1.068545e-06 0.00023651897
|
||||
76 4.5455283e-06 1.0952755e-06 0.00023624277
|
||||
77 4.6552095e-06 1.1222378e-06 0.00023596449
|
||||
78 4.7657869e-06 1.1494273e-06 0.00023568418
|
||||
79 4.8772416e-06 1.1768393e-06 0.0002354019
|
||||
80 4.9895545e-06 1.2044689e-06 0.00023511771
|
||||
81 5.1027067e-06 1.2323116e-06 0.00023483166
|
||||
82 5.2166788e-06 1.2603625e-06 0.00023454381
|
||||
83 5.3314515e-06 1.2886168e-06 0.00023425422
|
||||
84 5.4470054e-06 1.3170697e-06 0.00023396295
|
||||
85 5.5633208e-06 1.3457162e-06 0.00023367006
|
||||
86 5.6803783e-06 1.3745516e-06 0.0002333756
|
||||
87 5.798158e-06 1.403571e-06 0.00023307963
|
||||
88 5.9166402e-06 1.4327693e-06 0.00023278222
|
||||
89 6.0358049e-06 1.4621418e-06 0.00023248341
|
||||
90 6.1556323e-06 1.4916833e-06 0.00023218329
|
||||
91 6.2761023e-06 1.5213889e-06 0.00023188189
|
||||
92 6.3971948e-06 1.5512537e-06 0.00023157929
|
||||
93 6.5188897e-06 1.5812727e-06 0.00023127554
|
||||
94 6.6411667e-06 1.6114407e-06 0.0002309707
|
||||
95 6.7640056e-06 1.6417527e-06 0.00023066484
|
||||
96 6.8873862e-06 1.6722038e-06 0.00023035801
|
||||
97 7.011288e-06 1.7027888e-06 0.00023005028
|
||||
98 7.1356907e-06 1.7335027e-06 0.0002297417
|
||||
99 7.2605738e-06 1.7643404e-06 0.00022943234
|
||||
100 7.3859169e-06 1.7952968e-06 0.00022912226
|
||||
Loop time of 0.00195857 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 2205688634.372 fs/day, 0.000 hours/fs, 51057.607 timesteps/s, 153.173 katom-step/s
|
||||
39.2% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.602e-06 | 1.602e-06 | 1.602e-06 | 0.0 | 0.08
|
||||
Comm | 1.6951e-05 | 1.6951e-05 | 1.6951e-05 | 0.0 | 0.87
|
||||
Output | 0.00032627 | 0.00032627 | 0.00032627 | 0.0 | 16.66
|
||||
Modify | 0.0015486 | 0.0015486 | 0.0015486 | 0.0 | 79.07
|
||||
Other | | 6.514e-05 | | | 3.33
|
||||
|
||||
Nlocal: 3 ave 3 max 3 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 = 24
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,235 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
|
||||
Processor partition = 3
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188894 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
|
||||
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 0 0.00024796164
|
||||
1 8.5847879e-10 4.4463719e-10 0.00024796024
|
||||
2 3.4336684e-09 1.3183829e-09 0.00024795602
|
||||
3 7.7250055e-09 2.6210625e-09 0.000247949
|
||||
4 1.3731669e-08 4.3524371e-09 0.00024793917
|
||||
5 2.1452581e-08 6.5122035e-09 0.00024792653
|
||||
6 3.0886407e-08 9.0999942e-09 0.0002479111
|
||||
7 4.2031554e-08 1.2115377e-08 0.00024789287
|
||||
8 5.4886174e-08 1.5557858e-08 0.00024787185
|
||||
9 6.9448162e-08 1.9426875e-08 0.00024784804
|
||||
10 8.5715159e-08 2.3721806e-08 0.00024782146
|
||||
11 1.0368455e-07 2.8441963e-08 0.0002477921
|
||||
12 1.2335346e-07 3.3586595e-08 0.00024775998
|
||||
13 1.4471878e-07 3.9154888e-08 0.0002477251
|
||||
14 1.6777712e-07 4.5145965e-08 0.00024768748
|
||||
15 1.9252485e-07 5.1558884e-08 0.00024764712
|
||||
16 2.1895809e-07 5.8392642e-08 0.00024760403
|
||||
17 2.4707272e-07 6.5646173e-08 0.00024755823
|
||||
18 2.7686434e-07 7.3318348e-08 0.00024750973
|
||||
19 3.0832834e-07 8.1407976e-08 0.00024745854
|
||||
20 3.4145982e-07 8.9913804e-08 0.00024740467
|
||||
21 3.7625367e-07 9.8834518e-08 0.00024734813
|
||||
22 4.127045e-07 1.0816874e-07 0.00024728895
|
||||
23 4.5080671e-07 1.1791504e-07 0.00024722714
|
||||
24 4.9055443e-07 1.2807191e-07 0.00024716271
|
||||
25 5.3194155e-07 1.3863779e-07 0.00024709568
|
||||
26 5.7496174e-07 1.4961107e-07 0.00024702607
|
||||
27 6.1960841e-07 1.6099007e-07 0.00024695389
|
||||
28 6.6587473e-07 1.7277305e-07 0.00024687917
|
||||
29 7.1375365e-07 1.8495821e-07 0.00024680191
|
||||
30 7.6323786e-07 1.975437e-07 0.00024672216
|
||||
31 8.1431984e-07 2.1052759e-07 0.00024663991
|
||||
32 8.6699183e-07 2.2390793e-07 0.0002465552
|
||||
33 9.2124582e-07 2.3768267e-07 0.00024646805
|
||||
34 9.7707361e-07 2.5184974e-07 0.00024637847
|
||||
35 1.0344667e-06 2.6640698e-07 0.0002462865
|
||||
36 1.0934165e-06 2.813522e-07 0.00024619215
|
||||
37 1.1539141e-06 2.9668313e-07 0.00024609545
|
||||
38 1.2159503e-06 3.1239747e-07 0.00024599643
|
||||
39 1.2795157e-06 3.2849286e-07 0.00024589511
|
||||
40 1.344601e-06 3.4496686e-07 0.00024579151
|
||||
41 1.4111961e-06 3.61817e-07 0.00024568566
|
||||
42 1.4792913e-06 3.7904076e-07 0.0002455776
|
||||
43 1.5488762e-06 3.9663555e-07 0.00024546734
|
||||
44 1.6199404e-06 4.1459874e-07 0.00024535492
|
||||
45 1.6924734e-06 4.3292764e-07 0.00024524035
|
||||
46 1.7664643e-06 4.5161952e-07 0.00024512369
|
||||
47 1.841902e-06 4.7067159e-07 0.00024500494
|
||||
48 1.9187753e-06 4.90081e-07 0.00024488415
|
||||
49 1.9970729e-06 5.0984488e-07 0.00024476135
|
||||
50 2.076783e-06 5.2996028e-07 0.00024463656
|
||||
51 2.1578939e-06 5.5042422e-07 0.00024450981
|
||||
52 2.2403935e-06 5.7123366e-07 0.00024438115
|
||||
53 2.3242696e-06 5.9238553e-07 0.0002442506
|
||||
54 2.4095099e-06 6.138767e-07 0.00024411819
|
||||
55 2.4961017e-06 6.3570399e-07 0.00024398396
|
||||
56 2.5840323e-06 6.5786419e-07 0.00024384795
|
||||
57 2.6732887e-06 6.8035404e-07 0.00024371018
|
||||
58 2.7638579e-06 7.0317021e-07 0.0002435707
|
||||
59 2.8557265e-06 7.2630938e-07 0.00024342953
|
||||
60 2.9488811e-06 7.4976814e-07 0.00024328672
|
||||
61 3.0433081e-06 7.7354305e-07 0.0002431423
|
||||
62 3.1389936e-06 7.9763065e-07 0.00024299631
|
||||
63 3.2359238e-06 8.2202741e-07 0.00024284878
|
||||
64 3.3340844e-06 8.4672977e-07 0.00024269976
|
||||
65 3.4334612e-06 8.7173415e-07 0.00024254927
|
||||
66 3.5340397e-06 8.970369e-07 0.00024239736
|
||||
67 3.6358055e-06 9.2263435e-07 0.00024224406
|
||||
68 3.7387437e-06 9.4852279e-07 0.00024208942
|
||||
69 3.8428394e-06 9.7469849e-07 0.00024193348
|
||||
70 3.9480777e-06 1.0011576e-06 0.00024177626
|
||||
71 4.0544433e-06 1.0278964e-06 0.00024161782
|
||||
72 4.1619211e-06 1.054911e-06 0.0002414582
|
||||
73 4.2704954e-06 1.0821976e-06 0.00024129742
|
||||
74 4.3801508e-06 1.1097521e-06 0.00024113554
|
||||
75 4.4908716e-06 1.1375706e-06 0.0002409726
|
||||
76 4.6026419e-06 1.1656492e-06 0.00024080863
|
||||
77 4.7154459e-06 1.1939839e-06 0.00024064367
|
||||
78 4.8292673e-06 1.2225706e-06 0.00024047778
|
||||
79 4.9440901e-06 1.2514052e-06 0.00024031099
|
||||
80 5.059898e-06 1.2804837e-06 0.00024014333
|
||||
81 5.1766745e-06 1.309802e-06 0.00023997487
|
||||
82 5.2944032e-06 1.3393558e-06 0.00023980562
|
||||
83 5.4130674e-06 1.369141e-06 0.00023963565
|
||||
84 5.5326505e-06 1.3991534e-06 0.00023946499
|
||||
85 5.6531355e-06 1.4293887e-06 0.00023929369
|
||||
86 5.7745057e-06 1.4598429e-06 0.00023912178
|
||||
87 5.8967439e-06 1.4905114e-06 0.00023894931
|
||||
88 6.0198332e-06 1.5213902e-06 0.00023877633
|
||||
89 6.1437564e-06 1.5524748e-06 0.00023860287
|
||||
90 6.2684962e-06 1.5837609e-06 0.00023842898
|
||||
91 6.3940353e-06 1.6152441e-06 0.00023825471
|
||||
92 6.5203562e-06 1.6469202e-06 0.0002380801
|
||||
93 6.6474416e-06 1.6787847e-06 0.00023790518
|
||||
94 6.7752739e-06 1.7108332e-06 0.00023773001
|
||||
95 6.9038354e-06 1.7430613e-06 0.00023755463
|
||||
96 7.0331085e-06 1.7754645e-06 0.00023737908
|
||||
97 7.1630755e-06 1.8080385e-06 0.00023720341
|
||||
98 7.2937187e-06 1.8407787e-06 0.00023702765
|
||||
99 7.4250201e-06 1.8736806e-06 0.00023685186
|
||||
100 7.5569619e-06 1.9067398e-06 0.00023667607
|
||||
Loop time of 0.00197094 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 2191851993.165 fs/day, 0.000 hours/fs, 50737.315 timesteps/s, 152.212 katom-step/s
|
||||
37.5% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.652e-06 | 1.652e-06 | 1.652e-06 | 0.0 | 0.08
|
||||
Comm | 1.7965e-05 | 1.7965e-05 | 1.7965e-05 | 0.0 | 0.91
|
||||
Output | 0.00036011 | 0.00036011 | 0.00036011 | 0.0 | 18.27
|
||||
Modify | 0.0015231 | 0.0015231 | 0.0015231 | 0.0 | 77.28
|
||||
Other | | 6.806e-05 | | | 3.45
|
||||
|
||||
Nlocal: 3 ave 3 max 3 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 = 24
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
1
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh
Normal file
1
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh
Normal file
@ -0,0 +1 @@
|
||||
mpirun -np $NBEADS $LMP -in in.lmp -partition ${NBEADS}x1
|
||||
@ -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
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * ../../../../potentials/Cu_mishin1.eam.alloy Cu
|
||||
pair_coeff * * Cu_mishin1.eam.alloy Cu
|
||||
#------------------------------------------------------------------------------#
|
||||
|
||||
|
||||
|
||||
@ -112,6 +112,7 @@ snap: examples for using several bundled SNAP potentials
|
||||
srd: stochastic rotation dynamics (SRD) particles as solvent
|
||||
steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
|
||||
streitz: Streitz-Mintmire potential for Al2O3
|
||||
stress_vcm: removing binned rigid body motion from binned stress profile
|
||||
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
|
||||
template: examples for using atom_style template and comparing to atom style molecular
|
||||
tersoff: regression test input for Tersoff variants
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,45 +1,46 @@
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style spin
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
replicate 1 1 2
|
||||
|
||||
mass 1 58.93
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
#dump_modify 1 sort id
|
||||
run 100
|
||||
|
||||
@ -1,49 +1,49 @@
|
||||
# start a spin-lattice simulation from a data file
|
||||
units metal
|
||||
atom_style spin
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
atom_modify map array
|
||||
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
run 100
|
||||
|
||||
@ -1,54 +1,54 @@
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
lattice hcp 2.5071
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
set group all spin/atom/random 31 1.72
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice frozen
|
||||
timestep 0.0001
|
||||
fix 3 all nve/spin lattice frozen
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm pe v_emag temp etotal
|
||||
thermo 100
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 1000
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
#dump_modify 100 sort id
|
||||
run 1000
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
|
||||
136
examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1
Normal file
136
examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1
Normal file
@ -0,0 +1,136 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (15 28.32 13.68)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1024 atoms
|
||||
reading velocities ...
|
||||
1024 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
replicate 1 1 2
|
||||
Replication is creating a 1x1x2 = 2 times larger system...
|
||||
orthogonal box = (0 0 0) to (15 28.32 27.36)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2048 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
#dump_modify 1 sort id
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.499539
|
||||
ghost atom cutoff = 7.499539
|
||||
binsize = 3.7497695, bins = 5 8 8
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on, cut 7.499539
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.082 | 9.082 | 9.082 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng
|
||||
0 0 0.99566943155533 116726.359107918 -852.392312873949 34.9207785637842 0 116726.359107918
|
||||
20 0.002 0.995669416541629 70905.5692189811 -849.222504107045 34.647400481739 172820.122486868 116632.998844426
|
||||
40 0.004 0.995669401356638 71221.2391274615 -848.368415908416 34.9759984641547 171555.103338675 116613.950357609
|
||||
60 0.006 0.995669394598344 69647.7523345612 -845.585158124559 36.100016238044 177502.681559427 116614.166097826
|
||||
80 0.008 0.995669395756676 107415.560454437 -846.200871523815 37.9775024824566 35031.4099604677 116684.714477685
|
||||
100 0.01 0.995669403283478 63849.6798250643 -836.341677782106 39.680777051272 199492.565587335 116634.518317396
|
||||
Loop time of 2.97847 on 1 procs for 100 steps with 2048 atoms
|
||||
|
||||
Performance: 0.290 ns/day, 82.735 hours/ns, 33.574 timesteps/s, 68.760 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 | 1.0361 | 1.0361 | 1.0361 | 0.0 | 34.79
|
||||
Neigh | 0.78559 | 0.78559 | 0.78559 | 0.0 | 26.38
|
||||
Comm | 0.013262 | 0.013262 | 0.013262 | 0.0 | 0.45
|
||||
Output | 0.00026908 | 0.00026908 | 0.00026908 | 0.0 | 0.01
|
||||
Modify | 1.1415 | 1.1415 | 1.1415 | 0.0 | 38.33
|
||||
Other | | 0.001761 | | | 0.06
|
||||
|
||||
Nlocal: 2048 ave 2048 max 2048 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7952 ave 7952 max 7952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 314944 ave 314944 max 314944 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 629888 ave 629888 max 629888 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 629888
|
||||
Ave neighs/atom = 307.5625
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:03
|
||||
136
examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4
Normal file
136
examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4
Normal file
@ -0,0 +1,136 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (15 28.32 13.68)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1024 atoms
|
||||
reading velocities ...
|
||||
1024 velocities
|
||||
read_data CPU = 0.004 seconds
|
||||
replicate 1 1 2
|
||||
Replication is creating a 1x1x2 = 2 times larger system...
|
||||
orthogonal box = (0 0 0) to (15 28.32 27.36)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
2048 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
#dump_modify 1 sort id
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.499539
|
||||
ghost atom cutoff = 7.499539
|
||||
binsize = 3.7497695, bins = 5 8 8
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on, cut 7.499539
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.812 | 5.812 | 5.812 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng
|
||||
0 0 0.995669431555328 116726.359107923 -852.39231287395 34.9207785637843 0 116726.359107923
|
||||
20 0.002 0.995669419512638 70905.5692199804 -849.222502855646 34.6474282239503 172820.122483292 116632.998844479
|
||||
40 0.004 0.995669419108591 71221.2391285209 -848.368412494784 34.97611050919 171555.103335676 116613.950357875
|
||||
60 0.006 0.99566940895435 69647.7523345112 -845.585157291247 36.1001312564486 177502.681560664 116614.166098104
|
||||
80 0.008 0.995669417344697 107415.560454912 -846.200874451992 37.9776090859263 35031.4099596403 116684.714477941
|
||||
100 0.01 0.995669427709463 63849.6798245944 -836.341678212079 39.6809090980074 199492.565591024 116634.518317902
|
||||
Loop time of 0.991506 on 4 procs for 100 steps with 2048 atoms
|
||||
|
||||
Performance: 0.871 ns/day, 27.542 hours/ns, 100.857 timesteps/s, 206.554 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 | 0.31016 | 0.31287 | 0.31496 | 0.3 | 31.56
|
||||
Neigh | 0.21999 | 0.22957 | 0.23793 | 1.7 | 23.15
|
||||
Comm | 0.015231 | 0.025975 | 0.036137 | 6.0 | 2.62
|
||||
Output | 0.00012037 | 0.00014855 | 0.0001849 | 0.0 | 0.01
|
||||
Modify | 0.4213 | 0.42166 | 0.42201 | 0.0 | 42.53
|
||||
Other | | 0.001272 | | | 0.13
|
||||
|
||||
Nlocal: 512 ave 521 max 503 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 4112 ave 4121 max 4103 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 78736 ave 80265 max 77207 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 157472 ave 160276 max 154668 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 629888
|
||||
Ave neighs/atom = 307.5625
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:01
|
||||
135
examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1
Normal file
135
examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1
Normal file
@ -0,0 +1,135 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# start a spin-lattice simulation from a data file
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
Reading restart file ...
|
||||
restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025
|
||||
restoring atom style spin from restart
|
||||
orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style spin/exchange from restart
|
||||
500 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.499539
|
||||
ghost atom cutoff = 7.499539
|
||||
binsize = 3.7497695, bins = 4 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on, cut 7.499539
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.255 | 5.255 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng
|
||||
1000 0.1 0.0932563992120983 -2200.23506043127 -5.23510819573568 2608.1272233749 0 -2200.23506043127
|
||||
1020 0.102 0.0932564226983496 -2200.24431693921 -5.24438874766875 2636.89284253705 0.143502110493468 -2200.23506093651
|
||||
1040 0.104 0.0932564330551733 -2200.27026761331 -5.27068764778909 2646.09012775508 0.545814389665464 -2200.23506214178
|
||||
1060 0.106 0.0932564065525508 -2200.30841491752 -5.31025431862422 2627.26990645217 1.13721564075693 -2200.23506358487
|
||||
1080 0.108 0.0932563850278094 -2200.35339675793 -5.35874497582981 2585.24230543411 1.83458183455181 -2200.23506473927
|
||||
1100 0.11 0.0932563977118321 -2200.40087596139 -5.41289411193204 2540.00857034711 2.5706738278606 -2200.23506541119
|
||||
Loop time of 0.473574 on 1 procs for 100 steps with 500 atoms
|
||||
|
||||
Performance: 1.824 ns/day, 13.155 hours/ns, 211.160 timesteps/s, 105.580 katom-step/s
|
||||
98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12025 | 0.12025 | 0.12025 | 0.0 | 25.39
|
||||
Neigh | 0.14912 | 0.14912 | 0.14912 | 0.0 | 31.49
|
||||
Comm | 0.0047587 | 0.0047587 | 0.0047587 | 0.0 | 1.00
|
||||
Output | 0.07234 | 0.07234 | 0.07234 | 0.0 | 15.28
|
||||
Modify | 0.12645 | 0.12645 | 0.12645 | 0.0 | 26.70
|
||||
Other | | 0.0006494 | | | 0.14
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2534 ave 2534 max 2534 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 36500 ave 36500 max 36500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 73000 ave 73000 max 73000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 73000
|
||||
Ave neighs/atom = 146
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
136
examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4
Normal file
136
examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4
Normal file
@ -0,0 +1,136 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# start a spin-lattice simulation from a data file
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
Reading restart file ...
|
||||
restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025
|
||||
WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:628)
|
||||
restoring atom style spin from restart
|
||||
orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style spin/exchange from restart
|
||||
500 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.499539
|
||||
ghost atom cutoff = 7.499539
|
||||
binsize = 3.7497695, bins = 4 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on, cut 7.499539
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.188 | 5.188 | 5.188 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng
|
||||
1000 0.1 0.0932563992120983 -2200.23506043087 -5.23510819573568 2608.1272233749 0 -2200.23506043087
|
||||
1020 0.102 0.0932564663999882 -2200.24431693996 -5.24438874845296 2636.89226887198 0.14350212264756 -2200.23506093648
|
||||
1040 0.104 0.0932565837400281 -2200.27026761822 -5.27068765273516 2646.08966888271 0.545814465748645 -2200.23506214179
|
||||
1060 0.106 0.0932567073488227 -2200.30841492456 -5.31025432590717 2627.27001685206 1.13721574991944 -2200.23506358486
|
||||
1080 0.108 0.0932567401022577 -2200.35339675946 -5.35874497805351 2585.24242001276 1.83458185842719 -2200.23506473925
|
||||
1100 0.11 0.0932566884738387 -2200.4008759633 -5.41289411525345 2540.00813568378 2.57067385759474 -2200.23506541119
|
||||
Loop time of 0.180477 on 4 procs for 100 steps with 500 atoms
|
||||
|
||||
Performance: 4.787 ns/day, 5.013 hours/ns, 554.088 timesteps/s, 277.044 katom-step/s
|
||||
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.033968 | 0.034363 | 0.035109 | 0.2 | 19.04
|
||||
Neigh | 0.035043 | 0.03728 | 0.040013 | 0.9 | 20.66
|
||||
Comm | 0.0049574 | 0.0073867 | 0.0089549 | 1.7 | 4.09
|
||||
Output | 0.021087 | 0.023594 | 0.026417 | 1.3 | 13.07
|
||||
Modify | 0.074785 | 0.07749 | 0.079892 | 0.7 | 42.94
|
||||
Other | | 0.0003627 | | | 0.20
|
||||
|
||||
Nlocal: 125 ave 136 max 117 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 1387 ave 1395 max 1376 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 9125 ave 9972 max 8559 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
FullNghs: 18250 ave 19856 max 17082 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 73000
|
||||
Ave neighs/atom = 146
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
142
examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1
Normal file
142
examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1
Normal file
@ -0,0 +1,142 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/atom/random 31 1.72
|
||||
Setting atom values ...
|
||||
500 settings made for spin/atom/random
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice frozen
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm pe v_emag temp etotal
|
||||
thermo 100
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
#dump_modify 100 sort id
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 20 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.1
|
||||
ghost atom cutoff = 4.1
|
||||
binsize = 2.05, bins = 7 11 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.78 | 4.78 | 4.78 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag Temp TotEng
|
||||
0 0 0.076558814 0.89911794 0.89911794 0 0.89911794
|
||||
100 0.01 0.077627966 0.36694275 0.36694275 0 0.36694275
|
||||
200 0.02 0.076678387 -0.20241504 -0.20241504 0 -0.20241504
|
||||
300 0.03 0.079174207 -0.67593525 -0.67593525 0 -0.67593525
|
||||
400 0.04 0.085031074 -1.5172826 -1.5172826 0 -1.5172826
|
||||
500 0.05 0.087026279 -2.042653 -2.042653 0 -2.042653
|
||||
600 0.06 0.087064628 -2.6297295 -2.6297295 0 -2.6297295
|
||||
700 0.07 0.089787949 -3.3144767 -3.3144767 0 -3.3144767
|
||||
800 0.08 0.091698615 -4.028707 -4.028707 0 -4.028707
|
||||
900 0.09 0.090031988 -4.6007241 -4.6007241 0 -4.6007241
|
||||
1000 0.1 0.093256399 -5.2351082 -5.2351082 0 -5.2351082
|
||||
Loop time of 0.710555 on 1 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 12.160 ns/day, 1.974 hours/ns, 1407.350 timesteps/s, 703.675 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 | 0.12852 | 0.12852 | 0.12852 | 0.0 | 18.09
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.012387 | 0.012387 | 0.012387 | 0.0 | 1.74
|
||||
Output | 0.00014522 | 0.00014522 | 0.00014522 | 0.0 | 0.02
|
||||
Modify | 0.56835 | 0.56835 | 0.56835 | 0.0 | 79.99
|
||||
Other | | 0.001145 | | | 0.16
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1221 ave 1221 max 1221 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
|
||||
FullNghs: 10000 ave 10000 max 10000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10000
|
||||
Ave neighs/atom = 20
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
System init for write_restart ...
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Total wall time: 0:00:00
|
||||
142
examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4
Normal file
142
examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4
Normal file
@ -0,0 +1,142 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/atom/random 31 1.72
|
||||
Setting atom values ...
|
||||
500 settings made for spin/atom/random
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice frozen
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm pe v_emag temp etotal
|
||||
thermo 100
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
#dump_modify 100 sort id
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 20 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.1
|
||||
ghost atom cutoff = 4.1
|
||||
binsize = 2.05, bins = 7 11 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.732 | 4.732 | 4.733 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag Temp TotEng
|
||||
0 0 0.076558814 0.89911794 0.89911794 0 0.89911794
|
||||
100 0.01 0.078299852 0.44131103 0.44131103 0 0.44131103
|
||||
200 0.02 0.081260369 -0.2174146 -0.2174146 0 -0.2174146
|
||||
300 0.03 0.081195064 -0.87039697 -0.87039697 0 -0.87039697
|
||||
400 0.04 0.087298284 -1.7069593 -1.7069593 0 -1.7069593
|
||||
500 0.05 0.087663192 -2.1882865 -2.1882865 0 -2.1882865
|
||||
600 0.06 0.091713114 -2.926766 -2.926766 0 -2.926766
|
||||
700 0.07 0.093779218 -3.3532704 -3.3532704 0 -3.3532704
|
||||
800 0.08 0.097960251 -3.9343481 -3.9343481 0 -3.9343481
|
||||
900 0.09 0.10193598 -4.7944099 -4.7944099 0 -4.7944099
|
||||
1000 0.1 0.10832963 -5.3823924 -5.3823924 0 -5.3823924
|
||||
Loop time of 0.40066 on 4 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 21.564 ns/day, 1.113 hours/ns, 2495.885 timesteps/s, 1.248 Matom-step/s
|
||||
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.032435 | 0.033013 | 0.033957 | 0.3 | 8.24
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.016106 | 0.016898 | 0.017915 | 0.5 | 4.22
|
||||
Output | 0.00012331 | 0.00013523 | 0.00016852 | 0.0 | 0.03
|
||||
Modify | 0.34913 | 0.34974 | 0.35017 | 0.1 | 87.29
|
||||
Other | | 0.0008755 | | | 0.22
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 597.5 ave 600 max 595 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2500 ave 2500 max 2500 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10000
|
||||
Ave neighs/atom = 20
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
System init for write_restart ...
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Total wall time: 0:00:00
|
||||
@ -1,110 +0,0 @@
|
||||
LAMMPS (19 Mar 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
orthogonal box = (0 0 0) to (28.32 28.32 113.28)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
8192 atoms
|
||||
read_data CPU = 0.022048 secs
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.49954
|
||||
ghost atom cutoff = 7.49954
|
||||
binsize = 3.74977, bins = 8 8 31
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.99 | 19.99 | 19.99 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng
|
||||
0 0 0.0177864461018737 -36558.7284872918 -661.829206399896 1274.398774669 0 -36558.7284872918
|
||||
20 0.002 0.0177864377256184 -36558.7389378387 -661.839683504936 1259.94171978912 0.00986992693139795 -36558.7284878577
|
||||
40 0.004 0.017786472977471 -36558.7684525639 -661.869582914286 1224.05894016152 0.0377451568363827 -36558.7284891299
|
||||
60 0.006 0.0177865119543331 -36558.8126238543 -661.915330492427 1184.24369688088 0.0794631076347515 -36558.728490712
|
||||
80 0.008 0.0177865172048059 -36558.8659242367 -661.972562482488 1152.05459929593 0.129803482511904 -36558.7284922233
|
||||
100 0.01 0.0177865063752424 -36558.9229549739 -662.037138807935 1129.51470280479 0.183667498513087 -36558.7284933644
|
||||
Loop time of 14.3276 on 1 procs for 100 steps with 8192 atoms
|
||||
|
||||
Performance: 0.060 ns/day, 397.988 hours/ns, 6.980 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.0409 | 4.0409 | 4.0409 | 0.0 | 28.20
|
||||
Neigh | 3.6219 | 3.6219 | 3.6219 | 0.0 | 25.28
|
||||
Comm | 0.055327 | 0.055327 | 0.055327 | 0.0 | 0.39
|
||||
Output | 2.4259 | 2.4259 | 2.4259 | 0.0 | 16.93
|
||||
Modify | 4.1688 | 4.1688 | 4.1688 | 0.0 | 29.10
|
||||
Other | | 0.01477 | | | 0.10
|
||||
|
||||
Nlocal: 8192 ave 8192 max 8192 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 14621 ave 14621 max 14621 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 573440 ave 573440 max 573440 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1146880
|
||||
Ave neighs/atom = 140
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:14
|
||||
@ -1,110 +0,0 @@
|
||||
LAMMPS (19 Mar 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
orthogonal box = (0 0 0) to (28.32 28.32 113.28)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
8192 atoms
|
||||
read_data CPU = 0.013634 secs
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.49954
|
||||
ghost atom cutoff = 7.49954
|
||||
binsize = 3.74977, bins = 8 8 31
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.961 | 9.047 | 9.29 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng
|
||||
0 0 0.0177864461018739 -36558.7284872997 -661.829206399894 1274.398774669 0 -36558.7284872997
|
||||
20 0.002 0.0177863981273124 -36558.7389378386 -661.839683504262 1259.94177798388 0.00986992629371963 -36558.7284878582
|
||||
40 0.004 0.0177864622701489 -36558.7684525586 -661.869582908114 1224.05908191331 0.0377451510479599 -36558.7284891308
|
||||
60 0.006 0.0177865625037858 -36558.8126238326 -661.915330472361 1184.24389640891 0.0794630890177406 -36558.72849071
|
||||
80 0.008 0.0177865898045059 -36558.8659241943 -661.972562439245 1152.05483020781 0.129803443061299 -36558.7284922226
|
||||
100 0.01 0.017786565190115 -36558.9229549058 -662.037138735432 1129.51495182843 0.183667434061771 -36558.7284933646
|
||||
Loop time of 4.35911 on 4 procs for 100 steps with 8192 atoms
|
||||
|
||||
Performance: 0.198 ns/day, 121.086 hours/ns, 22.940 timesteps/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 | 1.0924 | 1.1043 | 1.1117 | 0.7 | 25.33
|
||||
Neigh | 0.93575 | 0.94926 | 0.98325 | 2.0 | 21.78
|
||||
Comm | 0.044663 | 0.088288 | 0.11128 | 8.7 | 2.03
|
||||
Output | 0.64199 | 0.6587 | 0.67226 | 1.4 | 15.11
|
||||
Modify | 1.5412 | 1.5535 | 1.5706 | 0.9 | 35.64
|
||||
Other | | 0.005046 | | | 0.12
|
||||
|
||||
Nlocal: 2048 ave 2061 max 2035 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 5765 ave 5778 max 5752 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 143360 ave 144262 max 142469 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
FullNghs: 286720 ave 288540 max 284900 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1146880
|
||||
Ave neighs/atom = 140
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:04
|
||||
@ -1,116 +0,0 @@
|
||||
LAMMPS (19 Mar 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# start a spin-lattice simulation from a data file
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
WARNING: Restart file used different # of processors: 4 vs. 1 (../read_restart.cpp:736)
|
||||
restoring atom style spin from restart
|
||||
orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style spin/exchange from restart
|
||||
500 atoms
|
||||
read_restart CPU = 0.00179696 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.49954
|
||||
ghost atom cutoff = 7.49954
|
||||
binsize = 3.74977, bins = 4 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.422 | 7.422 | 7.422 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng
|
||||
1000 0 0.108317262557656 -2200.38241212222 -5.38245988668244 2538.4247868621 0 -2200.38241212222
|
||||
1020 0.002 0.108317318495042 -2200.39172132133 -5.39179331134703 2513.42968070374 0.144319963844279 -2200.38241256643
|
||||
1040 0.004 0.108317415558744 -2200.41811580407 -5.418541526637 2478.87571728648 0.553516420254567 -2200.38241354532
|
||||
1060 0.006 0.108317473592946 -2200.45801216332 -5.45990062771403 2449.77257658726 1.17203792179707 -2200.38241476526
|
||||
1080 0.008 0.108317450745396 -2200.5068824087 -5.51245983698347 2427.25022669715 1.92968606059505 -2200.3824160902
|
||||
1100 0.01 0.108317381572202 -2200.55976028827 -5.57250071024394 2400.86131889957 2.74946927499959 -2200.38241728649
|
||||
Loop time of 0.954493 on 1 procs for 100 steps with 500 atoms
|
||||
|
||||
Performance: 0.905 ns/day, 26.514 hours/ns, 104.768 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.27043 | 0.27043 | 0.27043 | 0.0 | 28.33
|
||||
Neigh | 0.26148 | 0.26148 | 0.26148 | 0.0 | 27.40
|
||||
Comm | 0.0071123 | 0.0071123 | 0.0071123 | 0.0 | 0.75
|
||||
Output | 0.14169 | 0.14169 | 0.14169 | 0.0 | 14.84
|
||||
Modify | 0.2726 | 0.2726 | 0.2726 | 0.0 | 28.56
|
||||
Other | | 0.001178 | | | 0.12
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2534 ave 2534 max 2534 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 36500 ave 36500 max 36500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 73000 ave 73000 max 73000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 73000
|
||||
Ave neighs/atom = 146
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,115 +0,0 @@
|
||||
LAMMPS (19 Mar 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# start a spin-lattice simulation from a data file
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
restoring atom style spin from restart
|
||||
orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style spin/exchange from restart
|
||||
500 atoms
|
||||
read_restart CPU = 0.00173593 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.49954
|
||||
ghost atom cutoff = 7.49954
|
||||
binsize = 3.74977, bins = 4 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.324 | 7.324 | 7.324 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng
|
||||
1000 0 0.108317262557656 -2200.38241212182 -5.38245988668244 2538.4247868621 0 -2200.38241212182
|
||||
1020 0.002 0.108317316216432 -2200.39172132147 -5.39179331147409 2513.42945241007 0.14431996581917 -2200.38241256644
|
||||
1040 0.004 0.108317347939802 -2200.41811580574 -5.41854152831072 2478.87544274124 0.553516446104432 -2200.38241354532
|
||||
1060 0.006 0.108317342440309 -2200.45801216927 -5.45990063373049 2449.77218633122 1.17203801398165 -2200.38241476526
|
||||
1080 0.008 0.108317320345284 -2200.50688241767 -5.51245984623572 2427.2497145488 1.92968619968329 -2200.3824160902
|
||||
1100 0.01 0.10831728372281 -2200.55976028296 -5.57250070536486 2400.86059511731 2.74946919265255 -2200.38241728649
|
||||
Loop time of 0.405615 on 4 procs for 100 steps with 500 atoms
|
||||
|
||||
Performance: 2.130 ns/day, 11.267 hours/ns, 246.539 timesteps/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 | 0.075661 | 0.076798 | 0.077343 | 0.2 | 18.93
|
||||
Neigh | 0.063154 | 0.064974 | 0.066991 | 0.5 | 16.02
|
||||
Comm | 0.012538 | 0.013787 | 0.015151 | 0.8 | 3.40
|
||||
Output | 0.039155 | 0.040842 | 0.042502 | 0.6 | 10.07
|
||||
Modify | 0.20709 | 0.20883 | 0.21036 | 0.3 | 51.49
|
||||
Other | | 0.0003826 | | | 0.09
|
||||
|
||||
Nlocal: 125 ave 127 max 122 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 1387 ave 1390 max 1385 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 9125 ave 9272 max 8945 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
FullNghs: 18250 ave 18542 max 17812 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 73000
|
||||
Ave neighs/atom = 146
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,120 +0,0 @@
|
||||
LAMMPS (19 Mar 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
create_atoms CPU = 0.000952005 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
500 settings made for spin/random
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice frozen
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm pe v_emag temp etotal
|
||||
thermo 100
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.1
|
||||
ghost atom cutoff = 4.1
|
||||
binsize = 2.05, bins = 7 11 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.947 | 6.947 | 6.947 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag Temp TotEng
|
||||
0 0 0.076558814 0.89911794 0.89911794 0 0.89911794
|
||||
100 0.01 0.077628154 0.36693917 0.36693917 0 0.36693917
|
||||
200 0.02 0.076678996 -0.20242315 -0.20242315 0 -0.20242315
|
||||
300 0.03 0.079174837 -0.67595514 -0.67595514 0 -0.67595514
|
||||
400 0.04 0.085031632 -1.5172851 -1.5172851 0 -1.5172851
|
||||
500 0.05 0.08702747 -2.0426628 -2.0426628 0 -2.0426628
|
||||
600 0.06 0.087066482 -2.6297745 -2.6297745 0 -2.6297745
|
||||
700 0.07 0.089788894 -3.314538 -3.314538 0 -3.314538
|
||||
800 0.08 0.091699611 -4.0287043 -4.0287043 0 -4.0287043
|
||||
900 0.09 0.090038899 -4.600601 -4.600601 0 -4.600601
|
||||
1000 0.1 0.093257309 -5.2352261 -5.2352261 0 -5.2352261
|
||||
Loop time of 3.30071 on 1 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 2.618 ns/day, 9.169 hours/ns, 302.965 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 | 0.3844 | 0.3844 | 0.3844 | 0.0 | 11.65
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.019863 | 0.019863 | 0.019863 | 0.0 | 0.60
|
||||
Output | 1.3844 | 1.3844 | 1.3844 | 0.0 | 41.94
|
||||
Modify | 1.5084 | 1.5084 | 1.5084 | 0.0 | 45.70
|
||||
Other | | 0.00367 | | | 0.11
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1221 ave 1221 max 1221 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
|
||||
FullNghs: 10000 ave 10000 max 10000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10000
|
||||
Ave neighs/atom = 20
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
@ -1,120 +0,0 @@
|
||||
LAMMPS (19 Mar 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
create_atoms CPU = 0.000663042 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
500 settings made for spin/random
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice frozen
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm pe v_emag temp etotal
|
||||
thermo 100
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.1
|
||||
ghost atom cutoff = 4.1
|
||||
binsize = 2.05, bins = 7 11 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.868 | 6.868 | 6.868 Mbytes
|
||||
Step Time v_magnorm PotEng v_emag Temp TotEng
|
||||
0 0 0.076558814 0.89911794 0.89911794 0 0.89911794
|
||||
100 0.01 0.078299981 0.44129792 0.44129792 0 0.44129792
|
||||
200 0.02 0.081260508 -0.21742361 -0.21742361 0 -0.21742361
|
||||
300 0.03 0.081195603 -0.87041046 -0.87041046 0 -0.87041046
|
||||
400 0.04 0.087298495 -1.7069519 -1.7069519 0 -1.7069519
|
||||
500 0.05 0.087663924 -2.1883045 -2.1883045 0 -2.1883045
|
||||
600 0.06 0.091713683 -2.9267461 -2.9267461 0 -2.9267461
|
||||
700 0.07 0.093779119 -3.353314 -3.353314 0 -3.353314
|
||||
800 0.08 0.097960611 -3.9344284 -3.9344284 0 -3.9344284
|
||||
900 0.09 0.10193463 -4.7944004 -4.7944004 0 -4.7944004
|
||||
1000 0.1 0.10831726 -5.3824599 -5.3824599 0 -5.3824599
|
||||
Loop time of 1.7839 on 4 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 4.843 ns/day, 4.955 hours/ns, 560.569 timesteps/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 | 0.10068 | 0.10749 | 0.11461 | 1.5 | 6.03
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.052378 | 0.062171 | 0.07177 | 2.8 | 3.49
|
||||
Output | 0.4054 | 0.42334 | 0.44025 | 2.0 | 23.73
|
||||
Modify | 1.174 | 1.1893 | 1.2043 | 1.1 | 66.67
|
||||
Other | | 0.001558 | | | 0.09
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 597.5 ave 600 max 595 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2500 ave 2500 max 2500 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10000
|
||||
Ave neighs/atom = 20
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
Binary file not shown.
@ -50,5 +50,5 @@ thermo 200
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 100000
|
||||
run 10000
|
||||
# run 1
|
||||
|
||||
@ -0,0 +1,188 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bcc iron in a 3d periodic box
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
atom_style spin
|
||||
# atom_style spin/kk
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice bcc 2.8665
|
||||
Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
|
||||
region box block 0.0 3.0 0.0 3.0 0.0 3.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 54 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
|
||||
mass 1 55.845
|
||||
set group all spin/random 31 2.2
|
||||
Setting atom values ...
|
||||
WARNING: Set attribute spin/random is deprecated. Please use spin/atom/random instead. (src/set.cpp:293)
|
||||
54 settings made for spin/random
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 3.5
|
||||
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
|
||||
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.00 21
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_tmag temp v_emag ke pe etotal
|
||||
thermo 200
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 20 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.773367
|
||||
ghost atom cutoff = 5.773367
|
||||
binsize = 2.8866835, bins = 3 3 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on, cut 5.7733670002446
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Dump 1 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.626 | 5.626 | 5.626 Mbytes
|
||||
Step Time v_tmag Temp v_emag KinEng PotEng TotEng
|
||||
0 0 1836.2373 100.00358 -0.26674297 0.6851033 -231.38675 -230.70164
|
||||
200 0.02 1751.0384 48.019015 -0.27512361 0.32896808 -231.03061 -230.70164
|
||||
400 0.04 1776.2639 19.035769 -0.28188188 0.13041001 -230.83205 -230.70164
|
||||
600 0.06 1787.5802 60.069761 -0.2772323 0.41152518 -231.11317 -230.70164
|
||||
800 0.08 1706.5552 50.79606 -0.27292548 0.34799302 -231.04963 -230.70164
|
||||
1000 0.1 2120.1611 44.605193 -0.26987056 0.3055807 -231.00722 -230.70164
|
||||
1200 0.12 1754.9393 64.57232 -0.26943293 0.44237126 -231.14401 -230.70164
|
||||
1400 0.14 1912.6009 44.177766 -0.26857448 0.3026525 -231.00429 -230.70164
|
||||
1600 0.16 1875.5315 40.249733 -0.27481087 0.27574238 -230.97738 -230.70164
|
||||
1800 0.18 1837.1786 62.817536 -0.28092582 0.4303496 -231.13199 -230.70164
|
||||
2000 0.2 1860.1719 54.167659 -0.28282659 0.37109113 -231.07273 -230.70164
|
||||
2200 0.22 1691.658 46.643932 -0.29528237 0.31954767 -231.02119 -230.70164
|
||||
2400 0.24 1525.2579 57.361866 -0.30189945 0.39297397 -231.09462 -230.70164
|
||||
2600 0.26 1505.1726 56.239347 -0.30898994 0.38528383 -231.08693 -230.70164
|
||||
2800 0.28 1415.9555 47.818074 -0.31351411 0.32759147 -231.02923 -230.70164
|
||||
3000 0.3 1248.4308 49.608492 -0.31727375 0.33985725 -231.0415 -230.70164
|
||||
3200 0.32 1200.7605 51.495405 -0.31565357 0.35278409 -231.05443 -230.70164
|
||||
3400 0.34 1746.137 56.967184 -0.30906485 0.39027008 -231.09191 -230.70164
|
||||
3600 0.36 1805.3667 55.030692 -0.30799197 0.37700359 -231.07865 -230.70164
|
||||
3800 0.38 1609.9498 59.452017 -0.30520539 0.40729315 -231.10894 -230.70164
|
||||
4000 0.4 1686.1863 57.338707 -0.30240026 0.39281531 -231.09446 -230.70164
|
||||
4200 0.42 1961.3516 41.421108 -0.30479326 0.28376722 -230.98541 -230.70164
|
||||
4400 0.44 1971.1808 54.038289 -0.30876936 0.37020484 -231.07185 -230.70164
|
||||
4600 0.46 1819.428 56.766201 -0.3129157 0.38889319 -231.09054 -230.70164
|
||||
4800 0.48 1494.1263 47.402453 -0.32868332 0.32474414 -231.02639 -230.70164
|
||||
5000 0.5 1601.6127 63.404101 -0.33283819 0.43436803 -231.13601 -230.70164
|
||||
5200 0.52 1567.7429 62.783792 -0.34753005 0.43011843 -231.13176 -230.70164
|
||||
5400 0.54 1686.234 40.450417 -0.3603489 0.27711722 -230.97876 -230.70164
|
||||
5600 0.56 1651.1927 64.255456 -0.36569031 0.44020049 -231.14184 -230.70164
|
||||
5800 0.58 1380.639 75.386226 -0.36870019 0.51645503 -231.2181 -230.70164
|
||||
6000 0.6 1539.07 40.611642 -0.36303517 0.27822173 -230.97986 -230.70164
|
||||
6200 0.62 1442.2286 50.254503 -0.36560331 0.34428293 -231.04592 -230.70164
|
||||
6400 0.64 1263.6928 69.095161 -0.36822748 0.47335628 -231.175 -230.70164
|
||||
6600 0.66 1468.1529 54.534243 -0.37319988 0.37360252 -231.07524 -230.70164
|
||||
6800 0.68 1289.4927 60.381892 -0.38478834 0.41366352 -231.11531 -230.70164
|
||||
7000 0.7 1121.6702 58.691171 -0.39652609 0.40208075 -231.10372 -230.70164
|
||||
7200 0.72 1018.1068 53.528417 -0.40711639 0.36671182 -231.06835 -230.70164
|
||||
7400 0.74 1115.0342 78.62129 -0.41729373 0.53861776 -231.24026 -230.70164
|
||||
7600 0.76 1329.4621 65.650574 -0.41928751 0.44975815 -231.1514 -230.70164
|
||||
7800 0.78 1154.164 45.603278 -0.41263444 0.31241837 -231.01406 -230.70164
|
||||
8000 0.8 1090.2959 62.148282 -0.40987933 0.42576469 -231.12741 -230.70164
|
||||
8200 0.82 1303.4698 63.864431 -0.41301445 0.43752166 -231.13916 -230.70164
|
||||
8400 0.84 1144.2181 52.222297 -0.41645089 0.35776387 -231.05941 -230.70164
|
||||
8600 0.86 1005.3359 61.59129 -0.41282114 0.42194885 -231.12359 -230.70164
|
||||
8800 0.88 1453.8465 70.876149 -0.41920851 0.48555745 -231.1872 -230.70164
|
||||
9000 0.9 1325.9116 63.675151 -0.42450864 0.43622494 -231.13787 -230.70164
|
||||
9200 0.92 1213.5738 58.297881 -0.42722791 0.3993864 -231.10103 -230.70164
|
||||
9400 0.94 1227.437 57.375795 -0.44309693 0.39306939 -231.09471 -230.70164
|
||||
9600 0.96 1192.79 65.822598 -0.44760999 0.45093664 -231.15258 -230.70164
|
||||
9800 0.98 1231.5166 69.119896 -0.45335245 0.47352573 -231.17517 -230.70164
|
||||
10000 1 1284.2809 66.166068 -0.45872955 0.45328969 -231.15493 -230.70164
|
||||
Loop time of 5.97474 on 1 procs for 10000 steps with 54 atoms
|
||||
|
||||
Performance: 14.461 ns/day, 1.660 hours/ns, 1673.714 timesteps/s, 90.381 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.501 | 2.501 | 2.501 | 0.0 | 41.86
|
||||
Neigh | 0.016481 | 0.016481 | 0.016481 | 0.0 | 0.28
|
||||
Comm | 0.37576 | 0.37576 | 0.37576 | 0.0 | 6.29
|
||||
Output | 0.12311 | 0.12311 | 0.12311 | 0.0 | 2.06
|
||||
Modify | 2.9317 | 2.9317 | 2.9317 | 0.0 | 49.07
|
||||
Other | | 0.02661 | | | 0.45
|
||||
|
||||
Nlocal: 54 ave 54 max 54 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 777 ave 777 max 777 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1700 ave 1700 max 1700 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3400 ave 3400 max 3400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3400
|
||||
Ave neighs/atom = 62.962963
|
||||
Neighbor list builds = 58
|
||||
Dangerous builds = 0
|
||||
# run 1
|
||||
Total wall time: 0:00:06
|
||||
@ -49,4 +49,4 @@ variable tmag equal c_out_mag[6]
|
||||
thermo_style custom step time v_tmag temp v_emag ke pe etotal
|
||||
thermo 200
|
||||
|
||||
run 200000
|
||||
run 20000
|
||||
|
||||
@ -32,7 +32,7 @@ neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin 0.0 0.0 0.0 48279
|
||||
fix 2 all langevin 0.0 0.0 0.001 48279
|
||||
fix 3 all langevin/spin 200.0 0.01 321
|
||||
fix 4 all nve/spin lattice moving
|
||||
timestep 0.001
|
||||
@ -50,4 +50,4 @@ variable tmag equal c_out_mag[6]
|
||||
thermo_style custom step time v_tmag temp v_emag ke pe etotal
|
||||
thermo 200
|
||||
|
||||
run 200000
|
||||
run 20000
|
||||
|
||||
@ -0,0 +1,240 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bcc iron in a 3d periodic box
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
atom_style spin
|
||||
# atom_style spin/kk
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice bcc 2.8665
|
||||
Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
|
||||
region box block 0.0 3.0 0.0 3.0 0.0 3.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 54 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
|
||||
mass 1 55.845
|
||||
set group all spin 2.2 0.0 0.0 1.0
|
||||
Setting atom values ...
|
||||
WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268)
|
||||
54 settings made for spin
|
||||
velocity all create 400 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
|
||||
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
|
||||
pair_coeff * * spin/exchange exchange 3.4 0.1 0.2171 1.841
|
||||
pair_coeff * * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin 200.0 200.0 0.1 48279
|
||||
fix 3 all langevin/spin 0.0 0.0 321
|
||||
fix 4 all nve/spin lattice moving
|
||||
timestep 0.001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_tmag temp v_emag ke pe etotal
|
||||
thermo 200
|
||||
|
||||
run 20000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 20 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.773367
|
||||
ghost atom cutoff = 5.773367
|
||||
binsize = 2.8866835, bins = 3 3 3
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on, cut 5.7733670002446
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) pair spin/neel, perpetual, copy from (2)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes
|
||||
Step Time v_tmag Temp v_emag KinEng PotEng TotEng
|
||||
0 0 1.4336203e-31 400.01433 -22.021022 2.7404132 -253.14103 -250.40061
|
||||
200 0.2 0.26275543 188.91786 -21.983513 1.2942362 -251.94911 -250.65488
|
||||
400 0.4 0.56095049 204.95947 -21.977046 1.4041338 -251.914 -250.50987
|
||||
600 0.6 0.81480981 203.28763 -21.98548 1.3926804 -251.88478 -250.4921
|
||||
800 0.8 0.97590428 184.8694 -21.974142 1.266501 -251.73716 -250.47066
|
||||
1000 1 1.1324742 184.65547 -21.986309 1.2650354 -252.03248 -250.76744
|
||||
1200 1.2 1.5284342 207.55788 -21.974821 1.421935 -251.7769 -250.35497
|
||||
1400 1.4 1.8310776 220.75396 -21.979994 1.5123385 -251.93989 -250.42755
|
||||
1600 1.6 2.2057174 236.04272 -21.973951 1.6170785 -251.98625 -250.36917
|
||||
1800 1.8 2.7760928 195.92697 -21.96808 1.3422541 -251.7495 -250.40725
|
||||
2000 2 3.2171354 161.33811 -21.975129 1.1052932 -251.86337 -250.75808
|
||||
2200 2.2 3.8284998 193.21861 -21.968067 1.3236997 -251.86609 -250.54239
|
||||
2400 2.4 4.4109629 203.79368 -21.971813 1.3961472 -251.92264 -250.52649
|
||||
2600 2.6 4.5056291 200.81431 -21.960649 1.3757362 -251.80976 -250.43403
|
||||
2800 2.8 4.6221125 185.57027 -21.972664 1.2713025 -252.0384 -250.76709
|
||||
3000 3 4.9059897 216.00877 -21.966875 1.4798302 -252.13406 -250.65423
|
||||
3200 3.2 5.3958965 152.77626 -21.956779 1.0466377 -251.66 -250.61337
|
||||
3400 3.4 5.9881406 170.70538 -21.964189 1.1694663 -251.9061 -250.73663
|
||||
3600 3.6 6.134982 210.99981 -21.945137 1.4455149 -251.75025 -250.30474
|
||||
3800 3.8 6.5940545 239.12527 -21.953159 1.6381964 -251.90813 -250.26993
|
||||
4000 4 6.9355034 181.99614 -21.938591 1.2468169 -251.59724 -250.35043
|
||||
4200 4.2 7.3712919 242.52183 -21.932318 1.6614656 -251.71104 -250.04957
|
||||
4400 4.4 7.5924709 164.34328 -21.942361 1.1258809 -251.64032 -250.51444
|
||||
4600 4.6 8.1833481 205.94973 -21.941491 1.4109179 -251.57627 -250.16536
|
||||
4800 4.8 8.40416 169.96914 -21.945774 1.1644225 -251.87887 -250.71444
|
||||
5000 5 8.4422416 189.79518 -21.94955 1.3002465 -251.80055 -250.50031
|
||||
5200 5.2 8.3667008 195.86473 -21.934302 1.3418277 -251.64678 -250.30495
|
||||
5400 5.4 8.7075519 204.82319 -21.947339 1.4032002 -251.85712 -250.45392
|
||||
5600 5.6 8.6582399 191.25854 -21.933614 1.3102717 -251.51648 -250.2062
|
||||
5800 5.8 8.896287 180.44446 -21.923523 1.2361867 -251.68003 -250.44384
|
||||
6000 6 9.1379808 248.49596 -21.938845 1.7023931 -251.84502 -250.14263
|
||||
6200 6.2 8.9724294 181.67979 -21.939567 1.2446497 -251.81639 -250.57174
|
||||
6400 6.4 8.7735241 198.31668 -21.952115 1.3586255 -251.97841 -250.61979
|
||||
6600 6.6 9.0394523 218.6735 -21.934717 1.4980857 -251.85133 -250.35325
|
||||
6800 6.8 9.5779186 203.83536 -21.937873 1.3964328 -251.98448 -250.58804
|
||||
7000 7 9.7893273 185.56096 -21.949319 1.2712387 -252.09057 -250.81934
|
||||
7200 7.2 9.5292481 205.53224 -21.936466 1.4080577 -251.98037 -250.57231
|
||||
7400 7.4 9.7369072 200.76528 -21.944609 1.3754003 -251.88128 -250.50588
|
||||
7600 7.6 9.9385522 217.68239 -21.920768 1.4912959 -251.6169 -250.1256
|
||||
7800 7.8 9.8656638 219.17274 -21.92302 1.5015059 -251.50189 -250.00039
|
||||
8000 8 9.2380618 264.13229 -21.936112 1.8095143 -251.71532 -249.9058
|
||||
8200 8.2 9.3384949 239.58029 -21.941834 1.6413137 -251.73551 -250.0942
|
||||
8400 8.4 9.1684312 207.27974 -21.938426 1.4200295 -251.59062 -250.17059
|
||||
8600 8.6 8.8407032 200.79452 -21.933328 1.3756006 -251.48006 -250.10446
|
||||
8800 8.8 8.84683 218.44316 -21.949738 1.4965077 -251.92925 -250.43275
|
||||
9000 9 9.0686442 216.06373 -21.942255 1.4802067 -251.79797 -250.31776
|
||||
9200 9.2 9.2783597 187.56662 -21.93374 1.2849791 -251.87884 -250.59386
|
||||
9400 9.4 9.2794158 203.78139 -21.955284 1.396063 -252.09328 -250.69722
|
||||
9600 9.6 9.3563189 196.15871 -21.948544 1.3438417 -251.85685 -250.51301
|
||||
9800 9.8 9.6458819 215.38334 -21.94895 1.4755455 -251.92219 -250.44665
|
||||
10000 10 9.5073837 178.61601 -21.955281 1.2236604 -251.97306 -250.7494
|
||||
10200 10.2 9.3510908 185.21136 -21.94749 1.2688437 -251.83233 -250.56349
|
||||
10400 10.4 9.8171891 194.92192 -21.945394 1.3353687 -251.86067 -250.5253
|
||||
10600 10.6 9.5996138 213.90302 -21.945461 1.4654042 -251.72508 -250.25968
|
||||
10800 10.8 9.8602813 208.57912 -21.936736 1.4289312 -251.55778 -250.12885
|
||||
11000 11 10.652287 202.88507 -21.933085 1.3899225 -251.69631 -250.30639
|
||||
11200 11.2 10.413298 171.86972 -21.919711 1.1774429 -251.16232 -249.98488
|
||||
11400 11.4 10.589727 179.33897 -21.927537 1.2286132 -251.65266 -250.42405
|
||||
11600 11.6 11.099271 176.43012 -21.925025 1.2086853 -251.65796 -250.44927
|
||||
11800 11.8 11.49558 216.78529 -21.935923 1.48515 -251.51958 -250.03443
|
||||
12000 12 11.190687 206.45545 -21.941866 1.4143824 -251.55494 -250.14055
|
||||
12200 12.2 11.372777 216.26373 -21.934028 1.4815769 -251.75482 -250.27324
|
||||
12400 12.4 11.303952 218.67625 -21.928577 1.4981046 -251.73908 -250.24098
|
||||
12600 12.6 11.065605 188.25083 -21.925979 1.2896665 -251.49808 -250.20841
|
||||
12800 12.8 11.289265 209.423 -21.933529 1.4347125 -251.85142 -250.41671
|
||||
13000 13 11.412931 148.86392 -21.93732 1.0198351 -251.88347 -250.86364
|
||||
13200 13.2 11.677538 187.03356 -21.923919 1.2813272 -251.52124 -250.23991
|
||||
13400 13.4 12.451801 237.44268 -21.93385 1.6266694 -251.70112 -250.07445
|
||||
13600 13.6 12.981208 196.47947 -21.926751 1.3460391 -251.80509 -250.45905
|
||||
13800 13.8 13.301789 191.61721 -21.921891 1.3127288 -251.85541 -250.54268
|
||||
14000 14 13.726635 212.61693 -21.922086 1.4565934 -252.06804 -250.61145
|
||||
14200 14.2 13.715662 197.51397 -21.915949 1.3531263 -251.71314 -250.36002
|
||||
14400 14.4 13.340257 210.15601 -21.927197 1.4397342 -251.73271 -250.29297
|
||||
14600 14.6 14.118672 175.1782 -21.923635 1.2001087 -251.54286 -250.34275
|
||||
14800 14.8 14.52801 211.5541 -21.919371 1.4493122 -251.74119 -250.29188
|
||||
15000 15 14.522566 207.59406 -21.919623 1.4221828 -251.74192 -250.31974
|
||||
15200 15.2 15.1446 191.32404 -21.902291 1.3107204 -251.52754 -250.21682
|
||||
15400 15.4 15.815481 160.35385 -21.918453 1.0985502 -251.75506 -250.65651
|
||||
15600 15.6 16.942896 211.32891 -21.89554 1.4477695 -251.42064 -249.97287
|
||||
15800 15.8 17.339057 213.03178 -21.903747 1.4594355 -251.5815 -250.12207
|
||||
16000 16 17.610695 211.72009 -21.899083 1.4504494 -251.51043 -250.05998
|
||||
16200 16.2 18.352293 236.99887 -21.9043 1.623629 -251.79466 -250.17103
|
||||
16400 16.4 17.898896 208.62272 -21.904247 1.42923 -251.66653 -250.2373
|
||||
16600 16.6 18.005606 169.07581 -21.910252 1.1583025 -251.84184 -250.68353
|
||||
16800 16.8 18.884686 198.75251 -21.900417 1.3616113 -251.8573 -250.49569
|
||||
17000 17 19.454235 182.70172 -21.904544 1.2516507 -251.66187 -250.41021
|
||||
17200 17.2 19.497759 157.47203 -21.904461 1.0788075 -251.88582 -250.80701
|
||||
17400 17.4 19.470705 215.43531 -21.887158 1.4759016 -251.82426 -250.34836
|
||||
17600 17.6 19.553888 212.82066 -21.89372 1.4579892 -251.79955 -250.34157
|
||||
17800 17.8 19.646117 236.85339 -21.8983 1.6226323 -251.75304 -250.13041
|
||||
18000 18 20.205554 253.85283 -21.909061 1.7390919 -251.84228 -250.10319
|
||||
18200 18.2 20.065135 233.11058 -21.882631 1.5969911 -251.54972 -249.95273
|
||||
18400 18.4 20.76763 209.7018 -21.895306 1.4366225 -251.79971 -250.36309
|
||||
18600 18.6 21.369833 214.39422 -21.882332 1.4687693 -251.53344 -250.06467
|
||||
18800 18.8 21.939164 216.25928 -21.89097 1.4815464 -251.82112 -250.33958
|
||||
19000 19 22.817363 215.27695 -21.882698 1.4748166 -251.82572 -250.3509
|
||||
19200 19.2 23.705114 182.22745 -21.879076 1.2484016 -251.43044 -250.18204
|
||||
19400 19.4 23.441248 222.83743 -21.879144 1.5266119 -251.76376 -250.23715
|
||||
19600 19.6 23.435558 218.16026 -21.86114 1.4945696 -251.59729 -250.10272
|
||||
19800 19.8 24.074607 222.78958 -21.87264 1.5262841 -251.7863 -250.26001
|
||||
20000 20 23.618814 222.44332 -21.870985 1.5239119 -251.37299 -249.84908
|
||||
Loop time of 22.6158 on 1 procs for 20000 steps with 54 atoms
|
||||
|
||||
Performance: 76.407 ns/day, 0.314 hours/ns, 884.338 timesteps/s, 47.754 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 | 8.9116 | 8.9116 | 8.9116 | 0.0 | 39.40
|
||||
Neigh | 0.26535 | 0.26535 | 0.26535 | 0.0 | 1.17
|
||||
Comm | 0.65637 | 0.65637 | 0.65637 | 0.0 | 2.90
|
||||
Output | 0.0036141 | 0.0036141 | 0.0036141 | 0.0 | 0.02
|
||||
Modify | 12.725 | 12.725 | 12.725 | 0.0 | 56.26
|
||||
Other | | 0.05425 | | | 0.24
|
||||
|
||||
Nlocal: 54 ave 54 max 54 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 632 ave 632 max 632 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1677 ave 1677 max 1677 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3354 ave 3354 max 3354 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3354
|
||||
Ave neighs/atom = 62.111111
|
||||
Neighbor list builds = 1000
|
||||
Dangerous builds = 1000
|
||||
Total wall time: 0:00:22
|
||||
@ -0,0 +1,241 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bcc iron in a 3d periodic box
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
atom_style spin
|
||||
# atom_style spin/kk
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice bcc 2.8665
|
||||
Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
|
||||
region box block 0.0 3.0 0.0 3.0 0.0 3.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 54 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
|
||||
mass 1 55.845
|
||||
set group all spin 2.2 0.0 0.0 1.0
|
||||
Setting atom values ...
|
||||
WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268)
|
||||
54 settings made for spin
|
||||
velocity all create 0 4928459 rot yes dist gaussian
|
||||
|
||||
# pair_style hybrid/overlay eam/alloy spin/exchange 3.5
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
|
||||
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
|
||||
pair_coeff * * spin/exchange exchange 3.4 0.1 0.2171 1.841
|
||||
pair_coeff * * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin 0.0 0.0 0.001 48279
|
||||
fix 3 all langevin/spin 200.0 0.01 321
|
||||
fix 4 all nve/spin lattice moving
|
||||
timestep 0.001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_tmag temp v_emag ke pe etotal
|
||||
thermo 200
|
||||
|
||||
run 20000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
|
||||
|
||||
@article{tranchida2018massively,
|
||||
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
|
||||
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
|
||||
journal={Journal of Computational Physics},
|
||||
volume={372},
|
||||
pages={406--425},
|
||||
year={2018},
|
||||
publisher={Elsevier}
|
||||
doi={10.1016/j.jcp.2018.06.042}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 20 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.773367
|
||||
ghost atom cutoff = 5.773367
|
||||
binsize = 2.8866835, bins = 3 3 3
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on, cut 5.7733670002446
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) pair spin/neel, perpetual, copy from (2)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes
|
||||
Step Time v_tmag Temp v_emag KinEng PotEng TotEng
|
||||
0 0 1.4336203e-31 0 -22.021022 0 -253.14103 -253.14103
|
||||
200 0.2 185.03537 7.1508965e-05 -21.172867 4.8989274e-07 -252.29287 -252.29287
|
||||
400 0.4 209.70221 8.8414079e-05 -21.060203 6.0570608e-07 -252.1802 -252.1802
|
||||
600 0.6 185.48899 0.00010245242 -21.112413 7.0187977e-07 -252.23241 -252.23241
|
||||
800 0.8 223.05275 8.1457051e-05 -21.018423 5.5804496e-07 -252.13842 -252.13842
|
||||
1000 1 213.0164 8.9515898e-05 -21.048926 6.1325441e-07 -252.16892 -252.16892
|
||||
1200 1.2 246.36673 0.0001154676 -20.930718 7.9104402e-07 -252.05072 -252.05072
|
||||
1400 1.4 196.53774 6.2911172e-05 -21.154732 4.3099109e-07 -252.27473 -252.27473
|
||||
1600 1.6 182.01716 0.00010355261 -21.16282 7.0941692e-07 -252.28282 -252.28282
|
||||
1800 1.8 210.96677 8.7541641e-05 -21.088701 5.997292e-07 -252.2087 -252.2087
|
||||
2000 2 253.99717 0.00010826381 -20.86351 7.416924e-07 -251.98351 -251.98351
|
||||
2200 2.2 216.1501 9.6113637e-05 -21.030784 6.5845412e-07 -252.15078 -252.15078
|
||||
2400 2.4 223.43699 8.5950374e-05 -21.009537 5.8882776e-07 -252.12954 -252.12954
|
||||
2600 2.6 218.14727 0.00010110952 -20.970036 6.9267987e-07 -252.09004 -252.09004
|
||||
2800 2.8 232.40923 0.00011013217 -20.973661 7.5449212e-07 -252.09366 -252.09366
|
||||
3000 3 237.03942 0.0001227047 -20.923005 8.4062388e-07 -252.043 -252.043
|
||||
3200 3.2 193.18057 6.4453691e-05 -21.192632 4.4155855e-07 -252.31263 -252.31263
|
||||
3400 3.4 215.89559 0.00010926778 -20.99777 7.4857038e-07 -252.11777 -252.11777
|
||||
3600 3.6 166.54235 7.286928e-05 -21.241556 4.9921196e-07 -252.36156 -252.36156
|
||||
3800 3.8 159.38579 5.7560855e-05 -21.290065 3.9433719e-07 -252.41007 -252.41007
|
||||
4000 4 170.59358 7.7217892e-05 -21.234059 5.2900339e-07 -252.35406 -252.35406
|
||||
4200 4.2 215.77287 8.7497504e-05 -21.031438 5.9942683e-07 -252.15144 -252.15144
|
||||
4400 4.4 197.99439 8.3188835e-05 -21.136708 5.6990905e-07 -252.25671 -252.25671
|
||||
4600 4.6 225.89271 0.00015400081 -20.963516 1.0550269e-06 -252.08352 -252.08352
|
||||
4800 4.8 202.99311 0.00014034452 -21.013112 9.614705e-07 -252.13311 -252.13311
|
||||
5000 5 213.82643 0.00011505981 -21.058401 7.8825036e-07 -252.1784 -252.1784
|
||||
5200 5.2 185.50349 8.6160092e-05 -21.172207 5.902645e-07 -252.29221 -252.29221
|
||||
5400 5.4 201.98179 0.00010791717 -21.096481 7.3931764e-07 -252.21648 -252.21648
|
||||
5600 5.6 171.20549 6.8869235e-05 -21.197869 4.718085e-07 -252.31787 -252.31787
|
||||
5800 5.8 227.95465 0.00012603913 -21.009323 8.6346729e-07 -252.12932 -252.12932
|
||||
6000 6 200.21111 0.00010449734 -21.110701 7.1588912e-07 -252.2307 -252.2307
|
||||
6200 6.2 160.58077 7.2836942e-05 -21.267151 4.9899042e-07 -252.38715 -252.38715
|
||||
6400 6.4 200.05407 9.0509705e-05 -21.073988 6.2006277e-07 -252.19399 -252.19399
|
||||
6600 6.6 190.65275 0.0001033421 -21.158207 7.0797478e-07 -252.27821 -252.27821
|
||||
6800 6.8 228.26898 0.00014786596 -20.911618 1.0129983e-06 -252.03162 -252.03162
|
||||
7000 7 181.38559 7.164051e-05 -21.178965 4.9079392e-07 -252.29897 -252.29897
|
||||
7200 7.2 206.68689 0.00014900154 -20.996098 1.0207779e-06 -252.1161 -252.1161
|
||||
7400 7.4 192.31745 7.9639216e-05 -21.152927 5.4559136e-07 -252.27293 -252.27293
|
||||
7600 7.6 190.74433 8.1341909e-05 -21.140079 5.5725615e-07 -252.26008 -252.26008
|
||||
7800 7.8 174.0955 6.4367878e-05 -21.239195 4.4097067e-07 -252.3592 -252.35919
|
||||
8000 8 160.00011 0.00012761576 -21.159302 8.7426845e-07 -252.2793 -252.2793
|
||||
8200 8.2 210.43151 0.00014479042 -21.034928 9.9192846e-07 -252.15493 -252.15493
|
||||
8400 8.4 234.76455 0.00017824488 -20.929712 1.2211178e-06 -252.04971 -252.04971
|
||||
8600 8.6 186.41675 8.9522862e-05 -21.152624 6.1330212e-07 -252.27262 -252.27262
|
||||
8800 8.8 182.51437 8.1196096e-05 -21.169538 5.5625721e-07 -252.28954 -252.28954
|
||||
9000 9 205.7602 8.1712224e-05 -21.069704 5.597931e-07 -252.1897 -252.1897
|
||||
9200 9.2 169.12461 4.5311332e-05 -21.260803 3.1041832e-07 -252.3808 -252.3808
|
||||
9400 9.4 226.30809 0.00011391282 -20.976322 7.8039252e-07 -252.09632 -252.09632
|
||||
9600 9.6 167.17205 9.1023114e-05 -21.226931 6.2358003e-07 -252.34693 -252.34693
|
||||
9800 9.8 204.63476 0.00010727562 -21.045363 7.3492253e-07 -252.16536 -252.16536
|
||||
10000 10 236.18563 8.998006e-05 -20.973452 6.1643429e-07 -252.09345 -252.09345
|
||||
10200 10.2 194.32863 7.2352023e-05 -21.144235 4.9566835e-07 -252.26424 -252.26424
|
||||
10400 10.4 212.89479 0.00011913313 -21.041706 8.1615576e-07 -252.16171 -252.1617
|
||||
10600 10.6 215.20168 9.7714692e-05 -21.032571 6.6942261e-07 -252.15257 -252.15257
|
||||
10800 10.8 297.63322 0.00013498385 -20.721355 9.2474566e-07 -251.84135 -251.84135
|
||||
11000 11 221.40055 0.00010205784 -21.051231 6.9917662e-07 -252.17123 -252.17123
|
||||
11200 11.2 242.39307 0.00013617253 -20.890742 9.3288909e-07 -252.01074 -252.01074
|
||||
11400 11.4 165.26613 7.2237463e-05 -21.24741 4.9488352e-07 -252.36741 -252.36741
|
||||
11600 11.6 216.24435 8.1150764e-05 -21.036156 5.5594665e-07 -252.15616 -252.15616
|
||||
11800 11.8 183.53912 0.00010117662 -21.186918 6.9313953e-07 -252.30692 -252.30692
|
||||
12000 12 220.44994 9.647801e-05 -21.023611 6.6095036e-07 -252.14361 -252.14361
|
||||
12200 12.2 225.17986 9.472867e-05 -21.009823 6.48966e-07 -252.12982 -252.12982
|
||||
12400 12.4 216.68616 8.9352492e-05 -21.025818 6.1213495e-07 -252.14582 -252.14582
|
||||
12600 12.6 179.65027 6.5355297e-05 -21.199208 4.4773526e-07 -252.31921 -252.31921
|
||||
12800 12.8 210.22912 7.5167585e-05 -21.071447 5.1495716e-07 -252.19145 -252.19145
|
||||
13000 13 157.423 9.2895323e-05 -21.250615 6.3640614e-07 -252.37062 -252.37061
|
||||
13200 13.2 204.52025 0.00012645764 -21.049044 8.6633447e-07 -252.16904 -252.16904
|
||||
13400 13.4 198.28053 0.00012118522 -21.066084 8.3021421e-07 -252.18609 -252.18608
|
||||
13600 13.6 237.99318 8.644348e-05 -20.978488 5.9220593e-07 -252.09849 -252.09849
|
||||
13800 13.8 222.81023 0.00015789536 -20.951387 1.0817076e-06 -252.07139 -252.07139
|
||||
14000 14 218.31245 0.00011842157 -21.008674 8.1128101e-07 -252.12867 -252.12867
|
||||
14200 14.2 197.5018 0.00011399102 -21.081911 7.8092826e-07 -252.20191 -252.20191
|
||||
14400 14.4 228.11014 0.00015934606 -20.963235 1.091646e-06 -252.08323 -252.08323
|
||||
14600 14.6 216.45102 9.6033576e-05 -21.034352 6.5790564e-07 -252.15435 -252.15435
|
||||
14800 14.8 205.97376 0.00014278574 -21.018847 9.7819479e-07 -252.13885 -252.13885
|
||||
15000 15 230.09259 0.00012803086 -20.986446 8.7711221e-07 -252.10645 -252.10644
|
||||
15200 15.2 248.21379 0.0001784321 -20.84502 1.2224004e-06 -251.96502 -251.96502
|
||||
15400 15.4 223.07119 0.00013057001 -20.984451 8.9450744e-07 -252.10445 -252.10445
|
||||
15600 15.6 194.42126 8.4530618e-05 -21.127055 5.7910131e-07 -252.24705 -252.24705
|
||||
15800 15.8 207.23453 0.00013807606 -21.035173 9.4592974e-07 -252.15517 -252.15517
|
||||
16000 16 175.93234 8.2440767e-05 -21.208299 5.6478419e-07 -252.3283 -252.3283
|
||||
16200 16.2 225.63746 7.4767651e-05 -21.012845 5.1221731e-07 -252.13285 -252.13284
|
||||
16400 16.4 149.12667 6.624179e-05 -21.331981 4.5380844e-07 -252.45198 -252.45198
|
||||
16600 16.6 211.41275 0.00012606898 -21.042094 8.6367183e-07 -252.16209 -252.16209
|
||||
16800 16.8 199.88466 8.2345231e-05 -21.116203 5.641297e-07 -252.2362 -252.2362
|
||||
17000 17 212.37144 0.00010445794 -21.041826 7.1561919e-07 -252.16183 -252.16183
|
||||
17200 17.2 160.83603 5.4109632e-05 -21.294207 3.706936e-07 -252.41421 -252.41421
|
||||
17400 17.4 254.84209 0.00013687967 -20.886397 9.3773358e-07 -252.0064 -252.0064
|
||||
17600 17.6 237.6091 0.00012462019 -20.958967 8.5374644e-07 -252.07897 -252.07897
|
||||
17800 17.8 194.26242 7.0286952e-05 -21.145006 4.8152099e-07 -252.26501 -252.26501
|
||||
18000 18 175.14964 6.1470052e-05 -21.239458 4.2111827e-07 -252.35946 -252.35946
|
||||
18200 18.2 181.99258 7.2295849e-05 -21.195184 4.9528351e-07 -252.31519 -252.31519
|
||||
18400 18.4 197.11115 9.9207898e-05 -21.116471 6.7965225e-07 -252.23647 -252.23647
|
||||
18600 18.6 211.2814 8.4543325e-05 -21.074729 5.7918837e-07 -252.19473 -252.19473
|
||||
18800 18.8 198.62813 9.4052117e-05 -21.097909 6.4433109e-07 -252.21791 -252.21791
|
||||
19000 19 226.11003 0.00013827389 -20.951669 9.4728506e-07 -252.07167 -252.07167
|
||||
19200 19.2 233.61049 0.00013363448 -20.917911 9.1550145e-07 -252.03791 -252.03791
|
||||
19400 19.4 182.94749 9.0400181e-05 -21.139686 6.1931245e-07 -252.25969 -252.25968
|
||||
19600 19.6 155.99677 5.9871119e-05 -21.282519 4.1016433e-07 -252.40252 -252.40252
|
||||
19800 19.8 179.57217 8.5624245e-05 -21.193447 5.8659353e-07 -252.31345 -252.31345
|
||||
20000 20 243.60222 0.00015451915 -20.911769 1.0585779e-06 -252.03177 -252.03177
|
||||
Loop time of 21.9748 on 1 procs for 20000 steps with 54 atoms
|
||||
|
||||
Performance: 78.636 ns/day, 0.305 hours/ns, 910.134 timesteps/s, 49.147 katom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.1863 | 8.1863 | 8.1863 | 0.0 | 37.25
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.77445 | 0.77445 | 0.77445 | 0.0 | 3.52
|
||||
Output | 0.0037256 | 0.0037256 | 0.0037256 | 0.0 | 0.02
|
||||
Modify | 12.954 | 12.954 | 12.954 | 0.0 | 58.95
|
||||
Other | | 0.05601 | | | 0.25
|
||||
|
||||
Nlocal: 54 ave 54 max 54 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 801 ave 801 max 801 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1728 ave 1728 max 1728 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3456 ave 3456 max 3456 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3456
|
||||
Ave neighs/atom = 64
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:22
|
||||
103
examples/bpm/plasticity/in.bpm.plasticity
Normal file
103
examples/bpm/plasticity/in.bpm.plasticity
Normal file
@ -0,0 +1,103 @@
|
||||
# Load then unload four cantilevers with different plastic yield strains
|
||||
# model from DOI: 10.1016/j.powtec.2024.120563
|
||||
|
||||
units lj
|
||||
dimension 3
|
||||
boundary p s s
|
||||
atom_style bond
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.41
|
||||
region box block 0 20 -1 41 -5 5 units box
|
||||
create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
mass * 1.0
|
||||
|
||||
# Create initial disordered geometry somewhat near jamming
|
||||
|
||||
region cantilever block 3.0 12.0 0 40 -2.5 2.5 units box
|
||||
region cantileverw block 2.0 13.0 -1 41 -3.5 3.5 units box
|
||||
create_atoms 1 region cantilever
|
||||
|
||||
velocity all create 0.1 345910
|
||||
|
||||
pair_style bpm/spring
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
fix 1 all nve
|
||||
fix wtemp all wall/region cantileverw harmonic 1.0 1.0 1.0
|
||||
|
||||
thermo_style custom step ke pe pxx pyy pzz
|
||||
thermo 100
|
||||
|
||||
timestep 0.1
|
||||
run 20000
|
||||
unfix wtemp
|
||||
|
||||
# Replicate cylinder and add bonds
|
||||
|
||||
replicate 4 1 1
|
||||
|
||||
region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box
|
||||
|
||||
group c1 region r1
|
||||
group c2 region r2
|
||||
group c3 region r3
|
||||
group c4 region r4
|
||||
|
||||
set group c2 type 2
|
||||
set group c3 type 3
|
||||
set group c4 type 4
|
||||
|
||||
velocity all set 0.0 0.0 0.0
|
||||
neighbor 1.0 bin
|
||||
|
||||
create_bonds many c1 c1 1 0.0 1.5
|
||||
create_bonds many c2 c2 2 0.0 1.5
|
||||
create_bonds many c3 c3 3 0.0 1.5
|
||||
create_bonds many c4 c4 4 0.0 1.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring/plastic break no smooth no
|
||||
bond_coeff 1 1.0 0 1.0 1.0
|
||||
bond_coeff 2 1.0 0 1.0 0.022
|
||||
bond_coeff 3 1.0 0 1.0 0.0185
|
||||
bond_coeff 4 1.0 0 1.0 0.017
|
||||
|
||||
# apply load
|
||||
|
||||
region anchor block EDGE EDGE EDGE 2.0 EDGE EDGE units box
|
||||
region load block EDGE EDGE 38.0 EDGE EDGE EDGE units box
|
||||
group anchor region anchor
|
||||
group load region load
|
||||
|
||||
variable fload equal ramp(0.0,-0.0005)
|
||||
fix 2 anchor setforce 0.0 0.0 0.0
|
||||
fix 3 load addforce 0.0 0.0 v_fload
|
||||
fix 4 all viscous 0.0016
|
||||
|
||||
compute zmin1 c1 reduce min z
|
||||
compute zmin2 c2 reduce min z
|
||||
compute zmin3 c3 reduce min z
|
||||
compute zmin4 c4 reduce min z
|
||||
|
||||
thermo_style custom step ke c_zmin1 c_zmin2 c_zmin3 c_zmin4
|
||||
#dump 1 all custom 1000 atomDump id type x y z
|
||||
|
||||
run 30000
|
||||
|
||||
# hold load
|
||||
|
||||
unfix 3
|
||||
fix 3 load addforce 0.0 0.0 -0.0005
|
||||
run 50000
|
||||
|
||||
# remove load
|
||||
|
||||
unfix 3
|
||||
run 60000
|
||||
2024
examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1
Normal file
2024
examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
90
examples/bpm/poissons_ratio/in.bpm.poissons_ratio
Normal file
90
examples/bpm/poissons_ratio/in.bpm.poissons_ratio
Normal file
@ -0,0 +1,90 @@
|
||||
# Squish four pillars with different Poisson's ratios
|
||||
# going from nearly incompressible to auxetic
|
||||
# from left to right, nu ~ 0.5, 0.25, 0, <0
|
||||
# calibration from DOI: 10.1039/d3sm01373a
|
||||
|
||||
units lj
|
||||
dimension 3
|
||||
boundary p p s
|
||||
atom_style bond
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.41
|
||||
region box block 0 20 -10 10 -1 21 units box
|
||||
create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
mass * 1.0
|
||||
|
||||
# Create initial disordered geometry somewhat near jamming
|
||||
|
||||
region pillar cylinder z 10.0 0.0 7.0 0.0 20.0 units box
|
||||
region pillarw cylinder z 10.0 0.0 8.0 -1.0 21.0 units box
|
||||
create_atoms 1 region pillar
|
||||
|
||||
velocity all create 0.1 345910
|
||||
|
||||
pair_style bpm/spring
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
fix 1 all nve
|
||||
fix wtemp all wall/region pillarw harmonic 1.0 1.0 1.0
|
||||
|
||||
thermo_style custom step ke pe pxx pyy pzz
|
||||
thermo 100
|
||||
|
||||
timestep 0.1
|
||||
run 20000
|
||||
unfix wtemp
|
||||
|
||||
# Replicate cylinder and add bonds
|
||||
|
||||
replicate 4 1 1
|
||||
|
||||
region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box
|
||||
|
||||
group p1 region r1
|
||||
group p2 region r2
|
||||
group p3 region r3
|
||||
group p4 region r4
|
||||
|
||||
set group p2 type 2
|
||||
set group p3 type 3
|
||||
set group p4 type 4
|
||||
|
||||
velocity all set 0.0 0.0 0.0
|
||||
neighbor 1.0 bin
|
||||
|
||||
create_bonds many p1 p1 1 0.0 1.5
|
||||
create_bonds many p2 p2 2 0.0 1.5
|
||||
create_bonds many p3 p3 3 0.0 1.5
|
||||
create_bonds many p4 p4 4 0.0 1.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring break no smooth no volume/factor yes
|
||||
bond_coeff 1 1.0 0 1.0 -0.8
|
||||
bond_coeff 2 1.0 0 1.0 0.0
|
||||
bond_coeff 3 1.0 0 1.0 2.0
|
||||
bond_coeff 4 1.0 0 1.0 10.0
|
||||
|
||||
# squish
|
||||
|
||||
region b block EDGE EDGE EDGE EDGE -1.0 2.0 units box
|
||||
region t block EDGE EDGE EDGE EDGE 18.0 21.0 units box
|
||||
group bot region b
|
||||
group top region t
|
||||
|
||||
velocity top set 0.0 0.0 -0.0025
|
||||
fix 2 bot setforce 0.0 0.0 0.0
|
||||
fix 3 top setforce 0.0 0.0 0.0
|
||||
|
||||
compute zmax all reduce max z
|
||||
|
||||
thermo_style custom step ke pe pxx pyy pzz c_zmax
|
||||
#dump 1 all custom 100 atomDump id type x y z
|
||||
|
||||
run 10000
|
||||
@ -0,0 +1,635 @@
|
||||
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1028-g800a5f6310-modified)
|
||||
# Squish three pillars with different Poisson's ratios
|
||||
# from left to right, nu ~ 0.5, nu = 0.25 nu ~ 0, nu << 0
|
||||
|
||||
units lj
|
||||
dimension 3
|
||||
boundary p p s
|
||||
atom_style bond
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.41
|
||||
Lattice spacing in x,y,z = 1.4156209 1.4156209 1.4156209
|
||||
region box block 0 20 -10 10 -1 21 units box
|
||||
create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (0 -10 -1) to (20 10 21)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0
|
||||
|
||||
# Create roughly jammed initial disordered geometry
|
||||
|
||||
region pillar cylinder z 10.0 0.0 7.0 0.0 20.0 units box
|
||||
region pillarw cylinder z 10.0 0.0 8.0 -1.0 21.0 units box
|
||||
create_atoms 1 region pillar
|
||||
Created 4348 atoms
|
||||
using lattice units in orthogonal box = (0 -10 -1.0022) to (20 10 21.0022)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
velocity all create 0.1 345910
|
||||
|
||||
pair_style bpm/spring
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
fix 1 all nve
|
||||
fix wtemp all wall/region pillarw harmonic 1.0 1.0 1.0
|
||||
|
||||
thermo_style custom step ke pe pxx pyy pzz
|
||||
thermo 100
|
||||
|
||||
timestep 0.1
|
||||
run 20000
|
||||
Generated 0 of 6 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 = 1.3
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 0.65, bins = 31 31 34
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair bpm/spring, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.863 | 9.863 | 9.863 Mbytes
|
||||
Step KinEng PotEng Pxx Pyy Pzz
|
||||
0 0.1499655 0 0.055275974 0.054026613 0.05516469
|
||||
100 0.0045460156 0.0041409796 0.020750379 0.02025897 0.02055488
|
||||
200 0.0013178069 0.0013493823 0.011925094 0.011431479 0.012133526
|
||||
300 0.00061239509 0.00063111128 0.0078970462 0.0079941921 0.0081233289
|
||||
400 0.00035752073 0.00035219764 0.0058819816 0.0058434966 0.0059449021
|
||||
500 0.00024124423 0.00021786035 0.0046674184 0.0045620932 0.0045613656
|
||||
600 0.00016811016 0.0001529395 0.0037258758 0.0038555361 0.0038576669
|
||||
700 0.00012945096 0.00010987332 0.0031369246 0.0032615013 0.0032031682
|
||||
800 0.00010709448 8.0430402e-05 0.0026895825 0.0027732167 0.0027501992
|
||||
900 8.7153735e-05 6.3865397e-05 0.0024057711 0.0024050424 0.0024818746
|
||||
1000 7.3842889e-05 5.1564094e-05 0.0021520507 0.0021316601 0.0022291678
|
||||
1100 6.3710979e-05 4.3417308e-05 0.0019865788 0.0019506967 0.0020247423
|
||||
1200 5.6443217e-05 3.5839723e-05 0.0018116278 0.0017780415 0.0018009974
|
||||
1300 5.2117104e-05 2.9304564e-05 0.0016091295 0.001640217 0.0016494854
|
||||
1400 4.7722691e-05 2.4720323e-05 0.0014728954 0.0014850638 0.0015059012
|
||||
1500 4.3462545e-05 2.1647487e-05 0.0013643988 0.001374924 0.0013860842
|
||||
1600 4.0536322e-05 1.8288037e-05 0.0012573942 0.0012444583 0.0012755521
|
||||
1700 3.775762e-05 1.6253386e-05 0.0011940081 0.0011936534 0.0011875306
|
||||
1800 3.5608024e-05 1.4169135e-05 0.0011046597 0.0011124609 0.0011233068
|
||||
1900 3.3550883e-05 1.2504042e-05 0.0010287232 0.0010521058 0.0010397415
|
||||
2000 3.1777303e-05 1.1341947e-05 0.00099021486 0.000998969 0.0009824298
|
||||
2100 3.0397425e-05 1.0197816e-05 0.00093175155 0.0009356076 0.00093587614
|
||||
2200 2.9415297e-05 9.1442693e-06 0.00087450395 0.00088005632 0.00090292439
|
||||
2300 2.8707506e-05 8.0867687e-06 0.00083155793 0.00084280783 0.00081915094
|
||||
2400 2.8087223e-05 7.1902632e-06 0.0007805398 0.00077693415 0.00079586919
|
||||
2500 2.7412036e-05 6.5329159e-06 0.00074113675 0.00075460667 0.00075182142
|
||||
2600 2.679767e-05 5.9994917e-06 0.00071331838 0.00071107795 0.00071851862
|
||||
2700 2.635836e-05 5.4669016e-06 0.00067864938 0.00067012596 0.00068378851
|
||||
2800 2.5965243e-05 4.949289e-06 0.00064702706 0.00064070457 0.00065886675
|
||||
2900 2.559065e-05 4.5456845e-06 0.0006226747 0.00061715852 0.00061944402
|
||||
3000 2.5250954e-05 4.1940249e-06 0.00059390621 0.00060635122 0.00059577814
|
||||
3100 2.4986177e-05 3.8098655e-06 0.00057100922 0.00056783357 0.00056395219
|
||||
3200 2.4747099e-05 3.5558624e-06 0.00054231559 0.00054795569 0.00055365101
|
||||
3300 2.4583172e-05 3.2301482e-06 0.00052359125 0.00052829803 0.00051398925
|
||||
3400 2.4465352e-05 2.9399683e-06 0.000501977 0.00050484541 0.00050034857
|
||||
3500 2.4292908e-05 2.7427543e-06 0.00048102359 0.00048510374 0.00047731201
|
||||
3600 2.4101584e-05 2.5764805e-06 0.00045636206 0.00047866627 0.00046659816
|
||||
3700 2.3996774e-05 2.3958219e-06 0.00045065226 0.00045184729 0.0004429641
|
||||
3800 2.3876498e-05 2.2130338e-06 0.00043775075 0.00043861927 0.00042506898
|
||||
3900 2.3795887e-05 2.0489788e-06 0.00041988245 0.00041826647 0.00040894442
|
||||
4000 2.3728265e-05 1.8872709e-06 0.0004011638 0.00040340239 0.00039261217
|
||||
4100 2.361572e-05 1.8065046e-06 0.00038335165 0.00039918443 0.00037720392
|
||||
4200 2.3535095e-05 1.6942677e-06 0.00037114826 0.00038329691 0.0003685779
|
||||
4300 2.3470549e-05 1.5919892e-06 0.00036932669 0.00036792338 0.00034946519
|
||||
4400 2.3435028e-05 1.4707935e-06 0.00035224849 0.00035387592 0.00033687303
|
||||
4500 2.3379331e-05 1.3699313e-06 0.00033731606 0.00034141019 0.00032655896
|
||||
4600 2.3319696e-05 1.3018783e-06 0.0003294574 0.00032975202 0.00031755058
|
||||
4700 2.3261329e-05 1.2276139e-06 0.00031109085 0.00032618425 0.00030828008
|
||||
4800 2.3223647e-05 1.140323e-06 0.00030403794 0.00030819264 0.00029880154
|
||||
4900 2.3159354e-05 1.1062118e-06 0.00029932089 0.00031023756 0.0002883218
|
||||
5000 2.3107215e-05 1.0481984e-06 0.00028703077 0.00029791419 0.00028428891
|
||||
5100 2.3059227e-05 9.9631603e-07 0.00028386337 0.00029449929 0.00027691149
|
||||
5200 2.2992218e-05 9.7498165e-07 0.00028122064 0.00029160621 0.00026605841
|
||||
5300 2.2965927e-05 9.089863e-07 0.00026898334 0.00027744029 0.00025999853
|
||||
5400 2.2917228e-05 8.6905288e-07 0.00026737748 0.00026872859 0.00025247197
|
||||
5500 2.2888721e-05 8.1654344e-07 0.00025981052 0.00025927594 0.00024538697
|
||||
5600 2.2858634e-05 7.7918083e-07 0.00024981244 0.00025588577 0.00023814373
|
||||
5700 2.281493e-05 7.5493879e-07 0.00024608832 0.0002484983 0.00024049134
|
||||
5800 2.2768424e-05 7.3151987e-07 0.00024270273 0.00024299121 0.00022677616
|
||||
5900 2.2732815e-05 7.074362e-07 0.00023856426 0.00024317059 0.00022163128
|
||||
6000 2.2709157e-05 6.6558163e-07 0.00023134432 0.00023530205 0.00022005083
|
||||
6100 2.2662747e-05 6.5786116e-07 0.0002266164 0.00023346154 0.0002204147
|
||||
6200 2.2633078e-05 6.2893457e-07 0.00022245338 0.00022992048 0.00021358332
|
||||
6300 2.2609503e-05 5.9395689e-07 0.00021957435 0.00022236534 0.00020603821
|
||||
6400 2.2569287e-05 5.8419818e-07 0.00021444329 0.00022008074 0.00020680001
|
||||
6500 2.2558171e-05 5.5154822e-07 0.00020972278 0.00021475404 0.0001968296
|
||||
6600 2.2537593e-05 5.2835018e-07 0.00020614625 0.00021023961 0.00019204871
|
||||
6700 2.2502584e-05 5.1813436e-07 0.00020503279 0.00020643962 0.00019037754
|
||||
6800 2.2478356e-05 4.9790083e-07 0.00020102604 0.00020156032 0.00018515076
|
||||
6900 2.2455758e-05 4.8193847e-07 0.00019951327 0.00019687965 0.00017945937
|
||||
7000 2.2451788e-05 4.5334026e-07 0.00019179079 0.00019105513 0.00018131892
|
||||
7100 2.242032e-05 4.4768512e-07 0.00018785677 0.00019138466 0.00017575316
|
||||
7200 2.2399735e-05 4.3736624e-07 0.00018626883 0.00019360748 0.00017301675
|
||||
7300 2.2389231e-05 4.15585e-07 0.00018246126 0.00018633267 0.00016724368
|
||||
7400 2.2380183e-05 3.9716485e-07 0.00017807282 0.00017911936 0.00016526154
|
||||
7500 2.2360502e-05 3.8572453e-07 0.00017941834 0.00017481595 0.00016562917
|
||||
7600 2.2352618e-05 3.6544203e-07 0.0001738664 0.00017168235 0.00015859374
|
||||
7700 2.2334806e-05 3.607199e-07 0.00017225216 0.00017080992 0.00015661869
|
||||
7800 2.2324987e-05 3.4379759e-07 0.00016927498 0.00016663572 0.00015055472
|
||||
7900 2.2312673e-05 3.3388048e-07 0.00016641481 0.00016711678 0.00014572442
|
||||
8000 2.2301157e-05 3.2411769e-07 0.00016240031 0.00016423398 0.00014745631
|
||||
8100 2.2289999e-05 3.1300113e-07 0.00015980907 0.00016023173 0.00014648402
|
||||
8200 2.2290743e-05 2.9256755e-07 0.00015325928 0.00015691336 0.00013999402
|
||||
8300 2.2281125e-05 2.8428888e-07 0.00015228905 0.00015083585 0.00013859409
|
||||
8400 2.2276417e-05 2.7196488e-07 0.00014803522 0.00014827108 0.00013276633
|
||||
8500 2.2270336e-05 2.6090967e-07 0.00014433988 0.00014599154 0.00013300747
|
||||
8600 2.2263872e-05 2.4958292e-07 0.00013831677 0.00014270235 0.00012905707
|
||||
8700 2.2248712e-05 2.4963205e-07 0.00013872459 0.0001439154 0.00012481041
|
||||
8800 2.2250741e-05 2.3462546e-07 0.00013718378 0.00013836506 0.00012339897
|
||||
8900 2.224156e-05 2.2671444e-07 0.00013600425 0.00013296456 0.00011974963
|
||||
9000 2.223534e-05 2.2123093e-07 0.00013416263 0.00013296441 0.00011589796
|
||||
9100 2.2228222e-05 2.1383104e-07 0.00013107675 0.00012912031 0.0001145627
|
||||
9200 2.2227286e-05 2.0166229e-07 0.00012779654 0.00012790731 0.00011151855
|
||||
9300 2.2220754e-05 1.9643141e-07 0.00012495065 0.0001246298 0.00010931293
|
||||
9400 2.221898e-05 1.8787396e-07 0.00012142128 0.0001220759 0.00010842013
|
||||
9500 2.2213967e-05 1.8124491e-07 0.00011804877 0.00012238176 0.00010366211
|
||||
9600 2.2207421e-05 1.7767413e-07 0.00011648229 0.00012054702 0.00010322444
|
||||
9700 2.2204058e-05 1.7056842e-07 0.00011554095 0.00011498299 9.977342e-05
|
||||
9800 2.2199188e-05 1.6522097e-07 0.0001128848 0.00011236078 9.9036502e-05
|
||||
9900 2.2197504e-05 1.5746927e-07 0.00010946504 0.00010989886 9.6727132e-05
|
||||
10000 2.2192316e-05 1.5304623e-07 0.00010594185 0.00010914699 9.528986e-05
|
||||
10100 2.2184947e-05 1.5244045e-07 0.00010752432 0.00010893017 9.4551907e-05
|
||||
10200 2.2178334e-05 1.4903759e-07 0.00010714254 0.00010631136 9.3781244e-05
|
||||
10300 2.2176545e-05 1.4377101e-07 0.00010349821 0.00010615276 9.0627052e-05
|
||||
10400 2.2170858e-05 1.4070094e-07 0.00010356274 0.00010425909 8.9700967e-05
|
||||
10500 2.216613e-05 1.3820877e-07 0.00010184809 0.00010281562 8.9244415e-05
|
||||
10600 2.2164055e-05 1.3216024e-07 0.00010308437 9.8578026e-05 8.5149176e-05
|
||||
10700 2.2159491e-05 1.2984075e-07 9.8219521e-05 9.9602891e-05 8.4157228e-05
|
||||
10800 2.2154477e-05 1.2630119e-07 9.6387929e-05 9.8518691e-05 8.4474815e-05
|
||||
10900 2.2154048e-05 1.2065173e-07 9.7781796e-05 9.576565e-05 8.154014e-05
|
||||
11000 2.2149114e-05 1.1781869e-07 9.2783199e-05 9.5117475e-05 8.0363701e-05
|
||||
11100 2.2141212e-05 1.1917239e-07 9.5852588e-05 9.4366973e-05 8.1109475e-05
|
||||
11200 2.2137916e-05 1.1552597e-07 9.3462537e-05 9.3233749e-05 8.1109707e-05
|
||||
11300 2.213658e-05 1.1008603e-07 9.0556648e-05 9.0476596e-05 7.9879738e-05
|
||||
11400 2.2132896e-05 1.0849193e-07 9.0387656e-05 8.8771879e-05 7.7878167e-05
|
||||
11500 2.2131699e-05 1.0493084e-07 8.8911234e-05 8.9360083e-05 7.6820653e-05
|
||||
11600 2.212882e-05 1.0226714e-07 8.7730933e-05 8.9073361e-05 7.4566523e-05
|
||||
11700 2.2124982e-05 9.9910102e-08 8.477437e-05 8.7806303e-05 7.4307427e-05
|
||||
11800 2.2122352e-05 9.7448554e-08 8.7713138e-05 8.4813396e-05 7.2459814e-05
|
||||
11900 2.2115306e-05 9.9205622e-08 8.6813079e-05 8.772968e-05 7.320007e-05
|
||||
12000 2.211193e-05 9.6005824e-08 8.5655613e-05 8.5316917e-05 7.2326687e-05
|
||||
12100 2.2111397e-05 9.2687716e-08 8.307622e-05 8.4586949e-05 7.1199156e-05
|
||||
12200 2.2109506e-05 9.0349635e-08 8.3196249e-05 8.0047918e-05 7.1459883e-05
|
||||
12300 2.210352e-05 9.1828777e-08 8.3023487e-05 8.298801e-05 7.0680887e-05
|
||||
12400 2.2102016e-05 8.8266841e-08 8.1237167e-05 8.0897688e-05 6.8984427e-05
|
||||
12500 2.2100818e-05 8.4451868e-08 8.1241577e-05 7.9056657e-05 6.717288e-05
|
||||
12600 2.2099153e-05 8.2172667e-08 8.1099692e-05 7.7228294e-05 6.5679604e-05
|
||||
12700 2.2096311e-05 8.1609526e-08 7.8279774e-05 7.7218651e-05 6.5855028e-05
|
||||
12800 2.2092745e-05 8.0724331e-08 7.7558727e-05 7.7608398e-05 6.3769835e-05
|
||||
12900 2.2092691e-05 7.7030815e-08 7.6375935e-05 7.5224855e-05 6.3459282e-05
|
||||
13000 2.2090024e-05 7.6060223e-08 7.7017264e-05 7.4786591e-05 6.3026033e-05
|
||||
13100 2.2087518e-05 7.4543793e-08 7.6332555e-05 7.3188101e-05 6.1356128e-05
|
||||
13200 2.2084857e-05 7.418719e-08 7.6669987e-05 7.404012e-05 6.2432396e-05
|
||||
13300 2.2082212e-05 7.2196183e-08 7.4038422e-05 7.4260224e-05 6.1635001e-05
|
||||
13400 2.2080736e-05 7.0711865e-08 7.2995841e-05 7.2774089e-05 5.8837968e-05
|
||||
13500 2.2078436e-05 7.0246025e-08 7.2080944e-05 7.1699053e-05 6.0562467e-05
|
||||
13600 2.2076176e-05 6.8496408e-08 7.3283243e-05 7.0444762e-05 5.8434239e-05
|
||||
13700 2.207464e-05 6.6747696e-08 7.0510931e-05 7.0209957e-05 5.8512753e-05
|
||||
13800 2.2073094e-05 6.4951584e-08 7.221483e-05 6.8194771e-05 5.8326554e-05
|
||||
13900 2.2069993e-05 6.4329747e-08 7.108122e-05 6.7692383e-05 5.6975473e-05
|
||||
14000 2.2068384e-05 6.3826074e-08 7.0821331e-05 6.6802334e-05 5.68441e-05
|
||||
14100 2.2066879e-05 6.1895531e-08 6.9341143e-05 6.788505e-05 5.5082465e-05
|
||||
14200 2.2065117e-05 6.1337212e-08 6.9233584e-05 6.8817889e-05 5.5574272e-05
|
||||
14300 2.2064837e-05 5.8643765e-08 6.5620482e-05 6.5164345e-05 5.5025535e-05
|
||||
14400 2.2063445e-05 5.7670706e-08 6.5693047e-05 6.5227069e-05 5.3546255e-05
|
||||
14500 2.2062593e-05 5.538514e-08 6.696964e-05 6.4489522e-05 5.186144e-05
|
||||
14600 2.2059889e-05 5.6128076e-08 6.6606975e-05 6.3318574e-05 5.3065953e-05
|
||||
14700 2.2058311e-05 5.4197187e-08 6.5636138e-05 6.2862183e-05 5.1216722e-05
|
||||
14800 2.2056992e-05 5.3753302e-08 6.4166876e-05 6.2347682e-05 5.1644619e-05
|
||||
14900 2.2055144e-05 5.3731475e-08 6.2886449e-05 6.2665027e-05 5.1085737e-05
|
||||
15000 2.2055534e-05 5.1421678e-08 6.3216438e-05 6.2497955e-05 4.9420052e-05
|
||||
15100 2.2053654e-05 5.02402e-08 6.185253e-05 6.1020856e-05 4.8961501e-05
|
||||
15200 2.2052236e-05 4.9076779e-08 6.1894516e-05 5.8658526e-05 4.9270802e-05
|
||||
15300 2.2050986e-05 4.8464692e-08 6.1632248e-05 5.939126e-05 4.7954422e-05
|
||||
15400 2.2050221e-05 4.7362506e-08 5.9932389e-05 5.8619584e-05 4.8571134e-05
|
||||
15500 2.2049702e-05 4.5776499e-08 5.9343369e-05 5.6908271e-05 4.5799128e-05
|
||||
15600 2.2046842e-05 4.6074337e-08 6.0035433e-05 5.8667997e-05 4.6172612e-05
|
||||
15700 2.2046262e-05 4.542862e-08 5.8703316e-05 5.7704418e-05 4.6189812e-05
|
||||
15800 2.204616e-05 4.3329814e-08 5.6689179e-05 5.6845301e-05 4.5918735e-05
|
||||
15900 2.2044466e-05 4.3332045e-08 5.806419e-05 5.6030356e-05 4.5166944e-05
|
||||
16000 2.2043425e-05 4.2921122e-08 5.6716404e-05 5.5927539e-05 4.5500189e-05
|
||||
16100 2.2041966e-05 4.1774604e-08 5.6210966e-05 5.4580522e-05 4.4615956e-05
|
||||
16200 2.2041126e-05 4.1198995e-08 5.6314084e-05 5.5538584e-05 4.3793702e-05
|
||||
16300 2.2040394e-05 4.0405671e-08 5.6049147e-05 5.5461464e-05 4.1884999e-05
|
||||
16400 2.2040538e-05 3.8384306e-08 5.4398726e-05 5.3601303e-05 4.2580325e-05
|
||||
16500 2.2039103e-05 3.8153339e-08 5.46254e-05 5.3390447e-05 4.2089044e-05
|
||||
16600 2.2036976e-05 3.8358477e-08 5.2955748e-05 5.3742853e-05 4.1975739e-05
|
||||
16700 2.20354e-05 3.8227046e-08 5.3241934e-05 5.2684751e-05 4.1815545e-05
|
||||
16800 2.2034486e-05 3.7612842e-08 5.3915367e-05 5.3101063e-05 3.9996576e-05
|
||||
16900 2.2033757e-05 3.6901749e-08 5.324896e-05 5.2020981e-05 4.0209668e-05
|
||||
17000 2.2032483e-05 3.631797e-08 5.2504044e-05 5.1532024e-05 4.1841265e-05
|
||||
17100 2.2031907e-05 3.5761725e-08 5.2177113e-05 5.1853522e-05 4.0475234e-05
|
||||
17200 2.2030622e-05 3.5615934e-08 5.2153967e-05 5.1680185e-05 4.0255138e-05
|
||||
17300 2.2028906e-05 3.5769817e-08 5.3276095e-05 5.1713123e-05 3.9429947e-05
|
||||
17400 2.2027982e-05 3.5279634e-08 5.1720769e-05 5.1071287e-05 3.946136e-05
|
||||
17500 2.2027385e-05 3.4532852e-08 5.0897208e-05 5.0132128e-05 3.9770047e-05
|
||||
17600 2.2025743e-05 3.4705869e-08 5.1921573e-05 4.9849618e-05 3.9250188e-05
|
||||
17700 2.202442e-05 3.4664237e-08 5.1037538e-05 5.1309699e-05 3.8699028e-05
|
||||
17800 2.2024041e-05 3.3230639e-08 5.0676543e-05 4.9676967e-05 3.6992319e-05
|
||||
17900 2.2024009e-05 3.2185399e-08 4.9624741e-05 4.8805054e-05 3.8163917e-05
|
||||
18000 2.2023291e-05 3.1901464e-08 4.9090832e-05 4.9184392e-05 3.7458065e-05
|
||||
18100 2.202221e-05 3.1698456e-08 4.9178905e-05 4.8243736e-05 3.7166662e-05
|
||||
18200 2.2021437e-05 3.1022506e-08 4.8457604e-05 4.8875433e-05 3.5824097e-05
|
||||
18300 2.2020792e-05 3.0064688e-08 4.909522e-05 4.7180933e-05 3.5355876e-05
|
||||
18400 2.2021113e-05 2.9279611e-08 4.7111226e-05 4.7747191e-05 3.4625046e-05
|
||||
18500 2.2019843e-05 2.9077485e-08 4.7131195e-05 4.633375e-05 3.5061152e-05
|
||||
18600 2.201863e-05 2.9334156e-08 4.7778742e-05 4.7369011e-05 3.4559728e-05
|
||||
18700 2.2018219e-05 2.862088e-08 4.7260131e-05 4.5881586e-05 3.4305681e-05
|
||||
18800 2.2018393e-05 2.7165913e-08 4.6456933e-05 4.5912824e-05 3.3022256e-05
|
||||
18900 2.201532e-05 2.8873682e-08 4.7138874e-05 4.6487853e-05 3.5130117e-05
|
||||
19000 2.2014497e-05 2.8430782e-08 4.7563112e-05 4.6760097e-05 3.3226263e-05
|
||||
19100 2.2014081e-05 2.8050044e-08 4.6431839e-05 4.6219284e-05 3.4248177e-05
|
||||
19200 2.2013576e-05 2.7201031e-08 4.5709989e-05 4.5916792e-05 3.3897641e-05
|
||||
19300 2.2012609e-05 2.7374842e-08 4.561715e-05 4.5693439e-05 3.4284473e-05
|
||||
19400 2.2010667e-05 2.8105102e-08 4.6663945e-05 4.6539017e-05 3.3608877e-05
|
||||
19500 2.2010486e-05 2.6897595e-08 4.5576796e-05 4.6292499e-05 3.2656892e-05
|
||||
19600 2.2010302e-05 2.6248669e-08 4.4996903e-05 4.3675939e-05 3.4540503e-05
|
||||
19700 2.2009254e-05 2.6450724e-08 4.4868007e-05 4.5628545e-05 3.3413034e-05
|
||||
19800 2.2007283e-05 2.721852e-08 4.5939302e-05 4.5327011e-05 3.3411556e-05
|
||||
19900 2.2007538e-05 2.6295204e-08 4.5722301e-05 4.441743e-05 3.4023953e-05
|
||||
20000 2.2006515e-05 2.6089093e-08 4.4621124e-05 4.5449725e-05 3.2126359e-05
|
||||
Loop time of 7.03939 on 1 procs for 20000 steps with 4348 atoms
|
||||
|
||||
Performance: 24547586.015 tau/day, 2841.156 timesteps/s, 12.353 Matom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.55 | 4.55 | 4.55 | 0.0 | 64.64
|
||||
Bond | 0.00067765 | 0.00067765 | 0.00067765 | 0.0 | 0.01
|
||||
Neigh | 0.3745 | 0.3745 | 0.3745 | 0.0 | 5.32
|
||||
Comm | 0.013687 | 0.013687 | 0.013687 | 0.0 | 0.19
|
||||
Output | 0.006889 | 0.006889 | 0.006889 | 0.0 | 0.10
|
||||
Modify | 1.9222 | 1.9222 | 1.9222 | 0.0 | 27.31
|
||||
Other | | 0.1715 | | | 2.44
|
||||
|
||||
Nlocal: 4348 ave 4348 max 4348 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: 23350 ave 23350 max 23350 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 23350
|
||||
Ave neighs/atom = 5.3702852
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 222
|
||||
Dangerous builds = 0
|
||||
unfix wtemp
|
||||
|
||||
# Replicate cylinder and add bonds
|
||||
|
||||
replicate 4 1 1
|
||||
Replication is creating a 4x1x1 = 4 times larger system...
|
||||
orthogonal box = (0 -10 -0.0025658844) to (80 10 20.002511)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
17392 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
replicate CPU = 0.003 seconds
|
||||
|
||||
region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box
|
||||
region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box
|
||||
|
||||
group p1 region r1
|
||||
4348 atoms in group p1
|
||||
group p2 region r2
|
||||
4348 atoms in group p2
|
||||
group p3 region r3
|
||||
4348 atoms in group p3
|
||||
group p4 region r4
|
||||
4348 atoms in group p4
|
||||
|
||||
set group p2 type 2
|
||||
Setting atom values ...
|
||||
4348 settings made for type
|
||||
set group p3 type 3
|
||||
Setting atom values ...
|
||||
4348 settings made for type
|
||||
set group p4 type 4
|
||||
Setting atom values ...
|
||||
4348 settings made for type
|
||||
|
||||
velocity all set 0.0 0.0 0.0
|
||||
neighbor 1.0 bin
|
||||
|
||||
create_bonds many p1 p1 1 0.0 1.5
|
||||
Generated 0 of 6 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
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 80 20 21
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair bpm/spring, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 29229 bonds, new total = 29229
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
19 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
create_bonds many p2 p2 2 0.0 1.5
|
||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Bonds are defined but no bond style is set (../force.cpp:197)
|
||||
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199)
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 80 20 21
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair bpm/spring, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 29229 bonds, new total = 58458
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
19 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.003 seconds
|
||||
create_bonds many p3 p3 3 0.0 1.5
|
||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Bonds are defined but no bond style is set (../force.cpp:197)
|
||||
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199)
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 80 20 21
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair bpm/spring, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 29229 bonds, new total = 87687
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
19 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.004 seconds
|
||||
create_bonds many p4 p4 4 0.0 1.5
|
||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Bonds are defined but no bond style is set (../force.cpp:197)
|
||||
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199)
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 80 20 21
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair bpm/spring, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 29229 bonds, new total = 116916
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
19 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.005 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring break no smooth no volume/factor yes
|
||||
bond_coeff 1 1.0 0 1.0 -0.8
|
||||
bond_coeff 2 1.0 0 1.0 0.0
|
||||
bond_coeff 3 1.0 0 1.0 2.0
|
||||
bond_coeff 4 1.0 0 1.0 10.0
|
||||
|
||||
# squish
|
||||
|
||||
region b block EDGE EDGE EDGE EDGE -1.0 2.0 units box
|
||||
region t block EDGE EDGE EDGE EDGE 18.0 21.0 units box
|
||||
group bot region b
|
||||
2040 atoms in group bot
|
||||
group top region t
|
||||
2036 atoms in group top
|
||||
|
||||
velocity top set 0.0 0.0 -0.0025
|
||||
fix 2 bot setforce 0.0 0.0 0.0
|
||||
fix 3 top setforce 0.0 0.0 0.0
|
||||
|
||||
compute zmax all reduce max z
|
||||
|
||||
thermo_style custom step ke pe pxx pyy pzz c_zmax
|
||||
dump 1 all custom 100 atomDump id type x y z
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 6 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 = 1.3
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 0.65, bins = 124 31 31
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair bpm/spring, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 33.55 | 33.55 | 33.55 Mbytes
|
||||
Step KinEng PotEng Pxx Pyy Pzz c_zmax
|
||||
20000 7.3311514e-07 0 5.5082149e-05 5.6035691e-05 0.00016879881 20.000342
|
||||
20100 3.1226194e-06 4.1766539e-06 -0.00013996263 -0.00014393529 0.0029331928 19.964952
|
||||
20200 2.5567295e-06 1.4988852e-05 -0.00027674096 -0.00027610139 0.0056641847 19.929561
|
||||
20300 2.5665365e-06 3.3513395e-05 -0.00042198157 -0.0004191815 0.0083802213 19.894171
|
||||
20400 2.4143831e-06 5.9638373e-05 -0.00055373017 -0.00055236369 0.011083701 19.85878
|
||||
20500 2.2440232e-06 9.3155125e-05 -0.00070411826 -0.00070166982 0.013871936 19.82339
|
||||
20600 2.3036882e-06 0.00013415012 -0.00084108079 -0.00084004876 0.016564858 19.787999
|
||||
20700 2.4894579e-06 0.00018252868 -0.00098164122 -0.00097848101 0.019243173 19.752609
|
||||
20800 2.3533488e-06 0.0002383092 -0.0011196916 -0.0011163409 0.021906836 19.717218
|
||||
20900 2.3312562e-06 0.000301439 -0.0012662271 -0.0012625903 0.024743687 19.681828
|
||||
21000 2.3806649e-06 0.00037188609 -0.0014035798 -0.0013992731 0.02739958 19.646437
|
||||
21100 2.3212779e-06 0.00044964779 -0.0015396059 -0.0015348733 0.030041098 19.611047
|
||||
21200 2.3908442e-06 0.00053469194 -0.001674797 -0.0016694993 0.03266844 19.575656
|
||||
21300 2.3622478e-06 0.00062699617 -0.001822934 -0.0018167895 0.035552232 19.540266
|
||||
21400 2.349964e-06 0.00072653051 -0.0019569691 -0.0019503123 0.038170924 19.504875
|
||||
21500 2.3567592e-06 0.00083327134 -0.0020899915 -0.0020827032 0.040775314 19.469484
|
||||
21600 2.3616263e-06 0.00094719631 -0.0022220661 -0.0022140075 0.043365368 19.434094
|
||||
21700 2.353721e-06 0.0010682808 -0.0023711759 -0.0023623886 0.046296241 19.398703
|
||||
21800 2.3646799e-06 0.0011965 -0.0025021157 -0.0024925265 0.048877326 19.363313
|
||||
21900 2.3550746e-06 0.0013318277 -0.0026319662 -0.0026215842 0.051443901 19.327922
|
||||
22000 2.3552825e-06 0.0014742397 -0.0027607166 -0.0027495396 0.053995979 19.292532
|
||||
22100 2.3588762e-06 0.0016237112 -0.0028884164 -0.0028763855 0.05653356 19.257141
|
||||
22200 2.3566445e-06 0.0017802179 -0.0030385388 -0.0030255211 0.05951687 19.221751
|
||||
22300 2.3569128e-06 0.0019437341 -0.0031650443 -0.0031511287 0.062044959 19.18636
|
||||
22400 2.3573615e-06 0.0021142342 -0.0032904648 -0.0032756057 0.064558413 19.15097
|
||||
22500 2.3556792e-06 0.0022916926 -0.003414791 -0.0033989599 0.067057238 19.115579
|
||||
22600 2.3559622e-06 0.0024760839 -0.0035658051 -0.0035488398 0.070087637 19.080189
|
||||
22700 2.3565188e-06 0.0026673826 -0.0036888874 -0.0036708796 0.072576558 19.044798
|
||||
22800 2.3554654e-06 0.0028655631 -0.0038108556 -0.0037917743 0.075050709 19.009408
|
||||
22900 2.3556755e-06 0.0030705996 -0.0039317038 -0.0039115206 0.07751008 18.974017
|
||||
23000 2.3553906e-06 0.0032824663 -0.0040835075 -0.0040620186 0.080587643 18.938627
|
||||
23100 2.3549893e-06 0.0035011372 -0.0042030492 -0.0041803845 0.08303667 18.903236
|
||||
23200 2.3549869e-06 0.0037265864 -0.0043214571 -0.004297582 0.085470779 18.867846
|
||||
23300 2.3548674e-06 0.0039587875 -0.0044387217 -0.004413608 0.087889956 18.832455
|
||||
23400 2.3544804e-06 0.0041977141 -0.0045911895 -0.0045645946 0.091014737 18.797065
|
||||
23500 2.3543814e-06 0.0044433399 -0.0047070844 -0.0046791718 0.093423108 18.761674
|
||||
23600 2.3541461e-06 0.0046956382 -0.0048218198 -0.0047925569 0.09581641 18.726284
|
||||
23700 2.3539051e-06 0.0049545823 -0.0049353928 -0.0049047458 0.098194634 18.690893
|
||||
23800 2.3537612e-06 0.0052201456 -0.0050478006 -0.0050157354 0.10055777 18.655502
|
||||
23900 2.3535618e-06 0.0054923012 -0.0052005398 -0.0051667526 0.10373359 18.620112
|
||||
24000 2.353333e-06 0.005771022 -0.0053114912 -0.0052762067 0.10608529 18.584721
|
||||
24100 2.3531619e-06 0.006056281 -0.0054212598 -0.0053844406 0.10842176 18.549331
|
||||
24200 2.3529697e-06 0.0063480511 -0.0055298409 -0.0054914515 0.11074298 18.51394
|
||||
24300 2.352776e-06 0.0066463046 -0.0056829436 -0.0056426256 0.11396569 18.47855
|
||||
24400 2.3526011e-06 0.0069510143 -0.0057899993 -0.0057480274 0.11627496 18.443159
|
||||
24500 2.3524078e-06 0.0072621525 -0.0058958481 -0.0058521853 0.11856882 18.407769
|
||||
24600 2.3522128e-06 0.0075796913 -0.0060004865 -0.0059550957 0.12084728 18.372378
|
||||
24700 2.3520292e-06 0.0079036029 -0.0061538145 -0.0061062726 0.12411681 18.336988
|
||||
24800 2.3518453e-06 0.0082338593 -0.0062568585 -0.0062074978 0.12638278 18.301597
|
||||
24900 2.3516643e-06 0.0085704324 -0.0063586718 -0.0063074546 0.12863317 18.266207
|
||||
25000 2.3514892e-06 0.0089132938 -0.0064592514 -0.0064061393 0.13086797 18.230816
|
||||
25100 2.3513106e-06 0.0092624151 -0.0066126575 -0.0065571568 0.13418421 18.195426
|
||||
25200 2.3511362e-06 0.0096177679 -0.0067115701 -0.0066540785 0.13640596 18.160035
|
||||
25300 2.3509678e-06 0.0099793234 -0.0068092292 -0.0067497066 0.13861195 18.124645
|
||||
25400 2.3508006e-06 0.010347053 -0.0069056318 -0.0068440373 0.14080217 18.089254
|
||||
25500 2.3506356e-06 0.010720927 -0.0070007749 -0.0069370671 0.14297661 18.053864
|
||||
25600 2.3504737e-06 0.011100917 -0.0071536223 -0.0070872122 0.14634153 18.018473
|
||||
25700 2.3503117e-06 0.011486993 -0.007247006 -0.0071783805 0.14850216 17.983083
|
||||
25800 2.3501529e-06 0.011879126 -0.0073391102 -0.0072682259 0.15064682 17.947692
|
||||
25900 2.3499998e-06 0.012277287 -0.0074299315 -0.0073567446 0.1527755 17.912302
|
||||
26000 2.3498505e-06 0.012681445 -0.0075824884 -0.0075063219 0.15618632 17.876911
|
||||
26100 2.3497046e-06 0.013091571 -0.0076714736 -0.0075928957 0.15830056 17.84152
|
||||
26200 2.3495632e-06 0.013507634 -0.0077591555 -0.0076781204 0.16039862 17.80613
|
||||
26300 2.349426e-06 0.013929604 -0.0078455309 -0.0077619923 0.1624805 17.770739
|
||||
26400 2.3492932e-06 0.014357451 -0.0079976262 -0.0079108096 0.16593692 17.735349
|
||||
26500 2.349166e-06 0.014791144 -0.008082087 -0.0079926504 0.16800369 17.699958
|
||||
26600 2.3490444e-06 0.015230653 -0.0081652207 -0.0080731154 0.17005406 17.664568
|
||||
26700 2.3489277e-06 0.015675946 -0.008247024 -0.0081522008 0.17208804 17.629177
|
||||
26800 2.3488161e-06 0.016126992 -0.0083984781 -0.008300055 0.17558967 17.593787
|
||||
26900 2.3487105e-06 0.016583761 -0.0084782861 -0.0083770201 0.17760782 17.558396
|
||||
27000 2.3486117e-06 0.017046219 -0.0085567431 -0.008452582 0.17960935 17.523006
|
||||
27100 2.3485201e-06 0.017514336 -0.0086338458 -0.0085267367 0.18159424 17.487615
|
||||
27200 2.3484365e-06 0.017988079 -0.0087095911 -0.0085994803 0.18356247 17.452225
|
||||
27300 2.3483611e-06 0.018467417 -0.008859495 -0.0087453549 0.18710893 17.416834
|
||||
27400 2.3482941e-06 0.018952317 -0.0089331441 -0.0088158653 0.18906038 17.381444
|
||||
27500 2.3482362e-06 0.019442747 -0.0090054148 -0.0088849402 0.19099494 17.346053
|
||||
27600 2.3481885e-06 0.019938673 -0.009076304 -0.0089525756 0.19291257 17.310663
|
||||
27700 2.3481517e-06 0.020440063 -0.0092251203 -0.0090969772 0.19650266 17.275272
|
||||
27800 2.3481263e-06 0.020946883 -0.0092938279 -0.0091622823 0.1984027 17.239882
|
||||
27900 2.3481132e-06 0.0214591 -0.0093611327 -0.0092261226 0.20028558 17.204491
|
||||
28000 2.3481132e-06 0.02197668 -0.0094270316 -0.0092884939 0.20215126 17.169101
|
||||
28100 2.3481274e-06 0.02249959 -0.0095745512 -0.0094311779 0.20578425 17.13371
|
||||
28200 2.348157e-06 0.023027794 -0.0096381809 -0.0094911175 0.20763145 17.09832
|
||||
28300 2.3482036e-06 0.023561259 -0.0097003831 -0.0095495617 0.20946119 17.062929
|
||||
28400 2.3482687e-06 0.024099949 -0.0097611548 -0.0096065059 0.21127344 17.027538
|
||||
28500 2.3480319e-06 0.024643805 -0.0099071195 -0.0097471709 0.21494867 16.992148
|
||||
28600 2.3475123e-06 0.025192783 -0.0099654368 -0.0098014823 0.21674185 16.956757
|
||||
28700 2.3465283e-06 0.02574682 -0.010022297 -0.0098542782 0.21851751 16.921367
|
||||
28800 2.3462245e-06 0.026305935 -0.010077643 -0.0099055665 0.2202753 16.885976
|
||||
28900 2.3465001e-06 0.026870106 -0.010131548 -0.0099553377 0.22201519 16.850586
|
||||
29000 2.3468383e-06 0.027439281 -0.010274668 -0.010092595 0.22572932 16.815195
|
||||
29100 2.3470511e-06 0.028013406 -0.010326047 -0.010139547 0.22744875 16.779805
|
||||
29200 2.3477211e-06 0.02859243 -0.010375939 -0.01018496 0.22915025 16.744414
|
||||
29300 2.348195e-06 0.029176333 -0.010424252 -0.010228763 0.23083364 16.709024
|
||||
29400 2.3486217e-06 0.02976508 -0.010565133 -0.010363233 0.2345875 16.673633
|
||||
29500 2.3494547e-06 0.030358578 -0.010610824 -0.010404093 0.2362499 16.638243
|
||||
29600 2.350246e-06 0.030956806 -0.010654741 -0.010443743 0.23789521 16.602852
|
||||
29700 2.350645e-06 0.031559783 -0.010697062 -0.01048188 0.23952237 16.567462
|
||||
29800 2.3513205e-06 0.032167468 -0.010835186 -0.010613742 0.24331694 16.532071
|
||||
29900 2.3500682e-06 0.03277985 -0.010874694 -0.010649336 0.2449217 16.496681
|
||||
30000 2.348814e-06 0.033396866 -0.010912585 -0.010683036 0.24650812 16.46129
|
||||
Loop time of 96.3898 on 1 procs for 10000 steps with 17392 atoms
|
||||
|
||||
Performance: 896360.661 tau/day, 103.745 timesteps/s, 1.804 Matom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.4048 | 2.4048 | 2.4048 | 0.0 | 2.49
|
||||
Bond | 89.472 | 89.472 | 89.472 | 0.0 | 92.82
|
||||
Neigh | 0.25526 | 0.25526 | 0.25526 | 0.0 | 0.26
|
||||
Comm | 0.0489 | 0.0489 | 0.0489 | 0.0 | 0.05
|
||||
Output | 1.6355 | 1.6355 | 1.6355 | 0.0 | 1.70
|
||||
Modify | 1.8578 | 1.8578 | 1.8578 | 0.0 | 1.93
|
||||
Other | | 0.7153 | | | 0.74
|
||||
|
||||
Nlocal: 17392 ave 17392 max 17392 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 77 ave 77 max 77 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 102662 ave 102662 max 102662 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 102662
|
||||
Ave neighs/atom = 5.9028289
|
||||
Ave special neighs/atom = 13.444802
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
10000
|
||||
ERROR: Unknown command: 10000 (../input.cpp:314)
|
||||
Last input line: 10000
|
||||
20
examples/granular/3ps.dat
Normal file
20
examples/granular/3ps.dat
Normal file
@ -0,0 +1,20 @@
|
||||
LAMMPS data file
|
||||
|
||||
3 atoms
|
||||
2 atom types
|
||||
|
||||
-0.03 0.03 xlo xhi
|
||||
-0.02 0.02 ylo yhi
|
||||
-0.02 0.02 zlo zhi
|
||||
|
||||
Atoms # sphere
|
||||
|
||||
1 2 0.0005 2500 0.005 2.7937481665024794E-05 0.0016005372526493155 0 0 0
|
||||
2 1 0.01 2500 0.01 0.0 0.0 0 0 0
|
||||
3 1 0.01 2500 0.0 0.0 0.0 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0 0 0 0 0 0
|
||||
2 0 0 0 0 0 0
|
||||
3 0 0 0 0 0 0
|
||||
31
examples/granular/in.sync_verlet
Normal file
31
examples/granular/in.sync_verlet
Normal file
@ -0,0 +1,31 @@
|
||||
# Example problem demonstrating the use of synchronized_verlet
|
||||
# Refer https://doi.org/10.1016/j.cpc.2025.109524 for further details
|
||||
|
||||
units si
|
||||
atom_style sphere
|
||||
newton off
|
||||
|
||||
boundary p p f
|
||||
read_data 3ps.dat
|
||||
|
||||
group ps type 1
|
||||
group fine type 2
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution synchronized_verlet
|
||||
# pair_coeff * * hertz/material 5e8 0.5 0.3 tangential mindlin NULL 0.0 0.5 damping coeff_restitution #synchronized_verlet
|
||||
|
||||
timestep 1e-6
|
||||
fix frz ps freeze
|
||||
fix g fine gravity 9.81 vector 0 0 -1
|
||||
fix 1 fine nve/sphere
|
||||
fix 2 all wall/gran granular hooke 1e4 0.5 tangential linear_history 8235 0 0.5 damping coeff_restitution zplane $(zlo) $(zhi)
|
||||
|
||||
# dump 1 all custom 3000 op.dump id x y z vx vy vz type diameter
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
thermo 3000
|
||||
thermo_style custom step ke
|
||||
run_style verlet
|
||||
run 300000
|
||||
149
examples/granular/in.tableting.200
Normal file
149
examples/granular/in.tableting.200
Normal file
@ -0,0 +1,149 @@
|
||||
##################################### SIMULATION SETTINGS ###################################################
|
||||
|
||||
atom_style sphere 1
|
||||
atom_modify map array
|
||||
comm_modify vel yes
|
||||
units si
|
||||
newton off
|
||||
neighbor 1.0e-3 bin
|
||||
neigh_modify every 10 delay 60 check no
|
||||
timestep 4e-6
|
||||
#processors 2 2 1
|
||||
|
||||
############################## SIMULATION BOUNDING BOX AND INSERT PARTICLES #################################
|
||||
|
||||
boundary f f f
|
||||
read_data spheres200.data
|
||||
|
||||
#################################### ADD DIE AND ATOM PARAMETERIZATION ######################################
|
||||
|
||||
variable atomRadius equal 0.44e-3*1.25
|
||||
variable atomDiameter equal 2*${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}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user