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Fix merge conflicts, minor style fixes

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This commit is contained in:
Joel Thomas Clemmer
2021-11-01 18:13:06 -06:00
parent 69e600c404 b15c02e3cd
commit d7f7835069
1240 changed files with 46027 additions and 14730 deletions
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20
examples/COUPLE/lammps_quest/README
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@ -1,15 +1,21 @@
IMPORTANT NOTE: This example has not been updated since 2014,
so it is not likely to work anymore out of the box. There have
been changes to LAMMPS and its library interface that would need
to be applied. Please see the manual for the documentation of
the library interface.
This directory has an application that runs classical MD via LAMMPS,
but uses quantum forces calculated by the Quest DFT (density
functional) code in place of the usual classical MD forces calculated
by a pair style in LAMMPS.
lmpqst.cpp main program
it links LAMMPS as a library
it invokes Quest as an executable
in.lammps LAMMPS input script, without the run command
si_111.in Quest input script for an 8-atom Si unit cell
lmppath.h contains path to LAMMPS home directory
qstexe.h contains full pathname to Quest executable
lmpqst.cpp main program
it links LAMMPS as a library
it invokes Quest as an executable
in.lammps LAMMPS input script, without the run command
si_111.in Quest input script for an 8-atom Si unit cell
lmppath.h contains path to LAMMPS home directory
qstexe.h contains full pathname to Quest executable
After editing the Makefile, lmppath.h, and qstexe.h to make them
suitable for your box, type:

6
examples/COUPLE/lammps_spparks/README
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@ -1,3 +1,9 @@
IMPORTANT NOTE: This example has not been updated since 2013,
so it is not likely to work anymore out of the box. There have
been changes to LAMMPS and its library interface that would need
to be applied. Please see the manual for the documentation of
the library interface.
This directory has an application that models grain growth in the
presence of strain.

28
examples/COUPLE/multiple/multiple.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -28,13 +28,9 @@
#include <cstdlib>
#include <cstring>
#include "lammps.h" // these are LAMMPS include files
#include "input.h"
#include "atom.h"
#define LAMMPS_LIB_MPI // to make lammps_open() visible
#include "library.h"
using namespace LAMMPS_NS;
int main(int narg, char **arg)
{
// setup MPI and various communicators
@ -68,13 +64,13 @@ int main(int narg, char **arg)
int instance = me*ninstance / nprocs;
MPI_Comm comm_lammps;
MPI_Comm_split(MPI_COMM_WORLD,instance,0,&comm_lammps);
// each instance: unique screen file, log file, temperature
char str1[32],str2[32],str3[32];
char **lmparg = new char*[8];
lmparg[0] = NULL; // required placeholder for program name
lmparg[0] = (char *) "LAMMPS"; // required placeholder for program name
lmparg[1] = (char *) "-screen";
sprintf(str1,"screen.%d",instance);
lmparg[2] = str1;
@ -86,13 +82,9 @@ int main(int narg, char **arg)
sprintf(str3,"%g",temperature + instance*tdelta);
lmparg[7] = str3;
// open N instances of LAMMPS
// either of these methods will work
// create N instances of LAMMPS
LAMMPS *lmp = new LAMMPS(8,lmparg,comm_lammps);
//LAMMPS *lmp;
//lammps_open(8,lmparg,comm_lammps,(void **) &lmp);
void *lmp = lammps_open(8,lmparg,comm_lammps,NULL);
delete [] lmparg;
@ -102,8 +94,8 @@ int main(int narg, char **arg)
// query final temperature and print result for each instance
double *ptr = (double *)
lammps_extract_compute(lmp,(char *) "thermo_temp",0,0);
double *ptr = (double *)
lammps_extract_compute(lmp,"thermo_temp",LMP_STYLE_GLOBAL,LMP_TYPE_SCALAR);
double finaltemp = *ptr;
double *temps = new double[ninstance];
@ -112,7 +104,7 @@ int main(int narg, char **arg)
int me_lammps;
MPI_Comm_rank(comm_lammps,&me_lammps);
if (me_lammps == 0) temps[instance] = finaltemp;
double *alltemps = new double[ninstance];
MPI_Allreduce(temps,alltemps,ninstance,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
@ -125,7 +117,7 @@ int main(int narg, char **arg)
// delete LAMMPS instances
delete lmp;
lammps_close(lmp);
// close down MPI

2
examples/COUPLE/plugin/README
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@ -13,7 +13,7 @@ like below.
mpicc -c -O -Wall -g -I$HOME/lammps/src liblammpsplugin.c
mpicc -c -O -Wall -g simple.c
mpicc simple.o liblammsplugin.o -ldl -o simpleC
mpicc simple.o liblammpsplugin.o -ldl -o simpleC
You also need to build LAMMPS as a shared library
(see examples/COUPLE/README), e.g.

84
examples/COUPLE/plugin/liblammpsplugin.c
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@ -31,51 +31,105 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
if (lib == NULL) return NULL;
handle = dlopen(lib,RTLD_NOW|RTLD_GLOBAL);
if (handle == NULL) return NULL;
lmp = (liblammpsplugin_t *) malloc(sizeof(liblammpsplugin_t));
lmp->handle = handle;
#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)
ADDSYM(open);
ADDSYM(open_no_mpi);
ADDSYM(open_fortran);
ADDSYM(close);
ADDSYM(version);
ADDSYM(mpi_init);
ADDSYM(mpi_finalize);
ADDSYM(kokkos_finalize);
ADDSYM(python_finalize);
ADDSYM(file);
ADDSYM(command);
ADDSYM(commands_list);
ADDSYM(commands_string);
ADDSYM(free);
ADDSYM(extract_setting);
ADDSYM(extract_global);
ADDSYM(get_natoms);
ADDSYM(get_thermo);
ADDSYM(extract_box);
ADDSYM(reset_box);
ADDSYM(memory_usage);
ADDSYM(get_mpi_comm);
ADDSYM(extract_setting);
ADDSYM(extract_global_datatype);
ADDSYM(extract_global);
ADDSYM(extract_atom_datatype);
ADDSYM(extract_atom);
ADDSYM(extract_compute);
ADDSYM(extract_fix);
ADDSYM(extract_variable);
ADDSYM(get_thermo);
ADDSYM(get_natoms);
ADDSYM(set_variable);
ADDSYM(reset_box);
ADDSYM(gather_atoms);
ADDSYM(gather_atoms_concat);
ADDSYM(gather_atoms_subset);
ADDSYM(scatter_atoms);
ADDSYM(scatter_atoms_subset);
ADDSYM(gather_bonds);
ADDSYM(set_fix_external_callback);
ADDSYM(create_atoms);
ADDSYM(config_has_package);
ADDSYM(config_package_count);
ADDSYM(config_package_name);
ADDSYM(find_pair_neighlist);
ADDSYM(find_fix_neighlist);
ADDSYM(find_compute_neighlist);
ADDSYM(neighlist_num_elements);
ADDSYM(neighlist_element_neighbors);
ADDSYM(version);
ADDSYM(get_os_info);
ADDSYM(config_has_mpi_support);
ADDSYM(config_has_gzip_support);
ADDSYM(config_has_png_support);
ADDSYM(config_has_jpeg_support);
ADDSYM(config_has_ffmpeg_support);
ADDSYM(config_has_exceptions);
ADDSYM(create_atoms);
ADDSYM(config_has_package);
ADDSYM(config_package_count);
ADDSYM(config_package_name);
ADDSYM(config_accelerator);
ADDSYM(has_gpu_device);
ADDSYM(get_gpu_device_info);
ADDSYM(has_style);
ADDSYM(style_count);
ADDSYM(style_name);
ADDSYM(has_id);
ADDSYM(id_count);
ADDSYM(id_name);
ADDSYM(plugin_count);
ADDSYM(plugin_name);
ADDSYM(set_fix_external_callback);
ADDSYM(fix_external_get_force);
ADDSYM(fix_external_set_energy_global);
ADDSYM(fix_external_set_energy_peratom);
ADDSYM(fix_external_set_virial_global);
ADDSYM(fix_external_set_virial_peratom);
ADDSYM(fix_external_set_vector_length);
ADDSYM(fix_external_set_vector);
ADDSYM(free);
ADDSYM(is_running);
ADDSYM(force_timeout);
#ifdef LAMMPS_EXCEPTIONS
lmp->has_exceptions = 1;
ADDSYM(has_error);

128
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -39,75 +39,121 @@ extern "C" {
#if defined(LAMMPS_BIGBIG)
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
#elif defined(LAMMPS_SMALLBIG)
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
#else
#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
struct _liblammpsplugin {
int abiversion;
int has_exceptions;
void *handle;
void (*open)(int, char **, MPI_Comm, void **);
void (*open_no_mpi)(int, char **, void **);
void *(*open)(int, char **, MPI_Comm, void **);
void *(*open_no_mpi)(int, char **, void **);
void *(*open_fortran)(int, char **, void **, int);
void (*close)(void *);
int (*version)(void *);
void (*mpi_init)();
void (*mpi_finalize)();
void (*kokkos_finalize)();
void (*python_finalize)();
void (*file)(void *, char *);
char *(*command)(void *, char *);
void (*commands_list)(void *, int, char **);
void (*commands_string)(void *, char *);
void (*free)(void *);
int (*extract_setting)(void *, char *);
void *(*extract_global)(void *, char *);
void (*extract_box)(void *, double *, double *,
double *, double *, double *, int *, int *);
void *(*extract_atom)(void *, char *);
void *(*extract_compute)(void *, char *, int, int);
void *(*extract_fix)(void *, char *, int, int, int, int);
void *(*extract_variable)(void *, char *, char *);
char *(*command)(void *, const char *);
void (*commands_list)(void *, int, const char **);
void (*commands_string)(void *, const char *);
double (*get_natoms)(void *);
double (*get_thermo)(void *, char *);
int (*get_natoms)(void *);
int (*set_variable)(void *, char *, char *);
void (*extract_box)(void *, double *, double *,
double *, double *, double *, int *, int *);
void (*reset_box)(void *, double *, double *, double, double, double);
void (*memory_usage)(void *, double *);
int (*get_mpi_comm)(void *);
int (*extract_setting)(void *, const char *);
int *(*extract_global_datatype)(void *, const char *);
void *(*extract_global)(void *, const char *);
void *(*extract_atom_datatype)(void *, const char *);
void *(*extract_atom)(void *, const char *);
void *(*extract_compute)(void *, const char *, int, int);
void *(*extract_fix)(void *, const char *, int, int, int, int);
void *(*extract_variable)(void *, const char *, char *);
int (*set_variable)(void *, char *, char *);
void (*gather_atoms)(void *, char *, int, int, void *);
void (*gather_atoms_concat)(void *, char *, int, int, void *);
void (*gather_atoms_subset)(void *, char *, int, int, int, int *, void *);
void (*scatter_atoms)(void *, char *, int, int, void *);
void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *);
void (*set_fix_external_callback)(void *, char *, FixExternalFnPtr, void*);
void (*gather_bonds)(void *, void *);
// lammps_create_atoms() takes tagint and imageint as args
// ifdef insures they are compatible with rest of LAMMPS
// caller must match to how LAMMPS library is built
int (*config_has_package)(char * package_name);
int (*config_package_count)();
int (*config_package_name)(int index, char * buffer, int max_size);
#ifndef LAMMPS_BIGBIG
void (*create_atoms)(void *, int, int *, int *, double *,
double *, int *, int);
#else
void (*create_atoms)(void *, int, int64_t *, int *, double *,
double *, int64_t *, int);
#endif
int (*find_pair_neighlist)(void *, const char *, int, int, int);
int (*find_fix_neighlist)(void *, const char *, int);
int (*find_compute_neighlist)(void *, char *, int);
int (*neighlist_num_elements)(void *, int);
void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
int (*version)(void *);
void (*get_os_info)(char *, int);
int (*config_has_mpi_support)();
int (*config_has_gzip_support)();
int (*config_has_png_support)();
int (*config_has_jpeg_support)();
int (*config_has_ffmpeg_support)();
int (*config_has_exceptions)();
int (*find_pair_neighlist)(void* ptr, char * style, int exact, int nsub, int request);
int (*find_fix_neighlist)(void* ptr, char * id, int request);
int (*find_compute_neighlist)(void* ptr, char * id, int request);
int (*neighlist_num_elements)(void* ptr, int idx);
void (*neighlist_element_neighbors)(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);
int (*config_has_package)(const char *);
int (*config_package_count)();
int (*config_package_name)(int, char *, int);
// lammps_create_atoms() takes tagint and imageint as args
// ifdef insures they are compatible with rest of LAMMPS
// caller must match to how LAMMPS library is built
int (*config_accelerator)(const char *, const char *, const char *);
int (*has_gpu_device)();
void (*get_gpu_device_info)(char *, int);
#ifdef LAMMPS_BIGBIG
void (*create_atoms)(void *, int, int64_t *, int *,
double *, double *, int64_t *, int);
#else
void (*create_atoms)(void *, int, int *, int *,
double *, double *, int *, int);
#endif
int (*has_style)(void *, const char *, const char *);
int (*style_count)(void *, const char *);
int (*style_name)(void *, const char *, int, char *, int);
int (*has_id)(void *, const char *, const char *);
int (*id_count)(void *, const char *);
int (*id_name)(void *, const char *, int, char *, int);
int (*plugin_count)();
int (*plugin_name)(int, char *, char *, int);
void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void*);
void (*fix_external_get_force)(void *, const char *);
void (*fix_external_set_energy_global)(void *, const char *, double);
void (*fix_external_set_energy_peratom)(void *, const char *, double *);
void (*fix_external_set_virial_global)(void *, const char *, double *);
void (*fix_external_set_virial_peratom)(void *, const char *, double **);
void (*fix_external_set_vector_length)(void *, const char *, int);
void (*fix_external_set_vector)(void *, const char *, int, double);
void (*free)(void *);
void (*is_running)(void *);
void (*force_timeout)(void *);
int (*has_error)(void *);
int (*get_last_error_message)(void *, char *, int);
@ -117,7 +163,7 @@ typedef struct _liblammpsplugin liblammpsplugin_t;
liblammpsplugin_t *liblammpsplugin_load(const char *);
int liblammpsplugin_release(liblammpsplugin_t *);
#undef LAMMPS
#ifdef __cplusplus
}

225
examples/COUPLE/plugin/log.simple.plugin.1
View File

@ -1,9 +1,12 @@
LAMMPS (18 Feb 2020)
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
LAMMPS (31 Aug 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
1 by 1 by 1 MPI processor grid
Created 256 atoms
create_atoms CPU = 0.000297844 secs
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
create_atoms CPU = 0.001 seconds
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
@ -14,108 +17,108 @@ Neighbor list info ...
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6218056 -5.0244179
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
Loop time of 0.00164276 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00239712 on 1 procs for 10 steps with 256 atoms
Performance: 2629719.113 tau/day, 6087.313 timesteps/s
93.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1802163.347 tau/day, 4171.674 timesteps/s
97.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014956 | 0.0014956 | 0.0014956 | 0.0 | 91.04
Pair | 0.0020572 | 0.0020572 | 0.0020572 | 0.0 | 85.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.045e-05 | 8.045e-05 | 8.045e-05 | 0.0 | 4.90
Output | 1.1399e-05 | 1.1399e-05 | 1.1399e-05 | 0.0 | 0.69
Modify | 3.7431e-05 | 3.7431e-05 | 3.7431e-05 | 0.0 | 2.28
Other | | 1.789e-05 | | | 1.09
Comm | 0.00018731 | 0.00018731 | 0.00018731 | 0.0 | 7.81
Output | 4.478e-05 | 4.478e-05 | 4.478e-05 | 0.0 | 1.87
Modify | 6.3637e-05 | 6.3637e-05 | 6.3637e-05 | 0.0 | 2.65
Other | | 4.419e-05 | | | 1.84
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9984 ave 9984 max 9984 min
Neighs: 9984.00 ave 9984 max 9984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9984
Ave neighs/atom = 39
Ave neighs/atom = 39.000000
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 10
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
Loop time of 0.00199768 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00329271 on 1 procs for 10 steps with 256 atoms
Performance: 2162504.180 tau/day, 5005.797 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1311987.619 tau/day, 3037.008 timesteps/s
96.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018518 | 0.0018518 | 0.0018518 | 0.0 | 92.70
Pair | 0.0029015 | 0.0029015 | 0.0029015 | 0.0 | 88.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.9768e-05 | 7.9768e-05 | 7.9768e-05 | 0.0 | 3.99
Output | 1.1433e-05 | 1.1433e-05 | 1.1433e-05 | 0.0 | 0.57
Modify | 3.6904e-05 | 3.6904e-05 | 3.6904e-05 | 0.0 | 1.85
Other | | 1.773e-05 | | | 0.89
Comm | 0.00021807 | 0.00021807 | 0.00021807 | 0.0 | 6.62
Output | 4.9163e-05 | 4.9163e-05 | 4.9163e-05 | 0.0 | 1.49
Modify | 7.0573e-05 | 7.0573e-05 | 7.0573e-05 | 0.0 | 2.14
Other | | 5.339e-05 | | | 1.62
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9952 ave 9952 max 9952 min
Neighs: 9952.00 ave 9952 max 9952 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9952
Ave neighs/atom = 38.875
Ave neighs/atom = 38.875000
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 20
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
Loop time of 0.000304321 on 1 procs for 1 steps with 256 atoms
Loop time of 0.000638039 on 1 procs for 1 steps with 256 atoms
Performance: 1419553.695 tau/day, 3286.004 timesteps/s
98.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 677074.599 tau/day, 1567.302 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00027815 | 0.00027815 | 0.00027815 | 0.0 | 91.40
Pair | 0.00042876 | 0.00042876 | 0.00042876 | 0.0 | 67.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.321e-06 | 8.321e-06 | 8.321e-06 | 0.0 | 2.73
Output | 1.0513e-05 | 1.0513e-05 | 1.0513e-05 | 0.0 | 3.45
Modify | 3.968e-06 | 3.968e-06 | 3.968e-06 | 0.0 | 1.30
Other | | 3.365e-06 | | | 1.11
Comm | 5.2872e-05 | 5.2872e-05 | 5.2872e-05 | 0.0 | 8.29
Output | 0.00012218 | 0.00012218 | 0.00012218 | 0.0 | 19.15
Modify | 1.3762e-05 | 1.3762e-05 | 1.3762e-05 | 0.0 | 2.16
Other | | 2.047e-05 | | | 3.21
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9705 ave 9705 max 9705 min
Neighs: 9705.00 ave 9705 max 9705 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9705
Ave neighs/atom = 37.9102
Ave neighs/atom = 37.910156
Neighbor list builds = 0
Dangerous builds not checked
Force on 1 atom via extract_atom: 26.9581
@ -124,136 +127,136 @@ Setting up Verlet run ...
Unit style : lj
Current step : 21
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
Loop time of 0.00196027 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00281277 on 1 procs for 10 steps with 256 atoms
Performance: 2203779.175 tau/day, 5101.341 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1535852.558 tau/day, 3555.214 timesteps/s
92.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018146 | 0.0018146 | 0.0018146 | 0.0 | 92.57
Pair | 0.0024599 | 0.0024599 | 0.0024599 | 0.0 | 87.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.0268e-05 | 8.0268e-05 | 8.0268e-05 | 0.0 | 4.09
Output | 1.0973e-05 | 1.0973e-05 | 1.0973e-05 | 0.0 | 0.56
Modify | 3.6913e-05 | 3.6913e-05 | 3.6913e-05 | 0.0 | 1.88
Other | | 1.756e-05 | | | 0.90
Comm | 0.00020234 | 0.00020234 | 0.00020234 | 0.0 | 7.19
Output | 3.6436e-05 | 3.6436e-05 | 3.6436e-05 | 0.0 | 1.30
Modify | 6.7542e-05 | 6.7542e-05 | 6.7542e-05 | 0.0 | 2.40
Other | | 4.655e-05 | | | 1.65
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9688 ave 9688 max 9688 min
Neighs: 9688.00 ave 9688 max 9688 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9688
Ave neighs/atom = 37.8438
Ave neighs/atom = 37.843750
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 31
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
Loop time of 0.00433063 on 1 procs for 20 steps with 256 atoms
Loop time of 0.00560916 on 1 procs for 20 steps with 256 atoms
Performance: 1995088.941 tau/day, 4618.261 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1540338.414 tau/day, 3565.598 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0035121 | 0.0035121 | 0.0035121 | 0.0 | 81.10
Neigh | 0.00050258 | 0.00050258 | 0.00050258 | 0.0 | 11.61
Comm | 0.00019444 | 0.00019444 | 0.00019444 | 0.0 | 4.49
Output | 1.2092e-05 | 1.2092e-05 | 1.2092e-05 | 0.0 | 0.28
Modify | 7.2917e-05 | 7.2917e-05 | 7.2917e-05 | 0.0 | 1.68
Other | | 3.647e-05 | | | 0.84
Pair | 0.0044403 | 0.0044403 | 0.0044403 | 0.0 | 79.16
Neigh | 0.00056186 | 0.00056186 | 0.00056186 | 0.0 | 10.02
Comm | 0.00036797 | 0.00036797 | 0.00036797 | 0.0 | 6.56
Output | 3.676e-05 | 3.676e-05 | 3.676e-05 | 0.0 | 0.66
Modify | 0.00011282 | 0.00011282 | 0.00011282 | 0.0 | 2.01
Other | | 8.943e-05 | | | 1.59
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1421 ave 1421 max 1421 min
Nghost: 1421.00 ave 1421 max 1421 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9700 ave 9700 max 9700 min
Neighs: 9700.00 ave 9700 max 9700 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9700
Ave neighs/atom = 37.8906
Ave neighs/atom = 37.890625
Neighbor list builds = 1
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 51
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
Loop time of 0.00196567 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00373815 on 1 procs for 10 steps with 256 atoms
Performance: 2197727.285 tau/day, 5087.332 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1155650.623 tau/day, 2675.117 timesteps/s
98.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018222 | 0.0018222 | 0.0018222 | 0.0 | 92.70
Pair | 0.0030908 | 0.0030908 | 0.0030908 | 0.0 | 82.68
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.8285e-05 | 7.8285e-05 | 7.8285e-05 | 0.0 | 3.98
Output | 1.0862e-05 | 1.0862e-05 | 1.0862e-05 | 0.0 | 0.55
Modify | 3.6719e-05 | 3.6719e-05 | 3.6719e-05 | 0.0 | 1.87
Other | | 1.764e-05 | | | 0.90
Comm | 0.00038189 | 0.00038189 | 0.00038189 | 0.0 | 10.22
Output | 4.1615e-05 | 4.1615e-05 | 4.1615e-05 | 0.0 | 1.11
Modify | 0.00013851 | 0.00013851 | 0.00013851 | 0.0 | 3.71
Other | | 8.533e-05 | | | 2.28
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1421 ave 1421 max 1421 min
Nghost: 1421.00 ave 1421 max 1421 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9700 ave 9700 max 9700 min
Neighs: 9700.00 ave 9700 max 9700 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9700
Ave neighs/atom = 37.8906
Ave neighs/atom = 37.890625
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 61
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
81 0.77743907 -5.7735004 0 -4.6118971 0.090822641
Loop time of 0.00430528 on 1 procs for 20 steps with 256 atoms
Loop time of 0.00612177 on 1 procs for 20 steps with 256 atoms
Performance: 2006838.581 tau/day, 4645.460 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1411356.519 tau/day, 3267.029 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0034931 | 0.0034931 | 0.0034931 | 0.0 | 81.13
Neigh | 0.00050437 | 0.00050437 | 0.00050437 | 0.0 | 11.72
Comm | 0.0001868 | 0.0001868 | 0.0001868 | 0.0 | 4.34
Output | 1.1699e-05 | 1.1699e-05 | 1.1699e-05 | 0.0 | 0.27
Modify | 7.3308e-05 | 7.3308e-05 | 7.3308e-05 | 0.0 | 1.70
Other | | 3.604e-05 | | | 0.84
Pair | 0.0047211 | 0.0047211 | 0.0047211 | 0.0 | 77.12
Neigh | 0.00083088 | 0.00083088 | 0.00083088 | 0.0 | 13.57
Comm | 0.00032716 | 0.00032716 | 0.00032716 | 0.0 | 5.34
Output | 3.9891e-05 | 3.9891e-05 | 3.9891e-05 | 0.0 | 0.65
Modify | 0.00010926 | 0.00010926 | 0.00010926 | 0.0 | 1.78
Other | | 9.346e-05 | | | 1.53
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1405 ave 1405 max 1405 min
Nghost: 1405.00 ave 1405 max 1405 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9701 ave 9701 max 9701 min
Neighs: 9701.00 ave 9701 max 9701 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9701
Ave neighs/atom = 37.8945
Ave neighs/atom = 37.894531
Neighbor list builds = 1
Dangerous builds not checked
Deleted 256 atoms, new total = 0
@ -261,34 +264,34 @@ Setting up Verlet run ...
Unit style : lj
Current step : 81
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
81 0.6239063 -5.5404291 0 -4.6082254 1.0394285
91 0.75393007 -5.7375259 0 -4.6110484 0.39357367
Loop time of 0.00195843 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00319065 on 1 procs for 10 steps with 256 atoms
Performance: 2205851.941 tau/day, 5106.139 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1353954.393 tau/day, 3134.154 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018143 | 0.0018143 | 0.0018143 | 0.0 | 92.64
Pair | 0.0027828 | 0.0027828 | 0.0027828 | 0.0 | 87.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.8608e-05 | 7.8608e-05 | 7.8608e-05 | 0.0 | 4.01
Output | 1.0786e-05 | 1.0786e-05 | 1.0786e-05 | 0.0 | 0.55
Modify | 3.7106e-05 | 3.7106e-05 | 3.7106e-05 | 0.0 | 1.89
Other | | 1.762e-05 | | | 0.90
Comm | 0.00023286 | 0.00023286 | 0.00023286 | 0.0 | 7.30
Output | 4.0459e-05 | 4.0459e-05 | 4.0459e-05 | 0.0 | 1.27
Modify | 7.3576e-05 | 7.3576e-05 | 7.3576e-05 | 0.0 | 2.31
Other | | 6.094e-05 | | | 1.91
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9705 ave 9705 max 9705 min
Neighs: 9705.00 ave 9705 max 9705 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9705
Ave neighs/atom = 37.9102
Ave neighs/atom = 37.910156
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:00

213
examples/COUPLE/plugin/log.simple.plugin.4
View File

@ -1,9 +1,12 @@
LAMMPS (18 Feb 2020)
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
LAMMPS (31 Aug 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
1 by 1 by 2 MPI processor grid
Created 256 atoms
create_atoms CPU = 0.000265157 secs
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
create_atoms CPU = 0.003 seconds
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
@ -14,7 +17,7 @@ Neighbor list info ...
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : lj
@ -24,30 +27,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6218056 -5.0244179
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
Loop time of 0.00115264 on 2 procs for 10 steps with 256 atoms
Loop time of 0.00330899 on 2 procs for 10 steps with 256 atoms
Performance: 3747912.946 tau/day, 8675.724 timesteps/s
94.5% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 1305535.501 tau/day, 3022.073 timesteps/s
75.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00074885 | 0.00075021 | 0.00075156 | 0.0 | 65.09
Pair | 0.0013522 | 0.0013813 | 0.0014104 | 0.1 | 41.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00031829 | 0.00031943 | 0.00032056 | 0.0 | 27.71
Output | 9.306e-06 | 2.6673e-05 | 4.4041e-05 | 0.0 | 2.31
Modify | 2.0684e-05 | 2.0891e-05 | 2.1098e-05 | 0.0 | 1.81
Other | | 3.544e-05 | | | 3.07
Comm | 0.00049139 | 0.00054241 | 0.00059342 | 0.0 | 16.39
Output | 3.6986e-05 | 0.00056588 | 0.0010948 | 0.0 | 17.10
Modify | 4.3909e-05 | 4.3924e-05 | 4.3939e-05 | 0.0 | 1.33
Other | | 0.0007755 | | | 23.44
Nlocal: 128 ave 128 max 128 min
Nlocal: 128.000 ave 128 max 128 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 1109 ave 1109 max 1109 min
Nghost: 1109.00 ave 1109 max 1109 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 4992 ave 4992 max 4992 min
Neighs: 4992.00 ave 4992 max 4992 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9984
Ave neighs/atom = 39
Ave neighs/atom = 39.000000
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
@ -58,30 +61,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
Loop time of 0.00120443 on 2 procs for 10 steps with 256 atoms
Loop time of 0.00648485 on 2 procs for 10 steps with 256 atoms
Performance: 3586761.860 tau/day, 8302.689 timesteps/s
95.5% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 666168.017 tau/day, 1542.056 timesteps/s
44.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00087798 | 0.00091359 | 0.0009492 | 0.0 | 75.85
Pair | 0.0022373 | 0.0024405 | 0.0026437 | 0.4 | 37.63
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016739 | 0.00020368 | 0.00023997 | 0.0 | 16.91
Output | 1.0124e-05 | 3.0513e-05 | 5.0901e-05 | 0.0 | 2.53
Modify | 1.89e-05 | 1.9812e-05 | 2.0725e-05 | 0.0 | 1.64
Other | | 3.683e-05 | | | 3.06
Comm | 0.0024446 | 0.0026464 | 0.0028481 | 0.4 | 40.81
Output | 3.9069e-05 | 0.00059734 | 0.0011556 | 0.0 | 9.21
Modify | 4.869e-05 | 4.912e-05 | 4.9551e-05 | 0.0 | 0.76
Other | | 0.0007515 | | | 11.59
Nlocal: 128 ave 134 max 122 min
Nlocal: 128.000 ave 134 max 122 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1109 ave 1115 max 1103 min
Nghost: 1109.00 ave 1115 max 1103 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4976 ave 5205 max 4747 min
Neighs: 4976.00 ave 5205 max 4747 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9952
Ave neighs/atom = 38.875
Ave neighs/atom = 38.875000
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
@ -92,34 +95,34 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
Loop time of 0.000206062 on 2 procs for 1 steps with 256 atoms
Loop time of 0.00128072 on 2 procs for 1 steps with 256 atoms
Performance: 2096456.406 tau/day, 4852.908 timesteps/s
94.1% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 337310.921 tau/day, 780.812 timesteps/s
60.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00012947 | 0.00013524 | 0.00014101 | 0.0 | 65.63
Pair | 0.00047351 | 0.00049064 | 0.00050777 | 0.0 | 38.31
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.858e-05 | 2.4113e-05 | 2.9647e-05 | 0.0 | 11.70
Output | 8.699e-06 | 2.4204e-05 | 3.9708e-05 | 0.0 | 11.75
Modify | 2.34e-06 | 2.3705e-06 | 2.401e-06 | 0.0 | 1.15
Other | | 2.013e-05 | | | 9.77
Comm | 7.6767e-05 | 9.3655e-05 | 0.00011054 | 0.0 | 7.31
Output | 5.4217e-05 | 0.00026297 | 0.00047172 | 0.0 | 20.53
Modify | 1.1554e-05 | 1.2026e-05 | 1.2498e-05 | 0.0 | 0.94
Other | | 0.0004214 | | | 32.91
Nlocal: 128 ave 135 max 121 min
Nlocal: 128.000 ave 135 max 121 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1109 ave 1116 max 1102 min
Nghost: 1109.00 ave 1116 max 1102 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4852.5 ave 5106 max 4599 min
Neighs: 4852.50 ave 5106 max 4599 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9705
Ave neighs/atom = 37.9102
Force on 1 atom via extract_atom: -18.109
Force on 1 atom via extract_variable: -18.109
Ave neighs/atom = 37.910156
Neighbor list builds = 0
Dangerous builds not checked
Force on 1 atom via extract_atom: -18.109
Force on 1 atom via extract_variable: -18.109
Force on 1 atom via extract_atom: 26.9581
Force on 1 atom via extract_variable: 26.9581
Setting up Verlet run ...
@ -130,30 +133,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
Loop time of 0.00119048 on 2 procs for 10 steps with 256 atoms
Loop time of 0.00784933 on 2 procs for 10 steps with 256 atoms
Performance: 3628802.105 tau/day, 8400.005 timesteps/s
98.0% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 550365.761 tau/day, 1273.995 timesteps/s
59.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00085276 | 0.00089699 | 0.00094123 | 0.0 | 75.35
Pair | 0.0019235 | 0.0033403 | 0.0047572 | 2.5 | 42.56
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016896 | 0.00021444 | 0.00025992 | 0.0 | 18.01
Output | 9.413e-06 | 2.5939e-05 | 4.2465e-05 | 0.0 | 2.18
Modify | 1.8977e-05 | 2.0009e-05 | 2.1042e-05 | 0.0 | 1.68
Other | | 3.31e-05 | | | 2.78
Comm | 0.0016948 | 0.003118 | 0.0045411 | 2.5 | 39.72
Output | 3.6445e-05 | 0.00064636 | 0.0012563 | 0.0 | 8.23
Modify | 6.2842e-05 | 6.3209e-05 | 6.3577e-05 | 0.0 | 0.81
Other | | 0.0006814 | | | 8.68
Nlocal: 128 ave 135 max 121 min
Nlocal: 128.000 ave 135 max 121 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1109 ave 1116 max 1102 min
Nghost: 1109.00 ave 1116 max 1102 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4844 ave 5096 max 4592 min
Neighs: 4844.00 ave 5096 max 4592 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9688
Ave neighs/atom = 37.8438
Ave neighs/atom = 37.843750
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
@ -164,30 +167,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
Loop time of 0.00252603 on 2 procs for 20 steps with 256 atoms
Loop time of 0.00696051 on 2 procs for 20 steps with 256 atoms
Performance: 3420382.192 tau/day, 7917.551 timesteps/s
99.2% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 1241287.730 tau/day, 2873.351 timesteps/s
79.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016245 | 0.0017014 | 0.0017784 | 0.2 | 67.36
Neigh | 0.00025359 | 0.0002563 | 0.00025901 | 0.0 | 10.15
Comm | 0.00036863 | 0.00045124 | 0.00053385 | 0.0 | 17.86
Output | 9.839e-06 | 2.8031e-05 | 4.6223e-05 | 0.0 | 1.11
Modify | 3.7027e-05 | 3.9545e-05 | 4.2063e-05 | 0.0 | 1.57
Other | | 4.948e-05 | | | 1.96
Pair | 0.0028267 | 0.0036088 | 0.004391 | 1.3 | 51.85
Neigh | 0.00040272 | 0.00040989 | 0.00041707 | 0.0 | 5.89
Comm | 0.00081061 | 0.0015825 | 0.0023544 | 1.9 | 22.74
Output | 3.6006e-05 | 0.00062106 | 0.0012061 | 0.0 | 8.92
Modify | 6.8937e-05 | 7.1149e-05 | 7.336e-05 | 0.0 | 1.02
Other | | 0.0006671 | | | 9.58
Nlocal: 128 ave 132 max 124 min
Nlocal: 128.000 ave 132 max 124 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1100 ave 1101 max 1099 min
Nghost: 1100.00 ave 1101 max 1099 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4850 ave 4953 max 4747 min
Neighs: 4850.00 ave 4953 max 4747 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9700
Ave neighs/atom = 37.8906
Ave neighs/atom = 37.890625
Neighbor list builds = 1
Dangerous builds not checked
Setting up Verlet run ...
@ -198,30 +201,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
Loop time of 0.00115444 on 2 procs for 10 steps with 256 atoms
Loop time of 0.00155862 on 2 procs for 10 steps with 256 atoms
Performance: 3742065.976 tau/day, 8662.190 timesteps/s
96.5% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 2771678.197 tau/day, 6415.922 timesteps/s
95.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00087346 | 0.00089311 | 0.00091275 | 0.0 | 77.36
Pair | 0.0012369 | 0.001266 | 0.001295 | 0.1 | 81.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016192 | 0.0001823 | 0.00020269 | 0.0 | 15.79
Output | 9.49e-06 | 2.6234e-05 | 4.2978e-05 | 0.0 | 2.27
Modify | 1.9095e-05 | 1.9843e-05 | 2.0591e-05 | 0.0 | 1.72
Other | | 3.296e-05 | | | 2.85
Comm | 0.00019462 | 0.00022315 | 0.00025169 | 0.0 | 14.32
Output | 2.0217e-05 | 2.1945e-05 | 2.3673e-05 | 0.0 | 1.41
Modify | 2.562e-05 | 2.5759e-05 | 2.5898e-05 | 0.0 | 1.65
Other | | 2.181e-05 | | | 1.40
Nlocal: 128 ave 132 max 124 min
Nlocal: 128.000 ave 132 max 124 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1100 ave 1101 max 1099 min
Nghost: 1100.00 ave 1101 max 1099 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4850 ave 4953 max 4747 min
Neighs: 4850.00 ave 4953 max 4747 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9700
Ave neighs/atom = 37.8906
Ave neighs/atom = 37.890625
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
@ -232,30 +235,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
81 0.77743907 -5.7735004 0 -4.6118971 0.090822641
Loop time of 0.00244325 on 2 procs for 20 steps with 256 atoms
Loop time of 0.00351607 on 2 procs for 20 steps with 256 atoms
Performance: 3536279.919 tau/day, 8185.833 timesteps/s
99.0% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 2457288.612 tau/day, 5688.168 timesteps/s
97.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016916 | 0.0017038 | 0.001716 | 0.0 | 69.73
Neigh | 0.00025229 | 0.00025512 | 0.00025795 | 0.0 | 10.44
Comm | 0.00035772 | 0.00036918 | 0.00038064 | 0.0 | 15.11
Output | 1.0858e-05 | 2.7875e-05 | 4.4891e-05 | 0.0 | 1.14
Modify | 3.817e-05 | 3.9325e-05 | 4.048e-05 | 0.0 | 1.61
Other | | 4.796e-05 | | | 1.96
Pair | 0.0023896 | 0.0024147 | 0.0024397 | 0.1 | 68.67
Neigh | 0.00037331 | 0.00040456 | 0.0004358 | 0.0 | 11.51
Comm | 0.00050571 | 0.00051343 | 0.00052116 | 0.0 | 14.60
Output | 2.6424e-05 | 5.6547e-05 | 8.667e-05 | 0.0 | 1.61
Modify | 5.0287e-05 | 5.1071e-05 | 5.1856e-05 | 0.0 | 1.45
Other | | 7.58e-05 | | | 2.16
Nlocal: 128 ave 128 max 128 min
Nlocal: 128.000 ave 128 max 128 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 1088.5 ave 1092 max 1085 min
Nghost: 1088.50 ave 1092 max 1085 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4850.5 ave 4851 max 4850 min
Neighs: 4850.50 ave 4851 max 4850 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9701
Ave neighs/atom = 37.8945
Ave neighs/atom = 37.894531
Neighbor list builds = 1
Dangerous builds not checked
Deleted 256 atoms, new total = 0
@ -267,30 +270,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
81 0.6239063 -5.5404291 0 -4.6082254 1.0394285
91 0.75393007 -5.7375259 0 -4.6110484 0.39357367
Loop time of 0.00118092 on 2 procs for 10 steps with 256 atoms
Loop time of 0.0109747 on 2 procs for 10 steps with 256 atoms
Performance: 3658158.625 tau/day, 8467.960 timesteps/s
98.6% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 393631.731 tau/day, 911.185 timesteps/s
53.5% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0008476 | 0.00089265 | 0.00093771 | 0.0 | 75.59
Pair | 0.0012057 | 0.0012732 | 0.0013407 | 0.2 | 11.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016335 | 0.00020946 | 0.00025557 | 0.0 | 17.74
Output | 8.87e-06 | 2.5733e-05 | 4.2595e-05 | 0.0 | 2.18
Modify | 1.8755e-05 | 1.9814e-05 | 2.0872e-05 | 0.0 | 1.68
Other | | 3.326e-05 | | | 2.82
Comm | 0.00018882 | 0.00025686 | 0.00032489 | 0.0 | 2.34
Output | 2.1943e-05 | 0.0047067 | 0.0093915 | 6.8 | 42.89
Modify | 2.4614e-05 | 2.5439e-05 | 2.6264e-05 | 0.0 | 0.23
Other | | 0.004712 | | | 42.94
Nlocal: 128 ave 135 max 121 min
Nlocal: 128.000 ave 135 max 121 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1109 ave 1116 max 1102 min
Nghost: 1109.00 ave 1116 max 1102 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4852.5 ave 5106 max 4599 min
Neighs: 4852.50 ave 5106 max 4599 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9705
Ave neighs/atom = 37.9102
Ave neighs/atom = 37.910156
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:00

7
examples/COUPLE/plugin/simple.c
View File

@ -87,7 +87,7 @@ int main(int narg, char **arg)
MPI_Abort(MPI_COMM_WORLD,1);
}
}
if (lammps == 1) plugin->open(0,NULL,comm_lammps,&lmp);
if (lammps == 1) lmp = plugin->open(0,NULL,comm_lammps,NULL);
while (1) {
if (me == 0) {
@ -139,7 +139,7 @@ int main(int narg, char **arg)
cmds[0] = (char *)"run 10";
cmds[1] = (char *)"run 20";
if (lammps == 1) plugin->commands_list(lmp,2,cmds);
if (lammps == 1) plugin->commands_list(lmp,2,(const char **)cmds);
/* delete all atoms
create_atoms() to create new ones with old coords, vels
@ -164,12 +164,13 @@ int main(int narg, char **arg)
if (lammps == 1) {
plugin->close(lmp);
MPI_Barrier(comm_lammps);
MPI_Comm_free(&comm_lammps);
liblammpsplugin_release(plugin);
}
/* close down MPI */
if (lammps == 1) MPI_Comm_free(&comm_lammps);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
}

0
examples/MC/README → examples/MC-LOOP/README
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0
examples/MC/in.mc → examples/MC-LOOP/in.mc
View File

0
examples/MC/log.13Oct16.mc.g++.1 → examples/MC-LOOP/log.13Oct16.mc.g++.1
View File

2
examples/PACKAGES/charge_regulation/in.chreg-polymer
View File

@ -8,7 +8,7 @@ bond_style harmonic
bond_coeff 1 100 1.122462 # K R0
velocity all create 1.0 8008 loop geom
pair_style lj/cut/coul/long 1.122462 20
pair_style lj/cut/coul/long/soft 2 0.5 10.0 1.122462 20
pair_coeff * * 1.0 1.0 1.122462 # charges
kspace_style pppm 1.0e-3
pair_modify shift yes

5
examples/README
View File

@ -75,7 +75,6 @@ eim: NaCl using the EIM potential
ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
gcmc: Grand Canonical MC with fix gcmc, Widom insertion with fix widom
gjf: use of fix langevin Gronbech-Jensen/Farago option
granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics
@ -83,6 +82,7 @@ hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: use of LATTE density-functional tight-binding quantum code
mc: MC package models: GCMC, Widom, fix mol/swap
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
message: client/server coupling of 2 codes
@ -114,6 +114,7 @@ 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
threebody: regression test input for a variety of threebody potentials
ttm: two-temeperature model examples
vashishta: models using the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command
wall: use of reflective walls with different stochastic models
@ -166,7 +167,7 @@ The KAPPA directory has example scripts for computing the thermal
conductivity (kappa) of a LJ liquid using 5 different methods. See
the KAPPA/README file for more info.
The MC directory has an example script for using LAMMPS as an
The MC-LOOP directory has an example script for using LAMMPS as an
energy-evaluation engine in a iterative Monte Carlo energy-relaxation
loop.

0
examples/gcmc/CO2.txt → examples/mc/CO2.txt
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0
examples/gcmc/H2O.txt → examples/mc/H2O.txt
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11733
examples/mc/data.bead Normal file
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File diff suppressed because it is too large Load Diff

0
examples/gcmc/data.spce → examples/mc/data.spce
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0
examples/gcmc/data.widom.lj → examples/mc/data.widom.lj
View File

0
examples/gcmc/in.gcmc.co2 → examples/mc/in.gcmc.co2
View File

0
examples/gcmc/in.gcmc.h2o → examples/mc/in.gcmc.h2o
View File

0
examples/gcmc/in.gcmc.lj → examples/mc/in.gcmc.lj
View File

44
examples/mc/in.mixed Normal file
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@ -0,0 +1,44 @@
# test script for fix mol/swap
# initial system is 50/50 chains of type 1 and type 2
# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
# system will stay in equilibrium as a mix of both chain types
# fix mol/swap helps this happen quickly
# see the last 2 columns of thermo output for counts of 2 chain types
units lj
atom_style angle
neighbor 0.36 bin
neigh_modify delay 0
pair_style lj/cut 1.1224620483
bond_style fene
angle_style cosine
special_bonds lj 0.0 1.0 1.0
read_data data.bead
pair_coeff * * 1.0 1.0 1.1224620483
pair_coeff 1 2 1.02 1.0 1.1224620483
bond_coeff 1 30.0 1.5 1.0 1.0
angle_coeff 1 1.500
pair_modify shift yes
variable vt1 atom type==1
variable vt2 atom type==2
group g1 dynamic all var vt1 every 100
group g2 dynamic all var vt2 every 100
variable count1 equal count(g1)
variable count2 equal count(g2)
timestep 0.010
fix 1 all langevin 1.0 1.0 100.0 702547
fix 2 all nve
fix 3 all mol/swap 100 1 1 2 482794 1.0
compute p all pressure thermo_temp
thermo 1000
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
run 50000

44
examples/mc/in.pure Normal file
View File

@ -0,0 +1,44 @@
# test script for fix mol/swap
# initial system is 50/50 chains of type 1 and type 2
# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
# system will go to equilibrium as mostly one type or the other
# fix mol/swap helps this happen quickly
# see the last 2 columns of thermo output for counts of 2 chain types
units lj
atom_style angle
neighbor 0.36 bin
neigh_modify delay 0
pair_style lj/cut 1.1224620483
bond_style fene
angle_style cosine
special_bonds lj 0.0 1.0 1.0
read_data data.bead
pair_coeff * * 1.0 1.0 1.1224620483
pair_coeff 1 2 1.1 1.0 1.1224620483
bond_coeff 1 30.0 1.5 1.0 1.0
angle_coeff 1 1.500
pair_modify shift yes
variable vt1 atom type==1
variable vt2 atom type==2
group g1 dynamic all var vt1 every 100
group g2 dynamic all var vt2 every 100
variable count1 equal count(g1)
variable count2 equal count(g2)
timestep 0.010
fix 1 all langevin 1.0 1.0 100.0 702547
fix 2 all nve
fix 3 all mol/swap 100 1 1 2 482794 1.0
compute p all pressure thermo_temp
thermo 1000
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
run 50000

0
examples/gcmc/in.widom.lj → examples/mc/in.widom.lj
View File

0
examples/gcmc/in.widom.spce → examples/mc/in.widom.spce
View File

164
examples/mc/log.13Oct21.mixed.g++.4 Normal file
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@ -0,0 +1,164 @@
LAMMPS (29 Sep 2021)
# test script for fix mol/swap
# initial system is 50/50 chains of type 1 and type 2
# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
# system will stay in equilibrium as a mix of both chain types
# fix mol/swap helps this happen quickly
# see the last 2 columns of thermo output for counts of 2 chain types
units lj
atom_style angle
neighbor 0.36 bin
neigh_modify delay 0
pair_style lj/cut 1.1224620483
bond_style fene
angle_style cosine
special_bonds lj 0.0 1.0 1.0
read_data data.bead
Reading data file ...
orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
1 by 2 by 2 MPI processor grid
reading atoms ...
4000 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3900 bonds
reading angles ...
3800 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.028 seconds
pair_coeff * * 1.0 1.0 1.1224620483
pair_coeff 1 2 1.02 1.0 1.1224620483
bond_coeff 1 30.0 1.5 1.0 1.0
angle_coeff 1 1.500
pair_modify shift yes
variable vt1 atom type==1
variable vt2 atom type==2
group g1 dynamic all var vt1 every 100
dynamic group g1 defined
group g2 dynamic all var vt2 every 100
dynamic group g2 defined
variable count1 equal count(g1)
variable count2 equal count(g2)
timestep 0.010
fix 1 all langevin 1.0 1.0 100.0 702547
fix 2 all nve
fix 3 all mol/swap 100 1 1 2 482794 1.0
compute p all pressure thermo_temp
thermo 1000
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.482462
ghost atom cutoff = 1.482462
binsize = 0.74123102, bins = 23 23 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
0 0 21.451627 5.079399 0 0 2000 2000
1000 0.49011138 21.59359 4.2337989 10 10 2000 2000
2000 0.55288866 21.724374 4.4596786 20 20 2080 1920
3000 0.59299724 21.844178 4.6112243 30 29 2280 1720
4000 0.64746348 21.964318 4.9463669 40 39 2280 1720
5000 0.67853936 22.053147 5.1950218 50 48 2320 1680
6000 0.70751144 22.147453 5.0636869 60 58 2240 1760
7000 0.73570064 22.233705 5.4872622 70 68 2160 1840
8000 0.7677554 22.312938 5.4283736 80 77 2360 1640
9000 0.78493237 22.383155 5.8547233 90 87 2440 1560
10000 0.80634514 22.449402 5.8785731 100 96 2400 1600
11000 0.82563194 22.475286 5.8193738 110 104 2400 1600
12000 0.81684024 22.527492 6.0323967 120 114 2320 1680
13000 0.84497155 22.567888 6.0488755 130 122 2240 1760
14000 0.85452242 22.606908 6.1983634 140 132 2080 1920
15000 0.88109242 22.654336 6.1408279 150 141 1960 2040
16000 0.88925915 22.707597 6.1560975 160 150 2000 2000
17000 0.91598439 22.762791 6.1071728 170 160 2000 2000
18000 0.92453211 22.778304 6.3330693 180 170 2240 1760
19000 0.92839551 22.797316 6.2917909 190 180 2000 2000
20000 0.93054033 22.819289 6.091701 200 189 2200 1800
21000 0.93955351 22.844135 6.5833013 210 198 2000 2000
22000 0.94454858 22.856272 6.5661753 220 207 2200 1800
23000 0.95446407 22.878735 6.5957294 230 216 2160 1840
24000 0.94748257 22.894539 6.6187447 240 226 1920 2080
25000 0.95732202 22.912292 6.4795471 250 236 1680 2320
26000 0.96970172 22.908988 6.537366 260 245 1720 2280
27000 0.96032166 22.924899 6.6238248 270 255 1960 2040
28000 0.96197769 22.9358 6.8926097 280 264 1920 2080
29000 0.98745595 22.964694 6.5839025 290 271 2040 1960
30000 0.99264869 22.947884 6.3893499 300 280 1920 2080
31000 0.96953069 22.957927 6.6616047 310 289 1800 2200
32000 0.99955117 22.963979 6.5958456 320 298 1680 2320
33000 0.97090103 22.969029 6.9087296 330 307 1800 2200
34000 0.99818457 22.988477 6.6471994 340 316 1920 2080
35000 0.9965288 22.992883 6.9691785 350 325 2040 1960
36000 0.99533174 22.983774 6.6585089 360 334 2000 2000
37000 0.98819278 22.995387 6.618802 370 344 2080 1920
38000 0.99598576 22.991892 6.7536669 380 354 2080 1920
39000 0.99312702 22.989239 6.4028165 390 364 2080 1920
40000 1.0035821 23.001944 6.9307671 400 374 1920 2080
41000 0.99914733 23.00134 6.6251677 410 383 1880 2120
42000 0.98054536 22.981781 6.5918554 420 393 1880 2120
43000 0.99413829 23.008 6.7390795 430 403 1720 2280
44000 0.98867961 23.00521 6.8505543 440 412 1600 2400
45000 0.99626811 23.019995 6.827741 450 421 1640 2360
46000 1.0186043 23.020759 6.6195562 460 430 1680 2320
47000 1.0121335 23.019271 6.6022102 470 439 1800 2200
48000 0.99883756 23.013973 6.5255522 480 448 1920 2080
49000 0.99425223 23.022708 6.609746 490 458 2240 1760
50000 0.99505489 23.012641 6.4592863 500 468 2240 1760
Loop time of 19.4175 on 4 procs for 50000 steps with 4000 atoms
Performance: 2224796.830 tau/day, 2574.996 timesteps/s
95.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5467 | 2.6684 | 2.7896 | 6.3 | 13.74
Bond | 2.3037 | 2.4117 | 2.5085 | 5.3 | 12.42
Neigh | 7.3597 | 7.3633 | 7.3673 | 0.1 | 37.92
Comm | 3.0482 | 3.2694 | 3.4997 | 10.2 | 16.84
Output | 0.0014609 | 0.0017069 | 0.0021793 | 0.7 | 0.01
Modify | 2.9624 | 3.0581 | 3.1424 | 4.7 | 15.75
Other | | 0.6447 | | | 3.32
Nlocal: 1000.00 ave 1013 max 986 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 1186.25 ave 1198 max 1178 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 4927.00 ave 5028 max 4790 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 19708
Ave neighs/atom = 4.9270000
Ave special neighs/atom = 5.7000000
Neighbor list builds = 10721
Dangerous builds = 0
Total wall time: 0:00:19

164
examples/mc/log.13Oct21.pure.g++.4 Normal file
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@ -0,0 +1,164 @@
LAMMPS (29 Sep 2021)
# test script for fix mol/swap
# initial system is 50/50 chains of type 1 and type 2
# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
# system will go to equilibrium as mostly one type or the other
# fix mol/swap helps this happen quickly
# see the last 2 columns of thermo output for counts of 2 chain types
units lj
atom_style angle
neighbor 0.36 bin
neigh_modify delay 0
pair_style lj/cut 1.1224620483
bond_style fene
angle_style cosine
special_bonds lj 0.0 1.0 1.0
read_data data.bead
Reading data file ...
orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
1 by 2 by 2 MPI processor grid
reading atoms ...
4000 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3900 bonds
reading angles ...
3800 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.034 seconds
pair_coeff * * 1.0 1.0 1.1224620483
pair_coeff 1 2 1.1 1.0 1.1224620483
bond_coeff 1 30.0 1.5 1.0 1.0
angle_coeff 1 1.500
pair_modify shift yes
variable vt1 atom type==1
variable vt2 atom type==2
group g1 dynamic all var vt1 every 100
dynamic group g1 defined
group g2 dynamic all var vt2 every 100
dynamic group g2 defined
variable count1 equal count(g1)
variable count2 equal count(g2)
timestep 0.010
fix 1 all langevin 1.0 1.0 100.0 702547
fix 2 all nve
fix 3 all mol/swap 100 1 1 2 482794 1.0
compute p all pressure thermo_temp
thermo 1000
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.482462
ghost atom cutoff = 1.482462
binsize = 0.74123102, bins = 23 23 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
0 0 21.4699 5.230121 0 0 2000 2000
1000 0.50228459 21.61044 4.3659303 10 9 1960 2040
2000 0.55721903 21.75955 4.5695439 20 17 1960 2040
3000 0.61139287 21.892943 4.6514755 30 26 2240 1760
4000 0.65767189 22.002303 5.1854503 40 33 2280 1720
5000 0.69383416 22.110271 5.3803498 50 41 2280 1720
6000 0.72692038 22.205887 5.1756569 60 49 2280 1720
7000 0.77151336 22.306777 5.5743555 70 56 2240 1760
8000 0.78606858 22.37036 5.7745208 80 64 2560 1440
9000 0.79363653 22.420931 5.7369418 90 71 2680 1320
10000 0.82352629 22.488759 6.0238896 100 76 2720 1280
11000 0.83867685 22.534887 6.1263771 110 82 2800 1200
12000 0.85335127 22.590281 6.1499954 120 86 2800 1200
13000 0.86430985 22.632068 6.1654016 130 89 2760 1240
14000 0.88057592 22.680253 6.2162735 140 94 2800 1200
15000 0.89326694 22.719731 6.4789839 150 97 2760 1240
16000 0.90667644 22.737367 6.214481 160 101 2760 1240
17000 0.91190336 22.758572 6.2293336 170 105 2600 1400
18000 0.93182455 22.782019 6.2865382 180 111 2680 1320
19000 0.93002139 22.797048 6.5579988 190 117 2600 1400
20000 0.92396243 22.796108 6.6207461 200 122 2800 1200
21000 0.92949808 22.802813 6.3753268 210 125 2920 1080
22000 0.93415719 22.807112 6.4696121 220 130 3040 960
23000 0.9214833 22.82116 6.4146288 230 131 3080 920
24000 0.95693685 22.839738 6.4035728 240 135 2920 1080
25000 0.95421851 22.865199 6.4510751 250 138 2880 1120
26000 0.95476555 22.878082 6.4652888 260 145 3000 1000
27000 0.95773535 22.880671 6.757952 270 149 3000 1000
28000 0.95405332 22.896053 6.7425175 280 155 3080 920
29000 0.95955713 22.904144 6.6672832 290 161 3240 760
30000 0.95521498 22.886699 6.6197941 300 164 3360 640
31000 0.96431176 22.91094 6.6373887 310 168 3440 560
32000 0.96592495 22.903679 6.4245884 320 172 3520 480
33000 0.96457971 22.922681 6.6987987 330 175 3480 520
34000 0.96541889 22.92116 6.5992755 340 178 3600 400
35000 0.96892691 22.923361 6.7973298 350 178 3600 400
36000 0.97267726 22.923431 6.6577403 360 179 3640 360
37000 0.97514714 22.939979 6.4028068 370 183 3640 360
38000 0.98638599 22.952022 6.6518868 380 183 3640 360
39000 0.97864891 22.962534 6.3906837 390 184 3680 320
40000 0.9933016 22.975785 6.6819613 400 185 3720 280
41000 0.9861477 22.977271 6.6747347 410 187 3800 200
42000 0.98157369 22.963129 6.830028 420 187 3800 200
43000 0.98202452 22.966947 6.5257905 430 187 3800 200
44000 0.99540503 22.971262 6.5546513 440 187 3800 200
45000 0.98433653 22.978028 6.4316725 450 189 3800 200
46000 0.97912775 22.981328 6.9139851 460 189 3800 200
47000 0.9791927 22.981131 6.6417971 470 190 3840 160
48000 0.99601024 22.998536 6.6756953 480 191 3880 120
49000 0.99589958 22.998489 6.9262843 490 191 3880 120
50000 0.99294715 23.00399 6.6976013 500 192 3920 80
Loop time of 19.5161 on 4 procs for 50000 steps with 4000 atoms
Performance: 2213556.537 tau/day, 2561.987 timesteps/s
95.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6256 | 2.7183 | 2.8265 | 5.2 | 13.93
Bond | 2.3363 | 2.4406 | 2.5197 | 4.8 | 12.51
Neigh | 7.382 | 7.3884 | 7.3936 | 0.2 | 37.86
Comm | 3.014 | 3.2136 | 3.3994 | 9.4 | 16.47
Output | 0.0014574 | 0.0017086 | 0.0020613 | 0.5 | 0.01
Modify | 3.0282 | 3.1295 | 3.2034 | 4.1 | 16.04
Other | | 0.624 | | | 3.20
Nlocal: 1000.00 ave 1011 max 993 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 1187.25 ave 1202 max 1179 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 4939.25 ave 5067 max 4850 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 19757
Ave neighs/atom = 4.9392500
Ave special neighs/atom = 5.7000000
Neighbor list builds = 10714
Dangerous builds = 0
Total wall time: 0:00:19

0
examples/gcmc/log.27Nov18.gcmc.h2o.g++.1 → examples/mc/log.27Nov18.gcmc.h2o.g++.1
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0
examples/gcmc/log.27Nov18.gcmc.lj.g++.1 → examples/mc/log.27Nov18.gcmc.lj.g++.1
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0
examples/gcmc/log.27Nov18.gcmc.lj.g++.4 → examples/mc/log.27Nov18.gcmc.lj.g++.4
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0
examples/gcmc/log.30Jun20.widom.lj.g++.1 → examples/mc/log.30Jun20.widom.lj.g++.1
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0
examples/gcmc/log.30Jun20.widom.lj.g++.4 → examples/mc/log.30Jun20.widom.lj.g++.4
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0
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0
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33
examples/plugins/CMakeLists.txt
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@ -14,6 +14,15 @@ endif()
project(plugins VERSION 1.0 LANGUAGES CXX)
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# NOTE: the next line should be commented out when used outside of the LAMMPS package
get_filename_component(LAMMPS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../../src ABSOLUTE)
set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR} CACHE PATH "Location of LAMMPS headers")
@ -32,15 +41,10 @@ set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Need -restrict with Intel compilers
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
# bail out on windows
if(CMAKE_SYSTEM_NAME STREQUAL Windows)
message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows")
endif()
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR})
include(CheckIncludeFileCXX)
include(LAMMPSInterfaceCXX)
@ -62,12 +66,21 @@ add_library(zero2plugin MODULE zero2plugin.cpp pair_zero2.cpp bond_zero2.cpp
angle_zero2.cpp dihedral_zero2.cpp improper_zero2.cpp)
target_link_libraries(zero2plugin PRIVATE lammps)
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES
PREFIX ""
LINK_FLAGS "-rdynamic")
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES PREFIX "")
# MacOS seems to need this
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin
PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin
PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
if(CMAKE_CROSSCOMPILING)
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin
PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
else()
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES
LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
LINK_FLAGS "-rdynamic")
endif()

4
examples/plugins/LAMMPSInterfaceCXX.cmake
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@ -23,7 +23,9 @@ endfunction(validate_option)
# LAMMPS C++ interface. We only need the header related parts.
add_library(lammps INTERFACE)
target_include_directories(lammps INTERFACE ${LAMMPS_HEADER_DIR})
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
endif()
################################################################################
# MPI configuration
if(NOT CMAKE_CROSSCOMPILING)

1
examples/reaxff/water/acks2_ff.water Symbolic link
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@ -0,0 +1 @@
../../../potentials/acks2_ff.water

3016
examples/reaxff/water/data.water Normal file
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File diff suppressed because it is too large Load Diff

29
examples/reaxff/water/in.water.acks2 Normal file
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@ -0,0 +1,29 @@
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20

31
examples/reaxff/water/in.water.acks2.field Normal file
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@ -0,0 +1,31 @@
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20

29
examples/reaxff/water/in.water.qeq Normal file
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@ -0,0 +1,29 @@
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20

31
examples/reaxff/water/in.water.qeq.field Normal file
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@ -0,0 +1,31 @@
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20

129
examples/reaxff/water/log.13Oct21.reaxff.water-acks2-field.g++.1 Normal file
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@ -0,0 +1,129 @@
LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
1 by 1 by 1 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 361.2 | 361.2 | 361.2 Mbytes
Step Temp Press Density Volume
0 300 -20762.954 0.99996859 29916.212
10 396.27588 -18423.747 1.0000143 29914.844
20 518.59361 -10010.691 1.0000209 29914.647
Loop time of 29.8896 on 1 procs for 20 steps with 3000 atoms
Performance: 0.029 ns/day, 830.268 hours/ns, 0.669 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.611 | 11.611 | 11.611 | 0.0 | 38.85
Neigh | 0.6729 | 0.6729 | 0.6729 | 0.0 | 2.25
Comm | 0.0020791 | 0.0020791 | 0.0020791 | 0.0 | 0.01
Output | 0.00015777 | 0.00015777 | 0.00015777 | 0.0 | 0.00
Modify | 17.602 | 17.602 | 17.602 | 0.0 | 58.89
Other | | 0.001149 | | | 0.00
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5438.00 ave 5438 max 5438 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 787357.0 ave 787357 max 787357 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 787357
Ave neighs/atom = 262.45233
Neighbor list builds = 7
Dangerous builds = 0
Total wall time: 0:00:32

129
examples/reaxff/water/log.13Oct21.reaxff.water-acks2-field.g++.4 Normal file
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@ -0,0 +1,129 @@
LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.011 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
2 by 1 by 2 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 198.5 | 199.3 | 199.9 Mbytes
Step Temp Press Density Volume
0 300 -20761.724 0.99996859 29916.212
10 396.27588 -18420.441 1.0000144 29914.843
20 518.59146 -10012.622 1.0000207 29914.652
Loop time of 11.3556 on 4 procs for 20 steps with 3000 atoms
Performance: 0.076 ns/day, 315.433 hours/ns, 1.761 timesteps/s
94.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.7511 | 3.8123 | 3.9245 | 3.4 | 33.57
Neigh | 0.36492 | 0.3767 | 0.39023 | 1.5 | 3.32
Comm | 0.12022 | 0.23202 | 0.29307 | 13.8 | 2.04
Output | 8.0451e-05 | 0.00017452 | 0.00045489 | 0.0 | 0.00
Modify | 6.9172 | 6.9312 | 6.9431 | 0.4 | 61.04
Other | | 0.003189 | | | 0.03
Nlocal: 750.000 ave 758 max 737 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 4219.50 ave 4233 max 4198 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 230733.0 ave 233431 max 225531 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 922931
Ave neighs/atom = 307.64367
Neighbor list builds = 7
Dangerous builds = 0
Total wall time: 0:00:12

124
examples/reaxff/water/log.13Oct21.reaxff.water-acks2.g++.1 Normal file
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@ -0,0 +1,124 @@
LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 574.5 | 574.5 | 574.5 Mbytes
Step Temp Press Density Volume
0 300 1572.3474 1 29915.273
10 300.61522 8252.7686 1 29915.273
20 294.7387 2502.6624 1 29915.273
Loop time of 25.9579 on 1 procs for 20 steps with 3000 atoms
Performance: 0.033 ns/day, 721.052 hours/ns, 0.770 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.081 | 14.081 | 14.081 | 0.0 | 54.24
Neigh | 0.34284 | 0.34284 | 0.34284 | 0.0 | 1.32
Comm | 0.0027799 | 0.0027799 | 0.0027799 | 0.0 | 0.01
Output | 0.00012876 | 0.00012876 | 0.00012876 | 0.0 | 0.00
Modify | 11.53 | 11.53 | 11.53 | 0.0 | 44.42
Other | | 0.001007 | | | 0.00
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11077.0 ave 11077 max 11077 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 971815.0 ave 971815 max 971815 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 971815
Ave neighs/atom = 323.93833
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:27

124
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LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.013 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
3000 atoms
replicate CPU = 0.002 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 271.9 | 273.6 | 275.1 Mbytes
Step Temp Press Density Volume
0 300 1572.3807 1 29915.273
10 300.6152 8252.4834 1 29915.273
20 294.73868 2502.5661 1 29915.273
Loop time of 11.1133 on 4 procs for 20 steps with 3000 atoms
Performance: 0.078 ns/day, 308.702 hours/ns, 1.800 timesteps/s
92.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3609 | 4.7715 | 5.4812 | 19.5 | 42.94
Neigh | 0.15797 | 0.17176 | 0.19405 | 3.5 | 1.55
Comm | 0.21014 | 0.922 | 1.3353 | 44.6 | 8.30
Output | 8.815e-05 | 0.0002 | 0.00030501 | 0.0 | 0.00
Modify | 5.2267 | 5.2468 | 5.2584 | 0.5 | 47.21
Other | | 0.001074 | | | 0.01
Nlocal: 750.000 ave 760 max 735 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 6231.50 ave 6255 max 6192 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 277006.0 ave 280567 max 271394 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 1108026
Ave neighs/atom = 369.34200
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:12

128
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LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
1 by 1 by 1 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 332.3 | 332.3 | 332.3 Mbytes
Step Temp Press Density Volume
0 300 25015.837 0.99996859 29916.212
10 348.83356 31131.298 0.99964273 29925.965
20 414.67243 27564.999 0.99979791 29921.32
Loop time of 15.4107 on 1 procs for 20 steps with 3000 atoms
Performance: 0.056 ns/day, 428.074 hours/ns, 1.298 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.413 | 11.413 | 11.413 | 0.0 | 74.06
Neigh | 0.57486 | 0.57486 | 0.57486 | 0.0 | 3.73
Comm | 0.0019709 | 0.0019709 | 0.0019709 | 0.0 | 0.01
Output | 0.00013211 | 0.00013211 | 0.00013211 | 0.0 | 0.00
Modify | 3.4192 | 3.4192 | 3.4192 | 0.0 | 22.19
Other | | 0.001104 | | | 0.01
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5439.00 ave 5439 max 5439 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 786591.0 ave 786591 max 786591 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 786591
Ave neighs/atom = 262.19700
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:16

128
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LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.017 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
2 by 1 by 2 MPI processor grid
3000 atoms
replicate CPU = 0.002 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 188.9 | 189.5 | 190.1 Mbytes
Step Temp Press Density Volume
0 300 25015.837 0.99996859 29916.212
10 348.83356 31131.298 0.99964273 29925.965
20 414.67243 27564.999 0.99979791 29921.32
Loop time of 5.71549 on 4 procs for 20 steps with 3000 atoms
Performance: 0.151 ns/day, 158.764 hours/ns, 3.499 timesteps/s
94.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6678 | 3.8126 | 4.1402 | 9.8 | 66.71
Neigh | 0.31449 | 0.34639 | 0.38898 | 5.5 | 6.06
Comm | 0.032125 | 0.35935 | 0.50408 | 31.9 | 6.29
Output | 7.643e-05 | 0.00015959 | 0.00039876 | 0.0 | 0.00
Modify | 1.1534 | 1.1959 | 1.2283 | 3.0 | 20.92
Other | | 0.001099 | | | 0.02
Nlocal: 750.000 ave 757 max 738 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 4219.00 ave 4232 max 4198 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 230549.0 ave 233374 max 225849 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 922196
Ave neighs/atom = 307.39867
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:06

123
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LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes
Step Temp Press Density Volume
0 300 780.33989 1 29915.273
10 301.29205 5433.7415 1 29915.273
20 297.90652 1572.6111 1 29915.273
Loop time of 17.5765 on 1 procs for 20 steps with 3000 atoms
Performance: 0.049 ns/day, 488.237 hours/ns, 1.138 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.806 | 13.806 | 13.806 | 0.0 | 78.55
Neigh | 0.34211 | 0.34211 | 0.34211 | 0.0 | 1.95
Comm | 0.0028155 | 0.0028155 | 0.0028155 | 0.0 | 0.02
Output | 0.00012279 | 0.00012279 | 0.00012279 | 0.0 | 0.00
Modify | 3.4248 | 3.4248 | 3.4248 | 0.0 | 19.49
Other | | 0.001008 | | | 0.01
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11077.0 ave 11077 max 11077 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 971826.0 ave 971826 max 971826 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 971826
Ave neighs/atom = 323.94200
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:18

123
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@ -0,0 +1,123 @@
LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
Step Temp Press Density Volume
0 300 780.34006 1 29915.273
10 301.29205 5433.7414 1 29915.273
20 297.90652 1572.6111 1 29915.273
Loop time of 6.79573 on 4 procs for 20 steps with 3000 atoms
Performance: 0.127 ns/day, 188.770 hours/ns, 2.943 timesteps/s
93.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4827 | 4.6649 | 4.866 | 6.6 | 68.64
Neigh | 0.16329 | 0.17253 | 0.18074 | 1.6 | 2.54
Comm | 0.44871 | 0.64804 | 0.82827 | 17.5 | 9.54
Output | 9.9269e-05 | 0.00013061 | 0.00022048 | 0.0 | 0.00
Modify | 1.3028 | 1.3091 | 1.3201 | 0.6 | 19.26
Other | | 0.001043 | | | 0.02
Nlocal: 750.000 ave 759 max 735 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 6230.50 ave 6256 max 6190 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 277008.0 ave 280943 max 271394 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 1108032
Ave neighs/atom = 369.34400
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:07

83
examples/reaxff/water/qeq_ff.water Normal file
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@ -0,0 +1,83 @@
Reactive MD-force field: QEq Water [CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)]
39 ! Number of general parameters
50.0000 !Overcoordination parameter
9.5469 !Overcoordination parameter
26.5405 !Valency angle conjugation parameter
1.7224 !Triple bond stabilisation parameter
6.8702 !Triple bond stabilisation parameter
60.4850 !C2-correction
1.0588 !Undercoordination parameter
4.6000 !Triple bond stabilisation parameter
12.1176 !Undercoordination parameter
13.3056 !Undercoordination parameter
-70.5044 !Triple bond stabilization energy
0.0000 !Lower Taper-radius
10.0000 !Upper Taper-radius
2.8793 !Not used
33.8667 !Valency undercoordination
6.0891 !Valency angle/lone pair parameter
1.0563 !Valency angle
2.0384 !Valency angle parameter
6.1431 !Not used
6.9290 !Double bond/angle parameter
0.3989 !Double bond/angle parameter: overcoord
3.9954 !Double bond/angle parameter: overcoord
-2.4837 !Not used
5.7796 !Torsion/BO parameter
10.0000 !Torsion overcoordination
1.9487 !Torsion overcoordination
-1.2327 !Conjugation 0 (not used)
2.1645 !Conjugation
1.5591 !vdWaals shielding
0.1000 !Cutoff for bond order (*100)
2.1365 !Valency angle conjugation parameter
0.6991 !Overcoordination parameter
50.0000 !Overcoordination parameter
1.8512 !Valency/lone pair parameter
0.5000 !Not used
20.0000 !Not used
5.0000 !Molecular energy (not used)
0.0000 !Molecular energy (not used)
2.6962 !Valency angle conjugation parameter
3 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;#
alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u.
cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u.
ov/un;val1;n.u.;val3,vval4
H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000
8.2230 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000
-0.1000 0.0000 61.6606 3.0408 2.4197 0.0003 1.0698 0.0000
-19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000
O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000
9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000
0.9049 0.4056 59.0626 3.5027 0.7640 0.0021 0.9745 0.0000
-3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000
X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000
10.0000 2.5000 4.0000 0.0000 0.0000 8.5000 1.5000 0.0000
-0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.9745 0.0000
-11.0000 2.7466 1.0338 2.0000 2.8793 0.0000 0.0000 0.0000
3 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6
pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr
1 1 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300
6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000
2 2 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051
0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000
1 2 160.0000 0.0000 0.0000 -0.5725 0.0000 1.0000 6.0000 0.5626
1.1150 1.0000 0.0000 0.0000 -0.0920 4.2790 0.0000 0.0000
1 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2
1 2 0.0283 1.2885 10.9190 0.9215 -1.0000 -1.0000
6 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2
1 1 1 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400
2 2 2 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783
1 2 2 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680
1 2 1 85.8000 9.8453 2.2720 0.0000 2.8635 0.0000 1.5800
2 1 2 0.0000 15.0000 2.8900 0.0000 0.0000 0.0000 2.8774
1 1 2 0.0000 8.5744 3.0000 0.0000 0.0000 0.0000 1.0421
6 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n
1 2 2 1 2.5000 -4.0000 0.9000 -2.5000 -1.0000 0.0000 0.0000
1 2 2 2 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 0.0000 0.0000
2 2 2 2 -2.5000 -4.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000
0 1 1 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 1 2 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
0 2 2 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000
1 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1
2 1 2 2.1200 -3.5800 1.4500 19.5000

2
examples/rigid/data.rigid-property
View File

@ -99,7 +99,7 @@ Atoms
80 1 10 9.5 0
81 1 10 10 0
Bodies
Clumps
1 1
2 1

2
examples/rigid/in.rigid.property
View File

@ -8,7 +8,7 @@ pair_style lj/cut 2.5
fix 0 all property/atom i_bodies
read_data data.rigid-property fix 0 NULL Bodies
read_data data.rigid-property fix 0 NULL Clumps
velocity all create 100.0 4928459

4606
examples/ttm/FeVoter-ChenRecheck.fs Normal file
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File diff suppressed because it is too large Load Diff

43
examples/ttm/in.ttm Normal file
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@ -0,0 +1,43 @@
units metal
atom_style atomic
boundary p p p
variable latc equal 2.87
lattice bcc ${latc}
variable xmax equal 10.0
variable xmin equal -10.0
variable ymax equal 10.0
variable ymin equal -10.0
variable zmax equal 10.0
variable zmin equal -10.0
region sim_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} &
units lattice
create_box 1 sim_box
region atom_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} &
units lattice
create_atoms 1 region atom_box
mass 1 55.845
pair_style eam/fs
pair_coeff * * FeVoter-ChenRecheck.fs Fe
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm 342785 1.2470e-5 0.087614 &
0.005365 29.5917 47.5679 58.4613 10 10 10 set 1800.0
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000

43
examples/ttm/in.ttm.grid Normal file
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@ -0,0 +1,43 @@
units metal
atom_style atomic
boundary p p p
variable latc equal 2.87
lattice bcc ${latc}
variable xmax equal 10.0
variable xmin equal -10.0
variable ymax equal 10.0
variable ymin equal -10.0
variable zmax equal 10.0
variable zmin equal -10.0
region sim_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} &
units lattice
create_box 1 sim_box
region atom_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} &
units lattice
create_atoms 1 region atom_box
mass 1 55.845
pair_style eam/fs
pair_coeff * * FeVoter-ChenRecheck.fs Fe
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm/grid 342785 1.2470e-5 0.087614 &
0.005365 29.5917 47.5679 58.4613 10 10 10 set 1800.0
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000

113
examples/ttm/log.26Aug21.ttm.g++.1 Normal file
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@ -0,0 +1,113 @@
LAMMPS (30 Jul 2021)
units metal
atom_style atomic
boundary p p p
variable latc equal 2.87
lattice bcc ${latc}
lattice bcc 2.87
Lattice spacing in x,y,z = 2.8700000 2.8700000 2.8700000
variable xmax equal 10.0
variable xmin equal -10.0
variable ymax equal 10.0
variable ymin equal -10.0
variable zmax equal 10.0
variable zmin equal -10.0
region sim_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 10 ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 10 -10 ${zmax} units lattice
region sim_box block -10 10 -10 10 -10 10 units lattice
create_box 1 sim_box
Created orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000)
1 by 1 by 1 MPI processor grid
region atom_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 10 ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 10 -10 ${zmax} units lattice
region atom_box block -10 10 -10 10 -10 10 units lattice
create_atoms 1 region atom_box
Created 16000 atoms
using lattice units in orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000)
create_atoms CPU = 0.005 seconds
mass 1 55.845
include pot_iron.mod
pair_style eam/fs
pair_coeff * * FeVoter-ChenRecheck.fs Fe
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm 342785 1.2470e-5 0.087614 0.005365 29.5917 47.5679 58.4613 10 10 10 set 1800.0
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.524
ghost atom cutoff = 6.524
binsize = 3.262, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/fs, 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) = 10.97 | 10.97 | 10.97 Mbytes
Step Temp TotEng f_twotemp[1] f_twotemp[2]
0 0 -68483.52254543516 371.9188105082105 0
100 17.01353086098387 -68446.50228930202 334.6217068813629 0.3763710887774045
200 27.91331236535322 -68413.16008042906 301.3181773007303 0.3165912892484031
300 32.20115656493127 -68383.19634217303 271.3756381838044 0.2901111802983097
400 33.46056398887347 -68355.73057141017 243.9344715501159 0.2548133388123376
500 35.5346204243821 -68331.63060947017 219.84946888619 0.2388591367999412
600 40.61692458441595 -68309.36124792948 197.5527667607885 0.3056696014124333
700 46.20303146200327 -68290.12727395596 178.3775768561404 0.1982123493608405
800 50.43750181899325 -68272.72651051797 160.995046695269 0.1708386295858842
900 52.1701171463511 -68257.85059865141 146.1567281868866 0.1032829304640773
1000 53.49296457217385 -68244.38715993935 132.7166474251701 0.06428993394665879
Loop time of 17.1447 on 1 procs for 1000 steps with 16000 atoms
Performance: 0.504 ns/day, 47.624 hours/ns, 58.327 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.811 | 15.811 | 15.811 | 0.0 | 92.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.094539 | 0.094539 | 0.094539 | 0.0 | 0.55
Output | 0.00093974 | 0.00093974 | 0.00093974 | 0.0 | 0.01
Modify | 1.1898 | 1.1898 | 1.1898 | 0.0 | 6.94
Other | | 0.04797 | | | 0.28
Nlocal: 16000.0 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13449.0 ave 13449 max 13449 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 896000.0 ave 896000 max 896000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 896000
Ave neighs/atom = 56.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:17

113
examples/ttm/log.26Aug21.ttm.g++.4 Normal file
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@ -0,0 +1,113 @@
LAMMPS (30 Jul 2021)
units metal
atom_style atomic
boundary p p p
variable latc equal 2.87
lattice bcc ${latc}
lattice bcc 2.87
Lattice spacing in x,y,z = 2.8700000 2.8700000 2.8700000
variable xmax equal 10.0
variable xmin equal -10.0
variable ymax equal 10.0
variable ymin equal -10.0
variable zmax equal 10.0
variable zmin equal -10.0
region sim_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 10 ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 10 -10 ${zmax} units lattice
region sim_box block -10 10 -10 10 -10 10 units lattice
create_box 1 sim_box
Created orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000)
1 by 2 by 2 MPI processor grid
region atom_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 10 ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 10 -10 ${zmax} units lattice
region atom_box block -10 10 -10 10 -10 10 units lattice
create_atoms 1 region atom_box
Created 16000 atoms
using lattice units in orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000)
create_atoms CPU = 0.002 seconds
mass 1 55.845
include pot_iron.mod
pair_style eam/fs
pair_coeff * * FeVoter-ChenRecheck.fs Fe
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm 342785 1.2470e-5 0.087614 0.005365 29.5917 47.5679 58.4613 10 10 10 set 1800.0
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.524
ghost atom cutoff = 6.524
binsize = 3.262, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/fs, 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) = 4.845 | 4.845 | 4.845 Mbytes
Step Temp TotEng f_twotemp[1] f_twotemp[2]
0 0 -68483.52254530673 371.9188105082105 0
100 16.95536995775683 -68446.64765713879 334.7745598327934 0.3602932995006091
200 27.82619298359641 -68413.48663012494 301.6568409464845 0.2922875754523596
300 32.286609763559 -68383.41369945828 271.6030085280584 0.2698738824780399
400 33.33119316198579 -68356.74598240001 244.9747750036312 0.2061586600914007
500 35.14534756499593 -68332.73504057307 220.9328922343961 0.2800368538794571
600 39.58922469808519 -68311.03191758461 199.2602622784512 0.231030319616688
700 45.34652315787152 -68291.65247941406 179.9297699858465 0.1438135463248857
800 49.66707856481077 -68274.98092841901 163.2540575286428 0.1600890300738259
900 52.17692450487316 -68259.8031091165 148.1017576370546 0.1177316234407944
1000 54.24228199265477 -68245.58589458199 133.8816957314364 0.1314999893461338
Loop time of 5.03135 on 4 procs for 1000 steps with 16000 atoms
Performance: 1.717 ns/day, 13.976 hours/ns, 198.754 timesteps/s
98.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.1173 | 4.2634 | 4.3858 | 5.4 | 84.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.2218 | 0.34547 | 0.49422 | 19.4 | 6.87
Output | 0.00031185 | 0.00036952 | 0.00044986 | 0.0 | 0.01
Modify | 0.39294 | 0.39605 | 0.39877 | 0.4 | 7.87
Other | | 0.02604 | | | 0.52
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6329.00 ave 6329 max 6329 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 224000.0 ave 227436 max 220450 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 896000
Ave neighs/atom = 56.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05

113
examples/ttm/log.26Aug21.ttm.grid.g++.1 Normal file
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@ -0,0 +1,113 @@
LAMMPS (30 Jul 2021)
units metal
atom_style atomic
boundary p p p
variable latc equal 2.87
lattice bcc ${latc}
lattice bcc 2.87
Lattice spacing in x,y,z = 2.8700000 2.8700000 2.8700000
variable xmax equal 10.0
variable xmin equal -10.0
variable ymax equal 10.0
variable ymin equal -10.0
variable zmax equal 10.0
variable zmin equal -10.0
region sim_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 10 ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 10 -10 ${zmax} units lattice
region sim_box block -10 10 -10 10 -10 10 units lattice
create_box 1 sim_box
Created orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000)
1 by 1 by 1 MPI processor grid
region atom_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 10 ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 10 -10 ${zmax} units lattice
region atom_box block -10 10 -10 10 -10 10 units lattice
create_atoms 1 region atom_box
Created 16000 atoms
using lattice units in orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000)
create_atoms CPU = 0.005 seconds
mass 1 55.845
include pot_iron.mod
pair_style eam/fs
pair_coeff * * FeVoter-ChenRecheck.fs Fe
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm/grid 342785 1.2470e-5 0.087614 0.005365 29.5917 47.5679 58.4613 10 10 10 set 1800.0
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.524
ghost atom cutoff = 6.524
binsize = 3.262, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/fs, 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) = 10.99 | 10.99 | 10.99 Mbytes
Step Temp TotEng f_twotemp[1] f_twotemp[2]
0 0 -68483.52254543516 371.9188105082105 0
100 17.01353086098387 -68446.50228930202 334.6217068813629 0.3763710887774046
200 27.91331236535322 -68413.16008042906 301.3181773007303 0.3165912892484031
300 32.20115656493125 -68383.19634217303 271.3756381838045 0.2901111802983097
400 33.46056398887347 -68355.73057141017 243.9344715501159 0.2548133388123378
500 35.5346204243821 -68331.63060947017 219.84946888619 0.2388591367999414
600 40.61692458441596 -68309.36124792948 197.5527667607886 0.3056696014124338
700 46.20303146200326 -68290.12727395598 178.3775768561405 0.1982123493608406
800 50.4375018189932 -68272.72651051797 160.995046695269 0.1708386295858845
900 52.17011714635106 -68257.85059865142 146.1567281868867 0.1032829304640776
1000 53.49296457217382 -68244.38715993936 132.7166474251702 0.06428993394665769
Loop time of 14.8767 on 1 procs for 1000 steps with 16000 atoms
Performance: 0.581 ns/day, 41.324 hours/ns, 67.219 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.759 | 13.759 | 13.759 | 0.0 | 92.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.087429 | 0.087429 | 0.087429 | 0.0 | 0.59
Output | 0.00063941 | 0.00063941 | 0.00063941 | 0.0 | 0.00
Modify | 0.98561 | 0.98561 | 0.98561 | 0.0 | 6.63
Other | | 0.04396 | | | 0.30
Nlocal: 16000.0 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13449.0 ave 13449 max 13449 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 896000.0 ave 896000 max 896000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 896000
Ave neighs/atom = 56.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:14

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examples/ttm/log.26Aug21.ttm.grid.g++.4 Normal file
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LAMMPS (30 Jul 2021)
units metal
atom_style atomic
boundary p p p
variable latc equal 2.87
lattice bcc ${latc}
lattice bcc 2.87
Lattice spacing in x,y,z = 2.8700000 2.8700000 2.8700000
variable xmax equal 10.0
variable xmin equal -10.0
variable ymax equal 10.0
variable ymin equal -10.0
variable zmax equal 10.0
variable zmin equal -10.0
region sim_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 ${ymax} ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 10 ${zmin} ${zmax} units lattice
region sim_box block -10 10 -10 10 -10 ${zmax} units lattice
region sim_box block -10 10 -10 10 -10 10 units lattice
create_box 1 sim_box
Created orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000)
1 by 2 by 2 MPI processor grid
region atom_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 ${ymin} ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 ${ymax} ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 10 ${zmin} ${zmax} units lattice
region atom_box block -10 10 -10 10 -10 ${zmax} units lattice
region atom_box block -10 10 -10 10 -10 10 units lattice
create_atoms 1 region atom_box
Created 16000 atoms
using lattice units in orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000)
create_atoms CPU = 0.002 seconds
mass 1 55.845
include pot_iron.mod
pair_style eam/fs
pair_coeff * * FeVoter-ChenRecheck.fs Fe
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes
fix 1 all nve
fix twotemp all ttm/grid 342785 1.2470e-5 0.087614 0.005365 29.5917 47.5679 58.4613 10 10 10 set 1800.0
compute pe all pe/atom
compute ke all ke/atom
timestep 0.0001
thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
run 1000
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.524
ghost atom cutoff = 6.524
binsize = 3.262, bins = 18 18 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/fs, 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) = 4.843 | 4.843 | 4.843 Mbytes
Step Temp TotEng f_twotemp[1] f_twotemp[2]
0 0 -68483.52254530673 371.9188105082186 0
100 16.95536995775684 -68446.64765713879 334.7745598327931 0.3602932995006087
200 27.82619298359641 -68413.48663012494 301.6568409464847 0.2922875754523593
300 32.28660976355901 -68383.41369945828 271.6030085280586 0.26987388247804
400 33.33119316198579 -68356.74598240001 244.9747750036311 0.2061586600914003
500 35.14534756499593 -68332.73504057307 220.9328922343961 0.2800368538794578
600 39.58922469808521 -68311.03191758461 199.2602622784512 0.2310303196166884
700 45.34652315787151 -68291.65247941404 179.9297699858464 0.1438135463248855
800 49.66707856481075 -68274.98092841901 163.2540575286425 0.1600890300738265
900 52.17692450487317 -68259.8031091165 148.1017576370548 0.1177316234407941
1000 54.24228199265479 -68245.58589458198 133.8816957314364 0.1314999893461343
Loop time of 4.95173 on 4 procs for 1000 steps with 16000 atoms
Performance: 1.745 ns/day, 13.755 hours/ns, 201.949 timesteps/s
98.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.1159 | 4.2665 | 4.4446 | 7.1 | 86.16
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.14618 | 0.32518 | 0.47663 | 25.8 | 6.57
Output | 0.00030633 | 0.00034695 | 0.00044693 | 0.0 | 0.01
Modify | 0.33258 | 0.3333 | 0.33402 | 0.1 | 6.73
Other | | 0.0264 | | | 0.53
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6329.00 ave 6329 max 6329 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 224000.0 ave 227436 max 220450 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 896000
Ave neighs/atom = 56.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05