Merge branch 'develop' into collected-small-changes
This commit is contained in:
Axel Kohlmeyer
@ -48,9 +48,9 @@ Description
|
||||
|
||||
Pair style *pace* computes interactions using the Atomic Cluster
|
||||
Expansion (ACE), which is a general expansion of the atomic energy in
|
||||
multi-body basis functions. :ref:`(Drautz) <Drautz20191>`. The *pace*
|
||||
multi-body basis functions. :ref:`(Drautz19) <Drautz20191>`. The *pace*
|
||||
pair style provides an efficient implementation that is described in
|
||||
this paper :ref:`(Lysogorskiy) <Lysogorskiy20211>`.
|
||||
this paper :ref:`(Lysogorskiy21) <Lysogorskiy20211>`.
|
||||
|
||||
In ACE, the total energy is decomposed into a sum over atomic
|
||||
energies. The energy of atom *i* is expressed as a linear or non-linear
|
||||
@ -91,7 +91,7 @@ Extrapolation grade
|
||||
Calculation of extrapolation grade in PACE is implemented in `pair_style
|
||||
pace/extrapolation`. It is based on the MaxVol algorithm similar to
|
||||
Moment Tensor Potential (MTP) by Shapeev et al. and is described in
|
||||
:ref:`(Lysogorskiy2) <Lysogorskiy2022>`. In order to compute
|
||||
:ref:`(Lysogorskiy23) <Lysogorskiy2023>`. In order to compute
|
||||
extrapolation grade one needs to provide:
|
||||
|
||||
#. ACE potential in B-basis form (`.yaml` format) and
|
||||
@ -182,12 +182,12 @@ recursive, chunksize = 4096,
|
||||
|
||||
.. _Drautz20191:
|
||||
|
||||
**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
|
||||
**(Drautz19)** Drautz, Phys Rev B, 99, 014104 (2019).
|
||||
|
||||
.. _Lysogorskiy20211:
|
||||
|
||||
**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
|
||||
**(Lysogorskiy21)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
|
||||
|
||||
.. _Lysogorskiy2022:
|
||||
.. _Lysogorskiy2023:
|
||||
|
||||
**(Lysogorskiy2022)** Lysogorskiy, Bochkarev, Mrovec, Drautz, arXiv:2212.08716 (2022).
|
||||
**(Lysogorskiy23)** Lysogorskiy, Bochkarev, Mrovec, Drautz, Phys Rev Mater, 7, 043801 (2023) / arXiv:2212.08716 (2022).
|
||||
|
||||
@ -23,8 +23,9 @@ Description
|
||||
|
||||
This pair style computes a variable charge SMTB-Q (Second-Moment
|
||||
tight-Binding QEq) potential as described in :ref:`SMTB-Q_1 <SMTB-Q_1>` and
|
||||
:ref:`SMTB-Q_2 <SMTB-Q_2>`. Briefly, the energy of metallic-oxygen systems
|
||||
is given by three contributions:
|
||||
:ref:`SMTB-Q_2 <SMTB-Q_2>`.
|
||||
This potential was first proposed in :ref:`SMTB-Q_0 <SMTB-Q_0>`.
|
||||
Briefly, the energy of metallic-oxygen systems is given by three contributions:
|
||||
|
||||
.. math::
|
||||
|
||||
@ -208,7 +209,7 @@ For each cations (metal):
|
||||
6) Coordination parameter:
|
||||
|
||||
* First (:math:`r_{1n}`) and second (:math:`r_{2n}`) neighbor distances
|
||||
in Angstrom
|
||||
in angstroms
|
||||
* Divider line
|
||||
|
||||
7) Charge initialization mode:
|
||||
@ -306,6 +307,12 @@ and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
|
||||
|
||||
----------
|
||||
|
||||
.. _SMTB-Q_0:
|
||||
|
||||
**(SMTB-Q_0)** A. Hallil, E. Amzallag, S. Landron, R. Tetot,
|
||||
Surface Science 605 738-745 (2011);
|
||||
R. Tetot, A. Hallil, J. Creuze and I. Braems, EPL, 83 40001 (2008)
|
||||
|
||||
.. _SMTB-Q_1:
|
||||
|
||||
**(SMTB-Q_1)** N. Salles, O. Politano, E. Amzallag, R. Tetot,
|
||||
|
||||
@ -33,7 +33,6 @@ These are the sub-directories included in this directory:
|
||||
simple simple example of driver code calling LAMMPS as a lib
|
||||
multiple example of driver code calling multiple instances of LAMMPS
|
||||
plugin example for loading LAMMPS at runtime from a shared library
|
||||
lammps_quest MD with quantum forces, coupling to Quest DFT code
|
||||
lammps_spparks grain-growth Monte Carlo with strain via MD,
|
||||
coupling to SPPARKS kinetic MC code
|
||||
library collection of useful inter-code communication routines
|
||||
|
||||
@ -1,47 +0,0 @@
|
||||
# Makefile for MD with quantum forces via LAMMPS <-> Quest coupling
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# System-specific settings
|
||||
|
||||
LAMMPS = /home/sjplimp/lammps
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O -DMPICH_IGNORE_CXX_SEEK -I../library
|
||||
DEPFLAGS = -M
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O -L../library -L${LAMMPS}/src
|
||||
USRLIB = -lcouple -llammps_g++
|
||||
SYSLIB = -lfftw -lmpich -lpthread
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
|
||||
# Files
|
||||
|
||||
EXE = lmpqst
|
||||
SRC = $(wildcard *.cpp)
|
||||
INC = $(wildcard *.h)
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
|
||||
# Targets
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
clean:
|
||||
rm $(EXE) *.o
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
include $(DEPENDS)
|
||||
@ -1,70 +0,0 @@
|
||||
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
|
||||
|
||||
After editing the Makefile, lmppath.h, and qstexe.h to make them
|
||||
suitable for your box, type:
|
||||
|
||||
make -f Makefile.g++
|
||||
|
||||
and you should get the lmpqst executable.
|
||||
|
||||
NOTE: To run this coupled application, you must of course, have Quest
|
||||
built on your system. It's WWW site is http://dft.sandia.gov/Quest.
|
||||
It is not an open-source code, buy you can contact its authors to
|
||||
obtain a copy.
|
||||
|
||||
You can run lmpqst in serial or parallel as:
|
||||
|
||||
% lmpqst Niter in.lammps in.quest
|
||||
% mpirun -np 4 lmpqst Niter in.lammps in.quest
|
||||
|
||||
where
|
||||
|
||||
Niter = # of MD iterations
|
||||
in.lammps = LAMMPS input script
|
||||
in.quest = Quest input script
|
||||
|
||||
The log files are for this run:
|
||||
|
||||
% lmpqst 10 in.lammps si_111.in
|
||||
|
||||
This application is an example of a coupling where the driver code
|
||||
(lmpqst) runs one code (LAMMPS) as an outer code and facilitates it
|
||||
calling the other code (Quest) as an inner code. Specifically, the
|
||||
driver (lmpqst) invokes one code (LAMMPS) to perform its timestep
|
||||
loop, and grabs information from the other code (Quest) during its
|
||||
timestep. This is done in LAMMPS using the fix external command,
|
||||
which makes a "callback" to the driver application (lmpqst), which in
|
||||
turn invokes Quest with new atom coordinates, lets Quest compute
|
||||
forces, and returns those forces to the LAMMPS fix external.
|
||||
|
||||
The driver code launches LAMMPS in parallel. But Quest is only run on
|
||||
a single processor. It would be possible to change this by using a
|
||||
parallel build of Quest.
|
||||
|
||||
Since Quest does not currently have a library interface, the driver
|
||||
code interfaces with Quest via input and output files.
|
||||
|
||||
Note that essentially 100% of the run time for this coupled
|
||||
application is spent in Quest, as the quantum calculation of forces
|
||||
dominates the calculation.
|
||||
|
||||
You can look at the log files in the directory to see sample LAMMPS
|
||||
output for this simulation. Dump files produced by LAMMPS are stored
|
||||
as dump.md.
|
||||
@ -1,20 +0,0 @@
|
||||
# LAMMPS input for coupling MD/Quantum
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
lattice diamond 5.43
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 28.08
|
||||
|
||||
velocity all create 300.0 87293 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all external pf/callback 1 1
|
||||
|
||||
dump 1 all custom 1 dump.md id type x y z fx fy fz
|
||||
thermo 1
|
||||
@ -1 +0,0 @@
|
||||
#define LMPPATH /home/sjplimp/lammps
|
||||
@ -1,270 +0,0 @@
|
||||
// lmpqst = umbrella driver to couple LAMMPS + Quest
|
||||
// for MD using quantum forces
|
||||
|
||||
// Syntax: lmpqst Niter in.lammps in.quest
|
||||
// Niter = # of MD iterations
|
||||
// in.lammps = LAMMPS input script
|
||||
// in.quest = Quest input script
|
||||
|
||||
#include <mpi.h>
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "stdint.h"
|
||||
|
||||
#include "many2one.h"
|
||||
#include "one2many.h"
|
||||
#include "files.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#define QUOTE_(x) #x
|
||||
#define QUOTE(x) QUOTE_(x)
|
||||
|
||||
#include "lmppath.h"
|
||||
#include QUOTE(LMPPATH/src/lammps.h)
|
||||
#include QUOTE(LMPPATH/src/library.h)
|
||||
#include QUOTE(LMPPATH/src/input.h)
|
||||
#include QUOTE(LMPPATH/src/modify.h)
|
||||
#include QUOTE(LMPPATH/src/fix.h)
|
||||
#include QUOTE(LMPPATH/src/fix_external.h)
|
||||
|
||||
#include "qstexe.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define ANGSTROM_per_BOHR 0.529
|
||||
#define EV_per_RYDBERG 13.6056923
|
||||
|
||||
void quest_callback(void *, bigint, int, int *, double **, double **);
|
||||
|
||||
struct Info {
|
||||
int me;
|
||||
Memory *memory;
|
||||
LAMMPS *lmp;
|
||||
char *quest_input;
|
||||
};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
int n;
|
||||
char str[128];
|
||||
|
||||
// setup MPI
|
||||
|
||||
MPI_Init(&narg,&arg);
|
||||
MPI_Comm comm = MPI_COMM_WORLD;
|
||||
|
||||
int me,nprocs;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
Memory *memory = new Memory(comm);
|
||||
Error *error = new Error(comm);
|
||||
|
||||
// command-line args
|
||||
|
||||
if (narg != 4) error->all("Syntax: lmpqst Niter in.lammps in.quest");
|
||||
|
||||
int niter = atoi(arg[1]);
|
||||
n = strlen(arg[2]) + 1;
|
||||
char *lammps_input = new char[n];
|
||||
strcpy(lammps_input,arg[2]);
|
||||
n = strlen(arg[3]) + 1;
|
||||
char *quest_input = new char[n];
|
||||
strcpy(quest_input,arg[3]);
|
||||
|
||||
// instantiate LAMMPS
|
||||
|
||||
LAMMPS *lmp = new LAMMPS(0,NULL,MPI_COMM_WORLD);
|
||||
|
||||
// create simulation in LAMMPS from in.lammps
|
||||
|
||||
lmp->input->file(lammps_input);
|
||||
|
||||
// make info available to callback function
|
||||
|
||||
Info info;
|
||||
info.me = me;
|
||||
info.memory = memory;
|
||||
info.lmp = lmp;
|
||||
info.quest_input = quest_input;
|
||||
|
||||
// set callback to Quest inside fix external
|
||||
// this could also be done thru Python, using a ctypes callback
|
||||
|
||||
int ifix = lmp->modify->find_fix("2");
|
||||
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
|
||||
fix->set_callback(quest_callback,&info);
|
||||
|
||||
// run LAMMPS for Niter
|
||||
// each time it needs forces, it will invoke quest_callback
|
||||
|
||||
sprintf(str,"run %d",niter);
|
||||
lmp->input->one(str);
|
||||
|
||||
// clean up
|
||||
|
||||
delete lmp;
|
||||
|
||||
delete memory;
|
||||
delete error;
|
||||
|
||||
delete [] lammps_input;
|
||||
delete [] quest_input;
|
||||
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
callback to Quest with atom IDs and coords from each proc
|
||||
invoke Quest to compute forces, load them into f for LAMMPS to use
|
||||
f can be NULL if proc owns no atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void quest_callback(void *ptr, bigint ntimestep,
|
||||
int nlocal, int *id, double **x, double **f)
|
||||
{
|
||||
int i,j;
|
||||
char str[128];
|
||||
|
||||
Info *info = (Info *) ptr;
|
||||
|
||||
// boxlines = LAMMPS box size converted into Quest lattice vectors
|
||||
|
||||
char **boxlines = NULL;
|
||||
if (info->me == 0) {
|
||||
boxlines = new char*[3];
|
||||
for (i = 0; i < 3; i++) boxlines[i] = new char[128];
|
||||
}
|
||||
|
||||
double boxxlo = *((double *) lammps_extract_global(info->lmp,"boxxlo"));
|
||||
double boxxhi = *((double *) lammps_extract_global(info->lmp,"boxxhi"));
|
||||
double boxylo = *((double *) lammps_extract_global(info->lmp,"boxylo"));
|
||||
double boxyhi = *((double *) lammps_extract_global(info->lmp,"boxyhi"));
|
||||
double boxzlo = *((double *) lammps_extract_global(info->lmp,"boxzlo"));
|
||||
double boxzhi = *((double *) lammps_extract_global(info->lmp,"boxzhi"));
|
||||
double boxxy = *((double *) lammps_extract_global(info->lmp,"xy"));
|
||||
double boxxz = *((double *) lammps_extract_global(info->lmp,"xz"));
|
||||
double boxyz = *((double *) lammps_extract_global(info->lmp,"yz"));
|
||||
|
||||
double xprd = (boxxhi-boxxlo)/ANGSTROM_per_BOHR;
|
||||
double yprd = (boxyhi-boxylo)/ANGSTROM_per_BOHR;
|
||||
double zprd = (boxzhi-boxzlo)/ANGSTROM_per_BOHR;
|
||||
double xy = boxxy/ANGSTROM_per_BOHR;
|
||||
double xz = boxxz/ANGSTROM_per_BOHR;
|
||||
double yz = boxyz/ANGSTROM_per_BOHR;
|
||||
|
||||
if (info->me == 0) {
|
||||
sprintf(boxlines[0],"%g %g %g\n",xprd,0.0,0.0);
|
||||
sprintf(boxlines[1],"%g %g %g\n",xy,yprd,0.0);
|
||||
sprintf(boxlines[2],"%g %g %g\n",xz,yz,zprd);
|
||||
}
|
||||
|
||||
// xlines = x for atoms on each proc converted to text lines
|
||||
// xlines is suitable for insertion into Quest input file
|
||||
// convert LAMMPS Angstroms to Quest bohr
|
||||
|
||||
int natoms;
|
||||
MPI_Allreduce(&nlocal,&natoms,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD);
|
||||
|
||||
Many2One *lmp2qst = new Many2One(MPI_COMM_WORLD);
|
||||
lmp2qst->setup(nlocal,id,natoms);
|
||||
|
||||
char **xlines = NULL;
|
||||
double **xquest = NULL;
|
||||
if (info->me == 0) {
|
||||
xquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:xquest");
|
||||
xlines = new char*[natoms];
|
||||
for (i = 0; i < natoms; i++) xlines[i] = new char[128];
|
||||
}
|
||||
|
||||
if (info->me == 0) lmp2qst->gather(&x[0][0],3,&xquest[0][0]);
|
||||
else lmp2qst->gather(&x[0][0],3,NULL);
|
||||
|
||||
if (info->me == 0) {
|
||||
for (i = 0; i < natoms; i++) {
|
||||
xquest[i][0] /= ANGSTROM_per_BOHR;
|
||||
xquest[i][1] /= ANGSTROM_per_BOHR;
|
||||
xquest[i][2] /= ANGSTROM_per_BOHR;
|
||||
}
|
||||
for (i = 0; i < natoms; i++) {
|
||||
sprintf(xlines[i],"%d %d %g %g %g\n",i+1,1,
|
||||
xquest[i][0],xquest[i][1],xquest[i][2]);
|
||||
}
|
||||
}
|
||||
|
||||
// one-processor tasks:
|
||||
// whack all lcao.* files
|
||||
// cp quest_input to lcao.in
|
||||
// replace atom coords section of lcao.in with new atom coords
|
||||
// run Quest on one proc, save screen output to file
|
||||
// flines = atom forces extracted from Quest screen file
|
||||
// fquest = atom forces
|
||||
// convert Quest Ryd/bohr to LAMMPS eV/Angstrom
|
||||
|
||||
char **flines = NULL;
|
||||
double **fquest = NULL;
|
||||
if (info->me == 0) {
|
||||
fquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:fquest");
|
||||
flines = new char*[natoms];
|
||||
for (i = 0; i < natoms; i++) flines[i] = new char[128];
|
||||
}
|
||||
|
||||
if (info->me == 0) {
|
||||
system("rm lcao.*");
|
||||
sprintf(str,"cp %s lcao.in",info->quest_input);
|
||||
system(str);
|
||||
sprintf(str,"cp %s lcao.x",QUOTE(QUEST));
|
||||
system(str);
|
||||
replace("lcao.in","primitive lattice vectors",3,boxlines);
|
||||
replace("lcao.in","atom, type, position vector",natoms,xlines);
|
||||
system("lcao.x > lcao.screen");
|
||||
extract("lcao.screen","atom x force "
|
||||
"y force z force",natoms,flines);
|
||||
|
||||
int itmp;
|
||||
for (i = 0; i < natoms; i++)
|
||||
sscanf(flines[i],"%d %lg %lg %lg",&itmp,
|
||||
&fquest[i][0],&fquest[i][1],&fquest[i][2]);
|
||||
|
||||
for (i = 0; i < natoms; i++) {
|
||||
fquest[i][0] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
|
||||
fquest[i][1] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
|
||||
fquest[i][2] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
|
||||
}
|
||||
}
|
||||
|
||||
// convert fquest on one proc into f for atoms on each proc
|
||||
|
||||
One2Many *qst2lmp = new One2Many(MPI_COMM_WORLD);
|
||||
qst2lmp->setup(natoms,nlocal,id);
|
||||
double *fvec = NULL;
|
||||
if (f) fvec = &f[0][0];
|
||||
if (info->me == 0) qst2lmp->scatter(&fquest[0][0],3,fvec);
|
||||
else qst2lmp->scatter(NULL,3,fvec);
|
||||
|
||||
// clean up
|
||||
// some data only exists on proc 0
|
||||
|
||||
delete lmp2qst;
|
||||
delete qst2lmp;
|
||||
|
||||
info->memory->destroy_2d_double_array(xquest);
|
||||
info->memory->destroy_2d_double_array(fquest);
|
||||
|
||||
if (boxlines) {
|
||||
for (i = 0; i < 3; i++) delete [] boxlines[i];
|
||||
delete [] boxlines;
|
||||
}
|
||||
if (xlines) {
|
||||
for (i = 0; i < natoms; i++) delete [] xlines[i];
|
||||
delete [] xlines;
|
||||
}
|
||||
if (flines) {
|
||||
for (i = 0; i < natoms; i++) delete [] flines[i];
|
||||
delete [] flines;
|
||||
}
|
||||
}
|
||||
@ -1,58 +0,0 @@
|
||||
LAMMPS (20 Sep 2010)
|
||||
# LAMMPS input for coupling MD/Quantum
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
lattice diamond 5.43
|
||||
Lattice spacing in x,y,z = 5.43 5.43 5.43
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1 box
|
||||
Created 8 atoms
|
||||
mass 1 28.08
|
||||
|
||||
velocity all create 300.0 87293 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all external
|
||||
|
||||
dump 1 all custom 1 dump.md id type x y z fx fy fz
|
||||
thermo 1
|
||||
run 10
|
||||
Memory usage per processor = 1.25982 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 0.2714463 1810.9378
|
||||
1 298.22165 0 0 0.26983722 1800.2029
|
||||
2 293.2839 0 0 0.26536943 1770.3964
|
||||
3 286.18537 0 0 0.25894654 1727.5464
|
||||
4 277.61576 0 0 0.25119258 1675.8163
|
||||
5 267.3325 0 0 0.24188807 1613.7418
|
||||
6 254.94702 0 0 0.23068142 1538.9774
|
||||
7 240.91176 0 0 0.21798202 1454.2541
|
||||
8 226.27996 0 0 0.20474287 1365.9298
|
||||
9 212.1059 0 0 0.19191788 1280.3687
|
||||
10 199.27609 0 0 0.18030919 1202.922
|
||||
Loop time of 80.663 on 1 procs for 10 steps with 8 atoms
|
||||
|
||||
Pair time (%) = 0 (0)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 4.91142e-05 (6.08882e-05)
|
||||
Outpt time (%) = 0.00111485 (0.0013821)
|
||||
Other time (%) = 80.6618 (99.9986)
|
||||
|
||||
Nlocal: 8 ave 8 max 8 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
@ -1,58 +0,0 @@
|
||||
LAMMPS (20 Sep 2010)
|
||||
# LAMMPS input for coupling MD/Quantum
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
lattice diamond 5.43
|
||||
Lattice spacing in x,y,z = 5.43 5.43 5.43
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1 box
|
||||
Created 8 atoms
|
||||
mass 1 28.08
|
||||
|
||||
velocity all create 300.0 87293 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all external
|
||||
|
||||
dump 1 all custom 1 dump.md id type x y z fx fy fz
|
||||
thermo 1
|
||||
run 10
|
||||
Memory usage per processor = 1.25928 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 0.2714463 1810.9378
|
||||
1 298.22166 0 0 0.26983722 1800.2029
|
||||
2 293.28391 0 0 0.26536944 1770.3964
|
||||
3 286.18538 0 0 0.25894655 1727.5464
|
||||
4 277.61578 0 0 0.25119259 1675.8164
|
||||
5 267.33252 0 0 0.24188809 1613.7419
|
||||
6 254.94703 0 0 0.23068143 1538.9774
|
||||
7 240.91175 0 0 0.21798202 1454.254
|
||||
8 226.27997 0 0 0.20474287 1365.9299
|
||||
9 212.10594 0 0 0.19191791 1280.3689
|
||||
10 199.27613 0 0 0.18030923 1202.9223
|
||||
Loop time of 79.8256 on 4 procs for 10 steps with 8 atoms
|
||||
|
||||
Pair time (%) = 0 (0)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000365376 (0.000457718)
|
||||
Outpt time (%) = 0.00169969 (0.00212925)
|
||||
Other time (%) = 79.8236 (99.9974)
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5 ave 5 max 5 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
@ -1 +0,0 @@
|
||||
#define QUEST /home/sjplimp/csrf/quest/src/lcao.x
|
||||
@ -1,161 +0,0 @@
|
||||
do setup
|
||||
do iters
|
||||
do force
|
||||
no relax
|
||||
setup data
|
||||
title
|
||||
Si 1x1x1 unit cell
|
||||
functional
|
||||
PBE
|
||||
dimensions of system (0=cluster ... 3=bulk)
|
||||
3
|
||||
primitive lattice vectors
|
||||
10.261212 0.000000 0.000000
|
||||
0.000000 10.261212 0.000000
|
||||
0.000000 0.000000 10.261212
|
||||
grid dimensions
|
||||
10 10 10
|
||||
atom types
|
||||
1
|
||||
type number, label:
|
||||
1 Si_pbe
|
||||
notes5
|
||||
Originally constructed by Peter A. Schultz, 12Apr01
|
||||
potential generated by new Hamann program PUNSLDX
|
||||
Cite use with: D.R. Hamann, unpublished.
|
||||
Potential: "standard" setting out to l=2
|
||||
Basis: amended Jun05 for better (2d/1d not 1d/1d) d-function
|
||||
effective nuclear charge (s2p2 to 10.0)
|
||||
4.00000000d+00
|
||||
pseudopotentials: Lmax, and effective gaussian range
|
||||
2 0.86000000d+00
|
||||
functional type used in generating potential:
|
||||
PBE
|
||||
radial mesh: number of points for local and non-local pot integrals
|
||||
80 67
|
||||
mesh points for nuclear potential; ham2dh
|
||||
0.02500000 0.02696978 0.02909477 0.03138719 0.03386023 0.03652812
|
||||
0.03940622 0.04251109 0.04586060 0.04947402 0.05337215 0.05757741
|
||||
0.06211402 0.06700807 0.07228773 0.07798338 0.08412779 0.09075634
|
||||
0.09790716 0.10562140 0.11394345 0.12292121 0.13260635 0.14305458
|
||||
0.15432605 0.16648562 0.17960325 0.19375443 0.20902061 0.22548964
|
||||
0.24325628 0.26242278 0.28309943 0.30540522 0.32946852 0.35542780
|
||||
0.38343245 0.41364362 0.44623518 0.48139466 0.51932441 0.56024270
|
||||
0.60438500 0.65200533 0.70337773 0.75879783 0.81858456 0.88308197
|
||||
0.95266121 1.02772271 1.10869840 1.19605428 1.29029305 1.39195702
|
||||
1.50163124 1.61994684 1.74758469 1.88527930 2.03382306 2.19407079
|
||||
2.36694466 2.55343950 2.75462852 2.97166951 3.20581145 3.45840177
|
||||
3.73089402 4.02485632 4.34198031 4.68409093 5.05315693 5.45130215
|
||||
5.88081777 6.34417553 6.84404189 7.38329340 7.96503329 8.59260927
|
||||
9.26963282 10.00000000
|
||||
radwts: weights for radial points
|
||||
0.00189603 0.00204542 0.00220659 0.00238045 0.00256800 0.00277034
|
||||
0.00298862 0.00322410 0.00347813 0.00375218 0.00404781 0.00436675
|
||||
0.00471081 0.00508198 0.00548240 0.00591436 0.00638036 0.00688308
|
||||
0.00742541 0.00801047 0.00864162 0.00932251 0.01005704 0.01084945
|
||||
0.01170429 0.01262649 0.01362135 0.01469459 0.01585240 0.01710143
|
||||
0.01844888 0.01990249 0.02147064 0.02316234 0.02498733 0.02695611
|
||||
0.02908002 0.03137128 0.03384307 0.03650961 0.03938625 0.04248955
|
||||
0.04583736 0.04944895 0.05334510 0.05754823 0.06208254 0.06697411
|
||||
0.07225109 0.07794385 0.08408515 0.09071034 0.09785753 0.10556786
|
||||
0.11388570 0.12285891 0.13253914 0.14298208 0.15424783 0.16640123
|
||||
0.17951222 0.19365623 0.20891467 0.22537535 0.24313298 0.26228977
|
||||
0.28295594 0.30525043 0.32930153 0.35524766 0.38323811 0.41343397
|
||||
0.44600900 0.48115067 0.51906119 0.55995874 0.60407867 0.65167486
|
||||
0.70302122 0.75841323
|
||||
non-local potential: l,potential*integration weight
|
||||
0 0.62022930 0.62128855 0.62243016 0.62366033 0.62498568 0.62641328
|
||||
0.62795061 0.62960563 0.63138673 0.63330275 0.63536294 0.63757692
|
||||
0.63995464 0.64250630 0.64524218 0.64817253 0.65130735 0.65465605
|
||||
0.65822713 0.66202767 0.66606269 0.67033437 0.67484108 0.67957602
|
||||
0.68452576 0.68966817 0.69497006 0.70038419 0.70584566 0.71126756
|
||||
0.71653578 0.72150290 0.72598113 0.72973436 0.73246932 0.73382636
|
||||
0.73337030 0.73058243 0.72485505 0.71549107 0.70171167 0.68267654
|
||||
0.65752236 0.62542611 0.58570073 0.53792896 0.48213811 0.41900888
|
||||
0.35009536 0.27800640 0.20646172 0.14009458 0.08384960 0.04186877
|
||||
0.01596164 0.00423035 0.00115036 0.00066636 0.00047879 0.00029939
|
||||
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
|
||||
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000
|
||||
non-local potential: l,potential*integration weight
|
||||
1 0.59551624 0.59463303 0.59368033 0.59265268 0.59154422 0.59034862
|
||||
0.58905906 0.58766819 0.58616811 0.58455033 0.58280567 0.58092430
|
||||
0.57889565 0.57670833 0.57435015 0.57180802 0.56906791 0.56611482
|
||||
0.56293268 0.55950435 0.55581158 0.55183493 0.54755377 0.54294628
|
||||
0.53798942 0.53265896 0.52692951 0.52077458 0.51416671 0.50707751
|
||||
0.49947790 0.49133817 0.48262822 0.47331766 0.46337588 0.45277197
|
||||
0.44147437 0.42945016 0.41666374 0.40307468 0.38863443 0.37328165
|
||||
0.35693601 0.33949042 0.32080256 0.30068740 0.27891443 0.25521609
|
||||
0.22931791 0.20100526 0.17024474 0.13737521 0.10336405 0.07007167
|
||||
0.04035673 0.01767907 0.00470635 0.00076638 0.00047880 0.00029939
|
||||
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
|
||||
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000
|
||||
non-local potential: l,potential*integration weight
|
||||
2 0.56305372 0.55961728 0.55591134 0.55191498 0.54760572 0.54295941
|
||||
0.53795013 0.53255008 0.52672947 0.52045641 0.51369682 0.50641433
|
||||
0.49857022 0.49012333 0.48103004 0.47124429 0.46071759 0.44939919
|
||||
0.43723624 0.42417413 0.41015690 0.39512792 0.37903070 0.36181001
|
||||
0.34341340 0.32379300 0.30290805 0.28072780 0.25723539 0.23243242
|
||||
0.20634465 0.17902876 0.15058041 0.12114359 0.09092117 0.06018665
|
||||
0.02929636 -0.00129833 -0.03104046 -0.05926034 -0.08517498 -0.10789810
|
||||
-0.12646610 -0.13988656 -0.14721657 -0.14767751 -0.14080976 -0.12666296
|
||||
-0.10600305 -0.08049270 -0.05276798 -0.02629475 -0.00486427 0.00837657
|
||||
0.01228139 0.00892332 0.00342796 0.00074936 0.00047880 0.00029939
|
||||
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
|
||||
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000
|
||||
number of radial functions **** Si PBE Ham-II basis 20Feb01-PAS ****
|
||||
5
|
||||
angular momentum, number of alphas
|
||||
0 4
|
||||
alphas - s - 4s/2/4s407 (bulk Si dzp Eopt+reopt c1)
|
||||
0.10460000d+00 0.27226300d+00 1.30050800d+00 2.60103000d+00
|
||||
wave function coefficients
|
||||
0.20995300d+00 0.55978200d+00 -0.99128200d+00 0.33487100d+00
|
||||
angular momentum, number of alphas
|
||||
1 3
|
||||
alphas - p - 3p/2/3p492 (bulk Si dzp Eopt + reopt c1)
|
||||
0.09424100d+00 0.31767900d+00 1.56114500d+00
|
||||
wave function coefficients
|
||||
0.06761600d+00 0.31821200d+00 -0.06638300d+00
|
||||
angular momentum, number of alphas
|
||||
0 1
|
||||
alphas - s - second zeta s polarization
|
||||
0.10460000d+00
|
||||
wave function coefficients
|
||||
1.00000000d+00
|
||||
angular momentum, number of alphas
|
||||
1 1
|
||||
alphas - p - second zeta p polarization
|
||||
0.09424100d+00
|
||||
wave function coefficients
|
||||
1.00000000d+00
|
||||
angular momentum, number of alphas
|
||||
2 2
|
||||
alphas - d - angular polarization (dzp Eopt)
|
||||
0.32000000d+00 1.40000000d+00
|
||||
wave function coefficients
|
||||
0.31557000d+00 1.00000000d+00
|
||||
shell occupancies for this silicon, Si: s(2.00)p(2.00)
|
||||
2.00000000 2.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
end atom file
|
||||
number of atoms in unit cell
|
||||
8
|
||||
atom, type, position vector
|
||||
1 1 0.0000000000 0.0000000000 0.0000000000
|
||||
2 1 5.1306060590 5.1306060590 0.0000000000
|
||||
3 1 5.1306060590 0.0000000000 5.1306060590
|
||||
4 1 0.0000000000 5.1306060590 5.1306060590
|
||||
5 1 2.5653030295 2.5653030295 2.5653030295
|
||||
6 1 7.6959090885 7.6959090885 2.5653030295
|
||||
7 1 7.6959090885 2.5653030295 7.6959090885
|
||||
8 1 2.5653030295 7.6959090885 7.6959090885
|
||||
kgrid
|
||||
0 0 0
|
||||
end setup phase data
|
||||
run phase input data
|
||||
end of run phase data
|
||||
@ -2,18 +2,20 @@
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# Paths to your local LAMMPS and SPPARKS home directories
|
||||
|
||||
LAMMPS = /home/sjplimp/lammps/git
|
||||
SPPARKS = /home/sjplimp/spparks/git
|
||||
|
||||
# System-specific settings
|
||||
|
||||
LAMMPS = /home/sjplimp/lammps
|
||||
SPPARKS = /home/sjplimp/spparks
|
||||
|
||||
CC = g++
|
||||
CC = mpicxx
|
||||
CCFLAGS = -g -O -DMPICH_IGNORE_CXX_SEEK -I../library
|
||||
DEPFLAGS = -M
|
||||
LINK = g++
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -g -O -L../library -L${LAMMPS}/src -L${SPPARKS}/src
|
||||
USRLIB = -lcouple -llmp_g++ -lspk_g++
|
||||
SYSLIB = -lfftw -lmpich -lpthread
|
||||
USRLIB = -lcouple -llammps_mpi -lspparks_mpi
|
||||
SYSLIB =
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
@ -1,44 +1,67 @@
|
||||
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.
|
||||
|
||||
The grain growth is simulated by a Potts model in a kinetic Monte
|
||||
Carlo code SPPARKS. Clusters of like spins on a lattice represent
|
||||
grains. The Hamiltonian for the energy due of a collection of spins
|
||||
includes a strain term and is described on this page in the SPPARKS
|
||||
documentation:
|
||||
The grain growth is simulated by a Potts model in the kinetic Monte
|
||||
Carlo code SPPARKS -- https://spparks.github.io
|
||||
|
||||
http://spparks.sandia.gov/doc/app_potts_strain.html.
|
||||
Clusters of like spins on a lattice represent grains. The Hamiltonian
|
||||
for the energy due of a collection of spins includes a strain term and
|
||||
is described on this page in the SPPARKS documentation:
|
||||
|
||||
The strain is computed by the molecular dynamics code LAMMPS as a
|
||||
particle displacement where pairs of atoms across a grain boundary are
|
||||
of different types and thus push off from each other due to a
|
||||
Lennard-Jones sigma between particles of different types that is
|
||||
larger than the sigma between particles of the same type (interior to
|
||||
grains).
|
||||
https://spparks.github.io/doc/app_potts_strain.html
|
||||
|
||||
The strain is computed by the LAMMPS molecular dynamics code --
|
||||
https://www.lammps.org -- as a particle displacement where pairs of
|
||||
atoms across a grain boundary are of different types and thus push off
|
||||
from each other due to a Lennard-Jones sigma between particles of
|
||||
different types that is larger than the sigma between particles of the
|
||||
same type (interior to grains).
|
||||
|
||||
lmpspk.cpp main program
|
||||
it links LAMMPS and SPPARKS as libraries
|
||||
it links to LAMMPS and SPPARKS as libraries
|
||||
in.spparks SPPARKS input script, without the run command
|
||||
lmppath.h contains path to LAMMPS home directory
|
||||
spkpath.h contains path to SPPARKS home directory
|
||||
|
||||
After editing the Makefile, lmppath.h, and spkpath.h to make them
|
||||
suitable for your box, type:
|
||||
-----------------------------------
|
||||
|
||||
make -f Makefile.g++
|
||||
(1) To build and run this coupled application, you must have SPPARKS
|
||||
built on your system. It's WWW site is https://spparks.github.io and
|
||||
it can be downloaded as a tarball or cloned as a local Git repo.
|
||||
|
||||
and you should get the lmpspk executable.
|
||||
To build SPPARKS, do the following:
|
||||
|
||||
NOTE: To build and run this coupled application, you must of course,
|
||||
have SPPARKS built on your system. It's WWW site is
|
||||
http://www.sandia.gov/~sjplimp/spparks.html. It is an open-source
|
||||
code, written by two of the LAMMPS authors.
|
||||
% cd spparks/src
|
||||
% make mpi
|
||||
% make mode=lib mpi # build SPPARKS as a library
|
||||
|
||||
-----------------------------------
|
||||
|
||||
(2) You must also build the coupling library in
|
||||
lammps/examples/COUPLE/library.
|
||||
|
||||
To build the coupling library, do the following:
|
||||
|
||||
% cd lammps/examples/COUPLE/library
|
||||
% make -f Makefile.mpi
|
||||
|
||||
-----------------------------------
|
||||
|
||||
(3) Edit the Makefile.mpi, lmppath.h, and spkpath.h files in this
|
||||
directory to make them suitable for your box. Each of the 3 files
|
||||
has a comment telling you what to do.
|
||||
|
||||
-----------------------------------
|
||||
|
||||
(4) Build the coupled lmpspk application in this directory.
|
||||
|
||||
% make -f Makefile.mpi
|
||||
|
||||
This should give you a lmpspk executable.
|
||||
|
||||
-----------------------------------
|
||||
|
||||
(5) Run the test simulation
|
||||
|
||||
You can run lmpspk in serial or parallel as:
|
||||
|
||||
@ -52,7 +75,7 @@ Ndelta = time to run MC in each iteration
|
||||
Sfactor = multiplier on strain effect
|
||||
in.spparks = SPPARKS input script
|
||||
|
||||
The log files are for this run:
|
||||
The log files included in this directory are for this run:
|
||||
|
||||
% lmpspk 20 10.0 1 in.spparks
|
||||
|
||||
@ -70,11 +93,15 @@ The driver code launches both SPPARKS and LAMMPS in parallel and they
|
||||
both decompose their spatial domains in the same manner. The datums
|
||||
in SPPARKS (lattice sites) are the same as the datums in LAMMPS
|
||||
(coarse-grained particles). If this were not the case, more
|
||||
sophisticated inter-code communication could be performed.
|
||||
sophisticated inter-code communication could be performed. Note that
|
||||
the in.lammps and data.lammps files are not inputs; they are generated
|
||||
by the lmpspk driver.
|
||||
|
||||
You can look at the log files in the directory to see sample LAMMPS
|
||||
and SPPARKS output for this simulation. Dump files produced by the
|
||||
run are stored as dump.mc and dump.md. The image*.png files show
|
||||
snapshots from both the LAMMPS and SPPARKS output. Note that the
|
||||
in.lammps and data.lammps files are not inputs; they are generated by
|
||||
the lmpspk driver.
|
||||
You can look at the log files in the directory to see LAMMPS and
|
||||
SPPARKS output for this simulation run on 1 and 4 processors. Dump
|
||||
files produced by the run are named dump.mc and dump.md. The image
|
||||
PPM files show snapshots from the SPPARKS and LAMMPS output. Compare
|
||||
the image_spparks.0019.ppm and image_lammps.0190.ppm file. They were
|
||||
written at the same point in the simulation by both codes. The color
|
||||
maps for the 2 codes are not the same, but the morphology of the
|
||||
grains is.
|
||||
|
||||
@ -111,4 +111,6 @@ pair_coeff 100 100 1.0 1.0
|
||||
compute da all displace/atom
|
||||
|
||||
dump 1 all atom 10 dump.md
|
||||
dump 2 all image 10 image_lammps.*.ppm type type zoom 1.6
|
||||
dump_modify 2 pad 4 acolor * red/green/blue/aqua/magenta/yellow
|
||||
thermo 1
|
||||
|
||||
@ -20,4 +20,8 @@ diag_style energy
|
||||
temperature 1.0
|
||||
|
||||
stats 10.0
|
||||
dump 1 10.0 dump.mc
|
||||
dump 1 text 10.0 dump.mc id site x y
|
||||
|
||||
dump 2 image 1000 image_spparks.*.ppm site site view 0 0 box no 0.1 &
|
||||
crange 1 100 drange 1 1 shape cube zoom 1.5 size 512 512
|
||||
dump_modify 2 pad 4
|
||||
|
||||
@ -1 +1,3 @@
|
||||
#define LMPPATH /home/sjplimp/lammps
|
||||
// path to your LAMMPS home directory
|
||||
|
||||
#define LMPPATH /home/sjplimp/lammps/git
|
||||
|
||||
@ -14,8 +14,8 @@
|
||||
|
||||
#include "lammps_data_write.h"
|
||||
#include "many2many.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "memorylib.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
#define QUOTE_(x) #x
|
||||
#define QUOTE(x) QUOTE_(x)
|
||||
@ -51,8 +51,8 @@ int main(int narg, char **arg)
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
Memory *memory = new Memory(comm);
|
||||
Error *error = new Error(comm);
|
||||
MemoryLib *memory = new MemoryLib(comm);
|
||||
ErrorLib *error = new ErrorLib(comm);
|
||||
|
||||
// command-line args
|
||||
|
||||
@ -83,28 +83,28 @@ int main(int narg, char **arg)
|
||||
double **xyz;
|
||||
double *strain;
|
||||
|
||||
dimension = *((int *) spparks_extract(spk,"dimension"));
|
||||
nglobal = *((int *) spparks_extract(spk,"nglobal"));
|
||||
nlocal_spparks = *((int *) spparks_extract(spk,"nlocal"));
|
||||
dimension = *((int *) spparks_extract(spk,(char *) "dimension"));
|
||||
nglobal = *((int *) spparks_extract(spk,(char *) "nglobal"));
|
||||
nlocal_spparks = *((int *) spparks_extract(spk,(char *) "nlocal"));
|
||||
|
||||
boxxlo = *((double *) spparks_extract(spk,"boxxlo"));
|
||||
boxxhi = *((double *) spparks_extract(spk,"boxxhi"));
|
||||
boxylo = *((double *) spparks_extract(spk,"boxylo"));
|
||||
boxyhi = *((double *) spparks_extract(spk,"boxyhi"));
|
||||
boxxlo = *((double *) spparks_extract(spk,(char *) "boxxlo"));
|
||||
boxxhi = *((double *) spparks_extract(spk,(char *) "boxxhi"));
|
||||
boxylo = *((double *) spparks_extract(spk,(char *) "boxylo"));
|
||||
boxyhi = *((double *) spparks_extract(spk,(char *) "boxyhi"));
|
||||
if (dimension == 3) {
|
||||
boxzlo = *((double *) spparks_extract(spk,"boxzlo"));
|
||||
boxzhi = *((double *) spparks_extract(spk,"boxzhi"));
|
||||
boxzlo = *((double *) spparks_extract(spk,(char *) "boxzlo"));
|
||||
boxzhi = *((double *) spparks_extract(spk,(char *) "boxzhi"));
|
||||
} else {
|
||||
boxzlo = -0.5;
|
||||
boxzhi = 0.5;
|
||||
}
|
||||
|
||||
id_spparks = (int *) spparks_extract(spk,"id");
|
||||
spins = (int *) spparks_extract(spk,"site");
|
||||
xyz = (double **) spparks_extract(spk,"xyz");
|
||||
id_spparks = (int *) spparks_extract(spk,(char *) "id");
|
||||
spins = (int *) spparks_extract(spk,(char *) "site");
|
||||
xyz = (double **) spparks_extract(spk,(char *) "xyz");
|
||||
|
||||
nspins = *((int *) spparks_extract(spk,"nspins"));
|
||||
strain = (double *) spparks_extract(spk,"strain");
|
||||
nspins = *((int *) spparks_extract(spk,(char *) "nspins"));
|
||||
strain = (double *) spparks_extract(spk,(char *) "strain");
|
||||
|
||||
// write a LAMMPS input script using SPPARKS params
|
||||
|
||||
@ -114,7 +114,7 @@ int main(int narg, char **arg)
|
||||
|
||||
fprintf(fp,"units lj\n");
|
||||
sprintf(str,"dimension %d\n",dimension);
|
||||
fprintf(fp,str);
|
||||
fprintf(fp,"%s",str);
|
||||
fprintf(fp,"atom_style atomic\n\n");
|
||||
|
||||
fprintf(fp,"read_data data.lammps\n");
|
||||
@ -124,12 +124,14 @@ int main(int narg, char **arg)
|
||||
fprintf(fp,"pair_coeff * * 1.0 1.2\n");
|
||||
for (i = 0; i < nspins; i++) {
|
||||
sprintf(str,"pair_coeff %d %d 1.0 1.0\n",i+1,i+1);
|
||||
fprintf(fp,str);
|
||||
fprintf(fp,"%s",str);
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
|
||||
fprintf(fp,"compute da all displace/atom\n\n");
|
||||
fprintf(fp,"dump 1 all atom 10 dump.md\n");
|
||||
fprintf(fp,"dump 2 all image 10 image_lammps.*.ppm type type zoom 1.6\n");
|
||||
fprintf(fp,"dump_modify 2 pad 4 acolor * red/green/blue/aqua/magenta/yellow\n");
|
||||
fprintf(fp,"thermo 1\n");
|
||||
|
||||
fclose(fp);
|
||||
@ -138,12 +140,12 @@ int main(int narg, char **arg)
|
||||
// write a LAMMPS data file using SPPARKS data
|
||||
|
||||
LAMMPSDataWrite *lwd = new LAMMPSDataWrite(MPI_COMM_WORLD);
|
||||
lwd->file("data.lammps");
|
||||
lwd->header("%d atoms",nglobal);
|
||||
lwd->header("%d atom types",nspins);
|
||||
lwd->header("%g %g xlo xhi",boxxlo,boxxhi);
|
||||
lwd->header("%g %g ylo yhi",boxylo,boxyhi);
|
||||
lwd->header("%g %g zlo zhi",boxzlo,boxzhi);
|
||||
lwd->file((char *) "data.lammps");
|
||||
lwd->header((char *) "%d atoms",nglobal);
|
||||
lwd->header((char *) "%d atom types",nspins);
|
||||
lwd->header((char *) "%g %g xlo xhi",boxxlo,boxxhi);
|
||||
lwd->header((char *) "%g %g ylo yhi",boxylo,boxyhi);
|
||||
lwd->header((char *) "%g %g zlo zhi",boxzlo,boxzhi);
|
||||
lwd->atoms(nlocal_spparks);
|
||||
lwd->atoms(id_spparks);
|
||||
lwd->atoms(spins);
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,4 +1,4 @@
|
||||
SPPARKS (26 Aug 2010)
|
||||
SPPARKS (19 Sept 2022)
|
||||
# SPPARKS input for coupling MD/MC
|
||||
|
||||
seed 56789
|
||||
@ -28,244 +28,246 @@ diag_style energy
|
||||
temperature 1.0
|
||||
|
||||
stats 10.0
|
||||
dump 1 10.0 dump.mc
|
||||
dump 1 text 10.0 dump.mc id site x y
|
||||
run 10Setting up run ...
|
||||
Running with 32-bit site IDs
|
||||
Memory usage per processor = 2.375 Mbytes
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
0 0 0 0 0 19766
|
||||
10 17929 0 0 0.0776 5324
|
||||
Loop time of 0.077626 on 1 procs
|
||||
10 18978 0 13 0.0259 5500
|
||||
Loop time of 0.0258905 on 1 procs
|
||||
|
||||
Solve time (%) = 0.0070138 (9.03537)
|
||||
Solve time (%) = 0.00155363 (6.00079)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00146031 (1.88122)
|
||||
Outpt time (%) = 0.00415015 (5.34634)
|
||||
App time (%) = 0.0614648 (79.1807)
|
||||
Other time (%) = 0.00353694 (4.55639)
|
||||
Comm time (%) = 0.000642316 (2.4809)
|
||||
Outpt time (%) = 0.000680321 (2.62769)
|
||||
App time (%) = 0.0226682 (87.5542)
|
||||
Other time (%) = 0.000346003 (1.33641)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
10 17929 0 0 0 5324
|
||||
20 24582 0 0 0.0279 4750
|
||||
Loop time of 0.027904 on 1 procs
|
||||
10 18978 0 13 0 5500
|
||||
20 25374 0 18 0.00709 4552
|
||||
Loop time of 0.00708869 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00271416 (9.72676)
|
||||
Solve time (%) = 0.000496193 (6.99978)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000461817 (1.65502)
|
||||
Outpt time (%) = 0.0042181 (15.1165)
|
||||
App time (%) = 0.0191288 (68.5521)
|
||||
Other time (%) = 0.00138116 (4.94967)
|
||||
Comm time (%) = 0.000158039 (2.22945)
|
||||
Outpt time (%) = 0.0006739 (9.50669)
|
||||
App time (%) = 0.00564639 (79.6535)
|
||||
Other time (%) = 0.000114167 (1.61055)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
20 24582 0 0 0 4750
|
||||
30 30109 0 0 0.0234 4264
|
||||
Loop time of 0.023375 on 1 procs
|
||||
20 25374 0 18 0 4552
|
||||
30 30752 0 23 0.00575 4096
|
||||
Loop time of 0.00575649 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00216675 (9.2695)
|
||||
Solve time (%) = 0.000415252 (7.21363)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000342846 (1.46672)
|
||||
Outpt time (%) = 0.00416183 (17.8046)
|
||||
App time (%) = 0.015563 (66.5796)
|
||||
Other time (%) = 0.00114059 (4.87954)
|
||||
Comm time (%) = 0.00013092 (2.2743)
|
||||
Outpt time (%) = 0.000662723 (11.5126)
|
||||
App time (%) = 0.00445117 (77.3244)
|
||||
Other time (%) = 9.6422e-05 (1.67501)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
30 30109 0 0 0 4264
|
||||
40 35032 0 0 0.0208 3880
|
||||
Loop time of 0.020786 on 1 procs
|
||||
30 30752 0 23 0 4096
|
||||
40 35529 0 27 0.00589 3596
|
||||
Loop time of 0.00589801 on 1 procs
|
||||
|
||||
Solve time (%) = 0.0019896 (9.57182)
|
||||
Solve time (%) = 0.000424563 (7.19841)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000316858 (1.52438)
|
||||
Outpt time (%) = 0.00413609 (19.8984)
|
||||
App time (%) = 0.0132952 (63.962)
|
||||
Other time (%) = 0.00104833 (5.04341)
|
||||
Comm time (%) = 0.000114131 (1.93508)
|
||||
Outpt time (%) = 0.000763593 (12.9466)
|
||||
App time (%) = 0.0044969 (76.2443)
|
||||
Other time (%) = 9.8828e-05 (1.67562)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
40 35032 0 0 0 3880
|
||||
50 39543 0 0 0.0193 3784
|
||||
Loop time of 0.0193491 on 1 procs
|
||||
40 35529 0 27 0 3596
|
||||
50 39736 0 31 0.00444 3298
|
||||
Loop time of 0.00444854 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00185919 (9.60865)
|
||||
Solve time (%) = 0.000323247 (7.26637)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000333071 (1.72138)
|
||||
Outpt time (%) = 0.00412297 (21.3083)
|
||||
App time (%) = 0.0120728 (62.3946)
|
||||
Other time (%) = 0.000961065 (4.96698)
|
||||
Comm time (%) = 9.6777e-05 (2.17548)
|
||||
Outpt time (%) = 0.000637529 (14.3312)
|
||||
App time (%) = 0.00331502 (74.5193)
|
||||
Other time (%) = 7.5967e-05 (1.70769)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
50 39543 0 0 0 3784
|
||||
60 43899 0 0 0.0187 3706
|
||||
Loop time of 0.018713 on 1 procs
|
||||
50 39736 0 31 0 3298
|
||||
60 43567 0 35 0.00507 3296
|
||||
Loop time of 0.0050729 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00176001 (9.40526)
|
||||
Solve time (%) = 0.000354098 (6.98019)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000314474 (1.68051)
|
||||
Outpt time (%) = 0.00413895 (22.118)
|
||||
App time (%) = 0.0116153 (62.0706)
|
||||
Other time (%) = 0.000884295 (4.72556)
|
||||
Comm time (%) = 0.000114818 (2.26336)
|
||||
Outpt time (%) = 0.000893366 (17.6106)
|
||||
App time (%) = 0.00362051 (71.3697)
|
||||
Other time (%) = 9.0105e-05 (1.7762)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
60 43899 0 0 0 3706
|
||||
70 48028 0 0 0.0179 3392
|
||||
Loop time of 0.0178769 on 1 procs
|
||||
60 43567 0 35 0 3296
|
||||
70 47305 0 39 0.00417 3174
|
||||
Loop time of 0.00417405 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00174618 (9.76781)
|
||||
Solve time (%) = 0.00030627 (7.33747)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000296593 (1.65909)
|
||||
Outpt time (%) = 0.00414801 (23.2032)
|
||||
App time (%) = 0.0108221 (60.5367)
|
||||
Other time (%) = 0.000864029 (4.83322)
|
||||
Comm time (%) = 9.1156e-05 (2.18387)
|
||||
Outpt time (%) = 0.000689193 (16.5114)
|
||||
App time (%) = 0.00301511 (72.2347)
|
||||
Other time (%) = 7.232e-05 (1.73261)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
70 48028 0 0 0 3392
|
||||
80 51900 0 0 0.017 3208
|
||||
Loop time of 0.0169971 on 1 procs
|
||||
70 47305 0 39 0 3174
|
||||
80 51214 0 43 0.00437 3252
|
||||
Loop time of 0.00437516 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00157022 (9.23819)
|
||||
Solve time (%) = 0.000332427 (7.59805)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000290394 (1.70849)
|
||||
Outpt time (%) = 0.00416803 (24.522)
|
||||
App time (%) = 0.0101995 (60.0076)
|
||||
Other time (%) = 0.0007689 (4.52371)
|
||||
Comm time (%) = 9.1593e-05 (2.09348)
|
||||
Outpt time (%) = 0.00064481 (14.738)
|
||||
App time (%) = 0.00323051 (73.8375)
|
||||
Other time (%) = 7.5822e-05 (1.73301)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
80 51900 0 0 0 3208
|
||||
90 55450 0 0 0.0159 3162
|
||||
Loop time of 0.0158761 on 1 procs
|
||||
80 51214 0 43 0 3252
|
||||
90 54863 0 47 0.00417 3016
|
||||
Loop time of 0.00417621 on 1 procs
|
||||
|
||||
Solve time (%) = 0.0014894 (9.38143)
|
||||
Solve time (%) = 0.000285188 (6.82887)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000301123 (1.89671)
|
||||
Outpt time (%) = 0.00413799 (26.0644)
|
||||
App time (%) = 0.00924802 (58.2514)
|
||||
Other time (%) = 0.00069952 (4.40613)
|
||||
Comm time (%) = 9.0115e-05 (2.15782)
|
||||
Outpt time (%) = 0.000719767 (17.2349)
|
||||
App time (%) = 0.00301373 (72.1642)
|
||||
Other time (%) = 6.7413e-05 (1.61421)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
90 55450 0 0 0 3162
|
||||
100 59009 0 0 0.0158 3038
|
||||
Loop time of 0.0158172 on 1 procs
|
||||
90 54863 0 47 0 3016
|
||||
100 58060 0 51 0.00369 2766
|
||||
Loop time of 0.00369187 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00142503 (9.00938)
|
||||
Solve time (%) = 0.000253511 (6.86674)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000296831 (1.87664)
|
||||
Outpt time (%) = 0.00412178 (26.0589)
|
||||
App time (%) = 0.00923729 (58.4004)
|
||||
Other time (%) = 0.000736237 (4.65467)
|
||||
Comm time (%) = 8.878e-05 (2.40475)
|
||||
Outpt time (%) = 0.000686238 (18.5878)
|
||||
App time (%) = 0.00260318 (70.5111)
|
||||
Other time (%) = 6.0163e-05 (1.62961)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
100 59009 0 0 0 3038
|
||||
110 62454 0 0 0.0155 3066
|
||||
Loop time of 0.015537 on 1 procs
|
||||
100 58060 0 51 0 2766
|
||||
110 61110 0 55 0.00349 2840
|
||||
Loop time of 0.00349695 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00135612 (8.72834)
|
||||
Solve time (%) = 0.000239587 (6.85131)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000293732 (1.89053)
|
||||
Outpt time (%) = 0.00415182 (26.7221)
|
||||
App time (%) = 0.00904965 (58.2457)
|
||||
Other time (%) = 0.000685692 (4.41328)
|
||||
Comm time (%) = 8.1517e-05 (2.33109)
|
||||
Outpt time (%) = 0.000719507 (20.5753)
|
||||
App time (%) = 0.0023994 (68.614)
|
||||
Other time (%) = 5.6943e-05 (1.62836)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
110 62454 0 0 0 3066
|
||||
120 65856 0 0 0.0152 2898
|
||||
Loop time of 0.0152211 on 1 procs
|
||||
110 61110 0 55 0 2840
|
||||
120 64087 0 59 0.00325 2714
|
||||
Loop time of 0.00324861 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00139046 (9.13505)
|
||||
Solve time (%) = 0.000225271 (6.93437)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000291109 (1.91253)
|
||||
Outpt time (%) = 0.0041492 (27.2595)
|
||||
App time (%) = 0.00871038 (57.2257)
|
||||
Other time (%) = 0.00067997 (4.46728)
|
||||
Comm time (%) = 8.3445e-05 (2.56863)
|
||||
Outpt time (%) = 0.000647543 (19.9329)
|
||||
App time (%) = 0.00223748 (68.8748)
|
||||
Other time (%) = 5.4877e-05 (1.68924)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
120 65856 0 0 0 2898
|
||||
130 68856 0 0 0.0137 2798
|
||||
Loop time of 0.0137191 on 1 procs
|
||||
120 64087 0 59 0 2714
|
||||
130 67004 0 63 0.00333 2664
|
||||
Loop time of 0.00333198 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00130701 (9.52695)
|
||||
Solve time (%) = 0.00022963 (6.89169)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000296831 (2.16364)
|
||||
Outpt time (%) = 0.00412989 (30.1032)
|
||||
App time (%) = 0.00742817 (54.1448)
|
||||
Other time (%) = 0.000557184 (4.06138)
|
||||
Comm time (%) = 9.0368e-05 (2.71214)
|
||||
Outpt time (%) = 0.000650383 (19.5194)
|
||||
App time (%) = 0.00230627 (69.2163)
|
||||
Other time (%) = 5.5328e-05 (1.66051)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
130 68856 0 0 0 2798
|
||||
140 71967 0 0 0.0141 2700
|
||||
Loop time of 0.0141542 on 1 procs
|
||||
130 67004 0 63 0 2664
|
||||
140 69933 0 67 0.00324 2680
|
||||
Loop time of 0.00324401 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00132799 (9.38232)
|
||||
Solve time (%) = 0.000227399 (7.00982)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000284195 (2.00785)
|
||||
Outpt time (%) = 0.00414681 (29.2974)
|
||||
App time (%) = 0.00777125 (54.9042)
|
||||
Other time (%) = 0.000623941 (4.40817)
|
||||
Comm time (%) = 8.818e-05 (2.71824)
|
||||
Outpt time (%) = 0.000638812 (19.6921)
|
||||
App time (%) = 0.00223398 (68.8649)
|
||||
Other time (%) = 5.5635e-05 (1.71501)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
140 71967 0 0 0 2700
|
||||
150 74773 0 0 0.0132 2644
|
||||
Loop time of 0.0131881 on 1 procs
|
||||
140 69933 0 67 0 2680
|
||||
150 72830 0 71 0.00314 2664
|
||||
Loop time of 0.0031476 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00111961 (8.48956)
|
||||
Solve time (%) = 0.000213509 (6.78324)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000277758 (2.10612)
|
||||
Outpt time (%) = 0.00413394 (31.3459)
|
||||
App time (%) = 0.00711513 (53.951)
|
||||
Other time (%) = 0.000541687 (4.10738)
|
||||
Comm time (%) = 8.6263e-05 (2.7406)
|
||||
Outpt time (%) = 0.000676177 (21.4823)
|
||||
App time (%) = 0.00211915 (67.326)
|
||||
Other time (%) = 5.2495e-05 (1.66778)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
150 74773 0 0 0 2644
|
||||
160 77662 0 0 0.0134 2616
|
||||
Loop time of 0.0133891 on 1 procs
|
||||
150 72830 0 71 0 2664
|
||||
160 75877 0 75 0.00386 2640
|
||||
Loop time of 0.00386614 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00116301 (8.68621)
|
||||
Solve time (%) = 0.000262699 (6.79487)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00027895 (2.08341)
|
||||
Outpt time (%) = 0.00415397 (31.025)
|
||||
App time (%) = 0.00725079 (54.1544)
|
||||
Other time (%) = 0.000542402 (4.05107)
|
||||
Comm time (%) = 0.000115859 (2.99676)
|
||||
Outpt time (%) = 0.000745615 (19.2858)
|
||||
App time (%) = 0.00267785 (69.2643)
|
||||
Other time (%) = 6.4111e-05 (1.65827)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
160 77662 0 0 0 2616
|
||||
170 80475 0 0 0.0131 2538
|
||||
Loop time of 0.0130939 on 1 procs
|
||||
160 75877 0 75 0 2640
|
||||
170 78733 0 79 0.00555 2486
|
||||
Loop time of 0.0055484 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00108457 (8.28296)
|
||||
Solve time (%) = 0.000407211 (7.33925)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000279665 (2.13583)
|
||||
Outpt time (%) = 0.00412798 (31.5259)
|
||||
App time (%) = 0.00700951 (53.5324)
|
||||
Other time (%) = 0.000592232 (4.52294)
|
||||
Comm time (%) = 0.000168943 (3.04489)
|
||||
Outpt time (%) = 0.000823976 (14.8507)
|
||||
App time (%) = 0.00404893 (72.9746)
|
||||
Other time (%) = 9.9346e-05 (1.79053)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
170 80475 0 0 0 2538
|
||||
180 83407 0 0 0.0136 2660
|
||||
Loop time of 0.0136199 on 1 procs
|
||||
170 78733 0 79 0 2486
|
||||
180 81400 0 83 0.00291 2396
|
||||
Loop time of 0.00291697 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00117278 (8.61079)
|
||||
Solve time (%) = 0.000197105 (6.75718)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000262737 (1.92907)
|
||||
Outpt time (%) = 0.00413108 (30.3312)
|
||||
App time (%) = 0.0074532 (54.7229)
|
||||
Other time (%) = 0.0006001 (4.40605)
|
||||
Comm time (%) = 8.6733e-05 (2.97339)
|
||||
Outpt time (%) = 0.000641861 (22.0044)
|
||||
App time (%) = 0.00194335 (66.6221)
|
||||
Other time (%) = 4.7923e-05 (1.6429)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
180 83407 0 0 0 2660
|
||||
190 86407 0 0 0.0138 2656
|
||||
Loop time of 0.013859 on 1 procs
|
||||
180 81400 0 83 0 2396
|
||||
190 84097 0 86 0.00291 2418
|
||||
Loop time of 0.00290961 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00119066 (8.59124)
|
||||
Solve time (%) = 0.000198685 (6.82859)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000247717 (1.7874)
|
||||
Outpt time (%) = 0.00414801 (29.93)
|
||||
App time (%) = 0.00767326 (55.3665)
|
||||
Other time (%) = 0.000599384 (4.32486)
|
||||
Comm time (%) = 6.5496e-05 (2.25103)
|
||||
Outpt time (%) = 0.000671627 (23.0831)
|
||||
App time (%) = 0.00192582 (66.1883)
|
||||
Other time (%) = 4.7978e-05 (1.64895)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
190 86407 0 0 0 2656
|
||||
200 88961 0 0 0.0124 2374
|
||||
Loop time of 0.0124531 on 1 procs
|
||||
190 84097 0 86 0 2418
|
||||
200 86656 0 90 0.00332 2442
|
||||
Loop time of 0.00332468 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00107932 (8.6671)
|
||||
Solve time (%) = 0.000220838 (6.64238)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000233412 (1.87433)
|
||||
Outpt time (%) = 0.00414777 (33.3072)
|
||||
App time (%) = 0.00648117 (52.0447)
|
||||
Other time (%) = 0.000511408 (4.10668)
|
||||
Comm time (%) = 9.3912e-05 (2.82469)
|
||||
Outpt time (%) = 0.000744786 (22.4017)
|
||||
App time (%) = 0.00221113 (66.5064)
|
||||
Other time (%) = 5.402e-05 (1.62482)
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
SPPARKS (26 Aug 2010)
|
||||
SPPARKS (19 Sept 2022)
|
||||
# SPPARKS input for coupling MD/MC
|
||||
|
||||
seed 56789
|
||||
@ -28,244 +28,246 @@ diag_style energy
|
||||
temperature 1.0
|
||||
|
||||
stats 10.0
|
||||
dump 1 10.0 dump.mc
|
||||
dump 1 text 10.0 dump.mc id site x y
|
||||
run 10Setting up run ...
|
||||
Running with 32-bit site IDs
|
||||
Memory usage per processor = 2.375 Mbytes
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
0 0 0 0 0 19766
|
||||
10 18695 0 0 0.024 5696
|
||||
Loop time of 0.0240365 on 4 procs
|
||||
10 18709 0 14 0.00995 5410
|
||||
Loop time of 0.00996147 on 4 procs
|
||||
|
||||
Solve time (%) = 0.0017997 (7.48737)
|
||||
Solve time (%) = 0.000401817 (4.03371)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00263286 (10.9536)
|
||||
Outpt time (%) = 0.00416493 (17.3275)
|
||||
App time (%) = 0.0137114 (57.044)
|
||||
Other time (%) = 0.00172764 (7.18756)
|
||||
Comm time (%) = 0.00184758 (18.5473)
|
||||
Outpt time (%) = 0.000835493 (8.38724)
|
||||
App time (%) = 0.00643178 (64.5665)
|
||||
Other time (%) = 0.000444804 (4.46524)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
10 18695 0 0 0 5696
|
||||
20 25730 0 0 0.0114 4806
|
||||
Loop time of 0.0113776 on 4 procs
|
||||
10 18709 0 14 0 5410
|
||||
20 25405 0 20 0.00348 4414
|
||||
Loop time of 0.00348928 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000647247 (5.68877)
|
||||
Solve time (%) = 0.000145149 (4.15985)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.0013088 (11.5033)
|
||||
Outpt time (%) = 0.00417346 (36.6812)
|
||||
App time (%) = 0.0045594 (40.0733)
|
||||
Other time (%) = 0.000688732 (6.05338)
|
||||
Comm time (%) = 0.000562263 (16.114)
|
||||
Outpt time (%) = 0.0007944 (22.7669)
|
||||
App time (%) = 0.00176801 (50.6697)
|
||||
Other time (%) = 0.000219463 (6.28963)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
20 25730 0 0 0 4806
|
||||
30 31377 0 0 0.00985 4308
|
||||
Loop time of 0.00987101 on 4 procs
|
||||
20 25405 0 20 0 4414
|
||||
30 30724 0 25 0.00314 4092
|
||||
Loop time of 0.00314216 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000525832 (5.32704)
|
||||
Solve time (%) = 0.000123228 (3.92176)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.0012235 (12.3949)
|
||||
Outpt time (%) = 0.00415748 (42.1181)
|
||||
App time (%) = 0.00343758 (34.825)
|
||||
Other time (%) = 0.000526607 (5.33489)
|
||||
Comm time (%) = 0.000561445 (17.8681)
|
||||
Outpt time (%) = 0.00079681 (25.3586)
|
||||
App time (%) = 0.00146373 (46.5835)
|
||||
Other time (%) = 0.000196952 (6.26804)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
30 31377 0 0 0 4308
|
||||
40 36311 0 0 0.0092 3840
|
||||
Loop time of 0.00922179 on 4 procs
|
||||
30 30724 0 25 0 4092
|
||||
40 35289 0 30 0.00256 3496
|
||||
Loop time of 0.0025659 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000474155 (5.14168)
|
||||
Solve time (%) = 9.47535e-05 (3.6928)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00114667 (12.4344)
|
||||
Outpt time (%) = 0.00414455 (44.943)
|
||||
App time (%) = 0.00293165 (31.7905)
|
||||
Other time (%) = 0.000524759 (5.69043)
|
||||
Comm time (%) = 0.000508415 (19.8143)
|
||||
Outpt time (%) = 0.000788757 (30.74)
|
||||
App time (%) = 0.00106383 (41.4604)
|
||||
Other time (%) = 0.000110143 (4.29259)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
40 36311 0 0 0 3840
|
||||
50 40886 0 0 0.00891 3534
|
||||
Loop time of 0.0089252 on 4 procs
|
||||
40 35289 0 30 0 3496
|
||||
50 39511 0 35 0.00252 3294
|
||||
Loop time of 0.00252512 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000433862 (4.86109)
|
||||
Solve time (%) = 8.7092e-05 (3.44903)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00113171 (12.68)
|
||||
Outpt time (%) = 0.00413698 (46.3517)
|
||||
App time (%) = 0.00268257 (30.0561)
|
||||
Other time (%) = 0.000540078 (6.05116)
|
||||
Comm time (%) = 0.000631729 (25.0178)
|
||||
Outpt time (%) = 0.000780138 (30.8952)
|
||||
App time (%) = 0.000963016 (38.1375)
|
||||
Other time (%) = 6.31405e-05 (2.5005)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
50 40886 0 0 0 3534
|
||||
60 44888 0 0 0.00831 3306
|
||||
Loop time of 0.00833625 on 4 procs
|
||||
50 39511 0 35 0 3294
|
||||
60 43241 0 40 0.00254 3158
|
||||
Loop time of 0.00254794 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000383437 (4.59963)
|
||||
Solve time (%) = 8.5528e-05 (3.35675)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00106108 (12.7285)
|
||||
Outpt time (%) = 0.00413227 (49.5699)
|
||||
App time (%) = 0.00232393 (27.8774)
|
||||
Other time (%) = 0.000435531 (5.22455)
|
||||
Comm time (%) = 0.000598337 (23.4831)
|
||||
Outpt time (%) = 0.000777931 (30.5317)
|
||||
App time (%) = 0.000940118 (36.8971)
|
||||
Other time (%) = 0.00014603 (5.73128)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
60 44888 0 0 0 3306
|
||||
70 48583 0 0 0.00806 3078
|
||||
Loop time of 0.0080772 on 4 procs
|
||||
60 43241 0 40 0 3158
|
||||
70 46797 0 44 0.00248 3060
|
||||
Loop time of 0.00248266 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000353277 (4.37375)
|
||||
Solve time (%) = 8.14515e-05 (3.28081)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00102895 (12.739)
|
||||
Outpt time (%) = 0.0041061 (50.8357)
|
||||
App time (%) = 0.00213838 (26.4742)
|
||||
Other time (%) = 0.000450492 (5.57732)
|
||||
Comm time (%) = 0.000482648 (19.4407)
|
||||
Outpt time (%) = 0.000991271 (39.9277)
|
||||
App time (%) = 0.00085854 (34.5814)
|
||||
Other time (%) = 6.87532e-05 (2.76933)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
70 48583 0 0 0 3078
|
||||
80 52044 0 0 0.00786 2998
|
||||
Loop time of 0.00788343 on 4 procs
|
||||
70 46797 0 44 0 3060
|
||||
80 50183 0 48 0.0024 3102
|
||||
Loop time of 0.00240397 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000333607 (4.23175)
|
||||
Solve time (%) = 8.22802e-05 (3.42268)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00101435 (12.8669)
|
||||
Outpt time (%) = 0.00420028 (53.2799)
|
||||
App time (%) = 0.00198931 (25.234)
|
||||
Other time (%) = 0.000345886 (4.3875)
|
||||
Comm time (%) = 0.000494873 (20.5856)
|
||||
Outpt time (%) = 0.00085299 (35.4825)
|
||||
App time (%) = 0.000883469 (36.7504)
|
||||
Other time (%) = 9.03613e-05 (3.75883)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
80 52044 0 0 0 2998
|
||||
90 55352 0 0 0.0083 3026
|
||||
Loop time of 0.00831437 on 4 procs
|
||||
80 50183 0 48 0 3102
|
||||
90 53732 0 52 0.00272 3028
|
||||
Loop time of 0.00272017 on 4 procs
|
||||
|
||||
Solve time (%) = 0.00031358 (3.77154)
|
||||
Solve time (%) = 9.94713e-05 (3.6568)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00111783 (13.4445)
|
||||
Outpt time (%) = 0.00467652 (56.2462)
|
||||
App time (%) = 0.00188529 (22.6751)
|
||||
Other time (%) = 0.00032115 (3.86259)
|
||||
Comm time (%) = 0.000613542 (22.5553)
|
||||
Outpt time (%) = 0.000800183 (29.4166)
|
||||
App time (%) = 0.00108281 (39.8067)
|
||||
Other time (%) = 0.000124164 (4.56456)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
90 55352 0 0 0 3026
|
||||
100 58494 0 0 0.00733 2742
|
||||
Loop time of 0.00735307 on 4 procs
|
||||
90 53732 0 52 0 3028
|
||||
100 57112 0 56 0.0023 2942
|
||||
Loop time of 0.00230787 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000297189 (4.0417)
|
||||
Solve time (%) = 7.58975e-05 (3.28864)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000801027 (10.8938)
|
||||
Outpt time (%) = 0.00418043 (56.8529)
|
||||
App time (%) = 0.00179577 (24.422)
|
||||
Other time (%) = 0.000278652 (3.7896)
|
||||
Comm time (%) = 0.000502726 (21.7831)
|
||||
Outpt time (%) = 0.000796114 (34.4956)
|
||||
App time (%) = 0.000828819 (35.9127)
|
||||
Other time (%) = 0.000104316 (4.51999)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
100 58494 0 0 0 2742
|
||||
110 61498 0 0 0.00732 2636
|
||||
Loop time of 0.00733691 on 4 procs
|
||||
100 57112 0 56 0 2942
|
||||
110 60445 0 60 0.00192 2850
|
||||
Loop time of 0.00192261 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000282168 (3.84587)
|
||||
Solve time (%) = 6.89883e-05 (3.58826)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000877678 (11.9625)
|
||||
Outpt time (%) = 0.00414526 (56.4987)
|
||||
App time (%) = 0.00174332 (23.7609)
|
||||
Other time (%) = 0.000288486 (3.93199)
|
||||
Comm time (%) = 0.000257782 (13.4079)
|
||||
Outpt time (%) = 0.000791242 (41.1545)
|
||||
App time (%) = 0.000735212 (38.2403)
|
||||
Other time (%) = 6.9388e-05 (3.60905)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
110 61498 0 0 0 2636
|
||||
120 64343 0 0 0.00719 2518
|
||||
Loop time of 0.00721735 on 4 procs
|
||||
110 60445 0 60 0 2850
|
||||
120 63603 0 64 0.00193 2866
|
||||
Loop time of 0.00193198 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000270605 (3.74937)
|
||||
Solve time (%) = 6.44032e-05 (3.33354)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00078702 (10.9046)
|
||||
Outpt time (%) = 0.00416625 (57.7254)
|
||||
App time (%) = 0.00162369 (22.497)
|
||||
Other time (%) = 0.000369787 (5.12359)
|
||||
Comm time (%) = 0.00027428 (14.1969)
|
||||
Outpt time (%) = 0.000812462 (42.0534)
|
||||
App time (%) = 0.000682923 (35.3484)
|
||||
Other time (%) = 9.79088e-05 (5.0678)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
120 64343 0 0 0 2518
|
||||
130 66901 0 0 0.00709 2480
|
||||
Loop time of 0.00710845 on 4 procs
|
||||
120 63603 0 64 0 2866
|
||||
130 66749 0 68 0.0022 2710
|
||||
Loop time of 0.00220226 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000247002 (3.47476)
|
||||
Solve time (%) = 8.013e-05 (3.63854)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00100386 (14.1221)
|
||||
Outpt time (%) = 0.00416774 (58.6307)
|
||||
App time (%) = 0.00143349 (20.166)
|
||||
Other time (%) = 0.00025636 (3.60641)
|
||||
Comm time (%) = 0.000362387 (16.4552)
|
||||
Outpt time (%) = 0.000819649 (37.2186)
|
||||
App time (%) = 0.000844146 (38.3309)
|
||||
Other time (%) = 9.59462e-05 (4.35672)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
130 66901 0 0 0 2480
|
||||
140 69617 0 0 0.00723 2462
|
||||
Loop time of 0.00725645 on 4 procs
|
||||
130 66749 0 68 0 2710
|
||||
140 69868 0 72 0.00276 2822
|
||||
Loop time of 0.00276561 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000262678 (3.61992)
|
||||
Solve time (%) = 8.8444e-05 (3.19799)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000848353 (11.691)
|
||||
Outpt time (%) = 0.00418752 (57.7076)
|
||||
App time (%) = 0.00152171 (20.9704)
|
||||
Other time (%) = 0.000436187 (6.01102)
|
||||
Comm time (%) = 0.000566006 (20.4659)
|
||||
Outpt time (%) = 0.00100224 (36.2395)
|
||||
App time (%) = 0.000938724 (33.9427)
|
||||
Other time (%) = 0.000170192 (6.15388)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
140 69617 0 0 0 2462
|
||||
150 72516 0 0 0.0077 2368
|
||||
Loop time of 0.00771403 on 4 procs
|
||||
140 69868 0 72 0 2822
|
||||
150 72809 0 77 0.00203 2530
|
||||
Loop time of 0.00203296 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000279188 (3.61922)
|
||||
Solve time (%) = 6.10922e-05 (3.00508)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00115103 (14.9212)
|
||||
Outpt time (%) = 0.00420797 (54.5495)
|
||||
App time (%) = 0.00164241 (21.2911)
|
||||
Other time (%) = 0.000433445 (5.61892)
|
||||
Comm time (%) = 0.000430907 (21.196)
|
||||
Outpt time (%) = 0.000773949 (38.07)
|
||||
App time (%) = 0.000649508 (31.9488)
|
||||
Other time (%) = 0.000117508 (5.78011)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
150 72516 0 0 0 2368
|
||||
160 75201 0 0 0.00745 2384
|
||||
Loop time of 0.00747746 on 4 procs
|
||||
150 72809 0 77 0 2530
|
||||
160 75490 0 82 0.00243 2560
|
||||
Loop time of 0.00243939 on 4 procs
|
||||
|
||||
Solve time (%) = 0.00026089 (3.48901)
|
||||
Solve time (%) = 7.29237e-05 (2.98943)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00115579 (15.457)
|
||||
Outpt time (%) = 0.00416714 (55.7293)
|
||||
App time (%) = 0.0015164 (20.2796)
|
||||
Other time (%) = 0.000377238 (5.045)
|
||||
Comm time (%) = 0.000533877 (21.8857)
|
||||
Outpt time (%) = 0.000900521 (36.9159)
|
||||
App time (%) = 0.000753532 (30.8902)
|
||||
Other time (%) = 0.000178534 (7.31879)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
160 75201 0 0 0 2384
|
||||
170 77794 0 0 0.00709 2286
|
||||
Loop time of 0.00710869 on 4 procs
|
||||
160 75490 0 82 0 2560
|
||||
170 78382 0 86 0.00203 2424
|
||||
Loop time of 0.00203432 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000261724 (3.68175)
|
||||
Solve time (%) = 6.05745e-05 (2.97762)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000879705 (12.3751)
|
||||
Outpt time (%) = 0.00419676 (59.0371)
|
||||
App time (%) = 0.00145274 (20.4362)
|
||||
Other time (%) = 0.000317752 (4.46992)
|
||||
Comm time (%) = 0.000357404 (17.5687)
|
||||
Outpt time (%) = 0.000830967 (40.8473)
|
||||
App time (%) = 0.000642883 (31.6018)
|
||||
Other time (%) = 0.000142495 (7.00454)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
170 77794 0 0 0 2286
|
||||
180 80320 0 0 0.00723 2186
|
||||
Loop time of 0.00725418 on 4 procs
|
||||
170 78382 0 86 0 2424
|
||||
180 81046 0 90 0.00266 2450
|
||||
Loop time of 0.00266286 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000241041 (3.32279)
|
||||
Solve time (%) = 7.05732e-05 (2.65028)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00100464 (13.8491)
|
||||
Outpt time (%) = 0.00413877 (57.0535)
|
||||
App time (%) = 0.00144053 (19.8579)
|
||||
Other time (%) = 0.000429213 (5.91677)
|
||||
Comm time (%) = 0.000638214 (23.9672)
|
||||
Outpt time (%) = 0.00102986 (38.6749)
|
||||
App time (%) = 0.000760398 (28.5557)
|
||||
Other time (%) = 0.000163817 (6.15191)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
180 80320 0 0 0 2186
|
||||
190 82621 0 0 0.00686 2204
|
||||
Loop time of 0.00687295 on 4 procs
|
||||
180 81046 0 90 0 2450
|
||||
190 83562 0 94 0.00216 2402
|
||||
Loop time of 0.0021675 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000222385 (3.23565)
|
||||
Solve time (%) = 6.2358e-05 (2.87696)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000860512 (12.5203)
|
||||
Outpt time (%) = 0.00418121 (60.8357)
|
||||
App time (%) = 0.00126499 (18.4053)
|
||||
Other time (%) = 0.000343859 (5.00308)
|
||||
Comm time (%) = 0.000536287 (24.7422)
|
||||
Outpt time (%) = 0.000802317 (37.0158)
|
||||
App time (%) = 0.000649124 (29.9481)
|
||||
Other time (%) = 0.000117412 (5.41694)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
190 82621 0 0 0 2204
|
||||
200 84907 0 0 0.00681 2276
|
||||
Loop time of 0.0068413 on 4 procs
|
||||
190 83562 0 94 0 2402
|
||||
200 86036 0 98 0.0021 2306
|
||||
Loop time of 0.00210625 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000233412 (3.4118)
|
||||
Solve time (%) = 5.94018e-05 (2.82026)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000758171 (11.0823)
|
||||
Outpt time (%) = 0.00421125 (61.5562)
|
||||
App time (%) = 0.00125164 (18.2953)
|
||||
Other time (%) = 0.000386834 (5.65439)
|
||||
Comm time (%) = 0.000492842 (23.399)
|
||||
Outpt time (%) = 0.000817012 (38.7899)
|
||||
App time (%) = 0.000597335 (28.3601)
|
||||
Other time (%) = 0.00013966 (6.63072)
|
||||
|
||||
@ -1 +1,3 @@
|
||||
#define SPKPATH /home/sjplimp/spparks
|
||||
// path to your SPPARKS home directory
|
||||
|
||||
#define SPKPATH /home/sjplimp/spparks/git
|
||||
|
||||
@ -6,7 +6,7 @@ SPPARKS applications in 2 sister directories.
|
||||
The library dir has a Makefile (which you may need to edit for your
|
||||
box). If you type
|
||||
|
||||
g++ -f Makefile.g++
|
||||
g++ -f Makefile.mpi
|
||||
|
||||
you should create libcouple.a, which the other coupled applications
|
||||
link to.
|
||||
|
||||
@ -1,11 +1,11 @@
|
||||
#include <mpi.h>
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include "error.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Error::Error(MPI_Comm caller)
|
||||
ErrorLib::ErrorLib(MPI_Comm caller)
|
||||
{
|
||||
comm = caller;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
@ -15,7 +15,7 @@ Error::Error(MPI_Comm caller)
|
||||
called by all procs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::all(const char *str)
|
||||
void ErrorLib::all(const char *str)
|
||||
{
|
||||
if (me == 0) printf("ERROR: %s\n",str);
|
||||
MPI_Finalize();
|
||||
@ -26,7 +26,7 @@ void Error::all(const char *str)
|
||||
called by one proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::one(const char *str)
|
||||
void ErrorLib::one(const char *str)
|
||||
{
|
||||
printf("ERROR on proc %d: %s\n",me,str);
|
||||
MPI_Abort(comm,1);
|
||||
@ -36,7 +36,7 @@ void Error::one(const char *str)
|
||||
called by one proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::warning(const char *str)
|
||||
void ErrorLib::warning(const char *str)
|
||||
{
|
||||
printf("WARNING: %s\n",str);
|
||||
}
|
||||
@ -1,11 +1,11 @@
|
||||
#ifndef ERROR_H
|
||||
#define ERROR_H
|
||||
#ifndef ERRORLIB_H
|
||||
#define ERRORLIB_H
|
||||
|
||||
#include <mpi.h>
|
||||
|
||||
class Error {
|
||||
class ErrorLib {
|
||||
public:
|
||||
Error(MPI_Comm);
|
||||
ErrorLib(MPI_Comm);
|
||||
|
||||
void all(const char *);
|
||||
void one(const char *);
|
||||
@ -29,7 +29,7 @@ void replace(char *file, char *header, int n, char **lines)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
char **extract(char *file, char *header, int n, char **lines)
|
||||
void extract(char *file, char *header, int n, char **lines)
|
||||
{
|
||||
FILE *fp = fopen(file,"r");
|
||||
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
#ifndef FILES_H
|
||||
#define FILES_H
|
||||
void replace(char *, char *, int, char **);
|
||||
char **extract(char *, char *, int, char **);
|
||||
void extract(char *, char *, int, char **);
|
||||
#endif
|
||||
|
||||
@ -2,8 +2,8 @@
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "irregular.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "memorylib.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
|
||||
|
||||
@ -18,8 +18,8 @@ Irregular::Irregular(MPI_Comm caller)
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
memory = new MemoryLib(comm);
|
||||
error = new ErrorLib(comm);
|
||||
|
||||
init();
|
||||
|
||||
|
||||
@ -46,8 +46,8 @@ class Irregular {
|
||||
MPI_Status *status; // MPI statuses for Waitall
|
||||
MPI_Comm comm; // MPI communicator for all communication
|
||||
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
class MemoryLib *memory;
|
||||
class ErrorLib *error;
|
||||
|
||||
void exchange_same(char *, char *);
|
||||
void exchange_varying(char *, char *);
|
||||
|
||||
@ -2,8 +2,8 @@
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "lammps_data_write.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "memorylib.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
#define DELTA 4;
|
||||
|
||||
|
||||
@ -3,8 +3,8 @@
|
||||
#include <cstdio>
|
||||
#include "many2many.h"
|
||||
#include "irregular.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "memorylib.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
#include <map>
|
||||
|
||||
@ -18,8 +18,8 @@ Many2Many::Many2Many(MPI_Comm caller)
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
memory = new MemoryLib(comm);
|
||||
error = new ErrorLib(comm);
|
||||
|
||||
src_own = dest_own = NULL;
|
||||
src_off = dest_off = NULL;
|
||||
|
||||
@ -15,8 +15,8 @@ class Many2Many {
|
||||
protected:
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
class MemoryLib *memory;
|
||||
class ErrorLib *error;
|
||||
|
||||
int nown; // # of IDs common to src and dest
|
||||
int nsrc_off,ndest_off; // # of off-processor IDs
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include "many2one.h"
|
||||
#include "memory.h"
|
||||
#include "memorylib.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -12,7 +12,7 @@ Many2One::Many2One(MPI_Comm caller_comm)
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
memory = new MemoryLib(comm);
|
||||
|
||||
if (me == 0) {
|
||||
counts = new int[nprocs];
|
||||
|
||||
@ -14,7 +14,7 @@ class Many2One {
|
||||
protected:
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
class MemoryLib *memory;
|
||||
|
||||
int nsrc,nall;
|
||||
int *counts,*multicounts;
|
||||
|
||||
@ -1,19 +1,19 @@
|
||||
#include <mpi.h>
|
||||
#include <cstdlib>
|
||||
#include <cstdio>
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "memorylib.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Memory::Memory(MPI_Comm comm)
|
||||
MemoryLib::MemoryLib(MPI_Comm comm)
|
||||
{
|
||||
error = new Error(comm);
|
||||
error = new ErrorLib(comm);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Memory::~Memory()
|
||||
MemoryLib::~MemoryLib()
|
||||
{
|
||||
delete error;
|
||||
}
|
||||
@ -22,7 +22,7 @@ Memory::~Memory()
|
||||
safe malloc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void *Memory::smalloc(int n, const char *name)
|
||||
void *MemoryLib::smalloc(int n, const char *name)
|
||||
{
|
||||
if (n == 0) return NULL;
|
||||
void *ptr = malloc(n);
|
||||
@ -38,7 +38,7 @@ void *Memory::smalloc(int n, const char *name)
|
||||
safe free
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Memory::sfree(void *ptr)
|
||||
void MemoryLib::sfree(void *ptr)
|
||||
{
|
||||
if (ptr == NULL) return;
|
||||
free(ptr);
|
||||
@ -48,7 +48,7 @@ void Memory::sfree(void *ptr)
|
||||
safe realloc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void *Memory::srealloc(void *ptr, int n, const char *name)
|
||||
void *MemoryLib::srealloc(void *ptr, int n, const char *name)
|
||||
{
|
||||
if (n == 0) {
|
||||
sfree(ptr);
|
||||
@ -68,7 +68,7 @@ void *Memory::srealloc(void *ptr, int n, const char *name)
|
||||
create a 2d double array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double **Memory::create_2d_double_array(int n1, int n2, const char *name)
|
||||
double **MemoryLib::create_2d_double_array(int n1, int n2, const char *name)
|
||||
|
||||
{
|
||||
double *data = (double *) smalloc(n1*n2*sizeof(double),name);
|
||||
@ -89,7 +89,7 @@ double **Memory::create_2d_double_array(int n1, int n2, const char *name)
|
||||
if either dim is 0, return NULL
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double **Memory::grow_2d_double_array(double **array,
|
||||
double **MemoryLib::grow_2d_double_array(double **array,
|
||||
int n1, int n2, const char *name)
|
||||
|
||||
{
|
||||
@ -111,7 +111,7 @@ double **Memory::grow_2d_double_array(double **array,
|
||||
free a 2d double array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Memory::destroy_2d_double_array(double **array)
|
||||
void MemoryLib::destroy_2d_double_array(double **array)
|
||||
|
||||
{
|
||||
if (array == NULL) return;
|
||||
@ -1,12 +1,12 @@
|
||||
#ifndef MEMORY_H
|
||||
#define MEMORY_H
|
||||
#ifndef MEMORY_LIB_H
|
||||
#define MEMORY_LIB_H
|
||||
|
||||
#include <mpi.h>
|
||||
|
||||
class Memory {
|
||||
class MemoryLib {
|
||||
public:
|
||||
Memory(MPI_Comm);
|
||||
~Memory();
|
||||
MemoryLib(MPI_Comm);
|
||||
~MemoryLib();
|
||||
|
||||
void *smalloc(int n, const char *);
|
||||
void sfree(void *);
|
||||
@ -17,7 +17,7 @@ class Memory {
|
||||
void destroy_2d_double_array(double **);
|
||||
|
||||
private:
|
||||
class Error *error;
|
||||
class ErrorLib *error;
|
||||
};
|
||||
|
||||
#endif
|
||||
@ -1,7 +1,7 @@
|
||||
#include <mpi.h>
|
||||
#include <cstdlib>
|
||||
#include "one2many.h"
|
||||
#include "memory.h"
|
||||
#include "memorylib.h"
|
||||
|
||||
#include <map>
|
||||
|
||||
@ -13,7 +13,7 @@ One2Many::One2Many(MPI_Comm caller_comm)
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
memory = new MemoryLib(comm);
|
||||
hash = new std::map<int,int>();
|
||||
}
|
||||
|
||||
|
||||
@ -16,7 +16,7 @@ class One2Many {
|
||||
protected:
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
class MemoryLib *memory;
|
||||
std::map<int,int> *hash;
|
||||
int nsrc;
|
||||
};
|
||||
|
||||
@ -2,8 +2,8 @@
|
||||
#include <cstdlib>
|
||||
#include <cstdio>
|
||||
#include "send2one.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "memorylib.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -13,8 +13,8 @@ Send2One::Send2One(MPI_Comm caller_comm)
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
memory = new MemoryLib(comm);
|
||||
error = new ErrorLib(comm);
|
||||
|
||||
buf = NULL;
|
||||
maxbuf = 0;
|
||||
|
||||
@ -13,8 +13,8 @@ class Send2One {
|
||||
protected:
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
class MemoryLib *memory;
|
||||
class ErrorLib *error;
|
||||
|
||||
int maxbuf;
|
||||
char *buf;
|
||||
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (8 Feb 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for LJ simple fluid, no dynamics
|
||||
# T = 2.0
|
||||
@ -87,8 +88,10 @@ thermo 1000
|
||||
# run
|
||||
|
||||
run 10000
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
@ -97,45 +100,45 @@ 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
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.0603874 2.9024736 -3.2576986 3.0482443 0.584 73 0.069266074 0.066959582 0.11158434 0.53624 1.3978532 0.0014407586 64.19
|
||||
2000 2.1586837 1.5581387 -2.8420766 3.1857993 0.496 62 0.068487803 0.067570935 0.1126652 0.53128 1.3713694 0.020274019 63.41
|
||||
3000 2.4664064 0.65471138 -3.3428236 3.6435549 0.528 66 0.068182273 0.067547792 0.11226502 0.53472 1.3892234 0.0070204504 63.68
|
||||
4000 1.8880496 1.4802782 -2.7846019 2.785647 0.488 61 0.068250075 0.067843541 0.11299989 0.52744 1.299496 0.033918563 63.1
|
||||
5000 2.0578649 1.3204331 -3.5571862 3.0433213 0.568 71 0.067858571 0.067732262 0.11271981 0.5364 1.4237505 0.00065741209 64
|
||||
6000 2.3627973 0.97064566 -3.1107668 3.4879388 0.504 63 0.067846204 0.06757018 0.11272207 0.5332 1.3945131 0.014216594 63.7
|
||||
7000 1.6629817 0.98138972 -2.7780297 2.4514644 0.464 58 0.067451389 0.067269791 0.11263692 0.53688 1.4207486 -0.0012887793 63.82
|
||||
8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43
|
||||
9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23
|
||||
10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44
|
||||
Loop time of 27.8547 on 1 procs for 10000 steps with 64 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.4341 | 0.4341 | 0.4341 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.0603874 2.9024736 -3.2576986 3.0482443 0.584 73 0.069266074 0.066959582 0.11158434 0.53624 1.3978532 0.0014407586 67.03
|
||||
2000 2.1586837 1.5581387 -2.8420766 3.1857993 0.496 62 0.068487803 0.067570935 0.1126652 0.53128 1.3713694 0.020274019 66.41
|
||||
3000 2.4664064 0.65471138 -3.3428236 3.6435549 0.528 66 0.068182273 0.067547792 0.11226502 0.53472 1.3892234 0.0070204504 66.84
|
||||
4000 1.8880496 1.4802782 -2.7846019 2.785647 0.488 61 0.068250075 0.067843541 0.11299989 0.52744 1.299496 0.033918563 65.93
|
||||
5000 2.0578649 1.3204331 -3.5571862 3.0433213 0.568 71 0.067858571 0.067732262 0.11271981 0.5364 1.4237505 0.00065741209 67.05
|
||||
6000 2.3627973 0.97064566 -3.1107668 3.4879388 0.504 63 0.067846204 0.06757018 0.11272207 0.5332 1.3945131 0.014216594 66.65
|
||||
7000 1.6629817 0.98138972 -2.7780297 2.4514644 0.464 58 0.067451389 0.067269791 0.11263692 0.53688 1.4207486 -0.0012887793 67.11
|
||||
8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 65.92
|
||||
9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 66.34
|
||||
10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 65.89
|
||||
Loop time of 12.3703 on 1 procs for 10000 steps with 64 atoms
|
||||
|
||||
Performance: 155090.656 tau/day, 359.006 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 349224.803 tau/day, 808.391 timesteps/s, 51.737 katom-step/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.43892 | 0.43892 | 0.43892 | 0.0 | 1.58
|
||||
Neigh | 1.278 | 1.278 | 1.278 | 0.0 | 4.59
|
||||
Comm | 0.24105 | 0.24105 | 0.24105 | 0.0 | 0.87
|
||||
Output | 0.00032067 | 0.00032067 | 0.00032067 | 0.0 | 0.00
|
||||
Modify | 25.88 | 25.88 | 25.88 | 0.0 | 92.91
|
||||
Other | | 0.01693 | | | 0.06
|
||||
Pair | 0.28 | 0.28 | 0.28 | 0.0 | 2.26
|
||||
Neigh | 0.76133 | 0.76133 | 0.76133 | 0.0 | 6.15
|
||||
Comm | 0.073181 | 0.073181 | 0.073181 | 0.0 | 0.59
|
||||
Output | 0.00031081 | 0.00031081 | 0.00031081 | 0.0 | 0.00
|
||||
Modify | 11.24 | 11.24 | 11.24 | 0.0 | 90.87
|
||||
Other | | 0.01498 | | | 0.12
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 714 ave 714 max 714 min
|
||||
Nghost: 714 ave 714 max 714 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2423 ave 2423 max 2423 min
|
||||
Neighs: 2423 ave 2423 max 2423 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2423
|
||||
Ave neighs/atom = 37.8594
|
||||
Ave neighs/atom = 37.859375
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:27
|
||||
Total wall time: 0:00:12
|
||||
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (8 Feb 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for LJ simple fluid, no dynamics
|
||||
# T = 2.0
|
||||
@ -87,8 +88,10 @@ thermo 1000
|
||||
# run
|
||||
|
||||
run 10000
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
@ -97,45 +100,45 @@ 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
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 62.56
|
||||
2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 64.56
|
||||
3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 64.21
|
||||
4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 64.75
|
||||
5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 65.04
|
||||
6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 63.01
|
||||
7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 61.72
|
||||
8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45
|
||||
9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73
|
||||
10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04
|
||||
Loop time of 26.0069 on 4 procs for 10000 steps with 60 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.4492 | 0.4492 | 0.4492 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 65.69
|
||||
2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 67.75
|
||||
3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 66.92
|
||||
4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 67.68
|
||||
5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 67.96
|
||||
6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 66.39
|
||||
7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 64.96
|
||||
8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 66.63
|
||||
9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 67
|
||||
10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 65.34
|
||||
Loop time of 14.6475 on 4 procs for 10000 steps with 60 atoms
|
||||
|
||||
Performance: 166109.741 tau/day, 384.513 timesteps/s
|
||||
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 294930.892 tau/day, 682.710 timesteps/s, 40.963 katom-step/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10309 | 0.115 | 0.1225 | 2.2 | 0.44
|
||||
Neigh | 0.3907 | 0.40447 | 0.41957 | 1.7 | 1.56
|
||||
Comm | 0.44236 | 0.46678 | 0.49472 | 2.8 | 1.79
|
||||
Output | 0.0011411 | 0.0062903 | 0.0080109 | 3.7 | 0.02
|
||||
Modify | 25 | 25.002 | 25.005 | 0.0 | 96.14
|
||||
Other | | 0.01231 | | | 0.05
|
||||
Pair | 0.079336 | 0.086188 | 0.093829 | 2.2 | 0.59
|
||||
Neigh | 0.25224 | 0.26194 | 0.26946 | 1.4 | 1.79
|
||||
Comm | 0.31594 | 0.33181 | 0.34839 | 2.4 | 2.27
|
||||
Output | 0.00039633 | 0.00063799 | 0.00071881 | 0.0 | 0.00
|
||||
Modify | 13.956 | 13.957 | 13.958 | 0.0 | 95.29
|
||||
Other | | 0.01003 | | | 0.07
|
||||
|
||||
Nlocal: 15 ave 16 max 14 min
|
||||
Nlocal: 15 ave 16 max 14 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 437 ave 446 max 431 min
|
||||
Nghost: 437 ave 446 max 431 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 529 ave 595 max 437 min
|
||||
Neighs: 529 ave 595 max 437 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 2116
|
||||
Ave neighs/atom = 35.2667
|
||||
Ave neighs/atom = 35.266667
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:26
|
||||
Total wall time: 0:00:14
|
||||
|
||||
Reference in New Issue
Block a user