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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5724 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-02-23 15:25:00 +00:00
parent 2fd2543d88
commit 3a720230d9
4 changed files with 27 additions and 2 deletions
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1
src/REPLICA/tad.cpp
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@ -15,6 +15,7 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"

26
src/dump_cfg.cpp
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@ -15,6 +15,7 @@
Contributing author: Liang Wan (Chinese Academy of Sciences)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "dump_cfg.h"
@ -186,11 +187,27 @@ void DumpCFG::init_style()
void DumpCFG::write_header(bigint n)
{
// special handling for atom style peri
// use average volume of particles to scale particles to mimic C atoms
// scale box dimension to sc lattice for C with sigma = 1.44 Angstroms
double scale;
if (atom->style_match("peri")) {
int nlocal = atom->nlocal;
double vone = 0.0;
for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
double vave;
MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
if (atom->natoms) vave /= atom->natoms;
if (vave > 0.0) scale = 1.44 / pow(vave,1.0/3.0);
else scale = 1.0;
} else scale = 1.0;
if (me == 0 || multiproc) {
char str[64];
sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
fprintf(fp,str,n);
fprintf(fp,"A = 1.0 Angstrom (basic length-scale)\n");
fprintf(fp,"A = %g Angstrom (basic length-scale)\n",scale);
fprintf(fp,"H0(1,1) = %g A\n",domain->xprd);
fprintf(fp,"H0(1,2) = 0 A \n");
fprintf(fp,"H0(1,3) = 0 A \n");
@ -228,7 +245,11 @@ void DumpCFG::write_data(int n, double *mybuf)
{
int i,j,m,itype;
int tag_i,index;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
// transfer data from buf to rbuf
// if write by proc 0, transfer chunk by chunk
@ -246,7 +267,8 @@ void DumpCFG::write_data(int n, double *mybuf)
for (i = 0; i < nchosen; i++)
if (rbuf[i][1] == itype) break;
if (i < nchosen) {
fprintf(fp,"%g\n",mass[itype]);
if (rmass) fprintf(fp,"%g\n",rmass[i]);
else fprintf(fp,"%g\n",mass[itype]);
fprintf(fp,"%s\n",typenames[itype]);
for (; i < nchosen; i++) {
if (rbuf[i][1] == itype) {

1
src/minimize.cpp
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@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "stdlib.h"
#include "minimize.h"
#include "domain.h"

1
src/thermo.cpp
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@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"