Homec4science
Diffusion lammps (HEAD -> master) Browse

lammps/src/dump_atom.cpp
0cc1d090f44eHEAD -> master

Last Change
Raw File

dump_atom.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "dump_atom.h"
#include "domain.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal dump atom command");
scale_flag = 1;
image_flag = 0;
format_default = NULL;
// one-time file open
if (multifile == 0) openfile();
}
/* ---------------------------------------------------------------------- */
void DumpAtom::init()
{
// this error check cannot occur in constructor since scale_flag = 1
// is the default and it can be changed by dump_modify
if (scale_flag && domain->triclinic)
error->all("Cannot dump scaled coords with triclinic box");
if (image_flag == 0) size_one = 5;
else size_one = 8;
// default format depends on image flags
delete [] format;
if (format_user) {
int n = strlen(format_user) + 2;
format = new char[n];
strcpy(format,format_user);
strcat(format,"\n");
} else {
char *str;
if (image_flag == 0) str = (char *) "%d %d %g %g %g";
else str = (char *) "%d %d %g %g %g %d %d %d";
int n = strlen(str) + 2;
format = new char[n];
strcpy(format,str);
strcat(format,"\n");
}
// setup function ptrs
if (binary) header_choice = &DumpAtom::header_binary;
else header_choice = &DumpAtom::header_item;
if (scale_flag == 1 && image_flag == 0)
pack_choice = &DumpAtom::pack_scale_noimage;
else if (scale_flag == 1 && image_flag == 1)
pack_choice = &DumpAtom::pack_scale_image;
else if (scale_flag == 0 && image_flag == 0)
pack_choice = &DumpAtom::pack_noscale_noimage;
else if (scale_flag == 0 && image_flag == 1)
pack_choice = &DumpAtom::pack_noscale_image;
if (binary) write_choice = &DumpAtom::write_binary;
else if (image_flag == 0) write_choice = &DumpAtom::write_noimage;
else if (image_flag == 1) write_choice = &DumpAtom::write_image;
}
/* ---------------------------------------------------------------------- */
int DumpAtom::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"scale") == 0) {
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) scale_flag = 1;
else if (strcmp(arg[1],"no") == 0) scale_flag = 0;
else error->all("Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"image") == 0) {
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) image_flag = 1;
else if (strcmp(arg[1],"no") == 0) image_flag = 0;
else error->all("Illegal dump_modify command");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_header(int ndump)
{
if (me == 0) (this->*header_choice)(ndump);
}
/* ---------------------------------------------------------------------- */
int DumpAtom::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
int DumpAtom::pack()
{
return (this->*pack_choice)();
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_data(int n, double *buf)
{
(this->*write_choice)(n,buf);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::header_binary(int ndump)
{
fwrite(&update->ntimestep,sizeof(int),1,fp);
fwrite(&ndump,sizeof(int),1,fp);
fwrite(&boxxlo,sizeof(double),1,fp);
fwrite(&boxxhi,sizeof(double),1,fp);
fwrite(&boxylo,sizeof(double),1,fp);
fwrite(&boxyhi,sizeof(double),1,fp);
fwrite(&boxzlo,sizeof(double),1,fp);
fwrite(&boxzhi,sizeof(double),1,fp);
fwrite(&size_one,sizeof(int),1,fp);
if (multiproc) {
int one = 1;
fwrite(&one,sizeof(int),1,fp);
} else fwrite(&nprocs,sizeof(int),1,fp);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::header_item(int ndump)
{
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,"%d\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
fprintf(fp,"%d\n",ndump);
fprintf(fp,"ITEM: BOX BOUNDS\n");
fprintf(fp,"%g %g\n",boxxlo,boxxhi);
fprintf(fp,"%g %g\n",boxylo,boxyhi);
fprintf(fp,"%g %g\n",boxzlo,boxzhi);
fprintf(fp,"ITEM: ATOMS\n");
}
/* ---------------------------------------------------------------------- */
int DumpAtom::pack_scale_image()
{
int *tag = atom->tag;
int *type = atom->type;
int *image = atom->image;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
double invxprd = 1.0/domain->xprd;
double invyprd = 1.0/domain->yprd;
double invzprd = 1.0/domain->zprd;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = (x[i][0] - boxxlo) * invxprd;
buf[m++] = (x[i][1] - boxylo) * invyprd;
buf[m++] = (x[i][2] - boxzlo) * invzprd;
buf[m++] = (image[i] & 1023) - 512;
buf[m++] = (image[i] >> 10 & 1023) - 512;
buf[m++] = (image[i] >> 20) - 512;
}
return m;
}
/* ---------------------------------------------------------------------- */
int DumpAtom::pack_scale_noimage()
{
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
double invxprd = 1.0/domain->xprd;
double invyprd = 1.0/domain->yprd;
double invzprd = 1.0/domain->zprd;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = (x[i][0] - boxxlo) * invxprd;
buf[m++] = (x[i][1] - boxylo) * invyprd;
buf[m++] = (x[i][2] - boxzlo) * invzprd;
}
return m;
}
/* ---------------------------------------------------------------------- */
int DumpAtom::pack_noscale_image()
{
int *tag = atom->tag;
int *type = atom->type;
int *image = atom->image;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = (image[i] & 1023) - 512;
buf[m++] = (image[i] >> 10 & 1023) - 512;
buf[m++] = (image[i] >> 20) - 512;
}
return m;
}
/* ---------------------------------------------------------------------- */
int DumpAtom::pack_noscale_noimage()
{
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_binary(int n, double *buf)
{
n *= size_one;
fwrite(&n,sizeof(int),1,fp);
fwrite(buf,sizeof(double),n,fp);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_image(int n, double *buf)
{
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (buf[m]), static_cast<int> (buf[m+1]),
buf[m+2],buf[m+3],buf[m+4], static_cast<int> (buf[m+5]),
static_cast<int> (buf[m+6]), static_cast<int> (buf[m+7]));
m += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_noimage(int n, double *buf)
{
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (buf[m]), static_cast<int> (buf[m+1]),
buf[m+2],buf[m+3],buf[m+4]);
m += size_one;
}
}
c4science · Help