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dump_atom.cpp
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Sat, Jul 13, 18:24

dump_atom.cpp
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/* ----------------------------------------------------------------------
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 "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define ONELINE 256
#define DELTA 1048576
/* ---------------------------------------------------------------------- */
DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg != 5) error->all(FLERR,"Illegal dump atom command");
scale_flag = 1;
image_flag = 0;
buffer_allow = 1;
buffer_flag = 1;
format_default = NULL;
}
/* ---------------------------------------------------------------------- */
void DumpAtom::init_style()
{
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 boundary string
domain->boundary_string(boundstr);
// setup column string
if (scale_flag == 0 && image_flag == 0)
columns = (char *) "id type x y z";
else if (scale_flag == 0 && image_flag == 1)
columns = (char *) "id type x y z ix iy iz";
else if (scale_flag == 1 && image_flag == 0)
columns = (char *) "id type xs ys zs";
else if (scale_flag == 1 && image_flag == 1)
columns = (char *) "id type xs ys zs ix iy iz";
// setup function ptrs
if (binary && domain->triclinic == 0)
header_choice = &DumpAtom::header_binary;
else if (binary && domain->triclinic == 1)
header_choice = &DumpAtom::header_binary_triclinic;
else if (!binary && domain->triclinic == 0)
header_choice = &DumpAtom::header_item;
else if (!binary && domain->triclinic == 1)
header_choice = &DumpAtom::header_item_triclinic;
if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0)
pack_choice = &DumpAtom::pack_scale_noimage;
else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0)
pack_choice = &DumpAtom::pack_scale_image;
else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1)
pack_choice = &DumpAtom::pack_scale_noimage_triclinic;
else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1)
pack_choice = &DumpAtom::pack_scale_image_triclinic;
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 (image_flag == 0) convert_choice = &DumpAtom::convert_noimage;
else convert_choice = &DumpAtom::convert_image;
if (binary) write_choice = &DumpAtom::write_binary;
else if (buffer_flag == 1) write_choice = &DumpAtom::write_string;
else if (image_flag == 0) write_choice = &DumpAtom::write_lines_noimage;
else if (image_flag == 1) write_choice = &DumpAtom::write_lines_image;
// open single file, one time only
if (multifile == 0) openfile();
}
/* ---------------------------------------------------------------------- */
int DumpAtom::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"scale") == 0) {
if (narg < 2) error->all(FLERR,"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(FLERR,"Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"image") == 0) {
if (narg < 2) error->all(FLERR,"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(FLERR,"Illegal dump_modify command");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_header(bigint ndump)
{
if (multiproc) (this->*header_choice)(ndump);
else if (me == 0) (this->*header_choice)(ndump);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack(int *ids)
{
(this->*pack_choice)(ids);
}
/* ---------------------------------------------------------------------- */
int DumpAtom::convert_string(int n, double *mybuf)
{
return (this->*convert_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::header_binary(bigint ndump)
{
fwrite(&update->ntimestep,sizeof(bigint),1,fp);
fwrite(&ndump,sizeof(bigint),1,fp);
fwrite(&domain->triclinic,sizeof(int),1,fp);
fwrite(&domain->boundary[0][0],6*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) fwrite(&nclusterprocs,sizeof(int),1,fp);
else fwrite(&nprocs,sizeof(int),1,fp);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::header_binary_triclinic(bigint ndump)
{
fwrite(&update->ntimestep,sizeof(bigint),1,fp);
fwrite(&ndump,sizeof(bigint),1,fp);
fwrite(&domain->triclinic,sizeof(int),1,fp);
fwrite(&domain->boundary[0][0],6*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(&boxxy,sizeof(double),1,fp);
fwrite(&boxxz,sizeof(double),1,fp);
fwrite(&boxyz,sizeof(double),1,fp);
fwrite(&size_one,sizeof(int),1,fp);
if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
else fwrite(&nprocs,sizeof(int),1,fp);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::header_item(bigint ndump)
{
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
fprintf(fp,BIGINT_FORMAT "\n",ndump);
fprintf(fp,"ITEM: BOX BOUNDS %s\n",boundstr);
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 %s\n",columns);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::header_item_triclinic(bigint ndump)
{
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
fprintf(fp,BIGINT_FORMAT "\n",ndump);
fprintf(fp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
fprintf(fp,"%g %g %g\n",boxxlo,boxxhi,boxxy);
fprintf(fp,"%g %g %g\n",boxylo,boxyhi,boxxz);
fprintf(fp,"%g %g %g\n",boxzlo,boxzhi,boxyz);
fprintf(fp,"ITEM: ATOMS %s\n",columns);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_scale_image(int *ids)
{
int m,n;
int *tag = atom->tag;
int *type = atom->type;
imageint *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;
m = n = 00;
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] & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMG2BITS) - IMGMAX;
if (ids) ids[n++] = tag[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_scale_noimage(int *ids)
{
int m,n;
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;
m = n = 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;
if (ids) ids[n++] = tag[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_scale_image_triclinic(int *ids)
{
int m,n;
int *tag = atom->tag;
int *type = atom->type;
imageint *image = atom->image;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
double lamda[3];
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
domain->x2lamda(x[i],lamda);
buf[m++] = lamda[0];
buf[m++] = lamda[1];
buf[m++] = lamda[2];
buf[m++] = (image[i] & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMG2BITS) - IMGMAX;
if (ids) ids[n++] = tag[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_scale_noimage_triclinic(int *ids)
{
int m,n;
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
double lamda[3];
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
domain->x2lamda(x[i],lamda);
buf[m++] = lamda[0];
buf[m++] = lamda[1];
buf[m++] = lamda[2];
if (ids) ids[n++] = tag[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_noscale_image(int *ids)
{
int m,n;
int *tag = atom->tag;
int *type = atom->type;
imageint *image = atom->image;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
m = n = 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] & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMG2BITS) - IMGMAX;
if (ids) ids[n++] = tag[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_noscale_noimage(int *ids)
{
int m,n;
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
m = n = 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];
if (ids) ids[n++] = tag[i];
}
}
/* ----------------------------------------------------------------------
convert mybuf of doubles to one big formatted string in sbuf
return -1 if strlen exceeds an int, since used as arg in MPI calls in Dump
------------------------------------------------------------------------- */
int DumpAtom::convert_image(int n, double *mybuf)
{
int offset = 0;
int m = 0;
for (int i = 0; i < n; i++) {
if (offset + ONELINE > maxsbuf) {
if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
maxsbuf += DELTA;
memory->grow(sbuf,maxsbuf,"dump:sbuf");
}
offset += sprintf(&sbuf[offset],format,
static_cast<int> (mybuf[m]),
static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4],
static_cast<int> (mybuf[m+5]),
static_cast<int> (mybuf[m+6]),
static_cast<int> (mybuf[m+7]));
m += size_one;
}
return offset;
}
/* ---------------------------------------------------------------------- */
int DumpAtom::convert_noimage(int n, double *mybuf)
{
int offset = 0;
int m = 0;
for (int i = 0; i < n; i++) {
if (offset + ONELINE > maxsbuf) {
if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
maxsbuf += DELTA;
memory->grow(sbuf,maxsbuf,"dump:sbuf");
}
offset += sprintf(&sbuf[offset],format,
static_cast<int> (mybuf[m]),
static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
return offset;
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_binary(int n, double *mybuf)
{
n *= size_one;
fwrite(&n,sizeof(int),1,fp);
fwrite(mybuf,sizeof(double),n,fp);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_string(int n, double *mybuf)
{
fwrite(mybuf,sizeof(char),n,fp);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_lines_image(int n, double *mybuf)
{
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
m += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::write_lines_noimage(int n, double *mybuf)
{
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}

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