git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
319
src/dump_atom.cpp
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319
src/dump_atom.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "dump_atom.h"
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#include "domain.h"
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#include "atom.h"
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#include "update.h"
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#include "group.h"
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#include "error.h"
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/* ---------------------------------------------------------------------- */
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DumpAtom::DumpAtom(int narg, char **arg) : Dump(narg, arg)
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{
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if (narg != 5) error->all("Illegal dump atom command");
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scale_flag = 1;
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image_flag = 0;
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format_default = NULL;
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// one-time file open
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if (multifile == 0) openfile();
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::init()
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{
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if (image_flag == 0) size_one = 5;
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else size_one = 8;
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// default format depends on image flags
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delete [] format;
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if (format_user) {
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int n = strlen(format_user) + 2;
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format = new char[n];
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strcpy(format,format_user);
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strcat(format,"\n");
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} else {
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char *str;
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if (image_flag == 0) str = "%d %d %g %g %g";
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else str = "%d %d %g %g %g %d %d %d";
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int n = strlen(str) + 2;
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format = new char[n];
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strcpy(format,str);
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strcat(format,"\n");
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}
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// setup function ptrs
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if (binary) header_choice = &DumpAtom::header_binary;
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else header_choice = &DumpAtom::header_item;
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if (scale_flag == 1 && image_flag == 0)
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pack_choice = &DumpAtom::pack_scale_noimage;
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else if (scale_flag == 1 && image_flag == 1)
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pack_choice = &DumpAtom::pack_scale_image;
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else if (scale_flag == 0 && image_flag == 0)
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pack_choice = &DumpAtom::pack_noscale_noimage;
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else if (scale_flag == 0 && image_flag == 1)
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pack_choice = &DumpAtom::pack_noscale_image;
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if (binary) write_choice = &DumpAtom::write_binary;
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else if (image_flag == 0) write_choice = &DumpAtom::write_noimage;
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else if (image_flag == 1) write_choice = &DumpAtom::write_image;
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::modify_param(int narg, char **arg)
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{
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if (strcmp(arg[0],"scale") == 0) {
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if (narg < 2) error->all("Illegal dump_modify command");
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if (strcmp(arg[1],"yes") == 0) scale_flag = 1;
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else if (strcmp(arg[1],"no") == 0) scale_flag = 0;
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else error->all("Illegal dump_modify command");
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return 2;
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} else if (strcmp(arg[0],"image") == 0) {
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if (narg < 2) error->all("Illegal dump_modify command");
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if (strcmp(arg[1],"yes") == 0) image_flag = 1;
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else if (strcmp(arg[1],"no") == 0) image_flag = 0;
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else error->all("Illegal dump_modify command");
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return 2;
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}
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return 0;
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::write_header(int ndump)
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{
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(this->*header_choice)(ndump);
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::count()
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{
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if (igroup == 0) return atom->nlocal;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int m = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) m++;
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::pack()
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{
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return (this->*pack_choice)();
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::write_data(int n, double *buf)
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{
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(this->*write_choice)(n,buf);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_binary(int ndump)
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{
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fwrite(&update->ntimestep,sizeof(int),1,fp);
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fwrite(&ndump,sizeof(int),1,fp);
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fwrite(&domain->boxxlo,sizeof(double),1,fp);
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fwrite(&domain->boxxhi,sizeof(double),1,fp);
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fwrite(&domain->boxylo,sizeof(double),1,fp);
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fwrite(&domain->boxyhi,sizeof(double),1,fp);
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fwrite(&domain->boxzlo,sizeof(double),1,fp);
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fwrite(&domain->boxzhi,sizeof(double),1,fp);
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fwrite(&size_one,sizeof(int),1,fp);
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if (multiproc) {
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int one = 1;
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fwrite(&one,sizeof(int),1,fp);
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} else fwrite(&nprocs,sizeof(int),1,fp);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::header_item(int ndump)
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{
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fprintf(fp,"ITEM: TIMESTEP\n");
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fprintf(fp,"%d\n",update->ntimestep);
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fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
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fprintf(fp,"%d\n",ndump);
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fprintf(fp,"ITEM: BOX BOUNDS\n");
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fprintf(fp,"%g %g\n",domain->boxxlo,domain->boxxhi);
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fprintf(fp,"%g %g\n",domain->boxylo,domain->boxyhi);
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fprintf(fp,"%g %g\n",domain->boxzlo,domain->boxzhi);
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fprintf(fp,"ITEM: ATOMS\n");
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::pack_scale_image()
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{
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int *tag = atom->tag;
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int *type = atom->type;
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int *image = atom->image;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double boxxlo = domain->boxxlo;
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double boxylo = domain->boxylo;
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double boxzlo = domain->boxzlo;
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double invxprd = 1.0/domain->xprd;
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double invyprd = 1.0/domain->yprd;
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double invzprd = 1.0/domain->zprd;
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int m = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = (x[i][0] - boxxlo) * invxprd;
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buf[m++] = (x[i][1] - boxylo) * invyprd;
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buf[m++] = (x[i][2] - boxzlo) * invzprd;
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buf[m++] = (image[i] & 1023) - 512;
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buf[m++] = (image[i] >> 10 & 1023) - 512;
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buf[m++] = (image[i] >> 20) - 512;
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::pack_scale_noimage()
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{
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int *tag = atom->tag;
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int *type = atom->type;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double boxxlo = domain->boxxlo;
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double boxylo = domain->boxylo;
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double boxzlo = domain->boxzlo;
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double invxprd = 1.0/domain->xprd;
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double invyprd = 1.0/domain->yprd;
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double invzprd = 1.0/domain->zprd;
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int m = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = (x[i][0] - boxxlo) * invxprd;
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buf[m++] = (x[i][1] - boxylo) * invyprd;
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buf[m++] = (x[i][2] - boxzlo) * invzprd;
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::pack_noscale_image()
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{
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int *tag = atom->tag;
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int *type = atom->type;
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int *image = atom->image;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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int m = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = x[i][0];
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buf[m++] = x[i][1];
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buf[m++] = x[i][2];
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buf[m++] = (image[i] & 1023) - 512;
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buf[m++] = (image[i] >> 10 & 1023) - 512;
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buf[m++] = (image[i] >> 20) - 512;
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::pack_noscale_noimage()
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{
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int *tag = atom->tag;
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int *type = atom->type;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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int m = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = x[i][0];
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buf[m++] = x[i][1];
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buf[m++] = x[i][2];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::write_binary(int n, double *buf)
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{
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n *= size_one;
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fwrite(&n,sizeof(int),1,fp);
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fwrite(buf,sizeof(double),n,fp);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::write_image(int n, double *buf)
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{
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int m = 0;
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for (int i = 0; i < n; i++) {
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fprintf(fp,format,
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static_cast<int> (buf[m]), static_cast<int> (buf[m+1]),
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buf[m+2],buf[m+3],buf[m+4], static_cast<int> (buf[m+5]),
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static_cast<int> (buf[m+6]), static_cast<int> (buf[m+7]));
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m += size_one;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtom::write_noimage(int n, double *buf)
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{
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int m = 0;
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for (int i = 0; i < n; i++) {
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fprintf(fp,format,
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static_cast<int> (buf[m]), static_cast<int> (buf[m+1]),
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buf[m+2],buf[m+3],buf[m+4]);
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m += size_one;
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}
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}
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