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lammps/src/dump_cfg.cpp
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dump_cfg.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Liang Wan (Chinese Academy of Sciences)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "dump_cfg.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "fix.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#define UNWRAPEXPAND 10.0
using namespace LAMMPS_NS;
enum{INT,DOUBLE}; // same as in dump_custom.cpp
/* ---------------------------------------------------------------------- */
DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
if (narg < 10 ||
strcmp(arg[5],"id") != 0 || strcmp(arg[6],"type") != 0 ||
(strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) ||
(strcmp(arg[8],"ys") != 0 && strcmp(arg[8],"ysu") != 0) ||
(strcmp(arg[9],"zs") != 0 && strcmp(arg[9],"zsu") != 0))
error->all(FLERR,"Dump cfg arguments must start with "
"'id type xs ys zs' or 'id type xsu ysu zsu'");
if (strcmp(arg[7],"xs") == 0)
if (strcmp(arg[8],"ysu") == 0 || strcmp(arg[9],"zsu") == 0)
error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
else unwrapflag = 0;
else if (strcmp(arg[8],"ys") == 0 || strcmp(arg[9],"zs") == 0)
error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
else unwrapflag = 1;
// arrays for data rearrangement
rbuf = NULL;
nchosen = nlines = 0;
// setup auxiliary property name strings
// convert 'X_ID[m]' (X=c,f,v) to 'ID_m'
if (narg > 10) auxname = new char*[narg-10];
else auxname = NULL;
int i = 0;
for (int iarg = 10; iarg < narg; iarg++, i++) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Invalid keyword in dump cfg command");
*ptr = '\0';
*(ptr+2) = '\0';
auxname[i] = new char[strlen(suffix) + 3];
strcpy(auxname[i],suffix);
strcat(auxname[i],"_");
strcat(auxname[i],ptr+1);
} else {
auxname[i] = new char[strlen(suffix) + 1];
strcpy(auxname[i],suffix);
}
delete [] suffix;
} else {
auxname[i] = new char[strlen(arg[iarg]) + 1];
strcpy(auxname[i],arg[iarg]);
}
}
}
/* ---------------------------------------------------------------------- */
DumpCFG::~DumpCFG()
{
if (rbuf) memory->destroy(rbuf);
if (auxname) {
for (int i = 0; i < nfield-5; i++) delete [] auxname[i];
delete [] auxname;
}
}
/* ---------------------------------------------------------------------- */
void DumpCFG::init_style()
{
if (multifile == 0) error->all(FLERR,"Dump cfg requires one snapshot per file");
DumpCustom::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
// special handling for unwrapped coordinates
double scale;
if (atom->peri_flag) {
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 if (unwrapflag == 1) scale = UNWRAPEXPAND;
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 = %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");
fprintf(fp,"H0(2,1) = %g A \n",domain->xy);
fprintf(fp,"H0(2,2) = %g A\n",domain->yprd);
fprintf(fp,"H0(2,3) = 0 A \n");
fprintf(fp,"H0(3,1) = %g A \n",domain->xz);
fprintf(fp,"H0(3,2) = %g A \n",domain->yz);
fprintf(fp,"H0(3,3) = %g A\n",domain->zprd);
fprintf(fp,".NO_VELOCITY.\n");
fprintf(fp,"entry_count = %d\n",nfield-2);
for (int i = 0; i < nfield-5; i++)
fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
}
// calculate total # of data lines to be written on a writing proc
if (multiproc) nchosen = nme;
else MPI_Reduce(&nme,&nchosen,1,MPI_INT,MPI_SUM,0,world);
// allocate memory needed for data rearrangement on writing proc(s)
if (multiproc || me == 0) {
if (rbuf) memory->destroy(rbuf);
memory->create(rbuf,nchosen,size_one,"dump:rbuf");
}
}
/* ----------------------------------------------------------------------
write data lines to file in a block-by-block style
write head of block (mass & element name) only if has atoms of the type
------------------------------------------------------------------------- */
void DumpCFG::write_data(int n, double *mybuf)
{
int i,j,m,itype;
double *rmass = atom->rmass;
double *mass = atom->mass;
// transfer data from buf to rbuf
// if write by proc 0, transfer chunk by chunk
for (i = 0, m = 0; i < n; i++) {
for (j = 0; j < size_one; j++)
rbuf[nlines][j] = mybuf[m++];
nlines++;
}
// write data lines in rbuf to file after transfer is done
double unwrap_coord;
if (nlines == nchosen) {
for (itype = 1; itype <= ntypes; itype++) {
for (i = 0; i < nchosen; i++)
if (rbuf[i][1] == itype) break;
if (i < nchosen) {
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) {
if (unwrapflag == 0)
for (j = 2; j < size_one; j++) {
if (vtype[j] == INT)
fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
else fprintf(fp,vformat[j],rbuf[i][j]);
}
else {
// Unwrapped scaled coordinates are shifted to
// center of expanded box, to prevent
// rewrapping by AtomEye. Dividing by
// expansion factor restores correct
// interatomic distances.
for (j = 2; j < 5; j++) {
unwrap_coord = (rbuf[i][j] - 0.5)/UNWRAPEXPAND + 0.5;
fprintf(fp,vformat[j],unwrap_coord);
}
for (j = 5; j < size_one; j++) {
if (vtype[j] == INT)
fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
else fprintf(fp,vformat[j],rbuf[i][j]);
}
}
fprintf(fp,"\n");
}
}
}
}
nlines = 0;
}
}
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