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lammps_data_write.cpp
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Wed, Jul 31, 23:24

lammps_data_write.cpp
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#include "stdlib.h"
#include "string.h"
#include "lammps_data_write.h"
#include "memory.h"
#include "error.h"
#define DELTA 4;
enum{INT,DOUBLE,DOUBLE2};
/* ---------------------------------------------------------------------- */
LAMMPSDataWrite::LAMMPSDataWrite(MPI_Comm caller_comm) : Send2One(caller_comm)
{
outfile = NULL;
nheader = maxheader = 0;
format = NULL;
headtype = NULL;
ihead = NULL;
dhead = NULL;
ddhead = NULL;
nper = maxper = 0;
atomtype = NULL;
ivec = NULL;
dvec = NULL;
stride = NULL;
}
/* ---------------------------------------------------------------------- */
LAMMPSDataWrite::~LAMMPSDataWrite()
{
delete [] outfile;
for (int i = 0; i < nheader; i++) delete [] format[i];
memory->sfree(format);
memory->sfree(headtype);
memory->sfree(ihead);
memory->sfree(dhead);
memory->destroy_2d_double_array(ddhead);
memory->sfree(atomtype);
memory->sfree(ivec);
memory->sfree(dvec);
memory->sfree(stride);
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::pre()
{
if (me == 0) {
fp = fopen(outfile,"w");
if (fp == NULL)
error->one("Could not open data_write output file");
}
if (me == 0) {
fprintf(fp,"%s","LAMMPS data file\n\n");
for (int i = 0; i < nheader; i++)
if (headtype[i] == INT) fprintf(fp,format[i],ihead[i]);
else if (headtype[i] == DOUBLE) fprintf(fp,format[i],dhead[i]);
else if (headtype[i] == DOUBLE2) fprintf(fp,format[i],
ddhead[i][0],ddhead[i][1]);
fprintf(fp,"\nAtoms\n\n");
}
}
/* ---------------------------------------------------------------------- */
int LAMMPSDataWrite::size()
{
return nper*nlocal*sizeof(double);
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::pack(char *cbuf)
{
int i,j;
double *dbuf = (double *) cbuf;
int m = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < nper; j++) {
if (i == 0) {
if (atomtype[j] == 0)
printf("AT %d %d %p %d\n",
atomtype[j],stride[j],ivec[j],ivec[j][0]);
else
printf("AT %d %d %p %g\n",
atomtype[j],stride[j],dvec[j],dvec[j][0]);
}
if (atomtype[j] == INT) dbuf[m++] = ivec[j][i*stride[j]];
else if (atomtype[j] == DOUBLE) dbuf[m++] = dvec[j][i*stride[j]];
}
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::process(int nbuf, char *cbuf)
{
int i,j;
double *dbuf = (double *) cbuf;
int n = nbuf/nper/sizeof(double);
int m = 0;
for (i = 0; i < n; i++) {
for (j = 0; j < nper; j++) {
double dvalue = dbuf[m++];
if (atomtype[j] == INT) fprintf(fp,"%d ",static_cast<int> (dvalue));
else if (atomtype[j] == DOUBLE) fprintf(fp,"%g ",dvalue);
}
fprintf(fp,"\n");
}
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::post()
{
if (me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::file(char *fname)
{
int n = strlen(fname) + 1;
outfile = new char[n];
strcpy(outfile,fname);
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::header(char *str, int ivalue)
{
if (nheader == maxheader) grow_header();
int n = strlen(str) + 2;
format[nheader] = new char[n];
strcpy(format[nheader],str);
format[nheader][n-2] = '\n';
format[nheader][n-1] = '\0';
headtype[nheader] = INT;
ihead[nheader] = ivalue;
nheader++;
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::header(char *str, double dvalue)
{
if (nheader == maxheader) grow_header();
int n = strlen(str) + 2;
format[nheader] = new char[n];
strcpy(format[nheader],str);
format[nheader][n-2] = '\n';
format[nheader][n-1] = '\0';
headtype[nheader] = DOUBLE;
dhead[nheader] = dvalue;
nheader++;
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::header(char *str, double dvalue1, double dvalue2)
{
if (nheader == maxheader) grow_header();
int n = strlen(str) + 2;
format[nheader] = new char[n];
strcpy(format[nheader],str);
format[nheader][n-2] = '\n';
format[nheader][n-1] = '\0';
headtype[nheader] = DOUBLE2;
ddhead[nheader][0] = dvalue1;
ddhead[nheader][1] = dvalue2;
nheader++;
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::atoms(int n)
{
nlocal = n;
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::atoms(int *vec)
{
if (nper == maxper) grow_peratom();
atomtype[nper] = INT;
ivec[nper] = vec;
stride[nper] = 1;
nper++;
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::atoms(double *vec)
{
if (nper == maxper) grow_peratom();
atomtype[nper] = DOUBLE;
dvec[nper] = vec;
stride[nper] = 1;
nper++;
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::atoms(int n, double **vec)
{
if (nper+n >= maxper) grow_peratom();
for (int i = 0; i < n; i++) {
atomtype[nper] = DOUBLE;
dvec[nper] = &vec[0][i];
stride[nper] = n;
nper++;
}
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::grow_header()
{
int n = maxheader + DELTA;
format = (char **) memory->srealloc(format,n*sizeof(char *),"ldw:format");
headtype = (int *) memory->srealloc(headtype,n*sizeof(int),"ldw:headtype");
ihead = (int *) memory->srealloc(ihead,n*sizeof(int),"ldw:ihead");
dhead = (double *) memory->srealloc(dhead,n*sizeof(double),"ldw:dhead");
ddhead = memory->grow_2d_double_array(ddhead,n,2,"ldw:ddhead");
maxheader = n;
}
/* ---------------------------------------------------------------------- */
void LAMMPSDataWrite::grow_peratom()
{
int n = maxper + DELTA;
atomtype = (int *) memory->srealloc(atomtype,n*sizeof(int *),"ldw:atomtype");
ivec = (int **) memory->srealloc(ivec,n*sizeof(int *),"ldw:ihead");
dvec = (double **) memory->srealloc(dvec,n*sizeof(double *),"ldw:dhead");
stride = (int *) memory->srealloc(stride,n*sizeof(int *),"ldw:stride");
maxper = n;
}

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