Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F81677651
lammps_data_write.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, Sep 7, 09:24
Size
6 KB
Mime Type
text/x-c
Expires
Mon, Sep 9, 09:24 (1 d, 22 h)
Engine
blob
Format
Raw Data
Handle
20440698
Attached To
rLAMMPS lammps
lammps_data_write.cpp
View Options
#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;
}
Event Timeline
Log In to Comment