static int read_vaspoutcar_timestep(void *mydata, int natoms, molfile_timestep_t *ts)
{
vasp_plugindata_t *data = (vasp_plugindata_t *)mydata;
char lineptr[LINESIZE];
int atomcount;
/* Save coords only if we're given a timestep pointer,
* otherwise assume that VMD wants us to skip past it.
*/
if (!data || !ts) return MOLFILE_EOF;
atomcount = 0;
while (fgets(lineptr, LINESIZE, data->file) && atomcount == 0) {
if (strstr(lineptr, "TOTAL-FORCE") != NULL) {
int i;
fgets(lineptr, LINESIZE, data->file);
for (i = 0; i < data->numatoms; ++i, ++atomcount) {
float x, y, z;
fgets(lineptr, LINESIZE, data->file);
if (3 != sscanf(lineptr, "%f %f %f", &x, &y, &z)) return MOLFILE_EOF;
ts->coords[3*i ] = data->rotmat[0][0]*x+data->rotmat[0][1]*y+data->rotmat[0][2]*z;
ts->coords[3*i+1] = data->rotmat[1][0]*x+data->rotmat[1][1]*y+data->rotmat[1][2]*z;
ts->coords[3*i+2] = data->rotmat[2][0]*x+data->rotmat[2][1]*y+data->rotmat[2][2]*z;
}
}
}
if (atomcount != data->numatoms) return MOLFILE_EOF;
vasp_timestep_unitcell(ts, data);
return MOLFILE_SUCCESS;
}
static int read_vaspxml_timestep(void *mydata, int natoms, molfile_timestep_t *ts)
{
vasp_plugindata_t *data = (vasp_plugindata_t *)mydata;
char lineptr[LINESIZE];
/* only save coords if we're given a timestep pointer, */
/* otherwise assume that VMD wants us to skip past it. */
if (!data || !ts) return MOLFILE_EOF;
/* Scan xml file */
while (fgets(lineptr, LINESIZE, data->file)) {
/* Extract coordinates of all atoms */
if (strstr(lineptr, "positions") != NULL) {
int i;
for (i = 0; i < data->numatoms && fgets(lineptr, LINESIZE, data->file); ++i) {
float x, y, z, rotx, roty, rotz;
if (3 != sscanf(lineptr, " <v> %f %f %f </v>", &x, &y, &z)) return MOLFILE_EOF;
rotx = x*data->cell[0][0] + y*data->cell[1][0] + z*data->cell[2][0];
roty = x*data->cell[0][1] + y*data->cell[1][1] + z*data->cell[2][1];
rotz = x*data->cell[0][2] + y*data->cell[1][2] + z*data->cell[2][2];
ts->coords[3*i ] = data->rotmat[0][0]*rotx + data->rotmat[0][1]*roty + data->rotmat[0][2]*rotz;
ts->coords[3*i+1] = data->rotmat[1][0]*rotx + data->rotmat[1][1]*roty + data->rotmat[1][2]*rotz;
ts->coords[3*i+2] = data->rotmat[2][0]*rotx + data->rotmat[2][1]*roty + data->rotmat[2][2]*rotz;
}
vasp_timestep_unitcell(ts, data);
return MOLFILE_SUCCESS;
}
}
return MOLFILE_EOF;
}
static int read_vasp5xdatcar_timestep(void *mydata, int natoms, molfile_timestep_t *ts)
{
int i;
char lineptr[LINESIZE];
vasp_plugindata_t *data = (vasp_plugindata_t *)mydata;
/* Save coords only if we're given a timestep pointer,
* otherwise assume that VMD wants us to skip past it.
*/
if (!ts || !data) return MOLFILE_EOF;
for (i = 0; i < data->numatoms; ++i) {
float x, y, z, rotx, roty, rotz;
fgets(lineptr, LINESIZE, data->file);
if (3 != sscanf(lineptr, "%f %f %f", &x, &y, &z)) {
fprintf(stderr, "VASP5 XDATCAR read) missing type or coordinate(s) in file '%s' for atom '%d'\n", data->filename, i+1);
return MOLFILE_EOF;
}
rotx = x*data->cell[0][0]+y*data->cell[1][0]+z*data->cell[2][0];
roty = x*data->cell[0][1]+y*data->cell[1][1]+z*data->cell[2][1];
rotz = x*data->cell[0][2]+y*data->cell[1][2]+z*data->cell[2][2];
ts->coords[3*i ] = data->rotmat[0][0]*rotx+data->rotmat[0][1]*roty+data->rotmat[0][2]*rotz;
ts->coords[3*i+1] = data->rotmat[1][0]*rotx+data->rotmat[1][1]*roty+data->rotmat[1][2]*rotz;
ts->coords[3*i+2] = data->rotmat[2][0]*rotx+data->rotmat[2][1]*roty+data->rotmat[2][2]*rotz;
}
vasp_timestep_unitcell(ts, data);
/* VMD keeps calling for a next timestep, until we reach End-Of-File here */
if (fgets(lineptr, LINESIZE, data->file) == NULL) return MOLFILE_EOF;
return MOLFILE_SUCCESS;
}
static int read_vaspposcar_timestep(void *mydata, int natoms, molfile_timestep_t *ts)
{
int i, direct;
char lineptr[LINESIZE];
float lc;
vasp_plugindata_t *data = (vasp_plugindata_t *)mydata;
/* Save coords only if we're given a timestep pointer,
* otherwise assume that VMD wants us to skip past it.
*/
if (!ts || !data) return MOLFILE_EOF;
/* VMD keeps calling for a next timestep, until we reach End-Of-File here */
if (fgets(lineptr, LINESIZE, data->file) == NULL) return MOLFILE_EOF;
fgets(lineptr, LINESIZE, data->file);
sscanf(lineptr, "%f", &lc);
for (i = 0; i < 3; ++i) {
float x, y, z;
fgets(lineptr, LINESIZE, data->file);
sscanf(lineptr, "%f %f %f", &x, &y, &z);
data->cell[i][0] = x*lc;
data->cell[i][1] = y*lc;
data->cell[i][2] = z*lc;
}
vasp_buildrotmat(data);
/* Skip numbers of atom types */
for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file);
/* Skip selective tag-line, starting with 's' or 'S'. */
if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file);
/* Detect direct coordinates tag, starting with 'd' or 'D'. */
direct = (tolower(lineptr[0]) == 'd' ? 1 : 0);
for (i = 0; i < data->numatoms; ++i) {
float x, y, z, rotx, roty, rotz;
fgets(lineptr, LINESIZE, data->file);
if (3 != sscanf(lineptr, "%f %f %f", &x, &y, &z)) {
fprintf(stderr, "VASP POSCAR read) missing type or coordinate(s) in file '%s' for atom '%d'\n", data->filename, i+1);
return MOLFILE_EOF;
}
if (direct) {
rotx = x*data->cell[0][0]+y*data->cell[1][0]+z*data->cell[2][0];
roty = x*data->cell[0][1]+y*data->cell[1][1]+z*data->cell[2][1];
rotz = x*data->cell[0][2]+y*data->cell[1][2]+z*data->cell[2][2];
} else {
rotx = x*lc;
roty = y*lc;
rotz = z*lc;
}
ts->coords[3*i ] = data->rotmat[0][0]*rotx+data->rotmat[0][1]*roty+data->rotmat[0][2]*rotz;
ts->coords[3*i+1] = data->rotmat[1][0]*rotx+data->rotmat[1][1]*roty+data->rotmat[1][2]*rotz;
ts->coords[3*i+2] = data->rotmat[2][0]*rotx+data->rotmat[2][1]*roty+data->rotmat[2][2]*rotz;
}
vasp_timestep_unitcell(ts, data);
/* POSCAR type files have only one single timestep.
* Therefore proceed till end of file after reading the coordinates.
*/
fseek(data->file, 0, SEEK_END);
return MOLFILE_SUCCESS;
}
