static void *open_vaspoutcar_read(const char *filename, const char *filetype, int *natoms)
{
vasp_plugindata_t *data;
char lineptr[LINESIZE];
/* Verify that input is OK */
if (!filename || !natoms) return NULL;
/* Start with undefined value; set it after successful read */
*natoms = MOLFILE_NUMATOMS_UNKNOWN;
data = vasp_plugindata_malloc();
if (!data) return NULL;
data->file = fopen(filename, "rb");
if (!data->file) {
vasp_plugindata_free(data);
return NULL;
}
data->filename = strdup(filename);
/* Catch total number of atoms */
data->numatoms = 0;
while (fgets(lineptr, LINESIZE, data->file) && data->numatoms == 0) {
if (strstr(lineptr, "NIONS =") != NULL) {
sscanf(lineptr, " %*[ a-zA-Z] = %*d %*[ a-zA-Z] = %d", &data->numatoms);
break;
}
}
if (data->numatoms <= 0) {
vasp_plugindata_free(data);
fprintf(stderr, "\n\nVASP OUTCAR read) ERROR: file '%s' does not contain the number of atoms.\n", filename);
return NULL;
}
*natoms = data->numatoms;
/* Catch the lattice vectors */
while (fgets(lineptr, LINESIZE, data->file)) {
if (strstr(lineptr, "direct lattice vectors") != NULL) {
int i;
for (i = 0; i < 3; ++i) {
fgets(lineptr, LINESIZE, data->file);
if (3 != sscanf(lineptr, "%f %f %f", &data->cell[i][0], &data->cell[i][1], &data->cell[i][2])) {
vasp_plugindata_free(data);
fprintf(stderr, "\n\nVASP OUTCAR read) ERROR: file '%s' does not contain lattice vectors.\n", filename);
return NULL;
}
}
break;
}
}
vasp_buildrotmat(data);
rewind(data->file);
return data;
}
static void *open_vaspparchg_read(const char *filename, const char *filetype, int *natoms)
{
vasp_plugindata_t *data;
char lineptr[LINESIZE];
float lc;
int i;
/* Verify that input is OK */
if (!filename || !natoms) return NULL;
/* Start with undefined value; set it after successful read */
*natoms = MOLFILE_NUMATOMS_UNKNOWN;
data = vasp_plugindata_malloc();
if (!data) return NULL;
/* VASP4 is assumed in default */
data->version = 4;
data->file = fopen(filename, "rb");
if (!data->file) {
vasp_plugindata_free(data);
return NULL;
}
data->filename = strdup(filename);
/* Read system title */
fgets(lineptr, LINESIZE, data->file);
data->titleline = strdup(lineptr);
/* Read lattice constant */
fgets(lineptr, LINESIZE, data->file);
lc = atof(strtok(lineptr, " "));
/* Read unit cell lattice vectors and multiply by lattice constant */
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;
}
/* Build rotation matrix */
vasp_buildrotmat(data);
/* Count number of atoms */
fgets(lineptr, LINESIZE, data->file);
data->numatoms = 0;
for (i = 0; i < MAXATOMTYPES; ++i) {
char const *tmplineptr = strdup(lineptr);
char const *token = (i == 0 ? strtok(lineptr, " ") : strtok(NULL, " "));
int const n = (token ? atoi(token) : -1);
/* if fails to read number of atoms, then assume VASP5 */
if (i == 0 && n <= 0) {
data->version = 5;
data->titleline = strdup(tmplineptr);
fgets(lineptr, LINESIZE, data->file);
break;
} else if (n <= 0) break;
data->eachatom[i] = n;
data->numatoms += n;
}
if (data->version == 5) {
data->numatoms = 0;
for (i = 0; i < MAXATOMTYPES; ++i) {
char const *token = (i == 0 ? strtok(lineptr, " ") : strtok(NULL, " "));
int const n = (token ? atoi(token) : -1);
if (n <= 0) break;
data->eachatom[i] = n;
data->numatoms += n;
}
}
if (data->numatoms == 0) {
vasp_plugindata_free(data);
fprintf(stderr, "\n\nVASP PARCHG read) ERROR: file '%s' does not contain list of atom numbers.\n", filename);
return NULL;
}
/* Skip lines up to the grid numbers */
for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file);
*natoms = data->numatoms;
return data;
}
static void *open_vaspxml_read(const char *filename, const char *filetype, int *natoms)
{
vasp_plugindata_t *data;
char lineptr[LINESIZE];
int cellcoords, finished;
/* Verify that input is OK */
if (!filename || !natoms) return NULL;
/* Start with undefined value; set it after successful read */
*natoms = MOLFILE_NUMATOMS_UNKNOWN;
data = vasp_plugindata_malloc();
if (!data) return NULL;
data->file = fopen(filename, "rb");
if (!data->file) {
vasp_plugindata_free(data);
return NULL;
}
data->filename = strdup(filename);
/* Scan xml file */
data->numatoms = cellcoords = finished = 0;
while (fgets(lineptr, LINESIZE, data->file) && !finished) {
if (strstr(lineptr, "SYSTEM") != NULL && data->titleline == NULL) {
/* Extract title line */
char *begin = strstr(lineptr, ">") + 1;
char *end = strstr(lineptr, "</i>");
if (end) end = '\0';
if (begin) data->titleline = strdup(begin);
} else if (strstr(lineptr, "atominfo") != NULL && data->numatoms == 0) {
/* Extract number of atoms */
fgets(lineptr, LINESIZE, data->file);
sscanf(lineptr, " <atoms> %d </atoms>", &data->numatoms);
} else if (strstr(lineptr, "crystal") != NULL && cellcoords == 0) {
/* Extract lattice vectors */
int i;
fgets(lineptr, LINESIZE, data->file);
for (i = 0; i < 3 && fgets(lineptr, LINESIZE, data->file); ++i) cellcoords += sscanf(lineptr, " <v> %f %f %f </v>", &data->cell[i][0], &data->cell[i][1], &data->cell[i][2]);
}
finished = data->titleline != NULL && data->numatoms != 0 && cellcoords != 0;
}
if (data->numatoms <= 0) {
vasp_plugindata_free(data);
fprintf(stderr, "\n\nVASP xml read) ERROR: file '%s' does not contain the number of atoms.\n", filename);
return NULL;
}
if (cellcoords != 9) {
vasp_plugindata_free(data);
fprintf(stderr, "\n\nVASP xml read) ERROR: file '%s' does not contain lattice vectors.\n", filename);
return NULL;
}
vasp_buildrotmat(data);
*natoms = data->numatoms;
rewind(data->file);
return data;
}
static int read_vasp5xdatcar_structure(void *mydata, int *optflags, molfile_atom_t *atoms)
{
vasp_plugindata_t *data = (vasp_plugindata_t *)mydata;
FILE *potcar = NULL;
int atomcount, i;
char lineptr[LINESIZE], potcarfile[1000], *cp;
float lc;
if (!data || !optflags || !atoms) return MOLFILE_ERROR;
*optflags = MOLFILE_MASS; /* we set atom mass from the PTE. */
*optflags |= MOLFILE_ATOMICNUMBER | MOLFILE_RADIUS;
strcpy(potcarfile, data->filename);
cp = strstr(potcarfile, "XDATCAR");
if (cp) {
strcpy(cp, "POTCAR");
potcar = fopen(potcarfile, "r");
}
/* Read POTCAR file to determine atom types.
* Each atom type section in POTCAR starts with a line
* that contains the name of the element (H, He, C etc.).
* Otherwise try the title line instead.
*/
for (atomcount = i = 0; atomcount < data->numatoms; ++i) {
int idx, j;
char const *label;
float mass, radius;
if (potcar) {
char atomtype[5] = "X";
/* Obtain atom types from POTCAR file */
if (fgets(lineptr, LINESIZE, potcar)) sscanf(lineptr, "%*s %4[^_. 0-9]", atomtype);
idx = get_pte_idx(atomtype);
/* Skip lines in potcar file until next element */
while (fgets(lineptr, LINESIZE, potcar)) if (strstr(lineptr, "End of Dataset")) break;
} else {
/* Try to obtain atom types from title line */
char const *token = (i == 0 ? strtok(data->titleline, " ") : strtok(NULL, " "));
idx = get_pte_idx(token);
}
label = get_pte_label(idx);
mass = get_pte_mass(idx);
radius = get_pte_vdw_radius(idx);
for (j = 0; j < data->eachatom[i]; ++j, ++atomcount) {
molfile_atom_t *const atom = &(atoms[atomcount]);
/* Required settings */
strncpy(atom->name, label, sizeof(atom->name));
strncpy(atom->type, atom->name, sizeof(atom->type));
atom->resname[0] = '\0';
atom->resid = 1;
atom->segid[0]='\0';
atom->chain[0]='\0';
/* Optional flags (as defined in *optflags) */
atom->mass = mass;
atom->radius = radius;
atom->atomicnumber = idx;
}
}
if (potcar) fclose(potcar);
if (atomcount != data->numatoms) {
fprintf(stderr, "\n\nVASP5 XDATCAR read) ERROR: file '%s' doesn't seem to have list of atoms.\n", data->filename);
return MOLFILE_ERROR;
}
for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file);
sscanf(lineptr, "%f", &lc);
fprintf(stderr, "%f\n", 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);
/* Ignore header until X,Y,Z-coordinates */
for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file);
/* Check whether all coordinates are present in the file */
for (i = 0; i < data->numatoms; ++i) {
float coord;
fgets(lineptr, LINESIZE, data->file);
if (3 != sscanf(lineptr, "%f %f %f", &coord, &coord, &coord)) {
fprintf(stderr, "\n\nVASP5 XDATCAR read) ERROR: structure is missing type or coordinate(s) in file '%s' for atom '%d'\n", data->filename, i+1);
return MOLFILE_ERROR;
}
}
rewind(data->file);
/* Ignore header until X,Y,Z-coordinates */
for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file);
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;
}
