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_vasp5xdatcar_read(const char *filename, const char *filetype, int *natoms)
{
vasp_plugindata_t *data;
char lineptr[LINESIZE];
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;
/* VASP5 is assumed in default */
data->version = 5;
data->file = fopen(filename, "rb");
if (!data->file) {
vasp_plugindata_free(data);
return NULL;
}
data->filename = strdup(filename);
/* Ignore rest of header up to the line with atom numbers */
for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file);
/* Read title line */
fgets(lineptr, LINESIZE, data->file);
data->titleline = strdup(lineptr);
/* Read the number of atoms per atom type */
data->numatoms = 0;
fgets(lineptr, LINESIZE, data->file);
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\nVASP5 XDATCAR read) ERROR: file '%s' does not have list of atom numbers.\n", filename);
return NULL;
}
*natoms = data->numatoms;
rewind(data->file);
return data;
}
static void *open_vaspposcar_write(const char *filename, const char *filetype, int natoms)
{
vasp_plugindata_t *data;
data = vasp_plugindata_malloc();
if (!data) return NULL;
data->file = fopen(filename, "w");
if (!data->file) {
vasp_plugindata_free(data);
fprintf(stderr, "VASP POSCAR write) ERROR: Unable to open vaspposcar file '%s' for writing\n", filename);
return NULL;
}
data->filename = strdup(filename);
data->numatoms = natoms;
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;
}