static int read_binary_dx_data(dx_t *dx, int set, float *datablock) {
int i, j, k;
int xsize = dx->vol[0].xsize;
int ysize = dx->vol[0].ysize;
int zsize = dx->vol[0].zsize;
int xysize = xsize * ysize;
size_t total = xysize * zsize;
float *tmp = (float *)malloc(total*sizeof(float));
if (fread(tmp, sizeof(float), total, dx->fd) != total) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Failed to read %d binary floats\n", total);
free(tmp);
return MOLFILE_ERROR;
}
// take the transpose - nasty
int ind = 0;
for (i=0; i<xsize; i++) {
for (j=0; j<ysize; j++) {
for (k=0; k<zsize; k++) {
datablock[k * xysize + j*xsize + i] = tmp[ind++];
}
}
}
free( tmp );
return MOLFILE_SUCCESS;
}
static void *open_rst_write(const char *path, const char *filetype, int natoms) {
char title[82];
rstdata *rst;
FILE *fd;
int len;
fd = fopen(path, "wb");
if (!fd) {
vmdcon_printf(VMDCON_ERROR, "rst7plugin) Could not open file %s for writing\n", path);
return NULL;
}
/* write out fixed length fortran style string */
sprintf(title, "TITLE : Created by VMD with %d atoms",natoms);
len = strlen(title);
memset(title+len,(int)' ',82-len);
title[80] = '\n';
title[81] = '\0';
fputs(title,fd);
rst = (rstdata *)malloc(sizeof(rstdata));
rst->file = fd;
rst->numatoms = natoms;
rst->has_box = 1;
return rst;
}
// Get a string from a stream, printing any errors that occur
static char *dxgets(char *s, int n, FILE *stream) {
char *returnVal;
if (feof(stream)) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Unexpected end-of-file.\n");
return NULL;
} else if (ferror(stream)) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error reading file.\n");
return NULL;
} else {
returnVal = fgets(s, n, stream);
if (returnVal == NULL) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error reading line.\n");
}
}
return returnVal;
}
static void *open_dx_write(const char *filepath, const char *filetype,
int natoms) {
FILE *fd = fopen(filepath, "wb");
if (!fd) {
vmdcon_printf(VMDCON_ERROR,
"dxplugin) Could not open path '%s' for writing.\n",
filepath);
}
return fd;
}
/* flush current message queue to a registered
* console widget, if such a thing exists.
* since vmdcon_append() allocates the storage,
* for everything, we have to free the msg structs
* and the strings. */
int vmdcon_purge(void)
{
struct vmdcon_msg *msg;
const char *res;
wkf_mutex_lock(&vmdcon_status_lock);
/* purge message queue only if we have a working console window */
if ( ! ((vmdcon_status == VMDCON_UNDEF) || (vmdcon_status == VMDCON_NONE)
|| ((vmdcon_status == VMDCON_WIDGET) &&
((vmdcon_interp == NULL) || (vmdcon_wpath == NULL))) ) ) {
wkf_mutex_lock(&vmdcon_output_lock);
while (vmdcon_pending != NULL) {
msg=vmdcon_pending;
switch (vmdcon_status) {
case VMDCON_TEXT:
fputs(msg->txt,stdout);
break;
case VMDCON_WIDGET:
res = tcl_vmdcon_insert(vmdcon_interp, vmdcon_wpath,
vmdcon_mark, msg->txt);
/* handle errors writing to a tcl console window.
* unregister widget, don't free current message
* and append error message into holding buffer. */
if (res) {
wkf_mutex_unlock(&vmdcon_status_lock);
vmdcon_register(NULL, NULL, vmdcon_interp);
wkf_mutex_unlock(&vmdcon_output_lock);
vmdcon_printf(VMDCON_ERROR,
"Problem writing to text widget: %s\n", res);
return 1;
}
break;
default:
/* unknown console type */
return 1;
}
free(msg->txt);
vmdcon_pending=msg->next;
free(msg);
}
if (vmdcon_status == VMDCON_TEXT)
fflush(stdout);
wkf_mutex_unlock(&vmdcon_output_lock);
}
wkf_mutex_unlock(&vmdcon_status_lock);
return 0;
}
static int read_timestep_metadata(void *mydata,
molfile_timestep_metadata_t *meta) {
rstdata *data = (rstdata *)mydata;
meta->count = -1;
meta->has_velocities = data->ts_meta.has_velocities;
if (meta->has_velocities) {
vmdcon_printf(VMDCON_INFO,
"rst7plugin) Importing velocities from restart file.\n");
}
return MOLFILE_SUCCESS;
}
static int read_dx_data(void *v, int set, float *datablock,
float *colorblock) {
dx_t *dx = (dx_t *)v;
FILE *fd = dx->fd;
char inbuf[LINESIZE];
char *p;
float grid;
int x, y, z, xsize, ysize, zsize, xysize, count, total, i, line;
if (dx->isBinary)
return read_binary_dx_data(dx, set, datablock);
xsize = dx->vol[0].xsize;
ysize = dx->vol[0].ysize;
zsize = dx->vol[0].zsize;
xysize = xsize * ysize;
total = xysize * zsize;
/* Read the values from the file */
x = y = z = line = 0;
for (count = 0; count < total;) {
++line;
p=dxgets(inbuf, LINESIZE, fd);
if (p == NULL) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error reading grid data.\n");
vmdcon_printf(VMDCON_ERROR, "dxplugin) line: %d. item: %d/%d. last data: %s\n",
line, count, total, inbuf);
return MOLFILE_ERROR;
}
// chop line into whitespace separated tokens and parse them one by one.
while (*p != '\n' && *p != '\0') {
// skip over whitespace and try to parse non-blank as number
while (*p != '\0' && (*p == ' ' || *p == '\t' || *p == '\n')) ++p;
i = sscanf(p, "%e", &grid);
if (i < 0) break; // end of line/string. get a new one.
// a 0 return value means non-parsable as number.
if (i == 0) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error parsing grid data.\n");
vmdcon_printf(VMDCON_ERROR, "dxplugin) line: %d. item: %d/%d. data %s\n",
line, count, total, p);
return MOLFILE_ERROR;
}
// success! add to dataset.
if (i == 1) {
++count;
datablock[x + y*xsize + z*xysize] = grid;
z++;
if (z >= zsize) {
z = 0; y++;
if (y >= ysize) {
y = 0; x++;
}
}
}
// skip over the parsed text and search for next blank.
while (*p != '\0' && *p != ' ' && *p != '\t' && *p != '\n') ++p;
}
}
char dxname[256];
while (dxgets(inbuf, LINESIZE, dx->fd)) {
if (sscanf(inbuf, "object \"%[^\"]\" class field", dxname) == 1) {
// a dataset name has been found; override the default
strcpy(dx->vol[0].dataname, dxname);
break;
}
}
return MOLFILE_SUCCESS;
}
static void *open_dx_read(const char *filepath, const char *filetype,
int *natoms) {
FILE *fd;
dx_t *dx;
char inbuf[LINESIZE];
int xsize, ysize, zsize;
float orig[3], xdelta[3], ydelta[3], zdelta[3];
int isBinary = 0;
fd = fopen(filepath, "rb");
if (!fd) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error opening file.\n");
return NULL;
}
/* skip comments */
do {
if (dxgets(inbuf, LINESIZE, fd) == NULL)
return NULL;
} while (inbuf[0] == '#');
/* get the number of grid points */
if (sscanf(inbuf, "object 1 class gridpositions counts %d %d %d", &xsize, &ysize, &zsize) != 3) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error reading grid dimensions.\n");
return NULL;
}
/* get the cell origin */
if (dxgets(inbuf, LINESIZE, fd) == NULL) {
return NULL;
}
if (sscanf(inbuf, "origin %e %e %e", orig, orig+1, orig+2) != 3) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error reading grid origin.\n");
return NULL;
}
/* get the cell dimensions */
if (dxgets(inbuf, LINESIZE, fd) == NULL) {
return NULL;
}
if (sscanf(inbuf, "delta %e %e %e", xdelta, xdelta+1, xdelta+2) != 3) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error reading cell x-dimension.\n");
return NULL;
}
if (dxgets(inbuf, LINESIZE, fd) == NULL) {
return NULL;
}
if (sscanf(inbuf, "delta %e %e %e", ydelta, ydelta+1, ydelta+2) != 3) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error reading cell y-dimension.\n");
return NULL;
}
if (dxgets(inbuf, LINESIZE, fd) == NULL) {
return NULL;
}
if (sscanf(inbuf, "delta %e %e %e", zdelta, zdelta+1, zdelta+2) != 3) {
vmdcon_printf(VMDCON_ERROR, "dxplugin) Error reading cell z-dimension.\n");
return NULL;
}
/* skip the next line of the header (described at the beginning of
* the code), which aren't utilized by APBS-produced DX files. */
if (dxgets(inbuf, LINESIZE, fd) == NULL)
return NULL;
/* The next line tells us whether to expect ascii or binary format.
* We scan for the word 'binary' somewhere in the line, and if it's found
* we assume binary.
*/
if (dxgets(inbuf, LINESIZE, fd) == NULL)
return NULL;
if (strstr(inbuf, "binary")) {
isBinary = 1;
}
/* allocate and initialize the dx structure */
dx = new dx_t;
dx->fd = fd;
dx->vol = NULL;
dx->isBinary = isBinary;
*natoms = MOLFILE_NUMATOMS_NONE;
dx->nsets = 1; /* this file contains only one data set */
dx->vol = new molfile_volumetric_t[1];
strcpy(dx->vol[0].dataname, "DX map");
/* Set the unit cell origin and basis vectors */
for (int i=0; i<3; i++) {
dx->vol[0].origin[i] = orig[i];
dx->vol[0].xaxis[i] = xdelta[i] * ((xsize-1 > 0) ? (xsize-1) : 1);
dx->vol[0].yaxis[i] = ydelta[i] * ((ysize-1 > 0) ? (ysize-1) : 1);
dx->vol[0].zaxis[i] = zdelta[i] * ((zsize-1 > 0) ? (zsize-1) : 1);
}
dx->vol[0].xsize = xsize;
dx->vol[0].ysize = ysize;
dx->vol[0].zsize = zsize;
/* DX files contain no color information. Taken from edmplugin.C */
dx->vol[0].has_color = 0;
return dx;
}
static void *open_rst_read(const char *filename, const char *filetype,int *natoms) {
FILE *fd;
rstdata *data;
int numats=0,i,j,point2,kkk=1;
char title[82], *field;
char line[82];
float x, y, z,a=0.0,b=0.0,c=0.0;
double timesteprst;
/* Amber 7'coord' restart files have a second introduction line with
* possibly 2 entries only check for one now...
* they include three 90.00 ter cards at the end
* need to fix this, real crd files have atom record but no timestep and no
* velocity info...arggggg
*/
fd = fopen(filename, "rb");
if (!fd)
return NULL; /* failure */
data = (rstdata *)malloc(sizeof(rstdata));
memset(data, 0, sizeof(rstdata));
#if vmdplugin_ABIVERSION > 10
data->ts_meta.count = -1;
data->ts_meta.has_velocities = 0;
#endif
fgets(title, 82, fd);
vmdcon_printf(VMDCON_INFO, "rst7plugin) Title: %s\n",title);
fgets(line, 82, fd);
while (kkk==1) {
/* try to read first field */
field = strtok(line, " \t");
if (field==NULL) {
continue; /* no fields at all on this line */
}
numats = atoi(field);
/* try to read second field will be null if not there */
field = strtok(NULL, " \t");
if (field==NULL) {
kkk=0;
vmdcon_printf(VMDCON_INFO, "rst7plugin) This file has no velocity info.\n");
data->has_vels=0;
} else {
timesteprst = strtod(field, NULL);
vmdcon_printf(VMDCON_INFO, "rst7plugin) This file contains velocity info.\n");
data->has_vels=1;
#if vmdplugin_ABIVERSION > 10
data->ts_meta.has_velocities = 1;
#endif
kkk=0;
}
}
point2=ftell(fd);
data->file = fd;
vmdcon_printf(VMDCON_INFO, "rst7plugin) The Restartcrd has %d atoms.\n",numats);
/* skip over coordinate data */
for (i=0; i<numats; i++) {
j = fscanf(fd, "%f%f%f", &x, &y, &z);
}
/* skip over velocity data, if present */
if (data->has_vels) {
for (i=0; i<numats; i++) {
j = fscanf(fd, "%f%f%f", &x, &y, &z);
}
}
j = fscanf(fd, "%f%f%f%f%f%f", &x, &y, &z,&a,&b,&c);
if (j != EOF) {
vmdcon_printf(VMDCON_INFO, "rst7plugin) This restartcrd file has box info.\n");
data->has_box=1;
vmdcon_printf(VMDCON_INFO, "rst7plugin) Box Dimensions are %f %f %f %f %f %f\n",x,y,z,a,b,c);
}
*natoms=numats;
data->numatoms=numats;
data->rstfile=1;
fseek(fd,point2,SEEK_SET);
return data;
}
static int read_rst_timestep(void *mydata, int natoms, molfile_timestep_t *ts) {
rstdata *rst= (rstdata *)mydata;
int i, j;
float x, y, z, a, b, c;
/* check for rst and first read through already taken place */
if(rst->count==1 && rst->rstfile==1)
return MOLFILE_ERROR;
ts->A = ts->B = ts->C = 0.0f;
ts->alpha = ts->beta = ts->gamma = 90.0f;
for (i=0; i<rst->numatoms; i++) {
/* changed to i=1 BB */
j = fscanf(rst->file, "%f%f%f", &x, &y, &z);
if (j == EOF) {
return MOLFILE_ERROR;
} else if (j <= 0) {
vmdcon_printf(VMDCON_ERROR, "rst7plugin) Problem reading CRD file\n");
return MOLFILE_ERROR;
}
ts->coords[3*i] = x;
ts->coords[3*i+1] = y;
ts->coords[3*i+2] = z;
}
if (rst->has_vels) {
/* Read in optional velocity data. Units are Angstroms per 1/20.455ps. */
for (i=0; i<rst->numatoms; i++) {
j = fscanf(rst->file, "%f%f%f", &x, &y, &z);
if (j == EOF) {
return MOLFILE_ERROR;
} else if (j <= 0) {
vmdcon_printf(VMDCON_ERROR, "rst7plugin) Problem reading velocities\n");
return MOLFILE_ERROR;
}
#if vmdplugin_ABIVERSION > 10
if (ts->velocities != NULL) {
ts->velocities[3*i] = x;
ts->velocities[3*i+1] = y;
ts->velocities[3*i+2] = z;
}
#endif
}
}
if (rst->has_box) {
j = fscanf(rst->file, "%f%f%f%f%f%f", &x, &y, &z, &a, &b, &c);
if (j == EOF) {
vmdcon_printf(VMDCON_ERROR, "rst7plugin) Problem reading box data\n");
return MOLFILE_ERROR;
}
ts->A = x;
ts->B = y;
ts->C = z;
ts->alpha = a;
ts->beta = b;
ts->gamma = c;
}
rst->count++;
/* printf("rst->count: %d\n",rst->count); */
return MOLFILE_SUCCESS;
}
