static void close_js_write(void *v) {
jshandle *js = (jshandle *)v;
/* update the trajectory header information */
fio_fseek(js->fd, JSNFRAMESOFFSET, FIO_SEEK_SET);
fio_write_int32(js->fd, js->nframes);
fio_fseek(js->fd, 0, FIO_SEEK_END);
fio_fclose(js->fd);
#if JSMAJORVERSION > 1
if (js->bondfrom)
free(js->bondfrom);
if (js->bondto)
free(js->bondto);
if (js->bondorders)
free(js->bondorders);
if (js->angles)
free(js->angles);
if (js->dihedrals)
free(js->dihedrals);
if (js->impropers)
free(js->impropers);
if (js->cterms)
free(js->cterms);
#endif
free(js);
}
/*
* Skip past a timestep. If there are fixed atoms, this cannot be used with
* the first timestep.
* Input: fd - a file struct from which the header has already been read
* natoms - number of atoms per timestep
* nfixed - number of fixed atoms
* charmm - charmm flags as returned by read_dcdheader
* Output: 0 on success, negative error code on failure.
* Side effects: One timestep will be skipped; fd will be positioned at the
* next timestep.
*/
static int skip_dcdstep(fio_fd fd, int natoms, int nfixed, int charmm) {
int seekoffset = 0;
int rec_scale;
if (charmm & DCD_HAS_64BIT_REC) {
rec_scale=RECSCALE64BIT;
} else {
rec_scale=RECSCALE32BIT;
}
/* Skip charmm extra block */
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_EXTRA_BLOCK)) {
seekoffset += 4*rec_scale + 48 + 4*rec_scale;
}
/* For each atom set, seek past an int, the free atoms, and another int. */
seekoffset += 3 * (2*rec_scale + natoms - nfixed) * 4;
/* Assume that charmm 4th dim is the same size as the other three. */
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_4DIMS)) {
seekoffset += (2*rec_scale + natoms - nfixed) * 4;
}
if (fio_fseek(fd, seekoffset, FIO_SEEK_CUR)) return DCD_BADEOF;
return DCD_SUCCESS;
}
static int read_charmm_extrablock(fio_fd fd, int charmm, int reverseEndian,
float *unitcell) {
int i, input_integer[2], rec_scale;
if (charmm & DCD_HAS_64BIT_REC) {
rec_scale = RECSCALE64BIT;
} else {
rec_scale = RECSCALE32BIT;
}
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_EXTRA_BLOCK)) {
/* Leading integer must be 48 */
input_integer[1] = 0;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale)
return DCD_BADREAD;
if (reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) == 48) {
double tmp[6];
if (fio_fread(tmp, 48, 1, fd) != 1) return DCD_BADREAD;
if (reverseEndian)
swap8_aligned(tmp, 6);
for (i=0; i<6; i++) unitcell[i] = (float)tmp[i];
} else {
/* unrecognized block, just skip it */
if (fio_fseek(fd, (input_integer[0]+input_integer[1]), FIO_SEEK_CUR)) return DCD_BADREAD;
}
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
}
return DCD_SUCCESS;
}
int jump_to_frame(dcdhandle *dcd, int frame)
{
int rc;
if (frame > dcd->nsets) {
return -1;
}
// Calculate file offset
{
off_t extrablocksize, ndims, firstframesize, framesize;
off_t pos;
extrablocksize = dcd->charmm & DCD_HAS_EXTRA_BLOCK ? 48 + 8 : 0;
ndims = dcd->charmm & DCD_HAS_4DIMS ? 4 : 3;
firstframesize = (dcd->natoms+2) * ndims * sizeof(float) + extrablocksize;
framesize = (dcd->natoms-dcd->nfixed+2) * ndims * sizeof(float)
+ extrablocksize;
// Use zero indexing
if (frame == 0) {
pos = dcd->header_size;
dcd->first = 1;
}
else {
pos = dcd->header_size + firstframesize + framesize * (frame-1);
dcd->first = 0;
}
rc = fio_fseek(dcd->fd, pos, FIO_SEEK_SET);
}
dcd->setsread = frame;
return rc;
}
/*
* Write a timestep to a dcd file
* Input: fd - a file struct for which a dcd header has already been written
* curframe: Count of frames written to this file, starting with 1.
* curstep: Count of timesteps elapsed = istart + curframe * nsavc.
* natoms - number of elements in x, y, z arrays
* x, y, z: pointers to atom coordinates
* Output: 0 on success, negative error code on failure.
* Side effects: coordinates are written to the dcd file.
*/
static int write_dcdstep(fio_fd fd, int curframe, int curstep, int N,
const float *X, const float *Y, const float *Z,
const double *unitcell, int charmm) {
int out_integer;
if (charmm) {
/* write out optional unit cell */
if (unitcell != NULL) {
out_integer = 48; /* 48 bytes (6 floats) */
fio_write_int32(fd, out_integer);
WRITE(fd, unitcell, out_integer);
fio_write_int32(fd, out_integer);
}
}
/* write out coordinates */
out_integer = N*4; /* N*4 bytes per X/Y/Z array (N floats per array) */
fio_write_int32(fd, out_integer);
if (fio_fwrite((void *) X, out_integer, 1, fd) != 1) return DCD_BADWRITE;
fio_write_int32(fd, out_integer);
fio_write_int32(fd, out_integer);
if (fio_fwrite((void *) Y, out_integer, 1, fd) != 1) return DCD_BADWRITE;
fio_write_int32(fd, out_integer);
fio_write_int32(fd, out_integer);
if (fio_fwrite((void *) Z, out_integer, 1, fd) != 1) return DCD_BADWRITE;
fio_write_int32(fd, out_integer);
/* update the DCD header information */
fio_fseek(fd, NFILE_POS, FIO_SEEK_SET);
fio_write_int32(fd, curframe);
fio_fseek(fd, NSTEP_POS, FIO_SEEK_SET);
fio_write_int32(fd, curstep);
fio_fseek(fd, 0, FIO_SEEK_END);
return DCD_SUCCESS;
}
static int read_js_timestep(void *v, int natoms, molfile_timestep_t *ts) {
jshandle *js = (jshandle *)v;
int framelen = (natoms * 3 * sizeof(float)) + (6 * sizeof(double));;
/* if we have a valid ts pointer, read the timestep, otherwise skip it */
if (ts != NULL) {
int readlen;
fio_iovec iov[2];
double unitcell[6];
unitcell[0] = unitcell[2] = unitcell[5] = 1.0f;
unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
/* setup the I/O vector */
iov[0].iov_base = (fio_caddr_t) ts->coords; /* read coordinates */
iov[0].iov_len = natoms * 3 * sizeof(float);
iov[1].iov_base = (fio_caddr_t) &unitcell[0]; /* read PBC unit cell */
iov[1].iov_len = 6 * sizeof(double);
/* Do all of the reads with a single syscall, for peak efficiency. */
/* On smart kernels, readv() causes only one context switch, and */
/* can effeciently scatter the reads to the various buffers. */
readlen = fio_readv(js->fd, &iov[0], 2);
/* check the number of read bytes versus what we expected */
if (readlen != framelen)
return MOLFILE_EOF;
/* perform byte swapping if necessary */
if (js->reverseendian) {
swap4_aligned(ts->coords, natoms * 3);
swap8_aligned(unitcell, 6);
}
/* copy unit cell values into VMD */
ts->A = unitcell[0];
ts->B = unitcell[1];
ts->C = unitcell[2];
ts->alpha = 90.0 - asin(unitcell[3]) * 90.0 / M_PI_2;
ts->beta = 90.0 - asin(unitcell[4]) * 90.0 / M_PI_2;
ts->gamma = 90.0 - asin(unitcell[5]) * 90.0 / M_PI_2;
} else {
/* skip this frame, seek to the next frame */
if (fio_fseek(js->fd, framelen, FIO_SEEK_CUR))
return MOLFILE_EOF;
}
return MOLFILE_SUCCESS;
}
static int read_charmm_4dim(fio_fd fd, int charmm, int reverseEndian) {
int input_integer[2],rec_scale;
if (charmm & DCD_HAS_64BIT_REC) {
rec_scale=RECSCALE64BIT;
} else {
rec_scale=RECSCALE32BIT;
}
/* If this is a CHARMm file and contains a 4th dimension block, */
/* we must skip past it to avoid problems */
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_4DIMS)) {
input_integer[1]=0;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
if (reverseEndian) swap4_aligned(input_integer, rec_scale);
if (fio_fseek(fd, (input_integer[0]+input_integer[1]), FIO_SEEK_CUR)) return DCD_BADREAD;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
}
return DCD_SUCCESS;
}
static PyObject *
__reset_dcd_read(PyObject *self, PyObject *args)
{
PyObject* temp;
dcdhandle *dcd;
int rc;
if (! self) {
/* we were in fact called as a module function, try to retrieve
a matching object from args */
if( !PyArg_ParseTuple(args, "O", &self) )
return NULL;
} else {
/* we were obviously called as an object method so args should
only have the int value. */
if( !PyArg_ParseTuple(args, "") )
return NULL;
}
if ( !PyObject_HasAttrString(self, "_dcd_C_ptr") ) {
// Raise exception
PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
return NULL;
}
if ((temp = PyObject_GetAttrString(self, "_dcd_C_ptr")) == NULL) { // This gives me a New Reference
// Raise exception
PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
return NULL;
}
dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
dcd->setsread = 0;
dcd->first = 1;
Py_DECREF(temp);
Py_INCREF(Py_None);
return Py_None;
}
static void *open_dcd_read(const char *path, const char *filetype,
int *natoms) {
dcdhandle *dcd;
fio_fd fd;
int rc;
struct stat stbuf;
if (!path) return NULL;
/* See if the file exists, and get its size */
memset(&stbuf, 0, sizeof(struct stat));
if (stat(path, &stbuf)) {
printf("dcdplugin) Could not access file '%s'.\n", path);
return NULL;
}
if (fio_open(path, FIO_READ, &fd) < 0) {
printf("dcdplugin) Could not open file '%s' for reading.\n", path);
return NULL;
}
dcd = (dcdhandle *)malloc(sizeof(dcdhandle));
memset(dcd, 0, sizeof(dcdhandle));
dcd->fd = fd;
if ((rc = read_dcdheader(dcd->fd, &dcd->natoms, &dcd->nsets, &dcd->istart,
&dcd->nsavc, &dcd->delta, &dcd->nfixed, &dcd->freeind,
&dcd->fixedcoords, &dcd->reverse, &dcd->charmm))) {
print_dcderror("read_dcdheader", rc);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
/*
* Check that the file is big enough to really hold the number of sets
* it claims to have. Then we'll use nsets to keep track of where EOF
* should be.
*/
{
fio_size_t ndims, firstframesize, framesize, extrablocksize;
fio_size_t trjsize, filesize, curpos;
int newnsets;
extrablocksize = dcd->charmm & DCD_HAS_EXTRA_BLOCK ? 48 + 8 : 0;
ndims = dcd->charmm & DCD_HAS_4DIMS ? 4 : 3;
firstframesize = (dcd->natoms+2) * ndims * sizeof(float) + extrablocksize;
framesize = (dcd->natoms-dcd->nfixed+2) * ndims * sizeof(float)
+ extrablocksize;
/*
* It's safe to use ftell, even though ftell returns a long, because the
* header size is < 4GB.
*/
curpos = fio_ftell(dcd->fd); /* save current offset (end of header) */
#if defined(_MSC_VER) && defined(FASTIO_NATIVEWIN32)
/* the stat() call is not 64-bit savvy on Windows */
/* so we have to use the fastio fseek/ftell routines for this */
/* until we add a portable filesize routine for this purpose */
fio_fseek(dcd->fd, 0, FIO_SEEK_END); /* seek to end of file */
filesize = fio_ftell(dcd->fd);
fio_fseek(dcd->fd, curpos, FIO_SEEK_SET); /* return to end of header */
#else
filesize = stbuf.st_size; /* this works ok on Unix machines */
#endif
trjsize = filesize - curpos - firstframesize;
if (trjsize < 0) {
printf("dcdplugin) file '%s' appears to contain no timesteps.\n", path);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
newnsets = trjsize / framesize + 1;
if (dcd->nsets > 0 && newnsets != dcd->nsets) {
printf("dcdplugin) Warning: DCD header claims %d frames, file size indicates there are actually %d frames\n", dcd->nsets, newnsets);
}
dcd->nsets = newnsets;
dcd->setsread = 0;
}
dcd->first = 1;
dcd->x = (float *)malloc(dcd->natoms * sizeof(float));
dcd->y = (float *)malloc(dcd->natoms * sizeof(float));
dcd->z = (float *)malloc(dcd->natoms * sizeof(float));
if (!dcd->x || !dcd->y || !dcd->z) {
printf("dcdplugin) Unable to allocate space for %d atoms.\n", dcd->natoms);
if (dcd->x)
free(dcd->x);
if (dcd->y)
free(dcd->y);
if (dcd->z)
free(dcd->z);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
*natoms = dcd->natoms;
return dcd;
}
/*
* Read the header information from a dcd file.
* Input: fd - a file struct opened for binary reading.
* Output: 0 on success, negative error code on failure.
* Side effects: *natoms set to number of atoms per frame
* *nsets set to number of frames in dcd file
* *istart set to starting timestep of dcd file
* *nsavc set to timesteps between dcd saves
* *delta set to value of trajectory timestep
* *nfixed set to number of fixed atoms
* *freeind may be set to heap-allocated space
* *reverse set to one if reverse-endian, zero if not.
* *charmm set to internal code for handling charmm data.
*/
static int read_dcdheader(fio_fd fd, int *N, int *NSET, int *ISTART,
int *NSAVC, double *DELTA, int *NAMNF,
int **FREEINDEXES, float **fixedcoords, int *reverseEndian,
int *charmm)
{
unsigned int input_integer[2]; /* buffer space */
int i, ret_val, rec_scale;
union hdrufb_union {
char charvalue[84]; /* char buffer used to store header */
int intvalue;
} hdrbuf;
int NTITLE;
int dcdcordmagic;
char *corp = (char *) &dcdcordmagic;
/* coordinate dcd file magic string 'CORD' */
corp[0] = 'C';
corp[1] = 'O';
corp[2] = 'R';
corp[3] = 'D';
/* First thing in the file should be an 84.
* some 64-bit compiles have a 64-bit record length indicator,
* so we have to read two ints and check in a more complicated
* way. :-( */
ret_val = READ(fd, input_integer, 2*sizeof(unsigned int));
CHECK_FREAD(ret_val, "reading first int from dcd file");
CHECK_FEOF(ret_val, "reading first int from dcd file");
/* Check magic number in file header and determine byte order*/
if ((input_integer[0]+input_integer[1]) == 84) {
*reverseEndian=0;
rec_scale=RECSCALE64BIT;
printf("dcdplugin) detected CHARMM -i8 64-bit DCD file of native endianness\n");
} else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
*reverseEndian=0;
rec_scale=RECSCALE32BIT;
printf("dcdplugin) detected standard 32-bit DCD file of native endianness\n");
} else {
/* now try reverse endian */
swap4_aligned(input_integer, 2); /* will have to unswap magic if 32-bit */
if ((input_integer[0]+input_integer[1]) == 84) {
*reverseEndian=1;
rec_scale=RECSCALE64BIT;
printf("dcdplugin) detected CHARMM -i8 64-bit DCD file of opposite endianness\n");
} else {
swap4_aligned(&input_integer[1], 1); /* unswap magic (see above) */
if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
*reverseEndian=1;
rec_scale=RECSCALE32BIT;
printf("dcdplugin) detected standard 32-bit DCD file of opposite endianness\n");
} else {
/* not simply reversed endianism or -i8, something rather more evil */
printf("dcdplugin) unrecognized DCD header:\n");
printf("dcdplugin) [0]: %10d [1]: %10d\n", input_integer[0], input_integer[1]);
printf("dcdplugin) [0]: 0x%08x [1]: 0x%08x\n", input_integer[0], input_integer[1]);
return DCD_BADFORMAT;
}
}
}
/* check for magic string, in case of long record markers */
if (rec_scale == RECSCALE64BIT) {
ret_val = READ(fd, input_integer, sizeof(unsigned int));
if (input_integer[0] != dcdcordmagic) {
printf("dcdplugin) failed to find CORD magic in CHARMM -i8 64-bit DCD file\n");
return DCD_BADFORMAT;
}
}
/* Buffer the entire header for random access */
ret_val = READ(fd, hdrbuf.charvalue, 80);
CHECK_FREAD(ret_val, "buffering header");
CHECK_FEOF(ret_val, "buffering header");
/* CHARMm-genereate DCD files set the last integer in the */
/* header, which is unused by X-PLOR, to its version number. */
/* Checking if this is nonzero tells us this is a CHARMm file */
/* and to look for other CHARMm flags. */
if (*((int *) (hdrbuf.charvalue + 76)) != 0) {
(*charmm) = DCD_IS_CHARMM;
if (*((int *) (hdrbuf.charvalue + 40)) != 0)
(*charmm) |= DCD_HAS_EXTRA_BLOCK;
if (*((int *) (hdrbuf.charvalue + 44)) == 1)
(*charmm) |= DCD_HAS_4DIMS;
if (rec_scale == RECSCALE64BIT)
(*charmm) |= DCD_HAS_64BIT_REC;
} else {
(*charmm) = DCD_IS_XPLOR; /* must be an X-PLOR format DCD file */
}
if (*charmm & DCD_IS_CHARMM) {
/* CHARMM and NAMD versions 2.1b1 and later */
printf("dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)\n");
} else {
/* CHARMM and NAMD versions prior to 2.1b1 */
printf("dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)\n");
}
/* Store the number of sets of coordinates (NSET) */
(*NSET) = *((int *)(hdrbuf.charvalue));
if (*reverseEndian) swap4_unaligned(NSET, 1);
/* Store ISTART, the starting timestep */
(*ISTART) = *((int *) (hdrbuf.charvalue + 4));
if (*reverseEndian) swap4_unaligned(ISTART, 1);
/* Store NSAVC, the number of timesteps between dcd saves */
(*NSAVC) = *((int *) (hdrbuf.charvalue + 8));
if (*reverseEndian) swap4_unaligned(NSAVC, 1);
/* Store NAMNF, the number of fixed atoms */
(*NAMNF) = *((int *) (hdrbuf.charvalue + 32));
if (*reverseEndian) swap4_unaligned(NAMNF, 1);
/* Read in the timestep, DELTA */
/* Note: DELTA is stored as a double with X-PLOR but as a float with CHARMm */
if ((*charmm) & DCD_IS_CHARMM) {
float ftmp;
ftmp = *((float *)(hdrbuf.charvalue+36)); /* is this safe on Alpha? */
if (*reverseEndian)
swap4_aligned(&ftmp, 1);
*DELTA = (double)ftmp;
} else {
(*DELTA) = *((double *)(hdrbuf.charvalue + 36));
if (*reverseEndian) swap8_unaligned(DELTA, 1);
}
/* Get the end size of the first block */
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading second 84 from dcd file");
CHECK_FEOF(ret_val, "reading second 84 from dcd file");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if (rec_scale == RECSCALE64BIT) {
if ((input_integer[0]+input_integer[1]) != 84) {
return DCD_BADFORMAT;
}
} else {
if (input_integer[0] != 84) {
return DCD_BADFORMAT;
}
}
/* Read in the size of the next block */
input_integer[1] = 0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading size of title block");
CHECK_FEOF(ret_val, "reading size of title block");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((((input_integer[0]+input_integer[1])-4) % 80) == 0) {
/* Read NTITLE, the number of 80 character title strings there are */
ret_val = READ(fd, &NTITLE, sizeof(int));
CHECK_FREAD(ret_val, "reading NTITLE");
CHECK_FEOF(ret_val, "reading NTITLE");
if (*reverseEndian) swap4_aligned(&NTITLE, 1);
for (i=0; i<NTITLE; i++) {
fio_fseek(fd, 80, FIO_SEEK_CUR);
CHECK_FEOF(ret_val, "reading TITLE");
}
/* Get the ending size for this block */
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading size of title block");
CHECK_FEOF(ret_val, "reading size of title block");
} else {
return DCD_BADFORMAT;
}
/* Read in an integer '4' */
input_integer[1] = 0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading a '4'");
CHECK_FEOF(ret_val, "reading a '4'");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != 4) {
return DCD_BADFORMAT;
}
/* Read in the number of atoms */
ret_val = READ(fd, N, sizeof(int));
CHECK_FREAD(ret_val, "reading number of atoms");
CHECK_FEOF(ret_val, "reading number of atoms");
if (*reverseEndian) swap4_aligned(N, 1);
/* Read in an integer '4' */
input_integer[1] = 0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading a '4'");
CHECK_FEOF(ret_val, "reading a '4'");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != 4) {
return DCD_BADFORMAT;
}
*FREEINDEXES = NULL;
*fixedcoords = NULL;
if (*NAMNF != 0) {
(*FREEINDEXES) = (int *) calloc(((*N)-(*NAMNF)), sizeof(int));
if (*FREEINDEXES == NULL)
return DCD_BADMALLOC;
*fixedcoords = (float *) calloc((*N)*4 - (*NAMNF), sizeof(float));
if (*fixedcoords == NULL)
return DCD_BADMALLOC;
/* Read in index array size */
input_integer[1]=0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading size of index array");
CHECK_FEOF(ret_val, "reading size of index array");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
return DCD_BADFORMAT;
}
ret_val = READ(fd, (*FREEINDEXES), ((*N)-(*NAMNF))*sizeof(int));
CHECK_FREAD(ret_val, "reading size of index array");
CHECK_FEOF(ret_val, "reading size of index array");
if (*reverseEndian)
swap4_aligned((*FREEINDEXES), ((*N)-(*NAMNF)));
input_integer[1]=0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading size of index array");
CHECK_FEOF(ret_val, "reading size of index array");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
return DCD_BADFORMAT;
}
}
return DCD_SUCCESS;
}
static PyObject *
__read_timeseries(PyObject *self, PyObject *args)
{
PyObject *temp = NULL;
PyArrayObject *coord = NULL;
PyListObject *atoms = NULL;
int lowerb = 0, upperb = 0, range=0;
float *tempX = NULL, *tempY = NULL, *tempZ = NULL;
int rc;
int i, j, index;
int n_atoms = 0, n_frames = 0;
/* Stop = -1 is incorrect and causes an error, look for a fix of this in line
469 */
int start = 0, stop = -1, step = 1, numskip = 0, remaining_frames=0;
dcdhandle *dcd = NULL;
int *atomlist = NULL;
npy_intp dimensions[3];
float unitcell[6];
const char* format = "afc";
if (!self) {
/* we were in fact called as a module function, try to retrieve
a matching object from args */
if( !PyArg_ParseTuple(args, "OO!|iiis", &self, &PyList_Type, &atoms, &start, &stop, &step, &format) )
return NULL;
} else {
/* we were obviously called as an object method so args should
only have the int value. */
if( !PyArg_ParseTuple(args, "O!|iiis", &PyList_Type, &atoms, &start, &stop, &step, &format) )
return NULL;
}
if ((temp = PyObject_GetAttrString(self, "_dcd_C_ptr")) == NULL) { // This gives me a New Reference
// Raise exception
PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
return NULL;
}
dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
Py_DECREF(temp);
n_frames = ((stop-start) / step);
if ((stop-start) % step > 0) { n_frames++; }
//n_frames = dcd->nsets / skip;
n_atoms = PyList_Size((PyObject*)atoms);
if (n_atoms == 0) {
PyErr_SetString(PyExc_Exception, "No atoms passed into _read_timeseries function");
return NULL;
}
atomlist = (int*)malloc(sizeof(int)*n_atoms);
memset(atomlist, 0, sizeof(int)*n_atoms);
// Get the atom indexes
for (i=0;i<n_atoms;i++) {
temp = PyList_GetItem((PyObject*)atoms, i); // Borrowed Reference
if (temp==NULL) goto error;
// Make sure temp is an integer
/* TODO: this is not the proper check but [OB] cannot figure out how
to check if this is a numpy.int64 or similar; PyInt_Check would fail
on those (Issue 18)
*/
if (!PyArray_IsAnyScalar((PyObject*)temp)) {
PyErr_SetString(PyExc_ValueError, "Atom number is not an integer");
goto error;
}
atomlist[i] = PyInt_AsLong(temp);
}
lowerb = atomlist[0]; upperb = atomlist[n_atoms-1];
range = upperb-lowerb+1;
// Figure out the format string
if (strncasecmp(format, "afc", 3) == 0) {
dimensions[0] = n_atoms; dimensions[1] = n_frames; dimensions[2] = 3;
} else if (strncasecmp(format, "acf", 3) == 0) {
dimensions[0] = n_atoms; dimensions[1] = 3; dimensions[2] = n_frames;
} else if (strncasecmp(format, "fac", 3) == 0) {
dimensions[0] = n_frames; dimensions[1] = n_atoms; dimensions[2] = 3;
} else if (strncasecmp(format, "fca", 3) == 0) {
dimensions[0] = n_frames; dimensions[1] = 3; dimensions[2] = n_atoms;
} else if (strncasecmp(format, "caf", 3) == 0) {
dimensions[0] = 3; dimensions[1] = n_atoms; dimensions[2] = n_frames;
} else if (strncasecmp(format, "cfa", 3) == 0) {
dimensions[0] = 3; dimensions[1] = n_frames; dimensions[2] = n_atoms;
}
coord = (PyArrayObject*) PyArray_SimpleNew(3, dimensions, NPY_DOUBLE);
if (coord == NULL) goto error;
// Reset trajectory
rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
dcd->setsread = 0;
dcd->first = 1;
// Jump to starting frame
jump_to_frame(dcd, start);
// Now read through trajectory and get the atom pos
tempX = (float*)malloc(sizeof(float)*range);
tempY = (float*)malloc(sizeof(float)*range);
tempZ = (float*)malloc(sizeof(float)*range);
if ((tempX == NULL) | (tempY == NULL) || (tempZ == NULL)) {
PyErr_SetString(PyExc_MemoryError, "Can't allocate temporary space for coordinate arrays");
goto error;
}
remaining_frames = stop-start;
for (i=0;i<n_frames;i++) {
if (step > 1 && i>0) {
// Check if we have fixed atoms
// XXX not done
/* Figure out how many steps to step over, if step = n, np array
slicing treats this as skip over n-1, read the nth. */
numskip = step -1;
/* If the number to skip is greater than the number of frames left
to be jumped over, just take one more step to reflect np slicing
if there is a remainder, guaranteed to have at least one more
frame.
*/
if(remaining_frames < numskip){
numskip = 1;
}
rc = skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm, numskip);
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error skipping frame from DCD file");
goto error;
}
}
// on first iteration, numskip == 0, first set is always read.
dcd->setsread += numskip;
//now read from subset
rc = read_dcdsubset(dcd->fd, dcd->natoms, lowerb, upperb, tempX, tempY, tempZ,
unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
dcd->setsread++;
remaining_frames = stop - dcd->setsread;
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error reading frame from DCD file");
goto error;
}
// Copy into Numeric array only those atoms we are interested in
for (j=0;j<n_atoms;j++) {
index = atomlist[j]-lowerb;
/*
* coord[a][b][c] = *(float*)(coord->data + a*coord->strides[0] + b*coord->strides[1] + c*coord->strides[2])
*/
if (strncasecmp(format, "afc", 3) == 0) {
*(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 0*coord->strides[2]) = tempX[index];
*(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 1*coord->strides[2]) = tempY[index];
*(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 2*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "acf", 3) == 0) {
*(double*)(coord->data + j*coord->strides[0] + 0*coord->strides[1] + i*coord->strides[2]) = tempX[index];
*(double*)(coord->data + j*coord->strides[0] + 1*coord->strides[1] + i*coord->strides[2]) = tempY[index];
*(double*)(coord->data + j*coord->strides[0] + 2*coord->strides[1] + i*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "fac", 3) == 0) {
*(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 0*coord->strides[2]) = tempX[index];
*(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 1*coord->strides[2]) = tempY[index];
*(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 2*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "fca", 3) == 0) {
*(double*)(coord->data + i*coord->strides[0] + 0*coord->strides[1] + j*coord->strides[2]) = tempX[index];
*(double*)(coord->data + i*coord->strides[0] + 1*coord->strides[1] + j*coord->strides[2]) = tempY[index];
*(double*)(coord->data + i*coord->strides[0] + 2*coord->strides[1] + j*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "caf", 3) == 0) {
*(double*)(coord->data + 0*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempX[index];
*(double*)(coord->data + 1*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempY[index];
*(double*)(coord->data + 2*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempZ[index];
} else if (strncasecmp(format, "cfa", 3) == 0) {
*(double*)(coord->data + 0*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempX[index];
*(double*)(coord->data + 1*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempY[index];
*(double*)(coord->data + 2*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempZ[index];
}
}
// Check if we've been interupted by the user
if (PyErr_CheckSignals() == 1) goto error;
}
// Reset trajectory
rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
dcd->setsread = 0;
dcd->first = 1;
free(atomlist);
free(tempX);
free(tempY);
free(tempZ);
return PyArray_Return(coord);
error:
// Reset trajectory
rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
dcd->setsread = 0;
dcd->first = 1;
Py_XDECREF(coord);
if (atomlist != NULL) free(atomlist);
if (tempX != NULL) free(tempX);
if (tempY != NULL) free(tempY);
if (tempZ != NULL) free(tempZ);
return NULL;
}