static void *open_dcd_write(const char *path, const char *filetype,
int natoms) {
dcdhandle *dcd;
fio_fd fd;
int rc;
int istart, nsavc;
double delta;
int with_unitcell;
int charmm;
if (fio_open(path, FIO_WRITE, &fd) < 0) {
printf("dcdplugin) Could not open file '%s' for writing\n", path);
return NULL;
}
dcd = (dcdhandle *)malloc(sizeof(dcdhandle));
memset(dcd, 0, sizeof(dcdhandle));
dcd->fd = fd;
istart = 0; /* starting timestep of DCD file */
nsavc = 1; /* number of timesteps between written DCD frames */
delta = 1.0; /* length of a timestep */
if (getenv("VMDDCDWRITEXPLORFORMAT") != NULL) {
with_unitcell = 0; /* no unit cell info */
charmm = DCD_IS_XPLOR; /* X-PLOR format */
printf("dcdplugin) WARNING: Writing DCD file in X-PLOR format, \n");
printf("dcdplugin) WARNING: unit cell information will be lost!\n");
} else {
with_unitcell = 1; /* contains unit cell infor (Charmm format) */
charmm = DCD_IS_CHARMM; /* charmm-formatted DCD file */
if (with_unitcell)
charmm |= DCD_HAS_EXTRA_BLOCK;
}
rc = write_dcdheader(dcd->fd, "Created by DCD plugin", natoms,
istart, nsavc, delta, with_unitcell, charmm);
if (rc < 0) {
print_dcderror("write_dcdheader", rc);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
dcd->natoms = natoms;
dcd->nsets = 0;
dcd->istart = istart;
dcd->nsavc = nsavc;
dcd->with_unitcell = with_unitcell;
dcd->charmm = charmm;
dcd->x = (float *)malloc(natoms * sizeof(float));
dcd->y = (float *)malloc(natoms * sizeof(float));
dcd->z = (float *)malloc(natoms * sizeof(float));
return dcd;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
int
//sasio::Files::
sasio::
write_dcd_header(FILE *outfile, const std::string &filename, int &natoms, int &nset)
{
char *c_filename = new char[filename.size()+1] ;
c_filename[filename.size()] = 0 ;
memcpy(c_filename,filename.c_str(),filename.size()) ;
int istart = 0 , nsavc = 1 ;
double delta = 1.0 ;
int header_result = 0 ;
header_result = write_dcdheader(outfile, c_filename, natoms, nset, \
istart, nsavc, delta);
return header_result ;
}
static PyObject *
__write_dcd_header(PyObject *self, PyObject *args)
{
/* At this point we assume the file has been opened for writing */
PyObject *temp = NULL;
dcdhandle *dcd = NULL;
fio_fd fd;
int rc = 0;
int natoms = 0;
const char *remarks = "DCD";
int istart = 0; /* starting timestep of DCD file */
int nsavc = 1; /* number of timesteps between written DCD frames */
double delta = 1.0; /* length of a timestep */
int with_unitcell = 1; /* contains unit cell information (charmm format) */
int charmm = DCD_IS_CHARMM; /* charmm-formatted DCD file */
if (with_unitcell)
charmm |= DCD_HAS_EXTRA_BLOCK;
if (! self) {
/* we were in fact called as a module function, try to retrieve
a matching object from args */
if( !PyArg_ParseTuple(args, "Oi|iids", &self, &natoms, &istart, &nsavc, &delta, &remarks) )
return NULL;
} else {
/* we were obviously called as an object method so args should
only have the int value. */
if( !PyArg_ParseTuple(args, "i|iids", &natoms, &istart, &nsavc, &delta, &remarks) )
return NULL;
}
// Get the file object from the class
if (!PyObject_HasAttrString(self, "dcdfile")) {
// Raise exception
PyErr_SetString(PyExc_AttributeError, "dcdfile is not an attribute");
return NULL;
}
if ((temp = PyObject_GetAttrString(self, "dcdfile")) == NULL) { // This gives me a New Reference
// Raise exception
PyErr_SetString(PyExc_AttributeError, "dcdfile is not an attribute");
return NULL;
}
if (!PyFile_CheckExact(temp)) {
// Raise exception
PyErr_SetString(PyExc_TypeError, "dcdfile does not refer to a file object");
Py_DECREF(temp);
return NULL;
}
fd = fileno(PyFile_AsFile(temp));
// No longer need the reference to temp
Py_DECREF(temp);
dcd = (dcdhandle *)malloc(sizeof(dcdhandle));
memset(dcd, 0, sizeof(dcdhandle));
dcd->fd = fd;
if ((rc = write_dcdheader(dcd->fd, remarks, natoms, istart, nsavc, delta, with_unitcell, charmm)) < 0) {
PyErr_SetString(PyExc_IOError, "Cannot write header of DCD file");
free(dcd);
return NULL;
}
dcd->natoms = natoms;
dcd->nsets = 0;
dcd->istart = istart;
dcd->nsavc = nsavc;
dcd->delta = delta;
dcd->with_unitcell = with_unitcell;
dcd->charmm = charmm;
temp = PyCObject_FromVoidPtr(dcd, free); // Creates a New Reference
if (PyObject_SetAttrString(self, "_dcd_C_ptr", temp) == -1) {
// Raise exception - who knows what exception to raise??
PyErr_SetString(PyExc_AttributeError, "Could not create attribute _dcd_C_ptr");
Py_DECREF(temp);
return NULL;
}
Py_DECREF(temp);
// For debugging purposes
temp = PyBuffer_FromMemory(dcd, sizeof(dcdhandle)); // Creates a New Reference
if (PyObject_SetAttrString(self, "_dcd_C_str", temp) == -1) {
// Raise exception - who knows what exception to raise??
PyErr_SetString(PyExc_AttributeError, "Could not create attribute _dcd_C_str");
Py_DECREF(temp);
return NULL;
}
Py_DECREF(temp);
Py_INCREF(Py_None);
return Py_None;
}