static int write_timestep(void *v, const molfile_timestep_t *ts) {
dcdhandle *dcd = (dcdhandle *)v;
int i, rc, curstep;
float *pos = ts->coords;
double unitcell[6];
unitcell[0] = unitcell[2] = unitcell[5] = 1.0f;
unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
/* copy atom coords into separate X/Y/Z arrays for writing */
for (i=0; i<dcd->natoms; i++) {
dcd->x[i] = *(pos++);
dcd->y[i] = *(pos++);
dcd->z[i] = *(pos++);
}
dcd->nsets++;
curstep = dcd->istart + dcd->nsets * dcd->nsavc;
unitcell[0] = ts->A;
unitcell[2] = ts->B;
unitcell[5] = ts->C;
unitcell[1] = sin((M_PI_2 / 90.0) * (90.0 - ts->gamma)); /* cosAB */
unitcell[3] = sin((M_PI_2 / 90.0) * (90.0 - ts->beta)); /* cosAC */
unitcell[4] = sin((M_PI_2 / 90.0) * (90.0 - ts->alpha)); /* cosBC */
rc = write_dcdstep(dcd->fd, dcd->nsets, curstep, dcd->natoms,
dcd->x, dcd->y, dcd->z,
dcd->with_unitcell ? unitcell : NULL,
dcd->charmm);
if (rc < 0) {
print_dcderror("write_dcdstep", rc);
return MOLFILE_ERROR;
}
return MOLFILE_SUCCESS;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
write_dcd_step(FILE *outfile, int &frame, int &step)
{
int step_result = 0 ;
step_result = write_dcdstep(outfile,_natoms(),&_x()(0,frame),&_y()(0,frame),&_z()(0,frame),step+1) ;
return ;
}
static PyObject *
__write_next_frame(PyObject *self, PyObject *args)
{
dcdhandle *dcd;
PyObject *temp;
PyArrayObject *x, *y, *z, *uc;
int rc, curstep;
float* uc_array;
double unitcell[6];
if (!self) {
/* we were in fact called as a module function, try to retrieve
a matching object from args */
if( !PyArg_ParseTuple(args, "OO!O!O!O!", &self, &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc) )
return NULL;
} else {
/* we were obviously called as an object method so args should
only have the int value. */
if( !PyArg_ParseTuple(args, "O!O!O!O!", &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc) )
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);
dcd->nsets++;
curstep = dcd->istart + dcd->nsets * dcd->nsavc;
uc_array = (float*) uc->data;
unitcell[0] = uc_array[0]; /* A */
unitcell[2] = uc_array[2]; /* B */
unitcell[5] = uc_array[5]; /* C */
/* write angle cosines with NAMD ordering [orbeckst] */
/* (changed in MDAnalysis 0.9.0) */
unitcell[4] = sin((M_PI_2 / 90.0 ) * (90.0 - uc_array[4])); /* cos(alpha) */
unitcell[3] = sin((M_PI_2 / 90.0 ) * (90.0 - uc_array[3])); /* cos(beta) */
unitcell[1] = sin((M_PI_2 / 90.0 ) * (90.0 - uc_array[1])); /* cos(gamma) */
if ((rc = write_dcdstep(dcd->fd, dcd->nsets, curstep, dcd->natoms, (float*)x->data, (float*)y->data, (float*)z->data,
dcd->with_unitcell ? unitcell: NULL,
dcd->charmm)) < 0)
{
PyErr_SetString(PyExc_IOError, "Could not write timestep to dcd file");
return NULL;
}
Py_INCREF(Py_None);
return Py_None;
}
