///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_dcd_step(FILE *dcd_infile, int &frame, int &natoms, int &reverseEndian)
{
int charmm = 0 ;
int num_fixed = 0 ;
int result ;
std::vector<float> vector_x(natoms) ;
std::vector<float> vector_y(natoms) ;
std::vector<float> vector_z(natoms) ;
result = read_dcdstep(dcd_infile,natoms,&vector_x[0],&vector_y[0],&vector_z[0],num_fixed,frame,reverseEndian,charmm) ;
if(_x().cols() < frame)
{
std::cout << "resizing array: cols() = " << _x().cols() << " frame = " << frame << std::endl ;
resize_array() ;
}
for(int i = 0 ; i < _natoms() ; ++i)
{
_x()(i,frame) = vector_x[i] ;
_y()(i,frame) = vector_y[i] ;
_z()(i,frame) = vector_z[i] ;
}
_number_of_frames()++ ;
return ;
}
static int read_next_timestep(void *v, int natoms, molfile_timestep_t *ts) {
dcdhandle *dcd;
int i, j, rc;
float unitcell[6];
unitcell[0] = unitcell[2] = unitcell[5] = 1.0f;
unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
dcd = (dcdhandle *)v;
/* Check for EOF here; that way all EOF's encountered later must be errors */
if (dcd->setsread == dcd->nsets) return MOLFILE_EOF;
dcd->setsread++;
if (!ts) {
if (dcd->first && dcd->nfixed) {
/* We can't just skip it because we need the fixed atom coordinates */
rc = read_dcdstep(dcd->fd, dcd->natoms, dcd->x, dcd->y, dcd->z,
unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
return rc; /* XXX this needs to be updated */
}
dcd->first = 0;
/* XXX this needs to be changed */
return skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm);
}
rc = read_dcdstep(dcd->fd, dcd->natoms, dcd->x, dcd->y, dcd->z, unitcell,
dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
if (rc < 0) {
print_dcderror("read_dcdstep", rc);
return MOLFILE_ERROR;
}
/* copy timestep data from plugin-local buffers to VMD's buffer */
/* XXX
* This code is still the root of all evil. Just doing this extra copy
* cuts the I/O rate of the DCD reader from 728 MB/sec down to
* 394 MB/sec when reading from a ram filesystem.
* For a physical disk filesystem, the I/O rate goes from
* 187 MB/sec down to 122 MB/sec. Clearly this extra copy has to go.
*/
{
int natoms = dcd->natoms;
float *nts = ts->coords;
const float *bufx = dcd->x;
const float *bufy = dcd->y;
const float *bufz = dcd->z;
for (i=0, j=0; i<natoms; i++, j+=3) {
nts[j ] = bufx[i];
nts[j + 1] = bufy[i];
nts[j + 2] = bufz[i];
}
}
ts->A = unitcell[0];
ts->B = unitcell[2];
ts->C = unitcell[5];
if (unitcell[1] >= -1.0 && unitcell[1] <= 1.0 &&
unitcell[3] >= -1.0 && unitcell[3] <= 1.0 &&
unitcell[4] >= -1.0 && unitcell[4] <= 1.0) {
/* This file was generated by CHARMM, or by NAMD > 2.5, with the angle */
/* cosines of the periodic cell angles written to the DCD file. */
/* This formulation improves rounding behavior for orthogonal cells */
/* so that the angles end up at precisely 90 degrees, unlike acos(). */
ts->alpha = 90.0 - asin(unitcell[4]) * 90.0 / M_PI_2; /* cosBC */
ts->beta = 90.0 - asin(unitcell[3]) * 90.0 / M_PI_2; /* cosAC */
ts->gamma = 90.0 - asin(unitcell[1]) * 90.0 / M_PI_2; /* cosAB */
} else {
/* This file was likely generated by NAMD 2.5 and the periodic cell */
/* angles are specified in degrees rather than angle cosines. */
ts->alpha = unitcell[4]; /* angle between B and C */
ts->beta = unitcell[3]; /* angle between A and C */
ts->gamma = unitcell[1]; /* angle between A and B */
}
return MOLFILE_SUCCESS;
}
static PyObject *
__read_next_frame(PyObject *self, PyObject *args)
{
dcdhandle *dcd;
PyObject *temp;
PyArrayObject *x, *y, *z, *uc;
int skip=1;
int rc,numskip;
float* unitcell;
float alpha, beta, gamma;
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!|i", &self, &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc, &skip) )
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!|i", &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc, &skip) )
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);
unitcell = (float*) uc->data;
unitcell[0] = unitcell[2] = unitcell[5] = 0.0f;
unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
/* Check for EOF here; that way all EOF's encountered later must be errors */
if (dcd->setsread == dcd->nsets) {
// Is this an exception?
PyErr_SetString(PyExc_IOError, "End of file reached for dcd file");
return NULL;
//return MOLFILE_EOF;
}
if (skip > 1) {
if (dcd->first && dcd->nfixed) {
/* We can't just skip it because we need the fixed atom coordinates */
rc = read_dcdstep(dcd->fd, dcd->natoms, (float*)x->data, (float*)y->data, (float*)z->data,
unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error reading first frame from DCD file");
//fprintf(stderr, "read_dcdstep returned %d\n", rc);
return NULL;
//return MOLFILE_ERROR;
}
dcd->setsread++;
temp = Py_BuildValue("i", dcd->setsread);
return temp;
//return rc; /* XXX this needs to be updated */
}
dcd->first = 0;
// Figure out how many steps to skip
numskip = skip - (dcd->setsread % skip) - 1;
/* XXX this needs to be changed */
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");
//fprintf(stderr, "read_dcdstep returned %d\n", rc);
return NULL;
//return MOLFILE_ERROR;
}
dcd->setsread+=numskip;
}
rc = read_dcdstep(dcd->fd, dcd->natoms, (float*)x->data, (float*)y->data, (float*)z->data, unitcell,
dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
dcd->setsread++;
if (rc < 0) {
// return an exception
PyErr_SetString(PyExc_IOError, "Error reading frame from DCD file");
//fprintf(stderr, "read_dcdstep returned %d\n", rc);
return NULL;
//return MOLFILE_ERROR;
}
if (unitcell[1] >= -1.0 && unitcell[1] <= 1.0 &&
unitcell[3] >= -1.0 && unitcell[3] <= 1.0 &&
unitcell[4] >= -1.0 && unitcell[4] <= 1.0) {
/* This file was generated by Charmm, or by NAMD > 2.5, with the angle */
/* cosines of the periodic cell angles written to the DCD file. */
/* This formulation improves rounding behavior for orthogonal cells */
/* so that the angles end up at precisely 90 degrees, unlike acos(). */
/* (changed in MDAnalysis 0.9.0 to have NAMD ordering of the angles; */
/* see Issue 187) */
alpha = 90.0 - asin(unitcell[4]) * 90.0 / M_PI_2;
beta = 90.0 - asin(unitcell[3]) * 90.0 / M_PI_2;
gamma = 90.0 - asin(unitcell[1]) * 90.0 / M_PI_2;
} else {
/* This file was likely generated by NAMD 2.5 and the periodic cell */
/* angles are specified in degrees rather than angle cosines. */
alpha = unitcell[4];
beta = unitcell[3];
gamma = unitcell[1];
}
unitcell[4] = alpha;
unitcell[3] = beta;
unitcell[1] = gamma;
// Return the frame read
temp = Py_BuildValue("i", dcd->setsread);
return temp;
}
