static int xtc_coord(XDR *xd, int *natoms, rvec *box, rvec *x, real *prec, gmx_bool bRead)
{
int i, j, result;
#if GMX_DOUBLE
float *ftmp;
float fprec;
#endif
/* box */
result = 1;
for (i = 0; ((i < DIM) && result); i++)
{
for (j = 0; ((j < DIM) && result); j++)
{
result = XTC_CHECK("box", xdr_r2f(xd, &(box[i][j]), bRead));
}
}
if (!result)
{
return result;
}
#if GMX_DOUBLE
/* allocate temp. single-precision array */
snew(ftmp, (*natoms)*DIM);
/* Copy data to temp. array if writing */
if (!bRead)
{
for (i = 0; (i < *natoms); i++)
{
ftmp[DIM*i+XX] = x[i][XX];
ftmp[DIM*i+YY] = x[i][YY];
ftmp[DIM*i+ZZ] = x[i][ZZ];
}
fprec = *prec;
}
result = XTC_CHECK("x", xdr3dfcoord(xd, ftmp, natoms, &fprec));
/* Copy from temp. array if reading */
if (bRead)
{
for (i = 0; (i < *natoms); i++)
{
x[i][XX] = ftmp[DIM*i+XX];
x[i][YY] = ftmp[DIM*i+YY];
x[i][ZZ] = ftmp[DIM*i+ZZ];
}
*prec = fprec;
}
sfree(ftmp);
#else
result = XTC_CHECK("x", xdr3dfcoord(xd, x[0], natoms, prec));
#endif
return result;
}
void
F77_FUNC(xdrf3dfcoord,XDRF3DFCOORD)(int *xdrid, float *fp, int *size, float *precision, int *ret)
{
xdr_fortran_lock();
*ret = xdr3dfcoord(xdridptr[*xdrid], fp, size, precision);
xdr_fortran_unlock();
}
bool XtcFileFormat::read(std::istream &input, chemkit::TrajectoryFile *file)
{
// read data into temporary file
QTemporaryFile dataFile;
dataFile.open();
unsigned int dataSize = 0;
for(;;){
char c = input.get();
if(input.eof()){
break;
}
dataFile.write(&c, 1);
dataSize++;
}
dataFile.close();
XDR xdrs;
xdropen(&xdrs, dataFile.fileName().toAscii().constData(), "r");
chemkit::Trajectory *trajectory = new chemkit::Trajectory;
while(xdr_getpos(&xdrs) < dataSize){
// read magic (should be '1995')
int magic = 0;
xdr_int(&xdrs, &magic);
if(magic != 1995){
break;
}
// create new frame
chemkit::TrajectoryFrame *frame = trajectory->addFrame();
// read atom count
int atomCount = 0;
xdr_int(&xdrs, &atomCount);
// read frame number
int frameNumber = 0;
xdr_int(&xdrs, &frameNumber);
// read time
float time = 0;
xdr_float(&xdrs, &time);
// read unit cell
float box[3][3];
for(int i = 0; i < 3; i++){
for(int j = 0; j < 3; j++){
xdr_float(&xdrs, &box[i][j]);
}
}
chemkit::Vector3 x(box[0][0], box[0][1], box[0][2]);
chemkit::Vector3 y(box[1][0], box[1][1], box[1][2]);
chemkit::Vector3 z(box[2][0], box[2][1], box[2][2]);
frame->setUnitCell(new chemkit::UnitCell(x * 10, y * 10, z * 10));
// read coordinates
float coordinateData[3 * atomCount];
float precision = 1000.0f;
xdr3dfcoord(&xdrs, coordinateData, &atomCount, &precision);
chemkit::Coordinates coordinates(atomCount);
for(int i = 0; i < atomCount; i++){
// multiply each coordinate by 10 to convert
// from nanometers to angstroms
chemkit::Point3 position(coordinateData[i*3+0] * 10,
coordinateData[i*3+1] * 10,
coordinateData[i*3+2] * 10);
coordinates.setPosition(i, position);
}
frame->setCoordinates(&coordinates);
}
xdrclose(&xdrs);
if(trajectory->isEmpty()){
delete trajectory;
return false;
}
file->setTrajectory(trajectory);
return true;
}
void
F77_FUNC(xdrf3dfcoord,XDRF3DFCOORD)(int *xdrid, float *fp, int *size, float *precision, int *ret)
{
*ret = xdr3dfcoord(xdridptr[*xdrid], fp, size, precision);
}
