// Traj_AmberNetcdf::writeReservoir() TODO: Make Frame const&
int Traj_AmberNetcdf::writeReservoir(int set, Frame const& frame, double energy, int bin) {
start_[0] = ncframe_;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
// Coords
DoubleToFloat(Coord_, frame.xAddress());
if (checkNCerr(nc_put_vara_float(ncid_,coordVID_,start_,count_,Coord_)) ) {
mprinterr("Error: Netcdf writing reservoir coords %i\n",set);
return 1;
}
// Velo
if (velocityVID_ != -1) {
if (frame.vAddress() == 0) { // TODO: Make it so this can NEVER happen.
mprinterr("Error: Reservoir expects velocities, but no velocities in frame.\n");
return 1;
}
DoubleToFloat(Coord_, frame.vAddress());
if (checkNCerr(nc_put_vara_float(ncid_,velocityVID_,start_,count_,Coord_)) ) {
mprinterr("Error: Netcdf writing reservoir velocities %i\n",set);
return 1;
}
}
// Eptot, bins
if ( checkNCerr( nc_put_vara_double(ncid_,eptotVID_,start_,count_,&energy)) ) {
mprinterr("Error: Writing eptot.\n");
return 1;
}
if (binsVID_ != -1) {
if ( checkNCerr( nc_put_vara_int(ncid_,binsVID_,start_,count_,&bin)) ) {
mprinterr("Error: Writing bins.\n");
return 1;
}
}
// Write box
if (cellLengthVID_ != -1) {
count_[1] = 3;
count_[2] = 0;
if (checkNCerr(nc_put_vara_double(ncid_,cellLengthVID_,start_,count_,frame.bAddress())) ) {
mprinterr("Error: Writing cell lengths.\n");
return 1;
}
if (checkNCerr(nc_put_vara_double(ncid_,cellAngleVID_,start_,count_, frame.bAddress()+3)) ) {
mprinterr("Error: Writing cell angles.\n");
return 1;
}
}
nc_sync(ncid_); // Necessary after every write??
++ncframe_;
return 0;
}
int Traj_AmberNetcdf::parallelWriteFrame(int set, Frame const& frameOut) {
MPI_Offset pstart_[3];
MPI_Offset pcount_[3];
pstart_[0] = set;
pstart_[1] = 0;
pstart_[2] = 0;
pcount_[0] = 1;
pcount_[1] = Ncatom();
pcount_[2] = 3;
// TODO check error better
DoubleToFloat(Coord_, frameOut.xAddress());
//int err = ncmpi_put_vara_float_all(ncid_, coordVID_, pstart_, pcount_, Coord_);
int err = ncmpi_put_vara_float(ncid_, coordVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
if (velocityVID_ != -1) {
DoubleToFloat(Coord_, frameOut.vAddress());
//err = ncmpi_put_vara_float_all(ncid_, velocityVID_, pstart_, pcount_, Coord_);
err = ncmpi_put_vara_float(ncid_, velocityVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
}
if (frcVID_ != -1) {
DoubleToFloat(Coord_, frameOut.fAddress());
err = ncmpi_put_vara_float(ncid_, frcVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
}
pcount_[2] = 0;
if (cellLengthVID_ != -1) {
pcount_[1] = 3;
//err = ncmpi_put_vara_double_all(ncid_, cellLengthVID_, pstart_, pcount_, frameOut.bAddress());
err = ncmpi_put_vara_double(ncid_, cellLengthVID_, pstart_, pcount_, frameOut.bAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
//err = ncmpi_put_vara_double_all(ncid_, cellAngleVID_, pstart_, pcount_, frameOut.bAddress()+3);
err = ncmpi_put_vara_double(ncid_, cellAngleVID_, pstart_, pcount_, frameOut.bAddress()+3);
}
if (TempVID_ != -1) {
//err = ncmpi_put_vara_double_all(ncid_, TempVID_, pstart_, pcount_, frameOut.tAddress());
err = ncmpi_put_vara_double(ncid_, TempVID_, pstart_, pcount_, frameOut.tAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
}
if (timeVID_ != -1) {
float tVal = (float)frameOut.Time();
err = ncmpi_put_vara_float(ncid_, timeVID_, pstart_, pcount_, &tVal);
if (checkPNCerr(err)) return Parallel::Abort(err);
}
if (indicesVID_ != -1) {
pcount_[1] = remd_dimension_;
//err = ncmpi_put_vara_int_all(ncid_, indicesVID_, pstart_, pcount_, frameOut.iAddress());
err = ncmpi_put_vara_int(ncid_, indicesVID_, pstart_, pcount_, frameOut.iAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
}
return 0;
}
/*******************************************************************************
* ReadBBox
*
* Similar to ReadFloat above.
*
*/
static BOOL ReadBBox(FILE *file, CHAR buffer[], INT bufsize, AFM *afm,
BOOL *p_found)
{
CHAR *cp, *end_ptr;
double d;
if (FindLine(file, buffer, bufsize, "FontBBox") == FALSE)
return FALSE;
if (buffer[0] == '\0')
{
*p_found = FALSE;
return TRUE;
}
errno = 0;
cp = buffer + sizeof("FontBBox");
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0 ||
DoubleToFloat(&(afm->FontBBox.llx), d) == FALSE)
goto parse_error;
cp = end_ptr;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0 ||
DoubleToFloat(&(afm->FontBBox.lly), d) == FALSE)
goto parse_error;
cp = end_ptr;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0
|| DoubleToFloat(&(afm->FontBBox.urx), d) == FALSE)
goto parse_error;
cp = end_ptr;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0
|| DoubleToFloat(&(afm->FontBBox.ury), d) == FALSE)
goto parse_error;
*p_found = TRUE;
return TRUE;
parse_error:
WARN("Error parsing line '%s'\n", buffer);
*p_found = FALSE;
return TRUE;
}
/*******************************************************************************
* ReadFloat
*
* Finds and parses a line of the form '<key> <value>', where value is a
* number. Sets *p_found to FALSE if a corresponding line cannot be found, or
* it cannot be parsed; also sets *p_ret to 0.0, so calling functions can just
* skip the check of *p_found if the item is not required.
*
*/
static BOOL ReadFloat(FILE *file, CHAR buffer[], INT bufsize, LPCSTR key,
FLOAT *p_ret, BOOL *p_found)
{
CHAR *cp, *end_ptr;
double d;
if (FindLine(file, buffer, bufsize, key) == FALSE)
return FALSE;
if (buffer[0] == '\0') /* line not found */
{
*p_found = FALSE;
*p_ret = 0.0;
return TRUE;
}
cp = buffer + strlen(key); /* first char after key */
errno = 0;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0 || DoubleToFloat(p_ret, d) == FALSE)
{
WARN("Error parsing line '%s'\n", buffer);
*p_found = FALSE;
*p_ret = 0.0;
return TRUE;
}
*p_found = TRUE;
return TRUE;
}
/*******************************************************************************
*
* ParseB
*
* Fatal error: return FALSE (none defined)
*
* Non-fatal error: leave metrics->B.ury set to FLT_MAX
*
*/
static BOOL ParseB(LPSTR sz, OLD_AFMMETRICS *metrics)
{
CHAR *cp, *end_ptr;
double d;
errno = 0;
cp = sz + 1;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0 ||
DoubleToFloat(&(metrics->B.llx), d) == FALSE)
goto parse_error;
cp = end_ptr;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0 ||
DoubleToFloat(&(metrics->B.lly), d) == FALSE)
goto parse_error;
cp = end_ptr;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0 ||
DoubleToFloat(&(metrics->B.urx), d) == FALSE)
goto parse_error;
cp = end_ptr;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0 ||
DoubleToFloat(&(metrics->B.ury), d) == FALSE)
goto parse_error;
return TRUE;
parse_error:
WARN("Error parsing glyph bounding box '%s'\n", sz);
return TRUE;
}
TEST(DSP, FloatDoubleConversion)
{
float in[10] = {1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0};
double out[10];
float fout[10];
FloatToDouble(out, in, 10);
for (unsigned i = 0; i < 10; ++i)
{
ASSERT_DOUBLE_EQ((double)in[i], out[i]);
}
DoubleToFloat(fout, out, 10);
for (unsigned i = 0; i < 10; ++i)
{
ASSERT_FLOAT_EQ(in[i], fout[i]);
}
}
/*******************************************************************************
* ParseW
*
* Fatal error: return FALSE (none defined)
*
* Non-fatal error: leave metrics->WX set to FLT_MAX
*
*/
static BOOL ParseW(LPSTR sz, OLD_AFMMETRICS *metrics)
{
CHAR *cp, *end_ptr;
BOOL vector = TRUE;
double d;
cp = sz + 1;
if (*cp == '0')
++cp;
if (*cp == 'X')
{
vector = FALSE;
++cp;
}
if (!isspace(*cp))
goto parse_error;
errno = 0;
d = strtod(cp, &end_ptr);
if (end_ptr == cp || errno != 0 ||
DoubleToFloat(&(metrics->WX), d) == FALSE)
goto parse_error;
if (vector == FALSE)
return TRUE;
/* Make sure that Y component of vector is zero */
d = strtod(cp, &end_ptr); /* errno == 0 */
if (end_ptr == cp || errno != 0 || d != 0.0)
{
metrics->WX = FLT_MAX;
goto parse_error;
}
return TRUE;
parse_error:
WARN("Error parsing character width '%s'\n", sz);
return TRUE;
}
// Traj_AmberNetcdf::writeFrame()
int Traj_AmberNetcdf::writeFrame(int set, double *X, double *V, double *box, double T) {
DoubleToFloat(Coord_, X);
// Write coords
start_[0] = ncframe_;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
if (checkNCerr(nc_put_vara_float(ncid_,coordVID_,start_,count_,Coord_)) ) {
mprinterr("Error: Netcdf Writing frame %i\n",set);
return 1;
}
// Write box
if (cellLengthVID_ != -1) {
count_[1] = 3;
count_[2] = 0;
if (checkNCerr(nc_put_vara_double(ncid_,cellLengthVID_,start_,count_,box)) ) {
mprinterr("Error: Writing cell lengths.\n");
return 1;
}
if (checkNCerr(nc_put_vara_double(ncid_,cellAngleVID_,start_,count_, box+3)) ) {
mprinterr("Error: Writing cell angles.\n");
return 1;
}
}
// Write temperature
if (TempVID_!=-1) {
if ( checkNCerr( nc_put_vara_double(ncid_,TempVID_,start_,count_,&T)) ) {
mprinterr("Error: Writing temperature.\n");
return 1;
}
}
nc_sync(ncid_); // Necessary after every write??
++ncframe_;
return 0;
}
// Traj_NcEnsemble::writeArray() // TODO RemdValues
int Traj_NcEnsemble::writeArray(int set, FramePtrArray const& Farray) {
# ifdef HAS_PNETCDF
MPI_Offset pstart_[4];
MPI_Offset pcount_[4];
# define start_ pstart_
# define count_ pcount_
# endif
start_[0] = ncframe_; // Frame
start_[2] = 0; // Atoms
start_[3] = 0; // XYZ
count_[0] = 1; // Frame
count_[1] = 1; // Ensemble
count_[3] = 3; // XYZ
for (int member = ensembleStart_; member != ensembleEnd_; member++) {
//rprintf("DEBUG: Writing set %i, member %i\n", set+1, member);
# ifdef MPI
Frame* frm = Farray[0];
# else
Frame* frm = Farray[member];
# endif
start_[1] = member; // Ensemble
count_[2] = Ncatom(); // Atoms
// Write Coords
//DebugIndices(); // DEBUG
DoubleToFloat(Coord_, frm->xAddress());
# ifdef HAS_PNETCDF
if (ncmpi_put_vara_float_all(ncid_, coordVID_, start_, count_, Coord_))
# else
if (NC::CheckErr(nc_put_vara_float(ncid_, coordVID_, start_, count_, Coord_)))
# endif
{
mprinterr("Error: Netcdf Writing coords frame %i\n", set+1);
return 1;
}
// Write velocity.
if (velocityVID_ != -1) {
DoubleToFloat(Coord_, frm->vAddress());
# ifdef HAS_PNETCDF
if (ncmpi_put_vara_float_all(ncid_, velocityVID_, start_, count_, Coord_))
# else
if (NC::CheckErr(nc_put_vara_float(ncid_, velocityVID_, start_, count_, Coord_)) )
# endif
{
mprinterr("Error: Netcdf writing velocity frame %i\n", set+1);
return 1;
}
}
// Write box
if (cellLengthVID_ != -1) {
count_[2] = 3;
# ifdef HAS_PNETCDF
if (ncmpi_put_vara_double_all(ncid_,cellLengthVID_,start_,count_,frm->bAddress()))
# else
if (NC::CheckErr(nc_put_vara_double(ncid_,cellLengthVID_,start_,count_,frm->bAddress())) )
# endif
{
mprinterr("Error: Writing cell lengths frame %i.\n", set+1);
return 1;
}
# ifdef HAS_PNETCDF
if (ncmpi_put_vara_double_all(ncid_,cellAngleVID_,start_,count_,frm->bAddress()+3))
# else
if (NC::CheckErr(nc_put_vara_double(ncid_,cellAngleVID_,start_,count_,frm->bAddress()+3)))
# endif
{
mprinterr("Error: Writing cell angles frame %i.\n", set+1);
return 1;
}
}
// Write temperature
if (TempVID_!=-1) {
# ifdef HAS_PNETCDF
if (ncmpi_put_vara_double_all(ncid_,TempVID_,start_,count_,frm->tAddress()))
# else
if (NC::CheckErr(nc_put_vara_double(ncid_,TempVID_,start_,count_,frm->tAddress())))
# endif
{
mprinterr("Error: Writing temperature frame %i.\n", set+1);
return 1;
}
}
// Write indices
if (indicesVID_ != -1) {
count_[2] = remd_dimension_;
# ifdef HAS_PNETCDF
if (ncmpi_put_vara_int_all(ncid_,indicesVID_,start_,count_,frm->iAddress()))
# else
if (NC::CheckErr(nc_put_vara_int(ncid_,indicesVID_,start_,count_,frm->iAddress())))
# endif
{
mprinterr("Error: Writing indices frame %i.\n", set+1);
return 1;
}
}
}
# ifdef HAS_PNETCDF
//ncmpi_sync(ncid_);
# else
nc_sync(ncid_); // Necessary after every write??
# endif
++ncframe_;
# ifdef HAS_PNETCDF
// DEBUG
# undef start_
# undef count_
# endif
return 0;
}
// Traj_AmberNetcdf::writeFrame()
int Traj_AmberNetcdf::writeFrame(int set, Frame const& frameOut) {
DoubleToFloat(Coord_, frameOut.xAddress());
// Write coords
start_[0] = ncframe_;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
if (checkNCerr(nc_put_vara_float(ncid_,coordVID_,start_,count_,Coord_)) ) {
mprinterr("Error: Netcdf Writing coords frame %i\n", set+1);
return 1;
}
// Write velocity. FIXME: Should check in setup
if (CoordInfo().HasVel() && frameOut.HasVelocity()) {
DoubleToFloat(Coord_, frameOut.vAddress());
if (checkNCerr(nc_put_vara_float(ncid_, velocityVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Netcdf writing velocity frame %i\n", set+1);
return 1;
}
}
// Write box
if (cellLengthVID_ != -1) {
count_[1] = 3;
count_[2] = 0;
if (checkNCerr(nc_put_vara_double(ncid_,cellLengthVID_,start_,count_,frameOut.bAddress())) ) {
mprinterr("Error: Writing cell lengths frame %i.\n", set+1);
return 1;
}
if (checkNCerr(nc_put_vara_double(ncid_,cellAngleVID_,start_,count_, frameOut.bAddress()+3)) ) {
mprinterr("Error: Writing cell angles frame %i.\n", set+1);
return 1;
}
}
// Write temperature
if (TempVID_!=-1) {
if ( checkNCerr( nc_put_vara_double(ncid_,TempVID_,start_,count_,frameOut.tAddress())) ) {
mprinterr("Error: Writing temperature frame %i.\n", set+1);
return 1;
}
}
// Write time
if (timeVID_ != -1) {
float tVal = (float)frameOut.Time();
if ( checkNCerr( nc_put_vara_float(ncid_,timeVID_,start_,count_,&tVal)) ) {
mprinterr("Error: Writing time frame %i.\n", set+1);
return 1;
}
}
// Write indices
if (indicesVID_ != -1) {
count_[1] = remd_dimension_;
if ( checkNCerr(nc_put_vara_int(ncid_,indicesVID_,start_,count_,frameOut.iAddress())) ) {
mprinterr("Error: Writing indices frame %i.\n", set+1);
return 1;
}
}
nc_sync(ncid_); // Necessary after every write??
++ncframe_;
return 0;
}
