// TODO: Use Box class
int NetcdfFile::SetupBox(double* boxIn, NCTYPE typeIn) {
boxIn[0] = 0.0;
boxIn[1] = 0.0;
boxIn[2] = 0.0;
boxIn[3] = 0.0;
boxIn[4] = 0.0;
boxIn[5] = 0.0;
if ( nc_inq_varid(ncid_,NCCELL_LENGTHS,&cellLengthVID_)==NC_NOERR ) {
if (checkNCerr(nc_inq_varid(ncid_,NCCELL_ANGLES,&cellAngleVID_)) ) {
mprinterr("Error: Getting cell angles.\n");
return 1;
}
if (ncdebug_>0) mprintf(" Netcdf Box information found.\n");
// If present, get box angles. These will be used to determine the box
// type in TrajectoryFile.
start_[0]=0;
start_[1]=0;
start_[2]=0;
start_[3]=0;
switch (typeIn) {
case NC_AMBERRESTART:
count_[0]=3;
count_[1]=0;
count_[2]=0;
break;
case NC_AMBERTRAJ:
count_[0]=1;
count_[1]=3;
count_[2]=0;
break;
case NC_AMBERENSEMBLE:
count_[0]=1; // NOTE: All ensemble members must have same box type
count_[1]=1; // TODO: Check all members?
count_[2]=3;
break;
case NC_UNKNOWN:
return 1; // Sanity check
}
count_[3]=0;
if ( checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, boxIn )) )
{
mprinterr("Error: Getting cell lengths.\n");
return 1;
}
if ( checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, boxIn+3)) )
{
mprinterr("Error: Getting cell angles.\n");
return 1;
}
if (ncdebug_ > 0) mprintf("\tNetcdf Box: XYZ={%f %f %f} ABG={%f %f %f}\n",
boxIn[0], boxIn[1], boxIn[2], boxIn[3], boxIn[4], boxIn[5]);
return 0;
}
// No box information
return -1;
}
// NetcdfFile::NC_defineTemperature()
int NetcdfFile::NC_defineTemperature(int* dimensionID, int NDIM) {
if (checkNCerr(nc_def_var(ncid_,NCTEMPERATURE,NC_DOUBLE,NDIM,dimensionID,&TempVID_))) {
mprinterr("NetCDF error on defining temperature.\n");
return 1;
}
if (checkNCerr(nc_put_att_text(ncid_,TempVID_,"units",6,"kelvin"))) {
mprinterr("NetCDF error on defining temperature units.\n");
return 1;
}
return 0;
}
/** Get the specified frame from amber netcdf file
* Coords are a 1 dimensional array of format X1,Y1,Z1,X2,Y2,Z2,...
*/
int Traj_AmberNetcdf::readFrame(int set,double *X, double *V,double *box, double *T) {
// Get temperature
if (TempVID_!=-1) {
start_[0] = set;
count_[0] = 1;
if ( checkNCerr(nc_get_vara_double(ncid_, TempVID_, start_, count_, T)) ) {
mprinterr("Error: Getting replica temperature.\n");
return 1;
}
//fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
}
// Read Coords
start_[0] = set;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
if ( checkNCerr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting frame %i\n", set);
return 1;
}
FloatToDouble(X, Coord_);
// Read Velocities
if (velocityVID_ != -1) {
if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Veloc_)) ) {
mprinterr("Error: Getting velocities for frame %i\n", set);
return 1;
}
FloatToDouble(V, Veloc_);
}
// Read box info
if (cellLengthVID_ != -1) {
count_[1] = 3;
count_[2] = 0;
if ( checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, box)) ) {
mprinterr("Getting cell lengths.\n");
return 1;
}
if ( checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, box+3)) ) {
mprinterr("Getting cell angles.\n");
return 1;
}
}
return 0;
}
// NetcdfFile::NC_close()
void NetcdfFile::NC_close() {
if (ncid_ == -1) return;
bool err = checkNCerr( nc_close(ncid_) );
if (ncdebug_ > 0 && !err)
mprintf("Successfully closed ncid %i\n",ncid_);
ncid_ = -1;
}
/** Determine if Netcdf file contains time; set up timeVID and check units. */
int NetcdfFile::SetupTime() {
if ( nc_inq_varid(ncid_, NCTIME, &timeVID_) == NC_NOERR ) {
std::string attrText = GetAttrText(timeVID_, "units");
if (attrText!="picosecond")
mprintf("Warning: NetCDF file has time units of %s - expected picosecond.\n",
attrText.c_str());
// Check for time values which have NOT been filled, which was possible
// with netcdf trajectories created by older versions of ptraj/cpptraj.
if (ncframe_ > 0 && GetNetcdfConventions() == NC_AMBERTRAJ) {
float time;
start_[0] = 0;
count_[0] = 1;
if (checkNCerr(nc_get_vara_float(ncid_, timeVID_, start_, count_, &time))) {
mprinterr("Error: Getting time value for NetCDF file.\n");
return -1;
}
if (time == NC_FILL_FLOAT) {
mprintf("Warning: NetCDF file time variable defined but empty. Disabling.\n");
timeVID_ = -1;
}
}
return 0;
}
timeVID_=-1;
return 1;
}
/** Determine if Netcdf file contains multi-D REMD info. If so set the
* number of replica dimensions (remd_dimension_) and figure out
* the dimension types (remdDim)
*/
int NetcdfFile::SetupMultiD(ReplicaDimArray& remdDim) {
int dimensionDID;
if ( nc_inq_dimid(ncid_, NCREMD_DIMENSION, &dimensionDID) != NC_NOERR)
return 1;
// Although this is a second call to dimid, makes for easier code
if ( (dimensionDID = GetDimInfo(NCREMD_DIMENSION, &remd_dimension_))==-1 )
return -1;
if (ncdebug_ > 0)
mprintf("\tNetcdf file has multi-D REMD info, %i dimensions.\n",remd_dimension_);
// Ensure valid # dimensions
if (remd_dimension_ < 1) {
mprinterr("Error: Number of REMD dimensions is less than 1!\n");
return -1;
}
// Start and count for groupnum and dimtype, allocate mem
start_[0]=0;
start_[1]=0;
start_[2]=0;
count_[0]=remd_dimension_;
count_[1]=0;
count_[2]=0;
int* remd_dimtype = new int[ remd_dimension_ ];
// Get dimension types
int dimtypeVID;
if ( checkNCerr(nc_inq_varid(ncid_, NCREMD_DIMTYPE, &dimtypeVID)) ) {
mprinterr("Error: Getting dimension type variable ID for each dimension.\n");
return -1;
}
if ( checkNCerr(nc_get_vara_int(ncid_, dimtypeVID, start_, count_, remd_dimtype)) ) {
mprinterr("Error: Getting dimension type in each dimension.\n");
return -1;
}
// Get VID for replica indices
if ( checkNCerr(nc_inq_varid(ncid_, NCREMD_INDICES, &indicesVID_)) ) {
mprinterr("Error: Getting replica indices variable ID.\n");
return -1;
}
// Print info for each dimension
for (int dim = 0; dim < remd_dimension_; ++dim)
remdDim.AddRemdDimension( remd_dimtype[dim] );
delete[] remd_dimtype;
return 0;
}
/** Return the dimension ID of a given attribute in netcdf file ncid.
* Also set dimension length.
*/
int NetcdfFile::GetDimInfo(const char *attribute, int *length) {
int dimID;
size_t slength = 0;
*length = 0;
// Get dimid
if ( checkNCerr(nc_inq_dimid(ncid_, attribute, &dimID)) ) {
mprinterr("Error: Getting dimID for attribute %s\n",attribute);
return -1;
}
// get Dim length
if ( checkNCerr(nc_inq_dimlen(ncid_, dimID, &slength)) ) {
mprinterr("Error: Getting length for attribute %s\n",attribute);
return -1;
}
*length = (int) slength;
return dimID;
}
// 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;
}
/** Get the specified frame from amber netcdf file
* Coords are a 1 dimensional array of format X1,Y1,Z1,X2,Y2,Z2,...
*/
int Traj_AmberRestartNC::readFrame(int set,double *X, double *V,double *box, double *T) {
// Get temperature
if (TempVID_!=-1) {
if ( checkNCerr(nc_get_var_double(ncid_, TempVID_, T)) ) {
mprinterr("Error: Getting replica temperature.\n");
return 1;
}
if (debug_>1) mprintf("DEBUG: %s: Replica Temperature %lf\n",filename_.base(), T);
}
// Read Coords
start_[0] = 0;
start_[1] = 0;
count_[0] = Ncatom();
count_[1] = 3;
if ( checkNCerr(nc_get_vara_double(ncid_, coordVID_, start_, count_, X)) ) {
mprinterr("Error: Getting Coords\n");
return 1;
}
// Read Velocity
if (velocityVID_!=-1 && V!=0) {
if ( checkNCerr(nc_get_vara_double(ncid_, velocityVID_, start_, count_, V)) ) {
mprinterr("Error: Getting velocities\n");
return 1;
}
}
// Read box info
if (cellLengthVID_ != -1) {
count_[0] = 3;
count_[1] = 0;
if ( checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, box)) ) {
mprinterr("Error: Getting cell lengths.\n");
return 1;
}
if ( checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, box+3)) ) {
mprinterr("Error: Getting cell angles.\n");
return 1;
}
}
return 0;
}
int Traj_AmberRestartNC::readIndices(int set, int* remd_indices) {
if (indicesVID_!=-1) {
start_[0] = 0;
count_[1] = remd_dimension_;
if ( checkNCerr(nc_get_vara_int(ncid_, indicesVID_, start_, count_, remd_indices)) ) {
mprinterr("Error: Getting replica indices.\n");
return 1;
}
//mprintf("DEBUG:\tReplica Rst indices:");
//for (int dim=0; dim < remd_dimension_; dim++) mprintf(" %i",remd_indices[dim]);
//mprintf("\n");
}
return 0;
}
/** Get the information about a netcdf attribute with given vid and
* attribute text.
* Since there is no guarantee that null char at the end of retrieved string
* append one.
*/
std::string NetcdfFile::GetAttrText(int vid, const char *attribute) {
size_t attlen;
std::string attrOut;
// Get attr length
if ( checkNCerr(nc_inq_attlen(ncid_, vid, attribute, &attlen)) ) {
mprintf("Warning: Getting length for attribute '%s'\n",attribute);
return attrOut;
}
// Allocate space for attr text, plus one for null char
char *attrText = new char[ (attlen + 1) ];
// Get attr text
if ( checkNCerr(nc_get_att_text(ncid_, vid, attribute, attrText)) ) {
mprintf("Warning: Getting attribute text for '%s'\n",attribute);
delete[] attrText;
return attrOut;
}
// Append null char - NECESSARY?
attrText[attlen]='\0';
attrOut.assign( attrText );
delete[] attrText;
return attrOut;
}
// Traj_AmberNetcdf::readVelocity()
int Traj_AmberNetcdf::readVelocity(int set, Frame& frameIn) {
start_[0] = set;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
// Read Velocities
if (velocityVID_ != -1) {
if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting velocities for frame %i\n", set+1);
return 1;
}
FloatToDouble(frameIn.vAddress(), Coord_);
}
return 0;
}
// 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;
}
// NetcdfFile::NC_createReservoir()
int NetcdfFile::NC_createReservoir(bool hasBins, double reservoirT, int iseed,
int& eptotVID, int& binsVID)
{
int dimensionID[1];
dimensionID[0] = frameDID_;
if (ncid_ == -1 || dimensionID[0] == -1) return 1;
// Place file back in define mode
if ( checkNCerr( nc_redef( ncid_ ) ) ) return 1;
// Define eptot, bins, temp0
if ( checkNCerr( nc_def_var(ncid_, NCEPTOT, NC_DOUBLE, 1, dimensionID, &eptotVID)) ) {
mprinterr("Error: defining eptot variable ID.\n");
return 1;
}
if (hasBins) {
if ( checkNCerr( nc_def_var(ncid_, NCBINS, NC_INT, 1, dimensionID, &binsVID)) ) {
mprinterr("Error: defining bins variable ID.\n");
return 1;
}
} else
binsVID = -1;
if (NC_defineTemperature(dimensionID, 0)) return 1;
// Random seed, make global
if ( checkNCerr( nc_put_att_int(ncid_, NC_GLOBAL, "iseed", NC_INT, 1, &iseed) ) ) {
mprinterr("Error: setting random seed attribute.\n");
return 1;
}
// End definitions
if (checkNCerr(nc_enddef(ncid_))) {
mprinterr("NetCDF error on ending definitions.");
return 1;
}
// Write temperature
if (checkNCerr(nc_put_var_double(ncid_,TempVID_,&reservoirT)) ) {
mprinterr("Error: Writing reservoir temperature.\n");
return 1;
}
return 0;
}
// NetcdfFile::NC_create()
int NetcdfFile::NC_create(std::string const& Name, NCTYPE type, int natomIn,
CoordinateInfo const& coordInfo, std::string const& title)
{
if (Name.empty()) return 1;
int dimensionID[NC_MAX_VAR_DIMS];
int NDIM;
nc_type dataType;
if (ncdebug_>1)
mprintf("DEBUG: NC_create: %s natom=%i V=%i F=%i box=%i temp=%i time=%i\n",
Name.c_str(),natomIn,(int)coordInfo.HasVel(),
(int)coordInfo.HasForce(),(int)coordInfo.HasBox(),
(int)coordInfo.HasTemp(),(int)coordInfo.HasTime());
if ( checkNCerr( nc_create( Name.c_str(), NC_64BIT_OFFSET, &ncid_) ) )
return 1;
ncatom_ = natomIn;
ncatom3_ = ncatom_ * 3;
// Set number of dimensions based on file type
switch (type) {
case NC_AMBERENSEMBLE:
NDIM = 4;
dataType = NC_FLOAT;
break;
case NC_AMBERTRAJ:
NDIM = 3;
dataType = NC_FLOAT;
break;
case NC_AMBERRESTART:
NDIM = 2;
dataType = NC_DOUBLE;
break;
default:
mprinterr("Error: NC_create (%s): Unrecognized type (%i)\n",Name.c_str(),(int)type);
return 1;
}
if (type == NC_AMBERENSEMBLE) {
// Ensemble dimension for ensemble
if (coordInfo.EnsembleSize() < 1) {
mprinterr("Internal Error: NetcdfFile: ensembleSize < 1\n");
return 1;
}
if ( checkNCerr(nc_def_dim(ncid_, NCENSEMBLE, coordInfo.EnsembleSize(), &ensembleDID_)) ) {
mprinterr("Error: Defining ensemble dimension.\n");
return 1;
}
dimensionID[1] = ensembleDID_;
}
ncframe_ = 0;
if (type == NC_AMBERTRAJ || type == NC_AMBERENSEMBLE) {
// Frame dimension for traj
if ( checkNCerr( nc_def_dim( ncid_, NCFRAME, NC_UNLIMITED, &frameDID_)) ) {
mprinterr("Error: Defining frame dimension.\n");
return 1;
}
// Since frame is UNLIMITED, it must be lowest dim.
dimensionID[0] = frameDID_;
}
// Time variable and units
if (coordInfo.HasTime()) {
if ( checkNCerr( nc_def_var(ncid_, NCTIME, dataType, NDIM-2, dimensionID, &timeVID_)) ) {
mprinterr("Error: Defining time variable.\n");
return 1;
}
if ( checkNCerr( nc_put_att_text(ncid_, timeVID_, "units", 10, "picosecond")) ) {
mprinterr("Error: Writing time VID units.\n");
return 1;
}
}
// Spatial dimension and variable
if ( checkNCerr( nc_def_dim( ncid_, NCSPATIAL, 3, &spatialDID_)) ) {
mprinterr("Error: Defining spatial dimension.\n");
return 1;
}
dimensionID[0] = spatialDID_;
if ( checkNCerr( nc_def_var( ncid_, NCSPATIAL, NC_CHAR, 1, dimensionID, &spatialVID_)) ) {
mprinterr("Error: Defining spatial variable.\n");
return 1;
}
// Atom dimension
if ( checkNCerr( nc_def_dim( ncid_, NCATOM, ncatom_, &atomDID_)) ) {
mprinterr("Error: Defining atom dimension.\n");
return 1;
}
// Setup dimensions for Coords/Velocity
// NOTE: THIS MUST BE MODIFIED IF NEW TYPES ADDED
if (type == NC_AMBERENSEMBLE) {
dimensionID[0] = frameDID_;
dimensionID[1] = ensembleDID_;
dimensionID[2] = atomDID_;
dimensionID[3] = spatialDID_;
} else if (type == NC_AMBERTRAJ) {
dimensionID[0] = frameDID_;
dimensionID[1] = atomDID_;
dimensionID[2] = spatialDID_;
} else {
dimensionID[0] = atomDID_;
dimensionID[1] = spatialDID_;
}
// Coord variable
if ( checkNCerr( nc_def_var( ncid_, NCCOORDS, dataType, NDIM, dimensionID, &coordVID_)) ) {
mprinterr("Error: Defining coordinates variable.\n");
return 1;
}
if ( checkNCerr( nc_put_att_text( ncid_, coordVID_, "units", 8, "angstrom")) ) {
mprinterr("Error: Writing coordinates variable units.\n");
return 1;
}
// Velocity variable
if (coordInfo.HasVel()) {
if ( checkNCerr( nc_def_var( ncid_, NCVELO, dataType, NDIM, dimensionID, &velocityVID_)) ) {
mprinterr("Error: Defining velocities variable.\n");
return 1;
}
if ( checkNCerr( nc_put_att_text( ncid_, velocityVID_, "units", 19, "angstrom/picosecond")) )
{
mprinterr("Error: Writing velocities variable units.\n");
return 1;
}
if ( checkNCerr( nc_put_att_double( ncid_, velocityVID_, "scale_factor", NC_DOUBLE, 1,
&Constants::AMBERTIME_TO_PS)) )
{
mprinterr("Error: Writing velocities scale factor.\n");
return 1;
}
}
// Force variable
if (coordInfo.HasForce()) {
if ( checkNCerr( nc_def_var( ncid_, NCFRC, dataType, NDIM, dimensionID, &frcVID_)) ) {
mprinterr("Error: Defining forces variable\n");
return 1;
}
if ( checkNCerr( nc_put_att_text( ncid_, frcVID_, "units", 25, "kilocalorie/mole/angstrom")) )
{
mprinterr("Error: Writing forces variable units.\n");
return 1;
}
}
// Replica Temperature
if (coordInfo.HasTemp()) {
// NOTE: Setting dimensionID should be OK for Restart, will not be used.
dimensionID[0] = frameDID_;
if ( NC_defineTemperature( dimensionID, NDIM-2 ) ) return 1;
}
// Replica indices
int remDimTypeVID = -1;
if (coordInfo.HasReplicaDims()) {
// Define number of replica dimensions
remd_dimension_ = coordInfo.ReplicaDimensions().Ndims();
int remDimDID = -1;
if ( checkNCerr(nc_def_dim(ncid_, NCREMD_DIMENSION, remd_dimension_, &remDimDID)) ) {
mprinterr("Error: Defining replica indices dimension.\n");
return 1;
}
dimensionID[0] = remDimDID;
// For each dimension, store the type
if ( checkNCerr(nc_def_var(ncid_, NCREMD_DIMTYPE, NC_INT, 1, dimensionID, &remDimTypeVID)) )
{
mprinterr("Error: Defining replica dimension type variable.\n");
return 1;
}
// Need to store the indices of replica in each dimension each frame
// NOTE: THIS MUST BE MODIFIED IF NEW TYPES ADDED
if (type == NC_AMBERENSEMBLE) {
dimensionID[0] = frameDID_;
dimensionID[1] = ensembleDID_;
dimensionID[2] = remDimDID;
} else if (type == NC_AMBERTRAJ) {
dimensionID[0] = frameDID_;
dimensionID[1] = remDimDID;
} else {
dimensionID[0] = remDimDID;
}
if (checkNCerr(nc_def_var(ncid_, NCREMD_INDICES, NC_INT, NDIM-1, dimensionID, &indicesVID_)))
{
mprinterr("Error: Defining replica indices variable ID.\n");
return 1;
}
// TODO: Determine if groups are really necessary for restarts. If not,
// remove from AmberNetcdf.F90.
}
// Box Info
if (coordInfo.HasBox()) {
// Cell Spatial
if ( checkNCerr( nc_def_dim( ncid_, NCCELL_SPATIAL, 3, &cell_spatialDID_)) ) {
mprinterr("Error: Defining cell spatial dimension.\n");
return 1;
}
dimensionID[0] = cell_spatialDID_;
if ( checkNCerr( nc_def_var(ncid_, NCCELL_SPATIAL, NC_CHAR, 1, dimensionID, &cell_spatialVID_)))
{
mprinterr("Error: Defining cell spatial variable.\n");
return 1;
}
// Cell angular
if ( checkNCerr( nc_def_dim( ncid_, NCLABEL, NCLABELLEN, &labelDID_)) ) {
mprinterr("Error: Defining label dimension.\n");
return 1;
}
if ( checkNCerr( nc_def_dim( ncid_, NCCELL_ANGULAR, 3, &cell_angularDID_)) ) {
mprinterr("Error: Defining cell angular dimension.\n");
return 1;
}
dimensionID[0] = cell_angularDID_;
dimensionID[1] = labelDID_;
if ( checkNCerr( nc_def_var( ncid_, NCCELL_ANGULAR, NC_CHAR, 2, dimensionID,
&cell_angularVID_)) )
{
mprinterr("Error: Defining cell angular variable.\n");
return 1;
}
// Setup dimensions for Box
// NOTE: This must be modified if more types added
int boxdim;
if (type == NC_AMBERENSEMBLE) {
dimensionID[0] = frameDID_;
dimensionID[1] = ensembleDID_;
boxdim = 2;
} else if (type == NC_AMBERTRAJ) {
dimensionID[0] = frameDID_;
boxdim = 1;
} else {
boxdim = 0;
}
dimensionID[boxdim] = cell_spatialDID_;
if ( checkNCerr( nc_def_var( ncid_, NCCELL_LENGTHS, NC_DOUBLE, NDIM-1, dimensionID,
&cellLengthVID_)) )
{
mprinterr("Error: Defining cell length variable.\n");
return 1;
}
if ( checkNCerr( nc_put_att_text( ncid_, cellLengthVID_, "units", 8, "angstrom")) ) {
mprinterr("Error: Writing cell length variable units.\n");
return 1;
}
dimensionID[boxdim] = cell_angularDID_;
if ( checkNCerr( nc_def_var( ncid_, NCCELL_ANGLES, NC_DOUBLE, NDIM-1, dimensionID,
&cellAngleVID_)) )
{
mprinterr("Error: Defining cell angle variable.\n");
return 1;
}
if ( checkNCerr( nc_put_att_text( ncid_, cellAngleVID_, "units", 6, "degree")) ) {
mprinterr("Error: Writing cell angle variable units.\n");
return 1;
}
}
// Attributes
if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"title",title.size(),title.c_str())) ) {
mprinterr("Error: Writing title.\n");
return 1;
}
if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"application",5,"AMBER")) ) {
mprinterr("Error: Writing application.\n");
return 1;
}
if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"program",7,"cpptraj")) ) {
mprinterr("Error: Writing program.\n");
return 1;
}
if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"programVersion",
NETCDF_VERSION_STRLEN, NETCDF_VERSION_STRING)) )
{
mprinterr("Error: Writing program version.\n");
return 1;
}
// TODO: Make conventions a static string
bool errOccurred = false;
if ( type == NC_AMBERENSEMBLE )
errOccurred = checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"Conventions",13,"AMBERENSEMBLE"));
else if ( type == NC_AMBERTRAJ )
errOccurred = checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"Conventions",5,"AMBER"));
else
errOccurred = checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"Conventions",12,"AMBERRESTART"));
if (errOccurred) {
mprinterr("Error: Writing conventions.\n");
return 1;
}
if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"ConventionVersion",3,"1.0")) ) {
mprinterr("Error: Writing conventions version.\n");
return 1;
}
// Set fill mode
if (checkNCerr(nc_set_fill(ncid_, NC_NOFILL, dimensionID))) {
mprinterr("Error: NetCDF setting fill value.\n");
return 1;
}
// End netcdf definitions
if (checkNCerr(nc_enddef(ncid_))) {
mprinterr("NetCDF error on ending definitions.");
return 1;
}
// Specify spatial dimension labels
start_[0] = 0;
count_[0] = 3;
char xyz[3];
xyz[0] = 'x';
xyz[1] = 'y';
xyz[2] = 'z';
if (checkNCerr(nc_put_vara_text(ncid_, spatialVID_, start_, count_, xyz))) {
mprinterr("Error on NetCDF output of spatial VID 'x', 'y' and 'z'");
return 1;
}
if ( coordInfo.HasBox() ) {
xyz[0] = 'a';
xyz[1] = 'b';
xyz[2] = 'c';
if (checkNCerr(nc_put_vara_text(ncid_, cell_spatialVID_, start_, count_, xyz))) {
mprinterr("Error on NetCDF output of cell spatial VID 'a', 'b' and 'c'");
return 1;
}
char abc[15] = { 'a', 'l', 'p', 'h', 'a',
'b', 'e', 't', 'a', ' ',
'g', 'a', 'm', 'm', 'a'
};
start_[0] = 0;
start_[1] = 0;
count_[0] = 3;
count_[1] = NCLABELLEN;
if (checkNCerr(nc_put_vara_text(ncid_, cell_angularVID_, start_, count_, abc))) {
mprinterr("Error on NetCDF output of cell angular VID 'alpha', 'beta ' and 'gamma'");
return 1;
}
}
// Store the type of each replica dimension.
if (coordInfo.HasReplicaDims()) {
ReplicaDimArray const& remdDim = coordInfo.ReplicaDimensions();
start_[0] = 0;
count_[0] = remd_dimension_;
int* tempDims = new int[ remd_dimension_ ];
for (int i = 0; i < remd_dimension_; ++i)
tempDims[i] = remdDim[i];
if (checkNCerr(nc_put_vara_int(ncid_, remDimTypeVID, start_, count_, tempDims))) {
mprinterr("Error: writing replica dimension types.\n");
delete[] tempDims;
return 1;
}
delete[] tempDims;
}
return 0;
}
// Traj_AmberRestartNC::writeFrame()
int Traj_AmberRestartNC::writeFrame(int set, double *X, double *V,double *box, double T) {
// Set up file for this set
bool V_present = (HasV() && V != 0);
std::string fname;
// Create filename for this set
// If just writing 1 frame dont modify output filename
if (singleWrite_)
fname = filename_.Full();
else
fname = NumberFilename(filename_.Full(), set+1);
if ( NC_create( fname.c_str(), NC_AMBERRESTART, Ncatom(), V_present,
HasBox(), HasT(), (time0_ >= 0), Title() ) )
return 1;
// write coords
start_[0] = 0;
start_[1] = 0;
count_[0] = Ncatom();
count_[1] = 3;
if (checkNCerr(nc_put_vara_double(ncid_,coordVID_,start_,count_,X)) ) {
mprinterr("Error: Netcdf restart Writing coordinates %i\n",set);
return 1;
}
// write velocity
if (V_present) {
mprintf("DEBUG: Writing V, VID=%i\n",velocityVID_);
if (checkNCerr(nc_put_vara_double(ncid_,velocityVID_,start_,count_,V)) ) {
mprinterr("Error: Netcdf restart writing velocity %i\n",set);
return 1;
}
}
// write box
if (cellLengthVID_ != -1) {
count_[0] = 3;
count_[1] = 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 time
if (timeVID_ != -1) {
restartTime_ = (time0_ + (double)set) * dt_;
if (checkNCerr(nc_put_var_double(ncid_,timeVID_,&restartTime_)) ) {
mprinterr("Error: Writing restart time.\n");
return 1;
}
}
// write temperature
if (TempVID_ != -1) {
if (checkNCerr(nc_put_var_double(ncid_,TempVID_,&T)) ) {
mprinterr("Error: Writing restart temperature.\n");
return 1;
}
}
//nc_sync(ncid_); // Necessary? File about to close anyway...
// Close file for this set
closeTraj();
return 0;
}
// NetcdfFile::NC_openWrite()
int NetcdfFile::NC_openWrite(std::string const& Name) {
if (Name.empty()) return 1;
if ( checkNCerr( nc_open( Name.c_str(), NC_WRITE, &ncid_ ) ) )
return 1;
return 0;
}
// Traj_NcEnsemble::readArray()
int Traj_NcEnsemble::readArray(int set, FrameArray& f_ensemble) {
# ifdef HAS_PNETCDF
MPI_Offset pstart_[4];
MPI_Offset pcount_[4];
# define start_ pstart_
# define count_ pcount_
# endif
start_[0] = set; // Frame
start_[2] = 0; // Atoms
start_[3] = 0; // XYZ
count_[0] = 1; // Frame
count_[1] = 1; // Ensemble
count_[3] = 3; // XYZ
//rprintf("DEBUG: Reading frame %i\n", set+1);
for (int member = ensembleStart_; member != ensembleEnd_; member++) {
# ifdef MPI
Frame& frm = f_ensemble[0];
# else
Frame& frm = f_ensemble[member];
# endif
start_[1] = member; // Ensemble
count_[2] = Ncatom(); // Atoms
// Read Coords
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_float_all(ncid_, coordVID_, start_, count_, Coord_)))
# else
if (checkNCerr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)))
# endif
{
rprinterr("Error: Getting coordinates for frame %i\n", set+1);
return 1;
}
FloatToDouble(frm.xAddress(), Coord_);
//mprintf("Frm=%8i Rep=%8i ", set+1, member+1); // DEBUG
//frm.printAtomCoord(0); // DEBUG
// Read Velocities
if (velocityVID_ != -1) {
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_float_all(ncid_, velocityVID_, start_, count_, Coord_)))
# else
if (checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)))
# endif
{
rprinterr("Error: Getting velocities for frame %i\n", set+1);
return 1;
}
FloatToDouble(frm.vAddress(), Coord_);
}
// Read Box
if (cellLengthVID_ != -1) {
count_[2] = 3;
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, cellLengthVID_, start_, count_, frm.bAddress())))
# else
if (checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, frm.bAddress())))
# endif
{
rprinterr("Error: Getting cell lengths for frame %i.\n", set+1);
return 1;
}
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, cellAngleVID_, start_, count_, frm.bAddress()+3)))
# else
if (checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, frm.bAddress()+3)))
# endif
{
rprinterr("Error: Getting cell angles for frame %i.\n", set+1);
return 1;
}
}
// Read Temperature
if (TempVID_!=-1) {
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, TempVID_, start_, count_, frm.tAddress())))
# else
if (checkNCerr(nc_get_vara_double(ncid_, TempVID_, start_, count_, frm.tAddress())))
# endif
{
rprinterr("Error: Getting replica temperature for frame %i.\n", set+1);
return 1;
}
//fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
}
// Read indices
if (indicesVID_!=-1) {
count_[2] = remd_dimension_;
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_int_all(ncid_, indicesVID_, start_, count_, frm.iAddress())))
# else
if (checkNCerr(nc_get_vara_int(ncid_, indicesVID_, start_, count_, frm.iAddress())))
# endif
{
rprinterr("Error: Getting replica indices for frame %i.\n", set+1);
return 1;
}
// DEBUG
//char buffer[128];
//char* ptr = buffer;
//ptr += sprintf(buffer,"DEBUG:\tReplica indices:");
//for (int dim=0; dim < remd_dimension_; dim++) ptr += sprintf(ptr, " %i", frm.RemdIndices()[dim]);
//sprintf(ptr,"\n");
//rprintf("%s", buffer);
}
}
# ifdef HAS_PNETCDF
// DEBUG
# undef start_
# undef count_
# endif
return 0;
}
// Traj_NcEnsemble::writeArray()
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
//WriteIndices(); // DEBUG
DoubleToFloat(Coord_, frm->xAddress());
# ifdef HAS_PNETCDF
if (ncmpi_put_vara_float_all(ncid_, coordVID_, start_, count_, Coord_))
# else
if (checkNCerr(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 (CoordInfo().HasVel() && frm->HasVelocity()) { // TODO: Determine V beforehand
DoubleToFloat(Coord_, frm->vAddress());
# ifdef HAS_PNETCDF
if (ncmpi_put_vara_float_all(ncid_, velocityVID_, start_, count_, Coord_))
# else
if (checkNCerr(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 (checkNCerr(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 (checkNCerr(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 (checkNCerr(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 (checkNCerr(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;
}
/** Get the specified frame from amber netcdf file
* Coords are a 1 dimensional array of format X1,Y1,Z1,X2,Y2,Z2,...
*/
int Traj_AmberNetcdf::readFrame(int set, Frame& frameIn) {
start_[0] = set;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
// Get temperature
if (TempVID_!=-1) {
if ( checkNCerr(nc_get_vara_double(ncid_, TempVID_, start_, count_, frameIn.tAddress())) ) {
mprinterr("Error: Getting replica temperature for frame %i.\n", set+1);
return 1;
}
//fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
}
// Get time
if (timeVID_!=-1) {
float time;
if (checkNCerr(nc_get_vara_float(ncid_, timeVID_, start_, count_, &time))) {
mprinterr("Error: Getting time for frame %i.\n", set + 1);
return 1;
}
frameIn.SetTime( (double)time );
}
// Read Coords
if ( checkNCerr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting coordinates for frame %i\n", set+1);
return 1;
}
FloatToDouble(frameIn.xAddress(), Coord_);
// Read Velocities
if (velocityVID_ != -1) {
if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting velocities for frame %i\n", set+1);
return 1;
}
FloatToDouble(frameIn.vAddress(), Coord_);
}
// Read indices. Input array must be allocated to be size remd_dimension.
if (indicesVID_!=-1) {
count_[1] = remd_dimension_;
if ( checkNCerr(nc_get_vara_int(ncid_, indicesVID_, start_, count_, frameIn.iAddress())) ) {
mprinterr("Error: Getting replica indices for frame %i.\n", set+1);
return 1;
}
//mprintf("DEBUG:\tReplica indices:");
//for (int dim=0; dim < remd_dimension_; dim++) mprintf(" %i",remd_indices[dim]);
//mprintf("\n");
}
// Read box info
if (cellLengthVID_ != -1) {
count_[1] = 3;
count_[2] = 0;
if (checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, frameIn.bAddress())))
{
mprinterr("Error: Getting cell lengths for frame %i.\n", set+1);
return 1;
}
if (checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, frameIn.bAddress()+3)))
{
mprinterr("Error: Getting cell angles for frame %i.\n", set+1);
return 1;
}
}
return 0;
}
/** Setup ncatom, ncatom3, atomDID, coordVID, spatialDID, spatialVID,
* velocityVID, frcVID. Check units and spatial dimensions.
*/
int NetcdfFile::SetupCoordsVelo(bool useVelAsCoords) {
int spatial;
atomDID_ = GetDimInfo(NCATOM, &ncatom_);
if (atomDID_==-1) return 1;
ncatom3_ = ncatom_ * 3;
// Get coord info
coordVID_ = -1;
if ( nc_inq_varid(ncid_, NCCOORDS, &coordVID_) == NC_NOERR ) {
if (ncdebug_ > 0) mprintf("\tNetcdf file has coordinates.\n");
std::string attrText = GetAttrText(coordVID_, "units");
if (attrText!="angstrom")
mprintf("Warning: Netcdf file has length units of %s - expected angstrom.\n",
attrText.c_str());
}
// Get spatial info
spatialDID_ = GetDimInfo(NCSPATIAL, &spatial);
if (spatialDID_==-1) return 1;
if (spatial!=3) {
mprinterr("Error: Expected 3 spatial dimensions, got %i\n",spatial);
return 1;
}
if ( checkNCerr(nc_inq_varid(ncid_, NCSPATIAL, &spatialVID_)) ) {
mprintf("Warning: Could not get spatial VID. File may not be Amber NetCDF compliant.\n");
mprintf("Warning: Assuming spatial variables are 'x', 'y', 'z'\n");
} else {
start_[0] = 0;
count_[0] = 3;
char xyz[3];
if (checkNCerr(nc_get_vara_text(ncid_, spatialVID_, start_, count_, xyz))) {
mprinterr("Error: Getting spatial variables.\n");
return 1;
}
if (xyz[0] != 'x' || xyz[1] != 'y' || xyz[2] != 'z') {
mprinterr("Error: NetCDF spatial variables are '%c', '%c', '%c', not 'x', 'y', 'z'\n",
xyz[0], xyz[1], xyz[2]);
return 1;
}
}
// Get velocity info
velocityVID_ = -1;
if ( nc_inq_varid(ncid_, NCVELO, &velocityVID_) == NC_NOERR ) {
if (ncdebug_>0) mprintf("\tNetcdf file has velocities.\n");
}
// Return a error if no coords and no velocity
if ( coordVID_ == -1 && velocityVID_ == -1 ) {
mprinterr("Error: NetCDF file has no coords and no velocities.\n");
return 1;
}
// If using velocities as coordinates, swap them now.
if (useVelAsCoords) {
if (velocityVID_ == -1) {
mprinterr("Error: Cannot use velocities as coordinates; no velocities present.\n");
return 1;
}
mprintf("\tUsing velocities as coordinates.\n");
coordVID_ = velocityVID_;
velocityVID_ = -1;
}
// Get force info
frcVID_ = -1;
if ( nc_inq_varid(ncid_, NCFRC, &frcVID_) == NC_NOERR ) {
if (ncdebug_>0) mprintf("\tNetcdf file has forces.\n");
}
// Get overall replica and coordinate indices
crdidxVID_ = -1;
if ( nc_inq_varid(ncid_, NCREMD_REPIDX, &repidxVID_) == NC_NOERR ) {
//if (ncdebug_ > 0)
mprintf(" Netcdf file has overall replica indices.\n");
if ( checkNCerr(nc_inq_varid(ncid_, NCREMD_CRDIDX, &crdidxVID_)) ) {
mprinterr("Error: Getting overall coordinate index variable ID.\n");
return 1;
}
} else
repidxVID_ = -1;
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;
}
