/** Allocate a character buffer based on number of coords and whether
* velocities/box info is present.
*/
int Traj_AmberRestart::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
if (append) {
mprinterr("Error: Append not supported for Amber Restart.\n");
return 1;
}
CoordinateInfo cInfo = cInfoIn;
if (!cInfo.HasTemp() && outputTemp_) cInfo.SetTemperature(true);
// If temperature requested write time as well or format will break.
if (cInfo.HasTemp()) {
outputTime_ = true;
if (!cInfo.HasTime() && time0_ < 0.0) time0_ = 1.0;
}
if (cInfo.HasVel() && !outputVel_) cInfo.SetVelocity(false);
if (outputTime_) {
if (!cInfo.HasTime() && time0_ >= 0) cInfo.SetTime(true);
} else
cInfo.SetTime(false);
SetCoordInfo( cInfo );
if (file_.SetupWrite( fname, debug_ )) return 1;
readAccess_ = false;
// Set trajectory info
natom3_ = trajParm->Natom() * 3;
// Calculate the length of coordinate frame in bytes
file_.SetupFrameBuffer( natom3_, 12, 6 );
// Dont know ahead of time if velocities will be used, allocate space
// just in case. Velocity will not be written if V input is null.
file_.ResizeBuffer( natom3_ );
// If box coords are present, allocate extra space for them
if (CoordInfo().HasBox()) {
numBoxCoords_ = 6;
file_.ResizeBuffer( numBoxCoords_ );
}
// If number of frames to write == 1 set singleWrite so we dont append
// frame # to filename.
if (NframesToWrite==1) singleWrite_ = true;
// Set up title
std::string outTitle = Title();
if (outTitle.empty()) {
outTitle.assign("Cpptraj Generated Restart");
outTitle.resize(80, ' ');
} else {
if ( outTitle.size() > 80) {
mprintf("Warning: Amber restart title for %s too long: truncating.\n[%s]\n",
file_.Filename().base(), outTitle.c_str());
outTitle.resize(80);
}
}
SetTitle( outTitle );
return 0;
}
/** Create Netcdf file specified by filename and set up dimension and
* variable IDs.
*/
int Traj_AmberNetcdf::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
readAccess_ = false;
if (!append) {
CoordinateInfo cInfo = cInfoIn;
// Deal with output options
// For backwards compatibility always write temperature if remdtraj is true.
if (outputTemp_ && !cInfo.HasTemp()) cInfo.SetTemperature(true);
// Explicitly write velocity - initial frames may not have velocity info.
if (outputVel_ && !cInfo.HasVel()) cInfo.SetVelocity(true);
SetCoordInfo( cInfo );
filename_ = fname;
// Set up title
if (Title().empty())
SetTitle("Cpptraj Generated trajectory");
// Create NetCDF file.
if (NC_create( filename_.Full(), NC_AMBERTRAJ, trajParm->Natom(), CoordInfo(), Title() ))
return 1;
if (debug_>1) NetcdfDebug();
// Close Netcdf file. It will be reopened write.
NC_close();
// Allocate memory
if (Coord_!=0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
} else { // NOTE: File existence is checked for in Trajout
// Call setupTrajin to set input parameters. This will also allocate
// memory for coords.
if (setupTrajin(fname, trajParm) == TRAJIN_ERR) return 1;
// Check output options.
if (outputTemp_ && !CoordInfo().HasTemp())
mprintf("Warning: Cannot append temperature data to NetCDF file '%s'; no temperature dimension.\n",
filename_.base());
if (outputVel_ && !CoordInfo().HasVel())
mprintf("Warning: Cannot append velocity data to NetCDF file '%s'; no velocity dimension.\n",
filename_.base());
if (debug_ > 0)
mprintf("\tNetCDF: Appending %s starting at frame %i\n", filename_.base(), Ncframe());
}
// Open file
if ( NC_openWrite( filename_.Full() ) != 0 ) {
mprinterr("Error: Opening Netcdf file %s for Write.\n", filename_.base());
return 1;
}
return 0;
}
int DataSet_Coords_TRJ::CoordsSetup(Topology const& topIn, CoordinateInfo const& cInfoIn ) {
if (trajinList_.empty()) {
top_ = topIn;
cInfo_ = cInfoIn;
} else {
if ( topIn.Natom() != top_.Natom() ) {
mprinterr("Error: For TRAJ data set currently all trajectories must have same number\n"
"Error: of atoms: %i != %i. Recommended course of action is to\n"
"Error: create a trajectory where all frames have been stripped to the same\n"
"Error: number of atoms first.\n", topIn.Natom(), top_.Natom());
return 1;
}
// Since velocity/force info is not always allocated in Frame, if one traj
// has velocity/force info ensure that all do.
if (cInfoIn.HasVel()) cInfo_.SetVelocity( true );
if (cInfoIn.HasForce()) cInfo_.SetForce( true );
}
return 0;
}
// Action_CreateReservoir::Setup()
Action::RetType Action_CreateReservoir::Setup(ActionSetup& setup) {
// Check that input parm matches current parm
if (original_trajparm_->Pindex() != setup.Top().Pindex()) {
mprintf("Info: createreservoir was set up for topology %s\n", original_trajparm_->c_str());
mprintf("Info: skipping topology %s\n", setup.Top().c_str());
return Action::SKIP;
}
if (!trajIsOpen_) {
mprintf("\tCreating reservoir file %s\n", filename_.full());
CoordinateInfo cinfo = setup.CoordInfo();
if (!useVelocity_) cinfo.SetVelocity(false);
if (!useForce_) cinfo.SetForce(false);
if (reservoir_.InitReservoir(filename_, title_, cinfo, setup.Top().Natom(),
(bin_ != 0), reservoirT_, iseed_))
{
mprinterr("Error: Could not set up NetCDF reservoir.\n");
return Action::ERR;
}
trajIsOpen_ = true;
nframes_ = 0;
}
return Action::OK;
}
/** Like the strip action, closest will modify the current parm keeping info
* for atoms in mask plus the closestWaters solvent molecules. Set up the
* vector of MolDist objects, one for every solvent molecule in the original
* parm file. Atom masks for each solvent molecule will be set up.
*/
Action_Closest::RetType Action_Closest::Setup(Topology const& topIn, CoordinateInfo const& cInfoIn)
{
// If there are no solvent molecules this action is not valid.
if (topIn.Nsolvent()==0) {
mprintf("Warning: Parm %s does not contain solvent.\n",topIn.c_str());
return Action_Closest::SKIP;
}
// If # solvent to keep >= solvent in this parm the action is not valid.
if (closestWaters_ >= topIn.Nsolvent()) {
mprintf("Warning: # solvent to keep (%i) >= # solvent molecules in '%s' (%i)\n",
closestWaters_, topIn.c_str(), topIn.Nsolvent());
return Action_Closest::SKIP;
}
image_.SetupImaging( cInfoIn.TrajBox().Type() );
if (image_.ImagingEnabled())
mprintf("\tDistances will be imaged.\n");
else
mprintf("\tImaging off.\n");
// LOOP OVER MOLECULES
// 1: Check that all solvent molecules contain same # atoms. Solvent
// molecules must be identical for the command to work properly;
// the prmtop strip occurs only once so the solvent params become fixed.
// 2: Set up a mask for all solvent molecules.
SolventMols_.clear();
// NOTE: May not be necessary to init 'solvent'
MolDist solvent;
solvent.D = 0.0;
solvent.mol = 0;
SolventMols_.resize(topIn.Nsolvent(), solvent);
std::vector<MolDist>::iterator mdist = SolventMols_.begin();
// 3: Set up the soluteMask for all non-solvent molecules.
int molnum = 1;
int nclosest = 0;
int NsolventAtoms = -1;
for (Topology::mol_iterator Mol = topIn.MolStart();
Mol != topIn.MolEnd(); ++Mol)
{
if ( Mol->IsSolvent() ) {
// Solvent, check for same # of atoms.
if (NsolventAtoms == -1)
NsolventAtoms = Mol->NumAtoms();
else if ( NsolventAtoms != Mol->NumAtoms() ) {
mprinterr("Error: Solvent molecules in '%s' are not of uniform size.\n"
"Error: First solvent mol = %i atoms, solvent mol %i = %i atoms.\n",
topIn.c_str(), NsolventAtoms, molnum, (*Mol).NumAtoms());
return Action_Closest::ERR;
}
// mol here is the output molecule number which is why it starts from 1.
mdist->mol = molnum;
// Solvent molecule mask
mdist->mask.AddAtomRange( Mol->BeginAtom(), Mol->EndAtom() );
// Atoms in the solvent molecule to actually calculate distances to.
if (firstAtom_) {
mdist->solventAtoms.assign(1, Mol->BeginAtom() );
} else {
mdist->solventAtoms.clear();
mdist->solventAtoms.reserve( Mol->NumAtoms() );
for (int svatom = Mol->BeginAtom(); svatom < Mol->EndAtom(); svatom++)
mdist->solventAtoms.push_back( svatom );
}
if (debug_ > 0) {
mprintf("DEBUG:\tSet up mol %i:", mdist->mol); // DEBUG
mdist->mask.PrintMaskAtoms("solvent"); // DEBUG
mprintf("\n"); // DEBUG
}
++mdist;
}
++molnum;
}
// Setup distance atom mask
// NOTE: Should ensure that no solvent atoms are selected!
if ( topIn.SetupIntegerMask(distanceMask_) ) return Action_Closest::ERR;
if (distanceMask_.None()) {
mprintf("Warning: Distance mask '%s' contains no atoms.\n",
distanceMask_.MaskString());
return Action_Closest::SKIP;
}
distanceMask_.MaskInfo();
// Check the total number of solvent atoms to be kept.
NsolventAtoms *= closestWaters_;
mprintf("\tKeeping %i solvent atoms.\n",NsolventAtoms);
if (NsolventAtoms < 1) {
mprintf("Warning: # of solvent atoms to be kept is < 1.\n");
return Action_Closest::SKIP;
}
NsolventMolecules_ = (int)SolventMols_.size();
return Action_Closest::OK;
}
// Traj_NcEnsemble::setupTrajout()
int Traj_NcEnsemble::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
int err = 0;
# ifdef MPI
if (NoPnetcdf()) return 1;
# endif
readAccess_ = false;
if (!append) {
CoordinateInfo cInfo = cInfoIn;
// TODO: File output modifications
SetCoordInfo( cInfo );
# ifdef MPI
ensembleStart_ = Parallel::World().Rank();
ensembleEnd_ = Parallel::World().Rank() + 1;
# else
ensembleStart_ = 0;
ensembleEnd_ = cInfo.EnsembleSize();;
# endif
filename_ = fname;
// Set up title
if (Title().empty())
SetTitle("Cpptraj Generated trajectory");
# ifdef MPI
if (Parallel::World().Master()) { // Only master creates file.
# endif
// Create NetCDF file.
err = NC_create(filename_.Full(), NC_AMBERENSEMBLE, trajParm->Natom(), CoordInfo(),
Title(), debug_);
// Close Netcdf file. It will be reopened write. FIXME should NC_create leave it closed?
NC_close();
# ifdef MPI
}
Parallel::World().MasterBcast(&err, 1, MPI_INT);
# endif
if (err != 0) return 1;
# ifdef MPI
// Synchronize netcdf info on non-master threads
Sync(Parallel::World());
// DEBUG: Print info for all ranks
DebugVIDs();
# endif
// Allocate memory
if (Coord_!=0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
} else { // NOTE: File existence is checked for in Trajout
// Call setupTrajin to set input parameters. This will also allocate
// memory for coords.
if (setupTrajin(fname, trajParm) == TRAJIN_ERR) return 1;
if (debug_ > 0)
mprintf("\tNetCDF: Appending %s starting at frame %i\n", filename_.base(), Ncframe());
}
// Open file
# ifdef HAS_PNETCDF
err = ncmpi_open(MPI_COMM_WORLD, filename_.full(), NC_WRITE, MPI_INFO_NULL, &ncid_);
// TODO: Graceful error handling
# else
err = NC_openWrite( filename_.Full() );
# endif
if ( err != 0 ) {
mprinterr("Error: Opening Netcdf file %s for Write.\n", filename_.base());
return 1;
}
return 0;
}
/** Loop over all filenames in replica_filenames, set up TrajectoryIO. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
CoordinateInfo& cInfo, Topology* trajParm)
{
// Sanity check
if (!IOarray_.empty()) {
mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
return 1;
}
// Save arguments that have not been processed so they can be passed
// to each replica in turn. Only the lowest replica will use argIn.
ArgList argCopy( argIn );
bool lowestRep = true;
int rep0Frames = TrajectoryIO::TRAJIN_UNK; // Total frames in replica 0
int totalFrames = TrajectoryIO::TRAJIN_UNK; // Total # frames to be read from ensemble
TrajectoryFile::TrajFormatType lastRepFmt = TrajectoryFile::UNKNOWN_TRAJ;
// Right now enforce that all replicas have the same metadata as lowest
// replica, e.g. if replica 0 has temperature, replica 1 does too etc.
for (File::NameArray::const_iterator repfile = replica_filenames_.begin();
repfile != replica_filenames_.end(); ++repfile)
{
// Detect format
TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( *repfile, repformat );
if ( replica0 == 0 ) {
mprinterr("Error: Could not set up replica file %s\n", repfile->full());
return 1;
}
if (repformat != lastRepFmt)
mprintf("\tReading '%s' as %s\n", repfile->full(), TrajectoryFile::FormatString(repformat));
lastRepFmt = repformat;
replica0->SetDebug( debug_ );
// Pushing replica0 here allows the destructor to handle it on errors
IOarray_.push_back( replica0 );
// Process format-specific read args. Do not exit on error in case
// replicas have different formats supporting different args.
if (lowestRep) {
replica0->processReadArgs( argIn );
} else {
ArgList argtmp( argCopy );
replica0->processReadArgs( argtmp );
}
// Set up replica for reading and get the number of frames.
int nframes = replica0->setupTrajin( *repfile, trajParm );
if (nframes == TrajectoryIO::TRAJIN_ERR) {
mprinterr("Error: Could not set up %s for reading.\n", repfile->full());
return 1;
}
// TODO: Do not allow unknown number of frames?
if (lowestRep) {
cInfo = replica0->CoordInfo();
rep0Frames = nframes;
totalFrames = nframes;
if (cInfo.ReplicaDimensions().Ndims() > 0) {
mprintf("\tReplica dimensions:\n");
for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++)
mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd));
}
} else {
// Check total frames in this replica against lowest rep.
if (nframes != rep0Frames)
mprintf("Warning: Replica %s frames (%i) does not match # frames in first replica (%i).\n",
repfile->base(), nframes, rep0Frames);
//if (repframes < 0) {
// mprinterr("Error: RemdTraj: Unknown # of frames in replica.\n");
// return 1;
//}
if (nframes < totalFrames) {
totalFrames = nframes;
mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
totalFrames);
}
// Check box info against lowest rep.
if ( replica0->CoordInfo().HasBox() != cInfo.HasBox() ) {
mprinterr("Error: Replica %s box info does not match first replica.\n",
repfile->full());
return 1;
}
// TODO: Check specific box type
// Check velocity info against lowest rep.
if ( replica0->CoordInfo().HasVel() != cInfo.HasVel() ) {
mprinterr("Error: Replica %s velocity info does not match first replica.\n",
repfile->full());
return 1;
}
// Check # dimensions and types against lowest rep
if ( replica0->CoordInfo().ReplicaDimensions() != cInfo.ReplicaDimensions() ) {
mprinterr("Error: Replica %s dimension info does not match first replica.\n",
repfile->full());
ReplicaDimArray const& thisRepDims = replica0->CoordInfo().ReplicaDimensions();
for (int rd = 0; rd < thisRepDims.Ndims(); rd++)
mprinterr("\t\t%i: %s\n", rd+1, thisRepDims.Description(rd));
return 1;
}
// If temperature/time info does not match set to false.
if (cInfo.HasTemp() != replica0->CoordInfo().HasTemp())
cInfo.SetTemperature( false );
if (cInfo.HasTime() != replica0->CoordInfo().HasTime())
cInfo.SetTime( false );
}
lowestRep = false;
}
// Check how many frames will actually be read
if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
// Check for errors.
if (IOarray_.empty()) {
mprinterr("Error: No replica trajectories set up.\n");
return 1;
}
if (IOarray_.size() != replica_filenames_.size()) { // SANITY CHECK
mprinterr("Error: Not all replica files were set up.\n");
return 1;
}
// Update ensemble size
cInfo.SetEnsembleSize( (int)IOarray_.size() );
if (debug_ > 0)
cInfo.PrintCoordInfo( replica_filenames_[0].full(), trajParm->c_str() );
return 0;
}
/** Each rank only sets up file that it will process. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
CoordinateInfo& cInfo, Topology* trajParm,
Parallel::Comm const& ensComm, Parallel::Comm const& trajComm)
{
// Sanity check
if (!IOarray_.empty()) {
mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
return 1;
}
// Detect format
FileName const& repFname = replica_filenames_[ensComm.Rank()];
TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( repFname, repformat );
if ( replica0 == 0 ) {
mprinterr("Error: Could not set up replica file %s\n", repFname.full());
return 1;
}
mprintf("\tReading '%s' as %s\n", repFname.full(), TrajectoryFile::FormatString(repformat));
replica0->SetDebug( debug_ );
// Construct the IOarray_ with blanks for all except this rank.
for (int member = 0; member != ensComm.Size(); member++)
if (member == ensComm.Rank())
IOarray_.push_back( replica0 );
else
IOarray_.push_back( 0 );
// Process format-specific read args.
replica0->processReadArgs( argIn );
// Set up replica for reading and get # frames
int nframes = replica0->setupTrajin( repFname, trajParm );
if (nframes == TrajectoryIO::TRAJIN_ERR) {
mprinterr("Error: Could not set up %s for reading.\n", repFname.full());
return 1;
}
// Set coordinate info
cInfo = replica0->CoordInfo();
int totalFrames = nframes;
if (cInfo.ReplicaDimensions().Ndims() > 0) { // TODO put in common routine
mprintf("\tReplica dimensions:\n");
for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++)
mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd));
}
// Check # frames in all files, use lowest.
Parallel::World().AllReduce( &totalFrames, &nframes, 1, MPI_INT, MPI_MIN );
if (totalFrames != nframes) {
rprintf("Warning: Replica '%s' frames (%i) is > # frames in shortest replica.\n",
repFname.full(), nframes);
mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
totalFrames);
}
if (trajComm.Master()) {
static const int iSize = 6;
static const char* iTitle[iSize] = {"box", "velocity", "temperature", "time", "force",
"replica dimensions"};
// Check coordinate info of all files 0 1 2 3 4 5
std::vector<int> Info( iSize * ensComm.Size() ); // box, vel, temp, time, force, nRepDims
int rank_info[iSize];
rank_info[0] = (int)cInfo.TrajBox().Type();
rank_info[1] = (int)cInfo.HasVel();
rank_info[2] = (int)cInfo.HasTemp();
rank_info[3] = (int)cInfo.HasTime();
rank_info[4] = (int)cInfo.HasForce();
rank_info[5] = cInfo.ReplicaDimensions().Ndims();
ensComm.AllGather( rank_info, iSize, MPI_INT, &Info[0] );
// TODO Should mismatches be errors instead?
for (int midx = 0; midx != iSize; midx++) {
for (int ridx = midx + iSize; ridx < (int)Info.size(); ridx += iSize) {
if (Info[midx] != Info[ridx]) {
rprintf("Warning: Replica %i %s info does not match first replica.\n",
ridx/iSize, iTitle[midx]);
}
}
}
}
// TODO: Put code below into a common routine with serial version
// Check how many frames will actually be read
if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
// SANITY CHECK
if (IOarray_.size() != replica_filenames_.size()) {
mprinterr("Error: Not all replica files were set up.\n");
return 1;
}
// Update ensemble size
cInfo.SetEnsembleSize( (int)IOarray_.size() );
if (debug_ > 0)
cInfo.PrintCoordInfo( repFname.full(), trajParm->c_str() );
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;
}
