/** 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);
if (outputFrc_ && !cInfo.HasForce()) cInfo.SetForce(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 (outputFrc_ && !CoordInfo().HasForce())
mprintf("Warning: Cannot append force data to NetCDF file '%s'; no force 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;
}
// 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;
}