// Traj_AmberNetcdf::info()
void Traj_AmberNetcdf::Info() {
mprintf("is a NetCDF AMBER trajectory");
if (readAccess_ && !HasCoords()) mprintf(" (no coordinates)");
if (CoordInfo().HasVel()) mprintf(" containing velocities");
if (CoordInfo().HasTemp()) mprintf(" with replica temperatures");
if (remd_dimension_ > 0) mprintf(", with %i dimensions", remd_dimension_);
}
/** Set up trajectory for write. Calculate the length of each cooordinate
* frame. Set the title and titleSize. Calculate the full output file
* size, necessary only for seeking when MPI writing. Allocate memory for
* the frame buffer.
*/
int Traj_AmberCoord::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
// Set Temperature Write
// FIXME: Check for temperatures in input frames and when appending.
SetCoordInfo( cInfoIn );
if (outputTemp_) {
headerSize_ = REMD_HEADER_SIZE;
if (!CoordInfo().HasTemp())
mprintf("Warning: No temperature information in input frames.\n");
}
if (!append) {
// Write the title if not appending
if (file_.SetupWrite( fname, debug_ )) return 1;
std::string title = Title();
if (title.empty()) {
// Set up default title
title.assign("Cpptraj Generated trajectory");
title.resize(80,' ');
SetTitle( title );
} else {
// Check title length
if (title.size() > 80) {
mprintf("Warning: Amber traj title for %s too long: truncating.\n[%s]\n",
file_.Filename().base(), title.c_str());
title.resize(80);
}
}
if (file_.OpenFile()) return 1;
file_.Printf("%-s\n", title.c_str());
} else {
// Just set up for append
if (file_.SetupAppend( fname, debug_ )) return 1;
if (file_.OpenFile()) return 1;
}
// Allocate buffer. Will not buffer REMD header or need to seek.
// NOTE: This is done here since SetupFrameBuffer allocates based
// on write mode, which is not known until now.
natom3_ = trajParm->Natom() * 3;
file_.SetupFrameBuffer( natom3_, 8, 10 );
// If box coords are present, allocate extra space for them
switch (CoordInfo().TrajBox().Type()) {
case Box::NOBOX : numBoxCoords_ = 0; break;
case Box::ORTHO :
case Box::TRUNCOCT: numBoxCoords_ = 3; break;
default : numBoxCoords_ = 6;
}
file_.ResizeBuffer( numBoxCoords_ );
if (debug_>0)
rprintf("(%s): Each frame has %lu bytes.\n", file_.Filename().base(), file_.FrameSize());
return 0;
}
int Traj_GmxTrX::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
if (!append) {
SetCoordInfo( cInfoIn );
natoms_ = trajParm->Natom();
natom3_ = natoms_ * 3;
// Default to little endian, precision 4, TRR
format_ = TRR;
isBigEndian_ = false;
precision_ = 4;
// Set up title
if (Title().empty())
SetTitle("Cpptraj generated TRR file.");
// Set size defaults, box, velocity etc
ir_size_ = 0;
e_size_ = 0;
if (CoordInfo().HasBox())
box_size_ = precision_ * 9;
else
box_size_ = 0;
vir_size_ = 0;
pres_size_ = 0;
top_size_ = 0;
sym_size_ = 0;
x_size_ = natom3_ * precision_;
if (CoordInfo().HasVel())
v_size_ = natom3_ * precision_;
else
v_size_ = 0;
f_size_ = 0;
step_ = 0;
nre_ = 0;
dt_ = 0.0;
lambda_ = 0.0;
// Allocate temp space for coords/velo
AllocateCoords();
if (file_.SetupWrite( fname, debug_)) return 1;
if (file_.OpenFile()) return 1;
} else {
int nframes = setupTrajin( fname, trajParm );
if ( format_ == TRJ ) {
mprinterr("Error: Only writes to TRR files supported.\n");
return 1;
}
if ( nframes == TRAJIN_ERR ) return 1;
mprintf("\tAppending to TRR file starting at frame %i\n", nframes);
// Re-open for appending
if (file_.SetupAppend( fname, debug_ )) return 1;
if (file_.OpenFile()) return 1;
}
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;
}
int Traj_Gro::readFrame(int fnum, Frame& frm) {
if (fnum < currentSet_) {
file_.CloseFile();
file_.OpenFileRead( fname_ );
currentSet_ = 0;
}
// Position file
const char* ptr;
for (int set = currentSet_; set != fnum; set++) {
ptr = file_.Line(); // Title
ptr = file_.Line(); // Natoms
for (int i = 0; i != linesToRead_; i++)
ptr = file_.Line(); // Atom (and possibly box)
if (ptr == 0) return 1;
}
// Read current frame
ptr = file_.Line(); // Title
if (ptr == 0) return 1;
if (CoordInfo().HasTime())
frm.SetTime( GetTimeValue(ptr) );
ptr = file_.Line(); // Natoms TODO check?
double* Xptr = frm.xAddress();
if (CoordInfo().HasVel()) {
double* Vptr = frm.vAddress();
for (int i = 0; i != natom_; i++, Xptr += 3, Vptr += 3) {
ptr = file_.Line(); // Atom
sscanf(ptr, "%*5c%*5c%*5c%*5c%lf %lf %lf %lf %lf %lf",
Xptr, Xptr+1, Xptr+2, Vptr, Vptr+1, Vptr+2);
for (int n = 0; n != 3; n++) {
Xptr[n] *= 10.0;
Vptr[n] *= 10.0;
}
}
} else {
for (int i = 0; i != natom_; i++, Xptr += 3) {
ptr = file_.Line(); // Atom
sscanf(ptr, "%*5c%*5c%*5c%*5c%lf %lf %lf", Xptr, Xptr+1, Xptr+2);
for (int n = 0; n != 3; n++)
Xptr[n] *= 10.0;
}
}
// Box read
if (CoordInfo().HasBox()) {
ptr = file_.Line();
frm.SetBox( GetBox(ptr) );
}
++currentSet_;
return 0;
}
// Traj_AmberRestart::readVelocity()
int Traj_AmberRestart::readVelocity(int set, Frame& frameIn) {
if (CoordInfo().HasVel()) {
std::copy(VEL_.begin(), VEL_.end(), frameIn.vAddress());
return 0;
}
return 1;
}
// Traj_NcEnsemble::Info()
void Traj_NcEnsemble::Info() {
mprintf("is a NetCDF Ensemble AMBER trajectory");
if (readAccess_) {
mprintf(" with %s", CoordInfo().InfoString().c_str());
if (useVelAsCoords_) mprintf(" (using velocities as coordinates)");
if (useFrcAsCoords_) mprintf(" (using forces as coordinates)");
if (remd_dimension_ > 0) mprintf(", %i replica dimensions", remd_dimension_);
}
}
// Traj_AmberCoord::Info()
void Traj_AmberCoord::Info() {
if (CoordInfo().HasTemp())
mprintf("is an AMBER REMD trajectory");
else
mprintf("is an AMBER trajectory");
if (highPrecision_) mprintf(" (high precision)");
if (writeType_ == VEL) mprintf(" (MDVEL)");
else if (writeType_ == FRC) mprintf(" (MDFRC)");
}
/** 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;
}
/** Write coords in Frame to file in amber restart format. */
int Traj_AmberRestart::writeFrame(int set, Frame const& frameOut) {
// If just writing 1 frame dont modify output filename
if (singleWrite_) {
if (file_.OpenFile()) return 1;
} else {
if (file_.OpenWriteNumbered( set + 1 ) ) return 1;
}
// Write out title
file_.Printf("%-s\n", Title().c_str());
// Write out atoms
file_.Printf("%5i", frameOut.Natom());
// Write out restart time
if (CoordInfo().HasTime()) {
if (time0_>=0)
restartTime_ = (time0_ + (double)set) * dt_;
else
restartTime_ = frameOut.Time();
file_.Printf("%15.7lE",restartTime_);
}
// Write out temperature
if (CoordInfo().HasTemp())
file_.Printf("%15.7lE",frameOut.Temperature());
file_.Printf("\n");
// Write coords to buffer
file_.BufferBegin();
file_.DoubleToBuffer(frameOut.xAddress(), natom3_, "%12.7f");
// Write velocity to buffer. Check V since velocity not known ahead of time
if (CoordInfo().HasVel() && frameOut.HasVelocity())
file_.DoubleToBuffer(frameOut.vAddress(), natom3_, "%12.7f");
// Write box to buffer
if (numBoxCoords_!=0)
file_.DoubleToBuffer(frameOut.bAddress(), numBoxCoords_, "%12.7f");
if (file_.WriteFrame()) return 1;
file_.CloseFile();
return 0;
}
/** Copy buffered coords/velocities/box to input frame. */
int Traj_AmberRestart::readFrame(int set, Frame& frameIn) {
// Set frame temp
if (CoordInfo().HasTemp())
frameIn.SetTemperature( restartTemp_ );
// Set frame time
if (CoordInfo().HasTime())
frameIn.SetTime( restartTime_ );
// Get coords from buffer
std::copy(CRD_.begin(), CRD_.end(), frameIn.xAddress());
// Get velocity from buffer if present
if (CoordInfo().HasVel()) {
if (frameIn.HasVelocity()) {
if (useVelAsCoords_)
std::copy(VEL_.begin(), VEL_.end(), frameIn.xAddress());
else
std::copy(VEL_.begin(), VEL_.end(), frameIn.vAddress());
}
}
// Get box from buffer if present
if (numBoxCoords_!=0)
std::copy(boxInfo_.boxPtr(), boxInfo_.boxPtr()+6, frameIn.bAddress());
return 0;
}
void Traj_GmxTrX::AllocateCoords() {
// Allocate temp space for coords/velo
if (farray_ != 0) {
delete[] farray_;
farray_ = 0;
}
if (darray_ != 0) {
delete[] darray_;
darray_ = 0;
}
size_t arraySize = (size_t)natom3_;
if (CoordInfo().HasVel()) arraySize *= 2;
if (precision_ == sizeof(float))
farray_ = new float[ arraySize ];
else
darray_ = new double[ arraySize ];
}
// Traj_AmberRestart::Info()
void Traj_AmberRestart::Info() {
mprintf("is an AMBER restart file");
if (readAccess_) {
// If read access we know for sure whether there are velocities.
if (CoordInfo().HasVel())
mprintf(" with velocity info");
else
mprintf(", no velocities");
if (useVelAsCoords_) mprintf(" (using velocities as coords)");
} else {
// If write, not sure yet whether velocities will be written since
// it also depends on if the frame has velocity info, so only state
// if novelocity was specified.
if (!outputVel_) mprintf(", no velocities");
if (!outputTime_) mprintf(", no time");
}
}
// 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;
}
void Traj_Gro::Info() {
mprintf("is a GRO file");
if (CoordInfo().HasTime()) mprintf(", with time");
if (CoordInfo().HasVel()) mprintf(", with velocities");
if (CoordInfo().HasBox()) mprintf(", with box info");
}
// 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;
}
// 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;
}