/** Special version of AddSet that does NOT check if set already exists.
* Intended for use in Action Setup/DoAction where it is assumed that
* the Action is setting up DataSets in such a way that there will not
* be name conflicts, i.e. the DataSet name at least is unique.
* \param inType type of DataSet to add.
* \param metaIn DataSet MetaData.
* \return pointer to successfully set-up DataSet or 0 if error.
*/
DataSet* DataSetList::AddSet_NoCheck(DataSet::DataType inType, MetaData const& metaIn)
{ // TODO Pass in Nframes?
// Assume list does NOT have copies.
MetaData meta( metaIn );
meta.SetEnsembleNum( ensembleNum_ );
// Allocate DataSet
TokenPtr token = &(DataArray[inType]);
if ( token->Alloc == 0) {
mprinterr("Internal Error: No allocator for DataSet type [%s]\n", token->Description);
return 0;
}
DataSet* DS = (DataSet*)token->Alloc();
if (DS==0) {
mprinterr("Internal Error: DataSet %s memory allocation failed.\n", meta.PrintName().c_str());
return 0;
}
// If 1 dim set and time series status not set, set to true, allocate for frames.
if (meta.TimeSeries() == MetaData::UNKNOWN_TS && DS->Ndim() == 1) {
meta.SetTimeSeries( MetaData::IS_TS );
// Also set dimension default
DS->SetDim(Dimension::X, Dimension(1.0, 1.0, "Frame") );
//DS->Allocate( DataSet::SizeArray(1, Nframes) );
}
// Set up DataSet MetaData
if ( DS->SetMeta( meta ) ) {
mprinterr("Error setting up data set %s.\n", meta.PrintName().c_str());
delete DS;
return 0;
}
# ifdef MPI
if (newSetsNeedSync_) DS->SetNeedsSync( true );
# endif
// Add to list
Push_Back(DS);
return DS;
}
// Action_Density::Init()
Action::RetType Action_Density::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
std::string dsname = actionArgs.GetStringKey("name");
if (actionArgs.hasKey("x") ) {
axis_ = DX;
area_coord_[0] = DY;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("y") ) {
axis_ = DY;
area_coord_[0] = DX;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("z") ) {
axis_ = DZ;
area_coord_[0] = DX;
area_coord_[1] = DY;
}
property_ = NUMBER;
if (actionArgs.hasKey("number") ) property_ = NUMBER;
else if (actionArgs.hasKey("mass") ) property_ = MASS;
else if (actionArgs.hasKey("charge") ) property_ = CHARGE;
else if (actionArgs.hasKey("electron") ) property_ = ELECTRON;
binType_ = CENTER;
if (actionArgs.hasKey("bincenter")) binType_ = CENTER;
else if (actionArgs.hasKey("binedge") ) binType_ = EDGE;
delta_ = actionArgs.getKeyDouble("delta", 0.01);
if (delta_ <= 0) {
mprinterr("Error: Delta must be > 0.0\n");
return Action::ERR;
}
// for compatibility with ptraj, ignored because we rely on the atom code to
// do the right thing, see Atom.{h,cpp}
if (actionArgs.hasKey("efile"))
mprintf("Warning: The 'efile' keyword is deprecated.\n");
// read the rest of the command line as a series of masks
std::string maskstr;
unsigned int idx = 1;
while ( (maskstr = actionArgs.GetMaskNext() ) != emptystring) {
masks_.push_back( AtomMask(maskstr) );
if (dsname.empty())
dsname = init.DSL().GenerateDefaultName("DENSITY");
MetaData MD(dsname, "avg", idx);
MD.SetTimeSeries( MetaData::NOT_TS );
// Hold average density
DataSet* ads = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (ads == 0) return Action::ERR;
ads->SetLegend( NoWhitespace(masks_.back().MaskExpression()) );
AvSets_.push_back( ads );
if (outfile != 0) outfile->AddDataSet( ads );
// Hold SD density
MD.SetAspect("sd");
DataSet* sds = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (sds == 0) return Action::ERR;
sds->SetLegend( NoWhitespace("sd(" + masks_.back().MaskExpression() + ")") );
SdSets_.push_back( sds );
if (outfile != 0) outfile->AddDataSet( sds );
# ifdef MPI
ads->SetNeedsSync( false ); // Populated in Print()
sds->SetNeedsSync( false );
# endif
idx++;
}
if (masks_.empty()) {
// If no masks assume we want total system density.
if (dsname.empty())
dsname = actionArgs.GetStringNext();
density_ = init.DSL().AddSet(DataSet::DOUBLE, dsname, "DENSITY");
if (density_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet( density_ );
image_.InitImaging( true );
// Hijack delta for storing sum of masses
delta_ = 0.0;
} else {
// Density selected by mask(s) along an axis
density_ = 0;
histograms_.resize(masks_.size() );
}
mprintf(" DENSITY:");
if (density_ == 0) {
const char* binStr[] = {"center", "edge"};
mprintf(" Determining %s density for %zu masks.\n", PropertyStr_[property_], masks_.size());
mprintf("\troutine version: %s\n", ROUTINE_VERSION_STRING);
mprintf("\tDelta is %f\n", delta_);
mprintf("\tAxis is %s\n", AxisStr_[axis_]);
mprintf("\tData set name is '%s'\n", dsname.c_str());
mprintf("\tData set aspect [avg] holds the mean, aspect [sd] holds standard deviation.\n");
mprintf("\tBin coordinates will be to bin %s.\n", binStr[binType_]);
} else {
mprintf(" No masks specified, calculating total system density in g/cm^3.\n");
mprintf("\tData set name is '%s'\n", density_->legend());
}
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
return Action::OK;
}
/** Add a DataSet of specified type, set it up and return pointer to it.
* \param inType type of DataSet to add.
* \param metaIn DataSet MetaData.
* \return pointer to successfully set-up DataSet or 0 if error.
*/
DataSet* DataSetList::AddSet(DataSet::DataType inType, MetaData const& metaIn)
{ // TODO Always generate default name if empty?
# ifdef TIMER
time_total_.Start();
# endif
// Do not add to a list with copies
if (hasCopies_) {
mprinterr("Internal Error: Attempting to add DataSet (%s) to DataSetList with copies.\n",
metaIn.PrintName().c_str());
return 0;
}
MetaData meta( metaIn );
meta.SetEnsembleNum( ensembleNum_ );
# ifdef TIMER
time_check_.Start();
# endif
// Check if DataSet with same attributes already present.
DataSet* DS = CheckForSet(meta);
# ifdef TIMER
time_check_.Stop();
# endif
if (DS != 0) {
mprintf("Warning: DataSet '%s' already present.\n", DS->Meta().PrintName().c_str());
// NOTE: Should return found dataset?
return 0;
}
TokenPtr token = &(DataArray[inType]);
if ( token->Alloc == 0) {
mprinterr("Internal Error: No allocator for DataSet type [%s]\n", token->Description);
return 0;
}
# ifdef TIMER
time_setup_.Start();
# endif
DS = (DataSet*)token->Alloc();
if (DS==0) {
mprinterr("Internal Error: DataSet %s memory allocation failed.\n", meta.PrintName().c_str());
return 0;
}
// If 1 dim set and time series status not set, set to true.
if (meta.TimeSeries() == MetaData::UNKNOWN_TS && DS->Ndim() == 1) {
meta.SetTimeSeries( MetaData::IS_TS );
// Also set dimension default
DS->SetDim(Dimension::X, Dimension(1.0, 1.0, "Frame") );
}
// Set up dataset
if ( DS->SetMeta( meta ) ) {
mprinterr("Error setting up data set %s.\n", meta.PrintName().c_str());
delete DS;
return 0;
}
# ifdef MPI
if (newSetsNeedSync_) DS->SetNeedsSync( true );
# endif
# ifdef TIMER
time_setup_.Stop();
time_push_.Start();
# endif
Push_Back(DS);
# ifdef TIMER
time_push_.Stop();
# endif
//fprintf(stderr,"ADDED dataset %s\n",dsetName);
return DS;
}
// Action_Density::Init()
Action::RetType Action_Density::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
if (init.TrajComm().Size() > 1) {
mprinterr("Error: 'density' action does not work with > 1 thread (%i threads currently).\n",
init.TrajComm().Size());
return Action::ERR;
}
# endif
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
std::string dsname = actionArgs.GetStringKey("name");
if (dsname.empty())
dsname = init.DSL().GenerateDefaultName("DENSITY");
if (actionArgs.hasKey("x") ) {
axis_ = DX;
area_coord_[0] = DY;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("y") ) {
axis_ = DY;
area_coord_[0] = DX;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("z") ) {
axis_ = DZ;
area_coord_[0] = DX;
area_coord_[1] = DY;
}
property_ = NUMBER;
if (actionArgs.hasKey("number") ) property_ = NUMBER;
if (actionArgs.hasKey("mass") ) property_ = MASS;
if (actionArgs.hasKey("charge") ) property_ = CHARGE;
if (actionArgs.hasKey("electron") ) property_ = ELECTRON;
delta_ = actionArgs.getKeyDouble("delta", 0.01);
// for compatibility with ptraj, ignored because we rely on the atom code to
// do the right thing, see Atom.{h,cpp}
if (actionArgs.hasKey("efile"))
mprintf("Warning: The 'efile' keyword is deprecated.\n");
// read the rest of the command line as a series of masks
std::string maskstr;
unsigned int idx = 1;
while ( (maskstr = actionArgs.GetMaskNext() ) != emptystring) {
masks_.push_back( AtomMask(maskstr) );
MetaData MD(dsname, "avg", idx);
MD.SetTimeSeries( MetaData::NOT_TS );
// Hold average density
DataSet* ads = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (ads == 0) return Action::ERR;
ads->SetLegend( NoWhitespace(masks_.back().MaskExpression()) );
AvSets_.push_back( ads );
if (outfile != 0) outfile->AddDataSet( ads );
// Hold SD density
MD.SetAspect("sd");
DataSet* sds = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (sds == 0) return Action::ERR;
sds->SetLegend( NoWhitespace("sd(" + masks_.back().MaskExpression() + ")") );
SdSets_.push_back( sds );
if (outfile != 0) outfile->AddDataSet( sds );
# ifdef MPI
ads->SetNeedsSync( false ); // Populated in Print()
sds->SetNeedsSync( false );
# endif
idx++;
}
if (masks_.empty()) {
mprinterr("Error: No masks specified.\n");
return Action::ERR;
}
minus_histograms_.resize(masks_.size() );
plus_histograms_.resize(masks_.size() );
mprintf(" DENSITY: Determining %s density for %zu masks.\n", PropertyStr_[property_],
masks_.size());
mprintf("\troutine version: %s\n", ROUTINE_VERSION_STRING);
mprintf("\tDelta is %f\n", delta_);
mprintf("\tAxis is %s\n", AxisStr_[axis_]);
mprintf("\tData set name is '%s'\n", dsname.c_str());
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
return Action::OK;
}
