FMMSolver::FMMSolver(const Grid& g,
Vect<real_t>& phi,
bool HA)
{
_phi = φ
_dim = CheckDimension(g);
if (_dim==3)
_theFM = new FMM3D(g,_phi,HA);
else
_theFM = new FMM2D(g,_phi,HA);
}
/** Set up histogram with specified data sets. */
Analysis::RetType Analysis_Hist::Setup(ArgList& analyzeArgs, AnalysisSetup& setup, int debugIn)
{
debug_ = debugIn;
// Keywords
std::string histname = analyzeArgs.GetStringKey("name");
outfilename_ = analyzeArgs.GetStringKey("out");
if (outfilename_.empty()) {
mprinterr("Error: Hist: No output filename specified.\n");
return Analysis::ERR;
}
traj3dName_ = analyzeArgs.GetStringKey("traj3d");
traj3dFmt_ = TrajectoryFile::WriteFormatFromString( analyzeArgs.GetStringKey("trajfmt"),
TrajectoryFile::AMBERTRAJ );
parmoutName_ = analyzeArgs.GetStringKey("parmout");
// Create a DataFile here so any DataFile arguments can be processed. If it
// turns out later that native output is needed the DataFile will be removed.
outfile_ = setup.DFL().AddDataFile(outfilename_, analyzeArgs);
if (outfile_==0) return Analysis::ERR;
Temp_ = analyzeArgs.getKeyDouble("free",-1.0);
if (Temp_!=-1.0)
calcFreeE_ = true;
else
calcFreeE_ = false;
gnuplot_ = analyzeArgs.hasKey("gnu");
if (analyzeArgs.hasKey("norm"))
normalize_ = NORM_SUM;
else if (analyzeArgs.hasKey("normint"))
normalize_ = NORM_INT;
else
normalize_ = NO_NORM;
circular_ = analyzeArgs.hasKey("circular");
nativeOut_ = analyzeArgs.hasKey("nativeout");
if ( analyzeArgs.Contains("min") ) {
default_min_ = analyzeArgs.getKeyDouble("min", 0.0);
minArgSet_ = true;
}
if ( analyzeArgs.Contains("max") ) {
default_max_ = analyzeArgs.getKeyDouble("max", 0.0);
maxArgSet_ = true;
}
default_step_ = analyzeArgs.getKeyDouble("step", 0.0) ;
default_bins_ = analyzeArgs.getKeyInt("bins", -1);
calcAMD_ = false;
std::string amdname = analyzeArgs.GetStringKey("amd");
if (!amdname.empty()) {
DataSet* ds = setup.DSL().GetDataSet( amdname );
if (ds == 0) {
mprinterr("Error: AMD data set %s not found.\n", amdname.c_str());
return Analysis::ERR;
}
if (ds->Ndim() != 1) {
mprinterr("Error: AMD data set must be 1D.\n");
return Analysis::ERR;
}
amddata_ = (DataSet_1D*)ds;
calcAMD_ = true;
}
// Treat all remaining arguments as dataset names. Do not set up dimensions
// yet since the data sets may not be fully populated.
ArgList dsetNames = analyzeArgs.RemainingArgs();
for ( ArgList::const_iterator setname = dsetNames.begin();
setname != dsetNames.end(); ++setname)
{
if (CheckDimension( *setname, setup.DSL() )) return Analysis::ERR;
}
// histdata contains the DataSets to be histogrammed
if (histdata_.empty()) {
mprinterr("Error: Hist: No datasets specified.\n");
return Analysis::ERR;
}
// Total # of dimensions for the histogram is the number of sets to be binned.
N_dimensions_ = histdata_.size();
if (!nativeOut_) {
switch ( N_dimensions_ ) {
case 1: hist_ = setup.DSL().AddSet( DataSet::DOUBLE, histname, "Hist"); break;
case 2: hist_ = setup.DSL().AddSet( DataSet::MATRIX_DBL, histname, "Hist"); break;
// TODO: GRID_DBL
case 3: hist_ = setup.DSL().AddSet( DataSet::GRID_FLT, histname, "Hist"); break;
default: // FIXME: GET N DIMENSION CASE!
mprintf("Warning: Histogram dimension > 3. DataSet/DataFile output not supported.\n");
nativeOut_ = true;
}
}
// traj3d only supported with 3D histograms
if (!traj3dName_.empty() && N_dimensions_ != 3) {
mprintf("Warning: 'traj3d' only supported with 3D histograms.\n");
traj3dName_.clear();
parmoutName_.clear();
}
if (!nativeOut_) {
// DataFile output. Add DataSet to DataFile.
if (hist_ == 0) {
mprinterr("Error: Could not set up histogram data set.\n");
return Analysis::ERR;
}
outfile_->AddDataSet( hist_ );
} else {
// Native output. Remove DataFile from DataFileList
outfile_ = setup.DFL().RemoveDataFile( outfile_ );
native_ = setup.DFL().AddCpptrajFile( outfilename_, "Histogram output" );
if (native_ == 0) return Analysis::ERR;
}
mprintf("\tHist: %s: Set up for %zu dimensions using the following datasets:\n",
outfilename_.c_str(), N_dimensions_);
mprintf("\t[ ");
for (std::vector<DataSet_1D*>::iterator ds=histdata_.begin(); ds!=histdata_.end(); ++ds)
mprintf("%s ",(*ds)->legend());
mprintf("]\n");
if (calcAMD_)
mprintf("\tPopulating bins using AMD boost from data set %s\n",
amddata_->legend());
if (calcFreeE_)
mprintf("\tFree energy in kcal/mol will be calculated from bin populations at %f K.\n",Temp_);
if (nativeOut_)
mprintf("\tUsing internal routine for output. Data will not be stored on the data set list.\n");
//if (circular_ || gnuplot_) {
// mprintf("\tWarning: gnuplot and/or circular specified; advanced grace/gnuplot\n");
// mprintf("\t formatting disabled.\n");*/
if (circular_)
mprintf("\tcircular: Output coordinates will be wrapped.\n");
if (gnuplot_ && outfile_ == 0)
mprintf("\tgnuplot: Output will be in gnuplot-readable format.\n");
//}
if (normalize_ == NORM_SUM)
mprintf("\tnorm: Sum over bins will be normalized to 1.0.\n");
else if (normalize_ == NORM_INT)
mprintf("\tnormint: Integral over bins will be normalized to 1.0.\n");
if (!traj3dName_.empty()) {
mprintf("\tPseudo-trajectory will be written to '%s' with format %s\n",
traj3dName_.c_str(), TrajectoryFile::FormatString(traj3dFmt_));
if (!parmoutName_.empty())
mprintf("\tCorresponding pseudo-topology will be written to '%s'\n",
parmoutName_.c_str());
}
return Analysis::OK;
}