// Action_Grid::Init()
Action::RetType Action_Grid::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
debug_ = debugIn;
nframes_ = 0;
// Get output filename
std::string filename = actionArgs.GetStringKey("out");
// Get grid options
grid_ = GridInit( "GRID", actionArgs, init.DSL() );
if (grid_ == 0) return Action::ERR;
# ifdef MPI
if (ParallelGridInit(init.TrajComm(), grid_)) return Action::ERR;
# endif
// Get extra options
max_ = actionArgs.getKeyDouble("max", 0.80);
madura_ = actionArgs.getKeyDouble("madura", 0);
smooth_ = actionArgs.getKeyDouble("smoothdensity", 0);
invert_ = actionArgs.hasKey("invert");
pdbfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("pdb"),"Grid PDB",DataFileList::PDB,true);
density_ = actionArgs.getKeyDouble("density",0.033456);
if (actionArgs.hasKey("normframe")) normalize_ = TO_FRAME;
else if (actionArgs.hasKey("normdensity")) normalize_ = TO_DENSITY;
else normalize_ = NONE;
if (normalize_ != NONE && (smooth_ > 0.0 || madura_ > 0.0)) {
mprinterr("Error: Normalize options are not compatible with smoothdensity/madura options.\n");
init.DSL().RemoveSet( grid_ );
return Action::ERR;
}
// Get mask
std::string maskexpr = actionArgs.GetMaskNext();
if (maskexpr.empty()) {
mprinterr("Error: GRID: No mask specified.\n");
init.DSL().RemoveSet( grid_ );
return Action::ERR;
}
mask_.SetMaskString(maskexpr);
// Setup output file
// For backwards compat., if no 'out' assume next string is filename
if (filename.empty() && actionArgs.Nargs() > 1 && !actionArgs.Marked(1))
filename = actionArgs.GetStringNext();
DataFile* outfile = init.DFL().AddDataFile(filename, actionArgs);
if (outfile != 0) outfile->AddDataSet((DataSet*)grid_);
// Info
mprintf(" GRID:\n");
GridInfo( *grid_ );
if (outfile != 0) mprintf("\tGrid will be printed to file %s\n", outfile->DataFilename().full());
mprintf("\tGrid data set: '%s'\n", grid_->legend());
mprintf("\tMask expression: [%s]\n",mask_.MaskString());
if (pdbfile_ != 0)
mprintf("\tPseudo-PDB will be printed to %s\n", pdbfile_->Filename().full());
if (normalize_ == TO_FRAME)
mprintf("\tGrid will be normalized by number of frames.\n");
else if (normalize_ == TO_DENSITY)
mprintf("\tGrid will be normalized to a density of %g molecules/Ang^3.\n", density_);
// TODO: print extra options
return Action::OK;
}
inline int GridInit( int bHandle, const AbstractDistMatrix<scalarType>& A )
{
if( A.ColDist() != MC || A.RowDist() != MR )
LogicError
("Only (MC,MR) distributions are currently supported with ScaLAPACK");
const int context =
GridInit
( bHandle, A.Grid().Order()==COLUMN_MAJOR, A.ColStride(), A.RowStride() );
DEBUG_ONLY(
if( A.ColStride() != GridHeight(context) )
LogicError("Grid height did not match BLACS");
if( A.RowStride() != GridWidth(context) )
LogicError("Grid width did not match BLACS");
if( A.ColRank() != GridRow(context) )
LogicError("Grid row did not match BLACS");
if( A.RowRank() != GridCol(context) )
LogicError("Grid col did not match BLACS");
)
return context;
// Action_GridFreeEnergy::init()
Action::RetType Action_GridFreeEnergy::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Get output filename
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringNext(), actionArgs);
if (outfile == 0) {
mprinterr("Error: GridFreeEnergy: no output filename specified.\n");
return Action::ERR;
}
// Get grid options (<nx> <dx> <ny> <dy> <nz> <dz> [box|origin] [negative])
grid_ = GridInit( "GridFreeEnergy", actionArgs, init.DSL() );
if (grid_ == 0) return Action::ERR;
# ifdef MPI
if (ParallelGridInit(init.TrajComm(), grid_)) return Action::ERR;
# endif
//grid_.PrintXplor( filename_, "", "REMARKS Change in Free energy from bulk solvent with bin normalisation of " + integerToString(currentLargestVoxelOccupancyCount) );
// Get mask
std::string maskexpr = actionArgs.GetMaskNext();
if (maskexpr.empty()) {
mprinterr("Error: GridFreeEnergy: No mask specified.\n");
init.DSL().RemoveSet( grid_ );
return Action::ERR;
}
mask_.SetMaskString(maskexpr);
// Get extra args
tempInKevin_ = actionArgs.getKeyDouble("temp", 293.0);
outfile->AddDataSet( grid_ );
// Info
mprintf("Warning: DNAIONTRACKER is experimental code!\n");
mprintf(" GridFreeEnergy\n");
GridInfo( *grid_ );
mprintf("\tGrid will be printed to file %s\n",outfile->DataFilename().full());
mprintf("\tMask expression: [%s]\n",mask_.MaskString());
mprintf("\tTemp is : %f K\n",tempInKevin_);
// Allocate grid
//if (GridAllocate()) return 1;
return Action::OK;
}
void Init(char *langs, char *dialects, int anamorph)
{
Starting = 1;
GenOnAssert = 1;
LexEntryOff = 0;
SaveTime = 1;
/* SaveTime = 1: no spell correction hashing or phrase derivation,
* saves memory.
* SaveTime = 0: uses more time and memory.
*/
qallocInit();
DbgInit();
DbgSet(DBGALL, DBGBAD);
DbgSetStdoutLevel(DBGOK);
NoticePrint(stderr);
NoticePrint(Log);
EnvInit();
StringInit();
RandomInit();
GridInit();
ObjInit();
ObjListInit();
DbInit();
ContextInit();
TsInit();
TsRangeInit();
LexEntryInit();
Lex_WordForm2Init();
MorphInit(anamorph);
WordFormInit();
InferenceInit();
ReportInit();
CommentaryInit();
TranslateInit();
LearnInit();
StopAtInit();
TT_HTML_Init();
StdDiscourse = DiscourseCreate(langs, dialects);
DiscourseSetLang(StdDiscourse, F_ENGLISH);
Starting = 0;
}
