/** Given an argument with format, DataSet_Name[,min,max,step,bins], check
* that DataSet_Name exists and is valid. Add the argument to
* dimensionArgs and the corresponding dataset to histdata.
*/
int Analysis_Hist::CheckDimension(std::string const& input, DataSetList& DSLin) {
ArgList arglist;
// Separate input string by ','
arglist.SetList(input, ",");
if (arglist.Nargs()<1) {
mprinterr("Error: No arguments found in histogram argument: %s\n",input.c_str());
return 1;
}
// First argument should specify dataset name
if (debug_>0) mprintf("\tHist: Setting up histogram dimension using dataset %s\n",
arglist.Command());
DataSet* dset = DSLin.GetDataSet( arglist[0] );
if (dset == 0) {
mprinterr("Error: Dataset %s not found.\n",arglist.Command());
return 1;
}
// For now only 1D scalar data sets can be histogrammed
if (dset->Group() != DataSet::SCALAR_1D) {
mprinterr("Error: Cannot histogram data set '%s'\n", dset->legend());
mprinterr("Error: Currently only 1D scalar data sets can be histogrammed.\n");
return 1;
}
// TODO parse remaining args here, create data structure.
dimensionArgs_.push_back( arglist );
histdata_.push_back( (DataSet_1D*)dset );
return 0;
}
// Exec_CrdAction::ProcessArgs()
Exec::RetType Exec_CrdAction::ProcessArgs(CpptrajState& State, ArgList& argIn) {
std::string setname = argIn.GetStringNext();
if (setname.empty()) {
mprinterr("Error: %s: Specify COORDS dataset name.\n", argIn.Command());
return CpptrajState::ERR;
}
DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
if (CRD == 0) {
mprinterr("Error: %s: No COORDS set with name %s found.\n", argIn.Command(), setname.c_str());
return CpptrajState::ERR;
}
mprintf("\tUsing set '%s'\n", CRD->legend());
// Start, stop, offset
TrajFrameCounter frameCount;
ArgList crdarg( argIn.GetStringKey("crdframes"), "," );
if (frameCount.CheckFrameArgs( CRD->Size(), crdarg )) return CpptrajState::ERR;
frameCount.PrintInfoLine(CRD->legend());
ArgList actionargs = argIn.RemainingArgs();
actionargs.MarkArg(0);
Cmd const& cmd = Command::SearchTokenType( DispatchObject::ACTION, actionargs.Command() );
if ( cmd.Empty() ) return CpptrajState::ERR;
Action* act = (Action*)cmd.Alloc();
if (act == 0) return CpptrajState::ERR;
CpptrajState::RetType err = DoCrdAction(State, actionargs, CRD, act, frameCount);
delete act;
return err;
}
// Exec_CrdAction::Execute()
Exec::RetType Exec_CrdAction::Execute(CpptrajState& State, ArgList& argIn) {
# ifdef MPI
Exec::RetType ret = CpptrajState::OK;
int err = 0;
// Create a communicator that just contains the master.
int ID = MPI_UNDEFINED;
if (Parallel::TrajComm().IsNull()) {
if (Parallel::World().Master())
ID = 0;
} else if (Parallel::TrajComm().Master())
ID = Parallel::World().Rank();
//rprintf("DEBUG: About to create new comm, ID= %i\n", ID);
trajComm_ = Parallel::World().Split( ID );
if (ID != MPI_UNDEFINED) {
mprintf("Warning: '%s' command does not yet use multiple MPI threads.\n", argIn.Command());
ret = ProcessArgs(State, argIn);
if (ret != CpptrajState::OK)
err = 1;
}
trajComm_.Reset();
if (Parallel::World().CheckError( err ))
ret = CpptrajState::ERR;
return ret;
# else
return (ProcessArgs(State, argIn));
# endif
}
Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionargs,
DataSet_Coords* CRD, Action* act,
TrajFrameCounter const& frameCount) const
{
Timer total_time;
total_time.Start();
# ifdef MPI
ActionInit state(State.DSL(), State.DFL(), trajComm_);
# else
ActionInit state(State.DSL(), State.DFL());
# endif
if ( act->Init( actionargs, state, State.Debug() ) != Action::OK )
return CpptrajState::ERR;
actionargs.CheckForMoreArgs();
// Set up frame and parm for COORDS.
ActionSetup originalSetup( CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size() );
Frame originalFrame = CRD->AllocateFrame();
ActionFrame frm( &originalFrame, 0 );
// Set up for this topology
Action::RetType setup_ret = act->Setup( originalSetup );
if ( setup_ret == Action::ERR || setup_ret == Action::SKIP )
return CpptrajState::ERR;
// Loop over all frames in COORDS.
ProgressBar progress( frameCount.TotalReadFrames() );
int set = 0;
for (int frame = frameCount.Start(); frame < frameCount.Stop();
frame += frameCount.Offset(), ++set)
{
progress.Update( set );
CRD->GetFrame( frame, originalFrame );
frm.SetTrajoutNum( set );
Action::RetType ret = act->DoAction( set, frm );
if (ret == Action::ERR) {
mprinterr("Error: crdaction: Frame %i, set %i\n", frame + 1, set + 1);
break;
}
// Check if frame was modified. If so, update COORDS.
if ( ret == Action::MODIFY_COORDS )
CRD->SetCRD( frame, frm.Frm() );
}
# ifdef MPI
act->SyncAction();
# endif
// Check if parm was modified. If so, update COORDS.
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
mprintf("Info: crdaction: Parm for %s was modified by action %s\n",
CRD->legend(), actionargs.Command());
CRD->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() );
}
act->Print();
State.MasterDataFileWrite();
total_time.Stop();
mprintf("TIME: Total action execution time: %.4f seconds.\n", total_time.Total());
return CpptrajState::OK;
}
// Exec_Analyze::Execute()
Exec::RetType Exec_Analyze::Execute(CpptrajState& State, ArgList& argIn) {
// Remove 'analyze'
ArgList arg = argIn;
arg.RemoveFirstArg();
if (arg.empty()) {
mprinterr("Error: No analysis command specified.\n");
return CpptrajState::ERR;
}
mprintf("Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated.\n");
if (arg.CommandIs("matrix"))
mprintf("Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.\n");
else
mprintf("Warning: To add an analysis command the the queue, only the command name needs\n"
"Warning: to be specified, e.g. '%s <args>'.\n", arg.Command());
Cmd const& cmd = Command::SearchTokenType(DispatchObject::ANALYSIS, arg.Command());
if (cmd.Empty()) {
mprinterr("Error: Analysis command '%s' not found.\n", arg.Command());
return CpptrajState::ERR;
}
return State.AddToAnalysisQueue( (Analysis*)cmd.Alloc(), arg );
}
/** Add specified analysis to the analysis list with given args and
* DataSetList.
*/
int AnalysisList::AddAnalysis(DispatchObject::DispatchAllocatorType Alloc, ArgList& argIn,
DataSetList* DSLin, DataFileList* DFLin)
{
Analysis* ana = (Analysis*)Alloc();
// Attempt to set up analysis
if (ana->Setup( argIn, DSLin, DFLin, debug_) != Analysis::OK) {
mprinterr("Error: Could not setup analysis [%s]\n", argIn.Command());
delete ana;
return 1;
}
analysisList_.push_back( ana );
analysisCmd_.push_back( argIn.ArgLine() );
analysisStatus_.push_back( SETUP );
if (argIn.CheckForMoreArgs()) return 1;
return 0;
}
Exec::RetType Exec_ParmStrip::Execute(CpptrajState& State, ArgList& argIn) {
Topology* parm = State.DSL().GetTopByIndex( argIn );
if (parm == 0) return CpptrajState::ERR;
// Check if this topology has already been used to set up an input
// trajectory, as this will break the traj read.
bool topology_in_use = false;
const char* fname = 0;
for (TrajinList::trajin_it tIn = State.InputTrajList().trajin_begin();
tIn != State.InputTrajList().trajin_end(); ++tIn)
if ( (*tIn)->Traj().Parm() == parm ) {
topology_in_use = true;
fname = (*tIn)->Traj().Filename().full();
break;
}
if (!topology_in_use) {
for (TrajinList::ensemble_it eIn = State.InputTrajList().ensemble_begin();
eIn != State.InputTrajList().ensemble_end(); ++eIn)
if ( (*eIn)->Traj().Parm() == parm ) {
topology_in_use = true;
fname = (*eIn)->Traj().Filename().full();
break;
}
}
if (topology_in_use) {
mprinterr("Error: Topology '%s' has already been used to set up trajectory '%s'.\n"
"Error: To strip this topology use the 'strip' action.\n",
parm->c_str(), fname);
return CpptrajState::ERR;
}
AtomMask tempMask( argIn.GetMaskNext() );
// Since want to keep atoms outside mask, invert selection
tempMask.InvertMaskExpression();
if (parm->SetupIntegerMask( tempMask )) return CpptrajState::ERR;
mprintf("\tStripping atoms in mask [%s] (%i) from %s\n",tempMask.MaskString(),
parm->Natom() - tempMask.Nselected(), parm->c_str());
Topology* tempParm = parm->modifyStateByMask(tempMask);
if (tempParm==0) {
mprinterr("Error: %s: Could not strip parm.\n", argIn.Command());
return CpptrajState::ERR;
} else {
// Replace parm with stripped version
*parm = *tempParm;
parm->Brief("Stripped parm:");
delete tempParm;
}
return CpptrajState::OK;
}
/** Add specified analysis to the analysis list with given args and
* DataSetList.
*/
int AnalysisList::AddAnalysis(Analysis* anaIn, ArgList& argIn, AnalysisSetup& setup)
{
if (anaIn == 0) {
mprinterr("Internal Error: AddAnalysis() called with null Analysis.\n");
return 1;
}
AnaHolder ana;
ana.ptr_ = anaIn;
ana.args_ = argIn;
// Attempt to set up analysis
if (ana.ptr_->Setup( argIn, setup, debug_) != Analysis::OK) {
mprinterr("Error: Could not setup analysis [%s]\n", argIn.Command());
delete ana.ptr_;
return 1;
}
ana.status_ = SETUP;
analysisList_.push_back( ana );
if (argIn.CheckForMoreArgs()) return 1;
return 0;
}
// ActionList::AddAction()
int ActionList::AddAction(DispatchObject::DispatchAllocatorType Alloc, ArgList& argIn,
TopologyList* PFL, DataSetList* DSL, DataFileList* DFL)
{
int err = 0;
if (actionsAreSilent_) SetWorldSilent( true );
Action* act = (Action*)Alloc();
// Attempt to initialize action
if ( act->Init( argIn, PFL, DSL, DFL, debug_ ) != Action::OK ) {
mprinterr("Error: Could not initialize action [%s]\n", argIn.Command());
delete act;
err = 1;
} else {
actionlist_.push_back( act );
actioncmd_.push_back( argIn.ArgLine() );
actionAlloc_.push_back( Alloc );
actionstatus_.push_back( INIT );
if (argIn.CheckForMoreArgs()) err = 1;
}
if (actionsAreSilent_) SetWorldSilent( false );
return err;
}
Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionargs,
DataSet_Coords* CRD, Action* act,
TrajFrameCounter const& frameCount) const
{
Timer total_time;
total_time.Start();
# ifdef MPI
ActionInit state(State.DSL(), State.DFL(), trajComm_);
# else
ActionInit state(State.DSL(), State.DFL());
# endif
if ( act->Init( actionargs, state, State.Debug() ) != Action::OK )
return CpptrajState::ERR;
actionargs.CheckForMoreArgs();
// Set up frame and parm for COORDS.
ActionSetup originalSetup( CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size() );
Frame originalFrame = CRD->AllocateFrame();
// Set up for this topology
Action::RetType setup_ret = act->Setup( originalSetup );
if ( setup_ret == Action::ERR || setup_ret == Action::SKIP )
return CpptrajState::ERR;
// If the topology was modified, we will need a new COORDS set.
DataSet_Coords* crdOut = 0;
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
// This will not work for a TRJ set.
switch ( CRD->Type() ) {
case DataSet::TRAJ : mprinterr("Error: Cannot modify TRAJ data sets.\n"); break;
case DataSet::COORDS : crdOut = (DataSet_Coords*)new DataSet_Coords_CRD(); break;
case DataSet::REF_FRAME : crdOut = (DataSet_Coords*)new DataSet_Coords_REF(); break;
default: crdOut = 0; // SANITY
}
if (crdOut == 0) return CpptrajState::ERR;
mprintf("Info: crdaction: COORDS set '%s' will be modified by action '%s'\n",
CRD->legend(), actionargs.Command());
if (frameCount.TotalReadFrames() != (int)CRD->Size())
mprintf("Info: crdaction: Previous size= %zu, new size is %i\n",
CRD->Size(), frameCount.TotalReadFrames());
// Set up set, copy original metadata
crdOut->SetMeta( CRD->Meta() );
if (crdOut->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() ))
return CpptrajState::ERR;
DataSet::SizeArray mfArray(1, frameCount.TotalReadFrames());
if (crdOut->Allocate( mfArray )) return CpptrajState::ERR;
}
// Loop over all frames in COORDS.
ProgressBar* progress = 0;
if (State.ShowProgress())
progress = new ProgressBar( frameCount.TotalReadFrames() );
int set = 0;
for (int frame = frameCount.Start(); frame < frameCount.Stop();
frame += frameCount.Offset(), ++set)
{
// Since Frame can be modified by actions, save original and use currentFrame
ActionFrame frm( &originalFrame, set );
if (progress != 0) progress->Update( set );
CRD->GetFrame( frame, originalFrame );
Action::RetType ret = act->DoAction( set, frm );
if (ret == Action::ERR) {
mprinterr("Error: crdaction: Frame %i, set %i\n", frame + 1, set + 1);
break;
}
// Check if frame was modified. If so, update COORDS.
if ( ret == Action::MODIFY_COORDS ) {
if (crdOut != 0)
crdOut->AddFrame( frm.Frm() );
else
CRD->SetCRD( frame, frm.Frm() );
}
}
if (progress != 0) delete progress;
# ifdef MPI
act->SyncAction();
# endif
// If topology was modified, replace old set with new.
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
mprintf("Info: crdaction: Topology for '%s' was modified by action '%s'\n",
CRD->legend(), actionargs.Command());
State.DSL().RemoveSet( CRD );
State.DSL().AddSet( crdOut );
}
act->Print();
State.MasterDataFileWrite();
total_time.Stop();
mprintf("TIME: Total action execution time: %.4f seconds.\n", total_time.Total());
return CpptrajState::OK;
}
