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;
}
/** 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;
}
/** 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;
}
/** Process command relating to data files. */
int DataFileList::ProcessDataFileArgs(ArgList& dataArg) {
// Next string is DataFile name that command will be passed to.
std::string df_cmd = dataArg.GetStringNext();
if (df_cmd.empty()) {
mprintf("Warning: datafile: No filename given.\n");
return 0;
}
// Check for deprecated commands
if (df_cmd == "create" || df_cmd == "precision")
mprintf("Warning: 'datafile %s' is deprecated; use %s instead.\n",
df_cmd.c_str(), df_cmd.c_str());
//mprintf(" [%s]\n",(*dataArg).ArgLine());
DataFile* df = GetDataFile( df_cmd.c_str() );
if (df == 0) {
mprinterr("Error: datafile: File %s not found.\n", df_cmd.c_str());
return 1;
}
// Process command
int err = df->ProcessArgs( dataArg );
if (err != 0 || dataArg.CheckForMoreArgs()) return 1;
return 0;
}
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;
}
