// DataSetList::AddSet()
int DataSetList::AddSet( DataSet* dsIn ) {
if (dsIn == 0 ) return 1;
DataSet* ds = CheckForSet( dsIn->Meta() );
if (ds != 0) {
mprintf("Warning: DataSet '%s' already present.\n", ds->Meta().PrintName().c_str());
return 1;
}
Push_Back( dsIn );
return 0;
}
/** 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?
// 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_ );
// Check if DataSet with same attributes already present.
DataSet* DS = CheckForSet(meta);
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;
}
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;
}
Push_Back(DS);
//fprintf(stderr,"ADDED dataset %s\n",dsetName);
return DS;
}
// Exec_DataSetCmd::VectorCoord()
Exec::RetType Exec_DataSetCmd::VectorCoord(CpptrajState& State, ArgList& argIn) {
// Keywords
std::string name = argIn.GetStringKey("name");
int idx;
if (argIn.hasKey("X"))
idx = 0;
else if (argIn.hasKey("Y"))
idx = 1;
else if (argIn.hasKey("Z"))
idx = 2;
else {
mprinterr("Error: 'vectorcoord' requires specifying X, Y, or Z.\n");
return CpptrajState::ERR;
}
// Data set
DataSet* ds1 = State.DSL().GetDataSet( argIn.GetStringNext() );
if (ds1 == 0) return CpptrajState::ERR;
if (ds1->Type() != DataSet::VECTOR) {
mprinterr("Error: 'vectorcoord' only works with vector data sets.\n");
return CpptrajState::ERR;
}
if (ds1->Size() < 1) {
mprinterr("Error: '%s' is empty.\n", ds1->legend());
return CpptrajState::ERR;
}
// Create output set.
static const char* XYZ[3] = { "X", "Y", "Z" };
DataSet* out = State.DSL().AddSet( DataSet::DOUBLE, name, "COORD");
if (out == 0) return CpptrajState::ERR;
// Extract data
mprintf("\tExtracting %s coordinate from vector %s to %s\n",
XYZ[idx], ds1->legend(), out->Meta().PrintName().c_str());
DataSet_Vector const& vec = static_cast<DataSet_Vector const&>( *ds1 );
for (unsigned int n = 0; n != vec.Size(); n++) {
double d = vec.VXYZ(n)[idx];
out->Add( n, &d );
}
return CpptrajState::OK;
}
// Exec_SortEnsembleData::Sort_pH_Data()
int Exec_SortEnsembleData::Sort_pH_Data(DataSetList const& setsToSort, DataSetList& OutputSets,
unsigned int maxFrames)
const
{
// Cast sets back to DataSet_PHREMD
typedef std::vector<DataSet_PHREMD*> Parray;
Parray PHsets;
for (DataSetList::const_iterator ds = setsToSort.begin(); ds != setsToSort.end(); ++ds)
PHsets.push_back( (DataSet_PHREMD*)*ds );
// Gather initial pH data values, ensure no duplicates
typedef std::vector<double> Darray;
Darray pHvalues;
# ifdef MPI
pHvalues.resize( Parallel::Ensemble_Size() );
Darray phtmp;
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
phtmp.push_back( (*ds)->Initial_pH() );
if (comm_.AllGather(&phtmp[0], phtmp.size(), MPI_DOUBLE, &pHvalues[0])) {
rprinterr("Error: Gathering pH values.\n");
return 1;
}
# else
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
pHvalues.push_back( (*ds)->Initial_pH() );
# endif
ReplicaInfo::Map<double> pH_map;
if (pH_map.CreateMap( pHvalues )) {
rprinterr("Error: Duplicate pH value detected (%.2f) in ensemble.\n", pH_map.Duplicate());
return 1;
}
Darray sortedPH;
mprintf("\tInitial pH values:");
for (ReplicaInfo::Map<double>::const_iterator ph = pH_map.begin(); ph != pH_map.end(); ++ph)
{
mprintf(" %6.2f", ph->first);
sortedPH.push_back( ph->first );
}
mprintf("\n");
// Create sets to hold sorted pH values. Create a set for each pH value
// and each residue. Final output sets will be PH0R0, PH0R1, PH1R0, ...
// TODO check that residue info all the same
DataSet_PHREMD::Rarray const& Residues = PHsets[0]->Residues();
int defaultState = 0;
# ifdef MPI
if ( PHsets[0]->Type() == DataSet::PH_IMPL)
defaultState = -1;
# endif
if (debug_ > 0)
rprintf("DEBUG: Sorting %u frames for %zu sets, %zu pH values.\n",
maxFrames, PHsets.size(), sortedPH.size());
for (unsigned int idx = 0; idx != sortedPH.size(); idx++) {
OutputSets.SetEnsembleNum( idx );
for (unsigned int res = 0; res != Residues.size(); ++res) {
MetaData md(PHsets[0]->Meta().Name(), Residues[res].Name().Truncated(), Residues[res].Num());
DataSet_pH* out = (DataSet_pH*)OutputSets.AddSet( DataSet::PH, md );
if (out==0) return 1;
//out->SetLegend( "pH " + doubleToString( sortedPH[idx] ) );
out->Set_Solvent_pH( sortedPH[idx] );
out->SetResidueInfo( Residues[res] );
out->SetTimeValues(PHsets[0]->Time());
out->Resize( maxFrames, defaultState );
}
}
// ---------------------------------------------
if ( PHsets[0]->Type() == DataSet::PH_EXPL) {
// Loop over unsorted sets
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
{
DataSet_PHREMD_Explicit* in = (DataSet_PHREMD_Explicit*)*ds;
unsigned int phidx = 0;
for (unsigned int n = 0; n < maxFrames; n++)
{
float phval = in->pH_Values()[n];
int setidx = pH_map.FindIndex( phval ) * Residues.size();
//rprintf("DEBUG: %6u Set %10s pH= %6.2f going to %2i\n", n+1, in->legend(), phval, idx);
//mflush();
for (unsigned int res = 0; res < in->Residues().size(); res++, setidx++, phidx++)
{
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx];
//if (res == 0 && idx == 0) {
// rprintf("DEBUG: Frame %3u res %2u State %2i pH %6.2f\n",
// n, res, in->Res(res).State(n), phval);
// mflush();
//}
out->SetState(n, in->ResStates()[phidx], in->RecordType(n));
}
}
} // END loop over unsorted sets
# ifdef MPI
// Now we need to reduce down each set onto the thread where it belongs.
if (Parallel::World().Size() > 1) {
for (int idx = 0; idx != (int)OutputSets.size(); idx++) {
DataSet_pH* out = (DataSet_pH*)OutputSets[idx];
int ensembleRank = Parallel::MemberEnsCommRank( out->Meta().EnsembleNum() );
//rprintf("DEBUG: Reduce set %s to rank %i\n", out->legend(), ensembleRank);
out->Reduce( comm_, ensembleRank );
}
// Remove sets that do not belong on this rank
for (int idx = (int)OutputSets.size() - 1; idx > -1; idx--) {
DataSet* out = OutputSets[idx];
int ensembleRank = Parallel::MemberEnsCommRank( out->Meta().EnsembleNum() );
if (ensembleRank != comm_.Rank()) {
//rprintf("DEBUG: Remove set %s (%i) from rank %i\n", out->legend(),
// idx, comm_.Rank());
OutputSets.RemoveSet( out );
}
}
}
# endif
// ---------------------------------------------
} else if ( PHsets[0]->Type() == DataSet::PH_IMPL) {
# ifdef MPI
typedef std::vector<int> Iarray;
typedef std::vector<Iarray> Iarray2;
typedef std::vector<bool> Barray;
// True if I have this pH value
Barray isMyPh( sortedPH.size(), false );
// Which rank in ensemble has which pH
Iarray pHrank( sortedPH.size(), 0 );
for (int phidx = 0; phidx != (int)sortedPH.size(); phidx++)
{
int ensembleRank = Parallel::MemberEnsCommRank( phidx );
pHrank[phidx] = ensembleRank;
isMyPh[phidx] = (ensembleRank == comm_.Rank());
}
// DEBUG
for (unsigned int idx = 0; idx != pHrank.size(); idx++)
mprintf("\tpH %6.2f on rank %i\n", sortedPH[idx], pHrank[idx]);
// Hold frame-residue-state for each pH not on this rank.
Iarray2 FrmResState( sortedPH.size() );
// Loop over unsorted sets
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
{
DataSet_PHREMD_Implicit* in = (DataSet_PHREMD_Implicit*)*ds;
// Loop over frames
for (unsigned int n = 0; n < maxFrames; n++)
{
DataSet_PHREMD_Implicit::Record const& Rec = in->Records()[n];
float phval = Rec.pH();
int phidx = pH_map.FindIndex( phval );
if (isMyPh[phidx]) {
// This pH belongs to me. Set value.
int setidx = phidx * Residues.size();
if (Rec.RecType() == Cph::FULL_RECORD) {
// Info for all residues
for (unsigned int res = 0; res < in->Residues().size(); res++, setidx++)
((DataSet_pH*)OutputSets[setidx])->SetState(n, Rec.ResStates()[res], Rec.RecType());
} else if (Rec.RecType() > -1) {
// Info for single residue, record type for all residues
//rprintf("\tSetting my pH %6.2f frame %8i state %2i idx %6i res %6i '%s'\n", sortedPH[phidx], n, Rec.ResStates()[0], setidx, Rec.RecType(), OutputSets[setidx+Rec.RecType()]->legend());
for (int res = 0; res < (int)in->Residues().size(); res++, setidx++)
if (res == Rec.RecType())
((DataSet_pH*)OutputSets[setidx])->SetState(n, Rec.ResStates()[0], Rec.RecType());
else
((DataSet_pH*)OutputSets[setidx])->SetRecType(n, Rec.RecType());
}
} else {
// This pH belongs to another rank. Save it.
if (Rec.RecType() > -1) {
// Info for a single residue present
FrmResState[phidx].push_back( n );
FrmResState[phidx].push_back( Rec.RecType() );
FrmResState[phidx].push_back( Rec.ResStates()[0] );
} else {
// Info for all residues present
FrmResState[phidx].push_back( n );
FrmResState[phidx].push_back( Rec.RecType() );
for (unsigned int res = 0; res < in->Residues().size(); res++)
FrmResState[phidx].push_back( Rec.ResStates()[res] );
}
}
} // END loop over frames
} // END loop over sets
// DEBUG
/*
comm_.Barrier();
for (int rank = 0; rank < comm_.Size(); rank++)
{
if (rank == comm_.Rank())
{
for (unsigned int phidx = 0; phidx != sortedPH.size(); phidx++) {
rprintf("DEBUG: pH %6.2f: %8s %6s %2s\n", sortedPH[phidx], "Frm", "Res", "St");
Iarray const& FRS = FrmResState[phidx];
unsigned int idx = 0;
while (idx < FRS.size()) {
int rec = FRS[idx+1];
if (rec > -1) {
rprintf(" %8i %6i %2i\n", FRS[idx], rec, FRS[idx+2]);
idx += 3;
} else {
rprintf(" %8i %6i All Residues\n", FRS[idx], rec);
idx += (2 + Residues.size());
}
}
}
}
comm_.Barrier();
}
*/
// Communicate states to other ranks
typedef std::vector<unsigned int> Uarray;
Uarray sizeOnRank( comm_.Size() );
for (unsigned int phidx = 0; phidx != sortedPH.size(); phidx++)
{
// Each rank says how many frames of this pH they have collected and
// send to rank the pH belongs to.
unsigned int nph = FrmResState[phidx].size();
comm_.Gather(&nph, 1, MPI_UNSIGNED, &sizeOnRank[0], pHrank[phidx]);
if (pHrank[phidx] == comm_.Rank())
{
// This pH belongs to me. I should have no frames at this pH.
if (sizeOnRank[comm_.Rank()] > 0) {
rprinterr("Internal Error: Rank has frames to communicate at its pH\n");
Parallel::Abort(1);
}
unsigned int totalSize = 0;
for (unsigned int idx = 0; idx != sizeOnRank.size(); idx++) {
totalSize += sizeOnRank[idx];
//rprintf("DEBUG: Rank %4u has %8u frames of pH %6.2f\n",
// idx, sizeOnRank[idx], sortedPH[phidx]);
}
//rprintf("DEBUG: Total incoming size: %u\n", totalSize);
FrmResState[phidx].resize( totalSize );
// Receive state info for this pH from other ranks
int* frsArray = &(FrmResState[phidx][0]);
for (int rank = 0; rank != comm_.Size(); rank++) {
if (rank != comm_.Rank()) {
comm_.Recv(frsArray, sizeOnRank[rank], MPI_INT, rank, 1600+rank);
frsArray += sizeOnRank[rank];
}
}
} else {
// This pH belongs to another rank. Send my info there.
int* frsArray = &(FrmResState[phidx][0]);
comm_.Send(frsArray, nph, MPI_INT, pHrank[phidx], 1600+comm_.Rank());
}
comm_.Barrier();
}
// Fill in state info
std::vector<DataSet*> ToRemove;
for (unsigned int phidx = 0; phidx != sortedPH.size(); phidx++)
{
int setidx = phidx * Residues.size();
if (pHrank[phidx] == comm_.Rank())
{
Iarray const& FRS = FrmResState[phidx];
// This pH belongs to me. Fill in the information received from
// other ranks.
unsigned int idx = 0;
while (idx < FRS.size()) {
int rec = FRS[idx+1];
if (rec > -1) {
// Info for single residue, record type for all residues
//rprintf("\tSetting pH %6.2f frame %8i state %2i idx %6i res %6i '%s'\n", sortedPH[phidx], FRS[idx], FRS[idx+2], setidx, rec, OutputSets[setidx+rec]->legend());
for (int res = 0; res != (int)Residues.size(); res++) {
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx + res];
if (rec == res)
out->SetState( FRS[idx], FRS[idx+2], rec );
else
out->SetRecType( FRS[idx], rec );
}
idx += 3;
} else {
//rprintf(" %8i %6i All Residues\n", FRS[idx], rec);
int frm = FRS[idx];
idx += 2;
for (unsigned int res = 0; res != Residues.size(); res++, idx++) {
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx + res];
out->SetState( frm, FRS[idx], rec );
}
}
}
// Fill in any remaining data. FIXME safe to assume first frame is set?
for (unsigned int res = 0; res != Residues.size(); res++) {
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx + res];
for (unsigned int n = 1; n < maxFrames; n++)
if (out->State(n) == -1)
out->SetState(n, out->State(n-1), out->RecordType(n));
}
} else {
// This pH does not belong to me. Mark associated data sets to be removed.
for (unsigned int res = 0; res != Residues.size(); res++)
ToRemove.push_back( OutputSets[setidx + res] );
}
}
// Remove data sets that do not belong to me.
for (std::vector<DataSet*>::reverse_iterator it = ToRemove.rbegin();
it != ToRemove.rend(); ++it)
{
//rprintf("DEBUG: '%s' does not belong to me.\n", (*it)->legend());
OutputSets.RemoveSet( *it );
}
# else /* if not MPI */
// Loop over frames
for (unsigned int n = 0; n < maxFrames; n++)
{
// Loop over unsorted sets
for (Parray::const_iterator ds = PHsets.begin(); ds != PHsets.end(); ++ds)
{
DataSet_PHREMD_Implicit* in = (DataSet_PHREMD_Implicit*)*ds;
DataSet_PHREMD_Implicit::Record const& Rec = in->Records()[n];
float phval = Rec.pH();
int setidx = pH_map.FindIndex( phval ) * Residues.size();
if (Rec.RecType() == Cph::FULL_RECORD) {
for (unsigned int res = 0; res < in->Residues().size(); res++, setidx++)
{
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx];
//if (res == 0 && idx == 0) {
// rprintf("DEBUG: Frame %3u res %2u State %2i pH %6.2f\n",
// n, res, in->Res(res).State(n), phval);
// mflush();
//}
out->SetState(n, Rec.ResStates()[res], Rec.RecType());
}
} else {
for (int res = 0; res < (int)in->Residues().size(); res++, setidx++)
{
DataSet_pH* out = (DataSet_pH*)OutputSets[setidx];
if (res == Rec.RecType())
out->SetState(n, Rec.ResStates()[0], Rec.RecType());
else
// State for this residue not recorded - use previous state.
// Should be fine since first state always has all residues.
out->SetState(n, out->State(n-1), Rec.RecType());
}
}
} // END loop over unsorted sets
} // END loop over frames
# endif /* MPI */
// ---------------------------------------------
} else {
return 1; // Sanity check
}
return 0;
}
// Exec_DataSetCmd::ModifyPoints()
Exec::RetType Exec_DataSetCmd::ModifyPoints(CpptrajState& State, ArgList& argIn, bool drop) {
const char* mode;
if (drop)
mode = "Drop";
else
mode = "Kee";
// Keywords
std::string name = argIn.GetStringKey("name");
int start = argIn.getKeyInt("start", 0) - 1;
int stop = argIn.getKeyInt("stop", -1);
int offset = argIn.getKeyInt("offset", -1);
Range points;
if (start < 0 && stop < 0 && offset < 0) {
std::string rangearg = argIn.GetStringKey("range");
if (rangearg.empty()) {
mprinterr("Error: Must specify range or start/stop/offset.\n");
return CpptrajState::ERR;
}
points.SetRange( rangearg );
if (points.Empty()) {
mprinterr("Error: Range '%s' is empty.\n", rangearg.c_str());
return CpptrajState::ERR;
}
mprintf("\t%sping points in range %s\n", mode, rangearg.c_str());
// User args start from 1
points.ShiftBy(-1);
}
// Get data set to drop/keep points from
// Loop over all DataSet arguments
std::string ds_arg = argIn.GetStringNext();
while (!ds_arg.empty()) {
DataSetList dsl = State.DSL().GetMultipleSets( ds_arg );
for (DataSetList::const_iterator it = dsl.begin(); it != dsl.end(); ++it)
{
DataSet* DS = *it;
if (DS->Size() < 1) {
mprinterr("Error: Set '%s' is empty.\n", DS->legend());
return CpptrajState::ERR;
}
// Restrict to 1D sets for now TODO more types
if (DS->Group() != DataSet::SCALAR_1D) {
mprinterr("Error: Currently only works for 1D scalar data sets.\n");
return CpptrajState::ERR;
}
DataSet_1D* ds1 = (DataSet_1D*)DS;
// Output data set
DataSet* out = 0;
if (name.empty()) {
// Modifying this set. Create new temporary set.
out = State.DSL().Allocate( ds1->Type() );
if (out == 0) return CpptrajState::ERR;
*out = *ds1;
mprintf("\tOverwriting set '%s'\n", ds1->legend());
} else {
// Write to new set
MetaData md = ds1->Meta();
md.SetName( name );
out = State.DSL().AddSet(ds1->Type(), md);
if (out == 0) return CpptrajState::ERR;
mprintf("\tNew set is '%s'\n", out->Meta().PrintName().c_str());
}
out->Allocate(DataSet::SizeArray(1, ds1->Size()));
if (points.Empty()) {
// Drop by start/stop/offset. Set defaults if needed
if (start < 0) start = 0;
if (stop < 0) stop = ds1->Size();
if (offset < 0) offset = 1;
mprintf("\t%sping points from %i to %i, step %i\n", mode, start+1, stop, offset);
for (int idx = start; idx < stop; idx += offset)
points.AddToRange( idx );
} // TODO check that range values are valid?
if (State.Debug() > 0) mprintf("DEBUG: Keeping points:");
Range::const_iterator pt = points.begin();
int idx = 0;
int odx = 0;
if (drop) {
// Drop points
for (; idx < (int)ds1->Size(); idx++) {
if (pt == points.end()) break;
if (*pt != idx) {
if (State.Debug() > 0) mprintf(" %i", idx + 1);
KeepPoint(ds1, out, idx, odx);
} else
++pt;
}
// Keep all remaining points
for (; idx < (int)ds1->Size(); idx++) {
if (State.Debug() > 0) mprintf(" %i", idx + 1);
KeepPoint(ds1, out, idx, odx);
}
} else {
// Keep points
for (; pt != points.end(); pt++) {
if (*pt >= (int)ds1->Size()) break;
if (State.Debug() > 0) mprintf(" %i", *pt + 1);
KeepPoint(ds1, out, *pt, odx);
}
}
if (State.Debug() > 0) mprintf("\n");
if (name.empty()) {
// Replace old set with new set
State.DSL().RemoveSet( ds1 );
State.DSL().AddSet( out );
}
} // END loop over sets
ds_arg = argIn.GetStringNext();
} // END loop over set args
return CpptrajState::OK;
}
