Ejemplo n.º 1
0
// Analysis_TI::Calc_Increment()
int Analysis_TI::Calc_Increment() {
  // Determine max points if not given.
  int maxpts = avg_max_;
  if (maxpts == -1) {
    for (unsigned int idx = 0; idx != input_dsets_.size(); idx++) {
      DataSet_1D const& ds = static_cast<DataSet_1D const&>( *(input_dsets_[idx]) );
      if (maxpts == -1)
        maxpts = (int)ds.Size();
      else if (maxpts != (int)ds.Size()) {
        mprintf("Warning: # points in '%s' (%zu) is different than %i.\n",
                ds.legend(), ds.Size(), maxpts);
        maxpts = std::min( maxpts, (int)ds.Size() );
        mprintf("Warning:   Will only use %i points.\n", maxpts);
      }
    }
  }
  if (maxpts < 1) {
    mprinterr("Error: Max points to use is < 1.\n");
    return 1;
  }
  if (avg_skip_ >= maxpts) {
    mprinterr("Error: 'avgskip' (%i) > max (%i).\n", avg_skip_, maxpts);
    return 1;
  }
  // sum: Hold the results of integration for each curve (increment)
  Darray sum;
  // points: Hold point values at which each avg is being calculated
  Iarray points;
  // Loop over input data sets. 
  for (unsigned int idx = 0; idx != input_dsets_.size(); idx++) {
    DataSet_1D const& ds = static_cast<DataSet_1D const&>( *(input_dsets_[idx]) );
    if (CheckSet(ds)) return 1; 
    // Calculate averages for each increment
    Darray avg;
    Iarray increments;
    int count = 0;
    int endpt = maxpts -1;
    double currentSum = 0.0;
    if (debug_ > 0) mprintf("DEBUG: Lambda %g\n", xval_[idx]);
    for (int pt = avg_skip_; pt != maxpts; pt++)
    {
      currentSum += ds.Dval(pt);
      count++;
      if (count == avg_increment_ || pt == endpt) {
        avg.push_back( currentSum / ((double)(pt - avg_skip_ + 1)) );
        increments.push_back(pt+1);
        if (debug_ > 0)
          mprintf("DEBUG:\t\tAvg from %i to %i: %g\n", avg_skip_+1, pt+1, avg.back());
        count = 0;
      }
    }
    if (sum.empty()) {
      sum.resize(avg.size());
      points = increments;
    } else if (sum.size() != avg.size()) {
      mprinterr("Error: Different # of increments for set '%s'; got %zu, expected %zu.\n",
                ds.legend(), avg.size(), sum.size());
      return 1;
    }
    // Create increment curve data sets
    if (curve_.empty()) {
      MetaData md(dAout_->Meta().Name(), "TIcurve");
      for (unsigned int j = 0; j != avg.size(); j++) {
        md.SetIdx( increments[j] );
        DataSet* ds = masterDSL_->AddSet(DataSet::XYMESH, md);
        if (ds == 0) return Analysis::ERR;
        ds->ModifyDim(Dimension::X).SetLabel("Lambda");
        ds->SetLegend( md.Name() + "_Skip" + integerToString(increments[j]) );
        if (curveout_ != 0) curveout_->AddDataSet( ds );
        curve_.push_back( ds );
      }
    }
    for (unsigned int j = 0; j != avg.size(); j++) {
      DataSet_Mesh& CR = static_cast<DataSet_Mesh&>( *(curve_[j]) );
      CR.AddXY(xval_[idx], avg[j]);
      if (mode_ == GAUSSIAN_QUAD)
        sum[j] += (wgt_[idx] * avg[j]);
    }
  } // END loop over data sets
  if (mode_ == TRAPEZOID) Integrate_Trapezoid(sum);
  // Store final integration values
  DataSet_Mesh& DA = static_cast<DataSet_Mesh&>( *dAout_ );
  DA.ModifyDim(Dimension::X).SetLabel("Point");
  for (unsigned int j = 0; j != points.size(); j++)
    DA.AddXY(points[j], sum[j]);

  return 0;
}
Ejemplo n.º 2
0
//  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;
}