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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include <algorithm> |
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#include "io/ZConsWriter.hpp" |
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#include "utils/simError.h" |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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namespace oopse { |
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ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) { |
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//use master - slave mode, only master node writes to disk |
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namespace OpenMD { |
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ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) { |
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//use master - slave mode, only master node writes to disk |
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#ifdef IS_MPI |
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if(worldRank == 0){ |
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#endif |
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output_.open(filename.c_str()); |
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output_.open(filename.c_str()); |
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if(!output_){ |
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sprintf( painCave.errMsg, |
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"Could not open %s for z constrain output_ \n", filename.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if(!output_){ |
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sprintf( painCave.errMsg, |
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"Could not open %s for z constrain output_ \n", filename.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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output_ << "//time(fs)" << std::endl; |
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output_ << "//number of fixed z-constrain molecules" << std::endl; |
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output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl; |
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output_ << "//time(fs)" << std::endl; |
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output_ << "//number of fixed z-constrain molecules" << std::endl; |
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output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl; |
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#ifdef IS_MPI |
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} |
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#endif |
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} |
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} |
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ZConsWriter::~ZConsWriter() |
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{ |
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ZConsWriter::~ZConsWriter() |
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{ |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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if(worldRank == 0 ){ |
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#endif |
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output_.close(); |
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output_.close(); |
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#ifdef IS_MPI |
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} |
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} |
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#endif |
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} |
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} |
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void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){ |
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void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){ |
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#ifndef IS_MPI |
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output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; |
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output_ << fixedZmols.size() << std::endl; |
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std::list<ZconstraintMol>::const_iterator i; |
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for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) { |
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output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl; |
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output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl; |
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} |
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#else |
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int nproc; |
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MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
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int nproc = MPI::COMM_WORLD.Get_size(); |
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const int masterNode = 0; |
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int myNode = worldRank; |
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std::vector<int> tmpNFixedZmols(nproc, 0); |
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std::vector<int> nFixedZmolsInProc(nproc, 0); |
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tmpNFixedZmols[myNode] = fixedZmols.size(); |
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//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
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MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT, |
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MPI_SUM, MPI_COMM_WORLD); |
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//do MPI_ALLREDUCE to exchange the total number of atoms, |
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//rigidbodies and cutoff groups |
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MPI::COMM_WORLD.Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], |
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nproc, MPI::INT, MPI::SUM); |
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MPI_Status ierr; |
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MPI::Status ierr; |
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int zmolIndex; |
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double data[3]; |
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RealType data[3]; |
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if (masterNode == 0) { |
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std::vector<ZconsData> zconsData; |
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ZconsData tmpData; |
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for(int i =0 ; i < nproc; ++i) { |
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if (i == masterNode) { |
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std::list<ZconstraintMol>::const_iterator j; |
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for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { |
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tmpData.zmolIndex = j->mol->getGlobalIndex() ; |
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tmpData.zforce= j->fz; |
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tmpData.zpos = j->zpos; |
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tmpData.zconsPos = j->param.zTargetPos; |
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zconsData.push_back(tmpData); |
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} |
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std::vector<ZconsData> zconsData; |
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ZconsData tmpData; |
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for(int i =0 ; i < nproc; ++i) { |
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if (i == masterNode) { |
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std::list<ZconstraintMol>::const_iterator j; |
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for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { |
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tmpData.zmolIndex = j->mol->getGlobalIndex() ; |
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tmpData.zforce= j->fz; |
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tmpData.zpos = j->zpos; |
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tmpData.zconsPos = j->param.zTargetPos; |
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zconsData.push_back(tmpData); |
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} |
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} else { |
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for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) { |
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MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr); |
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MPI_Recv(data, 3, MPI_DOUBLE, i, 0, MPI_COMM_WORLD,&ierr); |
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tmpData.zmolIndex = zmolIndex; |
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tmpData.zforce= data[0]; |
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tmpData.zpos = data[1]; |
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tmpData.zconsPos = data[2]; |
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zconsData.push_back(tmpData); |
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} |
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} |
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} else { |
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for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) { |
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MPI::COMM_WORLD.Recv(&zmolIndex, 1, MPI::INT, i, 0, ierr); |
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MPI::COMM_WORLD.Recv(data, 3, MPI::REALTYPE, i, 0, ierr); |
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tmpData.zmolIndex = zmolIndex; |
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tmpData.zforce= data[0]; |
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tmpData.zpos = data[1]; |
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tmpData.zconsPos = data[2]; |
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zconsData.push_back(tmpData); |
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} |
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} |
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} |
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} |
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output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; |
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output_ << zconsData.size() << std::endl; |
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output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; |
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output_ << zconsData.size() << std::endl; |
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std::vector<ZconsData>::iterator l; |
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for (l = zconsData.begin(); l != zconsData.end(); ++l) { |
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output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl; |
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} |
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std::vector<ZconsData>::iterator l; |
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for (l = zconsData.begin(); l != zconsData.end(); ++l) { |
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output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl; |
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} |
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} else { |
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std::list<ZconstraintMol>::const_iterator j; |
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for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { |
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zmolIndex = j->mol->getGlobalIndex(); |
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data[0] = j->fz; |
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data[1] = j->zpos; |
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data[2] = j->param.zTargetPos; |
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MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
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MPI_Send(data, 3, MPI_DOUBLE, masterNode, 0, MPI_COMM_WORLD); |
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std::list<ZconstraintMol>::const_iterator j; |
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for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { |
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zmolIndex = j->mol->getGlobalIndex(); |
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data[0] = j->fz; |
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data[1] = j->zpos; |
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data[2] = j->param.zTargetPos; |
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MPI::COMM_WORLD.Send(&zmolIndex, 1, MPI::INT, masterNode, 0); |
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MPI::COMM_WORLD.Send(data, 3, MPI::REALTYPE, masterNode, 0); |
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} |
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} |
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} |
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#endif |
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} |
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} |
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} |
