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/* |
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* Copyright (c) 2009 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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* non-exclusive, royalty free, license to use, modify and |
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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. 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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, 234107 (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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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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#include <string> |
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#include <sstream> |
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#include <iostream> |
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|
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#include "io/RestWriter.hpp" |
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#include "utils/simError.h" |
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#include "brains/SnapshotManager.hpp" |
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|
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namespace OpenMD { |
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RestWriter::RestWriter(SimInfo* info, const std::string& filename, |
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std::vector<Restraint*> restraints ) : |
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info_(info){ |
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createRestFile_ = true; |
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|
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#ifdef IS_MPI |
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if(worldRank == 0){ |
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#endif |
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|
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output_ = new std::ofstream(filename.c_str()); |
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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 restraint output.\n", |
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filename.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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|
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|
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#ifdef IS_MPI |
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MPI_Status* istatus; |
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#endif |
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|
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#ifndef IS_MPI |
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|
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(*output_) << "#time\t"; |
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|
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std::vector<Restraint*>::const_iterator resti; |
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|
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for(resti=restraints.begin(); resti != restraints.end(); ++resti){ |
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if ((*resti)->getPrintRestraint()) { |
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|
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std::string myName = (*resti)->getRestraintName(); |
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int myType = (*resti)->getRestraintType(); |
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|
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(*output_) << myName << ":"; |
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|
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if (myType & Restraint::rtDisplacement) |
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(*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtTwist) |
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(*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtSwingX) |
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(*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtSwingY) |
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(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)"; |
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} |
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} |
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|
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(*output_) << "\n"; |
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(*output_).flush(); |
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|
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#else |
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|
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std::string buffer; |
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|
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std::vector<Restraint*>::const_iterator resti; |
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|
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for(resti=restraints.begin(); resti != restraints.end(); ++resti){ |
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if ((*resti)->getPrintRestraint()) { |
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|
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std::string myName = (*resti)->getRestraintName(); |
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int myType = (*resti)->getRestraintType(); |
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|
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buffer += (myName + ":"); |
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|
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if (myType & Restraint::rtDisplacement) |
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buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtTwist) |
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buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtSwingX) |
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buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtSwingY) |
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buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)"; |
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|
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buffer += "\n"; |
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} |
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} |
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|
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const int masterNode = 0; |
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|
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if (worldRank == masterNode) { |
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(*output_) << "#time\t"; |
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(*output_) << buffer; |
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|
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int nProc; |
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MPI_Comm_size( MPI_COMM_WORLD, &nProc); |
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|
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for (int i = 1; i < nProc; ++i) { |
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|
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// receive the length of the string buffer that was |
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// prepared by processor i |
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|
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int recvLength; |
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MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus); |
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char* recvBuffer = new char[recvLength]; |
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if (recvBuffer == NULL) { |
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} else { |
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MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, |
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istatus); |
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(*output_) << recvBuffer; |
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delete [] recvBuffer; |
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} |
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} |
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(*output_).flush(); |
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} else { |
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int sendBufferLength = buffer.size() + 1; |
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MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
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MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, |
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masterNode, 0, MPI_COMM_WORLD); |
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} |
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|
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#endif // is_mpi |
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|
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} |
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|
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void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) { |
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|
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#ifdef IS_MPI |
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MPI_Status* istatus; |
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#endif |
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|
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#ifndef IS_MPI |
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(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime(); |
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|
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// output some information about the molecules |
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std::vector<std::map<int, Restraint::RealPair> >::const_iterator i; |
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std::map<int, Restraint::RealPair>::const_iterator j; |
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|
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for( i = restInfo.begin(); i != restInfo.end(); ++i){ |
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for(j = (*i).begin(); j != (*i).end(); ++j){ |
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(*output_) << "\t" << (j->second).first << "\t" << (j->second).second; |
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} |
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(*output_) << std::endl; |
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} |
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(*output_).flush(); |
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#else |
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std::string buffer, first, second; |
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std::stringstream ss; |
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|
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std::vector<std::map<int, Restraint::RealPair> >::const_iterator i; |
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std::map<int, Restraint::RealPair>::const_iterator j; |
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|
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for( i = restInfo.begin(); i != restInfo.end(); ++i){ |
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for(j = (*i).begin(); j != (*i).end(); ++j){ |
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ss.clear(); |
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ss << (j->second).first; |
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ss >> first; |
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ss.clear(); |
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ss << (j->second).second; |
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ss >> second; |
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buffer += ("\t" + first + "\t" + second); |
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} |
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buffer += "\n"; |
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} |
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|
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const int masterNode = 0; |
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|
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if (worldRank == masterNode) { |
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(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime(); |
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(*output_) << buffer; |
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|
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int nProc; |
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MPI_Comm_size( MPI_COMM_WORLD, &nProc); |
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for (int i = 1; i < nProc; ++i) { |
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|
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// receive the length of the string buffer that was |
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// prepared by processor i |
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|
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int recvLength; |
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MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus); |
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char* recvBuffer = new char[recvLength]; |
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if (recvBuffer == NULL) { |
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} else { |
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MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, |
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istatus); |
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(*output_) << recvBuffer; |
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|
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delete [] recvBuffer; |
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} |
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} |
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(*output_).flush(); |
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} else { |
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int sendBufferLength = buffer.size() + 1; |
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MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
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MPI_Send((void *)buffer.c_str(), sendBufferLength, |
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MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
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} |
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#endif // is_mpi |
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} |
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|
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|
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RestWriter::~RestWriter() { |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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if (createRestFile_){ |
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writeClosing(*output_); |
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delete output_; |
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} |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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|
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void RestWriter::writeClosing(std::ostream& os) { |
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os.flush(); |
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} |
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|
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}// end namespace OpenMD |
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|
