--- trunk/src/io/ZConsWriter.cpp 2005/01/12 22:41:40 246 +++ trunk/src/io/ZConsWriter.cpp 2009/11/25 20:02:06 1390 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ #include @@ -46,54 +46,56 @@ #include "io/ZConsWriter.hpp" #include "utils/simError.h" +#ifdef IS_MPI +#include +#endif - -namespace oopse { -ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) { - //use master - slave mode, only master node writes to disk +namespace OpenMD { + ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) { + //use master - slave mode, only master node writes to disk #ifdef IS_MPI if(worldRank == 0){ #endif - output_.open(filename.c_str()); + output_.open(filename.c_str()); - if(!output_){ - sprintf( painCave.errMsg, - "Could not open %s for z constrain output_ \n", filename.c_str()); - painCave.isFatal = 1; - simError(); - } + if(!output_){ + sprintf( painCave.errMsg, + "Could not open %s for z constrain output_ \n", filename.c_str()); + painCave.isFatal = 1; + simError(); + } - output_ << "//time(fs)" << std::endl; - output_ << "//number of fixed z-constrain molecules" << std::endl; - output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl; + output_ << "//time(fs)" << std::endl; + output_ << "//number of fixed z-constrain molecules" << std::endl; + output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl; #ifdef IS_MPI } #endif -} + } -ZConsWriter::~ZConsWriter() -{ + ZConsWriter::~ZConsWriter() + { #ifdef IS_MPI - if(worldRank == 0 ){ + if(worldRank == 0 ){ #endif - output_.close(); + output_.close(); #ifdef IS_MPI - } + } #endif -} + } -void ZConsWriter::writeFZ(const std::list& fixedZmols){ + void ZConsWriter::writeFZ(const std::list& fixedZmols){ #ifndef IS_MPI output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; output_ << fixedZmols.size() << std::endl; std::list::const_iterator i; for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) { - output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos < zconsData; - ZconsData tmpData; - for(int i =0 ; i < nproc; ++i) { - if (i == masterNode) { - std::list::const_iterator j; - for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { - tmpData.zmolIndex = j->mol->getGlobalIndex() ; - tmpData.zforce= j->fz; - tmpData.zpos = j->zpos; - tmpData.zconsPos = j->param.zTargetPos; - zconsData.push_back(tmpData); - } + std::vector zconsData; + ZconsData tmpData; + for(int i =0 ; i < nproc; ++i) { + if (i == masterNode) { + std::list::const_iterator j; + for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { + tmpData.zmolIndex = j->mol->getGlobalIndex() ; + tmpData.zforce= j->fz; + tmpData.zpos = j->zpos; + tmpData.zconsPos = j->param.zTargetPos; + zconsData.push_back(tmpData); + } - } else { - for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) { - MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr); - MPI_Recv(data, 3, MPI_DOUBLE, i, 0, MPI_COMM_WORLD,&ierr); - tmpData.zmolIndex = zmolIndex; - tmpData.zforce= data[0]; - tmpData.zpos = data[1]; - tmpData.zconsPos = data[2]; - zconsData.push_back(tmpData); - } - } + } else { + for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) { + MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr); + MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr); + tmpData.zmolIndex = zmolIndex; + tmpData.zforce= data[0]; + tmpData.zpos = data[1]; + tmpData.zconsPos = data[2]; + zconsData.push_back(tmpData); + } + } - } + } - output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; - output_ << zconsData.size() << std::endl; + output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; + output_ << zconsData.size() << std::endl; - std::vector::iterator l; - for (l = zconsData.begin(); l != zconsData.end(); ++l) { - output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl; - } + std::vector::iterator l; + for (l = zconsData.begin(); l != zconsData.end(); ++l) { + output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl; + } } else { - std::list::const_iterator j; - for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { - zmolIndex = j->mol->getGlobalIndex(); - data[0] = j->fz; - data[1] = j->zpos; - data[2] = j->param.zTargetPos; - MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); - MPI_Send(data, 3, MPI_DOUBLE, masterNode, 0, MPI_COMM_WORLD); + std::list::const_iterator j; + for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) { + zmolIndex = j->mol->getGlobalIndex(); + data[0] = j->fz; + data[1] = j->zpos; + data[2] = j->param.zTargetPos; + MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); + MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD); - } + } } #endif -} + } }