--- trunk/src/io/ZConsWriter.cpp 2005/04/15 22:04:00 507 +++ trunk/src/io/ZConsWriter.cpp 2015/03/07 21:41:51 2071 @@ -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. @@ -37,46 +28,58 @@ * 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, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ +#ifdef IS_MPI +#include +#endif + #include #include #include - #include "io/ZConsWriter.hpp" #include "utils/simError.h" - -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()); if(!output_){ sprintf( painCave.errMsg, - "Could not open %s for z constrain output_ \n", filename.c_str()); + "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_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" + << std::endl; #ifdef IS_MPI } -#endif - +#endif } - + ZConsWriter::~ZConsWriter() { - + #ifdef IS_MPI if(worldRank == 0 ){ #endif @@ -88,32 +91,38 @@ namespace oopse { void ZConsWriter::writeFZ(const std::list& fixedZmols){ #ifndef IS_MPI - output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl; + 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 < tmpNFixedZmols(nproc, 0); std::vector nFixedZmolsInProc(nproc, 0); tmpNFixedZmols[myNode] = fixedZmols.size(); - //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups - MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT, - MPI_SUM, MPI_COMM_WORLD); - - MPI_Status ierr; + //do MPI_ALLREDUCE to exchange the total number of atoms, + //rigidbodies and cutoff groups + MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], + nproc, MPI_INT, MPI_SUM, MPI_COMM_WORLD); + + MPI_Status* ierr = NULL; int zmolIndex; - double data[3]; + RealType data[3]; - if (masterNode == 0) { - + if (myNode == masterNode) { + std::vector zconsData; ZconsData tmpData; for(int i =0 ; i < nproc; ++i) { @@ -126,44 +135,42 @@ namespace oopse { 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); + 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); + zconsData.push_back(tmpData); } - } - + } } - - output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << 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; + 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); - + MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); + MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD); } } #endif } - }