--- trunk/src/io/DumpWriter.cpp 2006/08/30 20:33:44 1025 +++ branches/development/src/io/DumpWriter.cpp 2011/11/22 20:38:56 1665 @@ -1,24 +1,15 @@ /* - * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a * non-exclusive, royalty free, license to use, modify and * 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 +28,16 @@ * 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "io/DumpWriter.hpp" @@ -46,11 +47,13 @@ #include "io/gzstream.hpp" #include "io/Globals.hpp" + #ifdef IS_MPI #include #endif //is_mpi -namespace oopse { +using namespace std; +namespace OpenMD { DumpWriter::DumpWriter(SimInfo* info) : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ @@ -58,6 +61,7 @@ namespace oopse { Globals* simParams = info->getSimParams(); needCompression_ = simParams->getCompressDumpFile(); needForceVector_ = simParams->getOutputForceVector(); + needParticlePot_ = simParams->getOutputParticlePotential(); createDumpFile_ = true; #ifdef HAVE_LIBZ if (needCompression_) { @@ -136,6 +140,7 @@ namespace oopse { needCompression_ = simParams->getCompressDumpFile(); needForceVector_ = simParams->getOutputForceVector(); + needParticlePot_ = simParams->getOutputParticlePotential(); #ifdef HAVE_LIBZ if (needCompression_) { @@ -194,11 +199,31 @@ namespace oopse { os << " \n"; RealType currentTime = s->getTime(); + + if (isinf(currentTime) || isnan(currentTime)) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the time"); + painCave.isFatal = 1; + simError(); + } + sprintf(buffer, " Time: %.10g\n", currentTime); os << buffer; Mat3x3d hmat; hmat = s->getHmat(); + + for (unsigned int i = 0; i < 3; i++) { + for (unsigned int j = 0; j < 3; j++) { + if (isinf(hmat(i,j)) || isnan(hmat(i,j))) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the box"); + painCave.isFatal = 1; + simError(); + } + } + } + sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", hmat(0, 0), hmat(1, 0), hmat(2, 0), hmat(0, 1), hmat(1, 1), hmat(2, 1), @@ -207,11 +232,30 @@ namespace oopse { RealType chi = s->getChi(); RealType integralOfChiDt = s->getIntegralOfChiDt(); + if (isinf(chi) || isnan(chi) || + isinf(integralOfChiDt) || isnan(integralOfChiDt)) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the thermostat"); + painCave.isFatal = 1; + simError(); + } sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); os << buffer; Mat3x3d eta; eta = s->getEta(); + + for (unsigned int i = 0; i < 3; i++) { + for (unsigned int j = 0; j < 3; j++) { + if (isinf(eta(i,j)) || isnan(eta(i,j))) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the barostat"); + painCave.isFatal = 1; + simError(); + } + } + } + sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", eta(0, 0), eta(1, 0), eta(2, 0), eta(0, 1), eta(1, 1), eta(2, 1), @@ -240,14 +284,15 @@ namespace oopse { os << " \n"; for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { - for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; integrableObject = mol->nextIntegrableObject(ii)) { - os << prepareDumpLine(integrableObject); - + os << prepareDumpLine(integrableObject); + } } os << " \n"; - + os << " \n"; os.flush(); @@ -255,15 +300,17 @@ namespace oopse { //every node prepares the dump lines for integrable objects belong to itself std::string buffer; for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { - + + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; integrableObject = mol->nextIntegrableObject(ii)) { - buffer += prepareDumpLine(integrableObject); + buffer += prepareDumpLine(integrableObject); } } const int masterNode = 0; - + int nProc; + MPI_Comm_size(MPI_COMM_WORLD, &nProc); if (worldRank == masterNode) { os << " \n"; writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); @@ -271,13 +318,12 @@ namespace oopse { os << buffer; - int nProc; - MPI_Comm_size(MPI_COMM_WORLD, &nProc); for (int i = 1; i < nProc; ++i) { // receive the length of the string buffer that was // prepared by processor i + MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD); int recvLength; MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); char* recvBuffer = new char[recvLength]; @@ -285,7 +331,7 @@ namespace oopse { } else { MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); os << recvBuffer; - delete recvBuffer; + delete [] recvBuffer; } } os << " \n"; @@ -294,8 +340,14 @@ namespace oopse { os.flush(); } else { int sendBufferLength = buffer.size() + 1; - MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); - MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); + int myturn = 0; + for (int i = 1; i < nProc; ++i){ + MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD); + if (myturn == worldRank){ + MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); + MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); + } + } } #endif // is_mpi @@ -312,7 +364,29 @@ namespace oopse { Vector3d pos; Vector3d vel; pos = integrableObject->getPos(); + + if (isinf(pos[0]) || isnan(pos[0]) || + isinf(pos[1]) || isnan(pos[1]) || + isinf(pos[2]) || isnan(pos[2]) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the position" + " for object %d", index); + painCave.isFatal = 1; + simError(); + } + vel = integrableObject->getVel(); + + if (isinf(vel[0]) || isnan(vel[0]) || + isinf(vel[1]) || isnan(vel[1]) || + isinf(vel[2]) || isnan(vel[2]) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the velocity" + " for object %d", index); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", pos[0], pos[1], pos[2], vel[0], vel[1], vel[2]); @@ -323,7 +397,30 @@ namespace oopse { Quat4d q; Vector3d ji; q = integrableObject->getQ(); + + if (isinf(q[0]) || isnan(q[0]) || + isinf(q[1]) || isnan(q[1]) || + isinf(q[2]) || isnan(q[2]) || + isinf(q[3]) || isnan(q[3]) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the quaternion" + " for object %d", index); + painCave.isFatal = 1; + simError(); + } + ji = integrableObject->getJ(); + + if (isinf(ji[0]) || isnan(ji[0]) || + isinf(ji[1]) || isnan(ji[1]) || + isinf(ji[2]) || isnan(ji[2]) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the angular" + " momentum for object %d", index); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", q[0], q[1], q[2], q[3], ji[0], ji[1], ji[2]); @@ -331,18 +428,62 @@ namespace oopse { } if (needForceVector_) { - type += "ft"; + type += "f"; Vector3d frc; - Vector3d trq; + frc = integrableObject->getFrc(); - trq = integrableObject->getTrq(); - - sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e", - frc[0], frc[1], frc[2], - trq[0], trq[1], trq[2]); + + if (isinf(frc[0]) || isnan(frc[0]) || + isinf(frc[1]) || isnan(frc[1]) || + isinf(frc[2]) || isnan(frc[2]) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the force" + " for object %d", index); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, " %13e %13e %13e", + frc[0], frc[1], frc[2]); line += tempBuffer; + + if (integrableObject->isDirectional()) { + type += "t"; + Vector3d trq; + + trq = integrableObject->getTrq(); + + if (isinf(trq[0]) || isnan(trq[0]) || + isinf(trq[1]) || isnan(trq[1]) || + isinf(trq[2]) || isnan(trq[2]) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the torque" + " for object %d", index); + painCave.isFatal = 1; + simError(); + } + + sprintf(tempBuffer, " %13e %13e %13e", + trq[0], trq[1], trq[2]); + line += tempBuffer; + } } - + if (needParticlePot_) { + type += "u"; + RealType particlePot; + + particlePot = integrableObject->getParticlePot(); + + if (isinf(particlePot) || isnan(particlePot)) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the particle " + " potential for object %d", index); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, " %13e", particlePot); + line += tempBuffer; + } + sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); return std::string(tempBuffer); } @@ -424,7 +565,7 @@ namespace oopse { newOStream = new std::ofstream(filename.c_str()); #endif //write out MetaData first - (*newOStream) << "" << std::endl; + (*newOStream) << "" << std::endl; (*newOStream) << " " << std::endl; (*newOStream) << info_->getRawMetaData(); (*newOStream) << " " << std::endl; @@ -433,8 +574,8 @@ namespace oopse { void DumpWriter::writeClosing(std::ostream& os) { - os << "\n"; + os << "\n"; os.flush(); } -}//end namespace oopse +}//end namespace OpenMD