--- trunk/src/io/DumpWriter.cpp 2008/01/23 21:23:02 1217 +++ branches/development/src/io/DumpWriter.cpp 2012/06/10 14:05:02 1752 @@ -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" @@ -46,18 +47,30 @@ #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()){ Globals* simParams = info->getSimParams(); - needCompression_ = simParams->getCompressDumpFile(); - needForceVector_ = simParams->getOutputForceVector(); + needCompression_ = simParams->getCompressDumpFile(); + needForceVector_ = simParams->getOutputForceVector(); + needParticlePot_ = simParams->getOutputParticlePotential(); + needFlucQ_ = simParams->getOutputFluctuatingCharges(); + needElectricField_ = simParams->getOutputElectricField(); + + if (needParticlePot_ || needFlucQ_ || needElectricField_) { + doSiteData_ = true; + } else { + doSiteData_ = false; + } + createDumpFile_ = true; #ifdef HAVE_LIBZ if (needCompression_) { @@ -95,8 +108,18 @@ namespace oopse { Globals* simParams = info->getSimParams(); eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; - needCompression_ = simParams->getCompressDumpFile(); - needForceVector_ = simParams->getOutputForceVector(); + needCompression_ = simParams->getCompressDumpFile(); + needForceVector_ = simParams->getOutputForceVector(); + needParticlePot_ = simParams->getOutputParticlePotential(); + needFlucQ_ = simParams->getOutputFluctuatingCharges(); + needElectricField_ = simParams->getOutputElectricField(); + + if (needParticlePot_ || needFlucQ_ || needElectricField_) { + doSiteData_ = true; + } else { + doSiteData_ = false; + } + createDumpFile_ = true; #ifdef HAVE_LIBZ if (needCompression_) { @@ -134,9 +157,18 @@ namespace oopse { Globals* simParams = info->getSimParams(); eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; - needCompression_ = simParams->getCompressDumpFile(); - needForceVector_ = simParams->getOutputForceVector(); - + needCompression_ = simParams->getCompressDumpFile(); + needForceVector_ = simParams->getOutputForceVector(); + needParticlePot_ = simParams->getOutputParticlePotential(); + needFlucQ_ = simParams->getOutputFluctuatingCharges(); + needElectricField_ = simParams->getOutputElectricField(); + + if (needParticlePot_ || needFlucQ_ || needElectricField_) { + doSiteData_ = true; + } else { + doSiteData_ = false; + } + #ifdef HAVE_LIBZ if (needCompression_) { filename_ += ".gz"; @@ -194,11 +226,31 @@ 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 +259,30 @@ 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), @@ -231,6 +302,8 @@ namespace oopse { StuntDouble* integrableObject; SimInfo::MoleculeIterator mi; Molecule::IntegrableObjectIterator ii; + RigidBody::AtomIterator ai; + Atom* atom; #ifndef IS_MPI os << " \n"; @@ -248,7 +321,32 @@ namespace oopse { } } os << " \n"; - + + if (doSiteData_) { + os << " \n"; + for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { + + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + + int ioIndex = integrableObject->getGlobalIntegrableObjectIndex(); + // do one for the IO itself + os << prepareSiteLine(integrableObject, ioIndex, 0); + + if (integrableObject->isRigidBody()) { + + RigidBody* rb = static_cast(integrableObject); + int siteIndex = 0; + for (atom = rb->beginAtom(ai); atom != NULL; + atom = rb->nextAtom(ai)) { + os << prepareSiteLine(atom, ioIndex, siteIndex); + siteIndex++; + } + } + } + } + os << " \n"; + } os << " \n"; os.flush(); @@ -265,7 +363,8 @@ namespace oopse { } const int masterNode = 0; - + int nProc; + MPI_Comm_size(MPI_COMM_WORLD, &nProc); if (worldRank == masterNode) { os << " \n"; writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); @@ -273,13 +372,12 @@ 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]; @@ -287,7 +385,7 @@ namespace oopse { } else { MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); os << recvBuffer; - delete recvBuffer; + delete [] recvBuffer; } } os << " \n"; @@ -296,8 +394,14 @@ 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 @@ -314,7 +418,29 @@ 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]); @@ -325,7 +451,30 @@ 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]); @@ -333,22 +482,135 @@ namespace oopse { } if (needForceVector_) { - type += "ft"; - 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]); + type += "f"; + Vector3d frc = integrableObject->getFrc(); + 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 = 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; + } } - + sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); return std::string(tempBuffer); } + std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) { + + + std::string id; + std::string type; + std::string line; + char tempBuffer[4096]; + + if (integrableObject->isRigidBody()) { + sprintf(tempBuffer, "%10d ", ioIndex); + id = std::string(tempBuffer); + } else { + sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex); + id = std::string(tempBuffer); + } + + if (needFlucQ_) { + type += "cw"; + RealType fqPos = integrableObject->getFlucQPos(); + if (isinf(fqPos) || isnan(fqPos) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the" + " fluctuating charge for object %s", id.c_str()); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, " %13e ", fqPos); + line += tempBuffer; + + RealType fqVel = integrableObject->getFlucQVel(); + if (isinf(fqVel) || isnan(fqVel) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the" + " fluctuating charge velocity for object %s", id.c_str()); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, " %13e ", fqVel); + line += tempBuffer; + + if (needForceVector_) { + type += "g"; + RealType fqFrc = integrableObject->getFlucQFrc(); + if (isinf(fqFrc) || isnan(fqFrc) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the" + " fluctuating charge force for object %s", id.c_str()); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, " %13e ", fqFrc); + line += tempBuffer; + } + } + + if (needElectricField_) { + type += "e"; + Vector3d eField= integrableObject->getElectricField(); + if (isinf(eField[0]) || isnan(eField[0]) || + isinf(eField[1]) || isnan(eField[1]) || + isinf(eField[2]) || isnan(eField[2]) ) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the electric" + " field for object %s", id.c_str()); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, " %13e %13e %13e", + eField[0], eField[1], eField[2]); + line += tempBuffer; + } + + + if (needParticlePot_) { + type += "u"; + RealType particlePot = integrableObject->getParticlePot(); + if (isinf(particlePot) || isnan(particlePot)) { + sprintf( painCave.errMsg, + "DumpWriter detected a numerical error writing the particle " + " potential for object %s", id.c_str()); + painCave.isFatal = 1; + simError(); + } + sprintf(tempBuffer, " %13e", particlePot); + line += tempBuffer; + } + + + sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str()); + return std::string(tempBuffer); + } + void DumpWriter::writeDump() { writeFrame(*dumpFile_); } @@ -426,7 +688,7 @@ 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; @@ -435,8 +697,8 @@ namespace oopse { void DumpWriter::writeClosing(std::ostream& os) { - os << "\n"; + os << "\n"; os.flush(); } -}//end namespace oopse +}//end namespace OpenMD