--- branches/development/src/io/DumpReader.cpp 2012/06/10 14:05:02 1752 +++ branches/development/src/io/DumpReader.cpp 2013/05/17 14:41:42 1875 @@ -35,7 +35,7 @@ * * [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). + * [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). */ @@ -58,16 +58,13 @@ #include "utils/simError.h" #include "utils/MemoryUtils.hpp" #include "utils/StringTokenizer.hpp" +#include "brains/Thermo.hpp" #ifdef IS_MPI - #include -#define TAKE_THIS_TAG_CHAR 0 -#define TAKE_THIS_TAG_INT 1 +#endif -#endif // is_mpi - namespace OpenMD { DumpReader::DumpReader(SimInfo* info, const std::string& filename) @@ -78,7 +75,8 @@ namespace OpenMD { if (worldRank == 0) { #endif - inFile_ = new std::ifstream(filename_.c_str()); + inFile_ = new std::ifstream(filename_.c_str(), + ifstream::in | ifstream::binary); if (inFile_->fail()) { sprintf(painCave.errMsg, @@ -130,7 +128,7 @@ namespace OpenMD { } void DumpReader::scanFile(void) { - int lineNo = 0; + std::streampos prevPos; std::streampos currPos; @@ -143,7 +141,8 @@ namespace OpenMD { prevPos = currPos; bool foundOpenSnapshotTag = false; bool foundClosedSnapshotTag = false; - bool foundOpenSiteDataTag = false; + + int lineNo = 0; while(inFile_->getline(buffer, bufferSize)) { ++lineNo; @@ -204,7 +203,7 @@ namespace OpenMD { #ifdef IS_MPI } - MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); + MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0); #endif // is_mpi @@ -229,7 +228,9 @@ namespace OpenMD { needVel_ = false; } - if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { + if (storageLayout & DataStorage::dslAmat || + storageLayout & DataStorage::dslDipole || + storageLayout & DataStorage::dslQuadrupole) { needQuaternion_ = true; } else { needQuaternion_ = false; @@ -245,20 +246,18 @@ namespace OpenMD { if (needCOMprops_) { Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); + Thermo thermo(info_); Vector3d com; - Vector3d comvel; - Vector3d comw; - if (needPos_ && needVel_){ - info_->getComAll(com, comvel); - comw = info_->getAngularMomentum(); - }else{ - com = info_->getCom(); - comvel = 0.0; - comw = 0.0; - } - s->setCOMprops(com, comvel, comw); + + if (needPos_ && needVel_) { + Vector3d comvel; + Vector3d comw; + thermo.getComAll(com, comvel); + comw = thermo.getAngularMomentum(); + } else { + com = thermo.getCom(); + } } - } void DumpReader::readSet(int whichFrame) { @@ -290,17 +289,18 @@ namespace OpenMD { } int sendBufferSize = sendBuffer.size(); - MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); - MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); + MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode); + MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize, + MPI::CHAR, masterNode); sstream.str(sendBuffer); } else { int sendBufferSize; - MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); + MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode); char * recvBuffer = new char[sendBufferSize+1]; assert(recvBuffer); recvBuffer[sendBufferSize] = '\0'; - MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); + MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode); sstream.str(recvBuffer); delete [] recvBuffer; } @@ -357,9 +357,9 @@ namespace OpenMD { int index = tokenizer.nextTokenAsInt(); - StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); + StuntDouble* sd = info_->getIOIndexToIntegrableObject(index); - if (integrableObject == NULL) { + if (sd == NULL) { return; } std::string type = tokenizer.nextToken(); @@ -379,7 +379,7 @@ namespace OpenMD { } } - if (integrableObject->isDirectional()) { + if (sd->isDirectional()) { if (needQuaternion_) { found = type.find("q"); if (found == std::string::npos) { @@ -402,7 +402,7 @@ namespace OpenMD { pos[1] = tokenizer.nextTokenAsDouble(); pos[2] = tokenizer.nextTokenAsDouble(); if (needPos_) { - integrableObject->setPos(pos); + sd->setPos(pos); } break; } @@ -412,14 +412,14 @@ namespace OpenMD { vel[1] = tokenizer.nextTokenAsDouble(); vel[2] = tokenizer.nextTokenAsDouble(); if (needVel_) { - integrableObject->setVel(vel); + sd->setVel(vel); } break; } case 'q' : { Quat4d q; - if (integrableObject->isDirectional()) { + if (sd->isDirectional()) { q[0] = tokenizer.nextTokenAsDouble(); q[1] = tokenizer.nextTokenAsDouble(); @@ -438,19 +438,19 @@ namespace OpenMD { q.normalize(); if (needQuaternion_) { - integrableObject->setQ(q); + sd->setQ(q); } } break; } case 'j' : { Vector3d ji; - if (integrableObject->isDirectional()) { + if (sd->isDirectional()) { ji[0] = tokenizer.nextTokenAsDouble(); ji[1] = tokenizer.nextTokenAsDouble(); ji[2] = tokenizer.nextTokenAsDouble(); if (needAngMom_) { - integrableObject->setJ(ji); + sd->setJ(ji); } } break; @@ -461,7 +461,7 @@ namespace OpenMD { force[0] = tokenizer.nextTokenAsDouble(); force[1] = tokenizer.nextTokenAsDouble(); force[2] = tokenizer.nextTokenAsDouble(); - integrableObject->setFrc(force); + sd->setFrc(force); break; } case 't' : { @@ -470,35 +470,35 @@ namespace OpenMD { torque[0] = tokenizer.nextTokenAsDouble(); torque[1] = tokenizer.nextTokenAsDouble(); torque[2] = tokenizer.nextTokenAsDouble(); - integrableObject->setTrq(torque); + sd->setTrq(torque); break; } case 'u' : { RealType particlePot; particlePot = tokenizer.nextTokenAsDouble(); - integrableObject->setParticlePot(particlePot); + sd->setParticlePot(particlePot); break; } case 'c' : { RealType flucQPos; flucQPos = tokenizer.nextTokenAsDouble(); - integrableObject->setFlucQPos(flucQPos); + sd->setFlucQPos(flucQPos); break; } case 'w' : { RealType flucQVel; flucQVel = tokenizer.nextTokenAsDouble(); - integrableObject->setFlucQVel(flucQVel); + sd->setFlucQVel(flucQVel); break; } case 'g' : { RealType flucQFrc; flucQFrc = tokenizer.nextTokenAsDouble(); - integrableObject->setFlucQFrc(flucQFrc); + sd->setFlucQFrc(flucQFrc); break; } case 'e' : { @@ -507,7 +507,7 @@ namespace OpenMD { eField[0] = tokenizer.nextTokenAsDouble(); eField[1] = tokenizer.nextTokenAsDouble(); eField[2] = tokenizer.nextTokenAsDouble(); - integrableObject->setElectricField(eField); + sd->setElectricField(eField); break; } default: { @@ -528,7 +528,7 @@ namespace OpenMD { StringTokenizer tokenizer(line); int nTokens; - + nTokens = tokenizer.countTokens(); if (nTokens < 2) { @@ -543,11 +543,10 @@ namespace OpenMD { */ int index = tokenizer.nextTokenAsInt(); - StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); - if (integrableObject == NULL) { + StuntDouble* sd = info_->getIOIndexToIntegrableObject(index); + if (sd == NULL) { return; } - StuntDouble* sd = integrableObject; /** * Test to see if the next token is an integer or not. If not, @@ -561,7 +560,7 @@ namespace OpenMD { if (i >> siteIndex) { // chew up this token and parse as an int: siteIndex = tokenizer.nextTokenAsInt(); - RigidBody* rb = static_cast(integrableObject); + RigidBody* rb = static_cast(sd); sd = rb->getAtoms()[siteIndex]; } @@ -649,14 +648,12 @@ namespace OpenMD { void DumpReader::readSiteData(std::istream& inputStream) { - inputStream.getline(buffer, bufferSize); std::string line(buffer); - - if (line.find("") == std::string::npos) { - // site data isn't required for a simulation, so skip - return; - } + // We already found the starting tag or we wouldn't be + // here, so just start parsing until we get to the ending + // tag: + while(inputStream.getline(buffer, bufferSize)) { line = buffer; @@ -714,10 +711,10 @@ namespace OpenMD { hmat(2, 2) = tokenizer.nextTokenAsDouble(); s->setHmat(hmat); } else if (propertyName == "Thermostat") { - RealType chi = tokenizer.nextTokenAsDouble(); - RealType integralOfChiDt = tokenizer.nextTokenAsDouble(); - s->setChi(chi); - s->setIntegralOfChiDt(integralOfChiDt); + pair thermostat; + thermostat.first = tokenizer.nextTokenAsDouble(); + thermostat.second = tokenizer.nextTokenAsDouble(); + s->setThermostat(thermostat); } else if (propertyName == "Barostat") { Mat3x3d eta; eta(0, 0) = tokenizer.nextTokenAsDouble(); @@ -729,7 +726,7 @@ namespace OpenMD { eta(2, 0) = tokenizer.nextTokenAsDouble(); eta(2, 1) = tokenizer.nextTokenAsDouble(); eta(2, 2) = tokenizer.nextTokenAsDouble(); - s->setEta(eta); + s->setBarostat(eta); } else { sprintf(painCave.errMsg, "DumpReader Error: %s is an invalid property in \n", propertyName.c_str());