--- trunk/src/io/DumpReader.cpp 2010/06/17 19:11:37 1450 +++ branches/development/src/io/DumpReader.cpp 2013/05/10 14:59:13 1871 @@ -35,8 +35,9 @@ * * [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). + * [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). */ #define _LARGEFILE_SOURCE64 @@ -57,16 +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) @@ -77,7 +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, @@ -142,6 +141,7 @@ namespace OpenMD { prevPos = currPos; bool foundOpenSnapshotTag = false; bool foundClosedSnapshotTag = false; + while(inFile_->getline(buffer, bufferSize)) { ++lineNo; @@ -202,7 +202,7 @@ 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 @@ -227,7 +227,9 @@ 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; @@ -243,20 +245,18 @@ 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) { @@ -288,17 +288,18 @@ 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; } @@ -324,13 +325,18 @@ namespace OpenMD { inputStream.getline(buffer, bufferSize); line = buffer; - if (line.find("") == std::string::npos) { - sprintf(painCave.errMsg, - "DumpReader Error: can not find \n"); - painCave.isFatal = 1; - simError(); - } - + + if (line.find("") != std::string::npos) { + //read SiteData + readSiteData(inputStream); + } else { + if (line.find("") == std::string::npos) { + sprintf(painCave.errMsg, + "DumpReader Error: can not find \n"); + painCave.isFatal = 1; + simError(); + } + } } void DumpReader::parseDumpLine(const std::string& line) { @@ -350,9 +356,9 @@ 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(); @@ -372,7 +378,7 @@ namespace OpenMD { } } - if (integrableObject->isDirectional()) { + if (sd->isDirectional()) { if (needQuaternion_) { found = type.find("q"); if (found == std::string::npos) { @@ -395,7 +401,7 @@ namespace OpenMD { pos[1] = tokenizer.nextTokenAsDouble(); pos[2] = tokenizer.nextTokenAsDouble(); if (needPos_) { - integrableObject->setPos(pos); + sd->setPos(pos); } break; } @@ -405,14 +411,14 @@ 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(); @@ -431,19 +437,19 @@ 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; @@ -454,7 +460,7 @@ namespace OpenMD { force[0] = tokenizer.nextTokenAsDouble(); force[1] = tokenizer.nextTokenAsDouble(); force[2] = tokenizer.nextTokenAsDouble(); - integrableObject->setFrc(force); + sd->setFrc(force); break; } case 't' : { @@ -463,9 +469,46 @@ 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(); + sd->setParticlePot(particlePot); + break; + } + case 'c' : { + + RealType flucQPos; + flucQPos = tokenizer.nextTokenAsDouble(); + sd->setFlucQPos(flucQPos); + break; + } + case 'w' : { + + RealType flucQVel; + flucQVel = tokenizer.nextTokenAsDouble(); + sd->setFlucQVel(flucQVel); + break; + } + case 'g' : { + + RealType flucQFrc; + flucQFrc = tokenizer.nextTokenAsDouble(); + sd->setFlucQFrc(flucQFrc); + break; + } + case 'e' : { + + Vector3d eField; + eField[0] = tokenizer.nextTokenAsDouble(); + eField[1] = tokenizer.nextTokenAsDouble(); + eField[2] = tokenizer.nextTokenAsDouble(); + sd->setElectricField(eField); + break; + } default: { sprintf(painCave.errMsg, "DumpReader Error: %s is an unrecognized type\n", type.c_str()); @@ -480,8 +523,106 @@ namespace OpenMD { } - void DumpReader::readStuntDoubles(std::istream& inputStream) { + void DumpReader::parseSiteLine(const std::string& line) { + StringTokenizer tokenizer(line); + int nTokens; + + nTokens = tokenizer.countTokens(); + + if (nTokens < 2) { + sprintf(painCave.errMsg, + "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); + painCave.isFatal = 1; + simError(); + } + + /** + * The first token is the global integrable object index. + */ + + int index = tokenizer.nextTokenAsInt(); + StuntDouble* sd = info_->getIOIndexToIntegrableObject(index); + if (sd == NULL) { + return; + } + + /** + * Test to see if the next token is an integer or not. If not, + * we've got data on the integrable object itself. If there is an + * integer, we're parsing data for a site on a rigid body. + */ + + std::string indexTest = tokenizer.peekNextToken(); + std::istringstream i(indexTest); + int siteIndex; + if (i >> siteIndex) { + // chew up this token and parse as an int: + siteIndex = tokenizer.nextTokenAsInt(); + RigidBody* rb = static_cast(sd); + sd = rb->getAtoms()[siteIndex]; + } + + /** + * The next token contains information on what follows. + */ + std::string type = tokenizer.nextToken(); + int size = type.size(); + + for(int i = 0; i < size; ++i) { + switch(type[i]) { + + case 'u' : { + + RealType particlePot; + particlePot = tokenizer.nextTokenAsDouble(); + sd->setParticlePot(particlePot); + break; + } + case 'c' : { + + RealType flucQPos; + flucQPos = tokenizer.nextTokenAsDouble(); + sd->setFlucQPos(flucQPos); + break; + } + case 'w' : { + + RealType flucQVel; + flucQVel = tokenizer.nextTokenAsDouble(); + sd->setFlucQVel(flucQVel); + break; + } + case 'g' : { + + RealType flucQFrc; + flucQFrc = tokenizer.nextTokenAsDouble(); + sd->setFlucQFrc(flucQFrc); + break; + } + case 'e' : { + + Vector3d eField; + eField[0] = tokenizer.nextTokenAsDouble(); + eField[1] = tokenizer.nextTokenAsDouble(); + eField[2] = tokenizer.nextTokenAsDouble(); + sd->setElectricField(eField); + break; + } + default: { + sprintf(painCave.errMsg, + "DumpReader Error: %s is an unrecognized type\n", type.c_str()); + painCave.isFatal = 1; + simError(); + break; + } + } + } + } + + + void DumpReader::readStuntDoubles(std::istream& inputStream) { + inputStream.getline(buffer, bufferSize); std::string line(buffer); @@ -504,6 +645,26 @@ namespace OpenMD { } + void DumpReader::readSiteData(std::istream& inputStream) { + + std::string line(buffer); + + // 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; + + if(line.find("") != std::string::npos) { + break; + } + + parseSiteLine(line); + } + + } + void DumpReader::readFrameProperties(std::istream& inputStream) { Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); @@ -549,10 +710,10 @@ 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(); @@ -564,7 +725,7 @@ 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());