--- trunk/src/io/DumpReader.cpp 2009/11/25 20:02:06 1390 +++ branches/development/src/io/DumpReader.cpp 2012/07/03 18:32:27 1764 @@ -36,7 +36,8 @@ * [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). + * [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) @@ -142,6 +140,7 @@ namespace OpenMD { prevPos = currPos; bool foundOpenSnapshotTag = false; bool foundClosedSnapshotTag = false; + bool foundOpenSiteDataTag = false; while(inFile_->getline(buffer, bufferSize)) { ++lineNo; @@ -243,20 +242,18 @@ 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) { @@ -324,13 +321,18 @@ 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) { @@ -341,7 +343,7 @@ namespace OpenMD { nTokens = tokenizer.countTokens(); - if (nTokens < 2) { + if (nTokens < 2) { sprintf(painCave.errMsg, "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); painCave.isFatal = 1; @@ -357,6 +359,34 @@ namespace OpenMD { } std::string type = tokenizer.nextToken(); int size = type.size(); + + size_t found; + + if (needPos_) { + found = type.find("p"); + if (found == std::string::npos) { + sprintf(painCave.errMsg, + "DumpReader Error: StuntDouble %d has no Position\n" + "\tField (\"p\") specified.\n%s\n", index, + line.c_str()); + painCave.isFatal = 1; + simError(); + } + } + + if (integrableObject->isDirectional()) { + if (needQuaternion_) { + found = type.find("q"); + if (found == std::string::npos) { + sprintf(painCave.errMsg, + "DumpReader Error: Directional StuntDouble %d has no\n" + "\tQuaternion Field (\"q\") specified.\n%s\n", index, + line.c_str()); + painCave.isFatal = 1; + simError(); + } + } + } for(int i = 0; i < size; ++i) { switch(type[i]) { @@ -438,6 +468,43 @@ namespace OpenMD { integrableObject->setTrq(torque); break; } + case 'u' : { + + RealType particlePot; + particlePot = tokenizer.nextTokenAsDouble(); + integrableObject->setParticlePot(particlePot); + break; + } + case 'c' : { + + RealType flucQPos; + flucQPos = tokenizer.nextTokenAsDouble(); + integrableObject->setFlucQPos(flucQPos); + break; + } + case 'w' : { + + RealType flucQVel; + flucQVel = tokenizer.nextTokenAsDouble(); + integrableObject->setFlucQVel(flucQVel); + break; + } + case 'g' : { + + RealType flucQFrc; + flucQFrc = tokenizer.nextTokenAsDouble(); + integrableObject->setFlucQFrc(flucQFrc); + break; + } + case 'e' : { + + Vector3d eField; + eField[0] = tokenizer.nextTokenAsDouble(); + eField[1] = tokenizer.nextTokenAsDouble(); + eField[2] = tokenizer.nextTokenAsDouble(); + integrableObject->setElectricField(eField); + break; + } default: { sprintf(painCave.errMsg, "DumpReader Error: %s is an unrecognized type\n", type.c_str()); @@ -452,8 +519,107 @@ 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* integrableObject = info_->getIOIndexToIntegrableObject(index); + if (integrableObject == NULL) { + return; + } + StuntDouble* sd = integrableObject; + + /** + * 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(integrableObject); + 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); @@ -476,6 +642,28 @@ 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; + } + + 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(); @@ -521,10 +709,10 @@ 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(); @@ -536,7 +724,7 @@ 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());