--- branches/development/src/io/DumpReader.cpp 2012/05/19 18:12:46 1714 +++ branches/development/src/io/DumpReader.cpp 2012/07/09 14:15:52 1769 @@ -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) @@ -143,6 +140,7 @@ namespace OpenMD { prevPos = currPos; bool foundOpenSnapshotTag = false; bool foundClosedSnapshotTag = false; + bool foundOpenSiteDataTag = false; while(inFile_->getline(buffer, bufferSize)) { ++lineNo; @@ -244,20 +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) { @@ -325,13 +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) { @@ -351,9 +352,9 @@ 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(); @@ -373,7 +374,7 @@ namespace OpenMD { } } - if (integrableObject->isDirectional()) { + if (sd->isDirectional()) { if (needQuaternion_) { found = type.find("q"); if (found == std::string::npos) { @@ -396,7 +397,7 @@ namespace OpenMD { pos[1] = tokenizer.nextTokenAsDouble(); pos[2] = tokenizer.nextTokenAsDouble(); if (needPos_) { - integrableObject->setPos(pos); + sd->setPos(pos); } break; } @@ -406,14 +407,14 @@ 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(); @@ -432,19 +433,19 @@ 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; @@ -455,7 +456,7 @@ namespace OpenMD { force[0] = tokenizer.nextTokenAsDouble(); force[1] = tokenizer.nextTokenAsDouble(); force[2] = tokenizer.nextTokenAsDouble(); - integrableObject->setFrc(force); + sd->setFrc(force); break; } case 't' : { @@ -464,35 +465,35 @@ 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' : { @@ -501,7 +502,7 @@ namespace OpenMD { eField[0] = tokenizer.nextTokenAsDouble(); eField[1] = tokenizer.nextTokenAsDouble(); eField[2] = tokenizer.nextTokenAsDouble(); - integrableObject->setElectricField(eField); + sd->setElectricField(eField); break; } default: { @@ -518,8 +519,106 @@ 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); @@ -542,6 +641,28 @@ 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(); @@ -587,10 +708,10 @@ 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(); @@ -602,7 +723,7 @@ 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());