--- trunk/OOPSE-4/src/io/DumpReader.cpp 2005/03/09 18:48:14 2100 +++ trunk/OOPSE-4/src/io/DumpReader.cpp 2005/03/10 15:10:24 2101 @@ -68,438 +68,439 @@ namespace oopse { namespace oopse { - -DumpReader::DumpReader(SimInfo* info, const std::string& filename) - : info_(info), filename_(filename), isScanned_(false), nframes_(0) { - + + DumpReader::DumpReader(SimInfo* info, const std::string& filename) + : info_(info), filename_(filename), isScanned_(false), nframes_(0) { + #ifdef IS_MPI - + if (worldRank == 0) { #endif - - inFile_ = fopen(filename_.c_str(), "r"); - - if (inFile_ == NULL) { - sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str()); - painCave.isFatal = 1; - simError(); - } - + + inFile_ = fopen(filename_.c_str(), "r"); + + if (inFile_ == NULL) { + sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str()); + painCave.isFatal = 1; + simError(); + } + #ifdef IS_MPI - + } - + strcpy(checkPointMsg, "Dump file opened for reading successfully."); MPIcheckPoint(); - + #endif - + return; -} - -DumpReader::~DumpReader() { - + } + + DumpReader::~DumpReader() { + #ifdef IS_MPI - + if (worldRank == 0) { #endif - - int error; - error = fclose(inFile_); - - if (error) { - sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str()); - painCave.isFatal = 1; - simError(); - } - - MemoryUtils::deletePointers(framePos_); - + + int error; + error = fclose(inFile_); + + if (error) { + sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str()); + painCave.isFatal = 1; + simError(); + } + + MemoryUtils::deletePointers(framePos_); + #ifdef IS_MPI - + } - + strcpy(checkPointMsg, "Dump file closed successfully."); MPIcheckPoint(); - + #endif - + return; -} - -int DumpReader::getNFrames(void) { - + } + + int DumpReader::getNFrames(void) { + if (!isScanned_) - scanFile(); - + scanFile(); + return nframes_; -} - -void DumpReader::scanFile(void) { - int i, j; - int lineNum = 0; - char readBuffer[maxBufferSize]; - fpos_t * currPos; - + } + + void DumpReader::scanFile(void) { + int i, j; + int lineNum = 0; + char readBuffer[maxBufferSize]; + fpos_t * currPos; + #ifdef IS_MPI - + if (worldRank == 0) { #endif // is_mpi - - rewind(inFile_); - - currPos = new fpos_t; - fgetpos(inFile_, currPos); + + rewind(inFile_); + + currPos = new fpos_t; + fgetpos(inFile_, currPos); + fgets(readBuffer, sizeof(readBuffer), inFile_); + lineNum++; + + if (feof(inFile_)) { + sprintf(painCave.errMsg, + "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", + filename_.c_str(), + lineNum); + painCave.isFatal = 1; + simError(); + } + + while (!feof(inFile_)) { + framePos_.push_back(currPos); + + i = atoi(readBuffer); + fgets(readBuffer, sizeof(readBuffer), inFile_); lineNum++; - + if (feof(inFile_)) { + sprintf(painCave.errMsg, + "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", + filename_.c_str(), + lineNum); + painCave.isFatal = 1; + simError(); + } + + for(j = 0; j < i; j++) { + fgets(readBuffer, sizeof(readBuffer), inFile_); + lineNum++; + + if (feof(inFile_)) { sprintf(painCave.errMsg, - "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", - filename_.c_str(), - lineNum); + "DumpReader Error: File \"%s\" ended unexpectedly at line %d," + " with atom %d\n", filename_.c_str(), + lineNum, + j); + painCave.isFatal = 1; simError(); + } } - - while (!feof(inFile_)) { - framePos_.push_back(currPos); - - i = atoi(readBuffer); - - fgets(readBuffer, sizeof(readBuffer), inFile_); - lineNum++; - - if (feof(inFile_)) { - sprintf(painCave.errMsg, - "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", - filename_.c_str(), - lineNum); - painCave.isFatal = 1; - simError(); - } - - for(j = 0; j < i; j++) { - fgets(readBuffer, sizeof(readBuffer), inFile_); - lineNum++; - - if (feof(inFile_)) { - sprintf(painCave.errMsg, - "DumpReader Error: File \"%s\" ended unexpectedly at line %d," - " with atom %d\n", filename_.c_str(), - lineNum, - j); - - painCave.isFatal = 1; - simError(); - } - } - - currPos = new fpos_t; - fgetpos(inFile_, currPos); - fgets(readBuffer, sizeof(readBuffer), inFile_); - lineNum++; - } - - delete currPos; - rewind(inFile_); - nframes_ = framePos_.size(); + currPos = new fpos_t; + fgetpos(inFile_, currPos); + fgets(readBuffer, sizeof(readBuffer), inFile_); + lineNum++; + } + + delete currPos; + rewind(inFile_); + + nframes_ = framePos_.size(); #ifdef IS_MPI } - + MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); - + strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); MPIcheckPoint(); - + #endif // is_mpi - + isScanned_ = true; -} - -void DumpReader::readFrame(int whichFrame) { + } + + void DumpReader::readFrame(int whichFrame) { int storageLayout = info_->getSnapshotManager()->getStorageLayout(); - + if (storageLayout & DataStorage::dslPosition) { - needPos_ = true; + needPos_ = true; } else { - needPos_ = false; + needPos_ = false; } - + if (storageLayout & DataStorage::dslVelocity) { - needVel_ = true; + needVel_ = true; } else { - needVel_ = false; + needVel_ = false; } - + if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { - needQuaternion_ = true; + needQuaternion_ = true; } else { - needQuaternion_ = false; + needQuaternion_ = false; } - + if (storageLayout & DataStorage::dslAngularMomentum) { - needAngMom_ = true; + needAngMom_ = true; } else { - needAngMom_ = false; + needAngMom_ = false; } - + readSet(whichFrame); -} - -void DumpReader::readSet(int whichFrame) { - int i; - int nTotObjs; // the number of atoms - char read_buffer[maxBufferSize]; //the line buffer for reading - char * eof_test; // ptr to see when we reach the end of the file - - Molecule* mol; - StuntDouble* integrableObject; - SimInfo::MoleculeIterator mi; - Molecule::IntegrableObjectIterator ii; - + } + + void DumpReader::readSet(int whichFrame) { + int i; + int nTotObjs; // the number of atoms + char read_buffer[maxBufferSize]; //the line buffer for reading + char * eof_test; // ptr to see when we reach the end of the file + + Molecule* mol; + StuntDouble* integrableObject; + SimInfo::MoleculeIterator mi; + Molecule::IntegrableObjectIterator ii; + #ifndef IS_MPI - + fsetpos(inFile_, framePos_[whichFrame]); eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); - + if (eof_test == NULL) { - sprintf(painCave.errMsg, - "DumpReader error: error reading 1st line of \"%s\"\n", - filename_.c_str()); - painCave.isFatal = 1; - simError(); + sprintf(painCave.errMsg, + "DumpReader error: error reading 1st line of \"%s\"\n", + filename_.c_str()); + painCave.isFatal = 1; + simError(); } - + nTotObjs = atoi(read_buffer); - + if (nTotObjs != info_->getNGlobalIntegrableObjects()) { - sprintf(painCave.errMsg, - "DumpReader error. %s nIntegrable, %d, " - "does not match the meta-data file's nIntegrable, %d.\n", - filename_.c_str(), - nTotObjs, - info_->getNGlobalIntegrableObjects()); - - painCave.isFatal = 1; - simError(); + sprintf(painCave.errMsg, + "DumpReader error. %s nIntegrable, %d, " + "does not match the meta-data file's nIntegrable, %d.\n", + filename_.c_str(), + nTotObjs, + info_->getNGlobalIntegrableObjects()); + + painCave.isFatal = 1; + simError(); } - + //read the box mat from the comment line - + eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); - + if (eof_test == NULL) { - sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", - filename_.c_str()); - painCave.isFatal = 1; - simError(); + sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", + filename_.c_str()); + painCave.isFatal = 1; + simError(); } - + parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); - + //parse dump lines - + + i = 0; for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { - - for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ii)) { - - eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); - - if (eof_test == NULL) { - sprintf(painCave.errMsg, - "DumpReader Error: error in reading file %s\n" - "natoms = %d; index = %d\n" - "error reading the line from the file.\n", - filename_.c_str(), - nTotObjs, - i); - - painCave.isFatal = 1; - simError(); - } - - parseDumpLine(read_buffer, integrableObject); - - } + + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + + eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); + + if (eof_test == NULL) { + sprintf(painCave.errMsg, + "DumpReader Error: error in reading file %s\n" + "natoms = %d; index = %d\n" + "error reading the line from the file.\n", + filename_.c_str(), + nTotObjs, + i); + + painCave.isFatal = 1; + simError(); + } + + parseDumpLine(read_buffer, integrableObject); + i++; + } } - + // MPI Section of code.......... - + #else //IS_MPI - + // first thing first, suspend fatalities. int masterNode = 0; int nCurObj; painCave.isEventLoop = 1; - + int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone int haveError; - + MPI_Status istatus; int nitems; - + nTotObjs = info_->getNGlobalIntegrableObjects(); haveError = 0; - + if (worldRank == masterNode) { - fsetpos(inFile_, framePos_[whichFrame]); - - eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); - - if (eof_test == NULL) { - sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", - filename_.c_str()); - painCave.isFatal = 1; - simError(); - } - - nitems = atoi(read_buffer); - - // Check to see that the number of integrable objects in the - // intial configuration file is the same as derived from the - // meta-data file. - - if (nTotObjs != nitems) { - sprintf(painCave.errMsg, - "DumpReader Error. %s nIntegrable, %d, " - "does not match the meta-data file's nIntegrable, %d.\n", - filename_.c_str(), - nTotObjs, - info_->getNGlobalIntegrableObjects()); - + fsetpos(inFile_, framePos_[whichFrame]); + + eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); + + if (eof_test == NULL) { + sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", + filename_.c_str()); + painCave.isFatal = 1; + simError(); + } + + nitems = atoi(read_buffer); + + // Check to see that the number of integrable objects in the + // intial configuration file is the same as derived from the + // meta-data file. + + if (nTotObjs != nitems) { + sprintf(painCave.errMsg, + "DumpReader Error. %s nIntegrable, %d, " + "does not match the meta-data file's nIntegrable, %d.\n", + filename_.c_str(), + nTotObjs, + info_->getNGlobalIntegrableObjects()); + + painCave.isFatal = 1; + simError(); + } + + //read the boxMat from the comment line + + eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); + + if (eof_test == NULL) { + sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", + filename_.c_str()); + painCave.isFatal = 1; + simError(); + } + + //Every single processor will parse the comment line by itself + //By using this way, we might lose some efficiency, but if we want to add + //more parameters into comment line, we only need to modify function + //parseCommentLine + + MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); + parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); + + for(i = 0; i < info_->getNGlobalMolecules(); i++) { + int which_node = info_->getMolToProc(i); + + if (which_node == masterNode) { + //molecules belong to master node + + mol = info_->getMoleculeByGlobalIndex(i); + + if (mol == NULL) { + sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); painCave.isFatal = 1; simError(); - } - - //read the boxMat from the comment line - - eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); - - if (eof_test == NULL) { - sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", - filename_.c_str()); - painCave.isFatal = 1; - simError(); - } - - //Every single processor will parse the comment line by itself - //By using this way, we might lose some efficiency, but if we want to add - //more parameters into comment line, we only need to modify function - //parseCommentLine - - MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); - parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); - - for(i = 0; i < info_->getNGlobalMolecules(); i++) { - int which_node = info_->getMolToProc(i); - - if (which_node == masterNode) { - //molecules belong to master node - - mol = info_->getMoleculeByGlobalIndex(i); - - if (mol == NULL) { - sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); - painCave.isFatal = 1; - simError(); - } - - for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ii)){ - - eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); - - if (eof_test == NULL) { - sprintf(painCave.errMsg, - "DumpReader Error: error in reading file %s\n" - "natoms = %d; index = %d\n" - "error reading the line from the file.\n", - filename_.c_str(), - nTotObjs, - i); - - painCave.isFatal = 1; - simError(); - } - - parseDumpLine(read_buffer, integrableObject); - } - } else { - //molecule belongs to slave nodes - - MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, - MPI_COMM_WORLD, &istatus); - - for(int j = 0; j < nCurObj; j++) { - eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); - - if (eof_test == NULL) { - sprintf(painCave.errMsg, - "DumpReader Error: error in reading file %s\n" - "natoms = %d; index = %d\n" - "error reading the line from the file.\n", - filename_.c_str(), - nTotObjs, - i); - - painCave.isFatal = 1; - simError(); - } - - MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, - TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); - } + } + + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)){ + + eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); + + if (eof_test == NULL) { + sprintf(painCave.errMsg, + "DumpReader Error: error in reading file %s\n" + "natoms = %d; index = %d\n" + "error reading the line from the file.\n", + filename_.c_str(), + nTotObjs, + i); + + painCave.isFatal = 1; + simError(); } + + parseDumpLine(read_buffer, integrableObject); + } + } else { + //molecule belongs to slave nodes + + MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, + MPI_COMM_WORLD, &istatus); + + for(int j = 0; j < nCurObj; j++) { + eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); + + if (eof_test == NULL) { + sprintf(painCave.errMsg, + "DumpReader Error: error in reading file %s\n" + "natoms = %d; index = %d\n" + "error reading the line from the file.\n", + filename_.c_str(), + nTotObjs, + i); + + painCave.isFatal = 1; + simError(); + } + + MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, + TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); + } } + } } else { - //actions taken at slave nodes - MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); - - /**@todo*/ - parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); - - for(i = 0; i < info_->getNGlobalMolecules(); i++) { - int which_node = info_->getMolToProc(i); - - if (which_node == worldRank) { - //molecule with global index i belongs to this processor - - mol = info_->getMoleculeByGlobalIndex(i); - if (mol == NULL) { - sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); - painCave.isFatal = 1; - simError(); - } - - nCurObj = mol->getNIntegrableObjects(); - - MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, - MPI_COMM_WORLD); - - for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ii)){ - - MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, - TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); - - parseDumpLine(read_buffer, integrableObject); - } - - } + //actions taken at slave nodes + MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); + + /**@todo*/ + parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); + + for(i = 0; i < info_->getNGlobalMolecules(); i++) { + int which_node = info_->getMolToProc(i); + + if (which_node == worldRank) { + //molecule with global index i belongs to this processor + + mol = info_->getMoleculeByGlobalIndex(i); + if (mol == NULL) { + sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); + painCave.isFatal = 1; + simError(); + } + + nCurObj = mol->getNIntegrableObjects(); + + MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, + MPI_COMM_WORLD); + + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)){ + MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, + TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); + + parseDumpLine(read_buffer, integrableObject); + } + } + } + } - + #endif - -} - -void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { - + + } + + void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { + Vector3d pos; // position place holders Vector3d vel; // velocity placeholders Quat4d q; // the quaternions @@ -508,92 +509,92 @@ void DumpReader::parseDumpLine(char *line, StuntDouble int nTokens; nTokens = tokenizer.countTokens(); - + if (nTokens < 14) { - sprintf(painCave.errMsg, - "DumpReader Error: Not enough Tokens.\n%s\n", line); - painCave.isFatal = 1; - simError(); + sprintf(painCave.errMsg, + "DumpReader Error: Not enough Tokens.\n%s\n", line); + painCave.isFatal = 1; + simError(); } - + std::string name = tokenizer.nextToken(); - + if (name != integrableObject->getType()) { - - sprintf(painCave.errMsg, - "DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", - name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); - painCave.isFatal = 1; - simError(); + + sprintf(painCave.errMsg, + "DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", + name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); + painCave.isFatal = 1; + simError(); } - + pos[0] = tokenizer.nextTokenAsDouble(); pos[1] = tokenizer.nextTokenAsDouble(); pos[2] = tokenizer.nextTokenAsDouble(); if (needPos_) { - integrableObject->setPos(pos); + integrableObject->setPos(pos); } vel[0] = tokenizer.nextTokenAsDouble(); vel[1] = tokenizer.nextTokenAsDouble(); vel[2] = tokenizer.nextTokenAsDouble(); if (needVel_) { - integrableObject->setVel(vel); + integrableObject->setVel(vel); } if (integrableObject->isDirectional()) { + + q[0] = tokenizer.nextTokenAsDouble(); + q[1] = tokenizer.nextTokenAsDouble(); + q[2] = tokenizer.nextTokenAsDouble(); + q[3] = tokenizer.nextTokenAsDouble(); + + double qlen = q.length(); + if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 - q[0] = tokenizer.nextTokenAsDouble(); - q[1] = tokenizer.nextTokenAsDouble(); - q[2] = tokenizer.nextTokenAsDouble(); - q[3] = tokenizer.nextTokenAsDouble(); - - double qlen = q.length(); - if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 - - sprintf(painCave.errMsg, - "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); - painCave.isFatal = 1; - simError(); - - } - - q.normalize(); - if (needQuaternion_) { - integrableObject->setQ(q); - } - - ji[0] = tokenizer.nextTokenAsDouble(); - ji[1] = tokenizer.nextTokenAsDouble(); - ji[2] = tokenizer.nextTokenAsDouble(); - if (needAngMom_) { - integrableObject->setJ(ji); - } + sprintf(painCave.errMsg, + "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); + painCave.isFatal = 1; + simError(); + + } + + q.normalize(); + if (needQuaternion_) { + integrableObject->setQ(q); + } + + ji[0] = tokenizer.nextTokenAsDouble(); + ji[1] = tokenizer.nextTokenAsDouble(); + ji[2] = tokenizer.nextTokenAsDouble(); + if (needAngMom_) { + integrableObject->setJ(ji); + } } - -} - - -void DumpReader::parseCommentLine(char* line, Snapshot* s) { + + } + + + void DumpReader::parseCommentLine(char* line, Snapshot* s) { double currTime; Mat3x3d hmat; double chi; double integralOfChiDt; Mat3x3d eta; - + StringTokenizer tokenizer(line); int nTokens; - + nTokens = tokenizer.countTokens(); - + //comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) if (nTokens < 10) { - sprintf(painCave.errMsg, - "DumpReader Error: Not enough tokens in comment line: %s", line); - painCave.isFatal = 1; - simError(); + sprintf(painCave.errMsg, + "DumpReader Error: Not enough tokens in comment line: %s", line); + painCave.isFatal = 1; + simError(); } - + //read current time currTime = tokenizer.nextTokenAsDouble(); s->setTime(currTime); @@ -612,29 +613,29 @@ void DumpReader::parseCommentLine(char* line, Snapshot //read chi and integralOfChidt, they should apprear in pair if (tokenizer.countTokens() >= 2) { - chi = tokenizer.nextTokenAsDouble(); - integralOfChiDt = tokenizer.nextTokenAsDouble(); - - s->setChi(chi); - s->setIntegralOfChiDt(integralOfChiDt); + chi = tokenizer.nextTokenAsDouble(); + integralOfChiDt = tokenizer.nextTokenAsDouble(); + + s->setChi(chi); + s->setIntegralOfChiDt(integralOfChiDt); } //read eta (eta is 3x3 matrix) if (tokenizer.countTokens() >= 9) { - eta(0, 0) = tokenizer.nextTokenAsDouble(); - eta(0, 1) = tokenizer.nextTokenAsDouble(); - eta(0, 2) = tokenizer.nextTokenAsDouble(); - eta(1, 0) = tokenizer.nextTokenAsDouble(); - eta(1, 1) = tokenizer.nextTokenAsDouble(); - eta(1, 2) = tokenizer.nextTokenAsDouble(); - eta(2, 0) = tokenizer.nextTokenAsDouble(); - eta(2, 1) = tokenizer.nextTokenAsDouble(); - eta(2, 2) = tokenizer.nextTokenAsDouble(); - - s->setEta(eta); + eta(0, 0) = tokenizer.nextTokenAsDouble(); + eta(0, 1) = tokenizer.nextTokenAsDouble(); + eta(0, 2) = tokenizer.nextTokenAsDouble(); + eta(1, 0) = tokenizer.nextTokenAsDouble(); + eta(1, 1) = tokenizer.nextTokenAsDouble(); + eta(1, 2) = tokenizer.nextTokenAsDouble(); + eta(2, 0) = tokenizer.nextTokenAsDouble(); + eta(2, 1) = tokenizer.nextTokenAsDouble(); + eta(2, 2) = tokenizer.nextTokenAsDouble(); + + s->setEta(eta); } - -} - + + } + }//end namespace oopse