--- trunk/src/io/DumpReader.cpp 2005/04/15 22:04:00 507
+++ trunk/src/io/DumpReader.cpp 2006/08/30 20:33:44 1025
@@ -1,641 +1,531 @@
-/*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
- *
- * The University of Notre Dame grants you ("Licensee") a
- * non-exclusive, royalty free, license to use, modify and
- * redistribute this software in source and binary code form, provided
- * that the following conditions are met:
- *
- * 1. Acknowledgement of the program authors must be made in any
- * publication of scientific results based in part on use of the
- * program. An acceptable form of acknowledgement is citation of
- * the article in which the program was described (Matthew
- * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- * Parallel Simulation Engine for Molecular Dynamics,"
- * J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- *
- * 3. Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the
- * distribution.
- *
- * This software is provided "AS IS," without a warranty of any
- * kind. All express or implied conditions, representations and
- * warranties, including any implied warranty of merchantability,
- * fitness for a particular purpose or non-infringement, are hereby
- * excluded. The University of Notre Dame and its licensors shall not
- * be liable for any damages suffered by licensee as a result of
- * using, modifying or distributing the software or its
- * derivatives. In no event will the University of Notre Dame or its
- * licensors be liable for any lost revenue, profit or data, or for
- * direct, indirect, special, consequential, incidental or punitive
- * damages, however caused and regardless of the theory of liability,
- * arising out of the use of or inability to use software, even if the
- * University of Notre Dame has been advised of the possibility of
- * such damages.
- */
-
-#define _LARGEFILE_SOURCE64
-#define _FILE_OFFSET_BITS 64
-
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#include <iostream>
-#include <math.h>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "io/DumpReader.hpp"
-#include "primitives/Molecule.hpp"
-#include "utils/simError.h"
-#include "utils/MemoryUtils.hpp"
-#include "utils/StringTokenizer.hpp"
-
-#ifdef IS_MPI
-
-#include <mpi.h>
-#define TAKE_THIS_TAG_CHAR 0
-#define TAKE_THIS_TAG_INT 1
-
-#endif // is_mpi
-
-
-namespace oopse {
+/*
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ *
+ * The University of Notre Dame grants you ("Licensee") a
+ * non-exclusive, royalty free, license to use, modify and
+ * redistribute this software in source and binary code form, provided
+ * that the following conditions are met:
+ *
+ * 1. Acknowledgement of the program authors must be made in any
+ * publication of scientific results based in part on use of the
+ * program. An acceptable form of acknowledgement is citation of
+ * the article in which the program was described (Matthew
+ * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
+ * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
+ * Parallel Simulation Engine for Molecular Dynamics,"
+ * J. Comput. Chem. 26, pp. 252-271 (2005))
+ *
+ * 2. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * 3. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the
+ * distribution.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded. The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * arising out of the use of or inability to use software, even if the
+ * University of Notre Dame has been advised of the possibility of
+ * such damages.
+ */
- DumpReader::DumpReader(SimInfo* info, const std::string& filename)
- : info_(info), filename_(filename), isScanned_(false), nframes_(0) {
+#define _LARGEFILE_SOURCE64
+#define _FILE_OFFSET_BITS 64
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <iostream>
+#include <math.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "io/DumpReader.hpp"
+#include "primitives/Molecule.hpp"
+#include "utils/simError.h"
+#include "utils/MemoryUtils.hpp"
+#include "utils/StringTokenizer.hpp"
+
+#ifdef IS_MPI
+
+#include <mpi.h>
+#define TAKE_THIS_TAG_CHAR 0
+#define TAKE_THIS_TAG_INT 1
+
+#endif // is_mpi
+
+
+namespace oopse {
+
+ DumpReader::DumpReader(SimInfo* info, const std::string& filename)
+ : info_(info), filename_(filename), isScanned_(false), nframes_(0) {
-#ifdef IS_MPI
+#ifdef IS_MPI
- if (worldRank == 0) {
-#endif
+ if (worldRank == 0) {
+#endif
- inFile_ = fopen(filename_.c_str(), "r");
+ inFile_ = new std::ifstream(filename_.c_str());
- if (inFile_ == NULL) {
- sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
- painCave.isFatal = 1;
- simError();
- }
+ if (inFile_->fail()) {
+ sprintf(painCave.errMsg,
+ "DumpReader: Cannot open file: %s\n",
+ filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
+ }
-#ifdef IS_MPI
+#ifdef IS_MPI
- }
+ }
- strcpy(checkPointMsg, "Dump file opened for reading successfully.");
- MPIcheckPoint();
+ strcpy(checkPointMsg, "Dump file opened for reading successfully.");
+ MPIcheckPoint();
-#endif
+#endif
- return;
- }
+ return;
+ }
- DumpReader::~DumpReader() {
+ DumpReader::~DumpReader() {
-#ifdef IS_MPI
+#ifdef IS_MPI
- if (worldRank == 0) {
-#endif
+ if (worldRank == 0) {
+#endif
- int error;
- error = fclose(inFile_);
+ delete inFile_;
- if (error) {
- sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
- painCave.isFatal = 1;
- simError();
- }
+#ifdef IS_MPI
- MemoryUtils::deletePointers(framePos_);
-
-#ifdef IS_MPI
-
- }
+ }
- strcpy(checkPointMsg, "Dump file closed successfully.");
- MPIcheckPoint();
+ strcpy(checkPointMsg, "Dump file closed successfully.");
+ MPIcheckPoint();
-#endif
+#endif
- return;
- }
+ return;
+ }
- int DumpReader::getNFrames(void) {
+ int DumpReader::getNFrames(void) {
+
+ if (!isScanned_)
+ scanFile();
+
+ return nframes_;
+ }
+
+ void DumpReader::scanFile(void) {
+ int lineNo = 0;
+ std::streampos prevPos;
+ std::streampos currPos;
- if (!isScanned_)
- scanFile();
+#ifdef IS_MPI
- return nframes_;
- }
-
- 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
+ if (worldRank == 0) {
+#endif // is_mpi
- 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++;
+ currPos = inFile_->tellg();
+ prevPos = currPos;
+ bool foundOpenSnapshotTag = false;
+ bool foundClosedSnapshotTag = false;
+ while(inFile_->getline(buffer, bufferSize)) {
+ ++lineNo;
+
+ std::string line = buffer;
+ currPos = inFile_->tellg();
+ if (line.find("<Snapshot>")!= std::string::npos) {
+ if (foundOpenSnapshotTag) {
+ sprintf(painCave.errMsg,
+ "DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
+ filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
+ }
+ foundOpenSnapshotTag = true;
+ foundClosedSnapshotTag = false;
+ framePos_.push_back(prevPos);
- 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();
+ } else if (line.find("</Snapshot>") != std::string::npos){
+ if (!foundOpenSnapshotTag) {
+ sprintf(painCave.errMsg,
+ "DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
+ filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
}
+
+ if (foundClosedSnapshotTag) {
+ sprintf(painCave.errMsg,
+ "DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
+ filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
+ }
+ foundClosedSnapshotTag = true;
+ foundOpenSnapshotTag = false;
}
-
- currPos = new fpos_t;
- fgetpos(inFile_, currPos);
- fgets(readBuffer, sizeof(readBuffer), inFile_);
- lineNum++;
+ prevPos = currPos;
}
- delete currPos;
- rewind(inFile_);
+ // only found <Snapshot> for the last frame means the file is corrupted, we should discard
+ // it and give a warning message
+ if (foundOpenSnapshotTag) {
+ sprintf(painCave.errMsg,
+ "DumpReader: last frame in %s is invalid\n", filename_.c_str());
+ painCave.isFatal = 0;
+ simError();
+ framePos_.pop_back();
+ }
- 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) {
- int storageLayout = info_->getSnapshotManager()->getStorageLayout();
-
- if (storageLayout & DataStorage::dslPosition) {
- needPos_ = true;
- } else {
- needPos_ = false;
- }
-
- if (storageLayout & DataStorage::dslVelocity) {
- needVel_ = true;
- } else {
- needVel_ = false;
- }
-
- if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
- needQuaternion_ = true;
- } else {
- needQuaternion_ = false;
- }
-
- if (storageLayout & DataStorage::dslAngularMomentum) {
- needAngMom_ = true;
- } else {
- 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;
-
-#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();
- }
-
- 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());
+ nframes_ = framePos_.size();
- 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();
- }
-
- 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);
- i++;
+ if (nframes_ == 0) {
+ sprintf(painCave.errMsg,
+ "DumpReader: %s does not contain a valid frame\n", filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
}
- }
+#ifdef IS_MPI
+ }
+
+ MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
- // MPI Section of code..........
+#endif // is_mpi
-#else //IS_MPI
-
- // first thing first, suspend fatalities.
+ isScanned_ = true;
+ }
+
+ void DumpReader::readFrame(int whichFrame) {
+ if (!isScanned_)
+ scanFile();
+
+ int storageLayout = info_->getSnapshotManager()->getStorageLayout();
+
+ if (storageLayout & DataStorage::dslPosition) {
+ needPos_ = true;
+ } else {
+ needPos_ = false;
+ }
+
+ if (storageLayout & DataStorage::dslVelocity) {
+ needVel_ = true;
+ } else {
+ needVel_ = false;
+ }
+
+ if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
+ needQuaternion_ = true;
+ } else {
+ needQuaternion_ = false;
+ }
+
+ if (storageLayout & DataStorage::dslAngularMomentum) {
+ needAngMom_ = true;
+ } else {
+ needAngMom_ = false;
+ }
+
+ readSet(whichFrame);
+ }
+
+ void DumpReader::readSet(int whichFrame) {
+ std::string line;
+
+#ifndef IS_MPI
+
+ inFile_->clear();
+ inFile_->seekg(framePos_[whichFrame]);
+
+ std::istream& inputStream = *inFile_;
+
+#else
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;
-
+ std::stringstream sstream;
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();
- }
+ std::string sendBuffer;
+
+ inFile_->clear();
+ inFile_->seekg(framePos_[whichFrame]);
- 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();
+ while (inFile_->getline(buffer, bufferSize)) {
+
+ line = buffer;
+ sendBuffer += line;
+ sendBuffer += '\n';
+ if (line.find("</Snapshot>") != std::string::npos) {
+ break;
+ }
}
+
+ 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);
- //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);
+ sstream.str(sendBuffer);
+ } else {
+ int sendBufferSize;
+ MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
+ char * recvBuffer = new char[sendBufferSize+1];
+ MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
+ sstream.str(recvBuffer);
+ }
+
+ std::istream& inputStream = sstream;
+#endif
+
+ inputStream.getline(buffer, bufferSize);
+
+ line = buffer;
+ if (line.find("<Snapshot>") == std::string::npos) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: can not find <Snapshot>\n");
+ painCave.isFatal = 1;
+ simError();
+ }
+
+ //read frameData
+ readFrameProperties(inputStream);
+
+ //read StuntDoubles
+ readStuntDoubles(inputStream);
+
+ inputStream.getline(buffer, bufferSize);
+ line = buffer;
+ if (line.find("</Snapshot>") == std::string::npos) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: can not find </Snapshot>\n");
+ painCave.isFatal = 1;
+ simError();
+ }
+
+ }
+
+ void DumpReader::parseDumpLine(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();
+ }
+
+ int index = tokenizer.nextTokenAsInt();
+
+ StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
+
+ if (integrableObject == NULL) {
+ return;
+ }
+ std::string type = tokenizer.nextToken();
+ int size = type.size();
+ for(int i = 0; i < size; ++i) {
+ switch(type[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);
+ case 'p': {
+ Vector3d pos;
+ pos[0] = tokenizer.nextTokenAsDouble();
+ pos[1] = tokenizer.nextTokenAsDouble();
+ pos[2] = tokenizer.nextTokenAsDouble();
+ if (needPos_) {
+ integrableObject->setPos(pos);
+ }
+ break;
+ }
+ case 'v' : {
+ Vector3d vel;
+ vel[0] = tokenizer.nextTokenAsDouble();
+ vel[1] = tokenizer.nextTokenAsDouble();
+ vel[2] = tokenizer.nextTokenAsDouble();
+ if (needVel_) {
+ integrableObject->setVel(vel);
+ }
+ break;
+ }
+
+ case 'q' : {
+ Quat4d q;
+ if (integrableObject->isDirectional()) {
- 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);
+ q[0] = tokenizer.nextTokenAsDouble();
+ q[1] = tokenizer.nextTokenAsDouble();
+ q[2] = tokenizer.nextTokenAsDouble();
+ q[3] = tokenizer.nextTokenAsDouble();
- painCave.isFatal = 1;
- simError();
- }
-
- MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
- TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
+ RealType 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);
+ }
+ }
+ break;
+ }
+ case 'j' : {
+ Vector3d ji;
+ if (integrableObject->isDirectional()) {
+ ji[0] = tokenizer.nextTokenAsDouble();
+ ji[1] = tokenizer.nextTokenAsDouble();
+ ji[2] = tokenizer.nextTokenAsDouble();
+ if (needAngMom_) {
+ integrableObject->setJ(ji);
+ }
}
+ }
+ case 'f': {
+
+ Vector3d force;
+ force[0] = tokenizer.nextTokenAsDouble();
+ force[1] = tokenizer.nextTokenAsDouble();
+ force[2] = tokenizer.nextTokenAsDouble();
+ integrableObject->setFrc(force);
+ break;
}
+ case 't' : {
+
+ Vector3d torque;
+ torque[0] = tokenizer.nextTokenAsDouble();
+ torque[1] = tokenizer.nextTokenAsDouble();
+ torque[2] = tokenizer.nextTokenAsDouble();
+ integrableObject->setTrq(torque);
+ break;
+ }
+ default: {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: %s is an unrecognized type\n", type.c_str());
+ painCave.isFatal = 1;
+ simError();
+ break;
+ }
+
}
- } else {
- //actions taken at slave nodes
- MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
-
- /**@todo*/
- parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
+ }
+
+ }
+
+
+ void DumpReader::readStuntDoubles(std::istream& inputStream) {
+
+ inputStream.getline(buffer, bufferSize);
+ std::string line(buffer);
+
+ if (line.find("<StuntDoubles>") == std::string::npos) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: Missing <StuntDoubles>\n");
+ painCave.isFatal = 1;
+ simError();
+ }
+
+ while(inputStream.getline(buffer, bufferSize)) {
+ line = buffer;
- 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);
- }
-
- }
-
+ if(line.find("</StuntDoubles>") != std::string::npos) {
+ break;
}
-
+
+ parseDumpLine(line);
}
-
-#endif
-
- }
- void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
-
- Vector3d pos; // position place holders
- Vector3d vel; // velocity placeholders
- Quat4d q; // the quaternions
- Vector3d ji; // angular velocity placeholders;
- StringTokenizer tokenizer(line);
- int nTokens;
-
- nTokens = tokenizer.countTokens();
-
- if (nTokens < 14) {
- sprintf(painCave.errMsg,
- "DumpReader Error: Not enough Tokens.\n%s\n", line);
- painCave.isFatal = 1;
- simError();
+ }
+
+ void DumpReader::readFrameProperties(std::istream& inputStream) {
+
+ Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
+ inputStream.getline(buffer, bufferSize);
+ std::string line(buffer);
+
+ if (line.find("<FrameData>") == std::string::npos) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: Missing <FrameData>\n");
+ painCave.isFatal = 1;
+ simError();
}
-
- std::string name = tokenizer.nextToken();
-
- if (name != integrableObject->getType()) {
+
+ while(inputStream.getline(buffer, bufferSize)) {
+ line = buffer;
- 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);
- }
-
- vel[0] = tokenizer.nextTokenAsDouble();
- vel[1] = tokenizer.nextTokenAsDouble();
- vel[2] = tokenizer.nextTokenAsDouble();
- if (needVel_) {
- 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
-
- 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);
+ if(line.find("</FrameData>") != std::string::npos) {
+ break;
}
- ji[0] = tokenizer.nextTokenAsDouble();
- ji[1] = tokenizer.nextTokenAsDouble();
- ji[2] = tokenizer.nextTokenAsDouble();
- if (needAngMom_) {
- integrableObject->setJ(ji);
+ StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
+ if (!tokenizer.hasMoreTokens()) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
+ painCave.isFatal = 1;
+ simError();
}
- }
-
- }
-
-
- 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();
- }
-
- //read current time
- currTime = tokenizer.nextTokenAsDouble();
- s->setTime(currTime);
-
- //read h-matrix
- hmat(0, 0) = tokenizer.nextTokenAsDouble();
- hmat(0, 1) = tokenizer.nextTokenAsDouble();
- hmat(0, 2) = tokenizer.nextTokenAsDouble();
- hmat(1, 0) = tokenizer.nextTokenAsDouble();
- hmat(1, 1) = tokenizer.nextTokenAsDouble();
- hmat(1, 2) = tokenizer.nextTokenAsDouble();
- hmat(2, 0) = tokenizer.nextTokenAsDouble();
- hmat(2, 1) = tokenizer.nextTokenAsDouble();
- hmat(2, 2) = tokenizer.nextTokenAsDouble();
- s->setHmat(hmat);
-
- //read chi and integralOfChidt, they should apprear in pair
- if (tokenizer.countTokens() >= 2) {
- chi = tokenizer.nextTokenAsDouble();
- integralOfChiDt = tokenizer.nextTokenAsDouble();
+
+ std::string propertyName = tokenizer.nextToken();
+ if (propertyName == "Time") {
+ RealType currTime = tokenizer.nextTokenAsDouble();
+ s->setTime(currTime);
+ } else if (propertyName == "Hmat"){
+ Mat3x3d hmat;
+ hmat(0, 0) = tokenizer.nextTokenAsDouble();
+ hmat(0, 1) = tokenizer.nextTokenAsDouble();
+ hmat(0, 2) = tokenizer.nextTokenAsDouble();
+ hmat(1, 0) = tokenizer.nextTokenAsDouble();
+ hmat(1, 1) = tokenizer.nextTokenAsDouble();
+ hmat(1, 2) = tokenizer.nextTokenAsDouble();
+ hmat(2, 0) = tokenizer.nextTokenAsDouble();
+ hmat(2, 1) = tokenizer.nextTokenAsDouble();
+ 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);
+ } else if (propertyName == "Barostat") {
+ Mat3x3d 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);
+ } else {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
+ painCave.isFatal = 0;
+ simError();
+ }
- 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);
- }
-
-
+
}
-
-}//end namespace oopse
+
+
+}//end namespace oopse