--- trunk/src/io/DumpReader.cpp 2005/03/07 22:39:33 398
+++ trunk/src/io/DumpReader.cpp 2006/05/17 21:51:42 963
@@ -1,640 +1,630 @@
- /*
- * 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.
- */
+/*
+ * 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
-#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
-
- 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();
- }
-
-#ifdef IS_MPI
-
- }
-
- strcpy(checkPointMsg, "Dump file opened for reading successfully.");
- MPIcheckPoint();
-
-#endif
-
- return;
-}
-
-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_);
-
-#ifdef IS_MPI
-
- }
-
- strcpy(checkPointMsg, "Dump file closed successfully.");
- MPIcheckPoint();
-
-#endif
-
- return;
-}
-
-int DumpReader::getNFrames(void) {
-
- if (!isScanned_)
- scanFile();
-
- 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
-
- 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,"
- " 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();
-#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());
-
- 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
-
- 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);
-
- }
- }
-
- // 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());
-
- 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);
- }
- }
- }
- } 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);
- }
-
- }
-
- }
-
- }
-
-#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();
- }
-
- 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();
- }
-
- 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();
-
+#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
+
+ if (worldRank == 0) {
+#endif
+
+ inFile_ = new std::ifstream(filename_.c_str());
+
+ if (inFile_->fail()) {
+ 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() {
+
+#ifdef IS_MPI
+
+ if (worldRank == 0) {
+#endif
+
+ delete inFile_;
+
+#ifdef IS_MPI
+
+ }
+
+ strcpy(checkPointMsg, "Dump file closed successfully.");
+ MPIcheckPoint();
+
+#endif
+
+ return;
+ }
+
+ int DumpReader::getNFrames(void) {
+
+ if (!isScanned_)
+ scanFile();
+
+ return nframes_;
+ }
+
+ void DumpReader::scanFile(void) {
+ int i, j;
+ int lineNum = 0;
+ char readBuffer[maxBufferSize];
+ std::streampos currPos;
+
+#ifdef IS_MPI
+
+ if (worldRank == 0) {
+#endif // is_mpi
+
+ inFile_->seekg (0, std::ios::beg);
+
+
+ currPos = inFile_->tellg();
+ inFile_->getline(readBuffer, sizeof(readBuffer));
+ lineNum++;
+
+ if (inFile_->eof()) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
+ filename_.c_str(),
+ lineNum);
+ painCave.isFatal = 1;
+ simError();
+ }
+
+ while (!inFile_->eof()) {
+ framePos_.push_back(currPos);
+
+ i = atoi(readBuffer);
+
+ inFile_->getline(readBuffer, sizeof(readBuffer));
+ lineNum++;
+
+ if (inFile_->eof()) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
+ filename_.c_str(),
+ lineNum);
+ 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) {
- 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();
-
- 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
+
+ for(j = 0; j < i; j++) {
+ inFile_->getline(readBuffer, sizeof(readBuffer));
+ lineNum++;
+
+ if (inFile_->eof()) {
+ 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 = inFile_->tellg();
+ inFile_->getline(readBuffer, sizeof(readBuffer));
+ lineNum++;
+ }
+
+ inFile_->seekg (0, std::ios::beg);
+
+ 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) {
+ 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) {
+ 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
+ inFile_->clear();
+ inFile_->seekg(framePos_[whichFrame]);
+
+ if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
+ 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();
+ }
+
+ //read the box mat from the comment line
+
+
+ if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
+ 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)) {
+
+
+
+ if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
+ 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) {
+ inFile_->clear();
+ inFile_->seekg(framePos_[whichFrame]);
+
+ if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
+ 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
+
+
+
+ if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
+ 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)){
+
+
+
+ if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
+ 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++) {
+
+
+ if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
+ 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);
+ }
+
+ }
+
+ }
+
+ }
+
+#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();
+ }
+
+ 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();
+ }
+
+ 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();
+
+ 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);
+ }
+
+ ji[0] = tokenizer.nextTokenAsDouble();
+ ji[1] = tokenizer.nextTokenAsDouble();
+ ji[2] = tokenizer.nextTokenAsDouble();
+ if (needAngMom_) {
+ integrableObject->setJ(ji);
+ }
+ }
+
+ }
+
+
+ void DumpReader::parseCommentLine(char* line, Snapshot* s) {
+ RealType currTime;
+ Mat3x3d hmat;
+ RealType chi;
+ RealType 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();
+
+ 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