--- trunk/src/io/DumpReader.cpp 2004/09/24 16:27:58 3
+++ trunk/src/io/DumpReader.cpp 2005/01/25 17:45:23 273
@@ -1,3 +1,44 @@
+ /*
+ * 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
@@ -11,756 +52,551 @@
#include <stdlib.h>
#include <string.h>
-
-#include "io/ReadWrite.hpp"
+#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>
-#include "brains/mpiSimulation.hpp"
#define TAKE_THIS_TAG_CHAR 0
#define TAKE_THIS_TAG_INT 1
+
#endif // is_mpi
-DumpReader :: DumpReader(const char *in_name ){
+namespace oopse {
- isScanned = false;
+DumpReader::DumpReader(SimInfo* info, const std::string& filename)
+ : info_(info), filename_(filename), isScanned_(false), nframes_(0) {
#ifdef IS_MPI
- if (worldRank == 0) {
+
+ if (worldRank == 0) {
#endif
- inFile = fopen(in_name, "r");
- if(inFile == NULL){
- sprintf(painCave.errMsg,
- "Cannot open file: %s\n", in_name);
- painCave.isFatal = 1;
- simError();
- }
-
- inFileName = in_name;
+ 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();
+
+ }
+
+ strcpy(checkPointMsg, "Dump file opened for reading successfully.");
+ MPIcheckPoint();
+
#endif
- return;
+
+ return;
}
-DumpReader :: ~DumpReader( ){
+DumpReader::~DumpReader() {
+
#ifdef IS_MPI
- if (worldRank == 0) {
+
+ if (worldRank == 0) {
#endif
- vector<fpos_t*>::iterator i;
- int error;
- error = fclose( inFile );
- if( error ){
- sprintf( painCave.errMsg,
- "Error closing %s\n", inFileName.c_str());
- simError();
- }
+ int error;
+ error = fclose(inFile_);
- for(i = framePos.begin(); i != framePos.end(); ++i)
- delete *i;
- framePos.clear();
-
+ if (error) {
+ sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
+ }
+
+ MemoryUtils::deleteVectorOfPointer(framePos_);
+
#ifdef IS_MPI
- }
- strcpy( checkPointMsg, "Dump file closed successfully." );
- MPIcheckPoint();
+
+ }
+
+ strcpy(checkPointMsg, "Dump file closed successfully.");
+ MPIcheckPoint();
+
#endif
- return;
+ return;
}
-int DumpReader::getNframes( void ){
+int DumpReader::getNFrames(void) {
- if( !isScanned )
- scanFile();
- return framePos.size();
+ if (!isScanned_)
+ scanFile();
+
+ return nframes_;
}
-void DumpReader::scanFile( void ){
-
+void DumpReader::scanFile(void) {
int i, j;
int lineNum = 0;
- char readBuffer[2000];
- fpos_t *currPos;
+ char readBuffer[maxBufferSize];
+ fpos_t * currPos;
#ifdef IS_MPI
- if( worldRank == 0 ){
+
+ 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,
- "File \"%s\" ended unexpectedly at line %d\n",
- inFileName.c_str(),
- lineNum );
- painCave.isFatal = 1;
- simError();
- }
- while( !feof( inFile ) ){
-
- framePos.push_back(currPos);
+ rewind(inFile_);
- i = atoi(readBuffer);
-
- fgets( readBuffer, sizeof( readBuffer ), inFile );
- lineNum++;
- if( feof( inFile ) ){
- sprintf( painCave.errMsg,
- "File \"%s\" ended unexpectedly at line %d\n",
- inFileName.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,
- "File \"%s\" ended unexpectedly at line %d,"
- " with atom %d\n",
- inFileName.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 );
-
- isScanned = true;
+ currPos = new fpos_t;
+ fgetpos(inFile_, currPos);
+ fgets(readBuffer, sizeof(readBuffer), inFile_);
+ lineNum++;
-#ifdef IS_MPI
- }
- strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
- MPIcheckPoint();
-#endif // is_mpi
-}
+ if (feof(inFile_)) {
+ sprintf(painCave.errMsg,
+ "File \"%s\" ended unexpectedly at line %d\n",
+ filename_.c_str(),
+ lineNum);
+ painCave.isFatal = 1;
+ simError();
+ }
-void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
+ while (!feof(inFile_)) {
+ framePos_.push_back(currPos);
- simnfo = the_simnfo;
+ i = atoi(readBuffer);
- this->readSet( whichFrame );
-}
+ fgets(readBuffer, sizeof(readBuffer), inFile_);
+ lineNum++;
+ if (feof(inFile_)) {
+ sprintf(painCave.errMsg,
+ "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++;
-void DumpReader :: readSet( int whichFrame ){
+ if (feof(inFile_)) {
+ sprintf(painCave.errMsg,
+ "File \"%s\" ended unexpectedly at line %d,"
+ " with atom %d\n", filename_.c_str(),
+ lineNum,
+ j);
- int i;
- unsigned int 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
- int done, which_node, which_atom; // loop counter
-#endif //is_mpi
+ }
- const int BUFFERSIZE = 2000; // size of the read buffer
- int nTotObjs; // the number of atoms
- char read_buffer[BUFFERSIZE]; //the line buffer for reading
+ MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
- char *eof_test; // ptr to see when we reach the end of the file
- char *parseErr;
+ strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
+ MPIcheckPoint();
- vector<StuntDouble*> integrableObjects;
+#endif // is_mpi
+ isScanned_ = true;
+}
-#ifndef IS_MPI
+void DumpReader::readFrame(int whichFrame) {
+ readSet(whichFrame);
+}
- 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",
- inFileName.c_str() );
- painCave.isFatal = 1;
- simError();
- }
+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
- nTotObjs = atoi( read_buffer );
+ Molecule* mol;
+ StuntDouble* integrableObject;
+ SimInfo::MoleculeIterator mi;
+ Molecule::IntegrableObjectIterator ii;
- if( nTotObjs != simnfo->getTotIntegrableObjects() ){
- sprintf( painCave.errMsg,
- "DumpReader error. %s nIntegrable, %d, "
- "does not match the meta-data file's nIntegrable, %d.\n",
- inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
- painCave.isFatal = 1;
- simError();
- }
+#ifndef IS_MPI
- //read the box mat from the comment line
+ fsetpos(inFile_, framePos_[whichFrame]);
+ eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
- eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
- if(eof_test == NULL){
- sprintf( painCave.errMsg,
- "error in reading commment in %s\n", inFileName.c_str());
- painCave.isFatal = 1;
- simError();
- }
-
- parseErr = parseCommentLine( read_buffer, simnfo);
- if( parseErr != NULL ){
- strcpy( painCave.errMsg, parseErr );
- painCave.isFatal = 1;
- simError();
- }
-
- //parse dump lines
-
- for( i=0; i < simnfo->n_mol; i++){
-
- integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
-
- for(j = 0; j < integrableObjects.size(); j++){
-
- eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
- if(eof_test == NULL){
+ if (eof_test == NULL) {
sprintf(painCave.errMsg,
- "error in reading file %s\n"
- "natoms = %d; index = %d\n"
- "error reading the line from the file.\n",
- inFileName.c_str(), nTotObjs, i );
+ "DumpReader error: error reading 1st line of \"%s\"\n",
+ filename_.c_str());
painCave.isFatal = 1;
simError();
- }
-
- parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
- if( parseErr != NULL ){
- strcpy( painCave.errMsg, parseErr );
- painCave.isFatal = 1;
- simError();
- }
}
- }
- // MPI Section of code..........
-#else //IS_MPI
+ nTotObjs = atoi(read_buffer);
- // first thing first, suspend fatalities.
- painCave.isEventLoop = 1;
+ 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());
- int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
- int haveError;
+ painCave.isFatal = 1;
+ simError();
+ }
- MPI_Status istatus;
- int *MolToProcMap = mpiSim->getMolToProcMap();
- int localIndex;
- int nCurObj;
- int nitems;
+ //read the box mat from the comment line
- nTotObjs = simnfo->getTotIntegrableObjects();
- haveError = 0;
- if (worldRank == 0) {
- fsetpos(inFile, framePos[whichFrame]);
+ eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
- eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
- if( eof_test == NULL ){
- sprintf( painCave.errMsg,
- "Error reading 1st line of %s \n ",inFileName.c_str());
- haveError = 1;
- simError();
+ if (eof_test == NULL) {
+ sprintf(painCave.errMsg, "error in reading commment in %s\n",
+ filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
}
- nitems = atoi( read_buffer );
+ parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
- // Check to see that the number of integrable objects in the
- // intial configuration file is the same as derived from the
- // meta-data file.
+ //parse dump lines
- if( nTotObjs != nitems){
- sprintf( painCave.errMsg,
- "DumpReader Error. %s nIntegrable, %d, "
- "does not match the meta-data file's nIntegrable, %d.\n",
- inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
- haveError= 1;
- simError();
- }
+ for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
- //read the boxMat from the comment line
+ 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,
- "error in reading commment in %s\n", inFileName.c_str());
- haveError = 1;
- simError();
- }
+ eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
- //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
+ if (eof_test == NULL) {
+ sprintf(painCave.errMsg,
+ "error in reading file %s\n"
+ "natoms = %d; index = %d\n"
+ "error reading the line from the file.\n",
+ filename_.c_str(),
+ nTotObjs,
+ i);
- MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
+ painCave.isFatal = 1;
+ simError();
+ }
- parseErr = parseCommentLine( read_buffer, simnfo);
-
- if( parseErr != NULL ){
- strcpy( painCave.errMsg, parseErr );
- haveError = 1;
- simError();
+ parseDumpLine(read_buffer, integrableObject);
+
+ }
}
- for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
- which_node = MolToProcMap[i];
- if(which_node == 0){
- //molecules belong to master node
+ // MPI Section of code..........
- localIndex = mpiSim->getGlobalToLocalMol(i);
+#else //IS_MPI
- if(localIndex == -1) {
- strcpy(painCave.errMsg, "Molecule not found on node 0!");
- haveError = 1;
- simError();
- }
+ // first thing first, suspend fatalities.
+ int masterNode = 0;
+ int nCurObj;
+ painCave.isEventLoop = 1;
- integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
- for(j=0; j < integrableObjects.size(); j++){
-
- eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
- if(eof_test == NULL){
- sprintf(painCave.errMsg,
- "error in reading file %s\n"
- "natoms = %d; index = %d\n"
- "error reading the line from the file.\n",
- inFileName.c_str(), nTotObjs, i );
- haveError= 1;
- simError();
- }
-
- if(haveError) nodeZeroError();
+ int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
+ int haveError;
- parseDumpLine(read_buffer, integrableObjects[j]);
-
- }
+ MPI_Status istatus;
+ int nitems;
+ nTotObjs = info_->getNGlobalIntegrableObjects();
+ haveError = 0;
- }
- else{
- //molecule belongs to slave nodes
+ if (worldRank == masterNode) {
+ fsetpos(inFile_, framePos_[whichFrame]);
- MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-
- for(j=0; j < nCurObj; j++){
-
- eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
- if(eof_test == NULL){
- sprintf(painCave.errMsg,
- "error in reading file %s\n"
- "natoms = %d; index = %d\n"
- "error reading the line from the file.\n",
- inFileName.c_str(), nTotObjs, i );
- haveError= 1;
- simError();
- }
-
- if(haveError) nodeZeroError();
+ eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
- MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
- TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
-
- }
-
- }
-
- }
-
- }
- else{
- //actions taken at slave nodes
- MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
-
- parseErr = parseCommentLine( read_buffer, simnfo);
-
- if( parseErr != NULL ){
- strcpy( painCave.errMsg, parseErr );
- haveError = 1;
- simError();
- }
-
- for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
- which_node = MolToProcMap[i];
-
- if(which_node == worldRank){
- //molecule with global index i belongs to this processor
-
- localIndex = mpiSim->getGlobalToLocalMol(i);
-
- if(localIndex == -1) {
- sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
- haveError = 1;
- simError();
+ if (eof_test == NULL) {
+ sprintf(painCave.errMsg, "Error reading 1st line of %s \n ",
+ filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
}
- integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
+ nitems = atoi(read_buffer);
- nCurObj = integrableObjects.size();
-
- MPI_Send(&nCurObj, 1, MPI_INT, 0,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
+ // Check to see that the number of integrable objects in the
+ // intial configuration file is the same as derived from the
+ // meta-data file.
- for(j = 0; j < integrableObjects.size(); j++){
-
- MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
- TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
-
- parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
-
- if( parseErr != NULL ){
- strcpy( painCave.errMsg, parseErr );
- simError();
- }
+ 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
-#endif
-}
+ eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
-char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
+ if (eof_test == NULL) {
+ sprintf(painCave.errMsg, "error in reading commment in %s\n",
+ filename_.c_str());
+ painCave.isFatal = 1;
+ simError();
+ }
- char *foo; // the pointer to the current string token
+ //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
- double pos[3]; // position place holders
- double vel[3]; // velocity placeholders
- double q[4]; // the quaternions
- double ji[3]; // angular velocity placeholders;
- double qSqr, qLength; // needed to normalize the quaternion vector.
+ 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);
- // set the string tokenizer
+ if (which_node == masterNode) {
+ //molecules belong to master node
- foo = strtok(readLine, " ,;\t");
+ mol = info_->getMoleculeByGlobalIndex(i);
- // check the atom name to the current atom
+ if (mol == NULL) {
+ sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
+ painCave.isFatal = 1;
+ simError();
+ }
- if( strcmp( foo, sd->getType() ) ){
- sprintf( painCave.errMsg,
- "DumpReader error. Does not"
- " match the meta-data atom %s.\n",
- sd->getType() );
- return strdup( painCave.errMsg );
- }
+ for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
+ integrableObject = mol->nextIntegrableObject(ii)){
+
+ eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
- // get the positions
+ if (eof_test == NULL) {
+ sprintf(painCave.errMsg,
+ "error in reading file %s\n"
+ "natoms = %d; index = %d\n"
+ "error reading the line from the file.\n",
+ filename_.c_str(),
+ nTotObjs,
+ i);
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading postition x from %s\n",
- inFileName.c_str());
- return strdup( painCave.errMsg );
- }
- pos[0] = atof( foo );
+ painCave.isFatal = 1;
+ simError();
+ }
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading postition y from %s\n",
- inFileName.c_str());
- return strdup( painCave.errMsg );
- }
- pos[1] = atof( foo );
+ parseDumpLine(read_buffer, integrableObject);
+ }
+ } else {
+ //molecule belongs to slave nodes
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading postition z from %s\n",
- inFileName.c_str());
- return strdup( painCave.errMsg );
- }
- pos[2] = atof( foo );
+ 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_);
- // get the velocities
+ if (eof_test == NULL) {
+ sprintf(painCave.errMsg,
+ "error in reading file %s\n"
+ "natoms = %d; index = %d\n"
+ "error reading the line from the file.\n",
+ filename_.c_str(),
+ nTotObjs,
+ i);
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- vel[0] = atof( foo );
+ 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);
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- vel[1] = atof( foo );
+ /**@todo*/
+ parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- vel[2] = atof( foo );
+ 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, "Molecule not found on node %d!", worldRank);
+ painCave.isFatal = 1;
+ simError();
+ }
+
+ nCurObj = mol->getNIntegrableObjects();
- // add the positions and velocities to the atom
+ MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
+ MPI_COMM_WORLD);
- sd->setPos( pos );
- sd->setVel( vel );
+ 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);
- if (!sd->isDirectional())
- return NULL;
+ parseDumpLine(read_buffer, integrableObject);
+ }
+
+ }
+
+ }
+
+ }
- // get the quaternions
+#endif
- if( sd->isDirectional() ){
+}
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- q[0] = atof( foo );
+void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- q[1] = atof( foo );
+ 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();
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
+ if (nTokens < 14) {
+ sprintf(painCave.errMsg,
+ "Not enough Tokens.\n");
+ painCave.isFatal = 1;
+ simError();
}
- q[2] = atof( foo );
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- q[3] = atof( foo );
+ std::string name = tokenizer.nextToken();
- // get the angular velocities
-
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
+ if (name != integrableObject->getType()) {
+
}
- ji[0] = atof( foo );
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- ji[1] = atof(foo );
+ pos[0] = tokenizer.nextTokenAsDouble();
+ pos[1] = tokenizer.nextTokenAsDouble();
+ pos[2] = tokenizer.nextTokenAsDouble();
+ integrableObject->setPos(pos);
+
+ vel[0] = tokenizer.nextTokenAsDouble();
+ vel[1] = tokenizer.nextTokenAsDouble();
+ vel[2] = tokenizer.nextTokenAsDouble();
+ integrableObject->setVel(vel);
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading velocity x from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- ji[2] = atof( foo );
+ 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,
+ "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
+ painCave.isFatal = 1;
+ simError();
+
+ }
- // check that the quaternion vector is normalized
-
- qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
-
- if (fabs(qSqr) < 1e-6) {
- sprintf(painCave.errMsg,
- "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
- return strdup(painCave.errMsg);
+ q.normalize();
+
+ integrableObject->setQ(q);
+
+ ji[0] = tokenizer.nextTokenAsDouble();
+ ji[1] = tokenizer.nextTokenAsDouble();
+ ji[2] = tokenizer.nextTokenAsDouble();
+ integrableObject->setJ(ji);
}
- qLength = sqrt( qSqr );
- q[0] = q[0] / qLength;
- q[1] = q[1] / qLength;
- q[2] = q[2] / qLength;
- q[3] = q[3] / qLength;
-
- // add quaternion and angular velocities
-
- sd->setQ( q );
- sd->setJ( ji );
- }
-
-
-
- return NULL;
}
-char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
+void DumpReader::parseCommentLine(char* line, Snapshot* s) {
+ double currTime;
+ Mat3x3d hmat;
+ double chi;
+ double integralOfChiDt;
+ Mat3x3d eta;
- double currTime;
- double boxMat[9];
- double theBoxMat3[3][3];
- double chi;
- double integralOfChidt;
- double eta[9];
+ StringTokenizer tokenizer(line);
+ int nTokens;
- char *foo; // the pointer to the current string token
+ nTokens = tokenizer.countTokens();
- // set the string tokenizer
-
- foo = strtok(readLine, " ,;\t");
- // set the timeToken.
-
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading Time from %s\n",
- inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
-
- currTime = atof( foo );
- entry_plug->setTime( currTime );
-
- //get H-Matrix
-
- for(int i = 0 ; i < 9; i++){
- foo = strtok(NULL, " ,;\t");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading H[%d] from %s\n", i, inFileName.c_str() );
- return strdup( painCave.errMsg );
+ //comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
+ if (nTokens < 10) {
+ sprintf(painCave.errMsg,
+ "Not enough tokens in comment line: %s", line);
+ painCave.isFatal = 1;
+ simError();
}
- boxMat[i] = atof( foo );
- }
- for(int i=0;i<3;i++)
- for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
+ //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 integrablOfChidt, they should apprear in pair
+ if (tokenizer.countTokens() >= 2) {
+ chi = tokenizer.nextTokenAsDouble();
+ integralOfChiDt = tokenizer.nextTokenAsDouble();
- //set H-Matrix
- entry_plug->setBoxM( theBoxMat3 );
-
- //get chi and integralOfChidt, they should appear by pair
-
- if( entry_plug->useInitXSstate ){
- foo = strtok(NULL, " ,;\t\n");
- if(foo != NULL){
- chi = atof(foo);
-
- foo = strtok(NULL, " ,;\t\n");
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- integralOfChidt = atof( foo );
-
- //push chi and integralOfChidt into SimInfo::properties which can be
- //retrieved by integrator later
- DoubleData* chiValue = new DoubleData();
- chiValue->setID(CHIVALUE_ID);
- chiValue->setData(chi);
- entry_plug->addProperty(chiValue);
-
- DoubleData* integralOfChidtValue = new DoubleData();
- integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
- integralOfChidtValue->setData(integralOfChidt);
- entry_plug->addProperty(integralOfChidtValue);
-
+ s->setChi(chi);
+ s->setIntegralOfChiDt(integralOfChiDt);
}
- else
- return NULL;
- //get eta
- foo = strtok(NULL, " ,;\t\n");
- if(foo != NULL ){
-
- for(int i = 0 ; i < 9; i++){
-
- if(foo == NULL){
- sprintf( painCave.errMsg,
- "error in reading eta[%d] from %s\n", i, inFileName.c_str() );
- return strdup( painCave.errMsg );
- }
- eta[i] = atof( foo );
- foo = strtok(NULL, " ,;\t\n");
- }
+ //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);
}
- else
- return NULL;
-
- //push eta into SimInfo::properties which can be
- //retrieved by integrator later
- //entry_plug->setBoxM( theBoxMat3 );
- DoubleArrayData* etaValue = new DoubleArrayData();
- etaValue->setID(ETAVALUE_ID);
- etaValue->setData(eta, 9);
- entry_plug->addProperty(etaValue);
- }
- return NULL;
+
}
-#ifdef IS_MPI
-void DumpReader::nodeZeroError( void ){
- int j, myStatus;
-
- myStatus = 0;
- for (j = 0; j < mpiSim->getNProcessors(); j++) {
- MPI_Send( &myStatus, 1, MPI_INT, j,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
- }
-
-
- MPI_Finalize();
- exit (0);
-
-}
-
-void DumpReader::anonymousNodeDie( void ){
-
- MPI_Finalize();
- exit (0);
-}
-#endif
+}//end namespace oopse