--- trunk/src/io/DumpReader.cpp 2004/09/24 04:16:43 2
+++ branches/development/src/io/DumpReader.cpp 2010/07/09 23:08:25 1465
@@ -1,766 +1,580 @@
-#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 "ReadWrite.hpp"
-#include "simError.h"
-
-#ifdef IS_MPI
-#include <mpi.h>
-#include "mpiSimulation.hpp"
-#define TAKE_THIS_TAG_CHAR 0
-#define TAKE_THIS_TAG_INT 1
-#endif // is_mpi
-
-
-DumpReader :: DumpReader(const char *in_name ){
-
- isScanned = false;
-
-#ifdef IS_MPI
- 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();
- }
+/*
+ * Copyright (c) 2009 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. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * 2. 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.
+ *
+ * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work. Good starting points are:
+ *
+ * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
+ * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
+ * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
+ * [4] Vardeman & Gezelter, in progress (2009).
+ */
- inFileName = in_name;
-#ifdef IS_MPI
- }
- strcpy( checkPointMsg, "Dump file opened for reading successfully." );
- MPIcheckPoint();
-#endif
- return;
-}
-
-DumpReader :: ~DumpReader( ){
-#ifdef IS_MPI
- 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();
- }
-
- for(i = framePos.begin(); i != framePos.end(); ++i)
- delete *i;
- framePos.clear();
+#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 OpenMD {
+
+ DumpReader::DumpReader(SimInfo* info, const std::string& filename)
+ : info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
+
+#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.");
+ errorCheckPoint();
+
+#endif
+
+ return;
+ }
-#ifdef IS_MPI
- }
- strcpy( checkPointMsg, "Dump file closed successfully." );
- MPIcheckPoint();
-#endif
-
- return;
-}
-
-int DumpReader::getNframes( void ){
-
- if( !isScanned )
- scanFile();
- return framePos.size();
-}
-
-void DumpReader::scanFile( void ){
-
- int i, j;
- int lineNum = 0;
- char readBuffer[2000];
- fpos_t *currPos;
-
-#ifdef IS_MPI
- if( worldRank == 0 ){
-#endif // is_mpi
+ DumpReader::~DumpReader() {
- rewind( inFile );
+#ifdef IS_MPI
- 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 ) ){
+ if (worldRank == 0) {
+#endif
- framePos.push_back(currPos);
-
- i = atoi(readBuffer);
+ delete inFile_;
- 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();
- }
-
- }
+#ifdef IS_MPI
- currPos = new fpos_t;
- fgetpos( inFile, currPos );
- fgets( readBuffer, sizeof( readBuffer ), inFile );
- lineNum++;
- }
+ }
- delete currPos;
- rewind( inFile );
+ strcpy(checkPointMsg, "Dump file closed successfully.");
+ errorCheckPoint();
+
+#endif
+
+ return;
+ }
+
+ int DumpReader::getNFrames(void) {
- isScanned = true;
-
-#ifdef IS_MPI
- }
- strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
- MPIcheckPoint();
-#endif // is_mpi
-}
-
-void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
-
- simnfo = the_simnfo;
-
- this->readSet( whichFrame );
-}
+ if (!isScanned_)
+ scanFile();
+
+ return nframes_;
+ }
+
+ void DumpReader::scanFile(void) {
+ int lineNo = 0;
+ std::streampos prevPos;
+ std::streampos currPos;
+
+#ifdef IS_MPI
+
+ if (worldRank == 0) {
+#endif // is_mpi
+
+ 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);
+
+ } 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;
+ }
+ prevPos = currPos;
+ }
+
+ // 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();
+
+ 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);
+
+#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);
+ if (needCOMprops_) {
+ Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
+ Vector3d com;
+ Vector3d comvel;
+ Vector3d comw;
+ if (needPos_ && needVel_){
+ info_->getComAll(com, comvel);
+ comw = info_->getAngularMomentum();
+ }else{
+ com = info_->getCom();
+ comvel = 0.0;
+ comw = 0.0;
+ }
+ s->setCOMprops(com, comvel, comw);
+ }
+ }
+
+ void DumpReader::readSet(int whichFrame) {
+ std::string line;
-void DumpReader :: readSet( int whichFrame ){
+#ifndef IS_MPI
+ inFile_->clear();
+ inFile_->seekg(framePos_[whichFrame]);
- int i;
- unsigned int j;
+ std::istream& inputStream = *inFile_;
-#ifdef IS_MPI
- int done, which_node, which_atom; // loop counter
-#endif //is_mpi
+#else
+ int masterNode = 0;
+ std::stringstream sstream;
+ if (worldRank == masterNode) {
+ std::string sendBuffer;
- const int BUFFERSIZE = 2000; // size of the read buffer
- int nTotObjs; // the number of atoms
- char read_buffer[BUFFERSIZE]; //the line buffer for reading
+ inFile_->clear();
+ inFile_->seekg(framePos_[whichFrame]);
+
+ while (inFile_->getline(buffer, bufferSize)) {
- char *eof_test; // ptr to see when we reach the end of the file
- char *parseErr;
+ line = buffer;
+ sendBuffer += line;
+ sendBuffer += '\n';
+ if (line.find("</Snapshot>") != std::string::npos) {
+ break;
+ }
+ }
- vector<StuntDouble*> integrableObjects;
+ 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);
+
+ sstream.str(sendBuffer);
+ } else {
+ int sendBufferSize;
+ MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
+ char * recvBuffer = new char[sendBufferSize+1];
+ assert(recvBuffer);
+ recvBuffer[sendBufferSize] = '\0';
+ MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
+ sstream.str(recvBuffer);
+ delete [] recvBuffer;
+ }
+ std::istream& inputStream = sstream;
+#endif
-#ifndef IS_MPI
+ inputStream.getline(buffer, bufferSize);
- 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();
- }
+ 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);
- nTotObjs = atoi( read_buffer );
+ //read StuntDoubles
+ readStuntDoubles(inputStream);
- 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();
- }
+ 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) {
- //read the box mat from the comment 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();
+ }
- 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();
- }
+ int index = tokenizer.nextTokenAsInt();
+
+ StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
- parseErr = parseCommentLine( read_buffer, simnfo);
- if( parseErr != NULL ){
- strcpy( painCave.errMsg, parseErr );
- painCave.isFatal = 1;
- simError();
- }
+ if (integrableObject == NULL) {
+ return;
+ }
+ std::string type = tokenizer.nextToken();
+ int size = type.size();
- //parse dump lines
+ size_t found;
+
+ if (needPos_) {
+ found = type.find("p");
+ if (found == std::string::npos) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: StuntDouble %d has no Position\n"
+ "\tField (\"p\") specified.\n%s\n", index,
+ line.c_str());
+ painCave.isFatal = 1;
+ simError();
+ }
+ }
+
+ if (integrableObject->isDirectional()) {
+ if (needQuaternion_) {
+ found = type.find("q");
+ if (found == std::string::npos) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: Directional StuntDouble %d has no\n"
+ "\tQuaternion Field (\"q\") specified.\n%s\n", index,
+ line.c_str());
+ painCave.isFatal = 1;
+ simError();
+ }
+ }
+ }
- for( i=0; i < simnfo->n_mol; i++){
+ for(int i = 0; i < size; ++i) {
+ switch(type[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()) {
+
+ q[0] = tokenizer.nextTokenAsDouble();
+ q[1] = tokenizer.nextTokenAsDouble();
+ q[2] = tokenizer.nextTokenAsDouble();
+ q[3] = tokenizer.nextTokenAsDouble();
+
+ RealType qlen = q.length();
+ if (qlen < OpenMD::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);
+ }
+ }
+ break;
+ }
+ case 'f': {
+
+ Vector3d force;
+ force[0] = tokenizer.nextTokenAsDouble();
+ force[1] = tokenizer.nextTokenAsDouble();
+ force[2] = tokenizer.nextTokenAsDouble();
+ integrableObject->setFrc(force);
+ break;
+ }
+ case 't' : {
- integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
+ 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;
+ }
- 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 );
- 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
+ void DumpReader::readStuntDoubles(std::istream& inputStream) {
- // first thing first, suspend fatalities.
- painCave.isEventLoop = 1;
-
- int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
- int haveError;
-
- MPI_Status istatus;
- int *MolToProcMap = mpiSim->getMolToProcMap();
- int localIndex;
- int nCurObj;
- int nitems;
-
- nTotObjs = simnfo->getTotIntegrableObjects();
- haveError = 0;
- if (worldRank == 0) {
- fsetpos(inFile, framePos[whichFrame]);
-
- 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();
+ 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();
}
- 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",
- inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
- haveError= 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,
- "error in reading commment in %s\n", inFileName.c_str());
- haveError = 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, 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 == 0){
- //molecules belong to master node
-
- localIndex = mpiSim->getGlobalToLocalMol(i);
-
- if(localIndex == -1) {
- strcpy(painCave.errMsg, "Molecule not found on node 0!");
- haveError = 1;
- simError();
- }
-
- 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();
-
- parseDumpLine(read_buffer, integrableObjects[j]);
-
- }
-
-
- }
- else{
- //molecule belongs to slave nodes
-
- MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
+ while(inputStream.getline(buffer, bufferSize)) {
+ line = buffer;
- 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();
-
- MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
- TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
-
- }
-
+ if(line.find("</StuntDoubles>") != std::string::npos) {
+ break;
}
-
- }
-
- }
- 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();
+ parseDumpLine(line);
}
- 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();
- }
+ void DumpReader::readFrameProperties(std::istream& inputStream) {
- integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
+ Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
+ inputStream.getline(buffer, bufferSize);
+ std::string line(buffer);
- nCurObj = integrableObjects.size();
-
- MPI_Send(&nCurObj, 1, MPI_INT, 0,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
+ if (line.find("<FrameData>") == std::string::npos) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: Missing <FrameData>\n");
+ painCave.isFatal = 1;
+ simError();
+ }
- 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();
- }
-
- }
-
+ while(inputStream.getline(buffer, bufferSize)) {
+ line = buffer;
+
+ if(line.find("</FrameData>") != std::string::npos) {
+ break;
}
- }
+ 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();
+ }
- }
-
-#endif
-}
-
-char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
-
- char *foo; // the pointer to the current string token
-
- 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.
-
-
- // set the string tokenizer
-
- foo = strtok(readLine, " ,;\t");
-
- // check the atom name to the current atom
-
- 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 );
- }
-
- // get the positions
-
- 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 );
-
- 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 );
-
- 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 );
-
-
- // get the 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 );
- }
- vel[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 );
- }
- vel[1] = 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 );
- }
- vel[2] = atof( foo );
-
-
- // add the positions and velocities to the atom
-
- sd->setPos( pos );
- sd->setVel( vel );
-
- if (!sd->isDirectional())
- return NULL;
-
- // get the quaternions
-
- 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 );
-
- 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 );
-
- 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[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 );
-
- // 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 );
- }
- 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 );
-
- 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 );
-
-
- // 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);
- }
-
- 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){
-
- double currTime;
- double boxMat[9];
- double theBoxMat3[3][3];
- double chi;
- double integralOfChidt;
- double eta[9];
-
- char *foo; // the pointer to the current string token
-
- // 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 );
- }
- 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];
-
- //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 );
+ 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();
}
- 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);
-
}
- 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");
- }
- }
- 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 OpenMD