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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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|
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#include <sys/types.h> |
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#include <sys/stat.h> |
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|
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#include <iostream> |
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#include <math.h> |
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|
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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|
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/StringTokenizer.hpp" |
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|
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#ifdef IS_MPI |
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|
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#include <mpi.h> |
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#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
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|
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#endif // is_mpi |
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|
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|
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namespace oopse { |
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|
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DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
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: info_(info), filename_(filename), isScanned_(false), nframes_(0) { |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif |
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|
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inFile_ = fopen(filename_.c_str(), "r"); |
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|
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if (inFile_ == NULL) { |
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sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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#ifdef IS_MPI |
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|
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} |
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|
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strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
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MPIcheckPoint(); |
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|
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#endif |
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|
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return; |
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} |
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|
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DumpReader::~DumpReader() { |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif |
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|
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int error; |
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error = fclose(inFile_); |
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|
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if (error) { |
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sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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MemoryUtils::deleteVectorOfPointer(framePos_); |
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|
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#ifdef IS_MPI |
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|
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} |
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|
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strcpy(checkPointMsg, "Dump file closed successfully."); |
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MPIcheckPoint(); |
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|
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#endif |
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|
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return; |
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} |
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|
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int DumpReader::getNFrames(void) { |
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|
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if (!isScanned_) |
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scanFile(); |
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|
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return nframes_; |
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} |
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|
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void DumpReader::scanFile(void) { |
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int i, j; |
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int lineNum = 0; |
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char readBuffer[maxBufferSize]; |
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fpos_t * currPos; |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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rewind(inFile_); |
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|
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currPos = new fpos_t; |
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fgetpos(inFile_, currPos); |
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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|
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if (feof(inFile_)) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
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filename_.c_str(), |
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lineNum); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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while (!feof(inFile_)) { |
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framePos_.push_back(currPos); |
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|
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i = atoi(readBuffer); |
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|
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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|
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if (feof(inFile_)) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
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filename_.c_str(), |
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lineNum); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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for(j = 0; j < i; j++) { |
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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|
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if (feof(inFile_)) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: File \"%s\" ended unexpectedly at line %d," |
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" with atom %d\n", filename_.c_str(), |
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lineNum, |
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j); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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currPos = new fpos_t; |
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fgetpos(inFile_, currPos); |
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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} |
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|
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delete currPos; |
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rewind(inFile_); |
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|
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nframes_ = framePos_.size(); |
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#ifdef IS_MPI |
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} |
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|
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MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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|
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strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
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|
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isScanned_ = true; |
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} |
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|
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void DumpReader::readFrame(int whichFrame) { |
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readSet(whichFrame); |
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} |
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|
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void DumpReader::readSet(int whichFrame) { |
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int i; |
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int nTotObjs; // the number of atoms |
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char read_buffer[maxBufferSize]; //the line buffer for reading |
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char * eof_test; // ptr to see when we reach the end of the file |
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|
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Molecule* mol; |
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StuntDouble* integrableObject; |
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SimInfo::MoleculeIterator mi; |
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Molecule::IntegrableObjectIterator ii; |
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|
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#ifndef IS_MPI |
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|
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fsetpos(inFile_, framePos_[whichFrame]); |
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eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
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|
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if (eof_test == NULL) { |
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sprintf(painCave.errMsg, |
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"DumpReader error: error reading 1st line of \"%s\"\n", |
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filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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nTotObjs = atoi(read_buffer); |
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|
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if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
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sprintf(painCave.errMsg, |
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"DumpReader error. %s nIntegrable, %d, " |
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"does not match the meta-data file's nIntegrable, %d.\n", |
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filename_.c_str(), |
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nTotObjs, |
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info_->getNGlobalIntegrableObjects()); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//read the box mat from the comment line |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
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|
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if (eof_test == NULL) { |
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sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
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filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
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|
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//parse dump lines |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
284 |
|
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if (eof_test == NULL) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: error in reading file %s\n" |
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"natoms = %d; index = %d\n" |
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"error reading the line from the file.\n", |
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filename_.c_str(), |
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nTotObjs, |
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i); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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parseDumpLine(read_buffer, integrableObject); |
299 |
|
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} |
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} |
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|
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// MPI Section of code.......... |
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|
305 |
#else //IS_MPI |
306 |
|
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// first thing first, suspend fatalities. |
308 |
int masterNode = 0; |
309 |
int nCurObj; |
310 |
painCave.isEventLoop = 1; |
311 |
|
312 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
313 |
int haveError; |
314 |
|
315 |
MPI_Status istatus; |
316 |
int nitems; |
317 |
|
318 |
nTotObjs = info_->getNGlobalIntegrableObjects(); |
319 |
haveError = 0; |
320 |
|
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if (worldRank == masterNode) { |
322 |
fsetpos(inFile_, framePos_[whichFrame]); |
323 |
|
324 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
325 |
|
326 |
if (eof_test == NULL) { |
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sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
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filename_.c_str()); |
329 |
painCave.isFatal = 1; |
330 |
simError(); |
331 |
} |
332 |
|
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nitems = atoi(read_buffer); |
334 |
|
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// Check to see that the number of integrable objects in the |
336 |
// intial configuration file is the same as derived from the |
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// meta-data file. |
338 |
|
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if (nTotObjs != nitems) { |
340 |
sprintf(painCave.errMsg, |
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"DumpReader Error. %s nIntegrable, %d, " |
342 |
"does not match the meta-data file's nIntegrable, %d.\n", |
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filename_.c_str(), |
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nTotObjs, |
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info_->getNGlobalIntegrableObjects()); |
346 |
|
347 |
painCave.isFatal = 1; |
348 |
simError(); |
349 |
} |
350 |
|
351 |
//read the boxMat from the comment line |
352 |
|
353 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
354 |
|
355 |
if (eof_test == NULL) { |
356 |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
357 |
filename_.c_str()); |
358 |
painCave.isFatal = 1; |
359 |
simError(); |
360 |
} |
361 |
|
362 |
//Every single processor will parse the comment line by itself |
363 |
//By using this way, we might lose some efficiency, but if we want to add |
364 |
//more parameters into comment line, we only need to modify function |
365 |
//parseCommentLine |
366 |
|
367 |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
368 |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
369 |
|
370 |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
371 |
int which_node = info_->getMolToProc(i); |
372 |
|
373 |
if (which_node == masterNode) { |
374 |
//molecules belong to master node |
375 |
|
376 |
mol = info_->getMoleculeByGlobalIndex(i); |
377 |
|
378 |
if (mol == NULL) { |
379 |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
380 |
painCave.isFatal = 1; |
381 |
simError(); |
382 |
} |
383 |
|
384 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
385 |
integrableObject = mol->nextIntegrableObject(ii)){ |
386 |
|
387 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
388 |
|
389 |
if (eof_test == NULL) { |
390 |
sprintf(painCave.errMsg, |
391 |
"DumpReader Error: error in reading file %s\n" |
392 |
"natoms = %d; index = %d\n" |
393 |
"error reading the line from the file.\n", |
394 |
filename_.c_str(), |
395 |
nTotObjs, |
396 |
i); |
397 |
|
398 |
painCave.isFatal = 1; |
399 |
simError(); |
400 |
} |
401 |
|
402 |
parseDumpLine(read_buffer, integrableObject); |
403 |
} |
404 |
} else { |
405 |
//molecule belongs to slave nodes |
406 |
|
407 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
408 |
MPI_COMM_WORLD, &istatus); |
409 |
|
410 |
for(int j = 0; j < nCurObj; j++) { |
411 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
412 |
|
413 |
if (eof_test == NULL) { |
414 |
sprintf(painCave.errMsg, |
415 |
"DumpReader Error: error in reading file %s\n" |
416 |
"natoms = %d; index = %d\n" |
417 |
"error reading the line from the file.\n", |
418 |
filename_.c_str(), |
419 |
nTotObjs, |
420 |
i); |
421 |
|
422 |
painCave.isFatal = 1; |
423 |
simError(); |
424 |
} |
425 |
|
426 |
MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
427 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
428 |
} |
429 |
} |
430 |
} |
431 |
} else { |
432 |
//actions taken at slave nodes |
433 |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
434 |
|
435 |
/**@todo*/ |
436 |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
437 |
|
438 |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
439 |
int which_node = info_->getMolToProc(i); |
440 |
|
441 |
if (which_node == worldRank) { |
442 |
//molecule with global index i belongs to this processor |
443 |
|
444 |
mol = info_->getMoleculeByGlobalIndex(i); |
445 |
if (mol == NULL) { |
446 |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
447 |
painCave.isFatal = 1; |
448 |
simError(); |
449 |
} |
450 |
|
451 |
nCurObj = mol->getNIntegrableObjects(); |
452 |
|
453 |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
454 |
MPI_COMM_WORLD); |
455 |
|
456 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
457 |
integrableObject = mol->nextIntegrableObject(ii)){ |
458 |
|
459 |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
460 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
461 |
|
462 |
parseDumpLine(read_buffer, integrableObject); |
463 |
} |
464 |
|
465 |
} |
466 |
|
467 |
} |
468 |
|
469 |
} |
470 |
|
471 |
#endif |
472 |
|
473 |
} |
474 |
|
475 |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
476 |
|
477 |
Vector3d pos; // position place holders |
478 |
Vector3d vel; // velocity placeholders |
479 |
Quat4d q; // the quaternions |
480 |
Vector3d ji; // angular velocity placeholders; |
481 |
StringTokenizer tokenizer(line); |
482 |
int nTokens; |
483 |
|
484 |
nTokens = tokenizer.countTokens(); |
485 |
|
486 |
if (nTokens < 14) { |
487 |
sprintf(painCave.errMsg, |
488 |
"DumpReader Error: Not enough Tokens.\n"); |
489 |
painCave.isFatal = 1; |
490 |
simError(); |
491 |
} |
492 |
|
493 |
std::string name = tokenizer.nextToken(); |
494 |
|
495 |
if (name != integrableObject->getType()) { |
496 |
|
497 |
sprintf(painCave.errMsg, |
498 |
"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
499 |
name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
500 |
painCave.isFatal = 1; |
501 |
simError(); |
502 |
} |
503 |
|
504 |
pos[0] = tokenizer.nextTokenAsDouble(); |
505 |
pos[1] = tokenizer.nextTokenAsDouble(); |
506 |
pos[2] = tokenizer.nextTokenAsDouble(); |
507 |
integrableObject->setPos(pos); |
508 |
|
509 |
vel[0] = tokenizer.nextTokenAsDouble(); |
510 |
vel[1] = tokenizer.nextTokenAsDouble(); |
511 |
vel[2] = tokenizer.nextTokenAsDouble(); |
512 |
integrableObject->setVel(vel); |
513 |
|
514 |
if (integrableObject->isDirectional()) { |
515 |
|
516 |
q[0] = tokenizer.nextTokenAsDouble(); |
517 |
q[1] = tokenizer.nextTokenAsDouble(); |
518 |
q[2] = tokenizer.nextTokenAsDouble(); |
519 |
q[3] = tokenizer.nextTokenAsDouble(); |
520 |
|
521 |
double qlen = q.length(); |
522 |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
523 |
|
524 |
sprintf(painCave.errMsg, |
525 |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
526 |
painCave.isFatal = 1; |
527 |
simError(); |
528 |
|
529 |
} |
530 |
|
531 |
q.normalize(); |
532 |
|
533 |
integrableObject->setQ(q); |
534 |
|
535 |
ji[0] = tokenizer.nextTokenAsDouble(); |
536 |
ji[1] = tokenizer.nextTokenAsDouble(); |
537 |
ji[2] = tokenizer.nextTokenAsDouble(); |
538 |
integrableObject->setJ(ji); |
539 |
} |
540 |
|
541 |
} |
542 |
|
543 |
|
544 |
void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
545 |
double currTime; |
546 |
Mat3x3d hmat; |
547 |
double chi; |
548 |
double integralOfChiDt; |
549 |
Mat3x3d eta; |
550 |
|
551 |
StringTokenizer tokenizer(line); |
552 |
int nTokens; |
553 |
|
554 |
nTokens = tokenizer.countTokens(); |
555 |
|
556 |
//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
557 |
if (nTokens < 10) { |
558 |
sprintf(painCave.errMsg, |
559 |
"DumpReader Error: Not enough tokens in comment line: %s", line); |
560 |
painCave.isFatal = 1; |
561 |
simError(); |
562 |
} |
563 |
|
564 |
//read current time |
565 |
currTime = tokenizer.nextTokenAsDouble(); |
566 |
s->setTime(currTime); |
567 |
|
568 |
//read h-matrix |
569 |
hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
570 |
hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
571 |
hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
572 |
hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
573 |
hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
574 |
hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
575 |
hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
576 |
hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
577 |
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
578 |
s->setHmat(hmat); |
579 |
|
580 |
//read chi and integrablOfChidt, they should apprear in pair |
581 |
if (tokenizer.countTokens() >= 2) { |
582 |
chi = tokenizer.nextTokenAsDouble(); |
583 |
integralOfChiDt = tokenizer.nextTokenAsDouble(); |
584 |
|
585 |
s->setChi(chi); |
586 |
s->setIntegralOfChiDt(integralOfChiDt); |
587 |
} |
588 |
|
589 |
//read eta (eta is 3x3 matrix) |
590 |
if (tokenizer.countTokens() >= 9) { |
591 |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
592 |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
593 |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
594 |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
595 |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
596 |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
597 |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
598 |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
599 |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
600 |
|
601 |
s->setEta(eta); |
602 |
} |
603 |
|
604 |
|
605 |
} |
606 |
|
607 |
}//end namespace oopse |