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/* |
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* Copyright (c) 2009 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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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#include "brains/Thermo.hpp" |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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|
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namespace OpenMD { |
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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), needCOMprops_(false) { |
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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_ = new std::ifstream(filename_.c_str()); |
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|
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if (inFile_->fail()) { |
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sprintf(painCave.errMsg, |
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"DumpReader: Cannot open file: %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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#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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errorCheckPoint(); |
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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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delete inFile_; |
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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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errorCheckPoint(); |
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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 lineNo = 0; |
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std::streampos prevPos; |
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std::streampos 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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currPos = inFile_->tellg(); |
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prevPos = currPos; |
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bool foundOpenSnapshotTag = false; |
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bool foundClosedSnapshotTag = false; |
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bool foundOpenSiteDataTag = false; |
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while(inFile_->getline(buffer, bufferSize)) { |
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++lineNo; |
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|
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std::string line = buffer; |
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currPos = inFile_->tellg(); |
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if (line.find("<Snapshot>")!= std::string::npos) { |
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if (foundOpenSnapshotTag) { |
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sprintf(painCave.errMsg, |
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"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo, |
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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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foundOpenSnapshotTag = true; |
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foundClosedSnapshotTag = false; |
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framePos_.push_back(prevPos); |
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|
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} else if (line.find("</Snapshot>") != std::string::npos){ |
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if (!foundOpenSnapshotTag) { |
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sprintf(painCave.errMsg, |
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"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo, |
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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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if (foundClosedSnapshotTag) { |
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sprintf(painCave.errMsg, |
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"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo, |
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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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foundClosedSnapshotTag = true; |
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foundOpenSnapshotTag = false; |
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} |
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prevPos = currPos; |
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} |
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|
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// only found <Snapshot> for the last frame means the file is corrupted, we should discard |
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// it and give a warning message |
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if (foundOpenSnapshotTag) { |
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sprintf(painCave.errMsg, |
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"DumpReader: last frame in %s is invalid\n", filename_.c_str()); |
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painCave.isFatal = 0; |
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simError(); |
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framePos_.pop_back(); |
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} |
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|
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nframes_ = framePos_.size(); |
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|
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if (nframes_ == 0) { |
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sprintf(painCave.errMsg, |
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"DumpReader: %s does not contain a valid frame\n", filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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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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#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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if (!isScanned_) |
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scanFile(); |
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|
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int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
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|
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if (storageLayout & DataStorage::dslPosition) { |
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needPos_ = true; |
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} else { |
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needPos_ = false; |
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} |
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|
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if (storageLayout & DataStorage::dslVelocity) { |
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needVel_ = true; |
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} else { |
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needVel_ = false; |
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} |
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|
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if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
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needQuaternion_ = true; |
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} else { |
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needQuaternion_ = false; |
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} |
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|
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if (storageLayout & DataStorage::dslAngularMomentum) { |
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needAngMom_ = true; |
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} else { |
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needAngMom_ = false; |
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} |
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|
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readSet(whichFrame); |
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|
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if (needCOMprops_) { |
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Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Thermo thermo(info_); |
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Vector3d com; |
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|
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if (needPos_ && needVel_) { |
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Vector3d comvel; |
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Vector3d comw; |
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thermo.getComAll(com, comvel); |
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comw = thermo.getAngularMomentum(); |
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} else { |
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com = thermo.getCom(); |
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} |
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} |
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} |
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|
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void DumpReader::readSet(int whichFrame) { |
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std::string line; |
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|
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#ifndef IS_MPI |
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inFile_->clear(); |
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inFile_->seekg(framePos_[whichFrame]); |
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|
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std::istream& inputStream = *inFile_; |
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|
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#else |
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int masterNode = 0; |
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std::stringstream sstream; |
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if (worldRank == masterNode) { |
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std::string sendBuffer; |
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|
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inFile_->clear(); |
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inFile_->seekg(framePos_[whichFrame]); |
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|
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while (inFile_->getline(buffer, bufferSize)) { |
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|
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line = buffer; |
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sendBuffer += line; |
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sendBuffer += '\n'; |
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if (line.find("</Snapshot>") != std::string::npos) { |
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break; |
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} |
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} |
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|
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int sendBufferSize = sendBuffer.size(); |
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MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
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MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
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|
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sstream.str(sendBuffer); |
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} else { |
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int sendBufferSize; |
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MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
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char * recvBuffer = new char[sendBufferSize+1]; |
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assert(recvBuffer); |
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recvBuffer[sendBufferSize] = '\0'; |
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MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
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sstream.str(recvBuffer); |
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delete [] recvBuffer; |
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} |
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|
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std::istream& inputStream = sstream; |
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#endif |
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|
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inputStream.getline(buffer, bufferSize); |
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|
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line = buffer; |
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if (line.find("<Snapshot>") == std::string::npos) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: can not find <Snapshot>\n"); |
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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 frameData |
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readFrameProperties(inputStream); |
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|
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//read StuntDoubles |
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readStuntDoubles(inputStream); |
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|
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inputStream.getline(buffer, bufferSize); |
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line = buffer; |
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|
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if (line.find("<SiteData>") != std::string::npos) { |
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//read SiteData |
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readSiteData(inputStream); |
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} else { |
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if (line.find("</Snapshot>") == std::string::npos) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: can not find </Snapshot>\n"); |
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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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|
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void DumpReader::parseDumpLine(const std::string& line) { |
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|
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|
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StringTokenizer tokenizer(line); |
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int nTokens; |
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|
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nTokens = tokenizer.countTokens(); |
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|
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if (nTokens < 2) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: Not enough Tokens.\n%s\n", line.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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int index = tokenizer.nextTokenAsInt(); |
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|
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StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); |
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|
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if (integrableObject == NULL) { |
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return; |
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} |
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std::string type = tokenizer.nextToken(); |
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int size = type.size(); |
| 362 |
|
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size_t found; |
| 364 |
|
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if (needPos_) { |
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found = type.find("p"); |
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if (found == std::string::npos) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: StuntDouble %d has no Position\n" |
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"\tField (\"p\") specified.\n%s\n", index, |
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line.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
| 375 |
} |
| 376 |
|
| 377 |
if (integrableObject->isDirectional()) { |
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if (needQuaternion_) { |
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found = type.find("q"); |
| 380 |
if (found == std::string::npos) { |
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sprintf(painCave.errMsg, |
| 382 |
"DumpReader Error: Directional StuntDouble %d has no\n" |
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"\tQuaternion Field (\"q\") specified.\n%s\n", index, |
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line.c_str()); |
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painCave.isFatal = 1; |
| 386 |
simError(); |
| 387 |
} |
| 388 |
} |
| 389 |
} |
| 390 |
|
| 391 |
for(int i = 0; i < size; ++i) { |
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switch(type[i]) { |
| 393 |
|
| 394 |
case 'p': { |
| 395 |
Vector3d pos; |
| 396 |
pos[0] = tokenizer.nextTokenAsDouble(); |
| 397 |
pos[1] = tokenizer.nextTokenAsDouble(); |
| 398 |
pos[2] = tokenizer.nextTokenAsDouble(); |
| 399 |
if (needPos_) { |
| 400 |
integrableObject->setPos(pos); |
| 401 |
} |
| 402 |
break; |
| 403 |
} |
| 404 |
case 'v' : { |
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Vector3d vel; |
| 406 |
vel[0] = tokenizer.nextTokenAsDouble(); |
| 407 |
vel[1] = tokenizer.nextTokenAsDouble(); |
| 408 |
vel[2] = tokenizer.nextTokenAsDouble(); |
| 409 |
if (needVel_) { |
| 410 |
integrableObject->setVel(vel); |
| 411 |
} |
| 412 |
break; |
| 413 |
} |
| 414 |
|
| 415 |
case 'q' : { |
| 416 |
Quat4d q; |
| 417 |
if (integrableObject->isDirectional()) { |
| 418 |
|
| 419 |
q[0] = tokenizer.nextTokenAsDouble(); |
| 420 |
q[1] = tokenizer.nextTokenAsDouble(); |
| 421 |
q[2] = tokenizer.nextTokenAsDouble(); |
| 422 |
q[3] = tokenizer.nextTokenAsDouble(); |
| 423 |
|
| 424 |
RealType qlen = q.length(); |
| 425 |
if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0 |
| 426 |
|
| 427 |
sprintf(painCave.errMsg, |
| 428 |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); |
| 429 |
painCave.isFatal = 1; |
| 430 |
simError(); |
| 431 |
|
| 432 |
} |
| 433 |
|
| 434 |
q.normalize(); |
| 435 |
if (needQuaternion_) { |
| 436 |
integrableObject->setQ(q); |
| 437 |
} |
| 438 |
} |
| 439 |
break; |
| 440 |
} |
| 441 |
case 'j' : { |
| 442 |
Vector3d ji; |
| 443 |
if (integrableObject->isDirectional()) { |
| 444 |
ji[0] = tokenizer.nextTokenAsDouble(); |
| 445 |
ji[1] = tokenizer.nextTokenAsDouble(); |
| 446 |
ji[2] = tokenizer.nextTokenAsDouble(); |
| 447 |
if (needAngMom_) { |
| 448 |
integrableObject->setJ(ji); |
| 449 |
} |
| 450 |
} |
| 451 |
break; |
| 452 |
} |
| 453 |
case 'f': { |
| 454 |
|
| 455 |
Vector3d force; |
| 456 |
force[0] = tokenizer.nextTokenAsDouble(); |
| 457 |
force[1] = tokenizer.nextTokenAsDouble(); |
| 458 |
force[2] = tokenizer.nextTokenAsDouble(); |
| 459 |
integrableObject->setFrc(force); |
| 460 |
break; |
| 461 |
} |
| 462 |
case 't' : { |
| 463 |
|
| 464 |
Vector3d torque; |
| 465 |
torque[0] = tokenizer.nextTokenAsDouble(); |
| 466 |
torque[1] = tokenizer.nextTokenAsDouble(); |
| 467 |
torque[2] = tokenizer.nextTokenAsDouble(); |
| 468 |
integrableObject->setTrq(torque); |
| 469 |
break; |
| 470 |
} |
| 471 |
case 'u' : { |
| 472 |
|
| 473 |
RealType particlePot; |
| 474 |
particlePot = tokenizer.nextTokenAsDouble(); |
| 475 |
integrableObject->setParticlePot(particlePot); |
| 476 |
break; |
| 477 |
} |
| 478 |
case 'c' : { |
| 479 |
|
| 480 |
RealType flucQPos; |
| 481 |
flucQPos = tokenizer.nextTokenAsDouble(); |
| 482 |
integrableObject->setFlucQPos(flucQPos); |
| 483 |
break; |
| 484 |
} |
| 485 |
case 'w' : { |
| 486 |
|
| 487 |
RealType flucQVel; |
| 488 |
flucQVel = tokenizer.nextTokenAsDouble(); |
| 489 |
integrableObject->setFlucQVel(flucQVel); |
| 490 |
break; |
| 491 |
} |
| 492 |
case 'g' : { |
| 493 |
|
| 494 |
RealType flucQFrc; |
| 495 |
flucQFrc = tokenizer.nextTokenAsDouble(); |
| 496 |
integrableObject->setFlucQFrc(flucQFrc); |
| 497 |
break; |
| 498 |
} |
| 499 |
case 'e' : { |
| 500 |
|
| 501 |
Vector3d eField; |
| 502 |
eField[0] = tokenizer.nextTokenAsDouble(); |
| 503 |
eField[1] = tokenizer.nextTokenAsDouble(); |
| 504 |
eField[2] = tokenizer.nextTokenAsDouble(); |
| 505 |
integrableObject->setElectricField(eField); |
| 506 |
break; |
| 507 |
} |
| 508 |
default: { |
| 509 |
sprintf(painCave.errMsg, |
| 510 |
"DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
| 511 |
painCave.isFatal = 1; |
| 512 |
simError(); |
| 513 |
break; |
| 514 |
} |
| 515 |
|
| 516 |
} |
| 517 |
} |
| 518 |
|
| 519 |
} |
| 520 |
|
| 521 |
|
| 522 |
void DumpReader::parseSiteLine(const std::string& line) { |
| 523 |
|
| 524 |
StringTokenizer tokenizer(line); |
| 525 |
int nTokens; |
| 526 |
|
| 527 |
nTokens = tokenizer.countTokens(); |
| 528 |
|
| 529 |
if (nTokens < 2) { |
| 530 |
sprintf(painCave.errMsg, |
| 531 |
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
| 532 |
painCave.isFatal = 1; |
| 533 |
simError(); |
| 534 |
} |
| 535 |
|
| 536 |
/** |
| 537 |
* The first token is the global integrable object index. |
| 538 |
*/ |
| 539 |
|
| 540 |
int index = tokenizer.nextTokenAsInt(); |
| 541 |
StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); |
| 542 |
if (integrableObject == NULL) { |
| 543 |
return; |
| 544 |
} |
| 545 |
StuntDouble* sd = integrableObject; |
| 546 |
|
| 547 |
/** |
| 548 |
* Test to see if the next token is an integer or not. If not, |
| 549 |
* we've got data on the integrable object itself. If there is an |
| 550 |
* integer, we're parsing data for a site on a rigid body. |
| 551 |
*/ |
| 552 |
|
| 553 |
std::string indexTest = tokenizer.peekNextToken(); |
| 554 |
std::istringstream i(indexTest); |
| 555 |
int siteIndex; |
| 556 |
if (i >> siteIndex) { |
| 557 |
// chew up this token and parse as an int: |
| 558 |
siteIndex = tokenizer.nextTokenAsInt(); |
| 559 |
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 560 |
sd = rb->getAtoms()[siteIndex]; |
| 561 |
} |
| 562 |
|
| 563 |
/** |
| 564 |
* The next token contains information on what follows. |
| 565 |
*/ |
| 566 |
std::string type = tokenizer.nextToken(); |
| 567 |
int size = type.size(); |
| 568 |
|
| 569 |
for(int i = 0; i < size; ++i) { |
| 570 |
switch(type[i]) { |
| 571 |
|
| 572 |
case 'u' : { |
| 573 |
|
| 574 |
RealType particlePot; |
| 575 |
particlePot = tokenizer.nextTokenAsDouble(); |
| 576 |
sd->setParticlePot(particlePot); |
| 577 |
break; |
| 578 |
} |
| 579 |
case 'c' : { |
| 580 |
|
| 581 |
RealType flucQPos; |
| 582 |
flucQPos = tokenizer.nextTokenAsDouble(); |
| 583 |
sd->setFlucQPos(flucQPos); |
| 584 |
break; |
| 585 |
} |
| 586 |
case 'w' : { |
| 587 |
|
| 588 |
RealType flucQVel; |
| 589 |
flucQVel = tokenizer.nextTokenAsDouble(); |
| 590 |
sd->setFlucQVel(flucQVel); |
| 591 |
break; |
| 592 |
} |
| 593 |
case 'g' : { |
| 594 |
|
| 595 |
RealType flucQFrc; |
| 596 |
flucQFrc = tokenizer.nextTokenAsDouble(); |
| 597 |
sd->setFlucQFrc(flucQFrc); |
| 598 |
break; |
| 599 |
} |
| 600 |
case 'e' : { |
| 601 |
|
| 602 |
Vector3d eField; |
| 603 |
eField[0] = tokenizer.nextTokenAsDouble(); |
| 604 |
eField[1] = tokenizer.nextTokenAsDouble(); |
| 605 |
eField[2] = tokenizer.nextTokenAsDouble(); |
| 606 |
sd->setElectricField(eField); |
| 607 |
break; |
| 608 |
} |
| 609 |
default: { |
| 610 |
sprintf(painCave.errMsg, |
| 611 |
"DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
| 612 |
painCave.isFatal = 1; |
| 613 |
simError(); |
| 614 |
break; |
| 615 |
} |
| 616 |
} |
| 617 |
} |
| 618 |
} |
| 619 |
|
| 620 |
|
| 621 |
void DumpReader::readStuntDoubles(std::istream& inputStream) { |
| 622 |
|
| 623 |
inputStream.getline(buffer, bufferSize); |
| 624 |
std::string line(buffer); |
| 625 |
|
| 626 |
if (line.find("<StuntDoubles>") == std::string::npos) { |
| 627 |
sprintf(painCave.errMsg, |
| 628 |
"DumpReader Error: Missing <StuntDoubles>\n"); |
| 629 |
painCave.isFatal = 1; |
| 630 |
simError(); |
| 631 |
} |
| 632 |
|
| 633 |
while(inputStream.getline(buffer, bufferSize)) { |
| 634 |
line = buffer; |
| 635 |
|
| 636 |
if(line.find("</StuntDoubles>") != std::string::npos) { |
| 637 |
break; |
| 638 |
} |
| 639 |
|
| 640 |
parseDumpLine(line); |
| 641 |
} |
| 642 |
|
| 643 |
} |
| 644 |
|
| 645 |
void DumpReader::readSiteData(std::istream& inputStream) { |
| 646 |
|
| 647 |
inputStream.getline(buffer, bufferSize); |
| 648 |
std::string line(buffer); |
| 649 |
|
| 650 |
if (line.find("<SiteData>") == std::string::npos) { |
| 651 |
// site data isn't required for a simulation, so skip |
| 652 |
return; |
| 653 |
} |
| 654 |
|
| 655 |
while(inputStream.getline(buffer, bufferSize)) { |
| 656 |
line = buffer; |
| 657 |
|
| 658 |
if(line.find("</SiteData>") != std::string::npos) { |
| 659 |
break; |
| 660 |
} |
| 661 |
|
| 662 |
parseSiteLine(line); |
| 663 |
} |
| 664 |
|
| 665 |
} |
| 666 |
|
| 667 |
void DumpReader::readFrameProperties(std::istream& inputStream) { |
| 668 |
|
| 669 |
Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 670 |
inputStream.getline(buffer, bufferSize); |
| 671 |
std::string line(buffer); |
| 672 |
|
| 673 |
if (line.find("<FrameData>") == std::string::npos) { |
| 674 |
sprintf(painCave.errMsg, |
| 675 |
"DumpReader Error: Missing <FrameData>\n"); |
| 676 |
painCave.isFatal = 1; |
| 677 |
simError(); |
| 678 |
} |
| 679 |
|
| 680 |
while(inputStream.getline(buffer, bufferSize)) { |
| 681 |
line = buffer; |
| 682 |
|
| 683 |
if(line.find("</FrameData>") != std::string::npos) { |
| 684 |
break; |
| 685 |
} |
| 686 |
|
| 687 |
StringTokenizer tokenizer(line, " ;\t\n\r{}:,"); |
| 688 |
if (!tokenizer.hasMoreTokens()) { |
| 689 |
sprintf(painCave.errMsg, |
| 690 |
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
| 691 |
painCave.isFatal = 1; |
| 692 |
simError(); |
| 693 |
} |
| 694 |
|
| 695 |
std::string propertyName = tokenizer.nextToken(); |
| 696 |
if (propertyName == "Time") { |
| 697 |
RealType currTime = tokenizer.nextTokenAsDouble(); |
| 698 |
s->setTime(currTime); |
| 699 |
} else if (propertyName == "Hmat"){ |
| 700 |
Mat3x3d hmat; |
| 701 |
hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
| 702 |
hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
| 703 |
hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
| 704 |
hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
| 705 |
hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
| 706 |
hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
| 707 |
hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
| 708 |
hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
| 709 |
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
| 710 |
s->setHmat(hmat); |
| 711 |
} else if (propertyName == "Thermostat") { |
| 712 |
pair<RealType, RealType> thermostat; |
| 713 |
thermostat.first = tokenizer.nextTokenAsDouble(); |
| 714 |
thermostat.second = tokenizer.nextTokenAsDouble(); |
| 715 |
s->setThermostat(thermostat); |
| 716 |
} else if (propertyName == "Barostat") { |
| 717 |
Mat3x3d eta; |
| 718 |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
| 719 |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
| 720 |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
| 721 |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
| 722 |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
| 723 |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
| 724 |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
| 725 |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
| 726 |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
| 727 |
s->setBarostat(eta); |
| 728 |
} else { |
| 729 |
sprintf(painCave.errMsg, |
| 730 |
"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str()); |
| 731 |
painCave.isFatal = 0; |
| 732 |
simError(); |
| 733 |
} |
| 734 |
|
| 735 |
} |
| 736 |
|
| 737 |
} |
| 738 |
|
| 739 |
|
| 740 |
}//end namespace OpenMD |
