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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_ = new std::ifstream(filename_.c_str()); |
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|
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if (inFile_->fail()) { |
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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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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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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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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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inFile_->seekg (0, std::ios::beg); |
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|
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|
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currPos = inFile_->tellg(); |
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inFile_->getline(readBuffer, sizeof(readBuffer)); |
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lineNum++; |
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|
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if (inFile_->eof()) { |
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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 (!inFile_->eof()) { |
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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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inFile_->getline(readBuffer, sizeof(readBuffer)); |
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lineNum++; |
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|
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if (inFile_->eof()) { |
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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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inFile_->getline(readBuffer, sizeof(readBuffer)); |
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lineNum++; |
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|
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if (inFile_->eof()) { |
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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 = inFile_->tellg(); |
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inFile_->getline(readBuffer, sizeof(readBuffer)); |
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lineNum++; |
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} |
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|
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inFile_->seekg (0, std::ios::beg); |
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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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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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|
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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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inFile_->clear(); |
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inFile_->seekg(framePos_[whichFrame]); |
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|
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if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
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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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|
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if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
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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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i = 0; |
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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; |
| 298 |
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integrableObject = mol->nextIntegrableObject(ii)) { |
| 299 |
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|
| 300 |
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|
| 301 |
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|
| 302 |
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if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
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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" |
| 306 |
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"error reading the line from the file.\n", |
| 307 |
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filename_.c_str(), |
| 308 |
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nTotObjs, |
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i); |
| 310 |
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|
| 311 |
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painCave.isFatal = 1; |
| 312 |
< |
simError(); |
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} |
| 314 |
< |
|
| 315 |
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parseDumpLine(read_buffer, integrableObject); |
| 316 |
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i++; |
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< |
} |
| 318 |
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} |
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|
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// MPI Section of code.......... |
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|
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#else //IS_MPI |
| 323 |
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|
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// first thing first, suspend fatalities. |
| 325 |
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int masterNode = 0; |
| 326 |
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int nCurObj; |
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painCave.isEventLoop = 1; |
| 328 |
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|
| 329 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 330 |
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int haveError; |
| 331 |
< |
|
| 332 |
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MPI_Status istatus; |
| 333 |
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int nitems; |
| 334 |
< |
|
| 335 |
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nTotObjs = info_->getNGlobalIntegrableObjects(); |
| 336 |
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haveError = 0; |
| 337 |
< |
|
| 338 |
< |
if (worldRank == masterNode) { |
| 339 |
< |
inFile_->clear(); |
| 340 |
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inFile_->seekg(framePos_[whichFrame]); |
| 341 |
< |
|
| 342 |
< |
if (!inFile_->getline(readBuffer, sizeof(readBuffer))) { |
| 343 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
| 344 |
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filename_.c_str()); |
| 345 |
< |
painCave.isFatal = 1; |
| 346 |
< |
simError(); |
| 347 |
< |
} |
| 348 |
< |
|
| 349 |
< |
nitems = atoi(read_buffer); |
| 350 |
< |
|
| 351 |
< |
// Check to see that the number of integrable objects in the |
| 352 |
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// intial configuration file is the same as derived from the |
| 353 |
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// meta-data file. |
| 354 |
< |
|
| 355 |
< |
if (nTotObjs != nitems) { |
| 356 |
< |
sprintf(painCave.errMsg, |
| 357 |
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"DumpReader Error. %s nIntegrable, %d, " |
| 358 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
| 359 |
< |
filename_.c_str(), |
| 360 |
< |
nTotObjs, |
| 361 |
< |
info_->getNGlobalIntegrableObjects()); |
| 362 |
< |
|
| 363 |
< |
painCave.isFatal = 1; |
| 364 |
< |
simError(); |
| 365 |
< |
} |
| 366 |
< |
|
| 367 |
< |
//read the boxMat from the comment line |
| 368 |
< |
|
| 369 |
< |
|
| 370 |
< |
|
| 371 |
< |
if (!inFile_->getline(readBuffer, sizeof(readBuffer))) { |
| 372 |
< |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
| 373 |
< |
filename_.c_str()); |
| 374 |
< |
painCave.isFatal = 1; |
| 375 |
< |
simError(); |
| 376 |
< |
} |
| 377 |
< |
|
| 378 |
< |
//Every single processor will parse the comment line by itself |
| 379 |
< |
//By using this way, we might lose some efficiency, but if we want to add |
| 380 |
< |
//more parameters into comment line, we only need to modify function |
| 381 |
< |
//parseCommentLine |
| 382 |
< |
|
| 383 |
< |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 384 |
< |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 385 |
< |
|
| 386 |
< |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 387 |
< |
int which_node = info_->getMolToProc(i); |
| 388 |
< |
|
| 389 |
< |
if (which_node == masterNode) { |
| 390 |
< |
//molecules belong to master node |
| 391 |
< |
|
| 392 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
| 393 |
< |
|
| 394 |
< |
if (mol == NULL) { |
| 395 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
| 396 |
< |
painCave.isFatal = 1; |
| 397 |
< |
simError(); |
| 398 |
< |
} |
| 399 |
< |
|
| 400 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 401 |
< |
integrableObject = mol->nextIntegrableObject(ii)){ |
| 402 |
< |
|
| 403 |
< |
|
| 404 |
< |
|
| 405 |
< |
if (!inFile_->getline(readBuffer, sizeof(readBuffer))) { |
| 406 |
< |
sprintf(painCave.errMsg, |
| 407 |
< |
"DumpReader Error: error in reading file %s\n" |
| 408 |
< |
"natoms = %d; index = %d\n" |
| 409 |
< |
"error reading the line from the file.\n", |
| 410 |
< |
filename_.c_str(), |
| 411 |
< |
nTotObjs, |
| 412 |
< |
i); |
| 413 |
< |
|
| 414 |
< |
painCave.isFatal = 1; |
| 415 |
< |
simError(); |
| 416 |
< |
} |
| 417 |
< |
|
| 418 |
< |
parseDumpLine(read_buffer, integrableObject); |
| 419 |
< |
} |
| 420 |
< |
} else { |
| 421 |
< |
//molecule belongs to slave nodes |
| 422 |
< |
|
| 423 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
| 424 |
< |
MPI_COMM_WORLD, &istatus); |
| 425 |
< |
|
| 426 |
< |
for(int j = 0; j < nCurObj; j++) { |
| 427 |
< |
|
| 428 |
< |
|
| 429 |
< |
if (!inFile_->getline(readBuffer, sizeof(readBuffer))) { |
| 430 |
< |
sprintf(painCave.errMsg, |
| 431 |
< |
"DumpReader Error: error in reading file %s\n" |
| 432 |
< |
"natoms = %d; index = %d\n" |
| 433 |
< |
"error reading the line from the file.\n", |
| 434 |
< |
filename_.c_str(), |
| 435 |
< |
nTotObjs, |
| 436 |
< |
i); |
| 437 |
< |
|
| 438 |
< |
painCave.isFatal = 1; |
| 439 |
< |
simError(); |
| 440 |
< |
} |
| 441 |
< |
|
| 442 |
< |
MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
| 443 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
| 444 |
< |
} |
| 445 |
< |
} |
| 446 |
< |
} |
| 447 |
< |
} else { |
| 448 |
< |
//actions taken at slave nodes |
| 449 |
< |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 450 |
< |
|
| 451 |
< |
/**@todo*/ |
| 452 |
< |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 453 |
< |
|
| 454 |
< |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 455 |
< |
int which_node = info_->getMolToProc(i); |
| 456 |
< |
|
| 457 |
< |
if (which_node == worldRank) { |
| 458 |
< |
//molecule with global index i belongs to this processor |
| 459 |
< |
|
| 460 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
| 461 |
< |
if (mol == NULL) { |
| 462 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
| 463 |
< |
painCave.isFatal = 1; |
| 464 |
< |
simError(); |
| 465 |
< |
} |
| 466 |
< |
|
| 467 |
< |
nCurObj = mol->getNIntegrableObjects(); |
| 468 |
< |
|
| 469 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
| 470 |
< |
MPI_COMM_WORLD); |
| 471 |
< |
|
| 472 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 473 |
< |
integrableObject = mol->nextIntegrableObject(ii)){ |
| 474 |
< |
|
| 475 |
< |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
| 476 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
| 477 |
< |
|
| 478 |
< |
parseDumpLine(read_buffer, integrableObject); |
| 479 |
< |
} |
| 480 |
< |
|
| 481 |
< |
} |
| 482 |
< |
|
| 483 |
< |
} |
| 484 |
< |
|
| 485 |
< |
} |
| 486 |
< |
|
| 487 |
< |
#endif |
| 488 |
< |
|
| 489 |
< |
} |
| 490 |
< |
|
| 491 |
< |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
| 492 |
< |
|
| 493 |
< |
Vector3d pos; // position place holders |
| 494 |
< |
Vector3d vel; // velocity placeholders |
| 495 |
< |
Quat4d q; // the quaternions |
| 496 |
< |
Vector3d ji; // angular velocity placeholders; |
| 497 |
< |
StringTokenizer tokenizer(line); |
| 498 |
< |
int nTokens; |
| 499 |
< |
|
| 500 |
< |
nTokens = tokenizer.countTokens(); |
| 501 |
< |
|
| 502 |
< |
if (nTokens < 14) { |
| 503 |
< |
sprintf(painCave.errMsg, |
| 504 |
< |
"DumpReader Error: Not enough Tokens.\n%s\n", line); |
| 505 |
< |
painCave.isFatal = 1; |
| 506 |
< |
simError(); |
| 507 |
< |
} |
| 508 |
< |
|
| 509 |
< |
std::string name = tokenizer.nextToken(); |
| 510 |
< |
|
| 511 |
< |
if (name != integrableObject->getType()) { |
| 512 |
< |
|
| 513 |
< |
sprintf(painCave.errMsg, |
| 514 |
< |
"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
| 515 |
< |
name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
| 516 |
< |
painCave.isFatal = 1; |
| 517 |
< |
simError(); |
| 518 |
< |
} |
| 519 |
< |
|
| 520 |
< |
pos[0] = tokenizer.nextTokenAsDouble(); |
| 521 |
< |
pos[1] = tokenizer.nextTokenAsDouble(); |
| 522 |
< |
pos[2] = tokenizer.nextTokenAsDouble(); |
| 523 |
< |
if (needPos_) { |
| 524 |
< |
integrableObject->setPos(pos); |
| 525 |
< |
} |
| 526 |
< |
|
| 527 |
< |
vel[0] = tokenizer.nextTokenAsDouble(); |
| 528 |
< |
vel[1] = tokenizer.nextTokenAsDouble(); |
| 529 |
< |
vel[2] = tokenizer.nextTokenAsDouble(); |
| 530 |
< |
if (needVel_) { |
| 531 |
< |
integrableObject->setVel(vel); |
| 532 |
< |
} |
| 533 |
< |
|
| 534 |
< |
if (integrableObject->isDirectional()) { |
| 535 |
< |
|
| 536 |
< |
q[0] = tokenizer.nextTokenAsDouble(); |
| 537 |
< |
q[1] = tokenizer.nextTokenAsDouble(); |
| 538 |
< |
q[2] = tokenizer.nextTokenAsDouble(); |
| 539 |
< |
q[3] = tokenizer.nextTokenAsDouble(); |
| 540 |
< |
|
| 541 |
< |
double qlen = q.length(); |
| 542 |
< |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
| 543 |
< |
|
| 544 |
< |
sprintf(painCave.errMsg, |
| 545 |
< |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
| 546 |
< |
painCave.isFatal = 1; |
| 547 |
< |
simError(); |
| 548 |
< |
|
| 549 |
< |
} |
| 550 |
< |
|
| 551 |
< |
q.normalize(); |
| 552 |
< |
if (needQuaternion_) { |
| 553 |
< |
integrableObject->setQ(q); |
| 554 |
< |
} |
| 555 |
< |
|
| 556 |
< |
ji[0] = tokenizer.nextTokenAsDouble(); |
| 557 |
< |
ji[1] = tokenizer.nextTokenAsDouble(); |
| 558 |
< |
ji[2] = tokenizer.nextTokenAsDouble(); |
| 559 |
< |
if (needAngMom_) { |
| 560 |
< |
integrableObject->setJ(ji); |
| 561 |
< |
} |
| 562 |
< |
} |
| 563 |
< |
|
| 564 |
< |
} |
| 565 |
< |
|
| 566 |
< |
|
| 567 |
< |
void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
| 568 |
< |
double currTime; |
| 569 |
< |
Mat3x3d hmat; |
| 570 |
< |
double chi; |
| 571 |
< |
double integralOfChiDt; |
| 572 |
< |
Mat3x3d eta; |
| 573 |
< |
|
| 574 |
< |
StringTokenizer tokenizer(line); |
| 575 |
< |
int nTokens; |
| 576 |
< |
|
| 577 |
< |
nTokens = tokenizer.countTokens(); |
| 578 |
< |
|
| 579 |
< |
//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
| 580 |
< |
if (nTokens < 10) { |
| 581 |
< |
sprintf(painCave.errMsg, |
| 582 |
< |
"DumpReader Error: Not enough tokens in comment line: %s", line); |
| 583 |
< |
painCave.isFatal = 1; |
| 584 |
< |
simError(); |
| 585 |
< |
} |
| 586 |
< |
|
| 587 |
< |
//read current time |
| 588 |
< |
currTime = tokenizer.nextTokenAsDouble(); |
| 589 |
< |
s->setTime(currTime); |
| 590 |
< |
|
| 591 |
< |
//read h-matrix |
| 592 |
< |
hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
| 593 |
< |
hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
| 594 |
< |
hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
| 595 |
< |
hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
| 596 |
< |
hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
| 597 |
< |
hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
| 598 |
< |
hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
| 599 |
< |
hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
| 600 |
< |
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
| 601 |
< |
s->setHmat(hmat); |
| 602 |
< |
|
| 603 |
< |
//read chi and integralOfChidt, they should apprear in pair |
| 604 |
< |
if (tokenizer.countTokens() >= 2) { |
| 605 |
< |
chi = tokenizer.nextTokenAsDouble(); |
| 606 |
< |
integralOfChiDt = tokenizer.nextTokenAsDouble(); |
| 607 |
< |
|
| 608 |
< |
s->setChi(chi); |
| 609 |
< |
s->setIntegralOfChiDt(integralOfChiDt); |
| 610 |
< |
} |
| 611 |
< |
|
| 612 |
< |
//read eta (eta is 3x3 matrix) |
| 613 |
< |
if (tokenizer.countTokens() >= 9) { |
| 614 |
< |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
| 615 |
< |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
| 616 |
< |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
| 617 |
< |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
| 618 |
< |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
| 619 |
< |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
| 620 |
< |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
| 621 |
< |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
| 622 |
< |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
| 623 |
< |
|
| 624 |
< |
s->setEta(eta); |
| 625 |
< |
} |
| 626 |
< |
|
| 627 |
< |
|
| 628 |
< |
} |
| 629 |
< |
|
| 630 |
< |
}//end namespace oopse |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
| 11 |
> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
| 13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
| 18 |
> |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
#define _LARGEFILE_SOURCE64 |
| 43 |
> |
#define _FILE_OFFSET_BITS 64 |
| 44 |
> |
|
| 45 |
> |
#include <sys/types.h> |
| 46 |
> |
#include <sys/stat.h> |
| 47 |
> |
|
| 48 |
> |
#include <iostream> |
| 49 |
> |
#include <math.h> |
| 50 |
> |
|
| 51 |
> |
#include <stdio.h> |
| 52 |
> |
#include <stdlib.h> |
| 53 |
> |
#include <string.h> |
| 54 |
> |
|
| 55 |
> |
#include "io/DumpReader.hpp" |
| 56 |
> |
#include "primitives/Molecule.hpp" |
| 57 |
> |
#include "utils/simError.h" |
| 58 |
> |
#include "utils/MemoryUtils.hpp" |
| 59 |
> |
#include "utils/StringTokenizer.hpp" |
| 60 |
> |
|
| 61 |
> |
#ifdef IS_MPI |
| 62 |
> |
|
| 63 |
> |
#include <mpi.h> |
| 64 |
> |
#define TAKE_THIS_TAG_CHAR 0 |
| 65 |
> |
#define TAKE_THIS_TAG_INT 1 |
| 66 |
> |
|
| 67 |
> |
#endif // is_mpi |
| 68 |
> |
|
| 69 |
> |
|
| 70 |
> |
namespace oopse { |
| 71 |
> |
|
| 72 |
> |
DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
| 73 |
> |
: info_(info), filename_(filename), isScanned_(false), nframes_(0) { |
| 74 |
> |
|
| 75 |
> |
#ifdef IS_MPI |
| 76 |
> |
|
| 77 |
> |
if (worldRank == 0) { |
| 78 |
> |
#endif |
| 79 |
> |
|
| 80 |
> |
inFile_ = new std::ifstream(filename_.c_str()); |
| 81 |
> |
|
| 82 |
> |
if (inFile_->fail()) { |
| 83 |
> |
sprintf(painCave.errMsg, |
| 84 |
> |
"DumpReader: Cannot open file: %s\n", |
| 85 |
> |
filename_.c_str()); |
| 86 |
> |
painCave.isFatal = 1; |
| 87 |
> |
simError(); |
| 88 |
> |
} |
| 89 |
> |
|
| 90 |
> |
#ifdef IS_MPI |
| 91 |
> |
|
| 92 |
> |
} |
| 93 |
> |
|
| 94 |
> |
strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
| 95 |
> |
MPIcheckPoint(); |
| 96 |
> |
|
| 97 |
> |
#endif |
| 98 |
> |
|
| 99 |
> |
return; |
| 100 |
> |
} |
| 101 |
> |
|
| 102 |
> |
DumpReader::~DumpReader() { |
| 103 |
> |
|
| 104 |
> |
#ifdef IS_MPI |
| 105 |
> |
|
| 106 |
> |
if (worldRank == 0) { |
| 107 |
> |
#endif |
| 108 |
> |
|
| 109 |
> |
delete inFile_; |
| 110 |
> |
|
| 111 |
> |
#ifdef IS_MPI |
| 112 |
> |
|
| 113 |
> |
} |
| 114 |
> |
|
| 115 |
> |
strcpy(checkPointMsg, "Dump file closed successfully."); |
| 116 |
> |
MPIcheckPoint(); |
| 117 |
> |
|
| 118 |
> |
#endif |
| 119 |
> |
|
| 120 |
> |
return; |
| 121 |
> |
} |
| 122 |
> |
|
| 123 |
> |
int DumpReader::getNFrames(void) { |
| 124 |
> |
|
| 125 |
> |
if (!isScanned_) |
| 126 |
> |
scanFile(); |
| 127 |
> |
|
| 128 |
> |
return nframes_; |
| 129 |
> |
} |
| 130 |
> |
|
| 131 |
> |
void DumpReader::scanFile(void) { |
| 132 |
> |
int i, j; |
| 133 |
> |
int lineNum = 0; |
| 134 |
> |
char readBuffer[maxBufferSize]; |
| 135 |
> |
std::streampos currPos; |
| 136 |
> |
|
| 137 |
> |
#ifdef IS_MPI |
| 138 |
> |
|
| 139 |
> |
if (worldRank == 0) { |
| 140 |
> |
#endif // is_mpi |
| 141 |
> |
|
| 142 |
> |
inFile_->seekg (0, std::ios::beg); |
| 143 |
> |
|
| 144 |
> |
|
| 145 |
> |
currPos = inFile_->tellg(); |
| 146 |
> |
inFile_->getline(readBuffer, sizeof(readBuffer)); |
| 147 |
> |
lineNum++; |
| 148 |
> |
|
| 149 |
> |
if (inFile_->eof()) { |
| 150 |
> |
sprintf(painCave.errMsg, |
| 151 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
| 152 |
> |
filename_.c_str(), |
| 153 |
> |
lineNum); |
| 154 |
> |
painCave.isFatal = 1; |
| 155 |
> |
simError(); |
| 156 |
> |
} |
| 157 |
> |
|
| 158 |
> |
while (!inFile_->eof()) { |
| 159 |
> |
framePos_.push_back(currPos); |
| 160 |
> |
|
| 161 |
> |
i = atoi(readBuffer); |
| 162 |
> |
|
| 163 |
> |
inFile_->getline(readBuffer, sizeof(readBuffer)); |
| 164 |
> |
lineNum++; |
| 165 |
> |
|
| 166 |
> |
if (inFile_->eof()) { |
| 167 |
> |
sprintf(painCave.errMsg, |
| 168 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
| 169 |
> |
filename_.c_str(), |
| 170 |
> |
lineNum); |
| 171 |
> |
painCave.isFatal = 1; |
| 172 |
> |
simError(); |
| 173 |
> |
} |
| 174 |
> |
|
| 175 |
> |
for(j = 0; j < i; j++) { |
| 176 |
> |
inFile_->getline(readBuffer, sizeof(readBuffer)); |
| 177 |
> |
lineNum++; |
| 178 |
> |
|
| 179 |
> |
if (inFile_->eof()) { |
| 180 |
> |
sprintf(painCave.errMsg, |
| 181 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d," |
| 182 |
> |
" with atom %d\n", filename_.c_str(), |
| 183 |
> |
lineNum, |
| 184 |
> |
j); |
| 185 |
> |
|
| 186 |
> |
painCave.isFatal = 1; |
| 187 |
> |
simError(); |
| 188 |
> |
} |
| 189 |
> |
} |
| 190 |
> |
|
| 191 |
> |
currPos = inFile_->tellg(); |
| 192 |
> |
inFile_->getline(readBuffer, sizeof(readBuffer)); |
| 193 |
> |
lineNum++; |
| 194 |
> |
} |
| 195 |
> |
|
| 196 |
> |
inFile_->seekg (0, std::ios::beg); |
| 197 |
> |
|
| 198 |
> |
nframes_ = framePos_.size(); |
| 199 |
> |
#ifdef IS_MPI |
| 200 |
> |
} |
| 201 |
> |
|
| 202 |
> |
MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
| 203 |
> |
|
| 204 |
> |
strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); |
| 205 |
> |
MPIcheckPoint(); |
| 206 |
> |
|
| 207 |
> |
#endif // is_mpi |
| 208 |
> |
|
| 209 |
> |
isScanned_ = true; |
| 210 |
> |
} |
| 211 |
> |
|
| 212 |
> |
void DumpReader::readFrame(int whichFrame) { |
| 213 |
> |
if (!isScanned_) |
| 214 |
> |
scanFile(); |
| 215 |
> |
|
| 216 |
> |
int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
| 217 |
> |
|
| 218 |
> |
if (storageLayout & DataStorage::dslPosition) { |
| 219 |
> |
needPos_ = true; |
| 220 |
> |
} else { |
| 221 |
> |
needPos_ = false; |
| 222 |
> |
} |
| 223 |
> |
|
| 224 |
> |
if (storageLayout & DataStorage::dslVelocity) { |
| 225 |
> |
needVel_ = true; |
| 226 |
> |
} else { |
| 227 |
> |
needVel_ = false; |
| 228 |
> |
} |
| 229 |
> |
|
| 230 |
> |
if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
| 231 |
> |
needQuaternion_ = true; |
| 232 |
> |
} else { |
| 233 |
> |
needQuaternion_ = false; |
| 234 |
> |
} |
| 235 |
> |
|
| 236 |
> |
if (storageLayout & DataStorage::dslAngularMomentum) { |
| 237 |
> |
needAngMom_ = true; |
| 238 |
> |
} else { |
| 239 |
> |
needAngMom_ = false; |
| 240 |
> |
} |
| 241 |
> |
|
| 242 |
> |
readSet(whichFrame); |
| 243 |
> |
} |
| 244 |
> |
|
| 245 |
> |
void DumpReader::readSet(int whichFrame) { |
| 246 |
> |
int i; |
| 247 |
> |
int nTotObjs; // the number of atoms |
| 248 |
> |
char read_buffer[maxBufferSize]; //the line buffer for reading |
| 249 |
> |
char * eof_test; // ptr to see when we reach the end of the file |
| 250 |
> |
|
| 251 |
> |
Molecule* mol; |
| 252 |
> |
StuntDouble* integrableObject; |
| 253 |
> |
SimInfo::MoleculeIterator mi; |
| 254 |
> |
Molecule::IntegrableObjectIterator ii; |
| 255 |
> |
|
| 256 |
> |
#ifndef IS_MPI |
| 257 |
> |
inFile_->clear(); |
| 258 |
> |
inFile_->seekg(framePos_[whichFrame]); |
| 259 |
> |
|
| 260 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
| 261 |
> |
sprintf(painCave.errMsg, |
| 262 |
> |
"DumpReader error: error reading 1st line of \"%s\"\n", |
| 263 |
> |
filename_.c_str()); |
| 264 |
> |
painCave.isFatal = 1; |
| 265 |
> |
simError(); |
| 266 |
> |
} |
| 267 |
> |
|
| 268 |
> |
nTotObjs = atoi(read_buffer); |
| 269 |
> |
|
| 270 |
> |
if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
| 271 |
> |
sprintf(painCave.errMsg, |
| 272 |
> |
"DumpReader error. %s nIntegrable, %d, " |
| 273 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
| 274 |
> |
filename_.c_str(), |
| 275 |
> |
nTotObjs, |
| 276 |
> |
info_->getNGlobalIntegrableObjects()); |
| 277 |
> |
|
| 278 |
> |
painCave.isFatal = 1; |
| 279 |
> |
simError(); |
| 280 |
> |
} |
| 281 |
> |
|
| 282 |
> |
//read the box mat from the comment line |
| 283 |
> |
|
| 284 |
> |
|
| 285 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
| 286 |
> |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
| 287 |
> |
filename_.c_str()); |
| 288 |
> |
painCave.isFatal = 1; |
| 289 |
> |
simError(); |
| 290 |
> |
} |
| 291 |
> |
|
| 292 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 293 |
> |
|
| 294 |
> |
//parse dump lines |
| 295 |
> |
|
| 296 |
> |
i = 0; |
| 297 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 298 |
> |
|
| 299 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 300 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 301 |
> |
|
| 302 |
> |
|
| 303 |
> |
|
| 304 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
| 305 |
> |
sprintf(painCave.errMsg, |
| 306 |
> |
"DumpReader Error: error in reading file %s\n" |
| 307 |
> |
"natoms = %d; index = %d\n" |
| 308 |
> |
"error reading the line from the file.\n", |
| 309 |
> |
filename_.c_str(), |
| 310 |
> |
nTotObjs, |
| 311 |
> |
i); |
| 312 |
> |
|
| 313 |
> |
painCave.isFatal = 1; |
| 314 |
> |
simError(); |
| 315 |
> |
} |
| 316 |
> |
|
| 317 |
> |
parseDumpLine(read_buffer, integrableObject); |
| 318 |
> |
i++; |
| 319 |
> |
} |
| 320 |
> |
} |
| 321 |
> |
|
| 322 |
> |
// MPI Section of code.......... |
| 323 |
> |
|
| 324 |
> |
#else //IS_MPI |
| 325 |
> |
|
| 326 |
> |
// first thing first, suspend fatalities. |
| 327 |
> |
int masterNode = 0; |
| 328 |
> |
int nCurObj; |
| 329 |
> |
painCave.isEventLoop = 1; |
| 330 |
> |
|
| 331 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 332 |
> |
int haveError; |
| 333 |
> |
|
| 334 |
> |
MPI_Status istatus; |
| 335 |
> |
int nitems; |
| 336 |
> |
|
| 337 |
> |
nTotObjs = info_->getNGlobalIntegrableObjects(); |
| 338 |
> |
haveError = 0; |
| 339 |
> |
|
| 340 |
> |
if (worldRank == masterNode) { |
| 341 |
> |
inFile_->clear(); |
| 342 |
> |
inFile_->seekg(framePos_[whichFrame]); |
| 343 |
> |
|
| 344 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
| 345 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
| 346 |
> |
filename_.c_str()); |
| 347 |
> |
painCave.isFatal = 1; |
| 348 |
> |
simError(); |
| 349 |
> |
} |
| 350 |
> |
|
| 351 |
> |
nitems = atoi(read_buffer); |
| 352 |
> |
|
| 353 |
> |
// Check to see that the number of integrable objects in the |
| 354 |
> |
// intial configuration file is the same as derived from the |
| 355 |
> |
// meta-data file. |
| 356 |
> |
|
| 357 |
> |
if (nTotObjs != nitems) { |
| 358 |
> |
sprintf(painCave.errMsg, |
| 359 |
> |
"DumpReader Error. %s nIntegrable, %d, " |
| 360 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
| 361 |
> |
filename_.c_str(), |
| 362 |
> |
nTotObjs, |
| 363 |
> |
info_->getNGlobalIntegrableObjects()); |
| 364 |
> |
|
| 365 |
> |
painCave.isFatal = 1; |
| 366 |
> |
simError(); |
| 367 |
> |
} |
| 368 |
> |
|
| 369 |
> |
//read the boxMat from the comment line |
| 370 |
> |
|
| 371 |
> |
|
| 372 |
> |
|
| 373 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
| 374 |
> |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
| 375 |
> |
filename_.c_str()); |
| 376 |
> |
painCave.isFatal = 1; |
| 377 |
> |
simError(); |
| 378 |
> |
} |
| 379 |
> |
|
| 380 |
> |
//Every single processor will parse the comment line by itself |
| 381 |
> |
//By using this way, we might lose some efficiency, but if we want to add |
| 382 |
> |
//more parameters into comment line, we only need to modify function |
| 383 |
> |
//parseCommentLine |
| 384 |
> |
|
| 385 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 386 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 387 |
> |
|
| 388 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 389 |
> |
int which_node = info_->getMolToProc(i); |
| 390 |
> |
|
| 391 |
> |
if (which_node == masterNode) { |
| 392 |
> |
//molecules belong to master node |
| 393 |
> |
|
| 394 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
| 395 |
> |
|
| 396 |
> |
if (mol == NULL) { |
| 397 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
| 398 |
> |
painCave.isFatal = 1; |
| 399 |
> |
simError(); |
| 400 |
> |
} |
| 401 |
> |
|
| 402 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 403 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
| 404 |
> |
|
| 405 |
> |
|
| 406 |
> |
|
| 407 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
| 408 |
> |
sprintf(painCave.errMsg, |
| 409 |
> |
"DumpReader Error: error in reading file %s\n" |
| 410 |
> |
"natoms = %d; index = %d\n" |
| 411 |
> |
"error reading the line from the file.\n", |
| 412 |
> |
filename_.c_str(), |
| 413 |
> |
nTotObjs, |
| 414 |
> |
i); |
| 415 |
> |
|
| 416 |
> |
painCave.isFatal = 1; |
| 417 |
> |
simError(); |
| 418 |
> |
} |
| 419 |
> |
|
| 420 |
> |
parseDumpLine(read_buffer, integrableObject); |
| 421 |
> |
} |
| 422 |
> |
} else { |
| 423 |
> |
//molecule belongs to slave nodes |
| 424 |
> |
|
| 425 |
> |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
| 426 |
> |
MPI_COMM_WORLD, &istatus); |
| 427 |
> |
|
| 428 |
> |
for(int j = 0; j < nCurObj; j++) { |
| 429 |
> |
|
| 430 |
> |
|
| 431 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
| 432 |
> |
sprintf(painCave.errMsg, |
| 433 |
> |
"DumpReader Error: error in reading file %s\n" |
| 434 |
> |
"natoms = %d; index = %d\n" |
| 435 |
> |
"error reading the line from the file.\n", |
| 436 |
> |
filename_.c_str(), |
| 437 |
> |
nTotObjs, |
| 438 |
> |
i); |
| 439 |
> |
|
| 440 |
> |
painCave.isFatal = 1; |
| 441 |
> |
simError(); |
| 442 |
> |
} |
| 443 |
> |
|
| 444 |
> |
MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
| 445 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
| 446 |
> |
} |
| 447 |
> |
} |
| 448 |
> |
} |
| 449 |
> |
} else { |
| 450 |
> |
//actions taken at slave nodes |
| 451 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 452 |
> |
|
| 453 |
> |
/**@todo*/ |
| 454 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 455 |
> |
|
| 456 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 457 |
> |
int which_node = info_->getMolToProc(i); |
| 458 |
> |
|
| 459 |
> |
if (which_node == worldRank) { |
| 460 |
> |
//molecule with global index i belongs to this processor |
| 461 |
> |
|
| 462 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
| 463 |
> |
if (mol == NULL) { |
| 464 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
| 465 |
> |
painCave.isFatal = 1; |
| 466 |
> |
simError(); |
| 467 |
> |
} |
| 468 |
> |
|
| 469 |
> |
nCurObj = mol->getNIntegrableObjects(); |
| 470 |
> |
|
| 471 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
| 472 |
> |
MPI_COMM_WORLD); |
| 473 |
> |
|
| 474 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 475 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
| 476 |
> |
|
| 477 |
> |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
| 478 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
| 479 |
> |
|
| 480 |
> |
parseDumpLine(read_buffer, integrableObject); |
| 481 |
> |
} |
| 482 |
> |
|
| 483 |
> |
} |
| 484 |
> |
|
| 485 |
> |
} |
| 486 |
> |
|
| 487 |
> |
} |
| 488 |
> |
|
| 489 |
> |
#endif |
| 490 |
> |
|
| 491 |
> |
} |
| 492 |
> |
|
| 493 |
> |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
| 494 |
> |
|
| 495 |
> |
Vector3d pos; // position place holders |
| 496 |
> |
Vector3d vel; // velocity placeholders |
| 497 |
> |
Quat4d q; // the quaternions |
| 498 |
> |
Vector3d ji; // angular velocity placeholders; |
| 499 |
> |
StringTokenizer tokenizer(line); |
| 500 |
> |
int nTokens; |
| 501 |
> |
|
| 502 |
> |
nTokens = tokenizer.countTokens(); |
| 503 |
> |
|
| 504 |
> |
if (nTokens < 14) { |
| 505 |
> |
sprintf(painCave.errMsg, |
| 506 |
> |
"DumpReader Error: Not enough Tokens.\n%s\n", line); |
| 507 |
> |
painCave.isFatal = 1; |
| 508 |
> |
simError(); |
| 509 |
> |
} |
| 510 |
> |
|
| 511 |
> |
std::string name = tokenizer.nextToken(); |
| 512 |
> |
|
| 513 |
> |
if (name != integrableObject->getType()) { |
| 514 |
> |
|
| 515 |
> |
sprintf(painCave.errMsg, |
| 516 |
> |
"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
| 517 |
> |
name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
| 518 |
> |
painCave.isFatal = 1; |
| 519 |
> |
simError(); |
| 520 |
> |
} |
| 521 |
> |
|
| 522 |
> |
pos[0] = tokenizer.nextTokenAsDouble(); |
| 523 |
> |
pos[1] = tokenizer.nextTokenAsDouble(); |
| 524 |
> |
pos[2] = tokenizer.nextTokenAsDouble(); |
| 525 |
> |
if (needPos_) { |
| 526 |
> |
integrableObject->setPos(pos); |
| 527 |
> |
} |
| 528 |
> |
|
| 529 |
> |
vel[0] = tokenizer.nextTokenAsDouble(); |
| 530 |
> |
vel[1] = tokenizer.nextTokenAsDouble(); |
| 531 |
> |
vel[2] = tokenizer.nextTokenAsDouble(); |
| 532 |
> |
if (needVel_) { |
| 533 |
> |
integrableObject->setVel(vel); |
| 534 |
> |
} |
| 535 |
> |
|
| 536 |
> |
if (integrableObject->isDirectional()) { |
| 537 |
> |
|
| 538 |
> |
q[0] = tokenizer.nextTokenAsDouble(); |
| 539 |
> |
q[1] = tokenizer.nextTokenAsDouble(); |
| 540 |
> |
q[2] = tokenizer.nextTokenAsDouble(); |
| 541 |
> |
q[3] = tokenizer.nextTokenAsDouble(); |
| 542 |
> |
|
| 543 |
> |
RealType qlen = q.length(); |
| 544 |
> |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
| 545 |
> |
|
| 546 |
> |
sprintf(painCave.errMsg, |
| 547 |
> |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); |
| 548 |
> |
painCave.isFatal = 1; |
| 549 |
> |
simError(); |
| 550 |
> |
|
| 551 |
> |
} |
| 552 |
> |
|
| 553 |
> |
q.normalize(); |
| 554 |
> |
if (needQuaternion_) { |
| 555 |
> |
integrableObject->setQ(q); |
| 556 |
> |
} |
| 557 |
> |
|
| 558 |
> |
ji[0] = tokenizer.nextTokenAsDouble(); |
| 559 |
> |
ji[1] = tokenizer.nextTokenAsDouble(); |
| 560 |
> |
ji[2] = tokenizer.nextTokenAsDouble(); |
| 561 |
> |
if (needAngMom_) { |
| 562 |
> |
integrableObject->setJ(ji); |
| 563 |
> |
} |
| 564 |
> |
} |
| 565 |
> |
|
| 566 |
> |
} |
| 567 |
> |
|
| 568 |
> |
|
| 569 |
> |
void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
| 570 |
> |
RealType currTime; |
| 571 |
> |
Mat3x3d hmat; |
| 572 |
> |
RealType chi; |
| 573 |
> |
RealType integralOfChiDt; |
| 574 |
> |
Mat3x3d eta; |
| 575 |
> |
|
| 576 |
> |
StringTokenizer tokenizer(line); |
| 577 |
> |
int nTokens; |
| 578 |
> |
|
| 579 |
> |
nTokens = tokenizer.countTokens(); |
| 580 |
> |
|
| 581 |
> |
//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
| 582 |
> |
if (nTokens < 10) { |
| 583 |
> |
sprintf(painCave.errMsg, |
| 584 |
> |
"DumpReader Error: Not enough tokens in comment line: %s", line); |
| 585 |
> |
painCave.isFatal = 1; |
| 586 |
> |
simError(); |
| 587 |
> |
} |
| 588 |
> |
|
| 589 |
> |
//read current time |
| 590 |
> |
currTime = tokenizer.nextTokenAsDouble(); |
| 591 |
> |
s->setTime(currTime); |
| 592 |
> |
|
| 593 |
> |
//read h-matrix |
| 594 |
> |
hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
| 595 |
> |
hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
| 596 |
> |
hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
| 597 |
> |
hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
| 598 |
> |
hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
| 599 |
> |
hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
| 600 |
> |
hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
| 601 |
> |
hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
| 602 |
> |
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
| 603 |
> |
s->setHmat(hmat); |
| 604 |
> |
|
| 605 |
> |
//read chi and integralOfChidt, they should apprear in pair |
| 606 |
> |
if (tokenizer.countTokens() >= 2) { |
| 607 |
> |
chi = tokenizer.nextTokenAsDouble(); |
| 608 |
> |
integralOfChiDt = tokenizer.nextTokenAsDouble(); |
| 609 |
> |
|
| 610 |
> |
s->setChi(chi); |
| 611 |
> |
s->setIntegralOfChiDt(integralOfChiDt); |
| 612 |
> |
} |
| 613 |
> |
|
| 614 |
> |
//read eta (eta is 3x3 matrix) |
| 615 |
> |
if (tokenizer.countTokens() >= 9) { |
| 616 |
> |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
| 617 |
> |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
| 618 |
> |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
| 619 |
> |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
| 620 |
> |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
| 621 |
> |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
| 622 |
> |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
| 623 |
> |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
| 624 |
> |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
| 625 |
> |
|
| 626 |
> |
s->setEta(eta); |
| 627 |
> |
} |
| 628 |
> |
|
| 629 |
> |
|
| 630 |
> |
} |
| 631 |
> |
|
| 632 |
> |
}//end namespace oopse |
