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/* |
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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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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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|
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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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|
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if (worldRank == 0) { |
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#endif |
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|
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inFile_ = fopen(filename_.c_str(), "r"); |
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|
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if (inFile_ == NULL) { |
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sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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|
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inFile_ = fopen(filename_.c_str(), "r"); |
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|
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if (inFile_ == NULL) { |
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sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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#ifdef IS_MPI |
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|
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} |
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|
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strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
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MPIcheckPoint(); |
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|
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|
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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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|
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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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|
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if (worldRank == 0) { |
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#endif |
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|
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int error; |
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error = fclose(inFile_); |
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|
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if (error) { |
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sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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MemoryUtils::deleteVectorOfPointer(framePos_); |
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|
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|
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int error; |
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error = fclose(inFile_); |
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|
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if (error) { |
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sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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MemoryUtils::deletePointers(framePos_); |
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|
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#ifdef IS_MPI |
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|
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|
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} |
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|
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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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|
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#endif |
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|
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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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} |
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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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scanFile(); |
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|
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return nframes_; |
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} |
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|
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void DumpReader::scanFile(void) { |
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int i, j; |
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int lineNum = 0; |
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char readBuffer[maxBufferSize]; |
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fpos_t * currPos; |
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|
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} |
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|
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void DumpReader::scanFile(void) { |
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int i, j; |
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int lineNum = 0; |
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char readBuffer[maxBufferSize]; |
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fpos_t * currPos; |
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|
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#ifdef IS_MPI |
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|
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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rewind(inFile_); |
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|
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currPos = new fpos_t; |
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fgetpos(inFile_, currPos); |
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|
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rewind(inFile_); |
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|
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currPos = new fpos_t; |
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fgetpos(inFile_, currPos); |
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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|
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if (feof(inFile_)) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
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filename_.c_str(), |
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lineNum); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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while (!feof(inFile_)) { |
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framePos_.push_back(currPos); |
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|
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i = atoi(readBuffer); |
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|
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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|
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|
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if (feof(inFile_)) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
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filename_.c_str(), |
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lineNum); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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for(j = 0; j < i; j++) { |
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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|
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if (feof(inFile_)) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
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filename_.c_str(), |
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lineNum); |
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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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while (!feof(inFile_)) { |
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framePos_.push_back(currPos); |
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|
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i = atoi(readBuffer); |
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|
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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|
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if (feof(inFile_)) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
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filename_.c_str(), |
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lineNum); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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for(j = 0; j < i; j++) { |
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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|
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if (feof(inFile_)) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: File \"%s\" ended unexpectedly at line %d," |
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" with atom %d\n", filename_.c_str(), |
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lineNum, |
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j); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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currPos = new fpos_t; |
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fgetpos(inFile_, currPos); |
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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} |
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|
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delete currPos; |
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rewind(inFile_); |
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|
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nframes_ = framePos_.size(); |
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currPos = new fpos_t; |
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fgetpos(inFile_, currPos); |
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fgets(readBuffer, sizeof(readBuffer), inFile_); |
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lineNum++; |
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} |
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|
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delete currPos; |
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rewind(inFile_); |
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|
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nframes_ = framePos_.size(); |
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#ifdef IS_MPI |
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} |
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|
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|
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MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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|
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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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|
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#endif // is_mpi |
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|
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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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} |
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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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|
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if (storageLayout & DataStorage::dslPosition) { |
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needPos_ = true; |
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needPos_ = true; |
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} else { |
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needPos_ = false; |
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needPos_ = false; |
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} |
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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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needVel_ = true; |
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} else { |
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needVel_ = false; |
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needVel_ = false; |
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} |
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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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needQuaternion_ = true; |
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} else { |
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needQuaternion_ = false; |
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needQuaternion_ = false; |
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} |
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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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needAngMom_ = true; |
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} else { |
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needAngMom_ = false; |
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needAngMom_ = false; |
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} |
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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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} |
253 |
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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 |
258 |
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char * eof_test; // ptr to see when we reach the end of the file |
259 |
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|
260 |
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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; |
264 |
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|
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#ifndef IS_MPI |
266 |
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|
266 |
> |
|
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fsetpos(inFile_, framePos_[whichFrame]); |
268 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
269 |
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|
269 |
> |
|
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if (eof_test == NULL) { |
271 |
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sprintf(painCave.errMsg, |
272 |
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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; |
275 |
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simError(); |
271 |
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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()); |
274 |
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painCave.isFatal = 1; |
275 |
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simError(); |
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} |
277 |
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|
277 |
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|
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nTotObjs = atoi(read_buffer); |
279 |
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|
279 |
> |
|
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if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
281 |
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sprintf(painCave.errMsg, |
282 |
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"DumpReader error. %s nIntegrable, %d, " |
283 |
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"does not match the meta-data file's nIntegrable, %d.\n", |
284 |
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filename_.c_str(), |
285 |
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nTotObjs, |
286 |
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info_->getNGlobalIntegrableObjects()); |
287 |
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|
288 |
< |
painCave.isFatal = 1; |
289 |
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simError(); |
281 |
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sprintf(painCave.errMsg, |
282 |
> |
"DumpReader error. %s nIntegrable, %d, " |
283 |
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"does not match the meta-data file's nIntegrable, %d.\n", |
284 |
> |
filename_.c_str(), |
285 |
> |
nTotObjs, |
286 |
> |
info_->getNGlobalIntegrableObjects()); |
287 |
> |
|
288 |
> |
painCave.isFatal = 1; |
289 |
> |
simError(); |
290 |
|
} |
291 |
< |
|
291 |
> |
|
292 |
|
//read the box mat from the comment line |
293 |
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|
293 |
> |
|
294 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
295 |
< |
|
295 |
> |
|
296 |
|
if (eof_test == NULL) { |
297 |
< |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
298 |
< |
filename_.c_str()); |
299 |
< |
painCave.isFatal = 1; |
300 |
< |
simError(); |
297 |
> |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
298 |
> |
filename_.c_str()); |
299 |
> |
painCave.isFatal = 1; |
300 |
> |
simError(); |
301 |
|
} |
302 |
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|
302 |
> |
|
303 |
|
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
304 |
< |
|
304 |
> |
|
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|
//parse dump lines |
306 |
< |
|
306 |
> |
|
307 |
> |
i = 0; |
308 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
309 |
< |
|
310 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
311 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
312 |
< |
|
313 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
314 |
< |
|
315 |
< |
if (eof_test == NULL) { |
316 |
< |
sprintf(painCave.errMsg, |
317 |
< |
"DumpReader Error: error in reading file %s\n" |
318 |
< |
"natoms = %d; index = %d\n" |
319 |
< |
"error reading the line from the file.\n", |
320 |
< |
filename_.c_str(), |
321 |
< |
nTotObjs, |
322 |
< |
i); |
323 |
< |
|
324 |
< |
painCave.isFatal = 1; |
325 |
< |
simError(); |
326 |
< |
} |
327 |
< |
|
328 |
< |
parseDumpLine(read_buffer, integrableObject); |
329 |
< |
|
330 |
< |
} |
309 |
> |
|
310 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
311 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
312 |
> |
|
313 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
314 |
> |
|
315 |
> |
if (eof_test == NULL) { |
316 |
> |
sprintf(painCave.errMsg, |
317 |
> |
"DumpReader Error: error in reading file %s\n" |
318 |
> |
"natoms = %d; index = %d\n" |
319 |
> |
"error reading the line from the file.\n", |
320 |
> |
filename_.c_str(), |
321 |
> |
nTotObjs, |
322 |
> |
i); |
323 |
> |
|
324 |
> |
painCave.isFatal = 1; |
325 |
> |
simError(); |
326 |
> |
} |
327 |
> |
|
328 |
> |
parseDumpLine(read_buffer, integrableObject); |
329 |
> |
i++; |
330 |
> |
} |
331 |
|
} |
332 |
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|
332 |
> |
|
333 |
|
// MPI Section of code.......... |
334 |
< |
|
334 |
> |
|
335 |
|
#else //IS_MPI |
336 |
< |
|
336 |
> |
|
337 |
|
// first thing first, suspend fatalities. |
338 |
|
int masterNode = 0; |
339 |
|
int nCurObj; |
340 |
|
painCave.isEventLoop = 1; |
341 |
< |
|
341 |
> |
|
342 |
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
343 |
|
int haveError; |
344 |
< |
|
344 |
> |
|
345 |
|
MPI_Status istatus; |
346 |
|
int nitems; |
347 |
< |
|
347 |
> |
|
348 |
|
nTotObjs = info_->getNGlobalIntegrableObjects(); |
349 |
|
haveError = 0; |
350 |
< |
|
350 |
> |
|
351 |
|
if (worldRank == masterNode) { |
352 |
< |
fsetpos(inFile_, framePos_[whichFrame]); |
353 |
< |
|
354 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
355 |
< |
|
356 |
< |
if (eof_test == NULL) { |
357 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
358 |
< |
filename_.c_str()); |
359 |
< |
painCave.isFatal = 1; |
360 |
< |
simError(); |
361 |
< |
} |
362 |
< |
|
363 |
< |
nitems = atoi(read_buffer); |
364 |
< |
|
365 |
< |
// Check to see that the number of integrable objects in the |
366 |
< |
// intial configuration file is the same as derived from the |
367 |
< |
// meta-data file. |
368 |
< |
|
369 |
< |
if (nTotObjs != nitems) { |
370 |
< |
sprintf(painCave.errMsg, |
371 |
< |
"DumpReader Error. %s nIntegrable, %d, " |
372 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
373 |
< |
filename_.c_str(), |
374 |
< |
nTotObjs, |
375 |
< |
info_->getNGlobalIntegrableObjects()); |
376 |
< |
|
352 |
> |
fsetpos(inFile_, framePos_[whichFrame]); |
353 |
> |
|
354 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
355 |
> |
|
356 |
> |
if (eof_test == NULL) { |
357 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
358 |
> |
filename_.c_str()); |
359 |
> |
painCave.isFatal = 1; |
360 |
> |
simError(); |
361 |
> |
} |
362 |
> |
|
363 |
> |
nitems = atoi(read_buffer); |
364 |
> |
|
365 |
> |
// Check to see that the number of integrable objects in the |
366 |
> |
// intial configuration file is the same as derived from the |
367 |
> |
// meta-data file. |
368 |
> |
|
369 |
> |
if (nTotObjs != nitems) { |
370 |
> |
sprintf(painCave.errMsg, |
371 |
> |
"DumpReader Error. %s nIntegrable, %d, " |
372 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
373 |
> |
filename_.c_str(), |
374 |
> |
nTotObjs, |
375 |
> |
info_->getNGlobalIntegrableObjects()); |
376 |
> |
|
377 |
> |
painCave.isFatal = 1; |
378 |
> |
simError(); |
379 |
> |
} |
380 |
> |
|
381 |
> |
//read the boxMat from the comment line |
382 |
> |
|
383 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
384 |
> |
|
385 |
> |
if (eof_test == NULL) { |
386 |
> |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
387 |
> |
filename_.c_str()); |
388 |
> |
painCave.isFatal = 1; |
389 |
> |
simError(); |
390 |
> |
} |
391 |
> |
|
392 |
> |
//Every single processor will parse the comment line by itself |
393 |
> |
//By using this way, we might lose some efficiency, but if we want to add |
394 |
> |
//more parameters into comment line, we only need to modify function |
395 |
> |
//parseCommentLine |
396 |
> |
|
397 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
398 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
399 |
> |
|
400 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
401 |
> |
int which_node = info_->getMolToProc(i); |
402 |
> |
|
403 |
> |
if (which_node == masterNode) { |
404 |
> |
//molecules belong to master node |
405 |
> |
|
406 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
407 |
> |
|
408 |
> |
if (mol == NULL) { |
409 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
410 |
|
painCave.isFatal = 1; |
411 |
|
simError(); |
412 |
< |
} |
413 |
< |
|
414 |
< |
//read the boxMat from the comment line |
415 |
< |
|
416 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
417 |
< |
|
418 |
< |
if (eof_test == NULL) { |
419 |
< |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
420 |
< |
filename_.c_str()); |
421 |
< |
painCave.isFatal = 1; |
422 |
< |
simError(); |
423 |
< |
} |
424 |
< |
|
425 |
< |
//Every single processor will parse the comment line by itself |
426 |
< |
//By using this way, we might lose some efficiency, but if we want to add |
427 |
< |
//more parameters into comment line, we only need to modify function |
428 |
< |
//parseCommentLine |
429 |
< |
|
393 |
< |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
394 |
< |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
395 |
< |
|
396 |
< |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
397 |
< |
int which_node = info_->getMolToProc(i); |
398 |
< |
|
399 |
< |
if (which_node == masterNode) { |
400 |
< |
//molecules belong to master node |
401 |
< |
|
402 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
403 |
< |
|
404 |
< |
if (mol == NULL) { |
405 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
406 |
< |
painCave.isFatal = 1; |
407 |
< |
simError(); |
408 |
< |
} |
409 |
< |
|
410 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
411 |
< |
integrableObject = mol->nextIntegrableObject(ii)){ |
412 |
< |
|
413 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
414 |
< |
|
415 |
< |
if (eof_test == NULL) { |
416 |
< |
sprintf(painCave.errMsg, |
417 |
< |
"DumpReader Error: error in reading file %s\n" |
418 |
< |
"natoms = %d; index = %d\n" |
419 |
< |
"error reading the line from the file.\n", |
420 |
< |
filename_.c_str(), |
421 |
< |
nTotObjs, |
422 |
< |
i); |
423 |
< |
|
424 |
< |
painCave.isFatal = 1; |
425 |
< |
simError(); |
426 |
< |
} |
427 |
< |
|
428 |
< |
parseDumpLine(read_buffer, integrableObject); |
429 |
< |
} |
430 |
< |
} else { |
431 |
< |
//molecule belongs to slave nodes |
432 |
< |
|
433 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
434 |
< |
MPI_COMM_WORLD, &istatus); |
435 |
< |
|
436 |
< |
for(int j = 0; j < nCurObj; j++) { |
437 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
438 |
< |
|
439 |
< |
if (eof_test == NULL) { |
440 |
< |
sprintf(painCave.errMsg, |
441 |
< |
"DumpReader Error: error in reading file %s\n" |
442 |
< |
"natoms = %d; index = %d\n" |
443 |
< |
"error reading the line from the file.\n", |
444 |
< |
filename_.c_str(), |
445 |
< |
nTotObjs, |
446 |
< |
i); |
447 |
< |
|
448 |
< |
painCave.isFatal = 1; |
449 |
< |
simError(); |
450 |
< |
} |
451 |
< |
|
452 |
< |
MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
453 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
454 |
< |
} |
412 |
> |
} |
413 |
> |
|
414 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
415 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
416 |
> |
|
417 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
418 |
> |
|
419 |
> |
if (eof_test == NULL) { |
420 |
> |
sprintf(painCave.errMsg, |
421 |
> |
"DumpReader Error: error in reading file %s\n" |
422 |
> |
"natoms = %d; index = %d\n" |
423 |
> |
"error reading the line from the file.\n", |
424 |
> |
filename_.c_str(), |
425 |
> |
nTotObjs, |
426 |
> |
i); |
427 |
> |
|
428 |
> |
painCave.isFatal = 1; |
429 |
> |
simError(); |
430 |
|
} |
431 |
+ |
|
432 |
+ |
parseDumpLine(read_buffer, integrableObject); |
433 |
+ |
} |
434 |
+ |
} else { |
435 |
+ |
//molecule belongs to slave nodes |
436 |
+ |
|
437 |
+ |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
438 |
+ |
MPI_COMM_WORLD, &istatus); |
439 |
+ |
|
440 |
+ |
for(int j = 0; j < nCurObj; j++) { |
441 |
+ |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
442 |
+ |
|
443 |
+ |
if (eof_test == NULL) { |
444 |
+ |
sprintf(painCave.errMsg, |
445 |
+ |
"DumpReader Error: error in reading file %s\n" |
446 |
+ |
"natoms = %d; index = %d\n" |
447 |
+ |
"error reading the line from the file.\n", |
448 |
+ |
filename_.c_str(), |
449 |
+ |
nTotObjs, |
450 |
+ |
i); |
451 |
+ |
|
452 |
+ |
painCave.isFatal = 1; |
453 |
+ |
simError(); |
454 |
+ |
} |
455 |
+ |
|
456 |
+ |
MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
457 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
458 |
+ |
} |
459 |
|
} |
460 |
+ |
} |
461 |
|
} else { |
462 |
< |
//actions taken at slave nodes |
463 |
< |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
464 |
< |
|
465 |
< |
/**@todo*/ |
466 |
< |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
467 |
< |
|
468 |
< |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
469 |
< |
int which_node = info_->getMolToProc(i); |
470 |
< |
|
471 |
< |
if (which_node == worldRank) { |
472 |
< |
//molecule with global index i belongs to this processor |
473 |
< |
|
474 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
475 |
< |
if (mol == NULL) { |
476 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
477 |
< |
painCave.isFatal = 1; |
478 |
< |
simError(); |
479 |
< |
} |
480 |
< |
|
481 |
< |
nCurObj = mol->getNIntegrableObjects(); |
482 |
< |
|
483 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
484 |
< |
MPI_COMM_WORLD); |
485 |
< |
|
486 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
487 |
< |
integrableObject = mol->nextIntegrableObject(ii)){ |
484 |
< |
|
485 |
< |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
486 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
487 |
< |
|
488 |
< |
parseDumpLine(read_buffer, integrableObject); |
489 |
< |
} |
490 |
< |
|
491 |
< |
} |
462 |
> |
//actions taken at slave nodes |
463 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
464 |
> |
|
465 |
> |
/**@todo*/ |
466 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
467 |
> |
|
468 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
469 |
> |
int which_node = info_->getMolToProc(i); |
470 |
> |
|
471 |
> |
if (which_node == worldRank) { |
472 |
> |
//molecule with global index i belongs to this processor |
473 |
> |
|
474 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
475 |
> |
if (mol == NULL) { |
476 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
477 |
> |
painCave.isFatal = 1; |
478 |
> |
simError(); |
479 |
> |
} |
480 |
> |
|
481 |
> |
nCurObj = mol->getNIntegrableObjects(); |
482 |
> |
|
483 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
484 |
> |
MPI_COMM_WORLD); |
485 |
> |
|
486 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
487 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
488 |
|
|
489 |
+ |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
490 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
491 |
+ |
|
492 |
+ |
parseDumpLine(read_buffer, integrableObject); |
493 |
+ |
} |
494 |
+ |
|
495 |
|
} |
496 |
|
|
497 |
+ |
} |
498 |
+ |
|
499 |
|
} |
500 |
< |
|
500 |
> |
|
501 |
|
#endif |
502 |
< |
|
503 |
< |
} |
504 |
< |
|
505 |
< |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
506 |
< |
|
502 |
> |
|
503 |
> |
} |
504 |
> |
|
505 |
> |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
506 |
> |
|
507 |
|
Vector3d pos; // position place holders |
508 |
|
Vector3d vel; // velocity placeholders |
509 |
|
Quat4d q; // the quaternions |
512 |
|
int nTokens; |
513 |
|
|
514 |
|
nTokens = tokenizer.countTokens(); |
515 |
< |
|
515 |
> |
|
516 |
|
if (nTokens < 14) { |
517 |
< |
sprintf(painCave.errMsg, |
518 |
< |
"DumpReader Error: Not enough Tokens.\n%s\n", line); |
519 |
< |
painCave.isFatal = 1; |
520 |
< |
simError(); |
517 |
> |
sprintf(painCave.errMsg, |
518 |
> |
"DumpReader Error: Not enough Tokens.\n%s\n", line); |
519 |
> |
painCave.isFatal = 1; |
520 |
> |
simError(); |
521 |
|
} |
522 |
< |
|
522 |
> |
|
523 |
|
std::string name = tokenizer.nextToken(); |
524 |
< |
|
524 |
> |
|
525 |
|
if (name != integrableObject->getType()) { |
526 |
< |
|
527 |
< |
sprintf(painCave.errMsg, |
528 |
< |
"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
529 |
< |
name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
530 |
< |
painCave.isFatal = 1; |
531 |
< |
simError(); |
526 |
> |
|
527 |
> |
sprintf(painCave.errMsg, |
528 |
> |
"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
529 |
> |
name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
530 |
> |
painCave.isFatal = 1; |
531 |
> |
simError(); |
532 |
|
} |
533 |
< |
|
533 |
> |
|
534 |
|
pos[0] = tokenizer.nextTokenAsDouble(); |
535 |
|
pos[1] = tokenizer.nextTokenAsDouble(); |
536 |
|
pos[2] = tokenizer.nextTokenAsDouble(); |
537 |
|
if (needPos_) { |
538 |
< |
integrableObject->setPos(pos); |
538 |
> |
integrableObject->setPos(pos); |
539 |
|
} |
540 |
|
|
541 |
|
vel[0] = tokenizer.nextTokenAsDouble(); |
542 |
|
vel[1] = tokenizer.nextTokenAsDouble(); |
543 |
|
vel[2] = tokenizer.nextTokenAsDouble(); |
544 |
|
if (needVel_) { |
545 |
< |
integrableObject->setVel(vel); |
545 |
> |
integrableObject->setVel(vel); |
546 |
|
} |
547 |
|
|
548 |
|
if (integrableObject->isDirectional()) { |
549 |
+ |
|
550 |
+ |
q[0] = tokenizer.nextTokenAsDouble(); |
551 |
+ |
q[1] = tokenizer.nextTokenAsDouble(); |
552 |
+ |
q[2] = tokenizer.nextTokenAsDouble(); |
553 |
+ |
q[3] = tokenizer.nextTokenAsDouble(); |
554 |
+ |
|
555 |
+ |
double qlen = q.length(); |
556 |
+ |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
557 |
|
|
558 |
< |
q[0] = tokenizer.nextTokenAsDouble(); |
559 |
< |
q[1] = tokenizer.nextTokenAsDouble(); |
560 |
< |
q[2] = tokenizer.nextTokenAsDouble(); |
561 |
< |
q[3] = tokenizer.nextTokenAsDouble(); |
562 |
< |
|
563 |
< |
double qlen = q.length(); |
564 |
< |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
565 |
< |
|
566 |
< |
sprintf(painCave.errMsg, |
567 |
< |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
568 |
< |
painCave.isFatal = 1; |
569 |
< |
simError(); |
570 |
< |
|
571 |
< |
} |
572 |
< |
|
573 |
< |
q.normalize(); |
574 |
< |
if (needQuaternion_) { |
575 |
< |
integrableObject->setQ(q); |
564 |
< |
} |
565 |
< |
|
566 |
< |
ji[0] = tokenizer.nextTokenAsDouble(); |
567 |
< |
ji[1] = tokenizer.nextTokenAsDouble(); |
568 |
< |
ji[2] = tokenizer.nextTokenAsDouble(); |
569 |
< |
if (needAngMom_) { |
570 |
< |
integrableObject->setJ(ji); |
571 |
< |
} |
558 |
> |
sprintf(painCave.errMsg, |
559 |
> |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
560 |
> |
painCave.isFatal = 1; |
561 |
> |
simError(); |
562 |
> |
|
563 |
> |
} |
564 |
> |
|
565 |
> |
q.normalize(); |
566 |
> |
if (needQuaternion_) { |
567 |
> |
integrableObject->setQ(q); |
568 |
> |
} |
569 |
> |
|
570 |
> |
ji[0] = tokenizer.nextTokenAsDouble(); |
571 |
> |
ji[1] = tokenizer.nextTokenAsDouble(); |
572 |
> |
ji[2] = tokenizer.nextTokenAsDouble(); |
573 |
> |
if (needAngMom_) { |
574 |
> |
integrableObject->setJ(ji); |
575 |
> |
} |
576 |
|
} |
577 |
< |
|
578 |
< |
} |
579 |
< |
|
580 |
< |
|
581 |
< |
void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
577 |
> |
|
578 |
> |
} |
579 |
> |
|
580 |
> |
|
581 |
> |
void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
582 |
|
double currTime; |
583 |
|
Mat3x3d hmat; |
584 |
|
double chi; |
585 |
|
double integralOfChiDt; |
586 |
|
Mat3x3d eta; |
587 |
< |
|
587 |
> |
|
588 |
|
StringTokenizer tokenizer(line); |
589 |
|
int nTokens; |
590 |
< |
|
590 |
> |
|
591 |
|
nTokens = tokenizer.countTokens(); |
592 |
< |
|
592 |
> |
|
593 |
|
//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
594 |
|
if (nTokens < 10) { |
595 |
< |
sprintf(painCave.errMsg, |
596 |
< |
"DumpReader Error: Not enough tokens in comment line: %s", line); |
597 |
< |
painCave.isFatal = 1; |
598 |
< |
simError(); |
595 |
> |
sprintf(painCave.errMsg, |
596 |
> |
"DumpReader Error: Not enough tokens in comment line: %s", line); |
597 |
> |
painCave.isFatal = 1; |
598 |
> |
simError(); |
599 |
|
} |
600 |
< |
|
600 |
> |
|
601 |
|
//read current time |
602 |
|
currTime = tokenizer.nextTokenAsDouble(); |
603 |
|
s->setTime(currTime); |
616 |
|
|
617 |
|
//read chi and integralOfChidt, they should apprear in pair |
618 |
|
if (tokenizer.countTokens() >= 2) { |
619 |
< |
chi = tokenizer.nextTokenAsDouble(); |
620 |
< |
integralOfChiDt = tokenizer.nextTokenAsDouble(); |
621 |
< |
|
622 |
< |
s->setChi(chi); |
623 |
< |
s->setIntegralOfChiDt(integralOfChiDt); |
619 |
> |
chi = tokenizer.nextTokenAsDouble(); |
620 |
> |
integralOfChiDt = tokenizer.nextTokenAsDouble(); |
621 |
> |
|
622 |
> |
s->setChi(chi); |
623 |
> |
s->setIntegralOfChiDt(integralOfChiDt); |
624 |
|
} |
625 |
|
|
626 |
|
//read eta (eta is 3x3 matrix) |
627 |
|
if (tokenizer.countTokens() >= 9) { |
628 |
< |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
629 |
< |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
630 |
< |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
631 |
< |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
632 |
< |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
633 |
< |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
634 |
< |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
635 |
< |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
636 |
< |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
637 |
< |
|
638 |
< |
s->setEta(eta); |
628 |
> |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
629 |
> |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
630 |
> |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
631 |
> |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
632 |
> |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
633 |
> |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
634 |
> |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
635 |
> |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
636 |
> |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
637 |
> |
|
638 |
> |
s->setEta(eta); |
639 |
|
} |
636 |
– |
|
640 |
|
|
641 |
< |
} |
642 |
< |
|
641 |
> |
|
642 |
> |
} |
643 |
> |
|
644 |
|
}//end namespace oopse |