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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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* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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#endif // is_mpi |
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namespace oopse { |
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namespace OpenMD { |
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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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: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) { |
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#ifdef IS_MPI |
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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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errorCheckPoint(); |
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#endif |
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} |
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strcpy(checkPointMsg, "Dump file closed successfully."); |
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MPIcheckPoint(); |
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errorCheckPoint(); |
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#endif |
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} |
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readSet(whichFrame); |
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|
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if (needCOMprops_) { |
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Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Vector3d com; |
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Vector3d comvel; |
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Vector3d comw; |
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if (needPos_ && needVel_){ |
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info_->getComAll(com, comvel); |
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comw = info_->getAngularMomentum(); |
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}else{ |
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com = info_->getCom(); |
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comvel = 0.0; |
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comw = 0.0; |
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} |
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s->setCOMprops(com, comvel, comw); |
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} |
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} |
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void DumpReader::readSet(int whichFrame) { |
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std::string line; |
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#ifndef IS_MPI |
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inFile_->clear(); |
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inFile_->seekg(framePos_[whichFrame]); |
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int sendBufferSize; |
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MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
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char * recvBuffer = new char[sendBufferSize+1]; |
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assert(recvBuffer); |
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recvBuffer[sendBufferSize] = '\0'; |
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MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
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sstream.str(recvBuffer); |
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delete [] recvBuffer; |
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} |
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std::istream& inputStream = sstream; |
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nTokens = tokenizer.countTokens(); |
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if (nTokens < 2) { |
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if (nTokens < 2) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
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painCave.isFatal = 1; |
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std::string type = tokenizer.nextToken(); |
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int size = type.size(); |
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size_t found; |
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|
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if (needPos_) { |
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found = type.find("p"); |
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if (found == std::string::npos) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: StuntDouble %d has no Position\n" |
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"\tField (\"p\") specified.\n%s\n", index, |
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line.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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if (integrableObject->isDirectional()) { |
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if (needQuaternion_) { |
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found = type.find("q"); |
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if (found == std::string::npos) { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: Directional StuntDouble %d has no\n" |
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"\tQuaternion Field (\"q\") specified.\n%s\n", index, |
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line.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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|
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for(int i = 0; i < size; ++i) { |
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switch(type[i]) { |
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q[3] = tokenizer.nextTokenAsDouble(); |
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RealType qlen = q.length(); |
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if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
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if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0 |
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sprintf(painCave.errMsg, |
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"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); |
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integrableObject->setTrq(torque); |
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break; |
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} |
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case 'u' : { |
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|
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RealType particlePot; |
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particlePot = tokenizer.nextTokenAsDouble(); |
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integrableObject->setParticlePot(particlePot); |
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break; |
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} |
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default: { |
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sprintf(painCave.errMsg, |
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"DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
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} |
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}//end namespace oopse |
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}//end namespace OpenMD |
