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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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/** |
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* @file DumpReader.hpp |
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#include <string> |
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#include "brains/SimInfo.hpp" |
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#include "primitives/StuntDouble.hpp" |
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namespace oopse { |
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namespace OpenMD { |
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/** |
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* @class DumpReader DumpReader.hpp "io/DumpReader.hpp" |
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DumpReader(SimInfo* info, const std::string & filename); |
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//DumpReader(SimInfo * info, istream & is); |
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~DumpReader(); |
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virtual ~DumpReader(); |
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/** Returns the number of frames in the dump file*/ |
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int getNFrames(); |
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void setNeedCOMprops(bool ncp) { |
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needCOMprops_ = ncp; |
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} |
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void readFrame(int whichFrame); |
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virtual void readFrame(int whichFrame); |
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private: |
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protected: |
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void scanFile(); |
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void readSet(int whichFrame); |
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void parseDumpLine(char *line, StuntDouble* integrableObject); |
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virtual void parseDumpLine(const std::string&); |
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void parseCommentLine(char* line, Snapshot* s); |
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#ifdef IS_MPI |
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void anonymousNodeDie(void); |
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void nodeZeroError(void); |
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#endif |
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// the maximum length of a typical MPI package is 15k |
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const static int maxBufferSize = 8192; |
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virtual void readFrameProperties(std::istream& inputStream); |
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void readStuntDoubles(std::istream& inputStream); |
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SimInfo* info_; |
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bool needPos_; |
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bool needVel_; |
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bool needQuaternion_; |
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bool needAngMom_; |
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bool needAngMom_; |
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bool needCOMprops_; |
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const static int bufferSize = 4096; |
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char buffer[bufferSize]; |
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}; |
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} //end namespace oopse |
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} //end namespace OpenMD |
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#endif //IO_DUMPREADER_HPP |
