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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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* 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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* 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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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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#ifndef IO_RESTREADER_HPP |
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#define IO_RESTREADER_HPP |
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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] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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/** |
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* @file RestReader.hpp |
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*/ |
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|
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#ifndef IO_RESTREADER_HPP |
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#define IO_RESTREADER_HPP |
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|
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#include "io/DumpReader.hpp" |
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|
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#define _LARGEFILE_SOURCE64 |
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#ifndef _FILE_OFFSET_BITS |
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#define _FILE_OFFSET_BITS 64 |
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#endif |
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#include <iostream> |
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#include <fstream> |
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#include <string> |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <unistd.h> |
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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 "brains/SimInfo.hpp" |
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#include "primitives/StuntDouble.hpp" |
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|
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namespace oopse { |
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|
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|
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/** |
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* @class RestReader RestReader.hpp "io/RestReader.hpp" |
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* @for extra file reading when using thermodynamic integration |
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*/ |
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class RestReader { |
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|
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public: |
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RestReader( SimInfo* theInfo ); |
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~RestReader(); |
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|
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void readIdealCrystal(); |
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void readZangle(); |
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void zeroZangle(); |
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|
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private: |
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char* parseIdealLine(char* readLine, StuntDouble* sd); |
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char *idealName; |
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FILE *inAngFile; |
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FILE *inIdealFile; |
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std::string inAngFileName; |
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std::string inIdealFileName; |
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bool isScanned; |
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|
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double angleTransfer; |
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std::vector<fpos_t*> framePos; |
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SimInfo *info_; |
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namespace OpenMD { |
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|
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/** |
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* @class RestReader RestReader.hpp "io/RestReader.hpp" |
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*/ |
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class RestReader : public DumpReader { |
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public: |
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RestReader(SimInfo* info, const std::string &filename) : DumpReader(info, filename){} |
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void readReferenceStructure(); |
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protected: |
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virtual void parseDumpLine(const std::string&); |
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virtual void readFrameProperties(std::istream& inputStream); |
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private: |
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std::vector<Vector3d> all_pos_; |
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}; |
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|
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} //end namespace oopse |
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#endif |
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|
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} //end namespace OpenMD |
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|
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#endif //IO_RESTREADER_HPP |
