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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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#include <iostream> |
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#include <fstream> |
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#include <string> |
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|
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#include "brains/Register.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "utils/simError.h" |
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|
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#include "applications/dynamicProps/DynamicPropsCmd.h" |
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#include "applications/dynamicProps/DipoleCorrFunc.hpp" |
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#include "applications/dynamicProps/RMSD.hpp" |
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#include "applications/dynamicProps/RCorrFunc.hpp" |
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#include "applications/dynamicProps/VCorrFunc.hpp" |
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#include "applications/dynamicProps/LegendreCorrFunc.hpp" |
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|
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|
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using namespace oopse; |
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|
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int main(int argc, char* argv[]){ |
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|
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//register force fields |
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registerForceFields(); |
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|
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gengetopt_args_info args_info; |
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|
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//parse the command line option |
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if (cmdline_parser (argc, argv, &args_info) != 0) { |
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exit(1) ; |
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} |
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|
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|
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//get the dumpfile name and meta-data file name |
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std::string dumpFileName = args_info.input_arg; |
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|
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std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; |
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|
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|
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std::string sele1; |
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std::string sele2; |
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|
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if (args_info.sele1_given) { |
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sele1 = args_info.sele1_arg; |
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}else { |
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char* sele1Env= getenv("OOPSE_SELE1"); |
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if (sele1Env) { |
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sele1 = sele1Env; |
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}else { |
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sprintf( painCave.errMsg, |
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"neither --sele1 option nor $OOPSE_SELE1 is set"); |
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painCave.severity = OOPSE_ERROR; |
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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 (args_info.sele2_given) { |
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sele2 = args_info.sele2_arg; |
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}else { |
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char* sele2Env = getenv("OOPSE_SELE2"); |
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if (sele2Env) { |
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sele2 = sele2Env; |
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} else { |
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sele2 = sele1; |
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} |
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} |
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|
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//parse md file and set up the system |
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SimCreator creator; |
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SimInfo* info = creator.createSim(mdFileName, false); |
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|
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|
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TimeCorrFunc* corrFunc; |
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if (args_info.rmsd_given) { |
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corrFunc = new RMSD(info, dumpFileName, sele1, sele2); |
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} else if (args_info.dcorr_given){ |
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corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2); |
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} else if (args_info.rcorr_given) { |
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corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2); |
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} |
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else if (args_info.vcorr_given) { |
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corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2); |
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} else if (args_info.lcorr_given) { |
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int order; |
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if (args_info.order_given) |
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order = args_info.order_arg; |
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else { |
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sprintf( painCave.errMsg, |
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"--order must be set if --lcoor is set\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order); |
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} |
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|
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if (args_info.output_given) { |
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corrFunc->setOutputName(args_info.output_arg); |
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} |
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|
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|
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corrFunc->doCorrelate(); |
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|
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delete corrFunc; |
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delete info; |
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|
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return 0; |
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} |
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|
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