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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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#include <iostream> |
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#include <fstream> |
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#include <string> |
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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 "io/DumpReader.hpp" |
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#include "utils/simError.h" |
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#include "applications/staticProps/StaticPropsCmd.h" |
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#include "applications/staticProps/GofR.hpp" |
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#include "applications/staticProps/GofRAngle.hpp" |
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#include "applications/staticProps/GofAngle2.hpp" |
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#include "applications/staticProps/GofXyz.hpp" |
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using namespace oopse; |
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int main(int argc, char* argv[]){ |
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//register force fields |
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registerForceFields(); |
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gengetopt_args_info args_info; |
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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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//get the dumpfile name and meta-data file name |
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std::string dumpFileName = args_info.input_arg; |
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std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; |
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std::string sele1; |
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std::string sele2; |
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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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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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sprintf( painCave.errMsg, |
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"neither --sele2 option nor $OOPSE_SELE2 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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//parse md file and set up the system |
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SimCreator creator; |
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SimInfo* info = creator.createSim(mdFileName); |
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double maxLen; |
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if (args_info.length_given) { |
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maxLen = args_info.length_arg; |
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} else { |
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Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
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maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2 ; |
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} |
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RadialDistrFunc* rdf; |
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if (args_info.gofr_given){ |
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GofR* r = new GofR(info, dumpFileName, sele1, sele2); |
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r->setNRBins(args_info.nrbins_arg); |
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r->setLength(maxLen); |
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rdf = r; |
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} else if (args_info.r_theta_given) { |
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GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2); |
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rTheta->setNRBins(args_info.nrbins_arg); |
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rTheta->setLength(maxLen); |
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rTheta->setNAngleBins(args_info.nanglebins_arg); |
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rdf = rTheta; |
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} |
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else if (args_info.r_omega_given) { |
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GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2); |
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rOmega->setNRBins(args_info.nrbins_arg); |
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rOmega->setLength(maxLen); |
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rOmega->setNAngleBins(args_info.nanglebins_arg); |
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rdf = rOmega; |
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} else if (args_info.theta_omega_given) { |
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GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2); |
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rAngle2->setNAngleBins(args_info.nanglebins_arg); |
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rdf = rAngle2; |
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} else if (args_info.xyz_given) { |
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GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2); |
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xyz->setNRBins(args_info.nrbins_arg); |
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xyz->setLength(maxLen); |
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rdf = xyz; |
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} |
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if (args_info.output_given) { |
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rdf->setOutputName(args_info.output_arg); |
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} |
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if (args_info.step_given) { |
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rdf->setStep(args_info.step_arg); |
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} |
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rdf->process(); |
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delete rdf; |
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delete info; |
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return 0; |
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} |
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