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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. 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, 234107 (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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#include <iostream> |
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#include <fstream> |
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#include <string> |
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|
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#include "brains/SimCreator.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "utils/StringUtils.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/SelectionCorrFunc.hpp" |
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#include "applications/dynamicProps/DipoleCorrFunc.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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#include "applications/dynamicProps/RadialRCorrFunc.hpp" |
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#include "applications/dynamicProps/ThetaCorrFunc.hpp" |
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#include "applications/dynamicProps/DirectionalRCorrFunc.hpp" |
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#include "applications/dynamicProps/EnergyCorrFunc.hpp" |
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#include "applications/dynamicProps/StressCorrFunc.hpp" |
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#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" |
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#include "applications/dynamicProps/MomentumCorrFunc.hpp" |
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|
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using namespace OpenMD; |
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|
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int main(int argc, char* argv[]){ |
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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 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("SELECTION1"); |
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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 $SELECTION1 is set"); |
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painCave.severity = OPENMD_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("SELECTION2"); |
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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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// use the memory string to figure out how much memory we can use: |
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char *end; |
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long long int memSize = memparse(args_info.memory_arg, &end); |
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sprintf( painCave.errMsg, |
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"Amount of memory being used: %llu bytes\n", memSize); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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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(dumpFileName, false); |
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|
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TimeCorrFunc* corrFunc; |
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if(args_info.sdcorr_given){ |
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corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.selecorr_given){ |
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corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.dcorr_given){ |
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corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.rcorr_given) { |
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corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.r_rcorr_given) { |
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corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.thetacorr_given) { |
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corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.drcorr_given) { |
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corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.vcorr_given) { |
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corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.helfandEcorr_given){ |
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corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.stresscorr_given){ |
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corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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} else if (args_info.momentum_given){ |
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corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
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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 = OPENMD_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, memSize); |
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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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|
