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/* |
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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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#include "utils/simError.h" |
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#include "applications/staticProps/StaticPropsCmd.h" |
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#include "applications/staticProps/StaticAnalyser.hpp" |
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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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#include "applications/staticProps/P2OrderParameter.hpp" |
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#include "applications/staticProps/BondOrderParameter.hpp" |
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#include "applications/staticProps/RippleOP.hpp" |
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#include "applications/staticProps/SCDOrderParameter.hpp" |
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#include "applications/staticProps/DensityPlot.hpp" |
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#include "applications/staticProps/RhoZ.hpp" |
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#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
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#include "applications/staticProps/Hxy.hpp" |
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#endif |
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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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//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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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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//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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//get the dumpfile name |
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std::string dumpFileName = args_info.input_arg; |
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std::string sele1; |
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std::string sele2; |
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bool userSpecifiedSelect1; |
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bool userSpecifiedSelect2; |
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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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// check the first selection argument, or set it to the environment |
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// variable, or failing that, set it to "select all" |
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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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|
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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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|
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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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|
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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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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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Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
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maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
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sele1 = "select all"; |
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} |
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|
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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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|
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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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// check the second selection argument, or set it to the environment |
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// variable, or failing that, set it to "select all" |
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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 = "select all"; |
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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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} |
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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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// Problems if sele1 wasn't specified, but |
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// if (!args_info.scd_given) { |
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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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rdf = rAngle2; |
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} else if (args_info.xyz_given) { |
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// Problems if sele1 wasn't specified |
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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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// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { |
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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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rdf = xyz; |
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} |
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bool batchMode; |
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if (args_info.scd_given){ |
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if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) { |
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batchMode = false; |
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} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) { |
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if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { |
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sprintf( painCave.errMsg, |
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"below conditions are not satisfied:\n" |
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"0 <= begin && 0<= end && begin <= end-2\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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batchMode = true; |
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} else{ |
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sprintf( painCave.errMsg, |
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"either --sele1, --sele2, --sele3 are specified," |
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" or --molname, --begin, --end are specified\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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if (args_info.output_given) { |
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rdf->setOutputName(args_info.output_arg); |
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} |
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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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//parse md file and set up the system |
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SimCreator creator; |
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SimInfo* info = creator.createSim(dumpFileName); |
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RealType 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)) /2.0; |
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} |
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StaticAnalyser* analyser; |
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if (args_info.gofr_given){ |
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analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
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} else if (args_info.r_theta_given) { |
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analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
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} else if (args_info.r_omega_given) { |
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analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
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} else if (args_info.theta_omega_given) { |
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analyser = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg); |
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} else if (args_info.gxyz_given) { |
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if (args_info.refsele_given) { |
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analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg); |
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} else { |
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sprintf( painCave.errMsg, |
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"--refsele must set when --gxyz is used"); |
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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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} else if (args_info.p2_given) { |
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analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
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} else if (args_info.rp2_given){ |
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analyser = new RippleOP(info, dumpFileName, sele1, sele2); |
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} else if (args_info.bo_given){ |
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if (args_info.rcut_given && args_info.LegendreL_given) { |
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analyser = new BondOrderParameter(info, dumpFileName, sele1, |
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args_info.rcut_arg, |
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args_info.LegendreL_arg); |
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} else { |
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sprintf( painCave.errMsg, |
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"Both the cutoff radius (rcut) and LegendreL must be specified when calculating Bond Order Parameters"); |
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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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} else if (args_info.scd_given) { |
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if (batchMode) { |
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analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, |
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args_info.begin_arg, args_info.end_arg); |
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} else{ |
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std::string sele3 = args_info.sele3_arg; |
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analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3); |
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} |
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}else if (args_info.density_given) { |
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analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
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} else if (args_info.slab_density_given) { |
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Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
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analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg); |
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#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
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}else if (args_info.hxy_given) { |
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analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg); |
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#endif |
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} |
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|
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if (args_info.output_given) { |
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analyser->setOutputName(args_info.output_arg); |
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} |
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if (args_info.step_given) { |
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analyser->setStep(args_info.step_arg); |
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} |
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rdf->process(); |
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analyser->process(); |
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delete rdf; |
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delete info; |
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delete analyser; |
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delete info; |
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return 0; |
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return 0; |
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} |
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