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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 "io/DumpReader.hpp" |
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#include "utils/simError.h" |
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|
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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/GofZ.hpp" |
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#include "applications/staticProps/GofRZ.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/TwoDGofR.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/BOPofR.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/ObjectCount.hpp" |
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#include "applications/staticProps/RhoZ.hpp" |
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#include "applications/staticProps/pAngle.hpp" |
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#include "applications/staticProps/BondAngleDistribution.hpp" |
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#include "applications/staticProps/NanoVolume.hpp" |
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#include "applications/staticProps/NanoLength.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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#include "applications/staticProps/RhoR.hpp" |
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#include "applications/staticProps/AngleR.hpp" |
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#include "applications/staticProps/TetrahedralityParam.hpp" |
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#include "applications/staticProps/TetrahedralityParamZ.hpp" |
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#include "applications/staticProps/TetrahedralityParamXYZ.hpp" |
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#include "applications/staticProps/RNEMDStats.hpp" |
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#include "applications/staticProps/NitrileFrequencyMap.hpp" |
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#include "applications/staticProps/MultipoleSum.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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|
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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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//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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|
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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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|
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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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sele1 = "select all"; |
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} |
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} |
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|
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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 the first selection |
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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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//If sele2 is not specified, then the default behavior |
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//should be what is already intended for sele1 |
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sele2 = sele1; |
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} |
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} |
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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 && |
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args_info.sele2_given && args_info.sele3_given) { |
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batchMode = false; |
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} else if (args_info.molname_given && |
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args_info.begin_given && args_info.end_given) { |
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if (args_info.begin_arg < 0 || |
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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 = OPENMD_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 = 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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//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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|
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RealType maxLen; |
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RealType zmaxLen; |
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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.zlength_given){ |
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zmaxLen = args_info.zlength_arg; |
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} |
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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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zmaxLen = hmat(2,2); |
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} |
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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, |
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args_info.nbins_arg); |
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} else if (args_info.gofz_given) { |
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analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen, |
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args_info.nbins_arg); |
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} else if (args_info.r_z_given) { |
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analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, |
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args_info.nbins_arg, args_info.nbins_z_arg); |
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} else if (args_info.r_theta_given) { |
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analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, |
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args_info.nbins_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, |
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args_info.nbins_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, |
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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, |
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args_info.refsele_arg, maxLen, args_info.nbins_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 = OPENMD_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.twodgofr_given){ |
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if (args_info.dz_given) { |
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analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen, |
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args_info.dz_arg, args_info.nbins_arg); |
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} else { |
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sprintf( painCave.errMsg, |
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"A slab width (dz) must be specified when calculating TwoDGofR"); |
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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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} else if (args_info.p2_given) { |
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if (args_info.sele1_given) { |
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if (args_info.sele2_given) |
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analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
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else |
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if (args_info.seleoffset_given) |
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analyser = new P2OrderParameter(info, dumpFileName, sele1, |
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args_info.seleoffset_arg); |
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else |
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analyser = new P2OrderParameter(info, dumpFileName, sele1); |
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} else { |
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sprintf( painCave.errMsg, |
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"At least one selection script (--sele1) must be specified when calculating P2 order parameters"); |
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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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} 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) { |
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analyser = new BondOrderParameter(info, dumpFileName, sele1, |
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args_info.rcut_arg, |
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args_info.nbins_arg); |
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} else { |
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sprintf( painCave.errMsg, |
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"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
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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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} else if (args_info.multipole_given){ |
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analyser = new MultipoleSum(info, dumpFileName, sele1, |
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maxLen, args_info.nbins_arg); |
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} else if (args_info.tet_param_given) { |
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if (args_info.rcut_given) { |
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analyser = new TetrahedralityParam(info, dumpFileName, sele1, |
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args_info.rcut_arg, |
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args_info.nbins_arg); |
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} else { |
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sprintf( painCave.errMsg, |
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"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters"); |
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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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} else if (args_info.tet_param_z_given) { |
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if (args_info.rcut_given) { |
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analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2, |
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args_info.rcut_arg, |
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args_info.nbins_arg); |
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} else { |
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sprintf( painCave.errMsg, |
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"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters"); |
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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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} else if (args_info.tet_param_xyz_given) { |
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if (!args_info.rcut_given) { |
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sprintf( painCave.errMsg, |
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"A cutoff radius (rcut) must be specified when calculating" |
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" Tetrahedrality Parameters"); |
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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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if (!args_info.voxelSize_given) { |
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sprintf( painCave.errMsg, |
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"A voxel size must be specified when calculating" |
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" volume-resolved Tetrahedrality Parameters"); |
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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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if (!args_info.gaussWidth_given) { |
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sprintf( painCave.errMsg, |
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"A gaussian width must be specified when calculating" |
| 295 |
" volume-resolved Tetrahedrality Parameters"); |
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painCave.severity = OPENMD_ERROR; |
| 297 |
painCave.isFatal = 1; |
| 298 |
simError(); |
| 299 |
} |
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analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2, |
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args_info.rcut_arg, |
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args_info.voxelSize_arg, |
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args_info.gaussWidth_arg); |
| 304 |
} else if (args_info.ior_given){ |
| 305 |
if (args_info.rcut_given) { |
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analyser = new IcosahedralOfR(info, dumpFileName, sele1, |
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args_info.rcut_arg, |
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args_info.nbins_arg, maxLen); |
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} else { |
| 310 |
sprintf( painCave.errMsg, |
| 311 |
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
| 312 |
painCave.severity = OPENMD_ERROR; |
| 313 |
painCave.isFatal = 1; |
| 314 |
simError(); |
| 315 |
} |
| 316 |
} else if (args_info.for_given){ |
| 317 |
if (args_info.rcut_given) { |
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analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg, |
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args_info.nbins_arg, maxLen); |
| 320 |
} else { |
| 321 |
sprintf( painCave.errMsg, |
| 322 |
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
| 323 |
painCave.severity = OPENMD_ERROR; |
| 324 |
painCave.isFatal = 1; |
| 325 |
simError(); |
| 326 |
} |
| 327 |
} else if (args_info.bad_given){ |
| 328 |
if (args_info.rcut_given) { |
| 329 |
analyser = new BondAngleDistribution(info, dumpFileName, sele1, |
| 330 |
args_info.rcut_arg, |
| 331 |
args_info.nbins_arg); |
| 332 |
} else { |
| 333 |
sprintf( painCave.errMsg, |
| 334 |
"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions"); |
| 335 |
painCave.severity = OPENMD_ERROR; |
| 336 |
painCave.isFatal = 1; |
| 337 |
simError(); |
| 338 |
} |
| 339 |
} else if (args_info.scd_given) { |
| 340 |
if (batchMode) { |
| 341 |
analyser = new SCDOrderParameter(info, dumpFileName, |
| 342 |
args_info.molname_arg, |
| 343 |
args_info.begin_arg, args_info.end_arg); |
| 344 |
} else{ |
| 345 |
std::string sele3 = args_info.sele3_arg; |
| 346 |
analyser = new SCDOrderParameter(info, dumpFileName, |
| 347 |
sele1, sele2, sele3); |
| 348 |
} |
| 349 |
}else if (args_info.density_given) { |
| 350 |
analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, |
| 351 |
args_info.nbins_arg); |
| 352 |
} else if (args_info.count_given) { |
| 353 |
analyser = new ObjectCount(info, dumpFileName, sele1 ); |
| 354 |
} else if (args_info.slab_density_given) { |
| 355 |
analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg); |
| 356 |
} else if (args_info.rnemdz_given) { |
| 357 |
analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg); |
| 358 |
} else if (args_info.rnemdr_given) { |
| 359 |
analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg); |
| 360 |
} else if (args_info.rnemdrt_given) { |
| 361 |
analyser = new RNEMDRTheta(info, dumpFileName, sele1, |
| 362 |
args_info.nbins_arg, args_info.nanglebins_arg); |
| 363 |
} else if (args_info.nitrile_given) { |
| 364 |
analyser = new NitrileFrequencyMap(info, dumpFileName, sele1, |
| 365 |
args_info.nbins_arg); |
| 366 |
} else if (args_info.p_angle_given) { |
| 367 |
if (args_info.sele1_given) { |
| 368 |
if (args_info.sele2_given) |
| 369 |
analyser = new pAngle(info, dumpFileName, sele1, sele2, |
| 370 |
args_info.nbins_arg); |
| 371 |
else |
| 372 |
if (args_info.seleoffset_given) { |
| 373 |
if (args_info.seleoffset2_given) { |
| 374 |
analyser = new pAngle(info, dumpFileName, sele1, |
| 375 |
args_info.seleoffset_arg, |
| 376 |
args_info.seleoffset2_arg, |
| 377 |
args_info.nbins_arg); |
| 378 |
} else { |
| 379 |
analyser = new pAngle(info, dumpFileName, sele1, |
| 380 |
args_info.seleoffset_arg, |
| 381 |
args_info.nbins_arg); |
| 382 |
} |
| 383 |
} else |
| 384 |
analyser = new pAngle(info, dumpFileName, sele1, |
| 385 |
args_info.nbins_arg); |
| 386 |
} else { |
| 387 |
sprintf( painCave.errMsg, |
| 388 |
"At least one selection script (--sele1) must be specified when " |
| 389 |
"calculating P(angle) distributions"); |
| 390 |
painCave.severity = OPENMD_ERROR; |
| 391 |
painCave.isFatal = 1; |
| 392 |
simError(); |
| 393 |
} |
| 394 |
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
| 395 |
}else if (args_info.hxy_given) { |
| 396 |
analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, |
| 397 |
args_info.nbins_y_arg, args_info.nbins_arg); |
| 398 |
#endif |
| 399 |
}else if (args_info.rho_r_given) { |
| 400 |
if (args_info.radius_given){ |
| 401 |
analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg); |
| 402 |
}else{ |
| 403 |
sprintf( painCave.errMsg, |
| 404 |
"A particle radius (radius) must be specified when calculating Rho(r)"); |
| 405 |
painCave.severity = OPENMD_ERROR; |
| 406 |
painCave.isFatal = 1; |
| 407 |
simError(); |
| 408 |
} |
| 409 |
} else if (args_info.hullvol_given) { |
| 410 |
analyser = new NanoVolume(info, dumpFileName, sele1); |
| 411 |
} else if (args_info.rodlength_given) { |
| 412 |
analyser = new NanoLength(info, dumpFileName, sele1); |
| 413 |
} else if (args_info.angle_r_given) { |
| 414 |
analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg); |
| 415 |
} |
| 416 |
|
| 417 |
if (args_info.output_given) { |
| 418 |
analyser->setOutputName(args_info.output_arg); |
| 419 |
} |
| 420 |
if (args_info.step_given) { |
| 421 |
analyser->setStep(args_info.step_arg); |
| 422 |
} |
| 423 |
|
| 424 |
analyser->process(); |
| 425 |
|
| 426 |
delete analyser; |
| 427 |
delete info; |
| 428 |
|
| 429 |
return 0; |
| 430 |
} |
