applications/staticProps/StaticProps.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "io/DumpReader.hpp"
#include "utils/simError.h"

#include "applications/staticProps/StaticPropsCmd.h"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "applications/staticProps/GofR.hpp"
#include "applications/staticProps/GofZ.hpp"
#include "applications/staticProps/GofRZ.hpp"
#include "applications/staticProps/GofRAngle.hpp"
#include "applications/staticProps/GofAngle2.hpp"
#include "applications/staticProps/GofXyz.hpp"
#include "applications/staticProps/TwoDGofR.hpp"
#include "applications/staticProps/P2OrderParameter.hpp"
#include "applications/staticProps/BondOrderParameter.hpp"
#include "applications/staticProps/BOPofR.hpp"
#include "applications/staticProps/RippleOP.hpp"
#include "applications/staticProps/SCDOrderParameter.hpp"
#include "applications/staticProps/DensityPlot.hpp"
#include "applications/staticProps/ObjectCount.hpp"
#include "applications/staticProps/RhoZ.hpp"
#include "applications/staticProps/pAngle.hpp"
#include "applications/staticProps/BondAngleDistribution.hpp"
#include "applications/staticProps/NanoVolume.hpp"
#include "applications/staticProps/NanoLength.hpp"
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
#include "applications/staticProps/Hxy.hpp"
#endif
#include "applications/staticProps/RhoR.hpp"
#include "applications/staticProps/AngleR.hpp"
#include "applications/staticProps/TetrahedralityParam.hpp"
#include "applications/staticProps/TetrahedralityParamZ.hpp"
#include "applications/staticProps/TetrahedralityParamXYZ.hpp"
#include "applications/staticProps/RNEMDStats.hpp"
#include "applications/staticProps/NitrileFrequencyMap.hpp"
#include "applications/staticProps/MultipoleSum.hpp"

using namespace OpenMD;

int main(int argc, char* argv[]){
  
  
  gengetopt_args_info args_info;
  
  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }
  
  //get the dumpfile name
  std::string dumpFileName = args_info.input_arg;
  std::string sele1;
  std::string sele2;
  std::string sele3;
  
  // check the first selection argument, or set it to the environment
  // variable, or failing that, set it to "select all"
  
  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  } else {
    char*  sele1Env= getenv("SELECTION1");
    if (sele1Env) {
      sele1 = sele1Env;
    } else {
      sele1 = "select all";
    }
  }
  
  // check the second selection argument, or set it to the environment
  // variable, or failing that, set it to the first selection
  
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  } else {
    char* sele2Env = getenv("SELECTION2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else { 
      //If sele2 is not specified, then the default behavior
      //should be what is already intended for sele1
      sele2 = sele1;
    }
  }

  // check the third selection argument, which is only set if
  // requested by the user

  if (args_info.sele3_given) sele3 = args_info.sele3_arg;

  bool batchMode;
  if (args_info.scd_given){
    if (args_info.sele1_given && 
        args_info.sele2_given && args_info.sele3_given) {
      batchMode = false;
    } else if (args_info.molname_given && 
               args_info.begin_given && args_info.end_given) {
      if (args_info.begin_arg < 0 || 
          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
        sprintf( painCave.errMsg,
                 "below conditions are not satisfied:\n"
                 "0 <= begin && 0<= end && begin <= end-2\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();                    
      }
      batchMode = true;        
    } else{
      sprintf( painCave.errMsg,
               "either --sele1, --sele2, --sele3 are specified,"
               " or --molname, --begin, --end are specified\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  }
  
  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(dumpFileName);

  RealType maxLen;
  RealType zmaxLen;
  if (args_info.length_given) {
    maxLen = args_info.length_arg;
    if (args_info.zlength_given){
      zmaxLen = args_info.zlength_arg;
    }
  } else {
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
    zmaxLen = hmat(2,2);    
  }    
  
  StaticAnalyser* analyser;
  if (args_info.gofr_given){
    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, 
                       args_info.nbins_arg);        
  } else if (args_info.gofz_given) {
    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
                       args_info.nbins_arg);
  } else if (args_info.r_z_given) {
    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, 
                          args_info.nbins_arg, args_info.nbins_z_arg);
  } else if (args_info.r_theta_given) {
    if (args_info.sele3_given) 
      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
                                args_info.nbins_arg, args_info.nanglebins_arg);
    else 
      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, 
                                args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.r_omega_given) {
    if (args_info.sele3_given) 
      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
                                args_info.nbins_arg, args_info.nanglebins_arg);
    else 
      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
                                args_info.nbins_arg, args_info.nanglebins_arg);

  } else if (args_info.theta_omega_given) {
    if (args_info.sele3_given) 
      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
                                args_info.nanglebins_arg);
    else
      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, 
                                args_info.nanglebins_arg);
  } else if (args_info.gxyz_given) {
    if (args_info.refsele_given) {
      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "--refsele must set when --gxyz is used");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
  } else if (args_info.twodgofr_given){
    if (args_info.dz_given) {
      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen, 
                             args_info.dz_arg, args_info.nbins_arg);        
    } else {
      sprintf( painCave.errMsg,
               "A slab width (dz) must be specified when calculating TwoDGofR");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }    
  } else if (args_info.p2_given) {
    if (args_info.sele1_given) {     
      if (args_info.sele2_given) 
        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
      else 
        if (args_info.seleoffset_given) 
          analyser  = new P2OrderParameter(info, dumpFileName, sele1, 
                                           args_info.seleoffset_arg);
        else 
          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
    } else {
      sprintf( painCave.errMsg,
               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.rp2_given){
    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
  } else if (args_info.bo_given){
    if (args_info.rcut_given) {
      analyser = new BondOrderParameter(info, dumpFileName, sele1, 
                                        args_info.rcut_arg, 
                                        args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.multipole_given){
    analyser = new MultipoleSum(info, dumpFileName, sele1, 
                                maxLen, args_info.nbins_arg);
  } else if (args_info.tet_param_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParam(info, dumpFileName, sele1, 
                                         args_info.rcut_arg, 
                                         args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.tet_param_z_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
                                          args_info.rcut_arg, 
                                          args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.tet_param_xyz_given) {
    if (!args_info.rcut_given) {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating"
               " Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    if (!args_info.voxelSize_given) {
      sprintf( painCave.errMsg,
               "A voxel size must be specified when calculating"
               " volume-resolved Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    if (!args_info.gaussWidth_given) {
      sprintf( painCave.errMsg,
               "A gaussian width must be specified when calculating"
               " volume-resolved Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
                                          args_info.rcut_arg, 
                                          args_info.voxelSize_arg,
                                          args_info.gaussWidth_arg);
  } else if (args_info.ior_given){
    if (args_info.rcut_given) {
      analyser = new IcosahedralOfR(info, dumpFileName, sele1, 
                                    args_info.rcut_arg,
                                    args_info.nbins_arg, maxLen);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.for_given){
    if (args_info.rcut_given) {
      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
                            args_info.nbins_arg, maxLen);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.bad_given){
    if (args_info.rcut_given) {
      analyser = new BondAngleDistribution(info, dumpFileName, sele1, 
                                           args_info.rcut_arg,
                                           args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.scd_given) {
    if (batchMode) {
      analyser  = new SCDOrderParameter(info, dumpFileName, 
                                        args_info.molname_arg, 
                                        args_info.begin_arg, args_info.end_arg);
    } else{
      analyser  = new SCDOrderParameter(info, dumpFileName, 
                                        sele1, sele2, sele3);
    }
  }else if (args_info.density_given) {
    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
                              args_info.nbins_arg);  
  } else if (args_info.count_given) {
    analyser = new ObjectCount(info, dumpFileName, sele1 );
  } else if (args_info.slab_density_given) {
    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.rnemdz_given) {
    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.rnemdr_given) {
    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.rnemdrt_given) {
    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
                               args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.nitrile_given) {
    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
                                       args_info.nbins_arg);
  } else if (args_info.p_angle_given) {
    if (args_info.sele1_given) {     
      if (args_info.sele2_given) 
        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
                               args_info.nbins_arg);
      else 
        if (args_info.seleoffset_given) {
          if (args_info.seleoffset2_given) {
            analyser  = new pAngle(info, dumpFileName, sele1, 
                                   args_info.seleoffset_arg, 
                                   args_info.seleoffset2_arg, 
                                   args_info.nbins_arg);
          } else {
            analyser  = new pAngle(info, dumpFileName, sele1, 
                                   args_info.seleoffset_arg, 
                                   args_info.nbins_arg);
          }
        } else 
          analyser  = new pAngle(info, dumpFileName, sele1, 
                                 args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "At least one selection script (--sele1) must be specified when "
               "calculating P(angle) distributions");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
  }else if (args_info.hxy_given) {
    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, 
                       args_info.nbins_y_arg, args_info.nbins_arg);
#endif
  }else if (args_info.rho_r_given) {
    if (args_info.radius_given){
      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
    }else{
      sprintf( painCave.errMsg,
               "A particle radius (radius) must be specified when calculating Rho(r)");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.hullvol_given) {
    analyser = new NanoVolume(info, dumpFileName, sele1);
  } else if (args_info.rodlength_given) {
    analyser = new NanoLength(info, dumpFileName, sele1);
  } else if (args_info.angle_r_given) {
    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
  }
  
  if (args_info.output_given) {
    analyser->setOutputName(args_info.output_arg);
  }
  if (args_info.step_given) {
    analyser->setStep(args_info.step_arg);
  }
  
  analyser->process();
  
  delete analyser;    
  delete info;
  
  return 0;   
}
Revision:	2023
Committed:	Thu Oct 2 14:35:14 2014 UTC (10 years, 6 months ago) by gezelter
File size:	17742 byte(s)
Log Message:	Added 3rd selection option for the 2d g(r) analyzers
#	User	Rev	Content
1	gezelter	507	/*
2	tim	310	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	310	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	310	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	310	*/
42
43			#include <iostream>
44			#include <fstream>
45			#include <string>
46
47			#include "brains/SimCreator.hpp"
48			#include "brains/SimInfo.hpp"
49			#include "io/DumpReader.hpp"
50			#include "utils/simError.h"
51
52	tim	311	#include "applications/staticProps/StaticPropsCmd.h"
53	tim	543	#include "applications/staticProps/StaticAnalyser.hpp"
54	tim	311	#include "applications/staticProps/GofR.hpp"
55	xsun	1213	#include "applications/staticProps/GofZ.hpp"
56	gezelter	1440	#include "applications/staticProps/GofRZ.hpp"
57	tim	311	#include "applications/staticProps/GofRAngle.hpp"
58			#include "applications/staticProps/GofAngle2.hpp"
59			#include "applications/staticProps/GofXyz.hpp"
60	gezelter	1454	#include "applications/staticProps/TwoDGofR.hpp"
61	tim	543	#include "applications/staticProps/P2OrderParameter.hpp"
62	gezelter	1039	#include "applications/staticProps/BondOrderParameter.hpp"
63	chuckv	1128	#include "applications/staticProps/BOPofR.hpp"
64	xsun	980	#include "applications/staticProps/RippleOP.hpp"
65	tim	544	#include "applications/staticProps/SCDOrderParameter.hpp"
66	tim	545	#include "applications/staticProps/DensityPlot.hpp"
67	gezelter	1513	#include "applications/staticProps/ObjectCount.hpp"
68	tim	840	#include "applications/staticProps/RhoZ.hpp"
69	gezelter	1413	#include "applications/staticProps/pAngle.hpp"
70	chuckv	1180	#include "applications/staticProps/BondAngleDistribution.hpp"
71			#include "applications/staticProps/NanoVolume.hpp"
72	gezelter	1585	#include "applications/staticProps/NanoLength.hpp"
73	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
74	xsun	955	#include "applications/staticProps/Hxy.hpp"
75	gezelter	956	#endif
76	chuckv	1091	#include "applications/staticProps/RhoR.hpp"
77	kstocke1	1522	#include "applications/staticProps/AngleR.hpp"
78			#include "applications/staticProps/TetrahedralityParam.hpp"
79	gezelter	1782	#include "applications/staticProps/TetrahedralityParamZ.hpp"
80	gezelter	2015	#include "applications/staticProps/TetrahedralityParamXYZ.hpp"
81	gezelter	1879	#include "applications/staticProps/RNEMDStats.hpp"
82	gezelter	1994	#include "applications/staticProps/NitrileFrequencyMap.hpp"
83	gezelter	1998	#include "applications/staticProps/MultipoleSum.hpp"
84	gezelter	1879
85	gezelter	1390	using namespace OpenMD;
86	tim	310
87			int main(int argc, char* argv[]){
88
89	gezelter	1513
90			gengetopt_args_info args_info;
91
92			//parse the command line option
93			if (cmdline_parser (argc, argv, &args_info) != 0) {
94			exit(1) ;
95			}
96
97			//get the dumpfile name
98			std::string dumpFileName = args_info.input_arg;
99			std::string sele1;
100			std::string sele2;
101	gezelter	2023	std::string sele3;
102	gezelter	1513
103			// check the first selection argument, or set it to the environment
104			// variable, or failing that, set it to "select all"
105
106			if (args_info.sele1_given) {
107			sele1 = args_info.sele1_arg;
108			} else {
109			char* sele1Env= getenv("SELECTION1");
110			if (sele1Env) {
111			sele1 = sele1Env;
112			} else {
113			sele1 = "select all";
114			}
115			}
116
117			// check the second selection argument, or set it to the environment
118	gezelter	1937	// variable, or failing that, set it to the first selection
119	gezelter	1513
120			if (args_info.sele2_given) {
121			sele2 = args_info.sele2_arg;
122			} else {
123	gezelter	1937	char* sele2Env = getenv("SELECTION2");
124	gezelter	1513	if (sele2Env) {
125			sele2 = sele2Env;
126			} else {
127	gezelter	1819	//If sele2 is not specified, then the default behavior
128			//should be what is already intended for sele1
129	jmichalk	1785	sele2 = sele1;
130	gezelter	1513	}
131			}
132	gezelter	1846
133	gezelter	2023	// check the third selection argument, which is only set if
134			// requested by the user
135
136			if (args_info.sele3_given) sele3 = args_info.sele3_arg;
137
138	gezelter	1513	bool batchMode;
139			if (args_info.scd_given){
140	gezelter	1846	if (args_info.sele1_given &&
141			args_info.sele2_given && args_info.sele3_given) {
142	gezelter	1513	batchMode = false;
143	gezelter	1846	} else if (args_info.molname_given &&
144			args_info.begin_given && args_info.end_given) {
145			if (args_info.begin_arg < 0 \|\|
146			args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
147	gezelter	1513	sprintf( painCave.errMsg,
148			"below conditions are not satisfied:\n"
149			"0 <= begin && 0<= end && begin <= end-2\n");
150			painCave.severity = OPENMD_ERROR;
151			painCave.isFatal = 1;
152			simError();
153			}
154			batchMode = true;
155			} else{
156			sprintf( painCave.errMsg,
157			"either --sele1, --sele2, --sele3 are specified,"
158			" or --molname, --begin, --end are specified\n");
159			painCave.severity = OPENMD_ERROR;
160			painCave.isFatal = 1;
161	gezelter	1846	simError();
162	gezelter	1513	}
163			}
164
165			//parse md file and set up the system
166			SimCreator creator;
167			SimInfo* info = creator.createSim(dumpFileName);
168	tim	310
169	gezelter	1513	RealType maxLen;
170			RealType zmaxLen;
171			if (args_info.length_given) {
172			maxLen = args_info.length_arg;
173			if (args_info.zlength_given){
174			zmaxLen = args_info.zlength_arg;
175	chuckv	1445	}
176	gezelter	1513	} else {
177			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
178			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
179			zmaxLen = hmat(2,2);
180			}
181	kstocke1	1522
182	gezelter	1513	StaticAnalyser* analyser;
183			if (args_info.gofr_given){
184			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
185	kstocke1	1522	args_info.nbins_arg);
186	gezelter	1513	} else if (args_info.gofz_given) {
187			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
188	kstocke1	1522	args_info.nbins_arg);
189	gezelter	1513	} else if (args_info.r_z_given) {
190			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
191	kstocke1	1522	args_info.nbins_arg, args_info.nbins_z_arg);
192	gezelter	1513	} else if (args_info.r_theta_given) {
193	gezelter	2023	if (args_info.sele3_given)
194			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
195			args_info.nbins_arg, args_info.nanglebins_arg);
196			else
197			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
198			args_info.nbins_arg, args_info.nanglebins_arg);
199	gezelter	1513	} else if (args_info.r_omega_given) {
200	gezelter	2023	if (args_info.sele3_given)
201			analyser = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
202			args_info.nbins_arg, args_info.nanglebins_arg);
203			else
204			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205			args_info.nbins_arg, args_info.nanglebins_arg);
206
207	gezelter	1513	} else if (args_info.theta_omega_given) {
208	gezelter	2023	if (args_info.sele3_given)
209			analyser = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
210			args_info.nanglebins_arg);
211			else
212			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
213			args_info.nanglebins_arg);
214	gezelter	1513	} else if (args_info.gxyz_given) {
215			if (args_info.refsele_given) {
216	gezelter	1846	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
217			args_info.refsele_arg, maxLen, args_info.nbins_arg);
218	gezelter	1039	} else {
219	gezelter	1513	sprintf( painCave.errMsg,
220	kstocke1	1522	"--refsele must set when --gxyz is used");
221	gezelter	1513	painCave.severity = OPENMD_ERROR;
222			painCave.isFatal = 1;
223			simError();
224	tim	310	}
225	gezelter	1513	} else if (args_info.twodgofr_given){
226			if (args_info.dz_given) {
227			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
228	kstocke1	1522	args_info.dz_arg, args_info.nbins_arg);
229	chuckv	1445	} else {
230	gezelter	1513	sprintf( painCave.errMsg,
231	kstocke1	1522	"A slab width (dz) must be specified when calculating TwoDGofR");
232	gezelter	1513	painCave.severity = OPENMD_ERROR;
233			painCave.isFatal = 1;
234			simError();
235	kstocke1	1522	}
236	gezelter	1513	} else if (args_info.p2_given) {
237	gezelter	1542	if (args_info.sele1_given) {
238			if (args_info.sele2_given)
239			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
240			else
241	gezelter	1819	if (args_info.seleoffset_given)
242			analyser = new P2OrderParameter(info, dumpFileName, sele1,
243			args_info.seleoffset_arg);
244			else
245			analyser = new P2OrderParameter(info, dumpFileName, sele1);
246	gezelter	1542	} else {
247			sprintf( painCave.errMsg,
248			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
249			painCave.severity = OPENMD_ERROR;
250			painCave.isFatal = 1;
251			simError();
252			}
253	gezelter	1513	} else if (args_info.rp2_given){
254			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
255			} else if (args_info.bo_given){
256			if (args_info.rcut_given) {
257			analyser = new BondOrderParameter(info, dumpFileName, sele1,
258	kstocke1	1522	args_info.rcut_arg,
259			args_info.nbins_arg);
260	gezelter	1513	} else {
261			sprintf( painCave.errMsg,
262	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
263	gezelter	1513	painCave.severity = OPENMD_ERROR;
264			painCave.isFatal = 1;
265			simError();
266	tim	544	}
267	gezelter	1998	} else if (args_info.multipole_given){
268	gezelter	1999	analyser = new MultipoleSum(info, dumpFileName, sele1,
269			maxLen, args_info.nbins_arg);
270	kstocke1	1522	} else if (args_info.tet_param_given) {
271			if (args_info.rcut_given) {
272			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
273			args_info.rcut_arg,
274			args_info.nbins_arg);
275			} else {
276			sprintf( painCave.errMsg,
277			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
278			painCave.severity = OPENMD_ERROR;
279			painCave.isFatal = 1;
280			simError();
281			}
282	gezelter	1782	} else if (args_info.tet_param_z_given) {
283			if (args_info.rcut_given) {
284	gezelter	1846	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
285			args_info.rcut_arg,
286			args_info.nbins_arg);
287	gezelter	1782	} else {
288			sprintf( painCave.errMsg,
289			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
290			painCave.severity = OPENMD_ERROR;
291			painCave.isFatal = 1;
292			simError();
293			}
294	gezelter	2015	} else if (args_info.tet_param_xyz_given) {
295			if (!args_info.rcut_given) {
296			sprintf( painCave.errMsg,
297			"A cutoff radius (rcut) must be specified when calculating"
298			" Tetrahedrality Parameters");
299			painCave.severity = OPENMD_ERROR;
300			painCave.isFatal = 1;
301			simError();
302			}
303			if (!args_info.voxelSize_given) {
304			sprintf( painCave.errMsg,
305			"A voxel size must be specified when calculating"
306			" volume-resolved Tetrahedrality Parameters");
307			painCave.severity = OPENMD_ERROR;
308			painCave.isFatal = 1;
309			simError();
310			}
311			if (!args_info.gaussWidth_given) {
312			sprintf( painCave.errMsg,
313			"A gaussian width must be specified when calculating"
314			" volume-resolved Tetrahedrality Parameters");
315			painCave.severity = OPENMD_ERROR;
316			painCave.isFatal = 1;
317			simError();
318			}
319			analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
320			args_info.rcut_arg,
321			args_info.voxelSize_arg,
322			args_info.gaussWidth_arg);
323	gezelter	1992	} else if (args_info.ior_given){
324	gezelter	1513	if (args_info.rcut_given) {
325	gezelter	1992	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
326			args_info.rcut_arg,
327			args_info.nbins_arg, maxLen);
328			} else {
329			sprintf( painCave.errMsg,
330			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
331			painCave.severity = OPENMD_ERROR;
332			painCave.isFatal = 1;
333			simError();
334			}
335			} else if (args_info.for_given){
336			if (args_info.rcut_given) {
337			analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
338	kstocke1	1522	args_info.nbins_arg, maxLen);
339	chuckv	1445	} else {
340	gezelter	1513	sprintf( painCave.errMsg,
341	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
342	gezelter	1513	painCave.severity = OPENMD_ERROR;
343			painCave.isFatal = 1;
344			simError();
345			}
346			} else if (args_info.bad_given){
347			if (args_info.rcut_given) {
348	gezelter	1846	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
349			args_info.rcut_arg,
350	kstocke1	1522	args_info.nbins_arg);
351	gezelter	1513	} else {
352			sprintf( painCave.errMsg,
353	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
354	gezelter	1513	painCave.severity = OPENMD_ERROR;
355			painCave.isFatal = 1;
356			simError();
357	gezelter	1846	}
358	gezelter	1513	} else if (args_info.scd_given) {
359			if (batchMode) {
360	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
361			args_info.molname_arg,
362	kstocke1	1522	args_info.begin_arg, args_info.end_arg);
363	gezelter	1513	} else{
364	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
365			sele1, sele2, sele3);
366	gezelter	1513	}
367			}else if (args_info.density_given) {
368			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
369	kstocke1	1522	args_info.nbins_arg);
370	gezelter	1513	} else if (args_info.count_given) {
371			analyser = new ObjectCount(info, dumpFileName, sele1 );
372			} else if (args_info.slab_density_given) {
373			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
374	gezelter	1879	} else if (args_info.rnemdz_given) {
375			analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
376			} else if (args_info.rnemdr_given) {
377			analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
378	gezelter	1953	} else if (args_info.rnemdrt_given) {
379			analyser = new RNEMDRTheta(info, dumpFileName, sele1,
380			args_info.nbins_arg, args_info.nanglebins_arg);
381	gezelter	1994	} else if (args_info.nitrile_given) {
382			analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
383			args_info.nbins_arg);
384	gezelter	1513	} else if (args_info.p_angle_given) {
385	gezelter	1979	if (args_info.sele1_given) {
386			if (args_info.sele2_given)
387			analyser = new pAngle(info, dumpFileName, sele1, sele2,
388			args_info.nbins_arg);
389			else
390	gezelter	1991	if (args_info.seleoffset_given) {
391			if (args_info.seleoffset2_given) {
392			analyser = new pAngle(info, dumpFileName, sele1,
393			args_info.seleoffset_arg,
394			args_info.seleoffset2_arg,
395			args_info.nbins_arg);
396			} else {
397			analyser = new pAngle(info, dumpFileName, sele1,
398			args_info.seleoffset_arg,
399			args_info.nbins_arg);
400			}
401			} else
402	gezelter	1979	analyser = new pAngle(info, dumpFileName, sele1,
403			args_info.nbins_arg);
404			} else {
405			sprintf( painCave.errMsg,
406			"At least one selection script (--sele1) must be specified when "
407			"calculating P(angle) distributions");
408			painCave.severity = OPENMD_ERROR;
409			painCave.isFatal = 1;
410			simError();
411			}
412	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
413	gezelter	1513	}else if (args_info.hxy_given) {
414			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
415	kstocke1	1522	args_info.nbins_y_arg, args_info.nbins_arg);
416	gezelter	956	#endif
417	gezelter	1513	}else if (args_info.rho_r_given) {
418			if (args_info.radius_given){
419			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
420			}else{
421			sprintf( painCave.errMsg,
422	kstocke1	1522	"A particle radius (radius) must be specified when calculating Rho(r)");
423	gezelter	1513	painCave.severity = OPENMD_ERROR;
424			painCave.isFatal = 1;
425			simError();
426	chuckv	1091	}
427	kstocke1	1522	} else if (args_info.hullvol_given) {
428	gezelter	1513	analyser = new NanoVolume(info, dumpFileName, sele1);
429	gezelter	1585	} else if (args_info.rodlength_given) {
430			analyser = new NanoLength(info, dumpFileName, sele1);
431	kstocke1	1522	} else if (args_info.angle_r_given) {
432			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
433	gezelter	1513	}
434	gezelter	1846
435	gezelter	1513	if (args_info.output_given) {
436			analyser->setOutputName(args_info.output_arg);
437			}
438			if (args_info.step_given) {
439			analyser->setStep(args_info.step_arg);
440			}
441	gezelter	1846
442	gezelter	1513	analyser->process();
443	kstocke1	1522
444	gezelter	1513	delete analyser;
445			delete info;
446	gezelter	1846
447	gezelter	1513	return 0;
448	tim	310	}