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/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;
  
  // 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;
    }
  }

  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) {
    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.r_omega_given) {
    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.theta_omega_given) {
    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){
    if (args_info.rcut_given) {
      analyser = new MultipoleSum(info, dumpFileName, sele1, 
                                        args_info.rcut_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Multipole Sums");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
  } 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.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{
      std::string sele3 = args_info.sele3_arg;
      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:	1998
Committed:	Fri May 30 19:48:35 2014 UTC (10 years, 11 months ago) by gezelter
File size:	15966 byte(s)
Log Message:	Added the MultipoleSum
#	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	1879	#include "applications/staticProps/RNEMDStats.hpp"
81	gezelter	1994	#include "applications/staticProps/NitrileFrequencyMap.hpp"
82	gezelter	1998	#include "applications/staticProps/MultipoleSum.hpp"
83	gezelter	1879
84	gezelter	1390	using namespace OpenMD;
85	tim	310
86			int main(int argc, char* argv[]){
87
88	gezelter	1513
89			gengetopt_args_info args_info;
90
91			//parse the command line option
92			if (cmdline_parser (argc, argv, &args_info) != 0) {
93			exit(1) ;
94			}
95
96			//get the dumpfile name
97			std::string dumpFileName = args_info.input_arg;
98			std::string sele1;
99			std::string sele2;
100
101			// check the first selection argument, or set it to the environment
102			// variable, or failing that, set it to "select all"
103
104			if (args_info.sele1_given) {
105			sele1 = args_info.sele1_arg;
106			} else {
107			char* sele1Env= getenv("SELECTION1");
108			if (sele1Env) {
109			sele1 = sele1Env;
110			} else {
111			sele1 = "select all";
112			}
113			}
114
115			// check the second selection argument, or set it to the environment
116	gezelter	1937	// variable, or failing that, set it to the first selection
117	gezelter	1513
118			if (args_info.sele2_given) {
119			sele2 = args_info.sele2_arg;
120			} else {
121	gezelter	1937	char* sele2Env = getenv("SELECTION2");
122	gezelter	1513	if (sele2Env) {
123			sele2 = sele2Env;
124			} else {
125	gezelter	1819	//If sele2 is not specified, then the default behavior
126			//should be what is already intended for sele1
127	jmichalk	1785	sele2 = sele1;
128	gezelter	1513	}
129			}
130	gezelter	1846
131	gezelter	1513	bool batchMode;
132			if (args_info.scd_given){
133	gezelter	1846	if (args_info.sele1_given &&
134			args_info.sele2_given && args_info.sele3_given) {
135	gezelter	1513	batchMode = false;
136	gezelter	1846	} else if (args_info.molname_given &&
137			args_info.begin_given && args_info.end_given) {
138			if (args_info.begin_arg < 0 \|\|
139			args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
140	gezelter	1513	sprintf( painCave.errMsg,
141			"below conditions are not satisfied:\n"
142			"0 <= begin && 0<= end && begin <= end-2\n");
143			painCave.severity = OPENMD_ERROR;
144			painCave.isFatal = 1;
145			simError();
146			}
147			batchMode = true;
148			} else{
149			sprintf( painCave.errMsg,
150			"either --sele1, --sele2, --sele3 are specified,"
151			" or --molname, --begin, --end are specified\n");
152			painCave.severity = OPENMD_ERROR;
153			painCave.isFatal = 1;
154	gezelter	1846	simError();
155	gezelter	1513	}
156			}
157
158			//parse md file and set up the system
159			SimCreator creator;
160			SimInfo* info = creator.createSim(dumpFileName);
161	tim	310
162	gezelter	1513	RealType maxLen;
163			RealType zmaxLen;
164			if (args_info.length_given) {
165			maxLen = args_info.length_arg;
166			if (args_info.zlength_given){
167			zmaxLen = args_info.zlength_arg;
168	chuckv	1445	}
169	gezelter	1513	} else {
170			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
171			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
172			zmaxLen = hmat(2,2);
173			}
174	kstocke1	1522
175	gezelter	1513	StaticAnalyser* analyser;
176			if (args_info.gofr_given){
177			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
178	kstocke1	1522	args_info.nbins_arg);
179	gezelter	1513	} else if (args_info.gofz_given) {
180			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
181	kstocke1	1522	args_info.nbins_arg);
182	gezelter	1513	} else if (args_info.r_z_given) {
183			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
184	kstocke1	1522	args_info.nbins_arg, args_info.nbins_z_arg);
185	gezelter	1513	} else if (args_info.r_theta_given) {
186			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
187	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
188	gezelter	1513	} else if (args_info.r_omega_given) {
189			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
190	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
191	gezelter	1513	} else if (args_info.theta_omega_given) {
192			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
193	kstocke1	1522	args_info.nanglebins_arg);
194	gezelter	1513	} else if (args_info.gxyz_given) {
195			if (args_info.refsele_given) {
196	gezelter	1846	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
197			args_info.refsele_arg, maxLen, args_info.nbins_arg);
198	gezelter	1039	} else {
199	gezelter	1513	sprintf( painCave.errMsg,
200	kstocke1	1522	"--refsele must set when --gxyz is used");
201	gezelter	1513	painCave.severity = OPENMD_ERROR;
202			painCave.isFatal = 1;
203			simError();
204	tim	310	}
205	gezelter	1513	} else if (args_info.twodgofr_given){
206			if (args_info.dz_given) {
207			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
208	kstocke1	1522	args_info.dz_arg, args_info.nbins_arg);
209	chuckv	1445	} else {
210	gezelter	1513	sprintf( painCave.errMsg,
211	kstocke1	1522	"A slab width (dz) must be specified when calculating TwoDGofR");
212	gezelter	1513	painCave.severity = OPENMD_ERROR;
213			painCave.isFatal = 1;
214			simError();
215	kstocke1	1522	}
216	gezelter	1513	} else if (args_info.p2_given) {
217	gezelter	1542	if (args_info.sele1_given) {
218			if (args_info.sele2_given)
219			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
220			else
221	gezelter	1819	if (args_info.seleoffset_given)
222			analyser = new P2OrderParameter(info, dumpFileName, sele1,
223			args_info.seleoffset_arg);
224			else
225			analyser = new P2OrderParameter(info, dumpFileName, sele1);
226	gezelter	1542	} else {
227			sprintf( painCave.errMsg,
228			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
229			painCave.severity = OPENMD_ERROR;
230			painCave.isFatal = 1;
231			simError();
232			}
233	gezelter	1513	} else if (args_info.rp2_given){
234			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
235			} else if (args_info.bo_given){
236			if (args_info.rcut_given) {
237			analyser = new BondOrderParameter(info, dumpFileName, sele1,
238	kstocke1	1522	args_info.rcut_arg,
239			args_info.nbins_arg);
240	gezelter	1513	} else {
241			sprintf( painCave.errMsg,
242	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
243	gezelter	1513	painCave.severity = OPENMD_ERROR;
244			painCave.isFatal = 1;
245			simError();
246	tim	544	}
247	gezelter	1998	} else if (args_info.multipole_given){
248			if (args_info.rcut_given) {
249			analyser = new MultipoleSum(info, dumpFileName, sele1,
250			args_info.rcut_arg);
251			} else {
252			sprintf( painCave.errMsg,
253			"A cutoff radius (rcut) must be specified when calculating Multipole Sums");
254			painCave.severity = OPENMD_ERROR;
255			painCave.isFatal = 1;
256			simError();
257			}
258	kstocke1	1522
259			} else if (args_info.tet_param_given) {
260			if (args_info.rcut_given) {
261			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
262			args_info.rcut_arg,
263			args_info.nbins_arg);
264			} else {
265			sprintf( painCave.errMsg,
266			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
267			painCave.severity = OPENMD_ERROR;
268			painCave.isFatal = 1;
269			simError();
270			}
271	gezelter	1782	} else if (args_info.tet_param_z_given) {
272			if (args_info.rcut_given) {
273	gezelter	1846	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
274			args_info.rcut_arg,
275			args_info.nbins_arg);
276	gezelter	1782	} else {
277			sprintf( painCave.errMsg,
278			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
279			painCave.severity = OPENMD_ERROR;
280			painCave.isFatal = 1;
281			simError();
282			}
283	gezelter	1992	} else if (args_info.ior_given){
284	gezelter	1513	if (args_info.rcut_given) {
285	gezelter	1992	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
286			args_info.rcut_arg,
287			args_info.nbins_arg, maxLen);
288			} else {
289			sprintf( painCave.errMsg,
290			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
291			painCave.severity = OPENMD_ERROR;
292			painCave.isFatal = 1;
293			simError();
294			}
295			} else if (args_info.for_given){
296			if (args_info.rcut_given) {
297			analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
298	kstocke1	1522	args_info.nbins_arg, maxLen);
299	chuckv	1445	} else {
300	gezelter	1513	sprintf( painCave.errMsg,
301	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
302	gezelter	1513	painCave.severity = OPENMD_ERROR;
303			painCave.isFatal = 1;
304			simError();
305			}
306			} else if (args_info.bad_given){
307			if (args_info.rcut_given) {
308	gezelter	1846	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
309			args_info.rcut_arg,
310	kstocke1	1522	args_info.nbins_arg);
311	gezelter	1513	} else {
312			sprintf( painCave.errMsg,
313	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
314	gezelter	1513	painCave.severity = OPENMD_ERROR;
315			painCave.isFatal = 1;
316			simError();
317	gezelter	1846	}
318	gezelter	1513	} else if (args_info.scd_given) {
319			if (batchMode) {
320	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
321			args_info.molname_arg,
322	kstocke1	1522	args_info.begin_arg, args_info.end_arg);
323	gezelter	1513	} else{
324			std::string sele3 = args_info.sele3_arg;
325	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
326			sele1, sele2, sele3);
327	gezelter	1513	}
328			}else if (args_info.density_given) {
329			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
330	kstocke1	1522	args_info.nbins_arg);
331	gezelter	1513	} else if (args_info.count_given) {
332			analyser = new ObjectCount(info, dumpFileName, sele1 );
333			} else if (args_info.slab_density_given) {
334			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
335	gezelter	1879	} else if (args_info.rnemdz_given) {
336			analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
337			} else if (args_info.rnemdr_given) {
338			analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
339	gezelter	1953	} else if (args_info.rnemdrt_given) {
340			analyser = new RNEMDRTheta(info, dumpFileName, sele1,
341			args_info.nbins_arg, args_info.nanglebins_arg);
342	gezelter	1994	} else if (args_info.nitrile_given) {
343			analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
344			args_info.nbins_arg);
345	gezelter	1513	} else if (args_info.p_angle_given) {
346	gezelter	1979	if (args_info.sele1_given) {
347			if (args_info.sele2_given)
348			analyser = new pAngle(info, dumpFileName, sele1, sele2,
349			args_info.nbins_arg);
350			else
351	gezelter	1991	if (args_info.seleoffset_given) {
352			if (args_info.seleoffset2_given) {
353			analyser = new pAngle(info, dumpFileName, sele1,
354			args_info.seleoffset_arg,
355			args_info.seleoffset2_arg,
356			args_info.nbins_arg);
357			} else {
358			analyser = new pAngle(info, dumpFileName, sele1,
359			args_info.seleoffset_arg,
360			args_info.nbins_arg);
361			}
362			} else
363	gezelter	1979	analyser = new pAngle(info, dumpFileName, sele1,
364			args_info.nbins_arg);
365			} else {
366			sprintf( painCave.errMsg,
367			"At least one selection script (--sele1) must be specified when "
368			"calculating P(angle) distributions");
369			painCave.severity = OPENMD_ERROR;
370			painCave.isFatal = 1;
371			simError();
372			}
373	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
374	gezelter	1513	}else if (args_info.hxy_given) {
375			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
376	kstocke1	1522	args_info.nbins_y_arg, args_info.nbins_arg);
377	gezelter	956	#endif
378	gezelter	1513	}else if (args_info.rho_r_given) {
379			if (args_info.radius_given){
380			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
381			}else{
382			sprintf( painCave.errMsg,
383	kstocke1	1522	"A particle radius (radius) must be specified when calculating Rho(r)");
384	gezelter	1513	painCave.severity = OPENMD_ERROR;
385			painCave.isFatal = 1;
386			simError();
387	chuckv	1091	}
388	kstocke1	1522	} else if (args_info.hullvol_given) {
389	gezelter	1513	analyser = new NanoVolume(info, dumpFileName, sele1);
390	gezelter	1585	} else if (args_info.rodlength_given) {
391			analyser = new NanoLength(info, dumpFileName, sele1);
392	kstocke1	1522	} else if (args_info.angle_r_given) {
393			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
394	gezelter	1513	}
395	gezelter	1846
396	gezelter	1513	if (args_info.output_given) {
397			analyser->setOutputName(args_info.output_arg);
398			}
399			if (args_info.step_given) {
400			analyser->setStep(args_info.step_arg);
401			}
402	gezelter	1846
403	gezelter	1513	analyser->process();
404	kstocke1	1522
405	gezelter	1513	delete analyser;
406			delete info;
407	gezelter	1846
408	gezelter	1513	return 0;
409	tim	310	}