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, 24107 (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"

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;
  bool userSpecifiedSelect1;
  bool userSpecifiedSelect2;
  
  // 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 "select all"
  
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  } else {
    char* sele2Env = getenv("SELECTION1");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else { 
      sele2 = "select all";
    }
  }
  
  
  // Problems if sele1 wasn't specified, but 
  // if (!args_info.scd_given) {
  //       sprintf( painCave.errMsg,
  //                "neither --sele1 option nor $SELECTION1 is set");
  //       painCave.severity = OPENMD_ERROR;
  //       painCave.isFatal = 1;
  //       simError();
  //     }
  //   }
  
  // Problems if sele1 wasn't specified
  
  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
  //       sprintf( painCave.errMsg,
  //                "neither --sele2 option nor $SELECTION1 is set");
  //       painCave.severity = OPENMD_ERROR;
  //       painCave.isFatal = 1;
  //       simError();        
  //     }
  //   }
  
  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;
  std::cout << "dumpFile = " << dumpFileName << "\n";
  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 
        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.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.bor_given){
    if (args_info.rcut_given) {
      analyser = new BOPofR(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.p_angle_given) {
    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
#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:	1725
Committed:	Sat May 26 18:13:43 2012 UTC (12 years, 11 months ago) by gezelter
File size:	13057 byte(s)
Log Message:	Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [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	1629	#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	1629	#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	gezelter	1629	#include "applications/staticProps/AngleR.hpp"
78			#include "applications/staticProps/TetrahedralityParam.hpp"
79	tim	311
80	gezelter	1390	using namespace OpenMD;
81	tim	310
82			int main(int argc, char* argv[]){
83
84	gezelter	1629
85			gengetopt_args_info args_info;
86
87			//parse the command line option
88			if (cmdline_parser (argc, argv, &args_info) != 0) {
89			exit(1) ;
90			}
91
92			//get the dumpfile name
93			std::string dumpFileName = args_info.input_arg;
94			std::string sele1;
95			std::string sele2;
96			bool userSpecifiedSelect1;
97			bool userSpecifiedSelect2;
98
99			// check the first selection argument, or set it to the environment
100			// variable, or failing that, set it to "select all"
101
102			if (args_info.sele1_given) {
103			sele1 = args_info.sele1_arg;
104			} else {
105			char* sele1Env= getenv("SELECTION1");
106			if (sele1Env) {
107			sele1 = sele1Env;
108			} else {
109			sele1 = "select all";
110	chuckv	1445	}
111	gezelter	1629	}
112
113			// check the second selection argument, or set it to the environment
114			// variable, or failing that, set it to "select all"
115
116			if (args_info.sele2_given) {
117			sele2 = args_info.sele2_arg;
118			} else {
119			char* sele2Env = getenv("SELECTION1");
120			if (sele2Env) {
121			sele2 = sele2Env;
122			} else {
123			sele2 = "select all";
124			}
125			}
126
127
128			// Problems if sele1 wasn't specified, but
129			// if (!args_info.scd_given) {
130			// sprintf( painCave.errMsg,
131			// "neither --sele1 option nor $SELECTION1 is set");
132			// painCave.severity = OPENMD_ERROR;
133			// painCave.isFatal = 1;
134			// simError();
135			// }
136			// }
137
138			// Problems if sele1 wasn't specified
139
140			// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
141			// sprintf( painCave.errMsg,
142			// "neither --sele2 option nor $SELECTION1 is set");
143			// painCave.severity = OPENMD_ERROR;
144			// painCave.isFatal = 1;
145			// simError();
146			// }
147			// }
148
149			bool batchMode;
150			if (args_info.scd_given){
151			if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
152			batchMode = false;
153			} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
154			if (args_info.begin_arg < 0 \|\| args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
155			sprintf( painCave.errMsg,
156			"below conditions are not satisfied:\n"
157			"0 <= begin && 0<= end && begin <= end-2\n");
158			painCave.severity = OPENMD_ERROR;
159			painCave.isFatal = 1;
160			simError();
161			}
162			batchMode = true;
163			} else{
164			sprintf( painCave.errMsg,
165			"either --sele1, --sele2, --sele3 are specified,"
166			" or --molname, --begin, --end are specified\n");
167			painCave.severity = OPENMD_ERROR;
168			painCave.isFatal = 1;
169			simError();
170
171			}
172			}
173
174			//parse md file and set up the system
175			SimCreator creator;
176			std::cout << "dumpFile = " << dumpFileName << "\n";
177			SimInfo* info = creator.createSim(dumpFileName);
178	tim	310
179	gezelter	1629	RealType maxLen;
180			RealType zmaxLen;
181			if (args_info.length_given) {
182			maxLen = args_info.length_arg;
183			if (args_info.zlength_given){
184			zmaxLen = args_info.zlength_arg;
185	tim	310	}
186	gezelter	1629	} else {
187			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
188			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
189			zmaxLen = hmat(2,2);
190			}
191	gezelter	1039
192	gezelter	1629	StaticAnalyser* analyser;
193			if (args_info.gofr_given){
194			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
195			args_info.nbins_arg);
196			} else if (args_info.gofz_given) {
197			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
198			args_info.nbins_arg);
199			} else if (args_info.r_z_given) {
200			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
201			args_info.nbins_arg, args_info.nbins_z_arg);
202			} else if (args_info.r_theta_given) {
203			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
204			args_info.nbins_arg, args_info.nanglebins_arg);
205			} else if (args_info.r_omega_given) {
206			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
207			args_info.nbins_arg, args_info.nanglebins_arg);
208			} else if (args_info.theta_omega_given) {
209			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
210			args_info.nanglebins_arg);
211			} else if (args_info.gxyz_given) {
212			if (args_info.refsele_given) {
213			analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
214			maxLen, args_info.nbins_arg);
215	chuckv	1445	} else {
216	gezelter	1629	sprintf( painCave.errMsg,
217			"--refsele must set when --gxyz is used");
218			painCave.severity = OPENMD_ERROR;
219			painCave.isFatal = 1;
220			simError();
221	tim	311	}
222	gezelter	1629	} else if (args_info.twodgofr_given){
223			if (args_info.dz_given) {
224			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
225			args_info.dz_arg, args_info.nbins_arg);
226			} else {
227			sprintf( painCave.errMsg,
228			"A slab width (dz) must be specified when calculating TwoDGofR");
229			painCave.severity = OPENMD_ERROR;
230			painCave.isFatal = 1;
231			simError();
232			}
233			} else if (args_info.p2_given) {
234			if (args_info.sele1_given) {
235			if (args_info.sele2_given)
236			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
237			else
238			analyser = new P2OrderParameter(info, dumpFileName, sele1);
239			} else {
240			sprintf( painCave.errMsg,
241			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
242			painCave.severity = OPENMD_ERROR;
243			painCave.isFatal = 1;
244			simError();
245			}
246			} else if (args_info.rp2_given){
247			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
248			} else if (args_info.bo_given){
249			if (args_info.rcut_given) {
250			analyser = new BondOrderParameter(info, dumpFileName, sele1,
251			args_info.rcut_arg,
252			args_info.nbins_arg);
253			} else {
254			sprintf( painCave.errMsg,
255			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
256			painCave.severity = OPENMD_ERROR;
257			painCave.isFatal = 1;
258			simError();
259			}
260	tim	544
261	gezelter	1629	} else if (args_info.tet_param_given) {
262			if (args_info.rcut_given) {
263			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
264			args_info.rcut_arg,
265			args_info.nbins_arg);
266			} else {
267			sprintf( painCave.errMsg,
268			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
269			painCave.severity = OPENMD_ERROR;
270			painCave.isFatal = 1;
271			simError();
272	tim	544	}
273	gezelter	1629	} else if (args_info.bor_given){
274			if (args_info.rcut_given) {
275			analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
276			args_info.nbins_arg, maxLen);
277	chuckv	1445	} else {
278	gezelter	1629	sprintf( painCave.errMsg,
279			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
280			painCave.severity = OPENMD_ERROR;
281			painCave.isFatal = 1;
282			simError();
283			}
284			} else if (args_info.bad_given){
285			if (args_info.rcut_given) {
286			analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
287			args_info.nbins_arg);
288			} else {
289			sprintf( painCave.errMsg,
290			"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
291			painCave.severity = OPENMD_ERROR;
292			painCave.isFatal = 1;
293			simError();
294	gezelter	1454	}
295	gezelter	1629	} else if (args_info.scd_given) {
296			if (batchMode) {
297			analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
298			args_info.begin_arg, args_info.end_arg);
299			} else{
300			std::string sele3 = args_info.sele3_arg;
301			analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
302			}
303			}else if (args_info.density_given) {
304			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
305			args_info.nbins_arg);
306			} else if (args_info.count_given) {
307			analyser = new ObjectCount(info, dumpFileName, sele1 );
308			} else if (args_info.slab_density_given) {
309			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
310			} else if (args_info.p_angle_given) {
311			analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
312	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
313	gezelter	1629	}else if (args_info.hxy_given) {
314			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
315			args_info.nbins_y_arg, args_info.nbins_arg);
316	gezelter	956	#endif
317	gezelter	1629	}else if (args_info.rho_r_given) {
318			if (args_info.radius_given){
319			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
320			}else{
321			sprintf( painCave.errMsg,
322			"A particle radius (radius) must be specified when calculating Rho(r)");
323			painCave.severity = OPENMD_ERROR;
324			painCave.isFatal = 1;
325			simError();
326	chuckv	1091	}
327	gezelter	1629	} else if (args_info.hullvol_given) {
328			analyser = new NanoVolume(info, dumpFileName, sele1);
329			} else if (args_info.rodlength_given) {
330			analyser = new NanoLength(info, dumpFileName, sele1);
331			} else if (args_info.angle_r_given) {
332			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
333			}
334
335			if (args_info.output_given) {
336			analyser->setOutputName(args_info.output_arg);
337			}
338			if (args_info.step_given) {
339			analyser->setStep(args_info.step_arg);
340			}
341	gezelter	1039
342	gezelter	1629	analyser->process();
343
344			delete analyser;
345			delete info;
346	tim	311
347	gezelter	1629	return 0;
348	tim	310	}
349