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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "brains/Register.hpp"
#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/RhoAngleR.hpp"
#include "applications/staticProps/TetrahedralityParam.hpp"

using namespace OpenMD;

int main(int argc, char* argv[]){
  
  //register force fields
  registerForceFields();
  
  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:	1585
Committed:	Sun Jun 19 17:51:15 2011 UTC (13 years, 10 months ago) by gezelter
File size:	13123 byte(s)
Log Message:	Added a module to compute the length of a nanorod
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	310	*/
41
42			#include <iostream>
43			#include <fstream>
44			#include <string>
45
46			#include "brains/Register.hpp"
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/RhoAngleR.hpp"
79			#include "applications/staticProps/TetrahedralityParam.hpp"
80	tim	311
81	gezelter	1390	using namespace OpenMD;
82	tim	310
83			int main(int argc, char* argv[]){
84
85	gezelter	1513	//register force fields
86			registerForceFields();
87
88			gengetopt_args_info args_info;
89
90			//parse the command line option
91			if (cmdline_parser (argc, argv, &args_info) != 0) {
92			exit(1) ;
93			}
94
95			//get the dumpfile name
96			std::string dumpFileName = args_info.input_arg;
97			std::string sele1;
98			std::string sele2;
99			bool userSpecifiedSelect1;
100			bool userSpecifiedSelect2;
101
102			// check the first selection argument, or set it to the environment
103			// variable, or failing that, set it to "select all"
104
105			if (args_info.sele1_given) {
106			sele1 = args_info.sele1_arg;
107			} else {
108			char* sele1Env= getenv("SELECTION1");
109			if (sele1Env) {
110			sele1 = sele1Env;
111			} else {
112			sele1 = "select all";
113			}
114			}
115
116			// check the second selection argument, or set it to the environment
117			// variable, or failing that, set it to "select all"
118
119			if (args_info.sele2_given) {
120			sele2 = args_info.sele2_arg;
121			} else {
122			char* sele2Env = getenv("SELECTION1");
123			if (sele2Env) {
124			sele2 = sele2Env;
125			} else {
126			sele2 = "select all";
127			}
128			}
129
130
131			// Problems if sele1 wasn't specified, but
132			// if (!args_info.scd_given) {
133			// sprintf( painCave.errMsg,
134			// "neither --sele1 option nor $SELECTION1 is set");
135			// painCave.severity = OPENMD_ERROR;
136			// painCave.isFatal = 1;
137			// simError();
138			// }
139			// }
140
141			// Problems if sele1 wasn't specified
142
143			// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
144			// sprintf( painCave.errMsg,
145			// "neither --sele2 option nor $SELECTION1 is set");
146			// painCave.severity = OPENMD_ERROR;
147			// painCave.isFatal = 1;
148			// simError();
149			// }
150			// }
151
152			bool batchMode;
153			if (args_info.scd_given){
154			if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
155			batchMode = false;
156			} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
157			if (args_info.begin_arg < 0 \|\| args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
158			sprintf( painCave.errMsg,
159			"below conditions are not satisfied:\n"
160			"0 <= begin && 0<= end && begin <= end-2\n");
161			painCave.severity = OPENMD_ERROR;
162			painCave.isFatal = 1;
163			simError();
164			}
165			batchMode = true;
166			} else{
167			sprintf( painCave.errMsg,
168			"either --sele1, --sele2, --sele3 are specified,"
169			" or --molname, --begin, --end are specified\n");
170			painCave.severity = OPENMD_ERROR;
171			painCave.isFatal = 1;
172			simError();
173
174			}
175			}
176
177			//parse md file and set up the system
178			SimCreator creator;
179			std::cout << "dumpFile = " << dumpFileName << "\n";
180			SimInfo* info = creator.createSim(dumpFileName);
181	tim	310
182	gezelter	1513	RealType maxLen;
183			RealType zmaxLen;
184			if (args_info.length_given) {
185			maxLen = args_info.length_arg;
186			if (args_info.zlength_given){
187			zmaxLen = args_info.zlength_arg;
188	chuckv	1445	}
189	gezelter	1513	} else {
190			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
191			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
192			zmaxLen = hmat(2,2);
193			}
194	kstocke1	1522
195	gezelter	1513	StaticAnalyser* analyser;
196			if (args_info.gofr_given){
197			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
198	kstocke1	1522	args_info.nbins_arg);
199	gezelter	1513	} else if (args_info.gofz_given) {
200			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
201	kstocke1	1522	args_info.nbins_arg);
202	gezelter	1513	} else if (args_info.r_z_given) {
203			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
204	kstocke1	1522	args_info.nbins_arg, args_info.nbins_z_arg);
205	gezelter	1513	} else if (args_info.r_theta_given) {
206			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
207	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
208	gezelter	1513	} else if (args_info.r_omega_given) {
209			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
210	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
211	gezelter	1513	} else if (args_info.theta_omega_given) {
212			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
213	kstocke1	1522	args_info.nanglebins_arg);
214	gezelter	1513	} else if (args_info.gxyz_given) {
215			if (args_info.refsele_given) {
216			analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
217	kstocke1	1522	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			analyser = new P2OrderParameter(info, dumpFileName, sele1);
242			} else {
243			sprintf( painCave.errMsg,
244			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
245			painCave.severity = OPENMD_ERROR;
246			painCave.isFatal = 1;
247			simError();
248			}
249	gezelter	1513	} else if (args_info.rp2_given){
250			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
251			} else if (args_info.bo_given){
252			if (args_info.rcut_given) {
253			analyser = new BondOrderParameter(info, dumpFileName, sele1,
254	kstocke1	1522	args_info.rcut_arg,
255			args_info.nbins_arg);
256	gezelter	1513	} else {
257			sprintf( painCave.errMsg,
258	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
259	gezelter	1513	painCave.severity = OPENMD_ERROR;
260			painCave.isFatal = 1;
261			simError();
262	tim	544	}
263	kstocke1	1522
264			} else if (args_info.tet_param_given) {
265			if (args_info.rcut_given) {
266			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
267			args_info.rcut_arg,
268			args_info.nbins_arg);
269			} else {
270			sprintf( painCave.errMsg,
271			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
272			painCave.severity = OPENMD_ERROR;
273			painCave.isFatal = 1;
274			simError();
275			}
276	gezelter	1513	} else if (args_info.bor_given){
277			if (args_info.rcut_given) {
278			analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
279	kstocke1	1522	args_info.nbins_arg, maxLen);
280	chuckv	1445	} else {
281	gezelter	1513	sprintf( painCave.errMsg,
282	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
283	gezelter	1513	painCave.severity = OPENMD_ERROR;
284			painCave.isFatal = 1;
285			simError();
286			}
287			} else if (args_info.bad_given){
288			if (args_info.rcut_given) {
289			analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
290	kstocke1	1522	args_info.nbins_arg);
291	gezelter	1513	} else {
292			sprintf( painCave.errMsg,
293	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
294	gezelter	1513	painCave.severity = OPENMD_ERROR;
295			painCave.isFatal = 1;
296			simError();
297	kstocke1	1522	}
298	gezelter	1513	} else if (args_info.scd_given) {
299			if (batchMode) {
300			analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
301	kstocke1	1522	args_info.begin_arg, args_info.end_arg);
302	gezelter	1513	} else{
303			std::string sele3 = args_info.sele3_arg;
304			analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
305			}
306			}else if (args_info.density_given) {
307			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
308	kstocke1	1522	args_info.nbins_arg);
309	gezelter	1513	} else if (args_info.count_given) {
310			analyser = new ObjectCount(info, dumpFileName, sele1 );
311			} else if (args_info.slab_density_given) {
312			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
313			} else if (args_info.p_angle_given) {
314			analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
315	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
316	gezelter	1513	}else if (args_info.hxy_given) {
317			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
318	kstocke1	1522	args_info.nbins_y_arg, args_info.nbins_arg);
319	gezelter	956	#endif
320	gezelter	1513	}else if (args_info.rho_r_given) {
321			if (args_info.radius_given){
322			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
323			}else{
324			sprintf( painCave.errMsg,
325	kstocke1	1522	"A particle radius (radius) must be specified when calculating Rho(r)");
326	gezelter	1513	painCave.severity = OPENMD_ERROR;
327			painCave.isFatal = 1;
328			simError();
329	chuckv	1091	}
330	kstocke1	1522	} else if (args_info.hullvol_given) {
331	gezelter	1513	analyser = new NanoVolume(info, dumpFileName, sele1);
332	gezelter	1585	} else if (args_info.rodlength_given) {
333			analyser = new NanoLength(info, dumpFileName, sele1);
334	kstocke1	1522	} else if (args_info.angle_r_given) {
335			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
336	gezelter	1513	}
337	kstocke1	1522
338	gezelter	1513	if (args_info.output_given) {
339			analyser->setOutputName(args_info.output_arg);
340			}
341			if (args_info.step_given) {
342			analyser->setStep(args_info.step_arg);
343			}
344	kstocke1	1522
345	gezelter	1513	analyser->process();
346	kstocke1	1522
347	gezelter	1513	delete analyser;
348			delete info;
349	tim	310
350	gezelter	1513	return 0;
351	tim	310	}
352