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"
#include "applications/staticProps/TetrahedralityParamZ.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 "select all"
  
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  } else {
    char* sele2Env = getenv("SELECTION1");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else { 
      //It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
      //should not be 'select all' but rather what is already intended for sele1
      //JRM 8/22/12
      sele2 = sele1;
      //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.tet_param_z_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParamZ(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:	1794
Committed:	Thu Sep 6 19:44:06 2012 UTC (12 years, 7 months ago) by gezelter
File size:	13729 byte(s)
Log Message:	Merging some of the trunk changes back to the development branch, cleaning up a datastorage bug
#	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	plouden	1762	#include "applications/staticProps/TetrahedralityParamZ.hpp"
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
97			// check the first selection argument, or set it to the environment
98			// variable, or failing that, set it to "select all"
99
100			if (args_info.sele1_given) {
101			sele1 = args_info.sele1_arg;
102			} else {
103			char* sele1Env= getenv("SELECTION1");
104			if (sele1Env) {
105			sele1 = sele1Env;
106			} else {
107			sele1 = "select all";
108	chuckv	1445	}
109	gezelter	1629	}
110
111			// check the second selection argument, or set it to the environment
112			// variable, or failing that, set it to "select all"
113
114			if (args_info.sele2_given) {
115			sele2 = args_info.sele2_arg;
116			} else {
117			char* sele2Env = getenv("SELECTION1");
118			if (sele2Env) {
119			sele2 = sele2Env;
120			} else {
121	gezelter	1794	//It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
122			//should not be 'select all' but rather what is already intended for sele1
123			//JRM 8/22/12
124			sele2 = sele1;
125			//sele2 = "select all";
126	gezelter	1629	}
127			}
128
129
130			// Problems if sele1 wasn't specified, but
131			// if (!args_info.scd_given) {
132			// sprintf( painCave.errMsg,
133			// "neither --sele1 option nor $SELECTION1 is set");
134			// painCave.severity = OPENMD_ERROR;
135			// painCave.isFatal = 1;
136			// simError();
137			// }
138			// }
139
140			// Problems if sele1 wasn't specified
141
142			// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
143			// sprintf( painCave.errMsg,
144			// "neither --sele2 option nor $SELECTION1 is set");
145			// painCave.severity = OPENMD_ERROR;
146			// painCave.isFatal = 1;
147			// simError();
148			// }
149			// }
150
151			bool batchMode;
152			if (args_info.scd_given){
153			if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
154			batchMode = false;
155			} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
156			if (args_info.begin_arg < 0 \|\| args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
157			sprintf( painCave.errMsg,
158			"below conditions are not satisfied:\n"
159			"0 <= begin && 0<= end && begin <= end-2\n");
160			painCave.severity = OPENMD_ERROR;
161			painCave.isFatal = 1;
162			simError();
163			}
164			batchMode = true;
165			} else{
166			sprintf( painCave.errMsg,
167			"either --sele1, --sele2, --sele3 are specified,"
168			" or --molname, --begin, --end are specified\n");
169			painCave.severity = OPENMD_ERROR;
170			painCave.isFatal = 1;
171			simError();
172
173			}
174			}
175
176			//parse md file and set up the system
177			SimCreator creator;
178			std::cout << "dumpFile = " << dumpFileName << "\n";
179			SimInfo* info = creator.createSim(dumpFileName);
180	tim	310
181	gezelter	1629	RealType maxLen;
182			RealType zmaxLen;
183			if (args_info.length_given) {
184			maxLen = args_info.length_arg;
185			if (args_info.zlength_given){
186			zmaxLen = args_info.zlength_arg;
187	tim	310	}
188	gezelter	1629	} else {
189			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
190			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
191			zmaxLen = hmat(2,2);
192			}
193	gezelter	1039
194	gezelter	1629	StaticAnalyser* analyser;
195			if (args_info.gofr_given){
196			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
197			args_info.nbins_arg);
198			} else if (args_info.gofz_given) {
199			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
200			args_info.nbins_arg);
201			} else if (args_info.r_z_given) {
202			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
203			args_info.nbins_arg, args_info.nbins_z_arg);
204			} else if (args_info.r_theta_given) {
205			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
206			args_info.nbins_arg, args_info.nanglebins_arg);
207			} else if (args_info.r_omega_given) {
208			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
209			args_info.nbins_arg, args_info.nanglebins_arg);
210			} else if (args_info.theta_omega_given) {
211			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
212			args_info.nanglebins_arg);
213			} else if (args_info.gxyz_given) {
214			if (args_info.refsele_given) {
215			analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
216			maxLen, args_info.nbins_arg);
217	chuckv	1445	} else {
218	gezelter	1629	sprintf( painCave.errMsg,
219			"--refsele must set when --gxyz is used");
220			painCave.severity = OPENMD_ERROR;
221			painCave.isFatal = 1;
222			simError();
223	tim	311	}
224	gezelter	1629	} else if (args_info.twodgofr_given){
225			if (args_info.dz_given) {
226			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
227			args_info.dz_arg, args_info.nbins_arg);
228			} else {
229			sprintf( painCave.errMsg,
230			"A slab width (dz) must be specified when calculating TwoDGofR");
231			painCave.severity = OPENMD_ERROR;
232			painCave.isFatal = 1;
233			simError();
234			}
235			} else if (args_info.p2_given) {
236			if (args_info.sele1_given) {
237			if (args_info.sele2_given)
238			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
239			else
240			analyser = new P2OrderParameter(info, dumpFileName, sele1);
241			} else {
242			sprintf( painCave.errMsg,
243			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
244			painCave.severity = OPENMD_ERROR;
245			painCave.isFatal = 1;
246			simError();
247			}
248			} else if (args_info.rp2_given){
249			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
250			} else if (args_info.bo_given){
251			if (args_info.rcut_given) {
252			analyser = new BondOrderParameter(info, dumpFileName, sele1,
253			args_info.rcut_arg,
254			args_info.nbins_arg);
255			} else {
256			sprintf( painCave.errMsg,
257			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
258			painCave.severity = OPENMD_ERROR;
259			painCave.isFatal = 1;
260			simError();
261			}
262	tim	544
263	gezelter	1629	} else if (args_info.tet_param_given) {
264			if (args_info.rcut_given) {
265			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
266			args_info.rcut_arg,
267			args_info.nbins_arg);
268			} else {
269			sprintf( painCave.errMsg,
270			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
271			painCave.severity = OPENMD_ERROR;
272			painCave.isFatal = 1;
273			simError();
274	tim	544	}
275	plouden	1762	} else if (args_info.tet_param_z_given) {
276			if (args_info.rcut_given) {
277			analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
278			args_info.rcut_arg,
279			args_info.nbins_arg);
280			} else {
281			sprintf( painCave.errMsg,
282			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
283			painCave.severity = OPENMD_ERROR;
284			painCave.isFatal = 1;
285			simError();
286			}
287	gezelter	1629	} else if (args_info.bor_given){
288			if (args_info.rcut_given) {
289			analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
290			args_info.nbins_arg, maxLen);
291	chuckv	1445	} else {
292	gezelter	1629	sprintf( painCave.errMsg,
293			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
294			painCave.severity = OPENMD_ERROR;
295			painCave.isFatal = 1;
296			simError();
297			}
298			} else if (args_info.bad_given){
299			if (args_info.rcut_given) {
300			analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
301			args_info.nbins_arg);
302			} else {
303			sprintf( painCave.errMsg,
304			"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
305			painCave.severity = OPENMD_ERROR;
306			painCave.isFatal = 1;
307			simError();
308	gezelter	1454	}
309	gezelter	1629	} else if (args_info.scd_given) {
310			if (batchMode) {
311			analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
312			args_info.begin_arg, args_info.end_arg);
313			} else{
314			std::string sele3 = args_info.sele3_arg;
315			analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
316			}
317			}else if (args_info.density_given) {
318			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
319			args_info.nbins_arg);
320			} else if (args_info.count_given) {
321			analyser = new ObjectCount(info, dumpFileName, sele1 );
322			} else if (args_info.slab_density_given) {
323			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
324			} else if (args_info.p_angle_given) {
325			analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
326	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
327	gezelter	1629	}else if (args_info.hxy_given) {
328			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
329			args_info.nbins_y_arg, args_info.nbins_arg);
330	gezelter	956	#endif
331	gezelter	1629	}else if (args_info.rho_r_given) {
332			if (args_info.radius_given){
333			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
334			}else{
335			sprintf( painCave.errMsg,
336			"A particle radius (radius) must be specified when calculating Rho(r)");
337			painCave.severity = OPENMD_ERROR;
338			painCave.isFatal = 1;
339			simError();
340	chuckv	1091	}
341	gezelter	1629	} else if (args_info.hullvol_given) {
342			analyser = new NanoVolume(info, dumpFileName, sele1);
343			} else if (args_info.rodlength_given) {
344			analyser = new NanoLength(info, dumpFileName, sele1);
345			} else if (args_info.angle_r_given) {
346			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
347			}
348
349			if (args_info.output_given) {
350			analyser->setOutputName(args_info.output_arg);
351			}
352			if (args_info.step_given) {
353			analyser->setStep(args_info.step_arg);
354			}
355	plouden	1762
356	gezelter	1629	analyser->process();
357
358			delete analyser;
359			delete info;
360	tim	311
361	gezelter	1629	return 0;
362	tim	310	}
363