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/RhoZ.hpp"
#include "applications/staticProps/pAngle.hpp"
#include "applications/staticProps/BondAngleDistribution.hpp"
#include "applications/staticProps/NanoVolume.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"

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) {
        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
    } 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.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.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);
    }
  
    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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	11548 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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	tim	840	#include "applications/staticProps/RhoZ.hpp"
68	gezelter	1413	#include "applications/staticProps/pAngle.hpp"
69	chuckv	1180	#include "applications/staticProps/BondAngleDistribution.hpp"
70			#include "applications/staticProps/NanoVolume.hpp"
71	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
72	xsun	955	#include "applications/staticProps/Hxy.hpp"
73	gezelter	956	#endif
74	chuckv	1091	#include "applications/staticProps/RhoR.hpp"
75	tim	311
76	gezelter	1390	using namespace OpenMD;
77	tim	310
78			int main(int argc, char* argv[]){
79
80	chuckv	1445	//register force fields
81			registerForceFields();
82	tim	310
83	chuckv	1445	gengetopt_args_info args_info;
84	tim	310
85	chuckv	1445	//parse the command line option
86			if (cmdline_parser (argc, argv, &args_info) != 0) {
87			exit(1) ;
88			}
89	tim	310
90	chuckv	1445	//get the dumpfile name
91			std::string dumpFileName = args_info.input_arg;
92			std::string sele1;
93			std::string sele2;
94			bool userSpecifiedSelect1;
95			bool userSpecifiedSelect2;
96	tim	310
97	chuckv	1445	// check the first selection argument, or set it to the environment
98			// variable, or failing that, set it to "select all"
99	gezelter	1039
100	chuckv	1445	if (args_info.sele1_given) {
101			sele1 = args_info.sele1_arg;
102	gezelter	1039	} else {
103	chuckv	1445	char* sele1Env= getenv("SELECTION1");
104			if (sele1Env) {
105			sele1 = sele1Env;
106			} else {
107			sele1 = "select all";
108			}
109	tim	310	}
110	gezelter	1039
111	chuckv	1445	// check the second selection argument, or set it to the environment
112			// variable, or failing that, set it to "select all"
113	gezelter	1039
114	chuckv	1445	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			sele2 = "select all";
122			}
123	tim	311	}
124	tim	310
125	gezelter	1039
126	chuckv	1445	// Problems if sele1 wasn't specified, but
127	gezelter	1039	// if (!args_info.scd_given) {
128			// sprintf( painCave.errMsg,
129	gezelter	1390	// "neither --sele1 option nor $SELECTION1 is set");
130			// painCave.severity = OPENMD_ERROR;
131	gezelter	1039	// painCave.isFatal = 1;
132			// simError();
133			// }
134			// }
135
136	chuckv	1445	// Problems if sele1 wasn't specified
137	gezelter	1039
138			// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
139			// sprintf( painCave.errMsg,
140	gezelter	1390	// "neither --sele2 option nor $SELECTION1 is set");
141			// painCave.severity = OPENMD_ERROR;
142	gezelter	1039	// painCave.isFatal = 1;
143			// simError();
144			// }
145			// }
146
147	chuckv	1445	bool batchMode;
148			if (args_info.scd_given){
149			if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
150			batchMode = false;
151			} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
152			if (args_info.begin_arg < 0 \|\| args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
153			sprintf( painCave.errMsg,
154			"below conditions are not satisfied:\n"
155			"0 <= begin && 0<= end && begin <= end-2\n");
156			painCave.severity = OPENMD_ERROR;
157			painCave.isFatal = 1;
158			simError();
159			}
160			batchMode = true;
161			} else{
162			sprintf( painCave.errMsg,
163			"either --sele1, --sele2, --sele3 are specified,"
164			" or --molname, --begin, --end are specified\n");
165			painCave.severity = OPENMD_ERROR;
166			painCave.isFatal = 1;
167			simError();
168	tim	544
169	chuckv	1445	}
170	tim	544	}
171
172	chuckv	1445	//parse md file and set up the system
173			SimCreator creator;
174			std::cout << "dumpFile = " << dumpFileName << "\n";
175			SimInfo* info = creator.createSim(dumpFileName);
176	tim	311
177	chuckv	1445	RealType maxLen;
178			RealType zmaxLen;
179			if (args_info.length_given) {
180			maxLen = args_info.length_arg;
181			if (args_info.zlength_given){
182			zmaxLen = args_info.zlength_arg;
183			}
184			} else {
185			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
186			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
187			zmaxLen = hmat(2,2);
188			}
189	gezelter	507
190	chuckv	1445	StaticAnalyser* analyser;
191			if (args_info.gofr_given){
192			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
193			args_info.nbins_arg);
194			} else if (args_info.gofz_given) {
195			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
196			args_info.nbins_arg);
197			} else if (args_info.r_z_given) {
198			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
199	gezelter	1440	args_info.nbins_arg, args_info.nbins_z_arg);
200	chuckv	1445	} else if (args_info.r_theta_given) {
201			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
202			args_info.nbins_arg, args_info.nanglebins_arg);
203			} else if (args_info.r_omega_given) {
204			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205			args_info.nbins_arg, args_info.nanglebins_arg);
206			} else if (args_info.theta_omega_given) {
207			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
208			args_info.nanglebins_arg);
209			} else if (args_info.gxyz_given) {
210			if (args_info.refsele_given) {
211			analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
212			maxLen, args_info.nbins_arg);
213			} else {
214			sprintf( painCave.errMsg,
215			"--refsele must set when --gxyz is used");
216			painCave.severity = OPENMD_ERROR;
217			painCave.isFatal = 1;
218			simError();
219			}
220	gezelter	1454	} else if (args_info.twodgofr_given){
221			if (args_info.dz_given) {
222			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
223			args_info.dz_arg, args_info.nbins_arg);
224			} else {
225			sprintf( painCave.errMsg,
226			"A slab width (dz) must be specified when calculating TwoDGofR");
227			painCave.severity = OPENMD_ERROR;
228			painCave.isFatal = 1;
229			simError();
230			}
231	chuckv	1445	} else if (args_info.p2_given) {
232			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
233			} 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			args_info.rcut_arg,
239			args_info.nbins_arg);
240			} else {
241			sprintf( painCave.errMsg,
242			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
243			painCave.severity = OPENMD_ERROR;
244			painCave.isFatal = 1;
245			simError();
246			}
247			} else if (args_info.bor_given){
248			if (args_info.rcut_given) {
249			analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
250			args_info.nbins_arg, maxLen);
251			} else {
252			sprintf( painCave.errMsg,
253			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
254			painCave.severity = OPENMD_ERROR;
255			painCave.isFatal = 1;
256			simError();
257			}
258			} else if (args_info.bad_given){
259			if (args_info.rcut_given) {
260			analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
261			args_info.nbins_arg);
262			} else {
263			sprintf( painCave.errMsg,
264			"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
265			painCave.severity = OPENMD_ERROR;
266			painCave.isFatal = 1;
267			simError();
268			}
269			} else if (args_info.scd_given) {
270			if (batchMode) {
271			analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
272			args_info.begin_arg, args_info.end_arg);
273			} else{
274			std::string sele3 = args_info.sele3_arg;
275			analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
276			}
277			}else if (args_info.density_given) {
278			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
279			args_info.nbins_arg);
280			} else if (args_info.slab_density_given) {
281			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
282			} else if (args_info.p_angle_given) {
283			analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
284	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
285	chuckv	1445	}else if (args_info.hxy_given) {
286			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
287			args_info.nbins_y_arg, args_info.nbins_arg);
288	gezelter	956	#endif
289	chuckv	1445	}else if (args_info.rho_r_given) {
290			if (args_info.radius_given){
291			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
292			}else{
293			sprintf( painCave.errMsg,
294			"A particle radius (radius) must be specified when calculating Rho(r)");
295			painCave.severity = OPENMD_ERROR;
296			painCave.isFatal = 1;
297			simError();
298			}
299			}else if (args_info.hullvol_given) {
300			analyser = new NanoVolume(info, dumpFileName, sele1);
301	chuckv	1091	}
302	gezelter	1039
303	chuckv	1445	if (args_info.output_given) {
304			analyser->setOutputName(args_info.output_arg);
305			}
306			if (args_info.step_given) {
307			analyser->setStep(args_info.step_arg);
308			}
309	tim	311
310	chuckv	1445	analyser->process();
311	tim	311
312	chuckv	1445	delete analyser;
313			delete info;
314	tim	310
315	chuckv	1445	return 0;
316	tim	310	}
317