applications/staticProps/StaticProps.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "io/DumpReader.hpp"
#include "utils/simError.h"

#include "applications/staticProps/StaticPropsCmd.h"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "applications/staticProps/GofR.hpp"
#include "applications/staticProps/GofZ.hpp"
#include "applications/staticProps/GofRZ.hpp"
#include "applications/staticProps/GofRAngle.hpp"
#include "applications/staticProps/GofAngle2.hpp"
#include "applications/staticProps/GofXyz.hpp"
#include "applications/staticProps/TwoDGofR.hpp"
#include "applications/staticProps/P2OrderParameter.hpp"
#include "applications/staticProps/BondOrderParameter.hpp"
#include "applications/staticProps/BOPofR.hpp"
#include "applications/staticProps/RippleOP.hpp"
#include "applications/staticProps/SCDOrderParameter.hpp"
#include "applications/staticProps/DensityPlot.hpp"
#include "applications/staticProps/ObjectCount.hpp"
#include "applications/staticProps/RhoZ.hpp"
#include "applications/staticProps/pAngle.hpp"
#include "applications/staticProps/BondAngleDistribution.hpp"
#include "applications/staticProps/NanoVolume.hpp"
#include "applications/staticProps/NanoLength.hpp"
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
#include "applications/staticProps/Hxy.hpp"
#endif
#include "applications/staticProps/RhoR.hpp"
#include "applications/staticProps/AngleR.hpp"
#include "applications/staticProps/TetrahedralityParam.hpp"
#include "applications/staticProps/TetrahedralityParamZ.hpp"
#include "applications/staticProps/RNEMDStats.hpp"

using namespace OpenMD;

int main(int argc, char* argv[]){
  
  
  gengetopt_args_info args_info;
  
  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }
  
  //get the dumpfile name
  std::string dumpFileName = args_info.input_arg;
  std::string sele1;
  std::string sele2;
  
  // check the first selection argument, or set it to the environment
  // variable, or failing that, set it to "select all"
  
  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  } else {
    char*  sele1Env= getenv("SELECTION1");
    if (sele1Env) {
      sele1 = sele1Env;
    } else {
      sele1 = "select all";
    }
  }
  
  // check the second selection argument, or set it to the environment
  // variable, or failing that, set it to the first selection
  
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  } else {
    char* sele2Env = getenv("SELECTION2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else { 
      //If sele2 is not specified, then the default behavior
      //should be what is already intended for sele1
      sele2 = sele1;
    }
  }

  bool batchMode;
  if (args_info.scd_given){
    if (args_info.sele1_given && 
        args_info.sele2_given && args_info.sele3_given) {
      batchMode = false;
    } else if (args_info.molname_given && 
               args_info.begin_given && args_info.end_given) {
      if (args_info.begin_arg < 0 || 
          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
        sprintf( painCave.errMsg,
                 "below conditions are not satisfied:\n"
                 "0 <= begin && 0<= end && begin <= end-2\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();                    
      }
      batchMode = true;        
    } else{
      sprintf( painCave.errMsg,
               "either --sele1, --sele2, --sele3 are specified,"
               " or --molname, --begin, --end are specified\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  }
  
  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(dumpFileName);

  RealType maxLen;
  RealType zmaxLen;
  if (args_info.length_given) {
    maxLen = args_info.length_arg;
    if (args_info.zlength_given){
      zmaxLen = args_info.zlength_arg;
    }
  } else {
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
    zmaxLen = hmat(2,2);    
  }    
  
  StaticAnalyser* analyser;
  if (args_info.gofr_given){
    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, 
                       args_info.nbins_arg);        
  } else if (args_info.gofz_given) {
    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
                       args_info.nbins_arg);
  } else if (args_info.r_z_given) {
    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, 
                          args_info.nbins_arg, args_info.nbins_z_arg);
  } else if (args_info.r_theta_given) {
    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.r_omega_given) {
    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.theta_omega_given) {
    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, 
                              args_info.nanglebins_arg);
  } else if (args_info.gxyz_given) {
    if (args_info.refsele_given) {
      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "--refsele must set when --gxyz is used");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
  } else if (args_info.twodgofr_given){
    if (args_info.dz_given) {
      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen, 
                             args_info.dz_arg, args_info.nbins_arg);        
    } else {
      sprintf( painCave.errMsg,
               "A slab width (dz) must be specified when calculating TwoDGofR");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }    
  } else if (args_info.p2_given) {
    if (args_info.sele1_given) {     
      if (args_info.sele2_given) 
        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
      else 
        if (args_info.seleoffset_given) 
          analyser  = new P2OrderParameter(info, dumpFileName, sele1, 
                                           args_info.seleoffset_arg);
        else 
          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
    } else {
      sprintf( painCave.errMsg,
               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.rp2_given){
    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
  } else if (args_info.bo_given){
    if (args_info.rcut_given) {
      analyser = new BondOrderParameter(info, dumpFileName, sele1, 
                                        args_info.rcut_arg, 
                                        args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
  } else if (args_info.tet_param_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParam(info, dumpFileName, sele1, 
                                         args_info.rcut_arg, 
                                         args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.tet_param_z_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
                                          args_info.rcut_arg, 
                                          args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.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.rnemdz_given) {
    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.rnemdr_given) {
    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.rnemdrt_given) {
    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
                               args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.p_angle_given) {
    if (args_info.sele1_given) {     
      if (args_info.sele2_given) 
        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
                               args_info.nbins_arg);
      else 
        if (args_info.seleoffset_given) 
          analyser  = new pAngle(info, dumpFileName, sele1, 
                                 args_info.seleoffset_arg, args_info.nbins_arg);
        else 
          analyser  = new pAngle(info, dumpFileName, sele1, 
                                 args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "At least one selection script (--sele1) must be specified when "
               "calculating P(angle) distributions");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
  }else if (args_info.hxy_given) {
    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, 
                       args_info.nbins_y_arg, args_info.nbins_arg);
#endif
  }else if (args_info.rho_r_given) {
    if (args_info.radius_given){
      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
    }else{
      sprintf( painCave.errMsg,
               "A particle radius (radius) must be specified when calculating Rho(r)");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.hullvol_given) {
    analyser = new NanoVolume(info, dumpFileName, sele1);
  } else if (args_info.rodlength_given) {
    analyser = new NanoLength(info, dumpFileName, sele1);
  } else if (args_info.angle_r_given) {
    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
  }
  
  if (args_info.output_given) {
    analyser->setOutputName(args_info.output_arg);
  }
  if (args_info.step_given) {
    analyser->setStep(args_info.step_arg);
  }
  
  analyser->process();
  
  delete analyser;    
  delete info;
  
  return 0;   
}
Revision:	1979
Committed:	Sat Apr 5 20:56:01 2014 UTC (11 years ago) by gezelter
File size:	14457 byte(s)
Log Message:	* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals * Added the ability to specify non-bonded constraints in a molecule * Added the ability to do selection offsets in the pAngle staticProps module
#	User	Rev	Content
1	gezelter	507	/*
2	tim	310	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	310	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	310	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	310	*/
42
43			#include <iostream>
44			#include <fstream>
45			#include <string>
46
47			#include "brains/SimCreator.hpp"
48			#include "brains/SimInfo.hpp"
49			#include "io/DumpReader.hpp"
50			#include "utils/simError.h"
51
52	tim	311	#include "applications/staticProps/StaticPropsCmd.h"
53	tim	543	#include "applications/staticProps/StaticAnalyser.hpp"
54	tim	311	#include "applications/staticProps/GofR.hpp"
55	xsun	1213	#include "applications/staticProps/GofZ.hpp"
56	gezelter	1440	#include "applications/staticProps/GofRZ.hpp"
57	tim	311	#include "applications/staticProps/GofRAngle.hpp"
58			#include "applications/staticProps/GofAngle2.hpp"
59			#include "applications/staticProps/GofXyz.hpp"
60	gezelter	1454	#include "applications/staticProps/TwoDGofR.hpp"
61	tim	543	#include "applications/staticProps/P2OrderParameter.hpp"
62	gezelter	1039	#include "applications/staticProps/BondOrderParameter.hpp"
63	chuckv	1128	#include "applications/staticProps/BOPofR.hpp"
64	xsun	980	#include "applications/staticProps/RippleOP.hpp"
65	tim	544	#include "applications/staticProps/SCDOrderParameter.hpp"
66	tim	545	#include "applications/staticProps/DensityPlot.hpp"
67	gezelter	1513	#include "applications/staticProps/ObjectCount.hpp"
68	tim	840	#include "applications/staticProps/RhoZ.hpp"
69	gezelter	1413	#include "applications/staticProps/pAngle.hpp"
70	chuckv	1180	#include "applications/staticProps/BondAngleDistribution.hpp"
71			#include "applications/staticProps/NanoVolume.hpp"
72	gezelter	1585	#include "applications/staticProps/NanoLength.hpp"
73	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
74	xsun	955	#include "applications/staticProps/Hxy.hpp"
75	gezelter	956	#endif
76	chuckv	1091	#include "applications/staticProps/RhoR.hpp"
77	kstocke1	1522	#include "applications/staticProps/AngleR.hpp"
78			#include "applications/staticProps/TetrahedralityParam.hpp"
79	gezelter	1782	#include "applications/staticProps/TetrahedralityParamZ.hpp"
80	gezelter	1879	#include "applications/staticProps/RNEMDStats.hpp"
81
82	gezelter	1390	using namespace OpenMD;
83	tim	310
84			int main(int argc, char* argv[]){
85
86	gezelter	1513
87			gengetopt_args_info args_info;
88
89			//parse the command line option
90			if (cmdline_parser (argc, argv, &args_info) != 0) {
91			exit(1) ;
92			}
93
94			//get the dumpfile name
95			std::string dumpFileName = args_info.input_arg;
96			std::string sele1;
97			std::string sele2;
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			}
111			}
112
113			// check the second selection argument, or set it to the environment
114	gezelter	1937	// variable, or failing that, set it to the first selection
115	gezelter	1513
116			if (args_info.sele2_given) {
117			sele2 = args_info.sele2_arg;
118			} else {
119	gezelter	1937	char* sele2Env = getenv("SELECTION2");
120	gezelter	1513	if (sele2Env) {
121			sele2 = sele2Env;
122			} else {
123	gezelter	1819	//If sele2 is not specified, then the default behavior
124			//should be what is already intended for sele1
125	jmichalk	1785	sele2 = sele1;
126	gezelter	1513	}
127			}
128	gezelter	1846
129	gezelter	1513	bool batchMode;
130			if (args_info.scd_given){
131	gezelter	1846	if (args_info.sele1_given &&
132			args_info.sele2_given && args_info.sele3_given) {
133	gezelter	1513	batchMode = false;
134	gezelter	1846	} else if (args_info.molname_given &&
135			args_info.begin_given && args_info.end_given) {
136			if (args_info.begin_arg < 0 \|\|
137			args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
138	gezelter	1513	sprintf( painCave.errMsg,
139			"below conditions are not satisfied:\n"
140			"0 <= begin && 0<= end && begin <= end-2\n");
141			painCave.severity = OPENMD_ERROR;
142			painCave.isFatal = 1;
143			simError();
144			}
145			batchMode = true;
146			} else{
147			sprintf( painCave.errMsg,
148			"either --sele1, --sele2, --sele3 are specified,"
149			" or --molname, --begin, --end are specified\n");
150			painCave.severity = OPENMD_ERROR;
151			painCave.isFatal = 1;
152	gezelter	1846	simError();
153	gezelter	1513	}
154			}
155
156			//parse md file and set up the system
157			SimCreator creator;
158			SimInfo* info = creator.createSim(dumpFileName);
159	tim	310
160	gezelter	1513	RealType maxLen;
161			RealType zmaxLen;
162			if (args_info.length_given) {
163			maxLen = args_info.length_arg;
164			if (args_info.zlength_given){
165			zmaxLen = args_info.zlength_arg;
166	chuckv	1445	}
167	gezelter	1513	} else {
168			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
169			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
170			zmaxLen = hmat(2,2);
171			}
172	kstocke1	1522
173	gezelter	1513	StaticAnalyser* analyser;
174			if (args_info.gofr_given){
175			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
176	kstocke1	1522	args_info.nbins_arg);
177	gezelter	1513	} else if (args_info.gofz_given) {
178			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
179	kstocke1	1522	args_info.nbins_arg);
180	gezelter	1513	} else if (args_info.r_z_given) {
181			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
182	kstocke1	1522	args_info.nbins_arg, args_info.nbins_z_arg);
183	gezelter	1513	} else if (args_info.r_theta_given) {
184			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
185	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
186	gezelter	1513	} else if (args_info.r_omega_given) {
187			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
188	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
189	gezelter	1513	} else if (args_info.theta_omega_given) {
190			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
191	kstocke1	1522	args_info.nanglebins_arg);
192	gezelter	1513	} else if (args_info.gxyz_given) {
193			if (args_info.refsele_given) {
194	gezelter	1846	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
195			args_info.refsele_arg, maxLen, args_info.nbins_arg);
196	gezelter	1039	} else {
197	gezelter	1513	sprintf( painCave.errMsg,
198	kstocke1	1522	"--refsele must set when --gxyz is used");
199	gezelter	1513	painCave.severity = OPENMD_ERROR;
200			painCave.isFatal = 1;
201			simError();
202	tim	310	}
203	gezelter	1513	} else if (args_info.twodgofr_given){
204			if (args_info.dz_given) {
205			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
206	kstocke1	1522	args_info.dz_arg, args_info.nbins_arg);
207	chuckv	1445	} else {
208	gezelter	1513	sprintf( painCave.errMsg,
209	kstocke1	1522	"A slab width (dz) must be specified when calculating TwoDGofR");
210	gezelter	1513	painCave.severity = OPENMD_ERROR;
211			painCave.isFatal = 1;
212			simError();
213	kstocke1	1522	}
214	gezelter	1513	} else if (args_info.p2_given) {
215	gezelter	1542	if (args_info.sele1_given) {
216			if (args_info.sele2_given)
217			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
218			else
219	gezelter	1819	if (args_info.seleoffset_given)
220			analyser = new P2OrderParameter(info, dumpFileName, sele1,
221			args_info.seleoffset_arg);
222			else
223			analyser = new P2OrderParameter(info, dumpFileName, sele1);
224	gezelter	1542	} else {
225			sprintf( painCave.errMsg,
226			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
227			painCave.severity = OPENMD_ERROR;
228			painCave.isFatal = 1;
229			simError();
230			}
231	gezelter	1513	} else if (args_info.rp2_given){
232			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
233			} else if (args_info.bo_given){
234			if (args_info.rcut_given) {
235			analyser = new BondOrderParameter(info, dumpFileName, sele1,
236	kstocke1	1522	args_info.rcut_arg,
237			args_info.nbins_arg);
238	gezelter	1513	} else {
239			sprintf( painCave.errMsg,
240	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
241	gezelter	1513	painCave.severity = OPENMD_ERROR;
242			painCave.isFatal = 1;
243			simError();
244	tim	544	}
245	kstocke1	1522
246			} else if (args_info.tet_param_given) {
247			if (args_info.rcut_given) {
248			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
249			args_info.rcut_arg,
250			args_info.nbins_arg);
251			} else {
252			sprintf( painCave.errMsg,
253			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
254			painCave.severity = OPENMD_ERROR;
255			painCave.isFatal = 1;
256			simError();
257			}
258	gezelter	1782	} else if (args_info.tet_param_z_given) {
259			if (args_info.rcut_given) {
260	gezelter	1846	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
261			args_info.rcut_arg,
262			args_info.nbins_arg);
263	gezelter	1782	} else {
264			sprintf( painCave.errMsg,
265			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
266			painCave.severity = OPENMD_ERROR;
267			painCave.isFatal = 1;
268			simError();
269			}
270	gezelter	1513	} else if (args_info.bor_given){
271			if (args_info.rcut_given) {
272			analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
273	kstocke1	1522	args_info.nbins_arg, maxLen);
274	chuckv	1445	} else {
275	gezelter	1513	sprintf( painCave.errMsg,
276	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
277	gezelter	1513	painCave.severity = OPENMD_ERROR;
278			painCave.isFatal = 1;
279			simError();
280			}
281			} else if (args_info.bad_given){
282			if (args_info.rcut_given) {
283	gezelter	1846	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
284			args_info.rcut_arg,
285	kstocke1	1522	args_info.nbins_arg);
286	gezelter	1513	} else {
287			sprintf( painCave.errMsg,
288	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
289	gezelter	1513	painCave.severity = OPENMD_ERROR;
290			painCave.isFatal = 1;
291			simError();
292	gezelter	1846	}
293	gezelter	1513	} else if (args_info.scd_given) {
294			if (batchMode) {
295	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
296			args_info.molname_arg,
297	kstocke1	1522	args_info.begin_arg, args_info.end_arg);
298	gezelter	1513	} else{
299			std::string sele3 = args_info.sele3_arg;
300	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
301			sele1, sele2, sele3);
302	gezelter	1513	}
303			}else if (args_info.density_given) {
304			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
305	kstocke1	1522	args_info.nbins_arg);
306	gezelter	1513	} 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	gezelter	1879	} else if (args_info.rnemdz_given) {
311			analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
312			} else if (args_info.rnemdr_given) {
313			analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
314	gezelter	1953	} else if (args_info.rnemdrt_given) {
315			analyser = new RNEMDRTheta(info, dumpFileName, sele1,
316			args_info.nbins_arg, args_info.nanglebins_arg);
317	gezelter	1513	} else if (args_info.p_angle_given) {
318	gezelter	1979	if (args_info.sele1_given) {
319			if (args_info.sele2_given)
320			analyser = new pAngle(info, dumpFileName, sele1, sele2,
321			args_info.nbins_arg);
322			else
323			if (args_info.seleoffset_given)
324			analyser = new pAngle(info, dumpFileName, sele1,
325			args_info.seleoffset_arg, args_info.nbins_arg);
326			else
327			analyser = new pAngle(info, dumpFileName, sele1,
328			args_info.nbins_arg);
329			} else {
330			sprintf( painCave.errMsg,
331			"At least one selection script (--sele1) must be specified when "
332			"calculating P(angle) distributions");
333			painCave.severity = OPENMD_ERROR;
334			painCave.isFatal = 1;
335			simError();
336			}
337	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
338	gezelter	1513	}else if (args_info.hxy_given) {
339			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
340	kstocke1	1522	args_info.nbins_y_arg, args_info.nbins_arg);
341	gezelter	956	#endif
342	gezelter	1513	}else if (args_info.rho_r_given) {
343			if (args_info.radius_given){
344			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
345			}else{
346			sprintf( painCave.errMsg,
347	kstocke1	1522	"A particle radius (radius) must be specified when calculating Rho(r)");
348	gezelter	1513	painCave.severity = OPENMD_ERROR;
349			painCave.isFatal = 1;
350			simError();
351	chuckv	1091	}
352	kstocke1	1522	} else if (args_info.hullvol_given) {
353	gezelter	1513	analyser = new NanoVolume(info, dumpFileName, sele1);
354	gezelter	1585	} else if (args_info.rodlength_given) {
355			analyser = new NanoLength(info, dumpFileName, sele1);
356	kstocke1	1522	} else if (args_info.angle_r_given) {
357			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
358	gezelter	1513	}
359	gezelter	1846
360	gezelter	1513	if (args_info.output_given) {
361			analyser->setOutputName(args_info.output_arg);
362			}
363			if (args_info.step_given) {
364			analyser->setStep(args_info.step_arg);
365			}
366	gezelter	1846
367	gezelter	1513	analyser->process();
368	kstocke1	1522
369	gezelter	1513	delete analyser;
370			delete info;
371	gezelter	1846
372	gezelter	1513	return 0;
373	tim	310	}