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root/OpenMD/trunk/src/applications/staticProps/StaticProps.cpp
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Comparing trunk/src/applications/staticProps/StaticProps.cpp (file contents):
Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 UTC

# Line 35 | Line 35
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <iostream>
44   #include <fstream>
45   #include <string>
46  
46 – #include "brains/Register.hpp"
47   #include "brains/SimCreator.hpp"
48   #include "brains/SimInfo.hpp"
49   #include "io/DumpReader.hpp"
# Line 57 | Line 57
57   #include "applications/staticProps/GofRAngle.hpp"
58   #include "applications/staticProps/GofAngle2.hpp"
59   #include "applications/staticProps/GofXyz.hpp"
60 + #include "applications/staticProps/TwoDGofR.hpp"
61   #include "applications/staticProps/P2OrderParameter.hpp"
62   #include "applications/staticProps/BondOrderParameter.hpp"
63   #include "applications/staticProps/BOPofR.hpp"
64   #include "applications/staticProps/RippleOP.hpp"
65   #include "applications/staticProps/SCDOrderParameter.hpp"
66   #include "applications/staticProps/DensityPlot.hpp"
67 + #include "applications/staticProps/ObjectCount.hpp"
68   #include "applications/staticProps/RhoZ.hpp"
69   #include "applications/staticProps/pAngle.hpp"
70   #include "applications/staticProps/BondAngleDistribution.hpp"
71   #include "applications/staticProps/NanoVolume.hpp"
72 + #include "applications/staticProps/NanoLength.hpp"
73   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
74   #include "applications/staticProps/Hxy.hpp"
75   #endif
76   #include "applications/staticProps/RhoR.hpp"
77 + #include "applications/staticProps/AngleR.hpp"
78 + #include "applications/staticProps/TetrahedralityParam.hpp"
79 + #include "applications/staticProps/TetrahedralityParamZ.hpp"
80 + #include "applications/staticProps/TetrahedralityParamXYZ.hpp"
81 + #include "applications/staticProps/RNEMDStats.hpp"
82 + #include "applications/staticProps/NitrileFrequencyMap.hpp"
83 + #include "applications/staticProps/MultipoleSum.hpp"
84  
85   using namespace OpenMD;
86  
87   int main(int argc, char* argv[]){
88    
89 <    //register force fields
90 <    registerForceFields();
91 <
92 <    gengetopt_args_info args_info;
93 <
94 <    //parse the command line option
95 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
96 <        exit(1) ;
97 <    }
98 <
99 <    //get the dumpfile name
100 <    std::string dumpFileName = args_info.input_arg;
101 <    std::string sele1;
102 <    std::string sele2;
103 <    bool userSpecifiedSelect1;
104 <    bool userSpecifiedSelect2;
105 <
106 <    // check the first selection argument, or set it to the environment
107 <    // variable, or failing that, set it to "select all"
108 <
109 <    if (args_info.sele1_given) {
110 <        sele1 = args_info.sele1_arg;
89 >  
90 >  gengetopt_args_info args_info;
91 >  
92 >  //parse the command line option
93 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
94 >    exit(1) ;
95 >  }
96 >  
97 >  //get the dumpfile name
98 >  std::string dumpFileName = args_info.input_arg;
99 >  std::string sele1;
100 >  std::string sele2;
101 >  std::string sele3;
102 >  
103 >  // check the first selection argument, or set it to the environment
104 >  // variable, or failing that, set it to "select all"
105 >  
106 >  if (args_info.sele1_given) {
107 >    sele1 = args_info.sele1_arg;
108 >  } else {
109 >    char*  sele1Env= getenv("SELECTION1");
110 >    if (sele1Env) {
111 >      sele1 = sele1Env;
112      } else {
113 <        char*  sele1Env= getenv("SELECTION1");
103 <        if (sele1Env) {
104 <            sele1 = sele1Env;
105 <        } else {
106 <            sele1 = "select all";
107 <        }
113 >      sele1 = "select all";
114      }
115 <
110 <    // check the second selection argument, or set it to the environment
111 <    // variable, or failing that, set it to "select all"
115 >  }
116    
117 <    if (args_info.sele2_given) {
118 <        sele2 = args_info.sele2_arg;
119 <    } else {
120 <        char* sele2Env = getenv("SELECTION1");
121 <        if (sele2Env) {
122 <            sele2 = sele2Env;            
123 <        } else {
124 <            sele2 = "select all";
125 <        }
117 >  // check the second selection argument, or set it to the environment
118 >  // variable, or failing that, set it to the first selection
119 >  
120 >  if (args_info.sele2_given) {
121 >    sele2 = args_info.sele2_arg;
122 >  } else {
123 >    char* sele2Env = getenv("SELECTION2");
124 >    if (sele2Env) {
125 >      sele2 = sele2Env;            
126 >    } else {
127 >      //If sele2 is not specified, then the default behavior
128 >      //should be what is already intended for sele1
129 >      sele2 = sele1;
130      }
131 +  }
132  
133 +  // check the third selection argument, which is only set if
134 +  // requested by the user
135  
136 <    // Problems if sele1 wasn't specified, but
126 < // if (!args_info.scd_given) {
127 < //       sprintf( painCave.errMsg,
128 < //                "neither --sele1 option nor $SELECTION1 is set");
129 < //       painCave.severity = OPENMD_ERROR;
130 < //       painCave.isFatal = 1;
131 < //       simError();
132 < //     }
133 < //   }
136 >  if (args_info.sele3_given) sele3 = args_info.sele3_arg;
137  
138 <    // Problems if sele1 wasn't specified
138 >  bool batchMode;
139 >  if (args_info.scd_given){
140 >    if (args_info.sele1_given &&
141 >        args_info.sele2_given && args_info.sele3_given) {
142 >      batchMode = false;
143 >    } else if (args_info.molname_given &&
144 >               args_info.begin_given && args_info.end_given) {
145 >      if (args_info.begin_arg < 0 ||
146 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
147 >        sprintf( painCave.errMsg,
148 >                 "below conditions are not satisfied:\n"
149 >                 "0 <= begin && 0<= end && begin <= end-2\n");
150 >        painCave.severity = OPENMD_ERROR;
151 >        painCave.isFatal = 1;
152 >        simError();                    
153 >      }
154 >      batchMode = true;        
155 >    } else{
156 >      sprintf( painCave.errMsg,
157 >               "either --sele1, --sele2, --sele3 are specified,"
158 >               " or --molname, --begin, --end are specified\n");
159 >      painCave.severity = OPENMD_ERROR;
160 >      painCave.isFatal = 1;
161 >      simError();
162 >    }
163 >  }
164 >  
165 >  //parse md file and set up the system
166 >  SimCreator creator;
167 >  SimInfo* info = creator.createSim(dumpFileName);
168  
169 < //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
170 < //       sprintf( painCave.errMsg,
171 < //                "neither --sele2 option nor $SELECTION1 is set");
172 < //       painCave.severity = OPENMD_ERROR;
173 < //       painCave.isFatal = 1;
174 < //       simError();        
143 < //     }
144 < //   }
145 <
146 <    bool batchMode;
147 <    if (args_info.scd_given){
148 <        if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
149 <            batchMode = false;
150 <        } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
151 <            if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
152 <                sprintf( painCave.errMsg,
153 <                         "below conditions are not satisfied:\n"
154 <                         "0 <= begin && 0<= end && begin <= end-2\n");
155 <                painCave.severity = OPENMD_ERROR;
156 <                painCave.isFatal = 1;
157 <                simError();                    
158 <            }
159 <            batchMode = true;        
160 <        } else{
161 <            sprintf( painCave.errMsg,
162 <                     "either --sele1, --sele2, --sele3 are specified,"
163 <                     " or --molname, --begin, --end are specified\n");
164 <            painCave.severity = OPENMD_ERROR;
165 <            painCave.isFatal = 1;
166 <            simError();        
167 <    
168 <        }
169 >  RealType maxLen;
170 >  RealType zmaxLen;
171 >  if (args_info.length_given) {
172 >    maxLen = args_info.length_arg;
173 >    if (args_info.zlength_given){
174 >      zmaxLen = args_info.zlength_arg;
175      }
176 +  } else {
177 +    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
178 +    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
179 +    zmaxLen = hmat(2,2);    
180 +  }    
181 +  
182 +  StaticAnalyser* analyser;
183 +  if (args_info.gofr_given){
184 +    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
185 +                       args_info.nbins_arg);        
186 +  } else if (args_info.gofz_given) {
187 +    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
188 +                       args_info.nbins_arg);
189 +  } else if (args_info.r_z_given) {
190 +    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
191 +                          args_info.nbins_arg, args_info.nbins_z_arg);
192 +  } else if (args_info.r_theta_given) {
193 +    if (args_info.sele3_given)
194 +      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
195 +                                args_info.nbins_arg, args_info.nanglebins_arg);
196 +    else
197 +      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
198 +                                args_info.nbins_arg, args_info.nanglebins_arg);
199 +  } else if (args_info.r_omega_given) {
200 +    if (args_info.sele3_given)
201 +      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
202 +                                args_info.nbins_arg, args_info.nanglebins_arg);
203 +    else
204 +      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205 +                                args_info.nbins_arg, args_info.nanglebins_arg);
206  
207 <    //parse md file and set up the system
208 <    SimCreator creator;
209 <    std::cout << "dumpFile = " << dumpFileName << "\n";
210 <    SimInfo* info = creator.createSim(dumpFileName);
211 <
212 <    RealType maxLen;
213 <    RealType zmaxLen;
214 <    if (args_info.length_given) {
215 <        maxLen = args_info.length_arg;
216 <        if (args_info.zlength_given){
217 <            zmaxLen = args_info.zlength_arg;
182 <        }
207 >  } else if (args_info.theta_omega_given) {
208 >    if (args_info.sele3_given)
209 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
210 >                                args_info.nanglebins_arg);
211 >    else
212 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
213 >                                args_info.nanglebins_arg);
214 >  } else if (args_info.gxyz_given) {
215 >    if (args_info.refsele_given) {
216 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
217 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
218      } else {
219 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
220 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
221 <        zmaxLen = hmat(2,2);    
219 >      sprintf( painCave.errMsg,
220 >               "--refsele must set when --gxyz is used");
221 >      painCave.severity = OPENMD_ERROR;
222 >      painCave.isFatal = 1;
223 >      simError();  
224 >    }
225 >  } else if (args_info.twodgofr_given){
226 >    if (args_info.dz_given) {
227 >      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
228 >                             args_info.dz_arg, args_info.nbins_arg);        
229 >    } else {
230 >      sprintf( painCave.errMsg,
231 >               "A slab width (dz) must be specified when calculating TwoDGofR");
232 >      painCave.severity = OPENMD_ERROR;
233 >      painCave.isFatal = 1;
234 >      simError();
235      }    
236 <
237 <    StaticAnalyser* analyser;
238 <    if (args_info.gofr_given){
239 <        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
240 <                           args_info.nbins_arg);        
241 <    } else if (args_info.gofz_given) {
242 <        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
243 <                           args_info.nbins_arg);
244 <    } else if (args_info.r_z_given) {
245 <        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
246 <                              args_info.nbins_arg, args_info.nbins_z_arg);
247 <    } else if (args_info.r_theta_given) {
248 <        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
249 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
250 <    } else if (args_info.r_omega_given) {
251 <        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
252 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
253 <    } else if (args_info.theta_omega_given) {
254 <        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
255 <                                  args_info.nanglebins_arg);
256 <    } else if (args_info.gxyz_given) {
257 <        if (args_info.refsele_given) {
258 <            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
259 <                                 maxLen, args_info.nbins_arg);        
260 <        } else {
261 <            sprintf( painCave.errMsg,
262 <                     "--refsele must set when --gxyz is used");
263 <            painCave.severity = OPENMD_ERROR;
264 <            painCave.isFatal = 1;
265 <            simError();  
266 <        }
267 <    } else if (args_info.p2_given) {
268 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
269 <    } else if (args_info.rp2_given){
270 <        analyser = new RippleOP(info, dumpFileName, sele1, sele2);
271 <    } else if (args_info.bo_given){
272 <        if (args_info.rcut_given) {
273 <            analyser = new BondOrderParameter(info, dumpFileName, sele1,
274 <                                              args_info.rcut_arg,
275 <                                              args_info.nbins_arg);
276 <        } else {
277 <            sprintf( painCave.errMsg,
278 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
279 <            painCave.severity = OPENMD_ERROR;
280 <            painCave.isFatal = 1;
281 <            simError();
282 <        }
283 <    } else if (args_info.bor_given){
284 <        if (args_info.rcut_given) {
285 <            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
286 <                                  args_info.nbins_arg, maxLen);
287 <        } else {
288 <            sprintf( painCave.errMsg,
289 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
290 <            painCave.severity = OPENMD_ERROR;
291 <            painCave.isFatal = 1;
292 <            simError();
293 <        }
294 <    } else if (args_info.bad_given){
295 <        if (args_info.rcut_given) {
296 <            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
297 <                                                 args_info.nbins_arg);
298 <        } else {
299 <            sprintf( painCave.errMsg,
300 <                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
301 <            painCave.severity = OPENMD_ERROR;
302 <            painCave.isFatal = 1;
303 <            simError();
304 <        }
305 <    } else if (args_info.scd_given) {
306 <        if (batchMode) {
307 <            analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
308 <                                              args_info.begin_arg, args_info.end_arg);
309 <        } else{
310 <            std::string sele3 = args_info.sele3_arg;
311 <            analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
312 <        }
313 <    }else if (args_info.density_given) {
314 <        analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
315 <                                  args_info.nbins_arg);  
316 <    } else if (args_info.slab_density_given) {
317 <        analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
318 <    } else if (args_info.p_angle_given) {
319 <        analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
236 >  } else if (args_info.p2_given) {
237 >    if (args_info.sele1_given) {    
238 >      if (args_info.sele2_given)
239 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
240 >      else
241 >        if (args_info.seleoffset_given)
242 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
243 >                                           args_info.seleoffset_arg);
244 >        else
245 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
246 >    } else {
247 >      sprintf( painCave.errMsg,
248 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
249 >      painCave.severity = OPENMD_ERROR;
250 >      painCave.isFatal = 1;
251 >      simError();
252 >    }
253 >  } else if (args_info.rp2_given){
254 >    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
255 >  } else if (args_info.bo_given){
256 >    if (args_info.rcut_given) {
257 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
258 >                                        args_info.rcut_arg,
259 >                                        args_info.nbins_arg);
260 >    } else {
261 >      sprintf( painCave.errMsg,
262 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
263 >      painCave.severity = OPENMD_ERROR;
264 >      painCave.isFatal = 1;
265 >      simError();
266 >    }
267 >  } else if (args_info.multipole_given){
268 >    analyser = new MultipoleSum(info, dumpFileName, sele1,
269 >                                maxLen, args_info.nbins_arg);
270 >  } else if (args_info.tet_param_given) {
271 >    if (args_info.rcut_given) {  
272 >      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
273 >                                         args_info.rcut_arg,
274 >                                         args_info.nbins_arg);
275 >    } else {
276 >      sprintf( painCave.errMsg,
277 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
278 >      painCave.severity = OPENMD_ERROR;
279 >      painCave.isFatal = 1;
280 >      simError();
281 >    }
282 >  } else if (args_info.tet_param_z_given) {
283 >    if (args_info.rcut_given) {  
284 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
285 >                                          args_info.rcut_arg,
286 >                                          args_info.nbins_arg);
287 >    } else {
288 >      sprintf( painCave.errMsg,
289 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
290 >      painCave.severity = OPENMD_ERROR;
291 >      painCave.isFatal = 1;
292 >      simError();
293 >    }
294 >  } else if (args_info.tet_param_xyz_given) {
295 >    if (!args_info.rcut_given) {
296 >      sprintf( painCave.errMsg,
297 >               "A cutoff radius (rcut) must be specified when calculating"
298 >               " Tetrahedrality Parameters");
299 >      painCave.severity = OPENMD_ERROR;
300 >      painCave.isFatal = 1;
301 >      simError();
302 >    }
303 >    if (!args_info.voxelSize_given) {
304 >      sprintf( painCave.errMsg,
305 >               "A voxel size must be specified when calculating"
306 >               " volume-resolved Tetrahedrality Parameters");
307 >      painCave.severity = OPENMD_ERROR;
308 >      painCave.isFatal = 1;
309 >      simError();
310 >    }
311 >    if (!args_info.gaussWidth_given) {
312 >      sprintf( painCave.errMsg,
313 >               "A gaussian width must be specified when calculating"
314 >               " volume-resolved Tetrahedrality Parameters");
315 >      painCave.severity = OPENMD_ERROR;
316 >      painCave.isFatal = 1;
317 >      simError();
318 >    }
319 >    analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
320 >                                          args_info.rcut_arg,
321 >                                          args_info.voxelSize_arg,
322 >                                          args_info.gaussWidth_arg);
323 >  } else if (args_info.ior_given){
324 >    if (args_info.rcut_given) {
325 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
326 >                                    args_info.rcut_arg,
327 >                                    args_info.nbins_arg, maxLen);
328 >    } else {
329 >      sprintf( painCave.errMsg,
330 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
331 >      painCave.severity = OPENMD_ERROR;
332 >      painCave.isFatal = 1;
333 >      simError();
334 >    }
335 >  } else if (args_info.for_given){
336 >    if (args_info.rcut_given) {
337 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
338 >                            args_info.nbins_arg, maxLen);
339 >    } else {
340 >      sprintf( painCave.errMsg,
341 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
342 >      painCave.severity = OPENMD_ERROR;
343 >      painCave.isFatal = 1;
344 >      simError();
345 >    }
346 >  } else if (args_info.bad_given){
347 >    if (args_info.rcut_given) {
348 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
349 >                                           args_info.rcut_arg,
350 >                                           args_info.nbins_arg);
351 >    } else {
352 >      sprintf( painCave.errMsg,
353 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
354 >      painCave.severity = OPENMD_ERROR;
355 >      painCave.isFatal = 1;
356 >      simError();
357 >    }
358 >  } else if (args_info.scd_given) {
359 >    if (batchMode) {
360 >      analyser  = new SCDOrderParameter(info, dumpFileName,
361 >                                        args_info.molname_arg,
362 >                                        args_info.begin_arg, args_info.end_arg);
363 >    } else{
364 >      analyser  = new SCDOrderParameter(info, dumpFileName,
365 >                                        sele1, sele2, sele3);
366 >    }
367 >  }else if (args_info.density_given) {
368 >    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
369 >                              args_info.nbins_arg);  
370 >  } else if (args_info.count_given) {
371 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
372 >  } else if (args_info.slab_density_given) {
373 >    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
374 >  } else if (args_info.rnemdz_given) {
375 >    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
376 >  } else if (args_info.rnemdr_given) {
377 >    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
378 >  } else if (args_info.rnemdrt_given) {
379 >    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
380 >                               args_info.nbins_arg, args_info.nanglebins_arg);
381 >  } else if (args_info.nitrile_given) {
382 >    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
383 >                                       args_info.nbins_arg);
384 >  } else if (args_info.p_angle_given) {
385 >    if (args_info.sele1_given) {    
386 >      if (args_info.sele2_given)
387 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
388 >                               args_info.nbins_arg);
389 >      else
390 >        if (args_info.seleoffset_given) {
391 >          if (args_info.seleoffset2_given) {
392 >            analyser  = new pAngle(info, dumpFileName, sele1,
393 >                                   args_info.seleoffset_arg,
394 >                                   args_info.seleoffset2_arg,
395 >                                   args_info.nbins_arg);
396 >          } else {
397 >            analyser  = new pAngle(info, dumpFileName, sele1,
398 >                                   args_info.seleoffset_arg,
399 >                                   args_info.nbins_arg);
400 >          }
401 >        } else
402 >          analyser  = new pAngle(info, dumpFileName, sele1,
403 >                                 args_info.nbins_arg);
404 >    } else {
405 >      sprintf( painCave.errMsg,
406 >               "At least one selection script (--sele1) must be specified when "
407 >               "calculating P(angle) distributions");
408 >      painCave.severity = OPENMD_ERROR;
409 >      painCave.isFatal = 1;
410 >      simError();
411 >    }
412   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
413 <    }else if (args_info.hxy_given) {
414 <        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
415 <                           args_info.nbins_y_arg, args_info.nbins_arg);
413 >  }else if (args_info.hxy_given) {
414 >    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
415 >                       args_info.nbins_y_arg, args_info.nbins_arg);
416   #endif
417 <    }else if (args_info.rho_r_given) {
418 <        if (args_info.radius_given){
419 <            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
420 <        }else{
421 <            sprintf( painCave.errMsg,
422 <                     "A particle radius (radius) must be specified when calculating Rho(r)");
423 <            painCave.severity = OPENMD_ERROR;
424 <            painCave.isFatal = 1;
425 <            simError();
286 <        }
287 <    }else if (args_info.hullvol_given) {
288 <        analyser = new NanoVolume(info, dumpFileName, sele1);
417 >  }else if (args_info.rho_r_given) {
418 >    if (args_info.radius_given){
419 >      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
420 >    }else{
421 >      sprintf( painCave.errMsg,
422 >               "A particle radius (radius) must be specified when calculating Rho(r)");
423 >      painCave.severity = OPENMD_ERROR;
424 >      painCave.isFatal = 1;
425 >      simError();
426      }
427 +  } else if (args_info.hullvol_given) {
428 +    analyser = new NanoVolume(info, dumpFileName, sele1);
429 +  } else if (args_info.rodlength_given) {
430 +    analyser = new NanoLength(info, dumpFileName, sele1);
431 +  } else if (args_info.angle_r_given) {
432 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
433 +  }
434    
435 <    if (args_info.output_given) {
436 <        analyser->setOutputName(args_info.output_arg);
437 <    }
438 <    if (args_info.step_given) {
439 <        analyser->setStep(args_info.step_arg);
440 <    }
441 <
442 <    analyser->process();
443 <
444 <    delete analyser;    
445 <    delete info;
446 <
447 <    return 0;  
435 >  if (args_info.output_given) {
436 >    analyser->setOutputName(args_info.output_arg);
437 >  }
438 >  if (args_info.step_given) {
439 >    analyser->setStep(args_info.step_arg);
440 >  }
441 >  
442 >  analyser->process();
443 >  
444 >  delete analyser;    
445 >  delete info;
446 >  
447 >  return 0;  
448   }
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