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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 1994 by gezelter, Wed Apr 30 18:50:45 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/RNEMDStats.hpp"
81 + #include "applications/staticProps/NitrileFrequencyMap.hpp"
82  
83   using namespace OpenMD;
84  
85   int main(int argc, char* argv[]){
86    
87 <    //register force fields
88 <    registerForceFields();
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 <    bool userSpecifiedSelect1;
102 <    bool userSpecifiedSelect2;
103 <
104 <    // check the first selection argument, or set it to the environment
105 <    // variable, or failing that, set it to "select all"
106 <
107 <    if (args_info.sele1_given) {
108 <        sele1 = args_info.sele1_arg;
87 >  
88 >  gengetopt_args_info args_info;
89 >  
90 >  //parse the command line option
91 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
92 >    exit(1) ;
93 >  }
94 >  
95 >  //get the dumpfile name
96 >  std::string dumpFileName = args_info.input_arg;
97 >  std::string sele1;
98 >  std::string sele2;
99 >  
100 >  // check the first selection argument, or set it to the environment
101 >  // variable, or failing that, set it to "select all"
102 >  
103 >  if (args_info.sele1_given) {
104 >    sele1 = args_info.sele1_arg;
105 >  } else {
106 >    char*  sele1Env= getenv("SELECTION1");
107 >    if (sele1Env) {
108 >      sele1 = sele1Env;
109      } else {
110 <        char*  sele1Env= getenv("SELECTION1");
103 <        if (sele1Env) {
104 <            sele1 = sele1Env;
105 <        } else {
106 <            sele1 = "select all";
107 <        }
110 >      sele1 = "select all";
111      }
112 <
110 <    // check the second selection argument, or set it to the environment
111 <    // variable, or failing that, set it to "select all"
112 >  }
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 <            sele2 = "select all";
122 <        }
114 >  // check the second selection argument, or set it to the environment
115 >  // variable, or failing that, set it to the first selection
116 >  
117 >  if (args_info.sele2_given) {
118 >    sele2 = args_info.sele2_arg;
119 >  } else {
120 >    char* sele2Env = getenv("SELECTION2");
121 >    if (sele2Env) {
122 >      sele2 = sele2Env;            
123 >    } else {
124 >      //If sele2 is not specified, then the default behavior
125 >      //should be what is already intended for sele1
126 >      sele2 = sele1;
127      }
128 +  }
129  
130 <
131 <    // Problems if sele1 wasn't specified, but
132 < // if (!args_info.scd_given) {
133 < //       sprintf( painCave.errMsg,
134 < //                "neither --sele1 option nor $SELECTION1 is set");
135 < //       painCave.severity = OPENMD_ERROR;
136 < //       painCave.isFatal = 1;
137 < //       simError();
138 < //     }
139 < //   }
140 <
141 <    // Problems if sele1 wasn't specified
142 <
143 < //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
144 < //       sprintf( painCave.errMsg,
145 < //                "neither --sele2 option nor $SELECTION1 is set");
146 < //       painCave.severity = OPENMD_ERROR;
147 < //       painCave.isFatal = 1;
148 < //       simError();        
149 < //     }
150 < //   }
151 <
152 <    bool batchMode;
153 <    if (args_info.scd_given){
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 <        }
130 >  bool batchMode;
131 >  if (args_info.scd_given){
132 >    if (args_info.sele1_given &&
133 >        args_info.sele2_given && args_info.sele3_given) {
134 >      batchMode = false;
135 >    } else if (args_info.molname_given &&
136 >               args_info.begin_given && args_info.end_given) {
137 >      if (args_info.begin_arg < 0 ||
138 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
139 >        sprintf( painCave.errMsg,
140 >                 "below conditions are not satisfied:\n"
141 >                 "0 <= begin && 0<= end && begin <= end-2\n");
142 >        painCave.severity = OPENMD_ERROR;
143 >        painCave.isFatal = 1;
144 >        simError();                    
145 >      }
146 >      batchMode = true;        
147 >    } else{
148 >      sprintf( painCave.errMsg,
149 >               "either --sele1, --sele2, --sele3 are specified,"
150 >               " or --molname, --begin, --end are specified\n");
151 >      painCave.severity = OPENMD_ERROR;
152 >      painCave.isFatal = 1;
153 >      simError();
154      }
155 +  }
156 +  
157 +  //parse md file and set up the system
158 +  SimCreator creator;
159 +  SimInfo* info = creator.createSim(dumpFileName);
160  
161 <    //parse md file and set up the system
162 <    SimCreator creator;
163 <    std::cout << "dumpFile = " << dumpFileName << "\n";
164 <    SimInfo* info = creator.createSim(dumpFileName);
165 <
166 <    RealType maxLen;
167 <    RealType zmaxLen;
168 <    if (args_info.length_given) {
169 <        maxLen = args_info.length_arg;
170 <        if (args_info.zlength_given){
171 <            zmaxLen = args_info.zlength_arg;
172 <        }
161 >  RealType maxLen;
162 >  RealType zmaxLen;
163 >  if (args_info.length_given) {
164 >    maxLen = args_info.length_arg;
165 >    if (args_info.zlength_given){
166 >      zmaxLen = args_info.zlength_arg;
167 >    }
168 >  } else {
169 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
170 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
171 >    zmaxLen = hmat(2,2);    
172 >  }    
173 >  
174 >  StaticAnalyser* analyser;
175 >  if (args_info.gofr_given){
176 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
177 >                       args_info.nbins_arg);        
178 >  } else if (args_info.gofz_given) {
179 >    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
180 >                       args_info.nbins_arg);
181 >  } else if (args_info.r_z_given) {
182 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
183 >                          args_info.nbins_arg, args_info.nbins_z_arg);
184 >  } else if (args_info.r_theta_given) {
185 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
186 >                              args_info.nbins_arg, args_info.nanglebins_arg);
187 >  } else if (args_info.r_omega_given) {
188 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
189 >                              args_info.nbins_arg, args_info.nanglebins_arg);
190 >  } else if (args_info.theta_omega_given) {
191 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
192 >                              args_info.nanglebins_arg);
193 >  } else if (args_info.gxyz_given) {
194 >    if (args_info.refsele_given) {
195 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
196 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
197      } else {
198 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
199 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
200 <        zmaxLen = hmat(2,2);    
198 >      sprintf( painCave.errMsg,
199 >               "--refsele must set when --gxyz is used");
200 >      painCave.severity = OPENMD_ERROR;
201 >      painCave.isFatal = 1;
202 >      simError();  
203 >    }
204 >  } else if (args_info.twodgofr_given){
205 >    if (args_info.dz_given) {
206 >      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
207 >                             args_info.dz_arg, args_info.nbins_arg);        
208 >    } else {
209 >      sprintf( painCave.errMsg,
210 >               "A slab width (dz) must be specified when calculating TwoDGofR");
211 >      painCave.severity = OPENMD_ERROR;
212 >      painCave.isFatal = 1;
213 >      simError();
214      }    
215 <
216 <    StaticAnalyser* analyser;
217 <    if (args_info.gofr_given){
218 <        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
219 <                           args_info.nbins_arg);        
220 <    } else if (args_info.gofz_given) {
221 <        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
222 <                           args_info.nbins_arg);
223 <    } else if (args_info.r_z_given) {
224 <        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
225 <                              args_info.nbins_arg, args_info.nbins_z_arg);
226 <    } else if (args_info.r_theta_given) {
227 <        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
228 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
229 <    } else if (args_info.r_omega_given) {
230 <        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
231 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
232 <    } else if (args_info.theta_omega_given) {
233 <        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
234 <                                  args_info.nanglebins_arg);
235 <    } else if (args_info.gxyz_given) {
236 <        if (args_info.refsele_given) {
237 <            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
238 <                                 maxLen, args_info.nbins_arg);        
239 <        } else {
240 <            sprintf( painCave.errMsg,
241 <                     "--refsele must set when --gxyz is used");
242 <            painCave.severity = OPENMD_ERROR;
243 <            painCave.isFatal = 1;
244 <            simError();  
245 <        }
246 <    } else if (args_info.p2_given) {
247 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
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 <    } else if (args_info.bor_given){
263 <        if (args_info.rcut_given) {
264 <            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
265 <                                  args_info.nbins_arg, maxLen);
266 <        } else {
267 <            sprintf( painCave.errMsg,
268 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
269 <            painCave.severity = OPENMD_ERROR;
270 <            painCave.isFatal = 1;
271 <            simError();
272 <        }
273 <    } else if (args_info.bad_given){
274 <        if (args_info.rcut_given) {
275 <            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
276 <                                                 args_info.nbins_arg);
277 <        } else {
278 <            sprintf( painCave.errMsg,
279 <                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
280 <            painCave.severity = OPENMD_ERROR;
281 <            painCave.isFatal = 1;
282 <            simError();
283 <        }
284 <    } else if (args_info.scd_given) {
285 <        if (batchMode) {
286 <            analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
287 <                                              args_info.begin_arg, args_info.end_arg);
288 <        } else{
289 <            std::string sele3 = args_info.sele3_arg;
290 <            analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
291 <        }
292 <    }else if (args_info.density_given) {
293 <        analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
294 <                                  args_info.nbins_arg);  
295 <    } else if (args_info.slab_density_given) {
296 <        analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
297 <    } else if (args_info.p_angle_given) {
298 <        analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
215 >  } else if (args_info.p2_given) {
216 >    if (args_info.sele1_given) {    
217 >      if (args_info.sele2_given)
218 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
219 >      else
220 >        if (args_info.seleoffset_given)
221 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
222 >                                           args_info.seleoffset_arg);
223 >        else
224 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
225 >    } else {
226 >      sprintf( painCave.errMsg,
227 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
228 >      painCave.severity = OPENMD_ERROR;
229 >      painCave.isFatal = 1;
230 >      simError();
231 >    }
232 >  } else if (args_info.rp2_given){
233 >    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
234 >  } else if (args_info.bo_given){
235 >    if (args_info.rcut_given) {
236 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
237 >                                        args_info.rcut_arg,
238 >                                        args_info.nbins_arg);
239 >    } else {
240 >      sprintf( painCave.errMsg,
241 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
242 >      painCave.severity = OPENMD_ERROR;
243 >      painCave.isFatal = 1;
244 >      simError();
245 >    }
246 >    
247 >  } else if (args_info.tet_param_given) {
248 >    if (args_info.rcut_given) {  
249 >      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
250 >                                         args_info.rcut_arg,
251 >                                         args_info.nbins_arg);
252 >    } else {
253 >      sprintf( painCave.errMsg,
254 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
255 >      painCave.severity = OPENMD_ERROR;
256 >      painCave.isFatal = 1;
257 >      simError();
258 >    }
259 >  } else if (args_info.tet_param_z_given) {
260 >    if (args_info.rcut_given) {  
261 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
262 >                                          args_info.rcut_arg,
263 >                                          args_info.nbins_arg);
264 >    } else {
265 >      sprintf( painCave.errMsg,
266 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
267 >      painCave.severity = OPENMD_ERROR;
268 >      painCave.isFatal = 1;
269 >      simError();
270 >    }
271 >  } else if (args_info.ior_given){
272 >    if (args_info.rcut_given) {
273 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
274 >                                    args_info.rcut_arg,
275 >                                    args_info.nbins_arg, maxLen);
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.for_given){
284 >    if (args_info.rcut_given) {
285 >      analyser = new FCCOfR(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,
297 >                                           args_info.rcut_arg,
298 >                                           args_info.nbins_arg);
299 >    } else {
300 >      sprintf( painCave.errMsg,
301 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
302 >      painCave.severity = OPENMD_ERROR;
303 >      painCave.isFatal = 1;
304 >      simError();
305 >    }
306 >  } else if (args_info.scd_given) {
307 >    if (batchMode) {
308 >      analyser  = new SCDOrderParameter(info, dumpFileName,
309 >                                        args_info.molname_arg,
310 >                                        args_info.begin_arg, args_info.end_arg);
311 >    } else{
312 >      std::string sele3 = args_info.sele3_arg;
313 >      analyser  = new SCDOrderParameter(info, dumpFileName,
314 >                                        sele1, sele2, sele3);
315 >    }
316 >  }else if (args_info.density_given) {
317 >    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
318 >                              args_info.nbins_arg);  
319 >  } else if (args_info.count_given) {
320 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
321 >  } else if (args_info.slab_density_given) {
322 >    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
323 >  } else if (args_info.rnemdz_given) {
324 >    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
325 >  } else if (args_info.rnemdr_given) {
326 >    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
327 >  } else if (args_info.rnemdrt_given) {
328 >    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
329 >                               args_info.nbins_arg, args_info.nanglebins_arg);
330 >  } else if (args_info.nitrile_given) {
331 >    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
332 >                                       args_info.nbins_arg);
333 >  } else if (args_info.p_angle_given) {
334 >    if (args_info.sele1_given) {    
335 >      if (args_info.sele2_given)
336 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
337 >                               args_info.nbins_arg);
338 >      else
339 >        if (args_info.seleoffset_given) {
340 >          if (args_info.seleoffset2_given) {
341 >            analyser  = new pAngle(info, dumpFileName, sele1,
342 >                                   args_info.seleoffset_arg,
343 >                                   args_info.seleoffset2_arg,
344 >                                   args_info.nbins_arg);
345 >          } else {
346 >            analyser  = new pAngle(info, dumpFileName, sele1,
347 >                                   args_info.seleoffset_arg,
348 >                                   args_info.nbins_arg);
349 >          }
350 >        } else
351 >          analyser  = new pAngle(info, dumpFileName, sele1,
352 >                                 args_info.nbins_arg);
353 >    } else {
354 >      sprintf( painCave.errMsg,
355 >               "At least one selection script (--sele1) must be specified when "
356 >               "calculating P(angle) distributions");
357 >      painCave.severity = OPENMD_ERROR;
358 >      painCave.isFatal = 1;
359 >      simError();
360 >    }
361   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
362 <    }else if (args_info.hxy_given) {
363 <        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
364 <                           args_info.nbins_y_arg, args_info.nbins_arg);
362 >  }else if (args_info.hxy_given) {
363 >    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
364 >                       args_info.nbins_y_arg, args_info.nbins_arg);
365   #endif
366 <    }else if (args_info.rho_r_given) {
367 <        if (args_info.radius_given){
368 <            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
369 <        }else{
370 <            sprintf( painCave.errMsg,
371 <                     "A particle radius (radius) must be specified when calculating Rho(r)");
372 <            painCave.severity = OPENMD_ERROR;
373 <            painCave.isFatal = 1;
374 <            simError();
286 <        }
287 <    }else if (args_info.hullvol_given) {
288 <        analyser = new NanoVolume(info, dumpFileName, sele1);
366 >  }else if (args_info.rho_r_given) {
367 >    if (args_info.radius_given){
368 >      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
369 >    }else{
370 >      sprintf( painCave.errMsg,
371 >               "A particle radius (radius) must be specified when calculating Rho(r)");
372 >      painCave.severity = OPENMD_ERROR;
373 >      painCave.isFatal = 1;
374 >      simError();
375      }
376 +  } else if (args_info.hullvol_given) {
377 +    analyser = new NanoVolume(info, dumpFileName, sele1);
378 +  } else if (args_info.rodlength_given) {
379 +    analyser = new NanoLength(info, dumpFileName, sele1);
380 +  } else if (args_info.angle_r_given) {
381 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
382 +  }
383    
384 <    if (args_info.output_given) {
385 <        analyser->setOutputName(args_info.output_arg);
386 <    }
387 <    if (args_info.step_given) {
388 <        analyser->setStep(args_info.step_arg);
389 <    }
390 <
391 <    analyser->process();
392 <
393 <    delete analyser;    
394 <    delete info;
395 <
396 <    return 0;  
384 >  if (args_info.output_given) {
385 >    analyser->setOutputName(args_info.output_arg);
386 >  }
387 >  if (args_info.step_given) {
388 >    analyser->setStep(args_info.step_arg);
389 >  }
390 >  
391 >  analyser->process();
392 >  
393 >  delete analyser;    
394 >  delete info;
395 >  
396 >  return 0;  
397   }
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