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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 1999 by gezelter, Sat May 31 21:00:46 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 + #include "applications/staticProps/MultipoleSum.hpp"
83  
84   using namespace OpenMD;
85  
86   int main(int argc, char* argv[]){
87    
88 <    //register force fields
89 <    registerForceFields();
90 <
91 <    gengetopt_args_info args_info;
92 <
93 <    //parse the command line option
94 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
95 <        exit(1) ;
96 <    }
97 <
98 <    //get the dumpfile name
99 <    std::string dumpFileName = args_info.input_arg;
100 <    std::string sele1;
101 <    std::string sele2;
102 <    bool userSpecifiedSelect1;
103 <    bool userSpecifiedSelect2;
104 <
105 <    // check the first selection argument, or set it to the environment
106 <    // variable, or failing that, set it to "select all"
107 <
108 <    if (args_info.sele1_given) {
109 <        sele1 = args_info.sele1_arg;
88 >  
89 >  gengetopt_args_info args_info;
90 >  
91 >  //parse the command line option
92 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
93 >    exit(1) ;
94 >  }
95 >  
96 >  //get the dumpfile name
97 >  std::string dumpFileName = args_info.input_arg;
98 >  std::string sele1;
99 >  std::string sele2;
100 >  
101 >  // check the first selection argument, or set it to the environment
102 >  // variable, or failing that, set it to "select all"
103 >  
104 >  if (args_info.sele1_given) {
105 >    sele1 = args_info.sele1_arg;
106 >  } else {
107 >    char*  sele1Env= getenv("SELECTION1");
108 >    if (sele1Env) {
109 >      sele1 = sele1Env;
110      } else {
111 <        char*  sele1Env= getenv("SELECTION1");
103 <        if (sele1Env) {
104 <            sele1 = sele1Env;
105 <        } else {
106 <            sele1 = "select all";
107 <        }
111 >      sele1 = "select all";
112      }
113 <
110 <    // check the second selection argument, or set it to the environment
111 <    // variable, or failing that, set it to "select all"
113 >  }
114    
115 <    if (args_info.sele2_given) {
116 <        sele2 = args_info.sele2_arg;
117 <    } else {
118 <        char* sele2Env = getenv("SELECTION1");
119 <        if (sele2Env) {
120 <            sele2 = sele2Env;            
121 <        } else {
122 <            sele2 = "select all";
123 <        }
115 >  // check the second selection argument, or set it to the environment
116 >  // variable, or failing that, set it to the first selection
117 >  
118 >  if (args_info.sele2_given) {
119 >    sele2 = args_info.sele2_arg;
120 >  } else {
121 >    char* sele2Env = getenv("SELECTION2");
122 >    if (sele2Env) {
123 >      sele2 = sele2Env;            
124 >    } else {
125 >      //If sele2 is not specified, then the default behavior
126 >      //should be what is already intended for sele1
127 >      sele2 = sele1;
128      }
129 +  }
130  
131 <
132 <    // Problems if sele1 wasn't specified, but
133 < // if (!args_info.scd_given) {
134 < //       sprintf( painCave.errMsg,
135 < //                "neither --sele1 option nor $SELECTION1 is set");
136 < //       painCave.severity = OPENMD_ERROR;
137 < //       painCave.isFatal = 1;
138 < //       simError();
139 < //     }
140 < //   }
141 <
142 <    // Problems if sele1 wasn't specified
143 <
144 < //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
145 < //       sprintf( painCave.errMsg,
146 < //                "neither --sele2 option nor $SELECTION1 is set");
147 < //       painCave.severity = OPENMD_ERROR;
148 < //       painCave.isFatal = 1;
149 < //       simError();        
150 < //     }
151 < //   }
152 <
153 <    bool batchMode;
154 <    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 <        }
131 >  bool batchMode;
132 >  if (args_info.scd_given){
133 >    if (args_info.sele1_given &&
134 >        args_info.sele2_given && args_info.sele3_given) {
135 >      batchMode = false;
136 >    } else if (args_info.molname_given &&
137 >               args_info.begin_given && args_info.end_given) {
138 >      if (args_info.begin_arg < 0 ||
139 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
140 >        sprintf( painCave.errMsg,
141 >                 "below conditions are not satisfied:\n"
142 >                 "0 <= begin && 0<= end && begin <= end-2\n");
143 >        painCave.severity = OPENMD_ERROR;
144 >        painCave.isFatal = 1;
145 >        simError();                    
146 >      }
147 >      batchMode = true;        
148 >    } else{
149 >      sprintf( painCave.errMsg,
150 >               "either --sele1, --sele2, --sele3 are specified,"
151 >               " or --molname, --begin, --end are specified\n");
152 >      painCave.severity = OPENMD_ERROR;
153 >      painCave.isFatal = 1;
154 >      simError();
155      }
156 +  }
157 +  
158 +  //parse md file and set up the system
159 +  SimCreator creator;
160 +  SimInfo* info = creator.createSim(dumpFileName);
161  
162 <    //parse md file and set up the system
163 <    SimCreator creator;
164 <    std::cout << "dumpFile = " << dumpFileName << "\n";
165 <    SimInfo* info = creator.createSim(dumpFileName);
166 <
167 <    RealType maxLen;
168 <    RealType zmaxLen;
169 <    if (args_info.length_given) {
170 <        maxLen = args_info.length_arg;
171 <        if (args_info.zlength_given){
172 <            zmaxLen = args_info.zlength_arg;
173 <        }
162 >  RealType maxLen;
163 >  RealType zmaxLen;
164 >  if (args_info.length_given) {
165 >    maxLen = args_info.length_arg;
166 >    if (args_info.zlength_given){
167 >      zmaxLen = args_info.zlength_arg;
168 >    }
169 >  } else {
170 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
171 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
172 >    zmaxLen = hmat(2,2);    
173 >  }    
174 >  
175 >  StaticAnalyser* analyser;
176 >  if (args_info.gofr_given){
177 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
178 >                       args_info.nbins_arg);        
179 >  } else if (args_info.gofz_given) {
180 >    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
181 >                       args_info.nbins_arg);
182 >  } else if (args_info.r_z_given) {
183 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
184 >                          args_info.nbins_arg, args_info.nbins_z_arg);
185 >  } else if (args_info.r_theta_given) {
186 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
187 >                              args_info.nbins_arg, args_info.nanglebins_arg);
188 >  } else if (args_info.r_omega_given) {
189 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
190 >                              args_info.nbins_arg, args_info.nanglebins_arg);
191 >  } else if (args_info.theta_omega_given) {
192 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
193 >                              args_info.nanglebins_arg);
194 >  } else if (args_info.gxyz_given) {
195 >    if (args_info.refsele_given) {
196 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
197 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
198      } else {
199 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
200 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
201 <        zmaxLen = hmat(2,2);    
199 >      sprintf( painCave.errMsg,
200 >               "--refsele must set when --gxyz is used");
201 >      painCave.severity = OPENMD_ERROR;
202 >      painCave.isFatal = 1;
203 >      simError();  
204 >    }
205 >  } else if (args_info.twodgofr_given){
206 >    if (args_info.dz_given) {
207 >      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
208 >                             args_info.dz_arg, args_info.nbins_arg);        
209 >    } else {
210 >      sprintf( painCave.errMsg,
211 >               "A slab width (dz) must be specified when calculating TwoDGofR");
212 >      painCave.severity = OPENMD_ERROR;
213 >      painCave.isFatal = 1;
214 >      simError();
215      }    
216 <
217 <    StaticAnalyser* analyser;
218 <    if (args_info.gofr_given){
219 <        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
220 <                           args_info.nbins_arg);        
221 <    } else if (args_info.gofz_given) {
222 <        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
223 <                           args_info.nbins_arg);
224 <    } else if (args_info.r_z_given) {
225 <        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
226 <                              args_info.nbins_arg, args_info.nbins_z_arg);
227 <    } else if (args_info.r_theta_given) {
228 <        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
229 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
230 <    } else if (args_info.r_omega_given) {
231 <        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
232 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
233 <    } else if (args_info.theta_omega_given) {
234 <        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
235 <                                  args_info.nanglebins_arg);
236 <    } else if (args_info.gxyz_given) {
237 <        if (args_info.refsele_given) {
238 <            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
239 <                                 maxLen, args_info.nbins_arg);        
240 <        } else {
241 <            sprintf( painCave.errMsg,
242 <                     "--refsele must set when --gxyz is used");
243 <            painCave.severity = OPENMD_ERROR;
244 <            painCave.isFatal = 1;
245 <            simError();  
246 <        }
247 <    } else if (args_info.p2_given) {
248 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
249 <    } else if (args_info.rp2_given){
250 <        analyser = new RippleOP(info, dumpFileName, sele1, sele2);
251 <    } else if (args_info.bo_given){
252 <        if (args_info.rcut_given) {
253 <            analyser = new BondOrderParameter(info, dumpFileName, sele1,
254 <                                              args_info.rcut_arg,
255 <                                              args_info.nbins_arg);
256 <        } else {
257 <            sprintf( painCave.errMsg,
258 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
259 <            painCave.severity = OPENMD_ERROR;
260 <            painCave.isFatal = 1;
261 <            simError();
262 <        }
263 <    } else if (args_info.bor_given){
264 <        if (args_info.rcut_given) {
265 <            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
266 <                                  args_info.nbins_arg, maxLen);
267 <        } else {
268 <            sprintf( painCave.errMsg,
269 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
270 <            painCave.severity = OPENMD_ERROR;
271 <            painCave.isFatal = 1;
272 <            simError();
273 <        }
274 <    } else if (args_info.bad_given){
275 <        if (args_info.rcut_given) {
276 <            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
277 <                                                 args_info.nbins_arg);
278 <        } else {
279 <            sprintf( painCave.errMsg,
280 <                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
281 <            painCave.severity = OPENMD_ERROR;
282 <            painCave.isFatal = 1;
283 <            simError();
284 <        }
285 <    } else if (args_info.scd_given) {
286 <        if (batchMode) {
287 <            analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
288 <                                              args_info.begin_arg, args_info.end_arg);
289 <        } else{
290 <            std::string sele3 = args_info.sele3_arg;
291 <            analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
292 <        }
293 <    }else if (args_info.density_given) {
294 <        analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
295 <                                  args_info.nbins_arg);  
296 <    } else if (args_info.slab_density_given) {
297 <        analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
298 <    } else if (args_info.p_angle_given) {
299 <        analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
216 >  } else if (args_info.p2_given) {
217 >    if (args_info.sele1_given) {    
218 >      if (args_info.sele2_given)
219 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
220 >      else
221 >        if (args_info.seleoffset_given)
222 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
223 >                                           args_info.seleoffset_arg);
224 >        else
225 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
226 >    } else {
227 >      sprintf( painCave.errMsg,
228 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
229 >      painCave.severity = OPENMD_ERROR;
230 >      painCave.isFatal = 1;
231 >      simError();
232 >    }
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.multipole_given){
248 >    analyser = new MultipoleSum(info, dumpFileName, sele1,
249 >                                maxLen, args_info.nbins_arg);
250 >  } else if (args_info.tet_param_given) {
251 >    if (args_info.rcut_given) {  
252 >      analyser = new TetrahedralityParam(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 Tetrahedrality Parameters");
258 >      painCave.severity = OPENMD_ERROR;
259 >      painCave.isFatal = 1;
260 >      simError();
261 >    }
262 >  } else if (args_info.tet_param_z_given) {
263 >    if (args_info.rcut_given) {  
264 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
265 >                                          args_info.rcut_arg,
266 >                                          args_info.nbins_arg);
267 >    } else {
268 >      sprintf( painCave.errMsg,
269 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
270 >      painCave.severity = OPENMD_ERROR;
271 >      painCave.isFatal = 1;
272 >      simError();
273 >    }
274 >  } else if (args_info.ior_given){
275 >    if (args_info.rcut_given) {
276 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
277 >                                    args_info.rcut_arg,
278 >                                    args_info.nbins_arg, maxLen);
279 >    } else {
280 >      sprintf( painCave.errMsg,
281 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
282 >      painCave.severity = OPENMD_ERROR;
283 >      painCave.isFatal = 1;
284 >      simError();
285 >    }
286 >  } else if (args_info.for_given){
287 >    if (args_info.rcut_given) {
288 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
289 >                            args_info.nbins_arg, maxLen);
290 >    } else {
291 >      sprintf( painCave.errMsg,
292 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
293 >      painCave.severity = OPENMD_ERROR;
294 >      painCave.isFatal = 1;
295 >      simError();
296 >    }
297 >  } else if (args_info.bad_given){
298 >    if (args_info.rcut_given) {
299 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
300 >                                           args_info.rcut_arg,
301 >                                           args_info.nbins_arg);
302 >    } else {
303 >      sprintf( painCave.errMsg,
304 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
305 >      painCave.severity = OPENMD_ERROR;
306 >      painCave.isFatal = 1;
307 >      simError();
308 >    }
309 >  } else if (args_info.scd_given) {
310 >    if (batchMode) {
311 >      analyser  = new SCDOrderParameter(info, dumpFileName,
312 >                                        args_info.molname_arg,
313 >                                        args_info.begin_arg, args_info.end_arg);
314 >    } else{
315 >      std::string sele3 = args_info.sele3_arg;
316 >      analyser  = new SCDOrderParameter(info, dumpFileName,
317 >                                        sele1, sele2, sele3);
318 >    }
319 >  }else if (args_info.density_given) {
320 >    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
321 >                              args_info.nbins_arg);  
322 >  } else if (args_info.count_given) {
323 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
324 >  } else if (args_info.slab_density_given) {
325 >    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
326 >  } else if (args_info.rnemdz_given) {
327 >    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
328 >  } else if (args_info.rnemdr_given) {
329 >    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
330 >  } else if (args_info.rnemdrt_given) {
331 >    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
332 >                               args_info.nbins_arg, args_info.nanglebins_arg);
333 >  } else if (args_info.nitrile_given) {
334 >    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
335 >                                       args_info.nbins_arg);
336 >  } else if (args_info.p_angle_given) {
337 >    if (args_info.sele1_given) {    
338 >      if (args_info.sele2_given)
339 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
340 >                               args_info.nbins_arg);
341 >      else
342 >        if (args_info.seleoffset_given) {
343 >          if (args_info.seleoffset2_given) {
344 >            analyser  = new pAngle(info, dumpFileName, sele1,
345 >                                   args_info.seleoffset_arg,
346 >                                   args_info.seleoffset2_arg,
347 >                                   args_info.nbins_arg);
348 >          } else {
349 >            analyser  = new pAngle(info, dumpFileName, sele1,
350 >                                   args_info.seleoffset_arg,
351 >                                   args_info.nbins_arg);
352 >          }
353 >        } else
354 >          analyser  = new pAngle(info, dumpFileName, sele1,
355 >                                 args_info.nbins_arg);
356 >    } else {
357 >      sprintf( painCave.errMsg,
358 >               "At least one selection script (--sele1) must be specified when "
359 >               "calculating P(angle) distributions");
360 >      painCave.severity = OPENMD_ERROR;
361 >      painCave.isFatal = 1;
362 >      simError();
363 >    }
364   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
365 <    }else if (args_info.hxy_given) {
366 <        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
367 <                           args_info.nbins_y_arg, args_info.nbins_arg);
365 >  }else if (args_info.hxy_given) {
366 >    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
367 >                       args_info.nbins_y_arg, args_info.nbins_arg);
368   #endif
369 <    }else if (args_info.rho_r_given) {
370 <        if (args_info.radius_given){
371 <            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
372 <        }else{
373 <            sprintf( painCave.errMsg,
374 <                     "A particle radius (radius) must be specified when calculating Rho(r)");
375 <            painCave.severity = OPENMD_ERROR;
376 <            painCave.isFatal = 1;
377 <            simError();
286 <        }
287 <    }else if (args_info.hullvol_given) {
288 <        analyser = new NanoVolume(info, dumpFileName, sele1);
369 >  }else if (args_info.rho_r_given) {
370 >    if (args_info.radius_given){
371 >      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
372 >    }else{
373 >      sprintf( painCave.errMsg,
374 >               "A particle radius (radius) must be specified when calculating Rho(r)");
375 >      painCave.severity = OPENMD_ERROR;
376 >      painCave.isFatal = 1;
377 >      simError();
378      }
379 +  } else if (args_info.hullvol_given) {
380 +    analyser = new NanoVolume(info, dumpFileName, sele1);
381 +  } else if (args_info.rodlength_given) {
382 +    analyser = new NanoLength(info, dumpFileName, sele1);
383 +  } else if (args_info.angle_r_given) {
384 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
385 +  }
386    
387 <    if (args_info.output_given) {
388 <        analyser->setOutputName(args_info.output_arg);
389 <    }
390 <    if (args_info.step_given) {
391 <        analyser->setStep(args_info.step_arg);
392 <    }
393 <
394 <    analyser->process();
395 <
396 <    delete analyser;    
397 <    delete info;
398 <
399 <    return 0;  
387 >  if (args_info.output_given) {
388 >    analyser->setOutputName(args_info.output_arg);
389 >  }
390 >  if (args_info.step_given) {
391 >    analyser->setStep(args_info.step_arg);
392 >  }
393 >  
394 >  analyser->process();
395 >  
396 >  delete analyser;    
397 >  delete info;
398 >  
399 >  return 0;  
400   }
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