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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 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1585 by gezelter, Sun Jun 19 17:51:15 2011 UTC

# 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/RhoAngleR.hpp"
79 + #include "applications/staticProps/TetrahedralityParam.hpp"
80  
81   using namespace OpenMD;
82  
# Line 78 | Line 84 | int main(int argc, char* argv[]){
84    
85    //register force fields
86    registerForceFields();
87 <
87 >  
88    gengetopt_args_info args_info;
89 <
89 >  
90    //parse the command line option
91    if (cmdline_parser (argc, argv, &args_info) != 0) {
92      exit(1) ;
93    }
94 <
94 >  
95    //get the dumpfile name
96    std::string dumpFileName = args_info.input_arg;
97    std::string sele1;
98    std::string sele2;
99    bool userSpecifiedSelect1;
100    bool userSpecifiedSelect2;
101 <
101 >  
102    // check the first selection argument, or set it to the environment
103    // variable, or failing that, set it to "select all"
104 <
104 >  
105    if (args_info.sele1_given) {
106      sele1 = args_info.sele1_arg;
107    } else {
# Line 106 | Line 112 | int main(int argc, char* argv[]){
112        sele1 = "select all";
113      }
114    }
115 <
115 >  
116    // check the second selection argument, or set it to the environment
117    // variable, or failing that, set it to "select all"
118    
# Line 120 | Line 126 | int main(int argc, char* argv[]){
126        sele2 = "select all";
127      }
128    }
129 <
130 <
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 <
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 <
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){
154      if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
# Line 164 | Line 170 | int main(int argc, char* argv[]){
170        painCave.severity = OPENMD_ERROR;
171        painCave.isFatal = 1;
172        simError();        
173 <    
173 >      
174      }
175    }
176 <
176 >  
177    //parse md file and set up the system
178    SimCreator creator;
179    std::cout << "dumpFile = " << dumpFileName << "\n";
180    SimInfo* info = creator.createSim(dumpFileName);
181  
182    RealType maxLen;
183 +  RealType zmaxLen;
184    if (args_info.length_given) {
185      maxLen = args_info.length_arg;
186 +    if (args_info.zlength_given){
187 +      zmaxLen = args_info.zlength_arg;
188 +    }
189    } else {
190      Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
191 <    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
191 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
192 >    zmaxLen = hmat(2,2);    
193    }    
194 <
194 >  
195    StaticAnalyser* analyser;
196    if (args_info.gofr_given){
197      analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
198 <                       args_info.nbins_arg);        
198 >                       args_info.nbins_arg);        
199    } else if (args_info.gofz_given) {
200      analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
201 <                       args_info.nbins_arg);
201 >                       args_info.nbins_arg);
202    } else if (args_info.r_z_given) {
203 <    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen,
204 <                              args_info.nbins_arg, args_info.nbins_z_arg);
203 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
204 >                          args_info.nbins_arg, args_info.nbins_z_arg);
205    } else if (args_info.r_theta_given) {
206      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
207 <                              args_info.nbins_arg, args_info.nanglebins_arg);
207 >                              args_info.nbins_arg, args_info.nanglebins_arg);
208    } else if (args_info.r_omega_given) {
209      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
210 <                              args_info.nbins_arg, args_info.nanglebins_arg);
210 >                              args_info.nbins_arg, args_info.nanglebins_arg);
211    } else if (args_info.theta_omega_given) {
212      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
213 <                              args_info.nanglebins_arg);
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,args_info.refsele_arg,
217 <                           maxLen, args_info.nbins_arg);        
217 >                           maxLen, args_info.nbins_arg);        
218      } else {
219        sprintf( painCave.errMsg,
220 <               "--refsele must set when --gxyz is used");
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    } else if (args_info.p2_given) {
237 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
237 >    if (args_info.sele1_given) {    
238 >      if (args_info.sele2_given)
239 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
240 >      else
241 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
242 >    } else {
243 >      sprintf( painCave.errMsg,
244 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
245 >      painCave.severity = OPENMD_ERROR;
246 >      painCave.isFatal = 1;
247 >      simError();
248 >    }
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);
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");
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 +    
264 +  } else if (args_info.tet_param_given) {
265 +    if (args_info.rcut_given) {  
266 +      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
267 +                                         args_info.rcut_arg,
268 +                                         args_info.nbins_arg);
269 +    } else {
270 +      sprintf( painCave.errMsg,
271 +               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
272 +      painCave.severity = OPENMD_ERROR;
273 +      painCave.isFatal = 1;
274 +      simError();
275 +    }
276    } else if (args_info.bor_given){
277      if (args_info.rcut_given) {
278        analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
279                              args_info.nbins_arg, maxLen);
280      } else {
281        sprintf( painCave.errMsg,
282 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
282 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
283        painCave.severity = OPENMD_ERROR;
284        painCave.isFatal = 1;
285        simError();
# Line 241 | Line 287 | int main(int argc, char* argv[]){
287    } else if (args_info.bad_given){
288      if (args_info.rcut_given) {
289        analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
290 <                            args_info.nbins_arg);
290 >                                           args_info.nbins_arg);
291      } else {
292        sprintf( painCave.errMsg,
293 <               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
293 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
294        painCave.severity = OPENMD_ERROR;
295        painCave.isFatal = 1;
296        simError();
297 <    }
297 >      }
298    } else if (args_info.scd_given) {
299      if (batchMode) {
300        analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
301 <                                        args_info.begin_arg, args_info.end_arg);
301 >                                        args_info.begin_arg, args_info.end_arg);
302      } else{
303        std::string sele3 = args_info.sele3_arg;
304        analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
305      }
306    }else if (args_info.density_given) {
307      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
308 <                              args_info.nbins_arg);  
308 >                              args_info.nbins_arg);  
309 >  } else if (args_info.count_given) {
310 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
311    } else if (args_info.slab_density_given) {
312      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
313    } else if (args_info.p_angle_given) {
# Line 267 | Line 315 | int main(int argc, char* argv[]){
315   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
316    }else if (args_info.hxy_given) {
317      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
318 <                       args_info.nbins_y_arg, args_info.nbins_arg);
318 >                       args_info.nbins_y_arg, args_info.nbins_arg);
319   #endif
320    }else if (args_info.rho_r_given) {
321      if (args_info.radius_given){
322        analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
323      }else{
324        sprintf( painCave.errMsg,
325 <               "A particle radius (radius) must be specified when calculating Rho(r)");
325 >               "A particle radius (radius) must be specified when calculating Rho(r)");
326        painCave.severity = OPENMD_ERROR;
327        painCave.isFatal = 1;
328        simError();
329      }
330 <        }else if (args_info.hullvol_given) {
330 >  } else if (args_info.hullvol_given) {
331      analyser = new NanoVolume(info, dumpFileName, sele1);
332 +  } else if (args_info.rodlength_given) {
333 +    analyser = new NanoLength(info, dumpFileName, sele1);
334 +  } else if (args_info.angle_r_given) {
335 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
336    }
337 <  
337 >    
338    if (args_info.output_given) {
339      analyser->setOutputName(args_info.output_arg);
340    }
341    if (args_info.step_given) {
342      analyser->setStep(args_info.step_arg);
343    }
344 <
344 >  
345    analyser->process();
346 <
346 >  
347    delete analyser;    
348    delete info;
349  

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