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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 1513 by gezelter, Tue Oct 19 18:40:54 2010 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

# Line 36 | Line 36
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).                        
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 69 | Line 69
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 <
77 > #include "applications/staticProps/AngleR.hpp"
78 > #include "applications/staticProps/TetrahedralityParam.hpp"
79 > #include "applications/staticProps/TetrahedralityParamZ.hpp"
80   using namespace OpenMD;
81  
82   int main(int argc, char* argv[]){
83    
81 –  //register force fields
82 –  registerForceFields();
84    
85    gengetopt_args_info args_info;
86    
# Line 92 | Line 93 | int main(int argc, char* argv[]){
93    std::string dumpFileName = args_info.input_arg;
94    std::string sele1;
95    std::string sele2;
95 –  bool userSpecifiedSelect1;
96 –  bool userSpecifiedSelect2;
96    
97    // check the first selection argument, or set it to the environment
98    // variable, or failing that, set it to "select all"
# Line 187 | Line 186 | int main(int argc, char* argv[]){
186      maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
187      zmaxLen = hmat(2,2);    
188    }    
189 <
189 >  
190    StaticAnalyser* analyser;
191    if (args_info.gofr_given){
192      analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
193 <                       args_info.nbins_arg);        
193 >                       args_info.nbins_arg);        
194    } else if (args_info.gofz_given) {
195      analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
196 <                       args_info.nbins_arg);
196 >                       args_info.nbins_arg);
197    } else if (args_info.r_z_given) {
198      analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
199 <                          args_info.nbins_arg, args_info.nbins_z_arg);
199 >                          args_info.nbins_arg, args_info.nbins_z_arg);
200    } else if (args_info.r_theta_given) {
201      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
202 <                              args_info.nbins_arg, args_info.nanglebins_arg);
202 >                              args_info.nbins_arg, args_info.nanglebins_arg);
203    } else if (args_info.r_omega_given) {
204      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205 <                              args_info.nbins_arg, args_info.nanglebins_arg);
205 >                              args_info.nbins_arg, args_info.nanglebins_arg);
206    } else if (args_info.theta_omega_given) {
207      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
208 <                              args_info.nanglebins_arg);
208 >                              args_info.nanglebins_arg);
209    } else if (args_info.gxyz_given) {
210      if (args_info.refsele_given) {
211        analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
212 <                           maxLen, args_info.nbins_arg);        
212 >                           maxLen, args_info.nbins_arg);        
213      } else {
214        sprintf( painCave.errMsg,
215 <               "--refsele must set when --gxyz is used");
215 >               "--refsele must set when --gxyz is used");
216        painCave.severity = OPENMD_ERROR;
217        painCave.isFatal = 1;
218        simError();  
# Line 221 | Line 220 | int main(int argc, char* argv[]){
220    } else if (args_info.twodgofr_given){
221      if (args_info.dz_given) {
222        analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
223 <                             args_info.dz_arg, args_info.nbins_arg);        
223 >                             args_info.dz_arg, args_info.nbins_arg);        
224      } else {
225        sprintf( painCave.errMsg,
226 <               "A slab width (dz) must be specified when calculating TwoDGofR");
226 >               "A slab width (dz) must be specified when calculating TwoDGofR");
227        painCave.severity = OPENMD_ERROR;
228        painCave.isFatal = 1;
229        simError();
230 <    }
230 >    }    
231    } else if (args_info.p2_given) {
232 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
232 >    if (args_info.sele1_given) {    
233 >      if (args_info.sele2_given)
234 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
235 >      else
236 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
237 >    } else {
238 >      sprintf( painCave.errMsg,
239 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
240 >      painCave.severity = OPENMD_ERROR;
241 >      painCave.isFatal = 1;
242 >      simError();
243 >    }
244    } else if (args_info.rp2_given){
245      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
246    } else if (args_info.bo_given){
247      if (args_info.rcut_given) {
248        analyser = new BondOrderParameter(info, dumpFileName, sele1,
249 <                                        args_info.rcut_arg,
250 <                                        args_info.nbins_arg);
249 >                                        args_info.rcut_arg,
250 >                                        args_info.nbins_arg);
251      } else {
252        sprintf( painCave.errMsg,
253 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
253 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
254        painCave.severity = OPENMD_ERROR;
255        painCave.isFatal = 1;
256        simError();
257      }
258 +    
259 +  } else if (args_info.tet_param_given) {
260 +    if (args_info.rcut_given) {  
261 +      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
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.tet_param_z_given) {
272 +    if (args_info.rcut_given) {  
273 +      analyser = new TetrahedralityParamZ(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 Tetrahedrality 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);
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");
289 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
290        painCave.severity = OPENMD_ERROR;
291        painCave.isFatal = 1;
292        simError();
# Line 259 | Line 294 | int main(int argc, char* argv[]){
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);
297 >                                           args_info.nbins_arg);
298      } else {
299        sprintf( painCave.errMsg,
300 <               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
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 <    }
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);
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);  
315 >                              args_info.nbins_arg);  
316    } else if (args_info.count_given) {
317      analyser = new ObjectCount(info, dumpFileName, sele1 );
318    } else if (args_info.slab_density_given) {
# Line 287 | Line 322 | int main(int argc, char* argv[]){
322   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
323    }else if (args_info.hxy_given) {
324      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
325 <                       args_info.nbins_y_arg, args_info.nbins_arg);
325 >                       args_info.nbins_y_arg, args_info.nbins_arg);
326   #endif
327    }else if (args_info.rho_r_given) {
328      if (args_info.radius_given){
329        analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
330      }else{
331        sprintf( painCave.errMsg,
332 <               "A particle radius (radius) must be specified when calculating Rho(r)");
332 >               "A particle radius (radius) must be specified when calculating Rho(r)");
333        painCave.severity = OPENMD_ERROR;
334        painCave.isFatal = 1;
335        simError();
336      }
337 <  }else if (args_info.hullvol_given) {
337 >  } else if (args_info.hullvol_given) {
338      analyser = new NanoVolume(info, dumpFileName, sele1);
339 +  } else if (args_info.rodlength_given) {
340 +    analyser = new NanoLength(info, dumpFileName, sele1);
341 +  } else if (args_info.angle_r_given) {
342 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
343    }
344 <  
344 >    
345    if (args_info.output_given) {
346      analyser->setOutputName(args_info.output_arg);
347    }
348    if (args_info.step_given) {
349      analyser->setStep(args_info.step_arg);
350    }
351 <
351 >
352    analyser->process();
353 <
353 >  
354    delete analyser;    
355    delete info;
356  

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