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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 1819 by gezelter, Thu Dec 13 16:57:39 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 119 | Line 118 | int main(int argc, char* argv[]){
118      if (sele2Env) {
119        sele2 = sele2Env;            
120      } else {
121 <      sele2 = "select all";
121 >      //If sele2 is not specified, then the default behavior
122 >      //should be what is already intended for sele1
123 >      sele2 = sele1;
124 >      //sele2 = "select all";
125      }
126    }
127    
# Line 187 | Line 189 | int main(int argc, char* argv[]){
189      maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
190      zmaxLen = hmat(2,2);    
191    }    
192 <
192 >  
193    StaticAnalyser* analyser;
194    if (args_info.gofr_given){
195      analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
196 <                       args_info.nbins_arg);        
196 >                       args_info.nbins_arg);        
197    } else if (args_info.gofz_given) {
198      analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
199 <                       args_info.nbins_arg);
199 >                       args_info.nbins_arg);
200    } else if (args_info.r_z_given) {
201      analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
202 <                          args_info.nbins_arg, args_info.nbins_z_arg);
202 >                          args_info.nbins_arg, args_info.nbins_z_arg);
203    } else if (args_info.r_theta_given) {
204      analyser  = new GofRTheta(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.r_omega_given) {
207      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
208 <                              args_info.nbins_arg, args_info.nanglebins_arg);
208 >                              args_info.nbins_arg, args_info.nanglebins_arg);
209    } else if (args_info.theta_omega_given) {
210      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
211 <                              args_info.nanglebins_arg);
211 >                              args_info.nanglebins_arg);
212    } else if (args_info.gxyz_given) {
213      if (args_info.refsele_given) {
214        analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
215 <                           maxLen, args_info.nbins_arg);        
215 >                           maxLen, args_info.nbins_arg);        
216      } else {
217        sprintf( painCave.errMsg,
218 <               "--refsele must set when --gxyz is used");
218 >               "--refsele must set when --gxyz is used");
219        painCave.severity = OPENMD_ERROR;
220        painCave.isFatal = 1;
221        simError();  
# Line 221 | Line 223 | int main(int argc, char* argv[]){
223    } else if (args_info.twodgofr_given){
224      if (args_info.dz_given) {
225        analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
226 <                             args_info.dz_arg, args_info.nbins_arg);        
226 >                             args_info.dz_arg, args_info.nbins_arg);        
227      } else {
228        sprintf( painCave.errMsg,
229 <               "A slab width (dz) must be specified when calculating TwoDGofR");
229 >               "A slab width (dz) must be specified when calculating TwoDGofR");
230        painCave.severity = OPENMD_ERROR;
231        painCave.isFatal = 1;
232        simError();
233 <    }
233 >    }    
234    } else if (args_info.p2_given) {
235 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
235 >    if (args_info.sele1_given) {    
236 >      if (args_info.sele2_given)
237 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
238 >      else
239 >        if (args_info.seleoffset_given)
240 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
241 >                                           args_info.seleoffset_arg);
242 >        else
243 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
244 >    } else {
245 >      sprintf( painCave.errMsg,
246 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
247 >      painCave.severity = OPENMD_ERROR;
248 >      painCave.isFatal = 1;
249 >      simError();
250 >    }
251    } else if (args_info.rp2_given){
252      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
253    } else if (args_info.bo_given){
254      if (args_info.rcut_given) {
255        analyser = new BondOrderParameter(info, dumpFileName, sele1,
256 <                                        args_info.rcut_arg,
257 <                                        args_info.nbins_arg);
256 >                                        args_info.rcut_arg,
257 >                                        args_info.nbins_arg);
258      } else {
259        sprintf( painCave.errMsg,
260 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
260 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
261        painCave.severity = OPENMD_ERROR;
262        painCave.isFatal = 1;
263        simError();
264      }
265 +    
266 +  } else if (args_info.tet_param_given) {
267 +    if (args_info.rcut_given) {  
268 +      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
269 +                                         args_info.rcut_arg,
270 +                                         args_info.nbins_arg);
271 +    } else {
272 +      sprintf( painCave.errMsg,
273 +               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
274 +      painCave.severity = OPENMD_ERROR;
275 +      painCave.isFatal = 1;
276 +      simError();
277 +    }
278 +  } else if (args_info.tet_param_z_given) {
279 +    if (args_info.rcut_given) {  
280 +      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
281 +                                         args_info.rcut_arg,
282 +                                         args_info.nbins_arg);
283 +    } else {
284 +      sprintf( painCave.errMsg,
285 +               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
286 +      painCave.severity = OPENMD_ERROR;
287 +      painCave.isFatal = 1;
288 +      simError();
289 +    }
290    } else if (args_info.bor_given){
291      if (args_info.rcut_given) {
292        analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
293 <                            args_info.nbins_arg, maxLen);
293 >                            args_info.nbins_arg, maxLen);
294      } else {
295        sprintf( painCave.errMsg,
296 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
296 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
297        painCave.severity = OPENMD_ERROR;
298        painCave.isFatal = 1;
299        simError();
# Line 259 | Line 301 | int main(int argc, char* argv[]){
301    } else if (args_info.bad_given){
302      if (args_info.rcut_given) {
303        analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
304 <                                           args_info.nbins_arg);
304 >                                           args_info.nbins_arg);
305      } else {
306        sprintf( painCave.errMsg,
307 <               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
307 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
308        painCave.severity = OPENMD_ERROR;
309        painCave.isFatal = 1;
310        simError();
311 <    }
311 >      }
312    } else if (args_info.scd_given) {
313      if (batchMode) {
314        analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
315 <                                        args_info.begin_arg, args_info.end_arg);
315 >                                        args_info.begin_arg, args_info.end_arg);
316      } else{
317        std::string sele3 = args_info.sele3_arg;
318        analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
319      }
320    }else if (args_info.density_given) {
321      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
322 <                              args_info.nbins_arg);  
322 >                              args_info.nbins_arg);  
323    } else if (args_info.count_given) {
324      analyser = new ObjectCount(info, dumpFileName, sele1 );
325    } else if (args_info.slab_density_given) {
# Line 287 | Line 329 | int main(int argc, char* argv[]){
329   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
330    }else if (args_info.hxy_given) {
331      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
332 <                       args_info.nbins_y_arg, args_info.nbins_arg);
332 >                       args_info.nbins_y_arg, args_info.nbins_arg);
333   #endif
334    }else if (args_info.rho_r_given) {
335      if (args_info.radius_given){
336        analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
337      }else{
338        sprintf( painCave.errMsg,
339 <               "A particle radius (radius) must be specified when calculating Rho(r)");
339 >               "A particle radius (radius) must be specified when calculating Rho(r)");
340        painCave.severity = OPENMD_ERROR;
341        painCave.isFatal = 1;
342        simError();
343      }
344 <  }else if (args_info.hullvol_given) {
344 >  } else if (args_info.hullvol_given) {
345      analyser = new NanoVolume(info, dumpFileName, sele1);
346 +  } else if (args_info.rodlength_given) {
347 +    analyser = new NanoLength(info, dumpFileName, sele1);
348 +  } else if (args_info.angle_r_given) {
349 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
350    }
351 <  
351 >    
352    if (args_info.output_given) {
353      analyser->setOutputName(args_info.output_arg);
354    }
355    if (args_info.step_given) {
356      analyser->setStep(args_info.step_arg);
357    }
358 <
358 >
359    analyser->process();
360 <
360 >  
361    delete analyser;    
362    delete info;
363  

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