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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 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC vs.
Revision 2031 by jmichalk, Fri Oct 31 18:40:40 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).          
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   */
# Line 77 | Line 77
77   #include "applications/staticProps/AngleR.hpp"
78   #include "applications/staticProps/TetrahedralityParam.hpp"
79   #include "applications/staticProps/TetrahedralityParamZ.hpp"
80 + #include "applications/staticProps/TetrahedralityParamXYZ.hpp"
81 + #include "applications/staticProps/RNEMDStats.hpp"
82 + #include "applications/staticProps/NitrileFrequencyMap.hpp"
83 + #include "applications/staticProps/MultipoleSum.hpp"
84 + #include "applications/staticProps/SurfaceDiffusion.hpp"
85 +
86   using namespace OpenMD;
87  
88   int main(int argc, char* argv[]){
# Line 93 | Line 99 | int main(int argc, char* argv[]){
99    std::string dumpFileName = args_info.input_arg;
100    std::string sele1;
101    std::string sele2;
102 +  std::string sele3;
103    
104    // check the first selection argument, or set it to the environment
105    // variable, or failing that, set it to "select all"
# Line 109 | Line 116 | int main(int argc, char* argv[]){
116    }
117    
118    // check the second selection argument, or set it to the environment
119 <  // variable, or failing that, set it to "select all"
119 >  // variable, or failing that, set it to the first selection
120    
121    if (args_info.sele2_given) {
122      sele2 = args_info.sele2_arg;
123    } else {
124 <    char* sele2Env = getenv("SELECTION1");
124 >    char* sele2Env = getenv("SELECTION2");
125      if (sele2Env) {
126        sele2 = sele2Env;            
127      } else {
128 <      //It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
129 <      //should not be 'select all' but rather what is already intended for sele1
123 <      //JRM 8/22/12
128 >      //If sele2 is not specified, then the default behavior
129 >      //should be what is already intended for sele1
130        sele2 = sele1;
125 –      //sele2 = "select all";
131      }
132    }
133 <  
134 <  
135 <  // Problems if sele1 wasn't specified, but
136 <  // if (!args_info.scd_given) {
137 <  //       sprintf( painCave.errMsg,
138 <  //                "neither --sele1 option nor $SELECTION1 is set");
134 <  //       painCave.severity = OPENMD_ERROR;
135 <  //       painCave.isFatal = 1;
136 <  //       simError();
137 <  //     }
138 <  //   }
139 <  
140 <  // Problems if sele1 wasn't specified
141 <  
142 <  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
143 <  //       sprintf( painCave.errMsg,
144 <  //                "neither --sele2 option nor $SELECTION1 is set");
145 <  //       painCave.severity = OPENMD_ERROR;
146 <  //       painCave.isFatal = 1;
147 <  //       simError();        
148 <  //     }
149 <  //   }
150 <  
133 >
134 >  // check the third selection argument, which is only set if
135 >  // requested by the user
136 >
137 >  if (args_info.sele3_given) sele3 = args_info.sele3_arg;
138 >
139    bool batchMode;
140    if (args_info.scd_given){
141 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
141 >    if (args_info.sele1_given &&
142 >        args_info.sele2_given && args_info.sele3_given) {
143        batchMode = false;
144 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
145 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
144 >    } else if (args_info.molname_given &&
145 >               args_info.begin_given && args_info.end_given) {
146 >      if (args_info.begin_arg < 0 ||
147 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
148          sprintf( painCave.errMsg,
149                   "below conditions are not satisfied:\n"
150                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 168 | Line 159 | int main(int argc, char* argv[]){
159                 " or --molname, --begin, --end are specified\n");
160        painCave.severity = OPENMD_ERROR;
161        painCave.isFatal = 1;
162 <      simError();        
172 <      
162 >      simError();
163      }
164    }
165    
166    //parse md file and set up the system
167    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
168    SimInfo* info = creator.createSim(dumpFileName);
169  
170    RealType maxLen;
# Line 202 | Line 191 | int main(int argc, char* argv[]){
191      analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
192                            args_info.nbins_arg, args_info.nbins_z_arg);
193    } else if (args_info.r_theta_given) {
194 <    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
195 <                              args_info.nbins_arg, args_info.nanglebins_arg);
194 >    if (args_info.sele3_given)
195 >      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
196 >                                args_info.nbins_arg, args_info.nanglebins_arg);
197 >    else
198 >      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
199 >                                args_info.nbins_arg, args_info.nanglebins_arg);
200    } else if (args_info.r_omega_given) {
201 <    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
202 <                              args_info.nbins_arg, args_info.nanglebins_arg);
201 >    if (args_info.sele3_given)
202 >      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
203 >                                args_info.nbins_arg, args_info.nanglebins_arg);
204 >    else
205 >      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
206 >                                args_info.nbins_arg, args_info.nanglebins_arg);
207 >
208    } else if (args_info.theta_omega_given) {
209 <    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
210 <                              args_info.nanglebins_arg);
209 >    if (args_info.sele3_given)
210 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
211 >                                args_info.nanglebins_arg);
212 >    else
213 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
214 >                                args_info.nanglebins_arg);
215    } else if (args_info.gxyz_given) {
216      if (args_info.refsele_given) {
217 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
218 <                           maxLen, args_info.nbins_arg);        
217 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
218 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
219      } else {
220        sprintf( painCave.errMsg,
221                 "--refsele must set when --gxyz is used");
# Line 237 | Line 239 | int main(int argc, char* argv[]){
239        if (args_info.sele2_given)
240          analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
241        else
242 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
242 >        if (args_info.seleoffset_given)
243 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
244 >                                           args_info.seleoffset_arg);
245 >        else
246 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
247      } else {
248        sprintf( painCave.errMsg,
249                 "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
# Line 259 | Line 265 | int main(int argc, char* argv[]){
265        painCave.isFatal = 1;
266        simError();
267      }
268 <    
268 >  } else if (args_info.multipole_given){
269 >    analyser = new MultipoleSum(info, dumpFileName, sele1,
270 >                                maxLen, args_info.nbins_arg);
271    } else if (args_info.tet_param_given) {
272      if (args_info.rcut_given) {  
273        analyser = new TetrahedralityParam(info, dumpFileName, sele1,
# Line 274 | Line 282 | int main(int argc, char* argv[]){
282      }
283    } else if (args_info.tet_param_z_given) {
284      if (args_info.rcut_given) {  
285 <      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
286 <                                         args_info.rcut_arg,
287 <                                         args_info.nbins_arg);
285 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
286 >                                          args_info.rcut_arg,
287 >                                          args_info.nbins_arg);
288      } else {
289        sprintf( painCave.errMsg,
290                 "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
# Line 284 | Line 292 | int main(int argc, char* argv[]){
292        painCave.isFatal = 1;
293        simError();
294      }
295 <  } else if (args_info.bor_given){
295 >  } else if (args_info.tet_param_xyz_given) {
296 >    if (!args_info.rcut_given) {
297 >      sprintf( painCave.errMsg,
298 >               "A cutoff radius (rcut) must be specified when calculating"
299 >               " Tetrahedrality Parameters");
300 >      painCave.severity = OPENMD_ERROR;
301 >      painCave.isFatal = 1;
302 >      simError();
303 >    }
304 >    if (!args_info.voxelSize_given) {
305 >      sprintf( painCave.errMsg,
306 >               "A voxel size must be specified when calculating"
307 >               " volume-resolved Tetrahedrality Parameters");
308 >      painCave.severity = OPENMD_ERROR;
309 >      painCave.isFatal = 1;
310 >      simError();
311 >    }
312 >    if (!args_info.gaussWidth_given) {
313 >      sprintf( painCave.errMsg,
314 >               "A gaussian width must be specified when calculating"
315 >               " volume-resolved Tetrahedrality Parameters");
316 >      painCave.severity = OPENMD_ERROR;
317 >      painCave.isFatal = 1;
318 >      simError();
319 >    }
320 >    analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
321 >                                          args_info.rcut_arg,
322 >                                          args_info.voxelSize_arg,
323 >                                          args_info.gaussWidth_arg);
324 >  } else if (args_info.ior_given){
325      if (args_info.rcut_given) {
326 <      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
326 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
327 >                                    args_info.rcut_arg,
328 >                                    args_info.nbins_arg, maxLen);
329 >    } else {
330 >      sprintf( painCave.errMsg,
331 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
332 >      painCave.severity = OPENMD_ERROR;
333 >      painCave.isFatal = 1;
334 >      simError();
335 >    }
336 >  } else if (args_info.for_given){
337 >    if (args_info.rcut_given) {
338 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
339                              args_info.nbins_arg, maxLen);
340      } else {
341        sprintf( painCave.errMsg,
# Line 297 | Line 346 | int main(int argc, char* argv[]){
346      }
347    } else if (args_info.bad_given){
348      if (args_info.rcut_given) {
349 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
349 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
350 >                                           args_info.rcut_arg,
351                                             args_info.nbins_arg);
352      } else {
353        sprintf( painCave.errMsg,
# Line 305 | Line 355 | int main(int argc, char* argv[]){
355        painCave.severity = OPENMD_ERROR;
356        painCave.isFatal = 1;
357        simError();
358 <      }
358 >    }
359    } else if (args_info.scd_given) {
360      if (batchMode) {
361 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
361 >      analyser  = new SCDOrderParameter(info, dumpFileName,
362 >                                        args_info.molname_arg,
363                                          args_info.begin_arg, args_info.end_arg);
364      } else{
365 <      std::string sele3 = args_info.sele3_arg;
366 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
365 >      analyser  = new SCDOrderParameter(info, dumpFileName,
366 >                                        sele1, sele2, sele3);
367      }
368    }else if (args_info.density_given) {
369      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
# Line 321 | Line 372 | int main(int argc, char* argv[]){
372      analyser = new ObjectCount(info, dumpFileName, sele1 );
373    } else if (args_info.slab_density_given) {
374      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
375 +  } else if (args_info.rnemdz_given) {
376 +    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
377 +  } else if (args_info.rnemdr_given) {
378 +    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
379 +  } else if (args_info.rnemdrt_given) {
380 +    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
381 +                               args_info.nbins_arg, args_info.nanglebins_arg);
382 +  } else if (args_info.nitrile_given) {
383 +    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
384 +                                       args_info.nbins_arg);
385    } else if (args_info.p_angle_given) {
386 <    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
386 >    if (args_info.sele1_given) {    
387 >      if (args_info.sele2_given)
388 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
389 >                               args_info.nbins_arg);
390 >      else
391 >        if (args_info.seleoffset_given) {
392 >          if (args_info.seleoffset2_given) {
393 >            analyser  = new pAngle(info, dumpFileName, sele1,
394 >                                   args_info.seleoffset_arg,
395 >                                   args_info.seleoffset2_arg,
396 >                                   args_info.nbins_arg);
397 >          } else {
398 >            analyser  = new pAngle(info, dumpFileName, sele1,
399 >                                   args_info.seleoffset_arg,
400 >                                   args_info.nbins_arg);
401 >          }
402 >        } else
403 >          analyser  = new pAngle(info, dumpFileName, sele1,
404 >                                 args_info.nbins_arg);
405 >    } else {
406 >      sprintf( painCave.errMsg,
407 >               "At least one selection script (--sele1) must be specified when "
408 >               "calculating P(angle) distributions");
409 >      painCave.severity = OPENMD_ERROR;
410 >      painCave.isFatal = 1;
411 >      simError();
412 >    }
413   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
414    }else if (args_info.hxy_given) {
415      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
416                         args_info.nbins_y_arg, args_info.nbins_arg);
417   #endif
418 +  }else if (args_info.surfDiffusion_given){
419 +    analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen);
420    }else if (args_info.rho_r_given) {
421      if (args_info.radius_given){
422        analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
# Line 345 | Line 434 | int main(int argc, char* argv[]){
434    } else if (args_info.angle_r_given) {
435      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
436    }
437 <    
437 >  
438    if (args_info.output_given) {
439      analyser->setOutputName(args_info.output_arg);
440    }
441    if (args_info.step_given) {
442      analyser->setStep(args_info.step_arg);
443    }
444 <
444 >  
445    analyser->process();
446    
447    delete analyser;    
448    delete info;
449 <
449 >  
450    return 0;  
451   }
363 –

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