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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 1522 by kstocke1, Fri Nov 19 20:26:36 2010 UTC vs.
Revision 2049 by gezelter, Tue Jan 6 21:44:10 2015 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 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   #include "applications/staticProps/AngleR.hpp"
77 – #include "applications/staticProps/RhoAngleR.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 + #include "applications/staticProps/HBondGeometric.hpp"
86  
87   using namespace OpenMD;
88  
89   int main(int argc, char* argv[]){
90    
84 –  //register force fields
85 –  registerForceFields();
91    
92    gengetopt_args_info args_info;
93    
# Line 95 | Line 100 | int main(int argc, char* argv[]){
100    std::string dumpFileName = args_info.input_arg;
101    std::string sele1;
102    std::string sele2;
103 <  bool userSpecifiedSelect1;
99 <  bool userSpecifiedSelect2;
103 >  std::string sele3;
104    
105    // check the first selection argument, or set it to the environment
106    // variable, or failing that, set it to "select all"
# Line 113 | Line 117 | int main(int argc, char* argv[]){
117    }
118    
119    // check the second selection argument, or set it to the environment
120 <  // variable, or failing that, set it to "select all"
120 >  // variable, or failing that, set it to the first selection
121    
122    if (args_info.sele2_given) {
123      sele2 = args_info.sele2_arg;
124    } else {
125 <    char* sele2Env = getenv("SELECTION1");
125 >    char* sele2Env = getenv("SELECTION2");
126      if (sele2Env) {
127        sele2 = sele2Env;            
128      } else {
129 <      sele2 = "select all";
129 >      //If sele2 is not specified, then the default behavior
130 >      //should be what is already intended for sele1
131 >      sele2 = sele1;
132      }
133    }
134 <  
135 <  
136 <  // Problems if sele1 wasn't specified, but
137 <  // if (!args_info.scd_given) {
138 <  //       sprintf( painCave.errMsg,
139 <  //                "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 <  
134 >
135 >  // check the third selection argument, which is only set if
136 >  // requested by the user
137 >
138 >  if (args_info.sele3_given) sele3 = args_info.sele3_arg;
139 >
140    bool batchMode;
141    if (args_info.scd_given){
142 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
142 >    if (args_info.sele1_given &&
143 >        args_info.sele2_given && args_info.sele3_given) {
144        batchMode = false;
145 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
146 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
145 >    } else if (args_info.molname_given &&
146 >               args_info.begin_given && args_info.end_given) {
147 >      if (args_info.begin_arg < 0 ||
148 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
149          sprintf( painCave.errMsg,
150                   "below conditions are not satisfied:\n"
151                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 168 | Line 160 | int main(int argc, char* argv[]){
160                 " or --molname, --begin, --end are specified\n");
161        painCave.severity = OPENMD_ERROR;
162        painCave.isFatal = 1;
163 <      simError();        
172 <      
163 >      simError();
164      }
165    }
166    
167    //parse md file and set up the system
168    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
169    SimInfo* info = creator.createSim(dumpFileName);
170  
171    RealType maxLen;
# Line 202 | Line 192 | int main(int argc, char* argv[]){
192      analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
193                            args_info.nbins_arg, args_info.nbins_z_arg);
194    } else if (args_info.r_theta_given) {
195 <    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
196 <                              args_info.nbins_arg, args_info.nanglebins_arg);
195 >    if (args_info.sele3_given)
196 >      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
197 >                                args_info.nbins_arg, args_info.nanglebins_arg);
198 >    else
199 >      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
200 >                                args_info.nbins_arg, args_info.nanglebins_arg);
201    } else if (args_info.r_omega_given) {
202 <    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
203 <                              args_info.nbins_arg, args_info.nanglebins_arg);
202 >    if (args_info.sele3_given)
203 >      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
204 >                                args_info.nbins_arg, args_info.nanglebins_arg);
205 >    else
206 >      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
207 >                                args_info.nbins_arg, args_info.nanglebins_arg);
208 >
209    } else if (args_info.theta_omega_given) {
210 <    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
211 <                              args_info.nanglebins_arg);
210 >    if (args_info.sele3_given)
211 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
212 >                                args_info.nanglebins_arg);
213 >    else
214 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
215 >                                args_info.nanglebins_arg);
216    } else if (args_info.gxyz_given) {
217      if (args_info.refsele_given) {
218 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
219 <                           maxLen, args_info.nbins_arg);        
218 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
219 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
220      } else {
221        sprintf( painCave.errMsg,
222                 "--refsele must set when --gxyz is used");
# Line 233 | Line 236 | int main(int argc, char* argv[]){
236        simError();
237      }    
238    } else if (args_info.p2_given) {
239 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
239 >    if (args_info.sele1_given) {    
240 >      if (args_info.sele2_given)
241 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
242 >      else
243 >        if (args_info.seleoffset_given)
244 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
245 >                                           args_info.seleoffset_arg);
246 >        else
247 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
248 >    } else {
249 >      sprintf( painCave.errMsg,
250 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
251 >      painCave.severity = OPENMD_ERROR;
252 >      painCave.isFatal = 1;
253 >      simError();
254 >    }
255    } else if (args_info.rp2_given){
256      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
257    } else if (args_info.bo_given){
# Line 248 | Line 266 | int main(int argc, char* argv[]){
266        painCave.isFatal = 1;
267        simError();
268      }
269 <    
269 >  } else if (args_info.multipole_given){
270 >    analyser = new MultipoleSum(info, dumpFileName, sele1,
271 >                                maxLen, args_info.nbins_arg);
272    } else if (args_info.tet_param_given) {
273      if (args_info.rcut_given) {  
274        analyser = new TetrahedralityParam(info, dumpFileName, sele1,
# Line 261 | Line 281 | int main(int argc, char* argv[]){
281        painCave.isFatal = 1;
282        simError();
283      }
284 <  } else if (args_info.bor_given){
284 >  } else if (args_info.tet_param_z_given) {
285 >    if (args_info.rcut_given) {  
286 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
287 >                                          args_info.rcut_arg,
288 >                                          args_info.nbins_arg);
289 >    } else {
290 >      sprintf( painCave.errMsg,
291 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
292 >      painCave.severity = OPENMD_ERROR;
293 >      painCave.isFatal = 1;
294 >      simError();
295 >    }
296 >  } else if (args_info.tet_param_xyz_given) {
297 >    if (!args_info.rcut_given) {
298 >      sprintf( painCave.errMsg,
299 >               "A cutoff radius (rcut) must be specified when calculating"
300 >               " Tetrahedrality Parameters");
301 >      painCave.severity = OPENMD_ERROR;
302 >      painCave.isFatal = 1;
303 >      simError();
304 >    }
305 >    if (!args_info.voxelSize_given) {
306 >      sprintf( painCave.errMsg,
307 >               "A voxel size must be specified when calculating"
308 >               " volume-resolved Tetrahedrality Parameters");
309 >      painCave.severity = OPENMD_ERROR;
310 >      painCave.isFatal = 1;
311 >      simError();
312 >    }
313 >    if (!args_info.gaussWidth_given) {
314 >      sprintf( painCave.errMsg,
315 >               "A gaussian width must be specified when calculating"
316 >               " volume-resolved Tetrahedrality Parameters");
317 >      painCave.severity = OPENMD_ERROR;
318 >      painCave.isFatal = 1;
319 >      simError();
320 >    }
321 >    analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
322 >                                          args_info.rcut_arg,
323 >                                          args_info.voxelSize_arg,
324 >                                          args_info.gaussWidth_arg);
325 >  } else if (args_info.ior_given){
326      if (args_info.rcut_given) {
327 <      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
327 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
328 >                                    args_info.rcut_arg,
329 >                                    args_info.nbins_arg, maxLen);
330 >    } else {
331 >      sprintf( painCave.errMsg,
332 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
333 >      painCave.severity = OPENMD_ERROR;
334 >      painCave.isFatal = 1;
335 >      simError();
336 >    }
337 >  } else if (args_info.for_given){
338 >    if (args_info.rcut_given) {
339 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
340                              args_info.nbins_arg, maxLen);
341      } else {
342        sprintf( painCave.errMsg,
# Line 274 | Line 347 | int main(int argc, char* argv[]){
347      }
348    } else if (args_info.bad_given){
349      if (args_info.rcut_given) {
350 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
350 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
351 >                                           args_info.rcut_arg,
352                                             args_info.nbins_arg);
353      } else {
354        sprintf( painCave.errMsg,
# Line 282 | Line 356 | int main(int argc, char* argv[]){
356        painCave.severity = OPENMD_ERROR;
357        painCave.isFatal = 1;
358        simError();
359 <      }
359 >    }
360    } else if (args_info.scd_given) {
361      if (batchMode) {
362 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
362 >      analyser  = new SCDOrderParameter(info, dumpFileName,
363 >                                        args_info.molname_arg,
364                                          args_info.begin_arg, args_info.end_arg);
365      } else{
366 <      std::string sele3 = args_info.sele3_arg;
367 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
366 >      analyser  = new SCDOrderParameter(info, dumpFileName,
367 >                                        sele1, sele2, sele3);
368      }
369    }else if (args_info.density_given) {
370      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
# Line 298 | Line 373 | int main(int argc, char* argv[]){
373      analyser = new ObjectCount(info, dumpFileName, sele1 );
374    } else if (args_info.slab_density_given) {
375      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
376 +  } else if (args_info.rnemdz_given) {
377 +    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
378 +  } else if (args_info.rnemdr_given) {
379 +    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
380 +  } else if (args_info.rnemdrt_given) {
381 +    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
382 +                               args_info.nbins_arg, args_info.nanglebins_arg);
383 +  } else if (args_info.nitrile_given) {
384 +    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
385 +                                       args_info.nbins_arg);
386    } else if (args_info.p_angle_given) {
387 <    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
387 >    if (args_info.sele1_given) {    
388 >      if (args_info.sele2_given)
389 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
390 >                               args_info.nbins_arg);
391 >      else
392 >        if (args_info.seleoffset_given) {
393 >          if (args_info.seleoffset2_given) {
394 >            analyser  = new pAngle(info, dumpFileName, sele1,
395 >                                   args_info.seleoffset_arg,
396 >                                   args_info.seleoffset2_arg,
397 >                                   args_info.nbins_arg);
398 >          } else {
399 >            analyser  = new pAngle(info, dumpFileName, sele1,
400 >                                   args_info.seleoffset_arg,
401 >                                   args_info.nbins_arg);
402 >          }
403 >        } else
404 >          analyser  = new pAngle(info, dumpFileName, sele1,
405 >                                 args_info.nbins_arg);
406 >    } else {
407 >      sprintf( painCave.errMsg,
408 >               "At least one selection script (--sele1) must be specified when "
409 >               "calculating P(angle) distributions");
410 >      painCave.severity = OPENMD_ERROR;
411 >      painCave.isFatal = 1;
412 >      simError();
413 >    }
414   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
415    }else if (args_info.hxy_given) {
416      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
417                         args_info.nbins_y_arg, args_info.nbins_arg);
418   #endif
419 +  }else if (args_info.surfDiffusion_given){
420 +    analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen);
421    }else if (args_info.rho_r_given) {
422      if (args_info.radius_given){
423        analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
# Line 317 | Line 430 | int main(int argc, char* argv[]){
430      }
431    } else if (args_info.hullvol_given) {
432      analyser = new NanoVolume(info, dumpFileName, sele1);
433 +  } else if (args_info.rodlength_given) {
434 +    analyser = new NanoLength(info, dumpFileName, sele1);
435    } else if (args_info.angle_r_given) {
436      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
437 +  } else if (args_info.hbond_given){
438 +    if (args_info.rcut_given) {
439 +      if (args_info.thetacut_given) {
440 +        
441 +        analyser = new HBondGeometric(info, dumpFileName, sele1, sele2,
442 +                                      args_info.rcut_arg,
443 +                                      args_info.thetacut_arg,
444 +                                      args_info.nbins_arg);
445 +      } else {
446 +        sprintf( painCave.errMsg,
447 +                 "A cutoff angle (thetacut) must be specified when calculating Hydrogen Bonding Statistics");
448 +        painCave.severity = OPENMD_ERROR;
449 +        painCave.isFatal = 1;
450 +        simError();
451 +      }
452 +    } else {
453 +      sprintf( painCave.errMsg,
454 +               "A cutoff radius (rcut) must be specified when calculating Hydrogen Bonding Statistics");
455 +      painCave.severity = OPENMD_ERROR;
456 +      painCave.isFatal = 1;
457 +      simError();
458 +    }    
459    }
460 <    
460 >  
461    if (args_info.output_given) {
462      analyser->setOutputName(args_info.output_arg);
463    }
# Line 332 | Line 469 | int main(int argc, char* argv[]){
469    
470    delete analyser;    
471    delete info;
472 <
472 >  
473    return 0;  
474   }
338 –

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