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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 2023 by gezelter, Thu Oct 2 14:35:14 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).          
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  
85   using namespace OpenMD;
86  
87   int main(int argc, char* argv[]){
88    
84 –  //register force fields
85 –  registerForceFields();
89    
90    gengetopt_args_info args_info;
91    
# Line 95 | Line 98 | int main(int argc, char* argv[]){
98    std::string dumpFileName = args_info.input_arg;
99    std::string sele1;
100    std::string sele2;
101 <  bool userSpecifiedSelect1;
99 <  bool userSpecifiedSelect2;
101 >  std::string sele3;
102    
103    // check the first selection argument, or set it to the environment
104    // variable, or failing that, set it to "select all"
# Line 113 | Line 115 | int main(int argc, char* argv[]){
115    }
116    
117    // check the second selection argument, or set it to the environment
118 <  // variable, or failing that, set it to "select all"
118 >  // variable, or failing that, set it to the first selection
119    
120    if (args_info.sele2_given) {
121      sele2 = args_info.sele2_arg;
122    } else {
123 <    char* sele2Env = getenv("SELECTION1");
123 >    char* sele2Env = getenv("SELECTION2");
124      if (sele2Env) {
125        sele2 = sele2Env;            
126      } else {
127 <      sele2 = "select all";
127 >      //If sele2 is not specified, then the default behavior
128 >      //should be what is already intended for sele1
129 >      sele2 = sele1;
130      }
131    }
132 <  
133 <  
134 <  // Problems if sele1 wasn't specified, but
135 <  // if (!args_info.scd_given) {
136 <  //       sprintf( painCave.errMsg,
137 <  //                "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 <  
132 >
133 >  // check the third selection argument, which is only set if
134 >  // requested by the user
135 >
136 >  if (args_info.sele3_given) sele3 = args_info.sele3_arg;
137 >
138    bool batchMode;
139    if (args_info.scd_given){
140 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
140 >    if (args_info.sele1_given &&
141 >        args_info.sele2_given && args_info.sele3_given) {
142        batchMode = false;
143 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
144 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
143 >    } else if (args_info.molname_given &&
144 >               args_info.begin_given && args_info.end_given) {
145 >      if (args_info.begin_arg < 0 ||
146 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
147          sprintf( painCave.errMsg,
148                   "below conditions are not satisfied:\n"
149                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 168 | Line 158 | int main(int argc, char* argv[]){
158                 " or --molname, --begin, --end are specified\n");
159        painCave.severity = OPENMD_ERROR;
160        painCave.isFatal = 1;
161 <      simError();        
172 <      
161 >      simError();
162      }
163    }
164    
165    //parse md file and set up the system
166    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
167    SimInfo* info = creator.createSim(dumpFileName);
168  
169    RealType maxLen;
# Line 202 | Line 190 | int main(int argc, char* argv[]){
190      analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
191                            args_info.nbins_arg, args_info.nbins_z_arg);
192    } else if (args_info.r_theta_given) {
193 <    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
194 <                              args_info.nbins_arg, args_info.nanglebins_arg);
193 >    if (args_info.sele3_given)
194 >      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
195 >                                args_info.nbins_arg, args_info.nanglebins_arg);
196 >    else
197 >      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
198 >                                args_info.nbins_arg, args_info.nanglebins_arg);
199    } else if (args_info.r_omega_given) {
200 <    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
201 <                              args_info.nbins_arg, args_info.nanglebins_arg);
200 >    if (args_info.sele3_given)
201 >      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
202 >                                args_info.nbins_arg, args_info.nanglebins_arg);
203 >    else
204 >      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205 >                                args_info.nbins_arg, args_info.nanglebins_arg);
206 >
207    } else if (args_info.theta_omega_given) {
208 <    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
209 <                              args_info.nanglebins_arg);
208 >    if (args_info.sele3_given)
209 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
210 >                                args_info.nanglebins_arg);
211 >    else
212 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
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);        
216 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
217 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
218      } else {
219        sprintf( painCave.errMsg,
220                 "--refsele must set when --gxyz is used");
# Line 233 | Line 234 | int main(int argc, char* argv[]){
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 >        if (args_info.seleoffset_given)
242 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
243 >                                           args_info.seleoffset_arg);
244 >        else
245 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
246 >    } else {
247 >      sprintf( painCave.errMsg,
248 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
249 >      painCave.severity = OPENMD_ERROR;
250 >      painCave.isFatal = 1;
251 >      simError();
252 >    }
253    } else if (args_info.rp2_given){
254      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
255    } else if (args_info.bo_given){
# Line 248 | Line 264 | int main(int argc, char* argv[]){
264        painCave.isFatal = 1;
265        simError();
266      }
267 <    
267 >  } else if (args_info.multipole_given){
268 >    analyser = new MultipoleSum(info, dumpFileName, sele1,
269 >                                maxLen, args_info.nbins_arg);
270    } else if (args_info.tet_param_given) {
271      if (args_info.rcut_given) {  
272        analyser = new TetrahedralityParam(info, dumpFileName, sele1,
# Line 261 | Line 279 | int main(int argc, char* argv[]){
279        painCave.isFatal = 1;
280        simError();
281      }
282 <  } else if (args_info.bor_given){
282 >  } else if (args_info.tet_param_z_given) {
283 >    if (args_info.rcut_given) {  
284 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
285 >                                          args_info.rcut_arg,
286 >                                          args_info.nbins_arg);
287 >    } else {
288 >      sprintf( painCave.errMsg,
289 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
290 >      painCave.severity = OPENMD_ERROR;
291 >      painCave.isFatal = 1;
292 >      simError();
293 >    }
294 >  } else if (args_info.tet_param_xyz_given) {
295 >    if (!args_info.rcut_given) {
296 >      sprintf( painCave.errMsg,
297 >               "A cutoff radius (rcut) must be specified when calculating"
298 >               " Tetrahedrality Parameters");
299 >      painCave.severity = OPENMD_ERROR;
300 >      painCave.isFatal = 1;
301 >      simError();
302 >    }
303 >    if (!args_info.voxelSize_given) {
304 >      sprintf( painCave.errMsg,
305 >               "A voxel size must be specified when calculating"
306 >               " volume-resolved Tetrahedrality Parameters");
307 >      painCave.severity = OPENMD_ERROR;
308 >      painCave.isFatal = 1;
309 >      simError();
310 >    }
311 >    if (!args_info.gaussWidth_given) {
312 >      sprintf( painCave.errMsg,
313 >               "A gaussian width must be specified when calculating"
314 >               " volume-resolved Tetrahedrality Parameters");
315 >      painCave.severity = OPENMD_ERROR;
316 >      painCave.isFatal = 1;
317 >      simError();
318 >    }
319 >    analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
320 >                                          args_info.rcut_arg,
321 >                                          args_info.voxelSize_arg,
322 >                                          args_info.gaussWidth_arg);
323 >  } else if (args_info.ior_given){
324      if (args_info.rcut_given) {
325 <      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
325 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
326 >                                    args_info.rcut_arg,
327 >                                    args_info.nbins_arg, maxLen);
328 >    } else {
329 >      sprintf( painCave.errMsg,
330 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
331 >      painCave.severity = OPENMD_ERROR;
332 >      painCave.isFatal = 1;
333 >      simError();
334 >    }
335 >  } else if (args_info.for_given){
336 >    if (args_info.rcut_given) {
337 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
338                              args_info.nbins_arg, maxLen);
339      } else {
340        sprintf( painCave.errMsg,
# Line 274 | Line 345 | int main(int argc, char* argv[]){
345      }
346    } else if (args_info.bad_given){
347      if (args_info.rcut_given) {
348 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
348 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
349 >                                           args_info.rcut_arg,
350                                             args_info.nbins_arg);
351      } else {
352        sprintf( painCave.errMsg,
# Line 282 | Line 354 | int main(int argc, char* argv[]){
354        painCave.severity = OPENMD_ERROR;
355        painCave.isFatal = 1;
356        simError();
357 <      }
357 >    }
358    } else if (args_info.scd_given) {
359      if (batchMode) {
360 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
360 >      analyser  = new SCDOrderParameter(info, dumpFileName,
361 >                                        args_info.molname_arg,
362                                          args_info.begin_arg, args_info.end_arg);
363      } else{
364 <      std::string sele3 = args_info.sele3_arg;
365 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
364 >      analyser  = new SCDOrderParameter(info, dumpFileName,
365 >                                        sele1, sele2, sele3);
366      }
367    }else if (args_info.density_given) {
368      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
# Line 298 | Line 371 | int main(int argc, char* argv[]){
371      analyser = new ObjectCount(info, dumpFileName, sele1 );
372    } else if (args_info.slab_density_given) {
373      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
374 +  } else if (args_info.rnemdz_given) {
375 +    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
376 +  } else if (args_info.rnemdr_given) {
377 +    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
378 +  } else if (args_info.rnemdrt_given) {
379 +    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
380 +                               args_info.nbins_arg, args_info.nanglebins_arg);
381 +  } else if (args_info.nitrile_given) {
382 +    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
383 +                                       args_info.nbins_arg);
384    } else if (args_info.p_angle_given) {
385 <    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
385 >    if (args_info.sele1_given) {    
386 >      if (args_info.sele2_given)
387 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
388 >                               args_info.nbins_arg);
389 >      else
390 >        if (args_info.seleoffset_given) {
391 >          if (args_info.seleoffset2_given) {
392 >            analyser  = new pAngle(info, dumpFileName, sele1,
393 >                                   args_info.seleoffset_arg,
394 >                                   args_info.seleoffset2_arg,
395 >                                   args_info.nbins_arg);
396 >          } else {
397 >            analyser  = new pAngle(info, dumpFileName, sele1,
398 >                                   args_info.seleoffset_arg,
399 >                                   args_info.nbins_arg);
400 >          }
401 >        } else
402 >          analyser  = new pAngle(info, dumpFileName, sele1,
403 >                                 args_info.nbins_arg);
404 >    } else {
405 >      sprintf( painCave.errMsg,
406 >               "At least one selection script (--sele1) must be specified when "
407 >               "calculating P(angle) distributions");
408 >      painCave.severity = OPENMD_ERROR;
409 >      painCave.isFatal = 1;
410 >      simError();
411 >    }
412   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
413    }else if (args_info.hxy_given) {
414      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
# Line 317 | Line 426 | int main(int argc, char* argv[]){
426      }
427    } else if (args_info.hullvol_given) {
428      analyser = new NanoVolume(info, dumpFileName, sele1);
429 +  } else if (args_info.rodlength_given) {
430 +    analyser = new NanoLength(info, dumpFileName, sele1);
431    } else if (args_info.angle_r_given) {
432      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
433    }
434 <    
434 >  
435    if (args_info.output_given) {
436      analyser->setOutputName(args_info.output_arg);
437    }
# Line 332 | Line 443 | int main(int argc, char* argv[]){
443    
444    delete analyser;    
445    delete info;
446 <
446 >  
447    return 0;  
448   }
338 –

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