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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 2015 by gezelter, Wed Aug 13 20:42:43 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 +
85   using namespace OpenMD;
86  
87   int main(int argc, char* argv[]){
# Line 109 | Line 114 | int main(int argc, char* argv[]){
114    }
115    
116    // check the second selection argument, or set it to the environment
117 <  // variable, or failing that, set it to "select all"
117 >  // variable, or failing that, set it to the first selection
118    
119    if (args_info.sele2_given) {
120      sele2 = args_info.sele2_arg;
121    } else {
122 <    char* sele2Env = getenv("SELECTION1");
122 >    char* sele2Env = getenv("SELECTION2");
123      if (sele2Env) {
124        sele2 = sele2Env;            
125      } else {
126 <      //It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
127 <      //should not be 'select all' but rather what is already intended for sele1
123 <      //JRM 8/22/12
126 >      //If sele2 is not specified, then the default behavior
127 >      //should be what is already intended for sele1
128        sele2 = sele1;
125 –      //sele2 = "select all";
129      }
130    }
131 <  
129 <  
130 <  // Problems if sele1 wasn't specified, but
131 <  // if (!args_info.scd_given) {
132 <  //       sprintf( painCave.errMsg,
133 <  //                "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 <  
131 >
132    bool batchMode;
133    if (args_info.scd_given){
134 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
134 >    if (args_info.sele1_given &&
135 >        args_info.sele2_given && args_info.sele3_given) {
136        batchMode = false;
137 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
138 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
137 >    } else if (args_info.molname_given &&
138 >               args_info.begin_given && args_info.end_given) {
139 >      if (args_info.begin_arg < 0 ||
140 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
141          sprintf( painCave.errMsg,
142                   "below conditions are not satisfied:\n"
143                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 168 | Line 152 | int main(int argc, char* argv[]){
152                 " or --molname, --begin, --end are specified\n");
153        painCave.severity = OPENMD_ERROR;
154        painCave.isFatal = 1;
155 <      simError();        
172 <      
155 >      simError();
156      }
157    }
158    
159    //parse md file and set up the system
160    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
161    SimInfo* info = creator.createSim(dumpFileName);
162  
163    RealType maxLen;
# Line 212 | Line 194 | int main(int argc, char* argv[]){
194                                args_info.nanglebins_arg);
195    } else if (args_info.gxyz_given) {
196      if (args_info.refsele_given) {
197 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
198 <                           maxLen, args_info.nbins_arg);        
197 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
198 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
199      } else {
200        sprintf( painCave.errMsg,
201                 "--refsele must set when --gxyz is used");
# Line 237 | Line 219 | int main(int argc, char* argv[]){
219        if (args_info.sele2_given)
220          analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
221        else
222 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
222 >        if (args_info.seleoffset_given)
223 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
224 >                                           args_info.seleoffset_arg);
225 >        else
226 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
227      } else {
228        sprintf( painCave.errMsg,
229                 "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
# Line 259 | Line 245 | int main(int argc, char* argv[]){
245        painCave.isFatal = 1;
246        simError();
247      }
248 <    
248 >  } else if (args_info.multipole_given){
249 >    analyser = new MultipoleSum(info, dumpFileName, sele1,
250 >                                maxLen, args_info.nbins_arg);
251    } else if (args_info.tet_param_given) {
252      if (args_info.rcut_given) {  
253        analyser = new TetrahedralityParam(info, dumpFileName, sele1,
# Line 274 | Line 262 | int main(int argc, char* argv[]){
262      }
263    } else if (args_info.tet_param_z_given) {
264      if (args_info.rcut_given) {  
265 <      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
266 <                                         args_info.rcut_arg,
267 <                                         args_info.nbins_arg);
265 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
266 >                                          args_info.rcut_arg,
267 >                                          args_info.nbins_arg);
268      } else {
269        sprintf( painCave.errMsg,
270                 "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
# Line 284 | Line 272 | int main(int argc, char* argv[]){
272        painCave.isFatal = 1;
273        simError();
274      }
275 <  } else if (args_info.bor_given){
275 >  } else if (args_info.tet_param_xyz_given) {
276 >    if (!args_info.rcut_given) {
277 >      sprintf( painCave.errMsg,
278 >               "A cutoff radius (rcut) must be specified when calculating"
279 >               " Tetrahedrality Parameters");
280 >      painCave.severity = OPENMD_ERROR;
281 >      painCave.isFatal = 1;
282 >      simError();
283 >    }
284 >    if (!args_info.voxelSize_given) {
285 >      sprintf( painCave.errMsg,
286 >               "A voxel size must be specified when calculating"
287 >               " volume-resolved Tetrahedrality Parameters");
288 >      painCave.severity = OPENMD_ERROR;
289 >      painCave.isFatal = 1;
290 >      simError();
291 >    }
292 >    if (!args_info.gaussWidth_given) {
293 >      sprintf( painCave.errMsg,
294 >               "A gaussian width must be specified when calculating"
295 >               " volume-resolved Tetrahedrality Parameters");
296 >      painCave.severity = OPENMD_ERROR;
297 >      painCave.isFatal = 1;
298 >      simError();
299 >    }
300 >    analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
301 >                                          args_info.rcut_arg,
302 >                                          args_info.voxelSize_arg,
303 >                                          args_info.gaussWidth_arg);
304 >  } else if (args_info.ior_given){
305      if (args_info.rcut_given) {
306 <      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
306 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
307 >                                    args_info.rcut_arg,
308 >                                    args_info.nbins_arg, maxLen);
309 >    } else {
310 >      sprintf( painCave.errMsg,
311 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
312 >      painCave.severity = OPENMD_ERROR;
313 >      painCave.isFatal = 1;
314 >      simError();
315 >    }
316 >  } else if (args_info.for_given){
317 >    if (args_info.rcut_given) {
318 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
319                              args_info.nbins_arg, maxLen);
320      } else {
321        sprintf( painCave.errMsg,
# Line 297 | Line 326 | int main(int argc, char* argv[]){
326      }
327    } else if (args_info.bad_given){
328      if (args_info.rcut_given) {
329 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
329 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
330 >                                           args_info.rcut_arg,
331                                             args_info.nbins_arg);
332      } else {
333        sprintf( painCave.errMsg,
# Line 305 | Line 335 | int main(int argc, char* argv[]){
335        painCave.severity = OPENMD_ERROR;
336        painCave.isFatal = 1;
337        simError();
338 <      }
338 >    }
339    } else if (args_info.scd_given) {
340      if (batchMode) {
341 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
341 >      analyser  = new SCDOrderParameter(info, dumpFileName,
342 >                                        args_info.molname_arg,
343                                          args_info.begin_arg, args_info.end_arg);
344      } else{
345        std::string sele3 = args_info.sele3_arg;
346 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
346 >      analyser  = new SCDOrderParameter(info, dumpFileName,
347 >                                        sele1, sele2, sele3);
348      }
349    }else if (args_info.density_given) {
350      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
# Line 321 | Line 353 | int main(int argc, char* argv[]){
353      analyser = new ObjectCount(info, dumpFileName, sele1 );
354    } else if (args_info.slab_density_given) {
355      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
356 +  } else if (args_info.rnemdz_given) {
357 +    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
358 +  } else if (args_info.rnemdr_given) {
359 +    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
360 +  } else if (args_info.rnemdrt_given) {
361 +    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
362 +                               args_info.nbins_arg, args_info.nanglebins_arg);
363 +  } else if (args_info.nitrile_given) {
364 +    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
365 +                                       args_info.nbins_arg);
366    } else if (args_info.p_angle_given) {
367 <    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
367 >    if (args_info.sele1_given) {    
368 >      if (args_info.sele2_given)
369 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
370 >                               args_info.nbins_arg);
371 >      else
372 >        if (args_info.seleoffset_given) {
373 >          if (args_info.seleoffset2_given) {
374 >            analyser  = new pAngle(info, dumpFileName, sele1,
375 >                                   args_info.seleoffset_arg,
376 >                                   args_info.seleoffset2_arg,
377 >                                   args_info.nbins_arg);
378 >          } else {
379 >            analyser  = new pAngle(info, dumpFileName, sele1,
380 >                                   args_info.seleoffset_arg,
381 >                                   args_info.nbins_arg);
382 >          }
383 >        } else
384 >          analyser  = new pAngle(info, dumpFileName, sele1,
385 >                                 args_info.nbins_arg);
386 >    } else {
387 >      sprintf( painCave.errMsg,
388 >               "At least one selection script (--sele1) must be specified when "
389 >               "calculating P(angle) distributions");
390 >      painCave.severity = OPENMD_ERROR;
391 >      painCave.isFatal = 1;
392 >      simError();
393 >    }
394   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
395    }else if (args_info.hxy_given) {
396      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
# Line 345 | Line 413 | int main(int argc, char* argv[]){
413    } else if (args_info.angle_r_given) {
414      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
415    }
416 <    
416 >  
417    if (args_info.output_given) {
418      analyser->setOutputName(args_info.output_arg);
419    }
420    if (args_info.step_given) {
421      analyser->setStep(args_info.step_arg);
422    }
423 <
423 >  
424    analyser->process();
425    
426    delete analyser;    
427    delete info;
428 <
428 >  
429    return 0;  
430   }
363 –

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