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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 1442 by gezelter, Mon May 10 17:28:26 2010 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).          
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 57 | Line 57
57   #include "applications/staticProps/GofRAngle.hpp"
58   #include "applications/staticProps/GofAngle2.hpp"
59   #include "applications/staticProps/GofXyz.hpp"
60 + #include "applications/staticProps/TwoDGofR.hpp"
61   #include "applications/staticProps/P2OrderParameter.hpp"
62   #include "applications/staticProps/BondOrderParameter.hpp"
63   #include "applications/staticProps/BOPofR.hpp"
64   #include "applications/staticProps/RippleOP.hpp"
65   #include "applications/staticProps/SCDOrderParameter.hpp"
66   #include "applications/staticProps/DensityPlot.hpp"
67 + #include "applications/staticProps/ObjectCount.hpp"
68   #include "applications/staticProps/RhoZ.hpp"
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"
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    
89 <  //register force fields
80 <  registerForceFields();
81 <
89 >  
90    gengetopt_args_info args_info;
91 <
91 >  
92    //parse the command line option
93    if (cmdline_parser (argc, argv, &args_info) != 0) {
94      exit(1) ;
95    }
96 <
96 >  
97    //get the dumpfile name
98    std::string dumpFileName = args_info.input_arg;
99    std::string sele1;
100    std::string sele2;
101 <  bool userSpecifiedSelect1;
94 <  bool userSpecifiedSelect2;
95 <
101 >  
102    // check the first selection argument, or set it to the environment
103    // variable, or failing that, set it to "select all"
104 <
104 >  
105    if (args_info.sele1_given) {
106      sele1 = args_info.sele1_arg;
107    } else {
# Line 106 | Line 112 | int main(int argc, char* argv[]){
112        sele1 = "select all";
113      }
114    }
115 <
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 <      sele2 = "select all";
126 >      //If sele2 is not specified, then the default behavior
127 >      //should be what is already intended for sele1
128 >      sele2 = sele1;
129      }
130    }
131  
124 –
125 –  // Problems if sele1 wasn't specified, but
126 – // if (!args_info.scd_given) {
127 – //       sprintf( painCave.errMsg,
128 – //                "neither --sele1 option nor $SELECTION1 is set");
129 – //       painCave.severity = OPENMD_ERROR;
130 – //       painCave.isFatal = 1;
131 – //       simError();
132 – //     }
133 – //   }
134 –
135 –  // Problems if sele1 wasn't specified
136 –
137 – //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
138 – //       sprintf( painCave.errMsg,
139 – //                "neither --sele2 option nor $SELECTION1 is set");
140 – //       painCave.severity = OPENMD_ERROR;
141 – //       painCave.isFatal = 1;
142 – //       simError();        
143 – //     }
144 – //   }
145 –
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 163 | 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();        
167 <    
155 >      simError();
156      }
157    }
158 <
158 >  
159    //parse md file and set up the system
160    SimCreator creator;
173 –  std::cout << "dumpFile = " << dumpFileName << "\n";
161    SimInfo* info = creator.createSim(dumpFileName);
162  
163    RealType maxLen;
164 +  RealType zmaxLen;
165    if (args_info.length_given) {
166      maxLen = args_info.length_arg;
167 +    if (args_info.zlength_given){
168 +      zmaxLen = args_info.zlength_arg;
169 +    }
170    } else {
171      Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
172 <    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
172 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
173 >    zmaxLen = hmat(2,2);    
174    }    
175 <
175 >  
176    StaticAnalyser* analyser;
177    if (args_info.gofr_given){
178      analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
179 <                       args_info.nbins_arg);        
179 >                       args_info.nbins_arg);        
180    } else if (args_info.gofz_given) {
181      analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
182 <                       args_info.nbins_arg);
182 >                       args_info.nbins_arg);
183    } else if (args_info.r_z_given) {
184 <    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen,
185 <                              args_info.nbins_arg, args_info.nbins_z_arg);
184 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
185 >                          args_info.nbins_arg, args_info.nbins_z_arg);
186    } else if (args_info.r_theta_given) {
187      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
188 <                              args_info.nbins_arg, args_info.nanglebins_arg);
188 >                              args_info.nbins_arg, args_info.nanglebins_arg);
189    } else if (args_info.r_omega_given) {
190      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
191 <                              args_info.nbins_arg, args_info.nanglebins_arg);
191 >                              args_info.nbins_arg, args_info.nanglebins_arg);
192    } else if (args_info.theta_omega_given) {
193      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
194 <                              args_info.nanglebins_arg);
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");
201 >               "--refsele must set when --gxyz is used");
202        painCave.severity = OPENMD_ERROR;
203        painCave.isFatal = 1;
204        simError();  
205      }
206 +  } else if (args_info.twodgofr_given){
207 +    if (args_info.dz_given) {
208 +      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
209 +                             args_info.dz_arg, args_info.nbins_arg);        
210 +    } else {
211 +      sprintf( painCave.errMsg,
212 +               "A slab width (dz) must be specified when calculating TwoDGofR");
213 +      painCave.severity = OPENMD_ERROR;
214 +      painCave.isFatal = 1;
215 +      simError();
216 +    }    
217    } else if (args_info.p2_given) {
218 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
218 >    if (args_info.sele1_given) {    
219 >      if (args_info.sele2_given)
220 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
221 >      else
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");
230 >      painCave.severity = OPENMD_ERROR;
231 >      painCave.isFatal = 1;
232 >      simError();
233 >    }
234    } else if (args_info.rp2_given){
235      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
236    } else if (args_info.bo_given){
237      if (args_info.rcut_given) {
238        analyser = new BondOrderParameter(info, dumpFileName, sele1,
239 <                                        args_info.rcut_arg,
240 <                                        args_info.nbins_arg);
239 >                                        args_info.rcut_arg,
240 >                                        args_info.nbins_arg);
241      } else {
242        sprintf( painCave.errMsg,
243 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
243 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
244        painCave.severity = OPENMD_ERROR;
245        painCave.isFatal = 1;
246        simError();
247      }
248 <  } else if (args_info.bor_given){
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,
254 >                                         args_info.rcut_arg,
255 >                                         args_info.nbins_arg);
256 >    } else {
257 >      sprintf( painCave.errMsg,
258 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
259 >      painCave.severity = OPENMD_ERROR;
260 >      painCave.isFatal = 1;
261 >      simError();
262 >    }
263 >  } else if (args_info.tet_param_z_given) {
264 >    if (args_info.rcut_given) {  
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");
271 >      painCave.severity = OPENMD_ERROR;
272 >      painCave.isFatal = 1;
273 >      simError();
274 >    }
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,
322 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
322 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
323        painCave.severity = OPENMD_ERROR;
324        painCave.isFatal = 1;
325        simError();
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,
330 <                            args_info.nbins_arg);
329 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
330 >                                           args_info.rcut_arg,
331 >                                           args_info.nbins_arg);
332      } else {
333        sprintf( painCave.errMsg,
334 <               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
334 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
335        painCave.severity = OPENMD_ERROR;
336        painCave.isFatal = 1;
337        simError();
338      }
339    } else if (args_info.scd_given) {
340      if (batchMode) {
341 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
342 <                                        args_info.begin_arg, args_info.end_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,
351 <                              args_info.nbins_arg);  
351 >                              args_info.nbins_arg);  
352 >  } else if (args_info.count_given) {
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,
397 <                       args_info.nbins_y_arg, args_info.nbins_arg);
397 >                       args_info.nbins_y_arg, args_info.nbins_arg);
398   #endif
399    }else if (args_info.rho_r_given) {
400      if (args_info.radius_given){
401        analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
402      }else{
403        sprintf( painCave.errMsg,
404 <               "A particle radius (radius) must be specified when calculating Rho(r)");
404 >               "A particle radius (radius) must be specified when calculating Rho(r)");
405        painCave.severity = OPENMD_ERROR;
406        painCave.isFatal = 1;
407        simError();
408      }
409 <        }else if (args_info.hullvol_given) {
409 >  } else if (args_info.hullvol_given) {
410      analyser = new NanoVolume(info, dumpFileName, sele1);
411 +  } else if (args_info.rodlength_given) {
412 +    analyser = new NanoLength(info, dumpFileName, sele1);
413 +  } else if (args_info.angle_r_given) {
414 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
415    }
416    
417    if (args_info.output_given) {
# Line 289 | Line 420 | int main(int argc, char* argv[]){
420    if (args_info.step_given) {
421      analyser->setStep(args_info.step_arg);
422    }
423 <
423 >  
424    analyser->process();
425 <
425 >  
426    delete analyser;    
427    delete info;
428 <
428 >  
429    return 0;  
430   }
300 –

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