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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 1999 by gezelter, Sat May 31 21:00:46 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/RNEMDStats.hpp"
81 + #include "applications/staticProps/NitrileFrequencyMap.hpp"
82 + #include "applications/staticProps/MultipoleSum.hpp"
83  
84   using namespace OpenMD;
85  
86   int main(int argc, char* argv[]){
87    
88 <  //register force fields
80 <  registerForceFields();
81 <
88 >  
89    gengetopt_args_info args_info;
90 <
90 >  
91    //parse the command line option
92    if (cmdline_parser (argc, argv, &args_info) != 0) {
93      exit(1) ;
94    }
95 <
95 >  
96    //get the dumpfile name
97    std::string dumpFileName = args_info.input_arg;
98    std::string sele1;
99    std::string sele2;
100 <  bool userSpecifiedSelect1;
94 <  bool userSpecifiedSelect2;
95 <
100 >  
101    // check the first selection argument, or set it to the environment
102    // variable, or failing that, set it to "select all"
103 <
103 >  
104    if (args_info.sele1_given) {
105      sele1 = args_info.sele1_arg;
106    } else {
# Line 106 | Line 111 | int main(int argc, char* argv[]){
111        sele1 = "select all";
112      }
113    }
114 <
114 >  
115    // check the second selection argument, or set it to the environment
116 <  // variable, or failing that, set it to "select all"
116 >  // variable, or failing that, set it to the first selection
117    
118    if (args_info.sele2_given) {
119      sele2 = args_info.sele2_arg;
120    } else {
121 <    char* sele2Env = getenv("SELECTION1");
121 >    char* sele2Env = getenv("SELECTION2");
122      if (sele2Env) {
123        sele2 = sele2Env;            
124      } else {
125 <      sele2 = "select all";
125 >      //If sele2 is not specified, then the default behavior
126 >      //should be what is already intended for sele1
127 >      sele2 = sele1;
128      }
129    }
130  
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 –
131    bool batchMode;
132    if (args_info.scd_given){
133 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
133 >    if (args_info.sele1_given &&
134 >        args_info.sele2_given && args_info.sele3_given) {
135        batchMode = false;
136 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
137 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
136 >    } else if (args_info.molname_given &&
137 >               args_info.begin_given && args_info.end_given) {
138 >      if (args_info.begin_arg < 0 ||
139 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
140          sprintf( painCave.errMsg,
141                   "below conditions are not satisfied:\n"
142                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 163 | Line 151 | int main(int argc, char* argv[]){
151                 " or --molname, --begin, --end are specified\n");
152        painCave.severity = OPENMD_ERROR;
153        painCave.isFatal = 1;
154 <      simError();        
167 <    
154 >      simError();
155      }
156    }
157 <
157 >  
158    //parse md file and set up the system
159    SimCreator creator;
173 –  std::cout << "dumpFile = " << dumpFileName << "\n";
160    SimInfo* info = creator.createSim(dumpFileName);
161  
162    RealType maxLen;
163 +  RealType zmaxLen;
164    if (args_info.length_given) {
165      maxLen = args_info.length_arg;
166 +    if (args_info.zlength_given){
167 +      zmaxLen = args_info.zlength_arg;
168 +    }
169    } else {
170      Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
171 <    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
171 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
172 >    zmaxLen = hmat(2,2);    
173    }    
174 <
174 >  
175    StaticAnalyser* analyser;
176    if (args_info.gofr_given){
177      analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
178 <                       args_info.nbins_arg);        
178 >                       args_info.nbins_arg);        
179    } else if (args_info.gofz_given) {
180      analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
181 <                       args_info.nbins_arg);
181 >                       args_info.nbins_arg);
182    } else if (args_info.r_z_given) {
183 <    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen,
184 <                              args_info.nbins_arg, args_info.nbins_z_arg);
183 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
184 >                          args_info.nbins_arg, args_info.nbins_z_arg);
185    } else if (args_info.r_theta_given) {
186      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
187 <                              args_info.nbins_arg, args_info.nanglebins_arg);
187 >                              args_info.nbins_arg, args_info.nanglebins_arg);
188    } else if (args_info.r_omega_given) {
189      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
190 <                              args_info.nbins_arg, args_info.nanglebins_arg);
190 >                              args_info.nbins_arg, args_info.nanglebins_arg);
191    } else if (args_info.theta_omega_given) {
192      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
193 <                              args_info.nanglebins_arg);
193 >                              args_info.nanglebins_arg);
194    } else if (args_info.gxyz_given) {
195      if (args_info.refsele_given) {
196 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
197 <                           maxLen, args_info.nbins_arg);        
196 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
197 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
198      } else {
199        sprintf( painCave.errMsg,
200 <               "--refsele must set when --gxyz is used");
200 >               "--refsele must set when --gxyz is used");
201        painCave.severity = OPENMD_ERROR;
202        painCave.isFatal = 1;
203        simError();  
204      }
205 +  } else if (args_info.twodgofr_given){
206 +    if (args_info.dz_given) {
207 +      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
208 +                             args_info.dz_arg, args_info.nbins_arg);        
209 +    } else {
210 +      sprintf( painCave.errMsg,
211 +               "A slab width (dz) must be specified when calculating TwoDGofR");
212 +      painCave.severity = OPENMD_ERROR;
213 +      painCave.isFatal = 1;
214 +      simError();
215 +    }    
216    } else if (args_info.p2_given) {
217 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
217 >    if (args_info.sele1_given) {    
218 >      if (args_info.sele2_given)
219 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
220 >      else
221 >        if (args_info.seleoffset_given)
222 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
223 >                                           args_info.seleoffset_arg);
224 >        else
225 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
226 >    } else {
227 >      sprintf( painCave.errMsg,
228 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
229 >      painCave.severity = OPENMD_ERROR;
230 >      painCave.isFatal = 1;
231 >      simError();
232 >    }
233    } else if (args_info.rp2_given){
234      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
235    } else if (args_info.bo_given){
236      if (args_info.rcut_given) {
237        analyser = new BondOrderParameter(info, dumpFileName, sele1,
238 <                                        args_info.rcut_arg,
239 <                                        args_info.nbins_arg);
238 >                                        args_info.rcut_arg,
239 >                                        args_info.nbins_arg);
240      } else {
241        sprintf( painCave.errMsg,
242 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
242 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
243        painCave.severity = OPENMD_ERROR;
244        painCave.isFatal = 1;
245        simError();
246      }
247 <  } else if (args_info.bor_given){
247 >  } else if (args_info.multipole_given){
248 >    analyser = new MultipoleSum(info, dumpFileName, sele1,
249 >                                maxLen, args_info.nbins_arg);
250 >  } else if (args_info.tet_param_given) {
251 >    if (args_info.rcut_given) {  
252 >      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
253 >                                         args_info.rcut_arg,
254 >                                         args_info.nbins_arg);
255 >    } else {
256 >      sprintf( painCave.errMsg,
257 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
258 >      painCave.severity = OPENMD_ERROR;
259 >      painCave.isFatal = 1;
260 >      simError();
261 >    }
262 >  } else if (args_info.tet_param_z_given) {
263 >    if (args_info.rcut_given) {  
264 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
265 >                                          args_info.rcut_arg,
266 >                                          args_info.nbins_arg);
267 >    } else {
268 >      sprintf( painCave.errMsg,
269 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
270 >      painCave.severity = OPENMD_ERROR;
271 >      painCave.isFatal = 1;
272 >      simError();
273 >    }
274 >  } else if (args_info.ior_given){
275      if (args_info.rcut_given) {
276 <      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
276 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
277 >                                    args_info.rcut_arg,
278 >                                    args_info.nbins_arg, maxLen);
279 >    } else {
280 >      sprintf( painCave.errMsg,
281 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
282 >      painCave.severity = OPENMD_ERROR;
283 >      painCave.isFatal = 1;
284 >      simError();
285 >    }
286 >  } else if (args_info.for_given){
287 >    if (args_info.rcut_given) {
288 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
289                              args_info.nbins_arg, maxLen);
290      } else {
291        sprintf( painCave.errMsg,
292 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
292 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
293        painCave.severity = OPENMD_ERROR;
294        painCave.isFatal = 1;
295        simError();
296      }
297    } else if (args_info.bad_given){
298      if (args_info.rcut_given) {
299 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
300 <                            args_info.nbins_arg);
299 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
300 >                                           args_info.rcut_arg,
301 >                                           args_info.nbins_arg);
302      } else {
303        sprintf( painCave.errMsg,
304 <               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
304 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
305        painCave.severity = OPENMD_ERROR;
306        painCave.isFatal = 1;
307        simError();
308      }
309    } else if (args_info.scd_given) {
310      if (batchMode) {
311 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
312 <                                        args_info.begin_arg, args_info.end_arg);
311 >      analyser  = new SCDOrderParameter(info, dumpFileName,
312 >                                        args_info.molname_arg,
313 >                                        args_info.begin_arg, args_info.end_arg);
314      } else{
315        std::string sele3 = args_info.sele3_arg;
316 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
316 >      analyser  = new SCDOrderParameter(info, dumpFileName,
317 >                                        sele1, sele2, sele3);
318      }
319    }else if (args_info.density_given) {
320      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
321 <                              args_info.nbins_arg);  
321 >                              args_info.nbins_arg);  
322 >  } else if (args_info.count_given) {
323 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
324    } else if (args_info.slab_density_given) {
325      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
326 +  } else if (args_info.rnemdz_given) {
327 +    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
328 +  } else if (args_info.rnemdr_given) {
329 +    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
330 +  } else if (args_info.rnemdrt_given) {
331 +    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
332 +                               args_info.nbins_arg, args_info.nanglebins_arg);
333 +  } else if (args_info.nitrile_given) {
334 +    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
335 +                                       args_info.nbins_arg);
336    } else if (args_info.p_angle_given) {
337 <    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
337 >    if (args_info.sele1_given) {    
338 >      if (args_info.sele2_given)
339 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
340 >                               args_info.nbins_arg);
341 >      else
342 >        if (args_info.seleoffset_given) {
343 >          if (args_info.seleoffset2_given) {
344 >            analyser  = new pAngle(info, dumpFileName, sele1,
345 >                                   args_info.seleoffset_arg,
346 >                                   args_info.seleoffset2_arg,
347 >                                   args_info.nbins_arg);
348 >          } else {
349 >            analyser  = new pAngle(info, dumpFileName, sele1,
350 >                                   args_info.seleoffset_arg,
351 >                                   args_info.nbins_arg);
352 >          }
353 >        } else
354 >          analyser  = new pAngle(info, dumpFileName, sele1,
355 >                                 args_info.nbins_arg);
356 >    } else {
357 >      sprintf( painCave.errMsg,
358 >               "At least one selection script (--sele1) must be specified when "
359 >               "calculating P(angle) distributions");
360 >      painCave.severity = OPENMD_ERROR;
361 >      painCave.isFatal = 1;
362 >      simError();
363 >    }
364   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
365    }else if (args_info.hxy_given) {
366      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
367 <                       args_info.nbins_y_arg, args_info.nbins_arg);
367 >                       args_info.nbins_y_arg, args_info.nbins_arg);
368   #endif
369    }else if (args_info.rho_r_given) {
370      if (args_info.radius_given){
371        analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
372      }else{
373        sprintf( painCave.errMsg,
374 <               "A particle radius (radius) must be specified when calculating Rho(r)");
374 >               "A particle radius (radius) must be specified when calculating Rho(r)");
375        painCave.severity = OPENMD_ERROR;
376        painCave.isFatal = 1;
377        simError();
378      }
379 <        }else if (args_info.hullvol_given) {
379 >  } else if (args_info.hullvol_given) {
380      analyser = new NanoVolume(info, dumpFileName, sele1);
381 +  } else if (args_info.rodlength_given) {
382 +    analyser = new NanoLength(info, dumpFileName, sele1);
383 +  } else if (args_info.angle_r_given) {
384 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
385    }
386    
387    if (args_info.output_given) {
# Line 289 | Line 390 | int main(int argc, char* argv[]){
390    if (args_info.step_given) {
391      analyser->setStep(args_info.step_arg);
392    }
393 <
393 >  
394    analyser->process();
395 <
395 >  
396    delete analyser;    
397    delete info;
398 <
398 >  
399    return 0;  
400   }
300 –

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