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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 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 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/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    
84 –  //register force fields
85 –  registerForceFields();
88    
89    gengetopt_args_info args_info;
90    
# Line 95 | Line 97 | int main(int argc, char* argv[]){
97    std::string dumpFileName = args_info.input_arg;
98    std::string sele1;
99    std::string sele2;
98 –  bool userSpecifiedSelect1;
99 –  bool userSpecifiedSelect2;
100    
101    // check the first selection argument, or set it to the environment
102    // variable, or failing that, set it to "select all"
# Line 113 | Line 113 | int main(int argc, char* argv[]){
113    }
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 <  
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 <  
130 >
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 168 | 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();        
172 <      
154 >      simError();
155      }
156    }
157    
158    //parse md file and set up the system
159    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
160    SimInfo* info = creator.createSim(dumpFileName);
161  
162    RealType maxLen;
# Line 212 | Line 193 | int main(int argc, char* argv[]){
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");
# Line 233 | Line 214 | int main(int argc, char* argv[]){
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){
# Line 248 | Line 244 | int main(int argc, char* argv[]){
244        painCave.isFatal = 1;
245        simError();
246      }
247 <    
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,
# Line 261 | Line 259 | int main(int argc, char* argv[]){
259        painCave.isFatal = 1;
260        simError();
261      }
262 <  } else if (args_info.bor_given){
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,
# Line 274 | Line 296 | int main(int argc, char* argv[]){
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,
299 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
300 >                                           args_info.rcut_arg,
301                                             args_info.nbins_arg);
302      } else {
303        sprintf( painCave.errMsg,
# Line 282 | Line 305 | int main(int argc, char* argv[]){
305        painCave.severity = OPENMD_ERROR;
306        painCave.isFatal = 1;
307        simError();
308 <      }
308 >    }
309    } else if (args_info.scd_given) {
310      if (batchMode) {
311 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_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,
# Line 298 | Line 323 | int main(int argc, char* argv[]){
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,
# Line 317 | Line 378 | int main(int argc, char* argv[]){
378      }
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 <    
386 >  
387    if (args_info.output_given) {
388      analyser->setOutputName(args_info.output_arg);
389    }
# Line 332 | Line 395 | int main(int argc, char* argv[]){
395    
396    delete analyser;    
397    delete info;
398 <
398 >  
399    return 0;  
400   }
338 –

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