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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 1992 by gezelter, Thu Apr 24 17:30:00 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/RNEMDStats.hpp"
81 +
82   using namespace OpenMD;
83  
84   int main(int argc, char* argv[]){
# Line 109 | Line 111 | int main(int argc, char* argv[]){
111    }
112    
113    // check the second selection argument, or set it to the environment
114 <  // variable, or failing that, set it to "select all"
114 >  // variable, or failing that, set it to the first selection
115    
116    if (args_info.sele2_given) {
117      sele2 = args_info.sele2_arg;
118    } else {
119 <    char* sele2Env = getenv("SELECTION1");
119 >    char* sele2Env = getenv("SELECTION2");
120      if (sele2Env) {
121        sele2 = sele2Env;            
122      } else {
123 <      //It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
124 <      //should not be 'select all' but rather what is already intended for sele1
123 <      //JRM 8/22/12
123 >      //If sele2 is not specified, then the default behavior
124 >      //should be what is already intended for sele1
125        sele2 = sele1;
125 –      //sele2 = "select all";
126      }
127    }
128 <  
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 <  
128 >
129    bool batchMode;
130    if (args_info.scd_given){
131 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
131 >    if (args_info.sele1_given &&
132 >        args_info.sele2_given && args_info.sele3_given) {
133        batchMode = false;
134 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
135 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
134 >    } else if (args_info.molname_given &&
135 >               args_info.begin_given && args_info.end_given) {
136 >      if (args_info.begin_arg < 0 ||
137 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
138          sprintf( painCave.errMsg,
139                   "below conditions are not satisfied:\n"
140                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 168 | Line 149 | int main(int argc, char* argv[]){
149                 " or --molname, --begin, --end are specified\n");
150        painCave.severity = OPENMD_ERROR;
151        painCave.isFatal = 1;
152 <      simError();        
172 <      
152 >      simError();
153      }
154    }
155    
156    //parse md file and set up the system
157    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
158    SimInfo* info = creator.createSim(dumpFileName);
159  
160    RealType maxLen;
# Line 212 | Line 191 | int main(int argc, char* argv[]){
191                                args_info.nanglebins_arg);
192    } else if (args_info.gxyz_given) {
193      if (args_info.refsele_given) {
194 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
195 <                           maxLen, args_info.nbins_arg);        
194 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
195 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
196      } else {
197        sprintf( painCave.errMsg,
198                 "--refsele must set when --gxyz is used");
# Line 237 | Line 216 | int main(int argc, char* argv[]){
216        if (args_info.sele2_given)
217          analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
218        else
219 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
219 >        if (args_info.seleoffset_given)
220 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
221 >                                           args_info.seleoffset_arg);
222 >        else
223 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
224      } else {
225        sprintf( painCave.errMsg,
226                 "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
# Line 274 | Line 257 | int main(int argc, char* argv[]){
257      }
258    } else if (args_info.tet_param_z_given) {
259      if (args_info.rcut_given) {  
260 <      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
261 <                                         args_info.rcut_arg,
262 <                                         args_info.nbins_arg);
260 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
261 >                                          args_info.rcut_arg,
262 >                                          args_info.nbins_arg);
263      } else {
264        sprintf( painCave.errMsg,
265                 "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
# Line 284 | Line 267 | int main(int argc, char* argv[]){
267        painCave.isFatal = 1;
268        simError();
269      }
270 <  } else if (args_info.bor_given){
270 >  } else if (args_info.ior_given){
271      if (args_info.rcut_given) {
272 <      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
272 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
273 >                                    args_info.rcut_arg,
274 >                                    args_info.nbins_arg, maxLen);
275 >    } else {
276 >      sprintf( painCave.errMsg,
277 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
278 >      painCave.severity = OPENMD_ERROR;
279 >      painCave.isFatal = 1;
280 >      simError();
281 >    }
282 >  } else if (args_info.for_given){
283 >    if (args_info.rcut_given) {
284 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
285                              args_info.nbins_arg, maxLen);
286      } else {
287        sprintf( painCave.errMsg,
# Line 297 | Line 292 | int main(int argc, char* argv[]){
292      }
293    } else if (args_info.bad_given){
294      if (args_info.rcut_given) {
295 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
295 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
296 >                                           args_info.rcut_arg,
297                                             args_info.nbins_arg);
298      } else {
299        sprintf( painCave.errMsg,
# Line 305 | Line 301 | int main(int argc, char* argv[]){
301        painCave.severity = OPENMD_ERROR;
302        painCave.isFatal = 1;
303        simError();
304 <      }
304 >    }
305    } else if (args_info.scd_given) {
306      if (batchMode) {
307 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
307 >      analyser  = new SCDOrderParameter(info, dumpFileName,
308 >                                        args_info.molname_arg,
309                                          args_info.begin_arg, args_info.end_arg);
310      } else{
311        std::string sele3 = args_info.sele3_arg;
312 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
312 >      analyser  = new SCDOrderParameter(info, dumpFileName,
313 >                                        sele1, sele2, sele3);
314      }
315    }else if (args_info.density_given) {
316      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
# Line 321 | Line 319 | int main(int argc, char* argv[]){
319      analyser = new ObjectCount(info, dumpFileName, sele1 );
320    } else if (args_info.slab_density_given) {
321      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
322 +  } else if (args_info.rnemdz_given) {
323 +    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
324 +  } else if (args_info.rnemdr_given) {
325 +    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
326 +  } else if (args_info.rnemdrt_given) {
327 +    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
328 +                               args_info.nbins_arg, args_info.nanglebins_arg);
329    } else if (args_info.p_angle_given) {
330 <    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
330 >    if (args_info.sele1_given) {    
331 >      if (args_info.sele2_given)
332 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
333 >                               args_info.nbins_arg);
334 >      else
335 >        if (args_info.seleoffset_given) {
336 >          if (args_info.seleoffset2_given) {
337 >            analyser  = new pAngle(info, dumpFileName, sele1,
338 >                                   args_info.seleoffset_arg,
339 >                                   args_info.seleoffset2_arg,
340 >                                   args_info.nbins_arg);
341 >          } else {
342 >            analyser  = new pAngle(info, dumpFileName, sele1,
343 >                                   args_info.seleoffset_arg,
344 >                                   args_info.nbins_arg);
345 >          }
346 >        } else
347 >          analyser  = new pAngle(info, dumpFileName, sele1,
348 >                                 args_info.nbins_arg);
349 >    } else {
350 >      sprintf( painCave.errMsg,
351 >               "At least one selection script (--sele1) must be specified when "
352 >               "calculating P(angle) distributions");
353 >      painCave.severity = OPENMD_ERROR;
354 >      painCave.isFatal = 1;
355 >      simError();
356 >    }
357   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
358    }else if (args_info.hxy_given) {
359      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
# Line 345 | Line 376 | int main(int argc, char* argv[]){
376    } else if (args_info.angle_r_given) {
377      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
378    }
379 <    
379 >  
380    if (args_info.output_given) {
381      analyser->setOutputName(args_info.output_arg);
382    }
383    if (args_info.step_given) {
384      analyser->setStep(args_info.step_arg);
385    }
386 <
386 >  
387    analyser->process();
388    
389    delete analyser;    
390    delete info;
391 <
391 >  
392    return 0;  
393   }
363 –

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