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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 1994 by gezelter, Wed Apr 30 18:50:45 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  
83   using namespace OpenMD;
84  
85   int main(int argc, char* argv[]){
86    
84 –  //register force fields
85 –  registerForceFields();
87    
88    gengetopt_args_info args_info;
89    
# Line 95 | Line 96 | int main(int argc, char* argv[]){
96    std::string dumpFileName = args_info.input_arg;
97    std::string sele1;
98    std::string sele2;
98 –  bool userSpecifiedSelect1;
99 –  bool userSpecifiedSelect2;
99    
100    // check the first selection argument, or set it to the environment
101    // variable, or failing that, set it to "select all"
# Line 113 | Line 112 | int main(int argc, char* argv[]){
112    }
113    
114    // check the second selection argument, or set it to the environment
115 <  // variable, or failing that, set it to "select all"
115 >  // variable, or failing that, set it to the first selection
116    
117    if (args_info.sele2_given) {
118      sele2 = args_info.sele2_arg;
119    } else {
120 <    char* sele2Env = getenv("SELECTION1");
120 >    char* sele2Env = getenv("SELECTION2");
121      if (sele2Env) {
122        sele2 = sele2Env;            
123      } else {
124 <      sele2 = "select all";
124 >      //If sele2 is not specified, then the default behavior
125 >      //should be what is already intended for sele1
126 >      sele2 = sele1;
127      }
128    }
129 <  
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 <  
129 >
130    bool batchMode;
131    if (args_info.scd_given){
132 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
132 >    if (args_info.sele1_given &&
133 >        args_info.sele2_given && args_info.sele3_given) {
134        batchMode = false;
135 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
136 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
135 >    } else if (args_info.molname_given &&
136 >               args_info.begin_given && args_info.end_given) {
137 >      if (args_info.begin_arg < 0 ||
138 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
139          sprintf( painCave.errMsg,
140                   "below conditions are not satisfied:\n"
141                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 168 | Line 150 | int main(int argc, char* argv[]){
150                 " or --molname, --begin, --end are specified\n");
151        painCave.severity = OPENMD_ERROR;
152        painCave.isFatal = 1;
153 <      simError();        
172 <      
153 >      simError();
154      }
155    }
156    
157    //parse md file and set up the system
158    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
159    SimInfo* info = creator.createSim(dumpFileName);
160  
161    RealType maxLen;
# Line 212 | Line 192 | int main(int argc, char* argv[]){
192                                args_info.nanglebins_arg);
193    } else if (args_info.gxyz_given) {
194      if (args_info.refsele_given) {
195 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
196 <                           maxLen, args_info.nbins_arg);        
195 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
196 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
197      } else {
198        sprintf( painCave.errMsg,
199                 "--refsele must set when --gxyz is used");
# Line 233 | Line 213 | int main(int argc, char* argv[]){
213        simError();
214      }    
215    } else if (args_info.p2_given) {
216 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
216 >    if (args_info.sele1_given) {    
217 >      if (args_info.sele2_given)
218 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
219 >      else
220 >        if (args_info.seleoffset_given)
221 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
222 >                                           args_info.seleoffset_arg);
223 >        else
224 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
225 >    } else {
226 >      sprintf( painCave.errMsg,
227 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
228 >      painCave.severity = OPENMD_ERROR;
229 >      painCave.isFatal = 1;
230 >      simError();
231 >    }
232    } else if (args_info.rp2_given){
233      analyser = new RippleOP(info, dumpFileName, sele1, sele2);
234    } else if (args_info.bo_given){
# Line 261 | Line 256 | int main(int argc, char* argv[]){
256        painCave.isFatal = 1;
257        simError();
258      }
259 <  } else if (args_info.bor_given){
259 >  } else if (args_info.tet_param_z_given) {
260 >    if (args_info.rcut_given) {  
261 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
262 >                                          args_info.rcut_arg,
263 >                                          args_info.nbins_arg);
264 >    } else {
265 >      sprintf( painCave.errMsg,
266 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
267 >      painCave.severity = OPENMD_ERROR;
268 >      painCave.isFatal = 1;
269 >      simError();
270 >    }
271 >  } else if (args_info.ior_given){
272      if (args_info.rcut_given) {
273 <      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
273 >      analyser = new IcosahedralOfR(info, dumpFileName, sele1,
274 >                                    args_info.rcut_arg,
275 >                                    args_info.nbins_arg, maxLen);
276 >    } else {
277 >      sprintf( painCave.errMsg,
278 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
279 >      painCave.severity = OPENMD_ERROR;
280 >      painCave.isFatal = 1;
281 >      simError();
282 >    }
283 >  } else if (args_info.for_given){
284 >    if (args_info.rcut_given) {
285 >      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
286                              args_info.nbins_arg, maxLen);
287      } else {
288        sprintf( painCave.errMsg,
# Line 274 | Line 293 | int main(int argc, char* argv[]){
293      }
294    } else if (args_info.bad_given){
295      if (args_info.rcut_given) {
296 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
296 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
297 >                                           args_info.rcut_arg,
298                                             args_info.nbins_arg);
299      } else {
300        sprintf( painCave.errMsg,
# Line 282 | Line 302 | int main(int argc, char* argv[]){
302        painCave.severity = OPENMD_ERROR;
303        painCave.isFatal = 1;
304        simError();
305 <      }
305 >    }
306    } else if (args_info.scd_given) {
307      if (batchMode) {
308 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
308 >      analyser  = new SCDOrderParameter(info, dumpFileName,
309 >                                        args_info.molname_arg,
310                                          args_info.begin_arg, args_info.end_arg);
311      } else{
312        std::string sele3 = args_info.sele3_arg;
313 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
313 >      analyser  = new SCDOrderParameter(info, dumpFileName,
314 >                                        sele1, sele2, sele3);
315      }
316    }else if (args_info.density_given) {
317      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
# Line 298 | Line 320 | int main(int argc, char* argv[]){
320      analyser = new ObjectCount(info, dumpFileName, sele1 );
321    } else if (args_info.slab_density_given) {
322      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
323 +  } else if (args_info.rnemdz_given) {
324 +    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
325 +  } else if (args_info.rnemdr_given) {
326 +    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
327 +  } else if (args_info.rnemdrt_given) {
328 +    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
329 +                               args_info.nbins_arg, args_info.nanglebins_arg);
330 +  } else if (args_info.nitrile_given) {
331 +    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
332 +                                       args_info.nbins_arg);
333    } else if (args_info.p_angle_given) {
334 <    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
334 >    if (args_info.sele1_given) {    
335 >      if (args_info.sele2_given)
336 >        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
337 >                               args_info.nbins_arg);
338 >      else
339 >        if (args_info.seleoffset_given) {
340 >          if (args_info.seleoffset2_given) {
341 >            analyser  = new pAngle(info, dumpFileName, sele1,
342 >                                   args_info.seleoffset_arg,
343 >                                   args_info.seleoffset2_arg,
344 >                                   args_info.nbins_arg);
345 >          } else {
346 >            analyser  = new pAngle(info, dumpFileName, sele1,
347 >                                   args_info.seleoffset_arg,
348 >                                   args_info.nbins_arg);
349 >          }
350 >        } else
351 >          analyser  = new pAngle(info, dumpFileName, sele1,
352 >                                 args_info.nbins_arg);
353 >    } else {
354 >      sprintf( painCave.errMsg,
355 >               "At least one selection script (--sele1) must be specified when "
356 >               "calculating P(angle) distributions");
357 >      painCave.severity = OPENMD_ERROR;
358 >      painCave.isFatal = 1;
359 >      simError();
360 >    }
361   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
362    }else if (args_info.hxy_given) {
363      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
# Line 317 | Line 375 | int main(int argc, char* argv[]){
375      }
376    } else if (args_info.hullvol_given) {
377      analyser = new NanoVolume(info, dumpFileName, sele1);
378 +  } else if (args_info.rodlength_given) {
379 +    analyser = new NanoLength(info, dumpFileName, sele1);
380    } else if (args_info.angle_r_given) {
381      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
382    }
383 <    
383 >  
384    if (args_info.output_given) {
385      analyser->setOutputName(args_info.output_arg);
386    }
# Line 332 | Line 392 | int main(int argc, char* argv[]){
392    
393    delete analyser;    
394    delete info;
395 <
395 >  
396    return 0;  
397   }
338 –

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