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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 1846 by gezelter, Thu Jan 31 15:55:47 2013 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).          
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 + #include "applications/staticProps/NitrileFrequencyMap.hpp"
82 +
83   using namespace OpenMD;
84  
85   int main(int argc, char* argv[]){
# Line 109 | 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 {
# Line 265 | Line 268 | int main(int argc, char* argv[]){
268        painCave.isFatal = 1;
269        simError();
270      }
271 <  } else if (args_info.bor_given){
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 305 | 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,

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