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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 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 {
# Line 265 | 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 305 | 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,

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