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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 1542 by gezelter, Thu Mar 3 20:32:49 2011 UTC vs.
Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

# Line 36 | Line 36
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).                        
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 <
79 > #include "applications/staticProps/TetrahedralityParamZ.hpp"
80   using namespace OpenMD;
81  
82   int main(int argc, char* argv[]){
83    
84 –  //register force fields
85 –  registerForceFields();
84    
85    gengetopt_args_info args_info;
86    
# Line 95 | Line 93 | int main(int argc, char* argv[]){
93    std::string dumpFileName = args_info.input_arg;
94    std::string sele1;
95    std::string sele2;
98 –  bool userSpecifiedSelect1;
99 –  bool userSpecifiedSelect2;
96    
97    // check the first selection argument, or set it to the environment
98    // variable, or failing that, set it to "select all"
# Line 122 | Line 118 | int main(int argc, char* argv[]){
118      if (sele2Env) {
119        sele2 = sele2Env;            
120      } else {
121 <      sele2 = "select all";
121 >      //If sele2 is not specified, then the default behavior
122 >      //should be what is already intended for sele1
123 >      sele2 = sele1;
124 >      //sele2 = "select all";
125      }
126    }
127    
# Line 237 | Line 236 | int main(int argc, char* argv[]){
236        if (args_info.sele2_given)
237          analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
238        else
239 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
239 >        if (args_info.seleoffset_given)
240 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
241 >                                           args_info.seleoffset_arg);
242 >        else
243 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
244      } else {
245        sprintf( painCave.errMsg,
246                 "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
# Line 272 | Line 275 | int main(int argc, char* argv[]){
275        painCave.isFatal = 1;
276        simError();
277      }
278 +  } else if (args_info.tet_param_z_given) {
279 +    if (args_info.rcut_given) {  
280 +      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
281 +                                         args_info.rcut_arg,
282 +                                         args_info.nbins_arg);
283 +    } else {
284 +      sprintf( painCave.errMsg,
285 +               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
286 +      painCave.severity = OPENMD_ERROR;
287 +      painCave.isFatal = 1;
288 +      simError();
289 +    }
290    } else if (args_info.bor_given){
291      if (args_info.rcut_given) {
292        analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
# Line 328 | Line 343 | int main(int argc, char* argv[]){
343      }
344    } else if (args_info.hullvol_given) {
345      analyser = new NanoVolume(info, dumpFileName, sele1);
346 +  } else if (args_info.rodlength_given) {
347 +    analyser = new NanoLength(info, dumpFileName, sele1);
348    } else if (args_info.angle_r_given) {
349      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
350    }
# Line 338 | Line 355 | int main(int argc, char* argv[]){
355    if (args_info.step_given) {
356      analyser->setStep(args_info.step_arg);
357    }
358 <  
358 >
359    analyser->process();
360    
361    delete analyser;    

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