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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 2015 by gezelter, Wed Aug 13 20:42:43 2014 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

# Line 81 | Line 81
81   #include "applications/staticProps/RNEMDStats.hpp"
82   #include "applications/staticProps/NitrileFrequencyMap.hpp"
83   #include "applications/staticProps/MultipoleSum.hpp"
84 + #include "applications/staticProps/SurfaceDiffusion.hpp"
85 + #include "applications/staticProps/HBondGeometric.hpp"
86  
87   using namespace OpenMD;
88  
# Line 98 | Line 100 | int main(int argc, char* argv[]){
100    std::string dumpFileName = args_info.input_arg;
101    std::string sele1;
102    std::string sele2;
103 +  std::string sele3;
104    
105    // check the first selection argument, or set it to the environment
106    // variable, or failing that, set it to "select all"
# Line 129 | Line 132 | int main(int argc, char* argv[]){
132      }
133    }
134  
135 <  bool batchMode;
135 >  // check the third selection argument, which is only set if
136 >  // requested by the user
137 >
138 >  if (args_info.sele3_given) sele3 = args_info.sele3_arg;
139 >
140 >  bool batchMode(false);
141    if (args_info.scd_given){
142      if (args_info.sele1_given &&
143          args_info.sele2_given && args_info.sele3_given) {
# Line 161 | Line 169 | int main(int argc, char* argv[]){
169    SimInfo* info = creator.createSim(dumpFileName);
170  
171    RealType maxLen;
172 <  RealType zmaxLen;
172 >  RealType zmaxLen(0.0);
173    if (args_info.length_given) {
174      maxLen = args_info.length_arg;
175      if (args_info.zlength_given){
# Line 184 | Line 192 | int main(int argc, char* argv[]){
192      analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
193                            args_info.nbins_arg, args_info.nbins_z_arg);
194    } else if (args_info.r_theta_given) {
195 <    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
196 <                              args_info.nbins_arg, args_info.nanglebins_arg);
195 >    if (args_info.sele3_given)
196 >      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
197 >                                args_info.nbins_arg, args_info.nanglebins_arg);
198 >    else
199 >      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
200 >                                args_info.nbins_arg, args_info.nanglebins_arg);
201    } else if (args_info.r_omega_given) {
202 <    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
203 <                              args_info.nbins_arg, args_info.nanglebins_arg);
202 >    if (args_info.sele3_given)
203 >      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
204 >                                args_info.nbins_arg, args_info.nanglebins_arg);
205 >    else
206 >      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
207 >                                args_info.nbins_arg, args_info.nanglebins_arg);
208 >
209    } else if (args_info.theta_omega_given) {
210 <    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
211 <                              args_info.nanglebins_arg);
210 >    if (args_info.sele3_given)
211 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
212 >                                args_info.nanglebins_arg);
213 >    else
214 >      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
215 >                                args_info.nanglebins_arg);
216    } else if (args_info.gxyz_given) {
217      if (args_info.refsele_given) {
218        analyser= new GofXyz(info, dumpFileName, sele1, sele2,
# Line 342 | Line 363 | int main(int argc, char* argv[]){
363                                          args_info.molname_arg,
364                                          args_info.begin_arg, args_info.end_arg);
365      } else{
345 –      std::string sele3 = args_info.sele3_arg;
366        analyser  = new SCDOrderParameter(info, dumpFileName,
367                                          sele1, sele2, sele3);
368      }
# Line 396 | Line 416 | int main(int argc, char* argv[]){
416      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
417                         args_info.nbins_y_arg, args_info.nbins_arg);
418   #endif
419 +  }else if (args_info.surfDiffusion_given){
420 +    analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen);
421    }else if (args_info.rho_r_given) {
422      if (args_info.radius_given){
423        analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
# Line 412 | Line 434 | int main(int argc, char* argv[]){
434      analyser = new NanoLength(info, dumpFileName, sele1);
435    } else if (args_info.angle_r_given) {
436      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
437 +  } else if (args_info.hbond_given){
438 +    if (args_info.rcut_given) {
439 +      if (args_info.thetacut_given) {
440 +        
441 +        analyser = new HBondGeometric(info, dumpFileName, sele1, sele2,
442 +                                      args_info.rcut_arg,
443 +                                      args_info.thetacut_arg,
444 +                                      args_info.nbins_arg);
445 +      } else {
446 +        sprintf( painCave.errMsg,
447 +                 "A cutoff angle (thetacut) must be specified when calculating Hydrogen Bonding Statistics");
448 +        painCave.severity = OPENMD_ERROR;
449 +        painCave.isFatal = 1;
450 +        simError();
451 +      }
452 +    } else {
453 +      sprintf( painCave.errMsg,
454 +               "A cutoff radius (rcut) must be specified when calculating Hydrogen Bonding Statistics");
455 +      painCave.severity = OPENMD_ERROR;
456 +      painCave.isFatal = 1;
457 +      simError();
458 +    }    
459    }
460    
461    if (args_info.output_given) {

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