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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 1444 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC

# Line 76 | Line 76 | int main(int argc, char* argv[]){
76  
77   int main(int argc, char* argv[]){
78    
79 <  //register force fields
80 <  registerForceFields();
79 >    //register force fields
80 >    registerForceFields();
81  
82 <  gengetopt_args_info args_info;
82 >    gengetopt_args_info args_info;
83  
84 <  //parse the command line option
85 <  if (cmdline_parser (argc, argv, &args_info) != 0) {
86 <    exit(1) ;
87 <  }
84 >    //parse the command line option
85 >    if (cmdline_parser (argc, argv, &args_info) != 0) {
86 >        exit(1) ;
87 >    }
88  
89 <  //get the dumpfile name
90 <  std::string dumpFileName = args_info.input_arg;
91 <  std::string sele1;
92 <  std::string sele2;
93 <  bool userSpecifiedSelect1;
94 <  bool userSpecifiedSelect2;
89 >    //get the dumpfile name
90 >    std::string dumpFileName = args_info.input_arg;
91 >    std::string sele1;
92 >    std::string sele2;
93 >    bool userSpecifiedSelect1;
94 >    bool userSpecifiedSelect2;
95  
96 <  // check the first selection argument, or set it to the environment
97 <  // variable, or failing that, set it to "select all"
96 >    // check the first selection argument, or set it to the environment
97 >    // variable, or failing that, set it to "select all"
98  
99 <  if (args_info.sele1_given) {
100 <    sele1 = args_info.sele1_arg;
101 <  } else {
102 <    char*  sele1Env= getenv("SELECTION1");
103 <    if (sele1Env) {
104 <      sele1 = sele1Env;
99 >    if (args_info.sele1_given) {
100 >        sele1 = args_info.sele1_arg;
101      } else {
102 <      sele1 = "select all";
102 >        char*  sele1Env= getenv("SELECTION1");
103 >        if (sele1Env) {
104 >            sele1 = sele1Env;
105 >        } else {
106 >            sele1 = "select all";
107 >        }
108      }
108 –  }
109  
110 <  // check the second selection argument, or set it to the environment
111 <  // variable, or failing that, set it to "select all"
110 >    // check the second selection argument, or set it to the environment
111 >    // variable, or failing that, set it to "select all"
112    
113 <  if (args_info.sele2_given) {
114 <    sele2 = args_info.sele2_arg;
115 <  } else {
116 <    char* sele2Env = getenv("SELECTION1");
117 <    if (sele2Env) {
118 <      sele2 = sele2Env;            
119 <    } else {
120 <      sele2 = "select all";
113 >    if (args_info.sele2_given) {
114 >        sele2 = args_info.sele2_arg;
115 >    } else {
116 >        char* sele2Env = getenv("SELECTION1");
117 >        if (sele2Env) {
118 >            sele2 = sele2Env;            
119 >        } else {
120 >            sele2 = "select all";
121 >        }
122      }
122 –  }
123  
124  
125 <  // Problems if sele1 wasn't specified, but
125 >    // Problems if sele1 wasn't specified, but
126   // if (!args_info.scd_given) {
127   //       sprintf( painCave.errMsg,
128   //                "neither --sele1 option nor $SELECTION1 is set");
# Line 132 | Line 132 | int main(int argc, char* argv[]){
132   //     }
133   //   }
134  
135 <  // Problems if sele1 wasn't specified
135 >    // Problems if sele1 wasn't specified
136  
137   //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
138   //       sprintf( painCave.errMsg,
# Line 143 | Line 143 | int main(int argc, char* argv[]){
143   //     }
144   //   }
145  
146 <  bool batchMode;
147 <  if (args_info.scd_given){
148 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
149 <      batchMode = false;
150 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
151 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
152 <        sprintf( painCave.errMsg,
153 <                 "below conditions are not satisfied:\n"
154 <                 "0 <= begin && 0<= end && begin <= end-2\n");
155 <        painCave.severity = OPENMD_ERROR;
156 <        painCave.isFatal = 1;
157 <        simError();                    
158 <      }
159 <      batchMode = true;        
160 <    } else{
161 <      sprintf( painCave.errMsg,
162 <               "either --sele1, --sele2, --sele3 are specified,"
163 <               " or --molname, --begin, --end are specified\n");
164 <      painCave.severity = OPENMD_ERROR;
165 <      painCave.isFatal = 1;
166 <      simError();        
146 >    bool batchMode;
147 >    if (args_info.scd_given){
148 >        if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
149 >            batchMode = false;
150 >        } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
151 >            if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
152 >                sprintf( painCave.errMsg,
153 >                         "below conditions are not satisfied:\n"
154 >                         "0 <= begin && 0<= end && begin <= end-2\n");
155 >                painCave.severity = OPENMD_ERROR;
156 >                painCave.isFatal = 1;
157 >                simError();                    
158 >            }
159 >            batchMode = true;        
160 >        } else{
161 >            sprintf( painCave.errMsg,
162 >                     "either --sele1, --sele2, --sele3 are specified,"
163 >                     " or --molname, --begin, --end are specified\n");
164 >            painCave.severity = OPENMD_ERROR;
165 >            painCave.isFatal = 1;
166 >            simError();        
167      
168 +        }
169      }
169 –  }
170  
171 <  //parse md file and set up the system
172 <  SimCreator creator;
173 <  std::cout << "dumpFile = " << dumpFileName << "\n";
174 <  SimInfo* info = creator.createSim(dumpFileName);
171 >    //parse md file and set up the system
172 >    SimCreator creator;
173 >    std::cout << "dumpFile = " << dumpFileName << "\n";
174 >    SimInfo* info = creator.createSim(dumpFileName);
175  
176 <  RealType maxLen;
177 <  if (args_info.length_given) {
178 <    maxLen = args_info.length_arg;
179 <  } else {
180 <    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
181 <    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
182 <  }    
176 >    RealType maxLen;
177 >    RealType zmaxLen;
178 >    if (args_info.length_given) {
179 >        maxLen = args_info.length_arg;
180 >        if (args_info.zlength_given){
181 >            zmaxLen = args_info.zlength_arg;
182 >        }
183 >    } else {
184 >        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
185 >        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
186 >        zmaxLen = hmat(2,2);    
187 >    }    
188  
189 <  StaticAnalyser* analyser;
190 <  if (args_info.gofr_given){
191 <    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
192 <                       args_info.nbins_arg);        
193 <  } else if (args_info.gofz_given) {
194 <    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
195 <                       args_info.nbins_arg);
196 <  } else if (args_info.r_z_given) {
197 <    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen,
189 >    StaticAnalyser* analyser;
190 >    if (args_info.gofr_given){
191 >        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
192 >                           args_info.nbins_arg);        
193 >    } else if (args_info.gofz_given) {
194 >        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
195 >                           args_info.nbins_arg);
196 >    } else if (args_info.r_z_given) {
197 >        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
198                                args_info.nbins_arg, args_info.nbins_z_arg);
199 <  } else if (args_info.r_theta_given) {
200 <    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
201 <                              args_info.nbins_arg, args_info.nanglebins_arg);
202 <  } else if (args_info.r_omega_given) {
203 <    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
204 <                              args_info.nbins_arg, args_info.nanglebins_arg);
205 <  } else if (args_info.theta_omega_given) {
206 <    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
207 <                              args_info.nanglebins_arg);
208 <  } else if (args_info.gxyz_given) {
209 <    if (args_info.refsele_given) {
210 <      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
211 <                           maxLen, args_info.nbins_arg);        
212 <    } else {
213 <      sprintf( painCave.errMsg,
214 <               "--refsele must set when --gxyz is used");
215 <      painCave.severity = OPENMD_ERROR;
216 <      painCave.isFatal = 1;
217 <      simError();  
218 <    }
219 <  } else if (args_info.p2_given) {
220 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
221 <  } else if (args_info.rp2_given){
222 <    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
223 <  } else if (args_info.bo_given){
224 <    if (args_info.rcut_given) {
225 <      analyser = new BondOrderParameter(info, dumpFileName, sele1,
226 <                                        args_info.rcut_arg,
227 <                                        args_info.nbins_arg);
228 <    } else {
229 <      sprintf( painCave.errMsg,
230 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
231 <      painCave.severity = OPENMD_ERROR;
232 <      painCave.isFatal = 1;
233 <      simError();
234 <    }
235 <  } else if (args_info.bor_given){
236 <    if (args_info.rcut_given) {
237 <      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
238 <                            args_info.nbins_arg, maxLen);
239 <    } else {
240 <      sprintf( painCave.errMsg,
241 <               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
242 <      painCave.severity = OPENMD_ERROR;
243 <      painCave.isFatal = 1;
244 <      simError();
245 <    }
246 <  } else if (args_info.bad_given){
247 <    if (args_info.rcut_given) {
248 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
249 <                            args_info.nbins_arg);
250 <    } else {
251 <      sprintf( painCave.errMsg,
252 <               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
253 <      painCave.severity = OPENMD_ERROR;
254 <      painCave.isFatal = 1;
255 <      simError();
256 <    }
257 <  } else if (args_info.scd_given) {
258 <    if (batchMode) {
259 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
260 <                                        args_info.begin_arg, args_info.end_arg);
261 <    } else{
262 <      std::string sele3 = args_info.sele3_arg;
263 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
264 <    }
265 <  }else if (args_info.density_given) {
266 <    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
267 <                              args_info.nbins_arg);  
268 <  } else if (args_info.slab_density_given) {
269 <    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
270 <  } else if (args_info.p_angle_given) {
271 <    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
199 >    } else if (args_info.r_theta_given) {
200 >        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
201 >                                  args_info.nbins_arg, args_info.nanglebins_arg);
202 >    } else if (args_info.r_omega_given) {
203 >        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
204 >                                  args_info.nbins_arg, args_info.nanglebins_arg);
205 >    } else if (args_info.theta_omega_given) {
206 >        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
207 >                                  args_info.nanglebins_arg);
208 >    } else if (args_info.gxyz_given) {
209 >        if (args_info.refsele_given) {
210 >            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
211 >                                 maxLen, args_info.nbins_arg);        
212 >        } else {
213 >            sprintf( painCave.errMsg,
214 >                     "--refsele must set when --gxyz is used");
215 >            painCave.severity = OPENMD_ERROR;
216 >            painCave.isFatal = 1;
217 >            simError();  
218 >        }
219 >    } else if (args_info.p2_given) {
220 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
221 >    } else if (args_info.rp2_given){
222 >        analyser = new RippleOP(info, dumpFileName, sele1, sele2);
223 >    } else if (args_info.bo_given){
224 >        if (args_info.rcut_given) {
225 >            analyser = new BondOrderParameter(info, dumpFileName, sele1,
226 >                                              args_info.rcut_arg,
227 >                                              args_info.nbins_arg);
228 >        } else {
229 >            sprintf( painCave.errMsg,
230 >                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
231 >            painCave.severity = OPENMD_ERROR;
232 >            painCave.isFatal = 1;
233 >            simError();
234 >        }
235 >    } else if (args_info.bor_given){
236 >        if (args_info.rcut_given) {
237 >            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
238 >                                  args_info.nbins_arg, maxLen);
239 >        } else {
240 >            sprintf( painCave.errMsg,
241 >                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
242 >            painCave.severity = OPENMD_ERROR;
243 >            painCave.isFatal = 1;
244 >            simError();
245 >        }
246 >    } else if (args_info.bad_given){
247 >        if (args_info.rcut_given) {
248 >            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
249 >                                                 args_info.nbins_arg);
250 >        } else {
251 >            sprintf( painCave.errMsg,
252 >                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
253 >            painCave.severity = OPENMD_ERROR;
254 >            painCave.isFatal = 1;
255 >            simError();
256 >        }
257 >    } else if (args_info.scd_given) {
258 >        if (batchMode) {
259 >            analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
260 >                                              args_info.begin_arg, args_info.end_arg);
261 >        } else{
262 >            std::string sele3 = args_info.sele3_arg;
263 >            analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
264 >        }
265 >    }else if (args_info.density_given) {
266 >        analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
267 >                                  args_info.nbins_arg);  
268 >    } else if (args_info.slab_density_given) {
269 >        analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
270 >    } else if (args_info.p_angle_given) {
271 >        analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
272   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
273 <  }else if (args_info.hxy_given) {
274 <    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
275 <                       args_info.nbins_y_arg, args_info.nbins_arg);
273 >    }else if (args_info.hxy_given) {
274 >        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
275 >                           args_info.nbins_y_arg, args_info.nbins_arg);
276   #endif
277 <  }else if (args_info.rho_r_given) {
278 <    if (args_info.radius_given){
279 <      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
280 <    }else{
281 <      sprintf( painCave.errMsg,
282 <               "A particle radius (radius) must be specified when calculating Rho(r)");
283 <      painCave.severity = OPENMD_ERROR;
284 <      painCave.isFatal = 1;
285 <      simError();
277 >    }else if (args_info.rho_r_given) {
278 >        if (args_info.radius_given){
279 >            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
280 >        }else{
281 >            sprintf( painCave.errMsg,
282 >                     "A particle radius (radius) must be specified when calculating Rho(r)");
283 >            painCave.severity = OPENMD_ERROR;
284 >            painCave.isFatal = 1;
285 >            simError();
286 >        }
287 >    }else if (args_info.hullvol_given) {
288 >        analyser = new NanoVolume(info, dumpFileName, sele1);
289      }
282 –        }else if (args_info.hullvol_given) {
283 –    analyser = new NanoVolume(info, dumpFileName, sele1);
284 –  }
290    
291 <  if (args_info.output_given) {
292 <    analyser->setOutputName(args_info.output_arg);
293 <  }
294 <  if (args_info.step_given) {
295 <    analyser->setStep(args_info.step_arg);
296 <  }
291 >    if (args_info.output_given) {
292 >        analyser->setOutputName(args_info.output_arg);
293 >    }
294 >    if (args_info.step_given) {
295 >        analyser->setStep(args_info.step_arg);
296 >    }
297  
298 <  analyser->process();
298 >    analyser->process();
299  
300 <  delete analyser;    
301 <  delete info;
300 >    delete analyser;    
301 >    delete info;
302  
303 <  return 0;  
303 >    return 0;  
304   }
305  

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