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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 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC vs.
Revision 1513 by gezelter, Tue Oct 19 18:40:54 2010 UTC

# Line 57 | Line 57
57   #include "applications/staticProps/GofRAngle.hpp"
58   #include "applications/staticProps/GofAngle2.hpp"
59   #include "applications/staticProps/GofXyz.hpp"
60 + #include "applications/staticProps/TwoDGofR.hpp"
61   #include "applications/staticProps/P2OrderParameter.hpp"
62   #include "applications/staticProps/BondOrderParameter.hpp"
63   #include "applications/staticProps/BOPofR.hpp"
64   #include "applications/staticProps/RippleOP.hpp"
65   #include "applications/staticProps/SCDOrderParameter.hpp"
66   #include "applications/staticProps/DensityPlot.hpp"
67 + #include "applications/staticProps/ObjectCount.hpp"
68   #include "applications/staticProps/RhoZ.hpp"
69   #include "applications/staticProps/pAngle.hpp"
70   #include "applications/staticProps/BondAngleDistribution.hpp"
# Line 76 | Line 78 | int main(int argc, char* argv[]){
78  
79   int main(int argc, char* argv[]){
80    
81 <    //register force fields
82 <    registerForceFields();
83 <
84 <    gengetopt_args_info args_info;
85 <
86 <    //parse the command line option
87 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
88 <        exit(1) ;
89 <    }
90 <
91 <    //get the dumpfile name
92 <    std::string dumpFileName = args_info.input_arg;
93 <    std::string sele1;
94 <    std::string sele2;
95 <    bool userSpecifiedSelect1;
96 <    bool userSpecifiedSelect2;
97 <
98 <    // check the first selection argument, or set it to the environment
99 <    // variable, or failing that, set it to "select all"
100 <
101 <    if (args_info.sele1_given) {
102 <        sele1 = args_info.sele1_arg;
81 >  //register force fields
82 >  registerForceFields();
83 >  
84 >  gengetopt_args_info args_info;
85 >  
86 >  //parse the command line option
87 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
88 >    exit(1) ;
89 >  }
90 >  
91 >  //get the dumpfile name
92 >  std::string dumpFileName = args_info.input_arg;
93 >  std::string sele1;
94 >  std::string sele2;
95 >  bool userSpecifiedSelect1;
96 >  bool userSpecifiedSelect2;
97 >  
98 >  // check the first selection argument, or set it to the environment
99 >  // variable, or failing that, set it to "select all"
100 >  
101 >  if (args_info.sele1_given) {
102 >    sele1 = args_info.sele1_arg;
103 >  } else {
104 >    char*  sele1Env= getenv("SELECTION1");
105 >    if (sele1Env) {
106 >      sele1 = sele1Env;
107      } else {
108 <        char*  sele1Env= getenv("SELECTION1");
103 <        if (sele1Env) {
104 <            sele1 = sele1Env;
105 <        } else {
106 <            sele1 = "select all";
107 <        }
108 >      sele1 = "select all";
109      }
110 <
110 <    // check the second selection argument, or set it to the environment
111 <    // variable, or failing that, set it to "select all"
110 >  }
111    
112 <    if (args_info.sele2_given) {
113 <        sele2 = args_info.sele2_arg;
114 <    } else {
115 <        char* sele2Env = getenv("SELECTION1");
116 <        if (sele2Env) {
117 <            sele2 = sele2Env;            
118 <        } else {
119 <            sele2 = "select all";
120 <        }
112 >  // check the second selection argument, or set it to the environment
113 >  // variable, or failing that, set it to "select all"
114 >  
115 >  if (args_info.sele2_given) {
116 >    sele2 = args_info.sele2_arg;
117 >  } else {
118 >    char* sele2Env = getenv("SELECTION1");
119 >    if (sele2Env) {
120 >      sele2 = sele2Env;            
121 >    } else {
122 >      sele2 = "select all";
123      }
124 +  }
125 +  
126 +  
127 +  // Problems if sele1 wasn't specified, but
128 +  // if (!args_info.scd_given) {
129 +  //       sprintf( painCave.errMsg,
130 +  //                "neither --sele1 option nor $SELECTION1 is set");
131 +  //       painCave.severity = OPENMD_ERROR;
132 +  //       painCave.isFatal = 1;
133 +  //       simError();
134 +  //     }
135 +  //   }
136 +  
137 +  // Problems if sele1 wasn't specified
138 +  
139 +  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
140 +  //       sprintf( painCave.errMsg,
141 +  //                "neither --sele2 option nor $SELECTION1 is set");
142 +  //       painCave.severity = OPENMD_ERROR;
143 +  //       painCave.isFatal = 1;
144 +  //       simError();        
145 +  //     }
146 +  //   }
147 +  
148 +  bool batchMode;
149 +  if (args_info.scd_given){
150 +    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
151 +      batchMode = false;
152 +    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
153 +      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
154 +        sprintf( painCave.errMsg,
155 +                 "below conditions are not satisfied:\n"
156 +                 "0 <= begin && 0<= end && begin <= end-2\n");
157 +        painCave.severity = OPENMD_ERROR;
158 +        painCave.isFatal = 1;
159 +        simError();                    
160 +      }
161 +      batchMode = true;        
162 +    } else{
163 +      sprintf( painCave.errMsg,
164 +               "either --sele1, --sele2, --sele3 are specified,"
165 +               " or --molname, --begin, --end are specified\n");
166 +      painCave.severity = OPENMD_ERROR;
167 +      painCave.isFatal = 1;
168 +      simError();        
169 +      
170 +    }
171 +  }
172 +  
173 +  //parse md file and set up the system
174 +  SimCreator creator;
175 +  std::cout << "dumpFile = " << dumpFileName << "\n";
176 +  SimInfo* info = creator.createSim(dumpFileName);
177  
178 <
179 <    // Problems if sele1 wasn't specified, but
180 < // if (!args_info.scd_given) {
181 < //       sprintf( painCave.errMsg,
182 < //                "neither --sele1 option nor $SELECTION1 is set");
183 < //       painCave.severity = OPENMD_ERROR;
130 < //       painCave.isFatal = 1;
131 < //       simError();
132 < //     }
133 < //   }
134 <
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,
139 < //                "neither --sele2 option nor $SELECTION1 is set");
140 < //       painCave.severity = OPENMD_ERROR;
141 < //       painCave.isFatal = 1;
142 < //       simError();        
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();        
167 <    
168 <        }
178 >  RealType maxLen;
179 >  RealType zmaxLen;
180 >  if (args_info.length_given) {
181 >    maxLen = args_info.length_arg;
182 >    if (args_info.zlength_given){
183 >      zmaxLen = args_info.zlength_arg;
184      }
185 +  } else {
186 +    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
187 +    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
188 +    zmaxLen = hmat(2,2);    
189 +  }    
190  
191 <    //parse md file and set up the system
192 <    SimCreator creator;
193 <    std::cout << "dumpFile = " << dumpFileName << "\n";
194 <    SimInfo* info = creator.createSim(dumpFileName);
195 <
196 <    RealType maxLen;
197 <    RealType zmaxLen;
198 <    if (args_info.length_given) {
199 <        maxLen = args_info.length_arg;
200 <        if (args_info.zlength_given){
201 <            zmaxLen = args_info.zlength_arg;
202 <        }
203 <    } else {
204 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
205 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
206 <        zmaxLen = hmat(2,2);    
207 <    }    
208 <
209 <    StaticAnalyser* analyser;
210 <    if (args_info.gofr_given){
211 <        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
212 <                           args_info.nbins_arg);        
213 <    } else if (args_info.gofz_given) {
214 <        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
215 <                           args_info.nbins_arg);
216 <    } else if (args_info.r_z_given) {
217 <        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
218 <                              args_info.nbins_arg, args_info.nbins_z_arg);
219 <    } else if (args_info.r_theta_given) {
220 <        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
221 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
222 <    } else if (args_info.r_omega_given) {
223 <        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
224 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
225 <    } else if (args_info.theta_omega_given) {
226 <        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
227 <                                  args_info.nanglebins_arg);
228 <    } else if (args_info.gxyz_given) {
229 <        if (args_info.refsele_given) {
230 <            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
231 <                                 maxLen, args_info.nbins_arg);        
232 <        } else {
233 <            sprintf( painCave.errMsg,
234 <                     "--refsele must set when --gxyz is used");
235 <            painCave.severity = OPENMD_ERROR;
236 <            painCave.isFatal = 1;
237 <            simError();  
238 <        }
239 <    } else if (args_info.p2_given) {
240 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
241 <    } else if (args_info.rp2_given){
242 <        analyser = new RippleOP(info, dumpFileName, sele1, sele2);
243 <    } else if (args_info.bo_given){
244 <        if (args_info.rcut_given) {
245 <            analyser = new BondOrderParameter(info, dumpFileName, sele1,
246 <                                              args_info.rcut_arg,
247 <                                              args_info.nbins_arg);
248 <        } else {
249 <            sprintf( painCave.errMsg,
250 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
251 <            painCave.severity = OPENMD_ERROR;
252 <            painCave.isFatal = 1;
253 <            simError();
254 <        }
255 <    } else if (args_info.bor_given){
256 <        if (args_info.rcut_given) {
257 <            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
258 <                                  args_info.nbins_arg, maxLen);
259 <        } else {
260 <            sprintf( painCave.errMsg,
261 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
262 <            painCave.severity = OPENMD_ERROR;
263 <            painCave.isFatal = 1;
264 <            simError();
265 <        }
266 <    } else if (args_info.bad_given){
267 <        if (args_info.rcut_given) {
268 <            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
269 <                                                 args_info.nbins_arg);
270 <        } else {
271 <            sprintf( painCave.errMsg,
272 <                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
273 <            painCave.severity = OPENMD_ERROR;
274 <            painCave.isFatal = 1;
275 <            simError();
276 <        }
277 <    } else if (args_info.scd_given) {
278 <        if (batchMode) {
279 <            analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
280 <                                              args_info.begin_arg, args_info.end_arg);
281 <        } else{
282 <            std::string sele3 = args_info.sele3_arg;
283 <            analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
284 <        }
285 <    }else if (args_info.density_given) {
286 <        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);
191 >  StaticAnalyser* analyser;
192 >  if (args_info.gofr_given){
193 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
194 >                       args_info.nbins_arg);        
195 >  } else if (args_info.gofz_given) {
196 >    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
197 >                       args_info.nbins_arg);
198 >  } else if (args_info.r_z_given) {
199 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
200 >                          args_info.nbins_arg, args_info.nbins_z_arg);
201 >  } else if (args_info.r_theta_given) {
202 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
203 >                              args_info.nbins_arg, args_info.nanglebins_arg);
204 >  } else if (args_info.r_omega_given) {
205 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
206 >                              args_info.nbins_arg, args_info.nanglebins_arg);
207 >  } else if (args_info.theta_omega_given) {
208 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
209 >                              args_info.nanglebins_arg);
210 >  } else if (args_info.gxyz_given) {
211 >    if (args_info.refsele_given) {
212 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
213 >                           maxLen, args_info.nbins_arg);        
214 >    } else {
215 >      sprintf( painCave.errMsg,
216 >               "--refsele must set when --gxyz is used");
217 >      painCave.severity = OPENMD_ERROR;
218 >      painCave.isFatal = 1;
219 >      simError();  
220 >    }
221 >  } else if (args_info.twodgofr_given){
222 >    if (args_info.dz_given) {
223 >      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
224 >                             args_info.dz_arg, args_info.nbins_arg);        
225 >    } else {
226 >      sprintf( painCave.errMsg,
227 >               "A slab width (dz) must be specified when calculating TwoDGofR");
228 >      painCave.severity = OPENMD_ERROR;
229 >      painCave.isFatal = 1;
230 >      simError();
231 >    }
232 >  } else if (args_info.p2_given) {
233 >    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
234 >  } else if (args_info.rp2_given){
235 >    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
236 >  } else if (args_info.bo_given){
237 >    if (args_info.rcut_given) {
238 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
239 >                                        args_info.rcut_arg,
240 >                                        args_info.nbins_arg);
241 >    } else {
242 >      sprintf( painCave.errMsg,
243 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
244 >      painCave.severity = OPENMD_ERROR;
245 >      painCave.isFatal = 1;
246 >      simError();
247 >    }
248 >  } else if (args_info.bor_given){
249 >    if (args_info.rcut_given) {
250 >      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
251 >                            args_info.nbins_arg, maxLen);
252 >    } else {
253 >      sprintf( painCave.errMsg,
254 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
255 >      painCave.severity = OPENMD_ERROR;
256 >      painCave.isFatal = 1;
257 >      simError();
258 >    }
259 >  } else if (args_info.bad_given){
260 >    if (args_info.rcut_given) {
261 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
262 >                                           args_info.nbins_arg);
263 >    } else {
264 >      sprintf( painCave.errMsg,
265 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
266 >      painCave.severity = OPENMD_ERROR;
267 >      painCave.isFatal = 1;
268 >      simError();
269 >    }
270 >  } else if (args_info.scd_given) {
271 >    if (batchMode) {
272 >      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
273 >                                        args_info.begin_arg, args_info.end_arg);
274 >    } else{
275 >      std::string sele3 = args_info.sele3_arg;
276 >      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
277 >    }
278 >  }else if (args_info.density_given) {
279 >    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
280 >                              args_info.nbins_arg);  
281 >  } else if (args_info.count_given) {
282 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
283 >  } else if (args_info.slab_density_given) {
284 >    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
285 >  } else if (args_info.p_angle_given) {
286 >    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
287   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
288 <    }else if (args_info.hxy_given) {
289 <        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
290 <                           args_info.nbins_y_arg, args_info.nbins_arg);
288 >  }else if (args_info.hxy_given) {
289 >    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
290 >                       args_info.nbins_y_arg, args_info.nbins_arg);
291   #endif
292 <    }else if (args_info.rho_r_given) {
293 <        if (args_info.radius_given){
294 <            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
295 <        }else{
296 <            sprintf( painCave.errMsg,
297 <                     "A particle radius (radius) must be specified when calculating Rho(r)");
298 <            painCave.severity = OPENMD_ERROR;
299 <            painCave.isFatal = 1;
300 <            simError();
286 <        }
287 <    }else if (args_info.hullvol_given) {
288 <        analyser = new NanoVolume(info, dumpFileName, sele1);
292 >  }else if (args_info.rho_r_given) {
293 >    if (args_info.radius_given){
294 >      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
295 >    }else{
296 >      sprintf( painCave.errMsg,
297 >               "A particle radius (radius) must be specified when calculating Rho(r)");
298 >      painCave.severity = OPENMD_ERROR;
299 >      painCave.isFatal = 1;
300 >      simError();
301      }
302 +  }else if (args_info.hullvol_given) {
303 +    analyser = new NanoVolume(info, dumpFileName, sele1);
304 +  }
305    
306 <    if (args_info.output_given) {
307 <        analyser->setOutputName(args_info.output_arg);
308 <    }
309 <    if (args_info.step_given) {
310 <        analyser->setStep(args_info.step_arg);
311 <    }
306 >  if (args_info.output_given) {
307 >    analyser->setOutputName(args_info.output_arg);
308 >  }
309 >  if (args_info.step_given) {
310 >    analyser->setStep(args_info.step_arg);
311 >  }
312  
313 <    analyser->process();
313 >  analyser->process();
314  
315 <    delete analyser;    
316 <    delete info;
315 >  delete analyser;    
316 >  delete info;
317  
318 <    return 0;  
318 >  return 0;  
319   }
320  

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