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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 1522 by kstocke1, Fri Nov 19 20:26:36 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 71 | Line 73
73   #include "applications/staticProps/Hxy.hpp"
74   #endif
75   #include "applications/staticProps/RhoR.hpp"
76 + #include "applications/staticProps/AngleR.hpp"
77 + #include "applications/staticProps/RhoAngleR.hpp"
78 + #include "applications/staticProps/TetrahedralityParam.hpp"
79  
80   using namespace OpenMD;
81  
82   int main(int argc, char* argv[]){
83    
84 <    //register force fields
85 <    registerForceFields();
86 <
87 <    gengetopt_args_info args_info;
88 <
89 <    //parse the command line option
90 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
91 <        exit(1) ;
92 <    }
93 <
94 <    //get the dumpfile name
95 <    std::string dumpFileName = args_info.input_arg;
96 <    std::string sele1;
97 <    std::string sele2;
98 <    bool userSpecifiedSelect1;
99 <    bool userSpecifiedSelect2;
100 <
101 <    // check the first selection argument, or set it to the environment
102 <    // variable, or failing that, set it to "select all"
103 <
104 <    if (args_info.sele1_given) {
105 <        sele1 = args_info.sele1_arg;
84 >  //register force fields
85 >  registerForceFields();
86 >  
87 >  gengetopt_args_info args_info;
88 >  
89 >  //parse the command line option
90 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
91 >    exit(1) ;
92 >  }
93 >  
94 >  //get the dumpfile name
95 >  std::string dumpFileName = args_info.input_arg;
96 >  std::string sele1;
97 >  std::string sele2;
98 >  bool userSpecifiedSelect1;
99 >  bool userSpecifiedSelect2;
100 >  
101 >  // check the first selection argument, or set it to the environment
102 >  // variable, or failing that, set it to "select all"
103 >  
104 >  if (args_info.sele1_given) {
105 >    sele1 = args_info.sele1_arg;
106 >  } else {
107 >    char*  sele1Env= getenv("SELECTION1");
108 >    if (sele1Env) {
109 >      sele1 = sele1Env;
110      } else {
111 <        char*  sele1Env= getenv("SELECTION1");
103 <        if (sele1Env) {
104 <            sele1 = sele1Env;
105 <        } else {
106 <            sele1 = "select all";
107 <        }
111 >      sele1 = "select all";
112      }
113 <
110 <    // check the second selection argument, or set it to the environment
111 <    // variable, or failing that, set it to "select all"
113 >  }
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 <        }
115 >  // check the second selection argument, or set it to the environment
116 >  // variable, or failing that, set it to "select all"
117 >  
118 >  if (args_info.sele2_given) {
119 >    sele2 = args_info.sele2_arg;
120 >  } else {
121 >    char* sele2Env = getenv("SELECTION1");
122 >    if (sele2Env) {
123 >      sele2 = sele2Env;            
124 >    } else {
125 >      sele2 = "select all";
126      }
127 <
128 <
129 <    // Problems if sele1 wasn't specified, but
130 < // if (!args_info.scd_given) {
131 < //       sprintf( painCave.errMsg,
132 < //                "neither --sele1 option nor $SELECTION1 is set");
133 < //       painCave.severity = OPENMD_ERROR;
134 < //       painCave.isFatal = 1;
135 < //       simError();
136 < //     }
137 < //   }
138 <
139 <    // Problems if sele1 wasn't specified
140 <
141 < //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
142 < //       sprintf( painCave.errMsg,
143 < //                "neither --sele2 option nor $SELECTION1 is set");
144 < //       painCave.severity = OPENMD_ERROR;
145 < //       painCave.isFatal = 1;
146 < //       simError();        
147 < //     }
148 < //   }
149 <
150 <    bool batchMode;
151 <    if (args_info.scd_given){
152 <        if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
153 <            batchMode = false;
154 <        } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
155 <            if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
156 <                sprintf( painCave.errMsg,
157 <                         "below conditions are not satisfied:\n"
158 <                         "0 <= begin && 0<= end && begin <= end-2\n");
159 <                painCave.severity = OPENMD_ERROR;
160 <                painCave.isFatal = 1;
161 <                simError();                    
162 <            }
163 <            batchMode = true;        
164 <        } else{
165 <            sprintf( painCave.errMsg,
166 <                     "either --sele1, --sele2, --sele3 are specified,"
167 <                     " or --molname, --begin, --end are specified\n");
168 <            painCave.severity = OPENMD_ERROR;
169 <            painCave.isFatal = 1;
170 <            simError();        
171 <    
172 <        }
127 >  }
128 >  
129 >  
130 >  // Problems if sele1 wasn't specified, but
131 >  // if (!args_info.scd_given) {
132 >  //       sprintf( painCave.errMsg,
133 >  //                "neither --sele1 option nor $SELECTION1 is set");
134 >  //       painCave.severity = OPENMD_ERROR;
135 >  //       painCave.isFatal = 1;
136 >  //       simError();
137 >  //     }
138 >  //   }
139 >  
140 >  // Problems if sele1 wasn't specified
141 >  
142 >  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
143 >  //       sprintf( painCave.errMsg,
144 >  //                "neither --sele2 option nor $SELECTION1 is set");
145 >  //       painCave.severity = OPENMD_ERROR;
146 >  //       painCave.isFatal = 1;
147 >  //       simError();        
148 >  //     }
149 >  //   }
150 >  
151 >  bool batchMode;
152 >  if (args_info.scd_given){
153 >    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
154 >      batchMode = false;
155 >    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
156 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
157 >        sprintf( painCave.errMsg,
158 >                 "below conditions are not satisfied:\n"
159 >                 "0 <= begin && 0<= end && begin <= end-2\n");
160 >        painCave.severity = OPENMD_ERROR;
161 >        painCave.isFatal = 1;
162 >        simError();                    
163 >      }
164 >      batchMode = true;        
165 >    } else{
166 >      sprintf( painCave.errMsg,
167 >               "either --sele1, --sele2, --sele3 are specified,"
168 >               " or --molname, --begin, --end are specified\n");
169 >      painCave.severity = OPENMD_ERROR;
170 >      painCave.isFatal = 1;
171 >      simError();        
172 >      
173      }
174 +  }
175 +  
176 +  //parse md file and set up the system
177 +  SimCreator creator;
178 +  std::cout << "dumpFile = " << dumpFileName << "\n";
179 +  SimInfo* info = creator.createSim(dumpFileName);
180  
181 <    //parse md file and set up the system
182 <    SimCreator creator;
183 <    std::cout << "dumpFile = " << dumpFileName << "\n";
184 <    SimInfo* info = creator.createSim(dumpFileName);
185 <
186 <    RealType maxLen;
187 <    RealType zmaxLen;
188 <    if (args_info.length_given) {
189 <        maxLen = args_info.length_arg;
190 <        if (args_info.zlength_given){
191 <            zmaxLen = args_info.zlength_arg;
192 <        }
181 >  RealType maxLen;
182 >  RealType zmaxLen;
183 >  if (args_info.length_given) {
184 >    maxLen = args_info.length_arg;
185 >    if (args_info.zlength_given){
186 >      zmaxLen = args_info.zlength_arg;
187 >    }
188 >  } else {
189 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
190 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
191 >    zmaxLen = hmat(2,2);    
192 >  }    
193 >  
194 >  StaticAnalyser* analyser;
195 >  if (args_info.gofr_given){
196 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
197 >                       args_info.nbins_arg);        
198 >  } else if (args_info.gofz_given) {
199 >    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
200 >                       args_info.nbins_arg);
201 >  } else if (args_info.r_z_given) {
202 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
203 >                          args_info.nbins_arg, args_info.nbins_z_arg);
204 >  } else if (args_info.r_theta_given) {
205 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
206 >                              args_info.nbins_arg, args_info.nanglebins_arg);
207 >  } else if (args_info.r_omega_given) {
208 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
209 >                              args_info.nbins_arg, args_info.nanglebins_arg);
210 >  } else if (args_info.theta_omega_given) {
211 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
212 >                              args_info.nanglebins_arg);
213 >  } else if (args_info.gxyz_given) {
214 >    if (args_info.refsele_given) {
215 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
216 >                           maxLen, args_info.nbins_arg);        
217      } else {
218 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
219 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
220 <        zmaxLen = hmat(2,2);    
218 >      sprintf( painCave.errMsg,
219 >               "--refsele must set when --gxyz is used");
220 >      painCave.severity = OPENMD_ERROR;
221 >      painCave.isFatal = 1;
222 >      simError();  
223 >    }
224 >  } else if (args_info.twodgofr_given){
225 >    if (args_info.dz_given) {
226 >      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
227 >                             args_info.dz_arg, args_info.nbins_arg);        
228 >    } else {
229 >      sprintf( painCave.errMsg,
230 >               "A slab width (dz) must be specified when calculating TwoDGofR");
231 >      painCave.severity = OPENMD_ERROR;
232 >      painCave.isFatal = 1;
233 >      simError();
234      }    
235 <
236 <    StaticAnalyser* analyser;
237 <    if (args_info.gofr_given){
238 <        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
239 <                           args_info.nbins_arg);        
240 <    } else if (args_info.gofz_given) {
241 <        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
242 <                           args_info.nbins_arg);
243 <    } else if (args_info.r_z_given) {
244 <        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
245 <                              args_info.nbins_arg, args_info.nbins_z_arg);
246 <    } else if (args_info.r_theta_given) {
247 <        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
248 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
249 <    } else if (args_info.r_omega_given) {
250 <        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
251 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
252 <    } else if (args_info.theta_omega_given) {
253 <        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
254 <                                  args_info.nanglebins_arg);
255 <    } else if (args_info.gxyz_given) {
256 <        if (args_info.refsele_given) {
257 <            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
258 <                                 maxLen, args_info.nbins_arg);        
259 <        } else {
260 <            sprintf( painCave.errMsg,
261 <                     "--refsele must set when --gxyz is used");
262 <            painCave.severity = OPENMD_ERROR;
263 <            painCave.isFatal = 1;
264 <            simError();  
265 <        }
266 <    } else if (args_info.p2_given) {
267 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
268 <    } else if (args_info.rp2_given){
269 <        analyser = new RippleOP(info, dumpFileName, sele1, sele2);
270 <    } else if (args_info.bo_given){
271 <        if (args_info.rcut_given) {
272 <            analyser = new BondOrderParameter(info, dumpFileName, sele1,
273 <                                              args_info.rcut_arg,
274 <                                              args_info.nbins_arg);
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.bor_given){
283 <        if (args_info.rcut_given) {
284 <            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
285 <                                  args_info.nbins_arg, maxLen);
286 <        } else {
287 <            sprintf( painCave.errMsg,
288 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
289 <            painCave.severity = OPENMD_ERROR;
290 <            painCave.isFatal = 1;
291 <            simError();
292 <        }
293 <    } else if (args_info.bad_given){
294 <        if (args_info.rcut_given) {
295 <            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
296 <                                                 args_info.nbins_arg);
297 <        } else {
298 <            sprintf( painCave.errMsg,
299 <                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
300 <            painCave.severity = OPENMD_ERROR;
301 <            painCave.isFatal = 1;
302 <            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);
235 >  } else if (args_info.p2_given) {
236 >    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
237 >  } else if (args_info.rp2_given){
238 >    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
239 >  } else if (args_info.bo_given){
240 >    if (args_info.rcut_given) {
241 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
242 >                                        args_info.rcut_arg,
243 >                                        args_info.nbins_arg);
244 >    } else {
245 >      sprintf( painCave.errMsg,
246 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
247 >      painCave.severity = OPENMD_ERROR;
248 >      painCave.isFatal = 1;
249 >      simError();
250 >    }
251 >    
252 >  } else if (args_info.tet_param_given) {
253 >    if (args_info.rcut_given) {  
254 >      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
255 >                                         args_info.rcut_arg,
256 >                                         args_info.nbins_arg);
257 >    } else {
258 >      sprintf( painCave.errMsg,
259 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
260 >      painCave.severity = OPENMD_ERROR;
261 >      painCave.isFatal = 1;
262 >      simError();
263 >    }
264 >  } else if (args_info.bor_given){
265 >    if (args_info.rcut_given) {
266 >      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
267 >                            args_info.nbins_arg, maxLen);
268 >    } else {
269 >      sprintf( painCave.errMsg,
270 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
271 >      painCave.severity = OPENMD_ERROR;
272 >      painCave.isFatal = 1;
273 >      simError();
274 >    }
275 >  } else if (args_info.bad_given){
276 >    if (args_info.rcut_given) {
277 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
278 >                                           args_info.nbins_arg);
279 >    } else {
280 >      sprintf( painCave.errMsg,
281 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
282 >      painCave.severity = OPENMD_ERROR;
283 >      painCave.isFatal = 1;
284 >      simError();
285 >      }
286 >  } else if (args_info.scd_given) {
287 >    if (batchMode) {
288 >      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
289 >                                        args_info.begin_arg, args_info.end_arg);
290 >    } else{
291 >      std::string sele3 = args_info.sele3_arg;
292 >      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
293 >    }
294 >  }else if (args_info.density_given) {
295 >    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
296 >                              args_info.nbins_arg);  
297 >  } else if (args_info.count_given) {
298 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
299 >  } else if (args_info.slab_density_given) {
300 >    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
301 >  } else if (args_info.p_angle_given) {
302 >    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
303   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
304 <    }else if (args_info.hxy_given) {
305 <        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
306 <                           args_info.nbins_y_arg, args_info.nbins_arg);
304 >  }else if (args_info.hxy_given) {
305 >    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
306 >                       args_info.nbins_y_arg, args_info.nbins_arg);
307   #endif
308 <    }else if (args_info.rho_r_given) {
309 <        if (args_info.radius_given){
310 <            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
311 <        }else{
312 <            sprintf( painCave.errMsg,
313 <                     "A particle radius (radius) must be specified when calculating Rho(r)");
314 <            painCave.severity = OPENMD_ERROR;
315 <            painCave.isFatal = 1;
316 <            simError();
286 <        }
287 <    }else if (args_info.hullvol_given) {
288 <        analyser = new NanoVolume(info, dumpFileName, sele1);
308 >  }else if (args_info.rho_r_given) {
309 >    if (args_info.radius_given){
310 >      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
311 >    }else{
312 >      sprintf( painCave.errMsg,
313 >               "A particle radius (radius) must be specified when calculating Rho(r)");
314 >      painCave.severity = OPENMD_ERROR;
315 >      painCave.isFatal = 1;
316 >      simError();
317      }
318 +  } else if (args_info.hullvol_given) {
319 +    analyser = new NanoVolume(info, dumpFileName, sele1);
320 +  } else if (args_info.angle_r_given) {
321 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
322 +  }
323 +    
324 +  if (args_info.output_given) {
325 +    analyser->setOutputName(args_info.output_arg);
326 +  }
327 +  if (args_info.step_given) {
328 +    analyser->setStep(args_info.step_arg);
329 +  }
330    
331 <    if (args_info.output_given) {
332 <        analyser->setOutputName(args_info.output_arg);
333 <    }
334 <    if (args_info.step_given) {
295 <        analyser->setStep(args_info.step_arg);
296 <    }
331 >  analyser->process();
332 >  
333 >  delete analyser;    
334 >  delete info;
335  
336 <    analyser->process();
299 <
300 <    delete analyser;    
301 <    delete info;
302 <
303 <    return 0;  
336 >  return 0;  
337   }
338  

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