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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 1454 by gezelter, Wed Jun 23 19:25:02 2010 UTC vs.
Revision 1585 by gezelter, Sun Jun 19 17:51:15 2011 UTC

# Line 64 | Line 64
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"
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"
78 + #include "applications/staticProps/RhoAngleR.hpp"
79 + #include "applications/staticProps/TetrahedralityParam.hpp"
80  
81   using namespace OpenMD;
82  
83   int main(int argc, char* argv[]){
84    
85 <    //register force fields
86 <    registerForceFields();
87 <
88 <    gengetopt_args_info args_info;
89 <
90 <    //parse the command line option
91 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
92 <        exit(1) ;
93 <    }
94 <
95 <    //get the dumpfile name
96 <    std::string dumpFileName = args_info.input_arg;
97 <    std::string sele1;
98 <    std::string sele2;
99 <    bool userSpecifiedSelect1;
100 <    bool userSpecifiedSelect2;
101 <
102 <    // check the first selection argument, or set it to the environment
103 <    // variable, or failing that, set it to "select all"
104 <
105 <    if (args_info.sele1_given) {
106 <        sele1 = args_info.sele1_arg;
85 >  //register force fields
86 >  registerForceFields();
87 >  
88 >  gengetopt_args_info args_info;
89 >  
90 >  //parse the command line option
91 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
92 >    exit(1) ;
93 >  }
94 >  
95 >  //get the dumpfile name
96 >  std::string dumpFileName = args_info.input_arg;
97 >  std::string sele1;
98 >  std::string sele2;
99 >  bool userSpecifiedSelect1;
100 >  bool userSpecifiedSelect2;
101 >  
102 >  // check the first selection argument, or set it to the environment
103 >  // variable, or failing that, set it to "select all"
104 >  
105 >  if (args_info.sele1_given) {
106 >    sele1 = args_info.sele1_arg;
107 >  } else {
108 >    char*  sele1Env= getenv("SELECTION1");
109 >    if (sele1Env) {
110 >      sele1 = sele1Env;
111      } else {
112 <        char*  sele1Env= getenv("SELECTION1");
104 <        if (sele1Env) {
105 <            sele1 = sele1Env;
106 <        } else {
107 <            sele1 = "select all";
108 <        }
112 >      sele1 = "select all";
113      }
114 <
111 <    // check the second selection argument, or set it to the environment
112 <    // variable, or failing that, set it to "select all"
114 >  }
115    
116 <    if (args_info.sele2_given) {
117 <        sele2 = args_info.sele2_arg;
118 <    } else {
119 <        char* sele2Env = getenv("SELECTION1");
120 <        if (sele2Env) {
121 <            sele2 = sele2Env;            
122 <        } else {
123 <            sele2 = "select all";
124 <        }
116 >  // check the second selection argument, or set it to the environment
117 >  // variable, or failing that, set it to "select all"
118 >  
119 >  if (args_info.sele2_given) {
120 >    sele2 = args_info.sele2_arg;
121 >  } else {
122 >    char* sele2Env = getenv("SELECTION1");
123 >    if (sele2Env) {
124 >      sele2 = sele2Env;            
125 >    } else {
126 >      sele2 = "select all";
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,
154 <                         "below conditions are not satisfied:\n"
155 <                         "0 <= begin && 0<= end && begin <= end-2\n");
156 <                painCave.severity = OPENMD_ERROR;
157 <                painCave.isFatal = 1;
158 <                simError();                    
159 <            }
160 <            batchMode = true;        
161 <        } else{
162 <            sprintf( painCave.errMsg,
163 <                     "either --sele1, --sele2, --sele3 are specified,"
164 <                     " or --molname, --begin, --end are specified\n");
165 <            painCave.severity = OPENMD_ERROR;
166 <            painCave.isFatal = 1;
167 <            simError();        
168 <    
169 <        }
170 <    }
171 <
172 <    //parse md file and set up the system
173 <    SimCreator creator;
174 <    std::cout << "dumpFile = " << dumpFileName << "\n";
175 <    SimInfo* info = creator.createSim(dumpFileName);
176 <
177 <    RealType maxLen;
178 <    RealType zmaxLen;
179 <    if (args_info.length_given) {
180 <        maxLen = args_info.length_arg;
181 <        if (args_info.zlength_given){
182 <            zmaxLen = args_info.zlength_arg;
183 <        }
184 <    } else {
185 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
186 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
187 <        zmaxLen = hmat(2,2);    
188 <    }    
189 <
190 <    StaticAnalyser* analyser;
191 <    if (args_info.gofr_given){
192 <        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
193 <                           args_info.nbins_arg);        
194 <    } else if (args_info.gofz_given) {
195 <        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
196 <                           args_info.nbins_arg);
197 <    } else if (args_info.r_z_given) {
198 <        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
199 <                              args_info.nbins_arg, args_info.nbins_z_arg);
200 <    } else if (args_info.r_theta_given) {
201 <        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
202 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
203 <    } else if (args_info.r_omega_given) {
204 <        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
206 <    } else if (args_info.theta_omega_given) {
207 <        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
208 <                                  args_info.nanglebins_arg);
209 <    } else if (args_info.gxyz_given) {
210 <        if (args_info.refsele_given) {
211 <            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
212 <                                 maxLen, args_info.nbins_arg);        
213 <        } else {
214 <            sprintf( painCave.errMsg,
215 <                     "--refsele must set when --gxyz is used");
216 <            painCave.severity = OPENMD_ERROR;
217 <            painCave.isFatal = 1;
218 <            simError();  
219 <        }
220 <    } else if (args_info.twodgofr_given){
221 <      if (args_info.dz_given) {
222 <        analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
223 <                               args_info.dz_arg, args_info.nbins_arg);        
224 <      } else {
128 >  }
129 >  
130 >  
131 >  // Problems if sele1 wasn't specified, but
132 >  // if (!args_info.scd_given) {
133 >  //       sprintf( painCave.errMsg,
134 >  //                "neither --sele1 option nor $SELECTION1 is set");
135 >  //       painCave.severity = OPENMD_ERROR;
136 >  //       painCave.isFatal = 1;
137 >  //       simError();
138 >  //     }
139 >  //   }
140 >  
141 >  // Problems if sele1 wasn't specified
142 >  
143 >  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
144 >  //       sprintf( painCave.errMsg,
145 >  //                "neither --sele2 option nor $SELECTION1 is set");
146 >  //       painCave.severity = OPENMD_ERROR;
147 >  //       painCave.isFatal = 1;
148 >  //       simError();        
149 >  //     }
150 >  //   }
151 >  
152 >  bool batchMode;
153 >  if (args_info.scd_given){
154 >    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
155 >      batchMode = false;
156 >    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
157 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
158          sprintf( painCave.errMsg,
159 <                 "A slab width (dz) must be specified when calculating TwoDGofR");
159 >                 "below conditions are not satisfied:\n"
160 >                 "0 <= begin && 0<= end && begin <= end-2\n");
161          painCave.severity = OPENMD_ERROR;
162          painCave.isFatal = 1;
163 <        simError();
163 >        simError();                    
164        }
165 <    } else if (args_info.p2_given) {
166 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
167 <    } else if (args_info.rp2_given){
168 <        analyser = new RippleOP(info, dumpFileName, sele1, sele2);
169 <    } else if (args_info.bo_given){
170 <        if (args_info.rcut_given) {
171 <            analyser = new BondOrderParameter(info, dumpFileName, sele1,
172 <                                              args_info.rcut_arg,
173 <                                              args_info.nbins_arg);
240 <        } else {
241 <            sprintf( painCave.errMsg,
242 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
243 <            painCave.severity = OPENMD_ERROR;
244 <            painCave.isFatal = 1;
245 <            simError();
246 <        }
247 <    } else if (args_info.bor_given){
248 <        if (args_info.rcut_given) {
249 <            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
250 <                                  args_info.nbins_arg, maxLen);
251 <        } else {
252 <            sprintf( painCave.errMsg,
253 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
254 <            painCave.severity = OPENMD_ERROR;
255 <            painCave.isFatal = 1;
256 <            simError();
257 <        }
258 <    } else if (args_info.bad_given){
259 <        if (args_info.rcut_given) {
260 <            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
261 <                                                 args_info.nbins_arg);
262 <        } else {
263 <            sprintf( painCave.errMsg,
264 <                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
265 <            painCave.severity = OPENMD_ERROR;
266 <            painCave.isFatal = 1;
267 <            simError();
268 <        }
269 <    } else if (args_info.scd_given) {
270 <        if (batchMode) {
271 <            analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
272 <                                              args_info.begin_arg, args_info.end_arg);
273 <        } else{
274 <            std::string sele3 = args_info.sele3_arg;
275 <            analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
276 <        }
277 <    }else if (args_info.density_given) {
278 <        analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
279 <                                  args_info.nbins_arg);  
280 <    } else if (args_info.slab_density_given) {
281 <        analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
282 <    } else if (args_info.p_angle_given) {
283 <        analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
284 < #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
285 <    }else if (args_info.hxy_given) {
286 <        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
287 <                           args_info.nbins_y_arg, args_info.nbins_arg);
288 < #endif
289 <    }else if (args_info.rho_r_given) {
290 <        if (args_info.radius_given){
291 <            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
292 <        }else{
293 <            sprintf( painCave.errMsg,
294 <                     "A particle radius (radius) must be specified when calculating Rho(r)");
295 <            painCave.severity = OPENMD_ERROR;
296 <            painCave.isFatal = 1;
297 <            simError();
298 <        }
299 <    }else if (args_info.hullvol_given) {
300 <        analyser = new NanoVolume(info, dumpFileName, sele1);
165 >      batchMode = true;        
166 >    } else{
167 >      sprintf( painCave.errMsg,
168 >               "either --sele1, --sele2, --sele3 are specified,"
169 >               " or --molname, --begin, --end are specified\n");
170 >      painCave.severity = OPENMD_ERROR;
171 >      painCave.isFatal = 1;
172 >      simError();        
173 >      
174      }
175 +  }
176    
177 <    if (args_info.output_given) {
178 <        analyser->setOutputName(args_info.output_arg);
177 >  //parse md file and set up the system
178 >  SimCreator creator;
179 >  std::cout << "dumpFile = " << dumpFileName << "\n";
180 >  SimInfo* info = creator.createSim(dumpFileName);
181 >
182 >  RealType maxLen;
183 >  RealType zmaxLen;
184 >  if (args_info.length_given) {
185 >    maxLen = args_info.length_arg;
186 >    if (args_info.zlength_given){
187 >      zmaxLen = args_info.zlength_arg;
188      }
189 <    if (args_info.step_given) {
190 <        analyser->setStep(args_info.step_arg);
189 >  } else {
190 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
191 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
192 >    zmaxLen = hmat(2,2);    
193 >  }    
194 >  
195 >  StaticAnalyser* analyser;
196 >  if (args_info.gofr_given){
197 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
198 >                       args_info.nbins_arg);        
199 >  } else if (args_info.gofz_given) {
200 >    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
201 >                       args_info.nbins_arg);
202 >  } else if (args_info.r_z_given) {
203 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
204 >                          args_info.nbins_arg, args_info.nbins_z_arg);
205 >  } else if (args_info.r_theta_given) {
206 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
207 >                              args_info.nbins_arg, args_info.nanglebins_arg);
208 >  } else if (args_info.r_omega_given) {
209 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
210 >                              args_info.nbins_arg, args_info.nanglebins_arg);
211 >  } else if (args_info.theta_omega_given) {
212 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
213 >                              args_info.nanglebins_arg);
214 >  } else if (args_info.gxyz_given) {
215 >    if (args_info.refsele_given) {
216 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
217 >                           maxLen, args_info.nbins_arg);        
218 >    } else {
219 >      sprintf( painCave.errMsg,
220 >               "--refsele must set when --gxyz is used");
221 >      painCave.severity = OPENMD_ERROR;
222 >      painCave.isFatal = 1;
223 >      simError();  
224      }
225 +  } else if (args_info.twodgofr_given){
226 +    if (args_info.dz_given) {
227 +      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
228 +                             args_info.dz_arg, args_info.nbins_arg);        
229 +    } else {
230 +      sprintf( painCave.errMsg,
231 +               "A slab width (dz) must be specified when calculating TwoDGofR");
232 +      painCave.severity = OPENMD_ERROR;
233 +      painCave.isFatal = 1;
234 +      simError();
235 +    }    
236 +  } else if (args_info.p2_given) {
237 +    if (args_info.sele1_given) {    
238 +      if (args_info.sele2_given)
239 +        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
240 +      else
241 +        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
242 +    } else {
243 +      sprintf( painCave.errMsg,
244 +               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
245 +      painCave.severity = OPENMD_ERROR;
246 +      painCave.isFatal = 1;
247 +      simError();
248 +    }
249 +  } else if (args_info.rp2_given){
250 +    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
251 +  } else if (args_info.bo_given){
252 +    if (args_info.rcut_given) {
253 +      analyser = new BondOrderParameter(info, dumpFileName, sele1,
254 +                                        args_info.rcut_arg,
255 +                                        args_info.nbins_arg);
256 +    } else {
257 +      sprintf( painCave.errMsg,
258 +               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
259 +      painCave.severity = OPENMD_ERROR;
260 +      painCave.isFatal = 1;
261 +      simError();
262 +    }
263 +    
264 +  } else if (args_info.tet_param_given) {
265 +    if (args_info.rcut_given) {  
266 +      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
267 +                                         args_info.rcut_arg,
268 +                                         args_info.nbins_arg);
269 +    } else {
270 +      sprintf( painCave.errMsg,
271 +               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
272 +      painCave.severity = OPENMD_ERROR;
273 +      painCave.isFatal = 1;
274 +      simError();
275 +    }
276 +  } else if (args_info.bor_given){
277 +    if (args_info.rcut_given) {
278 +      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
279 +                            args_info.nbins_arg, maxLen);
280 +    } else {
281 +      sprintf( painCave.errMsg,
282 +               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
283 +      painCave.severity = OPENMD_ERROR;
284 +      painCave.isFatal = 1;
285 +      simError();
286 +    }
287 +  } else if (args_info.bad_given){
288 +    if (args_info.rcut_given) {
289 +      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
290 +                                           args_info.nbins_arg);
291 +    } else {
292 +      sprintf( painCave.errMsg,
293 +               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
294 +      painCave.severity = OPENMD_ERROR;
295 +      painCave.isFatal = 1;
296 +      simError();
297 +      }
298 +  } else if (args_info.scd_given) {
299 +    if (batchMode) {
300 +      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
301 +                                        args_info.begin_arg, args_info.end_arg);
302 +    } else{
303 +      std::string sele3 = args_info.sele3_arg;
304 +      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
305 +    }
306 +  }else if (args_info.density_given) {
307 +    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
308 +                              args_info.nbins_arg);  
309 +  } else if (args_info.count_given) {
310 +    analyser = new ObjectCount(info, dumpFileName, sele1 );
311 +  } else if (args_info.slab_density_given) {
312 +    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
313 +  } else if (args_info.p_angle_given) {
314 +    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
315 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
316 +  }else if (args_info.hxy_given) {
317 +    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
318 +                       args_info.nbins_y_arg, args_info.nbins_arg);
319 + #endif
320 +  }else if (args_info.rho_r_given) {
321 +    if (args_info.radius_given){
322 +      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
323 +    }else{
324 +      sprintf( painCave.errMsg,
325 +               "A particle radius (radius) must be specified when calculating Rho(r)");
326 +      painCave.severity = OPENMD_ERROR;
327 +      painCave.isFatal = 1;
328 +      simError();
329 +    }
330 +  } else if (args_info.hullvol_given) {
331 +    analyser = new NanoVolume(info, dumpFileName, sele1);
332 +  } else if (args_info.rodlength_given) {
333 +    analyser = new NanoLength(info, dumpFileName, sele1);
334 +  } else if (args_info.angle_r_given) {
335 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
336 +  }
337 +    
338 +  if (args_info.output_given) {
339 +    analyser->setOutputName(args_info.output_arg);
340 +  }
341 +  if (args_info.step_given) {
342 +    analyser->setStep(args_info.step_arg);
343 +  }
344 +  
345 +  analyser->process();
346 +  
347 +  delete analyser;    
348 +  delete info;
349  
350 <    analyser->process();
311 <
312 <    delete analyser;    
313 <    delete info;
314 <
315 <    return 0;  
350 >  return 0;  
351   }
352  

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