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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 369 by tim, Fri Feb 18 23:07:32 2005 UTC vs.
Revision 1180 by chuckv, Mon Sep 17 20:05:51 2007 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 50 | Line 50
50   #include "utils/simError.h"
51  
52   #include "applications/staticProps/StaticPropsCmd.h"
53 + #include "applications/staticProps/StaticAnalyser.hpp"
54   #include "applications/staticProps/GofR.hpp"
55   #include "applications/staticProps/GofRAngle.hpp"
56   #include "applications/staticProps/GofAngle2.hpp"
57   #include "applications/staticProps/GofXyz.hpp"
58 + #include "applications/staticProps/P2OrderParameter.hpp"
59 + #include "applications/staticProps/BondOrderParameter.hpp"
60 + #include "applications/staticProps/BOPofR.hpp"
61 + #include "applications/staticProps/RippleOP.hpp"
62 + #include "applications/staticProps/SCDOrderParameter.hpp"
63 + #include "applications/staticProps/DensityPlot.hpp"
64 + #include "applications/staticProps/RhoZ.hpp"
65 + #include "applications/staticProps/BondAngleDistribution.hpp"
66 + #include "applications/staticProps/NanoVolume.hpp"
67 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
68 + #include "applications/staticProps/Hxy.hpp"
69 + #endif
70 + #include "applications/staticProps/RhoR.hpp"
71  
72   using namespace oopse;
73  
74   int main(int argc, char* argv[]){
75    
76 <    //register force fields
77 <    registerForceFields();
76 >  //register force fields
77 >  registerForceFields();
78  
79 <    gengetopt_args_info args_info;
79 >  gengetopt_args_info args_info;
80  
81 <    //parse the command line option
82 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
83 <        exit(1) ;
81 >  //parse the command line option
82 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
83 >    exit(1) ;
84 >  }
85 >
86 >  //get the dumpfile name
87 >  std::string dumpFileName = args_info.input_arg;
88 >  std::string sele1;
89 >  std::string sele2;
90 >  bool userSpecifiedSelect1;
91 >  bool userSpecifiedSelect2;
92 >
93 >  // check the first selection argument, or set it to the environment
94 >  // variable, or failing that, set it to "select all"
95 >
96 >  if (args_info.sele1_given) {
97 >    sele1 = args_info.sele1_arg;
98 >  } else {
99 >    char*  sele1Env= getenv("OOPSE_SELE1");
100 >    if (sele1Env) {
101 >      sele1 = sele1Env;
102 >    } else {
103 >      sele1 = "select all";
104      }
105 +  }
106  
107 +  // check the second selection argument, or set it to the environment
108 +  // variable, or failing that, set it to "select all"
109 +  
110 +  if (args_info.sele2_given) {
111 +    sele2 = args_info.sele2_arg;
112 +  } else {
113 +    char* sele2Env = getenv("OOPSE_SELE2");
114 +    if (sele2Env) {
115 +      sele2 = sele2Env;            
116 +    } else {
117 +      sele2 = "select all";
118 +    }
119 +  }
120  
73 –    //get the dumpfile name and meta-data file name
74 –    std::string dumpFileName = args_info.input_arg;
121  
122 <    std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
122 >  // Problems if sele1 wasn't specified, but
123 > // if (!args_info.scd_given) {
124 > //       sprintf( painCave.errMsg,
125 > //                "neither --sele1 option nor $OOPSE_SELE1 is set");
126 > //       painCave.severity = OOPSE_ERROR;
127 > //       painCave.isFatal = 1;
128 > //       simError();
129 > //     }
130 > //   }
131  
132 <    
79 <    std::string sele1;
80 <    std::string sele2;
132 >  // Problems if sele1 wasn't specified
133  
134 <    if (args_info.sele1_given) {
135 <        sele1 = args_info.sele1_arg;
136 <    }else {
137 <        char*  sele1Env= getenv("OOPSE_SELE1");
138 <        if (sele1Env) {
139 <            sele1 = sele1Env;
140 <        }else {
141 <            sprintf( painCave.errMsg,
142 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
143 <            painCave.severity = OOPSE_ERROR;
144 <            painCave.isFatal = 1;
145 <            simError();
146 <        }
147 <    }
134 > //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
135 > //       sprintf( painCave.errMsg,
136 > //                "neither --sele2 option nor $OOPSE_SELE2 is set");
137 > //       painCave.severity = OOPSE_ERROR;
138 > //       painCave.isFatal = 1;
139 > //       simError();        
140 > //     }
141 > //   }
142 >
143 >  bool batchMode;
144 >  if (args_info.scd_given){
145 >    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
146 >      batchMode = false;
147 >    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
148 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
149 >        sprintf( painCave.errMsg,
150 >                 "below conditions are not satisfied:\n"
151 >                 "0 <= begin && 0<= end && begin <= end-2\n");
152 >        painCave.severity = OOPSE_ERROR;
153 >        painCave.isFatal = 1;
154 >        simError();                    
155 >      }
156 >      batchMode = true;        
157 >    } else{
158 >      sprintf( painCave.errMsg,
159 >               "either --sele1, --sele2, --sele3 are specified,"
160 >               " or --molname, --begin, --end are specified\n");
161 >      painCave.severity = OOPSE_ERROR;
162 >      painCave.isFatal = 1;
163 >      simError();        
164      
97 –    if (args_info.sele2_given) {
98 –        sele2 = args_info.sele2_arg;
99 –    }else {
100 –        char* sele2Env = getenv("OOPSE_SELE2");
101 –        if (sele2Env) {
102 –            sele2 = sele2Env;            
103 –        } else {
104 –            sprintf( painCave.errMsg,
105 –               "neither --sele2 option nor $OOPSE_SELE2 is set");
106 –            painCave.severity = OOPSE_ERROR;
107 –            painCave.isFatal = 1;
108 –            simError();        
109 –        }
165      }
166 +  }
167  
168 <    //parse md file and set up the system
169 <    SimCreator creator;
170 <    SimInfo* info = creator.createSim(mdFileName);
168 >  //parse md file and set up the system
169 >  SimCreator creator;
170 >  std::cout << "dumpFile = " << dumpFileName << "\n";
171 >  SimInfo* info = creator.createSim(dumpFileName);
172  
173 <    double maxLen;
174 <    if (args_info.length_given) {
175 <        maxLen = args_info.length_arg;
176 <    } else {
177 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
178 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
179 <    }    
173 >  RealType maxLen;
174 >  if (args_info.length_given) {
175 >    maxLen = args_info.length_arg;
176 >  } else {
177 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
178 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
179 >  }    
180  
181 <    RadialDistrFunc* rdf;
182 <    if (args_info.gofr_given){
183 <        rdf= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);        
184 <    } else if (args_info.r_theta_given) {
185 <        rdf  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
186 <    } else if (args_info.r_omega_given) {
187 <        rdf  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
188 <    } else if (args_info.theta_omega_given) {
189 <        rdf  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
190 <    } else if (args_info.gxyz_given) {
191 <        if (args_info.refsele_given) {
192 <            rdf= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);        
193 <        } else {
194 <            sprintf( painCave.errMsg,
181 >  StaticAnalyser* analyser;
182 >  if (args_info.gofr_given){
183 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
184 >                       args_info.nbins_arg);        
185 >  } else if (args_info.r_theta_given) {
186 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
187 >                              args_info.nbins_arg, args_info.nanglebins_arg);
188 >  } else if (args_info.r_omega_given) {
189 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
190 >                              args_info.nbins_arg, args_info.nanglebins_arg);
191 >  } else if (args_info.theta_omega_given) {
192 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
193 >                              args_info.nanglebins_arg);
194 >  } else if (args_info.gxyz_given) {
195 >    if (args_info.refsele_given) {
196 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
197 >                           maxLen, args_info.nbins_arg);        
198 >    } else {
199 >      sprintf( painCave.errMsg,
200                 "--refsele must set when --gxyz is used");
201 <            painCave.severity = OOPSE_ERROR;
202 <            painCave.isFatal = 1;
203 <            simError();  
142 <        }
201 >      painCave.severity = OOPSE_ERROR;
202 >      painCave.isFatal = 1;
203 >      simError();  
204      }
205 <    
206 <    if (args_info.output_given) {
207 <        rdf->setOutputName(args_info.output_arg);
205 >  } else if (args_info.p2_given) {
206 >    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
207 >  } else if (args_info.rp2_given){
208 >    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
209 >  } else if (args_info.bo_given){
210 >    if (args_info.rcut_given) {
211 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
212 >                                        args_info.rcut_arg,
213 >                                        args_info.nbins_arg);
214 >    } else {
215 >      sprintf( painCave.errMsg,
216 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
217 >      painCave.severity = OOPSE_ERROR;
218 >      painCave.isFatal = 1;
219 >      simError();
220      }
221 <    if (args_info.step_given) {
222 <        rdf->setStep(args_info.step_arg);
221 >  } else if (args_info.bor_given){
222 >    if (args_info.rcut_given) {
223 >      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
224 >                            args_info.nbins_arg, maxLen);
225 >    } else {
226 >      sprintf( painCave.errMsg,
227 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
228 >      painCave.severity = OOPSE_ERROR;
229 >      painCave.isFatal = 1;
230 >      simError();
231      }
232 +  } else if (args_info.bad_given){
233 +    if (args_info.rcut_given) {
234 +      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
235 +                            args_info.nbins_arg);
236 +    } else {
237 +      sprintf( painCave.errMsg,
238 +               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
239 +      painCave.severity = OOPSE_ERROR;
240 +      painCave.isFatal = 1;
241 +      simError();
242 +    }
243 +  } else if (args_info.scd_given) {
244 +    if (batchMode) {
245 +      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
246 +                                        args_info.begin_arg, args_info.end_arg);
247 +    } else{
248 +      std::string sele3 = args_info.sele3_arg;
249 +      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
250 +    }
251 +  }else if (args_info.density_given) {
252 +    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
253 +                              args_info.nbins_arg);  
254 +  } else if (args_info.slab_density_given) {
255 +    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
256 +    analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
257 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
258 +  }else if (args_info.hxy_given) {
259 +    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
260 +                       args_info.nbins_y_arg, args_info.nbins_arg);
261 + #endif
262 +  }else if (args_info.rho_r_given) {
263 +    if (args_info.radius_given){
264 +      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
265 +    }else{
266 +      sprintf( painCave.errMsg,
267 +               "A particle radius (radius) must be specified when calculating Rho(r)");
268 +      painCave.severity = OOPSE_ERROR;
269 +      painCave.isFatal = 1;
270 +      simError();
271 +    }
272 +        }else if (args_info.hullvol_given) {
273 +    analyser = new NanoVolume(info, dumpFileName, sele1);
274 +  }
275 +  
276 +  if (args_info.output_given) {
277 +    analyser->setOutputName(args_info.output_arg);
278 +  }
279 +  if (args_info.step_given) {
280 +    analyser->setStep(args_info.step_arg);
281 +  }
282  
283 <    rdf->process();
283 >  analyser->process();
284  
285 <    delete rdf;    
286 <    delete info;
285 >  delete analyser;    
286 >  delete info;
287  
288 <    return 0;  
288 >  return 0;  
289   }
290  

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