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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 326 by tim, Sun Feb 13 20:05:42 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) ;
84 <    }
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 <    //get the dumpfile name and meta-data file name
94 <    std::string dumpFileName = args_info.input_arg;
93 >  // check the first selection argument, or set it to the environment
94 >  // variable, or failing that, set it to "select all"
95  
96 <    std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
97 <
98 <    
99 <    std::string sele1;
100 <    std::string sele2;
101 <
82 <    if (args_info.sele1_given) {
83 <        sele1 = args_info.sele1_arg;
84 <    }else {
85 <        char*  sele1Env= getenv("OOPSE_SELE1");
86 <        if (sele1Env) {
87 <            sele1 = sele1Env;
88 <        }else {
89 <            sprintf( painCave.errMsg,
90 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
91 <            painCave.severity = OOPSE_ERROR;
92 <            painCave.isFatal = 1;
93 <            simError();
94 <        }
95 <    }
96 <    
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 <        }
110 <    }
111 <
112 <    //parse md file and set up the system
113 <    SimCreator creator;
114 <    SimInfo* info = creator.createSim(mdFileName, false);
115 <
116 <    double maxLen;
117 <    if (args_info.length_given) {
118 <        maxLen = args_info.length_arg;
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 <        double rcut;
121 <        double rsw;
122 <        info->getCutoff(rcut, rsw);
123 <        maxLen = rcut + rsw;        
103 >      sele1 = "select all";
104      }
105 <    
105 >  }
106  
107 <    RadialDistrFunc* rdf;
108 <    if (args_info.gofr_given){
109 <        GofR* r = new GofR(info, dumpFileName, sele1, sele2);
110 <        
111 <        r->setNRBins(args_info.nrbins_arg);            
112 <        r->setLength(maxLen);
113 <        
114 <        rdf = r;
115 <    } else if (args_info.r_theta_given) {
116 <        GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2);
117 <          
138 <        rTheta->setNRBins(args_info.nrbins_arg);            
139 <        rTheta->setLength(maxLen);      
140 <        rTheta->setNAngleBins(args_info.nanglebins_arg);
141 <
142 <        
143 <        rdf = rTheta;
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 <    else if (args_info.r_omega_given) {
146 <        GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2);
119 >  }
120  
148 –      
149 –        rOmega->setNRBins(args_info.nrbins_arg);            
150 –        rOmega->setLength(maxLen);
151 –        rOmega->setNAngleBins(args_info.nanglebins_arg);
121  
122 <        rdf = rOmega;    
123 <    } else if (args_info.theta_omega_given) {
124 <        GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2);
125 <        rAngle2->setNAngleBins(args_info.nanglebins_arg);
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 <        rdf = rAngle2;  
159 <    } else if (args_info.xyz_given) {
132 >  // Problems if sele1 wasn't specified
133  
134 <        GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2);
135 <          
136 <        xyz->setNRBins(args_info.nrbins_arg);            
137 <        xyz->setLength(maxLen);
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 <        
144 <        rdf = xyz;
145 <    }
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      
170 –
171 –    if (args_info.output_given) {
172 –        rdf->setOutputName(args_info.output_arg);
165      }
166 +  }
167  
168 <    if (args_info.step_given) {
169 <        rdf->setStep(args_info.step_arg);
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 >  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 >  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();  
204      }
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 +  } 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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