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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 1128 by chuckv, Wed Apr 11 23:27:20 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 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
66 + #include "applications/staticProps/Hxy.hpp"
67 + #endif
68 + #include "applications/staticProps/RhoR.hpp"
69  
70   using namespace oopse;
71  
72   int main(int argc, char* argv[]){
73    
74 <    //register force fields
75 <    registerForceFields();
74 >  //register force fields
75 >  registerForceFields();
76  
77 <    gengetopt_args_info args_info;
77 >  gengetopt_args_info args_info;
78  
79 <    //parse the command line option
80 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
81 <        exit(1) ;
82 <    }
79 >  //parse the command line option
80 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
81 >    exit(1) ;
82 >  }
83  
84 +  //get the dumpfile name
85 +  std::string dumpFileName = args_info.input_arg;
86 +  std::string sele1;
87 +  std::string sele2;
88 +  bool userSpecifiedSelect1;
89 +  bool userSpecifiedSelect2;
90  
91 <    //get the dumpfile name and meta-data file name
92 <    std::string dumpFileName = args_info.input_arg;
91 >  // check the first selection argument, or set it to the environment
92 >  // variable, or failing that, set it to "select all"
93  
94 <    std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
95 <
96 <    
97 <    std::string sele1;
98 <    std::string sele2;
99 <
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;
94 >  if (args_info.sele1_given) {
95 >    sele1 = args_info.sele1_arg;
96 >  } else {
97 >    char*  sele1Env= getenv("OOPSE_SELE1");
98 >    if (sele1Env) {
99 >      sele1 = sele1Env;
100      } else {
101 <        double rcut;
121 <        double rsw;
122 <        info->getCutoff(rcut, rsw);
123 <        maxLen = rcut + rsw;        
101 >      sele1 = "select all";
102      }
103 <    
103 >  }
104  
105 <    RadialDistrFunc* rdf;
106 <    if (args_info.gofr_given){
107 <        GofR* r = new GofR(info, dumpFileName, sele1, sele2);
108 <        
109 <        r->setNRBins(args_info.nrbins_arg);            
110 <        r->setLength(maxLen);
111 <        
112 <        rdf = r;
113 <    } else if (args_info.r_theta_given) {
114 <        GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2);
115 <          
138 <        rTheta->setNRBins(args_info.nrbins_arg);            
139 <        rTheta->setLength(maxLen);      
140 <        rTheta->setNAngleBins(args_info.nanglebins_arg);
141 <
142 <        
143 <        rdf = rTheta;
105 >  // check the second selection argument, or set it to the environment
106 >  // variable, or failing that, set it to "select all"
107 >  
108 >  if (args_info.sele2_given) {
109 >    sele2 = args_info.sele2_arg;
110 >  } else {
111 >    char* sele2Env = getenv("OOPSE_SELE2");
112 >    if (sele2Env) {
113 >      sele2 = sele2Env;            
114 >    } else {
115 >      sele2 = "select all";
116      }
117 <    else if (args_info.r_omega_given) {
146 <        GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2);
117 >  }
118  
148 –      
149 –        rOmega->setNRBins(args_info.nrbins_arg);            
150 –        rOmega->setLength(maxLen);
151 –        rOmega->setNAngleBins(args_info.nanglebins_arg);
119  
120 <        rdf = rOmega;    
121 <    } else if (args_info.theta_omega_given) {
122 <        GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2);
123 <        rAngle2->setNAngleBins(args_info.nanglebins_arg);
120 >  // Problems if sele1 wasn't specified, but
121 > // if (!args_info.scd_given) {
122 > //       sprintf( painCave.errMsg,
123 > //                "neither --sele1 option nor $OOPSE_SELE1 is set");
124 > //       painCave.severity = OOPSE_ERROR;
125 > //       painCave.isFatal = 1;
126 > //       simError();
127 > //     }
128 > //   }
129  
130 <        rdf = rAngle2;  
159 <    } else if (args_info.xyz_given) {
130 >  // Problems if sele1 wasn't specified
131  
132 <        GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2);
133 <          
134 <        xyz->setNRBins(args_info.nrbins_arg);            
135 <        xyz->setLength(maxLen);
132 > //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
133 > //       sprintf( painCave.errMsg,
134 > //                "neither --sele2 option nor $OOPSE_SELE2 is set");
135 > //       painCave.severity = OOPSE_ERROR;
136 > //       painCave.isFatal = 1;
137 > //       simError();        
138 > //     }
139 > //   }
140  
141 <        
142 <        rdf = xyz;
143 <    }
141 >  bool batchMode;
142 >  if (args_info.scd_given){
143 >    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
144 >      batchMode = false;
145 >    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
146 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
147 >        sprintf( painCave.errMsg,
148 >                 "below conditions are not satisfied:\n"
149 >                 "0 <= begin && 0<= end && begin <= end-2\n");
150 >        painCave.severity = OOPSE_ERROR;
151 >        painCave.isFatal = 1;
152 >        simError();                    
153 >      }
154 >      batchMode = true;        
155 >    } else{
156 >      sprintf( painCave.errMsg,
157 >               "either --sele1, --sele2, --sele3 are specified,"
158 >               " or --molname, --begin, --end are specified\n");
159 >      painCave.severity = OOPSE_ERROR;
160 >      painCave.isFatal = 1;
161 >      simError();        
162      
170 –
171 –    if (args_info.output_given) {
172 –        rdf->setOutputName(args_info.output_arg);
163      }
164 +  }
165  
166 <    if (args_info.step_given) {
167 <        rdf->setStep(args_info.step_arg);
166 >  //parse md file and set up the system
167 >  SimCreator creator;
168 >  std::cout << "dumpFile = " << dumpFileName << "\n";
169 >  SimInfo* info = creator.createSim(dumpFileName);
170 >
171 >  RealType maxLen;
172 >  if (args_info.length_given) {
173 >    maxLen = args_info.length_arg;
174 >  } else {
175 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
176 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
177 >  }    
178 >
179 >  StaticAnalyser* analyser;
180 >  if (args_info.gofr_given){
181 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
182 >                       args_info.nbins_arg);        
183 >  } else if (args_info.r_theta_given) {
184 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
185 >                              args_info.nbins_arg, args_info.nanglebins_arg);
186 >  } else if (args_info.r_omega_given) {
187 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
188 >                              args_info.nbins_arg, args_info.nanglebins_arg);
189 >  } else if (args_info.theta_omega_given) {
190 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
191 >                              args_info.nanglebins_arg);
192 >  } else if (args_info.gxyz_given) {
193 >    if (args_info.refsele_given) {
194 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
195 >                           maxLen, args_info.nbins_arg);        
196 >    } else {
197 >      sprintf( painCave.errMsg,
198 >               "--refsele must set when --gxyz is used");
199 >      painCave.severity = OOPSE_ERROR;
200 >      painCave.isFatal = 1;
201 >      simError();  
202      }
203 +  } else if (args_info.p2_given) {
204 +    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
205 +  } else if (args_info.rp2_given){
206 +    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
207 +  } else if (args_info.bo_given){
208 +    if (args_info.rcut_given) {
209 +      analyser = new BondOrderParameter(info, dumpFileName, sele1,
210 +                                        args_info.rcut_arg,
211 +                                        args_info.nbins_arg);
212 +    } else {
213 +      sprintf( painCave.errMsg,
214 +               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
215 +      painCave.severity = OOPSE_ERROR;
216 +      painCave.isFatal = 1;
217 +      simError();
218 +    }
219 +  } else if (args_info.bor_given){
220 +    if (args_info.rcut_given) {
221 +      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
222 +                            args_info.nbins_arg, maxLen);
223 +    } else {
224 +      sprintf( painCave.errMsg,
225 +               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
226 +      painCave.severity = OOPSE_ERROR;
227 +      painCave.isFatal = 1;
228 +      simError();
229 +    }
230 +  } else if (args_info.scd_given) {
231 +    if (batchMode) {
232 +      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
233 +                                        args_info.begin_arg, args_info.end_arg);
234 +    } else{
235 +      std::string sele3 = args_info.sele3_arg;
236 +      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
237 +    }
238 +  }else if (args_info.density_given) {
239 +    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
240 +                              args_info.nbins_arg);  
241 +  } else if (args_info.slab_density_given) {
242 +    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
243 +    analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
244 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
245 +  }else if (args_info.hxy_given) {
246 +    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
247 +                       args_info.nbins_y_arg, args_info.nbins_arg);
248 + #endif
249 +  }else if (args_info.rho_r_given) {
250 +    if (args_info.radius_given){
251 +      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
252 +    }else{
253 +      sprintf( painCave.errMsg,
254 +               "A particle radius (radius) must be specified when calculating Rho(r)");
255 +      painCave.severity = OOPSE_ERROR;
256 +      painCave.isFatal = 1;
257 +      simError();
258 +    }
259 +  }
260 +  
261 +  if (args_info.output_given) {
262 +    analyser->setOutputName(args_info.output_arg);
263 +  }
264 +  if (args_info.step_given) {
265 +    analyser->setStep(args_info.step_arg);
266 +  }
267  
268 <    rdf->process();
268 >  analyser->process();
269  
270 <    delete rdf;    
271 <    delete info;
270 >  delete analyser;    
271 >  delete info;
272  
273 <    return 0;  
273 >  return 0;  
274   }
275  

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