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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 336 by tim, Mon Feb 14 18:51:48 2005 UTC vs.
Revision 1091 by chuckv, Fri Nov 10 18:45:29 2006 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/RippleOP.hpp"
61 + #include "applications/staticProps/SCDOrderParameter.hpp"
62 + #include "applications/staticProps/DensityPlot.hpp"
63 + #include "applications/staticProps/RhoZ.hpp"
64 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
65 + #include "applications/staticProps/Hxy.hpp"
66 + #endif
67 + #include "applications/staticProps/RhoR.hpp"
68  
69   using namespace oopse;
70  
71   int main(int argc, char* argv[]){
72    
73 <    //register force fields
74 <    registerForceFields();
73 >  //register force fields
74 >  registerForceFields();
75  
76 <    gengetopt_args_info args_info;
76 >  gengetopt_args_info args_info;
77  
78 <    //parse the command line option
79 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
80 <        exit(1) ;
81 <    }
78 >  //parse the command line option
79 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
80 >    exit(1) ;
81 >  }
82  
83 +  //get the dumpfile name
84 +  std::string dumpFileName = args_info.input_arg;
85 +  std::string sele1;
86 +  std::string sele2;
87 +  bool userSpecifiedSelect1;
88 +  bool userSpecifiedSelect2;
89  
90 <    //get the dumpfile name and meta-data file name
91 <    std::string dumpFileName = args_info.input_arg;
90 >  // check the first selection argument, or set it to the environment
91 >  // variable, or failing that, set it to "select all"
92  
93 <    std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
94 <
95 <    
96 <    std::string sele1;
97 <    std::string sele2;
98 <
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);
115 <
116 <    double maxLen;
117 <    if (args_info.length_given) {
118 <        maxLen = args_info.length_arg;
93 >  if (args_info.sele1_given) {
94 >    sele1 = args_info.sele1_arg;
95 >  } else {
96 >    char*  sele1Env= getenv("OOPSE_SELE1");
97 >    if (sele1Env) {
98 >      sele1 = sele1Env;
99      } else {
100 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
121 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
100 >      sele1 = "select all";
101      }
102 <    
102 >  }
103  
104 <    RadialDistrFunc* rdf;
105 <    if (args_info.gofr_given){
106 <        GofR* r = new GofR(info, dumpFileName, sele1, sele2);
107 <        
108 <        r->setNRBins(args_info.nrbins_arg);            
109 <        r->setLength(maxLen);
110 <        
111 <        rdf = r;
112 <    } else if (args_info.r_theta_given) {
113 <        GofRTheta* rTheta = new GofRTheta(info, dumpFileName, sele1, sele2);
114 <          
136 <        rTheta->setNRBins(args_info.nrbins_arg);            
137 <        rTheta->setLength(maxLen);      
138 <        rTheta->setNAngleBins(args_info.nanglebins_arg);
139 <
140 <        
141 <        rdf = rTheta;
104 >  // check the second selection argument, or set it to the environment
105 >  // variable, or failing that, set it to "select all"
106 >  
107 >  if (args_info.sele2_given) {
108 >    sele2 = args_info.sele2_arg;
109 >  } else {
110 >    char* sele2Env = getenv("OOPSE_SELE2");
111 >    if (sele2Env) {
112 >      sele2 = sele2Env;            
113 >    } else {
114 >      sele2 = "select all";
115      }
116 <    else if (args_info.r_omega_given) {
144 <        GofROmega* rOmega = new GofROmega(info, dumpFileName, sele1, sele2);
116 >  }
117  
146 –      
147 –        rOmega->setNRBins(args_info.nrbins_arg);            
148 –        rOmega->setLength(maxLen);
149 –        rOmega->setNAngleBins(args_info.nanglebins_arg);
118  
119 <        rdf = rOmega;    
120 <    } else if (args_info.theta_omega_given) {
121 <        GofAngle2* rAngle2 = new GofAngle2(info, dumpFileName, sele1, sele2);
122 <        rAngle2->setNAngleBins(args_info.nanglebins_arg);
119 >  // Problems if sele1 wasn't specified, but
120 > // if (!args_info.scd_given) {
121 > //       sprintf( painCave.errMsg,
122 > //                "neither --sele1 option nor $OOPSE_SELE1 is set");
123 > //       painCave.severity = OOPSE_ERROR;
124 > //       painCave.isFatal = 1;
125 > //       simError();
126 > //     }
127 > //   }
128  
129 <        rdf = rAngle2;  
157 <    } else if (args_info.xyz_given) {
129 >  // Problems if sele1 wasn't specified
130  
131 <        GofXyz* xyz = new GofXyz(info, dumpFileName, sele1, sele2);
132 <          
133 <        xyz->setNRBins(args_info.nrbins_arg);            
134 <        xyz->setLength(maxLen);
131 > //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
132 > //       sprintf( painCave.errMsg,
133 > //                "neither --sele2 option nor $OOPSE_SELE2 is set");
134 > //       painCave.severity = OOPSE_ERROR;
135 > //       painCave.isFatal = 1;
136 > //       simError();        
137 > //     }
138 > //   }
139  
140 <        
141 <        rdf = xyz;
142 <    }
140 >  bool batchMode;
141 >  if (args_info.scd_given){
142 >    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
143 >      batchMode = false;
144 >    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
145 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
146 >        sprintf( painCave.errMsg,
147 >                 "below conditions are not satisfied:\n"
148 >                 "0 <= begin && 0<= end && begin <= end-2\n");
149 >        painCave.severity = OOPSE_ERROR;
150 >        painCave.isFatal = 1;
151 >        simError();                    
152 >      }
153 >      batchMode = true;        
154 >    } else{
155 >      sprintf( painCave.errMsg,
156 >               "either --sele1, --sele2, --sele3 are specified,"
157 >               " or --molname, --begin, --end are specified\n");
158 >      painCave.severity = OOPSE_ERROR;
159 >      painCave.isFatal = 1;
160 >      simError();        
161      
168 –
169 –    if (args_info.output_given) {
170 –        rdf->setOutputName(args_info.output_arg);
162      }
163 +  }
164  
165 <    if (args_info.step_given) {
166 <        rdf->setStep(args_info.step_arg);
165 >  //parse md file and set up the system
166 >  SimCreator creator;
167 >  std::cout << "dumpFile = " << dumpFileName << "\n";
168 >  SimInfo* info = creator.createSim(dumpFileName);
169 >
170 >  RealType maxLen;
171 >  if (args_info.length_given) {
172 >    maxLen = args_info.length_arg;
173 >  } else {
174 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
175 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
176 >  }    
177 >
178 >  StaticAnalyser* analyser;
179 >  if (args_info.gofr_given){
180 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
181 >                       args_info.nbins_arg);        
182 >  } else if (args_info.r_theta_given) {
183 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
184 >                              args_info.nbins_arg, args_info.nanglebins_arg);
185 >  } else if (args_info.r_omega_given) {
186 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
187 >                              args_info.nbins_arg, args_info.nanglebins_arg);
188 >  } else if (args_info.theta_omega_given) {
189 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
190 >                              args_info.nanglebins_arg);
191 >  } else if (args_info.gxyz_given) {
192 >    if (args_info.refsele_given) {
193 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
194 >                           maxLen, args_info.nbins_arg);        
195 >    } else {
196 >      sprintf( painCave.errMsg,
197 >               "--refsele must set when --gxyz is used");
198 >      painCave.severity = OOPSE_ERROR;
199 >      painCave.isFatal = 1;
200 >      simError();  
201      }
202 +  } else if (args_info.p2_given) {
203 +    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
204 +  } else if (args_info.rp2_given){
205 +    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
206 +  } else if (args_info.bo_given){
207 +    if (args_info.rcut_given) {
208 +      analyser = new BondOrderParameter(info, dumpFileName, sele1,
209 +                                        args_info.rcut_arg,
210 +                                        args_info.nbins_arg);
211 +    } else {
212 +      sprintf( painCave.errMsg,
213 +               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
214 +      painCave.severity = OOPSE_ERROR;
215 +      painCave.isFatal = 1;
216 +      simError();
217 +    }
218 +  } else if (args_info.scd_given) {
219 +    if (batchMode) {
220 +      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
221 +                                        args_info.begin_arg, args_info.end_arg);
222 +    } else{
223 +      std::string sele3 = args_info.sele3_arg;
224 +      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
225 +    }
226 +  }else if (args_info.density_given) {
227 +    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
228 +                              args_info.nbins_arg);  
229 +  } else if (args_info.slab_density_given) {
230 +    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
231 +    analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
232 + #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
233 +  }else if (args_info.hxy_given) {
234 +    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
235 +                       args_info.nbins_y_arg, args_info.nbins_arg);
236 + #endif
237 +  }else if (args_info.rho_r_given) {
238 +    if (args_info.radius_given){
239 +      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
240 +    }else{
241 +      sprintf( painCave.errMsg,
242 +               "A particle radius (radius) must be specified when calculating Rho(r)");
243 +      painCave.severity = OOPSE_ERROR;
244 +      painCave.isFatal = 1;
245 +      simError();
246 +    }
247 +  }
248 +  
249 +  if (args_info.output_given) {
250 +    analyser->setOutputName(args_info.output_arg);
251 +  }
252 +  if (args_info.step_given) {
253 +    analyser->setStep(args_info.step_arg);
254 +  }
255  
256 <    rdf->process();
256 >  analyser->process();
257  
258 <    delete rdf;    
259 <    delete info;
258 >  delete analyser;    
259 >  delete info;
260  
261 <    return 0;  
261 >  return 0;  
262   }
263  

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