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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 545 by tim, Fri May 27 21:11:24 2005 UTC vs.
Revision 1180 by chuckv, Mon Sep 17 20:05:51 2007 UTC

# Line 56 | Line 56
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  
# Line 73 | Line 83 | int main(int argc, char* argv[]){
83      exit(1) ;
84    }
85  
86 <
77 <  //get the dumpfile name and meta-data file name
86 >  //get the dumpfile name
87    std::string dumpFileName = args_info.input_arg;
79 –
80 –  std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
81 –
82 –    
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 {
98 >  } else {
99      char*  sele1Env= getenv("OOPSE_SELE1");
100      if (sele1Env) {
101        sele1 = sele1Env;
102 <    }else if (!args_info.scd_given) {
103 <      sprintf( painCave.errMsg,
94 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
95 <      painCave.severity = OOPSE_ERROR;
96 <      painCave.isFatal = 1;
97 <      simError();
102 >    } else {
103 >      sele1 = "select all";
104      }
105    }
106 <    
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 {
112 >  } else {
113      char* sele2Env = getenv("OOPSE_SELE2");
114      if (sele2Env) {
115        sele2 = sele2Env;            
116 <    } else if(!args_info.scd_given && !args_info.density_given)  {
117 <      sprintf( painCave.errMsg,
109 <               "neither --sele2 option nor $OOPSE_SELE2 is set");
110 <      painCave.severity = OOPSE_ERROR;
111 <      painCave.isFatal = 1;
112 <      simError();        
116 >    } else {
117 >      sele2 = "select all";
118      }
119    }
120  
121 +
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 +  // Problems if sele1 wasn't specified
133 +
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;
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) {
122 <            sprintf( painCave.errMsg,
123 <                     "below conditions are not satisfied:\n"
124 <                     "0 <= begin && 0<= end && begin <= end-2\n");
125 <            painCave.severity = OOPSE_ERROR;
126 <            painCave.isFatal = 1;
127 <            simError();                    
128 <        }
129 <        batchMode = true;        
130 <    } else{
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 <                 "either --sele1, --sele2, --sele3 are specified,"
151 <                 " or --molname, --begin, --end are specified\n");
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();        
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      
165      }
166    }
167  
168    //parse md file and set up the system
169    SimCreator creator;
170 <  SimInfo* info = creator.createSim(mdFileName);
170 >  std::cout << "dumpFile = " << dumpFileName << "\n";
171 >  SimInfo* info = creator.createSim(dumpFileName);
172  
173 <  double maxLen;
173 >  RealType maxLen;
174    if (args_info.length_given) {
175      maxLen = args_info.length_arg;
176    } else {
# Line 152 | Line 180 | int main(int argc, char* argv[]){
180  
181    StaticAnalyser* analyser;
182    if (args_info.gofr_given){
183 <    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);        
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, args_info.nrbins_arg, args_info.nanglebins_arg);
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, args_info.nrbins_arg, args_info.nanglebins_arg);
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, args_info.nanglebins_arg);
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, maxLen, args_info.nrbins_arg);        
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");
# Line 170 | Line 203 | int main(int argc, char* argv[]){
203        simError();  
204      }
205    } else if (args_info.p2_given) {
206 <      analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
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 <      }
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, maxLen, args_info.nrbins_arg);  
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 <    
275 >  
276    if (args_info.output_given) {
277      analyser->setOutputName(args_info.output_arg);
278    }

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