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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 980 by xsun, Thu Jun 1 18:06:33 2006 UTC vs.
Revision 1128 by chuckv, Wed Apr 11 23:27:20 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"
# Line 63 | Line 65
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  
# Line 78 | Line 81 | int main(int argc, char* argv[]){
81      exit(1) ;
82    }
83  
84 <
82 <  //get the dumpfile name and meta-data file name
84 >  //get the dumpfile name
85    std::string dumpFileName = args_info.input_arg;
84 –
85 –  std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
86 –
87 –    
86    std::string sele1;
87    std::string sele2;
88 +  bool userSpecifiedSelect1;
89 +  bool userSpecifiedSelect2;
90  
91 +  // check the first selection argument, or set it to the environment
92 +  // variable, or failing that, set it to "select all"
93 +
94    if (args_info.sele1_given) {
95      sele1 = args_info.sele1_arg;
96 <  }else {
96 >  } else {
97      char*  sele1Env= getenv("OOPSE_SELE1");
98      if (sele1Env) {
99        sele1 = sele1Env;
100 <    }else if (!args_info.scd_given) {
101 <      sprintf( painCave.errMsg,
99 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
100 <      painCave.severity = OOPSE_ERROR;
101 <      painCave.isFatal = 1;
102 <      simError();
100 >    } else {
101 >      sele1 = "select all";
102      }
103    }
104 <    
104 >
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 {
110 >  } else {
111      char* sele2Env = getenv("OOPSE_SELE2");
112      if (sele2Env) {
113        sele2 = sele2Env;            
114 <    } else if (args_info.density_given) {
114 >    } else {
115        sele2 = "select all";
114 –    } else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
115 –      sprintf( painCave.errMsg,
116 –               "neither --sele2 option nor $OOPSE_SELE2 is set");
117 –      painCave.severity = OOPSE_ERROR;
118 –      painCave.isFatal = 1;
119 –      simError();        
116      }
117    }
118  
119 +
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 +  // Problems if sele1 wasn't specified
131 +
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    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;
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) {
129 <            sprintf( painCave.errMsg,
130 <                     "below conditions are not satisfied:\n"
131 <                     "0 <= begin && 0<= end && begin <= end-2\n");
132 <            painCave.severity = OOPSE_ERROR;
133 <            painCave.isFatal = 1;
134 <            simError();                    
135 <        }
136 <        batchMode = true;        
137 <    } else{
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 <                 "either --sele1, --sele2, --sele3 are specified,"
149 <                 " or --molname, --begin, --end are specified\n");
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();        
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      
163      }
164    }
165  
166    //parse md file and set up the system
167    SimCreator creator;
168 <  SimInfo* info = creator.createSim(mdFileName);
168 >  std::cout << "dumpFile = " << dumpFileName << "\n";
169 >  SimInfo* info = creator.createSim(dumpFileName);
170  
171    RealType maxLen;
172    if (args_info.length_given) {
# Line 159 | Line 178 | int main(int argc, char* argv[]){
178  
179    StaticAnalyser* analyser;
180    if (args_info.gofr_given){
181 <    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);        
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, args_info.nrbins_arg, args_info.nanglebins_arg);
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, args_info.nrbins_arg, args_info.nanglebins_arg);
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, args_info.nanglebins_arg);
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, maxLen, args_info.nrbins_arg);        
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");
# Line 177 | Line 201 | int main(int argc, char* argv[]){
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.scd_given) {
208 <      if (batchMode) {
209 <          analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
210 <            args_info.begin_arg, args_info.end_arg);
211 <      } else{
212 <          std::string sele3 = args_info.sele3_arg;
213 <          analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
214 <      }
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, args_info.nrbins_arg);  
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.nrbins_arg);
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, args_info.nbins_y_arg, args_info.nrbins_arg);
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 <    
260 >  
261    if (args_info.output_given) {
262      analyser->setOutputName(args_info.output_arg);
263    }

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