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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 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1513 by gezelter, Tue Oct 19 18:40:54 2010 UTC

# Line 53 | Line 53
53   #include "applications/staticProps/StaticAnalyser.hpp"
54   #include "applications/staticProps/GofR.hpp"
55   #include "applications/staticProps/GofZ.hpp"
56 + #include "applications/staticProps/GofRZ.hpp"
57   #include "applications/staticProps/GofRAngle.hpp"
58   #include "applications/staticProps/GofAngle2.hpp"
59   #include "applications/staticProps/GofXyz.hpp"
60 + #include "applications/staticProps/TwoDGofR.hpp"
61   #include "applications/staticProps/P2OrderParameter.hpp"
62   #include "applications/staticProps/BondOrderParameter.hpp"
63   #include "applications/staticProps/BOPofR.hpp"
64   #include "applications/staticProps/RippleOP.hpp"
65   #include "applications/staticProps/SCDOrderParameter.hpp"
66   #include "applications/staticProps/DensityPlot.hpp"
67 + #include "applications/staticProps/ObjectCount.hpp"
68   #include "applications/staticProps/RhoZ.hpp"
69 + #include "applications/staticProps/pAngle.hpp"
70   #include "applications/staticProps/BondAngleDistribution.hpp"
71   #include "applications/staticProps/NanoVolume.hpp"
72   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
# Line 76 | Line 80 | int main(int argc, char* argv[]){
80    
81    //register force fields
82    registerForceFields();
83 <
83 >  
84    gengetopt_args_info args_info;
85 <
85 >  
86    //parse the command line option
87    if (cmdline_parser (argc, argv, &args_info) != 0) {
88      exit(1) ;
89    }
90 <
90 >  
91    //get the dumpfile name
92    std::string dumpFileName = args_info.input_arg;
93    std::string sele1;
94    std::string sele2;
95    bool userSpecifiedSelect1;
96    bool userSpecifiedSelect2;
97 <
97 >  
98    // check the first selection argument, or set it to the environment
99    // variable, or failing that, set it to "select all"
100 <
100 >  
101    if (args_info.sele1_given) {
102      sele1 = args_info.sele1_arg;
103    } else {
# Line 104 | Line 108 | int main(int argc, char* argv[]){
108        sele1 = "select all";
109      }
110    }
111 <
111 >  
112    // check the second selection argument, or set it to the environment
113    // variable, or failing that, set it to "select all"
114    
# Line 118 | Line 122 | int main(int argc, char* argv[]){
122        sele2 = "select all";
123      }
124    }
125 <
126 <
125 >  
126 >  
127    // Problems if sele1 wasn't specified, but
128 < // if (!args_info.scd_given) {
129 < //       sprintf( painCave.errMsg,
130 < //                "neither --sele1 option nor $SELECTION1 is set");
131 < //       painCave.severity = OPENMD_ERROR;
132 < //       painCave.isFatal = 1;
133 < //       simError();
134 < //     }
135 < //   }
136 <
128 >  // if (!args_info.scd_given) {
129 >  //       sprintf( painCave.errMsg,
130 >  //                "neither --sele1 option nor $SELECTION1 is set");
131 >  //       painCave.severity = OPENMD_ERROR;
132 >  //       painCave.isFatal = 1;
133 >  //       simError();
134 >  //     }
135 >  //   }
136 >  
137    // Problems if sele1 wasn't specified
138 <
139 < //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
140 < //       sprintf( painCave.errMsg,
141 < //                "neither --sele2 option nor $SELECTION1 is set");
142 < //       painCave.severity = OPENMD_ERROR;
143 < //       painCave.isFatal = 1;
144 < //       simError();        
145 < //     }
146 < //   }
147 <
138 >  
139 >  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
140 >  //       sprintf( painCave.errMsg,
141 >  //                "neither --sele2 option nor $SELECTION1 is set");
142 >  //       painCave.severity = OPENMD_ERROR;
143 >  //       painCave.isFatal = 1;
144 >  //       simError();        
145 >  //     }
146 >  //   }
147 >  
148    bool batchMode;
149    if (args_info.scd_given){
150      if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
# Line 162 | Line 166 | int main(int argc, char* argv[]){
166        painCave.severity = OPENMD_ERROR;
167        painCave.isFatal = 1;
168        simError();        
169 <    
169 >      
170      }
171    }
172 <
172 >  
173    //parse md file and set up the system
174    SimCreator creator;
175    std::cout << "dumpFile = " << dumpFileName << "\n";
176    SimInfo* info = creator.createSim(dumpFileName);
177  
178    RealType maxLen;
179 +  RealType zmaxLen;
180    if (args_info.length_given) {
181      maxLen = args_info.length_arg;
182 +    if (args_info.zlength_given){
183 +      zmaxLen = args_info.zlength_arg;
184 +    }
185    } else {
186      Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
187 <    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
187 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
188 >    zmaxLen = hmat(2,2);    
189    }    
190  
191    StaticAnalyser* analyser;
# Line 186 | Line 195 | int main(int argc, char* argv[]){
195    } else if (args_info.gofz_given) {
196      analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
197                         args_info.nbins_arg);
198 +  } else if (args_info.r_z_given) {
199 +    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
200 +                          args_info.nbins_arg, args_info.nbins_z_arg);
201    } else if (args_info.r_theta_given) {
202      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
203                                args_info.nbins_arg, args_info.nanglebins_arg);
# Line 206 | Line 218 | int main(int argc, char* argv[]){
218        painCave.isFatal = 1;
219        simError();  
220      }
221 +  } else if (args_info.twodgofr_given){
222 +    if (args_info.dz_given) {
223 +      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
224 +                             args_info.dz_arg, args_info.nbins_arg);        
225 +    } else {
226 +      sprintf( painCave.errMsg,
227 +               "A slab width (dz) must be specified when calculating TwoDGofR");
228 +      painCave.severity = OPENMD_ERROR;
229 +      painCave.isFatal = 1;
230 +      simError();
231 +    }
232    } else if (args_info.p2_given) {
233      analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
234    } else if (args_info.rp2_given){
# Line 225 | Line 248 | int main(int argc, char* argv[]){
248    } else if (args_info.bor_given){
249      if (args_info.rcut_given) {
250        analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
251 <                            args_info.nbins_arg, maxLen);
251 >                            args_info.nbins_arg, maxLen);
252      } else {
253        sprintf( painCave.errMsg,
254                 "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
# Line 236 | Line 259 | int main(int argc, char* argv[]){
259    } else if (args_info.bad_given){
260      if (args_info.rcut_given) {
261        analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
262 <                            args_info.nbins_arg);
262 >                                           args_info.nbins_arg);
263      } else {
264        sprintf( painCave.errMsg,
265                 "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
# Line 255 | Line 278 | int main(int argc, char* argv[]){
278    }else if (args_info.density_given) {
279      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
280                                args_info.nbins_arg);  
281 +  } else if (args_info.count_given) {
282 +    analyser = new ObjectCount(info, dumpFileName, sele1 );
283    } else if (args_info.slab_density_given) {
284      analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
285 +  } else if (args_info.p_angle_given) {
286 +    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
287   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
288    }else if (args_info.hxy_given) {
289      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
# Line 272 | Line 299 | int main(int argc, char* argv[]){
299        painCave.isFatal = 1;
300        simError();
301      }
302 <        }else if (args_info.hullvol_given) {
302 >  }else if (args_info.hullvol_given) {
303      analyser = new NanoVolume(info, dumpFileName, sele1);
304    }
305    

Comparing trunk/src/applications/staticProps/StaticProps.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1513 by gezelter, Tue Oct 19 18:40:54 2010 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

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