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root/OpenMD/branches/development/src/applications/staticProps/StaticProps.cpp
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Comparing:
trunk/src/applications/staticProps/StaticProps.cpp (file contents), Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC vs.
branches/development/src/applications/staticProps/StaticProps.cpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <iostream>
44   #include <fstream>
45   #include <string>
46  
46 – #include "brains/Register.hpp"
47   #include "brains/SimCreator.hpp"
48   #include "brains/SimInfo.hpp"
49   #include "io/DumpReader.hpp"
# Line 57 | Line 57
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 + #include "applications/staticProps/NanoLength.hpp"
73   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
74   #include "applications/staticProps/Hxy.hpp"
75   #endif
76   #include "applications/staticProps/RhoR.hpp"
77 + #include "applications/staticProps/AngleR.hpp"
78 + #include "applications/staticProps/TetrahedralityParam.hpp"
79  
80   using namespace OpenMD;
81  
82   int main(int argc, char* argv[]){
83    
84 <    //register force fields
85 <    registerForceFields();
86 <
87 <    gengetopt_args_info args_info;
88 <
89 <    //parse the command line option
90 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
91 <        exit(1) ;
92 <    }
93 <
94 <    //get the dumpfile name
95 <    std::string dumpFileName = args_info.input_arg;
96 <    std::string sele1;
97 <    std::string sele2;
98 <    bool userSpecifiedSelect1;
99 <    bool userSpecifiedSelect2;
100 <
101 <    // check the first selection argument, or set it to the environment
102 <    // variable, or failing that, set it to "select all"
103 <
104 <    if (args_info.sele1_given) {
105 <        sele1 = args_info.sele1_arg;
84 >  
85 >  gengetopt_args_info args_info;
86 >  
87 >  //parse the command line option
88 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
89 >    exit(1) ;
90 >  }
91 >  
92 >  //get the dumpfile name
93 >  std::string dumpFileName = args_info.input_arg;
94 >  std::string sele1;
95 >  std::string sele2;
96 >  bool userSpecifiedSelect1;
97 >  bool userSpecifiedSelect2;
98 >  
99 >  // check the first selection argument, or set it to the environment
100 >  // variable, or failing that, set it to "select all"
101 >  
102 >  if (args_info.sele1_given) {
103 >    sele1 = args_info.sele1_arg;
104 >  } else {
105 >    char*  sele1Env= getenv("SELECTION1");
106 >    if (sele1Env) {
107 >      sele1 = sele1Env;
108      } else {
109 <        char*  sele1Env= getenv("SELECTION1");
103 <        if (sele1Env) {
104 <            sele1 = sele1Env;
105 <        } else {
106 <            sele1 = "select all";
107 <        }
109 >      sele1 = "select all";
110      }
111 <
110 <    // check the second selection argument, or set it to the environment
111 <    // variable, or failing that, set it to "select all"
111 >  }
112    
113 <    if (args_info.sele2_given) {
114 <        sele2 = args_info.sele2_arg;
115 <    } else {
116 <        char* sele2Env = getenv("SELECTION1");
117 <        if (sele2Env) {
118 <            sele2 = sele2Env;            
119 <        } else {
120 <            sele2 = "select all";
121 <        }
113 >  // check the second selection argument, or set it to the environment
114 >  // variable, or failing that, set it to "select all"
115 >  
116 >  if (args_info.sele2_given) {
117 >    sele2 = args_info.sele2_arg;
118 >  } else {
119 >    char* sele2Env = getenv("SELECTION1");
120 >    if (sele2Env) {
121 >      sele2 = sele2Env;            
122 >    } else {
123 >      sele2 = "select all";
124      }
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 <
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 <
148 <    bool batchMode;
149 <    if (args_info.scd_given){
150 <        if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
151 <            batchMode = false;
152 <        } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
153 <            if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
154 <                sprintf( painCave.errMsg,
155 <                         "below conditions are not satisfied:\n"
156 <                         "0 <= begin && 0<= end && begin <= end-2\n");
157 <                painCave.severity = OPENMD_ERROR;
158 <                painCave.isFatal = 1;
159 <                simError();                    
160 <            }
161 <            batchMode = true;        
162 <        } else{
163 <            sprintf( painCave.errMsg,
164 <                     "either --sele1, --sele2, --sele3 are specified,"
165 <                     " or --molname, --begin, --end are specified\n");
166 <            painCave.severity = OPENMD_ERROR;
167 <            painCave.isFatal = 1;
168 <            simError();        
169 <    
170 <        }
125 >  }
126 >  
127 >  
128 >  // Problems if sele1 wasn't specified, but
129 >  // if (!args_info.scd_given) {
130 >  //       sprintf( painCave.errMsg,
131 >  //                "neither --sele1 option nor $SELECTION1 is set");
132 >  //       painCave.severity = OPENMD_ERROR;
133 >  //       painCave.isFatal = 1;
134 >  //       simError();
135 >  //     }
136 >  //   }
137 >  
138 >  // Problems if sele1 wasn't specified
139 >  
140 >  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
141 >  //       sprintf( painCave.errMsg,
142 >  //                "neither --sele2 option nor $SELECTION1 is set");
143 >  //       painCave.severity = OPENMD_ERROR;
144 >  //       painCave.isFatal = 1;
145 >  //       simError();        
146 >  //     }
147 >  //   }
148 >  
149 >  bool batchMode;
150 >  if (args_info.scd_given){
151 >    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
152 >      batchMode = false;
153 >    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
154 >      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
155 >        sprintf( painCave.errMsg,
156 >                 "below conditions are not satisfied:\n"
157 >                 "0 <= begin && 0<= end && begin <= end-2\n");
158 >        painCave.severity = OPENMD_ERROR;
159 >        painCave.isFatal = 1;
160 >        simError();                    
161 >      }
162 >      batchMode = true;        
163 >    } else{
164 >      sprintf( painCave.errMsg,
165 >               "either --sele1, --sele2, --sele3 are specified,"
166 >               " or --molname, --begin, --end are specified\n");
167 >      painCave.severity = OPENMD_ERROR;
168 >      painCave.isFatal = 1;
169 >      simError();        
170 >      
171      }
172 +  }
173 +  
174 +  //parse md file and set up the system
175 +  SimCreator creator;
176 +  std::cout << "dumpFile = " << dumpFileName << "\n";
177 +  SimInfo* info = creator.createSim(dumpFileName);
178  
179 <    //parse md file and set up the system
180 <    SimCreator creator;
181 <    std::cout << "dumpFile = " << dumpFileName << "\n";
182 <    SimInfo* info = creator.createSim(dumpFileName);
183 <
184 <    RealType maxLen;
185 <    RealType zmaxLen;
186 <    if (args_info.length_given) {
187 <        maxLen = args_info.length_arg;
188 <        if (args_info.zlength_given){
189 <            zmaxLen = args_info.zlength_arg;
190 <        }
179 >  RealType maxLen;
180 >  RealType zmaxLen;
181 >  if (args_info.length_given) {
182 >    maxLen = args_info.length_arg;
183 >    if (args_info.zlength_given){
184 >      zmaxLen = args_info.zlength_arg;
185 >    }
186 >  } else {
187 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
188 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
189 >    zmaxLen = hmat(2,2);    
190 >  }    
191 >  
192 >  StaticAnalyser* analyser;
193 >  if (args_info.gofr_given){
194 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
195 >                       args_info.nbins_arg);        
196 >  } else if (args_info.gofz_given) {
197 >    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
198 >                       args_info.nbins_arg);
199 >  } else if (args_info.r_z_given) {
200 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
201 >                          args_info.nbins_arg, args_info.nbins_z_arg);
202 >  } else if (args_info.r_theta_given) {
203 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
204 >                              args_info.nbins_arg, args_info.nanglebins_arg);
205 >  } else if (args_info.r_omega_given) {
206 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
207 >                              args_info.nbins_arg, args_info.nanglebins_arg);
208 >  } else if (args_info.theta_omega_given) {
209 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
210 >                              args_info.nanglebins_arg);
211 >  } else if (args_info.gxyz_given) {
212 >    if (args_info.refsele_given) {
213 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
214 >                           maxLen, args_info.nbins_arg);        
215      } else {
216 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
217 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
218 <        zmaxLen = hmat(2,2);    
216 >      sprintf( painCave.errMsg,
217 >               "--refsele must set when --gxyz is used");
218 >      painCave.severity = OPENMD_ERROR;
219 >      painCave.isFatal = 1;
220 >      simError();  
221 >    }
222 >  } else if (args_info.twodgofr_given){
223 >    if (args_info.dz_given) {
224 >      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
225 >                             args_info.dz_arg, args_info.nbins_arg);        
226 >    } else {
227 >      sprintf( painCave.errMsg,
228 >               "A slab width (dz) must be specified when calculating TwoDGofR");
229 >      painCave.severity = OPENMD_ERROR;
230 >      painCave.isFatal = 1;
231 >      simError();
232      }    
233 <
234 <    StaticAnalyser* analyser;
235 <    if (args_info.gofr_given){
236 <        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
237 <                           args_info.nbins_arg);        
238 <    } else if (args_info.gofz_given) {
239 <        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
240 <                           args_info.nbins_arg);
241 <    } else if (args_info.r_z_given) {
242 <        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
243 <                              args_info.nbins_arg, args_info.nbins_z_arg);
244 <    } else if (args_info.r_theta_given) {
245 <        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
246 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
247 <    } else if (args_info.r_omega_given) {
248 <        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
249 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
250 <    } else if (args_info.theta_omega_given) {
251 <        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
252 <                                  args_info.nanglebins_arg);
253 <    } else if (args_info.gxyz_given) {
254 <        if (args_info.refsele_given) {
255 <            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
256 <                                 maxLen, args_info.nbins_arg);        
257 <        } else {
258 <            sprintf( painCave.errMsg,
259 <                     "--refsele must set when --gxyz is used");
260 <            painCave.severity = OPENMD_ERROR;
261 <            painCave.isFatal = 1;
262 <            simError();  
263 <        }
264 <    } else if (args_info.p2_given) {
265 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
266 <    } else if (args_info.rp2_given){
267 <        analyser = new RippleOP(info, dumpFileName, sele1, sele2);
268 <    } else if (args_info.bo_given){
269 <        if (args_info.rcut_given) {
270 <            analyser = new BondOrderParameter(info, dumpFileName, sele1,
271 <                                              args_info.rcut_arg,
272 <                                              args_info.nbins_arg);
273 <        } else {
274 <            sprintf( painCave.errMsg,
275 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
276 <            painCave.severity = OPENMD_ERROR;
277 <            painCave.isFatal = 1;
278 <            simError();
279 <        }
280 <    } else if (args_info.bor_given){
281 <        if (args_info.rcut_given) {
282 <            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
283 <                                  args_info.nbins_arg, maxLen);
284 <        } else {
285 <            sprintf( painCave.errMsg,
286 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
287 <            painCave.severity = OPENMD_ERROR;
288 <            painCave.isFatal = 1;
289 <            simError();
290 <        }
291 <    } else if (args_info.bad_given){
292 <        if (args_info.rcut_given) {
293 <            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
294 <                                                 args_info.nbins_arg);
295 <        } else {
296 <            sprintf( painCave.errMsg,
297 <                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
298 <            painCave.severity = OPENMD_ERROR;
299 <            painCave.isFatal = 1;
300 <            simError();
301 <        }
302 <    } else if (args_info.scd_given) {
303 <        if (batchMode) {
304 <            analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
305 <                                              args_info.begin_arg, args_info.end_arg);
306 <        } else{
307 <            std::string sele3 = args_info.sele3_arg;
308 <            analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
309 <        }
310 <    }else if (args_info.density_given) {
311 <        analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
267 <                                  args_info.nbins_arg);  
268 <    } else if (args_info.slab_density_given) {
269 <        analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
270 <    } else if (args_info.p_angle_given) {
271 <        analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
233 >  } else if (args_info.p2_given) {
234 >    if (args_info.sele1_given) {    
235 >      if (args_info.sele2_given)
236 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
237 >      else
238 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
239 >    } else {
240 >      sprintf( painCave.errMsg,
241 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
242 >      painCave.severity = OPENMD_ERROR;
243 >      painCave.isFatal = 1;
244 >      simError();
245 >    }
246 >  } else if (args_info.rp2_given){
247 >    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
248 >  } else if (args_info.bo_given){
249 >    if (args_info.rcut_given) {
250 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
251 >                                        args_info.rcut_arg,
252 >                                        args_info.nbins_arg);
253 >    } else {
254 >      sprintf( painCave.errMsg,
255 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
256 >      painCave.severity = OPENMD_ERROR;
257 >      painCave.isFatal = 1;
258 >      simError();
259 >    }
260 >    
261 >  } else if (args_info.tet_param_given) {
262 >    if (args_info.rcut_given) {  
263 >      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
264 >                                         args_info.rcut_arg,
265 >                                         args_info.nbins_arg);
266 >    } else {
267 >      sprintf( painCave.errMsg,
268 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
269 >      painCave.severity = OPENMD_ERROR;
270 >      painCave.isFatal = 1;
271 >      simError();
272 >    }
273 >  } else if (args_info.bor_given){
274 >    if (args_info.rcut_given) {
275 >      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
276 >                            args_info.nbins_arg, maxLen);
277 >    } else {
278 >      sprintf( painCave.errMsg,
279 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
280 >      painCave.severity = OPENMD_ERROR;
281 >      painCave.isFatal = 1;
282 >      simError();
283 >    }
284 >  } else if (args_info.bad_given){
285 >    if (args_info.rcut_given) {
286 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
287 >                                           args_info.nbins_arg);
288 >    } else {
289 >      sprintf( painCave.errMsg,
290 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
291 >      painCave.severity = OPENMD_ERROR;
292 >      painCave.isFatal = 1;
293 >      simError();
294 >      }
295 >  } else if (args_info.scd_given) {
296 >    if (batchMode) {
297 >      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
298 >                                        args_info.begin_arg, args_info.end_arg);
299 >    } else{
300 >      std::string sele3 = args_info.sele3_arg;
301 >      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
302 >    }
303 >  }else if (args_info.density_given) {
304 >    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
305 >                              args_info.nbins_arg);  
306 >  } else if (args_info.count_given) {
307 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
308 >  } else if (args_info.slab_density_given) {
309 >    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
310 >  } else if (args_info.p_angle_given) {
311 >    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
312   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
313 <    }else if (args_info.hxy_given) {
314 <        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
315 <                           args_info.nbins_y_arg, args_info.nbins_arg);
313 >  }else if (args_info.hxy_given) {
314 >    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
315 >                       args_info.nbins_y_arg, args_info.nbins_arg);
316   #endif
317 <    }else if (args_info.rho_r_given) {
318 <        if (args_info.radius_given){
319 <            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
320 <        }else{
321 <            sprintf( painCave.errMsg,
322 <                     "A particle radius (radius) must be specified when calculating Rho(r)");
323 <            painCave.severity = OPENMD_ERROR;
324 <            painCave.isFatal = 1;
325 <            simError();
286 <        }
287 <    }else if (args_info.hullvol_given) {
288 <        analyser = new NanoVolume(info, dumpFileName, sele1);
317 >  }else if (args_info.rho_r_given) {
318 >    if (args_info.radius_given){
319 >      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
320 >    }else{
321 >      sprintf( painCave.errMsg,
322 >               "A particle radius (radius) must be specified when calculating Rho(r)");
323 >      painCave.severity = OPENMD_ERROR;
324 >      painCave.isFatal = 1;
325 >      simError();
326      }
327 +  } else if (args_info.hullvol_given) {
328 +    analyser = new NanoVolume(info, dumpFileName, sele1);
329 +  } else if (args_info.rodlength_given) {
330 +    analyser = new NanoLength(info, dumpFileName, sele1);
331 +  } else if (args_info.angle_r_given) {
332 +    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
333 +  }
334 +    
335 +  if (args_info.output_given) {
336 +    analyser->setOutputName(args_info.output_arg);
337 +  }
338 +  if (args_info.step_given) {
339 +    analyser->setStep(args_info.step_arg);
340 +  }
341    
342 <    if (args_info.output_given) {
343 <        analyser->setOutputName(args_info.output_arg);
344 <    }
345 <    if (args_info.step_given) {
295 <        analyser->setStep(args_info.step_arg);
296 <    }
342 >  analyser->process();
343 >  
344 >  delete analyser;    
345 >  delete info;
346  
347 <    analyser->process();
299 <
300 <    delete analyser;    
301 <    delete info;
302 <
303 <    return 0;  
347 >  return 0;  
348   }
349  

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