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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 1454 by gezelter, Wed Jun 23 19:25:02 2010 UTC vs.
Revision 1846 by gezelter, Thu Jan 31 15:55:47 2013 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 64 | Line 64
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 <
77 > #include "applications/staticProps/AngleR.hpp"
78 > #include "applications/staticProps/TetrahedralityParam.hpp"
79 > #include "applications/staticProps/TetrahedralityParamZ.hpp"
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 >  
97 >  // check the first selection argument, or set it to the environment
98 >  // variable, or failing that, set it to "select all"
99 >  
100 >  if (args_info.sele1_given) {
101 >    sele1 = args_info.sele1_arg;
102 >  } else {
103 >    char*  sele1Env= getenv("SELECTION1");
104 >    if (sele1Env) {
105 >      sele1 = sele1Env;
106      } else {
107 <        char*  sele1Env= getenv("SELECTION1");
104 <        if (sele1Env) {
105 <            sele1 = sele1Env;
106 <        } else {
107 <            sele1 = "select all";
108 <        }
107 >      sele1 = "select all";
108      }
109 <
111 <    // check the second selection argument, or set it to the environment
112 <    // variable, or failing that, set it to "select all"
109 >  }
110    
111 <    if (args_info.sele2_given) {
112 <        sele2 = args_info.sele2_arg;
113 <    } else {
114 <        char* sele2Env = getenv("SELECTION1");
115 <        if (sele2Env) {
116 <            sele2 = sele2Env;            
117 <        } else {
118 <            sele2 = "select all";
119 <        }
111 >  // check the second selection argument, or set it to the environment
112 >  // variable, or failing that, set it to "select all"
113 >  
114 >  if (args_info.sele2_given) {
115 >    sele2 = args_info.sele2_arg;
116 >  } else {
117 >    char* sele2Env = getenv("SELECTION1");
118 >    if (sele2Env) {
119 >      sele2 = sele2Env;            
120 >    } else {
121 >      //If sele2 is not specified, then the default behavior
122 >      //should be what is already intended for sele1
123 >      sele2 = sele1;
124      }
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 < //     }
134 < //   }
135 <
136 <    // Problems if sele1 wasn't specified
137 <
138 < //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
139 < //       sprintf( painCave.errMsg,
140 < //                "neither --sele2 option nor $SELECTION1 is set");
141 < //       painCave.severity = OPENMD_ERROR;
142 < //       painCave.isFatal = 1;
143 < //       simError();        
144 < //     }
145 < //   }
146 <
147 <    bool batchMode;
148 <    if (args_info.scd_given){
149 <        if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
150 <            batchMode = false;
151 <        } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
152 <            if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
153 <                sprintf( painCave.errMsg,
154 <                         "below conditions are not satisfied:\n"
155 <                         "0 <= begin && 0<= end && begin <= end-2\n");
156 <                painCave.severity = OPENMD_ERROR;
157 <                painCave.isFatal = 1;
158 <                simError();                    
159 <            }
160 <            batchMode = true;        
161 <        } else{
162 <            sprintf( painCave.errMsg,
163 <                     "either --sele1, --sele2, --sele3 are specified,"
164 <                     " or --molname, --begin, --end are specified\n");
165 <            painCave.severity = OPENMD_ERROR;
166 <            painCave.isFatal = 1;
167 <            simError();        
168 <    
169 <        }
170 <    }
171 <
172 <    //parse md file and set up the system
173 <    SimCreator creator;
174 <    std::cout << "dumpFile = " << dumpFileName << "\n";
175 <    SimInfo* info = creator.createSim(dumpFileName);
176 <
177 <    RealType maxLen;
178 <    RealType zmaxLen;
179 <    if (args_info.length_given) {
180 <        maxLen = args_info.length_arg;
181 <        if (args_info.zlength_given){
182 <            zmaxLen = args_info.zlength_arg;
183 <        }
184 <    } else {
185 <        Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
186 <        maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
187 <        zmaxLen = hmat(2,2);    
188 <    }    
189 <
190 <    StaticAnalyser* analyser;
191 <    if (args_info.gofr_given){
192 <        analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
193 <                           args_info.nbins_arg);        
194 <    } else if (args_info.gofz_given) {
195 <        analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
196 <                           args_info.nbins_arg);
197 <    } else if (args_info.r_z_given) {
198 <        analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
199 <                              args_info.nbins_arg, args_info.nbins_z_arg);
200 <    } else if (args_info.r_theta_given) {
201 <        analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
202 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
203 <    } else if (args_info.r_omega_given) {
204 <        analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
205 <                                  args_info.nbins_arg, args_info.nanglebins_arg);
206 <    } else if (args_info.theta_omega_given) {
207 <        analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
208 <                                  args_info.nanglebins_arg);
209 <    } else if (args_info.gxyz_given) {
210 <        if (args_info.refsele_given) {
211 <            analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
212 <                                 maxLen, args_info.nbins_arg);        
213 <        } else {
214 <            sprintf( painCave.errMsg,
215 <                     "--refsele must set when --gxyz is used");
216 <            painCave.severity = OPENMD_ERROR;
217 <            painCave.isFatal = 1;
218 <            simError();  
219 <        }
220 <    } else if (args_info.twodgofr_given){
221 <      if (args_info.dz_given) {
222 <        analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
223 <                               args_info.dz_arg, args_info.nbins_arg);        
224 <      } else {
127 >  bool batchMode;
128 >  if (args_info.scd_given){
129 >    if (args_info.sele1_given &&
130 >        args_info.sele2_given && args_info.sele3_given) {
131 >      batchMode = false;
132 >    } else if (args_info.molname_given &&
133 >               args_info.begin_given && args_info.end_given) {
134 >      if (args_info.begin_arg < 0 ||
135 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
136          sprintf( painCave.errMsg,
137 <                 "A slab width (dz) must be specified when calculating TwoDGofR");
137 >                 "below conditions are not satisfied:\n"
138 >                 "0 <= begin && 0<= end && begin <= end-2\n");
139          painCave.severity = OPENMD_ERROR;
140          painCave.isFatal = 1;
141 <        simError();
141 >        simError();                    
142        }
143 <    } else if (args_info.p2_given) {
144 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
145 <    } else if (args_info.rp2_given){
146 <        analyser = new RippleOP(info, dumpFileName, sele1, sele2);
147 <    } else if (args_info.bo_given){
148 <        if (args_info.rcut_given) {
149 <            analyser = new BondOrderParameter(info, dumpFileName, sele1,
150 <                                              args_info.rcut_arg,
239 <                                              args_info.nbins_arg);
240 <        } else {
241 <            sprintf( painCave.errMsg,
242 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
243 <            painCave.severity = OPENMD_ERROR;
244 <            painCave.isFatal = 1;
245 <            simError();
246 <        }
247 <    } else if (args_info.bor_given){
248 <        if (args_info.rcut_given) {
249 <            analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
250 <                                  args_info.nbins_arg, maxLen);
251 <        } else {
252 <            sprintf( painCave.errMsg,
253 <                     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
254 <            painCave.severity = OPENMD_ERROR;
255 <            painCave.isFatal = 1;
256 <            simError();
257 <        }
258 <    } else if (args_info.bad_given){
259 <        if (args_info.rcut_given) {
260 <            analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
261 <                                                 args_info.nbins_arg);
262 <        } else {
263 <            sprintf( painCave.errMsg,
264 <                     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
265 <            painCave.severity = OPENMD_ERROR;
266 <            painCave.isFatal = 1;
267 <            simError();
268 <        }
269 <    } else if (args_info.scd_given) {
270 <        if (batchMode) {
271 <            analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
272 <                                              args_info.begin_arg, args_info.end_arg);
273 <        } else{
274 <            std::string sele3 = args_info.sele3_arg;
275 <            analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
276 <        }
277 <    }else if (args_info.density_given) {
278 <        analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
279 <                                  args_info.nbins_arg);  
280 <    } else if (args_info.slab_density_given) {
281 <        analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
282 <    } else if (args_info.p_angle_given) {
283 <        analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
284 < #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
285 <    }else if (args_info.hxy_given) {
286 <        analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
287 <                           args_info.nbins_y_arg, args_info.nbins_arg);
288 < #endif
289 <    }else if (args_info.rho_r_given) {
290 <        if (args_info.radius_given){
291 <            analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
292 <        }else{
293 <            sprintf( painCave.errMsg,
294 <                     "A particle radius (radius) must be specified when calculating Rho(r)");
295 <            painCave.severity = OPENMD_ERROR;
296 <            painCave.isFatal = 1;
297 <            simError();
298 <        }
299 <    }else if (args_info.hullvol_given) {
300 <        analyser = new NanoVolume(info, dumpFileName, sele1);
143 >      batchMode = true;        
144 >    } else{
145 >      sprintf( painCave.errMsg,
146 >               "either --sele1, --sele2, --sele3 are specified,"
147 >               " or --molname, --begin, --end are specified\n");
148 >      painCave.severity = OPENMD_ERROR;
149 >      painCave.isFatal = 1;
150 >      simError();
151      }
152 +  }
153    
154 <    if (args_info.output_given) {
155 <        analyser->setOutputName(args_info.output_arg);
154 >  //parse md file and set up the system
155 >  SimCreator creator;
156 >  SimInfo* info = creator.createSim(dumpFileName);
157 >
158 >  RealType maxLen;
159 >  RealType zmaxLen;
160 >  if (args_info.length_given) {
161 >    maxLen = args_info.length_arg;
162 >    if (args_info.zlength_given){
163 >      zmaxLen = args_info.zlength_arg;
164      }
165 <    if (args_info.step_given) {
166 <        analyser->setStep(args_info.step_arg);
165 >  } else {
166 >    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
167 >    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
168 >    zmaxLen = hmat(2,2);    
169 >  }    
170 >  
171 >  StaticAnalyser* analyser;
172 >  if (args_info.gofr_given){
173 >    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
174 >                       args_info.nbins_arg);        
175 >  } else if (args_info.gofz_given) {
176 >    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
177 >                       args_info.nbins_arg);
178 >  } else if (args_info.r_z_given) {
179 >    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
180 >                          args_info.nbins_arg, args_info.nbins_z_arg);
181 >  } else if (args_info.r_theta_given) {
182 >    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
183 >                              args_info.nbins_arg, args_info.nanglebins_arg);
184 >  } else if (args_info.r_omega_given) {
185 >    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
186 >                              args_info.nbins_arg, args_info.nanglebins_arg);
187 >  } else if (args_info.theta_omega_given) {
188 >    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2,
189 >                              args_info.nanglebins_arg);
190 >  } else if (args_info.gxyz_given) {
191 >    if (args_info.refsele_given) {
192 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
193 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
194 >    } else {
195 >      sprintf( painCave.errMsg,
196 >               "--refsele must set when --gxyz is used");
197 >      painCave.severity = OPENMD_ERROR;
198 >      painCave.isFatal = 1;
199 >      simError();  
200      }
201 <
202 <    analyser->process();
203 <
204 <    delete analyser;    
205 <    delete info;
206 <
207 <    return 0;  
201 >  } else if (args_info.twodgofr_given){
202 >    if (args_info.dz_given) {
203 >      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
204 >                             args_info.dz_arg, args_info.nbins_arg);        
205 >    } else {
206 >      sprintf( painCave.errMsg,
207 >               "A slab width (dz) must be specified when calculating TwoDGofR");
208 >      painCave.severity = OPENMD_ERROR;
209 >      painCave.isFatal = 1;
210 >      simError();
211 >    }    
212 >  } else if (args_info.p2_given) {
213 >    if (args_info.sele1_given) {    
214 >      if (args_info.sele2_given)
215 >        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
216 >      else
217 >        if (args_info.seleoffset_given)
218 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
219 >                                           args_info.seleoffset_arg);
220 >        else
221 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
222 >    } else {
223 >      sprintf( painCave.errMsg,
224 >               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
225 >      painCave.severity = OPENMD_ERROR;
226 >      painCave.isFatal = 1;
227 >      simError();
228 >    }
229 >  } else if (args_info.rp2_given){
230 >    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
231 >  } else if (args_info.bo_given){
232 >    if (args_info.rcut_given) {
233 >      analyser = new BondOrderParameter(info, dumpFileName, sele1,
234 >                                        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 Order Parameters");
239 >      painCave.severity = OPENMD_ERROR;
240 >      painCave.isFatal = 1;
241 >      simError();
242 >    }
243 >    
244 >  } else if (args_info.tet_param_given) {
245 >    if (args_info.rcut_given) {  
246 >      analyser = new TetrahedralityParam(info, dumpFileName, sele1,
247 >                                         args_info.rcut_arg,
248 >                                         args_info.nbins_arg);
249 >    } else {
250 >      sprintf( painCave.errMsg,
251 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
252 >      painCave.severity = OPENMD_ERROR;
253 >      painCave.isFatal = 1;
254 >      simError();
255 >    }
256 >  } else if (args_info.tet_param_z_given) {
257 >    if (args_info.rcut_given) {  
258 >      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
259 >                                          args_info.rcut_arg,
260 >                                          args_info.nbins_arg);
261 >    } else {
262 >      sprintf( painCave.errMsg,
263 >               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
264 >      painCave.severity = OPENMD_ERROR;
265 >      painCave.isFatal = 1;
266 >      simError();
267 >    }
268 >  } else if (args_info.bor_given){
269 >    if (args_info.rcut_given) {
270 >      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
271 >                            args_info.nbins_arg, maxLen);
272 >    } else {
273 >      sprintf( painCave.errMsg,
274 >               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
275 >      painCave.severity = OPENMD_ERROR;
276 >      painCave.isFatal = 1;
277 >      simError();
278 >    }
279 >  } else if (args_info.bad_given){
280 >    if (args_info.rcut_given) {
281 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
282 >                                           args_info.rcut_arg,
283 >                                           args_info.nbins_arg);
284 >    } else {
285 >      sprintf( painCave.errMsg,
286 >               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
287 >      painCave.severity = OPENMD_ERROR;
288 >      painCave.isFatal = 1;
289 >      simError();
290 >    }
291 >  } else if (args_info.scd_given) {
292 >    if (batchMode) {
293 >      analyser  = new SCDOrderParameter(info, dumpFileName,
294 >                                        args_info.molname_arg,
295 >                                        args_info.begin_arg, args_info.end_arg);
296 >    } else{
297 >      std::string sele3 = args_info.sele3_arg;
298 >      analyser  = new SCDOrderParameter(info, dumpFileName,
299 >                                        sele1, sele2, sele3);
300 >    }
301 >  }else if (args_info.density_given) {
302 >    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
303 >                              args_info.nbins_arg);  
304 >  } else if (args_info.count_given) {
305 >    analyser = new ObjectCount(info, dumpFileName, sele1 );
306 >  } else if (args_info.slab_density_given) {
307 >    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
308 >  } else if (args_info.p_angle_given) {
309 >    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
310 > #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
311 >  }else if (args_info.hxy_given) {
312 >    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
313 >                       args_info.nbins_y_arg, args_info.nbins_arg);
314 > #endif
315 >  }else if (args_info.rho_r_given) {
316 >    if (args_info.radius_given){
317 >      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
318 >    }else{
319 >      sprintf( painCave.errMsg,
320 >               "A particle radius (radius) must be specified when calculating Rho(r)");
321 >      painCave.severity = OPENMD_ERROR;
322 >      painCave.isFatal = 1;
323 >      simError();
324 >    }
325 >  } else if (args_info.hullvol_given) {
326 >    analyser = new NanoVolume(info, dumpFileName, sele1);
327 >  } else if (args_info.rodlength_given) {
328 >    analyser = new NanoLength(info, dumpFileName, sele1);
329 >  } else if (args_info.angle_r_given) {
330 >    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
331 >  }
332 >  
333 >  if (args_info.output_given) {
334 >    analyser->setOutputName(args_info.output_arg);
335 >  }
336 >  if (args_info.step_given) {
337 >    analyser->setStep(args_info.step_arg);
338 >  }
339 >  
340 >  analyser->process();
341 >  
342 >  delete analyser;    
343 >  delete info;
344 >  
345 >  return 0;  
346   }
317 –

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