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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 1522 by kstocke1, Fri Nov 19 20:26:36 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 69 | Line 69
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"
77 – #include "applications/staticProps/RhoAngleR.hpp"
78   #include "applications/staticProps/TetrahedralityParam.hpp"
79 <
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();
84    
85    gengetopt_args_info args_info;
86    
# Line 95 | Line 93 | int main(int argc, char* argv[]){
93    std::string dumpFileName = args_info.input_arg;
94    std::string sele1;
95    std::string sele2;
98 –  bool userSpecifiedSelect1;
99 –  bool userSpecifiedSelect2;
96    
97    // check the first selection argument, or set it to the environment
98    // variable, or failing that, set it to "select all"
# Line 122 | Line 118 | int main(int argc, char* argv[]){
118      if (sele2Env) {
119        sele2 = sele2Env;            
120      } else {
121 <      sele2 = "select all";
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 <  
129 <  
130 <  // Problems if sele1 wasn't specified, but
131 <  // if (!args_info.scd_given) {
132 <  //       sprintf( painCave.errMsg,
133 <  //                "neither --sele1 option nor $SELECTION1 is set");
134 <  //       painCave.severity = OPENMD_ERROR;
135 <  //       painCave.isFatal = 1;
136 <  //       simError();
137 <  //     }
138 <  //   }
139 <  
140 <  // Problems if sele1 wasn't specified
141 <  
142 <  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
143 <  //       sprintf( painCave.errMsg,
144 <  //                "neither --sele2 option nor $SELECTION1 is set");
145 <  //       painCave.severity = OPENMD_ERROR;
146 <  //       painCave.isFatal = 1;
147 <  //       simError();        
148 <  //     }
149 <  //   }
150 <  
126 >
127    bool batchMode;
128    if (args_info.scd_given){
129 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_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 && args_info.begin_given && args_info.end_given) {
133 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
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                   "below conditions are not satisfied:\n"
138                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 168 | Line 147 | int main(int argc, char* argv[]){
147                 " or --molname, --begin, --end are specified\n");
148        painCave.severity = OPENMD_ERROR;
149        painCave.isFatal = 1;
150 <      simError();        
172 <      
150 >      simError();
151      }
152    }
153    
154    //parse md file and set up the system
155    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
156    SimInfo* info = creator.createSim(dumpFileName);
157  
158    RealType maxLen;
# Line 212 | Line 189 | int main(int argc, char* argv[]){
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,args_info.refsele_arg,
193 <                           maxLen, args_info.nbins_arg);        
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");
# Line 233 | Line 210 | int main(int argc, char* argv[]){
210        simError();
211      }    
212    } else if (args_info.p2_given) {
213 <    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
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){
# Line 261 | Line 253 | int main(int argc, char* argv[]){
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,
# Line 274 | Line 278 | int main(int argc, char* argv[]){
278      }
279    } else if (args_info.bad_given){
280      if (args_info.rcut_given) {
281 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
281 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
282 >                                           args_info.rcut_arg,
283                                             args_info.nbins_arg);
284      } else {
285        sprintf( painCave.errMsg,
# Line 282 | Line 287 | int main(int argc, char* argv[]){
287        painCave.severity = OPENMD_ERROR;
288        painCave.isFatal = 1;
289        simError();
290 <      }
290 >    }
291    } else if (args_info.scd_given) {
292      if (batchMode) {
293 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
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, sele1, sele2, sele3);
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,
# Line 317 | Line 324 | int main(int argc, char* argv[]){
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 <    
332 >  
333    if (args_info.output_given) {
334      analyser->setOutputName(args_info.output_arg);
335    }
# Line 332 | Line 341 | int main(int argc, char* argv[]){
341    
342    delete analyser;    
343    delete info;
344 <
344 >  
345    return 0;  
346   }
338 –

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