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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 1542 by gezelter, Thu Mar 3 20:32:49 2011 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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 + #include "applications/staticProps/TetrahedralityParamZ.hpp"
80 + #include "applications/staticProps/RNEMDStats.hpp"
81  
82   using namespace OpenMD;
83  
84   int main(int argc, char* argv[]){
85    
84 –  //register force fields
85 –  registerForceFields();
86    
87    gengetopt_args_info args_info;
88    
# Line 95 | Line 95 | int main(int argc, char* argv[]){
95    std::string dumpFileName = args_info.input_arg;
96    std::string sele1;
97    std::string sele2;
98 –  bool userSpecifiedSelect1;
99 –  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"
# Line 113 | Line 111 | int main(int argc, char* argv[]){
111    }
112    
113    // check the second selection argument, or set it to the environment
114 <  // variable, or failing that, set it to "select all"
114 >  // variable, or failing that, set it to the first selection
115    
116    if (args_info.sele2_given) {
117      sele2 = args_info.sele2_arg;
118    } else {
119 <    char* sele2Env = getenv("SELECTION1");
119 >    char* sele2Env = getenv("SELECTION2");
120      if (sele2Env) {
121        sele2 = sele2Env;            
122      } else {
123 <      sele2 = "select all";
123 >      //If sele2 is not specified, then the default behavior
124 >      //should be what is already intended for sele1
125 >      sele2 = sele1;
126      }
127    }
128 <  
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 <  
128 >
129    bool batchMode;
130    if (args_info.scd_given){
131 <    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
131 >    if (args_info.sele1_given &&
132 >        args_info.sele2_given && args_info.sele3_given) {
133        batchMode = false;
134 <    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
135 <      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
134 >    } else if (args_info.molname_given &&
135 >               args_info.begin_given && args_info.end_given) {
136 >      if (args_info.begin_arg < 0 ||
137 >          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
138          sprintf( painCave.errMsg,
139                   "below conditions are not satisfied:\n"
140                   "0 <= begin && 0<= end && begin <= end-2\n");
# Line 168 | Line 149 | int main(int argc, char* argv[]){
149                 " or --molname, --begin, --end are specified\n");
150        painCave.severity = OPENMD_ERROR;
151        painCave.isFatal = 1;
152 <      simError();        
172 <      
152 >      simError();
153      }
154    }
155    
156    //parse md file and set up the system
157    SimCreator creator;
178 –  std::cout << "dumpFile = " << dumpFileName << "\n";
158    SimInfo* info = creator.createSim(dumpFileName);
159  
160    RealType maxLen;
# Line 212 | Line 191 | int main(int argc, char* argv[]){
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,
195 <                           maxLen, args_info.nbins_arg);        
194 >      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
195 >                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
196      } else {
197        sprintf( painCave.errMsg,
198                 "--refsele must set when --gxyz is used");
# Line 237 | Line 216 | int main(int argc, char* argv[]){
216        if (args_info.sele2_given)
217          analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
218        else
219 <        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
219 >        if (args_info.seleoffset_given)
220 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1,
221 >                                           args_info.seleoffset_arg);
222 >        else
223 >          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
224      } else {
225        sprintf( painCave.errMsg,
226                 "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
# Line 272 | Line 255 | int main(int argc, char* argv[]){
255        painCave.isFatal = 1;
256        simError();
257      }
258 +  } else if (args_info.tet_param_z_given) {
259 +    if (args_info.rcut_given) {  
260 +      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
261 +                                          args_info.rcut_arg,
262 +                                          args_info.nbins_arg);
263 +    } else {
264 +      sprintf( painCave.errMsg,
265 +               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
266 +      painCave.severity = OPENMD_ERROR;
267 +      painCave.isFatal = 1;
268 +      simError();
269 +    }
270    } else if (args_info.bor_given){
271      if (args_info.rcut_given) {
272        analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
# Line 285 | Line 280 | int main(int argc, char* argv[]){
280      }
281    } else if (args_info.bad_given){
282      if (args_info.rcut_given) {
283 <      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
283 >      analyser = new BondAngleDistribution(info, dumpFileName, sele1,
284 >                                           args_info.rcut_arg,
285                                             args_info.nbins_arg);
286      } else {
287        sprintf( painCave.errMsg,
# Line 293 | Line 289 | int main(int argc, char* argv[]){
289        painCave.severity = OPENMD_ERROR;
290        painCave.isFatal = 1;
291        simError();
292 <      }
292 >    }
293    } else if (args_info.scd_given) {
294      if (batchMode) {
295 <      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
295 >      analyser  = new SCDOrderParameter(info, dumpFileName,
296 >                                        args_info.molname_arg,
297                                          args_info.begin_arg, args_info.end_arg);
298      } else{
299        std::string sele3 = args_info.sele3_arg;
300 <      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
300 >      analyser  = new SCDOrderParameter(info, dumpFileName,
301 >                                        sele1, sele2, sele3);
302      }
303    }else if (args_info.density_given) {
304      analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
# Line 309 | Line 307 | int main(int argc, char* argv[]){
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.rnemdz_given) {
311 +    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
312 +  } else if (args_info.rnemdr_given) {
313 +    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
314 +  } else if (args_info.rnemdrt_given) {
315 +    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
316 +                               args_info.nbins_arg, args_info.nanglebins_arg);
317    } else if (args_info.p_angle_given) {
318      analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
319   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
# Line 328 | Line 333 | int main(int argc, char* argv[]){
333      }
334    } else if (args_info.hullvol_given) {
335      analyser = new NanoVolume(info, dumpFileName, sele1);
336 +  } else if (args_info.rodlength_given) {
337 +    analyser = new NanoLength(info, dumpFileName, sele1);
338    } else if (args_info.angle_r_given) {
339      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
340    }
341 <    
341 >  
342    if (args_info.output_given) {
343      analyser->setOutputName(args_info.output_arg);
344    }
# Line 343 | Line 350 | int main(int argc, char* argv[]){
350    
351    delete analyser;    
352    delete info;
353 <
353 >  
354    return 0;  
355   }
349 –

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