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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 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC vs.
Revision 1937 by gezelter, Tue Oct 29 16:02:58 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).          
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   */
# Line 77 | Line 77
77   #include "applications/staticProps/AngleR.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[]){
# Line 109 | 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        //If sele2 is not specified, then the default behavior
124        //should be what is already intended for sele1
125        sele2 = sele1;
124 –      //sele2 = "select all";
126      }
127    }
128 <  
128 <  
129 <  // Problems if sele1 wasn't specified, but
130 <  // if (!args_info.scd_given) {
131 <  //       sprintf( painCave.errMsg,
132 <  //                "neither --sele1 option nor $SELECTION1 is set");
133 <  //       painCave.severity = OPENMD_ERROR;
134 <  //       painCave.isFatal = 1;
135 <  //       simError();
136 <  //     }
137 <  //   }
138 <  
139 <  // Problems if sele1 wasn't specified
140 <  
141 <  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
142 <  //       sprintf( painCave.errMsg,
143 <  //                "neither --sele2 option nor $SELECTION1 is set");
144 <  //       painCave.severity = OPENMD_ERROR;
145 <  //       painCave.isFatal = 1;
146 <  //       simError();        
147 <  //     }
148 <  //   }
149 <  
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 167 | 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();        
171 <      
152 >      simError();
153      }
154    }
155    
156    //parse md file and set up the system
157    SimCreator creator;
177 –  std::cout << "dumpFile = " << dumpFileName << "\n";
158    SimInfo* info = creator.createSim(dumpFileName);
159  
160    RealType maxLen;
# Line 211 | 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 277 | Line 257 | int main(int argc, char* argv[]){
257      }
258    } else if (args_info.tet_param_z_given) {
259      if (args_info.rcut_given) {  
260 <      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
261 <                                         args_info.rcut_arg,
262 <                                         args_info.nbins_arg);
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");
# Line 300 | 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 308 | 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 324 | 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.p_angle_given) {
315      analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
316   #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
# Line 348 | Line 335 | int main(int argc, char* argv[]){
335    } else if (args_info.angle_r_given) {
336      analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
337    }
338 <    
338 >  
339    if (args_info.output_given) {
340      analyser->setOutputName(args_info.output_arg);
341    }
342    if (args_info.step_given) {
343      analyser->setStep(args_info.step_arg);
344    }
345 <
345 >  
346    analyser->process();
347    
348    delete analyser;    
349    delete info;
350 <
350 >  
351    return 0;  
352   }
366 –

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