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root/OpenMD/branches/development/src/applications/dump2Xyz/Dump2XYZ.cpp
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Comparing:
trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents), Revision 1456 by gezelter, Fri Jun 25 17:40:24 2010 UTC vs.
branches/development/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents), Revision 1706 by gezelter, Fri Apr 27 20:44:16 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>
# Line 63 | Line 64 | using namespace OpenMD;
64  
65   using namespace OpenMD;
66  
67 + using namespace std;
68   int main(int argc, char* argv[]){
69    
70    //register force fields
71    registerForceFields();
72    
73    gengetopt_args_info args_info;
74 <  std::string dumpFileName;
75 <  std::string xyzFileName;
76 <  bool printVel;
77 <  bool printFrc;
78 <  bool printVec;
79 <  bool printChrg;
74 >  string dumpFileName;
75 >  string xyzFileName;
76 >
77 >  bool printVel(false);
78 >  bool printFrc(false);
79 >  bool printVec(false);
80 >  bool printChrg(false);
81    
82    //parse the command line option
83    if (cmdline_parser (argc, argv, &args_info) != 0) {
# Line 85 | Line 88 | int main(int argc, char* argv[]){
88    if (args_info.input_given){
89      dumpFileName = args_info.input_arg;
90    } else {
91 <    std::cerr << "Does not have input file name" << std::endl;
91 >    cerr << "Does not have input file name" << endl;
92      exit(1);
93    }
94    
# Line 114 | Line 117 | int main(int argc, char* argv[]){
117    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
118    compositeVisitor->addVisitor(ssdVisitor, 800);
119    
120 +  //create GBtail atom visitor
121 +  GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
122 +  compositeVisitor->addVisitor(gbtVisitor, 790);
123 +  
124 +  //create GBhead atom visitor
125 +  GBheadVisitor* gbhVisitor = new GBheadVisitor(info);
126 +  compositeVisitor->addVisitor(gbhVisitor, 789);
127 +  
128    //create default atom visitor
129    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
130    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
# Line 130 | Line 141 | int main(int argc, char* argv[]){
141    if (args_info.basetype_flag) {
142      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
143      compositeVisitor->addVisitor(atomNameVisitor, 550);    
144 <    std::cout << compositeVisitor->toString();
144 >    cout << compositeVisitor->toString();
145    }
146    
147    //create ZconsVisitor
# Line 172 | Line 183 | int main(int argc, char* argv[]){
183                                                         args_info.refsele_arg),
184                                   250);
185    } else if (args_info.refsele_given || args_info.originsele_given) {
186 <    std::cerr << "Both of --refsele and --originsele should appear by pair"
187 <              << std::endl;
186 >    cerr << "Both of --refsele and --originsele should appear by pair"
187 >              << endl;
188      exit(1);
189    }
190    
# Line 212 | Line 223 | int main(int argc, char* argv[]){
223    DumpReader* dumpReader = new DumpReader(info, dumpFileName);
224    int nframes = dumpReader->getNFrames();
225    
226 <  std::ofstream xyzStream(xyzFileName.c_str());
226 >  ofstream xyzStream(xyzFileName.c_str());
227    
228    SimInfo::MoleculeIterator miter;
229    Molecule::IntegrableObjectIterator  iiter;
# Line 229 | Line 240 | int main(int argc, char* argv[]){
240    for (int i = 0; i < nframes; i += args_info.frame_arg){
241      dumpReader->readFrame(i);
242      
243 <    if (printFrc) forceMan->calcForces(true, false);
243 >    if (printFrc) forceMan->calcForces();
244      
245      //wrapping the molecule
246      if(args_info.periodicBox_flag) {

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