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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 1283 by gezelter, Wed Jul 30 18:48:01 2008 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
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).                        
40   */
41  
42   #include <iostream>
# Line 50 | Line 50
50   #include "io/DumpReader.hpp"
51   #include "utils/simError.h"
52   #include "visitors/AtomVisitor.hpp"
53 + #include "visitors/ReplacementVisitor.hpp"
54   #include "visitors/CompositeVisitor.hpp"
55   #include "visitors/RigidBodyVisitor.hpp"
56   #include "visitors/OtherVisitor.hpp"
# Line 59 | Line 60
60   #include "visitors/LipidTransVisitor.hpp"
61   #include "visitors/AtomNameVisitor.hpp"
62  
63 < using namespace oopse;
63 > using namespace OpenMD;
64  
65   int main(int argc, char* argv[]){
66    
# Line 94 | Line 95 | int main(int argc, char* argv[]){
95    SimCreator creator;
96    SimInfo* info = creator.createSim(dumpFileName, false);
97    
97 –
98    //create visitor list
99    CompositeVisitor* compositeVisitor = new CompositeVisitor();
100 <    
100 >  
101    //create RigidBody Visitor
102    if(args_info.rigidbody_flag){
103      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
# Line 108 | Line 108 | int main(int argc, char* argv[]){
108    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109    compositeVisitor->addVisitor(ssdVisitor, 800);
110    
111 –  LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
112 –  compositeVisitor->addVisitor(linearVisitor, 750);
113 –  if (args_info.gb_given) {
114 –    linearVisitor->addGayBerneAtomType(args_info.gb_arg);
115 –  }
116 –  
117 –  GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
118 –  compositeVisitor->addVisitor(gbLipidVisitor, 740);
119 –
120 –  Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info);
121 –  compositeVisitor->addVisitor(ring5Visitor, 730);
122 –
123 –  HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info);
124 –  compositeVisitor->addVisitor(headVisitor, 720);
125 –
111    //create default atom visitor
112    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
113    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
114    
115 <  //create waterType visitor
116 <  if(args_info.watertype_flag){
117 <    WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
118 <    compositeVisitor->addVisitor(waterTypeVisitor, 600);
119 <  }
120 <
115 >  // if we gave the -w option, we want to skip the waters:
116 >  if (!args_info.water_given) {
117 >    //create waterType visitor
118 >    if(args_info.watertype_flag){
119 >      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
120 >      compositeVisitor->addVisitor(waterTypeVisitor, 600);
121 >    }
122 >  }
123 >  
124    if (args_info.basetype_flag) {
125 <      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
126 <      compositeVisitor->addVisitor(atomNameVisitor, 550);
127 <
125 >    AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
126 >    compositeVisitor->addVisitor(atomNameVisitor, 550);    
127 >    std::cout << compositeVisitor->toString();
128    }
129    
130    //create ZconsVisitor
# Line 188 | Line 176 | int main(int argc, char* argv[]){
176      xyzVisitor->setPosOnly(posOnly);
177    }
178  
179 <  compositeVisitor->addVisitor(xyzVisitor, 200);
179 >  compositeVisitor->addVisitor(xyzVisitor, 200);
180    
193 –  std::cout << compositeVisitor->toString();
194 –  
181    //create prepareVisitor
182    PrepareVisitor* prepareVisitor = new PrepareVisitor();
183    

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 1283 by gezelter, Wed Jul 30 18:48:01 2008 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

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