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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# 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 57 | Line 57
57   #include "selection/SelectionEvaluator.hpp"
58   #include "selection/SelectionManager.hpp"
59   #include "visitors/LipidTransVisitor.hpp"
60 + #include "visitors/AtomNameVisitor.hpp"
61  
62 < using namespace oopse;
62 > using namespace OpenMD;
63  
64   int main(int argc, char* argv[]){
65    
# Line 67 | Line 68 | int main(int argc, char* argv[]){
68    
69    gengetopt_args_info args_info;
70    std::string dumpFileName;
70 –  std::string mdFileName;
71    std::string xyzFileName;
72    
73    //parse the command line option
# Line 83 | Line 83 | int main(int argc, char* argv[]){
83      exit(1);
84    }
85    
86 –  mdFileName = dumpFileName;
87 –  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88 –
86    if (args_info.output_given){
87      xyzFileName = args_info.output_arg;
88    } else {
# Line 95 | Line 92 | int main(int argc, char* argv[]){
92    
93    //parse md file and set up the system
94    SimCreator creator;
95 <  SimInfo* info = creator.createSim(mdFileName, false);
95 >  SimInfo* info = creator.createSim(dumpFileName, false);
96    
97 <  
98 <  
102 <  //creat visitor list
97 >
98 >  //create visitor list
99    CompositeVisitor* compositeVisitor = new CompositeVisitor();
100      
101 <  //creat RigidBody Visitor
101 >  //create RigidBody Visitor
102    if(args_info.rigidbody_flag){
103      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
104      compositeVisitor->addVisitor(rbCOMVisitor, 900);
105    }
106    
107 <  //creat SSD atom visitor
107 >  //create SSD atom visitor
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 <  //creat default atom visitor
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 >
126 >  //create default atom visitor
127    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
128    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
129    
130 <  //creat waterType visitor
131 <  if(args_info.watertype_flag){
132 <    WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
133 <    compositeVisitor->addVisitor(waterTypeVisitor, 600);
130 >  // if we gave the -w option, we want to skip the waters:
131 >  std::cerr << "-w flag was set to:" << args_info.water_given << "\n";
132 >  if (!args_info.water_given) {
133 >    //create waterType visitor
134 >    if(args_info.watertype_flag){
135 >      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
136 >      compositeVisitor->addVisitor(waterTypeVisitor, 600);
137 >    }
138 >  }
139 >
140 >  if (args_info.basetype_flag) {
141 >      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
142 >      compositeVisitor->addVisitor(atomNameVisitor, 550);
143 >
144    }
145    
146    //create ZconsVisitor
# Line 137 | Line 155 | int main(int argc, char* argv[]){
155      }
156    }
157    
158 <  //creat wrapping visitor
158 >  //create wrapping visitor
159    
160 <  if(args_info.periodicBox_flag){
161 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
162 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
163 <  }
160 >  //if(args_info.periodicBox_flag){
161 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
162 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
163 >  //}
164  
165 <  //creat replicate visitor
165 >  //create replicate visitor
166    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
167      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
168      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
# Line 160 | Line 178 | int main(int argc, char* argv[]){
178      exit(1);
179    }
180      
181 <  //creat xyzVisitor
181 >  //create xyzVisitor
182    XYZVisitor* xyzVisitor;
183 +
184    if (args_info.selection_given) {
185      xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
186    } else {
187      xyzVisitor = new XYZVisitor(info);
188    }
189 +
190 +  if(args_info.printPosOnly_flag){
191 +    bool posOnly = true;
192 +    xyzVisitor->setPosOnly(posOnly);
193 +  }
194 +
195    compositeVisitor->addVisitor(xyzVisitor, 200);
196    
197    std::cout << compositeVisitor->toString();
198    
199 <  //creat prepareVisitor
199 >  //create prepareVisitor
200    PrepareVisitor* prepareVisitor = new PrepareVisitor();
201    
202    //open dump file
# Line 179 | Line 204 | int main(int argc, char* argv[]){
204    int nframes = dumpReader->getNFrames();
205    
206    
207 <  std::ofstream xyzStream;    
183 <  xyzStream .open(xyzFileName.c_str());
207 >  std::ofstream xyzStream(xyzFileName.c_str());
208    
185 –  
209    SimInfo::MoleculeIterator miter;
210    Molecule::IntegrableObjectIterator  iiter;
211    Molecule::RigidBodyIterator rbIter;
212    Molecule* mol;
213    StuntDouble* integrableObject;
214    RigidBody* rb;
215 +  Vector3d molCom;
216 +  Vector3d newMolCom;
217 +  Vector3d displacement;
218 +  Mat3x3d hmat;
219 +  Snapshot* currentSnapshot;
220        
221    for (int i = 0; i < nframes; i += args_info.frame_arg){
222      dumpReader->readFrame(i);
223 <    
223 >
224 >    //wrapping the molecule
225 >    if(args_info.periodicBox_flag) {
226 >      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
227 >      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
228 >          molCom = mol->getCom();
229 >          newMolCom = molCom;
230 >          currentSnapshot->wrapVector(newMolCom);
231 >          displacement = newMolCom - molCom;
232 >        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
233 >             integrableObject = mol->nextIntegrableObject(iiter)) {  
234 >          integrableObject->setPos(integrableObject->getPos() + displacement);
235 >        }
236 >      }    
237 >    }
238      //update atoms of rigidbody
239      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
240        
# Line 226 | Line 268 | int main(int argc, char* argv[]){
268      xyzVisitor->clear();
269      
270    }//end for (int i = 0; i < nframes; i += args_info.frame_arg)
271 <  
271 >
272    xyzStream.close();
273 <  
232 <  
273 >  delete prepareVisitor;
274    delete compositeVisitor;
275    delete info;
235 –  
276   }

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