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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 1464 by gezelter, Fri Jul 9 19:29:05 2010 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 47 | Line 47
47   #include "brains/Register.hpp"
48   #include "brains/SimCreator.hpp"
49   #include "brains/SimInfo.hpp"
50 + #include "brains/ForceManager.hpp"
51   #include "io/DumpReader.hpp"
52   #include "utils/simError.h"
53   #include "visitors/AtomVisitor.hpp"
54 + #include "visitors/ReplacementVisitor.hpp"
55   #include "visitors/CompositeVisitor.hpp"
56   #include "visitors/RigidBodyVisitor.hpp"
57   #include "visitors/OtherVisitor.hpp"
# Line 57 | Line 59
59   #include "selection/SelectionEvaluator.hpp"
60   #include "selection/SelectionManager.hpp"
61   #include "visitors/LipidTransVisitor.hpp"
62 + #include "visitors/AtomNameVisitor.hpp"
63  
64 < using namespace oopse;
64 > using namespace OpenMD;
65  
66   int main(int argc, char* argv[]){
67    
# Line 67 | Line 70 | int main(int argc, char* argv[]){
70    
71    gengetopt_args_info args_info;
72    std::string dumpFileName;
70  std::string mdFileName;
73    std::string xyzFileName;
74 +  bool printVel;
75 +  bool printFrc;
76 +  bool printVec;
77 +  bool printChrg;
78    
79    //parse the command line option
80    if (cmdline_parser (argc, argv, &args_info) != 0) {
# Line 83 | Line 89 | int main(int argc, char* argv[]){
89      exit(1);
90    }
91    
86  mdFileName = dumpFileName;
87  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88
92    if (args_info.output_given){
93      xyzFileName = args_info.output_arg;
94    } else {
# Line 95 | Line 98 | int main(int argc, char* argv[]){
98    
99    //parse md file and set up the system
100    SimCreator creator;
101 <  SimInfo* info = creator.createSim(mdFileName, false);
101 >  SimInfo* info = creator.createSim(dumpFileName, false);
102 >  ForceManager* forceMan = new ForceManager(info);
103    
104 <  
101 <  
102 <  //creat visitor list
104 >  //create visitor list
105    CompositeVisitor* compositeVisitor = new CompositeVisitor();
106 <    
107 <  //creat RigidBody Visitor
106 >  
107 >  //create RigidBody Visitor
108    if(args_info.rigidbody_flag){
109      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
110      compositeVisitor->addVisitor(rbCOMVisitor, 900);
111    }
112    
113 <  //creat SSD atom visitor
113 >  //create SSD atom visitor
114    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
115    compositeVisitor->addVisitor(ssdVisitor, 800);
116    
117 <  LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
116 <  compositeVisitor->addVisitor(linearVisitor, 750);
117 <  
118 <  //creat default atom visitor
117 >  //create default atom visitor
118    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
119    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
120    
121 <  //creat waterType visitor
122 <  if(args_info.watertype_flag){
123 <    WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
124 <    compositeVisitor->addVisitor(waterTypeVisitor, 600);
121 >  // if we gave the -w option, we want to skip the waters:
122 >  if (!args_info.water_given) {
123 >    //create waterType visitor
124 >    if(args_info.watertype_flag){
125 >      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
126 >      compositeVisitor->addVisitor(waterTypeVisitor, 600);
127 >    }
128 >  }
129 >  
130 >  if (args_info.basetype_flag) {
131 >    AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
132 >    compositeVisitor->addVisitor(atomNameVisitor, 550);    
133 >    std::cout << compositeVisitor->toString();
134    }
135    
136    //create ZconsVisitor
# Line 137 | Line 145 | int main(int argc, char* argv[]){
145      }
146    }
147    
148 <  //creat wrapping visitor
148 >  //create wrapping visitor
149    
150 <  if(args_info.periodicBox_flag){
151 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
153 <  }
150 >  //if(args_info.periodicBox_flag){
151 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
153 >  //}
154  
155 <  //creat replicate visitor
156 <  if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
157 <    Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
158 <    ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
155 >  //create replicate visitor
156 >  if(args_info.repeatX_given > 0 ||
157 >     args_info.repeatY_given > 0 ||
158 >     args_info.repeatY_given > 0) {
159 >    Vector3i replicateOpt(args_info.repeatX_arg,
160 >                          args_info.repeatY_arg,
161 >                          args_info.repeatZ_arg);
162 >    ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info,
163 >                                                              replicateOpt);
164      compositeVisitor->addVisitor(replicateVisitor, 300);
165    }
166  
167  
168    //create rotation visitor
169    if (args_info.refsele_given&& args_info.originsele_given) {
170 <    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
170 >    compositeVisitor->addVisitor(new LipidTransVisitor(info,
171 >                                                       args_info.originsele_arg,
172 >                                                       args_info.refsele_arg),
173 >                                 250);
174    } else if (args_info.refsele_given || args_info.originsele_given) {
175 <    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
175 >    std::cerr << "Both of --refsele and --originsele should appear by pair"
176 >              << std::endl;
177      exit(1);
178    }
179 <    
180 <  //creat xyzVisitor
179 >  
180 >  //create xyzVisitor
181    XYZVisitor* xyzVisitor;
182 +
183    if (args_info.selection_given) {
184      xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
185    } else {
186      xyzVisitor = new XYZVisitor(info);
187    }
188 <  compositeVisitor->addVisitor(xyzVisitor, 200);
188 >
189 >  if(args_info.velocities_flag){
190 >    printVel = true;
191 >    xyzVisitor->doVelocities(printVel);
192 >  }
193 >  if(args_info.forces_flag){
194 >    printFrc = true;
195 >    xyzVisitor->doForces(printFrc);
196 >  }
197 >  if(args_info.vectors_flag){
198 >    printVec = true;
199 >    xyzVisitor->doVectors(printVec);
200 >  }
201 >  if(args_info.charges_flag){
202 >    printChrg = true;
203 >    xyzVisitor->doCharges(printChrg);
204 >  }
205    
206 <  std::cout << compositeVisitor->toString();
206 >  compositeVisitor->addVisitor(xyzVisitor, 200);
207    
208 <  //creat prepareVisitor
208 >  //create prepareVisitor
209    PrepareVisitor* prepareVisitor = new PrepareVisitor();
210    
211    //open dump file
212    DumpReader* dumpReader = new DumpReader(info, dumpFileName);
213    int nframes = dumpReader->getNFrames();
214    
215 +  std::ofstream xyzStream(xyzFileName.c_str());
216    
182  std::ofstream xyzStream;    
183  xyzStream .open(xyzFileName.c_str());
184  
185  
217    SimInfo::MoleculeIterator miter;
218    Molecule::IntegrableObjectIterator  iiter;
219    Molecule::RigidBodyIterator rbIter;
220    Molecule* mol;
221    StuntDouble* integrableObject;
222    RigidBody* rb;
223 +  Vector3d molCom;
224 +  Vector3d newMolCom;
225 +  Vector3d displacement;
226 +  Mat3x3d hmat;
227 +  Snapshot* currentSnapshot;
228        
229    for (int i = 0; i < nframes; i += args_info.frame_arg){
230      dumpReader->readFrame(i);
231      
232 +    if (printFrc) forceMan->calcForces();
233 +    
234 +    //wrapping the molecule
235 +    if(args_info.periodicBox_flag) {
236 +      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
237 +      for (mol = info->beginMolecule(miter); mol != NULL;
238 +           mol = info->nextMolecule(miter)) {
239 +          molCom = mol->getCom();
240 +          newMolCom = molCom;
241 +          currentSnapshot->wrapVector(newMolCom);
242 +          displacement = newMolCom - molCom;
243 +        for (integrableObject = mol->beginIntegrableObject(iiter);
244 +             integrableObject != NULL;
245 +             integrableObject = mol->nextIntegrableObject(iiter)) {  
246 +          integrableObject->setPos(integrableObject->getPos() + displacement);
247 +        }
248 +      }    
249 +    }
250      //update atoms of rigidbody
251 <    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
251 >    for (mol = info->beginMolecule(miter); mol != NULL;
252 >         mol = info->nextMolecule(miter)) {
253        
254        //change the positions of atoms which belong to the rigidbodies
255 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
255 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
256 >           rb = mol->nextRigidBody(rbIter)) {
257          rb->updateAtoms();
258 +        if (printVel) rb->updateAtomVel();
259        }
260      }
261      
262      //prepare visit
263 <    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
264 <      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
263 >    for (mol = info->beginMolecule(miter); mol != NULL;
264 >         mol = info->nextMolecule(miter)) {
265 >      for (integrableObject = mol->beginIntegrableObject(iiter);
266 >           integrableObject != NULL;
267             integrableObject = mol->nextIntegrableObject(iiter)) {
268          integrableObject->accept(prepareVisitor);
269        }
# Line 215 | Line 274 | int main(int argc, char* argv[]){
274  
275  
276      //visit stuntdouble
277 <    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
278 <      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
277 >    for (mol = info->beginMolecule(miter); mol != NULL;
278 >         mol = info->nextMolecule(miter)) {
279 >      for (integrableObject = mol->beginIntegrableObject(iiter);
280 >           integrableObject != NULL;
281             integrableObject = mol->nextIntegrableObject(iiter)) {
282          integrableObject->accept(compositeVisitor);
283        }
# Line 226 | Line 287 | int main(int argc, char* argv[]){
287      xyzVisitor->clear();
288      
289    }//end for (int i = 0; i < nframes; i += args_info.frame_arg)
290 <  
290 >
291    xyzStream.close();
292 <  
232 <  
292 >  delete prepareVisitor;
293    delete compositeVisitor;
294    delete info;
235  
295   }

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1464 by gezelter, Fri Jul 9 19:29:05 2010 UTC

# Line 0 | Line 1
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