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root/OpenMD/branches/development/src/applications/dump2Xyz/Dump2XYZ.cpp
Revision: 1874
Committed: Wed May 15 15:09:35 2013 UTC (12 years ago) by gezelter
File size: 10022 byte(s)
Log Message:
Fixed a bunch of cppcheck warnings.

File Contents

# User Rev Content
1 gezelter 507 /*
2 gezelter 246 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3     *
4     * The University of Notre Dame grants you ("Licensee") a
5     * non-exclusive, royalty free, license to use, modify and
6     * redistribute this software in source and binary code form, provided
7     * that the following conditions are met:
8     *
9 gezelter 1390 * 1. Redistributions of source code must retain the above copyright
10 gezelter 246 * notice, this list of conditions and the following disclaimer.
11     *
12 gezelter 1390 * 2. Redistributions in binary form must reproduce the above copyright
13 gezelter 246 * notice, this list of conditions and the following disclaimer in the
14     * documentation and/or other materials provided with the
15     * distribution.
16     *
17     * This software is provided "AS IS," without a warranty of any
18     * kind. All express or implied conditions, representations and
19     * warranties, including any implied warranty of merchantability,
20     * fitness for a particular purpose or non-infringement, are hereby
21     * excluded. The University of Notre Dame and its licensors shall not
22     * be liable for any damages suffered by licensee as a result of
23     * using, modifying or distributing the software or its
24     * derivatives. In no event will the University of Notre Dame or its
25     * licensors be liable for any lost revenue, profit or data, or for
26     * direct, indirect, special, consequential, incidental or punitive
27     * damages, however caused and regardless of the theory of liability,
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 gezelter 1390 *
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 gezelter 1850 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39 gezelter 1665 * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40     * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41 gezelter 246 */
42    
43 tim 12 #include <iostream>
44     #include <fstream>
45     #include <string>
46    
47     #include "applications/dump2Xyz/Dump2XYZCmd.h"
48 gezelter 246 #include "brains/Register.hpp"
49     #include "brains/SimCreator.hpp"
50     #include "brains/SimInfo.hpp"
51 gezelter 1456 #include "brains/ForceManager.hpp"
52 gezelter 246 #include "io/DumpReader.hpp"
53     #include "utils/simError.h"
54 tim 12 #include "visitors/AtomVisitor.hpp"
55 gezelter 1455 #include "visitors/ReplacementVisitor.hpp"
56 tim 12 #include "visitors/CompositeVisitor.hpp"
57     #include "visitors/RigidBodyVisitor.hpp"
58     #include "visitors/OtherVisitor.hpp"
59     #include "visitors/ZconsVisitor.hpp"
60 tim 291 #include "selection/SelectionEvaluator.hpp"
61 tim 324 #include "selection/SelectionManager.hpp"
62 tim 369 #include "visitors/LipidTransVisitor.hpp"
63 tim 543 #include "visitors/AtomNameVisitor.hpp"
64 tim 369
65 gezelter 1390 using namespace OpenMD;
66 tim 12
67 gezelter 1706 using namespace std;
68 tim 12 int main(int argc, char* argv[]){
69 gezelter 246
70 tim 12 gengetopt_args_info args_info;
71 gezelter 1706 string dumpFileName;
72     string xyzFileName;
73    
74     bool printVel(false);
75     bool printFrc(false);
76     bool printVec(false);
77     bool printChrg(false);
78 gezelter 1871 bool printField(false);
79 tim 12
80 gezelter 246 //parse the command line option
81     if (cmdline_parser (argc, argv, &args_info) != 0) {
82     exit(1) ;
83     }
84 tim 12
85     //get the dumpfile name and meta-data file name
86     if (args_info.input_given){
87     dumpFileName = args_info.input_arg;
88 gezelter 246 } else {
89 gezelter 1706 cerr << "Does not have input file name" << endl;
90 tim 12 exit(1);
91     }
92 gezelter 246
93 tim 12 if (args_info.output_given){
94     xyzFileName = args_info.output_arg;
95 gezelter 246 } else {
96 tim 12 xyzFileName = dumpFileName;
97     xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
98     }
99 gezelter 246
100 tim 12 //parse md file and set up the system
101 gezelter 246 SimCreator creator;
102 gezelter 1026 SimInfo* info = creator.createSim(dumpFileName, false);
103 gezelter 1456 ForceManager* forceMan = new ForceManager(info);
104 tim 12
105 chrisfen 527 //create visitor list
106 gezelter 246 CompositeVisitor* compositeVisitor = new CompositeVisitor();
107 gezelter 1455
108 chrisfen 527 //create RigidBody Visitor
109 tim 12 if(args_info.rigidbody_flag){
110 gezelter 246 RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
111 tim 12 compositeVisitor->addVisitor(rbCOMVisitor, 900);
112     }
113 gezelter 246
114 chrisfen 527 //create SSD atom visitor
115 gezelter 246 SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
116 tim 12 compositeVisitor->addVisitor(ssdVisitor, 800);
117 gezelter 246
118 gezelter 1629 //create GBtail atom visitor
119     GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
120     compositeVisitor->addVisitor(gbtVisitor, 790);
121    
122     //create GBhead atom visitor
123     GBheadVisitor* gbhVisitor = new GBheadVisitor(info);
124     compositeVisitor->addVisitor(gbhVisitor, 789);
125    
126 chrisfen 527 //create default atom visitor
127 gezelter 246 DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
128 tim 12 compositeVisitor->addVisitor(defaultAtomVisitor, 700);
129 gezelter 246
130 cli2 1303 // if we gave the -w option, we want to skip the waters:
131     if (!args_info.water_given) {
132     //create waterType visitor
133     if(args_info.watertype_flag){
134     WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
135     compositeVisitor->addVisitor(waterTypeVisitor, 600);
136     }
137 gezelter 1455 }
138    
139 tim 543 if (args_info.basetype_flag) {
140 gezelter 1455 AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
141     compositeVisitor->addVisitor(atomNameVisitor, 550);
142 gezelter 1706 cout << compositeVisitor->toString();
143 tim 543 }
144 gezelter 246
145 tim 12 //create ZconsVisitor
146     if(args_info.zconstraint_flag){
147 gezelter 246
148     ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
149 tim 12
150 gezelter 246 if(zconsVisitor->haveZconsMol()) {
151 tim 12 compositeVisitor->addVisitor(zconsVisitor, 500);
152 gezelter 246 } else {
153 tim 12 delete zconsVisitor;
154 gezelter 246 }
155 tim 12 }
156 gezelter 246
157 chrisfen 527 //create wrapping visitor
158 gezelter 246
159 tim 968 //if(args_info.periodicBox_flag){
160     // WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
161     // compositeVisitor->addVisitor(wrappingVisitor, 400);
162     //}
163 tim 369
164 chrisfen 527 //create replicate visitor
165 gezelter 1456 if(args_info.repeatX_given > 0 ||
166     args_info.repeatY_given > 0 ||
167 gezelter 1874 args_info.repeatZ_given > 0) {
168 gezelter 1456 Vector3i replicateOpt(args_info.repeatX_arg,
169     args_info.repeatY_arg,
170     args_info.repeatZ_arg);
171     ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info,
172     replicateOpt);
173 tim 12 compositeVisitor->addVisitor(replicateVisitor, 300);
174     }
175 tim 369
176    
177     //create rotation visitor
178     if (args_info.refsele_given&& args_info.originsele_given) {
179 gezelter 1456 compositeVisitor->addVisitor(new LipidTransVisitor(info,
180     args_info.originsele_arg,
181     args_info.refsele_arg),
182     250);
183 tim 369 } else if (args_info.refsele_given || args_info.originsele_given) {
184 gezelter 1706 cerr << "Both of --refsele and --originsele should appear by pair"
185 gezelter 1769 << endl;
186 tim 369 exit(1);
187     }
188 gezelter 1456
189 chrisfen 527 //create xyzVisitor
190 tim 413 XYZVisitor* xyzVisitor;
191 chuckv 1117
192 tim 413 if (args_info.selection_given) {
193     xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
194     } else {
195     xyzVisitor = new XYZVisitor(info);
196     }
197 chuckv 1117
198 gezelter 1456 if(args_info.velocities_flag){
199     printVel = true;
200     xyzVisitor->doVelocities(printVel);
201 chuckv 1117 }
202 gezelter 1456 if(args_info.forces_flag){
203     printFrc = true;
204     xyzVisitor->doForces(printFrc);
205     }
206     if(args_info.vectors_flag){
207     printVec = true;
208     xyzVisitor->doVectors(printVec);
209     }
210     if(args_info.charges_flag){
211     printChrg = true;
212     xyzVisitor->doCharges(printChrg);
213     }
214 gezelter 1871 if(args_info.efield_flag){
215     printField = true;
216     xyzVisitor->doElectricFields(printField);
217     }
218 gezelter 1456
219 gezelter 1455 compositeVisitor->addVisitor(xyzVisitor, 200);
220 gezelter 246
221 chrisfen 527 //create prepareVisitor
222 gezelter 246 PrepareVisitor* prepareVisitor = new PrepareVisitor();
223    
224 tim 12 //open dump file
225 gezelter 246 DumpReader* dumpReader = new DumpReader(info, dumpFileName);
226     int nframes = dumpReader->getNFrames();
227    
228 gezelter 1706 ofstream xyzStream(xyzFileName.c_str());
229 tim 12
230 gezelter 246 SimInfo::MoleculeIterator miter;
231     Molecule::IntegrableObjectIterator iiter;
232     Molecule::RigidBodyIterator rbIter;
233     Molecule* mol;
234 gezelter 1769 StuntDouble* sd;
235 gezelter 246 RigidBody* rb;
236 tim 968 Vector3d molCom;
237     Vector3d newMolCom;
238     Vector3d displacement;
239     Mat3x3d hmat;
240     Snapshot* currentSnapshot;
241 tim 413
242 tim 12 for (int i = 0; i < nframes; i += args_info.frame_arg){
243 gezelter 246 dumpReader->readFrame(i);
244 gezelter 1456
245 gezelter 1464 if (printFrc) forceMan->calcForces();
246 gezelter 1456
247 tim 968 //wrapping the molecule
248     if(args_info.periodicBox_flag) {
249     currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
250 gezelter 1456 for (mol = info->beginMolecule(miter); mol != NULL;
251     mol = info->nextMolecule(miter)) {
252 gezelter 1769
253     molCom = mol->getCom();
254     newMolCom = molCom;
255     currentSnapshot->wrapVector(newMolCom);
256     displacement = newMolCom - molCom;
257    
258     for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
259     sd = mol->nextIntegrableObject(iiter)) {
260    
261     sd->setPos(sd->getPos() + displacement);
262    
263 tim 968 }
264     }
265     }
266 gezelter 1769
267 tim 12 //update atoms of rigidbody
268 gezelter 1456 for (mol = info->beginMolecule(miter); mol != NULL;
269     mol = info->nextMolecule(miter)) {
270 gezelter 246
271     //change the positions of atoms which belong to the rigidbodies
272 gezelter 1456 for (rb = mol->beginRigidBody(rbIter); rb != NULL;
273     rb = mol->nextRigidBody(rbIter)) {
274 gezelter 1769
275 gezelter 246 rb->updateAtoms();
276 gezelter 1456 if (printVel) rb->updateAtomVel();
277 gezelter 1769
278 gezelter 246 }
279     }
280 tim 12
281     //prepare visit
282 gezelter 1456 for (mol = info->beginMolecule(miter); mol != NULL;
283     mol = info->nextMolecule(miter)) {
284 gezelter 1769
285     for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
286     sd = mol->nextIntegrableObject(iiter)) {
287    
288     sd->accept(prepareVisitor);
289    
290 gezelter 246 }
291     }
292    
293 tim 12 //update visitor
294     compositeVisitor->update();
295 tim 291
296 tim 413
297 tim 12 //visit stuntdouble
298 gezelter 1456 for (mol = info->beginMolecule(miter); mol != NULL;
299     mol = info->nextMolecule(miter)) {
300 gezelter 1769
301     for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
302     sd = mol->nextIntegrableObject(iiter)) {
303    
304     sd->accept(compositeVisitor);
305    
306 gezelter 246 }
307 tim 12 }
308 gezelter 246
309 tim 12 xyzVisitor->writeFrame(xyzStream);
310     xyzVisitor->clear();
311    
312     }//end for (int i = 0; i < nframes; i += args_info.frame_arg)
313 gezelter 1282
314 tim 12 xyzStream.close();
315 tim 466 delete prepareVisitor;
316 tim 12 delete compositeVisitor;
317     delete info;
318     }

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