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Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 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
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 < * 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
19 < *    notice, this list of conditions and the following disclaimer.
20 < *
21 < * 3. Redistributions in binary form must reproduce the above copyright
22 < *    notice, this list of conditions and the following disclaimer in the
23 < *    documentation and/or other materials provided with the
24 < *    distribution.
25 < *
26 < * This software is provided "AS IS," without a warranty of any
27 < * kind. All express or implied conditions, representations and
28 < * warranties, including any implied warranty of merchantability,
29 < * fitness for a particular purpose or non-infringement, are hereby
30 < * excluded.  The University of Notre Dame and its licensors shall not
31 < * be liable for any damages suffered by licensee as a result of
32 < * using, modifying or distributing the software or its
33 < * derivatives. In no event will the University of Notre Dame or its
34 < * licensors be liable for any lost revenue, profit or data, or for
35 < * direct, indirect, special, consequential, incidental or punitive
36 < * damages, however caused and regardless of the theory of liability,
37 < * arising out of the use of or inability to use software, even if the
38 < * University of Notre Dame has been advised of the possibility of
39 < * such damages.
40 < */
1 > /*
2 > * Copyright (c) 2009 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 > * 1. Redistributions of source code must retain the above copyright
10 > *    notice, this list of conditions and the following disclaimer.
11 > *
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.
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 > *
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   #define _LARGEFILE_SOURCE64
43   #define _FILE_OFFSET_BITS 64
# Line 67 | Line 67
67   #endif // is_mpi
68  
69  
70 < namespace oopse {
70 > namespace OpenMD {
71    
72    DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73 <    : info_(info), filename_(filename), isScanned_(false), nframes_(0) {
73 >    : info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
74      
75   #ifdef IS_MPI
76      
# Line 92 | Line 92 | namespace oopse {
92      }
93      
94      strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95 <    MPIcheckPoint();
95 >    errorCheckPoint();
96      
97   #endif
98      
# Line 113 | Line 113 | namespace oopse {
113      }
114      
115      strcpy(checkPointMsg, "Dump file closed successfully.");
116 <    MPIcheckPoint();
116 >    errorCheckPoint();
117      
118   #endif
119      
# Line 240 | Line 240 | namespace oopse {
240      }
241      
242      readSet(whichFrame);
243 +
244 +    if (needCOMprops_) {
245 +      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246 +      Vector3d com;
247 +      Vector3d comvel;
248 +      Vector3d comw;
249 +      if (needPos_ && needVel_){
250 +        info_->getComAll(com, comvel);
251 +        comw = info_->getAngularMomentum();
252 +      }else{
253 +        com = info_->getCom();
254 +        comvel = 0.0;
255 +        comw   = 0.0;
256 +      }
257 +      s->setCOMprops(com, comvel, comw);      
258 +    }
259 +
260    }
261    
262    void DumpReader::readSet(int whichFrame) {    
263      std::string line;
264  
265   #ifndef IS_MPI
249 –
266      inFile_->clear();  
267      inFile_->seekg(framePos_[whichFrame]);
268  
# Line 276 | Line 292 | namespace oopse {
292        MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
293        
294        sstream.str(sendBuffer);
279 –      std::cerr << sendBuffer;
295      } else {
296        int sendBufferSize;
297        MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
298        char * recvBuffer = new char[sendBufferSize+1];
299 +      assert(recvBuffer);
300 +      recvBuffer[sendBufferSize] = '\0';
301        MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
302        sstream.str(recvBuffer);
303 +      delete [] recvBuffer;
304      }      
305  
306      std::istream& inputStream = sstream;  
# Line 339 | Line 357 | namespace oopse {
357      }
358      std::string type = tokenizer.nextToken();
359      int size = type.size();
360 +
361      for(int i = 0; i < size; ++i) {
362        switch(type[i]) {
363          
# Line 373 | Line 392 | namespace oopse {
392               q[3] = tokenizer.nextTokenAsDouble();
393                
394               RealType qlen = q.length();
395 <             if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
395 >             if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
396                  
397                 sprintf(painCave.errMsg,
398                         "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
# Line 399 | Line 418 | namespace oopse {
418                 integrableObject->setJ(ji);
419               }
420            }
421 +          break;
422          }  
423          case 'f': {
424  
# Line 529 | Line 549 | namespace oopse {
549    }
550  
551    
552 < }//end namespace oopse
552 > }//end namespace OpenMD

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