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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1025 by gezelter, Wed Aug 30 20:33:44 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.
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. 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 "io/DumpWriter.hpp"
# Line 50 | Line 50
50   #include <mpi.h>
51   #endif //is_mpi
52  
53 < namespace oopse {
53 > namespace OpenMD {
54  
55    DumpWriter::DumpWriter(SimInfo* info)
56      : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
# Line 240 | Line 240 | namespace oopse {
240      os << "    <StuntDoubles>\n";
241      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
242  
243 <      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
243 >      
244 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
245             integrableObject = mol->nextIntegrableObject(ii)) {  
246 <        os << prepareDumpLine(integrableObject);
247 <
246 >          os << prepareDumpLine(integrableObject);
247 >          
248        }
249      }    
250      os << "    </StuntDoubles>\n";
251 <
251 >    
252      os << "  </Snapshot>\n";
253  
254      os.flush();
# Line 255 | Line 256 | namespace oopse {
256      //every node prepares the dump lines for integrable objects belong to itself
257      std::string buffer;
258      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
259 <      
259 >
260 >
261        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
262             integrableObject = mol->nextIntegrableObject(ii)) {  
263 <        buffer += prepareDumpLine(integrableObject);
263 >          buffer += prepareDumpLine(integrableObject);
264        }
265      }
266      
# Line 285 | Line 287 | namespace oopse {
287          } else {
288            MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
289            os << recvBuffer;
290 <          delete recvBuffer;
290 >          delete [] recvBuffer;
291          }
292        }
293        os << "    </StuntDoubles>\n";
# Line 424 | Line 426 | namespace oopse {
426      newOStream = new std::ofstream(filename.c_str());
427   #endif
428      //write out MetaData first
429 <    (*newOStream) << "<OOPSE version=4>" << std::endl;
429 >    (*newOStream) << "<OpenMD version=1>" << std::endl;
430      (*newOStream) << "  <MetaData>" << std::endl;
431      (*newOStream) << info_->getRawMetaData();
432      (*newOStream) << "  </MetaData>" << std::endl;
# Line 433 | Line 435 | namespace oopse {
435  
436    void DumpWriter::writeClosing(std::ostream& os) {
437  
438 <    os << "</OOPSE>\n";
438 >    os << "</OpenMD>\n";
439      os.flush();
440    }
441  
442 < }//end namespace oopse
442 > }//end namespace OpenMD

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