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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# 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   /**
# Line 79 | Line 79
79   #include "math/ParallelRandNumGen.hpp"
80   #endif
81  
82 < namespace oopse {
82 > namespace OpenMD {
83    
84    Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
85      Globals* simParams = NULL;
# Line 214 | Line 214 | namespace oopse {
214        painCave.isFatal = 1;
215        simError();        
216      }
217 <    catch (OOPSEException& e) {
217 >    catch (OpenMDException& e) {
218        sprintf(painCave.errMsg,
219                "%s\n",
220                e.getMessage().c_str());
# Line 262 | Line 262 | namespace oopse {
262        mdFile_.getline(buffer, bufferSize);
263        ++lineNo;
264        std::string line = trimLeftCopy(buffer);
265 <      i = CaseInsensitiveFind(line, "<OOPSE");
265 >      i = CaseInsensitiveFind(line, "<OpenMD");
266        if (static_cast<size_t>(i) == string::npos) {
267 +        // try the older file strings to see if that works:
268 +        i = CaseInsensitiveFind(line, "<OOPSE");
269 +      }
270 +      
271 +      if (static_cast<size_t>(i) == string::npos) {
272 +        // still no luck!
273          sprintf(painCave.errMsg,
274 <                "SimCreator: File: %s is not an OOPSE file!\n",
274 >                "SimCreator: File: %s is not a valid OpenMD file!\n",
275                  mdFileName.c_str());
276          painCave.isFatal = 1;
277          simError();
# Line 471 | Line 477 | namespace oopse {
477                "\tthe number of molecules.  This will not result in a \n"
478                "\tusable division of atoms for force decomposition.\n"
479                "\tEither try a smaller number of processors, or run the\n"
480 <              "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
480 >              "\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
481        
482        painCave.isFatal = 1;
483        simError();
# Line 813 | Line 819 | namespace oopse {
819      info->getSnapshotManager()->advance();
820    }
821    
822 < } //end namespace oopse
822 > } //end namespace OpenMD
823  
824  

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