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root/OpenMD/trunk/src/brains/MoleculeCreator.cpp
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Comparing trunk/src/brains/MoleculeCreator.cpp (file contents):
Revision 1290 by cli2, Wed Sep 10 19:51:45 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 59 | Line 59
59   #include "utils/simError.h"
60   #include "utils/StringUtils.hpp"
61  
62 < namespace oopse {
62 > namespace OpenMD {
63    
64    Molecule* MoleculeCreator::createMolecule(ForceField* ff,
65                                              MoleculeStamp *molStamp,
# Line 257 | Line 257 | namespace oopse {
257      //The third part is the index of the rigidbody defined in meta-data file
258      //For example, Butane_RB_0 is a valid rigid body name of butane molecule
259      /**@todo replace itoa by lexi_cast */
260 <    std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
260 >    std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
261      rb->setType(mol->getType() + "_RB_" + s.c_str());
262  
263      return rb;
# Line 438 | Line 438 | namespace oopse {
438                atomD->getType().c_str());
439        
440        painCave.isFatal = 0;
441 <      painCave.severity = OOPSE_INFO;
441 >      painCave.severity = OPENMD_INFO;
442        simError();
443        return NULL;
444      } else {

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