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Comparing trunk/src/visitors/OtherVisitor.cpp (file contents):
Revision 1219 by xsun, Wed Jan 23 21:23:32 2008 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 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   #include "selection/SelectionManager.hpp"
42   #include "visitors/OtherVisitor.hpp"
# Line 44 | Line 44
44   #include "primitives/RigidBody.hpp"
45   #include "primitives/Molecule.hpp"
46   #include "brains/SimInfo.hpp"
47 < namespace oopse {
47 > namespace OpenMD {
48  
49    void WrappingVisitor::visit(Atom *atom) {
50      internalVisit(atom);
# Line 296 | Line 296 | namespace oopse {
296             atomInfo = atomData->nextAtomInfo(i) ) {
297          if (atomInfo->hasCharge) {
298            sprintf(buffer,
299 <                "%s%15.8f%15.8f%15.8f%15.8f",
300 <                atomInfo->atomTypeName.c_str(),
301 <                atomInfo->pos[0],
302 <                atomInfo->pos[1],
303 <                atomInfo->pos[2],
304 <                atomInfo->charge);
299 >                  "%s%15.8f%15.8f%15.8f%15.8f",
300 >                  atomInfo->atomTypeName.c_str(),
301 >                  atomInfo->pos[0],
302 >                  atomInfo->pos[1],
303 >                  atomInfo->pos[2],
304 >                  atomInfo->charge);
305          } else {
306            sprintf(buffer,
307                  "%s%15.8f%15.8f%15.8f",
308 <                atomInfo->atomTypeName.c_str(),
309 <                atomInfo->pos[0],
310 <                atomInfo->pos[1],
311 <                atomInfo->pos[2]);
308 >                  atomInfo->atomTypeName.c_str(),
309 >                  atomInfo->pos[0],
310 >                  atomInfo->pos[1],
311 >                  atomInfo->pos[2]);
312          }
313          frame.push_back(buffer);
314        }
# Line 329 | Line 329 | namespace oopse {
329          } else {
330          sprintf(buffer,
331                  "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
332 <                atomInfo->atomTypeName.c_str(),
332 >                atomInfo->atomTypeName.c_str(),
333                  atomInfo->pos[0],
334                  atomInfo->pos[1],
335                  atomInfo->pos[2],
# Line 373 | Line 373 | namespace oopse {
373        outStream << *i << std::endl;
374    }
375  
376 +  std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {    
377 +    return atomTypeName.substr(0, atomTypeName.find('-'));
378 +  }
379 +
380    const std::string XYZVisitor::toString() {
381      char        buffer[65535];
382      std::string result;
# Line 540 | Line 544 | namespace oopse {
544      return result;
545    }
546  
547 < } //namespace oopse
547 > } //namespace OpenMD

Comparing trunk/src/visitors/OtherVisitor.cpp (property svn:keywords):
Revision 1219 by xsun, Wed Jan 23 21:23:32 2008 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

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