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Comparing trunk/src/visitors/OtherVisitor.cpp (file contents):
Revision 1118 by chuckv, Tue Jan 16 22:18:04 2007 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 294 | Line 294 | namespace oopse {
294      if (posOnly_){
295        for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
296             atomInfo = atomData->nextAtomInfo(i) ) {
297 <        sprintf(buffer,
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);
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        }
315      }else{
316        for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
317             atomInfo = atomData->nextAtomInfo(i) ) {
318 +        if (atomInfo->hasCharge) {
319          sprintf(buffer,
320 <                "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
320 >                "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
321                  atomInfo->atomTypeName.c_str(),
322                  atomInfo->pos[0],
323                  atomInfo->pos[1],
324                  atomInfo->pos[2],
325 +                atomInfo->charge,
326                  atomInfo->dipole[0],
327                  atomInfo->dipole[1],
328                  atomInfo->dipole[2]);
329 +        } else {
330 +        sprintf(buffer,
331 +                "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
332 +                atomInfo->atomTypeName.c_str(),
333 +                atomInfo->pos[0],
334 +                atomInfo->pos[1],
335 +                atomInfo->pos[2],
336 +                atomInfo->dipole[0],
337 +                atomInfo->dipole[1],
338 +                atomInfo->dipole[2]);
339 +        }
340          frame.push_back(buffer);
341        }
342      }
# Line 350 | 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 517 | 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 1118 by chuckv, Tue Jan 16 22:18:04 2007 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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