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root/OpenMD/trunk/src/brains/ForceManager.cpp
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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1245 by chuckv, Tue May 27 16:39:06 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 50 | Line 50
50   #include "brains/ForceManager.hpp"
51   #include "primitives/Molecule.hpp"
52   #include "UseTheForce/doForces_interface.h"
53 < #define __C
53 > #define __OPENMD_C
54   #include "UseTheForce/DarkSide/fInteractionMap.h"
55   #include "utils/simError.h"
56   #include "primitives/Bond.hpp"
57   #include "primitives/Bend.hpp"
58 < namespace oopse {
58 > #include "primitives/Torsion.hpp"
59 > #include "primitives/Inversion.hpp"
60 > namespace OpenMD {
61  
62    void ForceManager::calcForces(bool needPotential, bool needStress) {
63      
# Line 109 | Line 111 | namespace oopse {
111      Bond* bond;
112      Bend* bend;
113      Torsion* torsion;
114 +    Inversion* inversion;
115      SimInfo::MoleculeIterator mi;
116      Molecule::RigidBodyIterator rbIter;
117      Molecule::BondIterator bondIter;;
118      Molecule::BendIterator  bendIter;
119      Molecule::TorsionIterator  torsionIter;
120 +    Molecule::InversionIterator  inversionIter;
121      RealType bondPotential = 0.0;
122      RealType bendPotential = 0.0;
123      RealType torsionPotential = 0.0;
124 +    RealType inversionPotential = 0.0;
125  
126      //calculate short range interactions    
127      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 180 | Line 185 | namespace oopse {
185                                     i->second.prev.potential);
186          }      
187        }      
188 +
189 +      for (inversion = mol->beginInversion(inversionIter);
190 +           inversion != NULL;
191 +           inversion = mol->nextInversion(inversionIter)) {
192 +        RealType angle;
193 +        inversion->calcForce(angle);
194 +        RealType currInversionPot = inversion->getPotential();
195 +        inversionPotential += inversion->getPotential();
196 +        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
197 +        if (i == inversionDataSets.end()) {
198 +          InversionDataSet dataSet;
199 +          dataSet.prev.angle = dataSet.curr.angle = angle;
200 +          dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
201 +          dataSet.deltaV = 0.0;
202 +          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
203 +        }else {
204 +          i->second.prev.angle = i->second.curr.angle;
205 +          i->second.prev.potential = i->second.curr.potential;
206 +          i->second.curr.angle = angle;
207 +          i->second.curr.potential = currInversionPot;
208 +          i->second.deltaV =  fabs(i->second.curr.potential -  
209 +                                   i->second.prev.potential);
210 +        }      
211 +      }      
212      }
213      
214      RealType  shortRangePotential = bondPotential + bendPotential +
215 <      torsionPotential;    
215 >      torsionPotential +  inversionPotential;    
216      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
217      curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
218      curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
219      curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
220      curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
221 +    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
222      
223    }
224    
# Line 325 | Line 355 | namespace oopse {
355      }
356    }
357  
358 < } //end namespace oopse
358 > } //end namespace OpenMD

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