src/brains/ForceManager.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file ForceManager.cpp
 * @author tlin
 * @date 11/09/2004
 * @time 10:39am
 * @version 1.0
 */

#include "brains/ForceManager.hpp"
#include "primitives/Molecule.hpp"
#include "UseTheForce/doForces_interface.h"
#define __C
#include "UseTheForce/DarkSide/fInteractionMap.h"
#include "utils/simError.h"
#include "primitives/Bend.hpp"
#include "primitives/Bend.hpp"
namespace oopse {

  void ForceManager::calcForces(bool needPotential, bool needStress) {
    
    if (!info_->isFortranInitialized()) {
      info_->update();
    }
    
    preCalculation();
    
    calcShortRangeInteraction();

    calcLongRangeInteraction(needPotential, needStress);

    postCalculation(needStress);
    
  }
  
  void ForceManager::preCalculation() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    
    // forces are zeroed here, before any are accumulated.
    // NOTE: do not rezero the forces in Fortran.

    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        atom->zeroForcesAndTorques();
      }
      
      //change the positions of atoms which belong to the rigidbodies
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        rb->zeroForcesAndTorques();
      }        
    }
    
    // Zero out the stress tensor
    tau *= 0.0;
    
  }
  
  void ForceManager::calcShortRangeInteraction() {
    Molecule* mol;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;;
    Molecule::BendIterator  bendIter;
    Molecule::TorsionIterator  torsionIter;
    RealType bondPotential = 0.0;
    RealType bendPotential = 0.0;
    RealType torsionPotential = 0.0;

    //calculate short range interactions    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {

      //change the positions of atoms which belong to the rigidbodies
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        rb->updateAtoms();
      }

      for (bond = mol->beginBond(bondIter); bond != NULL; 
           bond = mol->nextBond(bondIter)) {
        bond->calcForce();
        bondPotential += bond->getPotential();
      }

      for (bend = mol->beginBend(bendIter); bend != NULL; 
           bend = mol->nextBend(bendIter)) {
        
        RealType angle;
        bend->calcForce(angle);
        RealType currBendPot = bend->getPotential();          
        bendPotential += bend->getPotential();
        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
        if (i == bendDataSets.end()) {
          BendDataSet dataSet;
          dataSet.prev.angle = dataSet.curr.angle = angle;
          dataSet.prev.potential = dataSet.curr.potential = currBendPot;
          dataSet.deltaV = 0.0;
          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
        }else {
          i->second.prev.angle = i->second.curr.angle;
          i->second.prev.potential = i->second.curr.potential;
          i->second.curr.angle = angle;
          i->second.curr.potential = currBendPot;
          i->second.deltaV =  fabs(i->second.curr.potential -  
                                   i->second.prev.potential);
        }
      }
      
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; 
           torsion = mol->nextTorsion(torsionIter)) {
        RealType angle;
        torsion->calcForce(angle);
        RealType currTorsionPot = torsion->getPotential();
        torsionPotential += torsion->getPotential();
        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
        if (i == torsionDataSets.end()) {
          TorsionDataSet dataSet;
          dataSet.prev.angle = dataSet.curr.angle = angle;
          dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
          dataSet.deltaV = 0.0;
          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
        }else {
          i->second.prev.angle = i->second.curr.angle;
          i->second.prev.potential = i->second.curr.potential;
          i->second.curr.angle = angle;
          i->second.curr.potential = currTorsionPot;
          i->second.deltaV =  fabs(i->second.curr.potential -  
                                   i->second.prev.potential);
        }      
      }      
    }
    
    RealType  shortRangePotential = bondPotential + bendPotential + 
      torsionPotential;    
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
    
  }
  
  void ForceManager::calcLongRangeInteraction(bool needPotential, 
                                              bool needStress) {
    Snapshot* curSnapshot;
    DataStorage* config;
    RealType* frc;
    RealType* pos;
    RealType* trq;
    RealType* A;
    RealType* electroFrame;
    RealType* rc;
    
    //get current snapshot from SimInfo
    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    
    //get array pointers
    config = &(curSnapshot->atomData);
    frc = config->getArrayPointer(DataStorage::dslForce);
    pos = config->getArrayPointer(DataStorage::dslPosition);
    trq = config->getArrayPointer(DataStorage::dslTorque);
    A   = config->getArrayPointer(DataStorage::dslAmat);
    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);

    //calculate the center of mass of cutoff group
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;
    Vector3d com;
    std::vector<Vector3d> rcGroup;
    
    if(info_->getNCutoffGroups() > 0){
      
      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for(cg = mol->beginCutoffGroup(ci); cg != NULL; 
            cg = mol->nextCutoffGroup(ci)) {
          cg->getCOM(com);
          rcGroup.push_back(com);
        }
      }// end for (mol)
       
      rc = rcGroup[0].getArrayPointer();
    } else {
      // center of mass of the group is the same as position of the atom  
      // if cutoff group does not exist
      rc = pos;
    }
    
    //initialize data before passing to fortran
    RealType longRangePotential[LR_POT_TYPES];
    RealType lrPot = 0.0;
    Vector3d totalDipole;
    short int passedCalcPot = needPotential;
    short int passedCalcStress = needStress;
    int isError = 0;

    for (int i=0; i<LR_POT_TYPES;i++){
      longRangePotential[i]=0.0; //Initialize array
    }
    
    doForceLoop( pos,
                 rc,
                 A,
                 electroFrame,
                 frc,
                 trq,
                 tau.getArrayPointer(),
                 longRangePotential, 
                 &passedCalcPot,
                 &passedCalcStress,
                 &isError );

    if( isError ){
      sprintf( painCave.errMsg,
               "Error returned from the fortran force calculation.\n" );
      painCave.isFatal = 1;
      simError();
    }
    for (int i=0; i<LR_POT_TYPES;i++){
      lrPot += longRangePotential[i]; //Quick hack
    }
    
    // grab the simulation box dipole moment if specified
    if (info_->getCalcBoxDipole()){
      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
      
      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
    }
    
    //store the tau and long range potential    
    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
  }

  
  void ForceManager::postCalculation(bool needStress) {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    
    // collect the atomic forces onto rigid bodies
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) { 
        if (needStress) {          
          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
          tau += rbTau;
        } else{
          rb->calcForcesAndTorques();
        }
      }
    }

    if (needStress) {
#ifdef IS_MPI
      Mat3x3d tmpTau(tau);
      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), 
                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#endif
      curSnapshot->statData.setTau(tau);
    } 
  }

} //end namespace oopse
Revision:	3126
Committed:	Fri Apr 6 21:53:43 2007 UTC (17 years, 5 months ago) by gezelter
File size:	11269 byte(s)
Log Message:	Massive update to do virials (both atomic and cutoff-group) correctly. The rigid body constraint contributions had been missing and this was masked by the use of cutoff groups...
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	gezelter	2204	/**
43			* @file ForceManager.cpp
44			* @author tlin
45			* @date 11/09/2004
46			* @time 10:39am
47			* @version 1.0
48			*/
49	gezelter	1930
50			#include "brains/ForceManager.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "UseTheForce/doForces_interface.h"
53	chuckv	2363	#define __C
54			#include "UseTheForce/DarkSide/fInteractionMap.h"
55	gezelter	1930	#include "utils/simError.h"
56	tim	2448	#include "primitives/Bend.hpp"
57			#include "primitives/Bend.hpp"
58	gezelter	1930	namespace oopse {
59
60	gezelter	2204	void ForceManager::calcForces(bool needPotential, bool needStress) {
61	gezelter	3126
62	gezelter	1930	if (!info_->isFortranInitialized()) {
63	gezelter	2204	info_->update();
64	gezelter	1930	}
65	gezelter	3126
66	gezelter	1930	preCalculation();
67
68			calcShortRangeInteraction();
69
70			calcLongRangeInteraction(needPotential, needStress);
71
72	gezelter	3126	postCalculation(needStress);
73	tim	2448
74	gezelter	2204	}
75	gezelter	3126
76	gezelter	2204	void ForceManager::preCalculation() {
77	gezelter	1930	SimInfo::MoleculeIterator mi;
78			Molecule* mol;
79			Molecule::AtomIterator ai;
80			Atom* atom;
81			Molecule::RigidBodyIterator rbIter;
82			RigidBody* rb;
83
84			// forces are zeroed here, before any are accumulated.
85			// NOTE: do not rezero the forces in Fortran.
86	gezelter	3126
87			for (mol = info_->beginMolecule(mi); mol != NULL;
88			mol = info_->nextMolecule(mi)) {
89	gezelter	2204	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
90			atom->zeroForcesAndTorques();
91			}
92	gezelter	3126
93	gezelter	2204	//change the positions of atoms which belong to the rigidbodies
94	gezelter	3126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
95			rb = mol->nextRigidBody(rbIter)) {
96	gezelter	2204	rb->zeroForcesAndTorques();
97			}
98	gezelter	1930	}
99
100	gezelter	3126	// Zero out the stress tensor
101			tau *= 0.0;
102
103	gezelter	2204	}
104	gezelter	3126
105	gezelter	2204	void ForceManager::calcShortRangeInteraction() {
106	gezelter	1930	Molecule* mol;
107			RigidBody* rb;
108			Bond* bond;
109			Bend* bend;
110			Torsion* torsion;
111			SimInfo::MoleculeIterator mi;
112			Molecule::RigidBodyIterator rbIter;
113			Molecule::BondIterator bondIter;;
114			Molecule::BendIterator bendIter;
115			Molecule::TorsionIterator torsionIter;
116	tim	2759	RealType bondPotential = 0.0;
117			RealType bendPotential = 0.0;
118			RealType torsionPotential = 0.0;
119	gezelter	1930
120			//calculate short range interactions
121	gezelter	3126	for (mol = info_->beginMolecule(mi); mol != NULL;
122			mol = info_->nextMolecule(mi)) {
123	gezelter	1930
124	gezelter	2204	//change the positions of atoms which belong to the rigidbodies
125	gezelter	3126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
126			rb = mol->nextRigidBody(rbIter)) {
127			rb->updateAtoms();
128	gezelter	2204	}
129	gezelter	1930
130	gezelter	3126	for (bond = mol->beginBond(bondIter); bond != NULL;
131			bond = mol->nextBond(bondIter)) {
132	tim	2448	bond->calcForce();
133			bondPotential += bond->getPotential();
134	gezelter	2204	}
135	gezelter	1930
136	gezelter	3126	for (bend = mol->beginBend(bendIter); bend != NULL;
137			bend = mol->nextBend(bendIter)) {
138
139			RealType angle;
140			bend->calcForce(angle);
141			RealType currBendPot = bend->getPotential();
142			bendPotential += bend->getPotential();
143			std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
144			if (i == bendDataSets.end()) {
145			BendDataSet dataSet;
146			dataSet.prev.angle = dataSet.curr.angle = angle;
147			dataSet.prev.potential = dataSet.curr.potential = currBendPot;
148			dataSet.deltaV = 0.0;
149			bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
150			}else {
151			i->second.prev.angle = i->second.curr.angle;
152			i->second.prev.potential = i->second.curr.potential;
153			i->second.curr.angle = angle;
154			i->second.curr.potential = currBendPot;
155			i->second.deltaV = fabs(i->second.curr.potential -
156			i->second.prev.potential);
157			}
158	gezelter	2204	}
159	gezelter	3126
160			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
161			torsion = mol->nextTorsion(torsionIter)) {
162	tim	2759	RealType angle;
163	gezelter	3126	torsion->calcForce(angle);
164	tim	2759	RealType currTorsionPot = torsion->getPotential();
165	gezelter	3126	torsionPotential += torsion->getPotential();
166			std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
167			if (i == torsionDataSets.end()) {
168			TorsionDataSet dataSet;
169			dataSet.prev.angle = dataSet.curr.angle = angle;
170			dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
171			dataSet.deltaV = 0.0;
172			torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
173			}else {
174			i->second.prev.angle = i->second.curr.angle;
175			i->second.prev.potential = i->second.curr.potential;
176			i->second.curr.angle = angle;
177			i->second.curr.potential = currTorsionPot;
178			i->second.deltaV = fabs(i->second.curr.potential -
179			i->second.prev.potential);
180			}
181			}
182	gezelter	1930	}
183
184	gezelter	3126	RealType shortRangePotential = bondPotential + bendPotential +
185			torsionPotential;
186	gezelter	1930	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
187			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
188	tim	2364	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
189			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
190			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
191
192	gezelter	2204	}
193	gezelter	3126
194			void ForceManager::calcLongRangeInteraction(bool needPotential,
195			bool needStress) {
196	gezelter	1930	Snapshot* curSnapshot;
197			DataStorage* config;
198	tim	2759	RealType* frc;
199			RealType* pos;
200			RealType* trq;
201			RealType* A;
202			RealType* electroFrame;
203			RealType* rc;
204	gezelter	1930
205			//get current snapshot from SimInfo
206			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
207	gezelter	3126
208	gezelter	1930	//get array pointers
209			config = &(curSnapshot->atomData);
210			frc = config->getArrayPointer(DataStorage::dslForce);
211			pos = config->getArrayPointer(DataStorage::dslPosition);
212			trq = config->getArrayPointer(DataStorage::dslTorque);
213			A = config->getArrayPointer(DataStorage::dslAmat);
214			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
215
216			//calculate the center of mass of cutoff group
217			SimInfo::MoleculeIterator mi;
218			Molecule* mol;
219			Molecule::CutoffGroupIterator ci;
220			CutoffGroup* cg;
221			Vector3d com;
222			std::vector<Vector3d> rcGroup;
223	gezelter	3126
224	gezelter	1930	if(info_->getNCutoffGroups() > 0){
225	gezelter	3126
226			for (mol = info_->beginMolecule(mi); mol != NULL;
227			mol = info_->nextMolecule(mi)) {
228			for(cg = mol->beginCutoffGroup(ci); cg != NULL;
229			cg = mol->nextCutoffGroup(ci)) {
230	gezelter	2204	cg->getCOM(com);
231			rcGroup.push_back(com);
232	gezelter	1930	}
233	gezelter	2204	}// end for (mol)
234	gezelter	1930
235	gezelter	2204	rc = rcGroup[0].getArrayPointer();
236	gezelter	1930	} else {
237	gezelter	3126	// center of mass of the group is the same as position of the atom
238			// if cutoff group does not exist
239	gezelter	2204	rc = pos;
240	gezelter	1930	}
241	gezelter	3126
242	gezelter	1930	//initialize data before passing to fortran
243	tim	2759	RealType longRangePotential[LR_POT_TYPES];
244			RealType lrPot = 0.0;
245	chrisfen	2917	Vector3d totalDipole;
246	gezelter	1930	short int passedCalcPot = needPotential;
247			short int passedCalcStress = needStress;
248			int isError = 0;
249
250	chuckv	2363	for (int i=0; i<LR_POT_TYPES;i++){
251			longRangePotential[i]=0.0; //Initialize array
252			}
253	gezelter	3126
254	gezelter	1930	doForceLoop( pos,
255	gezelter	2204	rc,
256			A,
257			electroFrame,
258			frc,
259			trq,
260			tau.getArrayPointer(),
261	chuckv	2363	longRangePotential,
262	gezelter	2204	&passedCalcPot,
263			&passedCalcStress,
264			&isError );
265	gezelter	1930
266			if( isError ){
267	gezelter	2204	sprintf( painCave.errMsg,
268			"Error returned from the fortran force calculation.\n" );
269			painCave.isFatal = 1;
270			simError();
271	gezelter	1930	}
272	chuckv	2363	for (int i=0; i<LR_POT_TYPES;i++){
273			lrPot += longRangePotential[i]; //Quick hack
274			}
275	gezelter	3126
276	chrisfen	2917	// grab the simulation box dipole moment if specified
277			if (info_->getCalcBoxDipole()){
278			getAccumulatedBoxDipole(totalDipole.getArrayPointer());
279	gezelter	3126
280	chrisfen	2917	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
281			curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
282			curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
283			}
284	gezelter	3126
285	gezelter	1930	//store the tau and long range potential
286	chuckv	2363	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
287	chrisfen	2390	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
288	tim	2380	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
289	gezelter	2204	}
290	gezelter	1930
291	gezelter	3126
292			void ForceManager::postCalculation(bool needStress) {
293	gezelter	1930	SimInfo::MoleculeIterator mi;
294			Molecule* mol;
295			Molecule::RigidBodyIterator rbIter;
296			RigidBody* rb;
297	gezelter	3126	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
298	gezelter	1930
299			// collect the atomic forces onto rigid bodies
300	gezelter	3126
301			for (mol = info_->beginMolecule(mi); mol != NULL;
302			mol = info_->nextMolecule(mi)) {
303			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
304			rb = mol->nextRigidBody(rbIter)) {
305			if (needStress) {
306			Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
307			tau += rbTau;
308			} else{
309			rb->calcForcesAndTorques();
310			}
311	gezelter	2204	}
312	gezelter	3126	}
313	gezelter	1930
314	gezelter	3126	if (needStress) {
315			#ifdef IS_MPI
316			Mat3x3d tmpTau(tau);
317			MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
318			9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
319			#endif
320			curSnapshot->statData.setTau(tau);
321			}
322	gezelter	2204	}
323	gezelter	1930
324			} //end namespace oopse