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 __OOPSE_C
#include "UseTheForce/DarkSide/fInteractionMap.h"
#include "utils/simError.h"
#include "primitives/Bond.hpp"
#include "primitives/Bend.hpp"
#include "primitives/Torsion.hpp"
#include "primitives/Inversion.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;
    Inversion* inversion;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;;
    Molecule::BendIterator  bendIter;
    Molecule::TorsionIterator  torsionIter;
    Molecule::InversionIterator  inversionIter;
    RealType bondPotential = 0.0;
    RealType bendPotential = 0.0;
    RealType torsionPotential = 0.0;
    RealType inversionPotential = 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);
        }      
      }      

      for (inversion = mol->beginInversion(inversionIter); 
           inversion != NULL; 
           inversion = mol->nextInversion(inversionIter)) {
        RealType angle;
        inversion->calcForce(angle);
        RealType currInversionPot = inversion->getPotential();
        inversionPotential += inversion->getPotential();
        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
        if (i == inversionDataSets.end()) {
          InversionDataSet dataSet;
          dataSet.prev.angle = dataSet.curr.angle = angle;
          dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
          dataSet.deltaV = 0.0;
          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, 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 = currInversionPot;
          i->second.deltaV =  fabs(i->second.curr.potential -  
                                   i->second.prev.potential);
        }      
      }      
    }
    
    RealType  shortRangePotential = bondPotential + bendPotential + 
      torsionPotential +  inversionPotential;    
    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;
    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
    
  }
  
  void ForceManager::calcLongRangeInteraction(bool needPotential, 
                                              bool needStress) {
    Snapshot* curSnapshot;
    DataStorage* config;
    RealType* frc;
    RealType* pos;
    RealType* trq;
    RealType* A;
    RealType* electroFrame;
    RealType* rc;
    RealType* particlePot;
    
    //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);
    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);

    //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, 
                particlePot,
                &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:	1292
Committed:	Fri Sep 12 20:51:22 2008 UTC (16 years, 7 months ago) by chuckv
Original Path:	*trunk/src/brains/ForceManager.cpp*
File size:	12979 byte(s)
Log Message:	fixed thermo bug
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	507	/**
43			* @file ForceManager.cpp
44			* @author tlin
45			* @date 11/09/2004
46			* @time 10:39am
47			* @version 1.0
48			*/
49	gezelter	246
50			#include "brains/ForceManager.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "UseTheForce/doForces_interface.h"
53	chuckv	1292	#define __OOPSE_C
54	chuckv	664	#include "UseTheForce/DarkSide/fInteractionMap.h"
55	gezelter	246	#include "utils/simError.h"
56	xsun	1215	#include "primitives/Bond.hpp"
57	tim	749	#include "primitives/Bend.hpp"
58	cli2	1275	#include "primitives/Torsion.hpp"
59			#include "primitives/Inversion.hpp"
60	gezelter	246	namespace oopse {
61
62	gezelter	507	void ForceManager::calcForces(bool needPotential, bool needStress) {
63	gezelter	1126
64	gezelter	246	if (!info_->isFortranInitialized()) {
65	gezelter	507	info_->update();
66	gezelter	246	}
67	gezelter	1126
68	gezelter	246	preCalculation();
69
70			calcShortRangeInteraction();
71
72			calcLongRangeInteraction(needPotential, needStress);
73
74	gezelter	1126	postCalculation(needStress);
75	tim	749
76	gezelter	507	}
77	gezelter	1126
78	gezelter	507	void ForceManager::preCalculation() {
79	gezelter	246	SimInfo::MoleculeIterator mi;
80			Molecule* mol;
81			Molecule::AtomIterator ai;
82			Atom* atom;
83			Molecule::RigidBodyIterator rbIter;
84			RigidBody* rb;
85
86			// forces are zeroed here, before any are accumulated.
87			// NOTE: do not rezero the forces in Fortran.
88	chuckv	1245
89	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
90			mol = info_->nextMolecule(mi)) {
91	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
92			atom->zeroForcesAndTorques();
93			}
94	chuckv	1245
95	gezelter	507	//change the positions of atoms which belong to the rigidbodies
96	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
97			rb = mol->nextRigidBody(rbIter)) {
98	gezelter	507	rb->zeroForcesAndTorques();
99			}
100	chuckv	1245
101	gezelter	246	}
102
103	gezelter	1126	// Zero out the stress tensor
104			tau *= 0.0;
105
106	gezelter	507	}
107	gezelter	1126
108	gezelter	507	void ForceManager::calcShortRangeInteraction() {
109	gezelter	246	Molecule* mol;
110			RigidBody* rb;
111			Bond* bond;
112			Bend* bend;
113			Torsion* torsion;
114	cli2	1275	Inversion* inversion;
115	gezelter	246	SimInfo::MoleculeIterator mi;
116			Molecule::RigidBodyIterator rbIter;
117			Molecule::BondIterator bondIter;;
118			Molecule::BendIterator bendIter;
119			Molecule::TorsionIterator torsionIter;
120	cli2	1275	Molecule::InversionIterator inversionIter;
121	tim	963	RealType bondPotential = 0.0;
122			RealType bendPotential = 0.0;
123			RealType torsionPotential = 0.0;
124	cli2	1275	RealType inversionPotential = 0.0;
125	gezelter	246
126			//calculate short range interactions
127	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
128			mol = info_->nextMolecule(mi)) {
129	gezelter	246
130	gezelter	507	//change the positions of atoms which belong to the rigidbodies
131	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
132			rb = mol->nextRigidBody(rbIter)) {
133			rb->updateAtoms();
134	gezelter	507	}
135	gezelter	246
136	gezelter	1126	for (bond = mol->beginBond(bondIter); bond != NULL;
137			bond = mol->nextBond(bondIter)) {
138	tim	749	bond->calcForce();
139			bondPotential += bond->getPotential();
140	gezelter	507	}
141	gezelter	246
142	gezelter	1126	for (bend = mol->beginBend(bendIter); bend != NULL;
143			bend = mol->nextBend(bendIter)) {
144
145			RealType angle;
146			bend->calcForce(angle);
147			RealType currBendPot = bend->getPotential();
148			bendPotential += bend->getPotential();
149			std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
150			if (i == bendDataSets.end()) {
151			BendDataSet dataSet;
152			dataSet.prev.angle = dataSet.curr.angle = angle;
153			dataSet.prev.potential = dataSet.curr.potential = currBendPot;
154			dataSet.deltaV = 0.0;
155			bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
156			}else {
157			i->second.prev.angle = i->second.curr.angle;
158			i->second.prev.potential = i->second.curr.potential;
159			i->second.curr.angle = angle;
160			i->second.curr.potential = currBendPot;
161			i->second.deltaV = fabs(i->second.curr.potential -
162			i->second.prev.potential);
163			}
164	gezelter	507	}
165	gezelter	1126
166			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
167			torsion = mol->nextTorsion(torsionIter)) {
168	tim	963	RealType angle;
169	gezelter	1126	torsion->calcForce(angle);
170	tim	963	RealType currTorsionPot = torsion->getPotential();
171	gezelter	1126	torsionPotential += torsion->getPotential();
172			std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
173			if (i == torsionDataSets.end()) {
174			TorsionDataSet dataSet;
175			dataSet.prev.angle = dataSet.curr.angle = angle;
176			dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
177			dataSet.deltaV = 0.0;
178			torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
179			}else {
180			i->second.prev.angle = i->second.curr.angle;
181			i->second.prev.potential = i->second.curr.potential;
182			i->second.curr.angle = angle;
183			i->second.curr.potential = currTorsionPot;
184			i->second.deltaV = fabs(i->second.curr.potential -
185			i->second.prev.potential);
186			}
187			}
188	cli2	1275
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	gezelter	246	}
213
214	gezelter	1126	RealType shortRangePotential = bondPotential + bendPotential +
215	cli2	1275	torsionPotential + inversionPotential;
216	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
217			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
218	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
219			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
220			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
221	cli2	1275	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
222	tim	665
223	gezelter	507	}
224	gezelter	1126
225			void ForceManager::calcLongRangeInteraction(bool needPotential,
226			bool needStress) {
227	gezelter	246	Snapshot* curSnapshot;
228			DataStorage* config;
229	tim	963	RealType* frc;
230			RealType* pos;
231			RealType* trq;
232			RealType* A;
233			RealType* electroFrame;
234			RealType* rc;
235	chuckv	1245	RealType* particlePot;
236	gezelter	246
237			//get current snapshot from SimInfo
238			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239	gezelter	1126
240	gezelter	246	//get array pointers
241			config = &(curSnapshot->atomData);
242			frc = config->getArrayPointer(DataStorage::dslForce);
243			pos = config->getArrayPointer(DataStorage::dslPosition);
244			trq = config->getArrayPointer(DataStorage::dslTorque);
245			A = config->getArrayPointer(DataStorage::dslAmat);
246			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
247	chuckv	1245	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
248	gezelter	246
249			//calculate the center of mass of cutoff group
250			SimInfo::MoleculeIterator mi;
251			Molecule* mol;
252			Molecule::CutoffGroupIterator ci;
253			CutoffGroup* cg;
254			Vector3d com;
255			std::vector<Vector3d> rcGroup;
256	gezelter	1126
257	gezelter	246	if(info_->getNCutoffGroups() > 0){
258	gezelter	1126
259			for (mol = info_->beginMolecule(mi); mol != NULL;
260			mol = info_->nextMolecule(mi)) {
261			for(cg = mol->beginCutoffGroup(ci); cg != NULL;
262			cg = mol->nextCutoffGroup(ci)) {
263	gezelter	507	cg->getCOM(com);
264			rcGroup.push_back(com);
265	gezelter	246	}
266	gezelter	507	}// end for (mol)
267	gezelter	246
268	gezelter	507	rc = rcGroup[0].getArrayPointer();
269	gezelter	246	} else {
270	gezelter	1126	// center of mass of the group is the same as position of the atom
271			// if cutoff group does not exist
272	gezelter	507	rc = pos;
273	gezelter	246	}
274	gezelter	1126
275	gezelter	246	//initialize data before passing to fortran
276	tim	963	RealType longRangePotential[LR_POT_TYPES];
277			RealType lrPot = 0.0;
278	chrisfen	998	Vector3d totalDipole;
279	gezelter	246	short int passedCalcPot = needPotential;
280			short int passedCalcStress = needStress;
281			int isError = 0;
282
283	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
284			longRangePotential[i]=0.0; //Initialize array
285			}
286	gezelter	1126
287	xsun	1215	doForceLoop(pos,
288			rc,
289			A,
290			electroFrame,
291			frc,
292			trq,
293			tau.getArrayPointer(),
294			longRangePotential,
295	chuckv	1245	particlePot,
296			&passedCalcPot,
297	xsun	1215	&passedCalcStress,
298			&isError );
299
300	gezelter	246	if( isError ){
301	gezelter	507	sprintf( painCave.errMsg,
302			"Error returned from the fortran force calculation.\n" );
303			painCave.isFatal = 1;
304			simError();
305	gezelter	246	}
306	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
307			lrPot += longRangePotential[i]; //Quick hack
308			}
309	gezelter	1126
310	chrisfen	998	// grab the simulation box dipole moment if specified
311			if (info_->getCalcBoxDipole()){
312			getAccumulatedBoxDipole(totalDipole.getArrayPointer());
313	gezelter	1126
314	chrisfen	998	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
315			curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
316			curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
317			}
318	gezelter	1126
319	gezelter	246	//store the tau and long range potential
320	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
321	chrisfen	691	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
322	tim	681	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
323	gezelter	507	}
324	gezelter	246
325	gezelter	1126
326			void ForceManager::postCalculation(bool needStress) {
327	gezelter	246	SimInfo::MoleculeIterator mi;
328			Molecule* mol;
329			Molecule::RigidBodyIterator rbIter;
330			RigidBody* rb;
331	gezelter	1126	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
332	gezelter	246
333			// collect the atomic forces onto rigid bodies
334	gezelter	1126
335			for (mol = info_->beginMolecule(mi); mol != NULL;
336			mol = info_->nextMolecule(mi)) {
337			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
338			rb = mol->nextRigidBody(rbIter)) {
339			if (needStress) {
340			Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
341			tau += rbTau;
342			} else{
343			rb->calcForcesAndTorques();
344			}
345	gezelter	507	}
346	gezelter	1126	}
347	gezelter	246
348	gezelter	1126	if (needStress) {
349			#ifdef IS_MPI
350			Mat3x3d tmpTau(tau);
351			MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
352			9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
353			#endif
354			curSnapshot->statData.setTau(tau);
355			}
356	gezelter	507	}
357	gezelter	246
358			} //end namespace oopse