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
File size:	12979 byte(s)
Log Message:	fixed thermo bug
#	Content
1	/*
2	* 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	/**
43	* @file ForceManager.cpp
44	* @author tlin
45	* @date 11/09/2004
46	* @time 10:39am
47	* @version 1.0
48	*/
49
50	#include "brains/ForceManager.hpp"
51	#include "primitives/Molecule.hpp"
52	#include "UseTheForce/doForces_interface.h"
53	#define __OOPSE_C
54	#include "UseTheForce/DarkSide/fInteractionMap.h"
55	#include "utils/simError.h"
56	#include "primitives/Bond.hpp"
57	#include "primitives/Bend.hpp"
58	#include "primitives/Torsion.hpp"
59	#include "primitives/Inversion.hpp"
60	namespace oopse {
61
62	void ForceManager::calcForces(bool needPotential, bool needStress) {
63
64	if (!info_->isFortranInitialized()) {
65	info_->update();
66	}
67
68	preCalculation();
69
70	calcShortRangeInteraction();
71
72	calcLongRangeInteraction(needPotential, needStress);
73
74	postCalculation(needStress);
75
76	}
77
78	void ForceManager::preCalculation() {
79	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
89	for (mol = info_->beginMolecule(mi); mol != NULL;
90	mol = info_->nextMolecule(mi)) {
91	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
92	atom->zeroForcesAndTorques();
93	}
94
95	//change the positions of atoms which belong to the rigidbodies
96	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
97	rb = mol->nextRigidBody(rbIter)) {
98	rb->zeroForcesAndTorques();
99	}
100
101	}
102
103	// Zero out the stress tensor
104	tau *= 0.0;
105
106	}
107
108	void ForceManager::calcShortRangeInteraction() {
109	Molecule* mol;
110	RigidBody* rb;
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;
128	mol = info_->nextMolecule(mi)) {
129
130	//change the positions of atoms which belong to the rigidbodies
131	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
132	rb = mol->nextRigidBody(rbIter)) {
133	rb->updateAtoms();
134	}
135
136	for (bond = mol->beginBond(bondIter); bond != NULL;
137	bond = mol->nextBond(bondIter)) {
138	bond->calcForce();
139	bondPotential += bond->getPotential();
140	}
141
142	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	}
165
166	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
167	torsion = mol->nextTorsion(torsionIter)) {
168	RealType angle;
169	torsion->calcForce(angle);
170	RealType currTorsionPot = torsion->getPotential();
171	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
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 + 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
225	void ForceManager::calcLongRangeInteraction(bool needPotential,
226	bool needStress) {
227	Snapshot* curSnapshot;
228	DataStorage* config;
229	RealType* frc;
230	RealType* pos;
231	RealType* trq;
232	RealType* A;
233	RealType* electroFrame;
234	RealType* rc;
235	RealType* particlePot;
236
237	//get current snapshot from SimInfo
238	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239
240	//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	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
248
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
257	if(info_->getNCutoffGroups() > 0){
258
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	cg->getCOM(com);
264	rcGroup.push_back(com);
265	}
266	}// end for (mol)
267
268	rc = rcGroup[0].getArrayPointer();
269	} else {
270	// center of mass of the group is the same as position of the atom
271	// if cutoff group does not exist
272	rc = pos;
273	}
274
275	//initialize data before passing to fortran
276	RealType longRangePotential[LR_POT_TYPES];
277	RealType lrPot = 0.0;
278	Vector3d totalDipole;
279	short int passedCalcPot = needPotential;
280	short int passedCalcStress = needStress;
281	int isError = 0;
282
283	for (int i=0; i<LR_POT_TYPES;i++){
284	longRangePotential[i]=0.0; //Initialize array
285	}
286
287	doForceLoop(pos,
288	rc,
289	A,
290	electroFrame,
291	frc,
292	trq,
293	tau.getArrayPointer(),
294	longRangePotential,
295	particlePot,
296	&passedCalcPot,
297	&passedCalcStress,
298	&isError );
299
300	if( isError ){
301	sprintf( painCave.errMsg,
302	"Error returned from the fortran force calculation.\n" );
303	painCave.isFatal = 1;
304	simError();
305	}
306	for (int i=0; i<LR_POT_TYPES;i++){
307	lrPot += longRangePotential[i]; //Quick hack
308	}
309
310	// grab the simulation box dipole moment if specified
311	if (info_->getCalcBoxDipole()){
312	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
313
314	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
319	//store the tau and long range potential
320	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
321	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
322	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
323	}
324
325
326	void ForceManager::postCalculation(bool needStress) {
327	SimInfo::MoleculeIterator mi;
328	Molecule* mol;
329	Molecule::RigidBodyIterator rbIter;
330	RigidBody* rb;
331	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
332
333	// collect the atomic forces onto rigid bodies
334
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	}
346	}
347
348	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	}
357
358	} //end namespace oopse