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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @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 __OPENMD_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 OpenMD {

  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 OpenMD
Revision:	1448
Committed:	Thu Jun 17 14:58:49 2010 UTC (14 years, 10 months ago) by gezelter
File size:	13033 byte(s)
Log Message:	mostly whitespace issues
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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	/**
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 __OPENMD_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 OpenMD {
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
149	bendPotential += bend->getPotential();
150	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
151	if (i == bendDataSets.end()) {
152	BendDataSet dataSet;
153	dataSet.prev.angle = dataSet.curr.angle = angle;
154	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
155	dataSet.deltaV = 0.0;
156	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
157	}else {
158	i->second.prev.angle = i->second.curr.angle;
159	i->second.prev.potential = i->second.curr.potential;
160	i->second.curr.angle = angle;
161	i->second.curr.potential = currBendPot;
162	i->second.deltaV = fabs(i->second.curr.potential -
163	i->second.prev.potential);
164	}
165	}
166
167	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
168	torsion = mol->nextTorsion(torsionIter)) {
169	RealType angle;
170	torsion->calcForce(angle);
171	RealType currTorsionPot = torsion->getPotential();
172	torsionPotential += torsion->getPotential();
173	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
174	if (i == torsionDataSets.end()) {
175	TorsionDataSet dataSet;
176	dataSet.prev.angle = dataSet.curr.angle = angle;
177	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
178	dataSet.deltaV = 0.0;
179	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
180	}else {
181	i->second.prev.angle = i->second.curr.angle;
182	i->second.prev.potential = i->second.curr.potential;
183	i->second.curr.angle = angle;
184	i->second.curr.potential = currTorsionPot;
185	i->second.deltaV = fabs(i->second.curr.potential -
186	i->second.prev.potential);
187	}
188	}
189
190	for (inversion = mol->beginInversion(inversionIter);
191	inversion != NULL;
192	inversion = mol->nextInversion(inversionIter)) {
193	RealType angle;
194	inversion->calcForce(angle);
195	RealType currInversionPot = inversion->getPotential();
196	inversionPotential += inversion->getPotential();
197	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
198	if (i == inversionDataSets.end()) {
199	InversionDataSet dataSet;
200	dataSet.prev.angle = dataSet.curr.angle = angle;
201	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
202	dataSet.deltaV = 0.0;
203	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
204	}else {
205	i->second.prev.angle = i->second.curr.angle;
206	i->second.prev.potential = i->second.curr.potential;
207	i->second.curr.angle = angle;
208	i->second.curr.potential = currInversionPot;
209	i->second.deltaV = fabs(i->second.curr.potential -
210	i->second.prev.potential);
211	}
212	}
213	}
214
215	RealType shortRangePotential = bondPotential + bendPotential +
216	torsionPotential + inversionPotential;
217	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
218	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
219	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
220	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
221	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
222	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
223
224	}
225
226	void ForceManager::calcLongRangeInteraction(bool needPotential,
227	bool needStress) {
228	Snapshot* curSnapshot;
229	DataStorage* config;
230	RealType* frc;
231	RealType* pos;
232	RealType* trq;
233	RealType* A;
234	RealType* electroFrame;
235	RealType* rc;
236	RealType* particlePot;
237
238	//get current snapshot from SimInfo
239	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
240
241	//get array pointers
242	config = &(curSnapshot->atomData);
243	frc = config->getArrayPointer(DataStorage::dslForce);
244	pos = config->getArrayPointer(DataStorage::dslPosition);
245	trq = config->getArrayPointer(DataStorage::dslTorque);
246	A = config->getArrayPointer(DataStorage::dslAmat);
247	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
248	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
249
250	//calculate the center of mass of cutoff group
251	SimInfo::MoleculeIterator mi;
252	Molecule* mol;
253	Molecule::CutoffGroupIterator ci;
254	CutoffGroup* cg;
255	Vector3d com;
256	std::vector<Vector3d> rcGroup;
257
258	if(info_->getNCutoffGroups() > 0){
259
260	for (mol = info_->beginMolecule(mi); mol != NULL;
261	mol = info_->nextMolecule(mi)) {
262	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
263	cg = mol->nextCutoffGroup(ci)) {
264	cg->getCOM(com);
265	rcGroup.push_back(com);
266	}
267	}// end for (mol)
268
269	rc = rcGroup[0].getArrayPointer();
270	} else {
271	// center of mass of the group is the same as position of the atom
272	// if cutoff group does not exist
273	rc = pos;
274	}
275
276	//initialize data before passing to fortran
277	RealType longRangePotential[LR_POT_TYPES];
278	RealType lrPot = 0.0;
279	Vector3d totalDipole;
280	short int passedCalcPot = needPotential;
281	short int passedCalcStress = needStress;
282	int isError = 0;
283
284	for (int i=0; i<LR_POT_TYPES;i++){
285	longRangePotential[i]=0.0; //Initialize array
286	}
287
288	doForceLoop(pos,
289	rc,
290	A,
291	electroFrame,
292	frc,
293	trq,
294	tau.getArrayPointer(),
295	longRangePotential,
296	particlePot,
297	&passedCalcPot,
298	&passedCalcStress,
299	&isError );
300
301	if( isError ){
302	sprintf( painCave.errMsg,
303	"Error returned from the fortran force calculation.\n" );
304	painCave.isFatal = 1;
305	simError();
306	}
307	for (int i=0; i<LR_POT_TYPES;i++){
308	lrPot += longRangePotential[i]; //Quick hack
309	}
310
311	// grab the simulation box dipole moment if specified
312	if (info_->getCalcBoxDipole()){
313	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
314
315	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
316	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
317	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
318	}
319
320	//store the tau and long range potential
321	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
322	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
323	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
324	}
325
326
327	void ForceManager::postCalculation(bool needStress) {
328	SimInfo::MoleculeIterator mi;
329	Molecule* mol;
330	Molecule::RigidBodyIterator rbIter;
331	RigidBody* rb;
332	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
333
334	// collect the atomic forces onto rigid bodies
335
336	for (mol = info_->beginMolecule(mi); mol != NULL;
337	mol = info_->nextMolecule(mi)) {
338	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
339	rb = mol->nextRigidBody(rbIter)) {
340	if (needStress) {
341	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
342	tau += rbTau;
343	} else{
344	rb->calcForcesAndTorques();
345	}
346	}
347	}
348
349	if (needStress) {
350	#ifdef IS_MPI
351	Mat3x3d tmpTau(tau);
352	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
353	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
354	#endif
355	curSnapshot->statData.setTau(tau);
356	}
357	}
358
359	} //end namespace OpenMD