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 {
  
  ForceManager::ForceManager(SimInfo * info) : info_(info), 
                                               NBforcesInitialized_(false) {
    lj_ = LJ::Instance();
    lj_->setForceField(info_->getForceField());

    gb_ = GB::Instance();
    gb_->setForceField(info_->getForceField());

    sticky_ = Sticky::Instance();
    sticky_->setForceField(info_->getForceField());

    eam_ = EAM::Instance();
    eam_->setForceField(info_->getForceField());
  }
 
  void ForceManager::calcForces() {
    
    if (!info_->isFortranInitialized()) {
      info_->update();
    }
    
    preCalculation();
    
    calcShortRangeInteraction();

    calcLongRangeInteraction();

    postCalculation();
    
  }
  
  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() {
    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;
    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,
                &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() {
    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)) { 
        Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
        tau += rbTau;
      }
    }
    
#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:	1485
Committed:	Wed Jul 28 19:52:00 2010 UTC (14 years, 9 months ago) by gezelter
Original Path:	*branches/development/src/brains/ForceManager.cpp*
File size:	13047 byte(s)
Log Message:	Converting Sticky over to C++
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	246	*/
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	gezelter	1390	#define __OPENMD_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	1467
61	gezelter	1390	namespace OpenMD {
62	gezelter	1469
63			ForceManager::ForceManager(SimInfo * info) : info_(info),
64			NBforcesInitialized_(false) {
65	gezelter	1470	lj_ = LJ::Instance();
66			lj_->setForceField(info_->getForceField());
67	gezelter	1480
68	gezelter	1483	gb_ = GB::Instance();
69			gb_->setForceField(info_->getForceField());
70
71	gezelter	1485	sticky_ = Sticky::Instance();
72			sticky_->setForceField(info_->getForceField());
73
74	gezelter	1480	eam_ = EAM::Instance();
75			eam_->setForceField(info_->getForceField());
76	gezelter	1469	}
77
78	gezelter	1464	void ForceManager::calcForces() {
79	gezelter	1126
80	gezelter	246	if (!info_->isFortranInitialized()) {
81	gezelter	507	info_->update();
82	gezelter	246	}
83	gezelter	1126
84	gezelter	246	preCalculation();
85
86			calcShortRangeInteraction();
87
88	gezelter	1464	calcLongRangeInteraction();
89	gezelter	246
90	gezelter	1464	postCalculation();
91	tim	749
92	gezelter	507	}
93	gezelter	1126
94	gezelter	507	void ForceManager::preCalculation() {
95	gezelter	246	SimInfo::MoleculeIterator mi;
96			Molecule* mol;
97			Molecule::AtomIterator ai;
98			Atom* atom;
99			Molecule::RigidBodyIterator rbIter;
100			RigidBody* rb;
101
102			// forces are zeroed here, before any are accumulated.
103			// NOTE: do not rezero the forces in Fortran.
104	chuckv	1245
105	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
106			mol = info_->nextMolecule(mi)) {
107	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
108			atom->zeroForcesAndTorques();
109			}
110	chuckv	1245
111	gezelter	507	//change the positions of atoms which belong to the rigidbodies
112	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
113			rb = mol->nextRigidBody(rbIter)) {
114	gezelter	507	rb->zeroForcesAndTorques();
115			}
116	chuckv	1245
117	gezelter	246	}
118
119	gezelter	1126	// Zero out the stress tensor
120			tau *= 0.0;
121
122	gezelter	507	}
123	gezelter	1126
124	gezelter	507	void ForceManager::calcShortRangeInteraction() {
125	gezelter	246	Molecule* mol;
126			RigidBody* rb;
127			Bond* bond;
128			Bend* bend;
129			Torsion* torsion;
130	cli2	1275	Inversion* inversion;
131	gezelter	246	SimInfo::MoleculeIterator mi;
132			Molecule::RigidBodyIterator rbIter;
133			Molecule::BondIterator bondIter;;
134			Molecule::BendIterator bendIter;
135			Molecule::TorsionIterator torsionIter;
136	cli2	1275	Molecule::InversionIterator inversionIter;
137	tim	963	RealType bondPotential = 0.0;
138			RealType bendPotential = 0.0;
139			RealType torsionPotential = 0.0;
140	cli2	1275	RealType inversionPotential = 0.0;
141	gezelter	246
142			//calculate short range interactions
143	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
144			mol = info_->nextMolecule(mi)) {
145	gezelter	246
146	gezelter	507	//change the positions of atoms which belong to the rigidbodies
147	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
148			rb = mol->nextRigidBody(rbIter)) {
149			rb->updateAtoms();
150	gezelter	507	}
151	gezelter	246
152	gezelter	1126	for (bond = mol->beginBond(bondIter); bond != NULL;
153			bond = mol->nextBond(bondIter)) {
154	tim	749	bond->calcForce();
155			bondPotential += bond->getPotential();
156	gezelter	507	}
157	gezelter	246
158	gezelter	1126	for (bend = mol->beginBend(bendIter); bend != NULL;
159			bend = mol->nextBend(bendIter)) {
160
161			RealType angle;
162			bend->calcForce(angle);
163			RealType currBendPot = bend->getPotential();
164	gezelter	1448
165	gezelter	1126	bendPotential += bend->getPotential();
166			std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
167			if (i == bendDataSets.end()) {
168			BendDataSet dataSet;
169			dataSet.prev.angle = dataSet.curr.angle = angle;
170			dataSet.prev.potential = dataSet.curr.potential = currBendPot;
171			dataSet.deltaV = 0.0;
172			bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, 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 = currBendPot;
178			i->second.deltaV = fabs(i->second.curr.potential -
179			i->second.prev.potential);
180			}
181	gezelter	507	}
182	gezelter	1126
183			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
184			torsion = mol->nextTorsion(torsionIter)) {
185	tim	963	RealType angle;
186	gezelter	1126	torsion->calcForce(angle);
187	tim	963	RealType currTorsionPot = torsion->getPotential();
188	gezelter	1126	torsionPotential += torsion->getPotential();
189			std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
190			if (i == torsionDataSets.end()) {
191			TorsionDataSet dataSet;
192			dataSet.prev.angle = dataSet.curr.angle = angle;
193			dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
194			dataSet.deltaV = 0.0;
195			torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
196			}else {
197			i->second.prev.angle = i->second.curr.angle;
198			i->second.prev.potential = i->second.curr.potential;
199			i->second.curr.angle = angle;
200			i->second.curr.potential = currTorsionPot;
201			i->second.deltaV = fabs(i->second.curr.potential -
202			i->second.prev.potential);
203			}
204			}
205	cli2	1275
206			for (inversion = mol->beginInversion(inversionIter);
207			inversion != NULL;
208			inversion = mol->nextInversion(inversionIter)) {
209			RealType angle;
210			inversion->calcForce(angle);
211			RealType currInversionPot = inversion->getPotential();
212			inversionPotential += inversion->getPotential();
213			std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
214			if (i == inversionDataSets.end()) {
215			InversionDataSet dataSet;
216			dataSet.prev.angle = dataSet.curr.angle = angle;
217			dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
218			dataSet.deltaV = 0.0;
219			inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
220			}else {
221			i->second.prev.angle = i->second.curr.angle;
222			i->second.prev.potential = i->second.curr.potential;
223			i->second.curr.angle = angle;
224			i->second.curr.potential = currInversionPot;
225			i->second.deltaV = fabs(i->second.curr.potential -
226			i->second.prev.potential);
227			}
228			}
229	gezelter	246	}
230
231	gezelter	1126	RealType shortRangePotential = bondPotential + bendPotential +
232	cli2	1275	torsionPotential + inversionPotential;
233	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
234			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
235	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
236			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
237			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
238	cli2	1275	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
239	tim	665
240	gezelter	507	}
241	gezelter	1126
242	gezelter	1464	void ForceManager::calcLongRangeInteraction() {
243	gezelter	246	Snapshot* curSnapshot;
244			DataStorage* config;
245	tim	963	RealType* frc;
246			RealType* pos;
247			RealType* trq;
248			RealType* A;
249			RealType* electroFrame;
250			RealType* rc;
251	chuckv	1245	RealType* particlePot;
252	gezelter	246
253			//get current snapshot from SimInfo
254			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
255	gezelter	1126
256	gezelter	246	//get array pointers
257			config = &(curSnapshot->atomData);
258			frc = config->getArrayPointer(DataStorage::dslForce);
259			pos = config->getArrayPointer(DataStorage::dslPosition);
260			trq = config->getArrayPointer(DataStorage::dslTorque);
261			A = config->getArrayPointer(DataStorage::dslAmat);
262			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
263	chuckv	1245	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
264	gezelter	246
265			//calculate the center of mass of cutoff group
266			SimInfo::MoleculeIterator mi;
267			Molecule* mol;
268			Molecule::CutoffGroupIterator ci;
269			CutoffGroup* cg;
270			Vector3d com;
271			std::vector<Vector3d> rcGroup;
272	gezelter	1126
273	gezelter	246	if(info_->getNCutoffGroups() > 0){
274	gezelter	1126
275			for (mol = info_->beginMolecule(mi); mol != NULL;
276			mol = info_->nextMolecule(mi)) {
277			for(cg = mol->beginCutoffGroup(ci); cg != NULL;
278			cg = mol->nextCutoffGroup(ci)) {
279	gezelter	507	cg->getCOM(com);
280			rcGroup.push_back(com);
281	gezelter	246	}
282	gezelter	507	}// end for (mol)
283	gezelter	246
284	gezelter	507	rc = rcGroup[0].getArrayPointer();
285	gezelter	246	} else {
286	gezelter	1126	// center of mass of the group is the same as position of the atom
287			// if cutoff group does not exist
288	gezelter	507	rc = pos;
289	gezelter	246	}
290	gezelter	1126
291	gezelter	246	//initialize data before passing to fortran
292	tim	963	RealType longRangePotential[LR_POT_TYPES];
293			RealType lrPot = 0.0;
294	chrisfen	998	Vector3d totalDipole;
295	gezelter	246	int isError = 0;
296
297	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
298			longRangePotential[i]=0.0; //Initialize array
299			}
300	gezelter	1126
301	xsun	1215	doForceLoop(pos,
302			rc,
303			A,
304			electroFrame,
305			frc,
306			trq,
307			tau.getArrayPointer(),
308			longRangePotential,
309	chuckv	1245	particlePot,
310	xsun	1215	&isError );
311
312	gezelter	246	if( isError ){
313	gezelter	507	sprintf( painCave.errMsg,
314			"Error returned from the fortran force calculation.\n" );
315			painCave.isFatal = 1;
316			simError();
317	gezelter	246	}
318	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
319			lrPot += longRangePotential[i]; //Quick hack
320			}
321	gezelter	1126
322	chrisfen	998	// grab the simulation box dipole moment if specified
323			if (info_->getCalcBoxDipole()){
324			getAccumulatedBoxDipole(totalDipole.getArrayPointer());
325	gezelter	1126
326	chrisfen	998	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
327			curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
328			curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
329			}
330	gezelter	1126
331	gezelter	246	//store the tau and long range potential
332	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
333	chrisfen	691	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
334	tim	681	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
335	gezelter	507	}
336	gezelter	246
337	gezelter	1126
338	gezelter	1464	void ForceManager::postCalculation() {
339	gezelter	246	SimInfo::MoleculeIterator mi;
340			Molecule* mol;
341			Molecule::RigidBodyIterator rbIter;
342			RigidBody* rb;
343	gezelter	1126	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
344	gezelter	246
345			// collect the atomic forces onto rigid bodies
346	gezelter	1126
347			for (mol = info_->beginMolecule(mi); mol != NULL;
348			mol = info_->nextMolecule(mi)) {
349			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
350			rb = mol->nextRigidBody(rbIter)) {
351	gezelter	1464	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
352			tau += rbTau;
353	gezelter	507	}
354	gezelter	1126	}
355	gezelter	1464
356	gezelter	1126	#ifdef IS_MPI
357	gezelter	1464	Mat3x3d tmpTau(tau);
358			MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
359			9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
360	gezelter	1126	#endif
361	gezelter	1464	curSnapshot->statData.setTau(tau);
362	gezelter	507	}
363	gezelter	246
364	gezelter	1390	} //end namespace OpenMD