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() {

    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* vel;
    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);
    vel = config->getArrayPointer(DataStorage::dslVelocity);
    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,
                vel,
                rc,
                A,
                electroFrame,
                frc,
                trq,
                tau.getArrayPointer(),
                Jv_.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);
    
    curSnapshot->statData.setJv(Jv_);
  }

} //end namespace OpenMD
Revision:	1671
Committed:	Mon Jan 30 21:31:09 2012 UTC (13 years, 5 months ago) by chuckv
File size:	12432 byte(s)
Log Message:	Adding support for atomic heat flux. Is broken w/ group based cuttoffs. Units need to be corrected and their may be a sign error in Jv.
#	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	chuckv	1671	*
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	chuckv	1671
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	1390	namespace OpenMD {
61	gezelter	246
62	gezelter	1464	void ForceManager::calcForces() {
63	chuckv	1671
64	gezelter	246	if (!info_->isFortranInitialized()) {
65	gezelter	507	info_->update();
66	gezelter	246	}
67	chuckv	1671
68	gezelter	246	preCalculation();
69	chuckv	1671
70	gezelter	246	calcShortRangeInteraction();
71
72	gezelter	1464	calcLongRangeInteraction();
73	gezelter	246
74	gezelter	1464	postCalculation();
75	chuckv	1671
76	gezelter	507	}
77	chuckv	1671
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	chuckv	1671
86	gezelter	246	// forces are zeroed here, before any are accumulated.
87			// NOTE: do not rezero the forces in Fortran.
88	chuckv	1671
89			for (mol = info_->beginMolecule(mi); mol != NULL;
90	gezelter	1126	mol = info_->nextMolecule(mi)) {
91	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
92	chuckv	1671	atom->zeroForcesAndTorques();
93	gezelter	507	}
94	chuckv	1671
95	gezelter	507	//change the positions of atoms which belong to the rigidbodies
96	chuckv	1671	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
97	gezelter	1126	rb = mol->nextRigidBody(rbIter)) {
98	chuckv	1671	rb->zeroForcesAndTorques();
99			}
100
101	gezelter	246	}
102	chuckv	1671
103	gezelter	1126	// Zero out the stress tensor
104			tau *= 0.0;
105	chuckv	1671
106	gezelter	507	}
107	chuckv	1671
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	chuckv	1671	//calculate short range interactions
127			for (mol = info_->beginMolecule(mi); mol != NULL;
128	gezelter	1126	mol = info_->nextMolecule(mi)) {
129	gezelter	246
130	gezelter	507	//change the positions of atoms which belong to the rigidbodies
131	chuckv	1671	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
132	gezelter	1126	rb = mol->nextRigidBody(rbIter)) {
133			rb->updateAtoms();
134	gezelter	507	}
135	gezelter	246
136	chuckv	1671	for (bond = mol->beginBond(bondIter); bond != NULL;
137	gezelter	1126	bond = mol->nextBond(bondIter)) {
138	tim	749	bond->calcForce();
139			bondPotential += bond->getPotential();
140	gezelter	507	}
141	gezelter	246
142	chuckv	1671	for (bend = mol->beginBend(bendIter); bend != NULL;
143	gezelter	1126	bend = mol->nextBend(bendIter)) {
144	chuckv	1671
145	gezelter	1126	RealType angle;
146			bend->calcForce(angle);
147	chuckv	1671	RealType currBendPot = bend->getPotential();
148
149	gezelter	1126	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	chuckv	1671	i->second.deltaV = fabs(i->second.curr.potential -
163	gezelter	1126	i->second.prev.potential);
164			}
165	gezelter	507	}
166	chuckv	1671
167			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
168	gezelter	1126	torsion = mol->nextTorsion(torsionIter)) {
169	tim	963	RealType angle;
170	gezelter	1126	torsion->calcForce(angle);
171	tim	963	RealType currTorsionPot = torsion->getPotential();
172	gezelter	1126	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	chuckv	1671	i->second.deltaV = fabs(i->second.curr.potential -
186	gezelter	1126	i->second.prev.potential);
187	chuckv	1671	}
188			}
189	cli2	1275
190	chuckv	1671	for (inversion = mol->beginInversion(inversionIter);
191			inversion != NULL;
192	cli2	1275	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	chuckv	1671	i->second.deltaV = fabs(i->second.curr.potential -
210	cli2	1275	i->second.prev.potential);
211	chuckv	1671	}
212			}
213	gezelter	246	}
214	chuckv	1671
215			RealType shortRangePotential = bondPotential + bendPotential +
216			torsionPotential + inversionPotential;
217	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
218			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
219	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
220			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
221			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
222	cli2	1275	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
223	chuckv	1671
224	gezelter	507	}
225	chuckv	1671
226	gezelter	1464	void ForceManager::calcLongRangeInteraction() {
227	gezelter	246	Snapshot* curSnapshot;
228			DataStorage* config;
229	tim	963	RealType* frc;
230			RealType* pos;
231	chuckv	1671	RealType* vel;
232	tim	963	RealType* trq;
233			RealType* A;
234			RealType* electroFrame;
235			RealType* rc;
236	chuckv	1245	RealType* particlePot;
237	chuckv	1671
238	gezelter	246	//get current snapshot from SimInfo
239			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
240	chuckv	1671
241	gezelter	246	//get array pointers
242			config = &(curSnapshot->atomData);
243			frc = config->getArrayPointer(DataStorage::dslForce);
244			pos = config->getArrayPointer(DataStorage::dslPosition);
245	chuckv	1671	vel = config->getArrayPointer(DataStorage::dslVelocity);
246	gezelter	246	trq = config->getArrayPointer(DataStorage::dslTorque);
247			A = config->getArrayPointer(DataStorage::dslAmat);
248			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
249	chuckv	1245	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
250	gezelter	246
251			//calculate the center of mass of cutoff group
252			SimInfo::MoleculeIterator mi;
253			Molecule* mol;
254			Molecule::CutoffGroupIterator ci;
255			CutoffGroup* cg;
256			Vector3d com;
257			std::vector<Vector3d> rcGroup;
258	chuckv	1671
259	gezelter	246	if(info_->getNCutoffGroups() > 0){
260	chuckv	1671
261			for (mol = info_->beginMolecule(mi); mol != NULL;
262	gezelter	1126	mol = info_->nextMolecule(mi)) {
263	chuckv	1671	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
264	gezelter	1126	cg = mol->nextCutoffGroup(ci)) {
265	chuckv	1671	cg->getCOM(com);
266			rcGroup.push_back(com);
267	gezelter	246	}
268	gezelter	507	}// end for (mol)
269	chuckv	1671
270	gezelter	507	rc = rcGroup[0].getArrayPointer();
271	gezelter	246	} else {
272	chuckv	1671	// center of mass of the group is the same as position of the atom
273	gezelter	1126	// if cutoff group does not exist
274	gezelter	507	rc = pos;
275	gezelter	246	}
276	chuckv	1671
277	gezelter	246	//initialize data before passing to fortran
278	tim	963	RealType longRangePotential[LR_POT_TYPES];
279			RealType lrPot = 0.0;
280	chrisfen	998	Vector3d totalDipole;
281	chuckv	1671
282
283
284	gezelter	246	int isError = 0;
285
286	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
287			longRangePotential[i]=0.0; //Initialize array
288			}
289	chuckv	1671
290	xsun	1215	doForceLoop(pos,
291	chuckv	1671	vel,
292	xsun	1215	rc,
293			A,
294			electroFrame,
295			frc,
296			trq,
297	chuckv	1671	tau.getArrayPointer(),
298			Jv_.getArrayPointer(),
299			longRangePotential,
300	chuckv	1245	particlePot,
301	xsun	1215	&isError );
302	chuckv	1671
303	gezelter	246	if( isError ){
304	gezelter	507	sprintf( painCave.errMsg,
305	chuckv	1671	"Error returned from the fortran force calculation.\n" );
306	gezelter	507	painCave.isFatal = 1;
307			simError();
308	gezelter	246	}
309	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
310			lrPot += longRangePotential[i]; //Quick hack
311			}
312	chuckv	1671
313	chrisfen	998	// grab the simulation box dipole moment if specified
314			if (info_->getCalcBoxDipole()){
315			getAccumulatedBoxDipole(totalDipole.getArrayPointer());
316	chuckv	1671
317	chrisfen	998	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
318			curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
319			curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
320			}
321	chuckv	1671
322			//store the tau and long range potential
323	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
324	chrisfen	691	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
325	tim	681	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
326	gezelter	507	}
327	gezelter	246
328	chuckv	1671
329	gezelter	1464	void ForceManager::postCalculation() {
330	gezelter	246	SimInfo::MoleculeIterator mi;
331			Molecule* mol;
332			Molecule::RigidBodyIterator rbIter;
333			RigidBody* rb;
334	gezelter	1126	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
335	chuckv	1671
336	gezelter	246	// collect the atomic forces onto rigid bodies
337	chuckv	1671
338			for (mol = info_->beginMolecule(mi); mol != NULL;
339	gezelter	1126	mol = info_->nextMolecule(mi)) {
340	chuckv	1671	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
341			rb = mol->nextRigidBody(rbIter)) {
342	gezelter	1464	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
343			tau += rbTau;
344	gezelter	507	}
345	gezelter	1126	}
346	chuckv	1671
347	gezelter	1126	#ifdef IS_MPI
348	gezelter	1464	Mat3x3d tmpTau(tau);
349	chuckv	1671	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
350	gezelter	1464	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
351	gezelter	1126	#endif
352	gezelter	1464	curSnapshot->statData.setTau(tau);
353	chuckv	1671
354			curSnapshot->statData.setJv(Jv_);
355	gezelter	507	}
356	gezelter	246
357	gezelter	1390	} //end namespace OpenMD