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 __C
#include "UseTheForce/DarkSide/fInteractionMap.h"
#include "utils/simError.h"
#include "primitives/Bend.hpp"
#include "primitives/Bend.hpp"
namespace oopse {

/*
  struct BendOrderStruct {
    Bend* bend;
    BendDataSet dataSet;
  };
  struct TorsionOrderStruct {
    Torsion* torsion;
    TorsionDataSet dataSet;
  };

  bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
    return b1.dataSet.deltaV < b2.dataSet.deltaV;
  }

  bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
    return t1.dataSet.deltaV < t2.dataSet.deltaV;
  }
  */
  void ForceManager::calcForces(bool needPotential, bool needStress) {

    if (!info_->isFortranInitialized()) {
      info_->update();
    }

    preCalculation();
    
    calcShortRangeInteraction();

    calcLongRangeInteraction(needPotential, needStress);

    postCalculation();

/*
    std::vector<BendOrderStruct> bendOrderStruct;
    for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
        BendOrderStruct tmp;
        tmp.bend= const_cast<Bend*>(i->first);
        tmp.dataSet = i->second;
        bendOrderStruct.push_back(tmp);
    }

    std::vector<TorsionOrderStruct> torsionOrderStruct;
    for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
        TorsionOrderStruct tmp;
        tmp.torsion = const_cast<Torsion*>(j->first);
        tmp.dataSet = j->second;
        torsionOrderStruct.push_back(tmp);
    }
    
    std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
    std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
    for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
        Bend* bend = k->bend;
        std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
        std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
    }
    for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
        Torsion* torsion = l->torsion;
        std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
        std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
    }
   */ 
  }

  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();
      }        
    }
    
  }

  void ForceManager::calcShortRangeInteraction() {
    Molecule* mol;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;;
    Molecule::BendIterator  bendIter;
    Molecule::TorsionIterator  torsionIter;
    RealType bondPotential = 0.0;
    RealType bendPotential = 0.0;
    RealType torsionPotential = 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);
          }      
      }

    }
    
    RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;    
    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;
    
  }

  void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
    Snapshot* curSnapshot;
    DataStorage* config;
    RealType* frc;
    RealType* pos;
    RealType* trq;
    RealType* A;
    RealType* electroFrame;
    RealType* rc;
    
    //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);

    //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;
    Mat3x3d tau;
    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, 
                 &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];

    curSnapshot->statData.setTau(tau);
  }


  void ForceManager::postCalculation() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    
    // 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)) {
        rb->calcForcesAndTorques();
      }
    }    

  }

} //end namespace oopse
Revision:	998
Committed:	Mon Jul 3 13:18:43 2006 UTC (18 years, 10 months ago) by chrisfen
File size:	12978 byte(s)
Log Message:	Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
#	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 __C
54	#include "UseTheForce/DarkSide/fInteractionMap.h"
55	#include "utils/simError.h"
56	#include "primitives/Bend.hpp"
57	#include "primitives/Bend.hpp"
58	namespace oopse {
59
60	/*
61	struct BendOrderStruct {
62	Bend* bend;
63	BendDataSet dataSet;
64	};
65	struct TorsionOrderStruct {
66	Torsion* torsion;
67	TorsionDataSet dataSet;
68	};
69
70	bool BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
71	return b1.dataSet.deltaV < b2.dataSet.deltaV;
72	}
73
74	bool TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
75	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	}
77	*/
78	void ForceManager::calcForces(bool needPotential, bool needStress) {
79
80	if (!info_->isFortranInitialized()) {
81	info_->update();
82	}
83
84	preCalculation();
85
86	calcShortRangeInteraction();
87
88	calcLongRangeInteraction(needPotential, needStress);
89
90	postCalculation();
91
92	/*
93	std::vector<BendOrderStruct> bendOrderStruct;
94	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
95	BendOrderStruct tmp;
96	tmp.bend= const_cast<Bend*>(i->first);
97	tmp.dataSet = i->second;
98	bendOrderStruct.push_back(tmp);
99	}
100
101	std::vector<TorsionOrderStruct> torsionOrderStruct;
102	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
103	TorsionOrderStruct tmp;
104	tmp.torsion = const_cast<Torsion*>(j->first);
105	tmp.dataSet = j->second;
106	torsionOrderStruct.push_back(tmp);
107	}
108
109	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
112	Bend* bend = k->bend;
113	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
114	std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
115	}
116	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
117	Torsion* torsion = l->torsion;
118	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
119	std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
120	}
121	*/
122	}
123
124	void ForceManager::preCalculation() {
125	SimInfo::MoleculeIterator mi;
126	Molecule* mol;
127	Molecule::AtomIterator ai;
128	Atom* atom;
129	Molecule::RigidBodyIterator rbIter;
130	RigidBody* rb;
131
132	// forces are zeroed here, before any are accumulated.
133	// NOTE: do not rezero the forces in Fortran.
134	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
135	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
136	atom->zeroForcesAndTorques();
137	}
138
139	//change the positions of atoms which belong to the rigidbodies
140	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
141	rb->zeroForcesAndTorques();
142	}
143	}
144
145	}
146
147	void ForceManager::calcShortRangeInteraction() {
148	Molecule* mol;
149	RigidBody* rb;
150	Bond* bond;
151	Bend* bend;
152	Torsion* torsion;
153	SimInfo::MoleculeIterator mi;
154	Molecule::RigidBodyIterator rbIter;
155	Molecule::BondIterator bondIter;;
156	Molecule::BendIterator bendIter;
157	Molecule::TorsionIterator torsionIter;
158	RealType bondPotential = 0.0;
159	RealType bendPotential = 0.0;
160	RealType torsionPotential = 0.0;
161
162	//calculate short range interactions
163	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
164
165	//change the positions of atoms which belong to the rigidbodies
166	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
167	rb->updateAtoms();
168	}
169
170	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
171	bond->calcForce();
172	bondPotential += bond->getPotential();
173	}
174
175
176	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
177
178	RealType angle;
179	bend->calcForce(angle);
180	RealType currBendPot = bend->getPotential();
181	bendPotential += bend->getPotential();
182	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
183	if (i == bendDataSets.end()) {
184	BendDataSet dataSet;
185	dataSet.prev.angle = dataSet.curr.angle = angle;
186	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
187	dataSet.deltaV = 0.0;
188	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
189	}else {
190	i->second.prev.angle = i->second.curr.angle;
191	i->second.prev.potential = i->second.curr.potential;
192	i->second.curr.angle = angle;
193	i->second.curr.potential = currBendPot;
194	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
195	}
196	}
197
198	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
199	RealType angle;
200	torsion->calcForce(angle);
201	RealType currTorsionPot = torsion->getPotential();
202	torsionPotential += torsion->getPotential();
203	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
204	if (i == torsionDataSets.end()) {
205	TorsionDataSet dataSet;
206	dataSet.prev.angle = dataSet.curr.angle = angle;
207	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
208	dataSet.deltaV = 0.0;
209	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
210	}else {
211	i->second.prev.angle = i->second.curr.angle;
212	i->second.prev.potential = i->second.curr.potential;
213	i->second.curr.angle = angle;
214	i->second.curr.potential = currTorsionPot;
215	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
216	}
217	}
218
219	}
220
221	RealType shortRangePotential = bondPotential + bendPotential + torsionPotential;
222	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
223	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
224	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
225	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
226	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
227
228	}
229
230	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
231	Snapshot* curSnapshot;
232	DataStorage* config;
233	RealType* frc;
234	RealType* pos;
235	RealType* trq;
236	RealType* A;
237	RealType* electroFrame;
238	RealType* rc;
239
240	//get current snapshot from SimInfo
241	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
242
243	//get array pointers
244	config = &(curSnapshot->atomData);
245	frc = config->getArrayPointer(DataStorage::dslForce);
246	pos = config->getArrayPointer(DataStorage::dslPosition);
247	trq = config->getArrayPointer(DataStorage::dslTorque);
248	A = config->getArrayPointer(DataStorage::dslAmat);
249	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
250
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
259	if(info_->getNCutoffGroups() > 0){
260
261	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
262	for(cg = mol->beginCutoffGroup(ci); cg != NULL; 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 if cutoff group does not exist
271	rc = pos;
272	}
273
274	//initialize data before passing to fortran
275	RealType longRangePotential[LR_POT_TYPES];
276	RealType lrPot = 0.0;
277	Vector3d totalDipole;
278	Mat3x3d tau;
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	&passedCalcPot,
296	&passedCalcStress,
297	&isError );
298
299	if( isError ){
300	sprintf( painCave.errMsg,
301	"Error returned from the fortran force calculation.\n" );
302	painCave.isFatal = 1;
303	simError();
304	}
305	for (int i=0; i<LR_POT_TYPES;i++){
306	lrPot += longRangePotential[i]; //Quick hack
307	}
308
309	// grab the simulation box dipole moment if specified
310	if (info_->getCalcBoxDipole()){
311	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
312
313	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
314	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
315	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
316	}
317
318	//store the tau and long range potential
319	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
320	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
321	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
322
323	curSnapshot->statData.setTau(tau);
324	}
325
326
327	void ForceManager::postCalculation() {
328	SimInfo::MoleculeIterator mi;
329	Molecule* mol;
330	Molecule::RigidBodyIterator rbIter;
331	RigidBody* rb;
332
333	// collect the atomic forces onto rigid bodies
334	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
335	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
336	rb->calcForcesAndTorques();
337	}
338	}
339
340	}
341
342	} //end namespace oopse