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));
    std::cout << "bend" << std::endl;
    for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
        Bend* bend = k->bend;
        std::cout << "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;
    }
    std::cout << "torsio" << std::endl;
    for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
        Torsion* torsion = l->torsion;
        std::cout << "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;
    double bondPotential = 0.0;
    double bendPotential = 0.0;
    double 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)) {

          double angle;
            bend->calcForce(angle);
          double 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)) {
        double angle;
          torsion->calcForce(angle);
        double 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);
          }      
      }

    }
    
    double  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;
    double* frc;
    double* pos;
    double* trq;
    double* A;
    double* electroFrame;
    double* 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
    double longRangePotential[LR_POT_TYPES];
    double lrPot = 0.0;
    
    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
    }

    //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:	2469
Committed:	Fri Dec 2 15:38:03 2005 UTC (18 years, 7 months ago) by tim
File size:	12619 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	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	std::cout << "bend" << std::endl;
112	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
113	Bend* bend = k->bend;
114	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
115	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;
116	}
117	std::cout << "torsio" << std::endl;
118	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
119	Torsion* torsion = l->torsion;
120	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
121	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;
122	}
123	*/
124	}
125
126	void ForceManager::preCalculation() {
127	SimInfo::MoleculeIterator mi;
128	Molecule* mol;
129	Molecule::AtomIterator ai;
130	Atom* atom;
131	Molecule::RigidBodyIterator rbIter;
132	RigidBody* rb;
133
134	// forces are zeroed here, before any are accumulated.
135	// NOTE: do not rezero the forces in Fortran.
136	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
137	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
138	atom->zeroForcesAndTorques();
139	}
140
141	//change the positions of atoms which belong to the rigidbodies
142	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
143	rb->zeroForcesAndTorques();
144	}
145	}
146
147	}
148
149	void ForceManager::calcShortRangeInteraction() {
150	Molecule* mol;
151	RigidBody* rb;
152	Bond* bond;
153	Bend* bend;
154	Torsion* torsion;
155	SimInfo::MoleculeIterator mi;
156	Molecule::RigidBodyIterator rbIter;
157	Molecule::BondIterator bondIter;;
158	Molecule::BendIterator bendIter;
159	Molecule::TorsionIterator torsionIter;
160	double bondPotential = 0.0;
161	double bendPotential = 0.0;
162	double torsionPotential = 0.0;
163
164	//calculate short range interactions
165	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
166
167	//change the positions of atoms which belong to the rigidbodies
168	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
169	rb->updateAtoms();
170	}
171
172	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
173	bond->calcForce();
174	bondPotential += bond->getPotential();
175	}
176
177
178	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
179
180	double angle;
181	bend->calcForce(angle);
182	double currBendPot = bend->getPotential();
183	bendPotential += bend->getPotential();
184	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
185	if (i == bendDataSets.end()) {
186	BendDataSet dataSet;
187	dataSet.prev.angle = dataSet.curr.angle = angle;
188	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
189	dataSet.deltaV = 0.0;
190	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
191	}else {
192	i->second.prev.angle = i->second.curr.angle;
193	i->second.prev.potential = i->second.curr.potential;
194	i->second.curr.angle = angle;
195	i->second.curr.potential = currBendPot;
196	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
197	}
198	}
199
200	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
201	double angle;
202	torsion->calcForce(angle);
203	double currTorsionPot = torsion->getPotential();
204	torsionPotential += torsion->getPotential();
205	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
206	if (i == torsionDataSets.end()) {
207	TorsionDataSet dataSet;
208	dataSet.prev.angle = dataSet.curr.angle = angle;
209	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
210	dataSet.deltaV = 0.0;
211	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
212	}else {
213	i->second.prev.angle = i->second.curr.angle;
214	i->second.prev.potential = i->second.curr.potential;
215	i->second.curr.angle = angle;
216	i->second.curr.potential = currTorsionPot;
217	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
218	}
219	}
220
221	}
222
223	double shortRangePotential = bondPotential + bendPotential + torsionPotential;
224	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
225	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
226	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
227	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
228	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
229
230	}
231
232	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
233	Snapshot* curSnapshot;
234	DataStorage* config;
235	double* frc;
236	double* pos;
237	double* trq;
238	double* A;
239	double* electroFrame;
240	double* rc;
241
242	//get current snapshot from SimInfo
243	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
244
245	//get array pointers
246	config = &(curSnapshot->atomData);
247	frc = config->getArrayPointer(DataStorage::dslForce);
248	pos = config->getArrayPointer(DataStorage::dslPosition);
249	trq = config->getArrayPointer(DataStorage::dslTorque);
250	A = config->getArrayPointer(DataStorage::dslAmat);
251	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
252
253	//calculate the center of mass of cutoff group
254	SimInfo::MoleculeIterator mi;
255	Molecule* mol;
256	Molecule::CutoffGroupIterator ci;
257	CutoffGroup* cg;
258	Vector3d com;
259	std::vector<Vector3d> rcGroup;
260
261	if(info_->getNCutoffGroups() > 0){
262
263	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
264	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
265	cg->getCOM(com);
266	rcGroup.push_back(com);
267	}
268	}// end for (mol)
269
270	rc = rcGroup[0].getArrayPointer();
271	} else {
272	// center of mass of the group is the same as position of the atom if cutoff group does not exist
273	rc = pos;
274	}
275
276	//initialize data before passing to fortran
277	double longRangePotential[LR_POT_TYPES];
278	double lrPot = 0.0;
279
280	Mat3x3d tau;
281	short int passedCalcPot = needPotential;
282	short int passedCalcStress = needStress;
283	int isError = 0;
284
285	for (int i=0; i<LR_POT_TYPES;i++){
286	longRangePotential[i]=0.0; //Initialize array
287	}
288
289	doForceLoop( pos,
290	rc,
291	A,
292	electroFrame,
293	frc,
294	trq,
295	tau.getArrayPointer(),
296	longRangePotential,
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	//store the tau and long range potential
312	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
313	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
314	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315
316	curSnapshot->statData.setTau(tau);
317	}
318
319
320	void ForceManager::postCalculation() {
321	SimInfo::MoleculeIterator mi;
322	Molecule* mol;
323	Molecule::RigidBodyIterator rbIter;
324	RigidBody* rb;
325
326	// collect the atomic forces onto rigid bodies
327	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
328	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
329	rb->calcForcesAndTorques();
330	}
331	}
332
333	}
334
335	} //end namespace oopse