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();
      }

      //int i =0;
      for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
          //std::cout << i++ << "\t";
          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:	749
Committed:	Wed Nov 16 23:10:02 2005 UTC (19 years, 11 months ago) by tim
File size:	12663 byte(s)
Log Message:	OptionSectionParser get compiled
#	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			* 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	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	chuckv	664	#define __C
54			#include "UseTheForce/DarkSide/fInteractionMap.h"
55	gezelter	246	#include "utils/simError.h"
56	tim	749	#include "primitives/Bend.hpp"
57			#include "primitives/Bend.hpp"
58	gezelter	246	namespace oopse {
59
60	tim	749	struct BendOrderStruct {
61			Bend* bend;
62			BendDataSet dataSet;
63			};
64			struct TorsionOrderStruct {
65			Torsion* torsion;
66			TorsionDataSet dataSet;
67			};
68
69			bool BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
70			return b1.dataSet.deltaV < b2.dataSet.deltaV;
71			}
72
73			bool TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
74			return t1.dataSet.deltaV < t2.dataSet.deltaV;
75			}
76
77	gezelter	507	void ForceManager::calcForces(bool needPotential, bool needStress) {
78	gezelter	246
79			if (!info_->isFortranInitialized()) {
80	gezelter	507	info_->update();
81	gezelter	246	}
82
83			preCalculation();
84
85			calcShortRangeInteraction();
86
87			calcLongRangeInteraction(needPotential, needStress);
88
89			postCalculation();
90	tim	749
91			std::vector<BendOrderStruct> bendOrderStruct;
92			for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
93			BendOrderStruct tmp;
94			tmp.bend= const_cast<Bend*>(i->first);
95			tmp.dataSet = i->second;
96			bendOrderStruct.push_back(tmp);
97			}
98
99			std::vector<TorsionOrderStruct> torsionOrderStruct;
100			for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
101			TorsionOrderStruct tmp;
102			tmp.torsion = const_cast<Torsion*>(j->first);
103			tmp.dataSet = j->second;
104			torsionOrderStruct.push_back(tmp);
105			}
106
107			std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
108			std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
109			std::cout << "bend" << std::endl;
110			for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
111			Bend* bend = k->bend;
112			std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
113			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;
114			}
115			std::cout << "torsio" << std::endl;
116			for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
117			Torsion* torsion = l->torsion;
118			std::cout << "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	gezelter	507	}
123	gezelter	246
124	gezelter	507	void ForceManager::preCalculation() {
125	gezelter	246	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	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
136			atom->zeroForcesAndTorques();
137			}
138	gezelter	246
139	gezelter	507	//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	gezelter	246	}
144
145	gezelter	507	}
146	gezelter	246
147	gezelter	507	void ForceManager::calcShortRangeInteraction() {
148	gezelter	246	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	tim	749	double bondPotential = 0.0;
159			double bendPotential = 0.0;
160			double torsionPotential = 0.0;
161	gezelter	246
162			//calculate short range interactions
163			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
164
165	gezelter	507	//change the positions of atoms which belong to the rigidbodies
166			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
167	tim	749	rb->updateAtoms();
168	gezelter	507	}
169	gezelter	246
170	gezelter	507	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
171	tim	749	bond->calcForce();
172			bondPotential += bond->getPotential();
173	gezelter	507	}
174	gezelter	246
175	tim	749	//int i =0;
176	gezelter	507	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
177	tim	749	//std::cout << i++ << "\t";
178			double angle;
179			bend->calcForce(angle);
180			double 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	gezelter	507	}
197	gezelter	246
198	gezelter	507	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
199	tim	749	double angle;
200			torsion->calcForce(angle);
201			double 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	gezelter	507	}
218	gezelter	246
219			}
220
221	tim	665	double shortRangePotential = bondPotential + bendPotential + torsionPotential;
222	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
223			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
224	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
225			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
226			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
227
228	gezelter	507	}
229	gezelter	246
230	gezelter	507	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
231	gezelter	246	Snapshot* curSnapshot;
232			DataStorage* config;
233			double* frc;
234			double* pos;
235			double* trq;
236			double* A;
237			double* electroFrame;
238			double* 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	chrisfen	645
259	gezelter	246	if(info_->getNCutoffGroups() > 0){
260	chrisfen	645
261	gezelter	507	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
262	gezelter	246	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
263	gezelter	507	cg->getCOM(com);
264			rcGroup.push_back(com);
265	gezelter	246	}
266	gezelter	507	}// end for (mol)
267	gezelter	246
268	gezelter	507	rc = rcGroup[0].getArrayPointer();
269	gezelter	246	} else {
270	gezelter	507	// center of mass of the group is the same as position of the atom if cutoff group does not exist
271			rc = pos;
272	gezelter	246	}
273
274			//initialize data before passing to fortran
275	chuckv	664	double longRangePotential[LR_POT_TYPES];
276			double lrPot = 0.0;
277
278	gezelter	246	Mat3x3d tau;
279			short int passedCalcPot = needPotential;
280			short int passedCalcStress = needStress;
281			int isError = 0;
282
283	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
284			longRangePotential[i]=0.0; //Initialize array
285			}
286
287	gezelter	246	doForceLoop( pos,
288	gezelter	507	rc,
289			A,
290			electroFrame,
291			frc,
292			trq,
293			tau.getArrayPointer(),
294	chuckv	664	longRangePotential,
295	gezelter	507	&passedCalcPot,
296			&passedCalcStress,
297			&isError );
298	gezelter	246
299			if( isError ){
300	gezelter	507	sprintf( painCave.errMsg,
301			"Error returned from the fortran force calculation.\n" );
302			painCave.isFatal = 1;
303			simError();
304	gezelter	246	}
305	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
306			lrPot += longRangePotential[i]; //Quick hack
307			}
308	gezelter	246
309			//store the tau and long range potential
310	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
311	chrisfen	691	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
312	tim	681	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313
314	gezelter	246	curSnapshot->statData.setTau(tau);
315	gezelter	507	}
316	gezelter	246
317
318	gezelter	507	void ForceManager::postCalculation() {
319	gezelter	246	SimInfo::MoleculeIterator mi;
320			Molecule* mol;
321			Molecule::RigidBodyIterator rbIter;
322			RigidBody* rb;
323
324			// collect the atomic forces onto rigid bodies
325			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
326	gezelter	507	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
327			rb->calcForcesAndTorques();
328			}
329	gezelter	246	}
330
331	gezelter	507	}
332	gezelter	246
333			} //end namespace oopse