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
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	2204	/**
43			* @file ForceManager.cpp
44			* @author tlin
45			* @date 11/09/2004
46			* @time 10:39am
47			* @version 1.0
48			*/
49	gezelter	1930
50			#include "brains/ForceManager.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "UseTheForce/doForces_interface.h"
53	chuckv	2363	#define __C
54			#include "UseTheForce/DarkSide/fInteractionMap.h"
55	gezelter	1930	#include "utils/simError.h"
56	tim	2448	#include "primitives/Bend.hpp"
57			#include "primitives/Bend.hpp"
58	gezelter	1930	namespace oopse {
59
60	tim	2469	/*
61	tim	2448	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	tim	2469	*/
78	gezelter	2204	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	gezelter	1930
80			if (!info_->isFortranInitialized()) {
81	gezelter	2204	info_->update();
82	gezelter	1930	}
83
84			preCalculation();
85
86			calcShortRangeInteraction();
87
88			calcLongRangeInteraction(needPotential, needStress);
89
90			postCalculation();
91	tim	2448
92	tim	2469	/*
93	tim	2448	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	tim	2469	*/
124	gezelter	2204	}
125	gezelter	1930
126	gezelter	2204	void ForceManager::preCalculation() {
127	gezelter	1930	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	gezelter	2204	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
138			atom->zeroForcesAndTorques();
139			}
140	gezelter	1930
141	gezelter	2204	//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	gezelter	1930	}
146
147	gezelter	2204	}
148	gezelter	1930
149	gezelter	2204	void ForceManager::calcShortRangeInteraction() {
150	gezelter	1930	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	tim	2448	double bondPotential = 0.0;
161			double bendPotential = 0.0;
162			double torsionPotential = 0.0;
163	gezelter	1930
164			//calculate short range interactions
165			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
166
167	gezelter	2204	//change the positions of atoms which belong to the rigidbodies
168			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
169	tim	2448	rb->updateAtoms();
170	gezelter	2204	}
171	gezelter	1930
172	gezelter	2204	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
173	tim	2448	bond->calcForce();
174			bondPotential += bond->getPotential();
175	gezelter	2204	}
176	gezelter	1930
177	tim	2469
178	gezelter	2204	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
179	tim	2469
180	tim	2448	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	gezelter	2204	}
199	gezelter	1930
200	gezelter	2204	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
201	tim	2448	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	gezelter	2204	}
220	gezelter	1930
221			}
222
223	tim	2364	double shortRangePotential = bondPotential + bendPotential + torsionPotential;
224	gezelter	1930	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
225			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
226	tim	2364	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
227			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
228			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
229
230	gezelter	2204	}
231	gezelter	1930
232	gezelter	2204	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
233	gezelter	1930	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	chrisfen	2344
261	gezelter	1930	if(info_->getNCutoffGroups() > 0){
262	chrisfen	2344
263	gezelter	2204	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
264	gezelter	1930	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
265	gezelter	2204	cg->getCOM(com);
266			rcGroup.push_back(com);
267	gezelter	1930	}
268	gezelter	2204	}// end for (mol)
269	gezelter	1930
270	gezelter	2204	rc = rcGroup[0].getArrayPointer();
271	gezelter	1930	} else {
272	gezelter	2204	// center of mass of the group is the same as position of the atom if cutoff group does not exist
273			rc = pos;
274	gezelter	1930	}
275
276			//initialize data before passing to fortran
277	chuckv	2363	double longRangePotential[LR_POT_TYPES];
278			double lrPot = 0.0;
279
280	gezelter	1930	Mat3x3d tau;
281			short int passedCalcPot = needPotential;
282			short int passedCalcStress = needStress;
283			int isError = 0;
284
285	chuckv	2363	for (int i=0; i<LR_POT_TYPES;i++){
286			longRangePotential[i]=0.0; //Initialize array
287			}
288
289	gezelter	1930	doForceLoop( pos,
290	gezelter	2204	rc,
291			A,
292			electroFrame,
293			frc,
294			trq,
295			tau.getArrayPointer(),
296	chuckv	2363	longRangePotential,
297	gezelter	2204	&passedCalcPot,
298			&passedCalcStress,
299			&isError );
300	gezelter	1930
301			if( isError ){
302	gezelter	2204	sprintf( painCave.errMsg,
303			"Error returned from the fortran force calculation.\n" );
304			painCave.isFatal = 1;
305			simError();
306	gezelter	1930	}
307	chuckv	2363	for (int i=0; i<LR_POT_TYPES;i++){
308			lrPot += longRangePotential[i]; //Quick hack
309			}
310	gezelter	1930
311			//store the tau and long range potential
312	chuckv	2363	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
313	chrisfen	2390	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
314	tim	2380	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315
316	gezelter	1930	curSnapshot->statData.setTau(tau);
317	gezelter	2204	}
318	gezelter	1930
319
320	gezelter	2204	void ForceManager::postCalculation() {
321	gezelter	1930	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	gezelter	2204	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
329			rb->calcForcesAndTorques();
330			}
331	gezelter	1930	}
332
333	gezelter	2204	}
334	gezelter	1930
335			} //end namespace oopse