src/brains/ForceManager.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @file ForceManager.cpp
 * @author tlin
 * @date 11/09/2004
 * @time 10:39am
 * @version 1.0
 */

#include "brains/ForceManager.hpp"
#include "primitives/Molecule.hpp"
#define __OPENMD_C
#include "utils/simError.h"
#include "primitives/Bond.hpp"
#include "primitives/Bend.hpp"
#include "primitives/Torsion.hpp"
#include "primitives/Inversion.hpp"
#include "nonbonded/NonBondedInteraction.hpp"
#include "parallel/ForceMatrixDecomposition.hpp"

using namespace std;
namespace OpenMD {
  
  ForceManager::ForceManager(SimInfo * info) : info_(info) {

    fDecomp_ = new ForceMatrixDecomposition(info_);
  }
  
  void ForceManager::calcForces() {
    
    if (!info_->isTopologyDone()) {
      info_->update();
      interactionMan_->setSimInfo(info_);
      interactionMan_->initialize();
      swfun_ = interactionMan_->getSwitchingFunction();
      info_->prepareTopology();
      fDecomp_->distributeInitialData();
    }
    
    preCalculation();   
    shortRangeInteractions();
    longRangeInteractions();
    postCalculation();
    
  }
  
  void ForceManager::preCalculation() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;
    
    // forces are zeroed here, before any are accumulated.
    
    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();
      }        

      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
        for(cg = mol->beginCutoffGroup(ci); cg != NULL; 
            cg = mol->nextCutoffGroup(ci)) {
          //calculate the center of mass of cutoff group
          cg->updateCOM();
        }
      }      
    }
   
    // Zero out the stress tensor
    tau *= 0.0;
    
  }
  
  void ForceManager::shortRangeInteractions() {
    Molecule* mol;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;;
    Molecule::BendIterator  bendIter;
    Molecule::TorsionIterator  torsionIter;
    Molecule::InversionIterator  inversionIter;
    RealType bondPotential = 0.0;
    RealType bendPotential = 0.0;
    RealType torsionPotential = 0.0;
    RealType inversionPotential = 0.0;

    //calculate short range interactions    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {

      //change the positions of atoms which belong to the rigidbodies
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        rb->updateAtoms();
      }

      for (bond = mol->beginBond(bondIter); bond != NULL; 
           bond = mol->nextBond(bondIter)) {
        bond->calcForce();
        bondPotential += bond->getPotential();
      }

      for (bend = mol->beginBend(bendIter); bend != NULL; 
           bend = mol->nextBend(bendIter)) {
        
        RealType angle;
        bend->calcForce(angle);
        RealType currBendPot = bend->getPotential();          
         
        bendPotential += bend->getPotential();
        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(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();
        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(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
        }else {
          i->second.prev.angle = i->second.curr.angle;
          i->second.prev.potential = i->second.curr.potential;
          i->second.curr.angle = angle;
          i->second.curr.potential = currTorsionPot;
          i->second.deltaV =  fabs(i->second.curr.potential -  
                                   i->second.prev.potential);
        }      
      }      
      
      for (inversion = mol->beginInversion(inversionIter); 
           inversion != NULL; 
           inversion = mol->nextInversion(inversionIter)) {
        RealType angle;
        inversion->calcForce(angle);
        RealType currInversionPot = inversion->getPotential();
        inversionPotential += inversion->getPotential();
        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
        if (i == inversionDataSets.end()) {
          InversionDataSet dataSet;
          dataSet.prev.angle = dataSet.curr.angle = angle;
          dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
          dataSet.deltaV = 0.0;
          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
        }else {
          i->second.prev.angle = i->second.curr.angle;
          i->second.prev.potential = i->second.curr.potential;
          i->second.curr.angle = angle;
          i->second.curr.potential = currInversionPot;
          i->second.deltaV =  fabs(i->second.curr.potential -  
                                   i->second.prev.potential);
        }      
      }      
    }
    
    RealType  shortRangePotential = bondPotential + bendPotential + 
      torsionPotential +  inversionPotential;    
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
  }
  
  void ForceManager::longRangeInteractions() {

    // some of this initial stuff will go away:
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    DataStorage* config = &(curSnapshot->atomData);
    DataStorage* cgConfig = &(curSnapshot->cgData);
    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
    RealType* rc;    

    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
    } 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[N_INTERACTION_FAMILIES];
    RealType lrPot = 0.0;
    int isError = 0;

    // dangerous to iterate over enums, but we'll live on the edge:
    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
      longRangePotential[i]=0.0; //Initialize array
    }

    // new stuff starts here:

    fDecomp_->distributeData();
 
    int cg1, cg2, atom1, atom2;
    Vector3d d_grp, dag;
    RealType rgrpsq, rgrp;
    RealType vij;
    Vector3d fij, fg;
    pair<int, int> gtypes;
    RealType rCutSq;
    bool in_switching_region;
    RealType sw, dswdr, swderiv;
    vector<int> atomListColumn, atomListRow, atomListLocal;
    InteractionData idat;
    SelfData sdat;
    RealType mf;

    int loopStart, loopEnd;

    loopEnd = PAIR_LOOP;
    if (info_->requiresPrepair() ) {
      loopStart = PREPAIR_LOOP;
    } else {
      loopStart = PAIR_LOOP;
    }

    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
      
      if (iLoop == loopStart) {
        bool update_nlist = fDecomp_->checkNeighborList();
        if (update_nlist) 
          neighborList = fDecomp_->buildNeighborList();
      }

      for (vector<pair<int, int> >::iterator it = neighborList.begin(); 
             it != neighborList.end(); ++it) {
        
        cg1 = (*it).first;
        cg2 = (*it).second;

        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
        curSnapshot->wrapVector(d_grp);        
        rgrpsq = d_grp.lengthSquare();
        rCutSq = groupCutoffMap[gtypes].first;

        if (rgrpsq < rCutSq) {
          *(idat.rcut) = groupCutoffMap[gtypes].second;
          if (iLoop == PAIR_LOOP) {
            vij *= 0.0;
            fij = V3Zero;
          }
          
          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr, 
                                                  rgrp);               
          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);

          for (vector<int>::iterator ia = atomListRow.begin(); 
               ia != atomListRow.end(); ++ia) {            
            atom1 = (*ia);
            
            for (vector<int>::iterator jb = atomListColumn.begin(); 
                 jb != atomListColumn.end(); ++jb) {              
              atom2 = (*jb);
              
              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
                
                idat = fDecomp_->fillInteractionData(atom1, atom2);

                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
                  *(idat.d) = d_grp;
                  *(idat.r2) = rgrpsq;
                } else {
                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
                  curSnapshot->wrapVector( *(idat.d) );
                  *(idat.r2) = idat.d->lengthSquare();
                }
                
                *(idat.rij) = sqrt( *(idat.r2) );
               
                if (iLoop == PREPAIR_LOOP) {
                  interactionMan_->doPrePair(idat);
                } else {
                  interactionMan_->doPair(idat);
                  vij += *(idat.vpair);
                  fij += *(idat.f1);
                  tau -= outProduct( *(idat.d), *(idat.f1));
                }
              }
            }
          }

          if (iLoop == PAIR_LOOP) {
            if (in_switching_region) {
              swderiv = vij * dswdr / rgrp;
              fg = swderiv * d_grp;

              fij += fg;

              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
                tau -= outProduct( *(idat.d), fg);
              }
          
              for (vector<int>::iterator ia = atomListRow.begin(); 
                   ia != atomListRow.end(); ++ia) {            
                atom1 = (*ia);                
                mf = fDecomp_->getMassFactorRow(atom1);
                // fg is the force on atom ia due to cutoff group's
                // presence in switching region
                fg = swderiv * d_grp * mf;
                fDecomp_->addForceToAtomRow(atom1, fg);

                if (atomListRow.size() > 1) {
                  if (info_->usesAtomicVirial()) {
                    // find the distance between the atom
                    // and the center of the cutoff group:
                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
                    tau -= outProduct(dag, fg);
                  }
                }
              }
              for (vector<int>::iterator jb = atomListColumn.begin(); 
                   jb != atomListColumn.end(); ++jb) {              
                atom2 = (*jb);
                mf = fDecomp_->getMassFactorColumn(atom2);
                // fg is the force on atom jb due to cutoff group's
                // presence in switching region
                fg = -swderiv * d_grp * mf;
                fDecomp_->addForceToAtomColumn(atom2, fg);

                if (atomListColumn.size() > 1) {
                  if (info_->usesAtomicVirial()) {
                    // find the distance between the atom
                    // and the center of the cutoff group:
                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
                    tau -= outProduct(dag, fg);
                  }
                }
              }
            }
            //if (!SIM_uses_AtomicVirial) {
            //  tau -= outProduct(d_grp, fij);
            //}
          }
        }
      }

      if (iLoop == PREPAIR_LOOP) {
        if (info_->requiresPrepair()) {            
          fDecomp_->collectIntermediateData();

          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
            sdat = fDecomp_->fillSelfData(atom1);
            interactionMan_->doPreForce(sdat);
          }

          fDecomp_->distributeIntermediateData();        
        }
      }

    }
    
    fDecomp_->collectData();
    
    if ( info_->requiresSkipCorrection() ) {
      
      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {

        vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
        
        for (vector<int>::iterator jb = skipList.begin(); 
             jb != skipList.end(); ++jb) {         
     
          atom2 = (*jb);
          idat = fDecomp_->fillSkipData(atom1, atom2);
          interactionMan_->doSkipCorrection(idat);

        }
      }
    }
    
    if (info_->requiresSelfCorrection()) {

      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
        sdat = fDecomp_->fillSelfData(atom1);
        interactionMan_->doSelfCorrection(sdat);
      }

    }

    // dangerous to iterate over enums, but we'll live on the edge:
    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++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[VANDERWAALS_FAMILY];
    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
  }

  
  void ForceManager::postCalculation() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    
    // collect the atomic forces onto rigid bodies
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) { 
        Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
        tau += rbTau;
      }
    }
    
#ifdef IS_MPI
    Mat3x3d tmpTau(tau);
    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), 
                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#endif
    curSnapshot->statData.setTau(tau);
  }

} //end namespace OpenMD
Revision:	1571
Committed:	Fri May 27 16:45:44 2011 UTC (13 years, 11 months ago) by gezelter
File size:	18402 byte(s)
Log Message:	Added Atypes to new C++ force decomposition.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
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	gezelter	1390	#define __OPENMD_C
53	gezelter	246	#include "utils/simError.h"
54	xsun	1215	#include "primitives/Bond.hpp"
55	tim	749	#include "primitives/Bend.hpp"
56	cli2	1275	#include "primitives/Torsion.hpp"
57			#include "primitives/Inversion.hpp"
58	gezelter	1551	#include "nonbonded/NonBondedInteraction.hpp"
59	gezelter	1549	#include "parallel/ForceMatrixDecomposition.hpp"
60	gezelter	1467
61	gezelter	1545	using namespace std;
62	gezelter	1390	namespace OpenMD {
63	gezelter	1469
64	gezelter	1545	ForceManager::ForceManager(SimInfo * info) : info_(info) {
65
66	gezelter	1549	fDecomp_ = new ForceMatrixDecomposition(info_);
67	gezelter	1469	}
68	gezelter	1545
69	gezelter	1464	void ForceManager::calcForces() {
70	gezelter	1126
71	gezelter	1569	if (!info_->isTopologyDone()) {
72	gezelter	507	info_->update();
73	gezelter	1546	interactionMan_->setSimInfo(info_);
74			interactionMan_->initialize();
75			swfun_ = interactionMan_->getSwitchingFunction();
76	gezelter	1571	info_->prepareTopology();
77	gezelter	1549	fDecomp_->distributeInitialData();
78	gezelter	246	}
79	gezelter	1126
80	gezelter	1544	preCalculation();
81	gezelter	1546	shortRangeInteractions();
82			longRangeInteractions();
83	gezelter	1464	postCalculation();
84	tim	749
85	gezelter	507	}
86	gezelter	1126
87	gezelter	507	void ForceManager::preCalculation() {
88	gezelter	246	SimInfo::MoleculeIterator mi;
89			Molecule* mol;
90			Molecule::AtomIterator ai;
91			Atom* atom;
92			Molecule::RigidBodyIterator rbIter;
93			RigidBody* rb;
94	gezelter	1540	Molecule::CutoffGroupIterator ci;
95			CutoffGroup* cg;
96	gezelter	246
97			// forces are zeroed here, before any are accumulated.
98	chuckv	1245
99	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
100			mol = info_->nextMolecule(mi)) {
101	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
102			atom->zeroForcesAndTorques();
103			}
104	chuckv	1245
105	gezelter	507	//change the positions of atoms which belong to the rigidbodies
106	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
107			rb = mol->nextRigidBody(rbIter)) {
108	gezelter	507	rb->zeroForcesAndTorques();
109			}
110	gezelter	1540
111			if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
112			for(cg = mol->beginCutoffGroup(ci); cg != NULL;
113			cg = mol->nextCutoffGroup(ci)) {
114			//calculate the center of mass of cutoff group
115			cg->updateCOM();
116			}
117			}
118	gezelter	246	}
119	gezelter	1540
120	gezelter	1126	// Zero out the stress tensor
121			tau *= 0.0;
122
123	gezelter	507	}
124	gezelter	1126
125	gezelter	1546	void ForceManager::shortRangeInteractions() {
126	gezelter	246	Molecule* mol;
127			RigidBody* rb;
128			Bond* bond;
129			Bend* bend;
130			Torsion* torsion;
131	cli2	1275	Inversion* inversion;
132	gezelter	246	SimInfo::MoleculeIterator mi;
133			Molecule::RigidBodyIterator rbIter;
134			Molecule::BondIterator bondIter;;
135			Molecule::BendIterator bendIter;
136			Molecule::TorsionIterator torsionIter;
137	cli2	1275	Molecule::InversionIterator inversionIter;
138	tim	963	RealType bondPotential = 0.0;
139			RealType bendPotential = 0.0;
140			RealType torsionPotential = 0.0;
141	cli2	1275	RealType inversionPotential = 0.0;
142	gezelter	246
143			//calculate short range interactions
144	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
145			mol = info_->nextMolecule(mi)) {
146	gezelter	246
147	gezelter	507	//change the positions of atoms which belong to the rigidbodies
148	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
149			rb = mol->nextRigidBody(rbIter)) {
150			rb->updateAtoms();
151	gezelter	507	}
152	gezelter	246
153	gezelter	1126	for (bond = mol->beginBond(bondIter); bond != NULL;
154			bond = mol->nextBond(bondIter)) {
155	tim	749	bond->calcForce();
156			bondPotential += bond->getPotential();
157	gezelter	507	}
158	gezelter	246
159	gezelter	1126	for (bend = mol->beginBend(bendIter); bend != NULL;
160			bend = mol->nextBend(bendIter)) {
161
162			RealType angle;
163			bend->calcForce(angle);
164			RealType currBendPot = bend->getPotential();
165	gezelter	1448
166	gezelter	1126	bendPotential += bend->getPotential();
167	gezelter	1545	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
168	gezelter	1126	if (i == bendDataSets.end()) {
169			BendDataSet dataSet;
170			dataSet.prev.angle = dataSet.curr.angle = angle;
171			dataSet.prev.potential = dataSet.curr.potential = currBendPot;
172			dataSet.deltaV = 0.0;
173	gezelter	1545	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
174	gezelter	1126	}else {
175			i->second.prev.angle = i->second.curr.angle;
176			i->second.prev.potential = i->second.curr.potential;
177			i->second.curr.angle = angle;
178			i->second.curr.potential = currBendPot;
179			i->second.deltaV = fabs(i->second.curr.potential -
180			i->second.prev.potential);
181			}
182	gezelter	507	}
183	gezelter	1126
184			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
185			torsion = mol->nextTorsion(torsionIter)) {
186	tim	963	RealType angle;
187	gezelter	1126	torsion->calcForce(angle);
188	tim	963	RealType currTorsionPot = torsion->getPotential();
189	gezelter	1126	torsionPotential += torsion->getPotential();
190	gezelter	1545	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
191	gezelter	1126	if (i == torsionDataSets.end()) {
192			TorsionDataSet dataSet;
193			dataSet.prev.angle = dataSet.curr.angle = angle;
194			dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
195			dataSet.deltaV = 0.0;
196	gezelter	1545	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
197	gezelter	1126	}else {
198			i->second.prev.angle = i->second.curr.angle;
199			i->second.prev.potential = i->second.curr.potential;
200			i->second.curr.angle = angle;
201			i->second.curr.potential = currTorsionPot;
202			i->second.deltaV = fabs(i->second.curr.potential -
203			i->second.prev.potential);
204			}
205			}
206	gezelter	1545
207	cli2	1275	for (inversion = mol->beginInversion(inversionIter);
208			inversion != NULL;
209			inversion = mol->nextInversion(inversionIter)) {
210			RealType angle;
211			inversion->calcForce(angle);
212			RealType currInversionPot = inversion->getPotential();
213			inversionPotential += inversion->getPotential();
214	gezelter	1545	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
215	cli2	1275	if (i == inversionDataSets.end()) {
216			InversionDataSet dataSet;
217			dataSet.prev.angle = dataSet.curr.angle = angle;
218			dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
219			dataSet.deltaV = 0.0;
220	gezelter	1545	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
221	cli2	1275	}else {
222			i->second.prev.angle = i->second.curr.angle;
223			i->second.prev.potential = i->second.curr.potential;
224			i->second.curr.angle = angle;
225			i->second.curr.potential = currInversionPot;
226			i->second.deltaV = fabs(i->second.curr.potential -
227			i->second.prev.potential);
228			}
229			}
230	gezelter	246	}
231
232	gezelter	1126	RealType shortRangePotential = bondPotential + bendPotential +
233	cli2	1275	torsionPotential + inversionPotential;
234	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
235			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
236	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
237			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
238			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
239	gezelter	1545	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
240	gezelter	507	}
241	gezelter	1126
242	gezelter	1546	void ForceManager::longRangeInteractions() {
243	gezelter	246
244	gezelter	1545	// some of this initial stuff will go away:
245			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
246			DataStorage* config = &(curSnapshot->atomData);
247			DataStorage* cgConfig = &(curSnapshot->cgData);
248			RealType* frc = config->getArrayPointer(DataStorage::dslForce);
249			RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
250			RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
251			RealType* A = config->getArrayPointer(DataStorage::dslAmat);
252			RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
253			RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
254			RealType* rc;
255
256	gezelter	1540	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
257			rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
258	gezelter	246	} else {
259	gezelter	1126	// center of mass of the group is the same as position of the atom
260			// if cutoff group does not exist
261	gezelter	507	rc = pos;
262	gezelter	246	}
263	gezelter	1126
264	gezelter	246	//initialize data before passing to fortran
265	gezelter	1550	RealType longRangePotential[N_INTERACTION_FAMILIES];
266	tim	963	RealType lrPot = 0.0;
267	gezelter	246	int isError = 0;
268
269	gezelter	1550	// dangerous to iterate over enums, but we'll live on the edge:
270			for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
271	chuckv	664	longRangePotential[i]=0.0; //Initialize array
272			}
273	gezelter	1545
274			// new stuff starts here:
275
276	gezelter	1549	fDecomp_->distributeData();
277	gezelter	1545
278	gezelter	1546	int cg1, cg2, atom1, atom2;
279			Vector3d d_grp, dag;
280	gezelter	1545	RealType rgrpsq, rgrp;
281	gezelter	1549	RealType vij;
282	gezelter	1545	Vector3d fij, fg;
283			pair<int, int> gtypes;
284			RealType rCutSq;
285			bool in_switching_region;
286			RealType sw, dswdr, swderiv;
287	gezelter	1549	vector<int> atomListColumn, atomListRow, atomListLocal;
288	gezelter	1545	InteractionData idat;
289	gezelter	1546	SelfData sdat;
290			RealType mf;
291	gezelter	1544
292	gezelter	1545	int loopStart, loopEnd;
293	gezelter	1544
294	gezelter	1545	loopEnd = PAIR_LOOP;
295	gezelter	1546	if (info_->requiresPrepair() ) {
296	gezelter	1545	loopStart = PREPAIR_LOOP;
297			} else {
298			loopStart = PAIR_LOOP;
299			}
300
301			for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
302
303			if (iLoop == loopStart) {
304	gezelter	1549	bool update_nlist = fDecomp_->checkNeighborList();
305	gezelter	1545	if (update_nlist)
306	gezelter	1549	neighborList = fDecomp_->buildNeighborList();
307	gezelter	1544	}
308	gezelter	1545
309			for (vector<pair<int, int> >::iterator it = neighborList.begin();
310			it != neighborList.end(); ++it) {
311
312			cg1 = (*it).first;
313			cg2 = (*it).second;
314
315	gezelter	1549	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
316			d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
317	gezelter	1545	curSnapshot->wrapVector(d_grp);
318			rgrpsq = d_grp.lengthSquare();
319	gezelter	1546	rCutSq = groupCutoffMap[gtypes].first;
320	gezelter	1545
321			if (rgrpsq < rCutSq) {
322	gezelter	1554	*(idat.rcut) = groupCutoffMap[gtypes].second;
323	gezelter	1545	if (iLoop == PAIR_LOOP) {
324	gezelter	1546	vij *= 0.0;
325	gezelter	1545	fij = V3Zero;
326			}
327
328	gezelter	1554	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
329			rgrp);
330	gezelter	1549	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
331			atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
332	gezelter	1545
333	gezelter	1549	for (vector<int>::iterator ia = atomListRow.begin();
334			ia != atomListRow.end(); ++ia) {
335	gezelter	1545	atom1 = (*ia);
336
337	gezelter	1549	for (vector<int>::iterator jb = atomListColumn.begin();
338			jb != atomListColumn.end(); ++jb) {
339	gezelter	1545	atom2 = (*jb);
340
341	gezelter	1549	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
342	gezelter	1545
343	gezelter	1549	idat = fDecomp_->fillInteractionData(atom1, atom2);
344	gezelter	1546
345	gezelter	1549	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
346	gezelter	1554	*(idat.d) = d_grp;
347			*(idat.r2) = rgrpsq;
348	gezelter	1545	} else {
349	gezelter	1554	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
350			curSnapshot->wrapVector( *(idat.d) );
351			*(idat.r2) = idat.d->lengthSquare();
352	gezelter	1545	}
353
354	gezelter	1554	(idat.rij) = sqrt( (idat.r2) );
355	gezelter	1546
356	gezelter	1545	if (iLoop == PREPAIR_LOOP) {
357			interactionMan_->doPrePair(idat);
358			} else {
359			interactionMan_->doPair(idat);
360	gezelter	1554	vij += *(idat.vpair);
361			fij += *(idat.f1);
362			tau -= outProduct( (idat.d), (idat.f1));
363	gezelter	1545	}
364			}
365			}
366			}
367
368			if (iLoop == PAIR_LOOP) {
369			if (in_switching_region) {
370			swderiv = vij * dswdr / rgrp;
371			fg = swderiv * d_grp;
372
373			fij += fg;
374
375	gezelter	1549	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
376	gezelter	1554	tau -= outProduct( *(idat.d), fg);
377	gezelter	1545	}
378
379	gezelter	1549	for (vector<int>::iterator ia = atomListRow.begin();
380			ia != atomListRow.end(); ++ia) {
381	gezelter	1545	atom1 = (*ia);
382	gezelter	1569	mf = fDecomp_->getMassFactorRow(atom1);
383	gezelter	1545	// fg is the force on atom ia due to cutoff group's
384			// presence in switching region
385			fg = swderiv * d_grp * mf;
386	gezelter	1549	fDecomp_->addForceToAtomRow(atom1, fg);
387	gezelter	1545
388	gezelter	1549	if (atomListRow.size() > 1) {
389	gezelter	1546	if (info_->usesAtomicVirial()) {
390	gezelter	1545	// find the distance between the atom
391			// and the center of the cutoff group:
392	gezelter	1549	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
393	gezelter	1545	tau -= outProduct(dag, fg);
394			}
395			}
396			}
397	gezelter	1549	for (vector<int>::iterator jb = atomListColumn.begin();
398			jb != atomListColumn.end(); ++jb) {
399	gezelter	1545	atom2 = (*jb);
400	gezelter	1569	mf = fDecomp_->getMassFactorColumn(atom2);
401	gezelter	1545	// fg is the force on atom jb due to cutoff group's
402			// presence in switching region
403			fg = -swderiv * d_grp * mf;
404	gezelter	1549	fDecomp_->addForceToAtomColumn(atom2, fg);
405	gezelter	1545
406	gezelter	1549	if (atomListColumn.size() > 1) {
407	gezelter	1546	if (info_->usesAtomicVirial()) {
408	gezelter	1545	// find the distance between the atom
409			// and the center of the cutoff group:
410	gezelter	1549	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
411	gezelter	1545	tau -= outProduct(dag, fg);
412			}
413			}
414			}
415			}
416			//if (!SIM_uses_AtomicVirial) {
417			// tau -= outProduct(d_grp, fij);
418			//}
419			}
420			}
421			}
422
423			if (iLoop == PREPAIR_LOOP) {
424	gezelter	1546	if (info_->requiresPrepair()) {
425	gezelter	1549	fDecomp_->collectIntermediateData();
426	gezelter	1570
427			for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
428	gezelter	1549	sdat = fDecomp_->fillSelfData(atom1);
429	gezelter	1545	interactionMan_->doPreForce(sdat);
430			}
431	gezelter	1570
432	gezelter	1549	fDecomp_->distributeIntermediateData();
433	gezelter	1545	}
434			}
435
436	gezelter	1544	}
437	gezelter	1545
438	gezelter	1549	fDecomp_->collectData();
439	gezelter	1545
440	gezelter	1570	if ( info_->requiresSkipCorrection() ) {
441
442			for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
443	gezelter	1544
444	gezelter	1570	vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
445
446			for (vector<int>::iterator jb = skipList.begin();
447			jb != skipList.end(); ++jb) {
448
449			atom2 = (*jb);
450			idat = fDecomp_->fillSkipData(atom1, atom2);
451			interactionMan_->doSkipCorrection(idat);
452
453	gezelter	1545	}
454			}
455	gezelter	246	}
456	gezelter	1570
457			if (info_->requiresSelfCorrection()) {
458	gezelter	1545
459	gezelter	1570	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
460			sdat = fDecomp_->fillSelfData(atom1);
461			interactionMan_->doSelfCorrection(sdat);
462			}
463
464			}
465
466	gezelter	1550	// dangerous to iterate over enums, but we'll live on the edge:
467			for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
468	chuckv	664	lrPot += longRangePotential[i]; //Quick hack
469			}
470	gezelter	1503
471	gezelter	246	//store the tau and long range potential
472	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
473	gezelter	1550	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
474			curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
475	gezelter	507	}
476	gezelter	246
477	gezelter	1126
478	gezelter	1464	void ForceManager::postCalculation() {
479	gezelter	246	SimInfo::MoleculeIterator mi;
480			Molecule* mol;
481			Molecule::RigidBodyIterator rbIter;
482			RigidBody* rb;
483	gezelter	1126	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
484	gezelter	246
485			// collect the atomic forces onto rigid bodies
486	gezelter	1126
487			for (mol = info_->beginMolecule(mi); mol != NULL;
488			mol = info_->nextMolecule(mi)) {
489			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
490			rb = mol->nextRigidBody(rbIter)) {
491	gezelter	1464	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
492			tau += rbTau;
493	gezelter	507	}
494	gezelter	1126	}
495	gezelter	1464
496	gezelter	1126	#ifdef IS_MPI
497	gezelter	1464	Mat3x3d tmpTau(tau);
498			MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
499			9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
500	gezelter	1126	#endif
501	gezelter	1464	curSnapshot->statData.setTau(tau);
502	gezelter	507	}
503	gezelter	246
504	gezelter	1390	} //end namespace OpenMD