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"
#include "UseTheForce/doForces_interface.h"
#define __OPENMD_C
#include "UseTheForce/DarkSide/fInteractionMap.h"
#include "utils/simError.h"
#include "primitives/Bond.hpp"
#include "primitives/Bend.hpp"
#include "primitives/Torsion.hpp"
#include "primitives/Inversion.hpp"
#include "parallel/ForceDecomposition.hpp"
//#include "parallel/SerialDecomposition.hpp"

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

#ifdef IS_MPI
    decomp_ = new ForceDecomposition(info_);
#else
    // decomp_ = new SerialDecomposition(info);
#endif
  }
  
  void ForceManager::calcForces() {
    
    if (!info_->isFortranInitialized()) {
      info_->update();
      interactionMan_->setSimInfo(info_);
      interactionMan_->initialize();
      swfun_ = interactionMan_->getSwitchingFunction();
      decomp_->distributeInitialData();
      info_->setupFortran();
    }
    
    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[LR_POT_TYPES];
    RealType lrPot = 0.0;
    int isError = 0;

    for (int i=0; i<LR_POT_TYPES;i++){
      longRangePotential[i]=0.0; //Initialize array
    }

    // new stuff starts here:

    decomp_->distributeData();
 
    int cg1, cg2, atom1, atom2;
    Vector3d d_grp, dag;
    RealType rgrpsq, rgrp;
    Vector<RealType, 4> vij;
    Vector3d fij, fg;
    pair<int, int> gtypes;
    RealType rCutSq;
    bool in_switching_region;
    RealType sw, dswdr, swderiv;
    vector<int> atomListI, atomListJ, atomList;
    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 = decomp_->checkNeighborList();
        if (update_nlist) 
          neighborList = decomp_->buildNeighborList();
      }

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

        gtypes = decomp_->getGroupTypes(cg1, cg2);
        d_grp  = decomp_->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);               
          atomListI = decomp_->getAtomsInGroupI(cg1);
          atomListJ = decomp_->getAtomsInGroupJ(cg2);

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

                if (atomListI.size() == 1 && atomListJ.size() == 1) {
                  idat.d = d_grp;
                  idat.r2 = rgrpsq;
                } else {
                  idat.d = decomp_->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 (atomListI.size() == 1 && atomListJ.size() == 1) {
                tau -= outProduct(idat.d, fg);
              }
          
              for (vector<int>::iterator ia = atomListI.begin(); 
                   ia != atomListI.end(); ++ia) {            
                atom1 = (*ia);                
                mf = decomp_->getMfactI(atom1);
                // fg is the force on atom ia due to cutoff group's
                // presence in switching region
                fg = swderiv * d_grp * mf;
                decomp_->addForceToAtomI(atom1, fg);

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

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

      if (iLoop == PREPAIR_LOOP) {
        if (info_->requiresPrepair()) {            
          decomp_->collectIntermediateData();
          atomList = decomp_->getAtomList();
          for (vector<int>::iterator ia = atomList.begin(); 
               ia != atomList.end(); ++ia) {              
            atom1 = (*ia);            
            sdat = decomp_->fillSelfData(atom1);
            interactionMan_->doPreForce(sdat);
          }
          decomp_->distributeIntermediateData();        
        }
      }

    }
    
    decomp_->collectData();
    
    if (info_->requiresSkipCorrection() || info_->requiresSelfCorrection()) {
      atomList = decomp_->getAtomList();
      for (vector<int>::iterator ia = atomList.begin(); 
           ia != atomList.end(); ++ia) {              
        atom1 = (*ia);     

        if (info_->requiresSkipCorrection()) {
          vector<int> skipList = decomp_->getSkipsForAtom(atom1);
          for (vector<int>::iterator jb = skipList.begin(); 
               jb != skipList.end(); ++jb) {              
            atom2 = (*jb);
            idat = decomp_->fillSkipData(atom1, atom2);
            interactionMan_->doSkipCorrection(idat);
          }
        }
          
        if (info_->requiresSelfCorrection()) {
          sdat = decomp_->fillSelfData(atom1);
          interactionMan_->doSelfCorrection(sdat);
      }
      
      
    }

    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];
  }

  
  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:	1546
Committed:	Sun Apr 10 15:16:39 2011 UTC (14 years, 6 months ago) by gezelter
File size:	18393 byte(s)
Log Message:	closer to a real force loop
#	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			#include "UseTheForce/doForces_interface.h"
53	gezelter	1390	#define __OPENMD_C
54	chuckv	664	#include "UseTheForce/DarkSide/fInteractionMap.h"
55	gezelter	246	#include "utils/simError.h"
56	xsun	1215	#include "primitives/Bond.hpp"
57	tim	749	#include "primitives/Bend.hpp"
58	cli2	1275	#include "primitives/Torsion.hpp"
59			#include "primitives/Inversion.hpp"
60	gezelter	1544	#include "parallel/ForceDecomposition.hpp"
61			//#include "parallel/SerialDecomposition.hpp"
62	gezelter	1467
63	gezelter	1545	using namespace std;
64	gezelter	1390	namespace OpenMD {
65	gezelter	1469
66	gezelter	1545	ForceManager::ForceManager(SimInfo * info) : info_(info) {
67
68	gezelter	1544	#ifdef IS_MPI
69			decomp_ = new ForceDecomposition(info_);
70			#else
71	gezelter	1545	// decomp_ = new SerialDecomposition(info);
72	gezelter	1544	#endif
73	gezelter	1469	}
74	gezelter	1545
75	gezelter	1464	void ForceManager::calcForces() {
76	gezelter	1126
77	gezelter	246	if (!info_->isFortranInitialized()) {
78	gezelter	507	info_->update();
79	gezelter	1546	interactionMan_->setSimInfo(info_);
80			interactionMan_->initialize();
81			swfun_ = interactionMan_->getSwitchingFunction();
82	gezelter	1544	decomp_->distributeInitialData();
83	gezelter	1535	info_->setupFortran();
84	gezelter	246	}
85	gezelter	1126
86	gezelter	1544	preCalculation();
87	gezelter	1546	shortRangeInteractions();
88			longRangeInteractions();
89	gezelter	1464	postCalculation();
90	tim	749
91	gezelter	507	}
92	gezelter	1126
93	gezelter	507	void ForceManager::preCalculation() {
94	gezelter	246	SimInfo::MoleculeIterator mi;
95			Molecule* mol;
96			Molecule::AtomIterator ai;
97			Atom* atom;
98			Molecule::RigidBodyIterator rbIter;
99			RigidBody* rb;
100	gezelter	1540	Molecule::CutoffGroupIterator ci;
101			CutoffGroup* cg;
102	gezelter	246
103			// forces are zeroed here, before any are accumulated.
104	chuckv	1245
105	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
106			mol = info_->nextMolecule(mi)) {
107	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
108			atom->zeroForcesAndTorques();
109			}
110	chuckv	1245
111	gezelter	507	//change the positions of atoms which belong to the rigidbodies
112	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
113			rb = mol->nextRigidBody(rbIter)) {
114	gezelter	507	rb->zeroForcesAndTorques();
115			}
116	gezelter	1540
117			if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
118			for(cg = mol->beginCutoffGroup(ci); cg != NULL;
119			cg = mol->nextCutoffGroup(ci)) {
120			//calculate the center of mass of cutoff group
121			cg->updateCOM();
122			}
123			}
124	gezelter	246	}
125	gezelter	1540
126	gezelter	1126	// Zero out the stress tensor
127			tau *= 0.0;
128
129	gezelter	507	}
130	gezelter	1126
131	gezelter	1546	void ForceManager::shortRangeInteractions() {
132	gezelter	246	Molecule* mol;
133			RigidBody* rb;
134			Bond* bond;
135			Bend* bend;
136			Torsion* torsion;
137	cli2	1275	Inversion* inversion;
138	gezelter	246	SimInfo::MoleculeIterator mi;
139			Molecule::RigidBodyIterator rbIter;
140			Molecule::BondIterator bondIter;;
141			Molecule::BendIterator bendIter;
142			Molecule::TorsionIterator torsionIter;
143	cli2	1275	Molecule::InversionIterator inversionIter;
144	tim	963	RealType bondPotential = 0.0;
145			RealType bendPotential = 0.0;
146			RealType torsionPotential = 0.0;
147	cli2	1275	RealType inversionPotential = 0.0;
148	gezelter	246
149			//calculate short range interactions
150	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
151			mol = info_->nextMolecule(mi)) {
152	gezelter	246
153	gezelter	507	//change the positions of atoms which belong to the rigidbodies
154	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
155			rb = mol->nextRigidBody(rbIter)) {
156			rb->updateAtoms();
157	gezelter	507	}
158	gezelter	246
159	gezelter	1126	for (bond = mol->beginBond(bondIter); bond != NULL;
160			bond = mol->nextBond(bondIter)) {
161	tim	749	bond->calcForce();
162			bondPotential += bond->getPotential();
163	gezelter	507	}
164	gezelter	246
165	gezelter	1126	for (bend = mol->beginBend(bendIter); bend != NULL;
166			bend = mol->nextBend(bendIter)) {
167
168			RealType angle;
169			bend->calcForce(angle);
170			RealType currBendPot = bend->getPotential();
171	gezelter	1448
172	gezelter	1126	bendPotential += bend->getPotential();
173	gezelter	1545	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
174	gezelter	1126	if (i == bendDataSets.end()) {
175			BendDataSet dataSet;
176			dataSet.prev.angle = dataSet.curr.angle = angle;
177			dataSet.prev.potential = dataSet.curr.potential = currBendPot;
178			dataSet.deltaV = 0.0;
179	gezelter	1545	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
180	gezelter	1126	}else {
181			i->second.prev.angle = i->second.curr.angle;
182			i->second.prev.potential = i->second.curr.potential;
183			i->second.curr.angle = angle;
184			i->second.curr.potential = currBendPot;
185			i->second.deltaV = fabs(i->second.curr.potential -
186			i->second.prev.potential);
187			}
188	gezelter	507	}
189	gezelter	1126
190			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
191			torsion = mol->nextTorsion(torsionIter)) {
192	tim	963	RealType angle;
193	gezelter	1126	torsion->calcForce(angle);
194	tim	963	RealType currTorsionPot = torsion->getPotential();
195	gezelter	1126	torsionPotential += torsion->getPotential();
196	gezelter	1545	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
197	gezelter	1126	if (i == torsionDataSets.end()) {
198			TorsionDataSet dataSet;
199			dataSet.prev.angle = dataSet.curr.angle = angle;
200			dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
201			dataSet.deltaV = 0.0;
202	gezelter	1545	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
203	gezelter	1126	}else {
204			i->second.prev.angle = i->second.curr.angle;
205			i->second.prev.potential = i->second.curr.potential;
206			i->second.curr.angle = angle;
207			i->second.curr.potential = currTorsionPot;
208			i->second.deltaV = fabs(i->second.curr.potential -
209			i->second.prev.potential);
210			}
211			}
212	gezelter	1545
213	cli2	1275	for (inversion = mol->beginInversion(inversionIter);
214			inversion != NULL;
215			inversion = mol->nextInversion(inversionIter)) {
216			RealType angle;
217			inversion->calcForce(angle);
218			RealType currInversionPot = inversion->getPotential();
219			inversionPotential += inversion->getPotential();
220	gezelter	1545	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
221	cli2	1275	if (i == inversionDataSets.end()) {
222			InversionDataSet dataSet;
223			dataSet.prev.angle = dataSet.curr.angle = angle;
224			dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
225			dataSet.deltaV = 0.0;
226	gezelter	1545	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
227	cli2	1275	}else {
228			i->second.prev.angle = i->second.curr.angle;
229			i->second.prev.potential = i->second.curr.potential;
230			i->second.curr.angle = angle;
231			i->second.curr.potential = currInversionPot;
232			i->second.deltaV = fabs(i->second.curr.potential -
233			i->second.prev.potential);
234			}
235			}
236	gezelter	246	}
237
238	gezelter	1126	RealType shortRangePotential = bondPotential + bendPotential +
239	cli2	1275	torsionPotential + inversionPotential;
240	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
241			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
242	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
243			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
244			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
245	gezelter	1545	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
246	gezelter	507	}
247	gezelter	1126
248	gezelter	1546	void ForceManager::longRangeInteractions() {
249	gezelter	246
250	gezelter	1545	// some of this initial stuff will go away:
251			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
252			DataStorage* config = &(curSnapshot->atomData);
253			DataStorage* cgConfig = &(curSnapshot->cgData);
254			RealType* frc = config->getArrayPointer(DataStorage::dslForce);
255			RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
256			RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
257			RealType* A = config->getArrayPointer(DataStorage::dslAmat);
258			RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
259			RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
260			RealType* rc;
261
262	gezelter	1540	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
263			rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
264	gezelter	246	} else {
265	gezelter	1126	// center of mass of the group is the same as position of the atom
266			// if cutoff group does not exist
267	gezelter	507	rc = pos;
268	gezelter	246	}
269	gezelter	1126
270	gezelter	246	//initialize data before passing to fortran
271	tim	963	RealType longRangePotential[LR_POT_TYPES];
272			RealType lrPot = 0.0;
273	gezelter	246	int isError = 0;
274
275	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
276			longRangePotential[i]=0.0; //Initialize array
277			}
278	gezelter	1545
279			// new stuff starts here:
280
281	gezelter	1544	decomp_->distributeData();
282	gezelter	1545
283	gezelter	1546	int cg1, cg2, atom1, atom2;
284			Vector3d d_grp, dag;
285	gezelter	1545	RealType rgrpsq, rgrp;
286	gezelter	1546	Vector<RealType, 4> vij;
287	gezelter	1545	Vector3d fij, fg;
288			pair<int, int> gtypes;
289			RealType rCutSq;
290			bool in_switching_region;
291			RealType sw, dswdr, swderiv;
292	gezelter	1546	vector<int> atomListI, atomListJ, atomList;
293	gezelter	1545	InteractionData idat;
294	gezelter	1546	SelfData sdat;
295			RealType mf;
296	gezelter	1544
297	gezelter	1545	int loopStart, loopEnd;
298	gezelter	1544
299	gezelter	1545	loopEnd = PAIR_LOOP;
300	gezelter	1546	if (info_->requiresPrepair() ) {
301	gezelter	1545	loopStart = PREPAIR_LOOP;
302			} else {
303			loopStart = PAIR_LOOP;
304			}
305
306			for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
307
308			if (iLoop == loopStart) {
309			bool update_nlist = decomp_->checkNeighborList();
310			if (update_nlist)
311			neighborList = decomp_->buildNeighborList();
312	gezelter	1544	}
313	gezelter	1545
314			for (vector<pair<int, int> >::iterator it = neighborList.begin();
315			it != neighborList.end(); ++it) {
316
317			cg1 = (*it).first;
318			cg2 = (*it).second;
319
320			gtypes = decomp_->getGroupTypes(cg1, cg2);
321			d_grp = decomp_->getIntergroupVector(cg1, cg2);
322			curSnapshot->wrapVector(d_grp);
323			rgrpsq = d_grp.lengthSquare();
324	gezelter	1546	rCutSq = groupCutoffMap[gtypes].first;
325	gezelter	1545
326			if (rgrpsq < rCutSq) {
327	gezelter	1546	idat.rcut = groupCutoffMap[gtypes].second;
328	gezelter	1545	if (iLoop == PAIR_LOOP) {
329	gezelter	1546	vij *= 0.0;
330	gezelter	1545	fij = V3Zero;
331			}
332
333	gezelter	1546	in_switching_region = swfun_->getSwitch(rgrpsq, idat.sw, dswdr, rgrp);
334	gezelter	1545	atomListI = decomp_->getAtomsInGroupI(cg1);
335			atomListJ = decomp_->getAtomsInGroupJ(cg2);
336
337			for (vector<int>::iterator ia = atomListI.begin();
338			ia != atomListI.end(); ++ia) {
339			atom1 = (*ia);
340
341			for (vector<int>::iterator jb = atomListJ.begin();
342			jb != atomListJ.end(); ++jb) {
343			atom2 = (*jb);
344
345			if (!decomp_->skipAtomPair(atom1, atom2)) {
346
347	gezelter	1546	idat = decomp_->fillInteractionData(atom1, atom2);
348
349	gezelter	1545	if (atomListI.size() == 1 && atomListJ.size() == 1) {
350			idat.d = d_grp;
351			idat.r2 = rgrpsq;
352			} else {
353			idat.d = decomp_->getInteratomicVector(atom1, atom2);
354			curSnapshot->wrapVector(idat.d);
355			idat.r2 = idat.d.lengthSquare();
356			}
357
358	gezelter	1546	idat.rij = sqrt(idat.r2);
359
360	gezelter	1545	if (iLoop == PREPAIR_LOOP) {
361			interactionMan_->doPrePair(idat);
362			} else {
363			interactionMan_->doPair(idat);
364			vij += idat.vpair;
365			fij += idat.f1;
366	gezelter	1546	tau -= outProduct(idat.d, idat.f1);
367	gezelter	1545	}
368			}
369			}
370			}
371
372			if (iLoop == PAIR_LOOP) {
373			if (in_switching_region) {
374			swderiv = vij * dswdr / rgrp;
375			fg = swderiv * d_grp;
376
377			fij += fg;
378
379			if (atomListI.size() == 1 && atomListJ.size() == 1) {
380			tau -= outProduct(idat.d, fg);
381			}
382
383			for (vector<int>::iterator ia = atomListI.begin();
384			ia != atomListI.end(); ++ia) {
385			atom1 = (*ia);
386			mf = decomp_->getMfactI(atom1);
387			// fg is the force on atom ia due to cutoff group's
388			// presence in switching region
389			fg = swderiv * d_grp * mf;
390			decomp_->addForceToAtomI(atom1, fg);
391
392			if (atomListI.size() > 1) {
393	gezelter	1546	if (info_->usesAtomicVirial()) {
394	gezelter	1545	// find the distance between the atom
395			// and the center of the cutoff group:
396			dag = decomp_->getAtomToGroupVectorI(atom1, cg1);
397			tau -= outProduct(dag, fg);
398			}
399			}
400			}
401			for (vector<int>::iterator jb = atomListJ.begin();
402			jb != atomListJ.end(); ++jb) {
403			atom2 = (*jb);
404			mf = decomp_->getMfactJ(atom2);
405			// fg is the force on atom jb due to cutoff group's
406			// presence in switching region
407			fg = -swderiv * d_grp * mf;
408			decomp_->addForceToAtomJ(atom2, fg);
409
410			if (atomListJ.size() > 1) {
411	gezelter	1546	if (info_->usesAtomicVirial()) {
412	gezelter	1545	// find the distance between the atom
413			// and the center of the cutoff group:
414			dag = decomp_->getAtomToGroupVectorJ(atom2, cg2);
415			tau -= outProduct(dag, fg);
416			}
417			}
418			}
419			}
420			//if (!SIM_uses_AtomicVirial) {
421			// tau -= outProduct(d_grp, fij);
422			//}
423			}
424			}
425			}
426
427			if (iLoop == PREPAIR_LOOP) {
428	gezelter	1546	if (info_->requiresPrepair()) {
429	gezelter	1545	decomp_->collectIntermediateData();
430			atomList = decomp_->getAtomList();
431			for (vector<int>::iterator ia = atomList.begin();
432			ia != atomList.end(); ++ia) {
433			atom1 = (*ia);
434	gezelter	1546	sdat = decomp_->fillSelfData(atom1);
435	gezelter	1545	interactionMan_->doPreForce(sdat);
436			}
437			decomp_->distributeIntermediateData();
438			}
439			}
440
441	gezelter	1544	}
442	gezelter	1545
443	gezelter	1544	decomp_->collectData();
444	gezelter	1545
445	gezelter	1546	if (info_->requiresSkipCorrection() \|\| info_->requiresSelfCorrection()) {
446	gezelter	1545	atomList = decomp_->getAtomList();
447			for (vector<int>::iterator ia = atomList.begin();
448			ia != atomList.end(); ++ia) {
449			atom1 = (*ia);
450	gezelter	1544
451	gezelter	1546	if (info_->requiresSkipCorrection()) {
452	gezelter	1545	vector<int> skipList = decomp_->getSkipsForAtom(atom1);
453			for (vector<int>::iterator jb = skipList.begin();
454			jb != skipList.end(); ++jb) {
455			atom2 = (*jb);
456	gezelter	1546	idat = decomp_->fillSkipData(atom1, atom2);
457	gezelter	1545	interactionMan_->doSkipCorrection(idat);
458			}
459			}
460
461	gezelter	1546	if (info_->requiresSelfCorrection()) {
462			sdat = decomp_->fillSelfData(atom1);
463	gezelter	1545	interactionMan_->doSelfCorrection(sdat);
464			}
465
466
467	gezelter	246	}
468	gezelter	1545
469	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
470			lrPot += longRangePotential[i]; //Quick hack
471			}
472	gezelter	1503
473	gezelter	246	//store the tau and long range potential
474	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
475	chrisfen	691	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
476	tim	681	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
477	gezelter	507	}
478	gezelter	246
479	gezelter	1126
480	gezelter	1464	void ForceManager::postCalculation() {
481	gezelter	246	SimInfo::MoleculeIterator mi;
482			Molecule* mol;
483			Molecule::RigidBodyIterator rbIter;
484			RigidBody* rb;
485	gezelter	1126	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
486	gezelter	246
487			// collect the atomic forces onto rigid bodies
488	gezelter	1126
489			for (mol = info_->beginMolecule(mi); mol != NULL;
490			mol = info_->nextMolecule(mi)) {
491			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
492			rb = mol->nextRigidBody(rbIter)) {
493	gezelter	1464	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
494			tau += rbTau;
495	gezelter	507	}
496	gezelter	1126	}
497	gezelter	1464
498	gezelter	1126	#ifdef IS_MPI
499	gezelter	1464	Mat3x3d tmpTau(tau);
500			MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
501			9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
502	gezelter	1126	#endif
503	gezelter	1464	curSnapshot->statData.setTau(tau);
504	gezelter	507	}
505	gezelter	246
506	gezelter	1390	} //end namespace OpenMD