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"

#include <cstdio>
#include <iostream>
#include <iomanip>

using namespace std;
namespace OpenMD {
  
  ForceManager::ForceManager(SimInfo * info) : info_(info) {
    forceField_ = info_->getForceField();
    interactionMan_ = new InteractionManager();
    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
  }

  /**
   * setupCutoffs
   *
   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
   *
   * cutoffRadius : realType
   *  If the cutoffRadius was explicitly set, use that value.
   *  If the cutoffRadius was not explicitly set:
   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
   *      No electrostatic atoms?  Poll the atom types present in the
   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
   *      Use the maximum suggested value that was found.
   *
   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
   *      If cutoffMethod was explicitly set, use that choice.
   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
   *
   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
   *      If cutoffPolicy was explicitly set, use that choice.
   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
   */
  void ForceManager::setupCutoffs() {
    
    Globals* simParams_ = info_->getSimParams();
    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
    
    if (simParams_->haveCutoffRadius()) {
      rCut_ = simParams_->getCutoffRadius();
    } else {      
      if (info_->usesElectrostaticAtoms()) {
        sprintf(painCave.errMsg,
                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
                "\tOpenMD will use a default value of 12.0 angstroms"
                "\tfor the cutoffRadius.\n");
        painCave.isFatal = 0;
        painCave.severity = OPENMD_INFO;
        simError();
        rCut_ = 12.0;
      } else {
        RealType thisCut;
        set<AtomType*>::iterator i;
        set<AtomType*> atomTypes;
        atomTypes = info_->getSimulatedAtomTypes();        
        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
          rCut_ = max(thisCut, rCut_);
        }
        sprintf(painCave.errMsg,
                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
                "\tOpenMD will use %lf angstroms.\n",
                rCut_);
        painCave.isFatal = 0;
        painCave.severity = OPENMD_INFO;
        simError();
      }
    }

    fDecomp_->setUserCutoff(rCut_);
    interactionMan_->setCutoffRadius(rCut_);

    map<string, CutoffMethod> stringToCutoffMethod;
    stringToCutoffMethod["HARD"] = HARD;
    stringToCutoffMethod["SWITCHED"] = SWITCHED;
    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
  
    if (simParams_->haveCutoffMethod()) {
      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
      map<string, CutoffMethod>::iterator i;
      i = stringToCutoffMethod.find(cutMeth);
      if (i == stringToCutoffMethod.end()) {
        sprintf(painCave.errMsg,
                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
                "\tShould be one of: "
                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
                cutMeth.c_str());
        painCave.isFatal = 1;
        painCave.severity = OPENMD_ERROR;
        simError();
      } else {
        cutoffMethod_ = i->second;
      }
    } else {
      sprintf(painCave.errMsg,
              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
              "\tOpenMD will use SHIFTED_FORCE.\n");
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      cutoffMethod_ = SHIFTED_FORCE;        
    }

    map<string, CutoffPolicy> stringToCutoffPolicy;
    stringToCutoffPolicy["MIX"] = MIX;
    stringToCutoffPolicy["MAX"] = MAX;
    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    

    std::string cutPolicy;
    if (forceFieldOptions_.haveCutoffPolicy()){
      cutPolicy = forceFieldOptions_.getCutoffPolicy();
    }else if (simParams_->haveCutoffPolicy()) {
      cutPolicy = simParams_->getCutoffPolicy();
    }

    if (!cutPolicy.empty()){
      toUpper(cutPolicy);
      map<string, CutoffPolicy>::iterator i;
      i = stringToCutoffPolicy.find(cutPolicy);

      if (i == stringToCutoffPolicy.end()) {
        sprintf(painCave.errMsg,
                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
                "\tShould be one of: "
                "MIX, MAX, or TRADITIONAL\n",
                cutPolicy.c_str());
        painCave.isFatal = 1;
        painCave.severity = OPENMD_ERROR;
        simError();
      } else {
        cutoffPolicy_ = i->second;
      }
    } else {
      sprintf(painCave.errMsg,
              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
              "\tOpenMD will use TRADITIONAL.\n");
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      cutoffPolicy_ = TRADITIONAL;        
    }
    fDecomp_->setCutoffPolicy(cutoffPolicy_);
  }

  /**
   * setupSwitching
   *
   * Sets the values of switchingRadius and 
   *  If the switchingRadius was explicitly set, use that value (but check it)
   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
   */
  void ForceManager::setupSwitching() {
    Globals* simParams_ = info_->getSimParams();

    // create the switching function object:
    switcher_ = new SwitchingFunction();
    
    if (simParams_->haveSwitchingRadius()) {
      rSwitch_ = simParams_->getSwitchingRadius();
      if (rSwitch_ > rCut_) {        
        sprintf(painCave.errMsg,
                "ForceManager::setupSwitching: switchingRadius (%f) is larger "
                "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
        painCave.isFatal = 1;
        painCave.severity = OPENMD_ERROR;
        simError();
      }
    } else {      
      rSwitch_ = 0.85 * rCut_;
      sprintf(painCave.errMsg,
              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
      painCave.isFatal = 0;
      painCave.severity = OPENMD_WARNING;
      simError();
    }           
    
    // Default to cubic switching function.
    sft_ = cubic;
    if (simParams_->haveSwitchingFunctionType()) {
      string funcType = simParams_->getSwitchingFunctionType();
      toUpper(funcType);
      if (funcType == "CUBIC") {
        sft_ = cubic;
      } else {
        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
          sft_ = fifth_order_poly;
        } else {
          // throw error        
          sprintf( painCave.errMsg,
                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
                   "\tswitchingFunctionType must be one of: "
                   "\"cubic\" or \"fifth_order_polynomial\".", 
                   funcType.c_str() );
          painCave.isFatal = 1;
          painCave.severity = OPENMD_ERROR;
          simError();
        }           
      }
    }
    switcher_->setSwitchType(sft_);
    switcher_->setSwitch(rSwitch_, rCut_);
    interactionMan_->setSwitchingRadius(rSwitch_);
  }
  
  void ForceManager::initialize() {

    if (!info_->isTopologyDone()) {
      info_->update();
      interactionMan_->setSimInfo(info_);
      interactionMan_->initialize();

      // We want to delay the cutoffs until after the interaction
      // manager has set up the atom-atom interactions so that we can
      // query them for suggested cutoff values

      setupCutoffs();
      setupSwitching();

      info_->prepareTopology();      
    }

    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    
    // Force fields can set options on how to scale van der Waals and electrostatic
    // interactions for atoms connected via bonds, bends and torsions
    // in this case the topological distance between atoms is:
    // 0 = topologically unconnected
    // 1 = bonded together 
    // 2 = connected via a bend
    // 3 = connected via a torsion
    
    vdwScale_.reserve(4);
    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);

    electrostaticScale_.reserve(4);
    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);

    vdwScale_[0] = 1.0;
    vdwScale_[1] = fopts.getvdw12scale();
    vdwScale_[2] = fopts.getvdw13scale();
    vdwScale_[3] = fopts.getvdw14scale();
    
    electrostaticScale_[0] = 1.0;
    electrostaticScale_[1] = fopts.getelectrostatic12scale();
    electrostaticScale_[2] = fopts.getelectrostatic13scale();
    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
    
    fDecomp_->distributeInitialData();
 
    initialized_ = true;

  }

  void ForceManager::calcForces() {
    
    if (!initialized_) initialize();

    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() {

    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    DataStorage* config = &(curSnapshot->atomData);
    DataStorage* cgConfig = &(curSnapshot->cgData);

    //calculate the center of mass of cutoff group

    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;

    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->updateCOM();
        }
      }      
    } else {
      // center of mass of the group is the same as position of the atom  
      // if cutoff group does not exist
      cgConfig->position = config->position;
    }

    fDecomp_->zeroWorkArrays();
    fDecomp_->distributeData();
    
    int cg1, cg2, atom1, atom2, topoDist;
    Vector3d d_grp, dag, d;
    RealType rgrpsq, rgrp, r2, r;
    RealType electroMult, vdwMult;
    RealType vij;
    Vector3d fij, fg, f1;
    tuple3<RealType, RealType, RealType> cuts;
    RealType rCutSq;
    bool in_switching_region;
    RealType sw, dswdr, swderiv;
    vector<int> atomListColumn, atomListRow, atomListLocal;
    InteractionData idat;
    SelfData sdat;
    RealType mf;
    RealType lrPot;
    RealType vpair;
    potVec longRangePotential(0.0);
    potVec workPot(0.0);

    int loopStart, loopEnd;

    idat.vdwMult = &vdwMult;
    idat.electroMult = &electroMult;
    idat.pot = &workPot;
    sdat.pot = fDecomp_->getEmbeddingPotential();
    idat.vpair = &vpair;
    idat.f1 = &f1;
    idat.sw = &sw;
    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
    
    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;
        
        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);

        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
        curSnapshot->wrapVector(d_grp);        
        rgrpsq = d_grp.lengthSquare();

        rCutSq = cuts.second;

        if (rgrpsq < rCutSq) {
          idat.rcut = &cuts.first;
          if (iLoop == PAIR_LOOP) {
            vij *= 0.0;
            fij = V3Zero;
          }
          
          in_switching_region = switcher_->getSwitch(rgrpsq, 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)) {
                vpair = 0.0;
                workPot = 0.0;
                f1 = V3Zero;

                fDecomp_->fillInteractionData(idat, atom1, atom2);
                
                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
                vdwMult = vdwScale_[topoDist];
                electroMult = electrostaticScale_[topoDist];

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

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

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

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

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

    }

    longRangePotential = *(fDecomp_->getEmbeddingPotential()) + 
      *(fDecomp_->getPairwisePotential());

    lrPot = longRangePotential.sum();

    //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:	1584
Committed:	Fri Jun 17 20:16:35 2011 UTC (13 years, 11 months ago) by gezelter
File size:	27497 byte(s)
Log Message:	bug fixes.