ComputeBonds.C

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#include "InfoStream.h"
#include "ComputeBonds.h"
#include "Molecule.h"
#include "Parameters.h"
#include "Node.h"
#include "ReductionMgr.h"
#include "Lattice.h"
#include "PressureProfile.h"
#include "Debug.h"


// static initialization
int BondElem::pressureProfileSlabs = 0;
int BondElem::pressureProfileAtomTypes = 1;
BigReal BondElem::pressureProfileThickness = 0;
BigReal BondElem::pressureProfileMin = 0;

void BondElem::getMoleculePointers
    (Molecule* mol, int* count, int32*** byatom, Bond** structarray)
{
#ifdef MEM_OPT_VERSION
  NAMD_die("Should not be called in BondElem::getMoleculePointers in memory optimized version!");
#else
  *count = mol->numBonds;
  *byatom = mol->bondsByAtom;
  *structarray = mol->bonds;
#endif
}

void BondElem::getParameterPointers(Parameters *p, const BondValue **v) {
  *v = p->bond_array;
}

void BondElem::computeForce(BondElem *tuples, int ntuple, BigReal *reduction, 
                            BigReal *pressureProfileData)
{
 SimParameters *const simParams = Node::Object()->simParameters;
 const Lattice & lattice = tuples[0].p[0]->p->lattice;

 //fepb BKR
 const int step = tuples[0].p[0]->p->flags.step;
 const BigReal alchLambda = simParams->getCurrentLambda(step);
 const BigReal alchLambda2 = simParams->getCurrentLambda2(step);
 const BigReal bond_lambda_1 = simParams->getBondLambda(alchLambda);
 const BigReal bond_lambda_2 = simParams->getBondLambda(1-alchLambda);
 const BigReal bond_lambda_12 = simParams->getBondLambda(alchLambda2);
 const BigReal bond_lambda_22 = simParams->getBondLambda(1-alchLambda2);
 Molecule *const mol = Node::Object()->molecule;
 //fepe

 for ( int ituple=0; ituple<ntuple; ++ituple ) {
  const BondElem &tup = tuples[ituple];
  enum { size = 2 };
  const AtomID (&atomID)[size](tup.atomID);
  const int    (&localIndex)[size](tup.localIndex);
  TuplePatchElem * const(&p)[size](tup.p);
  const Real (&scale)(tup.scale);
  const BondValue * const(&value)(tup.value);

  DebugM(1, "::computeForce() localIndex = " << localIndex[0] << " "
               << localIndex[1] << std::endl);

  // skip Lonepair bonds (other k=0. bonds have been filtered out)
  if (0. == value->k) continue;

  BigReal scal;         // force scaling
  BigReal energy;       // energy from the bond

  //DebugM(3, "::computeForce() -- starting with bond type " << bondType << std::endl);

  // get the bond information
  Real k = value->k * scale;
  Real x0 = value->x0;
  Real x1 = value->x1;

  // compute vectors between atoms and their distances
  const Vector r12 = lattice.delta(p[0]->x[localIndex[0]].position,
                                        p[1]->x[localIndex[1]].position);

  if (0. == x0) {
    BigReal r2 = r12.length2();
    scal = -2.0*k;    // bond interaction for equilibrium length 0
    energy = k*r2;
    // TODO: Instead flag by mass for Drude particles, otherwise mixing and 
    // matching Drude and alchemical "twin" particles will likely not work as 
    // expected.
    if( simParams->drudeOn && !simParams->drudeHardWallOn ) { // for Drude bonds
      BigReal drudeBondLen = simParams->drudeBondLen;
      BigReal drudeBondConst = simParams->drudeBondConst;
      if ( drudeBondConst > 0 && r2 > drudeBondLen*drudeBondLen ) {
        // add a quartic restraining potential to keep Drude bond short
        BigReal r = sqrt(r2);
        BigReal diff = r - drudeBondLen;
        BigReal diff2 = diff*diff;

        scal += -4*drudeBondConst * diff2 * diff / r;
        energy += drudeBondConst * diff2 * diff2;
      }
    }
  }
  else {
    BigReal r = r12.length();  // Distance between atoms
    BigReal diff = r - x0;     // Compare it to the rest bond

    if (x1) {
      // in this case, the bond represents a harmonic wall potential
      // where x0 is the lower wall and x1 is the upper
      diff = (r > x1 ? r - x1 : (r > x0 ? 0 : diff));
    }

    //  Add the energy from this bond to the total energy
    energy = k*diff*diff;

    //  Determine the magnitude of the force
    diff *= -2.0*k;

    //  Scale the force vector accordingly
    scal = (diff/r);
  }

  //fepb - BKR scaling of alchemical bonded terms
  //       NB: TI derivative is the _unscaled_ energy.
  if ( simParams->alchOn && !simParams->singleTopology) {
    switch ( mol->get_fep_bonded_type(atomID, 2) ) {
    case 1:
      reduction[bondEnergyIndex_ti_1] += energy;
      reduction[bondEnergyIndex_f] += (bond_lambda_12 - bond_lambda_1)*energy;
      energy *= bond_lambda_1;
      scal *= bond_lambda_1;
      break;
    case 2:
      reduction[bondEnergyIndex_ti_2] += energy;
      reduction[bondEnergyIndex_f] += (bond_lambda_22 - bond_lambda_2)*energy;
      energy *= bond_lambda_2;
      scal *= bond_lambda_2;
      break;
    }
  }
  //fepe
  const Force f12 = scal * r12;


  //  Now add the forces to each force vector
  p[0]->f[localIndex[0]] += f12;
  p[1]->f[localIndex[1]] -= f12;

  DebugM(3, "::computeForce() -- ending with delta energy " << energy << std::endl);
  reduction[bondEnergyIndex] += energy;
  reduction[virialIndex_XX] += f12.x * r12.x;
  reduction[virialIndex_XY] += f12.x * r12.y;
  reduction[virialIndex_XZ] += f12.x * r12.z;
  reduction[virialIndex_YX] += f12.y * r12.x;
  reduction[virialIndex_YY] += f12.y * r12.y;
  reduction[virialIndex_YZ] += f12.y * r12.z;
  reduction[virialIndex_ZX] += f12.z * r12.x;
  reduction[virialIndex_ZY] += f12.z * r12.y;
  reduction[virialIndex_ZZ] += f12.z * r12.z;

  if (pressureProfileData) {
    BigReal z1 = p[0]->x[localIndex[0]].position.z;
    BigReal z2 = p[1]->x[localIndex[1]].position.z;
    int n1 = (int)floor((z1-pressureProfileMin)/pressureProfileThickness);
    int n2 = (int)floor((z2-pressureProfileMin)/pressureProfileThickness);
    pp_clamp(n1, pressureProfileSlabs);
    pp_clamp(n2, pressureProfileSlabs);
    int p1 = p[0]->x[localIndex[0]].partition;
    int p2 = p[1]->x[localIndex[1]].partition;
    int pn = pressureProfileAtomTypes;
    pp_reduction(pressureProfileSlabs,
                n1, n2, 
                p1, p2, pn, 
                f12.x * r12.x, f12.y * r12.y, f12.z * r12.z,
                pressureProfileData);
  } 

 }
}

void BondElem::submitReductionData(BigReal *data, SubmitReduction *reduction)
{
  reduction->item(REDUCTION_BOND_ENERGY) += data[bondEnergyIndex];
  reduction->item(REDUCTION_BONDED_ENERGY_F) += data[bondEnergyIndex_f];
  reduction->item(REDUCTION_BONDED_ENERGY_TI_1) += data[bondEnergyIndex_ti_1];
  reduction->item(REDUCTION_BONDED_ENERGY_TI_2) += data[bondEnergyIndex_ti_2];
  ADD_TENSOR(reduction,REDUCTION_VIRIAL_NORMAL,data,virialIndex);
}