GromacsPairElem Class Reference

#include <ComputeGromacsPair.h>

Public Types
enum	{ size = 2 }
enum	{ gromacsPairEnergyIndex, TENSOR =(virialIndex), reductionDataSize }
enum	{ reductionChecksumLabel = REDUCTION_GRO_LJ_CHECKSUM }

Public Member Functions
int	hash () const
	GromacsPairElem ()
	GromacsPairElem (AtomID atom0, const TupleSignature *sig, const GromacsPairValue *v)
	GromacsPairElem (const GromacsPair *a, const GromacsPairValue *v)
	GromacsPairElem (AtomID atom0, AtomID atom1)
	~GromacsPairElem ()
int	operator== (const GromacsPairElem &a) const
int	operator< (const GromacsPairElem &a) const

Static Public Member Functions
static void	computeForce (GromacsPairElem *, int, BigReal *, BigReal *)
static void	getMoleculePointers (Molecule *, int *, int32 ***, GromacsPair **)
static void	getParameterPointers (Parameters *, const GromacsPairValue **)
static void	getTupleInfo (AtomSignature *sig, int *count, TupleSignature **t)
static void	submitReductionData (BigReal *, SubmitReduction *)

Public Attributes
AtomID	atomID [size]
int	localIndex [size]
TuplePatchElem *	p [size]
Real	scale
const GromacsPairValue *	value

Static Public Attributes
static int	pressureProfileSlabs = 0
static int	pressureProfileAtomTypes = 1
static BigReal	pressureProfileThickness = 0
static BigReal	pressureProfileMin = 0

Detailed Description

Definition at line 23 of file ComputeGromacsPair.h.

Member Enumeration Documentation

anonymous enum

anonymous enum

Enumerator
size

Definition at line 26 of file ComputeGromacsPair.h.

{ size = 2 };

anonymous enum

anonymous enum

Enumerator
gromacsPairEnergyIndex
TENSOR
reductionDataSize

Definition at line 53 of file ComputeGromacsPair.h.

{ gromacsPairEnergyIndex, TENSOR(virialIndex), reductionDataSize };

anonymous enum

anonymous enum

Enumerator
reductionChecksumLabel

Definition at line 55 of file ComputeGromacsPair.h.

{ reductionChecksumLabel = REDUCTION_GRO_LJ_CHECKSUM };

Constructor & Destructor Documentation

GromacsPairElem() [1/4]

GromacsPairElem::GromacsPairElem ( )

inline

Definition at line 12 of file ComputeGromacsPair.inl.

{ ; }

GromacsPairElem() [2/4]

GromacsPairElem::GromacsPairElem ( AtomID  atom0, const TupleSignature *  sig, const GromacsPairValue *  v  )

inline

Definition at line 14 of file ComputeGromacsPair.inl.

References atomID, TupleSignature::offset, TupleSignature::tupleParamType, and value.

                                                                                                         {
    atomID[0] = atom0;
    atomID[1] = atom0 + sig->offset[0];
    value = &v[sig->tupleParamType];
}

GromacsPairElem() [3/4]

GromacsPairElem::GromacsPairElem ( const GromacsPair *  a, const GromacsPairValue *  v  )

inline

Definition at line 20 of file ComputeGromacsPair.inl.

References gromacsPair::atom1, gromacsPair::atom2, atomID, gromacsPair::gromacsPair_type, and value.

  {
    atomID[0] = a->atom1;
    atomID[1] = a->atom2;
    value = &v[a->gromacsPair_type];
  }

GromacsPairElem() [4/4]

GromacsPairElem::GromacsPairElem ( AtomID  atom0, AtomID  atom1  )

inline

Definition at line 27 of file ComputeGromacsPair.inl.

References atomID.

  {
    if (atom0 > atom1) {  // Swap end atoms so lowest is first!
      AtomID tmp = atom1; atom1 = atom0; atom0 = tmp; 
    }
    atomID[0] = atom0;
    atomID[1] = atom1;
  }

~GromacsPairElem()

GromacsPairElem::~GromacsPairElem ( )

inline

Definition at line 61 of file ComputeGromacsPair.h.

{};

Member Function Documentation

computeForce()

void GromacsPairElem::computeForce ( GromacsPairElem *  tuples, int  ntuple, BigReal *  reduction, BigReal *  pressureProfileData  )

static

Definition at line 44 of file ComputeGromacsPair.C.

References atomID, DebugM, Lattice::delta(), TuplePatchElem::f, gromacsPairEnergyIndex, Patch::lattice, Vector::length2(), localIndex, Node::Object(), p, TuplePatchElem::p, GromacsPairValue::pairC12, GromacsPairValue::pairC6, CompAtom::partition, CompAtom::position, pp_clamp(), pp_reduction(), pressureProfileAtomTypes, pressureProfileMin, pressureProfileSlabs, pressureProfileThickness, scale, Node::simParameters, simParams, size, value, TuplePatchElem::x, Vector::x, Vector::y, and Vector::z.

{
 const Lattice & lattice = tuples[0].p[0]->p->lattice;

 for ( int ituple=0; ituple<ntuple; ++ituple ) {
  const GromacsPairElem &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 GromacsPairValue * const(&value)(tup.value);

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

    // 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 ( p[0]->patchID == p[1]->patchID && localIndex[0] == localIndex[1] ) {
        continue;
    }
    SimParameters *simParams = Node::Object()->simParameters;
    BigReal cutoff = simParams->cutoff;
    BigReal r12_len = r12.length2();
    if ( r12_len == 0 ) continue;
    //if ( r12_len > cutoff) {
        //continue;
    //}
    BigReal ri2 = 1.0/r12_len;
    BigReal ri = sqrt(ri2);
    BigReal ri6 = ri2*ri2*ri2;
    BigReal ri7 = ri*ri6;
    BigReal ri8 = ri2*ri2*ri2*ri2;
    BigReal ri12 = ri6*ri6;
    BigReal ri13 = ri12*ri;
    BigReal ri14 = ri12*ri2;

    BigReal energy = 0;
    BigReal diff = 0;
    BigReal pairC12 = value->pairC12;
    BigReal pairC6 = value->pairC6;

    // Add the energy for the 12-6 LJ interaction to the total energy
    energy = (pairC12*ri12) - (pairC6*ri6);
    // This is a dirty hack; currently the code is looping over N^2 instead of N(N-1)/2 
    // This is happening because the LJ list is 2x long as it has to be
    //energy *= 0.5; 

    // Determine the magnitude of the force
    diff = ((12*pairC12*ri14) - (6*pairC6*ri8));
    // This is a dirty hack; currently the code is looping over N^2 instead of N(N-1)/2 
    // This is happening because the LJ list is 2x long as it has to be
    //diff *= 0.5; 
    //std::cout << "Force: " << diff << " " << pairC12 << " " << pairC6 << " " << r12.length() << "\n";

    //Scale the force vector accordingly
    const Force f12 = diff * r12;
    //std::cout << "Atoms: " << localIndex[0] << " " << localIndex[1] << " " << f12.length() << " " << f12 << "\n";
    //std::cout << "Force2: " << f12 << "\n";

    // 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[gromacsPairEnergyIndex] += 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);
    } 

 }
}

getMoleculePointers()

void GromacsPairElem::getMoleculePointers ( Molecule *  mol, int *  count, int32 ***  byatom, GromacsPair **  structarray  )

static

Definition at line 27 of file ComputeGromacsPair.C.

References NAMD_die(), and Molecule::numLJPair.

{
#ifdef MEM_OPT_VERSION
    NAMD_die("Should not be called in GromacsPairElem::getMoleculePointers in memory optimized version!");
#else
    *count = mol->numLJPair;
    *byatom = mol->gromacsPairByAtom;
    *structarray = mol->gromacsPair;
#endif
}

getParameterPointers()

void GromacsPairElem::getParameterPointers ( Parameters *  p, const GromacsPairValue **  v  )

static

Definition at line 39 of file ComputeGromacsPair.C.

References p.

                                                                                    {
    // JLai
    *v=p->gromacsPair_array;
}

getTupleInfo()

static void GromacsPairElem::getTupleInfo ( AtomSignature *  sig, int *  count, TupleSignature **  t  )

inlinestatic

Definition at line 37 of file ComputeGromacsPair.h.

References AtomSignature::gromacsPairCnt, and AtomSignature::gromacsPairSigs.

                                                                                 {
        *count = sig->gromacsPairCnt;
        *t = sig->gromacsPairSigs;
    }

hash()

int GromacsPairElem::hash ( void  ) const

inline

Definition at line 48 of file ComputeGromacsPair.h.

References atomID.

{ return 0x7FFFFFFF & ( (atomID[0]<<16) + (atomID[1])); }

operator<()

int GromacsPairElem::operator< ( const GromacsPairElem &  a ) const

inline

Definition at line 41 of file ComputeGromacsPair.inl.

References atomID.

  {
    return (atomID[0] < a.atomID[0] ||
            (atomID[0] == a.atomID[0] &&
            (atomID[1] < a.atomID[1]) ));
  }

operator==()

int GromacsPairElem::operator== ( const GromacsPairElem &  a ) const

inline

Definition at line 36 of file ComputeGromacsPair.inl.

References atomID.

  {
    return (a.atomID[0] == atomID[0] && a.atomID[1] == atomID[1]);
  }

submitReductionData()

void GromacsPairElem::submitReductionData ( BigReal *  data, SubmitReduction *  reduction  )

static

Definition at line 143 of file ComputeGromacsPair.C.

References ADD_TENSOR, gromacsPairEnergyIndex, SubmitReduction::item(), and REDUCTION_GRO_LJ_ENERGY.

{
    // JLai
    reduction->item(REDUCTION_GRO_LJ_ENERGY) += data[gromacsPairEnergyIndex];
    ADD_TENSOR(reduction,REDUCTION_VIRIAL_NBOND,data,virialIndex);
    return;
}

Member Data Documentation

atomID

AtomID GromacsPairElem::atomID[size]

Definition at line 27 of file ComputeGromacsPair.h.

Referenced by computeForce(), GromacsPairElem(), hash(), operator<(), and operator==().

localIndex

int GromacsPairElem::localIndex[size]

Definition at line 28 of file ComputeGromacsPair.h.

Referenced by computeForce().

p

TuplePatchElem* GromacsPairElem::p[size]

Definition at line 29 of file ComputeGromacsPair.h.

Referenced by computeForce(), and getParameterPointers().

pressureProfileAtomTypes

int GromacsPairElem::pressureProfileAtomTypes = 1

static

Definition at line 44 of file ComputeGromacsPair.h.

Referenced by computeForce().

pressureProfileMin

BigReal GromacsPairElem::pressureProfileMin = 0

static

Definition at line 46 of file ComputeGromacsPair.h.

Referenced by computeForce().

pressureProfileSlabs

int GromacsPairElem::pressureProfileSlabs = 0

static

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 43 of file ComputeGromacsPair.h.

Referenced by computeForce().

pressureProfileThickness

BigReal GromacsPairElem::pressureProfileThickness = 0

static

Definition at line 45 of file ComputeGromacsPair.h.

Referenced by computeForce().

scale

Real GromacsPairElem::scale

Definition at line 30 of file ComputeGromacsPair.h.

Referenced by computeForce().

value

const GromacsPairValue* GromacsPairElem::value

Definition at line 51 of file ComputeGromacsPair.h.

Referenced by computeForce(), and GromacsPairElem().

---

The documentation for this class was generated from the following files:

• ComputeGromacsPair.h
• ComputeGromacsPair.C
• ComputeGromacsPair.inl