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BondElem Class Reference

#include <ComputeBonds.h>

List of all members.

Public Types

enum  { size = 2 }
enum  { bondEnergyIndex, virialIndex, reductionDataSize }
enum  { reductionChecksumLabel = REDUCTION_BOND_CHECKSUM }

Public Member Functions

void computeForce (BigReal *, BigReal *)
int hash () const
 BondElem ()
 BondElem (AtomID atom0, const TupleSignature *sig, const BondValue *v)
 BondElem (const Bond *a, const BondValue *v)
 BondElem (AtomID atom0, AtomID atom1)
 ~BondElem ()
int operator== (const BondElem &a) const
int operator< (const BondElem &a) const

Static Public Member Functions

void loadTuplesForAtom (void *, AtomID, Molecule *)
void getMoleculePointers (Molecule *, int *, int32 ***, Bond **)
void getParameterPointers (Parameters *, const BondValue **)
void getTupleInfo (AtomSignature *sig, int *count, TupleSignature **t)
void submitReductionData (BigReal *, SubmitReduction *)

Public Attributes

AtomID atomID [size]
int localIndex [size]
TuplePatchElem * p [size]
Real scale
const BondValue * value

Static Public Attributes

int pressureProfileSlabs = 0
int pressureProfileAtomTypes = 1
BigReal pressureProfileThickness = 0
BigReal pressureProfileMin = 0

Member Enumeration Documentation

anonymous enum
 

Enumeration values:
size 

Definition at line 23 of file ComputeBonds.h.

00023 { size = 2 };

anonymous enum
 

Enumeration values:
bondEnergyIndex 
virialIndex 
reductionDataSize 

Definition at line 49 of file ComputeBonds.h.

00049 { bondEnergyIndex, TENSOR(virialIndex), reductionDataSize };

anonymous enum
 

Enumeration values:
reductionChecksumLabel 

Definition at line 50 of file ComputeBonds.h.

00050 { reductionChecksumLabel = REDUCTION_BOND_CHECKSUM };

Constructor & Destructor Documentation

BondElem::BondElem (   )  [inline]
 

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

Definition at line 12 of file ComputeBonds.inl.

00012 { ; }

BondElem::BondElem (  AtomID  atom0,
const TupleSignature *  sig,
const BondValue *  v
)  [inline]
 

Definition at line 14 of file ComputeBonds.inl.

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

00014                                                                                     {
00015     atomID[0] = atom0;
00016     atomID[1] = atom0 + sig->offset[0];
00017     value = &v[sig->tupleParamType];
00018 }

BondElem::BondElem (  const Bond *  a,
const BondValue *  v
)  [inline]
 

Definition at line 20 of file ComputeBonds.inl.

References bond::atom1, bond::atom2, atomID, Bond, bond::bond_type, and value.

00021   {
00022     atomID[0] = a->atom1;
00023     atomID[1] = a->atom2;
00024     value = &v[a->bond_type];
00025   }

BondElem::BondElem (  AtomID  atom0,
AtomID  atom1
)  [inline]
 

Definition at line 27 of file ComputeBonds.inl.

References atomID, and AtomID.

00028   {
00029     if (atom0 > atom1) {  // Swap end atoms so lowest is first!
00030       AtomID tmp = atom1; atom1 = atom0; atom0 = tmp; 
00031     }
00032     atomID[0] = atom0;
00033     atomID[1] = atom1;
00034   }

BondElem::~BondElem (   )  [inline]
 

Definition at line 57 of file ComputeBonds.h.

00057 {};

Member Function Documentation

void BondElem::computeForce (  BigReal *  ,
BigReal * 
) 
 

Definition at line 65 of file ComputeBonds.C.

References BigReal, DebugM, Lattice::delta(), TuplePatchElem::f, Force, BondValue::k, Patch::lattice, Vector::length(), Vector::length2(), localIndex, TuplePatchElem::p, p, CompAtom::partition, CompAtom::position, pp_clamp(), pp_reduction(), pressureProfileMin, pressureProfileSlabs, pressureProfileThickness, Real, value, TuplePatchElem::x, Vector::x, BondValue::x0, Vector::y, and Vector::z.

00067 {
00068   DebugM(1, "::computeForce() localIndex = " << localIndex[0] << " "
00069                << localIndex[1] << std::endl);
00070 
00071   BigReal r;            // Distance between atoms
00072   BigReal scal;         // force scaling
00073   BigReal diff;         // difference between theta and theta0
00074   BigReal energy;       // energy from the bond
00075 
00076   //DebugM(3, "::computeForce() -- starting with bond type " << bondType << std::endl);
00077 
00078   // get the bond information
00079   Real k = value->k * scale;
00080   Real x0 = value->x0;
00081 
00082   // compute vectors between atoms and their distances
00083   const Lattice & lattice = p[0]->p->lattice;
00084   const Vector r12 = lattice.delta(p[0]->x[localIndex[0]].position,
00085                                         p[1]->x[localIndex[1]].position);
00086 
00087   if (0. == x0) {  // for Drude bonds
00088     scal = -2.0*k;
00089     energy = k * r12.length2();
00090   }
00091   else {
00092     r = r12.length();
00093 
00094     //  Compare it to the rest bond
00095     diff = r - x0;
00096 
00097     //  Add the energy from this bond to the total energy
00098     energy = k*diff*diff;
00099 
00100     //  Determine the magnitude of the force
00101     diff *= -2.0*k;
00102 
00103     //  Scale the force vector accordingly
00104     scal = (diff/r);
00105   }
00106   const Force f12 = scal * r12;
00107 
00108 
00109   //  Now add the forces to each force vector
00110   p[0]->f[localIndex[0]] += f12;
00111   p[1]->f[localIndex[1]] -= f12;
00112 
00113   DebugM(3, "::computeForce() -- ending with delta energy " << energy << std::endl);
00114   reduction[bondEnergyIndex] += energy;
00115   reduction[virialIndex_XX] += f12.x * r12.x;
00116   reduction[virialIndex_XY] += f12.x * r12.y;
00117   reduction[virialIndex_XZ] += f12.x * r12.z;
00118   reduction[virialIndex_YX] += f12.y * r12.x;
00119   reduction[virialIndex_YY] += f12.y * r12.y;
00120   reduction[virialIndex_YZ] += f12.y * r12.z;
00121   reduction[virialIndex_ZX] += f12.z * r12.x;
00122   reduction[virialIndex_ZY] += f12.z * r12.y;
00123   reduction[virialIndex_ZZ] += f12.z * r12.z;
00124 
00125   if (pressureProfileData) {
00126     BigReal z1 = p[0]->x[localIndex[0]].position.z;
00127     BigReal z2 = p[1]->x[localIndex[1]].position.z;
00128     int n1 = (int)floor((z1-pressureProfileMin)/pressureProfileThickness);
00129     int n2 = (int)floor((z2-pressureProfileMin)/pressureProfileThickness);
00130     pp_clamp(n1, pressureProfileSlabs);
00131     pp_clamp(n2, pressureProfileSlabs);
00132     int p1 = p[0]->x[localIndex[0]].partition;
00133     int p2 = p[1]->x[localIndex[1]].partition;
00134     int pn = pressureProfileAtomTypes;
00135     pp_reduction(pressureProfileSlabs,
00136                 n1, n2, 
00137                 p1, p2, pn, 
00138                 f12.x * r12.x, f12.y * r12.y, f12.z * r12.z,
00139                 pressureProfileData);
00140   } 
00141 }

void BondElem::getMoleculePointers (  Molecule *  ,
int *  ,
int32 ***  ,
Bond ** 
)  [static]
 

Definition at line 50 of file ComputeBonds.C.

References Bond, int32, and NAMD_die().

00051 {
00052 #ifdef MEM_OPT_VERSION
00053   NAMD_die("Should not be called in BondElem::getMoleculePointers in memory optimized version!");
00054 #else
00055   *count = mol->numBonds;
00056   *byatom = mol->bondsByAtom;
00057   *structarray = mol->bonds;
00058 #endif
00059 }

void BondElem::getParameterPointers (  Parameters *  ,
const BondValue ** 
)  [static]
 

Definition at line 61 of file ComputeBonds.C.

References Parameters::bond_array.

00061                                                                       {
00062   *v = p->bond_array;
00063 }

void BondElem::getTupleInfo (  AtomSignature *  sig,
int *  count,
TupleSignature **  t
)  [inline, static]
 

Definition at line 33 of file ComputeBonds.h.

References AtomSignature::bondCnt, and AtomSignature::bondSigs.

00033                                                                                  {
00034         *count = sig->bondCnt;
00035         *t = sig->bondSigs;
00036     }

int BondElem::hash (  void   )  const [inline]
 

Definition at line 44 of file ComputeBonds.h.

00044 { return 0x7FFFFFFF & ( (atomID[0]<<16) + (atomID[1])); }

void BondElem::loadTuplesForAtom (  void *  ,
AtomID  ,
Molecule * 
)  [static]
 

int BondElem::operator< (  const BondElem &  a  )  const [inline]
 

Definition at line 41 of file ComputeBonds.inl.

References atomID.

00042   {
00043     return (atomID[0] < a.atomID[0] ||
00044             (atomID[0] == a.atomID[0] &&
00045             (atomID[1] < a.atomID[1]) ));
00046   }

int BondElem::operator== (  const BondElem &  a  )  const [inline]
 

Definition at line 36 of file ComputeBonds.inl.

References atomID.

00037   {
00038     return (a.atomID[0] == atomID[0] && a.atomID[1] == atomID[1]);
00039   }

void BondElem::submitReductionData (  BigReal *  ,
SubmitReduction * 
)  [static]
 

Definition at line 143 of file ComputeBonds.C.

References ADD_TENSOR, SubmitReduction::item(), REDUCTION_BOND_ENERGY, REDUCTION_VIRIAL_NORMAL, and virialIndex.

00144 {
00145   reduction->item(REDUCTION_BOND_ENERGY) += data[bondEnergyIndex];
00146   ADD_TENSOR(reduction,REDUCTION_VIRIAL_NORMAL,data,virialIndex);
00147 }

Member Data Documentation

AtomID BondElem::atomID[size]
 

Definition at line 24 of file ComputeBonds.h.

Referenced by BondElem(), operator<(), and operator==().

int BondElem::localIndex[size]
 

Definition at line 25 of file ComputeBonds.h.

Referenced by computeForce().

TuplePatchElem* BondElem::p[size]
 

Definition at line 26 of file ComputeBonds.h.

Referenced by computeForce().

int BondElem::pressureProfileAtomTypes = 1 [static]
 

Definition at line 45 of file ComputeBonds.C.

BigReal BondElem::pressureProfileMin = 0 [static]
 

Definition at line 47 of file ComputeBonds.C.

Referenced by computeForce().

int BondElem::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 44 of file ComputeBonds.C.

Referenced by computeForce().

BigReal BondElem::pressureProfileThickness = 0 [static]
 

Definition at line 46 of file ComputeBonds.C.

Referenced by computeForce().

Real BondElem::scale
 

Definition at line 27 of file ComputeBonds.h.

const BondValue* BondElem::value
 

Definition at line 47 of file ComputeBonds.h.

Referenced by BondElem(), and computeForce().

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