#include <ComputeRestraints.h>

Inheritance diagram for ComputeRestraints:

Public Member Functions
	ComputeRestraints (ComputeID c, PatchID pid)

virtual	~ComputeRestraints ()

virtual void	doForce (FullAtom p, Results r)

Public Member Functions inherited from ComputeHomePatch
	ComputeHomePatch (ComputeID c, PatchID pid)

virtual	~ComputeHomePatch ()

virtual void	initialize ()

virtual void	atomUpdate ()

virtual void	doWork ()

Public Member Functions inherited from Compute
	Compute (ComputeID)

int	type ()

virtual	~Compute ()

void	setNumPatches (int n)

int	getNumPatches ()

virtual void	patchReady (PatchID, int doneMigration, int seq)

virtual int	noWork ()

virtual void	finishPatch (int)

int	sequence (void)

int	priority (void)

int	getGBISPhase (void)

virtual void	gbisP2PatchReady (PatchID, int seq)

virtual void	gbisP3PatchReady (PatchID, int seq)

Public Attributes
SubmitReduction *	reduction

Public Attributes inherited from Compute
const ComputeID	cid

LDObjHandle	ldObjHandle

LocalWorkMsg *const	localWorkMsg

Additional Inherited Members
Protected Member Functions inherited from Compute
void	enqueueWork ()

Protected Attributes inherited from ComputeHomePatch
int	numAtoms

Patch *	patch

HomePatch *	homePatch

Protected Attributes inherited from Compute
int	computeType

int	basePriority

int	gbisPhase

int	gbisPhasePriority [3]

Detailed Description

Definition at line 13 of file ComputeRestraints.h.

Constructor & Destructor Documentation

ComputeRestraints::ComputeRestraints	(	ComputeID	c,
		PatchID	pid
	)

Definition at line 20 of file ComputeRestraints.C.

References SimParameters::constraintExp, SimParameters::constrXOn, SimParameters::constrYOn, SimParameters::constrZOn, SimParameters::movingConstraintsOn, SimParameters::movingConsVel, Node::Object(), ReductionMgr::Object(), reduction, REDUCTIONS_BASIC, SimParameters::rotConsAxis, SimParameters::rotConsPivot, SimParameters::rotConstraintsOn, SimParameters::rotConsVel, SimParameters::selectConstraintsOn, Node::simParameters, simParams, and ReductionMgr::willSubmit().

   : ComputeHomePatch(c,pid)
 {
         reduction = ReductionMgr::Object()->willSubmit(REDUCTIONS_BASIC);
 
         SimParameters *simParams = Node::Object()->simParameters;
 
         //  Get parameters from the SimParameters object
         consExp = simParams->constraintExp;
         
         //****** BEGIN selective restraints (X,Y,Z) changes 
         consSelectOn = simParams->selectConstraintsOn;
         if (consSelectOn) {
           consSelectX = simParams->constrXOn;
           consSelectY = simParams->constrYOn;
           consSelectZ = simParams->constrZOn;
         }
         //****** END selective restraints (X,Y,Z) changes 
         
         //****** BEGIN moving constraints changes 
         consMoveOn = simParams->movingConstraintsOn;
         if (consMoveOn) {
           moveVel = simParams->movingConsVel;
         }
         //****** END moving constraints changes 
         //****** BEGIN rotating constraints changes 
         consRotOn = simParams->rotConstraintsOn;
         if (consRotOn) {
           rotVel = simParams->rotConsVel;
           rotAxis = simParams->rotConsAxis;
           rotPivot = simParams->rotConsPivot;
         }
         //****** END rotating constraints changes 
 
 }

ComputeRestraints::~ComputeRestraints ( )

virtual

Definition at line 65 of file ComputeRestraints.C.

References reduction.

 {
         delete reduction;
 }

Member Function Documentation

void ComputeRestraints::doForce	(	FullAtom *	p,
		Results *	r
	)

virtual

Implements ComputeHomePatch.

Definition at line 77 of file ComputeRestraints.C.

References ADD_TENSOR_OBJECT, ADD_VECTOR_OBJECT, SimParameters::constraintScaling, Lattice::delta(), Results::f, FullAtom::fixedPosition, Patch::flags, Molecule::get_cons_params(), CompAtomExt::id, Molecule::is_atom_constrained(), SubmitReduction::item(), Patch::lattice, Vector::length(), mat_multiply_vec(), Node::molecule, Results::normal, ComputeHomePatch::numAtoms, Node::Object(), outer(), ComputeHomePatch::patch, reduction, REDUCTION_BC_ENERGY, Node::simParameters, simParams, SimParameters::sphericalConstraintsOn, SimParameters::sphericalConstrCenter, Flags::step, SubmitReduction::submit(), vec_rotation_matrix(), and Vector::x.

 {
         Molecule *molecule = Node::Object()->molecule;
         Real k;                 //  Force constant
         SimParameters *simParams = Node::Object()->simParameters;
         BigReal scaling = simParams->constraintScaling;
         Vector refPos;          //  Reference position
         BigReal r, r2;  //  r=distance between atom position and the
                         //  reference position, r2 = r^2
         Vector Rij;     //  vector between current position and reference pos
         BigReal value;  //  Current calculated value
 
         // aliases to work with old code
         Force *f = res->f[Results::normal];
         BigReal energy = 0;
         BigReal m[9];
         Tensor virial;
         Vector netForce = 0;
 
         // BEGIN moving and rotating constraint changes ******
 
         // This version only allows one atom to be moved 
         // and only ALL ref positions to be rotated
 
         int currentTime = patch->flags.step;
         if (consRotOn) {
           vec_rotation_matrix(rotVel * currentTime, rotAxis, m);
         }
 
         // END moving and rotating constraint changes ******
 
           
         if (scaling != 0.) for (int localID=0; localID<numAtoms; ++localID)
         {
           if (molecule->is_atom_constrained(p[localID].id))
           {
 #ifndef MEM_OPT_VERSION
             molecule->get_cons_params(k, refPos, p[localID].id);
 #else
             k = 1.0;
             refPos = p[localID].fixedPosition;
 #endif
 
             k *= scaling;
 
             // BEGIN moving and rotating constraint changes ******
             
             if (consMoveOn) {
               refPos += currentTime * moveVel;
             }
             else if(consRotOn) {
               refPos = mat_multiply_vec(refPos - rotPivot, m) + rotPivot;
             }
 
             // END moving and rotating constraint changes *******
 
             if (simParams->sphericalConstraintsOn) {
               BigReal refRad = (refPos - simParams->sphericalConstrCenter).length();
               Vector relPos = patch->lattice.delta(p[localID].position, simParams->sphericalConstrCenter);
               refPos = simParams->sphericalConstrCenter + relPos * (refRad/relPos.length());
             }
 
             Rij = patch->lattice.delta(refPos,p[localID].position);
             Vector vpos = refPos - Rij;
 
             //****** BEGIN selective restraints (X,Y,Z) changes 
             if (consSelectOn) { // check which components we want to restrain:
               if (!consSelectX) {Rij.x=0.0;}  // by setting the appropriate
               if (!consSelectY) {Rij.y=0.0;}  // Cartesian component to zero
               if (!consSelectZ) {Rij.z=0.0;}  // we will avoid a restoring force
             }                                 // along that component, and the
                                               // energy will also be correct
             //****** END selective restraints (X,Y,Z) changes 
 
             
             //  Calculate the distance and the distance squared
             r2 = Rij.length2();
             r = sqrt(r2);
 
             //  Only calculate the energy and the force if the distance is
             //  non-zero.   Otherwise, you could end up dividing by 0, which
             //  is bad
             if (r>0.0)
             {
               value=k;
       
               //  Loop through and multiple k by r consExp times.
               //  i.e.  calculate kr^e
               //  I know, I could use pow(), but I don't trust it.
               for (int k=0; k<consExp; ++k)
               {
                 value *= r;
               }
 
               //  Add to the energy total
               energy += value;
       
               //  Now calculate the force, which is ekr^(e-1).  Also, divide
               //  by another factor of r to normalize the vector before we
               //  multiple it by the magnitude
               value *= consExp;
               value /= r2;
       
               Rij *= value;
               //iout << iINFO << "restraining force" << Rij        << "\n"; 
 
               f[localID] += Rij;
               netForce += Rij;
               virial += outer(Rij,vpos);
             }
           }
         }
 
         reduction->item(REDUCTION_BC_ENERGY) += energy;
         ADD_TENSOR_OBJECT(reduction,REDUCTION_VIRIAL_NORMAL,virial);
         ADD_VECTOR_OBJECT(reduction,REDUCTION_EXT_FORCE_NORMAL,netForce);
         reduction->submit();
 
 }

Member Data Documentation

SubmitReduction* ComputeRestraints::reduction

Definition at line 39 of file ComputeRestraints.h.

Referenced by ComputeRestraints(), doForce(), and ~ComputeRestraints().

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation