ComputeCylindricalBC.C

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#include "ComputeCylindricalBC.h"
#include "Node.h"
#include "SimParameters.h"
#include "Patch.h"

/************************************************************************/
/*                                                                      */
/*                      FUNCTION ComputeCylindricalBC                   */
/*                                                                      */
/*      This is the constructor for the ComputeCylindricalBC force object.*/
/*   It is responsible for getting all the parameters from the          */
/*   SimParameters object and then determining if this object needs     */
/*   to perform any computation.  It only needs to do so if there is    */
/*   some portion of the patch that lays outside of the cylindrical     */
/*   boundaries.                                                        */
/*                                                                      */
/************************************************************************/

ComputeCylindricalBC::ComputeCylindricalBC(ComputeID c, PatchID pid)
  : ComputePatch(c,pid)
{
        reduction = ReductionMgr::Object()->willSubmit(REDUCTIONS_BASIC);

        SimParameters *simParams = Node::Object()->simParameters;

        //  Get parameters from the SimParameters object
        axis = simParams->cylindricalBCAxis;
        r1 = simParams->cylindricalBCr1;
        r2 = simParams->cylindricalBCr2;
        r1_2 = r1*r1;
        r2_2 = r2*r2;
        k1 = simParams->cylindricalBCk1;
        k2 = simParams->cylindricalBCk2;
        exp1 = simParams->cylindricalBCexp1;
        exp2 = simParams->cylindricalBCexp2;
        //Additions for ends
        l1 = simParams->cylindricalBCl1;
        l2 = simParams->cylindricalBCl2;
        l1_2 = l1*l1;
        l2_2 = l2*l2;

        //  Check to see if this is one set of parameters or two
        if (r2 > -1.0)
        {
                twoForces = TRUE;
        }
        else
        {
                twoForces = FALSE;
        }

        center = simParams->cylindricalCenter;

}
/*                      END OF FUNCTION ComputeCylindricalBC            */

/************************************************************************/
/*                                                                      */
/*                      FUNCTION ~ComputeCylindricalBC                  */
/*                                                                      */
/*      This is the destructor for the ComputeCylindricalBC force object.       */
/*   It currently does ABSOLUTELY NOTHING!!                             */
/*                                                                      */
/************************************************************************/

ComputeCylindricalBC::~ComputeCylindricalBC()

{
        delete reduction;
}
/*                      END OF FUNCTION ~ComputeCylindricalBC           */

/************************************************************************/
/*                                                                      */
/*                              FUNCTION force                          */
/*                                                                      */
/*   INPUTS:                                                            */
/*      numAtoms - Number of coordinates being passed                   */
/*      x - Array of atom coordinates                                   */
/*      forces - Array of force vectors                                 */
/*                                                                      */
/*      This function calculates the force and energy for the cylindri. */
/*   boundary conditions for this patch.                                */
/*                                                                      */
/************************************************************************/

void ComputeCylindricalBC::doForce(CompAtom* p, CompAtomExt* pExt, Results* r)
{
        Vector diff;            //  Distance from atom to center of cylinder
        Vector f;               //  Calculated force vector
        int i, j;               //  Loop counters
        BigReal dist, dist_2;   //  Distance from atom to center, and this
                                //  distance squared
        BigReal rval;           //  Difference between distance from atom
                                //  to center and radius of cylinder
        BigReal eval;           //  Energy value for this atom
        BigReal fval;           //  Force magnitude for this atom

        // aliases to work with old code
        CompAtom *x = p;
        Force *forces = r->f[Results::normal];
        BigReal energy = 0;

        //  Loop through and check each atom
        for (i=0; i<numAtoms; i++)
        {
                //  Calculate the vector from the atom to the center of the
                //  cylinder
                diff.x = ( axis == 'x' ? 0.0 : x[i].position.x - center.x );
                diff.y = ( axis == 'y' ? 0.0 : x[i].position.y - center.y );
                diff.z = ( axis == 'z' ? 0.0 : x[i].position.z - center.z );
                
                //  Calculate the distance squared
                dist_2 = diff.x*diff.x + diff.y*diff.y + diff.z*diff.z;

                //  Look to see if we are outside either radius
                if ( (dist_2 > r1_2) || (twoForces && (dist_2 > r2_2)) )
                {
                        //  Calculate the distance to the center
                        dist = sqrt(dist_2);

                        //  Normalize the direction vector
                        diff /= dist;

                        //  Check to see if we are outside radius 1
                        if (dist > r1)
                        {
                                //  Assign the force vector to the
                                //  unit direction vector
                                f.x = diff.x;
                                f.y = diff.y;
                                f.z = diff.z;

                                //  Calculate the energy which is
                                //  e = k1*(r_i-r_center)^exp1
                                eval = k1;
                                rval = fabs(dist - r1);

                                for (j=0; j<exp1; j++)
                                {
                                        eval *= rval;
                                }

                                energy += eval;

                                //  Now calculate the force which is
                                //  e = -k1*exp1*(r_i-r_center1)^(exp1-1)
                                fval = -exp1*k1;

                                for (j=0; j<exp1-1; j++)
                                {
                                        fval *= rval;
                                }

                                //  Multiply the force magnitude to the
                                //  unit direction vector to get the
                                //  resulting force
                                f *= fval;

                                //  Add the force to the force vectors
                                forces[i].x += f.x;
                                forces[i].y += f.y;
                                forces[i].z += f.z;
                        }

                        //  Check to see if there is a second radius
                        //  and if we are outside of it
                        if (twoForces && (dist > r2) )
                        {
                                //  Assign the force vector to the
                                //  unit direction vector
                                f.x = diff.x;
                                f.y = diff.y;
                                f.z = diff.z;

                                //  Calculate the energy which is
                                //  e = k2*(r_i-r_center2)^exp2
                                eval = k2;
                                rval = fabs(dist - r2);

                                for (j=0; j<exp2; j++)
                                {
                                        eval *= rval;
                                }

                                energy += eval;

                                //  Now calculate the force which is
                                //  e = -k2*exp2*(r_i-r_center2)^(exp2-1)
                                fval = -exp2*k2;

                                for (j=0; j<exp2-1; j++)
                                {
                                        fval *= rval;
                                }

                                //  Multiply the force magnitude to the
                                //  unit direction vector to get the
                                //  resulting force
                                f *= fval;

                                //  Add the force to the force vectors
                                forces[i].x += f.x;
                                forces[i].y += f.y;
                                forces[i].z += f.z;
                        }
                }
        }
       //  Loop through and check each atom
        for (i=0; i<numAtoms; i++)
        {
                //  Calculate the vector from the atom to the center of the
                //  cylinder
                diff.x = ( axis != 'x' ? 0.0 : x[i].position.x - center.x );
                diff.y = ( axis != 'y' ? 0.0 : x[i].position.y - center.y );
                diff.z = ( axis != 'z' ? 0.0 : x[i].position.z - center.z );

                //  Calculate the distance squared
                dist_2 = diff.x*diff.x + diff.y*diff.y + diff.z*diff.z;

                //  Look to see if we are outside either radius
                if ( (dist_2 > l1_2)  || (twoForces && (dist_2 > l2_2)) )
                {
                        //  Calculate the distance to the center
                        dist = sqrt(dist_2);

                        //  Normalize the direction vector
                        diff /= dist;

                        //  Check to see if we are outside radius 1
                        if (dist > l1)
                        {
//printf ("Do faces one force z=%f\n", dist);
                                //  Assign the force vector to the
                                //  unit direction vector
                                f.x = diff.x;
                                f.y = diff.y;
                                f.z = diff.z;

                                //  Calculate the energy which is
                                //  e = k1*(r_i-r_center)^exp1
                                eval = k1;
                                rval = fabs(dist - l1);

                                for (j=0; j<exp1; j++)
                                {
                                        eval *= rval;
                                }

                                energy += eval;

                                //  Now calculate the force which is
                                //  e = -k1*exp1*(r_i-r_center1)^(exp1-1)
                                fval = -exp1*k1;

                                for (j=0; j<exp1-1; j++)
                                {
                                        fval *= rval;
                                }

                                //  Multiply the force magnitude to the
                                //  unit direction vector to get the
                                //  resulting force
                                f *= fval;

                                //  Add the force to the force vectors
                                forces[i].x += f.x;
                                forces[i].y += f.y;
                                forces[i].z += f.z;
                        }

                        //  Check to see if there is a second radius
                        //  and if we are outside of it
                        if (twoForces && (dist > l2) )
                        {
//printf ("Do faces two force z=%f\n", dist);
                                //  Assign the force vector to the
                                //  unit direction vector
                                f.x = diff.x;
                                f.y = diff.y;
                                f.z = diff.z;

                                //  Calculate the energy which is
                                //  e = k2*(r_i-r_center2)^exp2
                                eval = k2;
                                rval = fabs(dist - l2);

                                for (j=0; j<exp2; j++)
                                {
                                        eval *= rval;
                                }

                                energy += eval;

                                //  Now calculate the force which is
                                //  e = -k2*exp2*(r_i-r_center2)^(exp2-1)
                                fval = -exp2*k2;

                                for (j=0; j<exp2-1; j++)
                                {
                                        fval *= rval;
                                }

                                //  Multiply the force magnitude to the
                                //  unit direction vector to get the
                                //  resulting force
                                f *= fval;

                                //  Add the force to the force vectors
                                forces[i].x += f.x;
                                forces[i].y += f.y;
                                forces[i].z += f.z;
                        }
                }
        }

    reduction->item(REDUCTION_BC_ENERGY) += energy;
    reduction->submit();

}
/*                      END OF FUNCTION force                           */

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