FFTPoissonSolver.cpp

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// -*- C++ -*-
/***************************************************************************
 *
 *
 * FFTPoissonSolver.cc
 *
 *
 *
 *
 *
 *
 *
 ***************************************************************************/
 
#include "Solvers/FFTPoissonSolver.h"
#include "Algorithms/PartBunch.h"
#include "Physics/Physics.h"
#include "Utility/IpplTimings.h"
#include "BasicActions/Option.h"
#include "Utilities/Options.h"
#include "Utilities/Util.h"
#include <fstream>
 
extern Inform *gmsg;
// a little helper class to specialize the action of the Green's function
// calculation.  This should be specialized for each dimension
// to the proper action for computing the Green's function.  The first
// template parameter is the full type of the Field to compute, and the second
// is the dimension of the data, which should be specialized.
 
template<unsigned int Dim>
struct SpecializedGreensFunction { };
 
template<>
struct SpecializedGreensFunction<3> {
    template<class T, class FT, class FT2>
    static void calculate(Vektor<T, 3> &hrsq, FT &grn, FT2 *grnI) {
        grn = grnI[0] * hrsq[0] + grnI[1] * hrsq[1] + grnI[2] * hrsq[2];
        grn = 1.0 / sqrt(grn);
        grn[0][0][0] = grn[0][0][1];
    }
};
 
 
// constructor
 
 
FFTPoissonSolver::FFTPoissonSolver(Mesh_t *mesh, FieldLayout_t *fl, std::string greensFunction, std::string bcz):
    mesh_m(mesh),
    layout_m(fl),
    mesh2_m(nullptr),
    layout2_m(nullptr),
    mesh3_m(nullptr),
    layout3_m(nullptr),
    mesh4_m(nullptr),
    layout4_m(nullptr)
{
    bcz_m = (bcz == std::string("PERIODIC"));   // for DC beams, the z direction has periodic boundary conditions
    integratedGreens_m = (greensFunction == std::string("INTEGRATED"));
 
    initializeFields();
 
    GreensFunctionTimer_m = IpplTimings::getTimer("SF: GreensFTotal");
    ComputePotential_m = IpplTimings::getTimer("ComputePotential");
}
 
 
FFTPoissonSolver::FFTPoissonSolver(PartBunch &beam, std::string greensFunction):
    mesh_m(&beam.getMesh()),
    layout_m(&beam.getFieldLayout()),
    mesh2_m(nullptr),
    layout2_m(nullptr),
    mesh3_m(nullptr),
    layout3_m(nullptr),
    mesh4_m(nullptr),
    layout4_m(nullptr)
{
    integratedGreens_m = (greensFunction == std::string("INTEGRATED"));
 
    initializeFields();
 
    GreensFunctionTimer_m = IpplTimings::getTimer("SF: GreensFTotal");
    ComputePotential_m = IpplTimings::getTimer("ComputePotential");
}
 
// destructor
FFTPoissonSolver::~FFTPoissonSolver() {}
 
void FFTPoissonSolver::initializeFields() {
 
    domain_m = layout_m->getDomain();
 
    // For efficiency in the FFT's, we can use a parallel decomposition
    // which can be serial in the first dimension.
    e_dim_tag decomp[3];
    e_dim_tag decomp2[3];
    for(int d = 0; d < 3; ++ d) {
        decomp[d] = layout_m->getRequestedDistribution(d);
        decomp2[d] = layout_m->getRequestedDistribution(d);
    }
 
    if (bcz_m) {
        // The FFT's require double-sized field sizes in order to
        // simulate an isolated system.  The FFT of the charge density field, rho,
        // would otherwise mimic periodic boundary conditions, i.e. as if there were
        // several beams set a periodic distance apart.  The double-sized fields in x and
        // alleviate this problem, in z we have periodic BC's
        for (int i = 0; i < 2; ++ i) {
            hr_m[i] = mesh_m->get_meshSpacing(i);
            nr_m[i] = domain_m[i].length();
            domain2_m[i] = Index(2 * nr_m[i] + 1);
        }
 
        hr_m[2] = mesh_m->get_meshSpacing(2);
        nr_m[2] = domain_m[2].length();
        domain2_m[2] = Index(nr_m[2] + 1);
 
        for (int i = 0; i < 2 * 3; ++ i) {
            bc_m[i] = new ZeroFace<double, 3, Mesh_t, Center_t>(i);
            vbc_m[i] = new ZeroFace<Vector_t, 3, Mesh_t, Center_t>(i);
        }
        // z-direction
        bc_m[4] = new ParallelPeriodicFace<double,3,Mesh_t,Center_t>(4);
        bc_m[5] = new ParallelPeriodicFace<double,3,Mesh_t,Center_t>(5);
        vbc_m[4] = new ZeroFace<Vector_t, 3, Mesh_t, Center_t>(4);
        vbc_m[5] = new ZeroFace<Vector_t, 3, Mesh_t, Center_t>(5);
    }
    else {
        // The FFT's require double-sized field sizes in order to
        // simulate an isolated system.  The FFT of the charge density field, rho,
        // would otherwise mimic periodic boundary conditions, i.e. as if there were
        // several beams set a periodic distance apart.  The double-sized fields
        // alleviate this problem.
        for (int i = 0; i < 3; ++ i) {
            hr_m[i] = mesh_m->get_meshSpacing(i);
            nr_m[i] = domain_m[i].length();
            domain2_m[i] = Index(2 * nr_m[i] + 1);
        }
 
        for (int i = 0; i < 2 * 3; ++ i) {
            bc_m[i] = new ZeroFace<double, 3, Mesh_t, Center_t>(i);
            vbc_m[i] = new ZeroFace<Vector_t, 3, Mesh_t, Center_t>(i);
        }
    }
 
    // create double sized mesh and layout objects for the use in the FFT's
    mesh2_m = std::unique_ptr<Mesh_t>(new Mesh_t(domain2_m));
    layout2_m = std::unique_ptr<FieldLayout_t>(new FieldLayout_t(*mesh2_m, decomp));
 
    rho2_m.initialize(*mesh2_m, *layout2_m);
 
    NDIndex<3> tmpdomain;
    // Create the domain for the transformed (complex) fields.  Do this by
    // taking the domain from the doubled mesh, permuting it to the right, and
    // setting the 2nd dimension to have n/2 + 1 elements.
    if (bcz_m)
        domain3_m[0] = Index(nr_m[2] + 1);
    else
        domain3_m[0] = Index(2 * nr_m[2] + 1);
    domain3_m[1] = Index(nr_m[0] + 2);
    domain3_m[2] = Index(2 * nr_m[1] + 1);
 
    // create mesh and layout for the new real-to-complex FFT's, for the
    // complex transformed fields
    mesh3_m = std::unique_ptr<Mesh_t>(new Mesh_t(domain3_m));
    layout3_m = std::unique_ptr<FieldLayout_t>(new FieldLayout_t(*mesh3_m, decomp2));
 
    rho2tr_m.initialize(*mesh3_m, *layout3_m);
    imgrho2tr_m.initialize(*mesh3_m, *layout3_m);
    grntr_m.initialize(*mesh3_m, *layout3_m);
 
    // helper field for sin
    greentr_m.initialize(*mesh3_m, *layout3_m);
 
    for (int i = 0; i < 3; ++ i) {
        domain4_m[i] = Index(nr_m[i] + 2);
    }
    mesh4_m = std::unique_ptr<Mesh_t>(new Mesh_t(domain4_m));
    layout4_m = std::unique_ptr<FieldLayout_t>(new FieldLayout_t(*mesh4_m, decomp));
 
    tmpgreen_m.initialize(*mesh4_m, *layout4_m);
 
    // create a domain used to indicate to the FFT's how to construct it's
    // temporary fields.  This is the same as the complex field's domain,
    // but permuted back to the left.
    tmpdomain = layout3_m->getDomain();
    for (int i = 0; i < 3; ++ i)
        domainFFTConstruct_m[i] = tmpdomain[(i+1) % 3];
 
    // create the FFT object
    fft_m = std::unique_ptr<FFT_t>(new FFT_t(layout2_m->getDomain(), domainFFTConstruct_m));
 
    // these are fields that are used for calculating the Green's function.
    // they eliminate some calculation at each time-step.
    for (int i = 0; i < 3; ++ i) {
        grnIField_m[i].initialize(*mesh2_m, *layout2_m);
        grnIField_m[i][domain2_m] = where(lt(domain2_m[i], nr_m[i]),
                                          domain2_m[i] * domain2_m[i],
                                          (2 * nr_m[i] - domain2_m[i]) *
                                          (2 * nr_m[i] - domain2_m[i]));
    }
}
 
// given a charge-density field rho and a set of mesh spacings hr,
// compute the electric potential from the image charge by solving
// the Poisson's equation
 
void FFTPoissonSolver::computePotential(Field_t &rho, Vector_t hr, double zshift) {
 
    // use grid of complex doubled in both dimensions
    // and store rho in lower left quadrant of doubled grid
    rho2_m = 0.0;
 
    rho2_m[domain_m] = rho[domain_m];
 
    // needed in greens function
    hr_m = hr;
    // FFT double-sized charge density
    // we do a backward transformation so that we dont have to account for the normalization factor
    // that is used in the forward transformation of the IPPL FFT
    fft_m->transform(-1, rho2_m, rho2tr_m);
 
    // must be called if the mesh size has changed
    // have to check if we can do G with h = (1,1,1)
    // and rescale later
 
    // Do image charge.
    // The minus sign is due to image charge.
    // Convolute transformed charge density with shifted green's function.
    IpplTimings::startTimer(GreensFunctionTimer_m);
    shiftedIntGreensFunction(zshift);
    IpplTimings::stopTimer(GreensFunctionTimer_m);
 
    // Multiply transformed charge density and
    // transformed Green's function. Don't divide
    // by (2*nx_m)*(2*ny_m), as Ryne does; this
    // normalization is done in POOMA's fft routine.
    imgrho2tr_m = - rho2tr_m * grntr_m;
 
    // Inverse FFT to find image charge potential, rho2_m equals the electrostatic potential.
    fft_m->transform(+1, imgrho2tr_m, rho2_m);
 
    // Re-use rho to store image potential. Flip z coordinate since this is a mirror image.
    Index I = nr_m[0];
    Index J = nr_m[1];
    Index K = nr_m[2];
    rho[I][J][K] = rho2_m[I][J][nr_m[2] - K - 1];
 
}
 
 
// given a charge-density field rho and a set of mesh spacings hr,
// compute the electric field and put in eg by solving the Poisson's equation
 
void FFTPoissonSolver::computePotential(Field_t &rho, Vector_t hr) {
 
    IpplTimings::startTimer(ComputePotential_m);
 
    // use grid of complex doubled in both dimensions
    // and store rho in lower left quadrant of doubled grid
    rho2_m = 0.0;
 
    rho2_m[domain_m] = rho[domain_m];
 
    // needed in greens function
    hr_m = hr;
 
    // FFT double-sized charge density
    // we do a backward transformation so that we dont have to account for the normalization factor
    // that is used in the forward transformation of the IPPL FFT
    fft_m->transform(-1, rho2_m, rho2tr_m);
 
    // must be called if the mesh size has changed
    // have to check if we can do G with h = (1,1,1)
    // and rescale later
    IpplTimings::startTimer(GreensFunctionTimer_m);
    if(integratedGreens_m)
        integratedGreensFunction();
    else
        greensFunction();
    IpplTimings::stopTimer(GreensFunctionTimer_m);
    // multiply transformed charge density
    // and transformed Green function
    // Don't divide by (2*nx_m)*(2*ny_m), as Ryne does;
    // this normalization is done in POOMA's fft routine.
    rho2tr_m *= grntr_m;
 
    // inverse FFT, rho2_m equals to the electrostatic potential
    fft_m->transform(+1, rho2tr_m, rho2_m);
    // end convolution
 
    // back to physical grid
    // reuse the charge density field to store the electrostatic potential
    rho[domain_m] = rho2_m[domain_m];
    IpplTimings::stopTimer(ComputePotential_m);
}
 
// calculate the FFT of the Green's function for the given field
void FFTPoissonSolver::greensFunction() {
 
    //hr_m[0]=hr_m[1]=hr_m[2]=1;
 
    Vector_t hrsq(hr_m * hr_m);
    SpecializedGreensFunction<3>::calculate(hrsq, rho2_m, grnIField_m);
    // Green's function calculation complete at this point.
    // The next step is to FFT it.
    // FFT of Green's function
 
    // we do a backward transformation so that we dont have to account for the normalization factor
    // that is used in the forward transformation of the IPPL FFT
    fft_m->transform(-1, rho2_m, grntr_m);
}
 
void FFTPoissonSolver::integratedGreensFunction() {
 
 
 
    NDIndex<3> idx =  layout4_m->getLocalNDIndex();
    double cellVolume = hr_m[0] * hr_m[1] * hr_m[2];
    tmpgreen_m = 0.0;
 
    for(int k = idx[2].first(); k <= idx[2].last() + 1; k++) {
        for(int j = idx[1].first(); j <=  idx[1].last() + 1; j++) {
            for(int i = idx[0].first(); i <= idx[0].last() + 1; i++) {
 
                Vector_t vv = Vector_t(0.0);
                vv(0) = i * hr_m[0] - hr_m[0] / 2;
                vv(1) = j * hr_m[1] - hr_m[1] / 2;
                vv(2) = k * hr_m[2] - hr_m[2] / 2;
 
                double r = sqrt(vv(0) * vv(0) + vv(1) * vv(1) + vv(2) * vv(2));
                double tmpgrn  = -vv(2) * vv(2) * atan(vv(0) * vv(1) / (vv(2) * r)) / 2;
                tmpgrn += -vv(1) * vv(1) * atan(vv(0) * vv(2) / (vv(1) * r)) / 2;
                tmpgrn += -vv(0) * vv(0) * atan(vv(1) * vv(2) / (vv(0) * r)) / 2;
                tmpgrn += vv(1) * vv(2) * log(vv(0) + r);
                tmpgrn += vv(0) * vv(2) * log(vv(1) + r);
                tmpgrn += vv(0) * vv(1) * log(vv(2) + r);
 
                tmpgreen_m[i][j][k] = tmpgrn / cellVolume;
 
            }
        }
    }
 
 
    //assign seems to have problems when we need values that are on another CPU, i.e. [I+1]
    /*assign(rho2_m[I][J][K] ,
      tmpgreen_m[I+1][J+1][K+1] - tmpgreen_m[I][J+1][K+1] -
      tmpgreen_m[I+1][J][K+1] + tmpgreen_m[I][J][K+1] -
      tmpgreen_m[I+1][J+1][K] + tmpgreen_m[I][J+1][K] +
      tmpgreen_m[I+1][J][K] - tmpgreen_m[I][J][K]);*/
 
    Index I = nr_m[0] + 1;
    Index J = nr_m[1] + 1;
    Index K = nr_m[2] + 1;
 
 
    // the actual integration
    rho2_m = 0.0;
    rho2_m[I][J][K]  = tmpgreen_m[I+1][J+1][K+1];
    rho2_m[I][J][K] += tmpgreen_m[I+1][J][K];
    rho2_m[I][J][K] += tmpgreen_m[I][J+1][K];
    rho2_m[I][J][K] += tmpgreen_m[I][J][K+1];
    rho2_m[I][J][K] -= tmpgreen_m[I+1][J+1][K];
    rho2_m[I][J][K] -= tmpgreen_m[I+1][J][K+1];
    rho2_m[I][J][K] -= tmpgreen_m[I][J+1][K+1];
    rho2_m[I][J][K] -= tmpgreen_m[I][J][K];
 
    mirrorRhoField();
 
    fft_m->transform(-1, rho2_m, grntr_m);
 
}
 
void FFTPoissonSolver::shiftedIntGreensFunction(double zshift) {
 
    tmpgreen_m = 0.0;
    Field_t grn2(*mesh4_m, *layout4_m);
    grn2 = 0.0;
    NDIndex<3> idx =  layout4_m->getLocalNDIndex();
    double cellVolume = hr_m[0] * hr_m[1] * hr_m[2];
 
    for(int k = idx[2].first(); k <= idx[2].last(); k++) {
        for(int j = idx[1].first(); j <= idx[1].last(); j++) {
            for(int i = idx[0].first(); i <= idx[0].last(); i++) {
 
                Vector_t vv = Vector_t(0.0);
                vv(0) = i * hr_m[0] - hr_m[0] / 2;
                vv(1) = j * hr_m[1] - hr_m[1] / 2;
                vv(2) = k * hr_m[2] - hr_m[2] / 2 + zshift;
 
                double r = sqrt(vv(0) * vv(0) + vv(1) * vv(1) + vv(2) * vv(2));
                double tmpgrn  = -vv(2) * vv(2) * atan(vv(0) * vv(1) / (vv(2) * r)) / 2;
                tmpgrn += -vv(1) * vv(1) * atan(vv(0) * vv(2) / (vv(1) * r)) / 2;
                tmpgrn += -vv(0) * vv(0) * atan(vv(1) * vv(2) / (vv(0) * r)) / 2;
                tmpgrn += vv(1) * vv(2) * log(vv(0) + r);
                tmpgrn += vv(0) * vv(2) * log(vv(1) + r);
                tmpgrn += vv(0) * vv(1) * log(vv(2) + r);
 
                tmpgreen_m[i][j][k] = tmpgrn / cellVolume;
 
            }
        }
    }
 
    for(int k = idx[2].first(); k <= idx[2].last(); k++) {
        for(int j = idx[1].first(); j <= idx[1].last(); j++) {
            for(int i = idx[0].first(); i <= idx[0].last(); i++) {
 
                Vector_t vv = Vector_t(0.0);
                vv(0) = i * hr_m[0] - hr_m[0] / 2;
                vv(1) = j * hr_m[1] - hr_m[1] / 2;
                vv(2) = k * hr_m[2] - hr_m[2] / 2 + zshift - nr_m[2] * hr_m[2];
 
                double r = sqrt(vv(0) * vv(0) + vv(1) * vv(1) + vv(2) * vv(2));
                double tmpgrn  = -vv(2) * vv(2) * atan(vv(0) * vv(1) / (vv(2) * r)) / 2;
                tmpgrn += -vv(1) * vv(1) * atan(vv(0) * vv(2) / (vv(1) * r)) / 2;
                tmpgrn += -vv(0) * vv(0) * atan(vv(1) * vv(2) / (vv(0) * r)) / 2;
                tmpgrn += vv(1) * vv(2) * log(vv(0) + r);
                tmpgrn += vv(0) * vv(2) * log(vv(1) + r);
                tmpgrn += vv(0) * vv(1) * log(vv(2) + r);
 
                grn2[i][j][k] = tmpgrn / cellVolume;
 
            }
        }
    }
    Index I = nr_m[0] + 1;
    Index J = nr_m[1] + 1;
    Index K = nr_m[2] + 1;
 
    // the actual integration
    rho2_m = 0.0;
    rho2_m[I][J][K]  = tmpgreen_m[I+1][J+1][K+1];
    rho2_m[I][J][K] += tmpgreen_m[I+1][J][K];
    rho2_m[I][J][K] += tmpgreen_m[I][J+1][K];
    rho2_m[I][J][K] += tmpgreen_m[I][J][K+1];
    rho2_m[I][J][K] -= tmpgreen_m[I+1][J+1][K];
    rho2_m[I][J][K] -= tmpgreen_m[I+1][J][K+1];
    rho2_m[I][J][K] -= tmpgreen_m[I][J+1][K+1];
    rho2_m[I][J][K] -= tmpgreen_m[I][J][K];
 
    tmpgreen_m = 0.0;
    tmpgreen_m[I][J][K]  = grn2[I+1][J+1][K+1];
    tmpgreen_m[I][J][K] += grn2[I+1][J][K];
    tmpgreen_m[I][J][K] += grn2[I][J+1][K];
    tmpgreen_m[I][J][K] += grn2[I][J][K+1];
    tmpgreen_m[I][J][K] -= grn2[I+1][J+1][K];
    tmpgreen_m[I][J][K] -= grn2[I+1][J][K+1];
    tmpgreen_m[I][J][K] -= grn2[I][J+1][K+1];
    tmpgreen_m[I][J][K] -= grn2[I][J][K];
 
    mirrorRhoField(tmpgreen_m);
 
    fft_m->transform(-1, rho2_m, grntr_m);
}
 
void FFTPoissonSolver::mirrorRhoField() {
 
    Index aI(0, 2 * nr_m[0]);
    Index aJ(0, 2 * nr_m[1]);
 
    Index J(0, nr_m[1]);
    Index K(0, nr_m[2]);
 
    Index IE(nr_m[0] + 1, 2 * nr_m[0]);
    Index JE(nr_m[1] + 1, 2 * nr_m[1]);
    Index KE(nr_m[2] + 1, 2 * nr_m[2]);
 
    Index mirroredIE = 2 * nr_m[0] - IE;
    Index mirroredJE = 2 * nr_m[1] - JE;
    Index mirroredKE = 2 * nr_m[2] - KE;
 
    rho2_m[0][0][0] = rho2_m[0][0][1];
 
    rho2_m[IE][J ][K ] = rho2_m[mirroredIE][J         ][K         ];
    rho2_m[aI][JE][K ] = rho2_m[aI        ][mirroredJE][K         ];
    if (!bcz_m)
        rho2_m[aI][aJ][KE] = rho2_m[aI        ][aJ        ][mirroredKE];
 
}
 
void FFTPoissonSolver::mirrorRhoField(Field_t & ggrn2) {
 
    Index aI(0, 2 * nr_m[0]);
    Index aK(0, 2 * nr_m[2]);
 
    Index I(0, nr_m[0]);
    Index J(0, nr_m[1]);
    Index K(0, nr_m[2]);
 
    Index IE(nr_m[0] + 1, 2 * nr_m[0]);
    Index JE(nr_m[1] + 1, 2 * nr_m[1]);
    Index KE(nr_m[2] + 1, 2 * nr_m[2]);
 
    Index mirroredIE = 2*nr_m[0] - IE;
    Index mirroredJE = 2*nr_m[1] - JE;
    Index shiftedKE  = KE - nr_m[2];
 
    if (!bcz_m) {
        rho2_m[I ][J ][KE] = ggrn2[I          ][J         ][shiftedKE];
        rho2_m[IE][J ][aK] = rho2_m[mirroredIE][J         ][aK       ];
        rho2_m[aI][JE][aK] = rho2_m[aI        ][mirroredJE][aK       ];
    } else {
        rho2_m[IE][J ][K] = rho2_m[mirroredIE][J         ][K       ];
        rho2_m[aI][JE][K] = rho2_m[aI        ][mirroredJE][K       ];
    }
}
 
Inform &FFTPoissonSolver::print(Inform &os) const {
    os << "* ************* F F T P o i s s o n S o l v e r ************************************ " << endl;
    os << "* h " << hr_m << '\n';
    os << "* ********************************************************************************** " << endl;
    return os;
}