LandauDampingParameterList.cpp

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// Landau Damping Test that also has a parameterlist
// Modifications are tagged with MOD START , MOD END
//   Usage:
//     srun ./LandauDampingParameterList
//                  <nx> [<ny>...] <Np> <Nt> <stype [pre_args]>
//                  <lbthres> --overallocate <ovfactor> --info 10
//     nx           = No. cell-centered points in the x-direction
//     ny...        = No. cell-centered points in the y-, z-, ...-direction
//     Np           = Total no. of macro-particles in the simulation
//     Nt           = Number of time steps
//     stype        = Field solver type (FFT, CG and PCG supported) , PCG needs extra arguments
//     pre_args     = when using the PCG, a preconditioner and its corresponding parameters need to
//     be defined. Supported pre_args are: [jacobi, chebyshev <degree>, newton <level>,
//                              gauss-seidel <inner outer comm> , richardson <iter comm>]
//     jacobi       = diagonal preconditioner
//     chebyshev    = polynomial preconditioner (algo=chebyshev) of degree <degree>
//     newton       = polynomial preconditioner (algo=newton)    of degree 2^<level> - 1
//     gauss-seidel = symmetric 2-step gauss-seidel with <inner> inner iterations, <outer> outer
//     iterations richardson   = jacobi-richardson preconditioner with <iter> iterations comm = 0
//     means that there is no halo-exchange during preconditioning, 1 means there is halo-exchange
//     lbthres      = Load balancing threshold i.e., lbthres*100 is the maximum load imbalance
//                    percentage which can be tolerated and beyond which
//                    particle load balancing occurs. A value of 0.01 is good for many typical
//                    simulations.
//     ovfactor     = Over-allocation factor for the buffers used in the communication. Typical
//                values are 1.0, 2.0. Value 1.0 means no over-allocation.
//     Examples:
//     srun ./LandauDampingParameterList 64 64 64 10000 10 PCG chebyshev 31 0.01 --overallocate 2.0
//     --info 10 srun ./LandauDampingParameterList 64 64 64 10000 10 PCG gauss-seidel 5 2 0 0.01
//     --overallocate 2.0 --info 10
 
#include <Kokkos_MathematicalConstants.hpp>
#include <Kokkos_MathematicalFunctions.hpp>
#include <Kokkos_Random.hpp>
#include <chrono>
#include <iostream>
#include <random>
#include <set>
#include <string>
#include <vector>
 
#include "Utility/IpplTimings.h"
 
#include "ChargedParticles.hpp"
 
constexpr unsigned Dim = 3;
 
template <typename T>
struct Newton1D {
    double tol   = 1e-12;
    int max_iter = 20;
    double pi    = Kokkos::numbers::pi_v<double>;
 
    T k, alpha, u;
 
    KOKKOS_INLINE_FUNCTION Newton1D() {}
 
    KOKKOS_INLINE_FUNCTION Newton1D(const T& k_, const T& alpha_, const T& u_)
        : k(k_)
        , alpha(alpha_)
        , u(u_) {}
 
    KOKKOS_INLINE_FUNCTION ~Newton1D() {}
 
    KOKKOS_INLINE_FUNCTION T f(T& x) {
        T F;
        F = x + (alpha * (Kokkos::sin(k * x) / k)) - u;
        return F;
    }
 
    KOKKOS_INLINE_FUNCTION T fprime(T& x) {
        T Fprime;
        Fprime = 1 + (alpha * Kokkos::cos(k * x));
        return Fprime;
    }
 
    KOKKOS_FUNCTION
    void solve(T& x) {
        int iterations = 0;
        while (iterations < max_iter && Kokkos::fabs(f(x)) > tol) {
            x = x - (f(x) / fprime(x));
            iterations += 1;
        }
    }
};
 
template <typename T, class GeneratorPool, unsigned Dim>
struct generate_random {
    using view_type  = typename ippl::detail::ViewType<T, 1>::view_type;
    using value_type = typename T::value_type;
    // Output View for the random numbers
    view_type x, v;
 
    // The GeneratorPool
    GeneratorPool rand_pool;
 
    value_type alpha;
 
    T k, minU, maxU;
 
    // Initialize all members
    generate_random(view_type x_, view_type v_, GeneratorPool rand_pool_, value_type& alpha_, T& k_,
                    T& minU_, T& maxU_)
        : x(x_)
        , v(v_)
        , rand_pool(rand_pool_)
        , alpha(alpha_)
        , k(k_)
        , minU(minU_)
        , maxU(maxU_) {}
 
    KOKKOS_INLINE_FUNCTION void operator()(const size_t i) const {
        // Get a random number state from the pool for the active thread
        typename GeneratorPool::generator_type rand_gen = rand_pool.get_state();
 
        value_type u;
        for (unsigned d = 0; d < Dim; ++d) {
            u       = rand_gen.drand(minU[d], maxU[d]);
            x(i)[d] = u / (1 + alpha);
            Newton1D<value_type> solver(k[d], alpha, u);
            solver.solve(x(i)[d]);
            v(i)[d] = rand_gen.normal(0.0, 1.0);
        }
 
        // Give the state back, which will allow another thread to acquire it
        rand_pool.free_state(rand_gen);
    }
};
 
double CDF(const double& x, const double& alpha, const double& k) {
    double cdf = x + (alpha / k) * std::sin(k * x);
    return cdf;
}
 
KOKKOS_FUNCTION
double PDF(const Vector_t<double, Dim>& xvec, const double& alpha, const Vector_t<double, Dim>& kw,
           const unsigned Dim) {
    double pdf = 1.0;
 
    for (unsigned d = 0; d < Dim; ++d) {
        pdf *= (1.0 + alpha * Kokkos::cos(kw[d] * xvec[d]));
    }
    return pdf;
}
 
const char* TestName = "LandauDamping";
 
int main(int argc, char* argv[]) {
    ippl::initialize(argc, argv);
    {
        setSignalHandler();
 
        Inform msg("LandauDamping");
        Inform msg2all("LandauDamping", INFORM_ALL_NODES);
 
        auto start = std::chrono::high_resolution_clock::now();
 
        int arg = 1;
 
        Vector_t<int, Dim> nr;
        for (unsigned d = 0; d < Dim; d++) {
            nr[d] = std::atoi(argv[arg++]);
        }
 
        static IpplTimings::TimerRef mainTimer        = IpplTimings::getTimer("total");
        static IpplTimings::TimerRef particleCreation = IpplTimings::getTimer("particlesCreation");
        static IpplTimings::TimerRef dumpDataTimer    = IpplTimings::getTimer("dumpData");
        static IpplTimings::TimerRef PTimer           = IpplTimings::getTimer("pushVelocity");
        static IpplTimings::TimerRef RTimer           = IpplTimings::getTimer("pushPosition");
        static IpplTimings::TimerRef updateTimer      = IpplTimings::getTimer("update");
        static IpplTimings::TimerRef DummySolveTimer  = IpplTimings::getTimer("solveWarmup");
        static IpplTimings::TimerRef SolveTimer       = IpplTimings::getTimer("solve");
        static IpplTimings::TimerRef domainDecomposition = IpplTimings::getTimer("loadBalance");
 
        IpplTimings::startTimer(mainTimer);
 
        const size_type totalP = std::atoll(argv[arg++]);
        const unsigned int nt  = std::atoi(argv[arg++]);
 
        msg << "Landau damping" << endl
            << "nt " << nt << " Np= " << totalP << " grid = " << nr << endl;
 
        using bunch_type = ChargedParticles<PLayout_t<double, Dim>, double, Dim>;
 
        std::unique_ptr<bunch_type> P;
 
        ippl::NDIndex<Dim> domain;
        for (unsigned i = 0; i < Dim; i++) {
            domain[i] = ippl::Index(nr[i]);
        }
 
        std::array<bool, Dim> isParallel;
        isParallel.fill(true);
 
        // create mesh and layout objects for this problem domain
        Vector_t<double, Dim> kw = 0.5;
        double alpha             = 0.05;
        Vector_t<double, Dim> rmin(0.0);
        Vector_t<double, Dim> rmax = 2 * pi / kw;
 
        Vector_t<double, Dim> hr = rmax / nr;
        // Q = -\int\int f dx dv
        double Q = std::reduce(rmax.begin(), rmax.end(), -1., std::multiplies<double>());
        Vector_t<double, Dim> origin = rmin;
        const double dt              = std::min(.05, 0.5 * *std::min_element(hr.begin(), hr.end()));
 
        const bool isAllPeriodic = true;
        Mesh_t<Dim> mesh(domain, hr, origin);
        FieldLayout_t<Dim> FL(MPI_COMM_WORLD, domain, isParallel, isAllPeriodic);
        PLayout_t<double, Dim> PL(FL, mesh);
 
        std::string solver = argv[arg++];
        // MOD: Setup of Preconditioner Start
        int gauss_seidel_inner_iterations;
        int gauss_seidel_outer_iterations;
        int newton_level;
        int chebyshev_degree;
        int richardson_iterations;
        int communication;
        double ssor_omega;
        std::string preconditioner_type = "";
 
        if (solver == "OPEN") {
            throw IpplException("LandauDamping",
                                "Open boundaries solver incompatible with this simulation!");
        }
        ippl::ParameterList params;
        if (solver == "PCG") {
            preconditioner_type = argv[arg++];
            if (preconditioner_type == "newton") {
                newton_level = std::atoi(argv[arg++]);
            } else if (preconditioner_type == "chebyshev") {
                chebyshev_degree = std::atoi(argv[arg++]);
            } else if (preconditioner_type == "richardson") {
                richardson_iterations = std::atoi(argv[arg++]);
                communication         = std::atoi(argv[arg++]);
            } else if (preconditioner_type == "gauss-seidel") {
                gauss_seidel_inner_iterations = std::atoi(argv[arg++]);
                gauss_seidel_outer_iterations = std::atoi(argv[arg++]);
                communication                 = std::atoi(argv[arg++]);
            } else if (preconditioner_type == "ssor") {
                gauss_seidel_inner_iterations = std::atoi(argv[arg++]);
                gauss_seidel_outer_iterations = std::atoi(argv[arg++]);
                ssor_omega                    = std::stod(argv[arg++]);
            }
 
            params.add("preconditioner_type", preconditioner_type);
            params.add("gauss_seidel_inner_iterations", gauss_seidel_inner_iterations);
            params.add("gauss_seidel_outer_iterations", gauss_seidel_outer_iterations);
            params.add("newton_level", newton_level);
            params.add("chebyshev_degree", chebyshev_degree);
            params.add("richardson_iterations", richardson_iterations);
            params.add("communication", communication);
            params.add("ssor_omega", ssor_omega);
        }
 
        P = std::make_unique<bunch_type>(PL, hr, rmin, rmax, isParallel, Q, solver);
        // MOD END
 
        P->nr_m = nr;
 
        P->initializeFields(mesh, FL);
 
        P->initSolver(params);
        P->time_m                 = 0.0;
        P->loadbalancethreshold_m = std::atof(argv[arg++]);
 
        bool isFirstRepartition;
 
        if ((P->loadbalancethreshold_m != 1.0) && (ippl::Comm->size() > 1)) {
            msg << "Starting first repartition" << endl;
            IpplTimings::startTimer(domainDecomposition);
            isFirstRepartition             = true;
            const ippl::NDIndex<Dim>& lDom = FL.getLocalNDIndex();
            const int nghost               = P->rho_m.getNghost();
            auto rhoview                   = P->rho_m.getView();
 
            using index_array_type = typename ippl::RangePolicy<Dim>::index_array_type;
            ippl::parallel_for(
                "Assign initial rho based on PDF", P->rho_m.getFieldRangePolicy(),
                KOKKOS_LAMBDA(const index_array_type& args) {
                    // local to global index conversion
                    Vector_t<double, Dim> xvec = (args + lDom.first() - nghost + 0.5) * hr + origin;
 
                    // ippl::apply accesses the view at the given indices and obtains a
                    // reference; see src/Expression/IpplOperations.h
                    ippl::apply(rhoview, args) = PDF(xvec, alpha, kw, Dim);
                });
 
            Kokkos::fence();
 
            P->initializeORB(FL, mesh);
            P->repartition(FL, mesh, isFirstRepartition);
            IpplTimings::stopTimer(domainDecomposition);
        }
 
        msg << "First domain decomposition done" << endl;
        IpplTimings::startTimer(particleCreation);
 
        typedef ippl::detail::RegionLayout<double, Dim, Mesh_t<Dim>>::uniform_type RegionLayout_t;
        const RegionLayout_t& RLayout                           = PL.getRegionLayout();
        const typename RegionLayout_t::host_mirror_type Regions = RLayout.gethLocalRegions();
        Vector_t<double, Dim> Nr, Dr, minU, maxU;
        int myRank    = ippl::Comm->rank();
        double factor = 1;
        for (unsigned d = 0; d < Dim; ++d) {
            Nr[d] = CDF(Regions(myRank)[d].max(), alpha, kw[d])
                    - CDF(Regions(myRank)[d].min(), alpha, kw[d]);
            Dr[d]   = CDF(rmax[d], alpha, kw[d]) - CDF(rmin[d], alpha, kw[d]);
            minU[d] = CDF(Regions(myRank)[d].min(), alpha, kw[d]);
            maxU[d] = CDF(Regions(myRank)[d].max(), alpha, kw[d]);
            factor *= Nr[d] / Dr[d];
        }
 
        size_type nloc            = (size_type)(factor * totalP);
        size_type Total_particles = 0;
 
        MPI_Allreduce(&nloc, &Total_particles, 1, MPI_UNSIGNED_LONG, MPI_SUM,
                      ippl::Comm->getCommunicator());
 
        int rest = (int)(totalP - Total_particles);
 
        if (ippl::Comm->rank() < rest) {
            ++nloc;
        }
 
        P->create(nloc);
        Kokkos::Random_XorShift64_Pool<> rand_pool64((size_type)(42 + 100 * ippl::Comm->rank()));
        Kokkos::parallel_for(
            nloc, generate_random<Vector_t<double, Dim>, Kokkos::Random_XorShift64_Pool<>, Dim>(
                      P->R.getView(), P->P.getView(), rand_pool64, alpha, kw, minU, maxU));
 
        Kokkos::fence();
        ippl::Comm->barrier();
        IpplTimings::stopTimer(particleCreation);
 
        P->q = P->Q_m / totalP;
        msg << "particles created and initial conditions assigned " << endl;
        isFirstRepartition = false;
        // The update after the particle creation is not needed as the
        // particles are generated locally
 
        IpplTimings::startTimer(DummySolveTimer);
        P->rho_m = 0.0;
        P->runSolver();
        IpplTimings::stopTimer(DummySolveTimer);
 
        P->scatterCIC(totalP, 0, hr);
 
        IpplTimings::startTimer(SolveTimer);
        P->runSolver();
        IpplTimings::stopTimer(SolveTimer);
 
        P->gatherCIC();
 
        IpplTimings::startTimer(dumpDataTimer);
        P->dumpLandau();
        P->gatherStatistics(totalP);
        // P->dumpLocalDomains(FL, 0);
        IpplTimings::stopTimer(dumpDataTimer);
 
        // begin main timestep loop
        msg << "Starting iterations ..." << endl;
        for (unsigned int it = 0; it < nt; it++) {
            // LeapFrog time stepping https://en.wikipedia.org/wiki/Leapfrog_integration
            // Here, we assume a constant charge-to-mass ratio of -1 for
            // all the particles hence eliminating the need to store mass as
            // an attribute
            // kick
 
            IpplTimings::startTimer(PTimer);
            P->P = P->P - 0.5 * dt * P->E;
            IpplTimings::stopTimer(PTimer);
 
            // drift
            IpplTimings::startTimer(RTimer);
            P->R = P->R + dt * P->P;
            IpplTimings::stopTimer(RTimer);
            // P->R.print();
 
            // Since the particles have moved spatially update them to correct processors
            IpplTimings::startTimer(updateTimer);
            P->update();
            IpplTimings::stopTimer(updateTimer);
 
            // Domain Decomposition
            if (P->balance(totalP, it + 1)) {
                msg << "Starting repartition" << endl;
                IpplTimings::startTimer(domainDecomposition);
                P->repartition(FL, mesh, isFirstRepartition);
                IpplTimings::stopTimer(domainDecomposition);
                // IpplTimings::startTimer(dumpDataTimer);
                // P->dumpLocalDomains(FL, it+1);
                // IpplTimings::stopTimer(dumpDataTimer);
            }
 
            // scatter the charge onto the underlying grid
            P->scatterCIC(totalP, it + 1, hr);
 
            // Field solve
            IpplTimings::startTimer(SolveTimer);
            P->runSolver();
            IpplTimings::stopTimer(SolveTimer);
 
            // gather E field
            P->gatherCIC();
 
            // kick
            IpplTimings::startTimer(PTimer);
            P->P = P->P - 0.5 * dt * P->E;
            IpplTimings::stopTimer(PTimer);
 
            P->time_m += dt;
            IpplTimings::startTimer(dumpDataTimer);
            P->dumpLandau();
            P->gatherStatistics(totalP);
            IpplTimings::stopTimer(dumpDataTimer);
            msg << "Finished time step: " << it + 1 << " time: " << P->time_m << endl;
 
            if (checkSignalHandler()) {
                msg << "Aborting timestepping loop due to signal " << interruptSignalReceived
                    << endl;
                break;
            }
        }
 
        msg << "LandauDamping: End." << endl;
        IpplTimings::stopTimer(mainTimer);
        IpplTimings::print();
        IpplTimings::print(std::string("timing.dat"));
        auto end = std::chrono::high_resolution_clock::now();
 
        std::chrono::duration<double> time_chrono =
            std::chrono::duration_cast<std::chrono::duration<double>>(end - start);
        std::cout << "Elapsed time: " << time_chrono.count() << std::endl;
    }
    ippl::finalize();
 
    return 0;
}