grid_files.hpp

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#ifndef GRID_FILES_HPP
#define GRID_FILES_HPP

#ifdef USE_MPI
#include "my_mpi.hpp"
#endif
#include "file_reader.hpp"
#include "magnetic_field.hpp"
#include "grid_structs.hpp"
#include "grid_setup.hpp"
#include "space_settings.hpp"
#include "NamelistReader.hpp"


struct GridFiles{
    // Contents of .node
    int nnodes;
    View<RZPair*, HostType> x;
    View<int*, HostType> rgn;

    // Contents of .ele
    int ntriangles;
    View<Vertex*, HostType> nodes;

    // Contents of .flx.aif
    int nsurfaces;
    View<int*, HostType> nnodes_on_surface;
    int sum_nnodes_on_surfaces;
    View<int*, HostType> nodes_of_surfaces;

    void convert_to_x_rgn_format(const View<double**, CLayout, HostType>& tmp_nodes, View<RZPair*, HostType>& x, View<int*, HostType>& rgn){
        Kokkos::parallel_for("transpose_x_and_rgn", Kokkos::RangePolicy<HostExSpace>(0,tmp_nodes.extent(0)), KOKKOS_LAMBDA( const int i ){
            // tmp_nodes[i,0]; <-- first column is ignored
            x(i).r = tmp_nodes(i,1);
            x(i).z = tmp_nodes(i,2);
            rgn(i) = tmp_nodes(i,3);
        });
    }

    void convert_to_node_format(const View<int**, CLayout, HostType>& tmp_ele, View<Vertex*, HostType>& nodes){
        Kokkos::parallel_for("transpose_x_and_rgn", Kokkos::RangePolicy<HostExSpace>(0,tmp_ele.extent(0)), KOKKOS_LAMBDA( const int i ){
            // tmp_ele[i,0]; <-- first column is ignored
            nodes(i).vertex[0] = tmp_ele(i,1);
            nodes(i).vertex[1] = tmp_ele(i,2);
            nodes(i).vertex[2] = tmp_ele(i,3);
        });
    }

    // Read the files
    GridFiles(const std::string& node_file, const std::string& element_file, const std::string& flx_aif_file){
        // Only one MPI rank reads the files, then broadcasts to the others
        if(is_rank_zero()){

            FileReader file_reader;

            file_reader.open(node_file);
            file_reader.read(&nnodes, 1); // Get nnodes from file
            file_reader.skip(3); // Skip 3 unused values in file

            // Use dummy array since reformatting is needed
            View<double**, CLayout, HostType> tmp_nodes(NoInit("tmp_nodes"),nnodes,4); // 4 entries per node: index, r, z, region
            file_reader.read(tmp_nodes.data(), tmp_nodes.size());

            // Reformat to x and rgn
            x = View<RZPair*, HostType>(NoInit("x"),nnodes);
            rgn = View<int*, HostType>(NoInit("rgn"),nnodes);
            convert_to_x_rgn_format(tmp_nodes, x, rgn);

            file_reader.open(element_file);
            file_reader.read(&ntriangles, 1); // Get nnodes from file
            file_reader.skip(2); // Skip 2 unused values in file

            // Use dummy array since reformatting is needed
            View<int**, CLayout, HostType> tmp_ele(NoInit("tmp_ele"),ntriangles,4); // 4 entries per node: index, r, z, region
            file_reader.read(tmp_ele.data(), tmp_ele.size());

            // Reformat since first column is ignored
            nodes = View<Vertex*, HostType>("nodes",ntriangles);
            convert_to_node_format(tmp_ele, nodes);

/*
#ifndef NEW_FLX_AIF
            exit_XGC("\nError: C++ grid file reader can't read old flux files (i.e. NEW_FLX_AIF must be On)");
#endif
            file_reader.open(flx_aif_file);
            file_reader.skip(3); // Skip 3 unused values in file
            int nsurfaces1, nsurfaces2, nsurfaces3a, nsurfaces3b;
            file_reader.read(&nsurfaces1, 1); // Get number of surfaces
            file_reader.read(&nsurfaces2, 1); // Get number of surfaces
            file_reader.read(&nsurfaces3a, 1); // Get number of surfaces
            file_reader.read(&nsurfaces3b, 1); // Get number of surfaces
            // nsurfaces is actually the sum of these 4 inputs
            nsurfaces = nsurfaces1 + nsurfaces2 + nsurfaces3a + nsurfaces3b;

            file_reader.skip(2); // Skip 2 unused values in file

            // Read in nnodes on each surface
            nnodes_on_surface = std::vector<int>(nsurfaces);
            file_reader.read(nnodes_on_surface.data(), nnodes_on_surface.size());

            // Loop through surfaces to calculate sum total of nodes on surfaces
            sum_nnodes_on_surfaces = 0;
            for(int i=0; i<nsurfaces; i++) sum_nnodes_on_surfaces += nnodes_on_surface[i];

            // Allocate nodes_of_surfaces
            nodes_of_surfaces = std::vector<int>(sum_nnodes_on_surfaces);

            // Read in values
            file_reader.read(nodes_of_surfaces.data(), nodes_of_surfaces.size());
*/
        }

        /*** Broadcast grid contents to other MPI ranks ***/

        // First broadcast scalars so we know the sizes of the arrays
        View<int*, HostType> scalars("scalars", 4);
        scalars(0) = nnodes;
        scalars(1) = ntriangles;
//        scalars(2) = nsurfaces;
//        scalars(3) = sum_nnodes_on_surfaces;

        // Broadcast file size to other processes
#ifdef USE_MPI
        int root_rank = 0;
        MPI_Bcast(scalars.data(), scalars.size(), MPI_INT, root_rank, SML_COMM_WORLD);
#endif

        if(!is_rank_zero()){
            // Set scalars on non-root ranks
            nnodes = scalars(0);
            ntriangles = scalars(1);
//            nsurfaces = scalars(2);
//            sum_nnodes_on_surfaces = scalars(3);

            // Allocate vectors on non-root ranks
            Kokkos::resize(x, nnodes);
            Kokkos::resize(rgn, nnodes);
            Kokkos::resize(nodes, ntriangles);
//            nnodes_on_surface.resize(nsurfaces);
//            nodes_of_surfaces.resize(sum_nnodes_on_surfaces);
        }

        // Broadcast grid arrays
#ifdef USE_MPI
        MPI_Bcast( x.data(), x.size()*2, MPI_DOUBLE, root_rank, SML_COMM_WORLD);
        MPI_Bcast( rgn.data(), rgn.size(), MPI_INT, root_rank, SML_COMM_WORLD);
        MPI_Bcast( nodes.data(), nodes.size()*3, MPI_INT, root_rank, SML_COMM_WORLD);
//        MPI_Bcast( nnodes_on_surface.data(), nnodes_on_surface.size(), MPI_INT, root_rank, SML_COMM_WORLD);
//        MPI_Bcast( nodes_of_surfaces.data(), nodes_of_surfaces.size(), MPI_INT, root_rank, SML_COMM_WORLD);
#endif
    }

    // Options: hex vs circular
    enum GridCreateOpt{
        Hexagonal=0,
        Circular=1
    };

    void construct_hex_grid(int nshells, double raxis, double zaxis, double rscale, double zscale) {
        // First, build construction of what .node and .ele files would look like

        // Build hexagonal sample grid of concentric shells
        // Minimum 1 shell, which produces 7 nodes and 6 triangles

        // Grid construction uses this enum for directions
        enum { NE = 0, N, NW, SW, S, SE };

        // Work from center outward
        x(0).r = raxis;
        x(0).z = zaxis;
        rgn(0) = 0; // not wall
        int inode = 1;
        int itri = 0;
        for(int ish = 1; ish<=nshells; ish++){
            int nodes_in_shell = 6*ish;
            int first_inner_shell_node = ish==1 ? 0 : inode - 6*(ish-1);
            int first_node = inode;
            int inner_shell_node = first_inner_shell_node;
            // Starting position:
            double r_track = raxis + rscale*ish;
            double z_track = zaxis;
            for (int inodesh = 0; inodesh < nodes_in_shell; inodesh++){
                x(inode).r = r_track;
                x(inode).z = z_track;
                rgn(inode) = (ish==nshells? OnWall : Inside); // last shell is wall

                if (inodesh>0){
                    nodes(itri).vertex[0] = inner_shell_node;
                    nodes(itri).vertex[1] = inode-1;
                    nodes(itri).vertex[2] = inode;
                    itri++;
                    if (inodesh%ish>0){ // corners only add one triangle
                        nodes(itri).vertex[0] = inner_shell_node;
                        nodes(itri).vertex[1] = (inodesh == nodes_in_shell - 1) ? first_inner_shell_node : (inner_shell_node+1);
                        nodes(itri).vertex[2] = inode;
                        inner_shell_node++;
                        itri++;
                    }
                }

                // Determine position of next node
                int hex_region = inodesh/ish;
                double r_move, z_move;
                if(hex_region == NE)
                    {r_move = -0.5; z_move = 1.0;}
                else if (hex_region == N)
                    {r_move = -1.0; z_move = 0.0;}
                else if (hex_region == NW)
                    {r_move = -0.5; z_move = -1.0;}
                else if (hex_region == SW)
                    {r_move = 0.5; z_move = -1.0;}
                else if (hex_region == S)
                    {r_move = 1.0; z_move = 0.0;}
                else if (hex_region == SE)
                    {r_move = 0.5; z_move = 1.0;}
                r_track += rscale*r_move;
                z_track += zscale*z_move;
                inode++;
            }

            // Add last element to close ring
            nodes(itri).vertex[0] = first_inner_shell_node;
            nodes(itri).vertex[1] = inode-1;
            nodes(itri).vertex[2] = first_node;
            itri++;
        }

        // Shift node list to 1-indexing (input files are 1-indexed)
        for(int i = 0; i<ntriangles; i++){
            nodes(i).vertex[0]++;
            nodes(i).vertex[1]++;
            nodes(i).vertex[2]++;
        }

        // nsurfaces is 0 because the hex grid is not surface-aligned
        nsurfaces=0;
    }

    double node_to_node_dist(RZPair a, RZPair b){
        return sqrt((a.r-b.r)*(a.r-b.r) + (a.z-b.z)*(a.z-b.z));
    }

    void construct_circular_grid(int nshells, double raxis, double zaxis, double rscale, double zscale) {
        // First, build construction of what .node and .ele files would look like

        // Build circular sample grid of concentric shells
        // Minimum 1 shell, which produces 7 nodes and 6 triangles

        // Work from center outward
        x(0).r = raxis;
        x(0).z = zaxis;
        rgn(0) = 0; // not wall

        nnodes_on_surface(0) = 1;
        nodes_of_surfaces(0) = 0;
        int inode = 1;
        int itri = 0;
        for(int ish = 1; ish<=nshells; ish++){
            int nodes_in_shell = 6*ish;
            int nodes_in_inner_shell = ish==1 ? 1 : 6*(ish-1);
            int first_inner_shell_node = ish==1 ? 0 : inode - 6*(ish-1);
            int first_node = inode;
            int inner_shell_node = first_inner_shell_node;
            // Starting position:
            for (int inodesh = 0; inodesh <= nodes_in_shell; inodesh++){
                // Create node
                if(inodesh<nodes_in_shell){
                    double angle = TWOPI*double(inodesh)/double(nodes_in_shell);
                    x(inode).r = raxis + ish*rscale*cos(angle);
                    x(inode).z = zaxis + ish*zscale*sin(angle);
                    rgn(inode) = (ish==nshells? OnWall : Inside); // last shell is wall
                }

                // Create element(s)
                if (inodesh>0){
                    int outer_node = (inodesh < nodes_in_shell) ? inode : first_node;
                    int prev_outer_node = inode-1;

                    // First, check cross-distances
                    int next_inner_shell_node = inner_shell_node+1;
                    if(next_inner_shell_node-first_inner_shell_node==nodes_in_inner_shell) next_inner_shell_node = first_inner_shell_node;
                    double distance1 = node_to_node_dist(x(outer_node), x(inner_shell_node));
                    double distance2 = node_to_node_dist(x(prev_outer_node), x(next_inner_shell_node));

                    // The next node is far away enough that we need to add two elements
                    if(distance1>distance2 && next_inner_shell_node!=inner_shell_node){
                        if(itri>=nodes.size()) {printf("\nMore elements than expected in circular grid generation. Dynamically resize?"); exit(1); }
                        nodes(itri).vertex[0] = inner_shell_node;
                        nodes(itri).vertex[1] = next_inner_shell_node;
                        nodes(itri).vertex[2] = prev_outer_node;
                        inner_shell_node = next_inner_shell_node;
                        itri++;
                    }

                    if(itri>=nodes.size()) {printf("\nMore elements than expected in circular grid generation. Dynamically resize?"); exit(1); }
                    nodes(itri).vertex[0] = inner_shell_node;
                    nodes(itri).vertex[1] = prev_outer_node;
                    nodes(itri).vertex[2] = outer_node;
                    itri++;
                }

                if(inodesh<nodes_in_shell){
                    nodes_of_surfaces(inode) = inode;
                    inode++;
                }
            }

            nnodes_on_surface(ish) = nodes_in_shell;
        }

        if(itri!=nodes.size()) {printf("\nFewer elements than expected in circular grid generation. Dynamically resize?"); exit(1); }

        // Shift node list to 1-indexing (input files are 1-indexed)
        for(int i = 0; i<ntriangles; i++){
            nodes(i).vertex[0]++;
            nodes(i).vertex[1]++;
            nodes(i).vertex[2]++;
        }
    }


    GridFiles(int nshells, double raxis, double zaxis, double rscale, double zscale, GridCreateOpt grid_opt=Hexagonal)
      : nnodes(1 + 3*(nshells+1)*nshells),
        x(NoInit("x"),nnodes),
        rgn(NoInit("rgn"),nnodes),
        ntriangles(6*nshells*nshells),
        nodes(NoInit("nodes"),ntriangles),
        nsurfaces(nshells+1),
        nnodes_on_surface(NoInit("nnodes_on_surface"),nsurfaces),
        sum_nnodes_on_surfaces(nnodes),
        nodes_of_surfaces(NoInit("nodes_of_surfaces"),nnodes)
    {
        if(grid_opt==Hexagonal){
            construct_hex_grid(nshells, raxis, zaxis, rscale, zscale);
        }else{
            construct_circular_grid(nshells, raxis, zaxis, rscale, zscale);
        }
    }

    GridFiles(MagneticField<HostType>& magnetic_field, int nshells, GridCreateOpt grid_opt=Hexagonal)
      : nnodes(1 + 3*(nshells+1)*nshells),
        x(NoInit("x"),nnodes),
        rgn(NoInit("rgn"),nnodes),
        ntriangles(6*nshells*nshells),
        nodes(NoInit("nodes"),ntriangles),
        nsurfaces(nshells+1),
        nnodes_on_surface(NoInit("nnodes_on_surface"),nsurfaces),
        sum_nnodes_on_surfaces(nnodes),
        nodes_of_surfaces(NoInit("nodes_of_surfaces"),nnodes)
    {
        // Magnetic axis will be the center of the grid
        double raxis = magnetic_field.equil.axis_r;
        double zaxis = magnetic_field.equil.axis_z;

        // Since the axis is not necessarily centered in the field map, take the shorter
        // distance to the edge to use as the dimensions of the grid
        double width  = 2*std::min(magnetic_field.bd_max_r - magnetic_field.equil.axis_r,
                                   magnetic_field.equil.axis_r - magnetic_field.bd_min_r);

        double height = 2*std::min(magnetic_field.bd_max_z - magnetic_field.equil.axis_z,
                                   magnetic_field.equil.axis_z - magnetic_field.bd_min_z);

        // Make sure the grid is within the psi bounds
        width *= 0.99;
        height *= 0.99;

        if(grid_opt==Hexagonal){
            double triangle_width = width/(2*nshells);
            double triangle_height = height/(2*nshells);
            construct_hex_grid(nshells, raxis, zaxis, triangle_width, triangle_height);
        }else{
            // Circular grid; take the smaller of the width or height to make sure it fits
            double scale = std::min(width,height)/(2*nshells);
            construct_circular_grid(nshells, raxis, zaxis, scale, scale);
        }
    }

    /* Returns GridFiles object using the file-reader constructor. This may be updated so the input file
     * can specify an analytic grid.
     * */
    static GridFiles grid_files_from_namelist(NLReader::NamelistReader& nlr){
        // Read file names and path from input file
        nlr.use_namelist("sml_param");
        std::string node_file = nlr.get<std::string>("sml_node_file","example_file.node");
        std::string ele_file = nlr.get<std::string>("sml_ele_file","example_file.ele");
        std::string surf_file = nlr.get<std::string>("sml_surf_file","example_file.flx.aif");
        std::string input_file_dir = nlr.get<std::string>("sml_input_file_dir","./");

        // Add path to file names
        node_file = input_file_dir + "/" + node_file;
        ele_file = input_file_dir + "/" + ele_file;
        surf_file = input_file_dir + "/" + surf_file;

        // Read in grid files and return result
        return GridFiles(node_file, ele_file, surf_file);
    }

};

#endif