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"
#include "check_aif_flx_format.hpp"

extern "C" void set_fortran_flx_aif_format(int is_flx_aif_format_int);

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
    View<int*, HostType> i_x;

    int nsurfaces;
    int nsurfaces1, nsurfaces2, nsurfaces3a, nsurfaces3b;
    View<int*, HostType> i_surf_separatrices;
    View<int*, HostType> nnodes_on_surface;
    int sum_nnodes_on_surfaces;
    int num_non_aligned;
    View<int*, HostType> non_aligned_vert;
    View<int*, HostType> non_aligned_nsurf;
    View<int**, CLayout, HostType> non_aligned_surf_idx;
    View<int**, CLayout, HostType> surf_idx;

    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);
        });
    }

    // Default constructor, to use to deallocate the file arrays after use
    GridFiles(){}

    // Read the files
    GridFiles(const std::string& node_file, const std::string& element_file, const std::string& flx_aif_file){
        int max_nodes_on_surface;
        int n_xpts;
        int n_separatrices;
        // 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);

            if(nnodes==1) exit_XGC("\nGrid must have more than 1 nnode!\n"); // This is assumed in the flx format check
            bool old_flx_aif_format = is_old_flx_format(flx_aif_file);
            set_fortran_flx_aif_format(old_flx_aif_format ? 1 : 0);

            file_reader.open(flx_aif_file);

            if(old_flx_aif_format){
                file_reader.read(&nsurfaces, 1); // Get number of surfaces
                n_xpts = 0;
                n_separatrices = 0;
                i_x = View<int*, HostType>("i_x",0); // No xpoints specified
                i_surf_separatrices = View<int*, HostType>(NoInit("i_surf_separatrices"), 0); // No separatrices specified

                // These don't get read or used by the old format
                nsurfaces1 = 0;
                nsurfaces2 = 0;
                nsurfaces3a = 0;
                nsurfaces3b = 0;
            }else{
                file_reader.read(&n_xpts, 1); // Get number of x-points
                i_x = View<int*, HostType>("i_x", n_xpts);

                // Current flx.aif files list 2 x-point indices, regardless of n_xpts
                int i_xpt1, i_xpt2;
                file_reader.read(&i_xpt1, 1); // Get index of 1st x-point
                file_reader.read(&i_xpt2, 1); // Get index of 2nd x-point

                // Check for consistency
                if(n_xpts==1 && i_xpt2 != -1) exit_XGC("Error in flx.aif file: n_xpts=1, but i_xpt2 is specified.\n");
                if(n_xpts==2 && i_xpt2 <= 0) exit_XGC("Error in flx.aif file: n_xpts=2, but i_xpt2 is not specified.\n");

                if(n_xpts>=1) i_x(0) = i_xpt1 - 1; // switch to zero-index
                if(n_xpts>=2) i_x(1) = i_xpt2 - 1;

                // Next are the nsurface variables
                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;

                // Get surface index of separatrices
                // Hard-coded to 2, but generalize the read just in case
                n_separatrices = 2;
                i_surf_separatrices = View<int*, HostType>(NoInit("i_surf_separatrices"), n_separatrices);
                file_reader.read(&i_surf_separatrices(0), 1);
                file_reader.read(&i_surf_separatrices(1), 1);
            }

            // Read in nnodes on each surface
            nnodes_on_surface = View<int*, HostType>(NoInit("nnodes_on_surface"), nsurfaces);
            file_reader.read(nnodes_on_surface.data(), nnodes_on_surface.size());

            // Loop through surfaces to find max number of nodes in a surface
            max_nodes_on_surface = 0;
            for(int i=0; i<nnodes_on_surface.size(); i++) max_nodes_on_surface = std::max(nnodes_on_surface(i), max_nodes_on_surface);

            // Allocate surf_idx and initialize to 0
            surf_idx = View<int**, CLayout, HostType>("surf_idx",nsurfaces, max_nodes_on_surface);

            // Read in values
            for(int i=0; i<nnodes_on_surface.size(); i++){
                file_reader.read(&surf_idx(i,0), nnodes_on_surface(i));
            }

            // There is a "-1" in the file here to mark the end of the section
            int should_be_negative_one;
            file_reader.read(&should_be_negative_one, 1);
            if(should_be_negative_one != -1){
                printf("\nExpected -1 at end of section in surface file, encountered %d instead\n", should_be_negative_one);
                exit_XGC("Error reading surface file.\n");
            }

            file_reader.read(&num_non_aligned, 1);
            printf(" -  reading num_non_aligned: %d",num_non_aligned);

            // Read the non-aligned vertex data
            non_aligned_vert = View<int*, HostType>(NoInit("non_aligned_vert"), num_non_aligned);
            non_aligned_nsurf = View<int*, HostType>(NoInit("non_aligned_nsurf"), num_non_aligned);
            // Initialize to 0
            non_aligned_surf_idx = View<int**, CLayout, HostType>("non_aligned_surf_idx", num_non_aligned, 4);
            for(int i=0; i<num_non_aligned; i++){
                file_reader.read(&non_aligned_vert(i), 1);
                if(old_flx_aif_format){
                    file_reader.read(&non_aligned_nsurf(i), 1);
                }else{
                    // New format does not contain non_aligned_nsurf
                    non_aligned_nsurf(i)=2;
                }
                file_reader.read(&non_aligned_surf_idx(i,0), non_aligned_nsurf(i));
            }

            // Another "-1" at the end of the file
            file_reader.read(&should_be_negative_one, 1);
            if(should_be_negative_one != -1){
                printf("\nExpected -1 at end of the surface file, encountered %d instead\n", should_be_negative_one);
                exit_XGC("Error reading surface file.\n");
            }
        }

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

        // First broadcast scalars so we know the sizes of the arrays
        int n_scalars = 11;
        View<int*, HostType> scalars("scalars", n_scalars);
        scalars(0) = nnodes;
        scalars(1) = ntriangles;
        scalars(2) = nsurfaces;
        scalars(3) = max_nodes_on_surface;
        scalars(4) = num_non_aligned;
        scalars(5) = n_xpts;
        scalars(6) = n_separatrices;
        scalars(7) = nsurfaces1;
        scalars(8) = nsurfaces2;
        scalars(9) = nsurfaces3a;
        scalars(10) = nsurfaces3b;

        // 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);
            max_nodes_on_surface = scalars(3);
            num_non_aligned = scalars(4);
            n_xpts = scalars(5);
            n_separatrices = scalars(6);
            nsurfaces1 = scalars(7);
            nsurfaces2 = scalars(8);
            nsurfaces3a = scalars(9);
            nsurfaces3b = scalars(10);

            // node and ele views
            x = View<RZPair*, HostType>(NoInit("x"),nnodes);
            rgn = View<int*, HostType>(NoInit("rgn"),nnodes);
            nodes = View<Vertex*, HostType>("nodes",ntriangles);

            // flx.aif views
            i_x = View<int*, HostType>("i_x", n_xpts);
            i_surf_separatrices = View<int*, HostType>(NoInit("i_surf_separatrices"), n_separatrices);
            non_aligned_vert = View<int*, HostType>(NoInit("non_aligned_vert"), num_non_aligned);
            non_aligned_nsurf = View<int*, HostType>(NoInit("non_aligned_nsurf"), num_non_aligned);
            non_aligned_surf_idx = View<int**, CLayout, HostType>(NoInit("non_aligned_surf_idx"), num_non_aligned, 4);
            nnodes_on_surface = View<int*, HostType>(NoInit("nnodes_on_surface"), nsurfaces);
            surf_idx = View<int**, CLayout, HostType>(NoInit("surf_idx"),nsurfaces, max_nodes_on_surface);
        }

        // 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);

        if(i_x.size()>0) MPI_Bcast( i_x.data(), i_x.size(), MPI_INT, root_rank, SML_COMM_WORLD);
        if(i_surf_separatrices.size()>0) MPI_Bcast( i_surf_separatrices.data(), i_surf_separatrices.size(), MPI_INT, root_rank, SML_COMM_WORLD);
        MPI_Bcast( non_aligned_vert.data(), non_aligned_vert.size(), MPI_INT, root_rank, SML_COMM_WORLD);
        MPI_Bcast( non_aligned_nsurf.data(), non_aligned_nsurf.size(), MPI_INT, root_rank, SML_COMM_WORLD);
        MPI_Bcast( non_aligned_surf_idx.data(), non_aligned_surf_idx.size(), 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( surf_idx.data(), surf_idx.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 };

    // Node indices of each surface
        int max_nodes_on_surface = 6*nshells;
        surf_idx = View<int**, CLayout, HostType>(NoInit("surf_idx"),nsurfaces, max_nodes_on_surface);

        // Work from center outward
        x(0).r = raxis;
        x(0).z = zaxis;
        rgn(0) = 0; // not wall
    nnodes_on_surface(0) = 1;
        surf_idx(0, 0) = 1; // Since surf_idx is 1-indexed
        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

        surf_idx(ish, inodesh) = inode+1; // Since surf_idx is 1-indexed

                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++;

        nnodes_on_surface(ish) = nodes_in_shell;
        }

        // 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]++;
        }

    // Field geometry
        int n_xpts = 0; // Assume no X-points for now
        int n_separatrices = 0; // Assume no separatrices for now
        i_x = View<int*, HostType>("i_x", n_xpts);
        i_surf_separatrices = View<int*, HostType>(NoInit("i_surf_separatrices"), n_separatrices);

        // Assume no non-aligned surfaces for now
        num_non_aligned = 0;
        non_aligned_nsurf = View<int*, HostType>(NoInit("non_aligned_nsurf"), num_non_aligned);
        non_aligned_surf_idx = View<int**, CLayout, HostType>(NoInit("non_aligned_surf_idx"), num_non_aligned, 4);
    }

    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

        // Node indices of each surface
        int max_nodes_on_surface = 6*nshells;
        surf_idx = View<int**, CLayout, HostType>(NoInit("surf_idx"),nsurfaces, max_nodes_on_surface);

        nnodes_on_surface(0) = 1;
        surf_idx(0, 0) = 1; // Since surf_idx is 1-indexed
        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

                    surf_idx(ish, inodesh) = inode+1; // Since surf_idx is 1-indexed
                }

                // 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){
                    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]++;
        }

        // Field geometry
        int n_xpts = 0; // Assume no X-points for now
        int n_separatrices = 0; // Assume no separatrices for now
        i_x = View<int*, HostType>("i_x", n_xpts);
        i_surf_separatrices = View<int*, HostType>(NoInit("i_surf_separatrices"), n_separatrices);

        nsurfaces1 = nsurfaces;
        nsurfaces2 = 0;
        nsurfaces3a = 0;
        nsurfaces3b = 0;

        // Assume no non-aligned surfaces for now
        num_non_aligned = 0;
        non_aligned_nsurf = View<int*, HostType>(NoInit("non_aligned_nsurf"), num_non_aligned);
        non_aligned_surf_idx = View<int**, CLayout, HostType>(NoInit("non_aligned_surf_idx"), num_non_aligned, 4);
        non_aligned_vert = View<int*, HostType>(NoInit("non_aligned_vert"), num_non_aligned);
    }

    // Returns the number of shells needed to create a grid with at least nnodes nodes.
    static int nshells_from_nnodes(int nnodes){
        // nnodes = 1 + 3*(nshells+1)*nshells
        //     0  = 3s^2 + 3s + 1 - n
        // s = (-3 +/- sqrt(9 + 4*3*(n-1)))/6
        // s = sqrt(9 + 12*(n-1))/6 - 0.5
        if(nnodes<1) return 0;
        else return std::ceil(sqrt(12*nnodes - 3)/6 - 0.5);
    }

    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)
    {
        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)
    {
        // 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.bounds.max_r - magnetic_field.equil.axis_r,
                                   magnetic_field.equil.axis_r - magnetic_field.bounds.min_r);

        double height = 2*std::min(magnetic_field.bounds.max_z - magnetic_field.equil.axis_z,
                                   magnetic_field.equil.axis_z - magnetic_field.bounds.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);
        }
    }

    int n_specified_xpts(){
        return i_x.size();
    }

    View<Equil::XPoint*, HostType> get_xpts(){
        View<Equil::XPoint*, HostType> xpts(NoInit("xpts"), i_x.size());
        for(int i = 0; i<i_x.size(); i++){
            xpts(i).r = x(i_x(i)).r;
            xpts(i).z = x(i_x(i)).z;
        }
        return xpts;
    };

    /* 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");

        if(nlr.get<bool>("sml_create_analytic_grid", false)==true){
            // Keep analytic grid options simple: number of surfaces, and axis_r
            int nshells = 30;
            double axis_r = 1.5;
            if(nlr.namelist_present("analytic_grid_param")){
                nlr.use_namelist("analytic_grid_param");

                nshells = nlr.get<int>("nsurfaces", 30);
                axis_r = nlr.get<double>("axis_r", 1.5);
            }

            if(is_rank_zero()) printf("\nCreating a circular analytic grid with %d surfaces and %d nodes.\n", nshells, 1 + 3*(nshells+1)*nshells);

            double axis_z = 0.0;

            // Leave a margin so that all vertices are inside equilibrium
            double scale = 0.999/nshells; // Height of each triangle
            double rscale = scale; // rscale = zscale for circular
            double zscale = scale;
            return GridFiles(nshells, axis_r, axis_z, rscale, zscale, GridCreateOpt::Circular);
        }

        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