Mesh Outputs
============

This page is generated from in-code XGC I/O metadata by ``utils/python/document_outputs.py``.

Mesh, geometry, and f0 mesh-context outputs.

xgc.mesh.bp
-----------

.. list-table::
   :header-rows: 1
   :widths: 25 20 55

   * - Variable
     - Units
     - Description
   * - ``PEST_angle``
     - rad
     - PEST coordinate on the mesh nodes (only written for stellarator simulations).
   * - ``VMEC_angle``
     - rad
     - VMEC coordinate on the mesh nodes (only written for stellarator simulations).
   * - ``epsilon``
     - dimensionless
     - Inverse aspect ratio :math:`r_{\min}/R_{\maj}` for the flux surface.
   * - ``ff_1dp_p``
     - dimensionless
     - Barycentric interpolation weights at the full-plane field-following projection of each mesh node.
   * - ``ff_hdp_p``
     - dimensionless
     - Barycentric interpolation weights at the half-plane field-following projection of each mesh node.
   * - ``grid_nwall``
     - Positive integer
     - Number of nodes that make up the boundary of the domain (and represent the wall).
   * - ``grid_wall_nodes``
     - Positive integer
     - Node index for each wall node (0-indexed). Currently not "ordered", but in the order specified in .node file.
   * - ``m_max_surf``
     - Positive integer
     - Maximum resolvable poloidal mode number on each flux surface, defined from the largest spacing in straight-field-line poloidal angle between adjacent vertices: :math:`2\pi/[sml\_mode\_select\_cutoff \, \max_j(\theta_{j+1}-\theta_j)]`.
   * - ``n_geo``
     - Positive integer
     - Number of flux surfaces; same value as nsurf.
   * - ``n_n``
     - Positive integer
     - Number of mesh vertices (per plane).
   * - ``n_t``
     - Positive integer
     - Number of mesh triangles (per plane).
   * - ``nd_connect_list``
     - index
     - Triangle connectivity list for the poloidal plane mesh; each triplet contains zero-based mesh-node indices.
   * - ``nextnode``
     - Positive integer
     - Vertex indices closest to the intersection of the field line through vertex i on plane j with plane j+1 for rightward projection (tokamak only).
   * - ``node_vol``
     - m^3
     - Voronoi volume of the mesh vertices under linear interpolation and toroidal projection. The volume of the whole torus is :math:`N_{\mathrm{wedge}} N_{\phi,\mathrm{tot}} \sum_k V_k`, where :math:`V_k` is node_vol(k).
   * - ``node_vol_ff0``
     - m^3
     - Voronoi volume of the mesh vertices under linear interpolation and field-following projection (full toroidal step) from the midplane to the left.
   * - ``node_vol_ff0_l``
     - m^3
     - Voronoi volume of the mesh vertices under linear interpolation and field-following projection (full toroidal step) from the left plane to the left.
   * - ``node_vol_ff0_r``
     - m^3
     - Voronoi volume of the mesh vertices under linear interpolation and field-following projection (full toroidal step) from the right plane to the left.
   * - ``node_vol_ff1``
     - m^3
     - Voronoi volume of the mesh vertices under linear interpolation and field-following projection (full toroidal step) from the midplane to the right.
   * - ``node_vol_ff1_l``
     - m^3
     - Voronoi volume of the mesh vertices under linear interpolation and field-following projection (full toroidal step) from the left plane to the right.
   * - ``node_vol_ff1_r``
     - m^3
     - Voronoi volume of the mesh vertices under linear interpolation and field-following projection (full toroidal step) from the right plane to the right.
   * - ``node_vol_nearest``
     - m^3
     - Voronoi volume of the mesh vertices under nearest neighbor interpolation and field-following projection.
   * - ``nphi``
     - Positive integer
     - Number of toroidal mesh planes :math:`N_{\mathrm{planes}}` (only written for stellarator simulations).
   * - ``nsurf``
     - Positive integer
     - Number of flux surfaces.
   * - ``one_per_dx``
     - m
     - Distance traveled along the magnetic field line to adjacent full toroidal mesh planes.
   * - ``prefix+"delta_phi"``
     - rad
     - Toroidal angular spacing between neighboring mesh planes.
   * - ``prefix+"mapping"``
     - [1/m, 1/m, m]
     - Per-triangle affine mapping coefficients from physical (R,Z) coordinates to local barycentric triangle coordinates; entries 0 and 1 store the inverse edge matrix and entry 2 stores the reference vertex position.
   * - ``prefix+"nd_connect_list"``
     - index
     - Triangle connectivity list for each plane (multiple planes in case of stellarators); each triplet contains zero-based mesh-node indices.
   * - ``prefix+"region"``
     - index
     - Region identifier for each mesh vertex.
   * - ``prefix+"rz"``
     - m
     - Spatial location in (R,Z) coordinates of each mesh vertex in each stellarator plane.
   * - ``prefix+"wedge_angle"``
     - rad
     - Toroidal wedge angle represented by this simulation.
   * - ``psi``
     - Wb/rad
     - Toroidal magnetic flux for the flux surface that the node is on.
   * - ``psi_surf``
     - Wb/rad
     - Toroidal magnetic flux for the flux surface.
   * - ``qsafety``
     - dimensionless
     - Safety factor :math:`q` for the flux surface.
   * - ``rmaj``
     - m
     - Major radius of flux surface.
   * - ``rmin``
     - m
     - Minor radius of the flux surface.
   * - ``rz``
     - m
     - Spatial location of each mesh node in the poloidal plane; the first index selects the node and the second index selects the R or Z coordinate.
   * - ``surf_arc_len``
     - m
     - Poloidal arc-length of the complete flux surface.
   * - ``surf_idx``
     - Positive integer
     - Node index for each node on a flux surface. First index is flux surface label and second index is the node on the flux surface. Nodes counted from 1. Filled with zeros beyond surf_len.
   * - ``surf_len``
     - Positive integer
     - Number of nodes in each flux surface.
   * - ``surf_maxlen``
     - Positive integer
     - The maximum number of nodes on any flux surface. Used for indexing surf_idx.
   * - ``theta``
     - rad
     - Straight-field-line poloidal angle. Core: :math:`\theta=0` on the outer midplane; SOL: zero on the outer target and :math:`2\pi` on the inner target.
   * - ``tr_area``
     - m^2
     - Surface area of the triangles.
   * - ``trapped``
     - dimensionless
     - Trapped particle fraction for the flux surface.
   * - ``wedge_n``
     - Positive integer
     - Torus wedge number or toroidal periodicity (only written for stellarator simulations).

xgc.f0.mesh.bp
--------------

.. list-table::
   :header-rows: 1
   :widths: 25 20 55

   * - Variable
     - Units
     - Description
   * - ``f0_T_ev``
     - eV
     - Initial temperature for electrons (0) and ions (1).
   * - ``f0_den``
     - m^-3
     - Initial density in the simulation (currently only electrons and main ions).
   * - ``f0_dsmu``
     - species thermal speed sqrt(T_s/m_s)
     - :math:`\Delta v_{\perp}` in the 2D velocity grid of species :math:`s`.
   * - ``f0_dvp``
     - species thermal speed sqrt(T_s/m_s)
     - :math:`\Delta v_{\parallel}` in the 2D velocity grid of species :math:`s`.
   * - ``f0_fg_T_ev``
     - eV
     - Temperature used for calculating the thermal speed used to normalize velocities.
   * - ``f0_flow``
     - m/s
     - Initial parallel bulk flow of the plasma. Positive flow implies motion in the direction of the magnetic field.
   * - ``f0_grid_vol_vonly``
     - eV
     - Prefactor for calculating velocity-space moments: :math:`T_s/\sqrt{2\pi} \, dsmu_n \, dvp_n`. This assumes that the distribution function :math:`f` has absorbed the :math:`v_{\perp}` Jacobian factor and that the velocity-boundary coefficients mu_vol and vp_vol (0.5 on the boundary, 1 otherwise) are not included. For example, the density moment is :math:`n_s(k)=f0\_grid\_vol\_vonly(k) \sum_{i,j} mu\_vol(i) vp\_vol(j) f(i,j,k)`.
   * - ``f0_nmu``
     - Positive integer
     - Number of grid points in :math:`v_{\perp}` in the 2D velocity grid; equal to :math:`f0\_nmu + 1`. Same as input parameter f0_nmu.
   * - ``f0_nvp``
     - Positive integer
     - Number of grid points in :math:`v_{\parallel}` in the 2D velocity grid; equal to :math:`2 f0\_nvp + 1`. Same as input parameter f0_nvp.
   * - ``f0_smu_max``
     - species thermal speed sqrt(T_s/m_s)
     - Maximum :math:`v_{\perp}` in the 2D velocity grid (minimum is 0). Same as input parameter f0_smu_max.
   * - ``f0_vp_max``
     - species thermal speed sqrt(T_s/m_s)
     - Maximum absolute :math:`v_{\parallel}` in the 2D velocity grid; the minimum is the negative of this value. Same as input parameter f0_vp_max.
   * - ``gradpsi``
     - T m
     - Poloidal magnetic flux gradient at each mesh node.
   * - ``gvid0_pid``
     - Positive integer
     - Poloidal mesh partition table. It has length pe_per_plane + 1 and stores the first global vertex ID owned by each rank within a toroidal plane, using XGC's legacy 1-based convention.
   * - ``inode1m1``
     - Positive integer
     - Legacy decomposition metadata: offset of the first vertex on the last MPI rank that wrote to this file.
   * - ``n_n``
     - Positive integer
     - Number of mesh nodes per plane.
   * - ``nb_curl_nb``
     - m^-1
     - Part of the phase space Jacobian (D in XGC's equations), \hat{\boldsymbol{b}}\cdot\nabla\times\hat{\boldsymbol{b}}.
   * - ``ndata``
     - Positive integer
     - Legacy decomposition metadata: number of mesh vertices assigned to the last MPI rank that wrote to this file.
   * - ``nsp``
     - Positive integer
     - Number of species in the output.
   * - ``pe_per_plane``
     - Positive integer
     - Number of MPI ranks per plane.
   * - ``v_curv``
     - radial: T^2, poloidal and toroidal: T m^-1
     - Factors for curvature drift, :math:`\nabla\times B`, in radial, poloidal, and toroidal components. The radial component includes a factor :math:`\|\nabla\psi\|=R B_P`, hence the different units.
   * - ``v_gradb``
     - radial: T^3, poloidal and toroidal: T^2 m^-1
     - Factors for grad-B drift, :math:`B\times\nabla \|B\|`, in radial, poloidal, and toroidal components. The radial component includes a factor :math:`\|\nabla\psi\|=R B_P`, hence the different units.