Mesh
----

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There are two output files containing mesh parameters (the 5D mesh consists of a 3D unstructured triangular mesh in configuration space and a 2D structured rectangular grid in velocity space): xgc.f0.mesh.bp and xgc.mesh.bp.

**Remarks**

These files contain quantities that can be useful to calculate various averages.

# |nbsp| flux |nbsp| surfaces here includes the scrape-off layer, i.e. the open field-line region.

.. centered:: **xgc.f0.mesh.bp** |br| :smallbluegray:`Printed when: sml_f0_grid=.true..` |nbsp| |nbsp| |nbsp| :smallbluegray:`Output frequency: once at start/restart.`

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   * - *Output*
     - Dimension
     - Units
     - Description
   * - *f0_T_ev*
     - | :math:`N_{\mathrm{species}}~\times`
       | # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - :math:`\mathrm{eV}`
     - Temperature at start in all configuration space vertices for electrons (0) and ions (1).
   * - *f0_den*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - :math:`{\mathrm{m}}^{-3}`
     - Density at start in all configuration space vertices. :red:`Is n_e = n_i assumed?`
   * - *f0_dsmu*
     - Scalar
     - :math:`v_{Ts} = \sqrt{\frac{T_s}{m_s}}`
     - :math:`\Delta v_{\perp}` in the 2D velocity grid of species :math:`s`.
   * - *f0_dvp*
     - Scalar
     - :math:`v_{Ts} = \sqrt{\frac{T_s}{m_s}}`
     - :math:`\Delta v_{\|}` in the 2D velocity grid of species :math:`s`.
   * - *f0_grid_vol_vonly*
     - | :math:`N_{\mathrm{species}}~\times`
       | # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - Units
     - Prefactor for calculating velocity space moments. :math:`= \left( T_s/\sqrt{2 \pi} \right) \times ` ``dsmu_n`` :math:`\times` ``dvp_n``. Note that ``mu_vol`` and ``vp_vol`` are different and not included. In calculating density moment, for example: :math:`n_s(k)=` ``f0_grid_vol_vonly(k)`` :math:`\sum_{i,j}` ``mu_vol(i)`` ``vp_vol(j)`` f(i,j,k)
   * - *f0_nmu*
     - Scalar
     - Positive integer
     - Number of grid points in :math:`v_{\perp}` in the 2D velocity grid is *f0_nmu* + 1. Same as input parameter ``f0_nmu``.
   * - *f0_nvp*
     - Scalar
     - Positive integer
     - Number of grid points in :math:`v_{\|}` in the 2D velocity grid is 2 :math:`\times` *f0_nvp* + 1. Same as input parameter ``f0_nvp``.
   * - *f0_smu_max*
     - Scalar
     - :math:`v_{Ts} = \sqrt{\frac{T_s}{m_s}}`
     - Maximum :math:`v_{\perp}` in the 2D velocity grid (minimum is :math:`0`). Same as input parameter ``f0_smu_max``.
   * - *f0_vp_max*
     - Scalar
     - :math:`v_{Ts} = \sqrt{\frac{T_s}{m_s}}`
     - Maximum/minimum :math:`v_{\|}` (minimum with minus sign) in the 2D velocity grid. Same as input parameter ``f0_vp_max``.
   * - *gradpsi*
     - | # |nbsp| 3D |nbsp| mesh |nbsp| nodes
       | :math:`\times` |nbsp| 2
     - Units
     - Description
   * - *inode1m1*
     - Scalar
     - Units
     - Description
   * - *n_n*
     - Scalar
     - Positive integer
     - Number of |nbsp| 3D |nbsp| mesh |nbsp| nodes.
   * - *nb_curl_nb*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - Units
     - Description
   * - *ndata*
     - Scalar
     - Positive integer
     - Description
   * - *nsp*
     - Scalar
     - Positive integer
     - Number of kinetic species.
   * - *v_curv*
     - | # |nbsp| 3D |nbsp| mesh |nbsp| nodes
       | :math:`\times` |nbsp| 3
     - Units
     - Description
   * - *v_gradb*
     - | # |nbsp| 3D |nbsp| mesh |nbsp| nodes
       | :math:`\times` |nbsp| 3
     - Units
     - Description

.. * *n_n* [chr(12)] <scalar> [None] -- ??

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.. centered:: **xgc.mesh.bp** |br| :smallbluegray:`Printed when: always.` |nbsp| |nbsp| |nbsp| :smallbluegray:`Output frequency: once at start/restart.`

.. list-table::
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   :header-rows: 1

   * - *Output*
     - Dimension
     - Units
     - Description
   * - */cell_set[0]/node_connect_list*
     - | # |nbsp| 3D |nbsp| mesh |nbsp| triangles :math:`\times` |nbsp| 3
     - Integer
     - Defines triangular mesh on each poloidal plane (similar to, but indexed differently from .ele file). Same as ``nd_connect_list``. First index is triangle index and the second index is over the three nodes that make up the triangle's vertices. These are labelled by the index of the mesh node (from .node file). Index of nodes counts starting from zero.
   * - *nd_connect_list*
     - | # |nbsp| 3D |nbsp| mesh |nbsp| triangles :math:`\times` |nbsp| 3
     - Integer
     - Defines triangular mesh on each poloidal plane (similar to, but indexed differently from .ele file). Same as ``/cell_set[0]/node_connect_list``. First index is triangle index and the second index is over the three nodes that make up the triangle's vertices. These are labelled by the index of the mesh node (from .node file). Index of nodes counts starting from zero.
   * - */coordinates/values*
     - | # |nbsp| 3D |nbsp| mesh |nbsp| nodes
       | :math:`\times` |nbsp| 2
     - Meters
     - Defines the spatial location in the poloidal plane for each mesh node. First index defines the node. Second index is the :math:`(R,Z)` coordinate of the node. Same as ``rz``.
   * - *rz*
     - | # |nbsp| 3D |nbsp| mesh |nbsp| nodes
       | :math:`\times` |nbsp| 2
     - Meters
     - Defines the spatial location in the poloidal plane for each mesh node. First index defines the node. Second index is the :math:`(R,Z)` coordinate of the node. Same as ``/coordinates/values``.
   * - *epsilon*
     - # |nbsp| flux |nbsp| surfaces
     - Normalized
     - Inverse aspect ratio *rmin*/*rmaj* for the flux surface.
   * - *n_geo*
     - Scalar
     - Positive integer
     - Number of flux surfaces. Same as ``nsurf``.
   * - *n_n*
     - Scalar
     - Positive integer
     - Number of |nbsp| 2D |nbsp| mesh |nbsp| nodes.
   * - *n_t*
     - Scalar
     - Positive integer
     - Number of |nbsp| 2D |nbsp| mesh |nbsp| triangles.
   * - *grid_nwall*
     - Scalar
     - Positive integer
     - Number of nodes that make up the boundary of the domain (and represent the wall).
   * - *node_vol*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - :math:`\mathrm{m}^{3}`
     - Spatial volume of the 3D mesh node. Volume of whole torus is ``wedge_n`` :math:`\times` ``n_phi_tot`` :math:`\times \sum_k` ``node_vol(k)``.
   * - *node_vol_nearest*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - :math:`\mathrm{m}^{3}`
     - Description
   * - *nsurf*
     - Scalar
     - Positive integer
     - Number of flux surfaces.
   * - *psi*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - Weber/rad 
     - Toroidal magnetic flux for the flux surface that the node is on.
   * - *psi_surf*
     - # |nbsp| flux |nbsp| surfaces
     - Weber/rad 
     - Toroidal magnetic flux for the flux surface.
   * - *qsafety*
     - # |nbsp| flux |nbsp| surfaces
     - Normalized
     - Safety factor :math:`q` for the flux surface.
   * - *rmaj*
     - # |nbsp| flux |nbsp| surfaces
     - m
     - Major radius of flux surface.
   * - *rmin*
     - # |nbsp| flux |nbsp| surfaces
     - m
     - Minor radius of flux surface
   * - *surf_arc_len*
     - # |nbsp| flux |nbsp| surfaces
     - m
     - Poloidal arc-length of the complete flux surface.
   * - *surf_idx*
     - | # |nbsp| flux |nbsp| surfaces
       | :math:`\times` |nbsp| *surf_maxlen*
     - 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*
     - # |nbsp| flux |nbsp| surfaces
     - Positive integer
     - Number of nodes in each flux surface.
   * - *surf_maxlen*
     - Scalar
     - Positive integer
     - The maximum number of nodes on any flux surface. Used for indexing *surf_idx*.
   * - *theta*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - Normalized
     - Poloidal coordinate.
   * - *trapped*
     - # |nbsp| flux |nbsp| surfaces
     - Normalized
     - Trapped particle fraction for flux surface.
   * - *nextnode*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - Units
     - Description
   * - *mapping*
     - # |nbsp| 3D |nbsp| mesh |nbsp| triangles :math:`\times 3 \times 2`
     - m
     - Defines coordinates of triangle vertices. 
   * - *grid_wall_nodes*
     - *nwall*
     - Positive integer
     - Node index for each wall node. Currently not "ordered", but in the order specified in .node file.
   * - *m_max_surf*
     - # |nbsp| flux |nbsp| surfaces
     - Positive integer
     - Maximum resolvable poloidal mode number on each flux surface. Defined by field-following alignment when generating the mesh.
   * - *ff_1dp_p*
     - 2 :math:`\times` # |nbsp| 3D |nbsp| mesh |nbsp| nodes :math:`\times` 3
     - Units
     - Description
   * - *ff_hdp_p*
     - 2 :math:`\times` # |nbsp| 3D |nbsp| mesh |nbsp| nodes :math:`\times` 3
     - Units
     - Description

   * - *one_per_dx*
     - 2 :math:`\times` # |nbsp| 3D |nbsp| mesh |nbsp| nodes 
     - Units
     - Description
   * - *node_vol_ff0*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - Units
     - Description 
   * - *node_vol_ff1*
     - # |nbsp| 3D |nbsp| mesh |nbsp| nodes
     - Units
     - Description

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