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

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 \(r_{\min}/R_{\maj}\) 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: \(2\pi/[sml\_mode\_select\_cutoff \, \max_j(\theta_{j+1}-\theta_j)]\).
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 \(N_{\mathrm{wedge}} N_{\phi,\mathrm{tot}} \sum_k V_k\), where \(V_k\) 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 \(N_{\mathrm{planes}}\) (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 \(q\) 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: \(\theta=0\) on the outer midplane; SOL: zero on the outer target and \(2\pi\) 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

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)	\(\Delta v_{\perp}\) in the 2D velocity grid of species \(s\).
f0_dvp	species thermal speed sqrt(T_s/m_s)	\(\Delta v_{\parallel}\) in the 2D velocity grid of species \(s\).
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: \(T_s/\sqrt{2\pi} \, dsmu_n \, dvp_n\). This assumes that the distribution function \(f\) has absorbed the \(v_{\perp}\) 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 \(n_s(k)=f0\_grid\_vol\_vonly(k) \sum_{i,j} mu\_vol(i) vp\_vol(j) f(i,j,k)\).
f0_nmu	Positive integer	Number of grid points in \(v_{\perp}\) in the 2D velocity grid; equal to \(f0\_nmu + 1\). Same as input parameter f0_nmu.
f0_nvp	Positive integer	Number of grid points in \(v_{\parallel}\) in the 2D velocity grid; equal to \(2 f0\_nvp + 1\). Same as input parameter f0_nvp.
f0_smu_max	species thermal speed sqrt(T_s/m_s)	Maximum \(v_{\perp}\) 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 \(v_{\parallel}\) 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}}cdotnablatimeshat{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, \(\nabla\times B\), in radial, poloidal, and toroidal components. The radial component includes a factor \(\|\nabla\psi\|=R B_P\), hence the different units.
v_gradb	radial: T^3, poloidal and toroidal: T^2 m^-1	Factors for grad-B drift, \(B\times\nabla \|B\|\), in radial, poloidal, and toroidal components. The radial component includes a factor \(\|\nabla\psi\|=R B_P\), hence the different units.