ERF_TerrainMetrics.H File Reference

#include <AMReX.H>
#include <AMReX_Geometry.H>
#include <AMReX_MultiFab.H>
#include <ERF_IndexDefines.H>
#include <cmath>
#include <ERF_NumericalConstants.H>

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Enumerations
enum class	FineTerrain { None , Interpolate , Transform }

Functions
void	init_default_zphys (int lev, const amrex::Geometry &geom, amrex::MultiFab &z_phys_nd, amrex::MultiFab &z_phys_cc, amrex::Real z_offset=zero)
amrex::BoxArray	join_boxes_stacked_in_z (const amrex::BoxArray &ba)
void	init_zlevels (amrex::Vector< amrex::Vector< amrex::Real >> &zlevels_stag, amrex::Vector< amrex::Vector< amrex::Real >> &stretched_dz_h, amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real >> &stretched_dz_d, amrex::Vector< amrex::Geometry > const &geom, amrex::Vector< amrex::IntVect > const &ref_ratio, const amrex::Real grid_stretching_ratio, const amrex::Real zsurf, const amrex::Real dz0)
FineTerrain	which_fine_terrain ()
void	make_terrain_fitted_coords (int lev, const amrex::Geometry &geom, amrex::MultiFab &z_phys_nd, amrex::Vector< amrex::Real > const &z_levels_h, amrex::GpuArray< ERF_BC, AMREX_SPACEDIM *2 > &phys_bc_type, FineTerrain fine_terrain=FineTerrain::None, amrex::MultiFab const *z_phys_interp=nullptr)
void	init_which_terrain_grid (int lev, const amrex::Geometry &geom, amrex::MultiFab &z_phys_nd, amrex::Vector< amrex::Real > const &z_levels_h, FineTerrain fine_terrain=FineTerrain::None, amrex::MultiFab const *z_phys_interp=nullptr)
void	init_fine_terrain_grid (int lev, const amrex::Geometry &geom, amrex::MultiFab &z_phys_nd, amrex::Vector< amrex::Real > const &z_levels_h, FineTerrain fine_terrain, amrex::MultiFab const *z_phys_interp)
amrex::Real	get_dzmin_terrain (amrex::MultiFab &z_phys_nd)
void	update_stretched_dz (int lev, amrex::Vector< amrex::Vector< amrex::Real >> const &zlevels_stag, amrex::Vector< amrex::Vector< amrex::Real >> &stretched_dz_h, amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real >> &stretched_dz_d)
AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_zeta_AtCellCenter (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_xi_AtCellCenter (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_eta_AtCellCenter (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_zeta_AtIface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_xi_AtIface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_eta_AtIface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_zeta_AtJface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_xi_AtJface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_eta_AtJface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_zeta_AtKface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_xi_AtKface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_eta_AtKface (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_zeta_AtEdgeCenterK (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_xi_AtEdgeCenterK (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_eta_AtEdgeCenterK (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_zeta_AtEdgeCenterJ (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_xi_AtEdgeCenterJ (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_eta_AtEdgeCenterJ (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_zeta_AtEdgeCenterI (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_xi_AtEdgeCenterI (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_h_eta_AtEdgeCenterI (const int &i, const int &j, const int &k, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &cellSizeInv, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_Z_AtCellCenter (const int &i, const int &j, const int &k, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_Z_AtWFace (const int &i, const int &j, const int &k, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real	Compute_Zrel_AtCellCenter (const int &i, const int &j, const int &k, const amrex::Array4< const amrex::Real > &z_nd)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	OmegaFromW (int &i, int &j, int &k, amrex::Real w, const amrex::Array4< const amrex::Real > &u_arr, const amrex::Array4< const amrex::Real > &v_arr, const amrex::Array4< const amrex::Real > &mf_u, const amrex::Array4< const amrex::Real > &mf_v, const amrex::Array4< const amrex::Real > &z_nd, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &dxInv)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real	WFromOmega (int &i, int &j, int &k, amrex::Real omega, const amrex::Array4< const amrex::Real > &u_arr, const amrex::Array4< const amrex::Real > &v_arr, const amrex::Array4< const amrex::Real > &mf_u, const amrex::Array4< const amrex::Real > &mf_v, const amrex::Array4< const amrex::Real > &z_nd, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &dxInv)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE void	rotate_scalar_flux (const int &i, const int &j, const int &klo, const int &, const amrex::Real &flux, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &dxInv, const amrex::Array4< const amrex::Real > &zphys_arr, const amrex::Array4< amrex::Real > &phi1_arr, const amrex::Array4< amrex::Real > &phi2_arr, const amrex::Array4< amrex::Real > &phi3_arr)
AMREX_GPU_DEVICE AMREX_FORCE_INLINE void	rotate_stress_tensor (const int &i, const int &j, const int &klo, const int &, const amrex::Real &flux, const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &dxInv, const amrex::Array4< const amrex::Real > &zphys_arr, const amrex::Array4< const amrex::Real > &u_arr, const amrex::Array4< const amrex::Real > &v_arr, const amrex::Array4< const amrex::Real > &w_arr, const amrex::Array4< amrex::Real > &, const amrex::Array4< amrex::Real > &, const amrex::Array4< amrex::Real > &, const amrex::Array4< amrex::Real > &, const amrex::Array4< amrex::Real > &, const amrex::Array4< amrex::Real > &tau13_arr, const amrex::Array4< amrex::Real > &tau31_arr, const amrex::Array4< amrex::Real > &tau23_arr, const amrex::Array4< amrex::Real > &tau32_arr)

Enumeration Type Documentation

FineTerrain

enum FineTerrain

strong

How the terrain-fitted mesh on a fine level is built when erf.terrain_smoothing != 0.

The STF and Sullivan TF transformations are not defined on a level that does not reach the top of the domain, so on a fine level we instead start from the mesh interpolated from the coarse level. A caller that has done that interpolation – and, for Transform, has also written the fine-resolution terrain into the k=0 slab and saved the pre-overwrite field – says so by passing anything other than None. Every other caller keeps the historical behavior of aborting, because it has not prepared z_phys_nd in a way this path can use.

Enumerator
None	caller has not prepared a fine mesh from the coarse level
Interpolate	use the coordinates interpolated from the coarse level as-is
Transform	add the fine terrain as a correction that decays with height

                        {
    None,        //!< caller has not prepared a fine mesh from the coarse level
    Interpolate, //!< use the coordinates interpolated from the coarse level as-is
    Transform    //!< add the fine terrain as a correction that decays with height
};

Function Documentation

Compute_h_eta_AtCellCenter()

AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_eta_AtCellCenter	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the eta metric term at the cell center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Eta metric term.

{
    amrex::Real dyInv = cellSizeInv[1];
    amrex::Real met_h_eta  = fourth * dyInv *
      ( z_nd(i,j+1,k) + z_nd(i+1,j+1,k) + z_nd(i,j+1,k+1) + z_nd(i+1,j+1,k+1)
      - z_nd(i,j  ,k) - z_nd(i+1,j  ,k) - z_nd(i,j  ,k+1) - z_nd(i+1,j  ,k+1) );
    return met_h_eta;
}

Referenced by Compute_InvDt_Compressible(), ComputeStrain_T(), ComputeStressConsVisc_T(), ComputeStressVarVisc_T(), ERF::FillPlot3DVars(), ERFPhysBCFunct_cons::impose_vertical_cons_bcs(), ERF::poisson_wall_dist(), rotate_scalar_flux(), MOSTAverage::set_norm_indices_T(), and MOSTAverage::set_norm_positions_T().

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Compute_h_eta_AtEdgeCenterI()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_eta_AtEdgeCenterI	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the eta metric term at the i-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Eta metric term.

{
    amrex::Real dyInv = cellSizeInv[1];
    amrex::Real met_h_eta = fourth * dyInv *
      ( z_nd(i+1,j+1,k) + z_nd(i,j+1,k)
      - z_nd(i+1,j-1,k) - z_nd(i,j-1,k) );
    return met_h_eta;
}

Referenced by ComputeStrain_T(), ComputeStressConsVisc_T(), and ComputeStressVarVisc_T().

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Compute_h_eta_AtEdgeCenterJ()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_eta_AtEdgeCenterJ	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the eta metric term at the j-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Eta metric term.

{
    amrex::Real dyInv = cellSizeInv[1];
    amrex::Real met_h_eta = dyInv * ( z_nd(i,j+1,k) - z_nd(i,j,k) );
    return met_h_eta;
}

Referenced by ComputeStressConsVisc_T(), and ComputeStressVarVisc_T().

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Compute_h_eta_AtEdgeCenterK()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_eta_AtEdgeCenterK	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the eta metric term at the k-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Eta metric term.

{
    amrex::Real dyInv = cellSizeInv[1];
    amrex::Real met_h_eta = fourth * dyInv *
      ( z_nd(i,j+1,k) + z_nd(i,j+1,k+1)
      - z_nd(i,j-1,k) - z_nd(i,j-1,k+1) );
    return met_h_eta;
}

Referenced by ComputeStrain_T().

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Compute_h_eta_AtIface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_eta_AtIface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the eta metric term at the i-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Eta metric term.

{
    amrex::Real met_h_eta  = myhalf * cellSizeInv[1] * ( (z_nd(i,j+1,k  ) - z_nd(i,j,k  ))
                                                       + (z_nd(i,j+1,k+1) - z_nd(i,j,k+1)) );
    return met_h_eta;
}

Referenced by ERFPhysBCFunct_u::impose_vertical_xvel_bcs(), and rotate_stress_tensor().

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Compute_h_eta_AtJface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_eta_AtJface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the eta metric term at the j-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Eta metric term.

{
    amrex::Real met_h_eta  = amrex::Real(0.125) * cellSizeInv[1] *
      ( (z_nd(i  ,j+1,k  ) - z_nd(i  ,j-1,k  )) + (z_nd(i  ,j+1,k+1) - z_nd(i  ,j-1,k+1)) +
        (z_nd(i+1,j+1,k  ) - z_nd(i+1,j-1,k  )) + (z_nd(i+1,j+1,k+1) - z_nd(i+1,j-1,k+1)) );
    return met_h_eta;
}

Referenced by DiffusionSrcForState_T(), erf_substep_MT(), erf_substep_T(), ERFPhysBCFunct_v::impose_vertical_yvel_bcs(), ERF::poisson_wall_dist(), and MOSTAverage::set_rotated_fields().

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Compute_h_eta_AtKface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_eta_AtKface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the eta metric term at the k-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Eta metric term.

{
    amrex::Real met_h_eta  = myhalf * cellSizeInv[1] * ( (z_nd(i  ,j+1,k) - z_nd(i  ,j,k))
                                                       + (z_nd(i+1,j+1,k) - z_nd(i+1,j,k)) );
    return met_h_eta;
}

Referenced by DiffusionSrcForState_T(), and ERF::poisson_wall_dist().

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Compute_h_xi_AtCellCenter()

AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_xi_AtCellCenter	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the xi metric term at the cell center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Xi metric term.

{
    amrex::Real dxInv = cellSizeInv[0];
    amrex::Real met_h_xi   = fourth * dxInv *
      ( z_nd(i+1,j,k) + z_nd(i+1,j+1,k) + z_nd(i+1,j,k+1) + z_nd(i+1,j+1,k+1)
      - z_nd(i  ,j,k) - z_nd(i  ,j+1,k) - z_nd(i  ,j,k+1) - z_nd(i  ,j+1,k+1) );
    return met_h_xi;
}

Referenced by Compute_InvDt_Compressible(), ComputeStrain_T(), ComputeStressConsVisc_T(), ComputeStressVarVisc_T(), ERF::FillPlot3DVars(), ERFPhysBCFunct_cons::impose_vertical_cons_bcs(), ERF::poisson_wall_dist(), rotate_scalar_flux(), MOSTAverage::set_norm_indices_T(), and MOSTAverage::set_norm_positions_T().

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Compute_h_xi_AtEdgeCenterI()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_xi_AtEdgeCenterI	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the xi metric term at the i-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Xi metric term.

{
    amrex::Real dxInv = cellSizeInv[0];
    amrex::Real met_h_xi  = dxInv * ( z_nd(i+1,j,k) - z_nd(i,j,k) );
    return met_h_xi;
}

Referenced by ComputeStressConsVisc_T(), and ComputeStressVarVisc_T().

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Compute_h_xi_AtEdgeCenterJ()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_xi_AtEdgeCenterJ	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the xi metric term at the j-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Xi metric term.

{
    amrex::Real dxInv = cellSizeInv[0];
    amrex::Real met_h_xi = fourth * dxInv *
      ( z_nd(i+1,j+1,k) + z_nd(i+1,j  ,k)
      - z_nd(i-1,j+1,k) - z_nd(i-1,j  ,k) );
    return met_h_xi;
}

Referenced by ComputeStrain_T(), ComputeStressConsVisc_T(), and ComputeStressVarVisc_T().

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Compute_h_xi_AtEdgeCenterK()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_xi_AtEdgeCenterK	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the xi metric term at the k-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Xi metric term.

{
    amrex::Real dxInv = cellSizeInv[0];
    amrex::Real met_h_xi  = fourth * dxInv *
      ( z_nd(i+1,j,k) + z_nd(i+1,j,k+1)
      - z_nd(i-1,j,k) - z_nd(i-1,j,k+1) );
    return met_h_xi;
}

Referenced by ComputeStrain_T().

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Compute_h_xi_AtIface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_xi_AtIface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the xi metric term at the i-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Xi metric term.

{
    amrex::Real met_h_xi   = amrex::Real(0.125) * cellSizeInv[0] * (
      (z_nd(i+1,j  ,k  ) - z_nd(i-1,j  ,k  )) + (z_nd(i+1,j  ,k+1) - z_nd(i-1,j  ,k+1)) +
      (z_nd(i+1,j+1,k  ) - z_nd(i-1,j+1,k  )) + (z_nd(i+1,j+1,k+1) - z_nd(i-1,j+1,k+1)) );
    return met_h_xi;
}

Referenced by DiffusionSrcForState_T(), erf_substep_MT(), erf_substep_T(), ERFPhysBCFunct_u::impose_vertical_xvel_bcs(), ERF::poisson_wall_dist(), rotate_stress_tensor(), and MOSTAverage::set_rotated_fields().

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Compute_h_xi_AtJface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_xi_AtJface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the xi metric term at the j-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Xi metric term.

{
    amrex::Real met_h_xi   = myhalf * cellSizeInv[0] * ( (z_nd(i+1,j,k  ) - z_nd(i,j,k  ))
                                                       + (z_nd(i+1,j,k+1) - z_nd(i,j,k+1)) );
    return met_h_xi;
}

Referenced by ERFPhysBCFunct_v::impose_vertical_yvel_bcs().

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Compute_h_xi_AtKface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_xi_AtKface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the xi metric term at the k-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Xi metric term.

{
    amrex::Real met_h_xi   = myhalf * cellSizeInv[0] * ( (z_nd(i+1,j  ,k) - z_nd(i,j  ,k))
                                                       + (z_nd(i+1,j+1,k) - z_nd(i,j+1,k)) );
    return met_h_xi;
}

Referenced by DiffusionSrcForState_T(), and ERF::poisson_wall_dist().

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Compute_h_zeta_AtCellCenter()

AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_zeta_AtCellCenter	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the zeta metric term at the cell center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Zeta metric term.

{
    amrex::Real dzInv = cellSizeInv[2];
    amrex::Real met_h_zeta = fourth * dzInv *
      ( z_nd(i+1,j,k+1) + z_nd(i+1,j+1,k+1) + z_nd(i,j,k+1) + z_nd(i,j+1,k+1)
      - z_nd(i+1,j,k  ) - z_nd(i+1,j+1,k  ) - z_nd(i,j,k  ) - z_nd(i,j+1,k  ) );
    return met_h_zeta;
}

Referenced by Compute_InvDt_Anelastic(), Compute_InvDt_Compressible(), MOSTAverage::compute_region_averages(), ComputeDiffusivityMRF(), ComputeDiffusivityMYJ(), ComputeDiffusivityMYNN25(), ComputeDiffusivityMYNNEDMF(), ComputeDiffusivityYSU(), ComputeDiffusivityYSUNew(), ComputeTurbulentViscosityLES(), ComputeTurbulentViscosityRANS(), ERF::estTimeStep(), ERF::FillPlot3DVars(), ERFPhysBCFunct_cons::impose_vertical_cons_bcs(), and ERF::poisson_wall_dist().

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Compute_h_zeta_AtEdgeCenterI()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_zeta_AtEdgeCenterI	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the zeta metric term at the i-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Zeta metric term.

{
    amrex::Real dzInv = cellSizeInv[2];
    amrex::Real met_h_zeta = fourth * dzInv * ( z_nd(i,j,k+1) + z_nd(i+1,j,k+1)
                                              - z_nd(i,j,k-1) - z_nd(i+1,j,k-1) );
    return met_h_zeta;
}

Referenced by AdvectionSrcForMom_TF(), AdvectionSrcForZMom(), ComputeStrain_T(), ComputeStressConsVisc_T(), and ComputeStressVarVisc_T().

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Compute_h_zeta_AtEdgeCenterJ()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_zeta_AtEdgeCenterJ	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the zeta metric term at the j-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Zeta metric term.

{
    amrex::Real dzInv = cellSizeInv[2];
    amrex::Real met_h_zeta = fourth * dzInv * ( z_nd(i,j,k+1) + z_nd(i,j+1,k+1)
                                              - z_nd(i,j,k-1) - z_nd(i,j+1,k-1) );
    return met_h_zeta;
}

Referenced by AdvectionSrcForMom_TF(), AdvectionSrcForZMom(), ComputeStrain_T(), ComputeStressConsVisc_T(), and ComputeStressVarVisc_T().

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Compute_h_zeta_AtEdgeCenterK()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_zeta_AtEdgeCenterK	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the zeta metric term at the k-edge center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Zeta metric term.

{
    amrex::Real dzInv = cellSizeInv[2];
    amrex::Real met_h_zeta = dzInv * (z_nd(i,j,k+1) - z_nd(i,j,k));
    return met_h_zeta;
}

Referenced by AdvectionSrcForMom_TF(), AdvectionSrcForXMom(), AdvectionSrcForYMom(), ComputeStressConsVisc_T(), and ComputeStressVarVisc_T().

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Compute_h_zeta_AtIface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_zeta_AtIface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the zeta metric term at the i-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Zeta metric term.

{
    amrex::Real met_h_zeta = myhalf * cellSizeInv[2] * ( (z_nd(i,j  ,k+1) - z_nd(i,j  ,k))
                                                       + (z_nd(i,j+1,k+1) - z_nd(i,j+1,k)) );
    return met_h_zeta;
}

Referenced by erf_make_tau_terms(), erf_slow_rhs_pre(), erf_substep_MT(), erf_substep_T(), ERFPhysBCFunct_u::impose_vertical_xvel_bcs(), ERF::poisson_wall_dist(), and rotate_stress_tensor().

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Compute_h_zeta_AtJface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_zeta_AtJface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the zeta metric term at the j-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Zeta metric term.

{
    amrex::Real met_h_zeta = myhalf * cellSizeInv[2] * ( (z_nd(i  ,j,k+1) - z_nd(i  ,j,k  ))
                                                       + (z_nd(i+1,j,k+1) - z_nd(i+1,j,k  )) );
    return met_h_zeta;
}

Referenced by erf_make_tau_terms(), erf_slow_rhs_pre(), erf_substep_MT(), erf_substep_T(), ERFPhysBCFunct_v::impose_vertical_yvel_bcs(), and ERF::poisson_wall_dist().

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Compute_h_zeta_AtKface()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_h_zeta_AtKface	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	cellSizeInv,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the zeta metric term at the k-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	cellSizeInv	Inverse cell spacing.
[in]	z_nd	Nodal physical height field.

Returns

Zeta metric term.

{
    amrex::Real met_h_zeta = amrex::Real(0.125) * cellSizeInv[2] *
      ( (z_nd(i  ,j  ,k+1) - z_nd(i  ,j  ,k-1)) + (z_nd(i+1,j  ,k+1) - z_nd(i+1,j  ,k-1)) +
        (z_nd(i  ,j+1,k+1) - z_nd(i  ,j+1,k-1)) + (z_nd(i+1,j+1,k+1) - z_nd(i+1,j+1,k-1)) );
    return met_h_zeta;
}

Referenced by compute_gradp_interpz(), compute_gradp_z(), DiffusionSrcForState_T(), ImplicitDiffForMomLU_T(), ImplicitDiffForStateLU_T(), and ERF::poisson_wall_dist().

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Compute_Z_AtCellCenter()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_Z_AtCellCenter	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the physical height at the cell center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	z_nd	Nodal physical height field.

Returns

Physical height at cell center.

{
    const amrex::Real z_cc = amrex::Real(0.125)*(  z_nd(i  ,j  ,k) + z_nd(i  ,j  ,k+1)
                                                 + z_nd(i+1,j  ,k) + z_nd(i+1,j  ,k+1)
                                                 + z_nd(i  ,j+1,k) + z_nd(i  ,j+1,k+1)
                                                 + z_nd(i+1,j+1,k) + z_nd(i+1,j+1,k+1));
 
    return z_cc;
}

Referenced by SurfaceLayer::fill_qsurf_with_qsat(), sea_level_pressure_diagnostics::fill_sea_level_pressure(), SurfaceLayer::fill_tsurf_with_coupled_sst(), SurfaceLayer::fill_tsurf_with_sfc_sst(), ERFPhysBCFunct_cons::impose_vertical_cons_bcs(), SurfaceLayer::init_tke_from_ustar(), and plotfile2d::sampled_field_value().

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Compute_Z_AtWFace()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_Z_AtWFace	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the physical height at the W-face.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	z_nd	Nodal physical height field.

Returns

Physical height at W-face.

{
    const amrex::Real z_wf = fourth*( z_nd(i  ,j  ,k) + z_nd(i+1,j  ,k)
                                    + z_nd(i  ,j+1,k) + z_nd(i+1,j+1,k) );
 
    return z_wf;
}

Referenced by DiffusionSrcForState_T(), SurfaceLayer::fill_qsurf_with_qsat(), sea_level_pressure_diagnostics::fill_sea_level_pressure(), SurfaceLayer::fill_tsurf_with_coupled_sst(), SurfaceLayer::fill_tsurf_with_sfc_sst(), ERF::FillPlot2DVars(), get_dzmin_terrain(), OmegaFromW(), and WFromOmega().

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Compute_Zrel_AtCellCenter()

AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real Compute_Zrel_AtCellCenter	(	const int &	i,
		const int &	j,
		const int &	k,
		const amrex::Array4< const amrex::Real > &	z_nd
	)

Compute the relative height above the terrain surface at the cell center.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	z_nd	Nodal physical height field.

Returns

Relative height at cell center.

{
    const amrex::Real z_cc = amrex::Real(0.125)*(  z_nd(i  ,j  ,k) + z_nd(i  ,j  ,k+1) +
                                                 + z_nd(i+1,j  ,k) + z_nd(i+1,j  ,k+1)
                                                 + z_nd(i  ,j+1,k) + z_nd(i  ,j+1,k+1)
                                                 + z_nd(i+1,j+1,k) + z_nd(i+1,j+1,k+1));
 
    // Note: we assume the z_nd array spans from the bottom to top of the domain
    // i.e. no domain decomposition across processors in vertical direction
    const amrex::Real z0_cc = fourth*( z_nd(i  ,j  ,0) + z_nd(i  ,j+1,0)
                                     + z_nd(i+1,j  ,0) + z_nd(i+1,j+1,0));
 
    return (z_cc - z0_cc);
}

Referenced by ComputeDiffusivityMRF(), ComputeDiffusivityMYJ(), ComputeDiffusivityMYNN25(), ComputeDiffusivityMYNNEDMF(), ComputeDiffusivityYSU(), ComputeDiffusivityYSUNew(), near_surface_diagnostics::fill(), Radiation::mf_to_kokkos_buffers(), and plotfile2d::sampled_field_value().

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get_dzmin_terrain()

amrex::Real get_dzmin_terrain

(

amrex::MultiFab &

z_phys_nd

)

Compute the minimum vertical spacing with terrain.

Parameters

[in]

z_phys_nd

Nodal physical height field.

Returns

Minimum vertical grid spacing.

init_default_zphys()

void init_default_zphys	(	int	lev,
		const amrex::Geometry &	geom,
		amrex::MultiFab &	z_phys_nd,
		amrex::MultiFab &	z_phys_cc,
		amrex::Real	z_offset = zero
	)

Routine to define default z_phys_nd and z_phys_cc

init_fine_terrain_grid()

void init_fine_terrain_grid	(	int	lev,
		const amrex::Geometry &	geom,
		amrex::MultiFab &	z_phys_nd,
		amrex::Vector< amrex::Real > const &	z_levels_h,
		FineTerrain	fine_terrain,
		amrex::MultiFab const *	z_phys_interp
	)

Finish the terrain-fitted mesh on a fine level whose interior was set by interpolation from the coarse level (erf.terrain_smoothing != 0).

For FineTerrain::Transform this adds the fine-resolution terrain as a correction that decays linearly to zero at the top of the fine grids. For both modes it then fills the nodes outside the lateral domain boundary and the layer below the surface, which init_which_terrain_grid()'s BTF branch would otherwise have filled.

Parameters

[in]	lev	Level index.
[in]	geom	Geometry information.
[in,out]	z_phys_nd	Nodal physical height field.
[in]	z_levels_h	Host z-levels.
[in]	fine_terrain	Interpolate or Transform.
[in]	z_phys_interp	Mesh interpolated from the coarse level; see above.

init_which_terrain_grid()

void init_which_terrain_grid	(	int	lev,
		const amrex::Geometry &	geom,
		amrex::MultiFab &	z_phys_nd,
		amrex::Vector< amrex::Real > const &	z_levels_h,
		FineTerrain	fine_terrain = FineTerrain::None,
		amrex::MultiFab const *	z_phys_interp = nullptr
	)

Initialize the terrain grid mapping.

Parameters

[in]	lev	Level index.
[in]	geom	Geometry information.
[out]	z_phys_nd	Nodal physical height field.
[in]	z_levels_h	Host z-levels.
[in]	fine_terrain	How a fine level with terrain_smoothing != 0 is to be built.
[in]	z_phys_interp	Mesh interpolated from the coarse level; see above.

init_zlevels()

void init_zlevels	(	amrex::Vector< amrex::Vector< amrex::Real >> &	zlevels_stag,
		amrex::Vector< amrex::Vector< amrex::Real >> &	stretched_dz_h,
		amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real >> &	stretched_dz_d,
		amrex::Vector< amrex::Geometry > const &	geom,
		amrex::Vector< amrex::IntVect > const &	ref_ratio,
		const amrex::Real	grid_stretching_ratio,
		const amrex::Real	zsurf,
		const amrex::Real	dz0
	)

Utility routines for constructing terrain metric terms Initialize staggered z-levels and stretched vertical spacing.

Parameters

[out]	zlevels_stag	Staggered z-levels.
[out]	stretched_dz_h	Host stretched vertical spacing.
[out]	stretched_dz_d	Device stretched vertical spacing.
[in]	geom	Geometry information.
[in]	ref_ratio	Refinement ratios.
[in]	grid_stretching_ratio	Ratio for grid stretching.
[in]	zsurf	Surface height.
[in]	dz0	Initial vertical spacing.

join_boxes_stacked_in_z()

amrex::BoxArray join_boxes_stacked_in_z

(

const amrex::BoxArray &

ba

)

The cells of a (cell-centered) BoxArray as boxes that are never stacked on each other: wherever a box sits on the top face of another, the run of cells in z that the two belong to becomes a single box. Returns ba itself when no two boxes of ba are stacked.

Parameters

[in]

ba

cell-centered BoxArray

make_terrain_fitted_coords()

void make_terrain_fitted_coords	(	int	lev,
		const amrex::Geometry &	geom,
		amrex::MultiFab &	z_phys_nd,
		amrex::Vector< amrex::Real > const &	z_levels_h,
		amrex::GpuArray< ERF_BC, AMREX_SPACEDIM *2 > &	phys_bc_type,
		FineTerrain	fine_terrain = FineTerrain::None,
		amrex::MultiFab const *	z_phys_interp = nullptr
	)

Construct terrain-fitted coordinates.

Parameters

[in]	lev	Level index.
[in]	geom	Geometry information.
[out]	z_phys_nd	Nodal physical height field.
[in]	z_levels_h	Host z-levels.
[in]	phys_bc_type	Physical boundary condition types.
[in]	fine_terrain	How a fine level with terrain_smoothing != 0 is to be built.
[in]	z_phys_interp	Mesh interpolated from the coarse level before the fine terrain was written into the k=0 slab; required by, and only used for, FineTerrain::Transform.

OmegaFromW()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real OmegaFromW	(	int &	i,
		int &	j,
		int &	k,
		amrex::Real	w,
		const amrex::Array4< const amrex::Real > &	u_arr,
		const amrex::Array4< const amrex::Real > &	v_arr,
		const amrex::Array4< const amrex::Real > &	mf_u,
		const amrex::Array4< const amrex::Real > &	mf_v,
		const amrex::Array4< const amrex::Real > &	z_nd,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	dxInv
	)

Compute the contravariant vertical velocity omega from w.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	w	Vertical velocity.
[in]	u_arr	X-velocity array.
[in]	v_arr	Y-velocity array.
[in]	mf_u	X-velocity map factor.
[in]	mf_v	Y-velocity map factor.
[in]	z_nd	Nodal physical height field.
[in]	dxInv	Inverse cell spacing.

Returns

Contravariant vertical velocity.

{
    // This is dh/dxi at hi and lo edges
    amrex::Real z_x_p2  = Compute_Z_AtWFace(i+2,j,k,z_nd);
    amrex::Real z_x_p1  = Compute_Z_AtWFace(i+1,j,k,z_nd);
    amrex::Real z_x_m1  = Compute_Z_AtWFace(i-1,j,k,z_nd);
    amrex::Real z_x_m2  = Compute_Z_AtWFace(i-2,j,k,z_nd);
    amrex::Real met_xi  = (amrex::Real(1.0/amrex::Real(12.0))*(z_x_m2 - z_x_p2)
                         + amrex::Real(8.0/amrex::Real(12.0))*(z_x_p1 - z_x_m1)) * dxInv[0];
 
    // This is dh/deta at hi and lo edges
    amrex::Real z_y_p2   = Compute_Z_AtWFace(i,j+2,k,z_nd);
    amrex::Real z_y_p1   = Compute_Z_AtWFace(i,j+1,k,z_nd);
    amrex::Real z_y_m1   = Compute_Z_AtWFace(i,j-1,k,z_nd);
    amrex::Real z_y_m2   = Compute_Z_AtWFace(i,j-2,k,z_nd);
    amrex::Real met_eta  = (amrex::Real(1.0/amrex::Real(12.0))*(z_y_m2 - z_y_p2)
                          + amrex::Real(8.0/amrex::Real(12.0))*(z_y_p1 - z_y_m1)) * dxInv[1];
 
    // Use extrapolation instead of interpolation if at the bottom boundary
    amrex::Real u_hi = (k == 0) ? amrex::Real(1.5) *   u_arr(i+1,j  ,k  ) - myhalf * u_arr(i+1,j  ,k+1)  :
                                  myhalf * ( u_arr(i+1,j  ,k-1) +       u_arr(i+1,j  ,k  ) );
    amrex::Real u_lo = (k == 0) ? amrex::Real(1.5) *   u_arr(i  ,j  ,k  ) - myhalf * u_arr(i  ,j  ,k+1)  :
                                  myhalf * ( u_arr(i  ,j  ,k-1) +       u_arr(i  ,j  ,k  ) );
    amrex::Real mf_u_hi = mf_u(i+1,j,0);
    amrex::Real mf_u_lo = mf_u(i  ,j,0);
 
    amrex::Real v_hi = (k == 0) ? amrex::Real(1.5) *   v_arr(i  ,j+1,k  ) - myhalf * v_arr(i  ,j+1,k+1)  :
                                  myhalf * ( v_arr(i  ,j+1,k-1) +       v_arr(i  ,j+1,k  ) );
    amrex::Real v_lo = (k == 0) ? amrex::Real(1.5) *   v_arr(i  ,j  ,k  ) - myhalf * v_arr(i  ,j  ,k+1)  :
                                  myhalf * ( v_arr(i  ,j  ,k-1) +       v_arr(i  ,j  ,k  ) );
    amrex::Real mf_v_hi = mf_v(i,j+1,0);
    amrex::Real mf_v_lo = mf_v(i,j  ,0);
 
    amrex::Real u_met = met_xi  * myhalf * ( u_hi*mf_u_hi + u_lo*mf_u_lo );
    amrex::Real v_met = met_eta * myhalf * ( v_hi*mf_v_hi + v_lo*mf_v_lo );
 
    amrex::Real omega =  w - u_met - v_met;
    return omega;
}

Referenced by erf_make_tau_terms(), erf_slow_rhs_pre(), erf_substep_MT(), erf_substep_T(), ERF::estTimeStep(), and ERF::project_momenta().

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rotate_scalar_flux()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE void rotate_scalar_flux	(	const int &	i,
		const int &	j,
		const int &	klo,
		const int &	,
		const amrex::Real &	flux,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	dxInv,
		const amrex::Array4< const amrex::Real > &	zphys_arr,
		const amrex::Array4< amrex::Real > &	phi1_arr,
		const amrex::Array4< amrex::Real > &	phi2_arr,
		const amrex::Array4< amrex::Real > &	phi3_arr
	)

Rotate a scalar flux vector into terrain-following coordinates.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	klo	z-index
[in]	flux	Scalar flux value.
[in]	dxInv	Inverse cell spacing.
[in]	zphys_arr	Physical height field.
[out]	phi1_arr	Rotated flux component 1.
[out]	phi2_arr	Rotated flux component 2.
[out]	phi3_arr	Rotated flux component 3.

{
    amrex::Real h_xi  = Compute_h_xi_AtCellCenter(i, j, klo, dxInv, zphys_arr);
    amrex::Real h_eta = Compute_h_eta_AtCellCenter(i, j, klo, dxInv, zphys_arr);
    amrex::Real InvNorm  = one / std::sqrt(one + h_xi*h_xi + h_eta*h_eta);
    phi1_arr(i,j,klo) = -h_xi  * flux * InvNorm;
    phi2_arr(i,j,klo) = -h_eta * flux * InvNorm;
    phi3_arr(i,j,klo) =          flux * InvNorm;
}

Referenced by SurfaceLayer::compute_SurfaceLayer_bcs().

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rotate_stress_tensor()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE void rotate_stress_tensor	(	const int &	i,
		const int &	j,
		const int &	klo,
		const int &	,
		const amrex::Real &	flux,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	dxInv,
		const amrex::Array4< const amrex::Real > &	zphys_arr,
		const amrex::Array4< const amrex::Real > &	u_arr,
		const amrex::Array4< const amrex::Real > &	v_arr,
		const amrex::Array4< const amrex::Real > &	w_arr,
		const amrex::Array4< amrex::Real > &	,
		const amrex::Array4< amrex::Real > &	,
		const amrex::Array4< amrex::Real > &	,
		const amrex::Array4< amrex::Real > &	,
		const amrex::Array4< amrex::Real > &	,
		const amrex::Array4< amrex::Real > &	tau13_arr,
		const amrex::Array4< amrex::Real > &	tau31_arr,
		const amrex::Array4< amrex::Real > &	tau23_arr,
		const amrex::Array4< amrex::Real > &	tau32_arr
	)

Rotate the stress tensor for the MOST model.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	klo	z-index
[in]	flux	Flux value used for rotation.
[in]	dxInv	Inverse cell spacing.
[in]	zphys_arr	Physical height field.
[in]	u_arr	X-velocity array.
[in]	v_arr	Y-velocity array.
[in]	w_arr	Z-velocity array.
[out]	tau11_arr	Stress component tau11.
[out]	tau22_arr	Stress component tau22.
[out]	tau33_arr	Stress component tau33.
[out]	tau12_arr	Stress component tau12.
[out]	tau21_arr	Stress component tau21.
[out]	tau13_arr	Stress component tau13.
[out]	tau31_arr	Stress component tau31.
[out]	tau23_arr	Stress component tau23.
[out]	tau32_arr	Stress component tau32.

{
    // Unit-normal vector
    amrex::Array1D<amrex::Real,0,2> n_hat;
 
    // Unit-tangent vectors
    amrex::Array1D<amrex::Real,0,2> u_t_hat;
 
    // Final basis vector for right-hand coord sys
    amrex::Array1D<amrex::Real,0,2> a_hat;
 
    // Rotation matrix
    amrex::Array2D<amrex::Real,0,2,0,2> R_mat;
 
    // Metric data
    amrex::Real h_xi   =   Compute_h_xi_AtIface(i, j, klo, dxInv, zphys_arr);
    amrex::Real h_eta  =  Compute_h_eta_AtIface(i, j, klo, dxInv, zphys_arr);
    amrex::Real h_zeta = Compute_h_zeta_AtIface(i, j, klo, dxInv, zphys_arr);
 
    // Populate the inward normal vector
    amrex::Real Inormn = one/std::sqrt(one + h_xi*h_xi + h_eta*h_eta);
    n_hat(0) = -Inormn*h_xi; n_hat(1) = -Inormn*h_eta; n_hat(2) = Inormn;
 
    // Populate the u_t vector (u_t = u - (u \cdot n)n)
    amrex::Real u    = u_arr(i,j,klo);
    amrex::Real v    = fourth * ( v_arr(i  ,j,klo) + v_arr(i  ,j+1,klo)
                                + v_arr(i-1,j,klo) + v_arr(i-1,j+1,klo) );
    amrex::Real w    = myhalf * ( w_arr(i  ,j,klo) + w_arr(i-1,j  ,klo) );
    amrex::Real u_dot_n = n_hat(0)*u + n_hat(1)*v + n_hat(2)*w;
    u_t_hat(0) = u - u_dot_n*n_hat(0);
    u_t_hat(1) = v - u_dot_n*n_hat(1);
    u_t_hat(2) = w - u_dot_n*n_hat(2);
    amrex::Real Norm_u_t = u_t_hat(0)*u_t_hat(0)
                         + u_t_hat(1)*u_t_hat(1)
                         + u_t_hat(2)*u_t_hat(2);
 
    // NOTE: the direction of the tangential velocity is undefined when that
    //       velocity vanishes (a quiescent surface cell, or flow normal to the
    //       terrain), so we cannot normalize. Leaving u_t_hat as the zero vector
    //       is the only rotation-invariant choice, and it is the right limit for
    //       a quiescent cell since the flux vanishes with the surface wind too.
    amrex::Real Inorm_u_t = (Norm_u_t > zero) ? one/std::sqrt(Norm_u_t) : zero;
    for (int icol(0); icol<3; ++icol) {
        u_t_hat(icol) *= Inorm_u_t;
    }
 
    // Populate the a_hat = n_hat X u_t_hat vector
    a_hat(0) =   n_hat(1)*u_t_hat(2) - n_hat(2)*u_t_hat(1);
    a_hat(1) = -(n_hat(0)*u_t_hat(2) - n_hat(2)*u_t_hat(0));
    a_hat(2) =   n_hat(0)*u_t_hat(1) - n_hat(1)*u_t_hat(0);
 
    // Copy column vectors into R_mat
    // NOTE: basis vectors form rows of R_mat
    int icol = 0;
    for (int jrow(0); jrow<3; ++jrow) {
        R_mat(icol,jrow) = u_t_hat(jrow);
    }
    icol = 1;
    for (int jrow(0); jrow<3; ++jrow) {
        R_mat(icol,jrow) = a_hat(jrow);
    }
    icol = 2;
    for (int jrow(0); jrow<3; ++jrow) {
        R_mat(icol,jrow) = n_hat(jrow);
    }
 
    // Body-fixed stresses
    amrex::Real T11    = two*R_mat(0,0)*R_mat(2,0)*flux;
    amrex::Real T22    = two*R_mat(0,1)*R_mat(2,1)*flux;
    //amrex::Real T33    = two*R_mat(0,2)*R_mat(2,2)*flux;
    amrex::Real T12    = (R_mat(0,0)*R_mat(2,1) + R_mat(2,0)*R_mat(0,1))*flux;
    amrex::Real T13    = (R_mat(0,0)*R_mat(2,2) + R_mat(0,2)*R_mat(2,0))*flux;
    amrex::Real T23    = (R_mat(0,2)*R_mat(2,1) + R_mat(0,1)*R_mat(2,2))*flux;
 
    // Populate the stress tensor (apply JT)
    // NOTE: We cannot set the stresses that do not live at the
    //       bottom face --- e.g., tau11/22/33/12/21.
    tau13_arr(i,j,klo) =  -h_xi*T11 - h_eta*T12 + T13;
    tau31_arr(i,j,klo) = h_zeta*T13;
 
    tau23_arr(i,j,klo) =  -h_xi*T12 - h_eta*T22 + T23;
    tau32_arr(i,j,klo) = h_zeta*T23;
}

Referenced by SurfaceLayer::compute_SurfaceLayer_bcs().

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update_stretched_dz()

void update_stretched_dz	(	int	lev,
		amrex::Vector< amrex::Vector< amrex::Real >> const &	zlevels_stag,
		amrex::Vector< amrex::Vector< amrex::Real >> &	stretched_dz_h,
		amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real >> &	stretched_dz_d
	)

Re-derive the stretched vertical spacing at one level from the nominal z-levels.

init_zlevels() fills both zlevels_stag and stretched_dz_* together, but zlevels_stag can be replaced after construction (init_from_wrfinput() does this when erf.avg_grid_faces_to_nodes = false, and restart reads it back from the checkpoint). Call this whenever zlevels_stag[lev] changes so that the cell heights never drift out of sync with the levels they are supposed to describe.

Parameters

[in]	lev	Level index.
[in]	zlevels_stag	Staggered z-levels (the source of truth).
[out]	stretched_dz_h	Host stretched vertical spacing.
[out]	stretched_dz_d	Device stretched vertical spacing.

WFromOmega()

AMREX_GPU_DEVICE AMREX_FORCE_INLINE amrex::Real WFromOmega	(	int &	i,
		int &	j,
		int &	k,
		amrex::Real	omega,
		const amrex::Array4< const amrex::Real > &	u_arr,
		const amrex::Array4< const amrex::Real > &	v_arr,
		const amrex::Array4< const amrex::Real > &	mf_u,
		const amrex::Array4< const amrex::Real > &	mf_v,
		const amrex::Array4< const amrex::Real > &	z_nd,
		const amrex::GpuArray< amrex::Real, AMREX_SPACEDIM > &	dxInv
	)

Compute the vertical velocity w from the contravariant omega.

Parameters

[in]	i	x-index
[in]	j	y-index
[in]	k	z-index
[in]	omega	Contravariant vertical velocity.
[in]	u_arr	X-velocity array.
[in]	v_arr	Y-velocity array.
[in]	mf_u	X-velocity map factor.
[in]	mf_v	Y-velocity map factor.
[in]	z_nd	Nodal physical height field.
[in]	dxInv	Inverse cell spacing.

Returns

Vertical velocity w.

{
    // This is dh/dxi at hi and lo edges
    amrex::Real z_x_p2  = Compute_Z_AtWFace(i+2,j,k,z_nd);
    amrex::Real z_x_p1  = Compute_Z_AtWFace(i+1,j,k,z_nd);
    amrex::Real z_x_m1  = Compute_Z_AtWFace(i-1,j,k,z_nd);
    amrex::Real z_x_m2  = Compute_Z_AtWFace(i-2,j,k,z_nd);
    amrex::Real met_xi  = (amrex::Real(1.0/amrex::Real(12.0))*(z_x_m2 - z_x_p2)
                         + amrex::Real(8.0/amrex::Real(12.0))*(z_x_p1 - z_x_m1)) * dxInv[0];
 
    // This is dh/deta at hi and lo edges
    amrex::Real z_y_p2   = Compute_Z_AtWFace(i,j+2,k,z_nd);
    amrex::Real z_y_p1   = Compute_Z_AtWFace(i,j+1,k,z_nd);
    amrex::Real z_y_m1   = Compute_Z_AtWFace(i,j-1,k,z_nd);
    amrex::Real z_y_m2   = Compute_Z_AtWFace(i,j-2,k,z_nd);
    amrex::Real met_eta  = (amrex::Real(1.0/amrex::Real(12.0))*(z_y_m2 - z_y_p2)
                          + amrex::Real(8.0/amrex::Real(12.0))*(z_y_p1 - z_y_m1)) * dxInv[1];
 
    // Use extrapolation instead of interpolation if at the bottom boundary
    amrex::Real u_hi = (k == 0) ? amrex::Real(1.5) *   u_arr(i+1,j  ,k  ) - myhalf * u_arr(i+1,j  ,k+1)  :
                                  myhalf * ( u_arr(i+1,j  ,k-1) +       u_arr(i+1,j  ,k  ) );
    amrex::Real u_lo = (k == 0) ? amrex::Real(1.5) *   u_arr(i  ,j  ,k  ) - myhalf * u_arr(i  ,j  ,k+1)  :
                                  myhalf * ( u_arr(i  ,j  ,k-1) +       u_arr(i  ,j  ,k  ) );
    amrex::Real mf_u_hi = mf_u(i+1,j,0);
    amrex::Real mf_u_lo = mf_u(i  ,j,0);
 
    amrex::Real v_hi = (k == 0) ? amrex::Real(1.5) *   v_arr(i  ,j+1,k  ) - myhalf * v_arr(i  ,j+1,k+1)  :
                                  myhalf * ( v_arr(i  ,j+1,k-1) +       v_arr(i  ,j+1,k  ) );
    amrex::Real v_lo = (k == 0) ? amrex::Real(1.5) *   v_arr(i  ,j  ,k  ) - myhalf * v_arr(i  ,j  ,k+1)  :
                                  myhalf * ( v_arr(i  ,j  ,k-1) +       v_arr(i  ,j  ,k  ) );
    amrex::Real mf_v_hi = mf_v(i,j+1,0);
    amrex::Real mf_v_lo = mf_v(i,j  ,0);
 
    amrex::Real u_met = met_xi  * myhalf * ( u_hi*mf_u_hi + u_lo*mf_u_lo );
    amrex::Real v_met = met_eta * myhalf * ( v_hi*mf_v_hi + v_lo*mf_v_lo );
 
    amrex::Real w = omega + u_met + v_met;
    return w;
}

Referenced by erf_substep_MT(), erf_substep_T(), if(), ERFPhysBCFunct_w::impose_lateral_zvel_bcs(), ERFPhysBCFunct_w::impose_vertical_zvel_bcs(), ParallelFor(), and ERF::project_momenta().

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which_fine_terrain()

FineTerrain which_fine_terrain

(

)

Read erf.amr_terrain_refinement and translate it into a FineTerrain.

Aborts on any value other than "interpolate" or "transform" so that a typo cannot silently select a path that leaves the fine mesh untransformed.

Translate erf.amr_terrain_refinement into a FineTerrain.

{
    ParmParse pp("erf");
    std::string amr_terrain_refinement = "interpolate";
    pp.query("amr_terrain_refinement", amr_terrain_refinement);
 
    if (amr_terrain_refinement == "interpolate") {
        return FineTerrain::Interpolate;
    } else if (amr_terrain_refinement == "transform") {
        return FineTerrain::Transform;
    }
 
    Abort("erf.amr_terrain_refinement = " + amr_terrain_refinement +
          " is not recognized; it must be \"interpolate\" or \"transform\"");
    return FineTerrain::Interpolate;
}

Referenced by ERF::init_zphys(), and ERF::remake_zphys().

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