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8679f9097b Jeff* .. _sec_phys_pkg_gridalt:
                 
                 Gridalt - Alternate Grid Package
                 --------------------------------
                 
                 
                 Introduction
                 ++++++++++++
                 
                 The gridalt package :cite:`mol:09` is designed to allow different components of MITgcm
                 to be run using horizontal and/or vertical grids which are different
                 from the main model grid. The gridalt routines handle the definition of
                 the all the various alternative grid(s) and the mappings between them
                 and the MITgcm grid. The implementation of the gridalt package which
                 allows the high end atmospheric physics (fizhi) to be run on a high
                 resolution and quasi terrain-following vertical grid is documented here.
                 The package has also (with some user modifications) been used for other
                 calculations within the GCM.
                 
                 The rationale for implementing the atmospheric physics on a high
                 resolution vertical grid involves the fact that the MITgcm :math:`p^*`
                 (or any pressure-type) coordinate cannot maintain the vertical
                 resolution near the surface as the bottom topography rises above sea
                 level. The vertical length scales near the ground are small and can vary
                 on small time scales, and the vertical grid must be adequate to resolve
                 them. Many studies with both regional and global atmospheric models have
                 demonstrated the improvements in the simulations when the vertical
                 resolution near the surface is increased (). Some of the benefit of
                 increased resolution near the surface is realized by employing the
                 higher resolution for the computation of the forcing due to turbulent
                 and convective processes in the atmosphere.
                 
                 The parameterizations of atmospheric subgrid scale processes are all
                 essentially one-dimensional in nature, and the computation of the terms
                 in the equations of motion due to these processes can be performed for
                 the air column over one grid point at a time. The vertical grid on which
                 these computations take place can therefore be entirely independant of
                 the grid on which the equations of motion are integrated, and the
                 ’tendency’ terms can be interpolated to the vertical grid on which the
                 equations of motion are integrated. A modified :math:`p^*` coordinate,
                 which adjusts to the local terrain and adds additional levels between
                 the lower levels of the existing :math:`p^*` grid (and perhaps between
                 the levels near the tropopause as well), is implemented. The vertical
                 discretization is different for each grid point, although it consist of
                 the same number of levels. Additional ’sponge’ levels aloft are added
                 when needed. The levels of the physics grid are constrained to fit
                 exactly into the existing :math:`p^*` grid, simplifying the mapping
                 between the two vertical coordinates. This is illustrated as follows:
                 
                 
                  .. figure:: figs/vertical.*
                     :width: 70%
                     :align: center
                     :alt: vertical discretisation
                     :name: grid_alt_vertical
                 
                     Vertical discretization for MITgcm (dark grey lines) and for the atmospheric physics (light grey lines). In this implementation, all MITgcm level interfaces must coincide with atmospheric physics level interfaces.
                 
                 
                 The algorithm presented here retains the state variables on the high
                 resolution ’physics’ grid as well as on the coarser resolution
                 ’dynamics‘ grid, and ensures that the two estimates of the state ’agree’
                 on the coarse resolution grid. It would have been possible to implement
                 a technique in which the tendencies due to atmospheric physics are
                 computed on the high resolution grid and the state variables are
                 retained at low resolution only. This, however, for the case of the
                 turbulence parameterization, would mean that the turbulent kinetic
                 energy source terms, and all the turbulence terms that are written in
                 terms of gradients of the mean flow, cannot really be computed making
                 use of the fine structure in the vertical.
                 
                 Equations on Both Grids
                 +++++++++++++++++++++++
                 
                 In addition to computing the physical forcing terms of the momentum,
                 thermodynamic and humidity equations on the modified (higher resolution)
                 grid, the higher resolution structure of the atmosphere (the boundary
                 layer) is retained between physics calculations. This neccessitates a
                 second set of evolution equations for the atmospheric state variables on
                 the modified grid. If the equation for the evolution of :math:`U` on
                 :math:`p^*` can be expressed as:
                 
                 .. math::
                 
                    \left . \frac{\partial U}{\partial t} \right |_{p^*}^{total} = 
                    \left . \frac{\partial U}{\partial t} \right |_{p^*}^{dynamics} + 
                    \left . \frac{\partial U}{\partial t} \right |_{p^*}^{physics}
                 
                 where the physics forcing terms on :math:`p^*` have been mapped from the
                 modified grid, then an additional equation to govern the evolution of
                 :math:`U` (for example) on the modified grid is written:
                 
                 .. math::
                 
                    \left . \frac{\partial U}{\partial t} \right |_{p^{*m}}^{total} = 
                    \left . \frac{\partial U}{\partial t} \right |_{p^{*m}}^{dynamics} + 
                    \left . \frac{\partial U}{\partial t} \right |_{p^{*m}}^{physics} +
                    \gamma ({\left . U \right |_{p^*}} - {\left . U \right |_{p^{*m}}})
                 
                 where :math:`p^{*m}` refers to the modified higher resolution grid, and
                 the dynamics forcing terms have been mapped from :math:`p^*` space. The
                 last term on the RHS is a relaxation term, meant to constrain the state
                 variables on the modified vertical grid to ‘track’ the state variables
                 on the :math:`p^*` grid on some time scale, governed by :math:`\gamma`.
                 In the present implementation, :math:`\gamma = 1`, requiring an
                 immediate agreement between the two ’states’.
                 
                 Time stepping Sequence
                 ++++++++++++++++++++++
                 
                 If we write :math:`T_{phys}` as the temperature (or any other state
                 variable) on the high resolution physics grid, and :math:`T_{dyn}` as
                 the temperature on the coarse vertical resolution dynamics grid, then:
                 
                 #. Compute the tendency due to physics processes.
                 
                 #. Advance the physics state: :math:`{{T^{n+1}}^{**}}_{phys}(l) = {T^n}_{phys}(l) + \delta T_{phys}`.
                 
                 #. Interpolate the physics tendency to the dynamics grid, and advance the dynamics state by physics and dynamics tendencies: :math:`{T^{n+1}}_{dyn}(L) = {T^n}_{dyn}(L) + \delta T_{dyn}(L) + [\delta T _{phys}(l)](L)`.
                 
                 #. Interpolate the dynamics tendency to the physics grid, and update the physics grid due to dynamics tendencies: :math:`{{T^{n+1}}^*}_{phys}(l)` = :math:`{{T^{n+1}}^{**}}_{phys}(l) + {\delta T_{dyn}(L)}(l)`.
                 
                 #. Apply correction term to physics state to account for divergence from dynamics state: :math:`{T^{n+1}}_{phys}(l)` = :math:`{{T^{n+1}}^*}_{phys}(l) + \gamma \{  T_{dyn}(L) - [T_{phys}(l)](L) \}(l)`. Where :math:`\gamma=1` here.
                 
                 Interpolation
                 +++++++++++++
                 
                 In order to minimize the correction terms for the state variables on
                 the alternative, higher resolution grid, the vertical interpolation
                 scheme must be constructed so that a dynamics-to-physics interpolation
                 can be exactly reversed with a physics-to-dynamics mapping. The simple
                 scheme employed to achieve this is:
                 
bf89a37abc Phob* Coarse to fine: For all physics layers l in dynamics layer L, :math:`T_{phys}(l) = \{T_{dyn}(L)\} = T_{dyn}(L)`.
8679f9097b Jeff* 
bf89a37abc Phob* Fine to coarse: For all physics layers l in dynamics layer L, :math:`T_{dyn}(L) = [T_{phys}(l)] = \int{T_{phys} dp }`.
8679f9097b Jeff* 
                 Where :math:`\{\}` is defined as the dynamics-to-physics operator and
                 :math:`[ ]` is the physics-to-dynamics operator, :math:`T` stands for
                 any state variable, and the subscripts :math:`phys` and :math:`dyn`
                 stand for variables on the physics and dynamics grids, respectively.
                 
                 Key subroutines, parameters and files 
                 ++++++++++++++++++++++++++++++++++++++
                 
                 One of the central elements of the gridalt package is the routine which
bf89a37abc Phob* is called from subroutine :filelink:`gridalt_initialise <pkg/gridalt/gridalt_initialise.F>` to define the grid to be
                 used for the high end physics calculations. Routine :filelink:`make_phys_grid <pkg/gridalt/make_phys_grid.F>`
8679f9097b Jeff* passes back the parameters which define the grid, ultimately stored in
bf89a37abc Phob* the common block :filelink:`gridalt_mapping <pkg/gridalt/gridalt_mapping.F>`.
8679f9097b Jeff* 
                 ::
                 
                            subroutine make_phys_grid(drF,hfacC,im1,im2,jm1,jm2,Nr,
                          . Nsx,Nsy,i1,i2,j1,j2,bi,bj,Nrphys,Lbot,dpphys,numlevphys,nlperdyn)
                     c***********************************************************************
                     c Purpose: Define the grid that the will be used to run the high-end
                     c          atmospheric physics.
                     c
                     c Algorithm: Fit additional levels of some (~) known thickness in
                     c          between existing levels of the grid used for the dynamics
                     c
                     c Need:    Information about the dynamics grid vertical spacing
                     c
                     c Input:   drF         - delta r (p*) edge-to-edge
                     c          hfacC       - fraction of grid box above topography
                     c          im1, im2    - beginning and ending i - dimensions
                     c          jm1, jm2    - beginning and ending j - dimensions
                     c          Nr          - number of levels in dynamics grid
                     c          Nsx,Nsy     - number of processes in x and y direction
                     c          i1, i2      - beginning and ending i - index to fill
                     c          j1, j2      - beginning and ending j - index to fill
                     c          bi, bj      - x-dir and y-dir index of process
                     c          Nrphys      - number of levels in physics grid
                     c
                     c Output:  dpphys      - delta r (p*) edge-to-edge of physics grid
                     c          numlevphys  - number of levels used in the physics
                     c          nlperdyn    - physics level number atop each dynamics layer
                     c
                     c NOTES: 1) Pressure levs are built up from bottom, using p0, ps and dp:
                     c              p(i,j,k)=p(i,j,k-1) + dp(k)*ps(i,j)/p0(i,j)
                     c        2) Output dp's are aligned to fit EXACTLY between existing
                     c           levels of the dynamics vertical grid
                     c        3) IMPORTANT! This routine assumes the levels are numbered
                     c           from the bottom up, ie, level 1 is the surface.
                     c           IT WILL NOT WORK OTHERWISE!!!
                     c        4) This routine does NOT work for surface pressures less
                     c           (ie, above in the atmosphere) than about 350 mb
                     c***********************************************************************
                 
                 In the case of the grid used to compute the atmospheric physical forcing
bf89a37abc Phob* (:ref:`sub_phys_pkg_fizhi`), the locations of the grid points move in time with the
                 MITgcm :math:`p^*` coordinate, and subroutine :filelink:`gridalt_update <pkg/gridalt/gridalt_update.F>` is called
8679f9097b Jeff* during the run to update the locations of the grid points:
                 
                 ::
                 
                            subroutine gridalt_update(myThid)
                     c***********************************************************************
                     c Purpose: Update the pressure thicknesses of the layers of the
                     c          alternative vertical grid (used now for atmospheric physics).
                     c
                     c Calculate: dpphys    - new delta r (p*) edge-to-edge of physics grid
                     c                        using dpphys0 (initial value) and rstarfacC
                     c***********************************************************************
                 
                 The gridalt package also supplies utility routines which perform the
                 mappings from one grid to the other. These routines are called from the
                 code which computes the fields on the alternative (fizhi) grid.
                 
                 ::
                 
                           subroutine dyn2phys(qdyn,pedyn,im1,im2,jm1,jm2,lmdyn,Nsx,Nsy,
                          . idim1,idim2,jdim1,jdim2,bi,bj,windphy,pephy,Lbot,lmphy,nlperdyn,
                          . flg,qphy)
                     C***********************************************************************
                     C Purpose:
                     C   To interpolate an arbitrary quantity from the 'dynamics' eta (pstar)
                     C               grid to the higher resolution physics grid
                     C Algorithm:
                     C   Routine works one layer (edge to edge pressure) at a time.
                     C   Dynamics -> Physics retains the dynamics layer mean value,
                     C   weights the field either with the profile of the physics grid
                     C   wind speed (for U and V fields), or uniformly (T and Q)
                     C
                     C Input:
                     C   qdyn..... [im,jm,lmdyn] Arbitrary Quantity on Input Grid
                     C   pedyn.... [im,jm,lmdyn+1] Pressures at bottom edges of input levels
                     C   im1,2 ... Limits for Longitude Dimension of Input
                     C   jm1,2 ... Limits for Latitude  Dimension of Input
                     C   lmdyn.... Vertical  Dimension of Input
                     C   Nsx...... Number of processes in x-direction
                     C   Nsy...... Number of processes in y-direction
                     C   idim1,2.. Beginning and ending i-values to calculate
                     C   jdim1,2.. Beginning and ending j-values to calculate
                     C   bi....... Index of process number in x-direction
                     C   bj....... Index of process number in x-direction
                     C   windphy.. [im,jm,lmphy] Magnitude of the wind on the output levels
                     C   pephy.... [im,jm,lmphy+1] Pressures at bottom edges of output levels
                     C   lmphy.... Vertical  Dimension of Output
                     C   nlperdyn. [im,jm,lmdyn] Highest Physics level in each dynamics level
                     C   flg...... Flag to indicate field type (0 for T or Q, 1 for U or V)
                     C
                     C Output:
                     C   qphy..... [im,jm,lmphy] Quantity at output grid (physics grid)
                     C
                     C Notes:
                     C   1) This algorithm assumes that the output (physics) grid levels
                     C      fit exactly into the input (dynamics) grid levels
                     C***********************************************************************
                 
                 And similarly, gridalt contains subroutine phys2dyn.
                 
9ce7d74115 Jeff* .. _gridalt_diagnostics:
                 
8679f9097b Jeff* Gridalt Diagnostics
                 +++++++++++++++++++
                 
                 ::
                 
                 
                     ------------------------------------------------------------------------
                     <-Name->|Levs|<-parsing code->|<--  Units   -->|<- Tile (max=80c) 
                     ------------------------------------------------------------------------
                     DPPHYS  | 20 |SM      ML      |Pascal          |Pressure Thickness of Layers on Fizhi Grid
                 
                 Dos and donts
                 +++++++++++++
                 
                 Gridalt Reference
                 +++++++++++++++++
                 
                 Experiments and tutorials that use gridalt
                 ++++++++++++++++++++++++++++++++++++++++++
                 
bf89a37abc Phob* -  Fizhi experiment, in :filelink:`verification/fizhi-cs-32x32x10` verification directory
8679f9097b Jeff* 
                 

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