Merge pull request seahorce-scidac#222 from seahorce-scidac/fix_spelling

fix some spelling

.codespell-ignore-words

@@ -1,2 +1,4 @@
+Blocs
+inout
 parms
 ptd

Docs/sphinx_doc/BoundaryConditions.rst

@@ -84,7 +84,7 @@ As an example,
     xlo.temp                =   15.
     xlo.scalar              =   2.
 
-sets the boundary condtion type at the low x face to be an inflow with xlo.type = “Inflow”.
+sets the boundary condition type at the low x face to be an inflow with xlo.type = “Inflow”.
 
 We note that ``noslipwall`` allows for non-zero tangential velocities to be specified, such as
 

Docs/sphinx_doc/Discretizations.rst

@@ -402,12 +402,12 @@ The goal is to compute eddy viscosity at the *cell centers* and interpolated the
 .. math::
 
    \begin{matrix}
-   S_{12} = & \frac{1}{4}\left\lbrack S_{12i,j - \frac{1}{2}} + S_{12i,j + \frac{1}{2}} + S_{12i + 1,j - \frac{1}{2}} + S_{12i + 1,j + \frac{1}{2}} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrouding the cell}\end{smallmatrix} \\
-   S_{21} = & \frac{1}{4}\left\lbrack S_{21i - \frac{1}{2},j} + S_{21i + \frac{1}{2},j} + S_{21i - \frac{1}{2},j + 1} + S_{21i + \frac{1}{2},j + 1} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrouding the cell}\end{smallmatrix} \\
-   S_{13} = & \frac{1}{4}\left\lbrack S_{13i,k - \frac{1}{2}} + S_{13i,k + \frac{1}{2}} + S_{13i + 1,k - \frac{1}{2}} + S_{13i + 1,k + \frac{1}{2}} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrouding the cell}\end{smallmatrix} \\
-   S_{31} = & \frac{1}{4}\left\lbrack S_{31i - \frac{1}{2},k} + S_{31i + \frac{1}{2},k} + S_{31i - \frac{1}{2},k + 1} + S_{31i + \frac{1}{2},k + 1} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrouding the cell}\end{smallmatrix} \\
-   S_{23} = & \frac{1}{4}\left\lbrack S_{23j,k - \frac{1}{2}} + S_{23j,k + \frac{1}{2}} + S_{23j + 1,k - \frac{1}{2}} + S_{23j + 1,k + \frac{1}{2}} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrouding the cell}\end{smallmatrix} \\
-   S_{32} = & \frac{1}{4}\left\lbrack S_{32j - \frac{1}{2},k} + S_{32j + \frac{1}{2},k} + S_{32j - \frac{1}{2},k + 1} + S_{32j + \frac{1}{2},k + 1} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrouding the cell}\end{smallmatrix}
+   S_{12} = & \frac{1}{4}\left\lbrack S_{12i,j - \frac{1}{2}} + S_{12i,j + \frac{1}{2}} + S_{12i + 1,j - \frac{1}{2}} + S_{12i + 1,j + \frac{1}{2}} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrounding the cell}\end{smallmatrix} \\
+   S_{21} = & \frac{1}{4}\left\lbrack S_{21i - \frac{1}{2},j} + S_{21i + \frac{1}{2},j} + S_{21i - \frac{1}{2},j + 1} + S_{21i + \frac{1}{2},j + 1} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrounding the cell}\end{smallmatrix} \\
+   S_{13} = & \frac{1}{4}\left\lbrack S_{13i,k - \frac{1}{2}} + S_{13i,k + \frac{1}{2}} + S_{13i + 1,k - \frac{1}{2}} + S_{13i + 1,k + \frac{1}{2}} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrounding the cell}\end{smallmatrix} \\
+   S_{31} = & \frac{1}{4}\left\lbrack S_{31i - \frac{1}{2},k} + S_{31i + \frac{1}{2},k} + S_{31i - \frac{1}{2},k + 1} + S_{31i + \frac{1}{2},k + 1} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrounding the cell}\end{smallmatrix} \\
+   S_{23} = & \frac{1}{4}\left\lbrack S_{23j,k - \frac{1}{2}} + S_{23j,k + \frac{1}{2}} + S_{23j + 1,k - \frac{1}{2}} + S_{23j + 1,k + \frac{1}{2}} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrounding the cell}\end{smallmatrix} \\
+   S_{32} = & \frac{1}{4}\left\lbrack S_{32j - \frac{1}{2},k} + S_{32j + \frac{1}{2},k} + S_{32j - \frac{1}{2},k + 1} + S_{32j + \frac{1}{2},k + 1} \right\rbrack = \begin{smallmatrix} \text{Average of the 4 edges} \\ \text{surrounding the cell}\end{smallmatrix}
    \end{matrix}
 
 Note that:

Docs/sphinx_doc/Inputs.rst

@@ -482,7 +482,7 @@ Examples of Usage
      coarse time steps. The print statements have the form
    | ``TIME= 1.91717746 MASS= 1.792410279e+34``
    | for example. If this line is commented out or if **remora.v** :math:`<= 0`
-     then it will not compute and print these quanitities.
+     then it will not compute and print these quantities.
 
 Included terms
 ==============
@@ -657,8 +657,8 @@ List of Parameters
 |                                               | advection of momenta        | centered2         |             |
 +-----------------------------------------------+-----------------------------+-------------------+-------------+
 
-Vertical Stretch prameters
-==========================
+Vertical Stretch parameters
+===========================
 
 .. _list-of-parameters-17:
 

Docs/sphinx_doc/InputsPhysics.rst

@@ -39,7 +39,7 @@ List of Parameters
 Initialization
 ==============
 
-REMORA can be initialzed in different ways. These are listed below:
+REMORA can be initialized in different ways. These are listed below:
 
 - Custom initialization:
     Several problems under **Exec** are initialized in a custom manner. The state and velocity components are specific to the problem. These problems are meant for demonstration and do not include any terrain or map scale factors.

Docs/sphinx_doc/Numerical_Solution_Technique.rst

@@ -245,7 +245,7 @@ and
    :label: (12)
 
 When time stepping the model, we compute the right-hand-sides for the full 3-D momentum equations as well as the right-hand-sides for equations (11) and (12). The vertical integral of the 3-D right-hand-sides are obtained and then the 2-D right-hand-sides are subtracted. The resulting fields are the slow forcings :math:`R_{u_{\text{slow}}}` and :math:`R_{v_{\text{slow}}}`. This was found to be the easiest way to retain the baroclinic contributions of the non-linear terms such as :math:`\overline{uu}-\overline{u}\,\overline{u}`.
-The model is time stepped from time :math:`n` to time :math:`n+1` by using short time steps on equations (11), (12) and (6). Equation (6) is time stepped first, so that an estimate of the new :math:`D` is available for the time rate of change terms in equations (11) and (12). A third-order predictor-corrector time stepping is used. In practice, we actually time step all the way to time :math:`\left(n+\textbf{dtfast}\times M^*\right)` and while maintaining weighted averages of the values of :math:`\overline{u},\overline{v}` and :math:`\zeta`. The averages are used to replace the values at time :math:`n+1` in both the baroclinic and barotropic modes, and for recomputing the vertial grid spacing :math:`H_z`. The following figure shows one option for how these weights might look:
+The model is time stepped from time :math:`n` to time :math:`n+1` by using short time steps on equations (11), (12) and (6). Equation (6) is time stepped first, so that an estimate of the new :math:`D` is available for the time rate of change terms in equations (11) and (12). A third-order predictor-corrector time stepping is used. In practice, we actually time step all the way to time :math:`\left(n+\textbf{dtfast}\times M^*\right)` and while maintaining weighted averages of the values of :math:`\overline{u},\overline{v}` and :math:`\zeta`. The averages are used to replace the values at time :math:`n+1` in both the baroclinic and barotropic modes, and for recomputing the vertical grid spacing :math:`H_z`. The following figure shows one option for how these weights might look:
 
 .. image:: figures/Barostep.png
    :width: 100%

Docs/sphinx_doc/ProblemSetup.rst

@@ -16,4 +16,4 @@ Each problem setup with a different initial e.g. temperature profile and bathyme
 * ``Make.package``
 * ``amrvis.defaults`` (for visualization with AMRVis)
 
-The file ``prob.cpp`` contains a number of functions that set the initial temeprature profile, as well as surface stress, mixing coefficients, and bathymetry. New problem-specific input parameters can be defined by adding a variable to the ``ProbParm`` class in ``prob.H``, and reading in the value in ``amrex_probinit`` in ``prob.cpp``. See the AMReX documentation on `ParmParse <https://amrex-codes.github.io/amrex/docs_html/Basics.html#parmparse>`_ for how to add parameters.
+The file ``prob.cpp`` contains a number of functions that set the initial temperature profile, as well as surface stress, mixing coefficients, and bathymetry. New problem-specific input parameters can be defined by adding a variable to the ``ProbParm`` class in ``prob.H``, and reading in the value in ``amrex_probinit`` in ``prob.cpp``. See the AMReX documentation on `ParmParse <https://amrex-codes.github.io/amrex/docs_html/Basics.html#parmparse>`_ for how to add parameters.

Docs/sphinx_doc/Time_Stepping.rst

@@ -50,4 +50,4 @@ Time Stepping: Internal Velocity Modes and Tracers
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 The momentum equations are advanced before the tracer equation, by computing all the terms except the vertical viscosity and then using the implicit scheme described in ``#Vertical Friction and Diffusion`` to find the new values for :math:`u` and :math:`v`. The depth-averaged component is then removed and replaced by the :math:`\langle \overline{u} \rangle` and :math:`\langle \overline{v} \rangle` computed as in ``#Depth-Integrated Equations``. A third-order Adams-Bashforth (AB3) time step is used, requiring multiple right-hand-side time levels. These stored up r.h.s. values can be used to extrapolate to a value at time :math:`n+\frac{1}{2}`, obtained from the predictor step. The vertical diffusion is computed as in ``#Vertical Friction and Diffusion``. The predictor step cannot be both constancy=preserving and conservative; it was therefore decided to make it constancy-preserving. Also, since it is only being used to compute the advection for the corrector step, the expensive diffusion operations are not carried out on the predictor step.
 
-The preceeding notes on tracer advection refer to all but the MPDATA option. The MPDATA algorithm has its own predictor-corrector with emphasis on not allowing values to exceed their original range, and therefore gives up the constancy-preservation. This will be most noticeable in shallow areas with large tides.
+The preceding notes on tracer advection refer to all but the MPDATA option. The MPDATA algorithm has its own predictor-corrector with emphasis on not allowing values to exceed their original range, and therefore gives up the constancy-preservation. This will be most noticeable in shallow areas with large tides.

Docs/sphinx_doc/Visualization.rst

@@ -31,11 +31,11 @@ To open a plotfile
 
 #. If you have run the REMORA executable with terrain, then the mapped grid information will
    be stored as nodal data.  Choose the "point data" called "nu", then click on "Warp by Vector"
-   which can be found via Filters-->Alphabetical.  This wil then plot data onto the mapped grid
+   which can be found via Filters-->Alphabetical.  This will then plot data onto the mapped grid
    locations.
 
 #. Under the "Cell Arrays" field, select a variable (e.g., "x_velocity") and click
-   "Apply". Note that the default number of refinement levels loaded and vizualized is 1.
+   "Apply". Note that the default number of refinement levels loaded and visualized is 1.
    Change to the required number of AMR level before clicking "Apply".
 
 #. For "Representation" select "Surface".

Docs/sphinx_doc/coc.rst

@@ -6,7 +6,7 @@ Code of Conduct
 Our Pledge
 ----------
 
-In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socioeconomic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
 
 Our Standards
 -------------

Exec/Advection/inputs

@@ -54,7 +54,7 @@ remora.spatial_order = 2
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 35.0    # background salinity (nondimensional) constant
 remora.T0    = 14.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 1.0e-4  # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred
 

Exec/Advection/inputs_ml

@@ -55,7 +55,7 @@ remora.spatial_order = 2
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 35.0    # background salinity (nondimensional) constant
 remora.T0    = 14.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 0.0 #1.7e-4  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 0.0 #1.7e-4  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 0.0 #1.0e-4  # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred
 

Exec/DoublyPeriodic/inputs

@@ -54,7 +54,7 @@ remora.spatial_order = 2
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 35.0    # background salinity (nondimensional) constant
 remora.T0    = 14.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 0.0     # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred
 

Exec/IdealMiniGrid/inputs

@@ -62,7 +62,7 @@ remora.tcline = 100.
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 32.0    # background salinity (nondimensional) constant
 remora.T0    = 10.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 0.0  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 0.0  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 0.0     # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred
 

Exec/OCCAMS/inputs

@@ -63,7 +63,7 @@ remora.tcline = 100.
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 32.0    # background salinity (nondimensional) constant
 remora.T0    = 10.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 0.0     # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred
 

Exec/ParticlesOverSeaMount/inputs_ml

@@ -0,0 +1,80 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 300
+stop_time = 30000.0
+max_step = 80
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+geometry.prob_lo     =      0.     0.    -150.
+geometry.prob_hi     =  41000. 80000.       0.
+
+amr.n_cell           =  41     80      16
+
+# periodic in x to match WRF setup
+geometry.is_periodic = 1 1 0
+#ylo.type = "SlipWall"
+#yhi.type = "SlipWall"
+zlo.type = "SlipWall"
+zhi.type = "SlipWall"
+
+# TIME STEP CONTROL
+remora.fixed_dt       = 300.0 # Timestep size (seconds)
+# NDTFAST  = 30.0 # Number of baratropic steps => 300.0/30.0 = 10.0
+remora.fixed_fast_dt  = 10.0 # Baratropic timestep size (seconds)
+# remora.fixed_fast_dt  = 300.0 # Baratropic timestep size (seconds) testing value
+remora.fixed_ndtfast_ratio  = 30 # Baratropic timestep size (seconds)
+
+# PARTICLES
+remora.use_tracer_particles = 1
+tracer_particles.initial_distribution_type = box
+tracer_particles.particle_box_lo = 20000.  20000.  -100000.
+tracer_particles.particle_box_hi = 25000.  40000.   100000.
+tracer_particles.place_randomly_in_cells = false
+
+# DIAGNOSTICS & VERBOSITY
+remora.sum_interval   = 1       # timesteps between computing mass
+remora.v              = 0       # verbosity in REMORA.cpp (0: none, 1: print boxes, etc, 2: print values)
+amr.v              = 1       # verbosity in Amr.cpp
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 1       # maximum level number allowed
+amr.ref_ratio_vect  = 2 2 1
+
+remora.refinement_indicators = hi_pc
+remora.hi_pc.max_level     = 1
+remora.hi_pc.field_name    = tracer_particles_count
+remora.hi_pc.value_greater = 0.5
+
+# CHECKPOINT FILES
+remora.check_file      = chk        # root name of checkpoint file
+remora.check_int       = -57600      # number of timesteps between checkpoints
+
+# PLOTFILES
+remora.plot_file     = plt        # prefix of plotfile name
+remora.plot_int      = 5            # number of timesteps between plotfiles
+remora.plot_vars     = salt temp x_velocity y_velocity z_velocity tracer_particles_count
+remora.plotfile_type = amrex
+
+# SOLVER CHOICE
+remora.use_coriolis = true
+remora.horizontal_advection_scheme = "upstream3" # upstream3 or centered4
+remora.spatial_order = 2
+
+# Coriolis params
+remora.coriolis_f0 = -8.26e-5
+remora.coriolis_beta = 0.0
+
+# LINEAR EOS PARAMETERS (optional)
+remora.R0 = 1027.0
+remora.S0 = 35.0
+remora.T0 = 14.0
+
+# PROBLEM PARAMETERS (shear)
+prob.u_0   = 0.0
+prob.v_0   = 0.0
+prob.z0    = 0.1
+prob.zRef  = 80.0e-3
+prob.uRef  = 8.0e-3

Exec/Seamount/inputs

@@ -62,6 +62,6 @@ remora.tcline = 100.
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 32.0    # background salinity (nondimensional) constant
 remora.T0    = 10.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 0.0     # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred

Exec/Upwelling/inputs

@@ -53,7 +53,7 @@ remora.spatial_order = 2
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 35.0    # background salinity (nondimensional) constant
 remora.T0    = 14.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 0.0     # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred
 

Exec/Upwelling/inputs_gls

@@ -53,7 +53,7 @@ remora.spatial_order = 2
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 35.0    # background salinity (nondimensional) constant
 remora.T0    = 14.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 0.0     # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred
 

Exec/Upwelling_ML/inputs

@@ -55,7 +55,7 @@ remora.spatial_order = 2
 remora.R0    = 1027.0  # background density value (Kg/m3) used in Linear Equation of State
 remora.S0    = 35.0    # background salinity (nondimensional) constant
 remora.T0    = 14.0    # background potential temperature (Celsius) constant
-remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celcius)
+remora.Tcoef = 1.7e-4  # linear equation of state parameter (1/Celsius)
 remora.Scoef = 0.0     # linear equation of state parameter (nondimensional)
 remora.rho0  = 1025.0  # Mean density (Kg/m3) used when Boussinesq approx is inferred