From ddc70c11ec0ac2cb86379d9f7bdeec768791c267 Mon Sep 17 00:00:00 2001 From: Ann Almgren Date: Mon, 8 Jul 2024 18:22:10 -0700 Subject: [PATCH 1/4] fix some spelling --- Source/BoundaryConditions/REMORA_FillPatcher.cpp | 8 ++++---- Source/TimeIntegration/REMORA_gls.cpp | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Source/BoundaryConditions/REMORA_FillPatcher.cpp b/Source/BoundaryConditions/REMORA_FillPatcher.cpp index 15bebbd..2fa5078 100644 --- a/Source/BoundaryConditions/REMORA_FillPatcher.cpp +++ b/Source/BoundaryConditions/REMORA_FillPatcher.cpp @@ -9,10 +9,10 @@ using namespace amrex; * * @param[in] fba BoxArray of data to be filled at fine level * @param[in] fdm DistributionMapping of data to be filled at fine level - * @param[in] fgeom container of geometry infomation at fine level + * @param[in] fgeom container of geometry information at fine level * @param[in] cba BoxArray of data to be filled at coarse level * @param[in] cdm DistributionMapping of data to be filled at coarse level - * @param[in] cgeom container of geometry infomation at coarse level + * @param[in] cgeom container of geometry information at coarse level * @param[in] nghost number of ghost cells to be filled * @param[in] ncomp number of components to be filled * @param[in] interp interpolation operator to be used @@ -46,10 +46,10 @@ REMORAFillPatcher::REMORAFillPatcher (BoxArray const& fba, DistributionMapping c * * @param[in] fba BoxArray of data to be filled at fine level * @param[in] fdm DistributionMapping of data to be filled at fine level - * @param[in] fgeom container of geometry infomation at fine level + * @param[in] fgeom container of geometry information at fine level * @param[in] cba BoxArray of data to be filled at coarse level * @param[in] cdm DistributionMapping of data to be filled at coarse level - * @param[in] cgeom container of geometry infomation at coarse level + * @param[in] cgeom container of geometry information at coarse level * @param[in] nghost number of ghost cells to be filled * @param[in] ncomp number of components to be filled * @param[in] interp interpolation operator to be used diff --git a/Source/TimeIntegration/REMORA_gls.cpp b/Source/TimeIntegration/REMORA_gls.cpp index 09ccad8..d576a14 100644 --- a/Source/TimeIntegration/REMORA_gls.cpp +++ b/Source/TimeIntegration/REMORA_gls.cpp @@ -643,7 +643,7 @@ REMORA::gls_corrector (int lev, MultiFab* mf_gls, MultiFab* mf_tke, // Compute production and dissipation terms. ParallelFor(grow(bx,2,-1), [=] AMREX_GPU_DEVICE (int i, int j, int k) { - // Compute shear and bouyant production of turbulent energy (m3/s3) + // Compute shear and buoyant production of turbulent energy (m3/s3) // at W-points (ignore small negative values of buoyancy). Real strat2 = buoy2(i,j,k); Real gls_c3 = (strat2 > 0.0) ? gls_c3m : gls_c3p; From b9bfa1489d64b0449227e5f0aad9ce8f958f1956 Mon Sep 17 00:00:00 2001 From: Ann Almgren Date: Mon, 8 Jul 2024 18:26:42 -0700 Subject: [PATCH 2/4] fix more spellings --- .codespell-ignore-words | 2 + Docs/sphinx_doc/BoundaryConditions.rst | 2 +- Docs/sphinx_doc/InputsPhysics.rst | 2 +- .../Numerical_Solution_Technique.rst | 2 +- Docs/sphinx_doc/ProblemSetup.rst | 2 +- Docs/sphinx_doc/Visualization.rst | 2 +- Exec/Advection/inputs | 2 +- Exec/Advection/inputs_ml | 2 +- Exec/DoublyPeriodic/inputs | 2 +- Exec/IdealMiniGrid/inputs | 2 +- Exec/OCCAMS/inputs | 2 +- Exec/ParticlesOverSeaMount/inputs_ml | 80 +++++++++++++++++++ Exec/Seamount/inputs | 2 +- Exec/Upwelling/inputs | 2 +- Exec/Upwelling/inputs_gls | 2 +- Exec/Upwelling_ML/inputs | 2 +- .../Initialization/REMORA_make_new_level.cpp | 2 +- Source/REMORA.H | 4 +- Source/TimeIntegration/REMORA_gls.cpp | 2 +- paper/paper.md | 2 +- 20 files changed, 101 insertions(+), 19 deletions(-) create mode 100644 Exec/ParticlesOverSeaMount/inputs_ml diff --git a/.codespell-ignore-words b/.codespell-ignore-words index 4e0a361..641f66e 100644 --- a/.codespell-ignore-words +++ b/.codespell-ignore-words @@ -1,2 +1,4 @@ +Blocs +inout parms ptd diff --git a/Docs/sphinx_doc/BoundaryConditions.rst b/Docs/sphinx_doc/BoundaryConditions.rst index dd3de65..58eaf3a 100644 --- a/Docs/sphinx_doc/BoundaryConditions.rst +++ b/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 diff --git a/Docs/sphinx_doc/InputsPhysics.rst b/Docs/sphinx_doc/InputsPhysics.rst index 9fcadda..2bfe3e7 100644 --- a/Docs/sphinx_doc/InputsPhysics.rst +++ b/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. diff --git a/Docs/sphinx_doc/Numerical_Solution_Technique.rst b/Docs/sphinx_doc/Numerical_Solution_Technique.rst index 0bb2b41..a11b4fa 100644 --- a/Docs/sphinx_doc/Numerical_Solution_Technique.rst +++ b/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% diff --git a/Docs/sphinx_doc/ProblemSetup.rst b/Docs/sphinx_doc/ProblemSetup.rst index 404d6bd..3562d5c 100644 --- a/Docs/sphinx_doc/ProblemSetup.rst +++ b/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 `_ 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 `_ for how to add parameters. diff --git a/Docs/sphinx_doc/Visualization.rst b/Docs/sphinx_doc/Visualization.rst index 06036f3..459cd7d 100644 --- a/Docs/sphinx_doc/Visualization.rst +++ b/Docs/sphinx_doc/Visualization.rst @@ -31,7 +31,7 @@ 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 diff --git a/Exec/Advection/inputs b/Exec/Advection/inputs index 8401cd4..1eb5070 100644 --- a/Exec/Advection/inputs +++ b/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 diff --git a/Exec/Advection/inputs_ml b/Exec/Advection/inputs_ml index 9207150..2665a3e 100644 --- a/Exec/Advection/inputs_ml +++ b/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 diff --git a/Exec/DoublyPeriodic/inputs b/Exec/DoublyPeriodic/inputs index c188c16..5868dcb 100644 --- a/Exec/DoublyPeriodic/inputs +++ b/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 diff --git a/Exec/IdealMiniGrid/inputs b/Exec/IdealMiniGrid/inputs index 67e1e90..716fbe6 100644 --- a/Exec/IdealMiniGrid/inputs +++ b/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 diff --git a/Exec/OCCAMS/inputs b/Exec/OCCAMS/inputs index 5385753..d730c20 100644 --- a/Exec/OCCAMS/inputs +++ b/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 diff --git a/Exec/ParticlesOverSeaMount/inputs_ml b/Exec/ParticlesOverSeaMount/inputs_ml new file mode 100644 index 0000000..f16b187 --- /dev/null +++ b/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 diff --git a/Exec/Seamount/inputs b/Exec/Seamount/inputs index 41fefb8..239e612 100644 --- a/Exec/Seamount/inputs +++ b/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 diff --git a/Exec/Upwelling/inputs b/Exec/Upwelling/inputs index bbad962..a9b0341 100644 --- a/Exec/Upwelling/inputs +++ b/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 diff --git a/Exec/Upwelling/inputs_gls b/Exec/Upwelling/inputs_gls index b280570..1b01c57 100644 --- a/Exec/Upwelling/inputs_gls +++ b/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 diff --git a/Exec/Upwelling_ML/inputs b/Exec/Upwelling_ML/inputs index 241af8f..568857d 100644 --- a/Exec/Upwelling_ML/inputs +++ b/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 diff --git a/Source/Initialization/REMORA_make_new_level.cpp b/Source/Initialization/REMORA_make_new_level.cpp index 33938cb..4879d64 100644 --- a/Source/Initialization/REMORA_make_new_level.cpp +++ b/Source/Initialization/REMORA_make_new_level.cpp @@ -411,7 +411,7 @@ void REMORA::init_stuff (int lev, const BoxArray& ba, const DistributionMapping& vec_visc2_r[lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW,NGROW,0))); // harmonic viscosity at rho points vec_diff2[lev].reset(new MultiFab(ba,dm,NCONS,IntVect(NGROW,NGROW,0))); // harmonic diffusivity temperature/salt - //2d, (incl advection terms and surface/bottom stresses, integral over the whole columnn, k=0) + //2d, (incl advection terms and surface/bottom stresses, integral over the whole column, k=0) vec_rufrc[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0))); vec_rvfrc[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); //2d, same as above but v diff --git a/Source/REMORA.H b/Source/REMORA.H index e3cbc8f..67811d9 100644 --- a/Source/REMORA.H +++ b/Source/REMORA.H @@ -221,9 +221,9 @@ public: amrex::Vector> vec_Akv; /** Vertical diffusion coefficient (3D), set in .in file */ amrex::Vector> vec_Akt; - /** Harmonic viscosity devined on the psi points (corners of horizontal grid cells) */ + /** Harmonic viscosity defined on the psi points (corners of horizontal grid cells) */ amrex::Vector> vec_visc2_p; - /** Harmonic viscosity devined on the rho points (centers) */ + /** Harmonic viscosity defined on the rho points (centers) */ amrex::Vector> vec_visc2_r; /** Harmonic diffusivity for temperature / salinity */ amrex::Vector> vec_diff2; diff --git a/Source/TimeIntegration/REMORA_gls.cpp b/Source/TimeIntegration/REMORA_gls.cpp index d576a14..a510f34 100644 --- a/Source/TimeIntegration/REMORA_gls.cpp +++ b/Source/TimeIntegration/REMORA_gls.cpp @@ -852,7 +852,7 @@ REMORA::gls_corrector (int lev, MultiFab* mf_gls, MultiFab* mf_tke, Akt(i,j,k,n)=Akt_bak+Sh*ql; } - // Compute vertical mixing (m2/s) coefficents of turbulent kinetic + // Compute vertical mixing (m2/s) coefficients of turbulent kinetic // energy and generic statistical field. Akk(i,j,k)=Akk_bak+Sm*ql/gls_sigk; diff --git a/paper/paper.md b/paper/paper.md index cce505a..5d12c52 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -77,7 +77,7 @@ and incorporates temperature, salinity, and an arbitrary scalar which can be adv ### Time and Space Discretization and Terrain The time discretization in REMORA is the ... model as described on ROMS web page. -In each time step, the depth-averaged equations are first advanced to determine mean quanitities +In each time step, the depth-averaged equations are first advanced to determine mean quantities and ocean height, then the full three-dimensional equations are evolved for velocity and scalars. The spatial discretization in REMORA uses the classic Arakawa C-grid with From 01678e851760cf695c62c5d41dcf8d3b9daaf95f Mon Sep 17 00:00:00 2001 From: Ann Almgren Date: Mon, 8 Jul 2024 18:30:24 -0700 Subject: [PATCH 3/4] more spelling fixes --- Docs/sphinx_doc/Discretizations.rst | 12 ++++++------ Docs/sphinx_doc/Inputs.rst | 6 +++--- Docs/sphinx_doc/Time_Stepping.rst | 2 +- Docs/sphinx_doc/Visualization.rst | 2 +- Docs/sphinx_doc/coc.rst | 2 +- Source/BoundaryConditions/REMORA_FillPatcher.cpp | 2 +- Source/DataStruct.H | 2 +- Source/IO/NCFile.H | 2 +- Source/Particles/ParticleData.H | 2 +- Source/REMORA_Tagging.cpp | 2 +- Tests/test_files/Advection/Advection.i | 2 +- Tests/test_files/Advection_ML/Advection_ML.i | 2 +- Tests/test_files/DoublyPeriodic/DoublyPeriodic.i | 2 +- .../DoublyPeriodic_bathy/DoublyPeriodic_bathy.i | 2 +- Tests/test_files/Seamount/Seamount.i | 2 +- Tests/test_files/Upwelling/Upwelling.i | 2 +- Tests/test_files/Upwelling_GLS/Upwelling_GLS.i | 2 +- 17 files changed, 24 insertions(+), 24 deletions(-) diff --git a/Docs/sphinx_doc/Discretizations.rst b/Docs/sphinx_doc/Discretizations.rst index c73fda7..c82afbe 100644 --- a/Docs/sphinx_doc/Discretizations.rst +++ b/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: diff --git a/Docs/sphinx_doc/Inputs.rst b/Docs/sphinx_doc/Inputs.rst index 5ad0422..c283159 100644 --- a/Docs/sphinx_doc/Inputs.rst +++ b/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: diff --git a/Docs/sphinx_doc/Time_Stepping.rst b/Docs/sphinx_doc/Time_Stepping.rst index 1da9e42..1803a71 100644 --- a/Docs/sphinx_doc/Time_Stepping.rst +++ b/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. diff --git a/Docs/sphinx_doc/Visualization.rst b/Docs/sphinx_doc/Visualization.rst index 459cd7d..e28f999 100644 --- a/Docs/sphinx_doc/Visualization.rst +++ b/Docs/sphinx_doc/Visualization.rst @@ -35,7 +35,7 @@ To open a plotfile 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". diff --git a/Docs/sphinx_doc/coc.rst b/Docs/sphinx_doc/coc.rst index 9464cbb..a822f04 100644 --- a/Docs/sphinx_doc/coc.rst +++ b/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 ------------- diff --git a/Source/BoundaryConditions/REMORA_FillPatcher.cpp b/Source/BoundaryConditions/REMORA_FillPatcher.cpp index 2fa5078..af5b2e7 100644 --- a/Source/BoundaryConditions/REMORA_FillPatcher.cpp +++ b/Source/BoundaryConditions/REMORA_FillPatcher.cpp @@ -65,7 +65,7 @@ void REMORAFillPatcher::Define (BoxArray const& fba, DistributionMapping const& AMREX_ALWAYS_ASSERT(nghost_set <= 0); AMREX_ALWAYS_ASSERT(nghost <= nghost_set); - // Set data memebers + // Set data members m_fba = fba; m_cba = cba; m_fdm = fdm; m_cdm = cdm; m_fgeom = fgeom; m_cgeom = cgeom; diff --git a/Source/DataStruct.H b/Source/DataStruct.H index 9fa3b61..12b6bb3 100644 --- a/Source/DataStruct.H +++ b/Source/DataStruct.H @@ -350,7 +350,7 @@ struct SolverChoice { amrex::Real R0 = amrex::Real(1028); // background density value (Kg/m3) used in Linear Equation of State amrex::Real S0 = amrex::Real(35.0); // background salinity (nondimensional) constant amrex::Real T0 = amrex::Real(5.0); // background potential temperature (Celsius) constant - amrex::Real Tcoef = amrex::Real(1.7e-4); // linear equation of state parameter (1/Celcius) + amrex::Real Tcoef = amrex::Real(1.7e-4); // linear equation of state parameter (1/Celsius) amrex::Real Scoef = amrex::Real(0.0); // linear equation of state parameter (nondimensional) amrex::Real rho0 = amrex::Real(1025.0); // Mean density (Kg/m3) used when Boussinesq approx is inferred diff --git a/Source/IO/NCFile.H b/Source/IO/NCFile.H index 07fe1de..b17d59f 100644 --- a/Source/IO/NCFile.H +++ b/Source/IO/NCFile.H @@ -22,7 +22,7 @@ enum class NC_Data_Dims_Type { // NDArray is the datatype designed to hold any data, including scalars, multidimensional // arrays, that read from the NetCDF file. // -// The data read from NetCDF file are stored in a continuous memory, and the data layout is descriped +// The data read from NetCDF file are stored in a continuous memory, and the data layout is described // by using a vector (shape). AMRex Box can be constructed using the data shape information, and MultiFab // data array can be setup using the data that stored in the NDArray. // diff --git a/Source/Particles/ParticleData.H b/Source/Particles/ParticleData.H index b52bedf..351383e 100644 --- a/Source/Particles/ParticleData.H +++ b/Source/Particles/ParticleData.H @@ -210,7 +210,7 @@ class ParticleData return m_namelist_unalloc; } - /*! queries if containe has species of a certain name */ + /*! queries if container has species of a certain name */ inline bool contains ( const std::string& a_name ) const { BL_PROFILE("ParticleData::contains()"); diff --git a/Source/REMORA_Tagging.cpp b/Source/REMORA_Tagging.cpp index 5b12af8..24458f8 100644 --- a/Source/REMORA_Tagging.cpp +++ b/Source/REMORA_Tagging.cpp @@ -6,7 +6,7 @@ using namespace amrex; /** * Function to tag cells for refinement -- this overrides the pure virtual function in AmrCore * - * @param[in] levc level of refinement (0 is coarsest leve) + * @param[in] levc level of refinement (0 is coarsest level) * @param[out] tags array of tagged cells * @param[in] time current time */ diff --git a/Tests/test_files/Advection/Advection.i b/Tests/test_files/Advection/Advection.i index 5650293..d35721b 100644 --- a/Tests/test_files/Advection/Advection.i +++ b/Tests/test_files/Advection/Advection.i @@ -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 diff --git a/Tests/test_files/Advection_ML/Advection_ML.i b/Tests/test_files/Advection_ML/Advection_ML.i index 2f8b755..e4805df 100644 --- a/Tests/test_files/Advection_ML/Advection_ML.i +++ b/Tests/test_files/Advection_ML/Advection_ML.i @@ -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 = 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 diff --git a/Tests/test_files/DoublyPeriodic/DoublyPeriodic.i b/Tests/test_files/DoublyPeriodic/DoublyPeriodic.i index 04cd239..9bc5b03 100644 --- a/Tests/test_files/DoublyPeriodic/DoublyPeriodic.i +++ b/Tests/test_files/DoublyPeriodic/DoublyPeriodic.i @@ -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 diff --git a/Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i b/Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i index 1e5b408..ea5b7fe 100644 --- a/Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i +++ b/Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i @@ -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 diff --git a/Tests/test_files/Seamount/Seamount.i b/Tests/test_files/Seamount/Seamount.i index 65c0677..28dd6c7 100644 --- a/Tests/test_files/Seamount/Seamount.i +++ b/Tests/test_files/Seamount/Seamount.i @@ -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 diff --git a/Tests/test_files/Upwelling/Upwelling.i b/Tests/test_files/Upwelling/Upwelling.i index e03081d..68c0a69 100644 --- a/Tests/test_files/Upwelling/Upwelling.i +++ b/Tests/test_files/Upwelling/Upwelling.i @@ -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 diff --git a/Tests/test_files/Upwelling_GLS/Upwelling_GLS.i b/Tests/test_files/Upwelling_GLS/Upwelling_GLS.i index 3c4db5a..18c3f0b 100644 --- a/Tests/test_files/Upwelling_GLS/Upwelling_GLS.i +++ b/Tests/test_files/Upwelling_GLS/Upwelling_GLS.i @@ -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 From b756d53f680aae8b1829ab687f5a3e81e60b9b92 Mon Sep 17 00:00:00 2001 From: Ann Almgren Date: Mon, 8 Jul 2024 18:31:49 -0700 Subject: [PATCH 4/4] fix spelling --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 5ba3843..ad5d3d0 100644 --- a/README.rst +++ b/README.rst @@ -10,7 +10,7 @@ Getting Started ~~~~~~~~~~~~~~~ See `Getting Started `_ for instructions as to how to clone the REMORA -and AMReX codes, and for how to build and run a REMORA example. Mimimum requirements for system software are also given there. +and AMReX codes, and for how to build and run a REMORA example. Minimum requirements for system software are also given there. Documentation ~~~~~~~~~~~~~~~~~