Inputs
The REMORA executable reads run-time information from an “inputs” file which you put on the command line. This section describes the inputs which can be specified either in the inputs file or on the command line. If a value is specified on the command line, that value will override a value specified in the inputs file.
Problem Geometry
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
geometry.prob_lo |
physical location of low corner of the domain |
Real |
must be set |
geometry.prob_hi |
physical location of high corner of the domain |
Real |
must be set |
geometry.is_periodic |
is the domain periodic in this direction |
0 if false, 1 if true |
0 0 0 |
Examples of Usage
geometry.prob_lo = 0 0 0 defines the low corner of the domain at (0,0,0) in physical space.
geometry.prob_hi = 1.e8 2.e8 2.e8 defines the high corner of the domain at (1.e8,2.e8,2.e8) in physical space.
geometry.is_periodic = 0 1 0 says the domain is periodic in the y-direction only.
Domain Boundary Conditions
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
xlo.type |
boundary type of xlo face |
must be set if not periodic |
|
xhi.type |
boundary type of xhi face |
must be set if not periodic |
|
ylo.type |
boundary type of ylo face |
must be set if not periodic |
|
yhi.type |
boundary type of yhi face |
must be set if not periodic |
|
zlo.type |
boundary type of zlo face |
must be set if not periodic |
|
zhi.type |
boundary type of zhi face |
must be set if not periodic |
Resolution
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
amr.n_cell |
number of cells in each direction at the coarsest level |
Integer > 0 |
must be set |
amr.max_level |
number of levels of refinement above the coarsest level |
Integer >= 0 |
must be set |
amr.ref_ratio |
ratio of coarse to fine grid spacing between subsequent levels |
2 / 3 / 4 (one per level) |
2 for all levels |
amr.ref_ratio_vect |
ratio of coarse to fine grid spacing between subsequent levels |
3 integers (one per dir) 2 / 3 / 4 |
2 for all directions |
amr.regrid_int |
how often to regrid |
Integer > 0 |
must be set |
amr.regrid_on_restart |
should we regrid immediately after restarting |
0 or 1 |
0 |
Note: if amr.max_level = 0 then you do not need to set amr.ref_ratio or amr.regrid_int.
Examples of Usage
amr.n_cell = 32 64 64
would define the domain to have 32 cells in the x-direction, 64 cells in the y-direction, and 64 cells in the z-direction at the coarsest level.
- amr.max_level = 2would allow a maximum of 2 refined levels in addition to the coarse level. Note that these additional levels will only be created only if the tagging criteria are such that cells are flagged as needing refinement. The number of refined levels in a calculation must be \(\leq\) amr.max_level, but can change in time and need not always be equal to amr.max_level.
- amr.ref_ratio = 2 3would set factor 2 refinement between levels 0 and 1, and factor 3 refinement between levels 1 and 2. Note that you must have at least amr.max_level values of amr.ref_ratio (Additional values may appear in that line and they will be ignored).
- amr.ref_ratio_vect = 2 4 3would set factor {2 in x-dir, 4 in y-dir, 3 in z-dir} refinement between all adjacent levels. Note that you must specify 3 values, one for each coordinate direction.
- amr.regrid_int = 2 2tells the code to regrid every 2 steps. Thus in this example, new level-1 grids will be created every 2 level-0 time steps, and new level-2 grids will be created every 2 level-1 time steps.
Regridding
Overview
The user defines how to tag individual cells at a given level for refinement. This list of tagged cells is sent to a grid generation routine, which uses the Berger–Rigoutsos algorithm to create rectangular grids that contain the tagged cells.
See Mesh Refinement for more details on how to specify regions for refinement.
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
amr.regrid_file |
name of file from which to read the grids |
text |
no file |
amr.grid_eff |
grid efficiency at coarse level at which grids are created |
Real > 0, < 1 |
0.7 |
amr.n_error_buf |
radius of additional tagging around already tagged cells |
Integer >= 0 |
1 |
amr.max_grid_size |
maximum size of a grid in any direction |
Integer > 0 |
32 |
amr.max_grid_size |
maximum size |
Integer |
32 |
amr.blocking_factor |
grid size must be a multiple of this |
Integer > 0 |
2 |
amr.refine_grid_layout |
refine grids more if # of processors \(>\) # of grids |
0 if false, 1 if true |
1 |
Notes
amr.n_error_buf, amr.max_grid_size and amr.blocking_factor can be read in as a single value which is assigned to every level, or as multiple values, one for each level
amr.max_grid_size at every level must be even
amr.blocking_factor at every level must be a power of 2
the domain size amr.n_cell must be a multiple of amr.blocking_factor at level 0
amr.max_grid_size must be a multiple of amr.blocking_factor at every level
Examples of Usage
- amr.regrid_file = fixed_gridsIn this case the list of grids at each fine level are contained in the file fixed_grids, which will be read during the gridding procedure. These grids must not violate the amr.max_grid_size criterion. The rest of the gridding procedure described below will not occur if amr.regrid_file is set.
- amr.grid_eff = 0.9During the grid creation process, at least 90% of the cells in each grid at the level at which the grid creation occurs must be tagged cells. Note that this is applied at the coarsened level at which the grids are actually made, and before amr.max_grid_size is imposed.
- amr.max_grid_size = 64The final grids will be no longer than 64 cells on a side at every level.
- amr.max_grid_size = 64 32 16The final grids will be no longer than 64 cells on a side at level 0, 32 cells on a side at level 1, and 16 cells on a side at level 2.
- amr.blocking_factor = 32The dimensions of all the final grids will be multiples of 32 at all levels.
- amr.blocking_factor = 32 16 8The dimensions of all the final grids will be multiples of 32 at level 0, multiples of 16 at level 1, and multiples of 8 at level 2.
Simulation Time
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
max_step |
maximum number of level 0 time steps |
Integer >= 0 |
-1 |
stop_time |
final simulation time |
Real >= 0 |
-1.0 |
remora.start_time |
initial simulation time |
Real >= 0 |
0.0 |
Notes
To control the number of time steps, you can limit by the maximum number of level-0 time steps (max_step), or the final simulation time (stop_time), or both. The code will stop at whichever criterion comes first. Note that if the code reaches stop_time then the final time step will be shortened so as to end exactly at stop_time, not pass it.
Examples of Usage
max_step = 1000
stop_time = 1.0
will end the calculation when either the simulation time reaches 1.0 or the number of level-0 steps taken equals 1000, whichever comes first.
Time Step
List of Parameters for Single-Rate
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
remora.cfl |
CFL number for hydro |
Real > 0 and <= 1 |
0.8 |
remora.fixed_dt |
set level 0 dt as this value regardless of cfl or other settings |
Real > 0 |
unused if not set |
remora.fixed_fast_dt |
set fast dt as this value |
real > 0 |
inferred from fixed_dt and fixed_ndfast_ratio if not set |
remora.fixed_ndfast_ratio |
set fast dt as slow dt / this ratio |
int |
inferred from fixed_dt and fixed_fast_dt if not set |
remora.change_max |
factor by which dt can grow in subsequent steps |
Real >= 1 |
1.1 |
Examples of Usage
- remora.cfl = 0.9defines the timestep as dt = cfl * dx / (u+c). Only relevant if fixed_dt not set
- remora.change_max = 1.1allows the time step to increase by no more than 10% in this case. Note that the time step can shrink by any factor; this only controls the extent to which it can grow.
- remora.fixed_dt = 1.e-4sets the level-0 time step to be 1.e-4 for the entire simulation, ignoring the other timestep controls. Note that if remora.init_shrink \(\neq 1\) then the first time step will in fact be remora.init_shrink * remora.fixed_dt.
Restart Capability
See Checkpoint / Restart for how to control the checkpoint/restart capability.
Screen Output
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
amr.v |
verbosity of Amr.cpp |
0 or 1 |
0 |
remora.v |
verbosity of REMORA functions |
|
0 |
remora.sum_interval |
how often (in level-0 time steps) to compute integral quantities |
Integer |
-1 |
Examples of Usage
- remora.sum_interval = 2if remora.sum_interval \(> 0\) then the code computes and prints certain integral quantities, such as total mass, momentum and energy in the domain every remora.sum_interval level-0 steps. In this example the code will print these quantities every two 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 \(<= 0\) then it will not compute and print these quanitities.
Included terms
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
remora.use_coriolis |
Include Coriolis terms. |
true / false |
false |
remora.flat_bathymetry |
Use flat bathymetry. |
true / false |
true |
remora.use_prestep |
Do prestep terms. Only for debugging purposes. |
true / false |
true |
remora.use_uv3dmix |
Include harmonic viscosity. Only for debugging purposes. |
true / false |
true |
remora.use_barotropic |
Include 2d barotropic step. Only for debugging purposes. |
true / false |
true |
Physics Parameters
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
remora.ggrav |
Gravitational field strength [kg m/s^2] |
Real number |
9.81 |
remora.R0 |
Background density [kg/m^3] used in Linear Equation of State. May be used in setup of some problems. |
Real number |
1028 |
remora.S0 |
Background salinity (nondimensional) used in Linear Equation of State State. May be used in setup of some problems. |
Real number |
35 |
remora.T0 |
Background temperature (Celsius) used in Linear Equation of State State. May be used in setup of some problems. |
Real number |
5 |
remora.Tcoef |
Linear EOS parameter (1/Celsius) |
Real number |
1.7e-4 |
remora.Scoef |
Linear EOS parameter (nondimensional) |
Real number |
0.0 |
remora.rho0 |
Mean density (kg/m^3) used when Boussinesq approx is inferred |
Real number |
1025 |
remora.coriolis_type |
Type of Coriolis forcing.
|
|
|
remora.coriolis_f0 |
f-plane constant for Coriolis param \(f = f_0 + \beta y\) when using beta plane Coriolis type |
Real number |
0.0 |
remora.coriolis_beta |
beta-plane constant for Coriolis param \(f = f_0 + \beta y\) when using beta plane Coriolis type |
Real number |
0.0 |
Numerical Algorithms
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
remora.horizontal_advection_scheme |
Scheme for horizontal advection |
upstream3, centered4 |
upstream3 |
Vertical Stretch prameters
List of Parameters
Parameter |
Definition |
Acceptable Values |
Default |
---|---|---|---|
remora.theta_s |
Stretching parameter for surface refinement of vertical S-grid |
\(0 \leq \theta_S \leq 10\) |
3.0 |
remora.theta_b |
Stretching parameter for bottom refinement of vertical S-grid |
\(0 \leq \theta_B \leq 4\) |
0.0 |
remora.tcline |
Surface/bottom layer width (m) in vertical S-grid |
Positive number |
150 |
These parameters are used to calculate the vertical S-grid stretch/transform functions detailed in Vertical S-Coordinate.