Problem Setup
To setup a new problem you must specify:
intial conditions
resolution
problem geometry
boundary conditions
AMR tragging criteria (for multilevel runs only)
Many additional options are available, and are briefly described here and in following sections, Runtime Options and Algortihm Options.
Units
IAMR supports any selfconsistent units, as long as the length, time, and mass are consistent with the viscosity and diffusivity.
Initial Conditions
To define the initial conditions, we modify the function prob_initData()
within
IAMR/Source/prob/prob_init.cpp
. prob_initData()
reads in initial conditions
and problem parameters from the inputs file, and initializes the state data
(velocity, density, etc.). The easiest way to get started is to create a new probtype
by copying the code for an existing problem and modifying it to apply the desired initial state.
It is also possible to initialize the velocity using data from a previously generated plotfile.
To do this you must set BL_USE_VELOCITY=TRUE
in the makefile, and provide the plotfile in
the inputs file via ns.velocity_plotfile = my_plotfile_name
.
Resolution
The grid resolution is specified by defining the resolution at the coarsest level (level 0), the number of refinement levels, and factor of refinement between levels. The following inputs must be preceded by “amr.”
Description 
Type 
Default 


n_cell 
Number of cells at level 0 in each coordinate direction 
Int Int Int 
None 
max_level 
Maximum level of refinement allowed (0 when singlelevel) 
Int 
None 
ref_ratio 
Ratio of coarse to fine grid spacing between subsequent levels (2 or 4) 
Int 
None 
Some examples:
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. (If this line appears in a 2D inputs file then the final number will be ignored.)
amr.max_level = 2
would 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 4
would set factor of 2 refinement between levels 0 and 1, and factor of 4 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).
Problem Geometry
The following inputs must be preceded by “geometry.”
Description 
Type 
Default 


coord_sys 
0 for Cartesian 
Int 
0 
is_periodic 
1 for true, 0 for false (one value for each coordinate direction) 
Ints 
0 0 0 
prob_lo 
Low corner of physical domain (physical not index space) 
Reals 
None 
prob_hi 
High corner of physical domain (physical not index space) 
Reals 
None 
As an example, the following:
geometry.prob_lo = 0 0 0
geometry.prob_hi = 10.0 10.0 10.0
geometry.coord_sys = 0
geometry.is_periodic = 0 1 0
defines the domain to run from \((0,0,0)\) at the lower left to \((10,10,10)\) at the upper right in physical space, specifies a Cartesian geometry, and makes the domain periodic in the \(y\)direction only.
Domain Boundary Conditions
IAMR provides two ways to specify boundary condition types: integer keys or keywords. An inputs file must choose one style or the other, they cannot be mixed. Here we provide examples of both styles. We then discuss how to provide Dirichlet boundary conditions. For a more detailed discussion of boundaries, see Boundaries
Boundary conditions with integer keys
To specify boundary conditions with integer keys we use
ns.lo_bc: boundary type of each low face
ns.hi_bc: boundary type of each high face
The valid boundary types are:
0 – Interior / Periodic 
3 – Symmetry 
1 – Inflow 
4 – Slip Wall 
2 – Outflow 
5 – No Slip Wall 
Note: ns.lo_bc and ns.hi_bc must be consistent with geometry.is_periodic—if the domain is periodic in a particular direction then the low and high bc’s must be set to 0 for that direction.
As an example, the following:
ns.lo_bc = 1 4 0
ns.hi_bc = 2 4 0
geometry.is_periodic = 0 0 1
would define a problem with inflow (1) in the low \(x\) direction, outflow (2) in the high \(x\) direction, slip wall (4) on the low and high \(y\)faces, and periodic in the \(z\)direction.
Boundary conditions with keywords
To specify boundary conditions with keywords, we use the following options preceded by “xlo”, “xhi”, “ylo”, “yhi”, “zlo”, and “zhi”:
Description 
Type 
Default 


type 
Used to define boundary type. Available options include:

String 
None 
To use the same example problem as above, the following:
xlo.type = mi
xhi.type = po
ylo.type = sw
yhi.type = sw
geometry.is_periodic = 0 0 1
would define a problem with inflow in the low\(x\) direction, outflow in the high\(x\) direction, slip wall on the low and high \(y\)faces, and periodic in the \(z\)direction. Note that no keyword is needed for a periodic boundary, here only the specification in geometry.is_periodic is needed.
Dirichlet Boundary Conditions
IAMR provides the ability to specify constant Dirichlet BCs in the inputs file. We use the following options preceded by “xlo”, “xhi”, “ylo”, “yhi”, “zlo”, and “zhi”:
Description 
Type 
Default 


velocity 
Sets boundary velocity for mass inflows 
Real 
None 
density 
Sets boundary density for mass inflows 
Real 
None 
tracer 
Sets boundary tracer concentration for mass inflows 
Real 
None 
temp 
Sets temperature for mass inflows 
Real 
None 
pressure 
Sets boundary pressure for pressure inflows, outflows and mass inflows 
Real 
None 
As an example,
xlo.type = "mass_inflow"
xlo.velocity = 1. 0. 0.
xlo.density = 1.
xlo.tracer = 0.
xlo.temp = 1.
sets the boundary condtion type at the low x face to be an inflow with xlo.type = “mass_inflow”. Then xlo.velocity = 1. 0. 0. sets the inflow velocity, xlo.density = 1. sets the inflow density, xlo.tracer = 0. sets the inflow tracer value, and xlo.temp = 1. sets the inflow temperature. Another example, from the lid driven cavity problem setup, is
ns.lo_bc = 4 4 5
ns.hi_bc = 5 5 5
# 0 = Interior/Periodic 3 = Symmetry
# 1 = Inflow 4 = SlipWall
# 2 = Outflow 5 = NoSlipWall
# Boundary condition
zhi.velocity = 1. 0. 0.
Here, ns.hi_bc = 5 5 5 sets the boundary conditions on all high faces to no slip walls. zhi.velocity = 1. 0. 0. sets the wall at the high z face to be moving in the xdirection. Note that IAMR allows walls to move tangentially, but not in the normal direction.
Users can create more complex Dirichlet boundary condtions by writing
their own fill function in NS_bcfill.H
, then using that function to create
an amrex::StateDescriptor::BndryFunc
object and specifying which variables
will use it in NS_setup.cpp
. More information on boundary conditions is in
section Physical Boundaries.
Tagging criteria for creating AMR Levels
If amr.max_level
is greater than zero, then user specified tagging criteria are
used to define regions for higher levels of refinement.
For infomation on tagging see Tagging for Refinement
Constructing Embedded Boundaries
IAMR uses AMReX’s Embedded Boundary (cut cell) functionality to represent internal or external geometry in the flow. For details on AMReX’s approach to embedded boundaries, see the AMReX EB documentation (Embedded Boundaries).
Here we present a brief example of how to create an embedded boundary (EB) in IAMR. Additional examples and information are in AMReX’s documentation (Initializing the Geometric Database).
Create a new
geom_type
in the functioninitialize_eb2
in the fileSource/NS_init_eb2.cpp
Construct an implicit function representing the geometry (using the language of constructive solid geometry). For example
amrex::EB2::CylinderIF my_cyl(radius, height, direction, center, inside); auto gshop_cyl = amrex::EB2::makeShop(my_cyl);
Call
amrex::EB2::Build
. This function builds the EB levels and fills the implicit functionMultiFab
(the later being used to construct the levelset function).
Particles Initialization
Particles are initialized from an ASCII file, identified in the IAMR inputs file:
particles.particle_init_file = particle_file
Here particle_file
is the userspecified name of the file. The first line in this file is
assumed to contain the number of particles. Each line after that contains the position of the particle as
x y z
Tracers
IAMR includes one tracer field by default. A second tracer can be added with ns.do_trac2 = 1
.
IAMR can include additional tracers with only minor code modification: adding them to the
state variables in NS_setup.cpp
and providing initial conditions.
Temperature
IAMR has the option to solve for temperature, along with a modified divergence constraint on the velocity field (for more information, see Fluid Equations). To include temperature, you must specify two flags, both preceded by “ns.”:
Description 
Type 
Default 


do_temp 
If equal to 0, do not include temperature in the equation set 
int 
0 
temp_cond_coef 
Thermal diffusivity divided by specific heat at constant pressure 
Real 
None 
Physics Parameters
IAMR provides support for gravity, viscosity, and diffusivity. Default treatment is given in the table below. More sophiticated treatments are possible; if interested, please open an issue on github: https://github.com/AMReXCodes/IAMR/issues
The following inputs must be preceded by “ns.” For information on units, see Units.
Description 
Type 
Default 


gravity 
Gravity, taken to be in the y direction for 2d and z direction in 3d 
Real 
0 
vel_visc_coef 
Scalar viscosity 
Real 
None 
scal_diff_coefs 
Diffusivity of tracer(s). Must specify one value for each tracer. 
Real 
None 