Neko  0.8.0-rc2
A portable framework for high-order spectral element flow simulations
Case File

The case file defines all the parameters of a simulation. The format of the file is JSON, making it easy to read and write case files using the majority of the popular programming languages. JSON is heirarchical and, and consists of parameter blocks enclosed in curly braces. These blocks are referred to as objects. The case file makes use objects to separate the configuration of different parts of the solver. We refer the reader to the examples shipped with the code to get a good idea of how a case file looks. The table below provides a complete reference for all possible configuration choices.

High-level structure

The current high-level structure of the case file is shown below.

{
"version": 1.0
"case": {
"numerics": {}
"fluid": {}
"scalar": {}
"statistics": {}
"simulation_components" : []
"point_zones" : []
}
}

The version keywords is reserved to track changes in the format of the file. The the subsections below we list all the configuration options for each of the high-level objects. Some parameters will have default values, and are therefore optional.

Output frequency control

A common scheme for controlling the output frequency is applied for various outputs. It is described already now in order to clarify the meaning of several parameters found in the tables below.

The frequency is controlled by two paramters, ending with _control and _value, respectively. The latter name is perhaps not ideal, but it is somewhat difficult to come up with a good one, suggestions are welcome.

The _value parameter is a number, that defines the output frequency, but the interpretation of that number depends on the choice of _control. The three following options are possible.

  1. simulationtime, then _value is the time interval between the outputs.
  2. tsteps, then _value is the number of time steps between the outputs.
  3. nsamples, then _value is the total number of outputs that will be performed in the course of the simulation.
  4. never, then _value is ignored and output is never performed.

The case object

This object is mostly used as a high-level container for all the other objects, but also defines several parameters that pertain to the simulation as a whole.

Name Description Admissible values Default value
mesh_file The name of the mesh file. Strings ending with .nmsh -
output_boundary Whether to write a bdry0.f0000 file with boundary labels. Can be used to check boundary conditions. true or false false
output_directory Folder for redirecting solver output. Note that the folder has to exist! Path to an existing directory .
output_precision Whether to output snapshots in single or double precision single or double single
load_balancing Whether to apply load balancing. true or false false
output_partitions Whether to write a partitions.vtk file with domain partitioning. true or false false
output_checkpoints Whether to output checkpoints, i.e. restart files. true or false false
checkpoint_control Defines the interpretation of checkpoint_value to define the frequency of writing checkpoint files. nsamples, simulationtime, tsteps, never -
checkpoint_value The frequency of sampling in terms of checkpoint_control. Positive real or integer -
restart_file checkpoint to use for a restart from previous data Strings ending with .chkp -
timestep Time-step size Positive reals -
variable_timestep Whether to use variable dt true or false false
max_timestep Maximum time-step size when variable time step is activated Positive reals -
target_cfl The desired CFL number Positive real 0.4
cfl_max_update_frequency The minimum interval between two time-step-updating steps in terms of time steps Integer 0
cfl_running_avg_coeff The running average coefficient a where cfl_avg_new = a * cfl_new + (1-a) * cfl_avg_old Positive real between 0 and 1 0.5
max_dt_increase_factor The maximum scaling factor to increase time step Positive real greater than 1 1.2
min_dt_decrease_factor The minimum scaling factor to decrease time step Positive real less than 1 0.5
end_time Final time at which the simulation is stopped. Positive reals -
job_timelimit The maximum wall clock duration of the simulation. String formatted as HH:MM:SS No limit

Boundary type numbering in the output_boundary field

When the output_boundary setting is set to true, and additional .fld file will be stored in the beginning of the simulation, where the recognized boundaries will be marked with an integer number. This is a good way to debug the simulation setup. The value of the number depends on the type of the boundary as follows:

  1. A wall boundary, i.e. the w label.
  2. A Dirichlet boundary, i.e. the v label.
  3. An outlet boundary, i.e. the o label.
  4. A symmetry boundary, i.e. the sym label.
  5. A periodic boundary.
  6. An wall-normal transpiration boundary, i.e. the on label.

Note that the boundary conditions can be both prescribed via the labels in the case file or built into the mesh via conversion from a .re2 file. Both types will be picked up and marked in the field produced by output_boundary.

Numerics

Used to define the properties of the numerical discretization.

Name Description Admissible values Default value
polynomial_order The oder of the polynomial basis. Integers, typically 5 to 9 -
time_order The order of the time integration scheme. Refer to the time_scheme_controller type documention for details. 1,2, 3 -
dealias Whether to apply dealiasing to advection terms. true or false false
dealiased_polynomial order The polynomial order in the higher-order space used in the dealising. Integer 3/2(polynomial_order + 1) - 1

Fluid

The configuration of the fluid solver and the flow problem. Contains multiple subobjects for various parts of the setup.

Material properties

As per the governing equations, Neko requires the value of the density and dynamic viscosity to define the flow problem. These can be provided as rho and mu in the case file.

Alternatively, one may opt to provide the Reynolds number, Re, which corresponds to a non-dimensional formulation of the Navier-Stokes equations. This formulation can effectively be obtained by setting \( \rho = 1 \) and \( \mu = 1/Re \). This is exactly what Neko does under the hood, when Re is provided in the case file.

Note that if both Re and any of the dimensional material properties are provided, the simulation will issue an error.

As an alternative to providing material properties in the case file, it is possible to do that in a special routine in the user file. This is demonstrated in the rayleigh-benard-cylinder example. Ultimately, both rho and mu have to be set in the subroutine, but it can be based on arbitrary computations and arbitrary parameters read from the case file. Additionally, this allows to change the material properties in time.

Boundary types

The optional boundary_types keyword can be used to specify boundary conditions. The reason for it being optional, is that some conditions can be specified directly inside the mesh file. In particular, this happens when Nek5000 .re2 files are converted to .nmsh. Periodic boundary conditions are always defined inside the mesh file.

The value of the keyword is an array of strings, with the following possible values:

  • Standard boundary conditions
    • w, a no-slip wall.
    • v, a velocity Dirichlet boundary.
    • sym, a symmetry boundary.
    • o, outlet boundary.
    • on, Dirichlet for the boundary-parallel velocity and homogeneous Neumann for the wall-normal. The wall-parallel velocity is defined by the initial condition.
  • Advanced boundary conditions
    • d_vel_u, d_vel_v, d_vel_w (or a combination of them, separated by a "/"), a Dirichlet boundary for more complex velocity profiles. This boundary condition uses a more advanced user interface.
    • d_pres, a boundary for specified non-uniform pressure profiles, similar in essence to d_vel_u,d_vel_v and d_vel_w. Can be combined with other complex Dirichlet coonditions by specifying e.g.: "d_vel_u/d_vel_v/d_pres".
    • o+dong, outlet boundary using the Dong condition.
    • on+dong, an on boundary using the Dong condition, ensuring that the wall-normal velocity is directed outwards.

In some cases, only some boundary types have to be provided. For example, when one has periodic boundaries, like in the channel flow example. In this case, to put the specification of the boundary at the right index, preceding boundary types can be marked with an empty string. For example, if boundaries with index 1 and 2 are periodic, and the third one is a wall, we can set.

"boundary_types": ["", "", "w"]

Inflow boundary conditions

The object inflow_condition is used to specify velocity values at a Dirichlet boundary. This does not necessarily have to be an inflow boundary, so the name is not so good, and will most likely be changed along with type changes in the code. Since not all cases have Dirichlet boundaries (note, the special case of a no-slip boundary is treated separately in the configuration), this object is not obligatory. The means of prescribing the values are controlled via the type keyword:

  1. user, the values are set inside the compiled user file.
  2. uniform, the value is a constant vector, looked up under the value keyword.
  3. blasius, a Blasius profile is prescribed. Its properties are looked up in the case.fluid.blasius object, see below.

Initial conditions

The object initial_condition is used to provide initial conditions. It is mandatory. Note that this currently pertains to both the fluid, but also scalars. The means of prescribing the values are controlled via the type keyword:

  1. user, the values are set inside the compiled user file. The only way to initialize scalars.
  2. uniform, the value is a constant vector, looked up under the value keyword.
  3. blasius, a Blasius profile is prescribed. Its properties are looked up in the case.fluid.blasius object, see below.

Blasius profile

The blasius object is used to specify the Blasius profile that can be used for the initial and inflow condition. The boundary cannot be tilted with respect to the coordinate axes. It requires the following parameters:

  1. delta, the thickness of the boundary layer.
  2. freestream_velocity, the velocity value in the free stream.
  3. approximation, the numerical approximation to the Blasius profile.
    • linear, linear approximation.
    • quadratic, quadratic approximation.
    • cubic, cubic approximation.
    • quartic, quartic approximation.
    • sin, sine function approximation.

Source terms

The source_terms object should be used to specify the source terms in the momentum equation. The object is not mandatory, by default no forcing term is present. Each source term, is itself a JSON object, so source_terms is just an array of them. Note that with respect to the governing equations, the source terms define \( f^u \), meaning that the values are then multiplied by the density.

For each source, the type keyword defines the kind of forcing that will be introduced. Furthermore, the start_time and end_time keywords can be used to set a time frame for when the source term is active. Note, however, that these keywords have no effect on the user-defined source terms, but their execution can, of course, be directly controlled in the user code. By default, all source terms are active during the entire simulation.

The following types are currently implemented.

  1. constant, constant forcing. Strength defined by the values array with 3 reals corresponding to the 3 components of the forcing.
  2. boussinesq, a source term introducing boyancy based on the Boussinesq approximation, \( \rho \beta (T - T_{ref} \cdot g) \). Here, \( rho \) is density, \( \beta \) the thermal expansion coefficient, \( g \) the gravity vector, and $T_{ref}$ a reference value of the scalar, typically temperature.

    Reads the following entries:

    • scalar_field: The name of the scalar that drives the source term, defaults to "s".
    • reference_value: The reference value of the scalar.
    • g: The gravity vector.
    • beta: The thermal expansion coefficient, defaults to the inverse of ref_value.
  3. user_pointwise, the values are set inside the compiled user file, using the pointwise user file subroutine. Only works on CPUs!
  4. user_vector, the values are set inside the compiled user file, using the non-pointwise user file subroutine. Should be used when running on the GPU.
  1. brinkman, Brinkman permeability forcing inside a pre-defined region.

Brinkman

The Brinkman source term introduces regions of resistance in the fluid domain. The volume force \( f_i \) applied in the selected regions are proportional to the fluid velocity component \( u_i \).

\begin{eqnarray*} f_i(x) &=& - B(x) u_i(x), \\ B(x) &=& \kappa_0 + (\kappa_1 - \kappa_0) \xi(x) \frac{q + 1}{q + \xi(x)}, \end{eqnarray*}

where, \( x \) is the current location in the domain, \( \xi: x \mapsto [0,1] \) represent an indicator function for the resistance where \( \xi(x) = 0 \) is a free flow. \( \kappa_i \) describes the limits for the force application at \( \xi(x)=0 \) and \( \xi(x)=1 \). A penalty parameter \( q \) help us to reduce numerical problems.

The indicator function will be defined based on the object type. The following types are currently implemented.

  1. boundary_mesh, the indicator function for a boundary mesh is computed in two steps. First, the signed distance function is computed for the boundary mesh. Then, the indicator function is computed using the distance transform function specified in the case file.
  2. point_zone, the indicator function is defined as 1 inside the point zone and 0 outside.

Each object are added to a common indicator field by means of a point-wise max operator. This means that the indicator field will be the union of all the regions defined by the objects.

To assist correct placement and scaling of objects from external sources, the meshes can be transformed using the mesh_transform object. The object can be used to apply a transformation to the boundary mesh. The following types are currently implemented.

  1. none, no transformation is applied.
  2. bounding_box, the boundary mesh is transformed to fit inside a box defined by box_min and box_max. The box is defined by two vectors of 3 reals each. The keep_aspect_ratio keyword can be used to keep the aspect ratio of the boundary mesh.

After the indicator field is computed, it is filtered using a filter type specified in the case file. The filter is used to smooth the indicator field before computing the Brinkman force. The following types are currently implemented.

  1. none, no filtering is applied.

The filtering can be defined for each object separately. Additionally, the filter can be specified for the entire source term, in which case it will be applied to the final indicator field, after all sources have been added.

Additional keywords are available to modify the Brinkman force term.

Name Description Admissible values Default value
brinkman.limits Brinkman factor at free-flow ( \( \kappa_0 \)) and solid domain ( \( \kappa_1 \)). Vector of 2 reals. -
brinkman.penalty Penalty parameter \( q \) when estimating Brinkman factor. Real \( 1.0 \)
objects Array of JSON objects, defining the objects to be immersed. Each object must specify a type -
distance_transform.type How to map from distance field to indicator field. step, smooth_step -
distance_transform.value Values used to define the distance transform, such as cut-off distance for the step function. Real -
filter.type Type of filtering applied to the indicator field either globally or for the current object. none none
mesh_transform.type Apply a transformation to the boundary mesh. bounding_box, none none
mesh_transform.box_min Lower left front corner of the box to fit inside. Vector of 3 reals -
mesh_transform.box_max Upper right back corner of the box to fit inside. Vector of 3 reals -
mesh_transform.keep_aspect_ratio Keep the aspect ratio of the boundary mesh. true or false true

Example of a Brinkman source term where a boundary mesh and a point zone are combined to define the resistance in the fluid domain. The indicator field for the boundary mesh is computed using a step function with a cut-off distance of \( 0.1 \). The indicator field for the point zone is not filtered.

"source_terms": [
{
"type": "brinkman",
"objects": [
{
"type": "boundary_mesh",
"name": "some_mesh.stl",
"distance_transform": {
"type": "step",
"value": 0.1
},
},
{
"type": "point_zone",
"name": "cylinder_zone",
"filter": {
"type": "none"
}
}
],
"brinkman": {
"limits": [0.0, 100.0],
"penalty": 1.0
}
}
]

Linear solver configuration

The mandatory velocity_solver and pressure_solver objects are used to configure the solvers for the momentum and pressure-Poisson equation. The following keywords are used, with the corresponding options.

  • type, solver type.
    • cg, a conjugate gradient solver.
    • pipecg, a pipelined conjugate gradient solver.
    • bicgstab, a bi-conjugate gradient stabilized solver.
    • cacg, a communication-avoiding conjugate gradient solver.
    • gmres, a GMRES solver. Typically used for pressure.
    • fusedcg, a conjugate gradient solver optimised for accelerators using kernel fusion.
  • preconditioner, preconditioner type.
    • jacobi, a Jacobi preconditioner. Typically used for velocity.
    • hsmg, a hybrid-Schwarz multigrid preconditioner. Typically used for pressure.
    • ident, an identity matrix (no preconditioner).
  • absolute_tolerance, tolerance criterion for convergence.
  • max_iterations, maximum number of iterations before giving up.
  • projection_space_size, size of the vector space used for accelerating the solution procedure. If 0, then the projection space is not used. More important for the pressure equation.
  • projection_hold_steps, steps for which the simulation does not use projection after starting or time step changes. E.g. if 5, then the projection space will start to update at the 6th time step and the space will be utilized at the 7th time step.

Flow rate forcing

The optional flow_rate_force object can be used to force a particular flow rate through the domain. Useful for channel and pipe flows. The configuration uses the following parameters:

  • direction, the direction of the flow, defined as 0, 1, or 2, corresponding to x, y or z, respectively.
  • value, the desired flow rate.
  • use_averaged_flow, whether value specifies the domain-averaged (bulk) velocity or the volume flow rate.

Full parameter table

All the parameters are summarized in the table below. This includes all the subobjects discussed above, as well as keyword parameters that can be described concisely directly in the table.

Name Description Admissible values Default value
scheme The fluid solve type. pnpn -
Re The Reynolds number. Positive real -
rho The density of the fluid. Positive real -
mu The dynamic viscosity of the fluid. Positive real -
output_control Defines the interpretation of output_value to define the frequency of writing checkpoint files. nsamples, simulationtime, tsteps, never -
output_value The frequency of sampling in terms of output_control. Positive real or integer -
inflow_condition.type Velocity inflow condition type. user, uniform, blasius -
inflow_condition.value Value of the inflow velocity. Vector of 3 reals -
initial_condition.type Initial condition type. user, uniform, blasius -
initial_condition.value Value of the velocity initial condition. Vector of 3 reals -
blasius.delta Boundary layer thickness in the Blasius profile. Positive real -
blasius.freestream_velocity Free-stream velocity in the Blasius profile. Vector of 3 reals -
blasius.approximation Numerical approximation of the Blasius profile. linear, quadratic, cubic, quartic, sin -
source_terms Array of JSON objects, defining additional source terms. See list of source terms above -
boundary_types Boundary types/conditions labels. Array of strings -
velocity_solver.type Linear solver for the momentum equation. cg, pipecg, bicgstab, cacg, gmres -
velocity_solver.preconditioner Linear solver preconditioner for the momentum equation. ident, hsmg, jacobi -
velocity_solver.absolute_tolerance Linear solver convergence criterion for the momentum equation. Positive real -
velocity_solver.maxiter Linear solver max iteration count for the momentum equation. Positive real 800
velocity_solver.projection_space_size Projection space size for the momentum equation. Positive integer 20
velocity_solver.projection_hold_steps Holding steps of the projection for the momentum equation. Positive integer 5
pressure_solver.type Linear solver for the momentum equation. cg, pipecg, bicgstab, cacg, gmres -
pressure_solver.preconditioner Linear solver preconditioner for the momentum equation. ident, hsmg, jacobi -
pressure_solver.absolute_tolerance Linear solver convergence criterion for the momentum equation. Positive real -
pressure_solver.maxiter Linear solver max iteration count for the momentum equation. Positive real 800
pressure_solver.projection_space_size Projection space size for the momentum equation. Positive integer 20
pressure_solver.projection_hold_steps Holding steps of the projection for the momentum equation. Positive integer 5
flow_rate_force.direction Direction of the forced flow. 0, 1, 2 -
flow_rate_force.value Bulk velocity or volumetric flow rate. Positive real -
flow_rate_force.use_averaged_flow Whether bulk velocity or volumetric flow rate is given by the value parameter. true or false -
freeze Whether to fix the velocity field at initial conditions. true or false false

Scalar

The scalar object allows to add a scalar transport equation to the solution. The solution variable is called s, but saved as temperature in the fld files. Some properties of the object are inherited from fluid: the properties of the linear solver, the value of the density, and the output control.

The scalar equation requires defining additional material properties: the specific heat capacity and thermal conductivity. These are provided as cp and lambda. Similarly to the fluid, one can provide the Peclet number, Pe, as an alternative. In this case, cp is set to 1 and lambda to the inverse of Pe.

The boundary conditions for the scalar are specified through the boundary_types keyword. It is possible to directly specify a uniform value for a Dirichlet boundary. The syntax is, e.g. d=1, to set the value to 1, see the Ryleigh-Benard example case.

The configuration of source terms is the same as for the fluid. A demonstration of using source terms for the scalar can be found in the scalar_mms example.

Name Description Admissible values Default value
enabled Whether to enable the scalar computation. true or false true
Pe The Peclet number. Positive real -
cp Specific heat cpacity. Positive real -
lambda Thermal conductivity. Positive real -
boundary_types Boundary types/conditions labels. Array of strings -
initial_condition.type Initial condition type. user, uniform -
initial_condition.value Value of the velocity initial condition. Real -
source_terms Array of JSON objects, defining additional source terms. See list of source terms above -

Statistics

This object adds the collection of statistics for the fluid fields. For additional details on the workflow, see the corresponding page in the user manual.

Name Description Admissible values Default value
enabled Whether to enable the statistics computation. true or false true
start_time Time at which to start gathering statistics. Positive real 0
sampling_interval Interval, in timesteps, for sampling the flow fields for statistics. Positive integer 10

Simulation components

Simulation components enable the user to perform various additional operations, which are not strictly necessary to run the solver. An example could be computing and output of additional fields, e.g. vorticity.

A more detailed description as well as a full list of available components and their setup is provided in a separate page of the manual.

Point zones

Point zones enable the user to select GLL points in the computational domain according to some geometric criterion. Two predefined geometric shapes are selectable from the case file, boxes and spheres.

A point zone object defined in the case file can be retrieved from the point zone registry, neko_point_zone_registry, and can be used to perform any zone-specific operations (e.g. localized source term, probing...). User-specific point zones can also be added manually to the point zone registry from the user file.

A more detailed description as well as a full list of available components and their setup is provided in a separate page of the manual.