Enzo-E / Cello Parameters

This page documents all current parameters implemented in Enzo-E / Cello. Each parameter is summarized, its type or types are listed, and the default value (if any) is provided. The scope of the parameter is also listed, which is either “Cello” or “Enzo”, depending on whether the parameter is associated with Cello framework or Enzo-E application. Any assumptions associated with a parameter are also listed; for example, a parameter may only be valid if some other parameter is set to a certain value.

If you find any errors in the documentation, or have any specific suggestions, please contact the Enzo Project developers at github.

Adapt

Adapt parameters define how the mesh hierarchy dynamically adapts to the solution. It is closely related to the Mesh parameters, which defines the root grid size, number of blocks in the root grid, and size of blocks.

Parameter:

Adapt : interval

Summary:

Number of cycles between adapt steps

Type:

integer

Default:

1

Scope:

Cello

The interval parameter is used to set the number of root-level cycles between mesh adaptation. The default is 1.

Parameter:

Adapt : max_level

Summary:

Maximum level in the adaptive mesh hierarchy

Type:

integer

Default:

0

Scope:

Cello

This parameter specifies the level of the most highly refined Block in the mesh hierarchy. The default is 0, meaning there is no refinement past the initial root-level grid.

Parameter:

Adapt : min_level

Summary:

Minimum level in the adaptive mesh hierarchy

Type:

integer

Default:

0

Scope:

Cello

This parameter specifies the coarsest level of “sub-root” Blocks, and must non-positive. This is used primarily for multigrid methods, such as in the “mg0” solver. The default is 0, meaning no sub-root Blocks are created. If multigrid is used, then both Adapt : min_level and Method : <mg-solver> : min_level must be set..

Parameter:

Adapt : list

Summary:

List of refinement criteria

Type:

list ( string )

Default:

[]

Scope:

Cello

List of mesh refinement criteria, each of which has its own associated Adapt : <criteria> : parameters. When multiple criteria are used, if all refinement criteria evaluate to “coarsen”, then the block will be tagged to coarsen; if any refinement criteria evaluate as “refine”, then the block will be tagged to refine. (Note that a particular block will coarsen only if it and all other sibling blocks are tagged to coarsen as well.)

The items in the list need not be the same as the (required) Adapt : <criterion> : type parameter; they are solely used to identify and distinguish between different criteria in the simulation. This allows the user to use multiple criteria of the same type but with different parameters, e.g. “mask” with different masks:

Adapt {
   list = ["criterion_1", "criterion_2"];
   criterion_1 {
      type = "shock";
   }
   criterion_2 {
      type = "shear";
   }
}
Parameter:

Adapt : min_face_rank

Summary:

Minimum rank of Block faces to check for 2:1 refinement restriction

Type:

integer

Default:

0

Scope:

Cello

Many numerical methods require a 2:1 refinement restriction on adaptive meshes, such that no Block in level i is adjacent to another Block in a level j with |i - j|>1. This assumption may be required across corners and edges as well as 2D faces. This parameter specifies the minimum rank (dimensionality) of Block faces across which to enforce the 2:1 refinement restriction.

Parameter:

Adapt : <criterion> : field_list

Summary:

List of field the refinement criterion is applied to

Type:

[ string | list ( string ) ]

Default:

[] ( all fields )

Scope:

Cello

This parameter specifies the fields that the refinement criteria is applied to. For example, if type = “slope” and field_list = [“density”], then the “refine by slope” refinement criterion is applied to the density field.

Parameter:

Adapt : <criterion> : level_exponent

Summary:

Level exponent parameter

Type:

float

Default:

0.0

Scope:

Cello

Assumes:

<criterion> is of type “mass”

The level exponent parameter is used in the “mass” refinement criterion type only. It is used as a scaling factor for the refinement criteria for different mesh levels.

Parameter:

Adapt : <criterion> : max_coarsen

Summary:

Cutoff value for coarsening a block

Type:

[ float | list ( float ) ]

Default:

0.5*min_refine

Scope:

Cello

A block may coarsen if the refinement criterion applied to the block is smaller than this value everywhere in the block. A list is used for the “shock” refinement criterion type, in which case the first value is for pressure and the second is for the energy ratio.

Parameter:

Adapt : <criterion> : include_ghosts

Summary:

Whether to include ghost zones when applying the refinement criterion

Type:

logical

Default:

false

Scope:

Cello

When applying a mesh refinement criterion, this parameter specifies whether to apply it to ghost zones in the block as well as non-ghost zones.

Parameter:

Adapt : <criterion> : min_refine

Summary:

Cutoff value for refining a block

Type:

[ float | list ( float ) ]

Default:

0.3

Scope:

Cello

A block must refine if the refinement criterion applied to the block is larger than this value anywhere in the block. A list is used for the “shock” refinement criterion type, in which case the first value is for pressure and the second is for the energy ratio.

Parameter:

Adapt : <criterion> : output

Summary:

Name of a field in which to store the result of the refinement criterion

Type:

string

Default:

“”

Scope:

Cello

In addition to evolved field values, one may also output the refinement criteria. This may be useful for example for debugging or for finding appropriate values for :p:`max_coarsen and min_refine. A value of -1 specifies coarsening, +1 for refining, and 0 for staying the same.`

Parameter:

Adapt : <criterion> : max_level

Summary:

Maximum level to refine using this refinement criterion

Type:

integer

Default:

max (integer)

Scope:

Cello

Adapt will not refine past max_level when using this refinement criterion. Note if the global Adapt:max_level is smaller, than that takes precidence; also, another criterion may refine past this if both Adapt:max_level and Adapt : <criterion> : max_level for the other criterion are both larger.

Parameter:

Adapt : <criterion> : type

Summary:

Type of mesh refinement criteria

Type:

string

Default:

“unknown”

Scope:

Cello

Type of mesh refinement criteria. This is a required parameter, and must be one of “slope”, “shear”, “mask”, “mass”, “density”, “shock”, “particle_mass”, or “particle_count”.

Balance

Parameters for controlling dynamic load balancing are enclosed within the Balance group. Currently only one Balance parameter is available, which is used to control how frequently load balancing is performed.

Parameter:

Balance : schedule

Summary:

Scheduling parameters for dynamic load balancing

Type:

subgroup

Default:

none

Scope:

Cello

See the schedule subgroup for parameters used to define when to trigger the dynamic load balancing operation.

Boundary

Boundary group parameters define boundary conditions. For simple (non-mixed) boundary conditions, only the type parameter is required, e.g. Boundary { type = “periodic”; }. For more complicated boundary conditions, the list parameter is used to define Boundary subgroups, where each subgroup specifies boundary conditions for some subset of the domain. The axis and face parameters are available to restrict boundary conditions to a subset of faces, whereas the mask parameter is available for even finer control of mixed boundary conditions, which may be time-dependent. Inflow boundary conditions use the inflow parameter to specify field values at the boundary.

Parameter:

Boundary : list

Summary:

List of boundary condition subgroups

Type:

[ string | list ( string ) ]

Default:

[]

Scope:

Cello

For mixed boundary conditions, the list parameter specifies the list of names of subgroups that define boundary conditions on each portion of the domain boundary. Boundary conditions in each subgroup are applied in the order listed. In the example below, two subgroups “one” and “two” are defined, which specify reflecting boundary conditions along the x-axis and outflow boundary conditions along the y-axis:

Boundary {
   list = ["one", "two"];
   one {
      type = "reflecting";
      axis = "x";
   }
   two {
      type = "outflow";
      axis = "y";
   }
}
Parameter:

Boundary : <condition> : type

Summary:

Type of boundary condition

Type:

string

Default:

“undefined”

Scope:

Cello

Boundary conditions in Enzo-E include “reflecting” , “outflow” , “inflow” , and “periodic”. Other boundary condition types can be implemented by either a) modifying the existing EnzoBoundary class or b) creating a new class inherited from the Boundary base class. “inflow” boundary conditions additionally require inflow and field_list parameters.

Parameter:

Boundary : <condition> : axis

Summary:

Axis along which boundary conditions are to be enforced

Type:

string

Default:

“all”

Scope:

Cello

The axis parameter restricts the boundary conditions to the face orthogonal to the specified axis. axis must be “x” , “y” , “z” or “all”. The axis parameter may be used in conjunction with the face parameter, or by itself.

Parameter:

Boundary : <condition> : face

Summary:

Face along which boundary conditions are to be enforced

Type:

string

Default:

“all”

Scope:

Cello

The face parameter can restrict the boundary conditions to be applied only to the upper or lower faces. face orthogonal to the given face. face must be “upper” , “lower” or “all”. The face parameter may be used in conjunction with the axis parameter, or by itself.

Parameter:

Boundary : <condition> : mask

Summary:

Subregion in which boundary conditions are to be enforced

Type:

logical-expr

Default:

none

Scope:

Cello

The mask parameter specifies the subregion of the boundary on which to apply the boundary conditions. The logical expression may be a function of x, y, z, and t, and boundary conditions are restricted to where (and when) it evaluates to true:

Boundary {
   ...
   OUT {
      type = "outflow";
      mask = (x >= 4.0) ||
             (y >= 1.0 && (x >= 0.744017 + 11.547* t));
   }
}
Parameter:

Boundary : <condition> : inflow

Summary:

Value for inflow boundary conditions

Type:

float

Type:

float-expr

Type:

list ( float-expr [, logical-expr, float-expr [, … ] ] )

Default:

[]

Scope:

Cello

The inflow parameter is used to specify field values for inflow type boundary conditions. The inflow parameter is used in conjunction with the field_list parameter. inflow may be of type float, float-expr, or a list of alternating float-expr and logical-expr types. float-expr may be a function of x, y, z, and t. When a list is specified, the logical-expr is treated as a mask, similar to an ‘if-then-else’ clause

Boundary {
   ...
   VELOCITY_Y {
      type = "inflow";
      field_list = "velocity_y";
      inflow = [ -8.25*0.5,
                 ((x <= 0.166667) && (y <= 0.0) ) ||
                  (x <= 0.0) ||
                  ((x < 0.744017 + 11.547*t) && (y >= 1.0))
               ];
    }
}
Parameter:

Boundary : <condition> : field_list

Summary:

List of fields to apply boundary conditions to

Type:

list ( string )

Default:

[]

Scope:

Cello

The field_list parameter is used to restrict boundary conditions to the specified fields. An empty list, which is the default, is used to specify all fields.

Domain

Domain parameters specify the lower and upper extents of the computational domain, using the lower and upper parameters.

Parameter:

Domain : lower

Summary:

Lower domain extent

Type:

list ( float )

Default:

[0.0, 0.0, 0.0]

Scope:

Cello

Lower extent of the computational domain, [xmin], [ xmin, ymin], or [ xmin, ymin, zmin].

Parameter:

Domain : upper

Summary:

Upper domain extent

Type:

list ( float )

Default:

[1.0, 1.0, 1.0]

Scope:

Cello

Upper extent of the computational domain, [xmax], [ xmax, ymax], or [ xmax, ymax, zmax].

Field

Fields and their properties are defined using the Field parameter group. All fields must be explicitly defined using the list Field parameter, and must match the names expected by the respective Methods. Properties include the number of ghost zones, precision, and whether a field is centered or lies on some face, edge, or corner. Some performance-related parameters are available as well, including alignment in memory, and memory padding between fields.

Parameter:

Field : list

Summary:

List of fields

Type:

list ( string )

Default:

[]

Scope:

Cello

All fields must be explicitly listed in the list parameter. Field names depend on the Method(s) used; e.g., PPM uses “density”, “velocity_x”, “velocity_y”, “total_energy”, and “internal_energy”.

Parameter:

Field : gamma

Summary:

Adiabatic exponent

Type:

float

Default:

5.0 / 3.0

Scope:

Enzo

Todo:

perhaps move this to a different group, e.g. Physics

gamma specifies the ratio of specific heats for the ideal gas used by the PPM hydrodynamics solver.

Warning

This parameter is deprecated and will be removed in a future version. Going forward, pass this value to Physics:fluid_props:eos:gamma.

Parameter:

Field : alignment

Summary:

Force field data on each block to start on alignment bytes

Type:

integer

Default:

8

Scope:

Cello

Depending on the computer architecture, variables can be accessed from memory faster if they have at least 4-byte or 8-byte alignment. This parameter forces each field block array to have an address evenly divisible by the specified number of bytes.

Parameter:

Field : <field> : centering

Summary:

Specify the position of the given field variable within the computational cell.

Type:

list ( logical )

Default:

[ true, true, true ]

Scope:

Cello

By default, variables are centered within a computational cell. Some methods expect some variable, e.g. velocity components, to be positioned on a cell face. The effect of this parameter is to increase the dimension of the field block by one along each axis with a value of “false”. Numerical method implementations like PPML that assume (NX,NY,NZ) sized blocks even for offset variables, as opposed to e.g. (NX+1,NY,NZ), should still define the variable as centered.

Parameter:

Field : <field> : group_list

Summary:

Specify a list of groups that the Field belongs to

Type:

list ( string )

Default:

[ ]

Scope:

Cello

Different Fields may belong to any number of different “groups”. For example, Enzo uses “color fields”, which Enzo-E implements as defining color fields to belong to the group “color”.

Parameter:

Field : ghost_depth

Summary:

Field ghost zone depths

Type:

[ integer | list ( integer ) ]

Default:

[ 0, 0, 0 ]

Scope:

Cello

The default storage patch / block ghost zone depths [gx, gy, gz] along each axis for fields. If an integer, then the same ghost zone depth is used for each axis. Currently this value needs to be 4 for PPM when AMR is used.

Parameter:

Field : padding

Summary:

Add padding of the specified number of bytes between fields on each block.

Type:

integer

Default:

0

Scope:

Cello

If block sizes are large and a power of two, and if the computer’s cache has low associativity, performance can suffer due to cache thrashing. This can be avoided by introducing padding between fields. A value of twice the cache line width is recommended. Since field blocks are usually small, this should not usually be an issue.

Parameter:

Field : precision

Summary:

Default field precision

Type:

string

Default:

“default”

Scope:

Cello

Default precision for all fields. Supported precisions include “single” (32-bit) and “double” (64-bit). “quadruple” is accepted, but not implemented by most numerical methods (e.g. PPM). “default” is for compatibility with Enzo, and corresponds to either “single” or “double” depending on the CELLO_PREC configuration flag setting. This precision parameter must not conflict with the CELLO_PREC setting.

Parameter:

Field : prolong

Summary:

Type of prolongation (interpolation)

Type:

string

Default:

“linear”

Scope:

Cello

For adaptive mesh refinement, field values may need to be transferred from coarser to finer blocks, either from coarse neighbor blocks in the refresh phase, or to fine child blocks during refinement in the adapt phase. Valid values include “linear” ; other values accepted but not implemented include “enzo” and “MC1” :e:` ; which are unfinished implementations of Enzo’s` “InterpolationMethod” functionality.

Parameter:

Field : restrict

Summary:

Type of restriction (coarsening)

Type:

string

Default:

“linear”

Scope:

Cello

For adaptive mesh refinement, field values may need to be transferred from finer to coarser blocks, either from fine neighbor blocks in the refresh phase, or to the parent block during coarsening in the adapt phase. Valid values include “linear” ; ;other values accepted but not implemented include “enzo”.

Parameter:

Field : history

Summary:

How many generations of “old” fields to maintain

Type:

integer

Default:

0

Scope:

Cello

Many problems may require field values from the previous timestep, e.g. for flux-correction, updating particles, etc. Cello supports this by allowing one or more generations of all fields to be stored and maintained. The default is 0, though 1 may be fairly common, and even more generations are supported if needed.

Group

The Group parameter group is used to differentiate between different types of Field’s and Particles. For example, field groups may include “color” and “temporary”, and particle groups may include “dark_matter” and “star”.

Group {

   list = ["color", "temporary"];

   color {
      field_list = ["species_HI", "species_HII" ];
   }

   temporary {
      field_list = ["pressure", "temperature"];
   }

}

Field and Particle groups can analogously be defined in the respective Field and Particle parameter groups:

Field {

   list = ["density", "velocity_x", "species_HI"];

   species_HI {

      group_list = ["temporary"];

   }

}

Groups allow Cello applications to differentiate between these different types of fields and particles using the Grouping class (see src/Cello/data_Grouping.?pp).

Parameter:

Group : list

Summary:

List of groups

Type:

list ( string )

Default:

[]

Scope:

Cello

This parameter defines all groups.

Parameter:

Group : <group> : field_list

Summary:

List of fields belonging to the group

Type:

list ( string )

Default:

[]

Scope:

Cello

This parameter is used to assign fields to a given group.

Parameter:

Group : <group> : particle_list

Summary:

List of particle types belonging to the group

Type:

list ( string )

Default:

[]

Scope:

Cello

This parameter is used to assign particle groups to a given group.

Initial

The Initial group is used to specify initial conditions. cycle specifies the initial cycle number (usually 0), list specifies a list of initial conditions, which may include "value" for initializing fields directly, or other problem-specific initial condition generators.

Parameter:

Initial : cycle

Summary:

Initial cycle number

Type:

list ( integer )

Default:

0

Scope:

Cello

Initial value for the cycle number.

Parameter:

Initial : time

Summary:

Initial time

Type:

float

Default:

0.0

Scope:

Cello

Initial time in code units.

Parameter:

Initial : restart

Summary:

Set to true to restart from a checkpoint directory created by the “check” method

Type:

bool

Default:

false

Scope:

Cello

Restart the simulation to continue a previous run from a saved checkpoint. If true, the restart directory must be specified using the “restart_dir” parameter.

Parameter:

Initial : restart_dir

Summary:

Directory containing restart files from a checkpoint created using the “check” method

Type:

string

Default:

none

Scope:

Cello

When restarting a simulation from a “check” checkpoint directory, this parameter must specify the path to that directory.

value

Parameter:

Initial : value : <field> :

Summary:

Initialize field values

Type:

list ( float-expr, [ logical-expr, float-expr, [ … ] ] )

Default:

[]

Scope:

Cello

This initialization approach allows initializing field values directly. The first element of the list must be a float expression, and may include arithmetic operators, variables “x”, “y”, “z”, and most functions in the POSIX math library /include/math.h. The second optional list element is a logical expression, and serves as a “mask” of the domain. The third float expression parameter is required if a mask is supplied, and serves as the “else” case. Multiple such mask-value pairs may be used. For example:

Initial {

   list = ["value"];

   value {
      density = [ sin ( x + y ), x - y < 0.0, 1.0 ];
   }
}

is read as “Set the density field equal to sin ( x + y ) wherever x - y < 0.0 , otherwise set to 1.0 “.

accretion_test

The accretion_test Initial subgroup is used to initialize an accretion test problem. In particular, it initializes a single sink particle with a given initial mass, position, and velocity, in a background medium with constant density and pressure, and (possibly) an initial velocity field with constant magnitude, directed towards the sink particle’s initial position. Running this test problem requires the use of the “mhd_vlct”, “pm_update”, “merge_sinks”, and “accretion” methods. One can then test the accretion method by checking whether mass and momentum are conserved in this problem.

This initializer requires periodic boundary conditions, and three spatial dimensions.

Note: sink particles must have a "mass" attribute if this initializer is used.

Parameter:

Initial : accretion : sink_mass

Summary:

The initial mass of the sink particle.

Type:

float

Default:

0.0

Scope:

Enzo

The initial mass of the sink particle

Parameter:

Initial : accretion : sink_position

Summary:

The initial position of the sink particle.

Type:

list ( float )

Default:

[0.0,0.0,0.0]

Scope:

Enzo

The initial (3D) position of the sink particle

Parameter:

Initial : accretion : sink_velocity

Summary:

The initial velocity of the sink particle.

Type:

list ( float )

Default:

[0.0,0.0,0.0]

Scope:

Enzo

The initial (3D) velocity of the sink particle

Parameter:

Initial : accretion : gas_density

Summary:

The initial uniform density of the gas.

Type:

float

Default:

1.0e-6

Scope:

Enzo

The initial uniform density of the gas.

Parameter:

Initial : accretion : gas_pressure

Summary:

The initial uniform pressure of the gas.

Type:

float

Default:

1.0e-6

Scope:

Enzo

The initial uniform pressure of the gas.

Parameter:

Initial : accretion : gas_radial_velocity

Summary:

The (inwards) radial velocity of the gas, with respect to the initial sink particle position.

Type:

float

Default:

0.0

Scope:

Enzo

The gas velocity in every cell with have magnitude equal to the value of this parameter, directed towards the initial sink particle position.

bb_test

The bb_test Initial subgroup is used to initialize a “BB Test” problem, as described in Federrath et al 2010, ApJ, 713, 269. In particular, it initializes an isothermal sphere of gas with, with the gas having a constant (small) “external density” outside of the truncation radius. Within the truncation radius, the gas density has the following form:

\(\rho(\phi) = \rho_0 (1 + A \cos(2 \phi)),\)

where \(\rho\) is the gas density, \(\phi\) is the azimuthal angle in the spherical polar coordinate system, \(\rho_0\) is the mean density and \(A\) is the (small) fluctuation amplitude. The gas rotates around the z-axis as a solid-body, with an optional additional uniform “drift velocity”.

Running this test problem requires the use of the "pm_deposit", "gravity", "mhd_vlct", "sink_maker", and "pm_update" methods.

This initializer requires periodic boundary conditions, three spatial dimensions, and that the gas adiabatic index ("Field:gamma") is between 1.0 and 1.000001.

The following fields are required, and must be specified in the input parameter file: "density", "density_total", "density_particle", "density_particle_accumulate", "density_gas", "particle_mass", "potential", "potential_temp", "potential_copy", "total_energy", "pressure", "acceleration_x", "acceleration_y", "acceleration_z", "velocity_x", "velocity_y", "velocity_z", "X", "X_copy", "B", "B_copy", "density_source", "density_source_accumulate", "mom_dens_x_source", "mom_dens_x_source_accumulate", "mom_dens_y_source", "mom_dens_y_source_accumulate", "mom_dens_z_source", and "mom_dens_z_source_accumulate".

Sink particles must have the following attributes: "mass", "x", "y", "z", "vx", "vy", "vz", and "is_copy". These must all be of type "default", except for "is_copy", which should be of type "int64".

Sink particles must be in the "is_gravitating" particle group.

Parameter:

Initial : bb_test : center

Summary:

The coordinates of the center of the sphere.

Type:

list (float)

Default:

[0.0,0.0,0.0]

Scope:

Enzo

The coordinates of the center of the sphere.

Parameter:

Initial : bb_test : drift_velocity

Summary:

The initial additional uniform velocity of the gas.

Type:

list (float)

Default:

[0.0,0.0,0.0]

Scope:

Enzo

The initial additional uniform velocity of the gas. Inside the truncation radius, the initial gas velocity will be determined by solid body rotation, plus this additional velocity. Outside the truncation radius, the gas velocity is just this velocity.

Parameter:

Initial : bb_test : truncation_radius

Summary:

The truncation radius of the sphere.

Type:

float

Default:

1.0

Scope:

Enzo

The truncation radius of the isothermal sphere. Within this radius, the gas density is determined by the azimuthal angle; outside of this radius, it is equal to “external_density”.

Parameter:

Initial : bb_test : nominal_sound_speed

Summary:

The nominal uniform sound speed of the gas.

Type:

float

Default:

1.0

Scope:

Enzo

Nominal uniform sound speed of the gas used to initialise the total specific energy. In practice the actual sound speed will be different since the adiabatic index is not exactly 1.

Parameter:

Initial : bb_test : fluctuation_amplitude

Summary:

The amplitude of the density fluctuation which determines the initial gas density.

Type:

float

Default:

0.0

Scope:

Enzo

Within the truncation radius, the gas density has the following form:

\(\rho(\phi) = \rho_0 (1 + A \cos(2 \phi)),\)

where \(\rho\) is the gas density, \(\phi\) is the azimuthal angle in the spherical polar coordinate system, \(\rho_0\) is the mean density and \(A\) is the fluctuation amplitude.

Parameter:

Initial : bb_test : external_density

Summary:

The gas density outside of the truncation radius.

Type:

float

Default:

1.0e-6

Scope:

Enzo

The gas density outside of the truncation radius. Should be set to something much smaller than the mean gas density inside the truncation radius.

Parameter:

Initial : bb_test : mean_density

Summary:

The mean gas density inside the truncation radius.

Type:

float

Default:

1.0e-6

Scope:

Enzo

The mean gas density inside the truncation radius.

Parameter:

Initial : bb_test : angular_rotation_velocity

Summary:

The angular rotation velocity of gas inside the truncation radius in radians per second.

Type:

float

Default:

0.0

Scope:

Enzo

Inside the truncation radius, the gas rotates as a solid body around the z-axis. This parameter determines the angular rotation velocity in units of radians per second.

cloud

The cloud Initial subgroup is used to setup a Spherical cloud embedded in a hot wind. The cloud and wind are assumed to be in pressure equilibrium with one another.

The presence of (or lack thereof) the “bfield_x”, “bfield_y”, and “bfield_z” fields indicate whether the setup is purely hydrodynamic or involves magnetic fields. Presently, only uniform magnetic fields are supported if they are constant across the entire domain. The values of the magnetic fields are specified in one of 2 ways:

  1. If the uniform_bfield parameter is passed a list of 3 floats, the first, second, and third entries are used to initilize the x, y, and z componentents of a uniform magnetic field. If the “bfieldi_x”, “bfieldi_y”, and “bfieldi_z” face-centered fields are defined, then they will be correctly initialized for use with the VL+CT integrator.

  2. (Deprecated) If the uniform_bfield parameter is not specified (or is passed a list containing 0 entries), then the cell-centered magnetic fields are assumed to have been initialized by another Initial subgroup (e.g. value) prior to the call of this subgroup.

The initial density of a cell (from a uniform-resolution mesh) is initialized to \(f_{V} \rho_{\rm cl} \delta + (1 - f_{\rm V})\rho_{\rm w}\), where \(f_{V}\) is the fraction of the cell’s volume enclosed by the cloud (estimated by subsampling) and \(\delta\) is nominally 1. Machinery is provided to optionally produce perturbations to break symmetries in the initial density distribution. When this machinery is used, \(\delta\) is randomly drawn from a truncated Gaussian with \(\mu=1\). Pressure equilibria is maintained when this machinery is used.

Parameter:

Initial : cloud : subsample_n

Summary:

Determines the subsampling resolution

Type:

integer

Default:

0

Scope:

Enzo

Subsampling is used to initialize the fields in regions of overlap between the cloud and the wind. For cells in this region, the fraction of the volume enclosed by the cloud is estimated by subdividing a cell into \(2^n\) subcells along each axis (a value of 0, corresponds to no subsampling. The average density of the cells in this region are volume weighted and the average velocities are mass weighted. The total energy in a cell is currently computed by assuming constant internal energy density throughout the grid and using the average velocities and densities (and, if applicable, the magnetic fields).

Parameter:

Initial : cloud : cloud_radius

Summary:

Initial radius of the spherical cloud

Type:

float

Default:

none

Scope:

Enzo

This must be a positive value.

Parameter:

Initial : cloud : cloud_center_x

Summary:

x coordinate of the cloud center

Type:

float

Default:

0.0

Scope:

Enzo

Parameter:

Initial : cloud : cloud_center_y

Summary:

y coordinate of the cloud center

Type:

float

Default:

0.0

Scope:

Enzo

Parameter:

Initial : cloud : cloud_center_z

Summary:

z coordinate of the cloud center

Type:

float

Default:

0.0

Scope:

Enzo

Parameter:

Initial : cloud : cloud_density

Summary:

initial mass density of the cloud

Type:

float

Default:

none

Scope:

Enzo

This must be a positive value.

Parameter:

Initial : cloud : metal_mass_frac

Summary:

initial fraction of the mass density contributed by metals

Type:

float

Default:

0.0

Scope:

Enzo

If the ` `”metal_density_frac”`` field exists and is registered as a member of the ` `”colour”`` group, then the field is initialized by multiplying this value by the "density" field (this is done everywhere, regardless of proximity to the cloud center). Under these circumstances, this must have a positive value.

Parameter:

Initial : cloud : uniform_bfield

Summary:

initial uniform magnetic field values

Type:

list ( float )

Default:

[ ]

Scope:

Enzo

If specified, provides the values of the components of the initial magnetic field that are uniform throughout the entire domain. When employed this MUST have 3 entries. This will also initialize the face-centered fields magnetic fields (in addition to the cell-centered fields) if the appropriate fields have been defined. When this is not specified (i.e., when this has a list of 0 entries), the magnetic fields are assumed to have been pre-initialized by a separate problem initializer prior to the execution of the cloud initializer.

Parameter:

Initial : cloud : wind_density

Summary:

initial mass density of the wind

Type:

float

Default:

none

Scope:

Enzo

This must be a positive value.

Parameter:

Initial : cloud : wind_velocity

Summary:

initial velocity of the wind along the x-axis

Type:

float

Default:

0.0

Scope:

Enzo

Parameter:

Initial : cloud : wind_total_energy

Summary:

initial specific total energy of the wind

Type:

float

Default:

none

Scope:

Enzo

This must be a positive value.

Parameter:

Initial : cloud : wind_internal_energy

Summary:

initial specific internal energy of the wind

Type:

float

Default:

0

Scope:

Enzo

If the "internal_energy" field is defined, then this must be a positive value. In this case, the value is also used to help initialize the "total_energy" field for cells that overlap with the cloud. However, if the "internal_energy" field is not defined, then this must not have a specified value (i.e. it must have a value of 0).

Parameter:

Initial : cloud : perturb_standard_deviation

Summary:

standard deviation used for perturbations

Type:

float

Default:

0

Scope:

Enzo

This must be either 0 or a positive value. In the former case, the perturbation machinery is not used. In the latter case, it gives the standard deviation of the truncated gaussian for truncation (technically, it’s the standard deviation of the gaussian before truncation).

Parameter:

Initial : cloud : perturb_truncation_deviation

Summary:

number of deviation where perturbation gaussian is truncated

Type:

float

Default:

0

Scope:

Enzo

Meaningless unless Initial:cloud:perturb_standard_deviation is positive. This must be either 0 or a positive value. In the former case, the gaussian is not truncated (nominally allowing the possibility of negative values). In the latter case, this determines the number of standard deviations from the mean at which the gaussian should be truncated.

Parameter:

Initial : cloud : perturb_seed

Summary:

Seeds the perturbations to cloud density

Type:

integer

Default:

0

Scope:

Enzo

This must be a zero or larger. Meaningless unless Initial:cloud:perturb_standard_deviation is positive.

Warning

Due to reliance on std::normal_distribution the perturbations are not currently guaranteed to be the same (when the seed is the same) for different compilers or versions of the c++ standard library.

Changes in the grid resolution, domain size, way that mesh is divided across root blocks, or ghost depth will also affect the perturbations.

Parameter:

Initial : cloud : wind_total_energy

Summary:

initial specific total energy of the wind

Type:

float

Default:

none

Scope:

Enzo

This must be a positive value.

inclined_wave

The inclined_wave Initial subgroup is used to setup a HD, MHD, or Jeans wave at an angle inclined to the simulation domain for testing HD/MHD integrators. If applicable, magnetic fields fields are set to zero when a HD wave is initialized.

The initialization procedure was adopted from Gardiner & Stone (2008) . Specifically, a coordinate system “x0”, “x1”, “x2” is defined and the wave is initialized to travel along “x0”. The transformation between “x”, “y”, “z” and “x0”, “x1”, “x2”, is determined by the values of the alpha and beta parameters. They are explicitly related by

\[\begin{split}x &= x_0\cos\alpha\cos\beta - x_1\sin\beta - x_2\sin \alpha \cos \beta \\ y &= x_0\cos\alpha\sin\beta + x_1\cos\beta - x_2\sin \alpha \sin \beta \\ z &= x_0\sin\alpha + x_2 \cos\alpha\end{split}\]

As in that paper, non-zero magnetic fields are initialized using the vector potential to ensure that they are divergence-free.

Parameter:

Initial : inclined_wave : alpha

Summary:

Angle used to help determine wave inclination

Type:

float

Default:

0

Scope:

Enzo

The angle is assumed to have units of radians.

Parameter:

Initial : inclined_wave : beta

Summary:

Angle used to help determine wave inclination

Type:

float

Default:

0

Scope:

Enzo

The angle is assumed to have units of radians.

Parameter:

Initial : inclined_wave : wave_type

Summary:

Specifies the type of wave to initialize.

Type:

string

Default:

alfven

Scope:

Enzo

This value specifies the type of wave to initialize. We have provided more details about each option down below. Note, when using an MHD solver with a non-MHD wave, the mangetic fields are uniformly initialized to zero.

Hydro Waves

The values used to initialize hydrodynamical linear waves are taken from the columns of the matrix given in equation B3 of Stone et al. (2008) . Valid hydrodynamical waves include:

  • "sound" A linear sound wave.

  • "hd_entropy" A linear HD entropy wave with perturbations in v0 (velocity along the “x0”-axis).

  • "hd_transv_entropy_v1" A linear HD entropy wave with perturbations in velocity component v1 (transverse to the direction of bulk motion).

  • "hd_transv_entropy_v2" A linear HD entropy wave with perturbations in velocity component v2 (transverse to the direction of bulk motion).

MHD Waves

Each of the valid MHD waves are described in Gardiner & Stone (2008) . Valid MHD wave types include:

  • "alfven" A linear Alfven wave with perturbations to the magnetic field along the “x2”-axis.

  • "circ_alfven" A traveling circularly polarized Alfven wave.

  • "mhd_entropy" A linear MHD entropy wave.

  • "fast" A linear fast magnetosonic wave.

  • "slow" A linear slow magnetosonic wave.

Jeans Wave

To initialize a Jeans wave, set this parameter to "jeans". We use equations consistent with what Athena and (earlier versions of) Athena++ use. In detail, we use:

\[\begin{split}\rho &= \rho_{\rm bkg} \left( 1 + A \sin\left(\frac{2\pi}{\lambda} x_0 \right) \right) \\ \rho v_0 &= \rho_{\rm bkg} \frac{\sqrt{|\omega^2|}}{2\pi / \lambda} A \begin{cases} 0 & \omega^2 > 0 \\ \cos\left(\frac{2\pi}{\lambda} x_0 \right) & \omega^2 < 0 \\ \end{cases} \\ v_1 &= 0 \\ v_2 &= 0 \\ \rho E &= \frac{P_{\rm bkg}}{\gamma - 1} + \gamma A \sin\left(\frac{2\pi}{\lambda} x_0\right) \\\end{split}\]

in which:

  • \(E\) specifies the specific internal energy

  • \(\gamma\) is the adiabatic index.

  • \(A\) is the amplitude, specified by Initial:inclined_wave:amplitude and \(\lambda\) is the wavelength, specified by Initial:inclined_wave:lambda

  • \(\rho_{\rm bkg}=1\) and \(P_{\rm bkg}=1/\gamma\) in the appropriate code units

  • \(\omega^2=(2\pi c_{s,{\rm bkg}}/ \lambda)^2 (1 - (\lambda/\lambda_J)^2)\) is the dispersion relation. In this equation, \(c_{s,{\rm bkg}}^2=\gamma P_{\rm bkg}/\rho_{\rm bkg}\) and \(\lambda_J = c_{s,{\rm bkg}} \sqrt{\pi / (G \rho_{\rm bkg})}\). Note that the value of \(G\) is directly set by Method:gravity:grav_const.

Parameter:

Initial : inclined_wave : amplitude

Summary:

Sets the amplitudes of the waves.

Type:

float

Default:

1.e-6

Scope:

Enzo

This must be a positive value. This has no effect for the circularly polarized Alfven wave (for that case, amplitude is fixed at 0.1).

Parameter:

Initial : inclined_wave : lambda

Summary:

The wavelength of the wave.

Type:

float

Default:

1.

Scope:

Enzo

This must be a positive value.

Parameter:

Initial : inclined_wave : positive_vel

Summary:

Sets the sign of the wave speed.

Type:

logical

Default:

true

Scope:

Enzo

Do not specify this parameter when initializing a circularly polarized Alfven wave or a Jeans wave. This is ignored for linear HD entropy waves when Initial:inclined_wave:parallel_vel is specified.

Parameter:

Initial : inclined_wave : parallel_vel

Summary:

optionally sets the background velocity for HD waves

Type:

float

Default:

none

Scope:

Enzo

This can be used to specify a background velocity along v0 for HD linear waves. At present, this parameter should only be specified for the hydrodynamic waves.

merge_sinks_test

The merge_sinks_test Initial subgroup is used to read and initialise particle data from a text file. It is designed to be run with a small number of particles, in order to check conservation of mass and momentum (and potentially other quantities) when running with the “merge_sinks” method. The data are assumed to be arranged into seven columns, corresponding to mass, the x,y,z coordinates and the x,y,z-components of velocity, respectively. Each row corresponds to one sink particle.

Note: sink particles must have a "mass" attribute if this initializer is used.

Parameter:

Initial : merge_sinks_test : particle_data_filename

Summary:

Name of the file to read from.

Type:

string

Default:

none

Scope:

Enzo

Must point to a valid text file, with data arranged in seven columns seperated by blank space

music

The music Initial subgroup is used to read block data from HDF5 files generated by MUSIC initial conditions generator. Parameters are used to specify the HDF5 files to read from, the names of the HDF5 datasets, what type of data the datasets contain ("field" or "particle"), field or particle names, and particle attributes. Additionally, a coords parameter is used to specify the axis ordering used. The music group has its own list parameter, one for each field or particle type and attribute.

The following example reads the "density" field from "GridDensity" file, and the "dark" particle "position_x" attributes from the "ParticleDisplacements_x" file:

Initial {

  list = ["music"];
  music {

     file_list = ["FD","PX"];
     FD {
       type      = "field";
       name      = "density";
       coords    = ".zyx";
       file      = "GridDensity";
       dataset   = "GridDensity";
     }
     PX {
       type      = "particle";
       name      = "dark";
       coords    = ".zyx";
       attribute = "position_x";
       file      = "ParticleDisplacements_x";
       dataset   = "ParticleDisplacements_x";
     }
  }
}
Parameter:

Initial : music : list

Summary:

Name of the HDF5 to read from

Type:

string

Default:

none

Scope:

Enzo

List of file identifiers, one for each field or particle type+attribute.

Parameter:

Initial : music : <file> : type

Summary:

Type of data to read in

Type:

string

Default:

none

Scope:

Enzo

Type of data to read in, either “field” or “particle”.

Parameter:

Initial : music : <file> : file

Summary:

Name of the HDF5 file to read from

Type:

string

Default:

none

Scope:

Enzo

Name of the HDF5 file to read from.

Parameter:

Initial : music : <file> : dataset

Summary:

Name of the dataset to read from the the HDF5 file

Type:

string

Default:

none

Scope:

Enzo

Name of the dataset to read from the the HDF5 file.

Parameter:

Initial : music : <file> : name

Summary:

Name of the field or particle type

Type:

string

Default:

none

Scope:

Enzo

Name of the field or particle type.

Parameter:

Initial : music : <file> : attribute

Summary:

Name of the particle attribute to initialize

Type:

string

Default:

none

Scope:

Enzo

Name of the particle attribute to initialize..

Parameter:

Initial : music : <file> : coords

Summary:

Ordering of axes in the HDF5 file

Type:

string

Default:

“zyx”

Scope:

Enzo

String defining the axis ordering of ‘x’, ‘y’, and ‘z’ in the HDF5 file. For MUSIC initial conditions, which may have 4D datasets, “tzyx” can be used, where “t” is ignored and can be any character other than ‘x’, ‘y’, or ‘z’.

sedov

Parameter:

Initial : sedov : array

Summary:

Size of array of Sedov blasts

Type:

list ( integer )

Default:

[ 1, 1, 1 ]

Scope:

Enzo

This parameter defines the size of the array of Sedov blast waves. The default is a single blast.

Parameter:

Initial : sedov : radius_relative

Summary:

Initial radius of the Sedov blast

Type:

float

Default:

0.1

Scope:

Enzo

Todo:

write

Parameter:

Initial : sedov : pressure_in

Summary:

Pressure inside the Sedov blast

Type:

float

Default:

1.0

Scope:

Enzo

Todo:

write

Parameter:

Initial : sedov : pressure_out

Summary:

Pressure outside the Sedov blast

Type:

float

Default:

1.0e-5

Scope:

Enzo

Todo:

write

Parameter:

Initial : sedov : density

Summary:

Density for the Sedov blast array problem

Type:

float

Default:

1.0

Scope:

Enzo

Todo:

write

shock_tube

The shock_tube Initial subgroup is used to setup axis-aligned shock tube test problems.

Generically, a shock tube get’s set up to evolve along an axis given by the value of aligned_ax. The discontinuity is always placed at 0.5 along that axis (typically the domain should extend from 0.0 to 1.0).

Parameter:

Initial : shock_tube : setup_name

Summary:

Specifies the name of the shock tube problem to setup.

Type:

string

Default:

none

Scope:

Enzo

Valid shock tube problems include:

  • "rj2a" An MHD shock tube problem illustrated in Figure 2a of Ryu & Jones (1995) . The initialization assumes that the adiabatic index is 5/3.

  • "sod" The hydrodynamical Sod shock tube test problem. The canonical adiabatic is 1.4 (although this is not required).

Parameter:

Initial : shock_tube : aligned_ax

Summary:

Specify the axis along which the shock tube evolves along.

Type:

string

Default:

x

Scope:

Enzo

Allowed values are "x" , "y" , or "z" .

Parameter:

Initial : shock_tube : axis_velocity

Summary:

Value to add to velocity component along aligned_ax

Type:

float

Default:

0.

Scope:

Enzo

This value is added throughout the entire domain.

Parameter:

Initial : shock_tube : transverse_velocity

Summary:

Value to add to a velocity component perpendicular to aligned_ax

Type:

float

Default:

0.

Scope:

Enzo

This value is added throughout the entire domain. If aligned_ax is "x" , "y" , or "z" , then this value is added to the "velocity_y" , "velocity_z" , or "velocity_z" field.

Parameter:

Initial : shock_tube : flip_initialize

Summary:

Whether to mirror the initial condition across the discontinuity

Type:

logical

Default:

false

Scope:

Enzo

When this is "true" the entire setup is mirrored across the discontinuity. Basically the left and right states are swapped AND all components of the magnetic field and velocity (including contributions from axis_velocity and transverse_velocity) are multiplied by -1.

shu_collapse

The shu_collapse Initial subgroup is used to initialize a Shu Collapse problem, as described in Federrath et al 2010, ApJ, 713, 269. In particular, it initializes a gravitationally unstable isothermal sphere of gas with an inverse-square density profile, with an optional uniform “drift velocity”, and an optional sink particle at the center of the domain.

Running this test problem requires the use of the "pm_deposit", "gravity", "mhd_vlct", "sink_maker", and "pm_update" methods.

This initializer requires periodic boundary conditions, three spatial dimensions, and that the gas adiabatic index ("Field:gamma") is between 1.0 and 1.000001.

The following fields are required, and must be specified in the input parameter file: "density", "density_total", "density_particle", "density_particle_accumulate", "density_gas", "particle_mass", "potential", "potential_temp", "potential_copy", "total_energy", "pressure", "acceleration_x", "acceleration_y", "acceleration_z", "velocity_x", "velocity_y", "velocity_z", "X", "X_copy", "B", "B_copy", "density_source", "density_source_accumulate", "mom_dens_x_source", "mom_dens_x_source_accumulate", "mom_dens_y_source", "mom_dens_y_source_accumulate", "mom_dens_z_source", and "mom_dens_z_source_accumulate".

Sink particles must have the following attributes: "mass", "x", "y", "z", "vx", "vy", "vz", and "is_copy". These must all be of type "default", except for "is_copy", which should be of type "int64".

Sink particles must be in the "is_gravitating" particle group.

Parameter:

Initial : shu_collapse : center

Summary:

The coordinates of the center of the collapse.

Type:

list (float)

Default:

[0.0,0.0,0.0]

Scope:

Enzo

The coordinates of the center of the sphere.

Parameter:

Initial : shu_collapse : drift_velocity

Summary:

The initial uniform velocity of the gas.

Type:

list (float)

Default:

[0.0,0.0,0.0]

Scope:

Enzo

The initial uniform velocity of the gas.

Parameter:

Initial : shu_collapse : truncation_radius

Summary:

The truncation radius of the isothermal sphere.

Type:

float

Default:

1.0

Scope:

Enzo

The truncation radius of the isothermal sphere. Within this radius, the gas has an inverse square density profile; outside of this radius, the gas density is determined by “external_density”. Value must be at most a quarter of the domain width..

Parameter:

Initial : shu_collapse : nominal_sound_speed

Summary:

The nominal uniform sound speed of the gas.

Type:

float

Default:

1.0

Scope:

Enzo

Nominal uniform sound speed of the gas used to initialise the total specific energy. In practice the actual sound speed will be different since the adiabatic index is not exactly 1.

Parameter:

Initial : shu_collapse : instability_parameter

Summary:

The instability parameter which determines the gas density profile.

Type:

float

Default:

2.1

Scope:

Enzo

Instability parameter - sphere is gravitationally unstable if this is greater than 2.0. Determines density profile according to \(\rho(r) = \frac{A c_s^2}{4 \pi G r^2}\), where \(rho\) is the gas density, r is the distance from the center of the sphere, \(A\) is the instability parameter, \(c_s\) is the nominal sound speed, and \(G\) is the gravitational constant.

Parameter:

Initial : shu_collapse : external_density

Summary:

The gas density outside of the truncation radius.

Type:

float

Default:

1.0e-6

Scope:

Enzo

The gas density outside of the truncation radius. Should be set to something much smaller than the gas density just inside the truncation radius.

Parameter:

Initial : shu_collapse : central_sink_exists

Summary:

Controls whether a sink particle is placed at the center in the initial conditions.

Type:

logical

Default:

false

Scope:

Enzo

If true, a sink particle is initialised with position at the center of the sphere, and velocity equal to “drift_velocity”. Its mass is determined by “central_sink_mass”.

Parameter:

Initial : shu_collapse : central_sink_mass

Summary:

The mass of the central sink particle, if it exists.

Type:

float

Default:

0.0

Scope:

Enzo

If “central_sink_exists” is true, this determines the mass of the central sink particle. If false, this parameter is ignored.

turbulence

Parameter:

Initial : turbulence : density

Summary:

Initial density for turbulence initialization and method

Type:

float

Default:

1.0

Scope:

Enzo

Initial density for initializing the turbulence problem.

Parameter:

Initial : turbulence : pressure

Summary:

Initial pressure for turbulence initialization and method

Type:

float

Default:

0.0

Scope:

Enzo

Initial pressure for initializing the turbulence problem. Default is 0.0, meaning it is not used. Either pressure or temperature should be defined, but not both.

Parameter:

Initial : turbulence : temperature

Summary:

Initial temperature for turbulence initialization and method

Type:

float

Default:

0.0

Scope:

Enzo

Initial temperature for initializing the turbulence problem. Default is 0.0, meaning it is not used. Either pressure or temperature should be defined, but not both.

vlct_bfield

This is used to compute the cell-centered magnetic field for the VL + CT MHD method. This initializer can be utilized in 2 ways:

  1. Components of the vector potential ("Ax", "Ay", "Az") can be specified as parameters of the subgroup (functions can be specified for each component in the same way as functions are specified for the value subgroup. The initializer operates in this mode as long as the values for one of the components of the vector potential is specified (any unspecified components are assumed to be zero everywhere). In this mode, both the cell-centered and face-centered magnetic field values get specified.

  2. Initialize the cell-centered values of the magnetic fields after after another Initial subgroup (e.g. the value subgroup) has already to specified the face-centered magnetic fields ("bfieldi_x", "bfieldi_y", "bfieldi_z"). The cell-centered value is just the average of the corresponding face-centered component. The initializer operates in this mode if none of the components of the vector potential have specified values. (To properly specify use this mode, specify "vlct_bfield" in the Initial:list parameter list following the name of the Initial subgroup used to setup the face-centered values.

In both modes, the option to update partially initialized "total_energy" fields with the specific magnetic energy computed from the newly computed cell-centered bfields and pre-initialized "density" fields.

It might be nice to eventually generalize this initializer to be able to initialize cell-centered B-fields from vector potentials for MHD integrators that don’t require face-centered B-fields

Parameter:

Initial : value : update_etot :

Summary:

update total energy with the initialized magnetic fields

Type:

logical

Default:

false

Scope:

Enzo

If true, then the calculated cell-centered magnetic fields are used to update the specific total energy. This requires that the "total_energy" field has already been partially initialized (it just doesn’t include the specific magnetic energy), and that the "density" field has been initialized.

Parameter:

Initial : value : Ax :

Summary:

Expression for the x-component of the magnetic vector potential

Type:

list ( float-expr, [ logical-expr, float-expr, [ … ] ] )

Default:

[]

Scope:

Enzo

This parameter allows for the direct specification of the x-component of the magnetic vector potential (which will be used to compute magnetic fields). The arguements for this parameter follow the same sets of rules as the parameters of Initial:value. If this parameter is not specified, but the values of the other components of the magnetic vector potential are, then this component is assumed to be zero everywhere.

Parameter:

Initial : value : Ay :

Summary:

Expression for the y-component of the magnetic vector potential

Type:

list ( float-expr, [ logical-expr, float-expr, [ … ] ] )

Default:

[]

Scope:

Enzo

This parameter allows for the direct specification of the y-component of the magnetic vector potential (which will be used to compute magnetic fields). The arguements for this parameter follow the same sets of rules as the parameters of Initial:value. If this parameter is not specified, but the values of the other components of the magnetic vector potential are, then this component is assumed to be zero everywhere.

Parameter:

Initial : value : Az :

Summary:

Expression for the z-component of the magnetic vector potential

Type:

list ( float-expr, [ logical-expr, float-expr, [ … ] ] )

Default:

[]

Scope:

Enzo

This parameter allows for the direct specification of the z-component of the magnetic vector potential (which will be used to compute magnetic fields). The arguements for this parameter follow the same sets of rules as the parameters of Initial:value. If this parameter is not specified, but the values of the other components of the magnetic vector potential are, then this component is assumed to be zero everywhere.

Memory

Parameters in the Memory group are used to define the behavior of Cello’s dynamic memory allocation and deallocation.

Parameter:

Memory : active

Summary:

Whether to track memory usage

Type:

logical

Default:

true

Scope:

Cello

This parameter is used to turn on or off Cello’s build-in memory tracking. By default it is on, meaning it tracks the number and size of memory allocations, including the current number of bytes allocated, the maximum over the simulation, and the maximum over the current cycle. Cello implements this by overloading C’s new, new[], delete, and delete[] operators. This can be problematic on some systems, e.g. if an external library also redefines these operators, in which case this parameter should be set to false. This can be turned off completely by setting “memory” OFF (default value) as a cmake option.

Mesh

Parameter:

Mesh : root_blocks

Summary:

Number of Blocks used to tile the coarsest refinement level

Type:

list ( integer )

Default:

[ 1, 1, 1 ]

Scope:

Cello

This parameter specifies the number of Blocks along each axis in the mesh “array”. The product must not be smaller than the number of processors used.

Parameter:

Mesh : root_rank

Summary:

Physical dimensionality of the problem

Type:

integer

Default:

0

Scope:

Cello

Number of physical dimensions in the problem, 1, 2, or 3.

Parameter:

Mesh : root_size

Summary:

Coarsest Patch size

Type:

list ( integer )

Default:

[ 1, 1, 1 ]

Scope:

Cello

This parameter specifies the total size of the root-level mesh. For example, [400, 400] specifies a two dimensional root-level discretization of 400 x 400 zones, excluding ghost zones.

Method

Parameter:

Method : list

Summary:

Sequence of numerical methods to apply.

Type:

list ( string )

Default:

none

Scope:

Cello

This parameter specifies the list of numerical methods to use, and is analagous to “EvolveLevel” routine in ENZO. Each method in the list is applied in the order specified. Possible methods include:

  • “comoving_expansion” adds comoving expansion terms to the physical variables.

  • “cosmology” for writing redshift to monitor output.

  • “flux_correct” for performing flux corrections when using AMR.

  • “grackle” for heating and cooling methods in the Enzo Grackle library

  • “gravity” solves for the gravitational potential given gas and particle density fields.

  • “heat” for the forward-Euler heat-equation solver, which is used primarily for demonstrating how new Methods are implemented in Enzo-E

  • “pm_deposit” deposits “dark” particle density into “density_particle” field using CIC for “gravity” method.

  • “pm_update” moves cosmological “dark” particles based on positions, velocities, and accelerations. This will be phased out in favor of a more general “move_particles” method.

  • “ppm” for Enzo-E’s PPM hydrodynamics method. This may be phased out in favor of using a more general “hydro” method instead, with a specific hydro solver specified.

  • “ppml” for the PPML ideal MHD solver. This may be phased out in favor of using a more general “mhd” method instead, with a specific mhd solver specified.

  • “mhd_vlct” for the VL + CT (van Leer + Constrained Transport) MHD solver.

  • “trace” for moving tracer particles. This will be phased out in favor of a more general “move_particles” method.

  • “turbulence” computes random forcing for turbulence simulations.

Parameters specific to individual methods are specified in subgroups, e.g.:

Method {
   list = ["ppm"];
   ppm {
      diffusion   = true;
      flattening  = 3;
      steepening  = true;
      dual_energy = false;
   }
}

For more detailed documentation on Methods, see Enzo-E Methods

Parameter:

Method : courant

Summary:

Global Courant safety factor

Type:

float

Default:

1.0

Scope:

Cello

The global Courant safety factor is a multiplication factor for the time step applied on top of any Field or Particle specific Courant safety factors.

accretion

Parameter:

Method : accretion : accretion_radius_cells

Summary:

The radius of the spherical accretion zone around each sink particle, in units of the minimum cell width.

Type:

float

Default:

4.0

Scope:

Enzo

The accretion radius (i.e., the radius of the spherical accretion zone) in units of the minimum cell width (i.e., if the cell width along all the x, y, and z-axes are hx, hy, and hz, then the minimum cell width is the minimum of hx, hy, and hz),, at the highest refinement level. Its value must be less than one fewer than the minimum ghost depth for “flux” accretion, and less than the minimum ghost depth for other flavors of accretion. The ghost depth is 4 (along all axes) by default.

Parameter:

Method : accretion : flavor

Summary:

The flavor of accretion used.

Type:

string

Default:

“”

Scope:

Enzo

The flavor of accretion used, which can be either “threshold”, “bondi_hoyle”, “flux”, or “dummy”. If this parameter is not set in the parameter file, or if some other string is provided, then Enzo-E will exit with an error message.

Parameter:

Method : accretion : physical_density_threshold_cgs

Summary:

The value of the accretion (physical) density threshold in cgs units.

Type:

float

Default:

1.0e-24

Scope:

Enzo

The value of the (physical) density threshold in cgs units. The density in each cell in the accretion zone cannot go below this value during the accretion process. The value of this parameter in code density units must be greater than or equal to the value of the density floor imposed by the hydro method (either “ppm” or “mhd_vlct”. In cosmological simulations, the density unit is the mean matter density of the universe which decreases with time, which means that the value of a density quantity expressed in these units will increase with time, while the density floor is fixed in comoving units. The consequence is that is is sufficient for the density threshold to be above the density floor at the start of the simulation to guarantee that it will be above the floor at all subsequent times.

Parameter:

Method : accretion : max_mass_fraction

Summary:

The maximum fraction of mass which can be accreted from a cell in one timestep.

Type:

float

Default:

0.25

Scope:

Enzo

This parameter specifies the maximum fraction of mass which can be accreted from a cell in one timestep. This value of this parameter must be between 0 and 1.

flux_correct

Parameter:

Method : flux_correct : group

Summary:

Name of group of fields to apply flux correction to

Type:

string

Default:

“conserved”

Scope:

Cello

Flux correction must be applied to conserved fields in AMR simulations to maintain conserved quantities across mesh resolution jumps. This parameter selects the group of fields to which the “flux_correct” method will be applied.

Fields that store a conserved quantity divided by density (e.g. "total_energy", "velocity_x") have special handling. Such fields must be included in both the group specified by this parameter AND the "make_field_conservative" group. Flux corrections are applied to an element of such fields according to the following procedure:

  1. The element is multiplied by the corresponding element of the "density" field (before the flux corrections are applied to the "density" field).

  2. Flux corrections are applied to the product from step 1.

  3. Finally, the element in the original field is assigned the value computed in step 2 divided by the corresponding element from the "density" field (after flux corrections are applied to the "density" field).

An error will be raised if these special fields are detected, and the "density" field is not included in the group specified by this parameter.

Parameter:

Method : flux_correct : min_digits

Summary:

Number of digits expected to be conserved by fields in tests

Type:

list

Default:

[]

Scope:

Cello

Specifies the minimum number of digits that are expected to be conserved by fields. This is used for testing purposes (the simulation will check at each timestep whether this expectation has been met). Entries of this list should alternate between the name of fields (a string) and the expected number of conserved digits for that field (a float).

The example provided below indicates that the "density" field and the product of the "density" & "velocity_x" fields are expected to be conserved to 7.1 and 4.9 digits, respectively:

Method {
   flux_correct {
      min_digits = ["density", 7.1,
                    "velocity_x", 4.9];
   }
}

Group {
   list = [ "conserved", "make_field_conservative" ];
   conserved {
      field_list = [ "density", "velocity_x"];
   }
   make_field_conservative {
      field_list = [ "velocity_x"];
   }
}

For the sake of backwards compatibility, this parameter can be assigned a single float (that is not in a list). In this case, the value is assumed to be the expected minimum number of digits conserved by the "density" field. (Support for this type of parameter may be removed in the future)

gravity

Parameter:

Method : gravity : solver

Summary:

Name of the linear solver to use

Type:

string

Default:

“unknown”

Scope:

Enzo

Identifier for the linear solver to use, which must be included in the “Solver:list” parameter.

Parameter:

Method : gravity : grav_const

Summary:

Gravitational constant

Type:

float

Default:

6.67384e-8

Scope:

Enzo

Gravitational constant used in place of G. The default is G in cgs units. For non-cosmological simulations, if the user wants to use the standard value for the gravitational constant, the user must set a value which is consistent with their choice of units; i.e., its value must be \(G_{cgs}\times M \times T^2 \times L^{-3}\), or equivalently, \(G_{cgs}\times D \times T^2\), where \(M, D, T, L\) are the mass, density, time, and length units, and \(G_{cgs}\) is the value of the gravitational constant in cgs units.

In cosmological simulations, this parameter is ignored.

Parameter:

Method : gravity : order

Summary:

Order of accuracy discretization to use for the discrete Laplacian

Type:

integer

Default:

4

Scope:

Enzo

Second, fourth, and sixth order discretizations of the Laplacian are available; valid values are 2, 4, or 6.

Parameter:

Method : gravity : accumulate

Summary:

Whether to add one layer of ghost zones when refreshing particle density

Type:

logical

Default:

true

Scope:

Enzo

This should be true for all runs with particles, since particle mass deposited in the “density_particle” field may bleed into the first layer of ghost zones. This parameter ensures that that mass will be included in “density_total”.

Parameter:

Method : gravity : dt_max

Summary:

The maximum timestep returned by EnzoMethodGravity::timestep

Type:

float

Default:

1.0e10

Scope:

Enzo

The timestep returned by EnzoMethodGravity::timestep (when called on a block) is calculated as follows. First, the geometric mean of the cell-widths in all dimensions is found, which we call the “mean cell width”. Next, the quantity “epsilon” is calculated, as the mean cell width divided by the square of dt_max. Then, the maximum acceleration magnitude across all cells in the block is found, which we call “a_mag_max”. We then calculate the mean cell width divided by the sum of a_mag_max and epsilon. The timestep is then the square root of this quantity. This means that if all the accelerations are zero (such as at the first time step), the timestep is equal to dt_max. Defining the timestep in this way also means that the value of the timestep is independent of how the acceleration vectors are oriented relative to the mesh.

grackle

“Grackle is a chemistry and radiative cooling library for astrophysical simulations. It is a generalized and trimmed down version of the chemistry network of the Enzo simulation code.”

Most of the descriptions of the parameters come from the Grackle documentation; for the most up-to-date description of Grackle parameters, see the Grackle parameters section of the website.

Parameter:

Method : grackle : density_units

Summary:

Units for the density field

Type:

float

Default:

1.67e-24 (1 m_H/cc)

Scope:

Enzo

Units of density for the Grackle chemistry and cooling solver library.

Parameter:

Method : grackle : length_units

Summary:

Units for distance

Type:

float

Default:

3.086e21 (1 kpc)

Scope:

Enzo

Units of length for the Grackle chemistry and cooling solver library.

Parameter:

Method : grackle : time_units

Summary:

Units for time

Type:

float

Default:

3.15569e13 (1 Myr)

Scope:

Enzo

Units of time for the Grackle chemistry and cooling solver library.

Parameter:

Method : grackle : a_units

Summary:

Units for the cosmological expansion factor

Type:

float

Default:

1.0

Scope:

Enzo

Units of the cosmological expansion factor for the Grackle chemistry and cooling solver library.

Parameter:

Method : grackle : gamma

Summary:

The ratio of specific heats for an ideal gas

Type:

float

Default:

5/3

Scope:

Enzo

The ratio of specific heats for an ideal gas. A direct calculation for the molecular component is used if primordial_chemistry > 1.

Parameter:

Method : grackle : with_radiative_cooling

Summary:

Include radiative cooling

Type:

logical

Default:

true

Scope:

Enzo

Flag to include radiative cooling and actually update the thermal energy during the chemistry solver. If off, the chemistry species will still be updated. The most common reason to set this to off is to iterate the chemistry network to an equilibrium state.

Parameter:

Method : grackle : primordial_chemistry

Summary:

Flag to control which primordial chemistry network is used

Type:

logical

Default:

false

Scope:

Enzo

Flag to control which primordial chemistry network is used.

0: no chemistry network. Radiative cooling for primordial species is solved by interpolating from lookup tables calculated with Cloudy. A simplified set of functions are available (though not required) for use in this mode. For more information, see Pure Tabulated Mode.

1: 6-species atomic H and He. Active species: H, H+, He, He+, ++, e-.

2: 9-species network including atomic species above and species for molecular hydrogen formation. This network includes formation from the H- and H2+ channels, three-body formation ( H + H + H and H + H + H2), H2 rotational transitions, chemical heating, and collision-induced emission (optional). Active species: above + H-, H2, H2+.

3: 12-species network include all above plus HD rotation cooling. Active species: above plus D, D+, HD.

Note: In order to make use of the non-equilibrium chemistry network (primordial_chemistry options 1-3), you must add and advect baryon fields for each of the species used by that particular option.

Parameter:

Method : grackle : metal_cooling

Summary:

Flag to enable metal cooling using the Cloudy tables

Type:

logical

Default:

false

Scope:

Enzo

Flag to enable metal cooling using the Cloudy tables. If enabled, the cooling table to be used must be specified with the Grackle data_file parameter.

Note: In order to use the metal cooling, you must add and advect a metal density field.

Parameter:

Method : grackle : h2_on_dust

Summary:

Flag to enable H2 formation

Type:

logical

Default:

false

Scope:

Enzo

Flag to enable H2 formation on dust grains, dust cooling, and dust-gas heat transfer follow Omukai (2000). This assumes that the dust to gas ratio scales with the metallicity.

Parameter:

Method : grackle : cmb_temperature_floor

Summary:

Flag to enable an effective CMB temperature floor.

Type:

logical

Default:

true

Scope:

Enzo

Flag to enable an effective CMB temperature floor. This is implemented by subtracting the value of the cooling rate at TCMB from the total cooling rate.

Parameter:

Method : grackle : data_file

Summary:

Path to the data file containing the metal cooling and UV background tables.

Type:

string

Default:

“”

Scope:

Enzo

Path to the data file containing the metal cooling and UV background tables.

Parameter:

Method : grackle : three_body_rate

Summary:

Flag to control which three-body H2 formation rate is used.

Type:

integer

Default:

0

Scope:

Enzo

Status:

Not accessed

Flag to control which three-body H2 formation rate is used.

Parameter:

Method : grackle : cie_cooling

Summary:

Flag to enable |H2| collision-induced emission cooling

Type:

logical

Default:

false

Scope:

Enzo

Flag to enable H2 collision-induced emission cooling from Ripamonti & Abel (2004).

Parameter:

Method : grackle : h2_optical_depth_approximation

Summary:

Flag to enable |H2| cooling attenuation

Type:

logical

Default:

false

Scope:

Enzo

Flag to enable H2 cooling attenuation from Ripamonti & Abel (2004).

Parameter:

Method : grackle : photoelectric_heating

Summary:

Type:

Default:

Scope:

Enzo

Flag to enable a spatially uniform heating term approximating photo-electric heating from dust from Tasker & Bryan (2008)http://adsabs.harvard.edu/abs/2008ApJ…673..810T.

Parameter:

Method : grackle : photoelectric_heating_rate

Summary:

Type:

Default:

8.5e-26

Scope:

Enzo

If photoelectric_heating is enabled, the heating rate in units of erg cm-3 s-1.

Parameter:

Method : grackle : UVbackground

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Parameter:

Method : grackle : UVbackground_redshift_on

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : UVbackground_redshift_off

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : UVbackground_redshift_fullon

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : UVbackground_redshift_drop

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : Compton_xray_heating

Summary:

Type:

Default:

0

Scope:

Enzo

Flag to enable Compton heating from an X-ray background following Madau & Efstathiou (1999)http://adsabs.harvard.edu/abs/1999ApJ…517L…9M.

Parameter:

Method : grackle : LWbackground_intensity

Summary:

Type:

Default:

0

Scope:

Enzo

Intensity of a constant Lyman-Werner H2 photo-dissociating radiation field in units of 10-21 erg s-1 cm-2 Hz-1 sr-1.

Parameter:

Method : grackle : LWbackground_sawtooth_suppression

Summary:

Type:

Default:

0

Scope:

Enzo

Flag to enable suppression of Lyman-Werner flux due to Lyman-series absorption (giving a sawtooth pattern), taken from Haiman & Abel, & Rees (2000)http://adsabs.harvard.edu/abs/2000ApJ…534…11H.

Parameter:

Method : grackle : HydrogenFractionByMass

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : DeuteriumToHydrogenRatio

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : SolarMetalFractionByMass

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : NumberOfTemperatureBins

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : ih2co

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : ipiht

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : TemperatureStart

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : TemperatureEnd

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : comp_xray

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : temp_xray

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : CaseBRecombination

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : NumberOfDustTemperatureBins

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : DustTemperatureStart

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : DustTemperatureEnd

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

Parameter:

Method : grackle : cloudy_electron_fraction_factor

Summary:

Type:

Default:

Scope:

Enzo

Todo:

write

Status:

Not accessed

star_maker

..include:: method_star_maker.incl

feedback

..include:: method_feedback.incl

heat

Parameter:

Method : heat : alpha

Summary:

Parameter for the forward euler heat equation solver

Type:

float

Default:

1.0

Scope:

Enzo

Thermal diffusivity parameter for the heat equation.

merge_sinks

Parameter:

Method : merge_sinks : merging_radius_cells

Summary:

The distance within which sink particles merge with each other, in units of the minimum cell width

Type:

float

Default:

8.0

Scope:

Enzo

The distance within which sink particles merge with each other, in units of the minimum cell width, i.e., the minimum of the cell widths in all 3 dimensions, at the highest level of refinement.

mhd_vlct

Method:mhd_vlct parameters are used to initialize parameters for Enzo-E’s VL (+ CT) (magneto)hydrodynamic integrator.

The Method:mhd_vlct:mhd_choice determines whether the method is used as a pure hydrodynamic integrator or a MHD integrator that uses constrained transport.

Parameter:

Method : mhd_vlct : mhd_choice

Summary:

Denotes handling of bfields (or lack thereof)

Type:

string

Default:

none

Scope:

Enzo

Denotes how the integrator handles magentic fields. This must be specified. Valid choices include:

  • "no_bfield" The integrator acts as a pure hydrodynamical integrator; magnetic fields are ignored entirely.

  • "constrained_transport" Magnetic fields are evolved using constrained transport. The primary representation of the magnetic fields are stored in face-centered cello fields and cell-centered cello-fields are used to store a secondary representation.

This may be updated to include additional options in the future. For more details see "mhd_vlct": hydrodynamics/MHD

For debugging purposes, there is technically one last choice, `”unsafe_constant_uniform”. :e:`This is NOT meant for science runs. When this option is selected, the magnetic field is treated as a cell-centered conserved quantity and the magnetic fluxes computed in the Riemann solver are directly added to to the magnetic fields (magnetic field values are only stored in cell-centered Cello fields). Outside of very specific cases, this will NOT enforce the divergence-free constrain of the magnetic fields to grow. To use this option, you need to explicitly comment out an error in` ``"enzo_EnzoMethodMHDVlct.cpp".

Parameter:

Method : mhd_vlct : riemann_solver

Summary:

name of the Riemann solver to use

Type:

string

Default:

hlld

Scope:

Enzo

Name of the Riemann solver to use. For a list of options, see riemann solvers

Parameter:

Method : mhd_vlct : half_dt_reconstruct_method

Summary:

name of the reconstruction method to use for the full timestep

Type:

string

Default:

nn

Scope:

Enzo

Name of the interpolation method used to reconstruct face-centered primitives for the first half timestep. "nn" is recommended for this method (problems arise if "plm" or "plm_athena" are used). For a list of options, see reconstruction

Parameter:

Method : mhd_vlct : full_dt_reconstruct_method

Summary:

name of the reconstruction method to use for the full timestep

Type:

string

Default:

plm

Scope:

Enzo

Name of the interpolation method used to reconstruct face-centered primitives for the full timestep. For a list of options, see reconstruction

Parameter:

Method : mhd_vlct : theta_limiter

Summary:

controls the dissipation of certain slope limiters.

Type:

float

Default:

1.5

Scope:

Enzo

Modifies the disipation of the slope limiter of the "plm"/"plm_enzo" piecewise linear reconstruction algorithm. For more details, see reconstruction

Deprecated mhd_vlct parameters

The following parameters have all been deprecated and will be removed in a future version of Enzo-E. Going forwards, the corresponding parameters in Physics : fluid_props should be used instead.

Parameter:

Method : mhd_vlct : dual_energy

Summary:

Whether to use dual-energy formalism

Type:

logical

Default:

false

Scope:

Enzo

Whether to use the dual-energy formalism.

Parameter:

Method : mhd_vlct : dual_energy_eta

Summary:

Dual energy parameter eta

Type:

float

Default:

0.001

Scope:

Enzo

Dual-energy formalism parameter.

Parameter:

Method : mhd_vlct : density_floor

Summary:

Lower limit on density

Type:

float

Default:

none

Scope:

Enzo

Density floor, which must exceed 0. This is applied during reconstruction and quantity updates.

Parameter:

Method : mhd_vlct : pressure_floor

Summary:

Lower limit on thermal pressure

Type:

float

Default:

none

Scope:

Enzo

Thermal pressure floor, which must exceed 0. This is applied during reconstruction and quantity updates.

null

Parameter:

Method : null : dt

Summary:

Set the time step for the “null” Method

Type:

float

Default:

max (float)

Scope:

Enzo

Sets the time step for the null Method. This is typically used for testing the AMR meshing infrastructure without having to use any specific method. It can also be used to add an additional maximal time step value for other methods.

pm_deposit

Parameter:

Method : pm_deposit : alpha

Summary:

Compute the total gravitating density field at time t + alpha*dt

Type:

float

Default:

0.5

Scope:

Enzo

Sets the factor defining at what time to deposit mass into the density_total field. The default is 0.5, meaning density_total is computed at t + 0.5*dt.

ppm

Method:ppm parameters are used to initialize parameters for Enzo-E’s PPM hydrodynamics method.

Parameter:

Method : ppm : diffusion

Summary:

PPM diffusion parameter

Type:

logical

Default:

false

Scope:

Enzo

PPM diffusion parameter.

Parameter:

Method : ppm : flattening

Summary:

PPM flattening parameter

Type:

integer

Default:

3

Scope:

Enzo

PPM flattening parameter.

Parameter:

Method : ppm : minimum_pressure_support_parameter

Summary:

Enzo’s MinimumPressureSupportParameter

Type:

integer

Default:

100

Scope:

Enzo

Enzo’s MinimumPressureSupportParameter parameter.

Parameter:

Method : ppm : pressure_free

Summary:

Pressure-free flag

Type:

logical

Default:

false

Scope:

Enzo

Pressure-free flag.

Parameter:

Method : ppm : steepening

Summary:

PPM steepening parameter

Type:

logical

Default:

false

Scope:

Enzo

PPM steepening parameter.

Parameter:

Method : ppm : use_minimum_pressure_support

Summary:

Minimum pressure support

Type:

logical

Default:

false

Scope:

Enzo

Enzo’s UseMinimumPressureSupport parameter.

Deprecated ppm parameters

The following parameters have all been deprecated and will be removed in a future version of Enzo-E. Going forwards, the corresponding parameters in Physics : fluid_props should be used instead.

Parameter:

Method : ppm : density_floor

Summary:

Lower limit on density

Type:

float

Default:

1.0e-6

Scope:

Enzo

Density floor, which replaces Enzo’s “tiny_number”.

Parameter:

Method : ppm : dual_energy

Summary:

Whether to use dual-energy formalism

Type:

logical

Default:

false

Scope:

Enzo

Whether to use the dual-energy formalism.

Parameter:

Method : ppm : dual_energy_eta_1

Summary:

Dual energy parameter eta 1

Type:

float

Default:

0.001

Scope:

Enzo

First dual-energy formalism parameter.

Parameter:

Method : ppm : dual_energy_eta_2

Summary:

Dual energy parameter eta 2

Type:

float

Default:

0.1

Scope:

Enzo

Second dual-energy formalism parameter.

Parameter:

Method : ppm : mol_weight

Summary:

Enzo’s Mu parameter

Type:

float

Default:

0.6

Scope:

Enzo

Enzo’s Mu molecular weight parameter.

Parameter:

Method : ppm : number_density_floor

Summary:

Lower limit on number density

Type:

float

Default:

1.0e-6

Scope:

Enzo

Number density floor, which replaces Enzo’s “tiny_number”.

Parameter:

Method : ppm : pressure_floor

Summary:

Lower limit on pressure

Type:

float

Default:

1.0e-6

Scope:

Enzo

Pressure floor, which replaces Enzo’s “tiny_number”.

Parameter:

Method : ppm : temperature_floor

Summary:

Lower limit on temperature

Type:

float

Default:

1.0e-6

Scope:

Enzo

Temperature floor, which replaces Enzo’s “tiny_number”.

sink_maker

Parameter:

Method : sink_maker : jeans_length_resolution_cells

Summary:

Determines how many cell widths are required to resolve the local Jeans length for a cell not to form a sink.

Type:

float

Default:

4.0

Scope:

Enzo

If the local Jeans length in a cell is less than this quantity multiplied by the maximum cell width, then the cell is a candidate for forming a sink. The maximum cell width is maximum value out of hx, hy, and hz, where hx, hy, and hz are the cell widths across the x-, y- and z-axes, respectively.

Parameter:

Method : sink_maker : physical_density_threshold_cgs

Summary:

The minimum physical density required for a cell to form a sink particle in cgs units.

Type:

float

Default:

1.0e-24

Scope:

Enzo

The value of the physical density threshold in cgs units. The density in a cell must be greater than the density threshold to be able to form a sink. The density in a cell after sink formation will be no less than the density threshold. The value of the density threshold in code units must be greater than or equal to the value of the density floor imposed by the hydro method.

Parameter:

Method : sink_maker : max_mass_fraction

Summary:

The maximum fraction of a cell’s gas mass which can be turned into a sink particle in one timestep.

Type:

float

Default:

0.25

Scope:

Enzo

The mass of a newly-formed sink is bounded above by this parameter multiplied by the cell density multiplied by the cell volume. The value of this parameter must be between 0 and 1.

Parameter:

Method : sink_maker : min_sink_mass_solar

Summary:

The minimum mass of a newly-formed sink particle, in solar mass units.

Type:

float

Default:

0.0

Scope:

Enzo

The minimum mass of a newly-formed sink particle, in solar mass units. If there is not enough gas mass in a cell to form a sink with at least this mass, no sink is formed.

Parameter:

Method : sink_maker : check_density_maximum

Summary:

Determines whether a cell is required to be a local density maximum in order to form a sink particle.

Type:

logical

Default:

true

Scope:

Enzo

If true, then a cell will only form a sink particle if its density is larger than the density in all 26 neighboring cells.

Parameter:

Method : sink_maker : max_offset_cell_fraction

Summary:

Controls the size of the random displacement of a sink particle’s initial position relative to the center of the cell

Type:

float

Default:

0.0

Scope:

Enzo

When a cell creates a sink particle, the x/y/z coordinate of its initial position will be the x/y/z coordinate of the center of the cell, plus a random value generated from a uniform distribution on the interval [-A,A], where A is equal to this parameter multiplied by the cell width along the x/y/z axis.

Parameter:

Method : sink_maker : offset_seed_shift

Summary:

Seed used to generate the random displacement of a sink particle’s initial position relative to the center of the cell

Type:

integer

Default:

0

Scope:

Enzo

When computing the random offset for the initial position of a sink particle, we compute an unsigned 64 bit integer value from the cycle number, the block index, and the cell index, and then add on this value to give the seed for the random number generator.

turbulence

Parameter:

Method : turbulence : edot

Summary:

Initial value for edot for turbulence Method

Type:

float

Default:

-1.0

Scope:

Enzo

Todo:

write

Parameter:

Method : turbulence : mach_number

Summary:

Value for Mach number in turbulence problem

Type:

float

Default:

0.0

Scope:

Enzo

Todo:

write

Monitor

Parameter:

Monitor : debug

Summary:

Whether to display debugging output

Type:

logical

Default:

false

Scope:

Cello

If true, then process DEBUG() statements, writing the output to both stderr and appending to files out.debug.<proc>, where <proc> is the (physical) process rank. Note that out.debug.<proc> files are not erased at the start of a run. This parameter is not scalable and is inefficient since output files are continually opened and closed by each process.

Parameter:

Monitor : verbose

Summary:

Whether to display “verbose” output

Type:

logical

Default:

false

Scope:

Cello

If true, then output requests with Monitor::verbose() will be called. This will generally produce more detailed output, such as which specific Blocks are refining and coarsening, etc.

Output

Output parameters are used to specify what types of disk output to perform and on what schedule.

Parameter:

Output : list

Summary:

List of output file sets

Type:

list ( string )

Default:

[]

Scope:

Cello

List of active file sets, each of which has its own associated Output : <file_set> : parameters. Any file set parameters associated with a file set not in the list parameter are ignored.

Parameter:

Output : <file_set> : axis

Summary:

Axis of projections for image output

Type:

string

Default:

none

Scope:

Cello

Assumes:

<file_set> is of type “image”

For the “image” output type, the axis along which to project the data for 3D problems. Values are “x”, “y”, :e:`or “z”. See the associated type parameter.

Parameter:

Output : <file_set> : schedule

Summary:

Output schedule for the given file set

Type:

subgroup

Default:

none

Scope:

Cello

See the schedule subgroup for parameters used to define when to perform output for the given file set.

Parameter:

Output : <file_set> : colormap

Summary:

Color map for image output

Type:

list ( float )

Default:

[]

Scope:

Cello

Assumes:

<file_set> is of type “image”

For the “image” output type, a list of the form [r0, g0, b0, r1, g1, b1, …], where 0.0 ≤ ri,gi,bi≤ 1.0 are RGB values.

Parameter:

Output : <file_set> : field_list

Summary:

List of fields to output

Type:

list ( string )

Default:

[]

Scope:

Cello

List of fields for this output file set. For “image” field types, the field list must contain exactly one field.

Parameter:

Output : <file_set> : particle_list

Summary:

List of particle types to output

Type:

list ( string )

Default:

[]

Scope:

Cello

List of particles types for this output file set..

Parameter:

Output : <file_set> : name

Summary:

File names

Type:

list ( string )

Default:

“”

Scope:

Cello

Assumes:

<file_set> is not of type “restart”

This parameter specifies the names of files in the corresponding file_group. The first element is the file name, which may contain printf-style formatting fields. Subsequent values correspond to variables for the formatting fields, which may include “cycle”, “time”, “count” (a counter incremented each time output is performed), “proc” (the process rank), and “flipflop” (alternating 0 and 1, which can be useful for checkpoint directories). The file name should include an appropriate extension, e.g. “.png” for “image” output, and “.h5” or “.h5” for “data” output. Example: [“projection-%04d.png”, “cycle”].

Parameter:

Output : <file_set> : dir

Summary:

Name of the subdirectory for the output file

Type:

list ( string )

Default:

“”

Scope:

Cello

This parameter specifies the subdirectory for the output file. The first element is the file name, which may contain printf-style formatting fields. Subsequent values correspond to variables for the formatting fields, which may include “cycle”, “time”, “count” (a counter incremented each time output is performed), “proc” (the process rank), and “flipflop” (alternating 0 and 1, which can be useful for checkpoint directories). Example: [“Checkpoint-%d”, “flipflop”].

This parameter is required for file groups of type “checkpoint”. While optional for other file types, the behavior is different for groups of type “data”. In that case, two extra files are output: <DIR>.file_list, which contains a list of all data files output, and <DIR>.block_list, which contains a list of all names of Blocks and the corresponding data file containing each Block.

Parameter:

Output : <file_set> : stride_write

Summary:

Subset of processors to perform write

Type:

integer

Default:

1

Scope:

Cello

Assumes:

<file_set> is of type “data”

Status:

DEPRECIATED

This parameter allows for a strict subset of physical processors to output data, which is especially helpful for large process counts to reduce the load on parallel file systems. This parameter is depreciated, since the “output” method is preferered for writing data output.

Parameter:

Output : <file_set> : stride_wait

Summary:

Stride for sequencing processor data writes

Type:

integer

Default:

1

Scope:

Cello

Assumes:

<file_set> is of type “data”

Status:

DEPRECIATED

This parameter allows for processes to write sequentially to prevent too many processes overloading the file system. A good starting point would be the number of processes in a shared memory node, in which case at most one process per node will be writing at any point in time. This parameter is depreciated, since the “output” method is preferered for writing data output.

Parameter:

Output : <file_set> : type

Summary:

Type of output files

Type:

string

Default:

“unknown”

Scope:

Cello

The type of files to output in this output file set. Supported types include “image” (PNG file of 2D fields, or projection of 3D fields) and “data”. For “image” files, see the associated colormap and axis parameters.

Parameter:

Output : <file_set> : image_min

Summary:

Data value associated with the first color in the colormap

Type:

float

Default:

0.0

Scope:

Cello

Assumes:

<file_set> is of type “image”

This parameter specifies the Field value associated with the first color in the file set’s colormap.

Parameter:

Output : <file_set> : image_max

Summary:

Data value associated with the last color in the colormap

Type:

float

Default:

0.0

Scope:

Cello

Assumes:

<file_set> is of type “image”

This parameter specifies the Field value associated with the last color in the file set’s colormap.

Parameter:

Output : <file_set> : image_lower

Summary:

Lower bound on domain to be output in image

Type:

list ( float )

Default:

[min ( float ), min ( float ), min ( float )]

Scope:

Cello

Assumes:

<file_set> is of type “image”

This parameter specifies the lower limit of the domain to include in the image. This can be used for imaging “slices” of 3D data, or zeroing in on interesting region of the domain.

Parameter:

Output : <file_set> : image_upper

Summary:

Upper bound on domain to be output in image

Type:

list ( float )

Default:

[max ( float ), max ( float ), max ( float )]

Scope:

Cello

Assumes:

<file_set> is of type “image”

This parameter specifies the upper limit of the domain to include in the image. This can be used for imaging “slices” of 3D data, or zeroing in on interesting region of the domain.

Parameter:

Output : <file_set> : image_ghost

Summary:

Whether to include ghost zones in the image

Type:

logical

Default:

false

Scope:

Cello

Assumes:

<file_set> is of type “image”

Setting the image_ghost to true will include ghost zone values in the image output. This is typically used only when debugging. The default is false.

Parameter:

Output : <file_set> : image_reduce_type

Summary:

How to handle 3D field data orthogonal to the image

Type:

string

Default:

“sum”

Scope:

Cello

Assumes:

<file_set> is of type “image”

When images are generated for 3D problems, multiple data values will be associated with each pixel in the image. This parameter defines how to handle these multiple values, including “sum”, “min”, “max”, and, “avg”. For field data the default of “sum” is appropriate, though for images of meshes “max” should be used.

Parameter:

Output : <file_set> : image_face_rank

Summary:

Whether to include neighbor markers in the mesh image output

Type:

integer

Default:

3

Scope:

Cello

Assumes:

<file_set> is of type “image”

This parameter is primarily used for debugging. Internally, each node in the mesh keeps track of the mesh level of its neighbors. This parameter includes a marker on each face colored according to the neighbor’s level. The value of this parameter specifies the lower limit on the face “rank” (0 for corners, 1 for edges, 2 for faces). The default of 3 means no markers are displayed.

Parameter:

Output : <file_set> : image_size

Summary:

Set the size of the image

Type:

list ( integer )

Default:

[0,0]

Scope:

Cello

Assumes:

<file_set> is of type “image”

Specify the size of the output image. By default it is sized to be one pixel per field value at the finest mesh level. This is useful to keep images from being to big for large problems, or too small for small problems (e.g. for mesh images which could otherwise be too small).

Parameter:

Output : <file_set> : image_log

Summary:

Whether to output the log of the data

Type:

logical

Default:

false

Scope:

Cello

Assumes:

<file_set> is of type “image”

If true, then the natural logarithm of the field value is used for mapping values to the colormap, otherwise use the original field value.

Parameter:

Output : <file_set> : image_type

Summary:

Type of image to write

Type:

string

Default:

“data”

Scope:

Cello

Assumes:

<file_set> is of type “image”

This parameter is used to control whether field values are used to generate the image, whether it’s an image of the mesh structure, or a combination of both. Valid values are “data”, “mesh”, or “data+mesh”.

Parameter:

Output : <file_set> : image_block_size

Summary:

Number of pixels for fine-level blocks in a mesh image

Type:

integer

Default:

1

Scope:

Cello

Assumes:

<file_set> is of type “image”

Status:

DEPRECIATED

For images of meshes, this parameter defines how many pixels wide each finest-level block is in the image. This parameter and the image_size parameter should not both be set.

Parameter:

Output : <file_set> : image_mesh_color

Summary:

How to color blocks in a mesh image

Type:

string

Default:

“level”

Scope:

Cello

Assumes:

<file_set> is of type “image”

By default, blocks in mesh images are colored according to the level of the block. In addition to “level”, other possible ways to assign colors to blocks include “process” and “age”.

Particle

Cello supports any number of particle types–e.g. “dark” for dark matter particles, or “trace” for tracer particles. Each particle type in turn may have any number of attributes–e.g. “x” or “position_x” for position, “vx” or “velocity_x” for velocity, “mass”, “id”, etc. Attributes can have any basic floating-point or integer type.

All particle types must have at least attributes for position, defined using the position parameter. This allows Cello to know whether particles have moved off of a Block, and if so to relocate them to the correct new block.

Particle positions may be defined as integer types instead of floating-point. When a particle position attribute is defined as an integer, then the coordinate value is defined relative to the enclosed Block instead of a global coordinate system. This can be useful both to reduce memory usage, and to simultaneously improve accuracy–it avoids possible catastrophic cancellation errors that are especially large in “deep” Blocks in an AMR hierarchy whose position is far from 0. When positions are defined as integers, 0 is defined to be the center of the block, and [ -min-int / 2 , max-int / 2) are the bounds of the Block, where min-int is the minimum value of the signed integer of the corresponding size. Integer types allowed include “int8”, “int16”, “int32”, and “int64”. Two byte integers “int16” should be sufficient for most simulations: it has a range of [ -16384, 16384 ) within the particle’s containing Block, and ranges [-32768, -16384) and [16384, 32768) on either side of the associated Block.

Particles are allocated and operated on in “batches”. The batch_size parameter defines how many particles are in a batch. By operating on particles in batches, the frequency of memory operations is greatly reduced, and functions operating on particle attributes can be more efficient due to reduced overhead. It should also simplify writing particle methods to be executed on accelerators, such as NVIDIA or AMD GPU’s.

Just as with fields, particle types can be assigned to groups.

Parameter:

Particle : list

Summary:

List of particle types

Type:

list ( string )

Default:

[]

Scope:

Cello

Cello allows arbitrary parameter types (dark matter particles, tracer particles, star particles, etc.), each with arbitrary attributes (position, velocity, etc.). The list parameter defines which types of particles to use.

Particle {

    list = ["dark", "trace"];

}
Parameter:

Particle : batch_size

Summary:

Number of particles in a “batch” of particles

Type:

integer

Default:

1024

Scope:

Cello

Particles are allocated and operated on in batches. The number of particles in a batch is set using the batch_size parameter. The default batch size is 1024.

Parameter:

Particle : particle_type : attributes

Summary:

List of attribute names and data types

Type:

list ( string )

Default:

none

Scope:

Cello

Each particle type can have multiple attributes of varying types, which are defined by the attributes parameter. The attributes parameter is a list of strings, alternating between the name of the parameter, and its type. Names may include “position_x”, “velocity_z”, “mass”, “id”, etc. Types may include “single”, “double”, “quadruple”, “int8”, “int16”, “int32”, or “int64”. Ordering of attributes in memory is as in the attributes parameter.

Parameter {

    list = ["trace", "dark"];

        trace {

            attributes = ["id", "int64",
                          "x",  "single",
                          "y",  "single",
                          "z",  "single"];
         }

         dark {

             attributes = ["id",         "int64",
                           "mass",       "double",
                           "velocity_x", "single",
                           "velocity_y", "single",
                           "velocity_z", "single",
                           "position_x", "int16",
                           "position_y", "int16",
                           "position_z", "int16"];
       }
  }

Note that when attributes of multiple sizes are included in the same parameter type, it can be helpful to order the attributes so that larger-sized attributes are listed first, followed by smaller-sized attributes. This can help prevent allocating more memory than necessary, since attributes may be padded with unused bytes for correct memory alignment.

Parameter:

Particle : particle_type : interleaved

Summary:

Format of output files

Type:

logical

Default:

false

Scope:

Cello

Particle attributes within a batch of particles may be stored in memory either particle-by-particle, or “interleaved” (attribute-by-attribute). If ai,j represents the jth attribute of particle i, then with interleaved = false, attributes would be stored as a0,0 … am,0, a0,1 … am,1 … a0,n … am,n. If, however, interleaved = true, then attributes would be stored as a0,0 … a0,n, a1,0 … a1,n … am,0 … am,n. Non-interleaved particle attributes have array accesses of stride 1 and minimal storage overhead, but may not utilize cache well. Interleaved particle attributes may have improved cache utilization, but will have stride > 1, and may require memory padding for correct alignment of attributes in memory. The default is false.

Parameter:

Particle : particle_type : group_list

Summary:

Specify a list of groups that the Particle type belongs to

Type:

list ( string )

Default:

[ ]

Scope:

Cello

Different Particle types may belong to any number of different “groups”, which allows simulation code to loop over multiple related particle types.

Particle {
    list = ["trace","dark","star"];

    dark { group_list = ["is_gravitating"]; }
    star { group_list = ["is_gravitating"]; }
}

This example can be rewritten as follows, which is completely equivalent:

Particle
    list = ["trace","dark","star"];
}

Group {
    list = ["is_gravitating"];
    is_gravitating {
       particle_list = ["dark","star"];
    }
}
Parameter:

Particle : particle_type : position

Summary:

Format of output files

Type:

string

Default:

“”

Scope:

Cello

Cello needs to know which particle attributes represent position, so that it can determine when particles migrate out of a Block and need to be moved to a neighboring Block. This is done using the position parameter:

Particle {

   list = ["trace"];

   trace {

      attributes = ["id",
                    "x","single",
                    "y","single",
                    "z","single"];

      position = ["x","y","z"];
   }
}
Parameter:

Particle : particle_type : velocity

Summary:

Format of output files

Type:

string

Default:

“”

Scope:

Cello

Enzo may need to know which particle attributes represent velocity, for example for kick() or drift() operations. This is done using the velocity parameter, whose usage is analogous to the position parameter. While specifying position is required, specifying velocity is optional.

Particle {

   list = ["dark"];

   trace {

      attributes = [ "x","single",   "y","single",   "z","single",
                    "vx","single",  "vy","single",  "vz","single",
                    "mass","single"];

      velocity = ["vx","vy","vz"];
   }
}
Parameter:

Particle : mass_is_mass

Summary:

Flag for whether particle masses should be handled as a quantity with dimensions of mass.

Type:

any

Default:

none

Scope:

Cello

This parameter is not used by Enzo-E, but is rather used by yt to indicate whether particle “mass” should be treated as a quantity with dimensions of mass. If this parameter is absent, then “mass” is treated as a quantity with dimensions of density, which has a value equal to the true mass divided by the root level cell volume. The value of this parameter is not used: yt only checks whether this parameter is present, however, it must have some value which can be read in by yt. It is recommended to set the velue to be “true”.

Performance

Parameter:

Performance : warnings

Summary:

Whether to output performance-related warnings

Type:

logical

Default:

true

Scope:

Cello

If calls to the Performance API are incorrect, e.g. if stop_region() is called on a region that has not been started, then this parameter specifies whether or not to display warning messages

Parameter:

Performance : papi : counters

Summary:

List of PAPI counters

Type:

list ( string )

Default:

[]

Scope:

Cello

List of PAPI hardware performance counters to trace, e.g. ‘counters = [“PAPI_FP_OPS”, “PAPI_L3_TCA”];’. For a list of available counters, use the PAPI “papi_avail” utility.

Physics

Parameter:

Physics : list

Summary:

List of physics-sets

Type:

list ( string )

Default:

[]

Scope:

Cello

Specifies list of physics-sets, each of which has its own associated: Physics : <physics-set> : parameters. Any parameters associated with a physics-set subgroup that is not in this list parameter are ignored. Allowed values include:

  • “cosmology” specifies cosmological constants.

  • “fluid_props” specifies parameters related to gas properties.

cosmology

Parameter:

Physics : cosmology : comoving_box_size

Summary:

Enzo’s CosmologyComovingBoxSize parameter

Type:

float

Default:

64.0

Scope:

Enzo

Enzo’s CosmologyComovingBoxSize parameter.

Parameter:

Physics : cosmology : hubble_constant_now

Summary:

Hubble constant for Z=0

Type:

float

Default:

0.701

Scope:

Enzo

Hubble constant for Z=0.

Parameter:

Physics : cosmology : initial_redshift

Summary:

Enzo’s CosmologyInitialRedshift parameter.

Type:

float

Default:

20.0

Scope:

Enzo

Enzo’s CosmologyInitialRedshift parameter.

Parameter:

Physics : cosmology : max_expansion_rate

Summary:

Maximum expansion rate

Type:

float

Default:

0.01

Scope:

Enzo

Maximum expansion rate.

Parameter:

Physics : cosmology : omega_lamda_now

Summary:

Omega lambda for Z=0

Type:

float

Default:

0.721

Scope:

Enzo

Omega lamda for Z=0.

Parameter:

Physics : cosmology : omega_matter_now

Summary:

Omega matter for Z=0

Type:

float

Default:

0.279

Scope:

Enzo

Omega matter for Z=0.

fluid_props

Physics:fluid_props parameters are used to specify general fluid properties for the gas. The majority of these parameters are further divided into the following 3 subgroups: dual_energy, floors, eos.

An example configuration is described below:

Physics {
   list = ["fluid_props"];
   fluid_props {

      dual_energy { type = "disabled"; }

      eos {
         gamma = 1.4;
      }

      floors {
         density  = 1e-10;
         pressure = 1e-10;
      }

      mol_weight = 0.6;
   }
}
Parameter:

Physics : fluid_props : mol_weight

Summary:

Specifies the gas’s nominal mean molecular weight

Type:

float

Default:

0.6

Scope:

Enzo

Specifies the gas’s nominal mean molecular weight. This is used in operations like computing the temperature field. When the "grackle" method is in use, this parameter may not be used.

dual_energy

Physics:fluid_props:dual_energy parameters specify details about the dual-energy formalism (or the lack thereof). Significantly more detail about the different variants are provided in dual-energy formalism.

Parameter:

Physics : fluid_props : dual_energy : type

Summary:

specifies formulation of dual-energy formalism (if any)

Type:

string

Default:

disabled

Scope:

Enzo

Specifies the formulation of the dual-energy formalism that the simulation uses (if any). Valid choices include:

  • "disabled" The dual-energy formalism is not used. This is the default option.

  • "bryan95" Enables the formulation of the dual-energy formalism that is described in Bryan et al (1995)

  • "modern" Enables the formulation of the dual-energy formalism that is described in Overview

Parameter:

Physics : fluid_props : dual_energy : eta

Summary:

eta parameter(s) for the dual-energy formalism

Type:

list ( float )

Default:

[]

Scope:

Enzo

Specifies parameters used in the dual energy formalism. It expects a different number of parameters based on the value of Physics:fluid_props:dual_energy:type. The expectations are summarized below:

  • "disabled": This should always be an empty list.

  • "bryan95": The list should always contain two entries corresponding to [eta_1, eta_2]. An empty list (the default value) is treated as though it has the value [0.001, 0.1].

  • modern": The list should always one entry corresponding to [eta]. An empty list (the default value) is treated as though it has the value [0.001].

eos

Physics:fluid_props:dual_energy parameters specify details about the (caloric) equation of state. At this time, this only supports an ideal gas. But, in the future this will support alternative equations of state (like an isothermal equation of state).

See Compatability with hydro/mhd solvers for further discussion about how the equation of state is handled when Method:grackle:primordial_chemistry > 1 (under these conditions Grackle models a spatially varying adiabatic index).

Parameter:

Physics : fluid_props : eos : gamma

Summary:

Adiabatic exponent

Type:

float

Default:

5.0 / 3.0

Scope:

Enzo

gamma specifies the ratio of specific heats for the ideal gas used by the hydrodynamics solvers. This is used in a number other places like the "grackle" method, and various problem-initializers.

floors

Physics:fluid_props:floors parameters specify the floors that should be applied to different fluid quantities. Valid parameter values must be positive. Different methods selectively apply these floors. For more details, see Floors.

Parameter:

Physics : fluid_props : floors : density

Summary:

Lower limit on density field

Type:

float

Default:

none

Scope:

Enzo

Floor to be applied to the mass density field.

Parameter:

Physics : fluid_props : floors : pressure

Summary:

Lower limit on thermal pressure

Type:

float

Default:

none

Scope:

Enzo

Thermal pressure floor.

Parameter:

Physics : fluid_props : floors : temperature

Summary:

Lower limit on temperature

Type:

float

Default:

none

Scope:

Enzo

Temperature floor, which must exceed 0. Note that this is specified with units of Kelvin (since the `”temperature”`` field is always measured in Kelvin in Enzo-E)`

Parameter:

Physics : fluid_props : floors : metallicity

Summary:

Minimum metallicity in solar units

Type:

float

Default:

0.0

Scope:

Enzo

Minimum metallicity in solar units. This parameter is multiplied by the enzo_constants::metallicity_solar constant and the local value of the "density" field to give the local floor for the "metal_density" field

schedule

“schedule” is a parameter subgroup that defines when to do something, such as perform output, apply a method, or to apply the dynamic load balancer. Schedules can be specified as a list of values, or as an interval of values specified using some subset of start, stop, and step. The associated variable, set using var, can be “cycle”, “time”, or “seconds”. Here “time” refers to simulation time, and “seconds” to wall-clock time. At each cycle, all schedules are checked to see if the cycle number, simulation time or wall-clock seconds match the list or interval of values. If there is a match, the associated output or is performed; otherwise, it is skipped.

Note that when simulation “time” is specified, then the simulation’s time step may be reduced so that the corresponding output occurs exactly at the specified time.

Output {


   list = ["check", "dump", "image"];

   check {

      # **** write a checkpoint every 100.0 seconds ****

      schedule {
         var = "seconds";
         start = 100.0;
         step =  100.0;
      }
       ...
   }

   dump {

      # **** perform a data dump every 50 cycles until cycle 1000 ****

      schedule {
         var = "cycle";
         step =   50;
         stop = 1000;
       }
        ...
   }

   image {

      # **** write an image at times t = 1.0,  2.0, and 5.0 ****

      schedule {
         var = "time";
         list = [1.0, 2.0, 5.0];
       }
        ...
   }
}
Parameter:

schedule : var

Summary:

Variable associated with scheduling for the given file set

Type:

string

Default:

“none”

Scope:

Cello

The var parameter specifies what value is checked at each cycle, which may be “cycle”, “time”, or “seconds” Here “time” refers to simulation time, and “seconds” to wall-clock time. Note that when simulation “time” is specified, the simulation’s time step may be reduced such that the corresponding output occurs exactly at the specified time.

Parameter:

schedule : list

Summary:

List of scheduled values for the specified variable

Type:

[ list ( integer ) | list ( float ) ]

Default:

[]

Scope:

Cello

This parameter specifies a list of values to check against for output with respect to cycle, time, or seconds. If the “var” parameter associated with the schedule is “cycle”, then value must be a list of integers; otherwise, value must be a list of float’s The default is an empty list.

Parameter:

schedule : start

Summary:

Starting value for scheduled interval

Type:

[ integer | float ]

Default:

0 | 0.0

Scope:

Cello

Todo:

write

Parameter:

schedule : stop

Summary:

Last value for scheduled interval

Type:

[ integer | float ]

Default:

max (integer) | max (double)

Scope:

Cello

Todo:

write

Parameter:

schedule : step

Summary:

Stepping increment for interval

Type:

[ integer | float ]

Default:

1 | 1.0

Scope:

Cello

Todo:

write

Solver

Parameter:

Solver : solver : iter_max

Summary:

Iteration limit for the CG solver

Type:

int

Default:

100

Scope:

Enzo

Maximum number of CG iterations to take.

Parameter:

Solver : solver : res_tol

Summary:

Residual norm reduction tolerance for the CG solver

Type:

float

Default:

1e-6

Scope:

Enzo

Stopping tolerance on the 2-norm of the residual relative to the initial residual, i.e. CG is defined to have converged when ||R_i ||2 / ||R_0 ||2 < res_tol.

Parameter:

Solver : solver : grav_const

Summary:

Gravitational constant

Type:

float

Default:

6.67384e-8

Scope:

Enzo

Gravitational constant used in place of G. The default is G in cgs units.

Parameter:

Solver : solver : diag_precon

Summary:

Whether to apply diagonal preconditioning

Type:

logical

Default:

false

Scope:

Enzo

Whether to diagonally precondition the linear system A*X = B in EnzoSolverGravityCg by 1.0 / (h^2).

Parameter:

Solver : solver : monitor_iter

Summary:

How often to display progress

Type:

integer

Default:

1

Scope:

Enzo

The current iteration, and minimum, current, and maximum relative residuals, are displayed every monitor_iter iterations. If monitor_iter is 0, then only the first and last iteration are displayed.

Stopping

Parameter:

Stopping : cycle

Summary:

Stopping cycle

Type:

integer

Default:

max ( integer )

Scope:

Cello

Stopping cycle.

Parameter:

Stopping : time

Summary:

Stopping time

Type:

float

Default:

max ( double )

Scope:

Cello

Stopping time.

Parameter:

Stopping : seconds

Summary:

Stop after this number of seconds (wall-clock time)

Type:

float

Default:

max ( double )

Scope:

Cello

End the calculation after this many seconds of wall-clock time.

Parameter:

Stopping : interval

Summary:

Stopping interval

Type:

integer

Default:

1

Scope:

Cello

Number of cycles between applying the stopping criteria.

Testing

Parameter:

Testing : cycle_final

Summary:

Enzo-E unit test parameter for expected final cycle number

Type:

integer

Default:

0

Scope:

Cello

Enzo-E unit test parameter for expected final cycle number.

Parameter:

Testing : time_final

Summary:

Enzo-E unit test parameter for expected final time

Type:

float

Default:

0.0

Scope:

Cello

Enzo-E unit test parameter for expected final time.

Parameter:

Testing : time_tolerance

Summary:

Tolerance on the absolute error between actual final time and time_final

Type:

float

Default:

1.0e-6

Scope:

Cello

Enzo-E unit test parameter for tolerance on the expected final time.

Units

Parameter:

Units : length

Summary:

Units scaling factor for length

Type:

double

Default:

1.0

Scope:

Cello

Units scaling factor for length.

Parameter:

Units : mass

Summary:

Units scaling factor for mass

Type:

double

Default:

1.0

Scope:

Cello

Units scaling factor for mass. Only one of mass and density Units parameters can be initialized to ≠ 0.

Parameter:

Units : time

Summary:

Units scaling factor for time

Type:

double

Default:

1.0

Scope:

Cello

Units scaling factor for time.

Parameter:

Units : density

Summary:

Units scaling factor for density

Type:

double

Default:

1.0

Scope:

Cello

Units scaling factor for density. Only one of mass and density Units parameters can be initialized to ≠ 0.