Inputs¶

The Nyx executable reads run-time information from an “inputs” file which you put on the command line. This section describes the inputs which can be specified either in the inputs file or on the command line. If a value is specified on the command line, that value will override a value specified in the inputs file.

Problem Geometry¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
geometry.prob_lo	physical location of low corner of the domain	Real	must be set
geometry.prob_hi	physical location of high corner of the domain	Real	must be set
geometry.coord_sys	coordinate system	0 = Cartesian, 1 = r-z, 2 = spherical	must be set
geometry.is_periodic	is the domain periodic in this direction	0 if false, 1 if true	0 0 0

Examples of Usage¶

geometry.prob_lo = 0 0 0 defines the low corner of the domain at (0,0,0) in physical space.
geometry.prob_hi = 1.e8 2.e8 2.e8 defines the high corner of the domain at (1.e8,2.e8,2.e8) in physical space.
geometry.coord_sys = 0 defines the coordinate system as Cartesian
geometry.is_periodic = 0 1 0 says the domain is periodic in the y-direction only.

Domain Boundary Conditions¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
nyx.lo_bc	boundary type of each low face	0,1,2,3,4,5	must be set
nyx.hi_bc	boundary type of each high face	0,1,2,3,4,5	must be set

[Table:BC]

Notes¶

Boundary types are:

0 – Interior / Periodic	3 – Symmetry
1 – Inflow	4 – Slip Wall
2 – Outflow	5 – No Slip Wall

Note – nyx.lo_bc and nyx.hi_bc must be consistent with geometry.is_periodic – if the domain is periodic in a particular direction then the low and high bc’s must be set to 0 for that direction.

Examples of Usage¶

nyx.lo_bc = 1 4 0
nyx.hi_bc = 2 4 0
geometry.is_periodic = 0 0 1

would define a problem with inflow (1) in the low-x direction, outflow(2) in the high-x direction, slip wall (4) on the low and high y-faces, and periodic in the z-direction.

Resolution¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
amr.n_cell	number of cells in each direction at the coarsest level	Integer > 0	must be set
amr.max_level	number of levels of refinement above the coarsest level	Integer >= 0	must be set
amr.ref_ratio	ratio of coarse to fine grid spacing between subsequent levels	2 or 4	must be set
amr.regrid_int	how often to regrid	Integer > 0	must be set
amr.regrid_on_restart	should we regrid immediately after restarting	0 or 1	0

[Table:ResInputs]

Note: if amr.max_level = 0 then you do not need to set amr.ref_ratio or amr.regrid_int.

Examples of Usage¶

amr.n_cell = 32 64 64

would define the domain to have 32 cells in the x-direction, 64 cells in the y-direction, and 64 cells in the z-direction at the coarsest level. (If this line appears in a 2D inputs file then the final number will be ignored.)
amr.max_level = 2

would allow a maximum of 2 refined levels in addition to the coarse level. Note that these additional levels will only be created only if the tagging criteria are such that cells are flagged as needing refinement. The number of refined levels in a calculation must be \(\leq\) amr.max_level, but can change in time and need not always be equal to amr.max_level.
amr.ref_ratio = 2 4

would set factor 2 refinement between levels 0 and 1, and factor 4 refinement between levels 1 and 2. Note that you must have at least amr.>ax_level values of amr.ref_ratio (Additional values may appear in that line and they will be ignored).
amr.regrid_int = 2 2

tells the code to regrid every 2 steps. Thus in this example, new level-1 grids will be created every 2 level-0 time steps, and new level-2 grids will be created every 2 level-1 time steps.

Regridding¶

Overview¶

The details of the regridding strategy are described in Section 5.5, but first we cover how the input parameters can control the gridding.

As described later, the user defines Fortran subroutines which tag individual cells at a given level if they need refinement. This list of tagged cells is sent to a grid generation routine, which uses the Berger–Rigoutsos algorithm to create rectangular grids that contain the tagged cells.

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
amr.regrid_file	name of file from which to read the grids	text	no file
amr.grid_eff	grid efficiency at coarse level at which grids are created	Real > 0, < 1	0.7
amr.n_error_buf	radius of additional tagging around already tagged cells	Integer >= 0	1
amr.max_grid_size	maximum size of a grid in any direction	Integer > 0	128 in 2D, 32 in 3D
amr.max_grid_size	maximum size	Integer	128 in 2D, 32
amr.blocking_factor	grid size must be a multiple of this	Integer > 0	2
amr.refine_grid_layout	refine grids more if # of processors \(>\) # of grids	0 if false, 1 if true	1

[Table:GriddingInputs]

Notes¶

amr.n_error_buf, amr.max_grid_size and amr.blocking_factor can be read in as a single value which is assigned to every level, or as multiple values, one for each level
amr.max_grid_size at every level must be even
amr.blocking_factor at every level must be a power of 2
the domain size amr.n_cell must be a multiple of amr.blocking_factor at level 0
amr.max_grid_size must be a multiple of amr.blocking_factor at every level

Examples of Usage¶

amr.regrid_file = fixed_grids

In this case the list of grids at each fine level are contained in the file fixed_grids, which will be read during the gridding procedure. These grids must not violate the amr.max_grid_size criterion. The rest of the gridding procedure described below will not occur if amr.regrid_file is set.
amr.grid_eff = 0.9

During the grid creation process, at least 90% of the cells in each grid at the level at which the grid creation occurs must be tagged cells. Note that this is applied at the coarsened level at which the grids are actually made, and before amr.max_grid_size is imposed.
amr.max_grid_size = 64

The final grids will be no longer than 64 cells on a side at every level.
amr.max_grid_size = 64 32 16

The final grids will be no longer than 64 cells on a side at level 0, 32 cells on a side at level 1, and 16 cells on a side at level 2.
amr.blocking_factor = 32

The dimensions of all the final grids will be multiples of 32 at all levels.
amr.blocking_factor = 32 16 8

The dimensions of all the final grids will be multiples of 32 at level 0, multiples of 16 at level 1, and multiples of 8 at level 2.

Having grids that are large enough to coarsen multiple levels in a V-cycle is essential for good multigrid performance in simulations that use self-gravity.

How Grids are Created¶

The gridding algorithm proceeds in this order:

If at level 0, the domain is initially defined by n_cell as specified in the inputs file. If at level greater than 0, grids are created using the Berger–Rigoutsis clustering algorithm applied to the tagged cells, modified to ensure that the lengths of all new fine grids are divisible by blocking_factor.
Next, the grid list is chopped up if any grids have length longer than max_grid_size. Note that because max_grid_size is a multiple of blocking_factor (as long as max_grid_size is greater than blocking_factor), the blocking_factor criterion is still satisfied.
Next, if refine_grid_layout = 1 and there are more processors than grids at this level, then the grids at this level are further divided in order to ensure that no processor has fewer than one grid (at each level).
- if max_grid_size / 2 in the BL_SPACEDIM direction is a multiple of blocking_factor, then chop the grids in the BL_SPACEDIM direction so that none of the grids are longer in that direction than max_grid_size / 2
- If there are still fewer grids than processes, repeat the procedure in the BL_SPACEDIM-1 direction, and again in the BL_SPACEDIM-2 direction if necessary
- If after completing a sweep in all coordinate directions with max_grid_size / 2, there are still fewer grids than processes, repeat the steps above with max_grid_size / 4.

Simulation Time¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
max_step	maximum number of level 0 time steps	Integer >= 0	-1
stop_time	final simulation time	Real >= 0	-1.0
nyx.final_a	final value of a	Real > 0	-1.0
nyx.final_z	final value of z	Real > 0	-1.0

[Table:TimeInputs]

Notes¶

To control the number of time steps, you can limit by the maximum number of level-0 time steps (max_step), or the final simulation time (stop_time), or both. The code will stop at whichever criterion comes first. Note that if the code reaches stop_time then the final time step will be shortened so as to end exactly at stop_time, not pass it.

If running in comoving coordinates you can also set a final value of \(a\) by setting nyx.final_a, or a final value of \(z\) by setting nyx.final_z. You may only specify one or the other of these. Once this value of \(a\) or \(z\) is reached in a time step, the code will stop at the end of this full coarse time step. (Note it does not stop at \(a\) (or \(z\)) exactly equal to the final value, rather it stops once \(a\) is greater than (or \(z\) is less than) this value.)

Examples of Usage¶

max_step = 1000
stop_time = 1.0

will end the calculation when either the simulation time reaches 1.0 or the number of level-0 steps taken equals 1000, whichever comes first.

Time Step¶

If nyx.do_hydro\(= 1\), then typically the code chooses a time step based on the CFL number (dt = cfl * dx / max(u+c) ).
If nyx.do_hydro\(= 0\) and we are running with dark matter particles, then we use a time step based on the velocity of the particles, i.e., we set \(\Delta t\) so that the particle goes no further than \(f \Delta t\) in a coordinate direction where \(0 \leq f \leq 1.\) The value for \(f\) is currently hard-wired in Particles.H, but it will become an inputs parameter.

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
nyx.cfl	CFL number for hydro	Real > 0 and <= 1	0.8
particles.cfl	CFL number for particles	Real > 0 and <= 1	0.5
nyx.init_shrink	factor by which to shrink the initial time step	Real > 0 and <= 1	1.0
nyx.change_max	factor by which the time step can grow in subsequent steps	Real >= 1	1.1
nyx.fixed_dt	level-0 time step regardless of cfl or other settings	Real > 0	unused if not set
nyx.initial_dt	initial level-0 time step regardless of other settings	Real > 0	unused if not set
nyx.dt_cutoff	time step below which calculation will abort	Real > 0	0.0
nyx.dt_binpow	time step chosen to be a power of a half times the comoving time step	Real >= 0	-1.0
nyx.relative_max _change_a	max da/dt	Real > 0	0.01
nyx.absolute_max _change_a	a_new-a_old	Real > 0	-1.0

[Table:TimeStepInputs]

Examples of Usage¶

nyx.cfl = 0.9

defines the timestep as dt = cfl * dx / umax_hydro.
particles.cfl = 0.9

defines the timestep as dt = cfl * dx / umax_particles where umax_particles is the maximum velocity of any particle in the domain.
nyx.init_shrink = 0.01

sets the initial time step to 1% of what it would be otherwise.
nyx.change_max = 1.1

allows the time step to increase by no more than 10% in this case. Note that the time step can shrink by any factor; this only controls the extent to which it can grow.
nyx.fixed_dt = 1.e-4

sets the level-0 time step to be 1.e-4 for the entire simulation, ignoring the other timestep controls. Note that if nyx.init_shrink \(\neq 1\) then the first time step will in fact be nyx.init_shrink * nyx.fixed_dt.
nyx.initial_dt = 1.e-4

sets the initial level-0 time step to be 1.e-4 regardless of nyx.cfl or nyx.fixed_dt. The time step can grow in subsequent steps by a factor of nyx.change_max each step.
nyx.dt_cutoff = 1.e-20

tells the code to abort if the time step ever gets below 1.e-20. This is a safety mechanism so that if things go nuts you don’t burn through your entire computer allocation because you don’t realize the code is misbehaving.
nyx.dt_binpow = 1.0

sets \(\mathrm{dt}=\left(\frac{1}{2}\right)^{n}\mathrm{dt}_{\mathrm{a}}|n:\mathrm{dt}_{\mathrm{cfl}}>\left(\frac{1}{2}\right)^{n}\mathrm{dt_{a}}\) where \(\mathrm{dt}_{\mathrm{cfl}}\) is determined by the more restrictive timestep of nyx.cfl and particles.cfl, and where \(\mathrm{dt}_{\mathrm{a}}\) is determined by the relative_max_change_a, absolute_max_change_a, and the evolution of \(\frac{da}{dt}\)

Subcycling¶

supports a number of different modes for subcycling in time.

If amr.subcycling_mode\(=\)Auto (default), then the code will run with equal refinement in space and time. In other words, if level \(n+1\) is a factor of 2 refinement above level \(n\), then \(n+1\) will take 2 steps of half the duration for every level \(n\) step.
If amr.subcycling_mode\(=\)None, then the code will not refine in time. All levels will advance together with a timestep dictated by the level with the strictest \(dt\). Note that this is identical to the deprecated command amr.nosub = 1.
If amr.subcycling_mode\(=\)Manual, then the code will subcycle according to the values supplied by subcycling_iterations.

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
amr.sub cycling_mode	How shall we subcycle	Auto, None or Manual	Auto
amr.subcycli g_iterations	Number of cycles at each level	1 or `ref_ratio`	must be set in Manual mode

Examples of Usage¶

amr.subcycling_mode\(=\)Manual

Subcycle in manual mode with largest allowable timestep.
amr.subcycling_iterations = 1 2 1 2

Take 1 level-0 timestep at a time (required). Take 2 level-1 timesteps for each level-0 step, 1 timestep at level 2 for each level-1 step, and take 2 timesteps at level 3 for each level 2 step.
amr.subcycling_iterations = 2

Alternative form. Subcycle twice at every level (except level 0).

Restart Capability¶

has a standard sort of checkpointing and restarting capability. In the inputs file, the following options control the generation of checkpoint files (which are really directories):

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
amr.check_file	prefix for restart files	String	“chk”
amr.check_int	how often (by level-0 time steps) to write restart files	Integer \(> 0\)	-1
amr.check_per	how often (by simulation time) to write restart files	Real \(> 0\)	-1.0
amr.restart	name of the file (directory) from which to restart	String	not used if not set
amr.checkpoint_files_output	should we write checkpoint files	0 or 1	1
amr.check_nfiles	how parallel is the writing of the checkpoint files	Integer \(\geq 1\)	64
amr.checkpoint_on_restart	should we write a checkpoint immediately after restarting	0 or 1	0
nyx.checkpoint_z_values	The redshift values at which checkpoint file should be written in addition to what is specified using check_int	list of redshift values	NONE

Notes¶

You should specify either amr.check_int or amr.check_per. Do not try to specify both.
Note that if amr.check_per is used then in order to hit that exact time the code may modify the time step slightly, which will change your results ever so slightly than if you didn’t set this flag.
Note that amr.plotfile_on_restart and amr.checkpoint_on_restart only take effect if amr.regrid_on_restart is in effect.
See the Software Section for more details on parallel I/O and the amr.check_nfiles parameter.
If you are doing a scaling study then set amr.checkpoint_files_output = 0 so you can test scaling of the algorithm without I/O.

Examples of Usage¶

amr.check_file = chk_run
amr.check_int = 10

means that restart files (really directories) starting with the prefix “chk_run” will be generated every 10 level-0 time steps. The directory names will be chk_run00000, chk_run00010, chk_run00020, etc.

If instead you specify

amr.check_file = chk_run
amr.check_per = 0.5

then restart files (really directories) starting with the prefix “chk_run” will be generated every 0.1 units of simulation time. The directory names will be chk_run00000, chk_run00043, chk_run00061, etc, where \(t = 0.1\) after 43 level-0 steps, \(t = 0.2\) after 61 level-0 steps, etc.

To restart from chk_run00061,for example, then set

amr.restart = chk_run00061

Controlling PlotFile and Generation¶

The main output from is in the form of plotfiles (which are really directories). The following options in the inputs file control the generation of plotfiles

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
amr.plot_file	prefix for plotfiles	String	“plt”
amr.plot_int	how often (by level-0 time steps) to write plot files	Integer \(> 0\)	-1
amr.plot_per	how often (by simulation time) to write plot files	Real \(> 0\)	-1.0
amr.plot_vars	name of state variables to include in plotfiles	ALL, NONE or list	ALL
amr.derive_plot_vars	name of derived variables to include in plotfiles	ALL, NONE or list	NONE
amr.plot_files_output	should we write plot files	0 or 1	1
amr.plotfile_on_restart	should we write a plotfile immediately after restarting	0 or 1	0
amr.plot_nfiles	how parallel is the writing of the plotfiles	Integer \(\geq 1\)	64
nyx.plot_rank	should we plot the processor ID in the plotfiles	True / False	False
fab.format	Should we write the plotfile in double or single precision	NATIVE or IEEE32	NATIVE
nyx.plot_z_values	The redshift values at which plot files should be written in addition to what is specified using nyx.plot_int	list of redshift values	NONE

All the options for amr.derive_plot_vars are kept in derive_lst in Nyx_setup.cpp. Feel free to look at it and see what’s there.

Notes¶

You should specify either amr.plot_int or amr.plot_per. Do not try to specify both.
Note that if amr.plot_per is used then in order to hit that exact time the code may modify the time step slightly, which will change your results ever so slightly than if you didn’t set this flag.
See the Software Section for more details on parallel I/O and the amr.plot_nfiles parameter.
If you are doing a scaling study then set amr.plot_files_output = 0 so you can test scaling of the algorithm without I/O.
By default, plotfiles are written in double precision (NATIVE format). If you want to save space by writing them in single precision, set the fab.format flag to IEEE32.

Examples of Usage¶

amr.plot_file = plt_run
amr.plot_int = 10

means that plot files (really directories) starting with the prefix “plt_run” will be generated every 10 level-0 time steps. The directory names will be plt_run00000, plt_run00010, plt_run00020, etc.

If instead you specify

amr.plot_file = plt_run
amr.plot_per = 0.5

then restart files (really directories) starting with the prefix “plt_run” will be generated every 0.1 units of simulation time. The directory names will be plt_run00000, plt_run00043, plt_run00061, etc, where \(t = 0.1\) after 43 level-0 steps, \(t = 0.2\) after 61 level-0 steps, etc.

Plotfile Variables¶

Native variables¶

These variables come directly from the StateData, either the State_Type (for the hydrodynamic variables), DiagEOS_Type (for the nuclear energy generation quantities). PhiGrav_Type and Gravity_Type (for the gravity quantities)

variable name	description	units
`density`	Baryonic mass density, \(\rho\)	M\(_\odot\) / Mpc\(^3\)
`xmom`	x-momentum, \((\rho u)\)	\({\rm g~km^{-2}~s^{-1}}\)
`ymom`	y-momentum, \((\rho v)\)	\({\rm g~km^{-2}~s^{-1}}\)
`zmom`	z-momentum, \((\rho w)\)	\({\rm g~km^{-2}~s^{-1}}\)
`rho_E`	Total energy density	\({\rm erg~km^{-3}}\)
`rho_e`	Internal energy density	\({\rm erg~km^{-3}}\)
`Temp`	Temperature	\({\rm K}\)
`Ne`	Number density of electrons	dimensionless
`rho_X` (where X is H or He, the species defined in the network)	Mass density of species X (only valid for non- constant species)	dimensionless
`phiGrav`	Gravitational potential	\({\rm erg~g^{-1}}\)
`grav_x`, `grav_y`, `grav_z`	Gravitational acceleration	\({\rm km~s^{-2}}\)

Derived variables¶

variable name	description	derive routine	units
`divu`	\(\nabla \cdot \ub\)	`derdivu`	\({\rm s^{-1}}\)
`eint_e`	Specific internal energy computed from the conserved \((\rho e)\) state variable as \(e = (\rho e)/\rho\)	`dereint2`	\({\rm erg~g^{-1}}\)
`eint_E`	Specific internal energy computed from the total energy and momentum conserved state as \(e=[(\rho E)-\frac{1}{2}(\rho \ub^2)]/\rho\)	`dereint1`	\({\rm erg~g^{-1}}\)
`kineng`	Kinetic energy density, \(K = \frac{1}{2} \|(\rho \ub)\|^2\)	`derkineng`	\({\rm erg~km^{-3}}\)
`logden`	\(\log_{10} \rho\)	`derlogden`	M\(_\odot\) / Mpc\(^3\)
`MachNumber`	Fluid Mach number, \(\|\ub\|/c_s\)	`dermachnumber`	–
`maggrav`	Gravitational acceleration magnitude	`dermaggrav`	\({\rm km~s^{-2}}\)
`magmom`	Momentum density magnitude, \(\|\rho \ub\|\)	`dermagmom`	\({\rm g~km^{-2}~s^{-1}}\)
`magvel`	Velocity magnitude, \(\|\ub\|\)	`dermagvel`	\(\mathrm{km~s^{-1}}\)
`magvort`	Vorticity magnitude, \(\|\nabla\times\ub\|\)	`dermagvort`	\({\rm s^{-1}}\)
`pressure`	Total pressure, including ions and electrons	`derpres`	\({\rm dyn~km^{-2}}\)
`soundspeed`	Sound speed	`dersoundspeed`	\(\mathrm{km~s^{-1}}\)
`H` or `He`	Mass fraction of species H or He	`derspec`	–
`x_velocity`, `y_velocity`, `z_velocity`	Fluid velocity, \(\ub = (\rho \ub)/\rho\)	`dervel`	\(\mathrm{km~s^{-1}}\)

Screen Output¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
amr.v	verbosity of Amr.cpp	0 or 1	0
nyx.v	verbosity of Nyx.cpp	0 or 1	0
gravity.v	verbosity of Gravity.cpp	0 or 1	0
mg.v	verbosity of multigrid solver (for gravity)	0,1,2,3,4	0
particles.v	verbosity of particle-related processes	0,1,2,3,4	0
amr.grid_log	name of the file to which the grids are written	String	not used if not set
amr.run_log	name of the file to which certain output is written	String	not used if not set
amr.run_log_terse	name of the file to which certain (terser) output is written	String	not used if not set
amr.sum_interval	if \(> 0,\) how often (in level-0 time steps)
	to compute and print integral quantities	Integer	-1

Examples of Usage¶

amr.grid_log = grdlog

Every time the code regrids it prints a list of grids at all relevant levels. Here the code will write these grids lists into the file grdlog.
amr.run_log = runlog

Every time step the code prints certain statements to the screen (if amr.v = 1), such as

STEP = 1 TIME = 1.91717746 DT = 1.91717746

PLOTFILE: file = plt00001

Here these statements will be written into runlog as well.
amr.run_log_terse = runlogterse

This file, runlogterse, differs from runlog in that it only contains lines of the form

10 0.2 0.005

in which “10” is the number of steps taken, “0.2” is the simulation time, and “0.005” is the level-0 time step. This file can be plotted very easily to monitor the time step.
nyx.sum_interval = 2

if nyx.sum_interval \(> 0\) then the code computes and prints certain integral quantities, such as total mass, momentum and energy in the domain every nyx.sum_interval level-0 steps. In this example the code will print these quantities every two coarse time steps. The print statements have the form

TIME= 1.91717746 MASS= 1.792410279e+34

for example. If this line is commented out then it will not compute and print these quanitities.

Gravity¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
nyx.do_grav	Include gravity as a forcing term	0 if false 1 if true	must be set
gravity.no_sync	whether to perform the “sync solve”	0 if false 1 if true	0
gravity.no_composite	whether to perform a composite solve	0 if false 1 if true	0

Notes¶

To include gravity you must set nyx.do_grav = 1 in the inputs file

Physics¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
nyx.do_hydro	Time-advance the fluid dynamical equations	0 if false, 1 if true	must be set
nyx.ppm_type	Use PPM or PLM for hydro advance	0 for PLM 1 for PPM	1 (PPM)
nyx.enforce_min_density_type	how to enforce rho greater than small_dens	“floor” “cons”	“floor”
nyx.strang_split	Use strang splitting	0 if false, 1 if true	1
nyx.sdc_split	Use sdc splitting	0 if false, 1 if true	0
nyx.strang_grown_box	Use growntilebox to avoid comms	0 if false, 1 if true	1
nyx.add_ext_src	Include additional user-specified source term	0 if false, 1 if true	0
nyx.nghost_state	Set number of ghost cells for state variables	{1,2,3,4}	1
nyx.use_const_species	If 1 then read h_species and he_species	0 or 1	0
nyx.h_species	Concentration of H	0 \(<\) X \(<\) 1	0
nyx.he_species	Concentration of He	0 \(<\) X \(<\) 1	0

Cosmology¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
nyx.comoving_OmM	Relative (total) mass density	0 \(<\) X \(<\) 1	must be set
nyx.comoving_OmB	Relative baryon density	0 \(<\) X \(<\) 1	must be set
nyx.comoving_OmR	Relative radiation density	0 \(<\) X \(<\) 1	must be set
nyx.comoving_h	Dimensionless Hubble parameter	0 \(<\) X \(<\) 1	must be set
nyx.gamma	Dimensionless factor relating \(p, \rho, e\)	0 \(<\) X \(<\) 2	\(5/3\)

Examples of Usage¶

nyx.gamma This changes \(\gamma\) in the \(\gamma\) law gas: \(p = (\gamma - 1) \rho e.\)

Reionization models¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
uvb_rates_file	Name of the UVB (TREECOOL) file	string	must be set
uvb_density_A	Density-dependent heating	real	1.0
uvb_density_B	Density dependent heating	real	0.0
reionization_zHI_flash	Redshift of “flash” H reion.	0 \(<\) X or -1 if off	-1.0
reionization_zHeII_flash	Redshift of “flash” He reion.	0 \(<\) X of -1 if off	-1.0
inhomo_reion	Inhomogeneous reionization	0 or 1	0
inhomo_zhi_file	File with reionization map	string	must be set (if used)
inhomo_grid	Size of the reionization grid	integer	must be set (if used)
reionization_T_zHI	H reionization heat input	real	2.0e4
reionization_T_zHeII	He reionization heat input	real	1.5e4

Dark matter halo output using Reeber¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
reeber.min_halo_n_cells	Minimum number of cells required for a halo to be considered a valid structure	integer	10
reeber.halo_component_threshold	Threshold for identifying connected components within a halo	real	81.66
reeber.halo_extrema_threshold	Threshold for detecting local maxima or extrema in the density field	real	160.0

Multigrid Inputs¶

The following inputs can be set directly in the AMReX solver classes but we set them via the Nyx gravity routines.

These must be preceded by “gravity” in the inputs file:

	Description	Type	Default
v	Verbosity of Gravity class	Int	0
ml_tol	Relative tolerance for multilevel solves	Real	1.e-12
sl_tol	Relative tolerance for single-level solves	Real	1.e-12
delta_tol	Relative tolerance for synchronization solves	Real	1.e-12
mlmg_agglomeration	Should we agglomerate deep in the V-cycle	Int	1
mlmg_consolidation	Should we consolidate deep in the V-cycle	Int	1
dirichlet_bcs	Should we use homogeneous Dirichlet bcs in the gravity solves (used for testing only)	Int	0

These must be preceded by “mg” in the inputs file:

	Description	Type	Default
v	Verbosity of multigrid solver	Int	0
bottom_solver	What is the bottom solver? Options include “bicg”, “smoother”, “hypre”, etc	String	“bicg”
max_fmg_iter	Maximum number of F-cycles to do before continuing with V-cycles in a multigrid solve	Int	0

There are a number of additional inputs that can be used to control the multigrid solver.

See the AMReX Multigrid documentation for more details.

Memory Optimization¶

List of Parameters¶

Parameter	Definition	Acceptable Values	Default
nyx.shrink_to_fit	Shrink Particle vector to save memory	0 if false, 1 if true
nyx.minimize_memory	Use less temporary scratch memory in hydro	0 if false, 1 if true
nyx.load_balance_int	How often to load-balance particles	Int < 0 if never Int > 0	-1
nyx.load_balance_start_z	Redshift to start load-balancing particles	Real > 0	7.0
nyx.load_balance_wgt_stategy	Weight strategy to load-balance particles	{0, 1, 2}	0
nyx.load_balance_wgt_nmax	Max ranks to load-balance particles	0 < Int < Ranks	-1
nyx.load_balance_stategy	Dmap strategy type for particle load-balancing	{KNAPSACK, SFC, ROUNDROBIN	SFC