# 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.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:

1. 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.
2. 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.
3. 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

### 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.

• 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 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

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.

• 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

## 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