This template starts a fixed-bottom MHD simulation from a potential-field or magnetofrictional snapshot. Only the three magnetic components are inherited. The initial density, pressure/energy, and velocity are rebuilt by mod_usr.t; the velocity is reset to zero.

The normalization is shared with the potential and MF cases:

unit_length = 1e9 cm
unit_temperature = 1e6 K
unit_numberdensity = 1e9 cm^-3

Physics models

`mhd_model`	Variables	Atmospheres	Extra physics
`zero_beta`	7	uniform, coronal, or chromospheric density prescription	no pressure or gravity
`isothermal`	7	hydrostatic isothermal corona only	spherical solar gravity
`adiabatic`	8	hydrostatic corona/chromosphere or relaxed table	energy and gravity
`thermodynamic`	8	hydrostatic corona/chromosphere or relaxed table	energy, gravity, field-aligned conduction, cooling, heating

The model-specific parameter files are in par_zero_beta/, par_isothermal/, par_adiabatic/, and par_thermodynamic/. The top-level amrvac.par remains a compatibility copy of the zero-beta setup.

hydrostatic + chromosphere uses mod_solar_atmosphere and defaults to the AL-C7 temperature curve with n(10 Mm)=5e8 cm^-3. The coronal default is T=1 MK and n(z=0)=1e9 cm^-3. A relaxed atmosphere table must contain at least three code-unit columns:

# z rho p [optional extra columns]

Its height must increase strictly and cover the physical vertical domain. Density and pressure are logarithmically interpolated.

The thermodynamic background heating is H=H0 exp(-max(z,0)/lambda), with defaults H0=1e-4 erg cm^-3 s^-1 and lambda=50 Mm. Conduction and radiative-cooling controls remain ordinary AMRVAC settings in par_thermodynamic/amrvac.par.

Staging and restart behavior

Use stage_data_constrained_case(...) to select the model and write the data-specific override. For example:

stage_data_constrained_case(
    metadata,
    "DrivenFieldProject/DataConstrained",
    restart_file="DrivenFieldProject/MagnetofrictionalRelaxation/output/data_driven_mfr0000.dat",
    mhd_model="thermodynamic",
    atmosphere_model="chromosphere",
)

The generated initial override sets firstprocess, reset_time, and reset_it to true. Run the returned initial_run_command once. For an interrupted data-constrained run, restart from its own checkpoint with a new override that omits those three settings; otherwise the evolved plasma would be intentionally rebuilt and the clock reset.

The lower boundary is kept at the maximum AMR level. Its magnetic field, density, and pressure are fixed, and all three velocity components are zero. Standard AMRVAC .log, .dat, and VTU output is retained. Rank zero also writes output/initial_atmosphere.dat with code-unit columns z rho p T gravity heating.