Aux variables

There are a large number of variables that can be output to the aux file by putting the appropriate string in the mhd.in file. Here follows a list and explanation of each.

Enable these outputs by setting one of the following options in the aux parameter in the mhd.in file:

MHD module

Aux name	From Bifrost to CGS	CGS Units	From Bifrost to SI	SI Units	Aux description
'ca'	u_u	cm.s^-1	u_u * 1.e-2	m/s	Fast mode speed
'uv'	u_u	cm.s^-1	u_u * 1.e-2	m/s	The viscouse velocity : sqrt(c_s^2 + v_A^2)
'uv1'	u_u	cm.s^-1	u_u * 1.e-2	m/s	uv along the x direction
'uv2'	u_u	cm.s^-1	u_u * 1.e-2	m/s	uv along the y direction
'uv3'	u_u	cm.s^-1	u_u * 1.e-2	m/s	uv along the z direction
'ux'	u_u	cm.s^-1	u_u * 1.e-2	m/s	The fluid velocity along the x direction
'uy'	u_u	cm.s^-1	u_u * 1.e-2	m/s	The fluid velocity along the y direction
'uz'	u_u	cm.s^-1	u_u * 1.e-2	m/s	The fluid velocity along the z direction
'um'	u_u/u_l	s^-1	u_u/u_l	s^-1	Divergence of the perpendiculare velocity field, a type of magnetic diffusivity velocity
'um1'	u_u/u_l	s^-1	u_u/u_l	s^-1	um along the x direction
'um2'	u_u/u_l	s^-1	u_u/u_l	s^-1	um along the y direction
'um3'	u_u/u_l	s^-1	u_u/u_l	s^-1	um along the z direction
'Ix'	u_i$^*$	statA/cm^2 = G/s	u_i * 1.e-2 * 4pi / c_cgs / mu0_SI	A/m^2	Electric current density, x direction
'Iy'	u_i$^*$	statA/cm^2 = G/s	u_i * 1.e-2 * 4pi / c_cgs / mu0_SI	A/m^2	Electric current density, y direction
'Iz'	u_i$^*$	statA/cm^2 = G/s	u_i * 1.e-2 * 4pi / c_cgs / mu0_SI	A/m^2	Electric current density, z direction
'Ex'	u_el$^*$	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m	Electric field along the x direction
'Ey'	u_el$^*$	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m	Electric field along the y direction
'Ez'	u_el$^*$	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m	Electric field along the z direction
'etax'	u_el$^*$	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal resistive part of the electric field along the x direction
'etay'	u_el$^*$	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal resistive part of the electric field along the y direction
'etaz'	u_el$^*$	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal resistive part of the electric field along the z direction
'xdnr'	u_r	g/cm^3	u_r * 1.e3	kg/m^3	Mass density moved 0.5 grid steps in x direction, to cell interface
'ydnr'	u_r	g/cm^3	u_r * 1.e3	kg/m^3	Mass density moved 0.5 grid steps in y direction, to cell interface
'zdnr'	u_r	g/cm^3	u_r * 1.e3	kg/m^3	Mass density moved 0.5 grid steps in z direction, to cell interface
'fudge'					A checking factor for the alfven velocity

$^*$ where $c_{CGS}=2.998\times 10^{10}$, $mu0_{SI}=4\pi\times 10^{-7}$, u_i = c_cgs * u_b / u_l / 4pi and u_el = u_b * u_l / u_t / c_cgs. Please refer to unit factors derivation for computation of u_b, u_i and u_el

Heating terms of the internal energy equation

Aux name	From Bifrost to CGS	CGS Units	From Bifrost to SI	SI Units	Aux description
'qrdiff'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Density diffusion
'qediff'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Energy diffusion
'qeadv'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Energy advection
'qpdv'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Energy due to compression (change in energy due to compresion or expansion)
'qvisc'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Viscous heating
'qjoule'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Joule heating
'qeadv'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	heating advection
'qtot'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Radiative heating (flux divergence) (LTE, see below)
'qgenrad'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Radiative heating (flux divergence) from opt. thin losses + recipes (see below)
'qspitz'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Heating via Spitzer conduction (para. to mag. field)

Possible additional terms, see the Generalized Ohm's law section below.

Terms of the momentum equation

Aux name	From Bifrost to CGS	CGS Units	From Bifrost to SI	SI Units	Aux description
'fpadv1'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Reynolds stress term along x in the equation of motion ddx(rho.ux.ux)+ddy(rho.ux.uy)+ddz(rho.ux.uz) (careful! only diagonal term in old Bifrost)
'fpadv2'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Reynolds stress term along y in the equation of motion ddx(rho.uy.ux)+ddy(rho.uy.uy)+ddz(rho.uy.uz) (careful! only diagonal term in old Bifrost)
'fpadv3'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Reynolds stress term along z in the equation of motion ddx(rho.uz.ux)+ddy(rho.uz.uy)+ddz(rho.uz.uz) (careful! only diagonal term in old Bifrost)
'fpdiff1'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Diagonal term of the viscous stress along x ddx(Dxx)
'fpdiff2'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Diagonal term of the viscous stress along y ddx(Dyy)
'fpdiff3'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Diagonal term of the viscous stress along z ddx(Dzz)
'fstress1'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Non-diagonal term of the viscous stress along x ddy(Dxy) + ddz(Dxz)
'fstress2'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Non-diagonal term of the viscous stress along y ddx(Dyx) + ddz(Dyz)
'fstress3'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Non-diagonal term of the viscous stress along z ddx(Dzx) + ddy(Dzy)
'fpress1'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to the pressure gradient along x
'fpress2'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to the pressure gradient along y
'fpress3'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to the pressure gradient along z
'florentz1'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Lorentz force term along x
'florentz2'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Lorentz force term along y
'florentz3'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Lorentz force term along z
'frdiff1'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to mass diffusion along x
'frdiff2'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to mass diffusion along y
'frdiff3'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to mass diffusion along z
'fpdiff1'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to momentum diffusion along x
'fpdiff2'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to momentum diffusion along y
'fpdiff3'	u_e/u_l	dyn/cm^3	u_e/u_l * 10	N	Force term due to momentum diffusion along z
'term1'					cross term 1 in the equation of motion
'term2'					cross term 2 in the equation of motion
'term3'					cross term 3 in the equation of motion
'term4'					cross term 4 in the equation of motion
'term5'					cross term 5 in the equation of motion
'term6'					cross term 6 in the equation of motion

Equation of state

Aux name	From Bifrost to CGS	CGS Units	From Bifrost to SI	SI Units	Aux description
'tg'	already in cgs	K	already in SI	K	Temperature
'p'	u_p	dyne/cm^2	u_p * 1.e-1	Pa	Pressure
'cs'	u_u	cm/s	u_u * 1.e-2	m/s	Sound speed (from perfect gas law)
'cstab'	u_u	cm/s	u_u * 1.e-2	m/s	Sound speed (from tabulated EoS)
'nel'	already in cgs	cm^-3	1.e6	m^-3	Electron density

Radiation

Aux name	From Bifrost to CGS	CGS Units	From Bifrost to SI	SI Units	Aux description
'jn'	u_e/u_t*u_l	erg/cm^2/s	u_e / u_t * u_l *1.e-3	W/m^2	Mean radiation field in bin n
'sn'					Source function in bin n
'qn'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Flux divergence in bin n
'qtot'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	LTE Radiative heating (Total Flux divergence)
'Fx'	u_e/u_t*u_l	erg/cm^2/s	u_e / u_t * u_l *1.e-3	W/m^2	LTE Radiative Flux along x
'Fy'	u_e/u_t*u_l	erg/cm^2/s	u_e / u_t * u_l *1.e-3	W/m^2	LTE Radiative Flux along y
'Fz'	u_e/u_t*u_l	erg/cm^2/s	u_e / u_t * u_l *1.e-3	W/m^2	LTE Radiative Flux along z
'tn'					Tau along vertical inward ray in bin n
'in'					Specific intensities for all outgoing rays in bin n
'on'					Opacity in bin n
'en'					Photon destruction probability in bin n
'bn'					Thermal emission in bin n

Genrad

Aux name	From Bifrost to CGS	CGS Units	From Bifrost to SI	SI Units	Aux description
'qgenrad'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Total radiative heating from genrad
'qthin'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Thin radiative losses (always negative)
'qcwrm'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	An artificial heating term, to prevent the temperature to be below a certain value
'qcheat'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Ad hoc (cheating) term to ratiative heating
'qdeltat'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Radiative heating/cooling due to difference in local temperature to effective temperature (5780 K)
'qh'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Radiative heating/cooling from hydrogen bb transitions and Lyman continuum
'qca'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Radiative heating/cooling from calcium bb transitions
'qmg'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Radiative heating/cooling from magnesium bb transitions
'qhmbf'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Radiative heating/cooling from negative hydrogen ion, bound-free transitions
'qbalmer'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Radiative heating/cooling from hydrogen balmer continuum
'qincrad'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Heating from incoming radiation from the corona

Generalized Ohm's law

See Martinez-Sykora et al. 2012 for more details.

Aux name	From Bifrost to CGS	CGS Units	From Bifrost to SI	SI Units	Aux description
'hall_x'	u_el	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal hall part of the electric field along the x direction
'hall_y'	u_el	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal hall part of the electric field along the y direction
'hall_z'	u_el	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal hall part of the electric field along the z direction
'amb_x'	u_el	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal ambipolar part of the electric field along the x direction
'amb_y'	u_el	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal ambipolar part of the electric field along the y direction
'amb_z'	u_el	statV/cm = G	u_el * 1.e-6 * c_cgs	V/m^2	Non-ideal ambipolar part of the electric field along the z direction
'uhall_x'	u_u	cm.s^-1	u_u * 1.e-2	m.s^-1	Hall velocity along the x direction
'uhall_y'	u_u	cm.s^-1	u_u * 1.e-2	m.s^-1	Hall velocity along the y direction
'uhall_z'	u_u	cm.s^-1	u_u * 1.e-2	m.s^-1	Hall velocity along the z direction
'uamb_x'	u_u	cm.s^-1	u_u * 1.e-2	m.s^-1	Ambipolar velocity along the x direction
'uamb_y'	u_u	cm.s^-1	u_u * 1.e-2	m.s^-1	Ambipolar velocity along the y direction
'uamb_z'	u_u	cm.s^-1	u_u * 1.e-2	m.s^-1	Ambipolar velocity along the z direction
'eta_hall'	u_l^2/u_t	cm^2.s^-1	u_l^2/u_t * 1.e-4	m.s^-1	Hall term diffusion
'eta_hallb'	u_l^2/u_t/u_b	cm^2.s^-1.G^-1	u_l^2/u_t/u_b	m.s^-1	reduced Hall term diffusion
'eta_amb'	u_l^2/u_t	cm^2.s^-1	u_l^2/u_t * 1.e-4	m.s^-1	Ambipolar term diffusion
'eta_ambb'	u_l^2/u_t/u_b^2	cm^2.s^-1.G^-2	u_l^2/u_t/u_b * 1.e4	m.s^-1	reduced Ambipolar term diffusion
'qjamb'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Heating via ambipolar diffusion
'qh'	u_e/u_t	erg/cm^3/s	u_e / u_t *1.e-1	W/m^3	Heating via hall effect