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Getting started with analysis

Open up Python in your output directory and do the following:

sys.path.append('/path/to/nubhlight/scripts')
sys.path.append('/path/to/nubhlight/scripts/analysis')
import hdf5_to_dict as io
dr = io.load_hdr("dump_0000000.h5")  # loads dump header
geom = io.load_geom(hdr) # loads geometry/grid info
dump = io.load_dump('dump_file_name.h5',geom=geom)

Units

hdr['X_unit'] converts the quantity X from code units to cgs. For example hdr[RHO_unit'] converts density to cgs.

Items in the geom object:

gcov (192, 128, 4, 4)   : covariant metric (Kerr-Schild metric, HARM coordanates)
gcon (192, 128, 4, 4)   : contravariant metric (-- // --)
gdet (192, 128)         : \sqrt{-g}
alpha (192, 128, 66)    : lapse (extra dimension for plotting)
X1 (192, 128, 66)       : {X1(0:log(R)), X2(0:1), X3(0:tau)} -- code coorinates
X2 (192, 128, 66)
X3 (192, 128, 66)
x (192, 128, 66)        : {x, y, z} -- "corotating" Cartesian Kerr-Schild coordinates
y (192, 128, 66) 
z (192, 128, 66)
X1f (193, 129, 67)      : {X1f, X2f, X3f} -- same for the positions of grid nodes
X2f (193, 129, 67)
X3f (193, 129, 67)
xf (193, 129, 67)       : {xf, yf, zf} -- "corotating" Cartesian KS for grid nodes  
yf (193, 129, 67)
zf (193, 129, 67)
Lambda_h2cart_con (192, 128, 66, 4, 4) : transformation matrix \Lambda: HARM -> Cartesian
Lambda_h2cart_cov (192, 128, 66, 4, 4)
r (192, 128, 66)                       : {r, th, phi} -- corotating spherical Kerr-Schild
th (192, 128, 66)
phi (192, 128, 66)
rcyl (192, 128, 66)                    : cylindrical radius
Lambda_h2bl_con (192, 128, 4, 4)       : transformation: HARM -> Boyer-Lindquist
Lambda_h2bl_cov (192, 128, 4, 4)
Lambda_bl2cart_con (192, 128, 66, 4, 4) : transformation: Boyer-Lindquist -> Cartesian
Lambda_bl2cart_cov (192, 128, 66, 4, 4)
Lambda_h2bl_con_3d (192, 128, 66, 4, 4) : transformation: HARM -> Boyer-Lindquist
Lambda_h2bl_cov_3d (192, 128, 66, 4, 4)

Items in the dump object

hdr             : header
geom            : geometry object (see above)
t               : time in geomtric units of the output [GM/c^3]
dump_cnt        : index of the dump (dump count)
RHO             : density [geom]
UU              : internal energy density [geom?]
U1, U2, U3      : u^k/u^0  == dx^i/dt
B1, B2, B3      : magnetic field
Ye              : electron fraction
Ye_em           : -- // -- assuming no absorption happened
ATM             : 0..1: artificial atmosphere at the beginning of the simulation
jcon            : contravariant 4-current
divb            : divergence of the magnetic field: div(B)
fail_save       : records if fix-ups happened in this cell
Rmunu           : radiation energy-momentum
Nsph            : # of superphotons (= MC packets in a given cell)
nph             : number density of neutrinos in a cell
nuLnu           : \nu L_\nu (outgoing luminous flux of nus) binned in angles and energies
Jrad            : emissivity
Nem             : # of MC packets emitted
Nabs            : -- // -- absorbed
Nsc             : -- // -- scattered
radG_int        : source term of the fluid equations due to radiation, time-averaged between the dumps
tau_cool        : cooling time (neutrino cooling timescale)
dtau_avg        : optical depth experienced by an average nu in a cell over 1 time step
dtau_scatt      : -- // -- for scattering
dtau_tot        : -- // -- for both absorption and scattering
Nem_phys        : # of nu emitted 
Nabs_phys       : # of nu absorbed?
PRESS           : pressure [erg/cm3 = dyne/cm2]
TEMP            : temperature [MeV]
ENT             : entropy [k_B/baryon]
Theta           : dimensionless temperature / electron temperature (kb T / m_e c^2)
THETA           : ?
Thetae          : ?
tau_heat        : heating timescale
Qrad            : number of packets emitted per cooling time? (should worry if <10)
Nem_e           : alias to the neutrino component in the emitted neutrinos array Nem_phys
Nem_anti        : -- // -- for anti-neutrinos in Nem_phys
Nem_x           : -- // -- for heavy neutrinos in Nem_phys
Nabs_e          : alias to the neutrino component in the absorbed neutrinos array Nabs_phys 
Nabs_anti       : -- // -- for anti-neutrinos in Nabs_phys
Nabs_x          : -- // -- for heavy neutrinos in Nabs_phys
ucon, ucov      : 4-velocity in HARM coordinates: contra-/covariant components
bcon, bcov      : 4-vector of magnetic field: contra-/covariant components
bsq             : square of the magnetic field
beta            : gas pressure / magnetic pressure
ut,uX1,uX2,uX3  : components of ucon[]
jcov            : covariant current
j2              : square of the current
ur              : radiation pressure
betar           : gas pressure / radiation pressure
Jem             : = Jrad[0] - emission?
Jabs            : = Jrad[1] - absorption?
Jsc             : = Jrad[2] + Jrad[3] - scattering?
dtau_abs        
dtau_dens
dlepton_rad
dyedt_rad
ucon_bl         : BL = KS in corotating spherical coordinates (producing spherical horizon shape, so horizon is given by R = const)
ucov_bl
bcon_bl
bcov_bl
ucon_cart
ucov_cart
bcon_cart
bcov_cart