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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