Output Format

Introduction

One of the goals of iharm2d_v4 is to provide users with a GRMHD code that is as similar to production (HARM-based) GRMHD codes (e.g., iharm3d) as possible while doing away with several dependencies. Therefore, iharm2d_v4 writes fluid output to ASCII files.

The goal of this page is to explain the grid file and the fluid dump files that are written out by io.c. The grid is generated during problem initialization and cached in the struct GridGeom. The grid file - dumps/grid - is written only at the start of the simulation. The fluid state data meanwhile is continuously updated in the FluidState struct, and based on the cadence provided (Dtd) in param.dat, the code regularly writes output to dump files dumps/dump_*.

Grid file format

The grid file contains the grid coordinates, the covariant and contravariant components of the metric, the Jacobian ($\sqrt{-g}$), and the lapse $\big(\alpha\equiv 1/\sqrt{-g^{00}}\big)$. Each column in the grid file corresponds to each of these quantities with the values written in C-like index order. This means that the last index is changing fastest, and in the case of iharm2d_v4 this corresponds to X2. The slower-changing index corresponds to X1.

If one wants to read the grid file in python, the code would something look like,

grid  = numpy.loadtxt(os.path.join(dumpsdir,'grid'))
x     = grid[:,0].reshape((n1,n2))
z     = grid[:,1].reshape((n1,n2))
r     = grid[:,2].reshape((n1,n2))
th    = grid[:,3].reshape((n1,n2))
x1    = grid[:,4].reshape((n1,n2))
x2    = grid[:,5].reshape((n1,n2))
gdet  = grid[:,6].reshape((n1,n2))
lapse = grid[:,7].reshape((n1,n2))
gcon  = grid[:,8:24].reshape((n1, n2, ndim, ndim))
gcov  = grid[:,24:].reshape((n1, n2, ndim, ndim))

where n1 and n2 are the number of grid zones along X1 and X2 which can be read from the fluid dump header or the simulation compile-time parameter file parameters.h. ndim is the number of spacetime dimensions, or equivalently the matrix dimensions of the metric when represented in a coordinate basis, it's value is 4. grid is a numpy array that contains all the data stored in the grid file.

Dump file format

Just like iharm3d (see this), the fluid dump output can be schematically separated into two parts: the header - which in this case is the first line of the ASCII file - and the fluid state data.

Header

The header (for the torus problem) contains,

Variable	Description	Type	Notes
mad_type	Is the simulation SANE (0) or MAD (1)?	int
problem_type	Type of physical problem	string	"torus" in this case
rin	Inner radius of Fishbone-Moncrief torus	double	in code units
rmax	Pressure maximum radius of Fishbone-Moncrief torus	double	in code units
beta	Ratio of maximum fluid pressure to maximum magnetic pressure	double	$P_{g}/(b^2/2)$
u_jitter	Perturbation to the fluid internal energy	double
VERSION	Code version	string
has_electrons	Were electrons enabled?	int
gridfile	Grid file name	string
metric	Type of metric	string	Can be MINKOWSKI, MKS or FMKS
reconstruction	Reconstruction scheme	string	Can be LINEAR, WENO or MP5
N1	Number of grid zones along X1	int
N2	Number of grid zones along X2	int
n_prims	Number of primitives	int	Typically 8 for the vanilla ideal GRMHD problem
n_prims_passive	Number of passive primitives	int	Set to 0 for now
game	Adiabatic index of electrons	double	Only if ELECTRONS were enabled
gamp	Adiabatic index of protons	double	Only if ELECTRONS were enabled
fel0	Initial fraction of internal energy for electrons	double	Only if ELECTRONS were enabled
tptemin	Minimum ratio of temperature of protons to electrons	double	Only if ELECTRONS were enabled
tptemax	Minimum ratio of temperature of protons to electrons	double	Only if ELECTRONS were enabled
gam	Adiabatic index of the fluid	double
cour	Courant number	double
tf	Final simulation time	double	in code units
startx1	Logical grid left edge (X1)	double
startx2	Logical grid left edge (X2)	double
dx1	Logical grid width along X1	double
dx2	Logical grid width along X2	double
n_dim	Number of spacetime dimensions	int	4
poly_xt	FMKS coordinate transform parameter	double	Only if FMKS metric
poly_alpha	FMKS coordinate transform parameter	double	Only if FMKS metric
mks_smooth	FMKS coordinate transform parameter	double	Only if FMKS metric
Rin	Domain inner edge	double	Only if FMKS/MKS metric
Rout	Domain outer edge	double	Only if FMKS/MKS metric
Rhor	Event horizon radius	double	Only if FMKS/MKS metric
Risco	ISCO radius	double	Only if FMKS/MKS metric
hslope	MKS coordinate transformation parameter	double	Only if FMKS/MKS metric
a	Black hole spin	double	Only if FMKS/MKS metric
t	Simulation time	double	in code units
dt	Timestep	double	in code units
nstep	Timestep number	int
dump_cnt	Dump number	int
Dtd	Dump cadence	double	in code units
Dtf	Full fluid state cadence	double	Not used presently. Every dump is full fluid state dump

Fluid state data

The fluid state data contains,

Variable	Description	Type	Notes
p	Primitives	N1xN2xn_prims array of doubles	For vanilla, ideal GRMHD this contains arrays of RHO,UU,U1,U2,U3,B1,B2, and B3
jcon	The 4-current	N1xN2xn_dim array of doubles
gamma	Lorentz factor	N1xN2 array of doubles
divB	Magnetic field divergence values	N1xN2 array of doubles
fail_save	Zones where UtoP failed	N1xN2 array of ints	See u_top.c to understand failure code
fflag	Zones where fixup routine failed	N1xN2 array of ints

One can read the fluid primitives like,

prims = np.loadtxt('dumps/dump_000000000',skiprows=1)
rho = prims[:,0].reshape((n1,n2))
uu  = prims[:,1].reshape((n1,n2))
U1  = prims[:,2].reshape((n1,n2))
U2  = prims[:,3].reshape((n1,n2))
U3  = prims[:,4].reshape((n1,n2))
B1  = prims[:,5].reshape((n1,n2))
B2  = prims[:,6].reshape((n1,n2))
B3  = prims[:,7].reshape((n1,n2))

If you would like to write your own python script to read and plot iharm2d_v4 output, this page in addition to files/scripts/plot_torus.py should prove to be a good reference.