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"\n",
"\n",
"\n",
"# Equations of General Relativistic Magnetohydrodynamics (GRMHD)\n",
"\n",
"## Author: Zach Etienne\n",
"\n",
"## This notebook documents and constructs a number of quantities useful for building symbolic (SymPy) expressions for the equations of general relativistic magnetohydrodynamics (GRMHD), using the same (Valencia-like) formalism as `IllinoisGRMHD`.\n",
"\n",
"**Notebook Status:** Self-Validated; induction equation not yet implemented \n",
"\n",
"**Validation Notes:** This tutorial notebook has been confirmed to be self-consistent with its corresponding NRPy+ module, as documented [below](#code_validation). **Additional validation tests may have been performed, but are as yet, undocumented. (TODO)**\n",
"\n",
"## Introduction\n",
"\n",
"We write the equations of general relativistic magnetohydrodynamics in conservative form as follows (Eqs. 41-44 of [Duez *et al*](https://arxiv.org/pdf/astro-ph/0503420.pdf):\n",
"\n",
"\\begin{eqnarray}\n",
"\\ \\partial_t \\rho_* &+& \\partial_j \\left(\\rho_* v^j\\right) = 0 \\\\\n",
"\\partial_t \\tilde{\\tau} &+& \\partial_j \\left(\\alpha^2 \\sqrt{\\gamma} T^{0j} - \\rho_* v^j \\right) = s \\\\\n",
"\\partial_t \\tilde{S}_i &+& \\partial_j \\left(\\alpha \\sqrt{\\gamma} T^j{}_i \\right) = \\frac{1}{2} \\alpha\\sqrt{\\gamma} T^{\\mu\\nu} g_{\\mu\\nu,i} \\\\\n",
"\\partial_t \\tilde{B}^i &+& \\partial_j \\left(v^j \\tilde{B}^i - v^i \\tilde{B}^j\\right) = 0,\n",
"\\end{eqnarray}\n",
"where \n",
"\n",
"$$\n",
"s = \\alpha \\sqrt{\\gamma}\\left[\\left(T^{00}\\beta^i\\beta^j + 2 T^{0i}\\beta^j + T^{ij} \\right)K_{ij}\n",
"- \\left(T^{00}\\beta^i + T^{0i} \\right)\\partial_i\\alpha \\right].\n",
"$$\n",
"\n",
"We represent $T^{\\mu\\nu}$ as the sum of the stress-energy tensor of a perfect fluid $T^{\\mu\\nu}_{\\rm GRHD}$, plus the stress-energy associated with the electromagnetic fields in the force-free electrodynamics approximation $T^{\\mu\\nu}_{\\rm GRFFE}$ (equivalently, $T^{\\mu\\nu}_{\\rm em}$ in Duez *et al*):\n",
"\n",
"$$\n",
"T^{\\mu\\nu} = T^{\\mu\\nu}_{\\rm GRHD} + T^{\\mu\\nu}_{\\rm GRFFE},\n",
"$$\n",
"\n",
"where \n",
"\n",
"* $T^{\\mu\\nu}_{\\rm GRHD}$ is constructed from rest-mass density $\\rho_0$, pressure $P$, internal energy $\\epsilon$, 4-velocity $u^\\mu$, and ADM metric quantities as described in the [NRPy+ GRHD equations tutorial notebook](Tutorial-GRHD_Equations-Cartesian.ipynb); and \n",
"* $T^{\\mu\\nu}_{\\rm GRFFE}$ is constructed from the magnetic field vector $B^i$ and ADM metric quantities as described in the [NRPy+ GRFFE equations tutorial notebook](Tutorial-GRFFE_Equations-Cartesian.ipynb).\n",
"\n",
"All quantities can be written in terms of the full GRMHD stress-energy tensor $T^{\\mu\\nu}$ in precisely the same way they are defined in the GRHD equations. ***Therefore, we will not define special functions for generating these quantities, and instead refer the user to the appropriate functions in the [GRHD module](../edit/GRHD/equations.py)*** Namely,\n",
"\n",
"* The GRMHD conservative variables:\n",
" * $\\rho_* = \\alpha\\sqrt{\\gamma} \\rho_0 u^0$, via `GRHD.compute_rho_star(alpha, sqrtgammaDET, rho_b,u4U)`\n",
" * $\\tilde{\\tau} = \\alpha^2\\sqrt{\\gamma} T^{00} - \\rho_*$, via `GRHD.compute_tau_tilde(alpha, sqrtgammaDET, T4UU,rho_star)`\n",
" * $\\tilde{S}_i = \\alpha \\sqrt{\\gamma} T^0{}_i$, via `GRHD.compute_S_tildeD(alpha, sqrtgammaDET, T4UD)`\n",
"* The GRMHD fluxes:\n",
" * $\\rho_*$ flux: $\\left(\\rho_* v^j\\right)$, via `GRHD.compute_rho_star_fluxU(vU, rho_star)`\n",
" * $\\tilde{\\tau}$ flux: $\\left(\\alpha^2 \\sqrt{\\gamma} T^{0j} - \\rho_* v^j \\right)$, via `GRHD.compute_tau_tilde_fluxU(alpha, sqrtgammaDET, vU,T4UU,rho_star)`\n",
" * $\\tilde{S}_i$ flux: $\\left(\\alpha \\sqrt{\\gamma} T^j{}_i \\right)$, via `GRHD.compute_S_tilde_fluxUD(alpha, sqrtgammaDET, T4UD)`\n",
"* GRMHD source terms:\n",
" * $\\tilde{\\tau}$ source term $s$: defined above, via `GRHD.compute_s_source_term(KDD,betaU,alpha, sqrtgammaDET,alpha_dD, T4UU)` \n",
" * $\\tilde{S}_i$ source term: $\\frac{1}{2} \\alpha\\sqrt{\\gamma} T^{\\mu\\nu} g_{\\mu\\nu,i}$, via `GRHD.compute_S_tilde_source_termD(alpha, sqrtgammaDET,g4DD_zerotimederiv_dD, T4UU)`\n",
"\n",
"In summary, all terms in the GRMHD equations can be constructed once the full GRMHD stress-energy tensor $T^{\\mu\\nu} = T^{\\mu\\nu}_{\\rm GRHD} + T^{\\mu\\nu}_{\\rm GRFFE}$ is constructed. For completeness, the full set of input variables include:\n",
"* Spacetime quantities:\n",
" * ADM quantities $\\alpha$, $\\beta^i$, $\\gamma_{ij}$, $K_{ij}$\n",
"* Hydrodynamical quantities:\n",
" * Rest-mass density $\\rho_0$\n",
" * Pressure $P$\n",
" * Internal energy $\\epsilon$\n",
" * 4-velocity $u^\\mu$\n",
"* Electrodynamical quantities\n",
" * Magnetic field $B^i= \\tilde{B}^i / \\gamma$\n",
"\n",
"### A Note on Notation\n",
"\n",
"As is standard in NRPy+, \n",
"\n",
"* Greek indices refer to four-dimensional quantities where the zeroth component indicates temporal (time) component.\n",
"* Latin indices refer to three-dimensional quantities. This is somewhat counterintuitive since Python always indexes its lists starting from 0. As a result, the zeroth component of three-dimensional quantities will necessarily indicate the first *spatial* direction.\n",
"\n",
"For instance, in calculating the first term of $b^2 u^\\mu u^\\nu$, we use Greek indices:\n",
"\n",
"```python\n",
"T4EMUU = ixp.zerorank2(DIM=4)\n",
"for mu in range(4):\n",
" for nu in range(4):\n",
" # Term 1: b^2 u^{\\mu} u^{\\nu}\n",
" T4EMUU[mu][nu] = smallb2*u4U[mu]*u4U[nu]\n",
"```\n",
"\n",
"When we calculate $\\beta_i = \\gamma_{ij} \\beta^j$, we use Latin indices:\n",
"```python\n",
"betaD = ixp.zerorank1(DIM=3)\n",
"for i in range(3):\n",
" for j in range(3):\n",
" betaD[i] += gammaDD[i][j] * betaU[j]\n",
"```\n",
"\n",
"As a corollary, any expressions involving mixed Greek and Latin indices will need to offset one set of indices by one: A Latin index in a four-vector will be incremented and a Greek index in a three-vector will be decremented (however, the latter case does not occur in this tutorial notebook). This can be seen when we handle $\\frac{1}{2} \\alpha \\sqrt{\\gamma} T^{\\mu \\nu}_{\\rm EM} \\partial_i g_{\\mu \\nu}$:\n",
"```python\n",
"# \\alpha \\sqrt{\\gamma} T^{\\mu \\nu}_{\\rm EM} \\partial_i g_{\\mu \\nu} / 2\n",
"for i in range(3):\n",
" for mu in range(4):\n",
" for nu in range(4):\n",
" S_tilde_rhsD[i] += alpsqrtgam * T4EMUU[mu][nu] * g4DD_zerotimederiv_dD[mu][nu][i+1] / 2\n",
"```"
]
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"source": [
"\n",
"\n",
"# Table of Contents\n",
"$$\\label{toc}$$\n",
"\n",
"Each family of quantities is constructed within a given function (**boldfaced** below). This notebook is organized as follows\n",
"\n",
"\n",
"1. [Step 1](#importmodules): Import needed NRPy+ & Python modules\n",
"1. [Step 2](#stressenergy): Define the GRMHD stress-energy tensor $T^{\\mu\\nu}$ and $T^\\mu{}_\\nu$:\n",
" * **compute_T4UU()**, **compute_T4UD()**: \n",
"1. [Step 3](#declarevarsconstructgrhdeqs): Construct $T^{\\mu\\nu}$ from GRHD & GRFFE modules with ADM and GRMHD input variables, and construct GRMHD equations from the full GRMHD stress-energy tensor.\n",
"1. [Step 4](#code_validation): Code Validation against `GRMHD.equations` NRPy+ module\n",
"1. [Step 5](#latex_pdf_output): Output this notebook to $\\LaTeX$-formatted PDF file"
]
},
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"metadata": {},
"source": [
"\n",
"\n",
"# Step 1: Import needed NRPy+ & Python modules \\[Back to [top](#toc)\\]\n",
"$$\\label{importmodules}$$"
]
},
{
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"source": [
"# Step 1: Import needed core NRPy+ modules\n",
"import sympy as sp # SymPy: The Python computer algebra package upon which NRPy+ depends\n",
"import indexedexp as ixp # NRPy+: Symbolic indexed expression (e.g., tensors, vectors, etc.) support"
]
},
{
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"metadata": {},
"source": [
"\n",
"\n",
"# Step 2: Define the GRMHD stress-energy tensor $T^{\\mu\\nu}$ and $T^\\mu{}_\\nu$ \\[Back to [top](#toc)\\]\n",
"$$\\label{stressenergy}$$\n",
"\n",
"Recall from above that\n",
"\n",
"$$\n",
"T^{\\mu\\nu} = T^{\\mu\\nu}_{\\rm GRHD} + T^{\\mu\\nu}_{\\rm GRFFE},\n",
"$$\n",
"where\n",
"\n",
"* $T^{\\mu\\nu}_{\\rm GRHD}$ is constructed from the `GRHD.compute_T4UU(gammaDD,betaU,alpha, rho_b,P,epsilon,u4U)` [GRHD](../edit/GRHD/equations.py) [(**tutorial**)](Tutorial-GRHD_Equations-Cartesian.ipynb) function, and\n",
"* $T^{\\mu\\nu}_{\\rm GRFFE}$ is constructed from the `GRFFE.compute_TEM4UU(gammaDD,betaU,alpha, smallb4U, smallbsquared,u4U)` [GRFFE](../edit/GRFFE/equations.py) [(**tutorial**)](Tutorial-GRFFE_Equations-Cartesian.ipynb) function\n",
"\n",
"Since a lowering operation on a sum of tensors is equivalent to the lowering operation applied to the individual tensors in the sum,\n",
"\n",
"$$\n",
"T^\\mu{}_{\\nu} = T^\\mu{}_{\\nu}{}^{\\rm GRHD} + T^\\mu{}_{\\nu}{}^{\\rm GRFFE},\n",
"$$\n",
"\n",
"where\n",
"\n",
"* $T^\\mu{}_{\\nu}{}^{\\rm GRHD}$ is constructed from the `GRHD.compute_T4UD(gammaDD,betaU,alpha, T4UU)` [GRHD](../edit/GRHD/equations.py) [(**tutorial**)](Tutorial-GRHD_Equations-Cartesian.ipynb) function, and\n",
"* $T^{\\mu\\nu}_{\\rm GRFFE}$ is constructed from the `GRFFE.compute_TEM4UD(gammaDD,betaU,alpha, TEM4UU)` [GRFFE](../edit/GRFFE/equations.py) [(**tutorial**)](Tutorial-GRFFE_Equations-Cartesian.ipynb) function."
]
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"source": [
"import GRHD.equations as GRHD\n",
"import GRFFE.equations as GRFFE\n",
"\n",
"# Step 2.a: Define the GRMHD T^{mu nu} (a 4-dimensional tensor)\n",
"def compute_GRMHD_T4UU(gammaDD,betaU,alpha, rho_b,P,epsilon,u4U, smallb4U, smallbsquared):\n",
" global GRHDT4UU\n",
" global GRFFET4UU\n",
" global T4UU\n",
"\n",
" GRHD.compute_T4UU( gammaDD,betaU,alpha, rho_b,P,epsilon,u4U)\n",
" GRFFE.compute_TEM4UU(gammaDD,betaU,alpha, smallb4U, smallbsquared,u4U)\n",
"\n",
" GRHDT4UU = ixp.zerorank2(DIM=4)\n",
" GRFFET4UU = ixp.zerorank2(DIM=4)\n",
" T4UU = ixp.zerorank2(DIM=4)\n",
" for mu in range(4):\n",
" for nu in range(4):\n",
" GRHDT4UU[mu][nu] = GRHD.T4UU[mu][nu]\n",
" GRFFET4UU[mu][nu] = GRFFE.TEM4UU[mu][nu]\n",
" T4UU[mu][nu] = GRHD.T4UU[mu][nu] + GRFFE.TEM4UU[mu][nu]\n",
"\n",
"# Step 2.b: Define T^{mu}_{nu} (a 4-dimensional tensor)\n",
"def compute_GRMHD_T4UD(gammaDD,betaU,alpha, GRHDT4UU,GRFFET4UU):\n",
" global T4UD\n",
"\n",
" GRHD.compute_T4UD( gammaDD,betaU,alpha, GRHDT4UU)\n",
" GRFFE.compute_TEM4UD(gammaDD,betaU,alpha, GRFFET4UU)\n",
"\n",
" T4UD = ixp.zerorank2(DIM=4)\n",
" for mu in range(4):\n",
" for nu in range(4):\n",
" T4UD[mu][nu] = GRHD.T4UD[mu][nu] + GRFFE.TEM4UD[mu][nu]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Step 3: Declare ADM and hydrodynamical input variables, and construct all terms in GRMHD equations \\[Back to [top](#toc)\\]\n",
"$$\\label{declarevarsconstructgrhdeqs}$$"
]
},
{
"cell_type": "code",
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"source": [
"# First define hydrodynamical quantities\n",
"u4U = ixp.declarerank1(\"u4U\", DIM=4)\n",
"rho_b,P,epsilon = sp.symbols('rho_b P epsilon',real=True)\n",
"B_tildeU = ixp.declarerank1(\"B_tildeU\", DIM=3)\n",
"\n",
"# Then ADM quantities\n",
"gammaDD = ixp.declarerank2(\"gammaDD\",\"sym01\",DIM=3)\n",
"KDD = ixp.declarerank2(\"KDD\" ,\"sym01\",DIM=3)\n",
"betaU = ixp.declarerank1(\"betaU\", DIM=3)\n",
"alpha = sp.symbols('alpha', real=True)\n",
"\n",
"# Then numerical constant\n",
"sqrt4pi = sp.symbols('sqrt4pi', real=True)\n",
"\n",
"# First compute smallb4U & smallbsquared from BtildeU, which are needed\n",
"# for GRMHD stress-energy tensor T4UU and T4UD:\n",
"GRHD.compute_sqrtgammaDET(gammaDD)\n",
"GRFFE.compute_B_notildeU(GRHD.sqrtgammaDET, B_tildeU)\n",
"GRFFE.compute_smallb4U( gammaDD,betaU,alpha, u4U,GRFFE.B_notildeU, sqrt4pi)\n",
"GRFFE.compute_smallbsquared(gammaDD,betaU,alpha, GRFFE.smallb4U)\n",
"\n",
"# Then compute the GRMHD stress-energy tensor:\n",
"compute_GRMHD_T4UU(gammaDD,betaU,alpha, rho_b,P,epsilon,u4U, GRFFE.smallb4U, GRFFE.smallbsquared)\n",
"compute_GRMHD_T4UD(gammaDD,betaU,alpha, GRHDT4UU,GRFFET4UU)\n",
"\n",
"# Compute conservative variables in terms of primitive variables\n",
"GRHD.compute_rho_star( alpha, GRHD.sqrtgammaDET, rho_b,u4U)\n",
"GRHD.compute_tau_tilde(alpha, GRHD.sqrtgammaDET, T4UU,GRHD.rho_star)\n",
"GRHD.compute_S_tildeD( alpha, GRHD.sqrtgammaDET, T4UD)\n",
"\n",
"# Then compute v^i from u^mu\n",
"GRHD.compute_vU_from_u4U__no_speed_limit(u4U)\n",
"\n",
"# Next compute fluxes of conservative variables\n",
"GRHD.compute_rho_star_fluxU( GRHD.vU, GRHD.rho_star)\n",
"GRHD.compute_tau_tilde_fluxU(alpha, GRHD.sqrtgammaDET, GRHD.vU,T4UU,GRHD.rho_star)\n",
"GRHD.compute_S_tilde_fluxUD( alpha, GRHD.sqrtgammaDET, T4UD)\n",
"\n",
"# Then declare derivatives & compute g4DD_zerotimederiv_dD\n",
"gammaDD_dD = ixp.declarerank3(\"gammaDD_dD\",\"sym01\",DIM=3)\n",
"betaU_dD = ixp.declarerank2(\"betaU_dD\" ,\"nosym\",DIM=3)\n",
"alpha_dD = ixp.declarerank1(\"alpha_dD\" ,DIM=3)\n",
"GRHD.compute_g4DD_zerotimederiv_dD(gammaDD,betaU,alpha, gammaDD_dD,betaU_dD,alpha_dD)\n",
"\n",
"# Then compute source terms on tau_tilde and S_tilde equations\n",
"GRHD.compute_s_source_term(KDD,betaU,alpha, GRHD.sqrtgammaDET,alpha_dD, T4UU)\n",
"GRHD.compute_S_tilde_source_termD( alpha, GRHD.sqrtgammaDET,GRHD.g4DD_zerotimederiv_dD, T4UU)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Step 4: Code Validation against `GRMHD.equations` NRPy+ module \\[Back to [top](#toc)\\]\n",
"$$\\label{code_validation}$$\n",
"\n",
"As a code validation check, we verify agreement in the SymPy expressions for the GRHD equations generated in\n",
"1. this tutorial versus\n",
"2. the NRPy+ [GRMHD.equations](../edit/GRMHD/equations.py) module."
]
},
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"source": [
"import GRMHD.equations as GRMHD\n",
"\n",
"# Compute stress-energy tensor T4UU and T4UD:\n",
"GRMHD.compute_GRMHD_T4UU(gammaDD,betaU,alpha, rho_b,P,epsilon,u4U, GRFFE.smallb4U, GRFFE.smallbsquared)\n",
"GRMHD.compute_GRMHD_T4UD(gammaDD,betaU,alpha, GRMHD.GRHDT4UU,GRMHD.GRFFET4UU)"
]
},
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"scrolled": true
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"ALL TESTS PASSED!\n"
]
}
],
"source": [
"def comp_func(expr1,expr2,basename,prefixname2=\"Ge.\"):\n",
" if str(expr1-expr2)!=\"0\":\n",
" print(basename+\" - \"+prefixname2+basename+\" = \"+ str(expr1-expr2))\n",
" return 1\n",
" return 0\n",
"\n",
"def gfnm(basename,idx1,idx2=None,idx3=None):\n",
" if idx2 is None:\n",
" return basename+\"[\"+str(idx1)+\"]\"\n",
" if idx3 is None:\n",
" return basename+\"[\"+str(idx1)+\"][\"+str(idx2)+\"]\"\n",
" return basename+\"[\"+str(idx1)+\"][\"+str(idx2)+\"][\"+str(idx3)+\"]\"\n",
"\n",
"expr_list = []\n",
"exprcheck_list = []\n",
"namecheck_list = []\n",
"\n",
"for mu in range(4):\n",
" for nu in range(4):\n",
" namecheck_list.extend([gfnm(\"GRMHD.GRHDT4UU\",mu,nu),gfnm(\"GRMHD.GRFFET4UU\",mu,nu),\n",
" gfnm(\"GRMHD.T4UU\", mu,nu),gfnm(\"GRMHD.T4UD\", mu,nu)])\n",
" exprcheck_list.extend([GRMHD.GRHDT4UU[mu][nu],GRMHD.GRFFET4UU[mu][nu],\n",
" GRMHD.T4UU[mu][nu], GRMHD.T4UD[mu][nu]])\n",
" expr_list.extend([GRHDT4UU[mu][nu],GRFFET4UU[mu][nu],\n",
" T4UU[mu][nu], T4UD[mu][nu]])\n",
"\n",
"num_failures = 0\n",
"for i in range(len(expr_list)):\n",
" num_failures += comp_func(expr_list[i],exprcheck_list[i],namecheck_list[i])\n",
"\n",
"import sys\n",
"if num_failures == 0:\n",
" print(\"ALL TESTS PASSED!\")\n",
"else:\n",
" print(\"ERROR: \"+str(num_failures)+\" TESTS DID NOT PASS\")\n",
" sys.exit(1)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Step 5: Output this notebook to $\\LaTeX$-formatted PDF file \\[Back to [top](#toc)\\]\n",
"$$\\label{latex_pdf_output}$$\n",
"\n",
"The following code cell converts this Jupyter notebook into a proper, clickable $\\LaTeX$-formatted PDF file. After the cell is successfully run, the generated PDF may be found in the root NRPy+ tutorial directory, with filename\n",
"[Tutorial-GRMHD_Equations-Cartesian.pdf](Tutorial-GRMHD_Equations-Cartesian.pdf) (Note that clicking on this link may not work; you may need to open the PDF file through another means.)"
]
},
{
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"execution_count": 6,
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Created Tutorial-GRMHD_Equations-Cartesian.tex, and compiled LaTeX file to\n",
" PDF file Tutorial-GRMHD_Equations-Cartesian.pdf\n"
]
}
],
"source": [
"import cmdline_helper as cmd # NRPy+: Multi-platform Python command-line interface\n",
"cmd.output_Jupyter_notebook_to_LaTeXed_PDF(\"Tutorial-GRMHD_Equations-Cartesian\")"
]
}
],
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"display_name": "Python 3 (ipykernel)",
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"file_extension": ".py",
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