{
"cells": [
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"source": [
"\n",
"\n",
"\n",
"# Tutorial-IllinoisGRMHD: symmetry__set_gzs_staggered_gfs.C\n",
"\n",
"## Authors: Leo Werneck & Zach Etienne\n",
"\n",
"**This module is currently under development**\n",
"\n",
"## In this tutorial module we explain how `IllinoisGRMHD` handles symmetry options and the ghostzones of staggered gridfunctions. This module will likely be absorbed by another one once we finish documenting the code.\n",
"\n",
"### Required and recommended citations:\n",
"\n",
"* **(Required)** Etienne, Z. B., Paschalidis, V., Haas R., Mösta P., and Shapiro, S. L. IllinoisGRMHD: an open-source, user-friendly GRMHD code for dynamical spacetimes. Class. Quantum Grav. 32 (2015) 175009. ([arxiv:1501.07276](http://arxiv.org/abs/1501.07276)).\n",
"* **(Required)** Noble, S. C., Gammie, C. F., McKinney, J. C., Del Zanna, L. Primitive Variable Solvers for Conservative General Relativistic Magnetohydrodynamics. Astrophysical Journal, 641, 626 (2006) ([astro-ph/0512420](https://arxiv.org/abs/astro-ph/0512420)).\n",
"* **(Recommended)** Del Zanna, L., Bucciantini N., Londrillo, P. An efficient shock-capturing central-type scheme for multidimensional relativistic flows - II. Magnetohydrodynamics. A&A 400 (2) 397-413 (2003). DOI: 10.1051/0004-6361:20021641 ([astro-ph/0210618](https://arxiv.org/abs/astro-ph/0210618))."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Table of Contents\n",
"$$\\label{toc}$$\n",
"\n",
"This module is organized as follows\n",
"\n",
"0. [Step 0](#src_dir): **Source directory creation**\n",
"1. [Step 1](#introduction): **Introduction**\n",
"1. [Step 2](#symmetry__set_gzs_staggered_gfs__c): **`symmetry__set_gzs_staggered_gfs.C`**\n",
"1. [Step n-1](#code_validation): **Code validation**\n",
"1. [Step n](#latex_pdf_output): **Output this notebook to $\\LaTeX$-formatted PDF file**"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Step 0: Source directory creation \\[Back to [top](#toc)\\]\n",
"$$\\label{src_dir}$$\n",
"\n",
"We will now use the [cmdline_helper.py NRPy+ module](Tutorial-Tutorial-cmdline_helper.ipynb) to create the source directory within the `IllinoisGRMHD` NRPy+ directory, if it does not exist yet."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"# Step 0: Creation of the IllinoisGRMHD source directory\n",
"# Step 0a: Add NRPy's directory to the path\n",
"# https://stackoverflow.com/questions/16780014/import-file-from-parent-directory\n",
"import os,sys\n",
"nrpy_dir_path = os.path.join(\"..\",\"..\")\n",
"if nrpy_dir_path not in sys.path:\n",
" sys.path.append(nrpy_dir_path)\n",
"\n",
"# Step 0b: Load up cmdline_helper and create the directory\n",
"import cmdline_helper as cmd\n",
"IGM_src_dir_path = os.path.join(\"..\",\"src\")\n",
"cmd.mkdir(IGM_src_dir_path)\n",
"\n",
"# Step 0c: Create the output file path\n",
"outfile_path__symmetry__set_gzs_staggered_gfs__C = os.path.join(IGM_src_dir_path,\"symmetry__set_gzs_staggered_gfs.C\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Step 1: Introduction \\[Back to [top](#toc)\\]\n",
"$$\\label{introduction}$$"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Step 2: `symmetry__set_gzs_staggered_gfs.C` \\[Back to [top](#toc)\\]\n",
"$$\\label{symmetry__set_gzs_staggered_gfs__c}$$"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Writing ../src/symmetry__set_gzs_staggered_gfs.C\n"
]
}
],
"source": [
"%%writefile $outfile_path__symmetry__set_gzs_staggered_gfs__C\n",
"#include \"cctk.h\"\n",
"#include \"cctk_Parameters.h\"\n",
"#include \n",
"#include \n",
"#include \"IllinoisGRMHD_headers.h\"\n",
"\n",
"void IllinoisGRMHD_set_symmetry_gzs_staggered(const cGH *cctkGH, const int *cctk_lsh,CCTK_REAL *X,CCTK_REAL *Y,CCTK_REAL *Z, CCTK_REAL *gridfunc,\n",
" CCTK_REAL *gridfunc_syms,int stagger_x,int stagger_y,int stagger_z) {\n",
"\n",
" DECLARE_CCTK_PARAMETERS;\n",
"\n",
" if(CCTK_EQUALS(Symmetry, \"equatorial\"))\n",
" CCTK_VError(VERR_DEF_PARAMS,\"Warning: Symmetry==equatorial not supported! USE AT YOUR OWN RISK. You will need to comment this error message out.\");\n",
"\n",
" // No symmetries -> return.\n",
" if(CCTK_EQUALS(Symmetry, \"none\")) return;\n",
"\n",
" CCTK_REAL dz = Z[CCTK_GFINDEX3D(cctkGH,0,0,1)] - Z[CCTK_GFINDEX3D(cctkGH,0,0,0)];\n",
"\n",
" CCTK_REAL z_offset = dz*0.5*stagger_z;\n",
"\n",
" int num_gzs=0;\n",
" //FIXME: Might want to use cctk_nghostzones instead...\n",
" while( (Z[CCTK_GFINDEX3D(cctkGH,0,0,num_gzs)]+z_offset) < -dz*0.1 && num_gzs=cctk_lsh[2]) CCTK_VError(VERR_DEF_PARAMS,\"ERROR in symmetry__set_gzs_staggered_gfs.C\");\n",
"\n",
"#pragma omp parallel for\n",
" for(int k=0;k gridfunc[index 0] = gridfunc_syms[2]*gridfunc[index 1]\n",
" *\n",
" * if num_gzs==2 && stagger_z==1:\n",
" * z[] = {-3dz/2,-dz/2,dz/2,3dz/2 etc}\n",
" * -> gridfunc[index 0] = gridfunc_syms[2]*gridfunc[index 3]\n",
" * -> gridfunc[index 1] = gridfunc_syms[2]*gridfunc[index 2]\n",
" * .\n",
" * .\n",
" * .\n",
" * -> gridfunc[i] = gridfunc_syms[2]*gridfunc[(num_gz*2-1)-i]\n",
" *\n",
" * UNSTAGGERED PATTERN:\n",
" * if num_gzs==1 && stagger_z==0:\n",
" * z[] = {-dz,0,dz, etc} -> gridfunc[index 0] = gridfunc_syms[2]*gridfunc[index 2]\n",
" *\n",
" * if num_gzs==2 && stagger_z==0:\n",
" * z[] = {-2dz,-dz,0,dz,2dz, etc} -> gridfunc[index 0] = gridfunc_syms[2]*gridfunc[index 4]\n",
" * z[] = {-2dz,-dz,0,dz,2dz, etc} -> gridfunc[index 1] = gridfunc_syms[2]*gridfunc[index 3]\n",
" * .\n",
" * .\n",
" * .\n",
" * -> gridfunc[i] = gridfunc_syms[2]*gridfunc[(num_gz*2)-i]\n",
" *\n",
" * OVERALL PATTERN: gridfunc[i] = gridfunc_syms[2]*gridfunc[(num_gz*2-stagger_z)-i] */\n",
"\n",
" int matching_index_outside_sym_gz = CCTK_GFINDEX3D(cctkGH,i,j,(num_gzs*2-stagger_z)-k);\n",
"\n",
" gridfunc[index_inside__sym_gz] = gridfunc_syms[2]*gridfunc[matching_index_outside_sym_gz];\n",
" }\n",
"}\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Step n-1: Code validation \\[Back to [top](#toc)\\]\n",
"$$\\label{code_validation}$$\n",
"\n",
"First we download the original `IllinoisGRMHD` source code and then compare it to the source code generated by this tutorial notebook."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Validation test for symmetry__set_gzs_staggered_gfs.C: FAILED!\n",
"Diff:\n",
"12c12\n",
"< if(CCTK_EQUALS(Symmetry, \"equatorial\")) \n",
"---\n",
"> if(CCTK_EQUALS(Symmetry, \"equatorial\"))\n",
"34c34\n",
"< * if num_gzs==1 && stagger_z==1: \n",
"---\n",
"> * if num_gzs==1 && stagger_z==1:\n",
"37,38c37,38\n",
"< * if num_gzs==2 && stagger_z==1: \n",
"< * z[] = {-3dz/2,-dz/2,dz/2,3dz/2 etc} \n",
"---\n",
"> * if num_gzs==2 && stagger_z==1:\n",
"> * z[] = {-3dz/2,-dz/2,dz/2,3dz/2 etc}\n",
"64a65\n",
"> \n"
]
}
],
"source": [
"# Verify if the code generated by this tutorial module\n",
"# matches the original IllinoisGRMHD source code\n",
"\n",
"# First download the original IllinoisGRMHD source code\n",
"import urllib\n",
"from os import path\n",
"\n",
"original_IGM_file_url = \"https://bitbucket.org/zach_etienne/wvuthorns/raw/5611b2f0b17135538c9d9d17c7da062abe0401b6/IllinoisGRMHD/src/symmetry__set_gzs_staggered_gfs.C\"\n",
"original_IGM_file_name = \"symmetry__set_gzs_staggered_gfs-original.C\"\n",
"original_IGM_file_path = os.path.join(IGM_src_dir_path,original_IGM_file_name)\n",
"\n",
"# Then download the original IllinoisGRMHD source code\n",
"# We try it here in a couple of ways in an attempt to keep\n",
"# the code more portable\n",
"try:\n",
" original_IGM_file_code = urllib.request.urlopen(original_IGM_file_url).read().decode(\"utf-8\")\n",
" # Write down the file the original IllinoisGRMHD source code\n",
" with open(original_IGM_file_path,\"w\") as file:\n",
" file.write(original_IGM_file_code)\n",
"except:\n",
" try:\n",
" original_IGM_file_code = urllib.urlopen(original_IGM_file_url).read().decode(\"utf-8\")\n",
" # Write down the file the original IllinoisGRMHD source code\n",
" with open(original_IGM_file_path,\"w\") as file:\n",
" file.write(original_IGM_file_code)\n",
" except:\n",
" # If all else fails, hope wget does the job\n",
" !wget -O $original_IGM_file_path $original_IGM_file_url\n",
"\n",
"# Perform validation\n",
"Validation__symmetry__set_gzs_staggered_gfs__C = !diff $original_IGM_file_path $outfile_path__symmetry__set_gzs_staggered_gfs__C\n",
"\n",
"if Validation__symmetry__set_gzs_staggered_gfs__C == []:\n",
" # If the validation passes, we do not need to store the original IGM source code file\n",
" !rm $original_IGM_file_path\n",
" print(\"Validation test for symmetry__set_gzs_staggered_gfs.C: PASSED!\")\n",
"else:\n",
" # If the validation fails, we keep the original IGM source code file\n",
" print(\"Validation test for symmetry__set_gzs_staggered_gfs.C: FAILED!\")\n",
" # We also print out the difference between the code generated\n",
" # in this tutorial module and the original IGM source code\n",
" print(\"Diff:\")\n",
" for diff_line in Validation__symmetry__set_gzs_staggered_gfs__C:\n",
" print(diff_line)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"\n",
"# Step n: 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-IllinoisGRMHD__symmetry__set_gzs_staggered_gfs.pdf](Tutorial-IllinoisGRMHD__symmetry__set_gzs_staggered_gfs.pdf) (Note that clicking on this link may not work; you may need to open the PDF file through another means)."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"latex_nrpy_style_path = os.path.join(nrpy_dir_path,\"latex_nrpy_style.tplx\")\n",
"#!jupyter nbconvert --to latex --template $latex_nrpy_style_path --log-level='WARN' Tutorial-IllinoisGRMHD__symmetry__set_gzs_staggered_gfs.ipynb\n",
"#!pdflatex -interaction=batchmode Tutorial-IllinoisGRMHD__symmetry__set_gzs_staggered_gfs.tex\n",
"#!pdflatex -interaction=batchmode Tutorial-IllinoisGRMHD__symmetry__set_gzs_staggered_gfs.tex\n",
"#!pdflatex -interaction=batchmode Tutorial-IllinoisGRMHD__symmetry__set_gzs_staggered_gfs.tex\n",
"!rm -f Tut*.out Tut*.aux Tut*.log"
]
}
],
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"name": "python3"
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