{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Analyzing AMReX Outputs From FLEKS\n",
"\n",
"In this demo, we show how to analyze native AMReX field and particle outputs. Example data can be downloaded as follows:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import flekspy\n",
"from flekspy.util import download_testfile\n",
"\n",
"url = \"https://raw.githubusercontent.com/henry2004y/batsrus_data/master/fleks_particle_small.tar.gz\"\n",
"download_testfile(url, \"data\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Inheriting from the IDL procedures, we can pass strings to limit the plotting range (experimental, may be changed in the future):"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"ds = flekspy.load(\"data/fleks_particle_small/3d*amrex\")\n",
"dc = ds.get_slice(\"z\", 0.001)\n",
"\n",
"f, axes = dc.plot(\n",
" \"Bx<(1.5e4)>(-1.5e4) ({rhos0}+{rhos1})<(1.3e21) pS0 uxs0\", figsize=(12, 8)\n",
")\n",
"dc.add_stream(axes[0], \"Bx\", \"By\", color=\"w\")\n",
"dc.add_contour(axes[1], \"Bx\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Velocity Space Distributions"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from flekspy.util import unit_one\n",
"\n",
"filename = \"data/fleks_particle_small/cut_*amrex\"\n",
"ds = flekspy.load(filename)\n",
"\n",
"# Add a user defined field. See yt document for more information about derived field.\n",
"ds.add_field(\n",
" ds.pvar(\"unit_one\"), function=unit_one, sampling_type=\"particle\", units=\"code_mass\"\n",
")\n",
"\n",
"x_field = \"p_uy\"\n",
"y_field = \"p_uz\"\n",
"z_field = \"unit_one\"\n",
"# z_field = \"p_w\"\n",
"xleft = [-0.001, -0.001, -0.001]\n",
"xright = [0.001, 0.001, 0.001]\n",
"\n",
"### Select and plot the particles inside a box defined by xleft and xright\n",
"region = ds.box(xleft, xright)\n",
"pp = ds.plot_phase(\n",
" x_field,\n",
" y_field,\n",
" z_field,\n",
" region=region,\n",
" unit_type=\"si\",\n",
" x_bins=64,\n",
" y_bins=64,\n",
" domain_size=(-0.0002, 0.0002, -0.0002, 0.0002),\n",
")\n",
"\n",
"pp.set_cmap(pp.fields[0], \"turbo\")\n",
"\n",
"# plot.set_zlim(plot.fields[0], zmin, zmax)\n",
"pp.set_xlabel(r\"$V_y$\")\n",
"pp.set_ylabel(r\"$V_z$\")\n",
"# pp.set_colorbar_label(pp.fields[0], \"pw\")\n",
"pp.set_title(pp.fields[0], \"Number density\")\n",
"pp.set_font(\n",
" {\n",
" \"size\": 34,\n",
" \"family\": \"DejaVu Sans\",\n",
" }\n",
")\n",
"pp.set_log(pp.fields[0], False)\n",
"pp.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you need the direct phase space distributions together with the axis,"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"x, y, w = ds.get_phase(\n",
" x_field,\n",
" y_field,\n",
" z_field,\n",
" region=region,\n",
" x_bins=64,\n",
" y_bins=64,\n",
" domain_size=(-0.0002, 0.0002, -0.0002, 0.0002),\n",
")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"To check the newly added field,"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"ad = ds.all_data()\n",
"ad[(\"particles\", \"unit_one\")]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Plot the location of particles that are inside a sphere"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"center = [0, 0, 0]\n",
"radius = 0.001\n",
"z_field = \"unit_one\"\n",
"# Object sphere is defined in yt/data_objects/selection_objects/spheroids.py\n",
"sp = ds.sphere(center, radius)\n",
"pp = ds.plot_particles(\n",
" \"p_x\", \"p_y\", z_field, region=sp, unit_type=\"planet\", x_bins=64, y_bins=64\n",
")\n",
"pp.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Plot the phase space of particles that are inside a sphere"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pp = ds.plot_phase(\n",
" \"p_uy\", \"p_uz\", z_field, region=sp, unit_type=\"planet\", x_bins=64, y_bins=64\n",
")\n",
"pp.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Plot the location of particles that are inside a disk"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"center = [0, 0, 0]\n",
"normal = [1, 1, 0]\n",
"radius = 0.0005\n",
"height = 0.0004\n",
"z_field = \"unit_one\"\n",
"# Object sphere is defined in yt/data_objects/selection_objects/disk.py\n",
"disk = ds.disk(center, normal, radius, height)\n",
"pp = ds.plot_particles(\n",
" \"p_x\", \"p_y\", z_field, region=disk, unit_type=\"planet\", x_bins=64, y_bins=64\n",
")\n",
"pp.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Plot the phase space of particles that are inside a disk"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pp = ds.plot_phase(\n",
" \"p_uy\", \"p_uz\", z_field, region=disk, unit_type=\"planet\", x_bins=64, y_bins=64\n",
")\n",
"pp.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Transform the velocity coordinates and visualize the phase space distribution\n",
"\n",
"WIP"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import flekspy, yt\n",
"\n",
"l = [1, 0, 0]\n",
"m = [0, 1, 0]\n",
"n = [0, 0, 1]\n",
"\n",
"\n",
"def _vel_l(field, data):\n",
" res = (\n",
" l[0] * data[(\"particles\", \"p_ux\")]\n",
" + l[1] * data[(\"particles\", \"p_uy\")]\n",
" + l[2] * data[(\"particles\", \"p_uz\")]\n",
" )\n",
" return res\n",
"\n",
"\n",
"def _vel_m(field, data):\n",
" res = (\n",
" m[0] * data[(\"particles\", \"p_ux\")]\n",
" + m[1] * data[(\"particles\", \"p_uy\")]\n",
" + m[2] * data[(\"particles\", \"p_uz\")]\n",
" )\n",
" return res\n",
"\n",
"\n",
"def _vel_n(field, data):\n",
" res = (\n",
" n[0] * data[(\"particles\", \"p_ux\")]\n",
" + n[1] * data[(\"particles\", \"p_uy\")]\n",
" + n[2] * data[(\"particles\", \"p_uz\")]\n",
" )\n",
" return res\n",
"\n",
"\n",
"filename = \"data/fleks_particle_small/cut_*amrex\"\n",
"ds = flekspy.load(filename)\n",
"\n",
"# Add a user defined field. See yt document for more information about derived field.\n",
"vl_name = ds.pvar(\"vel_l\")\n",
"vm_name = ds.pvar(\"vel_m\")\n",
"vn_name = ds.pvar(\"vel_n\")\n",
"ds.add_field(vl_name, units=\"code_velocity\", function=_vel_l, sampling_type=\"particle\")\n",
"ds.add_field(vm_name, units=\"code_velocity\", function=_vel_m, sampling_type=\"particle\")\n",
"ds.add_field(vn_name, units=\"code_velocity\", function=_vel_n, sampling_type=\"particle\")\n",
"\n",
"######## Plot the location of particles that are inside a sphere ###########\n",
"center = [0, 0, 0]\n",
"radius = 0.001\n",
"# Object sphere is defined in yt/data_objects/selection_objects/spheroids.py\n",
"sp = ds.sphere(center, radius)\n",
"\n",
"x_field = vl_name\n",
"y_field = vm_name\n",
"z_field = ds.pvar(\"p_w\")\n",
"\n",
"logs = {x_field: False, y_field: False}\n",
"profile = yt.create_profile(\n",
" data_source=sp,\n",
" bin_fields=[x_field, y_field],\n",
" fields=z_field,\n",
" n_bins=[64, 64],\n",
" weight_field=None,\n",
" logs=logs,\n",
")\n",
"\n",
"pp = yt.PhasePlot.from_profile(profile)\n",
"\n",
"pp.set_unit(x_field, \"km/s\")\n",
"pp.set_unit(y_field, \"km/s\")\n",
"pp.set_unit(z_field, \"amu\")\n",
"\n",
"pp.set_cmap(pp.fields[0], \"turbo\")\n",
"# pp.set_zlim(pp.fields[0], zmin, zmax)\n",
"pp.set_xlabel(r\"$V_l$\")\n",
"pp.set_ylabel(r\"$V_m$\")\n",
"pp.set_colorbar_label(pp.fields[0], \"colorbar_label\")\n",
"pp.set_title(pp.fields[0], \"Density\")\n",
"pp.set_font(\n",
" {\n",
" \"size\": 34,\n",
" \"family\": \"DejaVu Sans\",\n",
" }\n",
")\n",
"pp.set_log(pp.fields[0], False)\n",
"pp.show()"
]
}
],
"metadata": {
"language_info": {
"name": "python"
}
},
"nbformat": 4,
"nbformat_minor": 2
}