From 92ad7c03ea28302b5b306f43a6da49915db7d1d8 Mon Sep 17 00:00:00 2001 From: Maxence Thevenet Date: Thu, 9 Aug 2018 18:22:38 -0700 Subject: updated Tools/Visualization.ipynb --- Tools/Visualization.ipynb | 1027 ++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 911 insertions(+), 116 deletions(-) (limited to 'Tools/Visualization.ipynb') diff --git a/Tools/Visualization.ipynb b/Tools/Visualization.ipynb index 6a598db02..948ab8688 100644 --- a/Tools/Visualization.ipynb +++ b/Tools/Visualization.ipynb @@ -15,22 +15,18 @@ }, { "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, - "outputs": [], - "source": [ - "data_path = '../Example/Langmuir/'" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, - "outputs": [], + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/mthevenet/anaconda2/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\n", + " from ._conv import register_converters as _register_converters\n" + ] + } + ], "source": [ "# Import statements\n", "import os, glob\n", @@ -38,127 +34,905 @@ "from IPython.display import clear_output\n", "import numpy as np\n", "from ipywidgets import interact, ToggleButtons, IntSlider\n", + "# read_raw_data.py is located in warpx/Tools\n", + "import read_raw_data\n", "import matplotlib.pyplot as plt\n", - "%matplotlib" + "%matplotlib notebook" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Read data in the simulation frame" ] }, { "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, - "outputs": [], + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/mthevenet/anaconda2/lib/python2.7/site-packages/yt-3.5.dev0-py2.7-macosx-10.6-x86_64.egg/yt/units/yt_array.py:1372: RuntimeWarning: invalid value encountered in divide\n", + " out=out, **kwargs)\n" + ] + }, + { + "data": { + "text/html": [ + "
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ - "# YT basic usage. Read this for practical examples\n", - "# ------------------------------------------------\n", + "ds = yt.load( './before/plt00000' ) # Create a dataset object\n", + "sl = yt.SlicePlot(ds, 2, 'Ex', aspect=.02) # Create a sliceplot object\n", + "sl.set_xlabel(r'$x (\\mu m)$') # Set labels x\n", + "sl.set_ylabel(r'$z (\\mu m)$') # Set labels y\n", + "sl.annotate_particles(width=(10.e-6, 'm'), p_size=2, ptype='ions', col='black') # Plot particles species=ions\n", + "sl.annotate_particles(width=(10.e-6, 'm'), p_size=2, ptype='electrons', col='black')\n", + "sl.annotate_particles(width=(10.e-6, 'm'), p_size=2, ptype='beam', col='black')\n", + "sl.annotate_grids() # Show grids\n", + "sl.show() # Show the plot\n", "\n", - "# Create a dataset object\n", - "ds = yt.load( './pml/plt00400' )\n", - "# List all fields in the datasert\n", - "ds.field_list\n", - "# Get All Data from the dataset\n", - "ad = ds.all_data()\n", - "# Get some data. \".v\" converts arrays from units-aware yt arrays to numpy arrays.\n", - "# Magnetic field\n", - "b = ad['boxlib', 'Bx'].v\n", - "# particle weight and z coordinate for species particle0\n", - "w = ad['particle0', 'particle_momentum_z'].v\n", - "z = ad['particle0', 'particle_weight'].v\n", - "\n", - "# Create a sliceplot object\n", - "sl = yt.SlicePlot(ds, 2, 'Ex')\n", - "# Set labels\n", - "sl.set_xlabel(r'$x (\\mu m)$')\n", - "sl.set_ylabel(r'$z (\\mu m)$')\n", - "# Set figure size\n", - "sl.figure_size = (9, 7)\n", - "# Plot particles\n", - "sl.annotate_particles(width=1., p_size=2, ptype='particle0', col='black')\n", - "# Show grids\n", - "sl.annotate_grids()\n", - "# show the plot\n", - "sl.show()\n", - "# Save image\n", + "#############################\n", + "### OTHER USEFUL COMMANDS ###\n", + "#############################\n", + "# # List all fields in the datasert\n", + "# ds.field_list\n", + "# # Get All Data from the dataset\n", + "# ad = ds.all_data()\n", + "# # Get some data. \".v\" converts arrays from units-aware yt arrays to numpy arrays.\n", + "# Bx = ad['boxlib', 'Bx'].v\n", + "# # particle \n", + "# # CAREFUL! For the moment, 2d WarpX simulations use (x, z) spatial coordinate \n", + "# # but they are stored as (particle_position_x, particle_position_y) in Yt\n", + "# x = ad['beam', 'particle_position_x'].v\n", + "# z = ad['beam', 'particle_position_y'].v\n", + "# # For 2d simulations, WarpX and Yt use (ux, uz)\n", + "# # ux/c should be the nirmalized momentum\n", + "# ux = ad['beam', 'particle_momentum_x'].v\n", + "# uy = ad['beam', 'particle_momentum_y'].v\n", + "# uz = ad['beam', 'particle_momentum_z']\n", + "# w = ad['beam', 'particle_weight'].v\n", + "# # Set figure size\n", + "# sl.figure_size = (9, 7)\n", + "# # Save image\n", "# sl.save('./toto.pdf')\n", - "# This returns the domain boundaries\n", - "sl.bounds" + "# # This returns the domain boundaries\n", + "# sl.bounds" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "# Functions to plot the fields" + "## Read data back-transformed to the lab frame when the simulation runs in the boosted frame" ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ - "def plot_field( iteration, field, slicing_direction='y', plotter='matplotlib' ):\n", - " ds = yt.load( os.path.join(data_path, 'plt%05d/' %iteration) )\n", - " all_data_level_0 = ds.covering_grid(level=0, \n", - " left_edge=ds.domain_left_edge, \n", - " dims=ds.domain_dimensions)\n", - " \n", - " if plotter == 'yt':\n", - " sl = yt.SlicePlot(ds, slicing_direction, field)\n", - " sl.set_log( field, False)\n", - " sl.annotate_grids()\n", - " # Show the new plot\n", - " clear_output()\n", - " sl.show()\n", - "\n", - " elif plotter == 'matplotlib':\n", - "\n", - " left_edge = ds.domain_left_edge.convert_to_mks()*1.e6\n", - " right_edge = ds.domain_right_edge.convert_to_mks()*1.e6\n", - " \n", - " if ds.dimensionality == 3:\n", - " if slicing_direction == 'x':\n", - " n = int( ds.domain_dimensions[0]//2 )\n", - " data2d = all_data_level_0[field][n, :, :]\n", - " extent = [ left_edge[2], right_edge[2], left_edge[1], right_edge[1] ]\n", - " elif slicing_direction == 'y':\n", - " n = int( ds.domain_dimensions[1]//2 )\n", - " data2d = all_data_level_0[field][:, n, :]\n", - " extent = [ left_edge[2], right_edge[2], left_edge[0], right_edge[0] ]\n", - " elif slicing_direction == 'z':\n", - " n = int( ds.domain_dimensions[2]//2 )\n", - " data2d = all_data_level_0[field][:, :, n]\n", - " extent = [ left_edge[1], right_edge[1], left_edge[0], right_edge[0] ]\n", - " elif ds.dimensionality == 2:\n", - " data2d = all_data_level_0[field][:,:,0].T\n", - " extent = [ left_edge[1], right_edge[1], left_edge[0], right_edge[0] ]\n", - "\n", - " plt.clf()\n", - " plt.imshow( data2d.to_ndarray(), interpolation='nearest', cmap='viridis',\n", - " origin='lower', extent=extent )\n", - " plt.colorbar()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Interactive viewer" + "# For the moment, the back-transformed diagnostics must be read with \n", + "# custom functions like this one.\n", + "# It should be OpenPMD-compliant hdf5 files soon, making this part outdated.\n", + "def get_particle_field(snapshot, species, field):\n", + " fn = snapshot + '/' + species\n", + " files = glob.glob(os.path.join(fn, field + '_*'))\n", + " all_data = np.array([])\n", + " for f in files:\n", + " data = np.fromfile(f)\n", + " all_data = np.concatenate((all_data, data))\n", + " return all_data" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "metadata": {}, "outputs": [ { "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "51d3a2c04a684310a3e87ee33674f728" - } + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "window.mpl = {};\n", + "\n", + "\n", + "mpl.get_websocket_type = function() {\n", + " if (typeof(WebSocket) !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof(MozWebSocket) !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert('Your browser does not have WebSocket support.' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. 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