![\"Open](\"https://colab.research.google.com/assets/colab-badge.svg\"){kind=icon}
\n",
"\n",
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## External dependencies"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you are working in Google Colab use this to install dependencies. "
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {},
"outputs": [],
"source": [
"import sys \n",
"if 'google.colab' in sys.modules:\n",
" !pip install -Uq multirex\n",
" !mkdir resources/"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"> **NOTE**: After installing you should reset Colab session before importing the package. This is to avoid an unintended behavior of the package `pybtex`."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you have already reset the Colab session, let's import `MultiREx` and any other package required for this example:"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Loading MultiREx version 0.1.5\n"
]
}
],
"source": [
"import multirex as mrex\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"import pandas as pd\n",
"# This is for developing purposes\n",
"%load_ext autoreload \n",
"%autoreload 2"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Creating a single system"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Components"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The central concept in `MultiREx` is that of a system. A system is made of a star, a planet and its atmosphere. Each component may have a wide range of properties useful for the purposes of the package. However, the key properties required for calculating a basic transmission spectra are defined below:\n",
"\n",
"- **Star**:\n",
" - Effective temperature in Kelvins (attribute `temperature`).\n",
" - Radius in solar radii (attribute `radius`).\n",
" - Mass in solar masses (attribute `mass`).\n",
"\n",
"- **Planet**:\n",
" - Radius in Earth radii (attribute `radius`).\n",
" - Mass in Earth masses (attribute `mass`).\n",
"\n",
"- **Atmosphere**: \n",
" - Surface temperature in Kelvins (attribute `temperature`).\n",
" - Surface pressure in Pascals (attribute `base_pressure`).\n",
" - Pressure at the top of the atmosphere in Pascals (attribute `top_pressure`).\n",
" - Composition (attribute `composition`). This is provided as a dictionary whose keys are the name of the gasses (e.g. 'CO2', 'CH4') and the value are the $log_{10}$ of the mixing ratio of the corresponding gas. \n",
" - Fill gass name (attribute `fill_gass`), i.e. the gass which fills the atmopshere (usually 'N2' for atmospheres of inhabited planets)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Available gasses"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you want to see the list of available gasses in the package use:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Available gases in the database:\n",
"['CO2', 'CH4', 'O2', 'O3', 'H2O']\n"
]
}
],
"source": [
"mrex.Util.list_gases()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"`MultiREx` comes along with [ExoTransmit](https://github.com/elizakempton/Exo_Transmit/tree/master/Opac) opacities for these particular gasses. These opacities are low resolution and light-weighted. They should be used only for testing purposes. For larger scientific applications, `MultiREx` provides a larger database of high-resolution opacities (most of them from [ExoMol](https://www.exomol.com/data/search/)) for a larger number of gasses. This database is hosted in a Google Drive repository and can be obtained and loaded into the running instance of `MultiREx` using:\n",
"\n",
"> **WARNING**: Be careful with this command: it will use as much as 4 GB of disk space."
]
},
{
"cell_type": "code",
"execution_count": 39,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The directory to the opacity database already exists in the specified path: /tmp\n"
]
}
],
"source": [
"mrex.Util.get_gases(path='/tmp')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Once downloaded, the list of available gasses are considerably larger:_"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Available gases in the database:\n",
"['DMS', 'NO2', 'SO2', 'CO', 'CO2', 'CH4', 'NH3', 'HCN', 'O2', 'O3', 'C2H6', 'CH3Cl', 'H2O', 'N2']\n"
]
}
],
"source": [
"mrex.Util.list_gases()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Creating components of the system"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's create a star:"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"star = mrex.Star(temperature=5777,radius=1,mass=1)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You may get the attributes of the star using:"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(1, 5777)"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"star.mass, star.temperature"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You may also modify the mass of the star:"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"star.set_mass(1.5)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now create the planet:"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"planet = mrex.Planet(radius=1,mass=1)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"And finally create the atmosphere:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"atmosphere = mrex.Atmosphere(\n",
" temperature=288, # in K\n",
" base_pressure=1e5, # in Pa\n",
" top_pressure=1, # in Pa\n",
" fill_gas='N2', # the gas that fills the atmosphere\n",
" composition=dict(\n",
" CO2=-4, # This is the log10(mix-ratio)\n",
" CH4=-6,\n",
" )\n",
")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Once created we can integrate the three components in a system:"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"planet.set_atmosphere(atmosphere)\n",
"system = mrex.System(star=star,planet=planet,sma=1)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"After ensembling the components you still have access to the properties independently:"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"1"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"system.planet.radius"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can ensemble a system using a single command like:"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"system = mrex.System(\n",
" star=mrex.Star(\n",
" temperature=5777,\n",
" radius=1,\n",
" mass=1\n",
" ),\n",
" planet=mrex.Planet(\n",
" radius=1,\n",
" mass=1,\n",
" atmosphere=mrex.Atmosphere(\n",
" temperature=290, # in K\n",
" base_pressure=1e5, # in Pa\n",
" top_pressure=1, # in Pa\n",
" fill_gas='N2', # the gas that fills the atmosphere\n",
" composition=dict(\n",
" CO2=-4, # This is the log10(mix-ratio)\n",
" CH4=-6,\n",
" )\n",
" )\n",
" ),\n",
" sma=1\n",
")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### The transmission model"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Once we have a system we can create the transmission model:"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"system.make_tm()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The transmission model is a `Taurex` class that allows us to create transmission spectra as desired. It encapsulates all the attributes and methods used to described the atmosphere that are taken into account when calculating the transmission spectra. `MultiREx` essentially simplify the interaction with the wide range of options of `TauREx` for specifying those attributes. "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You may take a quick look to the attributes of the transmission model using:"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'_log_name': 'taurex.TransmissionModel',\n",
" '_logger': | \n", " | noise | \n", "SNR | \n", "10.0 | \n", "9.971877349033692 | \n", "9.943833786417125 | \n", "9.915869089732885 | \n", "9.887983037189068 | \n", "9.860175407617508 | \n", "9.832445980472007 | \n", "9.804794535826622 | \n", "... | \n", "0.6154019907123947 | \n", "0.6136713171735172 | \n", "0.6119455107474266 | \n", "0.6102245577465119 | \n", "0.6085084445216544 | \n", "0.6067971574621212 | \n", "0.6050906829954558 | \n", "0.6033890075873711 | \n", "0.6016921177416427 | \n", "0.6 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "1.641670e-07 | \n", "10 | \n", "0.000084 | \n", "0.000084 | \n", "0.000084 | \n", "0.000084 | \n", "0.000084 | \n", "0.000084 | \n", "0.000084 | \n", "0.000084 | \n", "... | \n", "0.000084 | \n", "0.000085 | \n", "0.000085 | \n", "0.000084 | \n", "0.000084 | \n", "0.000084 | \n", "0.000084 | \n", "0.000085 | \n", "0.000085 | \n", "0.000085 | \n", "
1 rows × 1002 columns
\n", "