examples/cloud_parcel.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "6f3ab7ce",
   "metadata": {},
   "source": [
    "[![View notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/PyPartMC/blob/main/examples/cloud_parcel.ipynb)   \n",
    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/cloud_parcel.ipynb)    \n",
    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/cloud_parcel.ipynb)    \n",
    "[![ARM JupyterHub](https://img.shields.io/static/v1?label=launch%20in&logo=jupyter&color=lightblue&message=ARM+JupyterHub)](https://jupyterhub.arm.gov/hub/user-redirect/git-pull?repo=https%3A//github.com/open-atmos/PyPartMC&branch=main&urlPath=) (requires [logging in with ARM account](https://www.arm.gov/capabilities/computing-resources) and directing Jupyter to a notebook within the cloned repo)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "159edeb4",
   "metadata": {},
   "outputs": [],
   "source": [
    "# This file is a part of PyPartMC licensed under the GNU General Public License v3\n",
    "# Copyright (C) 2024 University of Illinois Urbana-Champaign\n",
    "# Authors:\n",
    "#  - https://github.com/compdyn/partmc/graphs/contributors\n",
    "#  - https://github.com/open-atmos/PyPartMC/graphs/contributors"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "4f8359c2",
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "import os\n",
    "if 'google.colab' in sys.modules:\n",
    "    !pip --quiet install open-atmos-jupyter-utils\n",
    "    from open_atmos_jupyter_utils import pip_install_on_colab\n",
    "    pip_install_on_colab('PyPartMC')\n",
    "elif 'JUPYTER_IMAGE' in os.environ and '.arm.gov' in os.environ['JUPYTER_IMAGE']:\n",
    "    !pip --quiet install PyPartMC open_atmos_jupyter_utils\n",
    "    _pypartmc_path = !pip show PyPartMC | fgrep Location | cut -f2 -d' '\n",
    "    sys.path.extend(_pypartmc_path if _pypartmc_path[0] not in sys.path else [])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "b494ea6e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "from open_atmos_jupyter_utils import show_plot\n",
    "import PyPartMC as ppmc\n",
    "from PyPartMC import si"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "df8d1a84",
   "metadata": {},
   "outputs": [],
   "source": [
    "gas_data = ppmc.GasData((\n",
    "    \"H2SO4\", \"HNO3\", \"HCl\", \"NH3\", \"NO\", \"NO2\", \"NO3\", \"N2O5\", \"HONO\", \"HNO4\",\n",
    "    \"O3\", \"O1D\", \"O3P\", \"OH\", \"HO2\", \"H2O2\", \"CO\", \"SO2\", \"CH4\", \"C2H6\",\n",
    "    \"CH3O2\", \"ETHP\", \"HCHO\", \"CH3OH\", \"ANOL\", \"CH3OOH\", \"ETHOOH\", \"ALD2\",\n",
    "    \"HCOOH\", \"RCOOH\", \"C2O3\", \"PAN\", \"ARO1\", \"ARO2\", \"ALK1\", \"OLE1\", \"API1\",\n",
    "    \"API2\", \"LIM1\", \"LIM2\", \"PAR\", \"AONE\", \"MGLY\", \"ETH\", \"OLET\", \"OLEI\",\n",
    "    \"TOL\", \"XYL\", \"CRES\", \"TO2\", \"CRO\", \"OPEN\", \"ONIT\", \"ROOH\", \"RO2\", \"ANO2\",\n",
    "    \"NAP\", \"XO2\", \"XPAR\", \"ISOP\", \"ISOPRD\", \"ISOPP\", \"ISOPN\", \"ISOPO2\", \"API\",\n",
    "    \"LIM\", \"DMS\", \"MSA\", \"DMSO\", \"DMSO2\", \"CH3SO2H\", \"CH3SCH2OO\", \"CH3SO2\",\n",
    "    \"CH3SO3\", \"CH3SO2OO\", \"CH3SO2CH2OO\", \"SULFHOX\"\n",
    "))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "a2d7bad8",
   "metadata": {},
   "outputs": [],
   "source": [
    "env_state = ppmc.EnvState({\n",
    "    \"rel_humidity\": 0.95,\n",
    "    \"latitude\": 0,\n",
    "    \"longitude\": 0,\n",
    "    \"altitude\": 0 * si.m,\n",
    "    \"start_time\": 21600 * si.s,\n",
    "    \"start_day\": 200,\n",
    "})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "815283a0",
   "metadata": {},
   "outputs": [],
   "source": [
    "aero_data = ppmc.AeroData((\n",
    "    #   density        ions in soln (1)    molecular weight    kappa (1)\n",
    "    #         \\                       \\    /                     |\n",
    "    {\"SO4\":  [1800 * si.kg / si.m**3, 1,  96.0 * si.g / si.mol, 0.00]},\n",
    "    {\"NO3\":  [1800 * si.kg / si.m**3, 1,  62.0 * si.g / si.mol, 0.00]},\n",
    "    {\"Cl\":   [2200 * si.kg / si.m**3, 1,  35.5 * si.g / si.mol, 0.00]},\n",
    "    {\"NH4\":  [1800 * si.kg / si.m**3, 1,  18.0 * si.g / si.mol, 0.00]},\n",
    "    {\"MSA\":  [1800 * si.kg / si.m**3, 0,  95.0 * si.g / si.mol, 0.53]},\n",
    "    {\"ARO1\": [1400 * si.kg / si.m**3, 0, 150.0 * si.g / si.mol, 0.10]},\n",
    "    {\"ARO2\": [1400 * si.kg / si.m**3, 0, 150.0 * si.g / si.mol, 0.10]},\n",
    "    {\"ALK1\": [1400 * si.kg / si.m**3, 0, 140.0 * si.g / si.mol, 0.10]},\n",
    "    {\"OLE1\": [1400 * si.kg / si.m**3, 0, 140.0 * si.g / si.mol, 0.10]},\n",
    "    {\"API1\": [1400 * si.kg / si.m**3, 0, 184.0 * si.g / si.mol, 0.10]},\n",
    "    {\"API2\": [1400 * si.kg / si.m**3, 0, 184.0 * si.g / si.mol, 0.10]},\n",
    "    {\"LIM1\": [1400 * si.kg / si.m**3, 0, 200.0 * si.g / si.mol, 0.10]},\n",
    "    {\"LIM2\": [1400 * si.kg / si.m**3, 0, 200.0 * si.g / si.mol, 0.10]},\n",
    "    {\"CO3\":  [2600 * si.kg / si.m**3, 1,  60.0 * si.g / si.mol, 0.00]},\n",
    "    {\"Na\":   [2200 * si.kg / si.m**3, 1,  23.0 * si.g / si.mol, 0.00]},\n",
    "    {\"Ca\":   [2600 * si.kg / si.m**3, 1,  40.0 * si.g / si.mol, 0.00]},\n",
    "    {\"OIN\":  [2600 * si.kg / si.m**3, 0,   1.0 * si.g / si.mol, 0.10]},\n",
    "    {\"OC\":   [1400 * si.kg / si.m**3, 0,   1.0 * si.g / si.mol, 0.10]},\n",
    "    {\"BC\":   [1800 * si.kg / si.m**3, 0,   1.0 * si.g / si.mol, 0.00]},\n",
    "    {\"H2O\":  [1000 * si.kg / si.m**3, 0,  18.0 * si.g / si.mol, 0.00]},\n",
    "))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "c822823d",
   "metadata": {},
   "outputs": [],
   "source": [
    "gas_state = ppmc.GasState(gas_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "58706963",
   "metadata": {},
   "outputs": [],
   "source": [
    "AERO_DIST_BACKGROUND = {\n",
    "    \"back_small\": {\n",
    "        \"mass_frac\": [{\"SO4\": [1]}, {\"OC\": [1.375]}, {\"NH4\": [0.375]}],\n",
    "        \"diam_type\": \"geometric\",\n",
    "        \"mode_type\": \"log_normal\",\n",
    "        \"num_conc\": 3.2e9 / si.m**3,\n",
    "        \"geom_mean_diam\": 0.02 * si.um,\n",
    "        \"log10_geom_std_dev\": 0.161,\n",
    "    },\n",
    "}\n",
    "\n",
    "AERO_DIST_EMIT = {\n",
    "    \"gasoline\": {\n",
    "        \"mass_frac\": [{\"OC\": [0.8]}, {\"BC\": [0.2]}],\n",
    "        \"diam_type\": \"geometric\",\n",
    "        \"mode_type\": \"log_normal\",\n",
    "        \"num_conc\": 5e7 / si.m**3,\n",
    "        \"geom_mean_diam\": 5e-8 * si.m,\n",
    "        \"log10_geom_std_dev\": 0.24,\n",
    "    },\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c6a96b7d",
   "metadata": {},
   "outputs": [],
   "source": [
    "time_timeseries = [0, 1200]\n",
    "pressure_timeseries = [1e5, 1e5]\n",
    "temp_timeseries = [290, 280]\n",
    "height_timeseries = [200, 200]\n",
    "times = [0 * si.s]\n",
    "gas_emit_times = [0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "920e41e3",
   "metadata": {},
   "outputs": [],
   "source": [
    "scenario = ppmc.Scenario(\n",
    "    gas_data,\n",
    "    aero_data,\n",
    "    {\n",
    "        \"temp_profile\": [\n",
    "            {\"time\": time_timeseries},\n",
    "            {\"temp\": temp_timeseries}\n",
    "        ],\n",
    "        \"pressure_profile\": [\n",
    "            {\"time\": time_timeseries},\n",
    "            {\"pressure\": pressure_timeseries},\n",
    "        ],\n",
    "        \"height_profile\": [\n",
    "            {\"time\": time_timeseries},\n",
    "            {\"height\": height_timeseries}\n",
    "        ],\n",
    "        \"gas_emissions\": [\n",
    "            {\"time\": gas_emit_times},\n",
    "            {\"rate\": [0.] * len(gas_emit_times)},\n",
    "        ],\n",
    "        \"gas_background\": [\n",
    "            {\"time\": times},\n",
    "            {\"rate\": [0.0 / si.s] * len(times)},\n",
    "        ],\n",
    "        \"aero_emissions\": [\n",
    "            {\"time\": [0 * si.s, 12 * 3600 * si.s]},\n",
    "            {\"rate\": [0 / si.s, 0 / si.s]},\n",
    "            {\"dist\": [[AERO_DIST_EMIT], [AERO_DIST_EMIT]]},\n",
    "        ],\n",
    "        \"aero_background\": [\n",
    "            {\"time\": [0 * si.s]},\n",
    "            {\"rate\": [0 / si.s]},\n",
    "            {\"dist\": [[AERO_DIST_BACKGROUND]]},\n",
    "        ],\n",
    "        \"loss_function\": \"none\",\n",
    "    },\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "6722ba83",
   "metadata": {},
   "outputs": [],
   "source": [
    "T_INITIAL = 0.0\n",
    "scenario.init_env_state(env_state, T_INITIAL)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "9781ca2f",
   "metadata": {},
   "outputs": [],
   "source": [
    "AERO_DIST_INIT = [{\n",
    "    \"init_small\": {\n",
    "        \"mass_frac\": [{\"SO4\": [1]}, {\"OC\": [1.375]}, {\"NH4\": [0.375]}],\n",
    "        \"diam_type\": \"geometric\",\n",
    "        \"mode_type\": \"log_normal\",\n",
    "        \"num_conc\": 3.2e9 / si.m**3,\n",
    "        \"geom_mean_diam\": 0.02 * si.um,\n",
    "        \"log10_geom_std_dev\": 0.161,\n",
    "    },\n",
    "    \"init_large\": {\n",
    "        \"mass_frac\": [{\"SO4\": [1]}, {\"OC\": [1.375]}, {\"NH4\": [0.375]}],\n",
    "        \"diam_type\": \"geometric\",\n",
    "        \"mode_type\": \"log_normal\",\n",
    "        \"num_conc\": 2.9e9 / si.m**3,\n",
    "        \"geom_mean_diam\": 0.16 * si.um,\n",
    "        \"log10_geom_std_dev\": 0.217,\n",
    "    },\n",
    "}]\n",
    "\n",
    "aero_dist_init = ppmc.AeroDist(aero_data, AERO_DIST_INIT)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "d8d9c8fd",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "244"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "run_part_opt = ppmc.RunPartOpt({\n",
    "    \"output_prefix\": \"urban_plume\",\n",
    "    \"do_coagulation\": False,\n",
    "    \"t_max\": 600 * si.s,\n",
    "    \"del_t\": 1 * si.s,\n",
    "    \"do_condensation\": True\n",
    "})\n",
    "\n",
    "N_PART = 500\n",
    "aero_state = ppmc.AeroState(aero_data, N_PART, 'flat_source')\n",
    "aero_state.dist_sample(\n",
    "    aero_dist_init,\n",
    "    sample_prop=1.0,\n",
    "    create_time=0.0,\n",
    "    allow_doubling=True,\n",
    "    allow_halving=True,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "10c018d8",
   "metadata": {},
   "outputs": [],
   "source": [
    "ppmc.condense_equilib_particles(env_state,aero_data, aero_state)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "5c8aef2b",
   "metadata": {},
   "outputs": [],
   "source": [
    "camp_core = ppmc.CampCore()\n",
    "photolysis = ppmc.Photolysis()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "0f7c29fe",
   "metadata": {},
   "outputs": [],
   "source": [
    "N_STEPS = int(run_part_opt.t_max / run_part_opt.del_t)\n",
    "\n",
    "output = {\n",
    "    aero_state: ('total_num_conc', 'total_mass_conc'),\n",
    "    env_state: ('height', 'temp', 'rh', 'air_density', 'elapsed_time'),\n",
    "}\n",
    "\n",
    "data = {\n",
    "    **{\n",
    "        attr: np.zeros(N_STEPS + 1)\n",
    "            for attrs in output.values()\n",
    "                for attr in attrs \n",
    "    },\n",
    "    **{\n",
    "        'gas_mix_rat': np.zeros((N_STEPS + 1, gas_state.n_spec)),\n",
    "        'dists': {}\n",
    "    }\n",
    "}\n",
    "\n",
    "diam_grid = ppmc.BinGrid(50, \"log\", 1e-9 * si.m, 1e-4 * si.m)\n",
    "\n",
    "last_output_time = 0.\n",
    "last_progress_time = 0.\n",
    "i_output = 1\n",
    "\n",
    "for i_time in range(0, N_STEPS + 1):\n",
    "    if i_time != 0:\n",
    "        last_output_time, last_progress_time, i_output = ppmc.run_part_timestep(\n",
    "            scenario,\n",
    "            env_state,\n",
    "            aero_data,\n",
    "            aero_state,\n",
    "            gas_data,\n",
    "            gas_state,\n",
    "            run_part_opt,\n",
    "            camp_core,\n",
    "            photolysis,\n",
    "            i_time,\n",
    "            T_INITIAL,\n",
    "            last_output_time,\n",
    "            last_progress_time,\n",
    "            i_output\n",
    "        )\n",
    "    for obj, attrs in output.items():\n",
    "        for attr in attrs:\n",
    "            data[attr][i_time] = getattr(obj, attr)\n",
    "    data['gas_mix_rat'][i_time, :] = gas_state.mix_rats\n",
    "    if np.mod(i_time * run_part_opt.del_t, 60 * si.s) == 0:\n",
    "        data['dists'][i_time] = ppmc.histogram_1d(\n",
    "            diam_grid,\n",
    "            aero_state.diameters(),\n",
    "            np.asarray(aero_state.num_concs) / env_state.air_density\n",
    "        )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "82c0cebb",
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.rcParams.update({'font.size': 9})\n",
    "plt.rcParams.update({'figure.figsize': (3.08, 2.5)})\n",
    "plt.rcParams.update({\"axes.grid\" : True})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "47474cd3",
   "metadata": {},
   "outputs": [
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   "source": [
    "plt.plot(data['elapsed_time'], data['temp'], 'r')\n",
    "plt.ylabel('Temperature (K)', color='r')\n",
    "plt.ylim([275, 300])\n",
    "plt.xticks(np.linspace(0, data['elapsed_time'][-1], 5))\n",
    "plt.xlim([0, data['elapsed_time'][-1]])\n",
    "plt.xlabel('Time (s)')\n",
    "plt.twinx()\n",
    "plt.plot(data['elapsed_time'], data['rh'] * 100, 'g')\n",
    "plt.ylabel('Relative humidity (%)', color='g')\n",
    "plt.ylim([50, 101])\n",
    "show_plot()"
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  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "8e1b89e0",
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   "source": [
    "plt.plot(\n",
    "    data['elapsed_time'],\n",
    "    data['total_mass_conc'] / data['air_density'],\n",
    "    \"b\", label=\"mass conc\"\n",
    ")\n",
    "plt.ylabel(r\"H2O mass mixing ratio (kg kg$_{\\rm dry air}^{-1}$)\", color='b')\n",
    "plt.xlabel(\"Time (s)\")\n",
    "plt.twinx()\n",
    "plt.plot(\n",
    "    data['elapsed_time'],\n",
    "    data['total_num_conc'] / data['air_density'],\n",
    "    \"g\", label=\"num conc\"\n",
    ")\n",
    "plt.xticks(np.linspace(0, data['elapsed_time'][-1], 5))\n",
    "plt.xlim([data['elapsed_time'][0], data['elapsed_time'][-1]])\n",
    "plt.ylabel(r\"Number density ($\\#$ kg$_{\\rm dry air}^{-1}$)\", color='g')\n",
    "show_plot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "faa1de28",
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   "outputs": [
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   "source": [
    "for i in (0, 5, 10):\n",
    "    plt.plot(\n",
    "        diam_grid.centers,\n",
    "        data['dists'][i * 60 * si.s / run_part_opt.del_t],\n",
    "        label=f'$t = {i}$ min'\n",
    "    )\n",
    "plt.xscale(\"log\")\n",
    "plt.xlabel(\"Diameter (m)\")\n",
    "plt.ylabel(r\"Number mixing ratio $n(D)$ ($\\#$ kg$_{\\rm dry air}^{-1}$)\")\n",
    "plt.ylim(bottom=0)\n",
    "plt.legend()\n",
    "plt.xlim(diam_grid.edges[0], diam_grid.edges[-1])\n",
    "show_plot()"
   ]
  },
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   "cell_type": "code",
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   "id": "ef17d66c-c058-4512-8da8-c0bc56856cb5",
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   "outputs": [],
   "source": []
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