interpolate_to_access-om2.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Create initial and boundary conditions for BGC of ACCESS-OM2*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### A few notes:\n",
    "\n",
    "1. Directory structure\n",
    "    - directories are based on `basepath`\n",
    "    - `input` contains input data\n",
    "    - `tmp` is where the regridded data will be stored initially (to be deleted manually after regridding is finished).\n",
    "    - `1deg, 025deg, 01deg` are where the regridded data used for model simulations will be stored (permanent locations).\n",
    "    - `insource` is where the input files are symlinked from.\n",
    "    - `cplpath` is the parent to the dirs that i2o.nc and o2i.nc are copied from.\n",
    "\n",
    "0. To run ACCESS-OM2* with BGC, the following files are required:\n",
    "    - bgc_param.nc (parameters)\n",
    "    - co2_iaf.nc or co2_ryf.nc (atmospheric co2 concentrations)\n",
    "    - csiro_bgc.res.nc (initial conditions)\n",
    "    - csiro_bgc_sediment.res.nc (initial sediment conditions)\n",
    "    - dust.nc (dust deposition for iron)\n",
    "\n",
    "0. In addition, the following files need to be updated by adding extra coupling tracers for ice BGC (initialised to zeros for simplicity):\n",
    "    - i2o.nc\n",
    "    - o2i.nc\n",
    "\n",
    "0. There are a few options for BGC initial conditions. The current version of this script supports generation of initial conditions either from:\n",
    "    - access-om2-1deg_omip2_cycle5 (adic,dic,alk)\n",
    "    - WOA13v2 (no3,o2; OMIP protocol)\n",
    "    - GLODAPv2 2016b (no3,o2,adic,dic,alk)\n",
    "    - FeMIP median (fe; mol L-1)\n",
    "    - 0.01 mmol m-3 is given to phy,zoo,det,caco3.\n",
    "\n",
    "0. Before regridding, input data are extrapolated over land to avoid missing values over the regridded ocean in case slight changes in the model bathymetry occurs in the future. This is done using `cdo fillmiss`.\n",
    "\n",
    "0. WOMBAT wants these fields in the units of mmol m-3 for all tracers except for iron (umol m-3). Therefore, appropriate unit conversion is needed if the input data are provided in different units. \n",
    "\n",
    "0. This script should be run using `gadi_jupyter` by requesting the maximum memory for a whole node i.e., `192 GB`."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Load relevant modules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "from scipy.interpolate import griddata,interpn\n",
    "import numpy as np\n",
    "import xarray as xr\n",
    "import xesmf as xe\n",
    "from pathlib import Path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
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       "        <h3 style=\"margin-bottom: 0px;\">Client</h3>\n",
       "        <p style=\"color: #9D9D9D; margin-bottom: 0px;\">Client-dcc48ede-4380-11ec-a8de-40f2e9c8ceea</p>\n",
       "        <table style=\"width: 100%; text-align: left;\">\n",
       "\n",
       "        <tr>\n",
       "        \n",
       "            <td style=\"text-align: left;\"><strong>Connection method:</strong> Cluster object</td>\n",
       "            <td style=\"text-align: left;\"><strong>Cluster type:</strong> distributed.LocalCluster</td>\n",
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       "                    <strong>Dashboard: </strong> <a href=\"/proxy/8787/status\" target=\"_blank\">/proxy/8787/status</a>\n",
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       "            <details>\n",
       "            <summary style=\"margin-bottom: 20px;\"><h3 style=\"display: inline;\">Cluster Info</h3></summary>\n",
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       "        <h3 style=\"margin-bottom: 0px; margin-top: 0px;\">LocalCluster</h3>\n",
       "        <p style=\"color: #9D9D9D; margin-bottom: 0px;\">f46abaca</p>\n",
       "        <table style=\"width: 100%; text-align: left;\">\n",
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       "                    <strong>Dashboard:</strong> <a href=\"/proxy/8787/status\" target=\"_blank\">/proxy/8787/status</a>\n",
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       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Workers:</strong> 27\n",
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       "            <tr>\n",
       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Total threads:</strong> 27\n",
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       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Total memory:</strong> 108.00 GiB\n",
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       "            \n",
       "            <tr>\n",
       "    <td style=\"text-align: left;\"><strong>Status:</strong> running</td>\n",
       "    <td style=\"text-align: left;\"><strong>Using processes:</strong> True</td>\n",
       "</tr>\n",
       "\n",
       "            \n",
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       "\n",
       "        <details>\n",
       "            <summary style=\"margin-bottom: 20px;\">\n",
       "                <h3 style=\"display: inline;\">Scheduler Info</h3>\n",
       "            </summary>\n",
       "\n",
       "            <div style=\"\">\n",
       "    <div>\n",
       "        <div style=\"width: 24px; height: 24px; background-color: #FFF7E5; border: 3px solid #FF6132; border-radius: 5px; position: absolute;\"> </div>\n",
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       "            <h3 style=\"margin-bottom: 0px;\">Scheduler</h3>\n",
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       "            <table style=\"width: 100%; text-align: left;\">\n",
       "                <tr>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Comm:</strong> tcp://127.0.0.1:37777\n",
       "                    </td>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Workers:</strong> 27\n",
       "                    </td>\n",
       "                </tr>\n",
       "                <tr>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Dashboard:</strong> <a href=\"/proxy/8787/status\" target=\"_blank\">/proxy/8787/status</a>\n",
       "                    </td>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Total threads:</strong> 27\n",
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       "                <tr>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Started:</strong> 3 hours ago\n",
       "                    </td>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Total memory:</strong> 108.00 GiB\n",
       "                    </td>\n",
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       "        </div>\n",
       "    </div>\n",
       "\n",
       "    <details style=\"margin-left: 48px;\">\n",
       "        <summary style=\"margin-bottom: 20px;\">\n",
       "            <h3 style=\"display: inline;\">Workers</h3>\n",
       "        </summary>\n",
       "\n",
       "        \n",
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       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
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       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 0</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:45591\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/45055/status\" target=\"_blank\">/proxy/45055/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:34533\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-x8wvuzuw\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
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       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
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       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 1</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:33117\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/40391/status\" target=\"_blank\">/proxy/40391/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:37669\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-gojtoi6m\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 2</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:39891\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/35265/status\" target=\"_blank\">/proxy/35265/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:37877\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-oughk8md\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 3</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:33679\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/45323/status\" target=\"_blank\">/proxy/45323/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:46721\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-w25517tf\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 4</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:44309\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/46125/status\" target=\"_blank\">/proxy/46125/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:39677\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-6wzc7qa3\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 5</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:38369\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/35659/status\" target=\"_blank\">/proxy/35659/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:42317\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-m7e7xl1g\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 6</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:42759\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/45159/status\" target=\"_blank\">/proxy/45159/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:43439\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-aqy1h3tk\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 7</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:40857\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/46657/status\" target=\"_blank\">/proxy/46657/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:44009\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-dfg46bnj\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 8</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:39061\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/39595/status\" target=\"_blank\">/proxy/39595/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:43859\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-4_i3kpw4\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 9</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:38367\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/34593/status\" target=\"_blank\">/proxy/34593/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:35199\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-tqnpsc7r\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 10</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:39671\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/36755/status\" target=\"_blank\">/proxy/36755/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:37355\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-_aih5yjh\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 11</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:40479\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/44007/status\" target=\"_blank\">/proxy/44007/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:35755\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-a747z7wy\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 12</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:46481\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/35633/status\" target=\"_blank\">/proxy/35633/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:43909\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-qqf_t39e\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 13</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:45103\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/40783/status\" target=\"_blank\">/proxy/40783/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:40407\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-06f06flk\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 14</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:45435\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/44001/status\" target=\"_blank\">/proxy/44001/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:36889\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-zm8bd9zg\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 15</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:39871\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/34313/status\" target=\"_blank\">/proxy/34313/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:40785\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-0db_ly_c\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 16</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:35643\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/40677/status\" target=\"_blank\">/proxy/40677/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:36161\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-_44r89lt\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 17</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:43957\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/33543/status\" target=\"_blank\">/proxy/33543/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:36055\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-32dpsu3g\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 18</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:39921\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/38637/status\" target=\"_blank\">/proxy/38637/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:33453\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-bbjmam7j\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 19</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:38407\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/42407/status\" target=\"_blank\">/proxy/42407/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:32987\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-7ax45tjp\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 20</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:43235\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/38933/status\" target=\"_blank\">/proxy/38933/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:40993\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-02ud7nvt\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 21</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:40915\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/34373/status\" target=\"_blank\">/proxy/34373/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:37429\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-7rpdsqob\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 22</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:40715\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/45135/status\" target=\"_blank\">/proxy/45135/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:44141\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-wsjzxv7y\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 23</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:36487\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/46361/status\" target=\"_blank\">/proxy/46361/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:43269\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-4ue577uk\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 24</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:38087\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/45293/status\" target=\"_blank\">/proxy/45293/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:37553\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-crixb4ec\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 25</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:41893\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/34285/status\" target=\"_blank\">/proxy/34285/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:36857\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-9s4ss1si\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 26</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://10.6.121.9:38795\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 1\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"/proxy/40559/status\" target=\"_blank\">/proxy/40559/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 4.00 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:35585\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> /jobfs/31122805.gadi-pbs/tmpmb6ubau2dask-worker-space/dask-worker-space/worker-66y8cvdn\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "\n",
       "    </details>\n",
       "</div>\n",
       "\n",
       "        </details>\n",
       "    </div>\n",
       "</div>\n",
       "            </details>\n",
       "        \n",
       "\n",
       "    </div>\n",
       "</div>"
      ],
      "text/plain": [
       "<Client: 'tcp://127.0.0.1:37777' processes=27 threads=27, memory=108.00 GiB>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import climtas.nci\n",
    "climtas.nci.GadiClient(malloc_trim_threshold='64kib')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Set up directories"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "#res_list = ['1','025','01']\n",
    "res_list = ['01']\n",
    "\n",
    "# basepath = '/g/data/v45/hh0162/projects/icebgc/prep_omip2/input_om2-bgc/'\n",
    "basepath = '/g/data/v45/aek156/input_om2-bgc/'\n",
    "inpath = basepath+'input/'\n",
    "tmppath = basepath+'tmp/'\n",
    "\n",
    "# insource is where the input files are copied/symlinked from\n",
    "insource = '/g/data/ik11/inputs/BGC/'\n",
    "\n",
    "# cplpath is parent to dirs that i2o.nc and o2i.nc are copied from\n",
    "cplpath = '/g/data/ik11/inputs/access-om2/input_20201102/'\n",
    "\n",
    "# create dirs if they don't already exist\n",
    "Path(inpath).mkdir(parents=True, exist_ok=True)\n",
    "Path(tmppath).mkdir(parents=True, exist_ok=True)\n",
    "for r in res_list:\n",
    "    Path(basepath+r+'deg').mkdir(parents=True, exist_ok=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash -s \"$insource\" \"$cplpath\" \"$basepath\" \"$inpath\" \"{\" \".join(res_list)}\"\n",
    "insource=$1\n",
    "cplpath=$2\n",
    "basepath=$3\n",
    "inpath=$4\n",
    "res=$5\n",
    "cp -nprs ${insource}input/* ${inpath} # symlink input files from insource to inpath if they aren't already there\n",
    "for ir in $res\n",
    "do # copy coupler files from cplpath to basepath if they aren't already there\n",
    "    cp -np `realpath ${cplpath}/cice_${ir}deg/i2o.nc` ${basepath}/${ir}deg\n",
    "    cp -np `realpath ${cplpath}/cice_${ir}deg/o2i.nc` ${basepath}/${ir}deg\n",
    "done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Create `csiro_bgc.res.nc`.\n",
    "\n",
    "- The input options `input_list` are:\n",
    "    - IRON = FEMIP median iron\n",
    "    - TAlk,TCO2,PI_TCO2,NO3,oxygen = GLODAPv2 2016b\n",
    "    - no3,o2 = WOA2013v2\n",
    "    - dic,adic,alk = 1deg_jra55_iaf_omip2_cycle5_restart304\n",
    "- `wombat_list` contains the names of variables that WOMBAT wants. The choices are `fe,dic,adic,alk,no3,o2`.\n",
    "\n",
    "- `wombat_list` must match the order of `input_list`. For example, if `input_list = ['NO3','oxygen']`, then `wombat_list = ['no3','o2']`\n",
    "\n",
    "- `res_list` is the output resolution you want to regrid to.\n",
    "\n",
    "- mean/min/max of both input and output data are printed to make sure that regridded values are reasonable and contains no NaNs."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Define `my_choice` to choose your input data based on your configuration, either `master+bgc`, `01deg_jra55v140_iaf_cycle4`, or `iamip2`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# my_choice = 'master+bgc' # 'master+bgc', '01deg_jra55v140_iaf_cycle4', or 'iamip2'\n",
    "my_choice = '01deg_jra55v140_iaf_cycle4' # 'master+bgc', '01deg_jra55v140_iaf_cycle4', or 'iamip2'\n",
    "\n",
    "BGC_vars = { \n",
    "    'master+bgc':                 ['NO3','oxygen','PI_TCO2','TAlk','TCO2','IRON'],\n",
    "    '01deg_jra55v140_iaf_cycle4': ['NO3','oxygen','dic',    'alk', 'adic','IRON'],\n",
    "    'iamip2':                     ['no3','o2',    'PI_TCO2','TAlk','TCO2','IRON']\n",
    "}\n",
    "\n",
    "input_list = BGC_vars[my_choice]\n",
    "wombat_list = ['no3','o2','dic'  ,'alk' ,'adic',    'fe'] # must be in the same order as in BGC_vars"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "jupyter": {
     "source_hidden": true
    },
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/coding/times.py:527: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  dtype = _decode_cf_datetime_dtype(data, units, calendar, self.use_cftime)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/core/indexing.py:419: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  return np.asarray(array[self.key], dtype=None)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xesmf/frontend.py:598: UserWarning: Using dimensions ('yt_ocean', 'xt_ocean') from data variable no3 as the horizontal dimensions for the regridding.\n",
      "  warnings.warn(\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xesmf/frontend.py:598: UserWarning: Using dimensions ('yt_ocean', 'xt_ocean') from data variable no3 as the horizontal dimensions for the regridding.\n",
      "  warnings.warn(\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['input: ', <xarray.DataArray 'no3' ()>\n",
      "array(23.00982795), <xarray.DataArray 'no3' ()>\n",
      "array(-0.4999066), <xarray.DataArray 'no3' ()>\n",
      "array(46.09739685)]\n",
      "['output: ', <xarray.DataArray 'no3' ()>\n",
      "array(20.5706646), <xarray.DataArray 'no3' ()>\n",
      "array(-0.49300141), <xarray.DataArray 'no3' ()>\n",
      "array(46.05384699)]\n",
      "01 NO3 done\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/coding/times.py:527: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  dtype = _decode_cf_datetime_dtype(data, units, calendar, self.use_cftime)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/core/indexing.py:419: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  return np.asarray(array[self.key], dtype=None)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xesmf/frontend.py:598: UserWarning: Using dimensions ('yt_ocean', 'xt_ocean') from data variable o2 as the horizontal dimensions for the regridding.\n",
      "  warnings.warn(\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['input: ', <xarray.DataArray 'o2' ()>\n",
      "array(208.60762603), <xarray.DataArray 'o2' ()>\n",
      "array(-0.49743176), <xarray.DataArray 'o2' ()>\n",
      "array(458.78067017)]\n",
      "['output: ', <xarray.DataArray 'o2' ()>\n",
      "array(232.22670776), <xarray.DataArray 'o2' ()>\n",
      "array(-0.43967125), <xarray.DataArray 'o2' ()>\n",
      "array(456.43481145)]\n",
      "01 oxygen done\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/coding/times.py:527: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  dtype = _decode_cf_datetime_dtype(data, units, calendar, self.use_cftime)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/core/indexing.py:419: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  return np.asarray(array[self.key], dtype=None)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['input: ', <xarray.DataArray 'dic' ()>\n",
      "array(2156.25, dtype=float32), <xarray.DataArray 'dic' ()>\n",
      "array(147.80667114), <xarray.DataArray 'dic' ()>\n",
      "array(2478.56494141)]\n",
      "['output: ', <xarray.DataArray 'dic' ()>\n",
      "array(2144.36123823), <xarray.DataArray 'dic' ()>\n",
      "array(170.94919116), <xarray.DataArray 'dic' ()>\n",
      "array(2574.30030627)]\n",
      "01 dic done\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/coding/times.py:527: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  dtype = _decode_cf_datetime_dtype(data, units, calendar, self.use_cftime)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/core/indexing.py:419: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  return np.asarray(array[self.key], dtype=None)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['input: ', <xarray.DataArray 'alk' ()>\n",
      "array(2333.12198623), <xarray.DataArray 'alk' ()>\n",
      "array(236.89623411), <xarray.DataArray 'alk' ()>\n",
      "array(2722.17376466)]\n",
      "['output: ', <xarray.DataArray 'alk' ()>\n",
      "array(2320.82518012), <xarray.DataArray 'alk' ()>\n",
      "array(275.95689388), <xarray.DataArray 'alk' ()>\n",
      "array(2721.86403995)]\n",
      "01 alk done\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/coding/times.py:527: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  dtype = _decode_cf_datetime_dtype(data, units, calendar, self.use_cftime)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/core/indexing.py:419: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  return np.asarray(array[self.key], dtype=None)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['input: ', <xarray.DataArray 'adic' ()>\n",
      "array(2163.82029871), <xarray.DataArray 'adic' ()>\n",
      "array(210.61384898), <xarray.DataArray 'adic' ()>\n",
      "array(2478.97542683)]\n",
      "['output: ', <xarray.DataArray 'adic' ()>\n",
      "array(2152.71645502), <xarray.DataArray 'adic' ()>\n",
      "array(244.71533825), <xarray.DataArray 'adic' ()>\n",
      "array(2573.98353997)]\n",
      "01 adic done\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/coding/times.py:527: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  dtype = _decode_cf_datetime_dtype(data, units, calendar, self.use_cftime)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/core/indexing.py:419: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  return np.asarray(array[self.key], dtype=None)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xesmf/frontend.py:598: UserWarning: Using dimensions ('yt_ocean', 'xt_ocean') from data variable fe as the horizontal dimensions for the regridding.\n",
      "  warnings.warn(\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['input: ', <xarray.DataArray 'fe' ()>\n",
      "array(5.46499738e-10), <xarray.DataArray 'fe' ()>\n",
      "array(5.71562964e-13), <xarray.DataArray 'fe' ()>\n",
      "array(7.53020216e-09)]\n",
      "['output: ', <xarray.DataArray 'fe' ()>\n",
      "array(5.52851049e-10), <xarray.DataArray 'fe' ()>\n",
      "array(1.58412526e-12), <xarray.DataArray 'fe' ()>\n",
      "array(6.86482349e-09)]\n",
      "01 IRON done\n"
     ]
    }
   ],
   "source": [
    "for ir in range(np.size(res_list)):\n",
    "    \n",
    "    for it in range(np.size(wombat_list)):\n",
    "\n",
    "        if input_list[it] == 'IRON':\n",
    "            ds_in = xr.open_dataset(inpath+'FEMIP_model_median_iron_2016_fillmiss.nc')\n",
    "            #rename the coordinates to the MOM coordinate names to enable interpolation.\n",
    "            ds_in = ds_in.rename(({'LON':'xt_ocean', 'LAT':'yt_ocean', 'DEPTH':'st_ocean'}))              \n",
    "        elif input_list[it] == 'no3':\n",
    "            ds_in = xr.open_dataset(inpath+'woa13_nitrate_OMIPinit_fillmiss.nc',decode_times=False)\n",
    "            ds_in = ds_in.rename(({'lon':'xt_ocean', 'lat':'yt_ocean', 'depth':'st_ocean'}))\n",
    "            ds_in = ds_in.isel(time=0,drop=True)\n",
    "        elif input_list[it] == 'o2':\n",
    "            ds_in = xr.open_dataset(inpath+'woa13_oxygen_OMIPinit_fillmiss.nc',decode_times=False)\n",
    "            ds_in = ds_in.rename(({'lon':'xt_ocean', 'lat':'yt_ocean', 'depth':'st_ocean'}))\n",
    "            ds_in = ds_in.isel(time=0,drop=True)\n",
    "        elif input_list[it] in ['alk','adic','dic']:\n",
    "            ds_in = xr.open_dataset(inpath+'1deg_jra55_iaf_omip2_cycle5_restart304_csiro_bgc.res_fillmiss.nc')\n",
    "            ds_in = ds_in.isel(time=0,drop=True)\n",
    "        elif input_list[it] in ['TAlk','TCO2','PI_TCO2','NO3','oxygen']:\n",
    "            ds_in = xr.open_dataset(inpath+'GLODAPv2.2016b.'+input_list[it]+'_fillmiss.nc')\n",
    "            ds_in = ds_in.rename(({'lon':'xt_ocean', 'lat':'yt_ocean', 'depth_surface':'st_ocean'}))\n",
    "            #the vertical coordinate (depth_surface) in GLODAPv2.2016b is wrong (it is index, not depth values).\n",
    "            #derive depth from FEMIP iron data (they are interpolated onto the same depths).\n",
    "            ds_tmp = xr.open_dataset(inpath+'FEMIP_model_median_iron_2016_fillmiss.nc')\n",
    "            ds_in['st_ocean'] = ds_tmp['DEPTH']    \n",
    "        ds_in = ds_in.rename({input_list[it]:wombat_list[it]})\n",
    "\n",
    "            \n",
    "        #first convert the lon coordinate system to the standard system (0-360) if not already in the standard system (e.g. -180 to 180)\n",
    "        #retain lon values less than 360, otherwise subtract 360\n",
    "        ds_in['xt_ocean'] = ds_in['xt_ocean'].where(ds_in['xt_ocean']<360,ds_in['xt_ocean']-360)\n",
    "        #retain lon values greater than 0, otherwise add 360\n",
    "        ds_in['xt_ocean'] = ds_in['xt_ocean'].where(ds_in['xt_ocean']>0,ds_in['xt_ocean']+360)\n",
    "\n",
    "        #now convert to the MOM lon coordinate system, which spans from -280 to 80 (yes, a bit weird)\n",
    "        #retain lon values less than 80, otherwise subtract 360\n",
    "        ds_in['xt_ocean'] = ds_in['xt_ocean'].where(ds_in['xt_ocean']<80,ds_in['xt_ocean']-360)\n",
    "        #retain lon values greater than -280, otherwise add 360\n",
    "        ds_in['xt_ocean'] = ds_in['xt_ocean'].where(ds_in['xt_ocean']>-280,ds_in['xt_ocean']+360)\n",
    "\n",
    "        \n",
    "        #read target grid\n",
    "        if res_list[ir] == '1':\n",
    "            ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_temp_salt.res.nc')\n",
    "            ds_gri = xr.open_dataset('/g/data/ik11/grids/ocean_grid_10.nc')\n",
    "        elif res_list[ir] == '025':\n",
    "            ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_025deg/ocean_temp_salt.res.nc')\n",
    "            ds_gri = xr.open_dataset('/g/data/ik11/grids/ocean_grid_025.nc')        \n",
    "        elif res_list[ir] == '01':\n",
    "            ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_01deg/ocean_temp_salt.res.nc')\n",
    "            ds_gri = xr.open_dataset('/g/data/ik11/grids/ocean_grid_01.nc')        \n",
    "        #rename to lon and lat so that xesmf understands\n",
    "        ds_gri = ds_gri.rename({'geolon_t': 'lon', 'geolat_t': 'lat'})\n",
    "        ds_tar = ds_tar.rename({'ZT': 'st_ocean', 'GRID_Y_T': 'yt_ocean', 'GRID_X_T':'xt_ocean'})\n",
    "\n",
    "        #vertical 1-d interpolation first\n",
    "        ar_zz = np.zeros((np.size(ds_tar['st_ocean']),np.size(ds_in['yt_ocean']),np.size(ds_in['xt_ocean'])))\n",
    "        ar_in = ds_in[wombat_list[it]].values\n",
    "        for ix in range(np.size(ar_zz,2)):\n",
    "            for iy in range(np.size(ar_zz,1)):\n",
    "                #fill_value=None will extrapolate\n",
    "                ar_zz[:,iy,ix] = interpn((ds_in['st_ocean'].values,),ar_in[:,iy,ix],ds_tar['st_ocean'].values,\n",
    "                                        method=\"linear\",fill_value=None,bounds_error=False)         \n",
    "        ds_zz = ds_in.copy()\n",
    "        ds_zz = ds_zz.isel(st_ocean=0,drop=True)\n",
    "        ds_zz = ds_zz.assign_coords(st_ocean=ds_tar['st_ocean'])\n",
    "        if input_list[it] in ['adic','alk','dic']:\n",
    "            ds_gri_1deg = xr.open_dataset('/g/data/ik11/grids/ocean_grid_10.nc')\n",
    "            ds_zz['lon'] = (['yt_ocean','xt_ocean'],ds_gri_1deg['geolon_t'].values)\n",
    "            ds_zz['lat'] = (['yt_ocean','xt_ocean'],ds_gri_1deg['geolat_t'].values)\n",
    "        else:        \n",
    "            ds_zz = ds_zz.rename({'xt_ocean': 'lon', 'yt_ocean': 'lat'})\n",
    "        ds_zz[wombat_list[it]] = (['st_ocean','yt_ocean','xt_ocean'],ar_zz)           \n",
    "        #use bilinear. i compared with nearest_s2d but the differences are minimal.\n",
    "        regridder = xe.Regridder(ds_zz,ds_gri,method='bilinear',periodic=True)\n",
    "        regridder        \n",
    "        ds_tar = ds_tar.rename({'temp':wombat_list[it]})\n",
    "        for attr in ['valid_range', 'longname', 'standard_name', 'units']:\n",
    "            try:\n",
    "                del ds_tar[wombat_list[it]].attrs[attr]\n",
    "            except KeyError:\n",
    "                pass\n",
    "        for iz in range(np.size(ds_zz['st_ocean'])):\n",
    "            ds_tar[wombat_list[it]][:,iz,:,:] = regridder(ds_zz[wombat_list[it]].isel(st_ocean=iz))\n",
    "        #some interpolated values are NaNs, so interpolate_na with the following options to fill in NaNs.\n",
    "        #dim='st_ocean' is essential. 'xt_ocean' produces NaNs.\n",
    "        #method='nearest' is essential. 'linear' gives extreme values.\n",
    "        #fill_value='extrapolate' is essential. without it, still NaNs exist.\n",
    "        ds_tar[wombat_list[it]] = ds_tar[wombat_list[it]].interpolate_na(dim='st_ocean',method='nearest',fill_value=\"extrapolate\")\n",
    "        print(['input: ',ds_in[wombat_list[it]].mean(),ds_in[wombat_list[it]].min(),ds_in[wombat_list[it]].max()])\n",
    "        print(['output: ',ds_tar[wombat_list[it]].mean(skipna=False),ds_tar[wombat_list[it]].min(skipna=False),ds_tar[wombat_list[it]].max(skipna=False)])\n",
    "        #set negative values to zero (negative values exist in NO3 input) \n",
    "        ds_tar[wombat_list[it]] = ds_tar[wombat_list[it]].where(ds_tar[wombat_list[it]]>0,0)\n",
    "\n",
    "        #unit conversion relevant for fe and o2\n",
    "        if wombat_list[it] == 'fe':\n",
    "            #conversion from mol l-1 to umol m-3\n",
    "            ds_tar[wombat_list[it]] = ds_tar[wombat_list[it]]*1e9\n",
    "        elif wombat_list[it] == 'o2':\n",
    "            #conversion from ml l-1 to mmol m-3\n",
    "            ds_tar[wombat_list[it]] = ds_tar[wombat_list[it]]*44.661\n",
    "        elif input_list[it] in ['TAlk','TCO2','PI_TCO2','NO3','oxygen']:\n",
    "            #conversion from umol kg-1 to mmol m-3\n",
    "            ds_tar[wombat_list[it]] = ds_tar[wombat_list[it]]*1.025            \n",
    "        \n",
    "        #rename to what wombat wants.\n",
    "        ds_tar = ds_tar.rename(({'xt_ocean':'xaxis_1', 'yt_ocean':'yaxis_1', 'st_ocean':'zaxis_1', 'time':'Time'}))    \n",
    "\n",
    "# convert units of 'degree_' to 'degrees_' so MOM will be able to infer the axis meaning\n",
    "# https://github.com/mom-ocean/MOM5/blob/1d9af9d262b/src/shared/axis_utils/axis_utils.F90#L92-L99\n",
    "        for dim in ds_tar.dims:\n",
    "            try:\n",
    "                units = ds_tar[dim].attrs['units'].lower()\n",
    "                if units.startswith('degree_'):\n",
    "                    ds_tar[dim].attrs['units'] = units.replace('degree_', 'degrees_', 1)\n",
    "            except KeyError:\n",
    "                pass\n",
    "\n",
    "        ds_tar.to_netcdf(tmppath+wombat_list[it]+'_init_'+res_list[ir]+'deg.nc',\n",
    "                         unlimited_dims='Time',\n",
    "                         encoding={wombat_list[it]:{'zlib': True,'complevel': 9}})\n",
    "        print(res_list[ir],input_list[it],'done')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Combine the regridded output for each tracer into a single `csiro_bgc.res.nc`. Also add tracers that are set to constant (0.01 mmol m-3; phy,zoo,det,caco3).\n",
    "- `dic_eq_adic = True` will set dic to be identical to adic (not using it for now)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/coding/times.py:527: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  dtype = _decode_cf_datetime_dtype(data, units, calendar, self.use_cftime)\n",
      "/g/data/hh5/public/apps/miniconda3/envs/analysis3-21.07/lib/python3.9/site-packages/xarray/core/indexing.py:419: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using cftime.datetime objects instead, reason: dates out of range\n",
      "  return np.asarray(array[self.key], dtype=None)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "01 done\n"
     ]
    }
   ],
   "source": [
    "# res_list = ['1','025','01']\n",
    "\n",
    "dic_eq_adic = False\n",
    "\n",
    "for ir in range(np.size(res_list)):\n",
    "    \n",
    "    for it in range(np.size(wombat_list)):\n",
    "        ds_tar = xr.open_dataset(tmppath+wombat_list[it]+'_init_'+res_list[ir]+'deg.nc')\n",
    "        try:\n",
    "            ds_tar_all = ds_tar_all.assign(ds_tar)\n",
    "        except NameError:\n",
    "            ds_tar_all = ds_tar.copy()\n",
    "    ds_new = ds_tar[wombat_list[-1]].copy()\n",
    "    if dic_eq_adic:\n",
    "        ds_tar_all = ds_tar_all.assign(dic=ds_new)\n",
    "    ds_new[:,:,:,:] = 0.01\n",
    "    ds_tar_all = ds_tar_all.assign(phy=ds_new)\n",
    "    ds_tar_all = ds_tar_all.assign(zoo=ds_new)\n",
    "    ds_tar_all = ds_tar_all.assign(det=ds_new)\n",
    "    ds_tar_all = ds_tar_all.assign(caco3=ds_new)\n",
    "    ds_tar_all.to_netcdf(tmppath+'csiro_bgc.res_'+res_list[ir]+'deg.nc')\n",
    "    del ds_tar_all\n",
    "    print(res_list[ir],'done')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Creation of `co2_iaf.nc` and `co2_ryf.nc`.\n",
    "\n",
    "1. Create atmospheric pCO2 (boundary conditions). one for IAF and one for RYF.\n",
    "1. prescribe annual mean (for saving storage) and global mean (for simplicity) data.\n",
    "1. follow omip2 protocol until 2014. from 2015-2020, use the global average data from https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_annmean_gl.txt (as of Oct  5 13:17:31 2021)\n",
    "1. For RYF, apply the mean of pco2 between 1957-58 (representative of 01/01/1958, the start of IAF). "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cftime import DatetimeNoLeap"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'np' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m/jobfs/30953042.gadi-pbs/ipykernel_867515/240001793.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0;31m#NOAA GML DATA for 2015-2020.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0matmco2\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;36m284.32\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m284.45\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m284.60\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m284.73\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m284.85\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m284.94\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m285.05\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m285.20\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m285.37\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m285.54\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m285.74\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m285.93\u001b[0m\u001b[0;34m,\u001b[0m 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\u001b[0;36m412.44\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 5\u001b[0;31m \u001b[0myrsco2\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1850\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m2020\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      6\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[0;31m#IAF spans from 1957 to 2020\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'np' is not defined"
     ]
    }
   ],
   "source": [
    "#combined atmospheric co2 data for input from 1850-2020.\n",
    "#OMIP2 protocol for 1850-2014.\n",
    "#NOAA GML DATA for 2015-2020.\n",
    "atmco2 = [284.32, 284.45, 284.60, 284.73, 284.85, 284.94, 285.05, 285.20, 285.37, 285.54, 285.74, 285.93, 286.10, 286.27, 286.44, 286.61, 286.78, 286.95, 287.10, 287.22, 287.35, 287.49, 287.66, 287.86, 288.06, 288.29, 288.52, 288.75, 288.99, 289.22, 289.47, 289.74, 290.02, 290.26, 290.51, 290.80, 291.10, 291.41, 291.76, 292.11, 292.46, 292.82, 293.17, 293.48, 293.79, 294.08, 294.36, 294.65, 294.95, 295.30, 295.67, 296.01, 296.32, 296.65, 296.95, 297.29, 297.66, 298.10, 298.52, 298.94, 299.38, 299.83, 300.35, 300.91, 301.42, 301.94, 302.48, 303.01, 303.45, 303.81, 304.25, 304.60, 304.94, 305.27, 305.63, 305.81, 305.95, 306.18, 306.33, 306.49, 306.62, 306.82, 307.09, 307.40, 307.78, 308.23, 309.01, 309.76, 310.29, 310.85, 311.36, 311.81, 312.17, 312.39, 312.41, 312.38, 312.39, 312.49, 312.52, 312.63, 312.82, 313.01, 313.34, 313.73, 314.09, 314.41, 314.70, 314.99, 315.34, 315.81, 316.62, 317.30, 318.04, 318.65, 319.33, 319.82, 320.88, 321.48, 322.39, 323.25, 324.78, 325.40, 327.35, 329.91, 330.76, 330.83, 331.54, 333.35, 335.01, 336.60, 338.70, 340.06, 340.64, 342.27, 344.01, 345.46, 346.90, 348.77, 351.28, 352.89, 354.07, 355.35, 356.23, 356.92, 358.25, 360.24, 362.00, 363.25, 365.93, 367.84, 369.12, 370.67, 372.83, 375.41, 376.99, 378.91, 381.01, 382.60, 384.74, 386.28, 388.72, 390.94, 393.02, 395.72, 397.55, 399.65, 403.08, 405.22, 407.62, 410.07, 412.44]\n",
    "yrsco2 = np.arange(1850,2020+1)\n",
    "\n",
    "#IAF spans from 1957 to 2020\n",
    "date_iaf = []\n",
    "for it in np.arange(1957,2020+1):\n",
    "    date_iaf.append(DatetimeNoLeap(it,7,1))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# res_list = ['1','025','01']\n",
    "\n",
    "for ir in range(np.size(res_list)):\n",
    "    if res_list[ir] == '1':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_temp_salt.res.nc')\n",
    "    elif res_list[ir] == '025':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_025deg/ocean_temp_salt.res.nc')\n",
    "    elif res_list[ir] == '01':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_01deg/ocean_temp_salt.res.nc')\n",
    "    ds_tar = ds_tar.rename({'ZT': 'st_ocean', 'GRID_Y_T': 'yt_ocean', 'GRID_X_T':'xt_ocean'})\n",
    "\n",
    "    ds_tar = ds_tar.drop_dims('st_ocean')\n",
    "    for v in ['time','time_bounds']:\n",
    "        try:\n",
    "            ds_tar = ds_tar.drop_vars(v)\n",
    "        except ValueError:\n",
    "            pass\n",
    "    ds_tar = ds_tar.rename(({'xt_ocean':'grid_x_T', 'yt_ocean':'grid_y_T'}))\n",
    "\n",
    "    #RYF first\n",
    "    #RYF only has two dates (the same concentration is used throughout the simulation.)    \n",
    "    date_ryf = [\n",
    "        DatetimeNoLeap(1800,7,1),\n",
    "        DatetimeNoLeap(2101,7,1)\n",
    "    ]    \n",
    "    co2_3d = np.zeros((np.size(date_ryf),np.size(ds_tar.grid_y_T),np.size(ds_tar.grid_x_T)))\n",
    "    #take the average of co2 between 1957-1958. fixed value is given to both RYF and nat_co2/dic\n",
    "    co2_fix = np.mean(atmco2[1957-1850:1958+1-1850])\n",
    "    co2_3d[:,:,:] = co2_fix\n",
    "    ds_tar = ds_tar.assign_coords({\"time\":date_ryf})\n",
    "    ds_tar['co2'] = xr.DataArray(co2_3d,dims=['time','grid_y_T','grid_x_T'])\n",
    "    ds_tar.to_netcdf(tmppath+'co2_ryf_'+res_list[ir]+'deg.nc',\n",
    "                     unlimited_dims='time',\n",
    "                     encoding={'co2':{'_FillValue': None,'zlib': True,'complevel': 9},'time':{'_FillValue':None,'dtype':'float64'}})\n",
    "    \n",
    "    ds_tar = ds_tar.drop_vars(['co2','time'])\n",
    "    \n",
    "    #IAF next\n",
    "    date_iaf = []\n",
    "    for it in range(1957,2020+1):\n",
    "        date_iaf.append(DatetimeNoLeap(it,7,1))    \n",
    "    co2_3d = np.zeros((np.size(date_iaf),np.size(ds_tar.grid_y_T),np.size(ds_tar.grid_x_T)))\n",
    "    for it in range(1957,2020+1):\n",
    "        co2_3d[it-1957,:,:] = atmco2[it-1850]\n",
    "    ds_tar = ds_tar.assign_coords({\"time\":date_iaf})\n",
    "    ds_tar['co2'] = xr.DataArray(co2_3d,dims=['time','grid_y_T','grid_x_T'])\n",
    "    ds_tar.to_netcdf(tmppath+'co2_iaf_'+res_list[ir]+'deg.nc',\n",
    "                     unlimited_dims='time',\n",
    "                     encoding={'co2':{'_FillValue': None,'zlib': True,'complevel': 9},'time':{'_FillValue':None,'dtype':'float64'}})\n",
    "    print(res_list[ir],'done')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash -s \"$tmppath\" \"{\" \".join(res_list)}\"\n",
    "cd $1\n",
    "for ir in $2\n",
    "do\n",
    "    for it in iaf ryf\n",
    "    do\n",
    "        filename=co2_${it}_${ir}deg.nc\n",
    "        ncatted -a cartesian_axis,grid_x_T,c,c,\"X\" $filename\n",
    "        ncatted -a cartesian_axis,grid_y_T,c,c,\"Y\" $filename\n",
    "    done\n",
    "    echo $ir,done\n",
    "done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Creation of `bgc_param.nc`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Define parameter values.\n",
    "- For the names and units of these parameters, see Table of Supporting Information of Hayashida et al. (2020): Background nutrient concentration determines phytoplankton bloom response to marine heatwaves. Global Change Biology. https://doi.org/10.1111/gcb.15255\n",
    "- However, note that units given below may be different from Table of Hayashida et al. (2020), because the model wants them in SI. For example, `abio = 0.27 d-1` in Hayashida et al. (2020), but `abio = 3.125e-6 s-1` in `bgc_param.nc` below. Parameters are given in the same units as Ziehn et al (2020) in `param_list_Ziehn2020`.\n",
    "- The parameter values specifed below are identical to those of Ziehn et al. (2020): The Australian Earth System Model: ACCESS-ESM1.5. Journal of Southern Hemisphere Earth Systems Science. https://doi.org/10.1071%2Fes19035, except for `nat_co2`.\n",
    "- `nat_co2` is the fixed atmospheric co2 concentration (ppm) applied to `dic`. Typically this is set to a pre-industrial co2 value, as long as `dic` is representative of natural DIC. However, in some applications, you might prescribe different values. We use `nat_co2`=284.32, which is the value used in the OMIP-BGC protocol (Orr et al. 2017, GMD)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "param_list = [\n",
    " ['abio',3.125e-6],\n",
    " ['alphabio',2.96296e-6],\n",
    " ['bbio',1.066],\n",
    " ['cbio',1],\n",
    " ['epsbio',1.85185e-5],\n",
    " ['fe_bkgnd',0.6],\n",
    " ['f_inorg',0.062], # CaCO3 inorganic fraction\n",
    " ['gam1bio',0.925],\n",
    " ['gam2bio',1.15741e-7],\n",
    " ['gbio',1.82292e-5],\n",
    " ['kcbio',21.2766], # required as an input in WOMBAT but not actually used; not in Ziehn et al (2020) or Hayashida et al (2020) tables\n",
    " ['kwbio',25], # required as an input in WOMBAT but not actually used; not in Ziehn et al (2020) or Hayashida et al (2020) tables\n",
    " ['k1bio',0.7],\n",
    " ['muecaco3',1.9838e-8], # CaCO3 remineralisation rate (matches 0.001714 day-1 in Ziehn et al 2020; differs from Hayashida et al 2020)\n",
    " ['muecaco3_sed',4.05093e-8],\n",
    " ['muedbio',5.55556e-7],\n",
    " ['muedbio_sed',2.31481e-7], # would normally equal muedbio, but we use this value to be consistent with what is in ESM1.5 (undocumented in Ziehn et al 2020)\n",
    " ['muepbio',4.62963e-7],\n",
    " ['muepsbio',2.89352e-6],\n",
    " ['muezbio',3.93519e-6],\n",
    " ['nat_co2',284.32], # 284.32 in the OMIP-BGC protocol (Orr et al. 2017, GMD)\n",
    " ['parbio',0.43],\n",
    " ['tscav_fe',3.17098e-8],\n",
    " ['wcaco3',6.94444e-5], # matches Ziehn et al 2020 but differs from Hayashida et al (2020)\n",
    " ['wdetbio',2.77778e-4] # matches Ziehn et al 2020 but differs from Hayashida et al (2020)\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Show parameters in same units as Ziehn et al. (2020) https://doi.org/10.1071%2Fes19035 for checking against their table 2\n",
    "param_list_Ziehn2020 = [ x if x[0] in ['parbio', 'bbio', 'cbio', 'k1bio', 'gam1bio', 'f_inorg', 'fe_bkgnd', 'nat_co2']\n",
    "                        else [x[0], x[1]*24*60*60] \n",
    "                        for x in param_list ]\n",
    "param_list_Ziehn2020"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# res_list = ['1','025','01']\n",
    "\n",
    "for ir in range(np.size(res_list)):\n",
    "    if res_list[ir] == '1':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_temp_salt.res.nc')\n",
    "    elif res_list[ir] == '025':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_025deg/ocean_temp_salt.res.nc')\n",
    "    elif res_list[ir] == '01':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_01deg/ocean_temp_salt.res.nc')\n",
    "    ds_tar = ds_tar.rename({'ZT': 'st_ocean', 'GRID_Y_T': 'yt_ocean', 'GRID_X_T':'xt_ocean'})\n",
    "\n",
    "    ds_tar['temp'] = ds_tar['temp'].isel(st_ocean=0,drop=True)\n",
    "    ds_tar = ds_tar.drop_dims('st_ocean')\n",
    "    try:\n",
    "        ds_tar = ds_tar.drop_vars('time_bounds')\n",
    "    except ValueError:\n",
    "        pass\n",
    "    ds_tar = ds_tar.rename(({'xt_ocean':'grid_x_T', 'yt_ocean':'grid_y_T'}))\n",
    "    for it in range(np.size(param_list,0)):\n",
    "        #where() is needed to remove the land mask.\n",
    "        ds_tar[param_list[it][0]] = ds_tar['temp'].where(ds_tar['temp']>0,0)*0 + param_list[it][1]\n",
    "    ds_tar = ds_tar.drop_vars('temp')\n",
    "    comp = dict(_FillValue=-1e34, missing_value=-1e34)\n",
    "    encoding = {var: comp for var in ds_tar.data_vars}\n",
    "\n",
    "# convert units of 'degree_' to 'degrees_' so MOM will be able to infer the axis meaning\n",
    "# https://github.com/mom-ocean/MOM5/blob/1d9af9d262b/src/shared/axis_utils/axis_utils.F90#L92-L99\n",
    "    for dim in ds_tar.dims:\n",
    "        try:\n",
    "            units = ds_tar[dim].attrs['units'].lower()\n",
    "            if units.startswith('degree_'):\n",
    "                ds_tar[dim].attrs['units'] = units.replace('degree_', 'degrees_', 1)\n",
    "        except KeyError:\n",
    "            pass\n",
    "\n",
    "    ds_tar.to_netcdf(tmppath+'bgc_param_'+res_list[ir]+'deg.nc',\n",
    "                     encoding=encoding,\n",
    "                     unlimited_dims='time')#,encoding={'time':{'_FillValue':None,'dtype':'float64'}})\n",
    "    print(res_list[ir],'done')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "%%bash -s \"$tmppath\" \"{\" \".join(res_list)}\"\n",
    "cd $1\n",
    "for ir in $2\n",
    "do\n",
    "    filename=bgc_param_${ir}deg.nc\n",
    "    ncatted -a cartesian_axis,grid_x_T,c,c,\"X\" $filename\n",
    "    ncatted -a cartesian_axis,grid_y_T,c,c,\"Y\" $filename\n",
    "    ncks -O -L 9 $filename $filename\n",
    "    echo $ir,done\n",
    "done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Creation of `dust.nc`\n",
    "1. The original source file for dust input is not available, so use the 1-degree interpolated file as input. the method is described in Mongin et al. (2011), https://doi.org/10.1016/j.dsr2.2011.06.001."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# res_list = ['1','025','01']\n",
    "\n",
    "for ir in range(np.size(res_list)):\n",
    "    #read target grid\n",
    "    if res_list[ir] == '1':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_temp_salt.res.nc')\n",
    "        ds_gri = xr.open_dataset('/g/data/ik11/grids/ocean_grid_10.nc')\n",
    "    elif res_list[ir] == '025':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_025deg/ocean_temp_salt.res.nc')\n",
    "        ds_gri = xr.open_dataset('/g/data/ik11/grids/ocean_grid_025.nc')        \n",
    "    elif res_list[ir] == '01':\n",
    "        ds_tar = xr.open_dataset('/g/data/ik11/inputs/access-om2/input_20201102/mom_01deg/ocean_temp_salt.res.nc')\n",
    "        ds_gri = xr.open_dataset('/g/data/ik11/grids/ocean_grid_01.nc')        \n",
    "    #rename to lon and lat so that xesmf understands\n",
    "    ds_gri = ds_gri.rename({'geolon_t': 'lon', 'geolat_t': 'lat'})\n",
    "    ds_tar = ds_tar.rename({'ZT': 'st_ocean', 'GRID_Y_T': 'yt_ocean', 'GRID_X_T':'xt_ocean'})\n",
    "\n",
    "    ds_in = xr.open_dataset(inpath+'dust.nc')\n",
    "    ds_gri_in = xr.open_dataset('/g/data/ik11/grids/ocean_grid_10.nc')\n",
    "    ds_gri_in = ds_gri_in.rename({'geolon_t': 'lon', 'geolat_t': 'lat'})\n",
    "    \n",
    "    ds_tar['temp'] = ds_tar['temp'].isel(st_ocean=0,drop=True)\n",
    "    ds_tar = ds_tar.drop_dims('st_ocean')\n",
    "    for v in ['time','time_bounds']:\n",
    "        try:\n",
    "            ds_tar = ds_tar.drop_vars(v)\n",
    "        except ValueError:\n",
    "            pass\n",
    "    ds_tar = ds_tar.drop_vars('temp')\n",
    "    ds_tar = ds_tar.assign_coords({\"time\":ds_in['time']})\n",
    "    ds_tar['lon'] = (['yt_ocean','xt_ocean'],ds_gri['lon'].values)\n",
    "    ds_tar['lat'] = (['yt_ocean','xt_ocean'],ds_gri['lat'].values)\n",
    "    ds_in['lon'] = (['yt_ocean','xt_ocean'],ds_gri_in['lon'].values)\n",
    "    ds_in['lat'] = (['yt_ocean','xt_ocean'],ds_gri_in['lat'].values)\n",
    "\n",
    "    regridder = xe.Regridder(ds_gri_in,ds_gri,method='bilinear',periodic=True)\n",
    "    ds_tar['dust'] = (['time','yt_ocean','xt_ocean'],regridder(ds_in['dust']).values)    \n",
    "    ds_tar = ds_tar.rename(({'xt_ocean':'grid_x_T', 'yt_ocean':'grid_y_T'}))\n",
    "    #some interpolated values are NaNs, so interpolate_na with the following options to fill in NaNs.\n",
    "    #dim='st_ocean' is essential. 'xt_ocean' produces NaNs.\n",
    "    #method='nearest' is essential. 'linear' gives extreme values.\n",
    "    #fill_value='extrapolate' is essential. without it, still NaNs exist.\n",
    "    ds_tar['dust'] = ds_tar['dust'].interpolate_na(dim='time',method='nearest',fill_value=\"extrapolate\")\n",
    "    print(['input: ',ds_in['dust'].mean(),ds_in['dust'].min(),ds_in['dust'].max()])\n",
    "    print(['output: ',ds_tar['dust'].mean(),ds_tar['dust'].min(),ds_tar['dust'].max()])\n",
    "\n",
    "# convert units of 'degree_' to 'degrees_' so MOM will be able to infer the axis meaning\n",
    "# https://github.com/mom-ocean/MOM5/blob/1d9af9d262b/src/shared/axis_utils/axis_utils.F90#L92-L99\n",
    "    for dim in ds_tar.dims:\n",
    "        try:\n",
    "            units = ds_tar[dim].attrs['units'].lower()\n",
    "            if units.startswith('degree_'):\n",
    "                ds_tar[dim].attrs['units'] = units.replace('degree_', 'degrees_', 1)\n",
    "        except KeyError:\n",
    "            pass\n",
    "\n",
    "    ds_tar.to_netcdf(tmppath+'dust_'+res_list[ir]+'deg.nc',\n",
    "                     unlimited_dims='time',\n",
    "                     encoding={'dust':{'zlib': True,'complevel': 1,\n",
    "                                       '_FillValue':-1.e34, 'missing_value':-1.e34}})\n",
    "    print(res_list[ir],'done')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Creation of `csiro_bgc_sediment.res.nc`\n",
    "1. for simplicity, initialise with zero values everywhere.\n",
    "1. the x and y dimensions of the input file are not helpful (given indices instead of actual lon/lat values), so replace them with dust.nc for interpolation purposes.\n",
    "1. This script relies on `csiro_bgc.res.nc`, so make sure to compute this after creating `csiro_bgc.res.nc`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# res_list = ['1','025','01']\n",
    "\n",
    "for ir in range(np.size(res_list)):\n",
    "    ds_in = xr.open_dataset(tmppath+'csiro_bgc.res_'+res_list[ir]+'deg.nc')\n",
    "    ds_tar = ds_in['phy'].isel(zaxis_1=0,drop=True)\n",
    "    ds_tar = ds_tar*0\n",
    "    ds_tar = ds_tar.rename('caco3_sediment')\n",
    "\n",
    "# convert units of 'degree_' to 'degrees_' so MOM will be able to infer the axis meaning\n",
    "# https://github.com/mom-ocean/MOM5/blob/1d9af9d262b/src/shared/axis_utils/axis_utils.F90#L92-L99\n",
    "    for dim in ds_tar.dims:\n",
    "        try:\n",
    "            units = ds_tar[dim].attrs['units'].lower()\n",
    "            if units.startswith('degree_'):\n",
    "                ds_tar[dim].attrs['units'] = units.replace('degree_', 'degrees_', 1)\n",
    "        except KeyError:\n",
    "            pass\n",
    "\n",
    "    ds_tar.to_netcdf(tmppath+'csiro_bgc_sediment.res_'+res_list[ir]+'deg.nc',unlimited_dims='Time',encoding={'Time':{'_FillValue':None,'dtype':'float64'}})\n",
    "    print(res_list[ir],'done')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "%%bash -s \"$tmppath\" \"{\" \".join(res_list)}\"\n",
    "cd $1\n",
    "for ir in $2\n",
    "do\n",
    "    filename=csiro_bgc_sediment.res_${ir}deg.nc\n",
    "    ncap2 -O -s 'det_sediment=caco3_sediment' $filename $filename\n",
    "    ncatted -a cartesian_axis,xaxis_1,c,c,\"X\" $filename\n",
    "    ncatted -a cartesian_axis,yaxis_1,c,c,\"Y\" $filename\n",
    "    ncks -O -L 9 $filename $filename\n",
    "done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Update `o2i.nc` and `i2o.nc`\n",
    "- two bgc tracers added to each file.\n",
    "- wind speed is added to `i2o.nc` for gas flux calculation.\n",
    "- these are the initial conditions for fluxes. set to zeros for simplicity."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash -s \"$basepath\" \"{\" \".join(res_list)}\"\n",
    "basepath=$1\n",
    "for ir in $2\n",
    "do\n",
    "    cd $basepath${ir}deg/\n",
    "    ncap2 -O -s 'ssn_i=sst_i*0' o2i.nc o2i.nc\n",
    "    ncap2 -O -s 'ssalg_i=sst_i*0' o2i.nc o2i.nc\n",
    "    ncap2 -O -s 'wnd10_io=licefh_io*0' i2o.nc i2o.nc\n",
    "    ncap2 -O -s 'nit_io=wnd10_io*0' i2o.nc i2o.nc\n",
    "    ncap2 -O -s 'alg_io=wnd10_io*0' i2o.nc i2o.nc\n",
    "done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Copy the regridded files to their respective destinations.\n",
    "1. the regridded files will be copied to each resolution directory and given the same file names (so that no need to customise ocean/field_table for each resolution)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash -s \"$tmppath\" \"{\" \".join(res_list)}\"\n",
    "cd $1\n",
    "for ir in $2\n",
    "do\n",
    "    for it in bgc_param co2_iaf co2_ryf dust csiro_bgc.res csiro_bgc_sediment.res\n",
    "    do\n",
    "        if [ -f ${it}_${ir}deg.nc ]; then\n",
    "            cp -p ${it}_${ir}deg.nc ../${ir}deg/${it}.nc\n",
    "        fi\n",
    "    done\n",
    "done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# That's it! If you are happy with the output stored in `1deg, 025deg, 01deg`, then delete `tmp`.\n",
    "# When it's completely finalised, run `finalise.sh`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Pre-processing of input and reference grid data (NOT NECESSARY, as these data already exist, but keeping it for reproducibility)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Download GLODAPv2 2016b and OMIP archives of WOA13v2 (no3, o2) and FEMIP (fe)\n",
    "#Extract GLODAPv2\n",
    "%%bash -s \"$inpath\"\n",
    "cd $1\n",
    "wget https://www.nodc.noaa.gov/archive/arc0107/0162565/1.1/data/0-data/mapped/GLODAPv2.2016b_MappedClimatologies.tar.gz\n",
    "tar -xvf GLODAPv2.2016b_MappedClimatologies.tar.gz\n",
    "wget https://vesg.ipsl.upmc.fr/thredds/fileServer/IPSLFS/jomce/OMIP/initconds/FEMIP_model_median_iron_2016.nc\n",
    "wget https://vesg.ipsl.upmc.fr/thredds/fileServer/IPSLFS/jomce/OMIP/initconds/woa13_oxygen_OMIPinit.nc\n",
    "wget https://vesg.ipsl.upmc.fr/thredds/fileServer/IPSLFS/jomce/OMIP/initconds/woa13_nitrate_OMIPinit.nc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Extrapolate over land\n",
    "%%bash -s \"$inpath\"\n",
    "cd $1\n",
    "cdo -O fillmiss woa13_oxygen_OMIPinit.nc woa13_oxygen_OMIPinit_fillmiss.nc\n",
    "cdo -O fillmiss woa13_nitrate_OMIPinit.nc woa13_nitrate_OMIPinit_fillmiss.nc\n",
    "cdo -O fillmiss FEMIP_model_median_iron_2016.nc FEMIP_model_median_iron_2016_fillmiss.nc\n",
    "for iv in oxygen NO3 PI_TCO2 TCO2 TAlk\n",
    "do\n",
    "    filename=GLODAPv2.2016b.${iv}\n",
    "    cdo -O fillmiss GLODAPv2.2016b_MappedClimatologies/${filename}.nc ${filename}_fillmiss.nc\n",
    "done "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Apply fillmiss for `adic` and `dic` of ACCESS-OM2 OMIP2 output. \n",
    "# For adic and alk, use the 1-deg omip2 cycle 5 restart 304. \n",
    "# Because restart files have weird values over land, i cannot do `cdo fillmiss`. \n",
    "# To resolve this issue, i need to first apply the landsea mask \n",
    "# and also give appropriate grid coordinates based on an output file.\n",
    "ds_in = xr.open_dataset('/g/data/ik11/outputs/access-om2/1deg_jra55_iaf_omip2_cycle5/restart304/ocean/csiro_bgc.res.nc')\n",
    "ds_ou = xr.open_dataset('/g/data/ik11/outputs/access-om2/1deg_jra55_iaf_omip2_cycle5/output304/ocean/ocean_bgc_ann.nc')\n",
    "ds_ou['adic'] = ds_ou['adic'].where(ds_ou['adic']!=ds_ou['adic'],ds_in['adic'].values)\n",
    "ds_ou['alk'] = ds_ou['alk'].where(ds_ou['alk']!=ds_ou['alk'],ds_in['alk'].values)\n",
    "ds_ou.to_netcdf(inpath+'1deg_jra55_iaf_omip2_cycle5_restart304_csiro_bgc.res.nc')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Extrapolate over land\n",
    "%%bash -s \"$inpath\"\n",
    "cd $1\n",
    "cdo -fillmiss 1deg_jra55_iaf_omip2_cycle5_restart304_csiro_bgc.res.nc 1deg_jra55_iaf_omip2_cycle5_restart304_csiro_bgc.res_fillmiss.nc\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Create a reference grid file for each resolution (used as a target grid for regridding)\n",
    "ncks -d time,1 -v temp /g/data/ik11/outputs/access-om2/1deg_jra55_iaf_omip2_cycle6/output365/ocean/ocean_month.nc 1deg/ocean_grid_xyz.nc\n",
    "ncks -d time,1 -v temp /g/data/ik11/outputs/access-om2-025/025deg_jra55_iaf_omip2_cycle6/output365/ocean/ocean_month.nc 025deg/ocean_grid_xyz.nc\n",
    "ncks -d time,1 -v temp /g/data/ik11/outputs/access-om2-01/01deg_jra55v140_iaf_cycle3/output700/ocean/ocean-3d-temp-1-daily-mean-ym_2011_01.nc 01deg/ocean_grid_xyz.nc\n"
   ]
  }
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