params/modify_params.ipynb

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   "metadata": {},
   "source": [
    "# Editing the CTSM paramfiles\n",
    "- some typical examples"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "81c94223-a9cd-4683-a298-a4d188f86d03",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import xarray as xr\n",
    "import os\n",
    "import netCDF4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "ab067e34-b931-443d-9b00-82c85e17afc5",
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   "outputs": [],
   "source": [
    "#this is the base paramfile that you will copy and edit\n",
    "basefile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/ctsm51_params.c210507.nc'\n",
    "\n",
    "#important that your paramfile match the version of CLM that you are using\n",
    "# consider examining bld/namelist_files/namelist_defaults_ctsm.xml"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "37b717ba-cb80-4ace-befc-2cdbd4b1dd4f",
   "metadata": {},
   "source": [
    "### examine a pft file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "3ac988fa-de04-44d7-af83-54b312b171d7",
   "metadata": {},
   "outputs": [],
   "source": [
    "ds = xr.open_dataset(basefile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "bc331c0b-0c9b-44f2-94f0-82e92aab4161",
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;kmax&#x27; (segment: 4, pft: 79)&gt;\n",
       "array([[0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08]])\n",
       "Coordinates:\n",
       "    pftname  (pft) |S40 b&#x27;not_vegetated                           &#x27; ... b&#x27;irr...\n",
       "  * segment  (segment) |S40 b&#x27;sunlit                                  &#x27; ... b...\n",
       "Dimensions without coordinates: pft\n",
       "Attributes:\n",
       "    units:      mm h2o (transpired)/mm h2o (water potential gradient)/sec\n",
       "    long_name:  plant segment max conductance</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'kmax'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>segment</span>: 4</li><li><span>pft</span>: 79</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-4977cc9a-7f42-41e8-868a-05b97eaf73f4' class='xr-array-in' type='checkbox' checked><label for='section-4977cc9a-7f42-41e8-868a-05b97eaf73f4' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>0.0 1.602e-08 2.235e-08 1.79e-08 3.317e-08 ... 2e-08 2e-08 2e-08 2e-08</span></div><div class='xr-array-data'><pre>array([[0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08]])</pre></div></div></li><li class='xr-section-item'><input id='section-4417d901-c9b9-4b36-aaca-5cb382b3fa83' class='xr-section-summary-in' type='checkbox'  checked><label for='section-4417d901-c9b9-4b36-aaca-5cb382b3fa83' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>pftname</span></div><div class='xr-var-dims'>(pft)</div><div class='xr-var-dtype'>|S40</div><div class='xr-var-preview xr-preview'>...</div><input id='attrs-7b90d4d5-ed11-4d1e-957b-cd9e6460a114' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7b90d4d5-ed11-4d1e-957b-cd9e6460a114' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7f280188-1b48-49dc-9cf9-836033751d40' class='xr-var-data-in' type='checkbox'><label for='data-7f280188-1b48-49dc-9cf9-836033751d40' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Description of plant type</dd><dt><span>units :</span></dt><dd>unitless</dd></dl></div><div class='xr-var-data'><pre>array([b&#x27;not_vegetated                           &#x27;,\n",
       "       b&#x27;needleleaf_evergreen_temperate_tree     &#x27;,\n",
       "       b&#x27;needleleaf_evergreen_boreal_tree        &#x27;,\n",
       "       b&#x27;needleleaf_deciduous_boreal_tree        &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_tropical_tree       &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_temperate_tree      &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_tropical_tree       &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_temperate_tree      &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_boreal_tree         &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_shrub               &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_temperate_shrub     &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_boreal_shrub        &#x27;,\n",
       "       b&#x27;c3_arctic_grass                         &#x27;,\n",
       "       b&#x27;c3_non-arctic_grass                     &#x27;,\n",
       "       b&#x27;c4_grass                                &#x27;,\n",
       "       b&#x27;c3_crop                                 &#x27;,\n",
       "       b&#x27;c3_irrigated                            &#x27;,\n",
       "       b&#x27;temperate_corn                          &#x27;,\n",
       "       b&#x27;irrigated_temperate_corn                &#x27;,\n",
       "       b&#x27;spring_wheat                            &#x27;,\n",
       "       b&#x27;irrigated_spring_wheat                  &#x27;,\n",
       "       b&#x27;winter_wheat                            &#x27;,\n",
       "       b&#x27;irrigated_winter_wheat                  &#x27;,\n",
       "       b&#x27;temperate_soybean                       &#x27;,\n",
       "       b&#x27;irrigated_temperate_soybean             &#x27;,\n",
       "       b&#x27;barley                                  &#x27;,\n",
       "       b&#x27;irrigated_barley                        &#x27;,\n",
       "       b&#x27;winter_barley                           &#x27;,\n",
       "       b&#x27;irrigated_winter_barley                 &#x27;,\n",
       "       b&#x27;rye                                     &#x27;,\n",
       "       b&#x27;irrigated_rye                           &#x27;,\n",
       "       b&#x27;winter_rye                              &#x27;,\n",
       "       b&#x27;irrigated_winter_rye                    &#x27;,\n",
       "       b&#x27;cassava                                 &#x27;,\n",
       "       b&#x27;irrigated_cassava                       &#x27;,\n",
       "       b&#x27;citrus                                  &#x27;,\n",
       "       b&#x27;irrigated_citrus                        &#x27;,\n",
       "       b&#x27;cocoa                                   &#x27;,\n",
       "       b&#x27;irrigated_cocoa                         &#x27;,\n",
       "       b&#x27;coffee                                  &#x27;,\n",
       "       b&#x27;irrigated_coffee                        &#x27;,\n",
       "       b&#x27;cotton                                  &#x27;,\n",
       "       b&#x27;irrigated_cotton                        &#x27;,\n",
       "       b&#x27;datepalm                                &#x27;,\n",
       "       b&#x27;irrigated_datepalm                      &#x27;,\n",
       "       b&#x27;foddergrass                             &#x27;,\n",
       "       b&#x27;irrigated_foddergrass                   &#x27;,\n",
       "       b&#x27;grapes                                  &#x27;,\n",
       "       b&#x27;irrigated_grapes                        &#x27;,\n",
       "       b&#x27;groundnuts                              &#x27;,\n",
       "       b&#x27;irrigated_groundnuts                    &#x27;,\n",
       "       b&#x27;millet                                  &#x27;,\n",
       "       b&#x27;irrigated_millet                        &#x27;,\n",
       "       b&#x27;oilpalm                                 &#x27;,\n",
       "       b&#x27;irrigated_oilpalm                       &#x27;,\n",
       "       b&#x27;potatoes                                &#x27;,\n",
       "       b&#x27;irrigated_potatoes                      &#x27;,\n",
       "       b&#x27;pulses                                  &#x27;,\n",
       "       b&#x27;irrigated_pulses                        &#x27;,\n",
       "       b&#x27;rapeseed                                &#x27;,\n",
       "       b&#x27;irrigated_rapeseed                      &#x27;,\n",
       "       b&#x27;rice                                    &#x27;,\n",
       "       b&#x27;irrigated_rice                          &#x27;,\n",
       "       b&#x27;sorghum                                 &#x27;,\n",
       "       b&#x27;irrigated_sorghum                       &#x27;,\n",
       "       b&#x27;sugarbeet                               &#x27;,\n",
       "       b&#x27;irrigated_sugarbeet                     &#x27;,\n",
       "       b&#x27;sugarcane                               &#x27;,\n",
       "       b&#x27;irrigated_sugarcane                     &#x27;,\n",
       "       b&#x27;sunflower                               &#x27;,\n",
       "       b&#x27;irrigated_sunflower                     &#x27;,\n",
       "       b&#x27;miscanthus                              &#x27;,\n",
       "       b&#x27;irrigated_miscanthus                    &#x27;,\n",
       "       b&#x27;switchgrass                             &#x27;,\n",
       "       b&#x27;irrigated_switchgrass                   &#x27;,\n",
       "       b&#x27;tropical_corn                           &#x27;,\n",
       "       b&#x27;irrigated_tropical_corn                 &#x27;,\n",
       "       b&#x27;tropical_soybean                        &#x27;,\n",
       "       b&#x27;irrigated_tropical_soybean              &#x27;], dtype=&#x27;|S40&#x27;)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>segment</span></div><div class='xr-var-dims'>(segment)</div><div class='xr-var-dtype'>|S40</div><div class='xr-var-preview xr-preview'>b&#x27;sunlit                        ...</div><input id='attrs-a2070be3-bdfc-4d85-8743-1781fde9a2bc' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a2070be3-bdfc-4d85-8743-1781fde9a2bc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-664ee6df-aee1-48ad-a2ec-6a1bb65b39ec' class='xr-var-data-in' type='checkbox'><label for='data-664ee6df-aee1-48ad-a2ec-6a1bb65b39ec' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>units :</span></dt><dd>unitless</dd><dt><span>long_name :</span></dt><dd>description of hydraulic segment</dd></dl></div><div class='xr-var-data'><pre>array([b&#x27;sunlit                                  &#x27;,\n",
       "       b&#x27;shaded                                  &#x27;,\n",
       "       b&#x27;xylem                                   &#x27;,\n",
       "       b&#x27;root                                    &#x27;], dtype=&#x27;|S40&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e4fe02a2-2a4e-4bc8-9c02-acd954aa66ee' class='xr-section-summary-in' type='checkbox'  checked><label for='section-e4fe02a2-2a4e-4bc8-9c02-acd954aa66ee' class='xr-section-summary' >Attributes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>units :</span></dt><dd>mm h2o (transpired)/mm h2o (water potential gradient)/sec</dd><dt><span>long_name :</span></dt><dd>plant segment max conductance</dd></dl></div></li></ul></div></div>"
      ],
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       "<xarray.DataArray 'kmax' (segment: 4, pft: 79)>\n",
       "array([[0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08],\n",
       "       [0.000000e+00, 1.602140e-08, 2.234574e-08, ..., 2.000000e-08,\n",
       "        2.000000e-08, 2.000000e-08]])\n",
       "Coordinates:\n",
       "    pftname  (pft) |S40 ...\n",
       "  * segment  (segment) |S40 b'sunlit                                  ' ... b...\n",
       "Dimensions without coordinates: pft\n",
       "Attributes:\n",
       "    units:      mm h2o (transpired)/mm h2o (water potential gradient)/sec\n",
       "    long_name:  plant segment max conductance"
      ]
     },
     "execution_count": 6,
     "metadata": {},
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    }
   ],
   "source": [
    "ds.kmax"
   ]
  },
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       "    pftname  (pft) |S40 b&#x27;not_vegetated                           &#x27; ... b&#x27;irr...\n",
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       "    long_name:  Medlyn slope of conductance-photosynthesis relationship\n",
       "    units:      umol H2O/umol CO2\n",
       "    comment:    Values come from the values used in the CABLE model</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'medlynslope'</div><ul class='xr-dim-list'><li><span>pft</span>: 79</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-27ff7dc5-6bd5-4810-b8c6-6372800971f0' class='xr-array-in' type='checkbox' checked><label for='section-27ff7dc5-6bd5-4810-b8c6-6372800971f0' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>0.0 2.35 2.35 2.35 4.12 4.12 4.45 ... 1.79 1.79 1.79 1.79 5.79 5.79</span></div><div class='xr-array-data'><pre>array([0.  , 2.35, 2.35, 2.35, 4.12, 4.12, 4.45, 4.45, 4.45, 4.7 , 4.7 , 4.7 ,\n",
       "       2.22, 5.25, 1.62, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 1.79,\n",
       "       1.79, 1.79, 1.79, 1.79, 1.79, 5.79, 5.79])</pre></div></div></li><li class='xr-section-item'><input id='section-bf003bc4-5bed-4957-87cb-f8116bba5d26' class='xr-section-summary-in' type='checkbox'  checked><label for='section-bf003bc4-5bed-4957-87cb-f8116bba5d26' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>pftname</span></div><div class='xr-var-dims'>(pft)</div><div class='xr-var-dtype'>|S40</div><div class='xr-var-preview xr-preview'>b&#x27;not_vegetated                 ...</div><input id='attrs-f85d4499-7346-4bb8-9ee6-6d2a1790da88' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f85d4499-7346-4bb8-9ee6-6d2a1790da88' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b9d3d8d4-df05-4cf6-8fb8-99691755eefc' class='xr-var-data-in' type='checkbox'><label for='data-b9d3d8d4-df05-4cf6-8fb8-99691755eefc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Description of plant type</dd><dt><span>units :</span></dt><dd>unitless</dd></dl></div><div class='xr-var-data'><pre>array([b&#x27;not_vegetated                           &#x27;,\n",
       "       b&#x27;needleleaf_evergreen_temperate_tree     &#x27;,\n",
       "       b&#x27;needleleaf_evergreen_boreal_tree        &#x27;,\n",
       "       b&#x27;needleleaf_deciduous_boreal_tree        &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_tropical_tree       &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_temperate_tree      &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_tropical_tree       &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_temperate_tree      &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_boreal_tree         &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_shrub               &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_temperate_shrub     &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_boreal_shrub        &#x27;,\n",
       "       b&#x27;c3_arctic_grass                         &#x27;,\n",
       "       b&#x27;c3_non-arctic_grass                     &#x27;,\n",
       "       b&#x27;c4_grass                                &#x27;,\n",
       "       b&#x27;c3_crop                                 &#x27;,\n",
       "       b&#x27;c3_irrigated                            &#x27;,\n",
       "       b&#x27;temperate_corn                          &#x27;,\n",
       "       b&#x27;irrigated_temperate_corn                &#x27;,\n",
       "       b&#x27;spring_wheat                            &#x27;,\n",
       "       b&#x27;irrigated_spring_wheat                  &#x27;,\n",
       "       b&#x27;winter_wheat                            &#x27;,\n",
       "       b&#x27;irrigated_winter_wheat                  &#x27;,\n",
       "       b&#x27;temperate_soybean                       &#x27;,\n",
       "       b&#x27;irrigated_temperate_soybean             &#x27;,\n",
       "       b&#x27;barley                                  &#x27;,\n",
       "       b&#x27;irrigated_barley                        &#x27;,\n",
       "       b&#x27;winter_barley                           &#x27;,\n",
       "       b&#x27;irrigated_winter_barley                 &#x27;,\n",
       "       b&#x27;rye                                     &#x27;,\n",
       "       b&#x27;irrigated_rye                           &#x27;,\n",
       "       b&#x27;winter_rye                              &#x27;,\n",
       "       b&#x27;irrigated_winter_rye                    &#x27;,\n",
       "       b&#x27;cassava                                 &#x27;,\n",
       "       b&#x27;irrigated_cassava                       &#x27;,\n",
       "       b&#x27;citrus                                  &#x27;,\n",
       "       b&#x27;irrigated_citrus                        &#x27;,\n",
       "       b&#x27;cocoa                                   &#x27;,\n",
       "       b&#x27;irrigated_cocoa                         &#x27;,\n",
       "       b&#x27;coffee                                  &#x27;,\n",
       "       b&#x27;irrigated_coffee                        &#x27;,\n",
       "       b&#x27;cotton                                  &#x27;,\n",
       "       b&#x27;irrigated_cotton                        &#x27;,\n",
       "       b&#x27;datepalm                                &#x27;,\n",
       "       b&#x27;irrigated_datepalm                      &#x27;,\n",
       "       b&#x27;foddergrass                             &#x27;,\n",
       "       b&#x27;irrigated_foddergrass                   &#x27;,\n",
       "       b&#x27;grapes                                  &#x27;,\n",
       "       b&#x27;irrigated_grapes                        &#x27;,\n",
       "       b&#x27;groundnuts                              &#x27;,\n",
       "       b&#x27;irrigated_groundnuts                    &#x27;,\n",
       "       b&#x27;millet                                  &#x27;,\n",
       "       b&#x27;irrigated_millet                        &#x27;,\n",
       "       b&#x27;oilpalm                                 &#x27;,\n",
       "       b&#x27;irrigated_oilpalm                       &#x27;,\n",
       "       b&#x27;potatoes                                &#x27;,\n",
       "       b&#x27;irrigated_potatoes                      &#x27;,\n",
       "       b&#x27;pulses                                  &#x27;,\n",
       "       b&#x27;irrigated_pulses                        &#x27;,\n",
       "       b&#x27;rapeseed                                &#x27;,\n",
       "       b&#x27;irrigated_rapeseed                      &#x27;,\n",
       "       b&#x27;rice                                    &#x27;,\n",
       "       b&#x27;irrigated_rice                          &#x27;,\n",
       "       b&#x27;sorghum                                 &#x27;,\n",
       "       b&#x27;irrigated_sorghum                       &#x27;,\n",
       "       b&#x27;sugarbeet                               &#x27;,\n",
       "       b&#x27;irrigated_sugarbeet                     &#x27;,\n",
       "       b&#x27;sugarcane                               &#x27;,\n",
       "       b&#x27;irrigated_sugarcane                     &#x27;,\n",
       "       b&#x27;sunflower                               &#x27;,\n",
       "       b&#x27;irrigated_sunflower                     &#x27;,\n",
       "       b&#x27;miscanthus                              &#x27;,\n",
       "       b&#x27;irrigated_miscanthus                    &#x27;,\n",
       "       b&#x27;switchgrass                             &#x27;,\n",
       "       b&#x27;irrigated_switchgrass                   &#x27;,\n",
       "       b&#x27;tropical_corn                           &#x27;,\n",
       "       b&#x27;irrigated_tropical_corn                 &#x27;,\n",
       "       b&#x27;tropical_soybean                        &#x27;,\n",
       "       b&#x27;irrigated_tropical_soybean              &#x27;], dtype=&#x27;|S40&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-4e635d03-b5de-48ef-9045-3a76f3f98601' class='xr-section-summary-in' type='checkbox'  checked><label for='section-4e635d03-b5de-48ef-9045-3a76f3f98601' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Medlyn slope of conductance-photosynthesis relationship</dd><dt><span>units :</span></dt><dd>umol H2O/umol CO2</dd><dt><span>comment :</span></dt><dd>Values come from the values used in the CABLE model</dd></dl></div></li></ul></div></div>"
      ],
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       "<xarray.DataArray 'medlynslope' (pft: 79)>\n",
       "array([0.  , 2.35, 2.35, 2.35, 4.12, 4.12, 4.45, 4.45, 4.45, 4.7 , 4.7 , 4.7 ,\n",
       "       2.22, 5.25, 1.62, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 1.79,\n",
       "       1.79, 1.79, 1.79, 1.79, 1.79, 5.79, 5.79])\n",
       "Coordinates:\n",
       "    pftname  (pft) |S40 b'not_vegetated                           ' ... b'irr...\n",
       "Dimensions without coordinates: pft\n",
       "Attributes:\n",
       "    long_name:  Medlyn slope of conductance-photosynthesis relationship\n",
       "    units:      umol H2O/umol CO2\n",
       "    comment:    Values come from the values used in the CABLE model"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.medlynslope"
   ]
  },
  {
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   "id": "27f831de-8631-4f30-800f-fd1c8735ee92",
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;jmaxb0&#x27; ()&gt;\n",
       "array(0.0311)\n",
       "Attributes:\n",
       "    long_name:  Baseline proportion of nitrogen allocated for electron transport\n",
       "    units:      J</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'jmaxb0'</div></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-8bcf1ea7-a461-4086-8993-9edacff58d76' class='xr-array-in' type='checkbox' checked><label for='section-8bcf1ea7-a461-4086-8993-9edacff58d76' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>0.0311</span></div><div class='xr-array-data'><pre>array(0.0311)</pre></div></div></li><li class='xr-section-item'><input id='section-1109a651-5a2c-4fed-aa2c-f6b751cfd688' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-1109a651-5a2c-4fed-aa2c-f6b751cfd688' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-680e6674-e98c-4490-bf80-ccfabb6032c4' class='xr-section-summary-in' type='checkbox'  checked><label for='section-680e6674-e98c-4490-bf80-ccfabb6032c4' class='xr-section-summary' >Attributes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Baseline proportion of nitrogen allocated for electron transport</dd><dt><span>units :</span></dt><dd>J</dd></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.DataArray 'jmaxb0' ()>\n",
       "array(0.0311)\n",
       "Attributes:\n",
       "    long_name:  Baseline proportion of nitrogen allocated for electron transport\n",
       "    units:      J"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.jmaxb0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "580e8d55-fbde-418c-a364-9800c0ebd6e9",
   "metadata": {},
   "source": [
    "## edit a paramfile\n",
    " - avoiding xarray for writing the new files, for some reason paramfiles written with xarray tend to crash the model"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f3d8f8b4-b282-4509-b99d-b5c266d9d61a",
   "metadata": {},
   "source": [
    "### jmaxb0, increase to 0.05"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "027b148d-3f2f-48c1-b4cc-e79044f27a0b",
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   "outputs": [
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     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## CREATE the new paramfile\n",
    "newfile = 'jmaxb0_5e-2.nc'\n",
    "cmd = 'cp '+basefile+' '+newfile\n",
    "os.system(cmd)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "7772f5b6-99ba-4f9c-aae9-aaadfcf2d77a",
   "metadata": {},
   "outputs": [],
   "source": [
    "param = 'jmaxb0'\n",
    "dset = netCDF4.Dataset(newfile,'r+')\n",
    "dset[param][:] = 0.05\n",
    "dset.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "6d39c684-ae26-482b-be5a-1fd9d2160e84",
   "metadata": {},
   "outputs": [
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       "Attributes:\n",
       "    long_name:  Baseline proportion of nitrogen allocated for electron transport\n",
       "    units:      J</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'jmaxb0'</div></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-92843621-27c3-4de8-b934-c4d3ff89f880' class='xr-array-in' type='checkbox' checked><label for='section-92843621-27c3-4de8-b934-c4d3ff89f880' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>0.05</span></div><div class='xr-array-data'><pre>array(0.05)</pre></div></div></li><li class='xr-section-item'><input id='section-fb1296a7-42a0-4373-854c-b0ee57e44da4' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-fb1296a7-42a0-4373-854c-b0ee57e44da4' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-f10dd162-2a55-4c4c-a739-0cf13d666e51' class='xr-section-summary-in' type='checkbox'  checked><label for='section-f10dd162-2a55-4c4c-a739-0cf13d666e51' class='xr-section-summary' >Attributes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Baseline proportion of nitrogen allocated for electron transport</dd><dt><span>units :</span></dt><dd>J</dd></dl></div></li></ul></div></div>"
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       "<xarray.DataArray 'jmaxb0' ()>\n",
       "array(0.05)\n",
       "Attributes:\n",
       "    long_name:  Baseline proportion of nitrogen allocated for electron transport\n",
       "    units:      J"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "xr.open_dataset(newfile)['jmaxb0']"
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   "source": [
    "### kmax, double all values\n",
    " - note that the shapes of the various parameters vary\n",
    " - some are scalar, some have a pft-dimension, and some have pft and plant-segment dimensions\n",
    " - easist to read in the example from basefile, and edit accordingly "
   ]
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   "source": [
    "## CREATE the new paramfile\n",
    "newfile = 'kmax_2x.nc'\n",
    "cmd = 'cp '+basefile+' '+newfile\n",
    "os.system(cmd)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "bcf2c053-b2ce-4406-a1ba-41d9684a23f2",
   "metadata": {},
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   "source": [
    "param = 'kmax'\n",
    "kmax = xr.open_dataset(basefile)[param].values\n",
    "newkmax = kmax*2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "1baf2f03-4da4-40b9-887e-f8afeb686b3d",
   "metadata": {},
   "outputs": [],
   "source": [
    "dset = netCDF4.Dataset(newfile,'r+')\n",
    "dset[param][:] = newkmax\n",
    "dset.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "62f01983-27c6-4c32-949b-a95580638685",
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;kmax&#x27; (segment: 4, pft: 79)&gt;\n",
       "array([[0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08],\n",
       "       [0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08],\n",
       "       [0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08],\n",
       "       [0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08]])\n",
       "Coordinates:\n",
       "    pftname  (pft) |S40 b&#x27;not_vegetated                           &#x27; ... b&#x27;irr...\n",
       "  * segment  (segment) |S40 b&#x27;sunlit                                  &#x27; ... b...\n",
       "Dimensions without coordinates: pft\n",
       "Attributes:\n",
       "    units:      mm h2o (transpired)/mm h2o (water potential gradient)/sec\n",
       "    long_name:  plant segment max conductance</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'kmax'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>segment</span>: 4</li><li><span>pft</span>: 79</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-f29506d1-b965-4de0-a56d-56692fd24438' class='xr-array-in' type='checkbox' checked><label for='section-f29506d1-b965-4de0-a56d-56692fd24438' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>0.0 3.204e-08 4.469e-08 3.58e-08 6.635e-08 ... 4e-08 4e-08 4e-08 4e-08</span></div><div class='xr-array-data'><pre>array([[0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08],\n",
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       "        4.000000e-08, 4.000000e-08],\n",
       "       [0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08],\n",
       "       [0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08]])</pre></div></div></li><li class='xr-section-item'><input id='section-ee5fdf28-8466-4545-a824-31330e8172f1' class='xr-section-summary-in' type='checkbox'  checked><label for='section-ee5fdf28-8466-4545-a824-31330e8172f1' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>pftname</span></div><div class='xr-var-dims'>(pft)</div><div class='xr-var-dtype'>|S40</div><div class='xr-var-preview xr-preview'>...</div><input id='attrs-6ed5bcfc-9105-484c-885d-d905a4af9b57' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6ed5bcfc-9105-484c-885d-d905a4af9b57' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-32f72024-d895-48f1-8113-bd0595e45e1a' class='xr-var-data-in' type='checkbox'><label for='data-32f72024-d895-48f1-8113-bd0595e45e1a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Description of plant type</dd><dt><span>units :</span></dt><dd>unitless</dd></dl></div><div class='xr-var-data'><pre>array([b&#x27;not_vegetated                           &#x27;,\n",
       "       b&#x27;needleleaf_evergreen_temperate_tree     &#x27;,\n",
       "       b&#x27;needleleaf_evergreen_boreal_tree        &#x27;,\n",
       "       b&#x27;needleleaf_deciduous_boreal_tree        &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_tropical_tree       &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_temperate_tree      &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_tropical_tree       &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_temperate_tree      &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_boreal_tree         &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_shrub               &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_temperate_shrub     &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_boreal_shrub        &#x27;,\n",
       "       b&#x27;c3_arctic_grass                         &#x27;,\n",
       "       b&#x27;c3_non-arctic_grass                     &#x27;,\n",
       "       b&#x27;c4_grass                                &#x27;,\n",
       "       b&#x27;c3_crop                                 &#x27;,\n",
       "       b&#x27;c3_irrigated                            &#x27;,\n",
       "       b&#x27;temperate_corn                          &#x27;,\n",
       "       b&#x27;irrigated_temperate_corn                &#x27;,\n",
       "       b&#x27;spring_wheat                            &#x27;,\n",
       "       b&#x27;irrigated_spring_wheat                  &#x27;,\n",
       "       b&#x27;winter_wheat                            &#x27;,\n",
       "       b&#x27;irrigated_winter_wheat                  &#x27;,\n",
       "       b&#x27;temperate_soybean                       &#x27;,\n",
       "       b&#x27;irrigated_temperate_soybean             &#x27;,\n",
       "       b&#x27;barley                                  &#x27;,\n",
       "       b&#x27;irrigated_barley                        &#x27;,\n",
       "       b&#x27;winter_barley                           &#x27;,\n",
       "       b&#x27;irrigated_winter_barley                 &#x27;,\n",
       "       b&#x27;rye                                     &#x27;,\n",
       "       b&#x27;irrigated_rye                           &#x27;,\n",
       "       b&#x27;winter_rye                              &#x27;,\n",
       "       b&#x27;irrigated_winter_rye                    &#x27;,\n",
       "       b&#x27;cassava                                 &#x27;,\n",
       "       b&#x27;irrigated_cassava                       &#x27;,\n",
       "       b&#x27;citrus                                  &#x27;,\n",
       "       b&#x27;irrigated_citrus                        &#x27;,\n",
       "       b&#x27;cocoa                                   &#x27;,\n",
       "       b&#x27;irrigated_cocoa                         &#x27;,\n",
       "       b&#x27;coffee                                  &#x27;,\n",
       "       b&#x27;irrigated_coffee                        &#x27;,\n",
       "       b&#x27;cotton                                  &#x27;,\n",
       "       b&#x27;irrigated_cotton                        &#x27;,\n",
       "       b&#x27;datepalm                                &#x27;,\n",
       "       b&#x27;irrigated_datepalm                      &#x27;,\n",
       "       b&#x27;foddergrass                             &#x27;,\n",
       "       b&#x27;irrigated_foddergrass                   &#x27;,\n",
       "       b&#x27;grapes                                  &#x27;,\n",
       "       b&#x27;irrigated_grapes                        &#x27;,\n",
       "       b&#x27;groundnuts                              &#x27;,\n",
       "       b&#x27;irrigated_groundnuts                    &#x27;,\n",
       "       b&#x27;millet                                  &#x27;,\n",
       "       b&#x27;irrigated_millet                        &#x27;,\n",
       "       b&#x27;oilpalm                                 &#x27;,\n",
       "       b&#x27;irrigated_oilpalm                       &#x27;,\n",
       "       b&#x27;potatoes                                &#x27;,\n",
       "       b&#x27;irrigated_potatoes                      &#x27;,\n",
       "       b&#x27;pulses                                  &#x27;,\n",
       "       b&#x27;irrigated_pulses                        &#x27;,\n",
       "       b&#x27;rapeseed                                &#x27;,\n",
       "       b&#x27;irrigated_rapeseed                      &#x27;,\n",
       "       b&#x27;rice                                    &#x27;,\n",
       "       b&#x27;irrigated_rice                          &#x27;,\n",
       "       b&#x27;sorghum                                 &#x27;,\n",
       "       b&#x27;irrigated_sorghum                       &#x27;,\n",
       "       b&#x27;sugarbeet                               &#x27;,\n",
       "       b&#x27;irrigated_sugarbeet                     &#x27;,\n",
       "       b&#x27;sugarcane                               &#x27;,\n",
       "       b&#x27;irrigated_sugarcane                     &#x27;,\n",
       "       b&#x27;sunflower                               &#x27;,\n",
       "       b&#x27;irrigated_sunflower                     &#x27;,\n",
       "       b&#x27;miscanthus                              &#x27;,\n",
       "       b&#x27;irrigated_miscanthus                    &#x27;,\n",
       "       b&#x27;switchgrass                             &#x27;,\n",
       "       b&#x27;irrigated_switchgrass                   &#x27;,\n",
       "       b&#x27;tropical_corn                           &#x27;,\n",
       "       b&#x27;irrigated_tropical_corn                 &#x27;,\n",
       "       b&#x27;tropical_soybean                        &#x27;,\n",
       "       b&#x27;irrigated_tropical_soybean              &#x27;], dtype=&#x27;|S40&#x27;)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>segment</span></div><div class='xr-var-dims'>(segment)</div><div class='xr-var-dtype'>|S40</div><div class='xr-var-preview xr-preview'>b&#x27;sunlit                        ...</div><input id='attrs-7045b6fa-b296-4982-902c-d19dab26ebc5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7045b6fa-b296-4982-902c-d19dab26ebc5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-011a4872-5721-4120-a644-a470d21eef03' class='xr-var-data-in' type='checkbox'><label for='data-011a4872-5721-4120-a644-a470d21eef03' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>units :</span></dt><dd>unitless</dd><dt><span>long_name :</span></dt><dd>description of hydraulic segment</dd></dl></div><div class='xr-var-data'><pre>array([b&#x27;sunlit                                  &#x27;,\n",
       "       b&#x27;shaded                                  &#x27;,\n",
       "       b&#x27;xylem                                   &#x27;,\n",
       "       b&#x27;root                                    &#x27;], dtype=&#x27;|S40&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-522aa3a6-d573-4df1-b2ad-72df88c4a879' class='xr-section-summary-in' type='checkbox'  checked><label for='section-522aa3a6-d573-4df1-b2ad-72df88c4a879' class='xr-section-summary' >Attributes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>units :</span></dt><dd>mm h2o (transpired)/mm h2o (water potential gradient)/sec</dd><dt><span>long_name :</span></dt><dd>plant segment max conductance</dd></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.DataArray 'kmax' (segment: 4, pft: 79)>\n",
       "array([[0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08],\n",
       "       [0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08],\n",
       "       [0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08],\n",
       "       [0.000000e+00, 3.204280e-08, 4.469149e-08, ..., 4.000000e-08,\n",
       "        4.000000e-08, 4.000000e-08]])\n",
       "Coordinates:\n",
       "    pftname  (pft) |S40 ...\n",
       "  * segment  (segment) |S40 b'sunlit                                  ' ... b...\n",
       "Dimensions without coordinates: pft\n",
       "Attributes:\n",
       "    units:      mm h2o (transpired)/mm h2o (water potential gradient)/sec\n",
       "    long_name:  plant segment max conductance"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "xr.open_dataset(newfile)['kmax']"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "84ba4bae-1b4e-4b5f-af7f-2411971fccd2",
   "metadata": {},
   "source": [
    "### medlynslope\n",
    "- substituting a value for just one pft"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "id": "6b184d47-246d-461f-9f11-09d599a2b689",
   "metadata": {},
   "outputs": [],
   "source": [
    "p = xr.open_dataset(basefile)\n",
    "mypft = 'broadleaf_deciduous_temperate_tree'\n",
    "ix    = np.array([mypft in str(n) for n in p.pftname.values])  #index vector for mypft"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "id": "006f879a-085e-4bea-904e-c0f1b4eaeb15",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([0.        , 2.3499999 , 2.3499999 , 2.3499999 , 4.11999989,\n",
       "       4.11999989, 4.44999981, 6.        , 4.44999981, 4.69999981,\n",
       "       4.69999981, 4.69999981, 2.22000003, 5.25      , 1.62      ,\n",
       "       5.78999996, 5.78999996, 1.78999996, 1.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 5.78999996, 5.78999996, 5.78999996,\n",
       "       5.78999996, 5.78999996, 1.78999996, 1.78999996, 5.78999996,\n",
       "       5.78999996, 1.78999996, 1.78999996, 1.78999996, 1.78999996,\n",
       "       1.78999996, 1.78999996, 5.78999996, 5.78999996])"
      ]
     },
     "execution_count": 53,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "param = 'medlynslope'\n",
    "m = p[param].values\n",
    "m[ix] = 6\n",
    "m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "id": "7b0a1d7d-1b76-48a1-bb8d-5b7ae496bc22",
   "metadata": {},
   "outputs": [],
   "source": [
    "newfile = 'medlynslope_BDT_6.nc'\n",
    "cmd = 'cp '+basefile+' '+newfile\n",
    "os.system(cmd)\n",
    "dset = netCDF4.Dataset(newfile,'r+')\n",
    "dset[param][:] = m\n",
    "dset.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "id": "300f8235-0c9f-4cc3-92a9-26ae32f4a31c",
   "metadata": {},
   "outputs": [
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;medlynslope&#x27; (pft: 79)&gt;\n",
       "array([0.  , 2.35, 2.35, 2.35, 4.12, 4.12, 4.45, 6.  , 4.45, 4.7 , 4.7 , 4.7 ,\n",
       "       2.22, 5.25, 1.62, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 1.79,\n",
       "       1.79, 1.79, 1.79, 1.79, 1.79, 5.79, 5.79])\n",
       "Coordinates:\n",
       "    pftname  (pft) |S40 b&#x27;not_vegetated                           &#x27; ... b&#x27;irr...\n",
       "Dimensions without coordinates: pft\n",
       "Attributes:\n",
       "    long_name:  Medlyn slope of conductance-photosynthesis relationship\n",
       "    units:      umol H2O/umol CO2\n",
       "    comment:    Values come from the values used in the CABLE model</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'medlynslope'</div><ul class='xr-dim-list'><li><span>pft</span>: 79</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-05e9362c-1994-4a78-95a7-32948c1297b4' class='xr-array-in' type='checkbox' checked><label for='section-05e9362c-1994-4a78-95a7-32948c1297b4' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>0.0 2.35 2.35 2.35 4.12 4.12 4.45 ... 1.79 1.79 1.79 1.79 5.79 5.79</span></div><div class='xr-array-data'><pre>array([0.  , 2.35, 2.35, 2.35, 4.12, 4.12, 4.45, 6.  , 4.45, 4.7 , 4.7 , 4.7 ,\n",
       "       2.22, 5.25, 1.62, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 1.79,\n",
       "       1.79, 1.79, 1.79, 1.79, 1.79, 5.79, 5.79])</pre></div></div></li><li class='xr-section-item'><input id='section-7be21ab7-4d2d-495f-8ecc-66d165c32462' class='xr-section-summary-in' type='checkbox'  checked><label for='section-7be21ab7-4d2d-495f-8ecc-66d165c32462' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>pftname</span></div><div class='xr-var-dims'>(pft)</div><div class='xr-var-dtype'>|S40</div><div class='xr-var-preview xr-preview'>...</div><input id='attrs-c2d05356-c0f5-47b7-85be-56439d08c6b5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c2d05356-c0f5-47b7-85be-56439d08c6b5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0d9b4f5f-2b09-457d-ac5e-0447b01fef62' class='xr-var-data-in' type='checkbox'><label for='data-0d9b4f5f-2b09-457d-ac5e-0447b01fef62' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Description of plant type</dd><dt><span>units :</span></dt><dd>unitless</dd></dl></div><div class='xr-var-data'><pre>array([b&#x27;not_vegetated                           &#x27;,\n",
       "       b&#x27;needleleaf_evergreen_temperate_tree     &#x27;,\n",
       "       b&#x27;needleleaf_evergreen_boreal_tree        &#x27;,\n",
       "       b&#x27;needleleaf_deciduous_boreal_tree        &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_tropical_tree       &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_temperate_tree      &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_tropical_tree       &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_temperate_tree      &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_boreal_tree         &#x27;,\n",
       "       b&#x27;broadleaf_evergreen_shrub               &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_temperate_shrub     &#x27;,\n",
       "       b&#x27;broadleaf_deciduous_boreal_shrub        &#x27;,\n",
       "       b&#x27;c3_arctic_grass                         &#x27;,\n",
       "       b&#x27;c3_non-arctic_grass                     &#x27;,\n",
       "       b&#x27;c4_grass                                &#x27;,\n",
       "       b&#x27;c3_crop                                 &#x27;,\n",
       "       b&#x27;c3_irrigated                            &#x27;,\n",
       "       b&#x27;temperate_corn                          &#x27;,\n",
       "       b&#x27;irrigated_temperate_corn                &#x27;,\n",
       "       b&#x27;spring_wheat                            &#x27;,\n",
       "       b&#x27;irrigated_spring_wheat                  &#x27;,\n",
       "       b&#x27;winter_wheat                            &#x27;,\n",
       "       b&#x27;irrigated_winter_wheat                  &#x27;,\n",
       "       b&#x27;temperate_soybean                       &#x27;,\n",
       "       b&#x27;irrigated_temperate_soybean             &#x27;,\n",
       "       b&#x27;barley                                  &#x27;,\n",
       "       b&#x27;irrigated_barley                        &#x27;,\n",
       "       b&#x27;winter_barley                           &#x27;,\n",
       "       b&#x27;irrigated_winter_barley                 &#x27;,\n",
       "       b&#x27;rye                                     &#x27;,\n",
       "       b&#x27;irrigated_rye                           &#x27;,\n",
       "       b&#x27;winter_rye                              &#x27;,\n",
       "       b&#x27;irrigated_winter_rye                    &#x27;,\n",
       "       b&#x27;cassava                                 &#x27;,\n",
       "       b&#x27;irrigated_cassava                       &#x27;,\n",
       "       b&#x27;citrus                                  &#x27;,\n",
       "       b&#x27;irrigated_citrus                        &#x27;,\n",
       "       b&#x27;cocoa                                   &#x27;,\n",
       "       b&#x27;irrigated_cocoa                         &#x27;,\n",
       "       b&#x27;coffee                                  &#x27;,\n",
       "       b&#x27;irrigated_coffee                        &#x27;,\n",
       "       b&#x27;cotton                                  &#x27;,\n",
       "       b&#x27;irrigated_cotton                        &#x27;,\n",
       "       b&#x27;datepalm                                &#x27;,\n",
       "       b&#x27;irrigated_datepalm                      &#x27;,\n",
       "       b&#x27;foddergrass                             &#x27;,\n",
       "       b&#x27;irrigated_foddergrass                   &#x27;,\n",
       "       b&#x27;grapes                                  &#x27;,\n",
       "       b&#x27;irrigated_grapes                        &#x27;,\n",
       "       b&#x27;groundnuts                              &#x27;,\n",
       "       b&#x27;irrigated_groundnuts                    &#x27;,\n",
       "       b&#x27;millet                                  &#x27;,\n",
       "       b&#x27;irrigated_millet                        &#x27;,\n",
       "       b&#x27;oilpalm                                 &#x27;,\n",
       "       b&#x27;irrigated_oilpalm                       &#x27;,\n",
       "       b&#x27;potatoes                                &#x27;,\n",
       "       b&#x27;irrigated_potatoes                      &#x27;,\n",
       "       b&#x27;pulses                                  &#x27;,\n",
       "       b&#x27;irrigated_pulses                        &#x27;,\n",
       "       b&#x27;rapeseed                                &#x27;,\n",
       "       b&#x27;irrigated_rapeseed                      &#x27;,\n",
       "       b&#x27;rice                                    &#x27;,\n",
       "       b&#x27;irrigated_rice                          &#x27;,\n",
       "       b&#x27;sorghum                                 &#x27;,\n",
       "       b&#x27;irrigated_sorghum                       &#x27;,\n",
       "       b&#x27;sugarbeet                               &#x27;,\n",
       "       b&#x27;irrigated_sugarbeet                     &#x27;,\n",
       "       b&#x27;sugarcane                               &#x27;,\n",
       "       b&#x27;irrigated_sugarcane                     &#x27;,\n",
       "       b&#x27;sunflower                               &#x27;,\n",
       "       b&#x27;irrigated_sunflower                     &#x27;,\n",
       "       b&#x27;miscanthus                              &#x27;,\n",
       "       b&#x27;irrigated_miscanthus                    &#x27;,\n",
       "       b&#x27;switchgrass                             &#x27;,\n",
       "       b&#x27;irrigated_switchgrass                   &#x27;,\n",
       "       b&#x27;tropical_corn                           &#x27;,\n",
       "       b&#x27;irrigated_tropical_corn                 &#x27;,\n",
       "       b&#x27;tropical_soybean                        &#x27;,\n",
       "       b&#x27;irrigated_tropical_soybean              &#x27;], dtype=&#x27;|S40&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e598bcba-2b37-49f6-b8dc-b3e2a30bccec' class='xr-section-summary-in' type='checkbox'  checked><label for='section-e598bcba-2b37-49f6-b8dc-b3e2a30bccec' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Medlyn slope of conductance-photosynthesis relationship</dd><dt><span>units :</span></dt><dd>umol H2O/umol CO2</dd><dt><span>comment :</span></dt><dd>Values come from the values used in the CABLE model</dd></dl></div></li></ul></div></div>"
      ],
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       "<xarray.DataArray 'medlynslope' (pft: 79)>\n",
       "array([0.  , 2.35, 2.35, 2.35, 4.12, 4.12, 4.45, 6.  , 4.45, 4.7 , 4.7 , 4.7 ,\n",
       "       2.22, 5.25, 1.62, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79,\n",
       "       5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 5.79, 1.79, 1.79, 5.79, 5.79, 1.79,\n",
       "       1.79, 1.79, 1.79, 1.79, 1.79, 5.79, 5.79])\n",
       "Coordinates:\n",
       "    pftname  (pft) |S40 ...\n",
       "Dimensions without coordinates: pft\n",
       "Attributes:\n",
       "    long_name:  Medlyn slope of conductance-photosynthesis relationship\n",
       "    units:      umol H2O/umol CO2\n",
       "    comment:    Values come from the values used in the CABLE model"
      ]
     },
     "execution_count": 55,
     "metadata": {},
     "output_type": "execute_result"
    }
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