{ "cells": [ { "cell_type": "code", "execution_count": 27, "id": "14641a7d", "metadata": {}, "outputs": [], "source": [ "from IPython.display import display, Markdown\n", "import os\n", "import json\n", "from libcbm import resources\n", "import pandas as pd\n", "import numpy as np\n", "from numpy.random import default_rng\n", "from libcbm.model.cbm_exn import cbm_exn_model\n", "from libcbm.model.cbm_exn import cbm_exn_spinup\n", "from libcbm.model.cbm_exn import cbm_exn_step\n", "from libcbm.model.cbm_exn.cbm_exn_parameters import parameters_factory\n", "from libcbm.model.model_definition.model_variables import ModelVariables" ] }, { "cell_type": "code", "execution_count": 28, "id": "1ef67854", "metadata": {}, "outputs": [], "source": [ "rng = default_rng()\n", "n_stands = 10" ] }, { "cell_type": "code", "execution_count": 29, "id": "ced55e55", "metadata": {}, "outputs": [], "source": [ "# load the default bundled parameters\n", "parameters = parameters_factory(resources.get_cbm_exn_parameters_dir())" ] }, { "cell_type": "markdown", "id": "9d6e18a4", "metadata": {}, "source": [ "# Fully dynamic modelling with cbm_exn\n", "\n", "This document illustrates a scheme to simulate with fully dynamic pools, fluxes and flow in libcbm using the cbm_exn package. \n", "\n", "This outlines a component of a highly efficient method for processing C flows in a CBM-Like model, producing outputs that are compatible with current reporting methods, and systems.\n", "\n", "The approach makes the hard coded model pool, flow, flux in CBM-CFS3 fully dynamic, and definable via high level language in the cbm_exn package. \n", "\n", "Prior to this improvement, using CBM-CFS3, it was only possible to modify parameters for the pool-flows withing the hard-coded model structure. This opens up opportunities to evaluate changes to model structure dynamically, in addition to modifiying pool flows. \n", "\n", "In addition the architecture opens opportunities for using machine learning both for informing pool flow parameters and the model structure itself.\n", "\n", "The document explains the basic structure of the default parameters and configuration in `cbm_exn`, and also shows the an example of the default pool flows generated in dataframe form, and describes their format. \n", "\n", "While only the default pool flows (based on CBM-CFS3) are presented here, it's important to note if the general format is followed it's possible to alter model pool-flow-flux structure via high level programming language. The default values could potentially be used as a template to accomplish this.\n", "\n", "Sections below are:\n", "\n", " * Operation DataFrame: a description of the storage scheme for mult-dimensional pool flow proportions within dataframe structures.\n", " * Default spinup operation dataframes: examples of spinup ops derived from the cbm_exn default parameters and example simulation area input\n", " * Default step operation dataframes: example of step ops also derived from the same inputs\n", " * Appendix1, Appendix2: the default parameters, and example simulation area used.\n" ] }, { "cell_type": "code", "execution_count": 30, "id": "ac59f1b9", "metadata": {}, "outputs": [], "source": [ "# read some packaged net increments, derived from a\n", "# simulation of the same growth curve used in CBM-CFS3\n", "# tutorial 1\n", "net_increments = pd.read_csv(\n", " os.path.join(\n", " resources.get_test_resources_dir(),\n", " \"cbm_exn_net_increments\",\n", " \"net_increments.csv\",\n", " )\n", ")" ] }, { "cell_type": "code", "execution_count": 31, "id": "7da385e2", "metadata": {}, "outputs": [], "source": [ "# the same set of increments are repeated for each stand in this example\n", "n_stands = 1000\n", "increments = None\n", "for s in range(n_stands):\n", " s_increments = net_increments.copy()\n", " s_increments.insert(0, \"row_idx\", s)\n", " s_increments = s_increments.rename(\n", " columns={\n", " \"SoftwoodMerch\": \"merch_inc\",\n", " \"SoftwoodFoliage\": \"foliage_inc\",\n", " \"SoftwoodOther\": \"other_inc\",\n", " }\n", " )\n", " increments = pd.concat([increments, s_increments])" ] }, { "cell_type": "code", "execution_count": 32, "id": "212a740c", "metadata": {}, "outputs": [], "source": [ "# create the require inputs for spinup\n", "spinup_input = {\n", " \"parameters\": pd.DataFrame(\n", " {\n", " # random age\n", " \"age\": rng.integers(low=0, high=60, size=n_stands, dtype=\"int\"),\n", " \"area\": np.full(n_stands, 1, dtype=\"int\"),\n", " \"delay\": np.full(n_stands, 0, dtype=\"int\"),\n", " \"return_interval\": np.full(n_stands, 125, dtype=\"int\"),\n", " \"min_rotations\": np.full(n_stands, 10, dtype=\"int\"),\n", " \"max_rotations\": np.full(n_stands, 30, dtype=\"int\"),\n", " \"spatial_unit_id\": np.full(\n", " n_stands, 17, dtype=\"int\"\n", " ), # ontario/mixedwood plains\n", " \"species\": np.full(n_stands, 20, dtype=\"int\"), # red pine\n", " \"mean_annual_temperature\": np.arange(\n", " 0, 2, 2 / n_stands\n", " ), # make a temperature ramp\n", " \"historical_disturbance_type\": np.full(n_stands, 1, dtype=\"int\"),\n", " \"last_pass_disturbance_type\": np.full(n_stands, 1, dtype=\"int\"),\n", " }\n", " ),\n", " \"increments\": increments,\n", "}" ] }, { "cell_type": "code", "execution_count": 33, "id": "24fc01cf", "metadata": {}, "outputs": [], "source": [ "spinup_vars = cbm_exn_spinup.prepare_spinup_vars(\n", " ModelVariables.from_pandas(spinup_input),\n", " parameters,\n", ")\n", "spinup_op_list = cbm_exn_spinup.get_default_op_list()\n", "spinup_ops = cbm_exn_spinup.get_default_ops(parameters, spinup_vars)" ] }, { "cell_type": "code", "execution_count": 34, "id": "a29b9a04", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['growth',\n", " 'snag_turnover',\n", " 'biomass_turnover',\n", " 'overmature_decline',\n", " 'growth',\n", " 'dom_decay',\n", " 'slow_decay',\n", " 'slow_mixing',\n", " 'disturbance']" ] }, "execution_count": 34, "metadata": {}, "output_type": "execute_result" } ], "source": [ "spinup_op_list" ] }, { "cell_type": "markdown", "id": "f738bb60", "metadata": {}, "source": [ "# Operation dataframes\n", "\n", "Operation dataframes are multi-dimensional sparse matrices, using column-name-formatting to denote the dimensions. \n", "\n", "The rationale for this design apporach is that multi-dimensional arrays lack interoperable standards that would work with many different high level languages simulataneously. Dataframes however are well supported by several high level languages.\n", "\n", "Each dataframe has pool flow columns, where the column name is of the form:\n", "\n", " pool_source_name.pool_sink_name\n", " \n", "Each row can be interpreted as a pool flow matrix (in sparse coordinate form). By default unspecified diagnal values (those where `pool_source_name` is equal to `pool_sink_name`) will be assigned a value of 1.\n", "\n", "There are 4 basic types of dataframes with regards to mapping to simulation space. These are covered in the next section\n", "\n", "## Single row \n", "\n", "The single row is a matrix that is applied to all simulation areas. See the `slow_mixing` dataframe in the following section.\n", "\n", "## Simulation-aligned \n", "\n", "the dataframe has a row for each simulation area in subsequent spinup or step calls. Each row represents a matrix that is 1:1 with simulation areas\n", "This type is appropriate for processes that vary by simulation area. See the `dom_decay` dataframe in the followin section.\n", "\n", "## Property-indexed \n", "\n", "A property-index dataframe has one or more values that correspond to values stored in the current simulation state. This type of dataframe contains 1 or more columns of the form:\n", "\n", " [table_name.variable_name]\n", "\n", "Where a simulation table, series name pair is surrounded by left and right brackets.\n", "\n", "An example of this is if one flow matrix is defined for each spatial unit identifier. See the `disturbance` dataframe in the following section for an example.\n", "\n", "## Both Simulation-aligned, and Property-indexed\n", "\n", "If a dataframe is both simulation aligned and property indexed each row corresponds to both a simulation area, and 1 or more properties within the simulation areas. The following pattern of columns is present in this type of dataframe:\n", "\n", " [row_idx], [table_name_1.variable_name_1], ... [table_name_N.variable_name_N]\n", "\n", "An example of this is a dataframe of matrices where each row corresponds to the simulation areas, and to simulation age. See the spinup growth dataframe in the following section." ] }, { "cell_type": "markdown", "id": "aa7127af", "metadata": {}, "source": [ "# Default spinup operation dataframes\n", "The default spinup operation dataframes are generated as a function of the default parameters (see appendix 1) and the simulation area input (Appendix 2). \n", "\n", "The [libcbm.model.cbm_exn.cbm_exn_spinup.spinup](https://github.com/cat-cfs/libcbm_py/blob/700b2febb73681ca2b4456d4db88d5c399008640/libcbm/model/cbm_exn/cbm_exn_spinup.py#L169) function can directly ingest operations in this format via the `ops` parameter.\n", "\n", "Within a spinup timestep these operations are applied in the following order by default. The order and naming of these operation is user-specifyable via passing a string list to the `op_sequence` parameter of the above linked function\n", "\n", " 1. growth\n", " 1. snag_turnover\n", " 1. biomass_turnover\n", " 1. overmature_decline\n", " 1. growth\n", " 1. dom_decay\n", " 1. slow_decay\n", " 1. slow_mixing\n", " 1. disturbance" ] }, { "cell_type": "code", "execution_count": 35, "id": "c8409a14", "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "## snag_turnover" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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[parameters.spatial_unit_id][parameters.sw_hw]StemSnag.StemSnagStemSnag.MediumSoilBranchSnag.BranchSnagBranchSnag.AboveGroundFastSoil
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" ], "text/plain": [ " [parameters.spatial_unit_id] [parameters.sw_hw] StemSnag.StemSnag \\\n", "0 1 0 0.968 \n", "1 3 0 0.968 \n", "2 4 0 0.968 \n", "3 5 0 0.968 \n", "4 6 0 0.968 \n", ".. ... ... ... \n", "91 52 1 0.968 \n", "92 53 1 0.968 \n", "93 54 1 0.968 \n", "94 58 1 0.968 \n", "95 59 1 0.968 \n", "\n", " StemSnag.MediumSoil BranchSnag.BranchSnag BranchSnag.AboveGroundFastSoil \n", "0 0.032 0.9 0.1 \n", "1 0.032 0.9 0.1 \n", "2 0.032 0.9 0.1 \n", "3 0.032 0.9 0.1 \n", "4 0.032 0.9 0.1 \n", ".. ... ... ... \n", "91 0.032 0.9 0.1 \n", "92 0.032 0.9 0.1 \n", "93 0.032 0.9 0.1 \n", "94 0.032 0.9 0.1 \n", "95 0.032 0.9 0.1 \n", "\n", "[96 rows x 6 columns]" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## biomass_turnover" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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[parameters.spatial_unit_id][parameters.sw_hw]Merch.StemSnagFoliage.AboveGroundVeryFastSoilOther.BranchSnagOther.AboveGroundFastSoilCoarseRoots.AboveGroundFastSoilCoarseRoots.BelowGroundFastSoilFineRoots.AboveGroundVeryFastSoilFineRoots.BelowGroundVeryFastSoil
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" ], "text/plain": [ " [parameters.spatial_unit_id] [parameters.sw_hw] Merch.StemSnag \\\n", "0 1 0 0.0050 \n", "1 3 0 0.0060 \n", "2 4 0 0.0050 \n", "3 5 0 0.0067 \n", "4 6 0 0.0067 \n", ".. ... ... ... \n", "91 52 1 0.0050 \n", "92 53 1 0.0060 \n", "93 54 1 0.0045 \n", "94 58 1 0.0060 \n", "95 59 1 0.0050 \n", "\n", " Foliage.AboveGroundVeryFastSoil Other.BranchSnag \\\n", "0 0.10 0.0100 \n", "1 0.05 0.0075 \n", "2 0.10 0.0100 \n", "3 0.15 0.0100 \n", "4 0.15 0.0100 \n", ".. ... ... \n", "91 0.95 0.0100 \n", "92 0.95 0.0100 \n", "93 0.95 0.0100 \n", "94 0.95 0.0075 \n", "95 0.95 0.0100 \n", "\n", " Other.AboveGroundFastSoil CoarseRoots.AboveGroundFastSoil \\\n", "0 0.0300 0.01 \n", "1 0.0225 0.01 \n", "2 0.0300 0.01 \n", "3 0.0300 0.01 \n", "4 0.0300 0.01 \n", ".. ... ... \n", "91 0.0300 0.01 \n", "92 0.0300 0.01 \n", "93 0.0300 0.01 \n", "94 0.0225 0.01 \n", "95 0.0300 0.01 \n", "\n", " CoarseRoots.BelowGroundFastSoil FineRoots.AboveGroundVeryFastSoil \\\n", "0 0.01 0.3205 \n", "1 0.01 0.3205 \n", "2 0.01 0.3205 \n", "3 0.01 0.3205 \n", "4 0.01 0.3205 \n", ".. ... ... \n", "91 0.01 0.3205 \n", "92 0.01 0.3205 \n", "93 0.01 0.3205 \n", "94 0.01 0.3205 \n", "95 0.01 0.3205 \n", "\n", " FineRoots.BelowGroundVeryFastSoil \n", "0 0.3205 \n", "1 0.3205 \n", "2 0.3205 \n", "3 0.3205 \n", "4 0.3205 \n", ".. ... \n", "91 0.3205 \n", "92 0.3205 \n", "93 0.3205 \n", "94 0.3205 \n", "95 0.3205 \n", "\n", "[96 rows x 10 columns]" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## dom_decay" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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" ], "text/plain": [ " [row_idx] [state.age] Merch.StemSnag Other.BranchSnag \\\n", "0 0 0 0.0 0.0 \n", "1 0 1 0.0 0.0 \n", "2 0 2 0.0 0.0 \n", "3 0 3 0.0 0.0 \n", "4 0 4 0.0 0.0 \n", "... ... ... ... ... \n", "70995 999 66 0.0 0.0 \n", "70996 999 67 0.0 0.0 \n", "70997 999 68 0.0 0.0 \n", "70998 999 69 0.0 0.0 \n", "70999 999 70 0.0 0.0 \n", "\n", " Other.AboveGroundFastSoil Foliage.AboveGroundVeryFastSoil \\\n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", "... ... ... \n", "70995 0.0 0.0 \n", "70996 0.0 0.0 \n", "70997 0.0 0.0 \n", "70998 0.0 0.0 \n", "70999 0.0 0.0 \n", "\n", " CoarseRoots.AboveGroundFastSoil CoarseRoots.BelowGroundFastSoil \\\n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", "... ... ... \n", "70995 0.0 0.0 \n", "70996 0.0 0.0 \n", "70997 0.0 0.0 \n", "70998 0.0 0.0 \n", "70999 0.0 0.0 \n", "\n", " FineRoots.AboveGroundVeryFastSoil FineRoots.BelowGroundVeryFastSoil \n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", "... ... ... \n", "70995 0.0 0.0 \n", "70996 0.0 0.0 \n", "70997 0.0 0.0 \n", "70998 0.0 0.0 \n", "70999 0.0 0.0 \n", "\n", "[71000 rows x 10 columns]" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "for op in spinup_ops:\n", " display(Markdown(f\"## {op['name']}\"))\n", " display(op[\"op_data\"])" ] }, { "cell_type": "markdown", "id": "cc083553", "metadata": {}, "source": [ "Run the spinup routine with the default operations passed as a parameter\n" ] }, { "cell_type": "code", "execution_count": 36, "id": "16db8725", "metadata": {}, "outputs": [], "source": [ "with cbm_exn_model.initialize() as model:\n", " cbm_vars = cbm_exn_spinup.spinup(\n", " model, spinup_vars, ops=spinup_ops, op_sequence=spinup_op_list\n", " )" ] }, { "cell_type": "code", "execution_count": 37, "id": "ba76e734", "metadata": {}, "outputs": [], "source": [ "# initialize parameters for stepping (values for illustration)\n", "cbm_vars[\"parameters\"][\"mean_annual_temperature\"].assign(1.1)\n", "cbm_vars[\"parameters\"][\"merch_inc\"].assign(0.1)\n", "cbm_vars[\"parameters\"][\"foliage_inc\"].assign(0.01)\n", "cbm_vars[\"parameters\"][\"other_inc\"].assign(0.05)\n", "cbm_vars[\"parameters\"][\"disturbance_type\"].assign(\n", " rng.choice([0, 1, 4], n_stands, p=[0.98, 0.01, 0.01])\n", ")" ] }, { "cell_type": "code", "execution_count": 38, "id": "5ba3b19c", "metadata": {}, "outputs": [], "source": [ "step_ops_sequence = cbm_exn_step.get_default_annual_process_op_sequence()\n", "step_disturbance_ops_sequence = (\n", " cbm_exn_step.get_default_disturbance_op_sequence()\n", ")\n", "step_ops = cbm_exn_step.get_default_ops(parameters, cbm_vars)" ] }, { "cell_type": "code", "execution_count": 39, "id": "7d93dd9b", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['disturbance']" ] }, "execution_count": 39, "metadata": {}, "output_type": "execute_result" } ], "source": [ "step_disturbance_ops_sequence" ] }, { "cell_type": "code", "execution_count": 40, "id": "92fc38c8", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['growth',\n", " 'snag_turnover',\n", " 'biomass_turnover',\n", " 'overmature_decline',\n", " 'growth',\n", " 'dom_decay',\n", " 'slow_decay',\n", " 'slow_mixing']" ] }, "execution_count": 40, "metadata": {}, "output_type": "execute_result" } ], "source": [ "step_ops_sequence" ] }, { "cell_type": "markdown", "id": "ee6a67dd", "metadata": {}, "source": [ "# Step processes\n", "\n", "With the exception of growth and overmature decline, the default step processes use an identical process for generation as the spinup processes, and so only growth and overmature decline are shown below.\n", "\n", "The difference is that by default in stepping, growth and overmature decline dataframes are both Simulation-aligned.\n", "\n", "\n", "The [libcbm.model.cbm_exn.cbm_exn_step.step](https://github.com/cat-cfs/libcbm_py/blob/700b2febb73681ca2b4456d4db88d5c399008640/libcbm/model/cbm_exn/cbm_exn_step.py#L190) function can directly ingest operations in this format via the `ops` parameter" ] }, { "cell_type": "code", "execution_count": 41, "id": "76ad77f5", "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "## growth" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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" ], "text/plain": [ " Merch.StemSnag Other.BranchSnag Other.AboveGroundFastSoil \\\n", "0 0.0 0.0 0.0 \n", "1 0.0 0.0 0.0 \n", "2 0.0 0.0 0.0 \n", "3 0.0 0.0 0.0 \n", "4 0.0 0.0 0.0 \n", ".. ... ... ... \n", "995 0.0 0.0 0.0 \n", "996 0.0 0.0 0.0 \n", "997 0.0 0.0 0.0 \n", "998 0.0 0.0 0.0 \n", "999 0.0 0.0 0.0 \n", "\n", " Foliage.AboveGroundVeryFastSoil CoarseRoots.AboveGroundFastSoil \\\n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", ".. ... ... \n", "995 0.0 0.0 \n", "996 0.0 0.0 \n", "997 0.0 0.0 \n", "998 0.0 0.0 \n", "999 0.0 0.0 \n", "\n", " CoarseRoots.BelowGroundFastSoil FineRoots.AboveGroundVeryFastSoil \\\n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", ".. ... ... \n", "995 0.0 0.0 \n", "996 0.0 0.0 \n", "997 0.0 0.0 \n", "998 0.0 0.0 \n", "999 0.0 0.0 \n", "\n", " FineRoots.BelowGroundVeryFastSoil \n", "0 0.0 \n", "1 0.0 \n", "2 0.0 \n", "3 0.0 \n", "4 0.0 \n", ".. ... \n", "995 0.0 \n", "996 0.0 \n", "997 0.0 \n", "998 0.0 \n", "999 0.0 \n", "\n", "[1000 rows x 8 columns]" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "for op in step_ops:\n", " name = op[\"name\"]\n", " if name in [\"growth\", \"overmature_decline\"]:\n", " display(Markdown(f\"## {name}\"))\n", " display(op[\"op_data\"])" ] }, { "cell_type": "markdown", "id": "15f85e32", "metadata": {}, "source": [ "run a timestep with the specified parameters" ] }, { "cell_type": "code", "execution_count": 42, "id": "15540ab3", "metadata": {}, "outputs": [], "source": [ "with cbm_exn_model.initialize() as model:\n", " cbm_vars = cbm_exn_step.step(\n", " model,\n", " cbm_vars,\n", " ops=step_ops,\n", " step_op_sequence=step_ops_sequence,\n", " disturbance_op_sequence=step_disturbance_ops_sequence,\n", " )" ] }, { "cell_type": "code", "execution_count": 43, "id": "15c1e03c", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ " Input Merch Foliage Other CoarseRoots FineRoots \\\n", "0 1.0 73.280370 7.178385 21.031789 20.379709 2.151192 \n", "1 1.0 7.774118 1.920598 5.284176 2.297170 1.028144 \n", "2 1.0 89.648104 8.665880 25.289823 25.107673 2.332372 \n", "3 1.0 86.794134 8.390010 24.485410 24.270207 2.296434 \n", "4 1.0 84.872181 8.204230 23.943693 23.705336 2.273127 \n", ".. ... ... ... ... ... ... \n", "995 1.0 9.338820 2.147632 6.058011 2.751865 1.143006 \n", "996 1.0 81.277491 7.856761 22.930502 22.646881 2.231494 \n", "997 1.0 17.020424 3.072825 9.243063 4.991417 1.521245 \n", "998 1.0 9.338820 2.147632 6.058011 2.751865 1.143006 \n", "999 1.0 29.410534 3.937428 11.838268 8.248054 1.783289 \n", "\n", " AboveGroundVeryFastSoil BelowGroundVeryFastSoil AboveGroundFastSoil \\\n", "0 9.947479 1.968485 10.564232 \n", "1 2.180844 0.769231 14.300553 \n", "2 12.248857 2.156594 13.017832 \n", "3 11.722687 2.114842 12.323974 \n", "4 11.412086 2.089355 11.959022 \n", ".. ... ... ... \n", "995 2.266580 0.757995 11.935299 \n", "996 9.202949 1.790814 9.963568 \n", "997 3.487677 1.076058 10.145725 \n", "998 2.265884 0.757736 11.929870 \n", "999 4.867150 1.355955 8.783199 \n", "\n", " BelowGroundFastSoil MediumSoil AboveGroundSlowSoil \\\n", "0 2.449042 57.708379 38.779972 \n", "1 6.267484 59.129590 34.133895 \n", "2 2.845668 52.095064 41.999048 \n", "3 2.721871 53.695097 41.024695 \n", "4 2.658248 54.497336 40.548368 \n", ".. ... ... ... \n", "995 4.905127 53.628358 32.404702 \n", "996 2.183926 48.055328 37.770128 \n", "997 3.619583 54.966027 32.991306 \n", "998 4.902391 53.611115 32.398762 \n", "999 2.640505 55.291161 33.722775 \n", "\n", " BelowGroundSlowSoil StemSnag BranchSnag CO2 CH4 \\\n", "0 127.722972 22.150185 1.350400 7723.799871 8.475443 \n", "1 129.648400 54.009079 3.155953 7608.867436 8.474532 \n", "2 127.418286 18.394004 1.710146 7789.726276 8.473622 \n", "3 127.446422 19.127702 1.623961 7770.320595 8.472711 \n", "4 127.473572 19.574634 1.574184 7760.799934 8.471801 \n", ".. ... ... ... ... ... \n", "995 124.955399 50.929667 2.618341 7638.111865 7.617916 \n", "996 122.998702 19.467886 1.445742 7774.280777 7.617101 \n", "997 124.594030 43.196613 1.716888 7654.197317 7.616286 \n", "998 124.940633 50.926692 2.617775 7638.186920 7.615472 \n", "999 124.187274 35.563809 1.235053 7674.474894 7.614657 \n", "\n", " CO NO2 Products \n", "0 76.277752 0.0 0.0 \n", "1 76.269556 0.0 0.0 \n", "2 76.261360 0.0 0.0 \n", "3 76.253165 0.0 0.0 \n", "4 76.244972 0.0 0.0 \n", ".. ... ... ... \n", "995 68.560102 0.0 0.0 \n", "996 68.552767 0.0 0.0 \n", "997 68.545434 0.0 0.0 \n", "998 68.538101 0.0 0.0 \n", "999 68.530769 0.0 0.0 \n", "\n", "[1000 rows x 20 columns]" ] }, "execution_count": 43, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cbm_vars[\"pools\"].to_pandas()" ] }, { "cell_type": "code", "execution_count": 44, "id": "8d76c8bc", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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DisturbanceCO2ProductionDisturbanceCH4ProductionDisturbanceCOProductionDisturbanceBioCO2EmissionDisturbanceBioCH4EmissionDisturbanceBioCOEmissionDecayDOMCO2EmissionDisturbanceProductionDisturbanceDOMProductionDeltaBiomass_AG...DisturbanceFineLitterInputDisturbanceVFastAGToAirDisturbanceVFastBGToAirDisturbanceFastAGToAirDisturbanceFastBGToAirDisturbanceMediumToAirDisturbanceSlowAGToAirDisturbanceSlowBGToAirDisturbanceStemSnagToAirDisturbanceBranchSnagToAir
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1000 rows × 47 columns

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" ], "text/plain": [ " DisturbanceCO2Production DisturbanceCH4Production \\\n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", ".. ... ... \n", "995 0.0 0.0 \n", "996 0.0 0.0 \n", "997 0.0 0.0 \n", "998 0.0 0.0 \n", "999 0.0 0.0 \n", "\n", " DisturbanceCOProduction DisturbanceBioCO2Emission \\\n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", ".. ... ... \n", "995 0.0 0.0 \n", "996 0.0 0.0 \n", "997 0.0 0.0 \n", "998 0.0 0.0 \n", "999 0.0 0.0 \n", "\n", " DisturbanceBioCH4Emission DisturbanceBioCOEmission DecayDOMCO2Emission \\\n", "0 0.0 0.0 4.819715 \n", "1 0.0 0.0 4.199927 \n", "2 0.0 0.0 5.308425 \n", "3 0.0 0.0 5.188081 \n", "4 0.0 0.0 5.118937 \n", ".. ... ... ... \n", "995 0.0 0.0 3.784433 \n", "996 0.0 0.0 4.391971 \n", "997 0.0 0.0 3.772003 \n", "998 0.0 0.0 3.783260 \n", "999 0.0 0.0 3.819926 \n", "\n", " DisturbanceProduction DisturbanceDOMProduction DeltaBiomass_AG ... \\\n", "0 0.0 0.0 0.16 ... \n", "1 0.0 0.0 0.16 ... \n", "2 0.0 0.0 0.16 ... \n", "3 0.0 0.0 0.16 ... \n", "4 0.0 0.0 0.16 ... \n", ".. ... ... ... ... \n", "995 0.0 0.0 0.16 ... \n", "996 0.0 0.0 0.16 ... \n", "997 0.0 0.0 0.16 ... \n", "998 0.0 0.0 0.16 ... \n", "999 0.0 0.0 0.16 ... \n", "\n", " DisturbanceFineLitterInput DisturbanceVFastAGToAir \\\n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", ".. ... ... \n", "995 0.0 0.0 \n", "996 0.0 0.0 \n", "997 0.0 0.0 \n", "998 0.0 0.0 \n", "999 0.0 0.0 \n", "\n", " DisturbanceVFastBGToAir DisturbanceFastAGToAir DisturbanceFastBGToAir \\\n", "0 0.0 0.0 0.0 \n", "1 0.0 0.0 0.0 \n", "2 0.0 0.0 0.0 \n", "3 0.0 0.0 0.0 \n", "4 0.0 0.0 0.0 \n", ".. ... ... ... \n", "995 0.0 0.0 0.0 \n", "996 0.0 0.0 0.0 \n", "997 0.0 0.0 0.0 \n", "998 0.0 0.0 0.0 \n", "999 0.0 0.0 0.0 \n", "\n", " DisturbanceMediumToAir DisturbanceSlowAGToAir DisturbanceSlowBGToAir \\\n", "0 0.0 0.0 0.0 \n", "1 0.0 0.0 0.0 \n", "2 0.0 0.0 0.0 \n", "3 0.0 0.0 0.0 \n", "4 0.0 0.0 0.0 \n", ".. ... ... ... \n", "995 0.0 0.0 0.0 \n", "996 0.0 0.0 0.0 \n", "997 0.0 0.0 0.0 \n", "998 0.0 0.0 0.0 \n", "999 0.0 0.0 0.0 \n", "\n", " DisturbanceStemSnagToAir DisturbanceBranchSnagToAir \n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", ".. ... ... \n", "995 0.0 0.0 \n", "996 0.0 0.0 \n", "997 0.0 0.0 \n", "998 0.0 0.0 \n", "999 0.0 0.0 \n", "\n", "[1000 rows x 47 columns]" ] }, "execution_count": 44, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cbm_vars[\"flux\"].to_pandas()" ] }, { "cell_type": "markdown", "id": "3fd2021f", "metadata": {}, "source": [ "## Appendix 1: CBM EXN Default parameters" ] }, { "cell_type": "code", "execution_count": 45, "id": "ff31330d", "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "## pools" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "```json\n", "[\n", " \"Input\",\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\",\n", " \"CoarseRoots\",\n", " \"FineRoots\",\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\",\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\",\n", " \"Products\"\n", "]\n", "```" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## flux" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "```json\n", "[\n", " {\n", " \"name\": \"DisturbanceCO2Production\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\",\n", " \"CoarseRoots\",\n", " \"FineRoots\",\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceCH4Production\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\",\n", " \"CoarseRoots\",\n", " \"FineRoots\",\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CH4\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceCOProduction\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\",\n", " \"CoarseRoots\",\n", " \"FineRoots\",\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceBioCO2Emission\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\",\n", " \"CoarseRoots\",\n", " \"FineRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceBioCH4Emission\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\",\n", " \"CoarseRoots\",\n", " \"FineRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"CH4\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceBioCOEmission\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\",\n", " \"CoarseRoots\",\n", " \"FineRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecayDOMCO2Emission\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceProduction\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\",\n", " \"CoarseRoots\",\n", " \"FineRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"Products\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceDOMProduction\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"Products\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DeltaBiomass_AG\",\n", " \"process\": \"Growth and Turnover\",\n", " \"source_pools\": [\n", " \"Input\"\n", " ],\n", " \"sink_pools\": [\n", " \"Merch\",\n", " \"Foliage\",\n", " \"Other\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DeltaBiomass_BG\",\n", " \"process\": \"Growth and Turnover\",\n", " \"source_pools\": [\n", " \"Input\"\n", " ],\n", " \"sink_pools\": [\n", " \"CoarseRoots\",\n", " \"FineRoots\"\n", " ]\n", " },\n", " {\n", " \"name\": \"TurnoverMerchLitterInput\",\n", " \"process\": \"Growth and Turnover\",\n", " \"source_pools\": [\n", " \"Merch\"\n", " ],\n", " \"sink_pools\": [\n", " \"StemSnag\"\n", " ]\n", " },\n", " {\n", " \"name\": \"TurnoverFolLitterInput\",\n", " \"process\": \"Growth and Turnover\",\n", " \"source_pools\": [\n", " \"Foliage\"\n", " ],\n", " \"sink_pools\": [\n", " \"AboveGroundVeryFastSoil\"\n", " ]\n", " },\n", " {\n", " \"name\": \"TurnoverOthLitterInput\",\n", " \"process\": \"Growth and Turnover\",\n", " \"source_pools\": [\n", " \"Other\"\n", " ],\n", " \"sink_pools\": [\n", " \"AboveGroundFastSoil\",\n", " \"BranchSnag\"\n", " ]\n", " },\n", " {\n", " \"name\": \"TurnoverCoarseLitterInput\",\n", " \"process\": \"Growth and Turnover\",\n", " \"source_pools\": [\n", " \"CoarseRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\"\n", " ]\n", " },\n", " {\n", " \"name\": \"TurnoverFineLitterInput\",\n", " \"process\": \"Growth and Turnover\",\n", " \"source_pools\": [\n", " \"FineRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecayVFastAGToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"AboveGroundVeryFastSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecayVFastBGToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"BelowGroundVeryFastSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecayFastAGToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"AboveGroundFastSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecayFastBGToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"BelowGroundFastSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecayMediumToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"MediumSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecaySlowAGToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"AboveGroundSlowSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecaySlowBGToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"BelowGroundSlowSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecayStemSnagToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"StemSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DecayBranchSnagToAir\",\n", " \"process\": \"Decay\",\n", " \"source_pools\": [\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceMerchToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceFolToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Foliage\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceOthToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Other\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceCoarseToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"CoarseRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceFineToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"FineRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceDOMCO2Emission\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceDOMCH4Emission\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CH4\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceDOMCOEmission\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\",\n", " \"BelowGroundSlowSoil\",\n", " \"StemSnag\",\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceMerchLitterInput\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Merch\"\n", " ],\n", " \"sink_pools\": [\n", " \"StemSnag\",\n", " \"MediumSoil\",\n", " \"AboveGroundSlowSoil\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceFolLitterInput\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Foliage\"\n", " ],\n", " \"sink_pools\": [\n", " \"AboveGroundVeryFastSoil\",\n", " \"BelowGroundVeryFastSoil\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceOthLitterInput\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"Other\"\n", " ],\n", " \"sink_pools\": [\n", " \"AboveGroundFastSoil\",\n", " \"BranchSnag\",\n", " \"BelowGroundFastSoil\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceCoarseLitterInput\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"CoarseRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceFineLitterInput\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"FineRoots\"\n", " ],\n", " \"sink_pools\": [\n", " \"AboveGroundVeryFastSoil\",\n", " \"AboveGroundFastSoil\",\n", " \"BelowGroundFastSoil\",\n", " \"BelowGroundVeryFastSoil\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceVFastAGToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"AboveGroundVeryFastSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceVFastBGToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"BelowGroundVeryFastSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceFastAGToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"AboveGroundFastSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceFastBGToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"BelowGroundFastSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceMediumToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"MediumSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceSlowAGToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"AboveGroundSlowSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceSlowBGToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"BelowGroundSlowSoil\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceStemSnagToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"StemSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " },\n", " {\n", " \"name\": \"DisturbanceBranchSnagToAir\",\n", " \"process\": \"Disturbance\",\n", " \"source_pools\": [\n", " \"BranchSnag\"\n", " ],\n", " \"sink_pools\": [\n", " \"CO2\",\n", " \"CH4\",\n", " \"CO\",\n", " \"NO2\"\n", " ]\n", " }\n", "]\n", "```" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## slow_mixing_rate" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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idrate
010.006
\n", "
" ], "text/plain": [ " id rate\n", "0 1 0.006" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## turnover_parameters" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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spatial_unit_idsw_hwFoliageFallRateStemAnnualTurnoverRateBranchTurnoverRateCoarseRootTurnPropFineRootTurnPropOtherToBranchSnagSplitCoarseRootAGSplitFineRootAGSplitStemSnagBranchSnag
0100.100.00500.040.020.6410.250.50.50.0320.1
1300.050.00600.030.020.6410.250.50.50.0320.1
2400.100.00500.040.020.6410.250.50.50.0320.1
3500.150.00670.040.020.6410.250.50.50.0320.1
4600.150.00670.040.020.6410.250.50.50.0320.1
.......................................
915210.950.00500.040.020.6410.250.50.50.0320.1
925310.950.00600.040.020.6410.250.50.50.0320.1
935410.950.00450.040.020.6410.250.50.50.0320.1
945810.950.00600.030.020.6410.250.50.50.0320.1
955910.950.00500.040.020.6410.250.50.50.0320.1
\n", "

96 rows × 12 columns

\n", "
" ], "text/plain": [ " spatial_unit_id sw_hw FoliageFallRate StemAnnualTurnoverRate \\\n", "0 1 0 0.10 0.0050 \n", "1 3 0 0.05 0.0060 \n", "2 4 0 0.10 0.0050 \n", "3 5 0 0.15 0.0067 \n", "4 6 0 0.15 0.0067 \n", ".. ... ... ... ... \n", "91 52 1 0.95 0.0050 \n", "92 53 1 0.95 0.0060 \n", "93 54 1 0.95 0.0045 \n", "94 58 1 0.95 0.0060 \n", "95 59 1 0.95 0.0050 \n", "\n", " BranchTurnoverRate CoarseRootTurnProp FineRootTurnProp \\\n", "0 0.04 0.02 0.641 \n", "1 0.03 0.02 0.641 \n", "2 0.04 0.02 0.641 \n", "3 0.04 0.02 0.641 \n", "4 0.04 0.02 0.641 \n", ".. ... ... ... \n", "91 0.04 0.02 0.641 \n", "92 0.04 0.02 0.641 \n", "93 0.04 0.02 0.641 \n", "94 0.03 0.02 0.641 \n", "95 0.04 0.02 0.641 \n", "\n", " OtherToBranchSnagSplit CoarseRootAGSplit FineRootAGSplit StemSnag \\\n", "0 0.25 0.5 0.5 0.032 \n", "1 0.25 0.5 0.5 0.032 \n", "2 0.25 0.5 0.5 0.032 \n", "3 0.25 0.5 0.5 0.032 \n", "4 0.25 0.5 0.5 0.032 \n", ".. ... ... ... ... \n", "91 0.25 0.5 0.5 0.032 \n", "92 0.25 0.5 0.5 0.032 \n", "93 0.25 0.5 0.5 0.032 \n", "94 0.25 0.5 0.5 0.032 \n", "95 0.25 0.5 0.5 0.032 \n", "\n", " BranchSnag \n", "0 0.1 \n", "1 0.1 \n", "2 0.1 \n", "3 0.1 \n", "4 0.1 \n", ".. ... \n", "91 0.1 \n", "92 0.1 \n", "93 0.1 \n", "94 0.1 \n", "95 0.1 \n", "\n", "[96 rows x 12 columns]" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## species" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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species_idspecies_namegenus_idgenus_nameforest_type_idforest_type_name
01Spruce1Spruce1Softwood
12Black spruce1Spruce1Softwood
23Red spruce1Spruce1Softwood
34Norway spruce1Spruce1Softwood
45Engelmann spruce1Spruce1Softwood
.....................
189191Other broadleaved species - Genus type12Other broad-leaved species3Hardwood
190192Unspecified broadleaved species - Genus type13Unspecified broad-leaved species3Hardwood
191193Missing value - Genus type14Missing Value1Softwood
192194Softwood forest type14Missing Value1Softwood
193195Hardwood forest type14Missing Value3Hardwood
\n", "

194 rows × 6 columns

\n", "
" ], "text/plain": [ " species_id species_name genus_id \\\n", "0 1 Spruce 1 \n", "1 2 Black spruce 1 \n", "2 3 Red spruce 1 \n", "3 4 Norway spruce 1 \n", "4 5 Engelmann spruce 1 \n", ".. ... ... ... \n", "189 191 Other broadleaved species - Genus type 12 \n", "190 192 Unspecified broadleaved species - Genus type 13 \n", "191 193 Missing value - Genus type 14 \n", "192 194 Softwood forest type 14 \n", "193 195 Hardwood forest type 14 \n", "\n", " genus_name forest_type_id forest_type_name \n", "0 Spruce 1 Softwood \n", "1 Spruce 1 Softwood \n", "2 Spruce 1 Softwood \n", "3 Spruce 1 Softwood \n", "4 Spruce 1 Softwood \n", ".. ... ... ... \n", "189 Other broad-leaved species 3 Hardwood \n", "190 Unspecified broad-leaved species 3 Hardwood \n", "191 Missing Value 1 Softwood \n", "192 Missing Value 1 Softwood \n", "193 Missing Value 3 Hardwood \n", "\n", "[194 rows x 6 columns]" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## root_parameters" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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idhw_asw_ahw_bfrp_afrp_bfrp_cbiomass_to_carbon_rate
011.5760.2220.6150.0720.354-0.0602120.5
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" ], "text/plain": [ " id hw_a sw_a hw_b frp_a frp_b frp_c biomass_to_carbon_rate\n", "0 1 1.576 0.222 0.615 0.072 0.354 -0.060212 0.5" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## decay_parameters" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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poolbase_decay_ratereference_tempq10prop_to_atmospheremax_rate
0AboveGroundVeryFastSoil0.3550010.02.650.8151.0
1BelowGroundVeryFastSoil0.5000010.02.000.8301.0
2AboveGroundFastSoil0.1435010.02.000.8301.0
3BelowGroundFastSoil0.1435010.02.000.8301.0
4MediumSoil0.0374010.02.000.8301.0
5AboveGroundSlowSoil0.0150010.02.651.0001.0
6BelowGroundSlowSoil0.0033010.01.001.0001.0
7StemSnag0.0187010.02.000.8301.0
8BranchSnag0.0717510.02.000.8301.0
\n", "
" ], "text/plain": [ " pool base_decay_rate reference_temp q10 \\\n", "0 AboveGroundVeryFastSoil 0.35500 10.0 2.65 \n", "1 BelowGroundVeryFastSoil 0.50000 10.0 2.00 \n", "2 AboveGroundFastSoil 0.14350 10.0 2.00 \n", "3 BelowGroundFastSoil 0.14350 10.0 2.00 \n", "4 MediumSoil 0.03740 10.0 2.00 \n", "5 AboveGroundSlowSoil 0.01500 10.0 2.65 \n", "6 BelowGroundSlowSoil 0.00330 10.0 1.00 \n", "7 StemSnag 0.01870 10.0 2.00 \n", "8 BranchSnag 0.07175 10.0 2.00 \n", "\n", " prop_to_atmosphere max_rate \n", "0 0.815 1.0 \n", "1 0.830 1.0 \n", "2 0.830 1.0 \n", "3 0.830 1.0 \n", "4 0.830 1.0 \n", "5 1.000 1.0 \n", "6 1.000 1.0 \n", "7 0.830 1.0 \n", "8 0.830 1.0 " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## disturbance_matrix_value" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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disturbance_matrix_idsource_poolsink_poolproportion
02MerchStemSnag0.68624
12MerchCO20.28102
22MerchCH40.00316
32MerchCO0.02842
42FoliageCO20.85570
...............
14788960MediumSoilMediumSoil1.00000
14789960AboveGroundSlowSoilAboveGroundSlowSoil1.00000
14790960BelowGroundSlowSoilBelowGroundSlowSoil1.00000
14791960StemSnagStemSnag1.00000
14792960BranchSnagBranchSnag1.00000
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14793 rows × 4 columns

\n", "
" ], "text/plain": [ " disturbance_matrix_id source_pool sink_pool \\\n", "0 2 Merch StemSnag \n", "1 2 Merch CO2 \n", "2 2 Merch CH4 \n", "3 2 Merch CO \n", "4 2 Foliage CO2 \n", "... ... ... ... \n", "14788 960 MediumSoil MediumSoil \n", "14789 960 AboveGroundSlowSoil AboveGroundSlowSoil \n", "14790 960 BelowGroundSlowSoil BelowGroundSlowSoil \n", "14791 960 StemSnag StemSnag \n", "14792 960 BranchSnag BranchSnag \n", "\n", " proportion \n", "0 0.68624 \n", "1 0.28102 \n", "2 0.00316 \n", "3 0.02842 \n", "4 0.85570 \n", "... ... \n", "14788 1.00000 \n", "14789 1.00000 \n", "14790 1.00000 \n", "14791 1.00000 \n", "14792 1.00000 \n", "\n", "[14793 rows x 4 columns]" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/markdown": [ "## disturbance_matrix_association" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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spatial_unit_iddisturbance_type_idsw_hwdisturbance_matrix_id
010027
130027
240027
350027
460027
...............
127475211850
127485311862
127495411845
127505811888
127515911880
\n", "

12752 rows × 4 columns

\n", "
" ], "text/plain": [ " spatial_unit_id disturbance_type_id sw_hw disturbance_matrix_id\n", "0 1 0 0 27\n", "1 3 0 0 27\n", "2 4 0 0 27\n", "3 5 0 0 27\n", "4 6 0 0 27\n", "... ... ... ... ...\n", "12747 52 1 1 850\n", "12748 53 1 1 862\n", "12749 54 1 1 845\n", "12750 58 1 1 888\n", "12751 59 1 1 880\n", "\n", "[12752 rows x 4 columns]" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "for k, v in parameters._data.items():\n", " display(Markdown(f\"## {k}\"))\n", " if isinstance(v, list):\n", " display(Markdown(f\"```json\\n{json.dumps(v, indent=4)}\\n```\"))\n", " else:\n", " display(v)" ] }, { "cell_type": "markdown", "id": "f3fce5f7", "metadata": {}, "source": [ "## Appendix 2: simulation parameters used to generate op-dataframes" ] }, { "cell_type": "markdown", "id": "493680fe", "metadata": {}, "source": [ "### Net C increments\n", "\n", "These are derived from Tutorial 1 of the CBM-CFS3 Operational-Scale toolbox. Each simulation area is assigned the same set of increments." ] }, { "cell_type": "code", "execution_count": 46, "id": "80cf90ea", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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row_idxagemerch_incfoliage_incother_inc
0010.0188970.0400120.018766
1020.0832300.0809840.099667
2030.1717000.1093220.188663
3040.2769970.1321480.276154
4050.3954540.1512600.359470
..................
65999660.0000000.0000000.000000
66999670.0000000.0000000.000000
67999680.0000000.0000000.000000
68999690.0000000.0000000.000000
69999700.0000000.0000000.000000
\n", "

70000 rows × 5 columns

\n", "
" ], "text/plain": [ " row_idx age merch_inc foliage_inc other_inc\n", "0 0 1 0.018897 0.040012 0.018766\n", "1 0 2 0.083230 0.080984 0.099667\n", "2 0 3 0.171700 0.109322 0.188663\n", "3 0 4 0.276997 0.132148 0.276154\n", "4 0 5 0.395454 0.151260 0.359470\n", ".. ... ... ... ... ...\n", "65 999 66 0.000000 0.000000 0.000000\n", "66 999 67 0.000000 0.000000 0.000000\n", "67 999 68 0.000000 0.000000 0.000000\n", "68 999 69 0.000000 0.000000 0.000000\n", "69 999 70 0.000000 0.000000 0.000000\n", "\n", "[70000 rows x 5 columns]" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "display(increments)" ] }, { "cell_type": "markdown", "id": "35ae2e3e", "metadata": {}, "source": [ "### Simulation areas" ] }, { "cell_type": "code", "execution_count": 47, "id": "778bb9e2", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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sw_hwageareadelayreturn_intervalmin_rotationsmax_rotationsspatial_unit_idspeciesmean_annual_temperaturehistorical_disturbance_typelast_pass_disturbance_type
004110125103017200.00011
101310125103017200.00211
205510125103017200.00411
305110125103017200.00611
404910125103017200.00811
.......................................
99501410125103017201.99011
99604610125103017201.99211
99701810125103017201.99411
99801410125103017201.99611
99902310125103017201.99811
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1000 rows × 12 columns

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" ], "text/plain": [ " sw_hw age area delay return_interval min_rotations max_rotations \\\n", "0 0 41 1 0 125 10 30 \n", "1 0 13 1 0 125 10 30 \n", "2 0 55 1 0 125 10 30 \n", "3 0 51 1 0 125 10 30 \n", "4 0 49 1 0 125 10 30 \n", ".. ... ... ... ... ... ... ... \n", "995 0 14 1 0 125 10 30 \n", "996 0 46 1 0 125 10 30 \n", "997 0 18 1 0 125 10 30 \n", "998 0 14 1 0 125 10 30 \n", "999 0 23 1 0 125 10 30 \n", "\n", " spatial_unit_id species mean_annual_temperature \\\n", "0 17 20 0.000 \n", "1 17 20 0.002 \n", "2 17 20 0.004 \n", "3 17 20 0.006 \n", "4 17 20 0.008 \n", ".. ... ... ... \n", "995 17 20 1.990 \n", "996 17 20 1.992 \n", "997 17 20 1.994 \n", "998 17 20 1.996 \n", "999 17 20 1.998 \n", "\n", " historical_disturbance_type last_pass_disturbance_type \n", "0 1 1 \n", "1 1 1 \n", "2 1 1 \n", "3 1 1 \n", "4 1 1 \n", ".. ... ... \n", "995 1 1 \n", "996 1 1 \n", "997 1 1 \n", "998 1 1 \n", "999 1 1 \n", "\n", "[1000 rows x 12 columns]" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "display(spinup_input[\"parameters\"])" ] }, { "cell_type": "code", "execution_count": null, "id": "c4c53352", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "jupytext": { "formats": "ipynb,md" }, "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.11.3" } }, "nbformat": 4, "nbformat_minor": 5 }