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Add get and set state examples #27

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Add get and set state examples #27

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4110d16
close to first implementation of set and get state
RolfHut Sep 23, 2022
dc2eaca
fixed filenames for now
RolfHut Sep 24, 2022
2b8d7b5
debugging get_value_at_indeces
RolfHut Sep 25, 2022
67aef71
finished! Needs cleaning up of library files to correct folders
RolfHut Sep 26, 2022
534152b
removed local version of bmipy
RolfHut Sep 26, 2022
cf7affa
put Heat folder back in its place
RolfHut Sep 26, 2022
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386 changes: 386 additions & 0 deletions examples/.ipynb_checkpoints/run-model-from-bmi-checkpoint.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Run the `Heat` model through its BMI"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"`Heat` models the diffusion of temperature on a uniform rectangular plate with Dirichlet boundary conditions. View the source code for the [model](https://github.com/csdms/bmi-example-python/blob/master/heat/heat.py) and its [BMI](https://github.com/csdms/bmi-example-python/blob/master/heat/bmi_heat.py) on GitHub."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Start by importing `os`, `numpy` and the `Heat` BMI:"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"import numpy as np\n",
"\n",
"from heat import BmiHeat"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Create an instance of the model's BMI."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"x = BmiHeat()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"What's the name of this model?"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The 2D Heat Equation\n"
]
}
],
"source": [
"print(x.get_component_name())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Start the `Heat` model through its BMI using a configuration file:"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"# Heat model configuration\n",
"shape:\n",
" - 6\n",
" - 8\n",
"spacing:\n",
" - 1.0\n",
" - 1.0\n",
"origin:\n",
" - 0.0\n",
" - 0.0\n",
"alpha: 1.0\n"
]
}
],
"source": [
"cat heat.yaml"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"x.initialize(\"heat.yaml\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Check the time information for the model."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Start time: 0.0\n",
"End time: 1.7976931348623157e+308\n",
"Current time: 0.0\n",
"Time step: 0.25\n",
"Time units: s\n"
]
}
],
"source": [
"print(\"Start time:\", x.get_start_time())\n",
"print(\"End time:\", x.get_end_time())\n",
"print(\"Current time:\", x.get_current_time())\n",
"print(\"Time step:\", x.get_time_step())\n",
"print(\"Time units:\", x.get_time_units())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Show the input and output variables for the component (aside on [Standard Names](https://csdms.colorado.edu/wiki/CSDMS_Standard_Names)):"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"print(x.get_input_var_names())\n",
"print(x.get_output_var_names())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Next, get the identifier for the grid on which the temperature variable is defined:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"grid_id = x.get_var_grid(\"plate_surface__temperature\")\n",
"print(\"Grid id:\", grid_id)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Then get the grid attributes:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"print(\"Grid type:\", x.get_grid_type(grid_id))\n",
"\n",
"rank = x.get_grid_rank(grid_id)\n",
"print(\"Grid rank:\", rank)\n",
"\n",
"shape = np.ndarray(rank, dtype=int)\n",
"x.get_grid_shape(grid_id, shape)\n",
"print(\"Grid shape:\", shape)\n",
"\n",
"spacing = np.ndarray(rank, dtype=float)\n",
"x.get_grid_spacing(grid_id, spacing)\n",
"print(\"Grid spacing:\", spacing)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"These commands are made somewhat un-Pythonic by the generic design of the BMI."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Through the model's BMI, zero out the initial temperature field, except for an impulse near the middle.\n",
"Note that *set_value* expects a one-dimensional array for input."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"temperature = np.zeros(shape)\n",
"temperature[3, 4] = 100.0\n",
"x.set_value(\"plate_surface__temperature\", temperature)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Check that the temperature field has been updated. Note that *get_value* expects a one-dimensional array to receive output."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"temperature_flat = np.empty_like(temperature).flatten()\n",
"x.get_value(\"plate_surface__temperature\", temperature_flat)\n",
"print(temperature_flat.reshape(shape))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now advance the model by a single time step:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"x.update()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"View the new state of the temperature field:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"x.get_value(\"plate_surface__temperature\", temperature_flat)\n",
"print(temperature_flat.reshape(shape))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"There's diffusion!"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Advance the model to some distant time:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"distant_time = 2.0\n",
"while x.get_current_time() < distant_time:\n",
" x.update()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"View the final state of the temperature field:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"np.set_printoptions(formatter={\"float\": \"{: 5.1f}\".format})\n",
"x.get_value(\"plate_surface__temperature\", temperature_flat)\n",
"print(temperature_flat.reshape(shape))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Note that temperature isn't conserved on the plate:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"print(temperature_flat.sum())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"End the model:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"x.finalize()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"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": "3.7.1"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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