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LevanBokeriaLevanBokeria
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Merge pull request #71 from alan-turing-institute/dev
Adding a variation of KorakianitisMixedModel with passive component
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‎sandbox/notebooks/generate_KMMPP_KGO.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Description\n",
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"\n",
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"This notebook is to generate known good outputs (KGOs) for solving KorakianitisMixedModelPP (KMMPP) after we have added a cycle step size argument to the `advance_cycle()` function of the solver.\n",
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"\n",
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"With different step sizes, there are slightly different solutions reached, so tests need these different KGOs to have as comparisons."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"import json\n",
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"\n",
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"from ModularCirc.Solver import Solver\n",
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"\n",
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"from ModularCirc.Models.KorakianitisMixedModelPP import KorakianitisMixedModelPP\n",
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"from ModularCirc.Models.KorakianitisMixedModel_parameters import KorakianitisMixedModel_parameters"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Running simulation with cycle step size: 1\n",
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"Running simulation with cycle step size: 1\n",
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"Running simulation with cycle step size: 3\n",
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"Running simulation with cycle step size: 3\n",
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"Running simulation with cycle step size: 5\n",
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"Running simulation with cycle step size: 5\n",
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"Running simulation with cycle step size: 7\n",
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"Running simulation with cycle step size: 7\n"
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]
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}
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],
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"source": [
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"time_setup_dict = {\n",
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" 'name': 'TimeTest',\n",
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" 'ncycles': 40,\n",
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" 'tcycle': 1.0,\n",
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" 'dt': 0.001,\n",
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" 'export_min': 1\n",
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" }\n",
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"\n",
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"# Start the loop with different cycle step size to generate JSON files for each loop:\n",
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"cycle_step_sizes = [1, 3, 5, 7]\n",
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"\n",
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"# Dictionary to store the results for all cycle step sizes\n",
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"all_results = {\n",
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" \"metadata\": {\n",
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" \"description\": \"Results for different cycle_step_size values\",\n",
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" \"cycle_step_sizes\": cycle_step_sizes\n",
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" },\n",
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" \"results\": {}\n",
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"}\n",
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"\n",
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"# Loop through each cycle step size\n",
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"for i_cycle_step_size in cycle_step_sizes:\n",
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"\n",
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" print(f\"Running simulation with cycle step size: {i_cycle_step_size}\")\n",
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"\n",
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" # Initializing the parameter object\n",
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" parobj = KorakianitisMixedModel_parameters()\n",
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"\n",
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" # Initializing the model \n",
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" model = KorakianitisMixedModelPP(time_setup_dict=time_setup_dict, \n",
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" parobj=parobj, \n",
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" suppress_printing=True)\n",
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"\n",
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" # Initializing the solver\n",
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" solver = Solver(model=model)\n",
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"\n",
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" # Initializing the parameter object\n",
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" parobj = KorakianitisMixedModel_parameters()\n",
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"\n",
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" # Initializing the model \n",
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" model = KorakianitisMixedModelPP(time_setup_dict=time_setup_dict, \n",
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" parobj=parobj, \n",
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" suppress_printing=True)\n",
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"\n",
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" # Initializing the solver\n",
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" solver = Solver(model=model)\n",
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"\n",
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" # Solver is being setup: switching off console printing and setting the solver method to \"LSODA\"\n",
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" solver.setup(suppress_output=True, \n",
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" method='LSODA',\n",
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" step=i_cycle_step_size)\n",
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"\n",
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" # Running the model\n",
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" solver.solve()\n",
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"\n",
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" # Define the indexes of the equivalent to the last cycles\n",
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" tind_fin = np.arange(start=model.time_object.n_t-model.time_object.n_c,\n",
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" stop=model.time_object.n_t)\n",
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"\n",
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" # Dictionary to store the final cycle values for each component for the current step size\n",
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" final_cycle_values = {}\n",
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"\n",
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" # From each of the components, retrieve the volume (<V>), pressure (<P_i>) and flow (<Q_i>)\n",
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" for key, value in model.components.items():\n",
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" final_cycle_values[key] = {\n",
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" 'V': value.V.values[tind_fin].mean(),\n",
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" 'P_i': value.P_i.values[tind_fin].mean(),\n",
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" 'Q_i': value.Q_i.values[tind_fin].mean()\n",
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" }\n",
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"\n",
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" # Add the results for the current cycle step size to the main dictionary\n",
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" all_results[\"results\"][i_cycle_step_size] = final_cycle_values\n",
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"\n",
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"# Save all results to a single JSON file in the tests/expected_outputs directory\n",
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"with open('../../tests/expected_outputs/KorakianitisMixedModelPP_expected_output.json', 'w') as f:\n",
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" json.dump(all_results, f, indent=4)"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "venv",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.4"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎sandbox/notebooks/generate_KMM_KGO.ipynb

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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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" # Initializing the solver\n",
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" solver = Solver(model=model)\n",
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"\n",
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" print(f\"Running simulation with cycle step size: {i_cycle_step_size}\")\n",
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"\n",
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" # Initializing the parameter object\n",
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" parobj = KorakianitisMixedModel_parameters()\n",
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"\n",

‎src/ModularCirc/Components/HC_mixed_elastance_pp.py

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from .ComponentBase import ComponentBase
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from ..HelperRoutines import activation_function_1, \
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chamber_volume_rate_change, \
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time_shift
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from ..Time import TimeClass
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import pandas as pd
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import numpy as np
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def dvdt(t, q_in=None, q_out=None, v=None, v_ref=0.0, y=None):
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if y is not None:
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q_in, q_out, v = y[:3]
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if q_in - q_out > 0.0 or v > v_ref:
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return q_in - q_out
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else:
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return 0.0
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def gen_active_p(E_act, v_ref):
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def active_p(v):
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return E_act * (v - v_ref)
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return active_p
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def gen_active_dpdt(E_act):
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def active_dpdt(q_i, q_o):
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return E_act * (q_i - q_o)
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return active_dpdt
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def gen_passive_p(E_pas, k_pas, v_ref):
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def passive_p(v):
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return E_pas * (np.exp(k_pas * (v - v_ref)) - 1.0)
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return passive_p
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def gen_passive_dpdt(E_pas, k_pas, v_ref):
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def passive_dpdt(v, q_i, q_o):
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return E_pas * k_pas * np.exp(k_pas * (v - v_ref)) * (q_i - q_o)
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return passive_dpdt
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def gen_total_p(_af, active_p, passive_p):
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def total_p(t, y):
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_af_t = _af(t)
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return _af_t * active_p(y) + passive_p(y)
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return total_p
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def gen_total_dpdt(active_p, passive_p, _af, active_dpdt, passive_dpdt):
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def total_dpdt(t, y):
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_af_t = _af(t)
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_d_af_dt = _af(t, dt=True)
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return (_d_af_dt * active_p(y[0]) + _af_t * active_dpdt(y[1], y[2]) + passive_dpdt(y[0], y[1], y[2]))
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return total_dpdt
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def gen_comp_v(E_pas, v_ref, k_pas):
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def comp_v(t, y):
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return v_ref + np.log(y[0] / E_pas + 1.0) / k_pas
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return comp_v
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def gen_time_shifter(delay_, T):
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def time_shifter(t):
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return time_shift(t, delay_, T)
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return time_shifter
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def gen__af(af, time_shifter, kwargs):
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varnames = [name for name in af.__code__.co_varnames if name != 'coeff' and name != 't']
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kwargs2 = {key: val for key,val in kwargs.items() if key in varnames}
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def _af(t, dt=False):
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return af(time_shifter(t), dt=dt, **kwargs2)
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return _af
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class HC_mixed_elastance_pp(ComponentBase):
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def __init__(self,
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name:str,
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time_object: TimeClass,
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E_pas: float,
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E_act: float,
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k_pas: float,
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v_ref: float,
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v : float = None,
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p : float = None,
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af = activation_function_1,
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*args, **kwargs
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) -> None:
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super().__init__(name=name, time_object=time_object, v=v, p=p)
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self.E_pas = E_pas
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self.k_pas = k_pas
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self.E_act = E_act
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self.v_ref = v_ref
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self.eps = 1.0e-3
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self.kwargs = kwargs
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self.af = af
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self.make_unique_io_state_variable(p_flag=True, q_flag=False)
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@property
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def P(self):
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return self._P_i._u
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def setup(self) -> None:
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E_pas = self.E_pas
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k_pas = self.k_pas
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E_act = self.E_act
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v_ref = self.v_ref
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eps = self.eps
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kwargs= self.kwargs
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T = self._to.tcycle
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af = self.af
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time_shifter = gen_time_shifter(delay_=kwargs['delay'], T=T)
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_af = gen__af(af=af, time_shifter=time_shifter, kwargs=kwargs)
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active_p = gen_active_p(E_act=E_act, v_ref=v_ref)
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active_dpdt = gen_active_dpdt(E_act=E_act)
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passive_p = gen_passive_p(E_pas=E_pas, k_pas=k_pas, v_ref=v_ref)
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passive_dpdt = gen_passive_dpdt(E_pas=E_pas, k_pas=k_pas, v_ref=v_ref)
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total_p = gen_total_p(_af=_af, active_p=active_p, passive_p=passive_p)
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total_dpdt = gen_total_dpdt(active_p=active_p, passive_p=passive_p,
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_af=_af, active_dpdt=active_dpdt, passive_dpdt=passive_dpdt)
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comp_v = gen_comp_v(E_pas=E_pas, v_ref=v_ref, k_pas=k_pas)
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self._V.set_dudt_func(chamber_volume_rate_change,
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function_name='chamber_volume_rate_change')
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self._V.set_inputs(pd.Series({'q_in' :self._Q_i.name,
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'q_out':self._Q_o.name}))
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self._P_i.set_dudt_func(total_dpdt, function_name='total_dpdt')
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self._P_i.set_inputs(pd.Series({'v' :self._V.name,
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'q_i':self._Q_i.name,
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'q_o':self._Q_o.name}))
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if self.p0 is None or self.p0 is np.NaN:
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self._P_i.set_i_func(total_p, function_name='total_p')
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self._P_i.set_i_inputs(pd.Series({'v':self._V.name}))
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else:
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self.P_i.loc[0] = self.p0
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if self.v0 is None or self.v0 is np.NaN:
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self._V.set_i_func(comp_v, function_name='comp_v')
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self._V.set_i_inputs(pd.Series({'p':self._P_i.name}))
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if (self.v0 is None or self.v0 is np.NaN) and (self.p0 is None or self.p0 is np.NaN):
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raise Exception("Solver needs at least the initial volume or pressure to be defined!")

‎src/ModularCirc/Components/__init__.py

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from .ComponentBase import ComponentBase
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from .HC_constant_elastance import HC_constant_elastance
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from .HC_mixed_elastance import HC_mixed_elastance
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from .HC_mixed_elastance_pp import HC_mixed_elastance_pp
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from .R_component import R_component
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from .Rc_component import Rc_component
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from .Rlc_component import Rlc_component

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