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Merge branch 'development' into dokken/deprecated_unused_functions
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Also resolves reviwer comments
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@jorgensd
jorgensd committed Mar 1, 2023
2 parents 63cf5c2 + 49bcfc3 commit 6ab5e69
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2 changes: 1 addition & 1 deletion .github/workflows/build_docs.yml
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build:
runs-on: ubuntu-22.04
container: ghcr.io/scientificcomputing/fenics:2023-01-16
container: ghcr.io/scientificcomputing/fenics-gmsh:2023-02-17a
env:
DEB_PYTHON_INSTALL_LAYOUT: deb_system
PUBLISH_DIR: ./_build/html
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2 changes: 1 addition & 1 deletion .github/workflows/test_fenics_stubs.yml
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check-code:
runs-on: ubuntu-22.04
# Runs against FEniCS main branch built the 16-01-2023
container: ghcr.io/scientificcomputing/fenics:2023-01-16
container: ghcr.io/scientificcomputing/fenics-gmsh:2023-02-17a
steps:
# This action sets the current path to the root of your github repo
- uses: actions/checkout@v3
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18 changes: 5 additions & 13 deletions docker/Dockerfile_dev
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# $ docker run -ti --name stubs --init -p 8080:8888 -v $HOME:/home/fenics/shared stubs:latest

# Base fenics dev image
FROM quay.io/fenicsproject/dev
FROM ghcr.io/scientificcomputing/fenics:2023-01-16


# ======================================================
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# this is to install just the dependencies so that we can use the local version of stubs
RUN python3 -m pip install fenics-stubs
RUN python3 -m pip uninstall --yes fenics-stubs
# now we add the local repo to the pythonpath
ENV PYTHONPATH "${PYTHONPATH}:$FENICS_HOME/shared/gitrepos/stubs"
# now we add the local repo to the pythonpath
ENV FENICS_HOME "/root"
ENV PYTHONPATH "/root/shared/gitrepos/stubs-dev"


# bashrc settings (this appends to the top of the file)
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RUN ["/bin/bash", "-c", "source $FENICS_HOME/.bashrc"]
#RUN cd $FENICS_SRC_DIR/dolfin
#build cmake
#build pybind11 cd $FENICS_SRC_DIR/dolfin




# dont want my email floating around on the internet
RUN email_name="justinglaughlin"
RUN git config --global user.email "[email protected]"
RUN git config --global user.name "justinlaughlin"

#build pybind11 cd $FENICS_SRC_DIR/dolfin
4,014 changes: 6 additions & 4,008 deletions examples/example1/example1.ipynb
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3,796 changes: 3,796 additions & 0 deletions examples/example1/example1_sphere.ipynb
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245 changes: 245 additions & 0 deletions examples/example2/example2.ipynb
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{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"id": "f65f18d7",
"metadata": {},
"source": [
"# Example for system in Meyers, Craig and Odde 2006\n",
"\n",
"Geometry is divided into 2 domains; one volume and one surface:\n",
"- PM\n",
"- Cytosol\n",
"\n",
"This model has a single species, A, which is phosphorylated at the cell membrane. The unphosphorylated form of A ($A_{dephos}$) can be inferred from mass conservation; everywhere $c_{A_{phos}} + c_{A_{dephos}} = c_{Tot}$, which is a constant in both time and space if the phosphorylated vs. unphosphorylated forms have the same diffusion coefficient.\n",
"\n",
"There are two reactions - one in the PM and other in the cytosol. At the membrane, $A_{dephos}$ is phosphorylated by a first-order reaction with rate $k_{kin}$, and in the cytosolic volume, $A_{phos}$ is dephosphorylated by a first order reaction with rate $k_p$.\n",
"\n",
"Currently, this code includes a dummy variable, kinMem, which represents relative kinase activity at the membrane, currently set as constant at 1 (dimensionless). Without this additional species, the code currently does not solve the system (it seems that there needs to be variables in at least two compartments to solve the monolithic system).\n"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "cc398816",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Authorization required, but no authorization protocol specified\n",
"Authorization required, but no authorization protocol specified\n"
]
}
],
"source": [
"import os\n",
"\n",
"import dolfin as d\n",
"import sympy as sym\n",
"import numpy as np\n",
"\n",
"from stubs import unit, config, common, mesh, model\n",
"from stubs.model_assembly import Compartment, Parameter, Reaction, Species, sbmodel_from_locals"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "95b9d865",
"metadata": {},
"source": [
"First, we define the various units for the inputs"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "4f4023cf",
"metadata": {},
"outputs": [],
"source": [
"# Aliases - base units\n",
"uM = unit.uM\n",
"um = unit.um\n",
"molecule = unit.molecule\n",
"sec = unit.sec\n",
"dimensionless = unit.dimensionless\n",
"# Aliases - units used in model\n",
"D_unit = um**2 / sec\n",
"flux_unit = molecule / (um**2 * sec)\n",
"vol_unit = uM\n",
"surf_unit = molecule / um**2"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "46582d26",
"metadata": {},
"source": [
"Next we generate the model."
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "09079b17",
"metadata": {},
"outputs": [],
"source": [
"def make_model(curRadius):\n",
" # =============================================================================================\n",
" # Species\n",
" # =============================================================================================\n",
" # name, initial concentration, concentration units, diffusion, diffusion units, compartment\n",
" Aphos = Species(\"Aphos\", 0.1, vol_unit, 10.0, D_unit, \"Cyto\")\n",
" kinMem = Species(\"kinMem\", 1.0, dimensionless, 0.0, D_unit, \"PM\") # dummy variable; without this, the current version of SMART throws an error\n",
"\n",
" # =============================================================================================\n",
" # Compartments\n",
" # =============================================================================================\n",
" # name, topological dimensionality, length scale units, marker value\n",
" Cyto = Compartment(\"Cyto\", 3, um, 1)\n",
" PM = Compartment(\"PM\", 2, um, 10)\n",
"\n",
" # =============================================================================================\n",
" # Parameters and Reactions\n",
" # =============================================================================================\n",
" Atot = Parameter(\"Atot\", 1.0, vol_unit)\n",
" # Phosphorylation of Adephos at the PM\n",
" kkin = Parameter(\"kkin\", 50.0, 1/sec) \n",
" VolSA = Parameter(\"VolSA\", curRadius/3, um) # vol to surface area ratio of the cell\n",
" r1 = Reaction(\"r1\", [], [\"Aphos\"], param_map={\"kon\": \"kkin\", \"Atot\": \"Atot\", \"VolSA\": \"VolSA\"},\n",
" eqn_f_str=\"kinMem*kon*VolSA*(Atot - Aphos)\", species_map={\"Aphos\": \"Aphos\",\"kinMem\": \"kinMem\"}, explicit_restriction_to_domain=\"PM\")\n",
" # Dephosphorylation of Aphos in the cytosol\n",
" kp = Parameter(\"kp\", 10.0, 1/sec)\n",
" r2 = Reaction(\"r2\", [\"Aphos\"], [], param_map={\"kon\": \"kp\"},\n",
" eqn_f_str=\"kon*Aphos\", species_map={\"Aphos\": \"Aphos\"})\n",
"\n",
" # =============================================================================================\n",
" # Gather all parameters, species, compartments and reactions\n",
" # =============================================================================================\n",
" return sbmodel_from_locals(locals().values())"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "15c35d39",
"metadata": {},
"source": [
"We load the model generated above, and load in the mesh we will use in this example, iterating over 10 different values of cell radius, log-spaced between 1 and 10."
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "fe56e162",
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "module 'stubs.common' has no attribute 'sbmodel_from_locals'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[4], line 4\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[39mfor\u001b[39;00m i \u001b[39min\u001b[39;00m \u001b[39mrange\u001b[39m(\u001b[39m10\u001b[39m):\n\u001b[1;32m 3\u001b[0m curRadius \u001b[39m=\u001b[39m radiusVec[i]\n\u001b[0;32m----> 4\u001b[0m pc, sc, cc, rc \u001b[39m=\u001b[39m make_model(curRadius)\n\u001b[1;32m 6\u001b[0m \u001b[39m# =============================================================================================\u001b[39;00m\n\u001b[1;32m 7\u001b[0m \u001b[39m# Create/load in mesh\u001b[39;00m\n\u001b[1;32m 8\u001b[0m \u001b[39m# =============================================================================================\u001b[39;00m\n\u001b[1;32m 9\u001b[0m \u001b[39m# Base mesh\u001b[39;00m\n\u001b[1;32m 10\u001b[0m domain, facet_markers, cell_markers \u001b[39m=\u001b[39m common\u001b[39m.\u001b[39mDemoSpheresMesh(curRadius, \u001b[39m0\u001b[39m) \u001b[39m#0 in second argument corresponds to no ER\u001b[39;00m\n",
"Cell \u001b[0;32mIn[3], line 33\u001b[0m, in \u001b[0;36mmake_model\u001b[0;34m(curRadius)\u001b[0m\n\u001b[1;32m 27\u001b[0m r2 \u001b[39m=\u001b[39m Reaction(\u001b[39m\"\u001b[39m\u001b[39mr2\u001b[39m\u001b[39m\"\u001b[39m, [\u001b[39m\"\u001b[39m\u001b[39mAphos\u001b[39m\u001b[39m\"\u001b[39m], [], param_map\u001b[39m=\u001b[39m{\u001b[39m\"\u001b[39m\u001b[39mkon\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mkp\u001b[39m\u001b[39m\"\u001b[39m},\n\u001b[1;32m 28\u001b[0m eqn_f_str\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mkon*Aphos\u001b[39m\u001b[39m\"\u001b[39m, species_map\u001b[39m=\u001b[39m{\u001b[39m\"\u001b[39m\u001b[39mAphos\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mAphos\u001b[39m\u001b[39m\"\u001b[39m})\n\u001b[1;32m 30\u001b[0m \u001b[39m# =============================================================================================\u001b[39;00m\n\u001b[1;32m 31\u001b[0m \u001b[39m# Gather all parameters, species, compartments and reactions\u001b[39;00m\n\u001b[1;32m 32\u001b[0m \u001b[39m# =============================================================================================\u001b[39;00m\n\u001b[0;32m---> 33\u001b[0m \u001b[39mreturn\u001b[39;00m common\u001b[39m.\u001b[39;49msbmodel_from_locals(\u001b[39mlocals\u001b[39m()\u001b[39m.\u001b[39mvalues())\n",
"\u001b[0;31mAttributeError\u001b[0m: module 'stubs.common' has no attribute 'sbmodel_from_locals'"
]
}
],
"source": [
"radiusVec = np.logspace(0,1,num=10) # currently testing 10 radius values\n",
"for i in range(10):\n",
" curRadius = radiusVec[i]\n",
" pc, sc, cc, rc = make_model(curRadius)\n",
"\n",
" # =============================================================================================\n",
" # Create/load in mesh\n",
" # =============================================================================================\n",
" # Base mesh\n",
" domain, facet_markers, cell_markers = common.DemoSpheresMesh(curRadius, 0) #0 in second argument corresponds to no ER\n",
" # Write mesh and meshfunctions to file\n",
" os.makedirs(f\"mesh_{i:03d}\", exist_ok=True)\n",
" common.write_mesh(domain, facet_markers, cell_markers, filename=f\"mesh_{i:03d}/DemoSphere\")\n",
"\n",
" # # Define solvers\n",
" parent_mesh = mesh.ParentMesh(\n",
" mesh_filename=f\"mesh_{i:03d}/DemoSphere.h5\",\n",
" mesh_filetype=\"hdf5\",\n",
" name=\"parent_mesh\",\n",
" )\n",
" configCur = config.Config()\n",
" modelCur = model.Model(pc, sc, cc, rc, configCur, parent_mesh)\n",
" configCur.solver.update(\n",
" {\n",
" \"final_t\": 1,\n",
" \"initial_dt\": 0.01,\n",
" \"time_precision\": 6,\n",
" \"use_snes\": True,\n",
" \"print_assembly\": False,\n",
" }\n",
" )\n",
"\n",
" modelCur.initialize(initialize_solver=False)\n",
" modelCur.initialize_discrete_variational_problem_and_solver()\n",
" # Write initial condition(s) to file\n",
" results = dict()\n",
" os.makedirs(f\"resultsSphere_{i:03d}\", exist_ok=True)\n",
" for species_name, species in modelCur.sc.items:\n",
" results[species_name] = d.XDMFFile(\n",
" modelCur.mpi_comm_world, f\"resultsSphere_{i:03d}/{species_name}.xdmf\"\n",
" )\n",
" results[species_name].parameters[\"flush_output\"] = True\n",
" results[species_name].write(modelCur.sc[species_name].u[\"u\"], modelCur.t)\n",
"\n",
" # Solve\n",
" while True:\n",
" # Solve the system\n",
" modelCur.monolithic_solve()\n",
" # Save results for post processing\n",
" for species_name, species in modelCur.sc.items:\n",
" results[species_name].write(modelCur.sc[species_name].u[\"u\"], modelCur.t)\n",
" # End if we've passed the final time\n",
" if modelCur.t >= modelCur.final_t:\n",
" break"
]
}
],
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"jupytext": {
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