Fixes to model files

.gitignore

@@ -1,5 +1,5 @@
 _build
-examples/example1/mesh/
+meshes/
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

ca2+-examples/pre_process_mesh.py

@@ -13,6 +13,11 @@ def main(input_mesh_file, output_mesh_file, num_refinements):
     spine_mesh = d.Mesh(Path(input_mesh_file).as_posix())
     cell_markers = d.MeshFunction("size_t", spine_mesh, 3, spine_mesh.domains())
     facet_markers = d.MeshFunction("size_t", spine_mesh, 2, spine_mesh.domains())
+    int_domain = d.MeshFunction("size_t", spine_mesh, 3)
+    psd_domain = d.MeshFunction("size_t", spine_mesh, 2, spine_mesh.domains())
+    for i in range(len(int_domain.mesh().coordinates())):
+        if int_domain.mesh().coordinates()[i][2] > 0.5:
+            int_domain.array()[i] = 1
 
     if num_refinements > 0:
         print(
@@ -25,21 +30,23 @@ def main(input_mesh_file, output_mesh_file, num_refinements):
             spine_mesh = d.adapt(spine_mesh)
             cell_markers = d.adapt(cell_markers, spine_mesh)
             facet_markers = d.adapt(facet_markers, spine_mesh)
+            psd_domain = d.adapt(psd_domain, spine_mesh)
+            int_domain = d.adapt(int_domain, spine_mesh)
         print(
             f"Refined mesh has {spine_mesh.num_cells()} cells, "
             f"{spine_mesh.num_facets()} facets and "
             f"{spine_mesh.num_vertices()} vertices"
         )
-
-
-    # for i in range(len(facet_array)):
-    #     if (
-    #         facet_array[i] == 11
-    #     ):  # this indicates PSD; in this case, set to 10 to indicate it is a part of the PM
-    #         facet_array[i] = 10
+    
+    facet_array = facet_markers.array()[:]
+    for i in range(len(facet_array)):
+        if (
+            facet_array[i] == 11
+        ):  # this indicates PSD; in this case, set to 10 to indicate it is a part of the PM
+            facet_array[i] = 10
 
     Path(output_mesh_file).parent.mkdir(exist_ok=True, parents=True)
-    mesh_tools.write_mesh(spine_mesh, facet_markers, cell_markers, output_mesh_file)
+    mesh_tools.write_mesh(spine_mesh, facet_markers, cell_markers, output_mesh_file, [psd_domain, int_domain])
 
 
 if __name__ == "__main__":

ex3_scripts/main.py

@@ -61,6 +61,111 @@ def add_argument_preprocess_mech_mesh(parser: argparse.ArgumentParser):
 
     mech_parser_args.add_preprocess_mech_mesh_arguments(parser)
 
+def add_argument_mito_example(parser: argparse.ArgumentParser):
+    sys.path.insert(0, (here / ".." / "mito-example").as_posix())
+    import mito_parser_args
+
+    mito_parser_args.add_run_mito_arguments(parser)
+
+
+def add_argument_preprocess_mito_mesh(parser: argparse.ArgumentParser):
+    sys.path.insert(0, (here / ".." / "mito-example").as_posix())
+    import mito_parser_args
+
+    mito_parser_args.add_preprocess_mito_mesh_arguments(parser)
+
+def run_preprocess_mito_mesh(
+    input_mesh_file: Path,
+    output_mesh_file: Path,
+    input_curv_file: Path,
+    output_curv_file: Path,
+    dry_run: bool,
+    num_refinements: int,
+    **kwargs,
+):
+    args = [
+        "--input-mesh-file",
+        Path(input_mesh_file).as_posix(),
+        "--output-mesh-file",
+        Path(output_mesh_file).as_posix(),
+        "--input-curv-file",
+        Path(input_curv_file).as_posix(),
+        "--output-curv-file",
+        Path(output_curv_file).as_posix(),
+        "--num-refinements",
+        num_refinements,
+    ]
+
+    script = (
+        (here / ".." / "mito-example" / "pre_process_mesh.py")
+        .absolute()
+        .resolve()
+        .as_posix()
+    )
+    args = list(map(str, args))
+    if dry_run:
+        print(f"Run command: {sys.executable} {script} {' '.join(args)}")
+        return
+
+    sp.run([sys.executable, script, *args])
+
+
+def run_mito_example(
+    mesh_file: Path,
+    curv_file: Path,
+    outdir: Path,
+    time_step: float,
+    curv_dep: float,
+    enforce_mass_conservation: bool,
+    dry_run: bool = False,
+    submit_ex3: bool = False,
+    **kwargs,
+):
+    args = [
+        "--mesh-file",
+        Path(mesh_file).as_posix(),
+        "--curv-file",
+        Path(curv_file).as_posix(),
+        "--time-step",
+        time_step,
+        "--curv-dep",
+        curv_dep,
+    ]
+    if enforce_mass_conservation:
+        args.append("--enforce-mass-conservation")
+
+    if not submit_ex3:
+        args.extend(["--outdir", Path(outdir).as_posix()])
+
+    script = (
+        (here / ".." / "mito-example" / "mito_atp_dynamics.py")
+        .absolute()
+        .resolve()
+        .as_posix()
+    )
+    # Turn all arguments into strings
+    args = list(map(str, args))
+    args_str = " ".join(args)
+    if dry_run:
+        print(f"Run command: {sys.executable} {script} {args_str}")
+        return
+
+    if submit_ex3:
+        job_file = Path("tmp_job.sbatch")
+        job_file.write_text(
+            ex3_template.format(
+                job_name="mito",
+                python=sys.executable,
+                script=script,
+                args=args_str,
+            )
+        )
+
+        sp.run(["sbatch", job_file])
+        job_file.unlink()
+    else:
+        sp.run([sys.executable, script, *args])
+
 
 def run_pre_preprocess_mech_mesh(
     mesh_folder: Path,
@@ -104,6 +209,7 @@ def run_mechanotransduction_example(
     e_val: float,
     z_cutoff: float,
     axisymmetric: bool,
+    well_mixed: bool,
     no_enforce_mass_conservation: bool = False,
     dry_run: bool = False,
     submit_ex3: bool = False,
@@ -119,6 +225,7 @@ def run_mechanotransduction_example(
         "--z-cutoff",
         z_cutoff,
         "--axisymmetric" if axisymmetric else "",
+        "--well-mixed" if well_mixed else "",
     ]
     if no_enforce_mass_conservation:
         args.append("--no-enforce-mass-conservation")
@@ -296,6 +403,17 @@ def main():
     )
     add_argument_mechanotransduction_example(dendritic_spine)
 
+    # Mito example
+    preprocess_spine_mesh = subparsers.add_parser(
+        "preprocess-mito-mesh", help="Preprocess mesh for mito example"
+    )
+    add_argument_preprocess_mito_mesh(preprocess_spine_mesh)
+
+    mito = subparsers.add_parser(
+        "mito", help="Run mito example"
+    )
+    add_argument_mito_example(mito)
+
     args = vars(parser.parse_args())
     # if args[""]
 
@@ -318,6 +436,14 @@ def main():
     elif args["command"] == "mechanotransduction":
         print("Run mechanotransduction example")
         run_mechanotransduction_example(**args)
+
+    elif args["command"] == "preprocess-mito-mesh":
+        print("Run preprocess mito mesh")
+        run_preprocess_mito_mesh(**args)
+
+    elif args["command"] == "mito":
+        print("Run mito example")
+        run_mito_example(**args)
 
 
 if __name__ == "__main__":

ex3_scripts/run_mito.sh

@@ -0,0 +1,12 @@
+python3 main.py preprocess-mito-mesh --input-mesh-file /root/shared/gitrepos/smart-comp-sci/meshes/mito1_mesh.xml --output-mesh-file meshes/mito_mesh.h5 --input-curv-file /root/shared/gitrepos/smart-comp-sci/meshes/mito1_curvature.xml --output-curv-file meshes/mito_curv.xdmf
+python3 main.py mito --mesh-file meshes/mito_mesh.h5  --curv-file meshes/mito_curv.xdmf --outdir /root/scratch/eafrancis/mito/sweep_gamer_curv/results_curvdepneg40 --curv-dep=-40 --enforce-mass-conservation &
+sleep 10
+python3 main.py mito --mesh-file meshes/mito_mesh.h5  --curv-file meshes/mito_curv.xdmf --outdir /root/scratch/eafrancis/mito/sweep_gamer_curv/results_curvdepneg20 --curv-dep=-20 --enforce-mass-conservation &
+sleep 10
+python3 main.py mito --mesh-file meshes/mito_mesh.h5  --curv-file meshes/mito_curv.xdmf --outdir /root/scratch/eafrancis/mito/sweep_gamer_curv/results_curvdepneg10 --curv-dep=-10 --enforce-mass-conservation &
+sleep 10
+python3 main.py mito --mesh-file meshes/mito_mesh.h5  --curv-file meshes/mito_curv.xdmf --outdir /root/scratch/eafrancis/mito/sweep_gamer_curv/results_curvdep10 --curv-dep 10 --enforce-mass-conservation &
+sleep 10
+python3 main.py mito --mesh-file meshes/mito_mesh.h5  --curv-file meshes/mito_curv.xdmf --outdir /root/scratch/eafrancis/mito/sweep_gamer_curv/results_curvdep20 --curv-dep 20 --enforce-mass-conservation &
+sleep 10
+python3 main.py mito --mesh-file meshes/mito_mesh.h5  --curv-file meshes/mito_curv.xdmf --outdir /root/scratch/eafrancis/mito/sweep_gamer_curv/results_curvdep40 --curv-dep 40 --enforce-mass-conservation

mechanotransduction-example/mech_parser_args.py

@@ -61,6 +61,11 @@ def add_mechanotransduction_arguments(parser: argparse.ArgumentParser) -> None:
         action="store_true",
         default=False,
     )
+    parser.add_argument(
+        "--well-mixed",
+        action="store_true",
+        default=False,
+    )
     parser.add_argument(
         "--no-enforce-mass-conservation",
         action="store_true",