phiFEM 0.8.0.dev1__tar.gz → 0.8.2.dev1__tar.gz

{phifem-0.8.0.dev1 → phifem-0.8.2.dev1}/.vscode/settings.json

@@ -25,7 +25,8 @@
         "statusBar.debuggingBackground": "#0a7f02",
         "statusBar.debuggingForeground": "#e7e7e7",
         "activityBar.activeBorder": "#e7e7e7",
-        "activityBarTop.activeBorder": "#e7e7e7"
+        "activityBarTop.activeBorder": "#e7e7e7",
+        "statusBar.inactiveBackground": "#0a7f02"
     },
     "peacock.color": "#0a7f02",
     "peacock.favoriteColors": [

{phifem-0.8.0.dev1 → phifem-0.8.2.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: phiFEM
-Version: 0.8.0.dev1
+Version: 0.8.2.dev1
 Summary: phiFEM: convenience tools to use the phiFEM immersed boundary finite element method with dolfinx.
 Project-URL: Homepage, https://github.com/PhiFEM/phiFEM
 Project-URL: Issues, https://github.com/PhiFEM/phiFEM/issues
@@ -12,7 +12,7 @@ License-File: COPYING.lesser
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.9
-Requires-Dist: fenics-dolfinx==0.9.0
+Requires-Dist: fenics-dolfinx<0.11,>=0.9.0
 Description-Content-Type: text/markdown
 
 <p align="center" width="100%">

{phifem-0.8.0.dev1 → phifem-0.8.2.dev1}/demo/neumann/square/main.py

@@ -1,5 +1,6 @@
 import argparse
 import os
+import shutil
 
 import dolfinx as dfx
 import numpy as np
@@ -29,7 +30,8 @@ mesh_type = args.mesh_type
 
 output_dir = os.path.join(parent_dir, mesh_type + "_output")
 
-if not os.path.isdir(output_dir):
+world_comm = MPI.COMM_WORLD
+if world_comm.rank == 0 and not os.path.isdir(output_dir):
     print(f"{output_dir} directory not found, we create it.")
     os.mkdir(os.path.join(parent_dir, output_dir))
 
@@ -70,6 +72,18 @@ elif mesh_type == "sub":
     )
     ds = ufl.Measure("ds", domain=mesh)
 
+dg0_element = element("DG", cell_name, 0)
+dg0_space = dfx.fem.functionspace(mesh, dg0_element)
+
+cells_tags_h = dfx.fem.Function(dg0_space)
+cells_tags_h.name = "cells tags"
+
+local_num_dofs = dg0_space.dofmap.index_map.size_local
+ghosts_dofs = dg0_space.dofmap.index_map.ghosts
+l2g_map = dg0_space.dofmap.index_map.local_to_global(np.arange(local_num_dofs))
+l2g_map = np.sort(np.hstack([l2g_map, ghosts_dofs]))
+cells_tags_h.x.array[:] = cells_tags.values
+
 gdim = mesh.geometry.dim
 primal_element = element("Lagrange", cell_name, primal_degree)
 auxiliary_element = element("DG", cell_name, auxiliary_degree)
@@ -156,6 +170,7 @@ L = ufl.inner(f_h, v) * dx((1, 2)) + (
 
 linear_form = dfx.fem.form(L)
 b = assemble_vector(linear_form)
+b.ghostUpdate(addv=PETSc.InsertMode.ADD, mode=PETSc.ScatterMode.REVERSE)
 
 """
 =========================
@@ -182,6 +197,7 @@ pc.getFactorMatrix().setMumpsIcntl(icntl=25, ival=0)
 solution_wh = dfx.fem.Function(mixed_space)
 ksp.solve(b, solution_wh.x.petsc_vec)
 ksp.destroy()
+solution_wh.x.scatter_forward()
 
 # Recover the primal solution from the mixed solution
 solution_uh, _, _ = solution_wh.split()
@@ -192,58 +208,63 @@ solution_uh.collapse()
  Save solution for visualization
 =================================
 """
-with XDMFFile(mesh.comm, os.path.join(output_dir, "solution.xdmf"), "w") as of:
-    of.write_mesh(mesh)
-    of.write_function(solution_uh)
 
 u_exact_h = dfx.fem.Function(primal_space)
 u_exact_h.interpolate(exact_solution)
 
-with XDMFFile(mesh.comm, os.path.join(output_dir, "exact_solution.xdmf"), "w") as of:
+solution_uh.name = "uh"
+u_exact_h.name = "exact"
+with XDMFFile(mesh.comm, os.path.join(output_dir, "solutions.xdmf"), "w") as of:
     of.write_mesh(mesh)
+    of.write_function(solution_uh)
     of.write_function(u_exact_h)
+    of.write_function(cells_tags_h)
 
 """
 =========================
  Local error computation
 =========================
 """
-ref_element = element("Lagrange", cell_name, primal_degree + 2)
-ref_space = dfx.fem.functionspace(mesh, ref_element)
-
-ref_exact_solution = dfx.fem.Function(ref_space)
-ref_exact_solution.interpolate(exact_solution)
-ref_solution = dfx.fem.Function(ref_space)
-ref_solution.interpolate(solution_uh)
-ref_error = dfx.fem.Function(ref_space)
-ref_error.x.array[:] = ref_exact_solution.x.array[:] - ref_solution.x.array[:]
-
-dg0_element = element("DG", cell_name, 0)
-dg0_space = dfx.fem.functionspace(mesh, dg0_element)
-v0 = ufl.TestFunction(dg0_space)
-
-h1_error = ufl.inner(
-    ufl.inner(ufl.grad(ref_error), ufl.grad(ref_error))
-    + ufl.inner(ref_error, ref_error),
-    v0,
-) * dx((1, 2))
-
-h1_error_form = dfx.fem.form(h1_error)
-h1_error_vec = assemble_vector(h1_error_form)
-
-h1_error_fct = dfx.fem.Function(dg0_space)
-h1_error_fct.x.array[:] = h1_error_vec.array[:]
-
-with XDMFFile(mesh.comm, os.path.join(output_dir, "h1_error.xdmf"), "w") as of:
-    of.write_mesh(mesh)
-    of.write_function(h1_error_fct)
-
-h1_norm_exact_solution = (
-    ufl.inner(ufl.grad(ref_exact_solution), ufl.grad(ref_exact_solution))
-    + ufl.inner(ref_exact_solution, ref_exact_solution)
-) * dx((1, 2))
-h1_norm_exact_solution_form = dfx.fem.form(h1_norm_exact_solution)
-h1_norm_exact_solution = dfx.fem.assemble_scalar(h1_norm_exact_solution_form)
-
-print("Relative H1 error:")
-print(np.sqrt(h1_error_fct.x.array.sum() / h1_norm_exact_solution))
+# ref_element = element("Lagrange", cell_name, primal_degree + 2)
+# ref_space = dfx.fem.functionspace(mesh, ref_element)
+
+# ref_exact_solution = dfx.fem.Function(ref_space)
+# ref_exact_solution.interpolate(exact_solution)
+# ref_solution = dfx.fem.Function(ref_space)
+# ref_solution.interpolate(solution_uh)
+# ref_error = dfx.fem.Function(ref_space)
+# ref_error.x.array[:] = ref_exact_solution.x.array[:] - ref_solution.x.array[:]
+
+# dg0_element = element("DG", cell_name, 0)
+# dg0_space = dfx.fem.functionspace(mesh, dg0_element)
+# v0 = ufl.TestFunction(dg0_space)
+
+# h1_error = ufl.inner(
+#     ufl.inner(ufl.grad(ref_error), ufl.grad(ref_error))
+#     + ufl.inner(ref_error, ref_error),
+#     v0,
+# ) * dx((1, 2))
+
+# h1_error_form = dfx.fem.form(h1_error)
+# h1_error_vec = assemble_vector(h1_error_form)
+
+# h1_error_fct = dfx.fem.Function(dg0_space)
+# if mesh.comm.rank == 0:
+#     h1_error_fct.x.array[:] = h1_error_vec.array[:]
+
+# h1_error_fct.x.array[:] = mesh.comm.bcast(h1_error_fct.x.array[:], root=0)
+
+# with XDMFFile(mesh.comm, os.path.join(output_dir, "h1_error.xdmf"), "w") as of:
+#     of.write_mesh(mesh)
+#     of.write_function(h1_error_fct)
+
+# h1_norm_exact_solution = (
+#     ufl.inner(ufl.grad(ref_exact_solution), ufl.grad(ref_exact_solution))
+#     + ufl.inner(ref_exact_solution, ref_exact_solution)
+# ) * dx((1, 2))
+# h1_norm_exact_solution_form = dfx.fem.form(h1_norm_exact_solution)
+# h1_norm_exact_solution = dfx.fem.assemble_scalar(h1_norm_exact_solution_form)
+
+# if mesh.comm.rank == 0:
+#     print("Relative H1 error:")
+#     print(np.sqrt(h1_error_fct.x.array.sum() / h1_norm_exact_solution))

phifem-0.8.2.dev1/phifem-env.yml

@@ -0,0 +1,9 @@
+name: phifem
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.11.10
+  - numpy>=1.26.3
+  - fenics-dolfinx>=0.9.0,<0.11
+  - pip:
+    - phifem==0.7.1.dev2