fix typo

playground/benchmark-umut-at2/vs_analytics_at2.py

@@ -17,19 +17,34 @@
 import ufl
 import yaml
 from dolfinx.common import list_timings
-from dolfinx.fem import (Constant, Function, assemble_scalar, dirichletbc,
-                         form, locate_dofs_geometrical)
+from dolfinx.fem import (
+    Constant,
+    Function,
+    assemble_scalar,
+    dirichletbc,
+    form,
+    locate_dofs_geometrical,
+)
 from dolfinx.io import XDMFFile
 from mpi4py import MPI
 from petsc4py import PETSc
-from pyvista.plotting.utilities import xvfbimport basix.ufl
+from pyvista.plotting.utilities import xvfb
+import basix.ufl
 
 from irrevolutions.algorithms.am import HybridSolver
 from irrevolutions.algorithms.so import BifurcationSolver, StabilitySolver
-from irrevolutions.utils import (ColorPrint, Visualization, _logger,
-                                 _write_history_data, history_data)
-from irrevolutions.utils.plots import (plot_AMit_load, plot_energies,
-                                       plot_force_displacement)
+from irrevolutions.utils import (
+    ColorPrint,
+    Visualization,
+    _logger,
+    _write_history_data,
+    history_data,
+)
+from irrevolutions.utils.plots import (
+    plot_AMit_load,
+    plot_energies,
+    plot_force_displacement,
+)
 from irrevolutions.utils.viz import plot_profile, plot_scalar
 
 petsc4py.init(sys.argv)

playground/benchmark-umut-at2/vs_analytics_at2_2d.py

@@ -16,22 +16,35 @@
 import ufl
 import yaml
 from dolfinx.common import list_timings
-from dolfinx.fem import (Constant, Function, assemble_scalar, form,
-                         locate_dofs_geometrical)
+from dolfinx.fem import (
+    Constant,
+    Function,
+    assemble_scalar,
+    form,
+    locate_dofs_geometrical,
+)
 from dolfinx.io import XDMFFile, gmshio
 from mpi4py import MPI
 from petsc4py import PETSc
-from pyvista.plotting.utilities import xvfbimport basix.ufl
+from pyvista.plotting.utilities import xvfb
+import basix.ufl
 
 from irrevolutions.algorithms.am import HybridSolver
 from irrevolutions.algorithms.so import BifurcationSolver, StabilitySolver
 from irrevolutions.meshes.primitives import mesh_bar_gmshapi
-from irrevolutions.models import \
-    BrittleMembraneOverElasticFoundation as ThinFilm
-from irrevolutions.utils import (ColorPrint, Visualization, _logger,
-                                 _write_history_data, history_data)
-from irrevolutions.utils.plots import (plot_AMit_load, plot_energies,
-                                       plot_force_displacement)
+from irrevolutions.models import BrittleMembraneOverElasticFoundation as ThinFilm
+from irrevolutions.utils import (
+    ColorPrint,
+    Visualization,
+    _logger,
+    _write_history_data,
+    history_data,
+)
+from irrevolutions.utils.plots import (
+    plot_AMit_load,
+    plot_energies,
+    plot_force_displacement,
+)
 from irrevolutions.utils.viz import plot_profile, plot_scalar, plot_vector
 
 petsc4py.init(sys.argv)
@@ -101,7 +114,9 @@ def run_computation(parameters, storage=None):
         file.write_mesh(mesh)
 
     # Functional Setting
-    element_u = basix.ufl.element("Lagrange", mesh.basix_cell(), degree=1, shape=(tdim,))
+    element_u = basix.ufl.element(
+        "Lagrange", mesh.basix_cell(), degree=1, shape=(tdim,)
+    )
     element_alpha = basix.ufl.element("Lagrange", mesh.basix_cell(), degree=1)
 
     V_u = dolfinx.fem.functionspace(mesh, element_u)

src/irrevolutions/practice/pacman-cone.py

@@ -23,14 +23,24 @@
 import ufl
 import yaml
 from dolfinx.common import list_timings, timing
-from dolfinx.fem import (Constant, Function, FunctionSpace, assemble_scalar,
-                         dirichletbc, form, locate_dofs_topological, set_bc)
+from dolfinx.fem import (
+    Constant,
+    Function,
+    FunctionSpace,
+    assemble_scalar,
+    dirichletbc,
+    form,
+    locate_dofs_topological,
+    set_bc,
+)
 from dolfinx.io import XDMFFile, gmshio
 from dolfinx.mesh import locate_entities_boundary
+
 #
 from mpi4py import MPI
 from petsc4py import PETSc
-from pyvista.plotting.utilities import xvfbimport basix.ufl
+from pyvista.plotting.utilities import xvfb
+import basix.ufl
 
 sys.path.append("../")
 

src/irrevolutions/practice/pacman_hybrid.py

@@ -22,11 +22,18 @@
 import matplotlib.pyplot as plt
 import pyvista
 import yaml
-from dolfinx.fem import (Function, FunctionSpace, dirichletbc,
-                         locate_dofs_topological, set_bc)
+from dolfinx.fem import (
+    Function,
+    FunctionSpace,
+    dirichletbc,
+    locate_dofs_topological,
+    set_bc,
+)
 from dolfinx.io import XDMFFile, gmshio
 from dolfinx.mesh import locate_entities_boundary
-from pyvista.plotting.utilities import xvfbimport basix.ufl
+from pyvista.plotting.utilities import xvfb
+import basix.ufl
+
 sys.path.append("../")
 
 

src/irrevolutions/practice/thinfilm-bar.py

@@ -24,13 +24,23 @@
 import ufl
 import yaml
 from dolfinx.common import list_timings
-from dolfinx.fem import (Constant, Function, FunctionSpace, assemble_scalar,
-                         dirichletbc, form, locate_dofs_geometrical, set_bc)
+from dolfinx.fem import (
+    Constant,
+    Function,
+    FunctionSpace,
+    assemble_scalar,
+    dirichletbc,
+    form,
+    locate_dofs_geometrical,
+    set_bc,
+)
 from dolfinx.io import XDMFFile, gmshio
+
 #
 from mpi4py import MPI
 from petsc4py import PETSc
-from pyvista.plotting.utilities import xvfbimport basix.ufl
+from pyvista.plotting.utilities import xvfb
+import basix.ufl
 
 sys.path.append("../")
 # from meshes.pacman import mesh_pacman
@@ -131,7 +141,9 @@ def main(parameters, storage=None):
     mesh, mts, fts = gmshio.model_to_mesh(gmsh_model, comm, model_rank, tdim)
 
     # functional space
-    element_u = basix.ufl.element("Lagrange", mesh.basix_cell(), degree=1, shape=(tdim,))
+    element_u = basix.ufl.element(
+        "Lagrange", mesh.basix_cell(), degree=1, shape=(tdim,)
+    )
     V_u = FunctionSpace(mesh, element_u)
 
     element_alpha = basix.ufl.element("Lagrange", mesh.basix_cell(), degree=1)
@@ -469,7 +481,7 @@ def load_parameters(file_path):
 
     if "--ell_e" in sys.argv:
         parameters, signature = parameters_vs_elle(
-            parameters= base_parameters, elle=np.float(args.ell_e)
+            parameters=base_parameters, elle=np.float(args.ell_e)
         )
         _storage = (
             f"output/parametric/thinfilm-bar/vs_ell_e/{base_signature}/{signature}"

src/irrevolutions/practice/traction-AT1_cone.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 from utils.viz import plot_scalar, plot_vector
-from pyvista.plotting.utilities import xvfbimport pyvista
+from pyvista.plotting.utilities import xvfb
+import pyvista
 from utils.plots import plot_AMit_load, plot_force_displacement
 import hashlib
 from irrevolutions.utils import ColorPrint
@@ -24,8 +25,16 @@
 import ufl
 import yaml
 from dolfinx.common import list_timings
-from dolfinx.fem import (Constant, Function, FunctionSpace, assemble_scalar,
-                         dirichletbc, form, locate_dofs_geometrical, set_bc)
+from dolfinx.fem import (
+    Constant,
+    Function,
+    FunctionSpace,
+    assemble_scalar,
+    dirichletbc,
+    form,
+    locate_dofs_geometrical,
+    set_bc,
+)
 from dolfinx.io import XDMFFile, gmshio
 from mpi4py import MPI
 from petsc4py import PETSc
@@ -100,7 +109,6 @@
 mesh, mts, fts = gmshio.model_to_mesh(gmsh_model, comm, model_rank, tdim)
 
 
-
 signature = hashlib.md5(str(parameters).encode("utf-8")).hexdigest()
 
 if comm.rank == 0:
@@ -157,7 +165,9 @@
 alpha_ub.interpolate(lambda x: np.ones_like(x[0]))
 
 for f in [zero_u, zero_alpha, u_, alpha_lb, alpha_ub]:
-    f.x.petsc_vec.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
+    f.x.petsc_vec.ghostUpdate(
+        addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD
+    )
 
 bc_u_left = dirichletbc(np.array([0, 0], dtype=PETSc.ScalarType), dofs_u_left, V_u)
 
@@ -242,7 +252,9 @@
 for i_t, t in enumerate(loads):
     # for i_t, t in enumerate([0., .99, 1.0, 1.01]):
     u_.interpolate(lambda x: (t * np.ones_like(x[0]), np.zeros_like(x[1])))
-    u_.x.petsc_vec.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
+    u_.x.petsc_vec.ghostUpdate(
+        addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD
+    )
 
     # update the lower bound
     alpha.x.petsc_vec.copy(alpha_lb.x.petsc_vec)
@@ -367,8 +379,6 @@
     plot_force_displacement(history_data, file=f"{prefix}/{_nameExp}_stress-load.pdf")
 
 
-
-
 #
 xvfb.start_xvfb(wait=0.05)
 pyvista.OFF_SCREEN = True

src/irrevolutions/practice/traction-AT1_first_order.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 from utils.viz import plot_scalar, plot_vector
-from pyvista.plotting.utilities import xvfbimport pyvista
+from pyvista.plotting.utilities import xvfb
+import pyvista
 from utils.plots import plot_AMit_load, plot_force_displacement
 import hashlib
 from irrevolutions.utils import ColorPrint
@@ -24,8 +25,16 @@
 import ufl
 import yaml
 from dolfinx.common import list_timings
-from dolfinx.fem import (Constant, Function, FunctionSpace, assemble_scalar,
-                         dirichletbc, form, locate_dofs_geometrical, set_bc)
+from dolfinx.fem import (
+    Constant,
+    Function,
+    FunctionSpace,
+    assemble_scalar,
+    dirichletbc,
+    form,
+    locate_dofs_geometrical,
+    set_bc,
+)
 from dolfinx.io import XDMFFile, gmshio
 from mpi4py import MPI
 from petsc4py import PETSc
@@ -103,7 +112,6 @@
 mesh, mts, fts = gmshio.model_to_mesh(gmsh_model, comm, model_rank, tdim)
 
 
-
 signature = hashlib.md5(str(parameters).encode("utf-8")).hexdigest()
 
 if comm.rank == 0:
@@ -160,7 +168,9 @@
 alpha_ub.interpolate(lambda x: np.ones_like(x[0]))
 
 for f in [zero_u, zero_alpha, u_, alpha_lb, alpha_ub]:
-    f.x.petsc_vec.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
+    f.x.petsc_vec.ghostUpdate(
+        addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD
+    )
 
 bc_u_left = dirichletbc(np.array([0, 0], dtype=PETSc.ScalarType), dofs_u_left, V_u)
 
@@ -245,7 +255,9 @@
 for i_t, t in enumerate(loads):
     # for i_t, t in enumerate([0., .99, 1.0, 1.01]):
     u_.interpolate(lambda x: (t * np.ones_like(x[0]), np.zeros_like(x[1])))
-    u_.x.petsc_vec.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
+    u_.x.petsc_vec.ghostUpdate(
+        addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD
+    )
 
     # update the lower bound
     alpha.x.petsc_vec.copy(alpha_lb.x.petsc_vec)
@@ -362,8 +374,6 @@
     plot_force_displacement(history_data, file=f"{prefix}/{_nameExp}_stress-load.pdf")
 
 
-
-
 #
 xvfb.start_xvfb(wait=0.05)
 pyvista.OFF_SCREEN = True

src/irrevolutions/practice/traction-AT2_cone.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 from utils.viz import plot_scalar, plot_vector
-from pyvista.plotting.utilities import xvfbimport pyvista
+from pyvista.plotting.utilities import xvfb
+import pyvista
 from utils.plots import plot_AMit_load, plot_force_displacement
 import hashlib
 from irrevolutions.utils import ColorPrint
@@ -22,8 +23,16 @@
 import petsc4py
 import ufl
 import yaml
-from dolfinx.fem import (Constant, Function, FunctionSpace, assemble_scalar,
-                         dirichletbc, form, locate_dofs_geometrical, set_bc)
+from dolfinx.fem import (
+    Constant,
+    Function,
+    FunctionSpace,
+    assemble_scalar,
+    dirichletbc,
+    form,
+    locate_dofs_geometrical,
+    set_bc,
+)
 from dolfinx.io import XDMFFile, gmshio
 from mpi4py import MPI
 from petsc4py import PETSc
@@ -134,7 +143,9 @@ def w(self, alpha):
 alpha_ub.interpolate(lambda x: np.ones_like(x[0]))
 
 for f in [zero_u, zero_alpha, u_, alpha_lb, alpha_ub]:
-    f.x.petsc_vec.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
+    f.x.petsc_vec.ghostUpdate(
+        addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD
+    )
 
 bc_u_left = dirichletbc(np.array([0, 0], dtype=PETSc.ScalarType), dofs_u_left, V_u)
 bc_u_right = dirichletbc(u_, dofs_u_right)
@@ -203,7 +214,9 @@ def w(self, alpha):
 
 for i_t, t in enumerate(loads):
     u_.interpolate(lambda x: (t * np.ones_like(x[0]), np.zeros_like(x[1])))
-    u_.x.petsc_vec.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
+    u_.x.petsc_vec.ghostUpdate(
+        addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD
+    )
 
     alpha.x.petsc_vec.copy(alpha_lb.x.petsc_vec)
     alpha_lb.x.petsc_vec.ghostUpdate(
@@ -310,7 +323,6 @@ def w(self, alpha):
     plot_force_displacement(history_data, file=f"{prefix}/{_nameExp}_stress-load.pdf")
 
 
-
 xvfb.start_xvfb(wait=0.05)
 pyvista.OFF_SCREEN = True