Merge pull request #105 from kumiori/andres-practice

Andres practice

demo/demo_elasticity.py

@@ -17,13 +17,13 @@
 from dolfinx.io import XDMFFile, gmshio
 from mpi4py import MPI
 from petsc4py import PETSc
-from pyvista.utilities import xvfb
-
+from pyvista.plotting.utilities import xvfb
 from irrevolutions.meshes.primitives import mesh_bar_gmshapi
 from irrevolutions.models import ElasticityModel
 from irrevolutions.solvers import SNESSolver as ElasticitySolver
 from irrevolutions.utils.viz import plot_vector
 import basix.ufl
+
 logging.basicConfig(level=logging.INFO)
 
 
@@ -69,7 +69,7 @@
 element_u = basix.ufl.element("Lagrange", mesh.basix_cell(), degree=1, shape=(tdim,))
 V_u = dolfinx.fem.functionspace(mesh, element_u)
 V_ux = dolfinx.fem.functionspace(
-    mesh,basix.ufl.element("Lagrange", mesh.basix_cell(), degree=1)
+    mesh, basix.ufl.element("Lagrange", mesh.basix_cell(), degree=1)
 )
 
 # Define the state
@@ -96,7 +96,9 @@
 ux_.interpolate(lambda x: np.ones_like(x[0]))
 
 for f in [zero_u, ux_]:
-    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
+    )
 
 bcs_u = [
     dolfinx.fem.dirichletbc(zero_u, dofs_u_left),
@@ -133,7 +135,9 @@
 
 for i_t, t in enumerate(loads):
     u_.interpolate(lambda x: (t * np.ones_like(x[0]), 0 * np.ones_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
+    )
 
     logging.info(f"-- Solving for t = {t:3.2f} --")
 

demo/demo_traction.py

@@ -15,19 +15,27 @@
 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.utilities import xvfb
-
+from pyvista.plotting.utilities import xvfb
 from irrevolutions.algorithms.am import AlternateMinimisation, HybridSolver
 from irrevolutions.meshes.primitives import mesh_bar_gmshapi
 from irrevolutions.models import DamageElasticityModel as Brittle
 from irrevolutions.utils.plots import plot_energies, plot_force_displacement
 from irrevolutions.utils.viz import plot_scalar, plot_vector
 import basix.ufl
+
 logging.basicConfig(level=logging.INFO)
 
 
@@ -115,7 +123,9 @@
 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)
 
@@ -177,7 +187,9 @@
 
 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
+    )
 
     # update the lower bound
     alpha.x.petsc_vec.copy(alpha_lb.x.petsc_vec)

demo/demo_vi.py

@@ -16,8 +16,7 @@
 from dolfinx.fem.assemble import assemble_scalar
 from dolfinx.mesh import CellType
 from mpi4py import MPI
-from pyvista.utilities import xvfb
-
+from pyvista.plotting.utilities import xvfb
 from irrevolutions.solvers import SNESSolver
 from irrevolutions.utils.viz import plot_profile, plot_scalar
 

playground/IDRIS-CAMPAING-HYDRA/parameters/1d_parameters.yaml

@@ -0,0 +1,128 @@
+# === Loading === #
+loading:
+    min: 0
+    max: 1.001
+    steps: 10
+
+#  === Geometry === #
+geometry:
+    geometric_dimension: 2
+    geom_type: "bar"
+    Lx: 1.
+    Ly: .1
+    lc: 0.02
+    mesh_size_factor: 3
+
+#  === Material === #
+model:
+    E: 1.
+    sigma_D0: 1.
+    ell: 0.1
+    model_dimension: 1
+    model_type: "1D"
+    kappa: 10.
+    # could be "2D"/ "3D" / "plane_stress" / "plane_strain"
+# === Solver === #
+solvers:
+    elasticity:
+        prefix: elasticity
+        snes:
+            snes_type: newtontr
+            snes_stol: 1e-8
+            snes_atol: 1e-8
+            snes_rtol: 1e-8
+            snes_max_it: 200
+            # snes_divergence_tolerance: -1.0
+            snes_monitor: ""
+            ksp_type: preonly
+            pc_type: lu
+            pc_factor_mat_solver_type: mumps
+
+    # Damage solver parameters
+    damage:
+        type: SNES
+        prefix: damage
+        snes:
+            # Options in the case of SNES solver
+            snes_type: vinewtonrsls
+            snes_linesearch_type: basic
+            ksp_type: preonly
+            pc_type: lu
+            pc_factor_mat_solver_type: mumps
+            snes_atol: 1.0e-8
+            snes_rtol: 1.0e-8
+            # snes_stol: 0.0
+            snes_max_it: 50
+            # snes_divergence_tolerance: -1.0
+            snes_monitor: ""
+        tao:
+            # Options in the case of TAO solver
+            tao_type: tron
+            tao_gpcg_maxpgits: 50
+            tao_max_it: 100
+            tao_steptol: 1.0e-7
+            tao_gatol: 1.0e-8
+            tao_grtol: 1.0e-8
+            tao_gttol: 1.0e-8
+            tao_catol: 0.
+            tao_crtol: 0.
+            tao_ls_ftol: 1e-5
+            tao_ls_gtol: 1e-5
+            tao_ls_rtol: 1e-5
+            ksp_rtol: 1e-6
+            tao_ls_stepmin: 1e-8
+            tao_ls_stepmax: 1e6
+            pc_type: lu
+            tao_monitor: ""
+
+    # Damage Elasticity Solver parameters
+    damage_elasticity:
+        max_it: 200
+        alpha_rtol: 1.0e-4
+        criterion: "alpha_H1"
+
+    newton:
+        snes_type: "vinewtonrsls"
+        snes_linesearch_type: "basic"
+        snes_rtol: 1.0e-8
+        snes_atol: 1.0e-8
+        snes_max_it: 30
+        snes_monitor: ""
+        linesearch_damping: 0.5
+
+stability:
+    order: 3
+    maxmodes: 10
+    checkstability: "True"
+    continuation: "False"
+    cont_rtol: 1.0e-10
+    inactiveset_gatol: 1.e-6
+    inactiveset_pwtol: 1.e-6
+    is_elastic_tol: 1.e-6
+
+    inertia:
+        # MUMPS
+        ksp_type: "preonly"
+        pc_type: "cholesky"
+        pc_factor_mat_solver_type: "mumps"
+        mat_mumps_icntl_24: 1
+        mat_mumps_icntl_13: 1
+
+    eigen:
+        eps_type: "krylovschur"
+        # eps_type: "lanczos"
+        # eps_monitor: ""
+        eps_tol: 1.e-5
+        eig_rtol: 1.e-8
+        eps_max_it: 100
+
+    cone:
+        cone_atol: 1.0e-06
+        cone_max_it: 3000
+        cone_rtol: 1.0e-06
+        maxmodes: 3
+        scaling: 1.e-5
+
+    linesearch:
+        order: 4
+        method: 'min'

playground/IDRIS-CAMPAING-HYDRA/parameters/2d_parameters.yaml

@@ -0,0 +1,127 @@
+# === Loading === #
+loading:
+    min: 0
+    max: 1.001
+    steps: 10
+
+#  === Geometry === #
+geometry:
+    geometric_dimension: 2
+    geom_type: "circle"
+    R: 1.
+    lc: 0.02
+    mesh_size_factor: 3
+
+#  === Material === #
+model:
+    E: 1.
+    sigma_D0: 1.
+    ell: 0.1
+    model_dimension: 1
+    model_type: "2D"
+    kappa: 10.
+    # could be "2D"/ "3D" / "plane_stress" / "plane_strain"
+# === Solver === #
+solvers:
+    elasticity:
+        prefix: elasticity
+        snes:
+            snes_type: newtontr
+            snes_stol: 1e-8
+            snes_atol: 1e-8
+            snes_rtol: 1e-8
+            snes_max_it: 200
+            # snes_divergence_tolerance: -1.0
+            snes_monitor: ""
+            ksp_type: preonly
+            pc_type: lu
+            pc_factor_mat_solver_type: mumps
+
+    # Damage solver parameters
+    damage:
+        type: SNES
+        prefix: damage
+        snes:
+            # Options in the case of SNES solver
+            snes_type: vinewtonrsls
+            snes_linesearch_type: basic
+            ksp_type: preonly
+            pc_type: lu
+            pc_factor_mat_solver_type: mumps
+            snes_atol: 1.0e-8
+            snes_rtol: 1.0e-8
+            # snes_stol: 0.0
+            snes_max_it: 50
+            # snes_divergence_tolerance: -1.0
+            snes_monitor: ""
+        tao:
+            # Options in the case of TAO solver
+            tao_type: tron
+            tao_gpcg_maxpgits: 50
+            tao_max_it: 100
+            tao_steptol: 1.0e-7
+            tao_gatol: 1.0e-8
+            tao_grtol: 1.0e-8
+            tao_gttol: 1.0e-8
+            tao_catol: 0.
+            tao_crtol: 0.
+            tao_ls_ftol: 1e-5
+            tao_ls_gtol: 1e-5
+            tao_ls_rtol: 1e-5
+            ksp_rtol: 1e-6
+            tao_ls_stepmin: 1e-8
+            tao_ls_stepmax: 1e6
+            pc_type: lu
+            tao_monitor: ""
+
+    # Damage Elasticity Solver parameters
+    damage_elasticity:
+        max_it: 200
+        alpha_rtol: 1.0e-4
+        criterion: "alpha_H1"
+
+    newton:
+        snes_type: "vinewtonrsls"
+        snes_linesearch_type: "basic"
+        snes_rtol: 1.0e-8
+        snes_atol: 1.0e-8
+        snes_max_it: 30
+        snes_monitor: ""
+        linesearch_damping: 0.5
+
+stability:
+    order: 3
+    maxmodes: 10
+    checkstability: "True"
+    continuation: "False"
+    cont_rtol: 1.0e-10
+    inactiveset_gatol: 1.e-6
+    inactiveset_pwtol: 1.e-6
+    is_elastic_tol: 1.e-6
+
+    inertia:
+        # MUMPS
+        ksp_type: "preonly"
+        pc_type: "cholesky"
+        pc_factor_mat_solver_type: "mumps"
+        mat_mumps_icntl_24: 1
+        mat_mumps_icntl_13: 1
+
+    eigen:
+        eps_type: "krylovschur"
+        # eps_type: "lanczos"
+        # eps_monitor: ""
+        eps_tol: 1.e-5
+        eig_rtol: 1.e-8
+        eps_max_it: 100
+
+    cone:
+        cone_atol: 1.0e-06
+        cone_max_it: 3000
+        cone_rtol: 1.0e-06
+        maxmodes: 3
+        scaling: 1.e-5
+
+    linesearch:
+        order: 4
+        method: 'min'