From 364a1b97468ae2fe093540e095fc44a9bf191eaf Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Thu, 31 Oct 2024 12:19:37 -0400
Subject: [PATCH 1/3] petsc_options as args

---
 src/festim/hydrogen_transport_problem.py |  2 ++
 src/festim/problem.py                    | 18 ++++++++++++++----
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/src/festim/hydrogen_transport_problem.py b/src/festim/hydrogen_transport_problem.py
index ddefd98f1..6ff1cd98f 100644
--- a/src/festim/hydrogen_transport_problem.py
+++ b/src/festim/hydrogen_transport_problem.py
@@ -149,6 +149,7 @@ def __init__(
         settings=None,
         exports=None,
         traps=None,
+        petsc_options=None,
     ):
         super().__init__(
             mesh=mesh,
@@ -157,6 +158,7 @@ def __init__(
             subdomains=subdomains,
             boundary_conditions=boundary_conditions,
             settings=settings,
+            petsc_options=petsc_options,
         )
 
         self.species = species or []
diff --git a/src/festim/problem.py b/src/festim/problem.py
index 223f79ad1..76ecaf326 100644
--- a/src/festim/problem.py
+++ b/src/festim/problem.py
@@ -7,6 +7,7 @@
 import ufl
 from dolfinx import fem
 from dolfinx.nls.petsc import NewtonSolver
+from petsc4py import PETSc
 
 import festim as F
 from festim.mesh.mesh import Mesh as _Mesh
@@ -41,7 +42,7 @@ def __init__(
         subdomains=None,
         boundary_conditions=None,
         settings=None,
-        petcs_options=None,
+        petsc_options=None,
     ) -> None:
         self.mesh = mesh
         # for arguments to initialise as empty list
@@ -60,7 +61,7 @@ def __init__(
         self.formulation = None
         self.bc_forms = []
         self.show_progress_bar = True
-        self.petcs_options = petcs_options
+        self.petsc_options = petsc_options
 
     @property
     def volume_subdomains(self):
@@ -123,12 +124,21 @@ def create_solver(self):
         self.solver.rtol = self.settings.rtol
         self.solver.max_it = self.settings.max_iterations
 
-        if self.petcs_options is None:
-            ksp = self.solver.krylov_solver
+        ksp = self.solver.krylov_solver
+
+        if self.petsc_options is None:
             ksp.setType("preonly")
             ksp.getPC().setType("lu")
             ksp.getPC().setFactorSolverType("mumps")
             ksp.setErrorIfNotConverged(True)
+        else:
+            # Set PETSc options
+            opts = PETSc.Options()
+            for k, v in self.petsc_options.items():
+                opts[k] = v
+            ksp.setFromOptions()
+
+            print(opts)
 
     def run(self):
         """Runs the model"""

From 3f9767fbd2b52b3a9a230f62d8225470518e2ae3 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Thu, 31 Oct 2024 12:56:45 -0400
Subject: [PATCH 2/3] added prefix

---
 src/festim/problem.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/festim/problem.py b/src/festim/problem.py
index 76ecaf326..ff4b36c26 100644
--- a/src/festim/problem.py
+++ b/src/festim/problem.py
@@ -134,12 +134,11 @@ def create_solver(self):
         else:
             # Set PETSc options
             opts = PETSc.Options()
+            option_prefix = ksp.getOptionsPrefix()
             for k, v in self.petsc_options.items():
-                opts[k] = v
+                opts[f"{option_prefix}{k}"] = v
             ksp.setFromOptions()
 
-            print(opts)
-
     def run(self):
         """Runs the model"""
 

From dcb89e917fee13de189456dd25b163de013262db Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Thu, 31 Oct 2024 15:37:06 -0400
Subject: [PATCH 3/3] added a test that adds a unused variable to the petsc
 options

---
 test/system_tests/test_misc.py | 39 ++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 test/system_tests/test_misc.py

diff --git a/test/system_tests/test_misc.py b/test/system_tests/test_misc.py
new file mode 100644
index 000000000..ba622cb1b
--- /dev/null
+++ b/test/system_tests/test_misc.py
@@ -0,0 +1,39 @@
+import dolfinx
+import festim as F
+import numpy as np
+
+
+def test_petsc_options():
+    my_model = F.HydrogenTransportProblem(
+        petsc_options={
+            "ksp_type": "preonly",
+            "pc_type": "lu",
+            "pc_factor_mat_solver_type": "mumps",
+            "coucoucou": 3,
+        }
+    )
+
+    tungsten = F.Material(D_0=1, E_D=0, K_S_0=1, E_K_S=0)
+
+    my_model.mesh = F.Mesh1D(vertices=np.linspace(0, 1, num=100))
+    vol1 = F.VolumeSubdomain1D(id=1, material=tungsten, borders=[0, 1])
+    surface1 = F.SurfaceSubdomain1D(id=4, x=0)
+    surface2 = F.SurfaceSubdomain1D(id=5, x=1)
+
+    my_model.subdomains = [vol1, surface1, surface2]
+
+    mobile = F.Species(name="H", mobile=True)
+
+    my_model.species = [mobile]
+
+    my_model.temperature = 600
+
+    my_model.boundary_conditions = [
+        F.FixedConcentrationBC(subdomain=surface1, species=mobile, value=1),
+        F.FixedConcentrationBC(subdomain=surface2, species=mobile, value=0),
+    ]
+
+    my_model.settings = F.Settings(atol=1e-6, rtol=1e-6, transient=False)
+
+    my_model.initialise()
+    my_model.run()