Merge branch 'development' into Quick_Start_Docs

.github/workflows/publish.yml

@@ -6,7 +6,6 @@ on:
     branches:
       - main # Occurs on protected branch through PR
       - development
-      - Quick_Start_Docs # Testing branch (delete later)
 
 name: Quarto Publish
 

setup.py

@@ -10,19 +10,7 @@
 import numpy
 import petsc4py
 
-if os.environ.get("CC") is None:
-    import warnings
-
-    warnings.warn(
-        "CC environment variable not set. Using mpi4py's compiler configuration"
-    )
-    # Get CC from mpi4py
-    import mpi4py
-
-    conf = mpi4py.get_config()
-    os.environ["CC"] = conf["mpicc"]
-
-# PETSc version check - 3.16 or higher
+# PETSc version check - 3.18 or higher
 from petsc4py import PETSc
 
 petscVer = PETSc.Sys().getVersion()
@@ -35,7 +23,6 @@
     )
     raise RuntimeError(msg)
 
-
 def configure():
 
     INCLUDE_DIRS = []

src/underworld3/function/_function.pyx

@@ -763,7 +763,7 @@ def dm_swarm_get_migrate_type(swarm):
 
     return mtype
 
-def dm_swarm_set_migrate_type(swarm, mtype:PETSc.DMSwarm.MigrateType):
+def dm_swarm_set_migrate_type(swarm, mtype:PETsc.DMSwarm.MigrateType):
 
     cdef DM dm = swarm.dm
     cdef PetscErrorCode ierr

src/underworld3/meshing.py

@@ -206,6 +206,8 @@ class boundary_normals_3D(Enum):
 
     def box_return_coords_to_bounds(coords):
 
+        epsilon = 1.0e-3
+
         x00s = coords[:, 0] < minCoords[0]
         x01s = coords[:, 0] > maxCoords[0]
         x10s = coords[:, 1] < minCoords[1]
@@ -215,14 +217,14 @@ def box_return_coords_to_bounds(coords):
             x20s = coords[:, 2] < minCoords[2]
             x21s = coords[:, 2] > maxCoords[2]
 
-        coords[x00s, 0] = minCoords[0]
-        coords[x01s, 0] = maxCoords[0]
-        coords[x10s, 1] = minCoords[1]
-        coords[x11s, 1] = maxCoords[1]
+        coords[x00s, 0] = minCoords[0] + epsilon
+        coords[x01s, 0] = maxCoords[0] - epsilon
+        coords[x10s, 1] = minCoords[1] + epsilon
+        coords[x11s, 1] = maxCoords[1] - epsilon
 
         if dim == 3:
-            coords[x20s, 2] = minCoords[2]
-            coords[x21s, 2] = maxCoords[2]
+            coords[x20s, 2] = minCoords[2] + epsilon
+            coords[x21s, 2] = maxCoords[2] - epsilon
 
         return coords
 

src/underworld3/swarm.py

@@ -1,3 +1,4 @@
+from posixpath import pardir
 import petsc4py.PETSc as PETSc
 
 import numpy as np
@@ -1935,6 +1936,8 @@ def __init__(
             nswarm,
             vtype=trackedVariable.vtype,
             _proxy=False,
+            # proxy_degree=trackedVariable.degree,
+            # proxy_continuous=trackedVariable.continuous,
             varsymbol=symbol,
         )
 

src/underworld3/systems/ddt.py

@@ -216,7 +216,6 @@ def update_pre_solve(
 
         # We use the u_star variable as a working value here so we have to work backwards
         # so we don't over-write the history terms
-        #
 
         for i in range(self.order - 1, -1, -1):
             with self._nswarm_psi.access(self._nswarm_psi._X0):
@@ -314,7 +313,6 @@ def update_pre_solve(
             # the data when we put it back onto the nodes
 
             with self._nswarm_psi.access():
-
                 orig_index = self._nswarm_psi._nI0.data.copy().reshape(-1)
 
                 with self.mesh.access(self._workVar):

tests/parallel/ptest_002_projection.py

@@ -45,6 +45,8 @@
     print(s_values.data[0:10,0])
     s_values.data[:, 0] = 1.0 # uw.function.evalf(sympy.sympify(1), s_values.coords)
 
+print(f"{uw.mpi.rank} - solve projection", flush=True)
+mesh1.dm.view()
 
 scalar_projection.solve()