Merge branch 'main' into pep639

Author: finsberg

.cspell_dict.txt

@@ -42,6 +42,7 @@ finsberg
 Francesco
 functionspace
 geodir
+gmsh
 gradu
 Grice
 Guccione

demo/time_dependent_land_circ_biv.py

@@ -85,11 +85,11 @@
 robin_base = pulse.RobinBC(value=alpha_base, marker=geometry.markers["BASE"][0])
 
 
-lvv_initial = geometry.volume("ENDO_LV")
+lvv_initial = geo.mesh.comm.allreduce(geometry.volume("ENDO_LV"), op=MPI.SUM)
 lv_volume = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(lvv_initial))
 lv_cavity = pulse.problem.Cavity(marker="ENDO_LV", volume=lv_volume)
 
-rvv_initial = geometry.volume("ENDO_RV")
+rvv_initial = geo.mesh.comm.allreduce(geometry.volume("ENDO_RV"), op=MPI.SUM)
 rv_volume = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(rvv_initial))
 rv_cavity = pulse.problem.Cavity(marker="ENDO_RV", volume=rv_volume)
 
@@ -179,7 +179,8 @@ def solve_beat(times, states, dt, p, V_index, Ca_index, Vs, Cais, Tas):
     ax[2, 1].set_xlabel("Time [ms]")
 
     fig.savefig(outdir / "Ta_ORdLand.png")
-    np.save(state_file, y)
+    if comm.rank == 0:
+        np.save(state_file, y)
 
 y = np.load(state_file)
 
@@ -287,9 +288,7 @@ def p_BiV_func(V_LV, V_RV, t):
 
 mL = circulation.units.ureg("mL")
 add_units = False
-surface_area_lv = geometry.surface_area("ENDO_LV")
 lvv_init = geo.mesh.comm.allreduce(geometry.volume("ENDO_LV", u=problem.u), op=MPI.SUM) * 1e6 * 1.0  # Increase the volume by 5%
-surface_area_rv = geometry.surface_area("ENDO_RV")
 rvv_init = geo.mesh.comm.allreduce(geometry.volume("ENDO_RV", u=problem.u), op=MPI.SUM) * 1e6 * 1.0  # Increase the volume by 5%
 logger.info(f"Initial volume (LV): {lvv_init} mL and (RV): {rvv_init} mL")
 init_state = {"V_LV": lvv_initial * 1e6 * mL, "V_RV": rvv_initial * 1e6 * mL}

tests/test_geometry.py

@@ -1,5 +1,6 @@
 import math
 
+import gmsh
 import numpy as np
 import pytest
 import ufl
@@ -111,6 +112,7 @@ def test_HeartGeometry_lv(tmp_path):
     # assert np.isclose(geo2.volume("ENDO"), endo_volume, atol=1e-7)
 
 
+@pytest.mark.skipif(gmsh.__version__ == "4.14.0", reason="GMSH 4.14.0 has a bug with fuse")
 def test_HeartGeometry_biv(tmp_path):
     geo1 = cardiac_geometries.mesh.biv_ellipsoid(
         outdir=tmp_path,