Fix for new biv geometry

Author: finsberg

demo/time_dependent_land_circ_biv.py

@@ -46,7 +46,30 @@
     comm=comm,
     folder=geodir,
 )
-geo.mesh.geometry.x[:] *= 3e-2
+# Scale the geometry to meters and adjust the size so that LV and RV volumes are reasonable
+geo.mesh.geometry.x[:] *= 1.4e-2
+
+# Now we need to redefine the markers to have so that facets on the endo- and epicardium combine both
+# free wall and the septum.
+
+markers = {"ENDO_LV": [1, 2], "ENDO_RV": [2, 2], "BASE": [3, 2], "EPI": [4, 2]}
+marker_values = geo.ffun.values.copy()
+marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_ENDO_FW"][0]))] = markers["ENDO_LV"][0]
+marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_SEPTUM"][0]))] = markers["ENDO_LV"][0]
+marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_ENDO_FW"][0]))] = markers["ENDO_RV"][0]
+marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_SEPTUM"][0]))] = markers["ENDO_RV"][0]
+marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["BASE"][0]))] = markers["BASE"][0]
+marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_EPI_FW"][0]))] = markers["EPI"][0]
+marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_EPI_FW"][0]))] = markers["EPI"][0]
+
+geo.markers = markers
+ffun = dolfinx.mesh.meshtags(
+    geo.mesh,
+    geo.ffun.dim,
+    geo.ffun.indices,
+    marker_values,
+)
+geo.ffun = ffun
 
 geometry = pulse.HeartGeometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 6})
 
@@ -182,6 +205,7 @@ def solve_beat(times, states, dt, p, V_index, Ca_index, Vs, Cais, Tas):
     if comm.rank == 0:
         np.save(state_file, y)
 
+comm.barrier()
 y = np.load(state_file)