Rename python package from fenicsx_pulse to pulse

Author: finsberg

demo/benchmark/problem1.py

@@ -6,7 +6,7 @@
 import numpy as np
 import dolfinx
 from dolfinx import log
-import fenicsx_pulse
+import pulse
 
 # Next we create the beam, which should have a length og 10 mm and a width of 1 mm
 
@@ -20,43 +20,43 @@
 left = 1
 bottom = 2
 boundaries = [
-    fenicsx_pulse.Marker(name="left", marker=left, dim=2, locator=lambda x: np.isclose(x[0], 0)),
-    fenicsx_pulse.Marker(name="bottom", marker=bottom, dim=2, locator=lambda x: np.isclose(x[2], 0)),
+    pulse.Marker(name="left", marker=left, dim=2, locator=lambda x: np.isclose(x[0], 0)),
+    pulse.Marker(name="bottom", marker=bottom, dim=2, locator=lambda x: np.isclose(x[2], 0)),
 ]
 
 # and assemble the geometry
 
-geo = fenicsx_pulse.Geometry(
+geo = pulse.Geometry(
     mesh=mesh,
     boundaries=boundaries,
     metadata={"quadrature_degree": 4},
 )
 
-# The material model used in this benchmark is the {py:class}`Guccione <fenicsx_pulse.material_models.guccione.Guccione>` model.
+# The material model used in this benchmark is the {py:class}`Guccione <pulse.material_models.guccione.Guccione>` model.
 
 material_params = {
-    "C": fenicsx_pulse.Variable(dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(2.0)), "kPa"),
+    "C": pulse.Variable(dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(2.0)), "kPa"),
     "bf": dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(8.0)),
     "bt": dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(2.0)),
     "bfs": dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(4.0)),
 }
 f0 = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type((1.0, 0.0, 0.0)))
 s0 = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type((0.0, 1.0, 0.0)))
 n0 = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type((0.0, 0.0, 1.0)))
-material = fenicsx_pulse.Guccione(f0=f0, s0=s0, n0=n0, **material_params)
+material = pulse.Guccione(f0=f0, s0=s0, n0=n0, **material_params)
 
 # There are now active contraction, so we choose a pure passive model
 
-active_model = fenicsx_pulse.active_model.Passive()
+active_model = pulse.active_model.Passive()
 
 # and the model should be incompressible
 
-comp_model = fenicsx_pulse.Incompressible()
+comp_model = pulse.Incompressible()
 
 # We can now assemble the `CardiacModel`
 #
 
-model = fenicsx_pulse.CardiacModel(
+model = pulse.CardiacModel(
     material=material,
     active=active_model,
     compressibility=comp_model,
@@ -79,15 +79,15 @@ def dirichlet_bc(
 # and the traction force
 
 traction = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(0.0))
-neumann = fenicsx_pulse.NeumannBC(traction=traction, marker=bottom)
+neumann = pulse.NeumannBC(traction=traction, marker=bottom)
 
 # We assemble all the boundary conditions
 
-bcs = fenicsx_pulse.BoundaryConditions(dirichlet=(dirichlet_bc,), neumann=(neumann,))
+bcs = pulse.BoundaryConditions(dirichlet=(dirichlet_bc,), neumann=(neumann,))
 
 # and create a mechanics problem
 
-problem = fenicsx_pulse.StaticProblem(model=model, geometry=geo, bcs=bcs)
+problem = pulse.StaticProblem(model=model, geometry=geo, bcs=bcs)
 
 # Now let us turn on some more logging
 

demo/benchmark/problem2.py

@@ -10,7 +10,7 @@
 import numpy as np
 import math
 import cardiac_geometries
-import fenicsx_pulse
+import pulse
 
 
 logging.basicConfig(level=logging.INFO)
@@ -40,34 +40,34 @@
     folder=geodir,
 )
 
-# Now, lets convert the geometry to a `fenicsx_pulse.Geometry` object.
+# Now, lets convert the geometry to a `pulse.Geometry` object.
 
-geometry = fenicsx_pulse.HeartGeometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 4})
+geometry = pulse.HeartGeometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 4})
 
 
-# The material model used in this benchmark is the {py:class}`Guccione <fenicsx_pulse.material_models.guccione.Guccione>` model.
+# The material model used in this benchmark is the {py:class}`Guccione <pulse.material_models.guccione.Guccione>` model.
 
 material_params = {
     "C": dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(10.0)),
     "bf": dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1.0)),
     "bt": dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1.0)),
     "bfs": dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1.0)),
 }
-material = fenicsx_pulse.Guccione(**material_params)
+material = pulse.Guccione(**material_params)
 
 
 # There are now active contraction, so we choose a pure passive model
 
-active_model = fenicsx_pulse.active_model.Passive()
+active_model = pulse.active_model.Passive()
 
 # and the model should be incompressible
 
-comp_model = fenicsx_pulse.Incompressible()
+comp_model = pulse.Incompressible()
 
 
 # and assembles the `CardiacModel`
 
-model = fenicsx_pulse.CardiacModel(
+model = pulse.CardiacModel(
     material=material,
     active=active_model,
     compressibility=comp_model,
@@ -78,19 +78,19 @@
 # We apply a traction in endocardium
 
 traction = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0))
-neumann = fenicsx_pulse.NeumannBC(
-    traction=fenicsx_pulse.Variable(traction, "kPa"),
+neumann = pulse.NeumannBC(
+    traction=pulse.Variable(traction, "kPa"),
     marker=geo.markers["ENDO"][0],
 )
 
 # and finally combine all the boundary conditions
 
-bcs = fenicsx_pulse.BoundaryConditions(neumann=(neumann,))
+bcs = pulse.BoundaryConditions(neumann=(neumann,))
 
 # and create a Mixed problem
 
-problem = fenicsx_pulse.StaticProblem(
-    model=model, geometry=geometry, bcs=bcs, parameters={"base_bc": fenicsx_pulse.BaseBC.fixed},
+problem = pulse.StaticProblem(
+    model=model, geometry=geometry, bcs=bcs, parameters={"base_bc": pulse.BaseBC.fixed},
 )
 
 # Now we can solve the problem
@@ -183,12 +183,12 @@
 U = dolfinx.fem.Function(problem.u.function_space)
 U.interpolate(lambda x: (x[0], x[1], x[2]))
 
-endo_apex_coord = fenicsx_pulse.utils.evaluate_at_vertex_tag(U, geo.vfun, geo.markers["ENDOPT"][0])
-u_endo_apex = fenicsx_pulse.utils.evaluate_at_vertex_tag(problem.u, geo.vfun, geo.markers["ENDOPT"][0])
-endo_apex_pos = fenicsx_pulse.utils.gather_broadcast_array(geo.mesh.comm, endo_apex_coord + u_endo_apex)
+endo_apex_coord = pulse.utils.evaluate_at_vertex_tag(U, geo.vfun, geo.markers["ENDOPT"][0])
+u_endo_apex = pulse.utils.evaluate_at_vertex_tag(problem.u, geo.vfun, geo.markers["ENDOPT"][0])
+endo_apex_pos = pulse.utils.gather_broadcast_array(geo.mesh.comm, endo_apex_coord + u_endo_apex)
 print(f"\nGet longitudinal position of endocardial apex: {endo_apex_pos[0, 0]:4f} mm")
 
-epi_apex_coord = fenicsx_pulse.utils.evaluate_at_vertex_tag(U, geo.vfun, geo.markers["EPIPT"][0])
-u_epi_apex = fenicsx_pulse.utils.evaluate_at_vertex_tag(problem.u, geo.vfun, geo.markers["EPIPT"][0])
-epi_apex_pos = fenicsx_pulse.utils.gather_broadcast_array(geo.mesh.comm, epi_apex_coord + u_epi_apex)
+epi_apex_coord = pulse.utils.evaluate_at_vertex_tag(U, geo.vfun, geo.markers["EPIPT"][0])
+u_epi_apex = pulse.utils.evaluate_at_vertex_tag(problem.u, geo.vfun, geo.markers["EPIPT"][0])
+epi_apex_pos = pulse.utils.gather_broadcast_array(geo.mesh.comm, epi_apex_coord + u_epi_apex)
 print(f"\nGet longitudinal position of epicardial apex: {epi_apex_pos[0, 0]:4f} mm")

demo/benchmark/problem3.py

@@ -10,7 +10,7 @@
 import numpy as np
 import math
 import cardiac_geometries
-import fenicsx_pulse
+import pulse
 
 # Next we will create the geometry and save it in the folder called `lv_ellipsoid`. Now we will also generate fibers and use a sixth order quadrature space for the fibers
 
@@ -43,35 +43,35 @@
     folder=geodir,
 )
 
-# Now, lets convert the geometry to a `fenicsx_pulse.Geometry` object.
+# Now, lets convert the geometry to a `pulse.Geometry` object.
 
-geometry = fenicsx_pulse.HeartGeometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 6})
+geometry = pulse.HeartGeometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 6})
 
 
-# The material model used in this benchmark is the {py:class}`Guccione <fenicsx_pulse.material_models.guccione.Guccione>` model.
+# The material model used in this benchmark is the {py:class}`Guccione <pulse.material_models.guccione.Guccione>` model.
 
 material_params = {
     "C": dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(2.0)),
     "bf": dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(8.0)),
     "bt": dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(2.0)),
     "bfs": dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(4.0)),
 }
-material = fenicsx_pulse.Guccione(f0=geo.f0, s0=geo.s0, n0=geo.n0, **material_params)
+material = pulse.Guccione(f0=geo.f0, s0=geo.s0, n0=geo.n0, **material_params)
 
 
 # We use an active stress approach with 60% transverse active stress
 
 Ta = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0))
-active_model = fenicsx_pulse.ActiveStress(geo.f0, activation=fenicsx_pulse.Variable(Ta, "kPa"))
+active_model = pulse.ActiveStress(geo.f0, activation=pulse.Variable(Ta, "kPa"))
 
 # and the model should be incompressible
 
-comp_model = fenicsx_pulse.Incompressible()
+comp_model = pulse.Incompressible()
 
 
 # and assembles the `CardiacModel`
 
-model = fenicsx_pulse.CardiacModel(
+model = pulse.CardiacModel(
     material=material,
     active=active_model,
     compressibility=comp_model,
@@ -82,19 +82,19 @@
 # We apply a traction in endocardium
 
 traction = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0))
-neumann = fenicsx_pulse.NeumannBC(
-    traction=fenicsx_pulse.Variable(traction, "kPa"),
+neumann = pulse.NeumannBC(
+    traction=pulse.Variable(traction, "kPa"),
     marker=geo.markers["ENDO"][0],
 )
 
 # and finally combine all the boundary conditions
 
-bcs = fenicsx_pulse.BoundaryConditions(neumann=(neumann,))
+bcs = pulse.BoundaryConditions(neumann=(neumann,))
 
 # and create a Mixed problem
 
-problem = fenicsx_pulse.StaticProblem(
-    model=model, geometry=geometry, bcs=bcs, parameters={"base_bc": fenicsx_pulse.BaseBC.fixed},
+problem = pulse.StaticProblem(
+    model=model, geometry=geometry, bcs=bcs, parameters={"base_bc": pulse.BaseBC.fixed},
 )
 
 # Now we can solve the problem
@@ -153,12 +153,12 @@
 U = dolfinx.fem.Function(problem.u.function_space)
 U.interpolate(lambda x: (x[0], x[1], x[2]))
 
-endo_apex_coord = fenicsx_pulse.utils.evaluate_at_vertex_tag(U, geo.vfun, geo.markers["ENDOPT"][0])
-u_endo_apex = fenicsx_pulse.utils.evaluate_at_vertex_tag(problem.u, geo.vfun, geo.markers["ENDOPT"][0])
-endo_apex_pos = fenicsx_pulse.utils.gather_broadcast_array(geo.mesh.comm, endo_apex_coord + u_endo_apex)
+endo_apex_coord = pulse.utils.evaluate_at_vertex_tag(U, geo.vfun, geo.markers["ENDOPT"][0])
+u_endo_apex = pulse.utils.evaluate_at_vertex_tag(problem.u, geo.vfun, geo.markers["ENDOPT"][0])
+endo_apex_pos = pulse.utils.gather_broadcast_array(geo.mesh.comm, endo_apex_coord + u_endo_apex)
 print(f"\nGet longitudinal position of endocardial apex: {endo_apex_pos[0, 0]:4f} mm")
 
-epi_apex_coord = fenicsx_pulse.utils.evaluate_at_vertex_tag(U, geo.vfun, geo.markers["EPIPT"][0])
-u_epi_apex = fenicsx_pulse.utils.evaluate_at_vertex_tag(problem.u, geo.vfun, geo.markers["EPIPT"][0])
-epi_apex_pos = fenicsx_pulse.utils.gather_broadcast_array(geo.mesh.comm, epi_apex_coord + u_epi_apex)
+epi_apex_coord = pulse.utils.evaluate_at_vertex_tag(U, geo.vfun, geo.markers["EPIPT"][0])
+u_epi_apex = pulse.utils.evaluate_at_vertex_tag(problem.u, geo.vfun, geo.markers["EPIPT"][0])
+epi_apex_pos = pulse.utils.gather_broadcast_array(geo.mesh.comm, epi_apex_coord + u_epi_apex)
 print(f"\nGet longitudinal position of epicardial apex: {epi_apex_pos[0, 0]:4f} mm")

demo/biv_ellipsoid.py

@@ -8,10 +8,10 @@
 from mpi4py import MPI
 import dolfinx
 from dolfinx import log
-import fenicsx_pulse
 import ldrb
 import cardiac_geometries
 import cardiac_geometries.geometry
+import pulse
 
 # and lets turn on logging so that we can see more info from `dolfinx`
 
@@ -34,18 +34,18 @@
     folder=geodir,
 )
 
-# In order to use the geometry with `pulse` we need to convert it to a `fenicsx_pulse.Geometry` object. We can do this by using the `from_cardiac_geometries` method. We also specify that we want to use a quadrature degree of 4
+# In order to use the geometry with `pulse` we need to convert it to a `pulse.Geometry` object. We can do this by using the `from_cardiac_geometries` method. We also specify that we want to use a quadrature degree of 4
 #
 
-geometry = fenicsx_pulse.Geometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 4})
+geometry = pulse.Geometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 4})
 
-# Next we create the material object, and we will use the transversely isotropic version of the {py:class}`Neo Hookean model <fenicsx_pulse.neo_hookean.NeoHookean>`
+# Next we create the material object, and we will use the transversely isotropic version of the {py:class}`Neo Hookean model <pulse.neo_hookean.NeoHookean>`
 
-material = fenicsx_pulse.NeoHookean(mu=dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(15.0)))
+material = pulse.NeoHookean(mu=dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(15.0)))
 # and use an active stress approach
 
 Ta = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0))
-active_model = fenicsx_pulse.ActiveStress(geo.f0, activation=Ta)
+active_model = pulse.ActiveStress(geo.f0, activation=Ta)
 
 # Now we will also implement two different versions, one where we use a compressible model and one where we use an incompressible model. To do this we will introduce a flag
 
@@ -54,14 +54,14 @@
 # And in both cases we will use different compressible models, mechanics problems and different ways to get the displacement.
 
 if incompressible:
-    comp_model: fenicsx_pulse.Compressibility = fenicsx_pulse.Incompressible()
+    comp_model: pulse.Compressibility = pulse.Incompressible()
 else:
-    comp_model = fenicsx_pulse.Compressible()
+    comp_model = pulse.Compressible()
 
 
 # Now we can assemble the `CardiacModel`
 
-model = fenicsx_pulse.CardiacModel(
+model = pulse.CardiacModel(
     material=material,
     active=active_model,
     compressibility=comp_model,
@@ -71,25 +71,25 @@
 # We will add a pressure on the LV endocarium
 
 lvp = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0))
-neumann_lv = fenicsx_pulse.NeumannBC(traction=lvp, marker=geometry.markers["ENDO_LV"][0])
+neumann_lv = pulse.NeumannBC(traction=lvp, marker=geometry.markers["ENDO_LV"][0])
 
 # and on the RV endocardium
 
 rvp = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0))
-neumann_rv = fenicsx_pulse.NeumannBC(traction=lvp, marker=geometry.markers["ENDO_RV"][0])
+neumann_rv = pulse.NeumannBC(traction=lvp, marker=geometry.markers["ENDO_RV"][0])
 
 # We will also add a Robin type spring on the epicardial surface to mimic the pericardium.
 
 pericardium = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1.0))
-robin_per = fenicsx_pulse.RobinBC(value=pericardium, marker=geometry.markers["EPI"][0])
+robin_per = pulse.RobinBC(value=pericardium, marker=geometry.markers["EPI"][0])
 
 # We collect all the boundary conditions
 
-bcs = fenicsx_pulse.BoundaryConditions(neumann=(neumann_lv, neumann_rv), robin=(robin_per,))
+bcs = pulse.BoundaryConditions(neumann=(neumann_lv, neumann_rv), robin=(robin_per,))
 
 # create the problem
 
-problem = fenicsx_pulse.StaticProblem(model=model, geometry=geometry, bcs=bcs, parameters={"base_bc": fenicsx_pulse.BaseBC.fixed})
+problem = pulse.StaticProblem(model=model, geometry=geometry, bcs=bcs, parameters={"base_bc": pulse.BaseBC.fixed})
 
 # and solve