Skip to content

Showcase how to get data from SOFA components and fix RegularGridTopology #20

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Fimache merged 2 commits into from
May 13, 2026
Merged

Showcase how to get data from SOFA components and fix RegularGridTopology #20

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ec50d0e
use SOFA components for the nodal force quadrature computation
th-skam May 12, 2026
10b9a22
fix regular grid topology order
th-skam May 12, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
204 changes: 76 additions & 128 deletions examples/Freefem/3D/mms_structured/mms_utils_3d.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,93 +40,52 @@ def node_idx(i, j, k, nx, ny): return i + j * nx + k * nx * ny



def compute_nodal_forces(nodes, L, E, nu, nx, ny, nz):

dx = L / (nx - 1)
dy = L / (ny - 1)
dz = L / (nz - 1)
F = np.zeros((len(nodes), 3))

def compute_nodal_forces(nodes, quads, E, nu, L):
gp = np.array([-1/np.sqrt(3), 1/np.sqrt(3)])
gw = np.array([1.0, 1.0])
F = np.zeros((len(nodes), 3))
centroid = nodes.mean(axis=0)

for quad in quads:
x = nodes[quad] # (4, 3)
# determine outward normal sign at quad centre (xi=eta=0)
dN_dxi0 = np.array([-1., 1., 1., -1.]) / 4
dN_deta0 = np.array([-1., -1., 1., 1.]) / 4
J0 = np.cross(dN_dxi0 @ x, dN_deta0 @ x)
sign = 1.0 if np.dot(J0, x.mean(axis=0) - centroid) > 0 else -1.0

for gi, xi in enumerate(gp):
for gj, eta in enumerate(gp):
N = np.array([(1-xi)*(1-eta), (1+xi)*(1-eta),
(1+xi)*(1+eta), (1-xi)*(1+eta)]) / 4
dN_dxi = np.array([-(1-eta), (1-eta), (1+eta), -(1+eta)]) / 4
dN_deta = np.array([-(1-xi), -(1+xi), (1+xi), (1-xi)]) / 4
J_vec = np.cross(dN_dxi @ x, dN_deta @ x)
Jmag = np.linalg.norm(J_vec)
n_hat = sign * J_vec / Jmag
xg = N @ x
T = np.array(traction(*xg, *n_hat, E, nu, L))
F[quad] += np.outer(N, T) * (gw[gi] * gw[gj] * Jmag)

def _integrate_face(face, eta_f, zeta_f, Jf, p_coords_fn, traction_fn):
for gi, p1 in enumerate(gp):
for gj, p2 in enumerate(gp):
w = gw[gi] * gw[gj] * Jf
coords = p_coords_fn(p1, p2)
Tx, Ty, Tz = traction_fn(*coords)
for a in range(4):
Na = (1 + eta_f[a]*p1) * (1 + zeta_f[a]*p2) / 4.
F[face[a], 0] += Na * Tx * w
F[face[a], 1] += Na * Ty * w
F[face[a], 2] += Na * Tz * w

eta_yz = [-1, 1, 1, -1]
zeta_yz = [-1, -1, 1, 1]
eta_xz = [-1, 1, 1, -1]
zeta_xz = [-1, -1, 1, 1]
xi_xy = [-1, 1, 1, -1]
eta_xy = [-1, -1, 1, 1]

Jf = (dy/2) * (dz/2)
for k in range(nz - 1):
for j in range(ny - 1):
y0, z0 = j*dy, k*dz
for x_val, nx_c, jj in [(L, +1., ny-1 if False else None),
(0., -1., None)]:
i_node = nx-1 if nx_c > 0 else 0
face = [node_idx(i_node, j, k, nx, ny),
node_idx(i_node, j+1, k, nx, ny),
node_idx(i_node, j+1, k+1, nx, ny),
node_idx(i_node, j, k+1, nx, ny)]
_integrate_face(
face, eta_yz, zeta_yz, Jf,
lambda p1, p2, y0=y0, z0=z0:
(x_val, y0 + dy/2 + p1*(dy/2), z0 + dz/2 + p2*(dz/2)),
lambda x, y, z: traction(x, y, z, nx_c, 0., 0., E, nu, L),
)

Jf = (dx/2) * (dz/2)
for k in range(nz - 1):
for i in range(nx - 1):
x0, z0 = i*dx, k*dz
for y_val, ny_c in [(L, +1.), (0., -1.)]:
j_node = ny-1 if ny_c > 0 else 0
face = [node_idx(i, j_node, k, nx, ny),
node_idx(i+1, j_node, k, nx, ny),
node_idx(i+1, j_node, k+1, nx, ny),
node_idx(i, j_node, k+1, nx, ny)]
_integrate_face(
face, eta_xz, zeta_xz, Jf,
lambda p1, p2, x0=x0, z0=z0:
(x0 + dx/2 + p1*(dx/2), y_val, z0 + dz/2 + p2*(dz/2)),
lambda x, y, z: traction(x, y, z, 0., ny_c, 0., E, nu, L),
)

Jf = (dx/2) * (dy/2)
for j in range(ny - 1):
for i in range(nx - 1):
x0, y0 = i*dx, j*dy
for z_val, nz_c in [(L, +1.), (0., -1.)]:
k_node = nz-1 if nz_c > 0 else 0
face = [node_idx(i, j, k_node, nx, ny),
node_idx(i+1, j, k_node, nx, ny),
node_idx(i+1, j+1, k_node, nx, ny),
node_idx(i, j+1, k_node, nx, ny)]
_integrate_face(
face, xi_xy, eta_xy, Jf,
lambda p1, p2, x0=x0, y0=y0:
(x0 + dx/2 + p1*(dx/2), y0 + dy/2 + p2*(dy/2), z_val),
lambda x, y, z: traction(x, y, z, 0., 0., nz_c, E, nu, L),
)


res = np.abs(F.sum(axis=0))
assert res.max() < 1e-6 * np.abs(F).max()

return F
# =========================== SOFA scene =============================
class MMSForceController(Sofa.Core.Controller):
def __init__(self, dofs, cff, quad_topo, E, nu, L, *args, **kwargs):
super().__init__(*args, **kwargs)
self.dofs = dofs
self.cff = cff
self.quad_topo = quad_topo
self.E, self.nu, self.L = E, nu, L

def onSimulationInitDoneEvent(self, event):
nodes = self.dofs.position.array().copy()
quads = np.array(self.quad_topo.quads.array())
F = compute_nodal_forces(nodes, quads, self.E, self.nu, self.L)
self.cff.forces.value = F.tolist()


def build_scene_3d(rootNode, L=1.0, E=1e6, nu=0.3, nx=6, ny=6, nz=6,
visual=False):

Expand Down Expand Up @@ -154,6 +113,15 @@ def build_scene_3d(rootNode, L=1.0, E=1e6, nu=0.3, nx=6, ny=6, nz=6,
rootNode.gravity.value = [0, 0, 0]
rootNode.dt.value = 1.0

# This component has to be added at a different node because one Node
# cannot have 2 topology components
regGrid = rootNode.addChild('GridTopology')
regGrid.addObject('RegularGridTopology',
name="grid",
nx=nx, ny=ny, nz=nz,
min=[0., 0., 0.],
max=[L, L, L])

solid = rootNode.addChild('Solid3D')

solid.addObject('NewtonRaphsonSolver',
Expand All @@ -176,22 +144,15 @@ def build_scene_3d(rootNode, L=1.0, E=1e6, nu=0.3, nx=6, ny=6, nz=6,
newtonSolver="@newtonSolver",
linearSolver="@linearSolver")

# ===================== Mesh via RegularGridTopology =================================
solid.addObject('RegularGridTopology',
name="grid",
nx=nx, ny=ny, nz=nz,
min=[0., 0., 0.],
max=[L, L, L])
solid.addObject('HexahedronSetTopologyContainer',
name="topology",
src="@../GridTopology/grid")
solid.addObject('HexahedronSetTopologyModifier')

dofs = solid.addObject('MechanicalObject',
name="dofs",
template="Vec3d",
src="@grid")

solid.addObject('HexahedronSetTopologyContainer',
name="topology",
src="@grid")
solid.addObject('HexahedronSetTopologyModifier')
src="@topology")

solid.addObject('LinearSmallStrainFEMForceField',
name="FEM",
Expand Down Expand Up @@ -219,42 +180,30 @@ def build_scene_3d(rootNode, L=1.0, E=1e6, nu=0.3, nx=6, ny=6, nz=6,
indices="@fixC.indices",
fixedDirections=[0, 0, 1])

dx = L / (nx - 1)
dy = L / (ny - 1)
dz = L / (nz - 1)
nodes_pre = np.array(
[[i*dx, j*dy, k*dz]
for k in range(nz)
for j in range(ny)
for i in range(nx)],
dtype=float,
)
F = compute_nodal_forces(nodes_pre, L, E, nu, nx, ny, nz)

all_idx = " ".join(str(m) for m in range(len(nodes_pre)))
all_forces = " ".join(
f"{F[m,0]} {F[m,1]} {F[m,2]}" for m in range(len(nodes_pre))
)
solid.addObject('ConstantForceField',
name="MMS_forces",
template="Vec3d",
indices=all_idx,
forces=all_forces)

n_nodes = nx * ny * nz
cff = solid.addObject('ConstantForceField',
name="MMS_forces",
template="Vec3d",
indices=list(range(n_nodes)),
forces=[[0., 0., 0.]] * n_nodes)

surf = solid.addChild('Surface')
quad_topo = surf.addObject('QuadSetTopologyContainer', name="surfTopo")
surf.addObject('QuadSetTopologyModifier')
surf.addObject('Hexa2QuadTopologicalMapping',
input="@../topology",
output="@surfTopo")
if visual:
visu = solid.addChild('Visual')
visu.addObject('QuadSetTopologyContainer', name="quadTopo")
visu.addObject('QuadSetTopologyModifier')
visu.addObject('Hexa2QuadTopologicalMapping',
input="@../topology",
output="@quadTopo")
visu.addObject('OglModel',
surf.addObject('OglModel',
name="ogl",
src="@quadTopo",
src="@surfTopo",
color=[0.2, 0.6, 1.0, 0.9])
visu.addObject('IdentityMapping')
surf.addObject('IdentityMapping')

solid.addObject(MMSForceController(dofs, cff, quad_topo, E, nu, L,
name="MMSForceController"))

return dofs, nodes_pre
return dofs



Expand All @@ -263,8 +212,7 @@ def run_simulation_3d(L, E, nu, nx, ny, nz):
root = Sofa.Core.Node("root")
root.dt.value = 1.0

dofs, nodes_pre = build_scene_3d(root, L=L, E=E, nu=nu,
nx=nx, ny=ny, nz=nz, visual=False)
dofs = build_scene_3d(root, L=L, E=E, nu=nu, nx=nx, ny=ny, nz=nz, visual=False)
Sofa.Simulation.init(root)
pos_init = dofs.position.array().copy()
Sofa.Simulation.animate(root, root.dt.value)
Expand All @@ -274,7 +222,7 @@ def run_simulation_3d(L, E, nu, nx, ny, nz):
ux = pos_final[:, 0] - pos_init[:, 0]
uy = pos_final[:, 1] - pos_init[:, 1]
uz = pos_final[:, 2] - pos_init[:, 2]
return nodes_pre, ux, uy, uz
return pos_init, ux, uy, uz

def l2_error_3d(nodes, ux, uy, uz, L):

Expand Down Expand Up @@ -386,4 +334,4 @@ def nidx(i, j, k):
plt.tight_layout()
out2 = os.path.join(RESULTS_DIR, f'2d_visual_nx{nx}.png')
plt.savefig(out2, dpi=150), plt.close()


Loading