Sandia Libmesh

Introduction
Object Models
System Assembly
Examples
libMesh Finite Element Library

Roy Stogner
roystgnr@cfdlab.ae.utexas.edu
Derek Gaston
drgasto@sandia.gov
1 Univ.
of Texas at Austin
2 Sandia
National Laboratories
Albuquerque,NM
August 22, 2007
Summary
Introduction
Object Models
System Assembly
Outline
1
2
Introduction
Object Models
Core Classes
BVP Framework
System Assembly
Basic Example
Coupled Variables
Essential Boundary Conditions
Examples
Fluid Dynamics
Biology
Material Science
Summary
Examples
Summary
Introduction
Object Models
Goals
libMesh is not
System Assembly
Examples
Summary
Introduction
Object Models
System Assembly
Goals
libMesh is not
A physics implementation.
Examples
Summary
Introduction
Object Models
System Assembly
Goals
libMesh is not
A stand-alone application.
Examples
Summary
Introduction
Object Models
System Assembly
Goals
libMesh is not
libMesh is
Examples
Summary
Introduction
Object Models
System Assembly
Goals
libMesh is not
libMesh is
A software library and toolkit.
Examples
Summary
Introduction
Object Models
System Assembly
Examples
Goals
libMesh is not
libMesh is
Classes and functions for writing parallel adaptive
finite element applications.
Summary
Introduction
Object Models
System Assembly
Examples
Goals
libMesh is not
libMesh is
Classes and functions for writing parallel adaptive
finite element applications.
An interface to linear algebra, meshing, partitioning,
etc. libraries.
Summary
=
=
=
=
D
System Assembly
N
0
uD D
0 N
u0 (x)
= F(u)
For most applications we

assume there is a Boundary
Value Problem to be
approximated in a Finite
Element function space
u
M
t
G(u)
u
N(u)
u(x, 0)
Object Models
Introduction
Examples
Summary
Introduction
Object Models
Associated to is the
Mesh data structure
A Mesh is basically a
collection of geometric
elements and nodes
[
h :=
e
e
System Assembly
Examples
Summary
Introduction
Object Models
System Assembly
Object Oriented Programming
Examples
Summary
Introduction
Object Models
System Assembly
Examples
Abstract Base Classes define user interfaces.
Summary
Introduction
Object Models
System Assembly
Examples

Concrete Subclasses implement functionality.
Summary
Introduction
Object Models
System Assembly
Examples

Concrete Subclasses implement functionality.
One physics code can work with many
discretizations.
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Geometric Element Classes

DofObject
-_n_systems: unsigned char
-_n_vars: unsigned char *
-_n_comp: unsigned char **
-_dof_ids: unsigned int **
-_id: unsigned int
-_processor_id: unsigned short int
Node
Elem
#_nodes: Node **
#_neighbors: Elem **
#_parent: Elem *
#_children: Elem **
#_*flag: RefinementState
#_p_level: unsigned char
#_subdomain_id: unsigned char
+n_{faces,sides,vertices,edges,children}(): unsigned int
+centroid(): Point
+hmin,hmax(): Real
NodeElem
Edge
Prism
Hex8
Face
Cell
Hex
Pyramid
Hex20
InfQuad
Hex27
Tet
InfCell
Abstract interface
gives mesh topology
Concrete
instantiations of
mesh geometry
Hides element type
from most
applications
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Finite Element Classes

FEBase
+phi, dphi, d2phi
+quadrature_rule, JxW
+reinit(Elem)
+reinit(Elem,side)
Lagrange
Hermite
Hierarchic
Monomial
Finite Element object

builds data for each
Geometric object
User only deals with
shape function,
quadrature data
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Core Features
Mixed element geometries in unstructured grids

Adaptive mesh h refinement with hanging nodes, p
refinement
Integration w/ PETSc, LASPack, METIS, ParMETIS,
Triangle, TetGen
Support for UNV, ExodusII, Tecplot, GMV, UCD files
Mesh creation, modification utilities
Summary
Introduction
Object Models
System Assembly
Core Classes
Degree of Freedom Handling
Examples
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
DofObject subclasses store global Degree of

Freedom indices
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes

Freedom indices
DofMap class assigns indices to a partitioned mesh
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes

Freedom indices
FE classes calculate hanging node, periodic
constraints
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes

Freedom indices
constraints
DofMap class applies constraints
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes

Freedom indices
constraints
DofMap class applies constraints
System class handles AMR/C projections
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Generic Constraint Calculations

To maintain function space continuity, constrain hanging
node Degrees of Freedom coefficients on fine elements
in terms of DoFs on coarse neighbors.
uF = uC
X
uCj Cj
uFi Fi =
Aki ui = Bkj uj
ui = A1
ki Bkj uj
1
Integrated values (and fluxes, for C continuity) give
element-independent matrices:
Aki (Fi , Fk )
Bkj (Cj , Ck )
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Generic Projection Calculations

Upon element coarsening (or refinement in non-nested
spaces):
Copy nodal Degree of Freedom coefficients
Project edge DoFs, holding nodal DoFs constant
Project face DoFs, holding nodes/edges constant
Project interior DoFs, holding boundaries constant
Advantages / Disadvantages
Requires only local solves
Consistent in parallel
May violate physical conservation laws
Summary
Introduction
Object Models
System Assembly
Core Classes
libMesh Parallelization
Parallel code
Examples
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Parallel code
PetscVector, DistributedVector classes for Linear
Algebra
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Parallel code
Algebra
Parallel assembly, error indicators, etc.
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Parallel code
Algebra
Mesh partitioning with ParMETIS, etc.
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Parallel code
Algebra
Serial code
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Parallel code
Algebra
Serial code
Mesh storage on every node
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Parallel code
Algebra
Serial code
DoF renumbering, constraint calculations
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Parallel code
Algebra
Serial code
Refinement/Coarsening flagging
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
Parallel code
Algebra
Serial code
Refinement/Coarsening flagging
Mesh, solution I/O
Summary
Introduction
Object Models
System Assembly
Examples
Core Classes
ParallelMesh
Parallel subclassing of MeshBase
Start from unstructured Mesh class
Add methods to delete, reconstruct non-semilocal
Elem and Node objects
Parallelize DofMap methods
Parallelize MeshRefinement methods
Add parallel or chunked I/O support
Add load balancing support
Also want parallel BoundaryInfo, BoundaryMesh, Data,
Function, Generation, Modification, Smoother, and Tools
classes
Summary
Introduction
Object Models
System Assembly
Examples
Summary
BVP Framework
Boundary Value Problem Framework Goals

Goals
Improved test coverage and reliability
Hiding implementation details from user code
Rapid prototyping of new formulations
Physics-dependent error estimators
Methods
Object-oriented System and Solver subclasses
Factoring common patterns into library code
Per-element Numerical Jacobian verification
Introduction
Object Models
System Assembly
Examples
BVP Framework
FEM System Classes
FEMSystem
+elem_solution: DenseVector<Number>
+elem_residual: DenseVector<Number>
+elem_jacobian: DenseMatrix<Number>
#elem_fixed_solution: DenseVector<Number>
#*_fe_var: std::vector<FEBase *>
#elem: Elem *
+*_time_derivative(request_jacobian)
+*_constraint(request_jacobian)
+*_postprocess()
NavierStokesSystem
CahnHilliardSystem
LaplaceYoungSystem
SurfactantSystem
Generalized IBVP
representation
FEMSystem does all
initialization, global
assembly
User code only
needs weighted time
derivative residuals
( u
, vi ) = Fi (u) and/or
t
constraints
Gi (u, vi ) = 0
Summary
Introduction
Object Models
System Assembly
Examples
BVP Framework
ODE Solver Classes
TimeSolver
+*_residual(request_jacobian)
+solve()
+advance_timestep()
SteadySolver
AdamsMoultonSolver
EulerSolver
EigenSolver
Calls user code on

each element
Assembles
element-by-element
time derivatives,
constraints, and
weighted old
solutions
Summary
Introduction
Object Models
System Assembly
Examples
BVP Framework
Nonlinear Solver Classes
NonlinearSolver
+*_tolerance
+*_max_iterations
+solve()
LinearSolver
ContinuationSolver
QuasiNewtonSolver
Acquires residuals,
jacobians from
FEMSystem
assembly
Handles inner loops,
inner solvers and
tolerances,
convergence tests,
etc
Summary
Introduction
Object Models
System Assembly
Examples
Basic Example
System Assembly
For simplicity we will focus on the weighted residual

statement arising from the Poisson equation, with
N = ,
(R(uh ), vh ) :=
Z
h

u vh fvh dx = 0
h
vh V h
Summary
Introduction
Object Models
System Assembly
Basic Example
The element integrals . . .

Z
h

u vh fvh dx
e
Examples
Summary
Introduction
Object Models
System Assembly
Examples
Basic Example

Z
h

u vh fvh dx
e
are written in terms of the local i basis functions

Ns
X
j=1
Z
j i dx
uj
e
f i dx ,
e
i = 1, . . . , Ns
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

Z
h

u vh fvh dx
e
are written in terms of the local i basis functions

Ns
X
j=1
Z
j i dx
uj
e
f i dx ,
i = 1, . . . , Ns
This can be expressed naturally in matrix notation as

K e U e Fe
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example
The integrals are performed on a reference element

e , transformed via Lagrange basis to the geometric
element.
x()
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

element.
x()
The Jacobian of the map x() is J.

Fei
Z
=
Z
f i dx =
f (x())i |J|d
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

element.
x()
Introduction
Object Models
System Assembly
Examples
Basic Example
The integrals on the reference element are

approximated via numerical quadrature.
Summary
Introduction
Object Models
System Assembly
Examples
Basic Example

The quadrature rule has Nq points q and weights
wq .
Summary
Introduction
Object Models
System Assembly
Examples
Basic Example

wq .
Fei
Z
=
e
Nq
X
q=1
f i |J|d
f (x(q ))i (q )|J(q )|wq
Summary
Introduction
Object Models
System Assembly
Examples
Basic Example

wq .
K eij
Z
=
e
Nq
X
q=1
j i |J|d
j (q ) i (q )|J(q )|wq
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example
At the qth quadrature point, LibMesh can provide

variables including:
Code
Math
Description
JxW[q]
|J(q )|wq
Jacobian times weight
phi[i][q]
i (q )
value of ith shape fn.
dphi[i][q]
i (q )
value of ith shape fn. gradient
d2phi[i][q]
i (q ) value of ith shape fn. Hessian
xyz[q]
x(q )
location of q in physical space
normals[q]
~n(x(q ))
normal vector at x on a side
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example
The LibMesh representation of the matrix and rhs

assembly is similar to the mathematical statements.
for (q=0; q<Nq; ++q)
for (i=0; i<Ns; ++i) {
Fe(i)
+= JxW[q]*f(xyz[q])*phi[i][q];
for (j=0; j<Ns; ++j)
Ke(i,j) += JxW[q]*(dphi[j][q]*dphi[i][q]);
}
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

for (i=0; i<Ns; ++i) {
Fe(i)
}
Fei
Nq
X
q=1
f (x(q ))i (q )|J(q )|wq
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

for (i=0; i<Ns; ++i) {
Fe(i)
}
Fei
Nq
X
q=1
f (x(q ))i (q )|J(q )|wq
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

for (i=0; i<Ns; ++i) {
Fe(i)
}
Fei
Nq
X
q=1
f (x(q ))i (q )|J(q )|wq
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

for (i=0; i<Ns; ++i) {
Fe(i)
}
Fei
Nq
X
q=1
f (x(q ))i (q )|J(q )|wq
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

for (i=0; i<Ns; ++i) {
Fe(i)
}
K eij
Nq
X
q=1
j (q )
i (q )|J(q )|wq
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

for (i=0; i<Ns; ++i) {
Fe(i)
}
K eij
Nq
X
q=1
j (q )
i (q )|J(q )|wq
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example

for (i=0; i<Ns; ++i) {
Fe(i)
}
K eij
Nq
X
q=1
j (q )
i (q )|J(q )|wq
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example
Convection-Diffusion Equation
The matrix assembly routine for the linear
convection-diffusion equation,
ku + b u = f
for (i=0; i<Ns; ++i) {
Fe(i)
Ke(i,j) += JxW[q]*(k*(dphi[j][q]*dphi[i][q])
+ (b*dphi[j][q])*phi[i][q]);
}
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example
ku + b u = f
for (i=0; i<Ns; ++i) {
Fe(i)
}
Introduction
Object Models
System Assembly
Examples
Summary
Basic Example
ku + b u = f
for (i=0; i<Ns; ++i) {
Fe(i)
}
Introduction
Object Models
System Assembly
Examples
Summary
Coupled Variables
Stokes Flow
For multi-variable systems like Stokes flow,
p u = f
u = 0
R2
The element stiffness matrix concept can extended to

include sub-matrices
e
e e
Ku1 u1 Kue1 u2 Kue1 p
Uu1
Fu1
Kue u Kue u Kue p Uue Fue
2 1
2 2
2
2
2
e
e
e
e
e
U
F
Kpu
K
K
p
p
pu2
pp
1
We have an array of submatrices: Ke[ ][ ]
Introduction
Object Models
System Assembly
Examples
Summary
Coupled Variables
Stokes Flow
p u = f
u = 0
R2

e
e e
Uu1
Fu1
2 1
2 2
2
2
2
e
e
e
e
e
U
F
Kpu
K
K
p
p
pu2
pp
1
We have an array of submatrices: Ke[1][1]
Introduction
Object Models
System Assembly
Examples
Summary
Coupled Variables
Stokes Flow
p u = f
u = 0
R2

e
e e
Uu1
Fu1
2 1
2 2
2
2
2
e
e
e
e
e
U
F
Kpu
K
K
p
p
pu2
pp
1
Introduction
Object Models
System Assembly
Examples
Summary
Coupled Variables
Stokes Flow
p u = f
u = 0
R2

e
e e
Uu1
Fu1
2 1
2 2
2
2
2
e
e
e
e
e
U
F
Kpu
K
K
p
p
pu2
pp
1
Introduction
Object Models
System Assembly
Examples
Summary
Coupled Variables
Stokes Flow
p u = f
u = 0
R2

e
e e
Uu1
Fu1
2 1
2 2
2
2
2
e
e
e
e
e
U
F
Kpu
K
K
p
p
pu2
pp
1
And an array of right-hand sides: Fe[].
Introduction
Object Models
System Assembly
Examples
Summary
Coupled Variables
Stokes Flow
p u = f
u = 0
R2

e
e e
Uu1
Fu1
2 1
2 2
2
2
2
e
e
e
e
e
U
F
Kpu
K
K
p
p
pu2
pp
1
And an array of right-hand sides: Fe[1].
Introduction
Object Models
System Assembly
Examples
Summary
Coupled Variables
Stokes Flow
p u = f
u = 0
R2

e
e e
Uu1
Fu1
2 1
2 2
2
2
2
e
e
e
e
e
U
F
Kpu
K
K
p
p
pu2
pp
1
And an array of right-hand sides: Fe[2].
Introduction
Object Models
System Assembly
Examples
Summary
Coupled Variables
Stokes Flow
The matrix assembly can proceed in essentially the
same way.
For the momentum equations:
for (d=0; d<2; ++d)
for (i=0; i<Ns; ++i) {
Fe[d](i) += JxW[q]*f(xyz[q],d)*phi[i][q];
Ke[d][d](i,j) +=
JxW[q]*nu*(dphi[j][q]*dphi[i][q]);
}
Introduction
Object Models
System Assembly
Examples
Essential Boundary Data

Dirichlet boundary conditions can be enforced after
the global stiffness matrix K has been assembled
This usually involves
1
placing a 1 on the main diagonal of the global

stiffness matrix
Summary
Introduction
Object Models
System Assembly
Examples

1

stiffness matrix
zeroing out the row entries
Summary
Introduction
Object Models
System Assembly
Examples

1
2
3

stiffness matrix
placing the Dirichlet value in the rhs vector
Summary
Introduction
Object Models
System Assembly
Examples

1
2
3
4

stiffness matrix
subtracting off the column entries from the rhs
Summary
Introduction
Object Models
System Assembly
Examples
Summary

1
2
3
4

stiffness matrix
subtracting off the column entries from the rhs
k11 k12 k13

k21 k22 k23
k31 k32 k33

.
.
.
f1
1 0 0
.
. f2
0 k22 k23
,
0 k32 k33
. f3
.
0 .
.
.
0
g1
.
, f2 k21 g1
. f3 k31 g1
.
.
Introduction
Object Models
System Assembly
Cons of this approach :
Examples
Summary
Introduction
Object Models
System Assembly
Examples
Summary

Works for an interpolary finite element basis but not in
general.
Introduction
Object Models
System Assembly
Examples
Summary

general.
May be inefficient to change individual entries once
the global matrix is assembled.
Introduction
Object Models
System Assembly
Examples
Summary

general.
May be inefficient to change individual entries once
the global matrix is assembled.
Need to enforce boundary conditions for a generic

finite element basis at the element stiffness matrix
level.
Introduction
Object Models
System Assembly
Examples
A penalty term is added to the standard weighted

residual statement
Z
1
(R(u), v) +
v V
(u uD )v dx = 0
D
{z
}
|
penalty term
Summary
Introduction
Object Models
System Assembly
Examples

residual statement
Z
1
(R(u), v) +
v V
(u uD )v dx = 0
D
{z
}
|
penalty term
Here 1 is chosen so that, in floating point

arithmetic, 1 + 1 = 1 .
Summary
Introduction
Object Models
System Assembly
Examples
Summary

residual statement
Z
1
(R(u), v) +
v V
(u uD )v dx = 0
D
{z
}
|
penalty term
Here 1 is chosen so that, in floating point

arithmetic, 1 + 1 = 1 .
This weakly enforces u = uD on the Dirichlet
boundary, and works for general finite element bases.
Introduction
Object Models
System Assembly
Examples
LibMesh provides:
A quadrature rule with Nqf points and JxW f[]
A finite element coincident with the boundary face
that has shape function values phi f[][]
for (qf=0; qf<Nqf; ++qf) {
for (i=0; i<Nf; ++i) {
Fe(i) += JxW_f[qf]*
penalty*uD(xyz[q])*phi_f[i][qf];
for (j=0; j<Nf; ++j)
Ke(i,j) += JxW_f[qf]*
penalty*phi_f[j][qf]*phi_f[i][qf];
}
}
Summary
Introduction
Object Models
System Assembly
Examples
LibMesh provides:
for (i=0; i<Nf; ++i) {
Fe(i) += JxW_f[qf]*
}
}
Summary
Introduction
Object Models
System Assembly
Examples
LibMesh provides:
for (i=0; i<Nf; ++i) {
Fe(i) += JxW_f[qf]*
}
}
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
Introduction
Laplace-Young equation model surface tension effects for
enclosed liquids.
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Introduction
enclosed liquids.
Combining surface tension, gravity and contact the energy
functional for Laplace-Young is:
Z
Z
Z q
1 2
2
1 + |u| d +
u d
u ds
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Introduction
enclosed liquids.
Z
Z
Z q
1 2
2
1 + |u| d +
u d
u ds
Where is the ratio of surface energy to gravitational

energy and u is the height of the liquid.
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Introduction
enclosed liquids.
Z
Z
Z q
1 2
2
1 + |u| d +
u d
u ds

While the weak formulation of the stationary condition is
given by:
!
u
p
,
+ (u, ) = (1, )
(1)
1 + |u|2
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Introduction
enclosed liquids.
Z
Z
Z q
1 2
2
1 + |u| d +
u d
u ds

While the weak formulation of the stationary condition is
given by:
!
u
p
,
+ (u, ) = (1, )
(1)
1 + |u|2
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
Instead of explicitly finding the Jacobian, well use FEMSystem to finite difference the weak form.
element constraint()
for (unsigned int qp=0; qp != n_qpoints; qp++) {
Number u = interior_value(0, qp);
Gradient grad_u = interior_gradient(0, qp);
Number K = 1. / sqrt(1. + (grad_u * grad_u));
for (unsigned int i=0; i != n_u_dofs; i++) {
Fu(i) += JxW[qp] * ((_kappa * u * phi[i][qp]) +
(K * grad_u * dphi[i][qp]));
}
}
side constraint()
Fu(i) -= JxW[qp] * _gamma * phi[i][qp];
}
}
1
u
B
C
, A
@q
1 + |u|2
+ (u, ) (1, ) = 0
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
}
}
side constraint()
}
}
1
u
B
C
, A
@q
1 + |u|2
+ (u, ) (1, ) = 0
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
}
}
side constraint()
}
}
1
u
B
C
, A
@q
1 + |u|2
+ (u, ) (1, ) = 0
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
}
}
side constraint()
}
}
1
u
B
C
, A
@q
1 + |u|2
+ (u, ) (1, ) = 0
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
}
}
side constraint()
}
}
1
u
B
C
, A
@q
1 + |u|2
+ (u, ) (1, ) = 0
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
}
}
side constraint()
}
}
1
u
B
C
, A
@q
1 + |u|2
+ (u, ) (1, ) = 0
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
Solution
An overkill solution containing 200,000 DOFs.
(a) 2D.
(b) Contour Elevation.
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
Compressible Shocked Flow
Original compressible flow code written by Ben Kirk

utilizing libMesh.
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics

utilizing libMesh.
Solves both Compressible Navier Stokes and Inviscid
Euler.
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics

utilizing libMesh.
Solves both Compressible Navier Stokes and Inviscid
Euler.
Includes both SUPG and a shock capturing scheme.
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
Problem Specification
The problem studied is that of an oblique shock
generated by a 10o wedge angle.
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
This problem has an exact solution for density which
is a step function.
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
is a step function.
Utilizing libmeshs exact solution capability the exact
L2 error can be solved for.
Summary
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
is a step function.
Utilizing libmeshs exact solution capability the exact
L2 error can be solved for.
The exact solution is shown below:
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Uniformly Refined Solutions

For comparison purposes, here is a mesh and a
solution after 1 uniform refinement with 10890 DOFs.
1
0.8
0.8
0.6
0.6
r
1.45
1.4
1.35
1.3
1.25
1.2
1.15
1.1
1.05
1
0.4
0.4
0.2
0.2
0.2
0.4
0.6
0.8
(c) Mesh after 1 uniform
0.2
0.4
0.6
0.8
(d) Solution after 1 uni-
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
H-Adapted Solutions
A flux jump indicator was employed as the error
indcator along with a statistical flagging scheme.
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
H-Adapted Solutions
A flux jump indicator was employed as the error
indcator along with a statistical flagging scheme.
Here is a mesh and solution after 2 adaptive
refinements containing 10800 DOFs:
1
0.8
0.8
0.6
0.6
r
1.45
1.4
1.35
1.3
1.25
1.2
1.15
1.1
1.05
1
0.4
0.4
0.2
0.2
0.2
0.4
0.6
0.8
0.2
0.4
0.6
0.8
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Redistributed Solutions
Redistribution utilizing the same flux jump indicator.
1
0.8
0.8
0.6
0.6
r
1.45
1.4
1.35
1.3
1.25
1.2
1.15
1.1
1.05
1
0.4
0.4
0.2
0.2
0.2
0.4
0.6
0.8
(i) Mesh after 8 redistributions.
0.2
0.4
0.6
0.8
(j) Solution after 8 redistributions.
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Redistributed and Adapted

Now combining the two, here are the mesh and
solution after 2 adaptations beyond the previous
redistribution containing 10190 DOFs.
1
0.8
0.8
0.6
0.6
r
1.45
1.4
1.35
1.3
1.25
1.2
1.15
1.1
1.05
1
0.4
0.4
0.2
0.2
0.2
0.4
0.6
0.8
0.2
0.4
0.6
0.8
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Solution Comparison
For a better comparison here are 3 of the solutions,
each with around 11000 DOFs:
1
1
r
0.81.45
0.6
0.4
0.4
0.2
0.2
0.2
0.2
0.4
0.6
0.8
(m) Uniform.
0.2
0.4
0.6
0.8
(n) Adaptive.
1.45
1.4
1.35
1.3
1.25
1.2
1.15
1.1
1.05
1
1.4
1.35
1.3
1.25
0.61.2
1.15
1.1
1.05
1
0.4
0.81.45
1.4
1.35
1.3
1.25
0.61.2
1.15
1.1
1.05
1
0.8
0.2
0.4
0.6
(o) R + H.
0.8
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Error Plot
libmesh provides capability for computing error norms
against an exact solution.
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Error Plot
libmesh provides capability for computing error norms
against an exact solution.
The exact solution is not in H 1 therefore we only
obtain the L2 convergence plot:
Uniform
Adaptivity
Redist + Adapt
-1.2
log10(L2Error)
-1.4
-1.6
-1.8
-2.0
-2.2
3.5
4.0
4.5
log10(N Dofs)
5.0
Introduction
Fluid Dynamics
Object Models
System Assembly
Examples
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Natural Convection
Tetrahedral mesh of pipe geometry. Stream ribbons

colored by temperature.
Introduction
Object Models
System Assembly
Examples
Fluid Dynamics
Surface-Tension-Driven Flow
Adaptive grid solution shown with temperature

contours and velocity vectors.
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Fluid Dynamics
Double-Diffusive Convection
Solute contours: a plume of warm, low-salinity fluid is

convected upward through a porous medium.
Introduction
Object Models
System Assembly
Examples
Biology
Tumor Angiogenesis
The tumor secretes a chemical which stimulates

blood vessel formation.
Summary
Introduction
Object Models
System Assembly
Examples
Summary
Material Science
Free Energy Formulation

Cahn-Hilliard systems model phase separation and
interface evolution
f (c, c) f0 (c) + f (c)
2
f (c) c c c
2
f0 (c) NkT (c ln (c) + (1 c) ln (1 c)) + Nc(1 c)

c
= Mc f00 (c) 2c c
t
Introduction
Object Models
System Assembly
Examples
Summary
Material Science
Phase Separation - Spinodal Decomposition

Initial Evolution
Initial homogeneous blend quenched below critical T
Random perturbations anti-diffuse into two phases
divided by narrow interfaces
Gradual coalescence of single-phase regions
Additional physics leads to pattern self-assembly
Introduction
Object Models
System Assembly
Examples
Summary
libMesh Development
Open Source (LGPL)
Leveraging existing libraries
Public site, mailing lists, CVS tree, examples, etc. at
http://libmesh.sf.net/
18 examples including:
Infinite Elements for the wave equation.
Helmholtz with complex numbers.
Laplace in L-Shaped Domain.
Biharmonic Equation.
Using SLEPc for an Eigen Problem.
Unsteady Navier Stokes.
And More!
Summary

Sandia Libmesh

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Introduction

libMesh Finite Element Library

August 22, 2007

For most applications we

Object Oriented Programming

Object Oriented Programming

Abstract Base Classes define user interfaces.

Object Oriented Programming

Abstract Base Classes define user interfaces.

Object Oriented Programming

Abstract Base Classes define user interfaces.

Geometric Element Classes

Finite Element Classes

Finite Element object

Mixed element geometries in unstructured grids

Degree of Freedom Handling

Degree of Freedom Handling

DofObject subclasses store global Degree of

Degree of Freedom Handling

DofObject subclasses store global Degree of

Degree of Freedom Handling

DofObject subclasses store global Degree of

Degree of Freedom Handling

DofObject subclasses store global Degree of

Degree of Freedom Handling

DofObject subclasses store global Degree of

Generic Constraint Calculations

Generic Projection Calculations

Boundary Value Problem Framework Goals

FEM System Classes

ODE Solver Classes

Calls user code on

Nonlinear Solver Classes

For simplicity we will focus on the weighted residual

The element integrals . . .

The element integrals . . .

are written in terms of the local i basis functions

The element integrals . . .

are written in terms of the local i basis functions

This can be expressed naturally in matrix notation as

The integrals are performed on a reference element

The integrals are performed on a reference element

The Jacobian of the map x() is J.

The integrals are performed on a reference element

The integrals on the reference element are

The integrals on the reference element are

The integrals on the reference element are

The integrals on the reference element are

At the qth quadrature point, LibMesh can provide

Jacobian times weight

value of ith shape fn.

value of ith shape fn. gradient

i (q ) value of ith shape fn. Hessian

location of q in physical space

normal vector at x on a side

The LibMesh representation of the matrix and rhs

The LibMesh representation of the matrix and rhs

f (x(q ))i (q )|J(q )|wq

The LibMesh representation of the matrix and rhs

f (x(q ))i (q )|J(q )|wq

The LibMesh representation of the matrix and rhs

f (x(q ))i (q )|J(q )|wq

The LibMesh representation of the matrix and rhs

f (x(q ))i (q )|J(q )|wq

Here 1 is chosen so that, in floating point

Here 1 is chosen so that, in floating point