2005 03 01 Wheeler Presentation

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FiPy A Finite Volume PDE Solver Using Python

D. Wheeler, J. E. Guyer & J. A. Warren

www.ctcms.nist.gov/fipy/

Metallurgy Division & Center for Theoretical and Computational Materials Science

Materials Science and Engineering Laboratory

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Motivation

PDEs are ubiquitous in Materials Science problems

Solve PDEs in weird and unique ways

Easy to pose problems

Easy to customize

Dont care about numerical methods

Dendrites

What Are Dendrites:

A vast amount of the products and devices that we use everyday,everything from aluminum foil and soda cans, to cars, jet engines andcomputers, are made from metals and alloys. Early in the creation of allthese products the metals are in a liquid, or molten state, that freezes toform a solid, just like water freezes to form ice. Now, if you were to lookat some just frozen, or freshly solidified metallic alloy with a strongmagnifying glass you would see that its structure is not uniform, but ismade up of tiny individual crystalline grains. Moreover, If you were able tolook even more carefully at the individual grains through a powerfulmicroscope, you would see that each grain is made up from what looks likea bunch of tiny metallic snowflakes crowding and growing into each other.Scientists and engineers call these tiny metallic snowflakes dendrites. Thepicture to the right shows what a surface cut through a "forest" of dendrites in a metal would look likethrough a microscope.

The term dendrite comes from the Greek word "dendron", which means a tree.This description is appropriate because we often describe the form and structure ofa metallic dendrite as that of a tree (see figure to left), with a main branch or trunk,from which grow side branches, from which grow smaller side branches, and soon, until all the main branches and the side branches grow into each other and thereis no room for any more branches to grow. The figure to

the right shows a few dendrites growing out of the surface of a metal. Infact, almost all freshly crystallized alloys are composed of many thousands,or even millions of dendritic crystals all stuck together. What's mostimportant is that the shape, size, and speed of growth of these dendrites areall factors that profoundly influence the final properties of cast and weldedmetals.For example, the dendrites affect how hard or soft a material is, howstretchable or springy it behaves, and how much you can bend or stretch itbefore it breaks. The dendrites also affect both how long and under whatenvironmental conditions you can use an alloy before it wears out or rusts.The dendrites affect whether the material is a good or a poor conductor of electricity. The dendriteseven affect how easily you can weld one piece of metal to another, and what's the best way to do thewelding. In short, the dendritic pattern formed during solidification profoundly influences a material'smechanical, electrical, and chemical properties.

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What is FiPy?

FiPy is a computer program written in Python to solve partial differential equations (PDEs) using the Finite Volume method

Python is a powerful object oriented scripting language with tools for numericsThe Finite Volume method is a way to solve a set of PDEs, similar to the Finite Element or Finite Difference methods

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Why a common code?Many interface motion codes for solving Materials Science problems at NIST.

Phase Field for solidification and meltingPhase Field for grain boundary motionPhase Field for elasticityPhase Field for electrochemistryLevel Set code for electrochemistryetc

Need for code homogeneity

Institutional memory is lost with constant rewriting of codesNeed for preservation and reuseLeverage different skill sets

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Design

Implement interface tracking

Phase Field, Level Set, Volume of Fluid, particle tracking

Object-oriented structure

Encapsulation and Inheritance

Adapt, extend, reuse

Test-based development

Open Source

CVS and compressed source archives

Bug tracker and mailing lists

High-level scripting language

Python programming language

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Design: test-based development

485 major tests, comprising thousands of low-level tests

Tests are documentation (and vice versa)

298 Module fipy.variables.variable

ge (self, other)

Test if a Variable is greater than or equal to another quantity>>> a = Variable(value = 3)>>> b = (a >= 4)>>> b(Variable(value = 3) >= 4)>>> b()0>>> a.setValue(4)>>> b()1>>> a.setValue(5)>>> b()1

getitem (self, index )

Evaluate the variable and return the specified element>>> a = Variable(value = ((3.,4.),(5.,6.)), unit = "m") + "4 m">>> print a[1,1]10.0 m

It is an error to slice a Variable whose value is not sliceable>>> Variable(value = 3)[2]Traceback (most recent call last):

...TypeError: unsubscriptable object

gt (self, other)

Test if a Variable is greater than another quantity>>> a = Variable(value = 3)>>> b = (a > 4)>>> b(Variable(value = 3) > 4)>>> b()0>>> a.setValue(5)>>> b()1

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Design: test-based development

485 major tests, comprising thousands of low-level tests

Tests are documentation (and vice versa)

Running __main__.Variable.__gt__.__doc__Trying: a = Variable(value = 3)Expecting: nothingokTrying: b = (a > 4)Expecting: nothingokTrying: bExpecting: (Variable(value = 3) > 4)okTrying: b()Expecting: 0okTrying: a.setValue(5)Expecting: nothingokTrying: b()Expecting: 1ok0 of 6 examples failed in __main__.Variable.__gt__.__doc__

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Finite Volume MethodSolve a general PDE on a given domain for a field

!("#)!t

transient

+$.("u#) convection

= $.(%$#) diffusion

+ S#source

a11 a12

a21 a22. . .

. . . . . . . . .. . . ann

12...n

=

b1b2...bn

()t

transient

+ ($u) convection

= () diffusion

+ Ssource

V

()t

dV transient

+

S($n $u) dS convection

=

S($n ) dS

diffusion

+

VS dV

source

V (V )oldt

transient

+face

[($n $u)A]face convection

=face

[A$n ]face diffusion

+ V Ssource

1

domain

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion

[ (i)]n nth order diffusion

(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion

S(#n #u) dS convection

VS dV

source

= 0

V (V )oldt

transient

face

[A#n ]face diffusion

face

[A#n { }]face nth order diffusion

face

[(#n #u)A]face convection

V Ssource

= 0

1

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Integrate PDE over arbitrary control volumes

!("#)!t

transient

+$.("u#) convection

= $.(%$#) diffusion

+ S#source

a11 a12

a21 a22. . .

. . . . . . . . .. . . ann

12...n

=

b1b2...bn

()t

transient

+ ($u) convection

= () diffusion

+ Ssource

V

()t

dV transient

+


=

S($n ) dS

diffusion

+

VS dV

source

V (V )oldt

transient

+face


=face


+ V Ssource

1

controlvolume

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion


(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion


VS dV

source

= 0

V (V )oldt

transient

face


face


face


V Ssource

= 0

1

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Evaluate PDE over polyhedral control volumes !("#)!t

transient

+$.("u#) convection

= $.(%$#) diffusion

+ S#source

a11 a12

a21 a22. . .

. . . . . . . . .. . . ann

12...n

=

b1b2...bn

()t

transient

+ ($u) convection

= () diffusion

+ Ssource

V

()t

dV transient

+


=

S($n ) dS

diffusion

+

VS dV

source

V (V )oldt

transient

+face


=face


+ V Ssource

1

face

cell

vertex

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion


(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion


VS dV

source

= 0

V (V )oldt

transient

face


face


face


V Ssource

= 0

1

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Evaluate PDE over polyhedral control volumes

Obtain a large coupled set of linear equations in

!("#)!t

transient

+$.("u#) convection

= $.(%$#) diffusion

+ S#source

a11 a12

a21 a22. . .

. . . . . . . . .. . . ann

12...n

=

b1b2...bn

()t

transient

+ ($u) convection

= () diffusion

+ Ssource

V

()t

dV transient

+


=

S($n ) dS

diffusion

+

VS dV

source

V (V )oldt

transient

+face


=face


+ V Ssource

1

a11 a12

a21 a22. . .

. . . . . . . . .. . . ann

12...n

=

b1b2...bn

()t

transient

+ ($u) convection

= () diffusion

+ Ssource

V

()t

dV transient

+


=

S($n ) dS

diffusion

+

VS dV

source

V (V )oldt

transient

+face


=face


+ V Ssource

1

a11 a12

a21 a22. . .

. . . . . . . . .. . . ann

12...n

=

b1b2...bn

()t

transient

+ ($u) convection

= () diffusion

+ Ssource

V

()t

dV transient

+


=

S($n ) dS

diffusion

+

VS dV

source

V (V )oldt

transient

+face


=face


+ V Ssource

1

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# create a mesh

# create a field variable

# create the equation terms

# create the equation

# create a viewer

# solve

Diffusion Example

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion

+ [ (i)]n nth order diffusion

+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

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Diffusion Example

# create a mesh

L = nx * dxfrom fipy.meshes.grid2D import Grid2Dmesh = Grid2D(nx = nx, dx = dx)



# create a viewer

# solve

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

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Diffusion Example

# create a mesh


from fipy.variables.cellVariable import CellVariablevar = CellVariable(mesh = mesh, value = 0)

def centerCells(cell): return abs(cell.getCenter()[0] - L/2.) < L/10.

var.setValue(value = 1., cells = mesh.getCells(filter = centerCells))


# create a viewer

# solve

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

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Diffusion Example

# create a mesh


# set the initial conditionsdef centerCells(cell): return abs(cell.getCenter()[0] - L/2.) < L/10.

var.setValue(value = 1., cells = mesh.getCells(filter = centerCells))


# create a viewer

# solve

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

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Diffusion Example

# create a mesh



from fipy.terms.transientTerm import TransientTermfrom fipy.terms.implicitDiffusionTerm import ImplicitDiffusionTerm

## equivalent forms

## eq = (TransientTerm() == ImplicitDiffusionTerm(coeff = 1))

## eq = TransientTerm() - ImplicitDiffusionTerm(coeff = 1)

eq = (TransientTerm() - ImplicitDiffusionTerm(coeff = 1) == 0)

# create a viewer

# solve

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

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Diffusion Example

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

# create a mesh




# create a viewer

from fipy.viewers.gist1DViewer import Gist1DViewerviewer = Gist1DViewer(vars = (var,), limits = ('e', 'e', 0, 1))viewer.plot()

# solve

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# create a mesh




# create a viewer

# solve

for i in range(steps): var.updateOld() eq.solve() viewer.plot()

Diffusion Example

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

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Convection Example

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

# create a mesh


# create the boundary conditions


# create a viewer

# solve

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

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Convection Example

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

# create a mesh



from fipy.boundaryConditions.fixedValue import FixedValuebcs = ( FixedValue(mesh.getFacesLeft(), 0), FixedValue(mesh.getFacesRight(), 1),)


# create a viewer

# solve

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

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Convection Example

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

# create a mesh




from fipy.terms.implicitDiffusionTerm import ImplicitDiffusionTermdiffusionTerm = ImplicitDiffusionTerm(coeff = 1)

from fipy.terms.exponentialConvectionTerm import ExponentialConvectionTermconvectionTerm = ExponentialConvectionTerm(coeff = (10,0),

diffusionTerm = diffusionTerm)

eq = (diffusionTerm + convectionTerm == 0)

# create a viewer

# solve

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

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Convection Example

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

1.0

0.8

0.6

0.4

0.2

0.0

210

# create a mesh




# create a viewer

# solve

from fipy.solvers.linearCGSSolver import LinearCGSSolver

eq.solve(var = var, solver = LinearCGSSolver(tolerance = 1.e-15, steps = 2000), boundaryConditions = boundaryConditions)

viewer.plot()

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

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# create a mesh

# create the field variables

# create the phase equation

# create the temperature equation

# create a viewer

# solve

Phase Field Dendrite Exampleafter J. A. Warren, R. Kobayashi, A. E. Lobkovsky,

and W. C. Carter, Acta Materialia 51(20), (2003) 60356058

ttransient

= () diffusion

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t 22 (1 )m2(, T ) = 0

T

tDT2T

t= 0

transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion


(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion


VS dV

source

= 0

V (V )oldt

transient

face


face


face


V Ssource

= 0

1

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Phase Field Dendrite Example

# create a mesh



m2 = phase - 0.5 - kappa1 * arctan(kappa2 * temperatue)

phaseEq = (TransientTerm(coeff = tau) == \

ImplicitDiffusionTerm(coeff = alpha**2) + \

ImplicitSourceTerm(coeff = m2 * ((m2 < 0) - phase)) + \

(m2 > 0) * m2 * phase)


# create an iterator

# create a viewer

# solve

after J. A. Warren, R. Kobayashi, A. E. Lobkovsky, and W. C. Carter, Acta Materialia 51(20), (2003) 60356058

ttransient

= () diffusion

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t 22 (1 )m2(, T ) = 0

T

tDT2T

t= 0

transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion


(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion


VS dV

source

= 0

V (V )oldt

transient

face


face


face


V Ssource

= 0

1

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Phase Field Dendrite Example

# create a mesh



# create the temperature equationtemperatureEq = (TransientTerm() == \

ImplicitDiffusionTerm(coeff = tempDiffCoeff) + \

(phase - phase.getOld()) / timeStepDuration)

# create a viewer

# solve

after J. A. Warren, R. Kobayashi, A. E. Lobkovsky, and W. C. Carter, Acta Materialia 51(20), (2003) 60356058

ttransient

= () diffusion

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t 22 (1 )m2(, T ) = 0

T

tDT2T

t= 0

transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion


(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion


VS dV

source

= 0

V (V )oldt

transient

face


face


face


V Ssource

= 0

1

pipi

1

# create a mesh





# create a viewer

# solve

for i for range(steps): phase.updateOld() temperature.updateOld() phaseEq.solve(phase, dt = timeStepDuration) temperatureEq.solve(temperature, dt = timeStepDuration) if i%frameRate == 0: phaseViewer.plot() temperatureViewer.plot()

Phase Field Dendrite Exampleafter J. A. Warren, R. Kobayashi, A. E. Lobkovsky,

and W. C. Carter, Acta Materialia 51(20), (2003) 60356058

ttransient

= () diffusion

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

= () diffusion


+ (#u) convection

+ Ssource

V

()t

dV transient

=

S(#n ) dS

diffusion

+

Sn(#n ) dS

nth order diffusion

+


+

VS dV

source

V (V )oldt

transient

=face


+face


+face


+ V Ssource

1

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t 22 (1 )m2(, T ) = 0

T

tDT2T

t= 0

transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion


(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion


VS dV

source

= 0

V (V )oldt

transient

face


face


face


V Ssource

= 0

1

ttransient

= () diffusion

transient

t=

diffusion 22+

source (1 )m2(, T )

T

t= DT2T + L

cp

t

m2(, T ) = 12 1pi

arctan (2T )

1

pipi

1

Cahn-Hilliard Example

# create a mesh

# create the field variable



# create a viewer

# solve

t D

(f

#22

)= 0

f =a2

22(1 )2

= 0 on all boundaries3 = 0 on all boundaries

ttransient

D [1 6 (1 )] 2nd order diffusion

+ D#22 4th order diffusion

= 0

3

t D

(f

#22

)= 0

f =a2

22(1 )2

$n = 0 on all boundaries$n 3 = 0 on all boundaries

ttransient



= 0

3

pipi

1


# create a mesh




# create a viewer

# solve

t D

(f

#22

)= 0

f =a2

22(1 )2


ttransient



= 0

3

t D

(f

#22

)= 0

f =a2

22(1 )2


ttransient

Da2 [1 6 (1 )] 2nd order diffusion


= 0

3

pipi

1


# create a mesh



faceVar = var.getArithmeticFaceValue()doubleWellDerivative = a**2 * ( 1 - 6 * faceVar * (1 - faceVar))

from fipy.terms.nthOrderDiffusionTerm import NthOrderDiffusionTermfrom fipy.terms.transientTerm import TransientTermeq = (TransientTerm() == \ NthOrderDiffusionTerm(coeffs = (diffusionCoeff * doubleWellDerivative,)) -\ NthOrderDiffusionTerm(coeffs = (diffusionCoeff, epsilon**2)))


# create a viewer

# solve

t D

(f

#22

)= 0

f =a2

22(1 )2


ttransient



= 0

3

t D

(f

#22

)= 0

f =a2

22(1 )2


ttransient



= 0

3

pipi

1


# create a mesh




from fipy.boundaryConditions.nthOrderBoundaryCondition \ import NthOrderBoundaryCondition

BCs = (NthOrderBoundaryCondition(mesh.getExteriorFaces(), 0, 3),)

# create a viewer

# solve

t D

(f

#22

)= 0

f =a2

22(1 )2


ttransient



= 0

3

t D

(f

#22

)= 0

f =a2

22(1 )2


ttransient



= 0

3

pipi

1

# create a mesh




# create a viewer

# solve

dexp = 0.01 for step in range(steps): dt = Numeric.exp(dexp) dt = min(100, dt) dexp += 0.01 var.updateOld() eq.solve(var, boundaryConditions = BCs, solver = solver, dt = dt) viewer.plot()

t D

(f

#22

)= 0

f =a2

22(1 )2


ttransient



= 0

3


t D

(f

#22

)= 0

f =a2

22(1 )2


ttransient



= 0

3

pipi

1

CEAC Example

Copper electodeposition in submicron features

electrolyte additives influence deposition rate

CEAC - Curvature Enhanced Accelerator Coverage.

Bottom Up fill

Momentum plating

Curvature

l =Klcl

1 + Klcl(1 s)

i = (1 s)i0 exp(cF

RT)

dsdt

= ks [s K(1 s)]

K = k exp(1/2a

)

dadt

= |%v|a + ka(0a a)

s = 0s at t = 0

a = 0a at t = 0

0s =K0

1 + K0

K0 = k exp(

(0a)1/2)

i = i0 exp(F

RT)

i0 = i00 + i

10a

= 0 + 1a

4

Interface speed

fixed point moving with the interface

Accelerator coverage

Experimental sequence

45 degree side wall tilt

The Electrochemical Society Interface Winter 2004 51

FIG. 8. Seedless superfill is demonstrated by a sequence of images of direct copper deposition on trenches coatedwith a ruthenium barrier.3

FIG. 7. (a) A time sequence of images showing bottom-up copper superfilling of a via. (b) Tracking the interface midheight position during via filling provides a compari-son between the simulation and experiment. The inset shows a SPS colorized contour plot of simulated bottom-up film growth.16

(a) (b)

With further increases in the differentialdeposition rate being so constrained, thesidewalls impinge before the bottom sur-face is able to escape the trench. For ini-tial catalyst coverage of 0.88, the deposi-tion rate is predicted to be effectively sat-urated at the start of metal depositionwith geometrically driven changes incatalyst coverage on the concave sur-faces being minimal. Depletion effects

are considered only across the hydrody-namic boundary in these simulations.However, for the higher deposition ratesassociated with higher catalyst cover-ages, significant depletion of the Cu2+ion occurs within the trench, resultingin faster deposition toward the top of thefeature. This leads to an earlier impinge-ment at this location and void forma-tion as observed in two experimental

specimens ( = 0.44 and 0.88) ratherthan the predicted seams. Such deple-tion effects have been fully modeledelsewhere.15

Via Filling Experiments andSimulationsDeposition in vias, unliketrenches, is a three-dimensional prob-lem by virtue of the nonzero curvatureof the cylindrical sidewalls. Cross sec-tions detailing the filling of cylindricalvias with a 4.5 sidewall slope areshown in 10 s increments in Fig. 7.16 Inthis experiment the catalyst is adsorbedsimultaneously with copper plating inaccord with conventional practice.Wafer fragments were immersed in theSPS-PEG-Cl electrolyte, containing 6.4mol/L SPS, with a -0.25 V (Cu/Cu2+)growth potential already applied.Growth is essentially conformal for thefirst 60 s followed by the onset of bot-tom-up superfilling at 70 s. The fillingprocess is summarized by tracking theheight of the deposit along the center-line of the via, as a function of deposi-tion time. Favorable agreement withthe CEAC simulation is evident and thecorresponding simulated growth con-tours are given in the inset.16

Seedless Superfill

Current metallization technologyemploys three layers, a barrier metal,

LEVELER

ACCELERATOR

INHIBITOR

pipi

1

# create a mesh


# create the governing equations


# solve

CEAC Exampleafter D. Josell, D. Wheeler, W. H. Huber, and T. P. Moffat,

Physical Review Letters, 87(1), (2001) 016102

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =

{DLm when 0,0 when < 0

Dmn cm = v on = 0

ct

= Dc

D =

{DL when 00 when < 0

Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + (k0 + k33)ci(1 )

cmt

= Dmcmct

= Dc

Dmn cm = v on = 0Dn c = kc(1 ) on = 0

2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + kci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0

|| = 1


2

pipi

1

# create a meshfrom gapFillMesh import TrenchMesh mesh = TrenchMesh(cellSize = 0.002e-6, trenchSpacing = 1e-6, trenchDepth = 0.5e-6, boundaryLayerDepth = 50e-6, aspectRatio = 2.)




# solve



v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + (k0 + k33)ci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + kci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0

|| = 1


2

pipi

1

# create a mesh


# distance variable

# surface accelerator concentration

# bulk accelerator concentration

# metal ion concentration

# interfacial velocity

exchangeCurrentDensity = constantCurrentDensity \ + acceleratorDependenceCurrentDensity * acceleratorVar.getInterfaceVar()

currentDensity = exchangeCurrentDensity * metalVar / bulkMetalConcentration * Numeric.exp(-transferCoefficient * faradaysConstant * overpotential \ / gasConstant / temperature)

depositionRateVariable = currentDensity * atomicVolume / charge / faradaysC



# create the viewers

# solve



v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + (k0 + k33)ci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + kci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0

|| = 1


2

pipi

1

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0

|| = 1


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + (k0 + k33)ci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + kci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2



# create a mesh



# advection equation

from fipy.terms.transientTerm import TransientTermfrom fipy.models.levelSet.advection.higherOrderAdvectionTerm \ import HigherOrderAdvectionTerm

advectionEquation = TransientTerm() + HigherOrderAdvectionTerm(coeff = extensionVelocityVariable)

# surfactant equation

# metal equation

# bulk accelerator equation


# solve

pipi

1



v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + (k0 + k33)ci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t= vext||

t= Jv + kci(1 )

cmt

= Dmcmct

= Dc


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0


2

# create a mesh




# solve

for step in range(numberOfSteps): if step % levelSetUpdateFrequency == 0: distanceVar.calcDistanceFunction() for var in (distanceVar, acceleratorVar, metalVar, bulAcceleratorVar): var.updateOld() dt = cflNumber * cellSize / max(extensionVelocityVariable) distanceVar.extendVariable(extensionVelocityVariable)

advectionEquation.solve(distanceVar, dt = dt) surfactantEquation.solve(acceleratorVar, dt = dt) metalEquation.solve(metalVar, dt = dt, boundaryConditions = metalEquationBCs) bulkAcceleratorEquation.solve(bulkAcceleratorVar, dt = dt,

boundaryConditions = acceleratorBCs)

v =inF

i = i0cimcm

exp(F

RT

)i0() = b0 + b1

cmt

= Dmcm

Dm =


Dmn cm = v on = 0

ct

= Dc

D =


Dn c = kc(1 ) on = 0

t= Jv + (k0 + k33)ci(1 )

v =nF

(b0 + b1)cimcm

exp(F

RT

)

t+ vext|| = 0

t Jv kci(1 ) = 0cmt

Dmcm = 0ct Dc = 0

|| = 1


2

pipi

1



no leveler

acce

lera

tor

cove

rage

pipi

1


Physical Review Letters, 87(1), (2001) 016102with leveler

(just add another surfactant equation set)no leveler

acce

lera

tor

cove

rage

pipi

1

Term

Solver

BoundaryCondition

Variable Viewer

SparseMatrix

Mesh

Cell

Face

Vertex

FiPy Design - Objects

pipi

1

FiPy Design - Terms

Term

Solver

BoundaryCondition

Variable Viewer

SparseMatrix

Mesh

Cell

Face

Vertex

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion


(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion


VS dV

source

= 0

V (V )oldt

transient

face


face


face


V Ssource

= 0

1

Variable

Term

Solver

BoundaryCondition

FaceTermNthOrderTerm

SparseMatrix

CellTerm

TransientTerm SourceTerm DiffusionTerm ConvectionTerm

cell

adjacentcell

face

vertex

pipi

1

FiPy Design - Variables

ttransient

() diffusion

= 0

(#u) convection

+ () diffusion

= 0

|x=0 = 0 |x=L = 1

t= 22+ (1 )m2(, T )

T

t= DT2T +

t transient

diffusion

source

m2(, T ) = 12 1pi

arctan (2T )

()t

transient

() diffusion


(#u) convection

Ssource

= 0

V

()t

dV transient

S(#n ) dS

diffusion

Sn(#n ) dS

nth order diffusion


VS dV

source

= 0

V (V )oldt

transient

face


face


face


V Ssource

= 0

1

Term

Solver

BoundaryCondition

Variable Viewer

SparseMatrix

Mesh

Cell

Face

Vertex

Term

Variable

CellVariable FaceVariable GradVariable

Viewer Mesh

CellGradVariable FaceGradVariable

Either:

solution variables (evaluated by Term)set by intermediate calculation

Lazy evaluation

Physical dimensions

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Efficiency Issues

Tested efficiency against Ryo Kobayashis FORTRAN code specifically written to solve grain impingement problem.

Naive all-Python FiPy was 200X as slow

Smarter all-Python FiPy is 30X as slow

After optimization and judicious C-inline, FiPy is now 7X as slow

Development time is reduced considerably

FORTRAN requires 1800 lines of single-use codePython smart requires 100 linesPython inline requires 300 lines

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Future Work

Adaptive meshes

Multigrid

Cell-centered finite volume

Repair/improve support for physical dimensions

Export (formatted text, HDF, etc.)

Viewers (refactor and add more, e.g., OpenDX (Dan Lewis?))

More examples:

Fluid flowElasticityElectrochemistry Phase Field (implemented, but vexing)

???

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Summary

Cross-platform, Open Source code for solving phase transformation problems

Capable of solving multivariate, coupled, non-linear PDEs

Extensive documentation, dozens of examples, hundreds of tests

Python syntax both easy to learn and powerful

Object-oriented structure easy to adapt to unique problems

Slower to run than hand-tailored FORTRAN or C

but much faster to write

www.ctcms.nist.gov/fipy/

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Acknowledgements

Alex Mont Montgomery Blair High School

John Dukovic Applied Materials

Daniel Josell NIST Metallurgy Division

Tom Moffat NIST Metallurgy Division

Steve Langer NIST Information Technology Laboratory

Andrew Reid NIST Materials Science and Engineering Laboratory

Edwin Garca NIST Materials Science and Engineering Laboratory

Daniel Lewis GE Ceramic and Metallurgy Technologies

2005 03 01 Wheeler Presentation

Documents

Transcript of 2005 03 01 Wheeler Presentation