SIAM Workshop Introduction To Python For Mathematicians and Scientists

SIAM Workshop
Introduction to Python for mathematicians

and scientists
Mike Sussman
[email protected]
http://www.math.pitt.edu/%7esussmanm
October 18, 2014
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Topics
Introduction
Python, the language
Python language specifics
Python basics, Example 1
Functions, flow control, and import, Example 2
Watch out, Alexander!
Classes
A finite element program
Gauß integration, Example 3
BVP by FEM
Shape functions, Example 4
Code, Example 4
FEM code, Example 5
Python language comments
FEniCS
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Who am I?
I Part-time faculty in Math Dept.

I Experience at Bettis lab
I Administer 2070/2071 Numerical Analysis lab
I Interested in numerical applications associated with fluid flow
I Interested in large-scale scientific computing
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Objectives
I Introduce Python programming

I Focus on use in scientific work
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References
I Recent Python and NumPy/SciPy books from oreilly.com

I Python Reference:
https://docs.python.org/2/reference/index.html
I The Python Tutorial
https://docs.python.org/2/tutorial
I 10-minute Python tutorial
http://www.stavros.io/tutorials/python/
I Tentative NumPy Tutorial
http://wiki.scipy.org/Tentative_NumPy_Tutorial
I Wonderful scientific Python blog by Greg von Winckel
http://www.scientificpython.net/
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Getting Python
1. Recommend using WinPython on MS-Windows

http://sourceforge.net/p/winpython/wiki/Installation
2. Download version for Python 2.7
3. Run the installer
4. Do not “register” it
5. Navigate to Downloads\WinPython...
6. Run Spyder (not light)
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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What is Python?
I Computer programming language

I Interpreted
I Object-oriented
I Extended using “modules” and “packages”
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Python and modules
I Core Python: bare-bones

https://docs.python.org/2/reference/index.html
I “Standard Library”
https://docs.python.org/2/library/index.html
I “Python package index” (50,000 packages)
https://pypi.python.org
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Python for scientific use
I numpy
I scipy
I matplotlib.pylab
I sympy
I SAGE
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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Running Python
I Use Spyder IDE

I Run python in a Cygwin command window
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File structure and line syntax
I No mandatory statement termination character.

I Blocks are determined by indentation
I Statements requiring a following block end with a colon (:)
I Comments start with octothorpe (#), end at end of line
I Multiline comments are surrounded by triple double quotes (""")
I Continue lines with \
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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Python basics
example1.py
1. Debugger
2. x/3, -x/3
3. float(x)/3
4. conjugate(z), abs(w), w*w
5. y0==y1
6. 2**100 (answer is long)
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Basic data types
I Integers: 0, -5, 100

I Floating-point numbers: 3.14159, 6.02e23
I Complex numbers: 1.5 + 0.5j
I Strings: "A string"
I Can use single quotes
I Long (integers of arbitrary length)
I Logical or Boolean: True, False
I None
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Basic operations
I +, -, *, /
I ** (raise to power)
I % (remainder)
I and, or, not
I >, <, >=, <=, ==, != (logical comparison)
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Python array-type data types
I List: [0,"string",another list ]

I Tuple: immutable list, surrounded by ()
I Dictionary (dict): {"key1":"value1",2:3,"pi":3.14}
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Getting help
>>> help(complex)
class complex(object)
| complex(real[, imag]) -> complex number
|
| Create a complex number from a real part and an optional imaginary part.
| This is equivalent to (real + imag*1j) where imag defaults to 0.
|
| Methods defined here:
|
| __abs__(...)
| x.__abs__() <==> abs(x)
|
| __add__(...)
| x.__add__(y) <==> x+y
|
| __div__(...)
| x.__div__(y) <==> x/y
|
| conjugate(...)
| complex.conjugate() -> complex
|
| Return the complex conjugate of its argument. (3-4j).conjugate() == 3+4j
| -----------------------------------------------
| Data descriptors defined here:
|
| imag
| the imaginary part of a complex number
|
| real
| the real part of a complex number
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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Functions, flow control, and import
example2.py
1. Debugger
2. i/10
3. n, term, partialSum out of workspace after return!
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Functions
I Functions begin with def

I The def line ends with a colon
I Function bodies are indented
I Functions use return to return values
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Flow control
I if ... elif ... else

I for
I while
I Bodies are indented
I range(N) generates 0, 1, ... , (N-1)
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Importing and naming
I Include external libraries using import

I import numpy
Imports all numpy functions, call as numpy.sin(x)
I import numpy as np
Imports all numpy functions, call as np.sin(x)
I from numpy import *
Imports all numpy functions, call as sin(x)
I from numpy import sin
Imports only sin()
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Pylab in Spyder
Automatically does following imports

from pylab import *
from numpy import *
from scipy import *
You must do your own importing when writing code in files
I strongly suggest using names.
import numpy as np
import scipy.linalg as la
import matplotlib.pyplot as plt
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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Subscripts
I x = [ ’a’, ’b’, ’c’, ’d’ ]
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Subscripts
I x = [ ’a’, ’b’, ’c’, ’d’ ]

I x[0] is ’a’
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Subscripts
I x = [ ’a’, ’b’, ’c’, ’d’ ]

I x[0] is ’a’
I x[3] is ’d’
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Subscripts
I x = [ ’a’, ’b’, ’c’, ’d’ ]

I x[0] is ’a’
I x[3] is ’d’
I x[0:2] is [ ’a’, ’b’ ]
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Subscripts
I x = [ ’a’, ’b’, ’c’, ’d’ ]

I x[0] is ’a’
I x[3] is ’d’
I x[0:2] is [ ’a’, ’b’ ]
I x[-1] is ’d’
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Equals, Copies, and Deep Copies
>>> import copy as cp
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> d=cp.deepcopy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [1, 2]] z= ["*", 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [1, 2]] z= ["*", 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> z[2][0]=9
>>> print "y=",y," z=",z," c=",c," d=",d
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [1, 2]] z= ["*", 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> z[2][0]=9
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, 2]] z= ["*", 4, [9, 2]] c= [3, 4, [9, 2]] d= [3, 4, [1, 2]]
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [1, 2]] z= ["*", 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> z[2][0]=9
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, 2]] z= ["*", 4, [9, 2]] c= [3, 4, [9, 2]] d= [3, 4, [1, 2]]
>>> c[2][1]=’c’
>>> print "y=",y," z=",z," c=",c," d=",d
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [1, 2]] z= ["*", 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> z[2][0]=9
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, 2]] z= ["*", 4, [9, 2]] c= [3, 4, [9, 2]] d= [3, 4, [1, 2]]
>>> c[2][1]=’c’
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, c]] z= ["*", 4, [9, c]] c= [3, 4, [9, c]] d= [3, 4, [1, 2]]
>>> x
[9, c]
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [1, 2]] z= ["*", 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> z[2][0]=9
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, 2]] z= ["*", 4, [9, 2]] c= [3, 4, [9, 2]] d= [3, 4, [1, 2]]
>>> c[2][1]=’c’
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, c]] z= ["*", 4, [9, c]] c= [3, 4, [9, c]] d= [3, 4, [1, 2]]
>>> x
[9, c]
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [1, 2]] z= ["*", 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> z[2][0]=9
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, 2]] z= ["*", 4, [9, 2]] c= [3, 4, [9, 2]] d= [3, 4, [1, 2]]
>>> c[2][1]=’c’
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, c]] z= ["*", 4, [9, c]] c= [3, 4, [9, c]] d= [3, 4, [1, 2]]
>>> x
[9, c]
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>>> x=[1,2]
>>> y=[3,4,x]
>>> z=y
>>> print "x=",x," y=",y," z=",z
x= [1, 2] y= [3, 4, [1, 2]] z= [3, 4, [1, 2]]
>>> c=cp.copy(y)
>>> print "y=",y," z=",z," c=",c," d=",d
y= [3, 4, [1, 2]] z= [3, 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> y[0]="*"
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [1, 2]] z= ["*", 4, [1, 2]] c= [3, 4, [1, 2]] d= [3, 4, [1, 2]]
>>> z[2][0]=9
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, 2]] z= ["*", 4, [9, 2]] c= [3, 4, [9, 2]] d= [3, 4, [1, 2]]
>>> c[2][1]=’c’
>>> print "y=",y," z=",z," c=",c," d=",d
y= ["*", 4, [9, c]] z= ["*", 4, [9, c]] c= [3, 4, [9, c]] d= [3, 4, [1, 2]]
>>> x
[9, c]
Moral: Only deepcopy does it right! 28 / 56

Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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A Class is a generalized data type
I numpy defines a class called ndarray

I Define variable x of type ndarray, a one-dimensional array of
length 10:
import numpy as np
x=np.ndarray([10])
I Varibles of type ndarray are usually just called “array”.
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Classes define members’ “attributes”
I Attributes can be data

I Usually, data attributes are “hidden”
I Names start with double-underscore
I Programmers are trusted not to access such data
I Attributes can be functions
I Functions are provided to access “hidden” data
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Examples of attributes
One way to generate a numpy array is:
import numpy as np
x=np.array( [0, 0.1, 0.2, 0.4, 0.9, 3.14] )
I (data attribute) x.size is 6.

I (data attribute) x.dtype is "float64" (quotes mean “string”)
I (function attribute) x.item(2) is 0.2 (parentheses mean
“function”)
I Copy function is provided by numpy:
y = x.copy() or
y = np.copy(x)
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Operators can be overridden
I Multiplication and division are pre-defined (overridden)

>>> 3*x
array([ 0. , 0.3 , 0.6 , 1.2 , 2.7 , 9.42])
I Brackets can be overridden to make things look “normal”
>>> x[2] # bracket overridden
0.2
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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Gauß integration
R1
I Integrate Q = 0
f (ξ)dξ
P3
I Approximate it as Q ≈ i=1 wi f (gi )
I wi and gi come from reference materials.
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Example 3
example3.py
I Function of a vector returns a vector
I np.not
I Extensive testing!
I y=0.0*x+1.0 ⇐⇒ y=np.zeros_like(x) ⇐⇒
y=np.zeros( shape(x) )
I append() is a List attribute (function)
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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A boundary value problem by the finite element
method
−u 00 + u = f on [0, L]
0
u (0) = 0 = u 0 (L)
1. Pick a basis of functions φi (x)

P
2. Write u(x) ≈ i ui φi (x)
3. Plug into equation
4. Multiply equation through by φj (x) and integrate
5. Solve system of equations for ui
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FEM formulation
−u 00 + u = f (x) u 0 (0) = u 0 (L) = 0
Multiply through by a function v and integrate
Z L h iL Z L Z L
u 0 (x)v 0 (x)dx + u 0 (x)v (x) + u(x)v (x)dx = f (x)v (x)dx
0 0 0 0
The bracketed term drops out because of boundary values.

Assume that an approximate solution can be written as
N
X
u(x) = uj φj (x)
j=1
Choosing v (x) = φi (x) yields

N
!
X Z L Z L Z L
φ0i (x)φ0j (x)dx + φi (x)φj (x)dx uj = f (x)φi (x)dx .
0 0
j=1
| {z } |0 {z }
aij fi
AU = F.
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Do integrations elementwise
I Break [0, L] into N uniform subintervals ek : k = 0, . . . , N − 1,

each of width ∆x
RL P R
I φ (x)f (x) dx = k ek φi (x)f (x) dx
0 i
R R1
I φ (x)f (x) dx = 0 φi (ξ)f (ξ)∆x dξ
ek i
I Inside ek , define
φ0 (ξ) = 2.0(ξ − 0.5)(ξ − 1.0),

φ1 (ξ) = 4.0ξ(1.0 − ξ),
φ2 (ξ) = 2.0ξ(ξ − 0.5)
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
42 / 56
What do the shape functions look like?
I Suppose ∆x = L/N so that ek = [k ∆x, (k + 1)∆x]

I Define xi = i∆x/2 for i = 0, 1, . . . , 2N
I x2N = L
I ek = [x2k , x2K +2 ] for k = 0, 1, . . . , (N − 1)
I Map ek → [0, 1] is given by x = (k + ξ)∆x
I Inside ek ,
ξ = (x − k ∆x)/∆x
φ0k (x) = 2.0(ξ − 0.5)(ξ − 1.0),
φ1k (x) = 4.0ξ(1.0 − ξ),
φ2k (x) = 2.0ξ(ξ − 0.5)
I Outside ek , φik = 0
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Shape functions are a “partition of unity”
I Each φik is 1 at ξi ∈ ek and 0 elsewhere

I Each φ is piecewise quadratic
I The unique piecewise quadratic function satisfying φi (xj ) = δij
agrees with one of the φik when xj ∈ ek .
P
i φi (x) = 1
I
I φi form a basis of the space of piecewise quadratic functions with

breaks at xi .
P
I u piecewise quadratic ⇒ u(x) = i ui φi (x)
I ui are called “degrees of freedom.”
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
45 / 56
Example 4
example4.py
I φ21 and φ02 together make φ4
I 2D subscripting: (Amat1[ m, n ])
I plt.plot and plt.hold are like Matlab
I np.linspace is like Matlab
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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Example 5
example5.py
I Solves −u 00 + u = f in weak form
R 0 0 R R
u v + uv = fv with
Neumann boundary conditions on [0, 5]
I Two tests: f0 (x) = 1 and f1 (x) = x
I Two exact solutions: u0 (x) = x and
u1 (x) = cosh(5)−1
sinh(5) cosh(x) − sinh(x) + x
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Convergence results
Convergence results
N error ratio
5 0.000142449953558
10 8.60661737944e-06 16.55121254702143
Fourth-order
20 5.21196552761e-07 16.51318937903001
40 3.19766785929e-08 16.29927108429344
80 1.97897364593e-09 16.1582134550725
160 1.23080146312e-10 16.0787397905218
convergence is too high, a consequence of “superconvergence.”
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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Some differences with C++
I Indentation
I **, and, or
I long
I (=) and copying
I Interpreted vs. compiled
I No private variables
I Programmer must pretend not to see variables starting with __
I No const
I Cannot have two functions with same name
I Allowed in C++ if signatures different
I Automatic garbage collection
I Variable types are implicit
I Constructor syntax
I Extra parameter self
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Some versions/variants of Python
I CPython: reference implementation of Python, written in C

I Cython: superset of Python. Easy to write integrated C or C++
and Python code
I Jython: version of Python written in Java, can easily call Java
methods
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Topics
Introduction
Classes
BVP by FEM
Code, Example 4
FEM code, Example 5
FEniCS
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FEniCS
FEniCS is a package for solving partial differential equations

expressed in weak form.
1. You write a script in high-level Python
I Uses UFL form language
I Can use numpy, scipy, matplotlib.pyplot, etc.
I Can use Viper for plotting
2. DOLFIN interprets the script
3. UFL is passed to FFC for compilation
4. Instant turns it into C++ callable from Python (“swig”)
5. Linear algebra is passed to PETSc or UMFPACK
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DOLFIN classes
I Sparse matrices and vectors via PETSc

I Solvers via PETSc can run in parallel
I Eigenvalues via SLEPc
I Newton solver for nonlinear equations
I Connected to ParaView for plotting solutions
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FEniCS example
from dolfin import *
# Create mesh and define function space

mesh = UnitSquareMesh(6, 4)
V = FunctionSpace(mesh, ’Lagrange’, 1)
# Define boundary conditions

u0 = Expression(’1 + x[0]*x[0] + 2*x[1]*x[1]’)
def u0_boundary(x, on_boundary):

return on_boundary
bc = DirichletBC(V, u0, u0_boundary)

Always start with this
# Define variational problem
u = TrialFunction(V)
v = TestFunction(V)
f = Constant(-6.0)
a = inner(nabla_grad(u), nabla_grad(v))*dx
L = f*v*dx
# Compute solution
u = Function(V)
solve(a == L, u, bc)
# Plot solution and mesh

plot(u,interactive=True)
plot(mesh,interactive=True)
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FEniCS example



return on_boundary
bc = DirichletBC(V, u0, u0_boundary) I Mesh on [0, 1] × [0, 1]

I Uniform 6 cells in x0 , 4 in x1
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary

Linear Lagrange shape functions
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary
bc = DirichletBC(V, u0, u0_boundary) I “Expression” causes a

compilation
u = TrialFunction(V) I x is a “global variable”
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary

I on_boundary is a “global”
# Define variational problem variable
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary
I Set Dirichlet b.c.
I Can be more than one
# Define variational problem boundary
v = TestFunction(V) I u0_boundary is used
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary
I This is UFL
I Specify weak form
R
I −∆u
R = f ⇐⇒ ∇u∇v dx =
v = TestFunction(V) f v dx
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary
bc = DirichletBC(V, u0, u0_boundary) Define trial and test function

# Define variational problem spaces
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary

R
Define L(v ) = f (x)v (x) dx with
# Define variational problem f = −6
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary
bc = DirichletBC(V, u0, u0_boundary) R

Define a(u, v ) = ∇u · ∇v dx
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary

u is redefined as a Function
# Define variational problem insteadof TrialFunction
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



return on_boundary
bc = DirichletBC(V, u0, u0_boundary) Solve the system

L(v ) = a(u, v ) ∀v subject to
u = TrialFunction(V) boundary conditions.
v = TestFunction(V)
f = Constant(-6.0)
L = f*v*dx
# Compute solution
u = Function(V)

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FEniCS example



I Plot u and mesh in two
return on_boundary frames.
bc = DirichletBC(V, u0, u0_boundary) I interactive=True causes
the plot to remain displayed
u = TrialFunction(V) until destroyed by mouse.
v = TestFunction(V)
f = Constant(-6.0) I Can also put
a = inner(nabla_grad(u), nabla_grad(v))*dx interactive() at the end.
L = f*v*dx
# Compute solution
u = Function(V)

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SIAM Workshop Introduction To Python For Mathematicians and Scientists

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SIAM Workshop Introduction To Python For Mathematicians and Scientists

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SIAM Workshop

Introduction to Python for mathematicians

October 18, 2014

I Part-time faculty in Math Dept.

I Introduce Python programming

I Recent Python and NumPy/SciPy books from oreilly.com

1. Recommend using WinPython on MS-Windows

I Computer programming language

I Core Python: bare-bones

I Use Spyder IDE

I No mandatory statement termination character.

I Integers: 0, -5, 100

I List: [0,"string",another list ]

I Functions begin with def

I if ... elif ... else

I Include external libraries using import

Automatically does following imports

I x = [ ’a’, ’b’, ’c’, ’d’ ]

I x = [ ’a’, ’b’, ’c’, ’d’ ]

I x = [ ’a’, ’b’, ’c’, ’d’ ]

I x = [ ’a’, ’b’, ’c’, ’d’ ]

I x = [ ’a’, ’b’, ’c’, ’d’ ]

Moral: Only deepcopy does it right! 28 / 56

I numpy defines a class called ndarray

I Attributes can be data

One way to generate a numpy array is:

I (data attribute) x.size is 6.

I Multiplication and division are pre-defined (overridden)

1. Pick a basis of functions φi (x)

The bracketed term drops out because of boundary values.

Choosing v (x) = φi (x) yields

I Break [0, L] into N uniform subintervals ek : k = 0, . . . , N − 1,

φ0 (ξ) = 2.0(ξ − 0.5)(ξ − 1.0),

I Suppose ∆x = L/N so that ek = [k ∆x, (k + 1)∆x]

I Each φik is 1 at ξi ∈ ek and 0 elsewhere

I φi form a basis of the space of piecewise quadratic functions with

I CPython: reference implementation of Python, written in C

FEniCS is a package for solving partial differential equations

I Sparse matrices and vectors via PETSc

# Create mesh and define function space

# Define boundary conditions

def u0_boundary(x, on_boundary):

bc = DirichletBC(V, u0, u0_boundary)

# Plot solution and mesh

# Create mesh and define function space

# Define boundary conditions

def u0_boundary(x, on_boundary):

bc = DirichletBC(V, u0, u0_boundary) I Mesh on [0, 1] × [0, 1]

# Plot solution and mesh

# Create mesh and define function space

# Define boundary conditions

def u0_boundary(x, on_boundary):

bc = DirichletBC(V, u0, u0_boundary)

# Plot solution and mesh

# Create mesh and define function space

# Define boundary conditions

def u0_boundary(x, on_boundary):

bc = DirichletBC(V, u0, u0_boundary) I “Expression” causes a