pycse - Python Computations in Science and

Engineering
John Kitchin
2013-01-21 Mon

Contents
1 Overview 8

2 Basic python usage 8

2.1 Basic math . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2 Advanced mathematical operators . . . . . . . . . . . . . . . . . 9
2.2.1 Exponential and logarithmic functions . . . . . . . . . . . 10
2.3 Creating your own functions . . . . . . . . . . . . . . . . . . . . . 10
2.4 Defining functions in python . . . . . . . . . . . . . . . . . . . . . 11
2.5 Advanced function creation . . . . . . . . . . . . . . . . . . . . . 13
2.6 Lambda Lambda Lambda . . . . . . . . . . . . . . . . . . . . . . 16
2.6.1 Applications of lambda functions . . . . . . . . . . . . . . 18
2.6.2 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.7 Creating arrays in python . . . . . . . . . . . . . . . . . . . . . . 19
2.8 Functions on arrays of values . . . . . . . . . . . . . . . . . . . . 22
2.9 Some basic data structures in python . . . . . . . . . . . . . . . . 24
2.9.1 the list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.9.2 tuples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.9.3 struct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.9.4 dictionaries . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.9.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
2.10 Indexing vectors and arrays in Python . . . . . . . . . . . . . . . 26
2.10.1 2d arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.10.2 Using indexing to assign values to rows and columns . . . 28
2.10.3 3D arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.10.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.11 Controlling the format of printed variables . . . . . . . . . . . . . 29
2.12 Advanced string formatting . . . . . . . . . . . . . . . . . . . . . 32

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3 Math 33
3.1 Numeric derivatives by differences . . . . . . . . . . . . . . . . . 33
3.2 Vectorized numeric derivatives . . . . . . . . . . . . . . . . . . . 35
3.3 2-point vs. 4-point numerical derivatives . . . . . . . . . . . . . . 36
3.4 Derivatives by polynomial fitting . . . . . . . . . . . . . . . . . . 37
3.5 Derivatives by fitting a function and taking the analytical derivative 39
3.6 Derivatives by FFT . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.7 A novel way to numerically estimate the derivative of a function
- complex-step derivative approximation . . . . . . . . . . . . . . 42
3.8 Vectorized piecewise functions . . . . . . . . . . . . . . . . . . . . 44
3.9 Smooth transitions between discontinuous functions . . . . . . . 47
3.9.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.10 Smooth transitions between two constants . . . . . . . . . . . . . 52
3.11 On the quad or trapz’d in ChemE heaven . . . . . . . . . . . . . 53
3.11.1 Numerical data integration . . . . . . . . . . . . . . . . . 54
3.11.2 Combining numerical data with quad . . . . . . . . . . . 55
3.11.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.12 Polynomials in python . . . . . . . . . . . . . . . . . . . . . . . . 56
3.12.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
3.13 The trapezoidal method of integration . . . . . . . . . . . . . . . 58
3.14 Numerical Simpsons rule . . . . . . . . . . . . . . . . . . . . . . . 59
3.15 Integrating functions in python . . . . . . . . . . . . . . . . . . . 60
3.15.1 double integrals . . . . . . . . . . . . . . . . . . . . . . . . 60
3.15.2 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
3.16 Integrating equations in python . . . . . . . . . . . . . . . . . . . 61
3.17 Function integration by the Romberg method . . . . . . . . . . . 62
3.18 Symbolic math in python . . . . . . . . . . . . . . . . . . . . . . 62
3.18.1 Solve the quadratic equation . . . . . . . . . . . . . . . . 62
3.18.2 differentiation . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.18.3 integration . . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.18.4 Analytically solve a simple ODE . . . . . . . . . . . . . . 63
3.19 Is your ice cream float bigger than mine . . . . . . . . . . . . . . 64

4 Linear algebra 65
4.1 Potential gotchas in linear algebra in numpy . . . . . . . . . . . . 65
4.2 Solving linear equations . . . . . . . . . . . . . . . . . . . . . . . 67
4.3 Rules for transposition . . . . . . . . . . . . . . . . . . . . . . . . 69
4.3.1 The transpose in Python . . . . . . . . . . . . . . . . . . 69
4.3.2 Rule 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
4.3.3 Rule 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
4.3.4 Rule 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
4.3.5 Rule 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
4.3.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
4.4 Sums products and linear algebra notation - avoiding loops where
possible . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
4.4.1 Old-fashioned way with a loop . . . . . . . . . . . . . . . 71

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 4.4.2 The numpy approach . . . . . . . . . . . . . . . . . . . . 71
4.4.3 Matrix algebra approach. . . . . . . . . . . . . . . . . . . 72
4.4.4 Another example . . . . . . . . . . . . . . . . . . . . . . . 72
4.4.5 Last example . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.4.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.5 Determining linear independence of a set of vectors . . . . . . . . 73
4.5.1 another example . . . . . . . . . . . . . . . . . . . . . . . 75
4.5.2 Near deficient rank . . . . . . . . . . . . . . . . . . . . . . 75
4.5.3 Application to independent chemical reactions. . . . . . . 75
4.6 Reduced row echelon form . . . . . . . . . . . . . . . . . . . . . . 77
4.7 Computing determinants from matrix decompositions . . . . . . 78
4.8 Calling lapack directly from scipy . . . . . . . . . . . . . . . . . . 79

5 Nonlinear algebra 80
5.1 Know your tolerance . . . . . . . . . . . . . . . . . . . . . . . . . 81
5.2 Solving integral equations with fsolve . . . . . . . . . . . . . . . . 82
5.2.1 Summary notes . . . . . . . . . . . . . . . . . . . . . . . . 84
5.3 Method of continuity for nonlinear equation solving . . . . . . . . 84
5.4 Method of continuity for solving nonlinear equations - Part II . . 88
5.5 Counting roots . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
5.5.1 Use roots for this polynomial . . . . . . . . . . . . . . . . 91
5.5.2 method 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.5.3 Method 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.6 Finding the nth root of a periodic function . . . . . . . . . . . . 93

6 Statistics 95
6.1 Introduction to statistical data analysis . . . . . . . . . . . . . . 95
6.2 Basic statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
6.3 Confidence interval on an average . . . . . . . . . . . . . . . . . . 97
6.4 Are averages different . . . . . . . . . . . . . . . . . . . . . . . . 97
6.5 Model selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
6.6 Numerical propagation of errors . . . . . . . . . . . . . . . . . . . 107
6.6.1 Addition and subtraction . . . . . . . . . . . . . . . . . . 108
6.6.2 Multiplication . . . . . . . . . . . . . . . . . . . . . . . . . 108
6.6.3 Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
6.6.4 exponents . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
6.6.5 the chain rule in error propagation . . . . . . . . . . . . . 109
6.6.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
6.7 Another approach to error propagation . . . . . . . . . . . . . . . 110
6.7.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
6.8 Random thoughts . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
6.8.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

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7 Data analysis 117
7.1 Fit a line to numerical data . . . . . . . . . . . . . . . . . . . . . 117
7.2 Linear least squares fitting with linear algebra . . . . . . . . . . . 118
7.3 Linear regression with confidence intervals. . . . . . . . . . . . . 119
7.4 Nonlinear curve fitting . . . . . . . . . . . . . . . . . . . . . . . . 121
7.5 Nonlinear curve fitting by direct least squares minimization . . . 122
7.6 Parameter estimation by directly minimizing summed squared
errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
7.7 Nonlinear curve fitting with parameter confidence intervals . . . 127
7.8 Nonlinear curve fitting with confidence intervals . . . . . . . . . . 129
7.9 Graphical methods to help get initial guesses for multivariate
nonlinear regression . . . . . . . . . . . . . . . . . . . . . . . . . 130
7.10 Fitting a numerical ODE solution to data . . . . . . . . . . . . . 134
7.11 Reading in delimited text files . . . . . . . . . . . . . . . . . . . . 135

8 Interpolation 136
8.1 Better interpolate than never . . . . . . . . . . . . . . . . . . . . 136
8.1.1 Estimate the value of f at t=2. . . . . . . . . . . . . . . . 136
8.1.2 improved interpolation? . . . . . . . . . . . . . . . . . . . 137
8.1.3 The inverse question . . . . . . . . . . . . . . . . . . . . . 138
8.1.4 A harder problem . . . . . . . . . . . . . . . . . . . . . . 139
8.1.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
8.2 Interpolation of data . . . . . . . . . . . . . . . . . . . . . . . . . 141
8.3 Interpolation with splines . . . . . . . . . . . . . . . . . . . . . . 142

9 Optimization 142
9.1 Constrained optimization . . . . . . . . . . . . . . . . . . . . . . 142
9.2 Using Lagrange multipliers in optimization . . . . . . . . . . . . 144
9.2.1 Construct the Lagrange multiplier augmented function . . 145
9.2.2 Finding the partial derivatives . . . . . . . . . . . . . . . 145
9.2.3 Now we solve for the zeros in the partial derivatives . . . 145
9.2.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
9.3 Linear programming example with inequality constraints . . . . . 146
9.4 Find the minimum distance from a point to a curve. . . . . . . . 147

10 Differential equations 149

10.1 Ordinary differential equations . . . . . . . . . . . . . . . . . . . 150
10.1.1 Numerical solution to a simple ode . . . . . . . . . . . . . 150
10.1.2 Plotting ODE solutions in cylindrical coordinates . . . . . 151
10.1.3 ODEs with discontinuous forcing functions . . . . . . . . 152
10.1.4 Simulating the events feature of Matlab’s ode solvers . . . 153
10.1.5 Mimicking ode events in python . . . . . . . . . . . . . . 155
10.1.6 Solving an ode for a specific solution value . . . . . . . . . 158
10.1.7 A simple first order ode evaluated at specific points . . . 161
10.1.8 Stopping the integration of an ODE at some condition . . 161
10.1.9 Finding minima and maxima in ODE solutions with events162

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 10.1.10 Error tolerance in numerical solutions to ODEs . . . . . . 163
10.1.11 Solving parameterized ODEs over and over conveniently . 167
10.1.12 Yet another way to parameterize an ODE . . . . . . . . . 168
10.1.13 Another way to parameterize an ODE - nested function . 169
10.1.14 Solving a second order ode . . . . . . . . . . . . . . . . . 170
10.1.15 Solving Bessel’s Equation numerically . . . . . . . . . . . 172
10.1.16 Phase portraits of a system of ODEs . . . . . . . . . . . . 174
10.1.17 Linear algebra approaches to solving systems of constant
coefficient ODEs . . . . . . . . . . . . . . . . . . . . . . . 177
10.2 Delay Differential Equations . . . . . . . . . . . . . . . . . . . . . 179
10.3 Differential algebraic systems of equations . . . . . . . . . . . . . 179
10.4 Boundary value equations . . . . . . . . . . . . . . . . . . . . . . 179
10.4.1 Plane Poiseuille flow - BVP solve by shooting method . . 179
10.4.2 Plane poiseuelle flow solved by finite difference . . . . . . 184
10.4.3 Boundary value problem in heat conduction . . . . . . . . 187
10.4.4 BVP in pycse . . . . . . . . . . . . . . . . . . . . . . . . . 189
10.4.5 A nonlinear BVP . . . . . . . . . . . . . . . . . . . . . . . 190
10.4.6 Another look at nonlinear BVPs . . . . . . . . . . . . . . 192
10.4.7 Solving the Blasius equation . . . . . . . . . . . . . . . . . 194
10.5 Partial differential equations . . . . . . . . . . . . . . . . . . . . . 196
10.5.1 Modeling a transient plug flow reactor . . . . . . . . . . . 196
10.5.2 Transient heat conduction - partial differential equations . 200
10.5.3 Transient diffusion - partial differential equations . . . . . 203

11 Plotting 206
11.1 Plot customizations - Modifying line, text and figure properties . 206
11.1.1 setting all the text properties in a figure. . . . . . . . . . 207
11.2 Plotting two datasets with very different scales . . . . . . . . . . 208
11.2.1 Make two plots! . . . . . . . . . . . . . . . . . . . . . . . . 209
11.2.2 Scaling the results . . . . . . . . . . . . . . . . . . . . . . 211
11.2.3 Double-y axis plot . . . . . . . . . . . . . . . . . . . . . . 212
11.2.4 Subplots . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
11.3 Customizing plots after the fact . . . . . . . . . . . . . . . . . . . 214
11.4 Fancy, built-in colors in Python . . . . . . . . . . . . . . . . . . . 217
11.5 Picasso’s short lived blue period with Python . . . . . . . . . . . 218
11.6 Interactive plotting . . . . . . . . . . . . . . . . . . . . . . . . . . 220
11.6.1 Basic mouse clicks . . . . . . . . . . . . . . . . . . . . . . 220
11.6.2 Mouse movement . . . . . . . . . . . . . . . . . . . . . . . 224
11.6.3 key press events . . . . . . . . . . . . . . . . . . . . . . . 225
11.6.4 Picking lines . . . . . . . . . . . . . . . . . . . . . . . . . 226
11.6.5 Picking data points . . . . . . . . . . . . . . . . . . . . . . 226

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12 Programming 227
12.1 Some of this, sum of that . . . . . . . . . . . . . . . . . . . . . . 227
12.1.1 Nested lists . . . . . . . . . . . . . . . . . . . . . . . . . . 228
12.2 Sorting in python . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
12.3 Unique entries in a vector . . . . . . . . . . . . . . . . . . . . . . 230
12.4 Lather, rinse and repeat . . . . . . . . . . . . . . . . . . . . . . . 231
12.4.1 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . 232
12.5 Brief intro to regular expressions . . . . . . . . . . . . . . . . . . 232
12.6 Working with lists . . . . . . . . . . . . . . . . . . . . . . . . . . 233
12.7 Making word files in python . . . . . . . . . . . . . . . . . . . . . 235
12.8 Interacting with Excel in python . . . . . . . . . . . . . . . . . . 236
12.8.1 Writing Excel workbooks . . . . . . . . . . . . . . . . . . 237
12.8.2 Updating an existing Excel workbook . . . . . . . . . . . 237
12.8.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
12.9 Using Excel in Python . . . . . . . . . . . . . . . . . . . . . . . . 238
12.10Running Aspen via Python . . . . . . . . . . . . . . . . . . . . . 239
12.11Using an external solver with Aspen . . . . . . . . . . . . . . . . 241
12.12Redirecting the print function . . . . . . . . . . . . . . . . . . . . 242
12.13Modifying functions with decorators . . . . . . . . . . . . . . . . 246
12.14Getting a dictionary of counts . . . . . . . . . . . . . . . . . . . . 246
12.15About your python . . . . . . . . . . . . . . . . . . . . . . . . . . 247
12.16Automatic, temporary directory changing . . . . . . . . . . . . . 248
12.17multiprocessing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250

13 Miscellaneous 250
13.1 Mail merge with python . . . . . . . . . . . . . . . . . . . . . . . 250

14 Worked examples 253

14.1 Peak finding in Raman spectroscopy . . . . . . . . . . . . . . . . 253
14.1.1 Summary notes . . . . . . . . . . . . . . . . . . . . . . . . 258
14.2 Curve fitting to get overlapping peak areas . . . . . . . . . . . . 258
14.2.1 Notable differences from Matlab . . . . . . . . . . . . . . 263
14.3 Estimating the boiling point of water . . . . . . . . . . . . . . . . 264
14.3.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
14.4 Gibbs energy minimization and the NIST webbook . . . . . . . . 266
14.4.1 Compute mole fractions and partial pressures . . . . . . . 268
14.4.2 Computing equilibrium constants . . . . . . . . . . . . . . 268
14.5 Finding equilibrium composition by direct minimization of Gibbs
free energy on mole numbers . . . . . . . . . . . . . . . . . . . . 269
14.5.1 The Gibbs energy of a mixture . . . . . . . . . . . . . . . 269
14.5.2 Linear equality constraints for atomic mass conservation . 269
14.5.3 Equilibrium constant based on mole numbers . . . . . . . 271
14.5.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
14.6 The Gibbs free energy of a reacting mixture and the equilibrium
composition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
14.6.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 276

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14.7 Water gas shift equilibria via the NIST Webbook . . . . . . . . . 276
14.7.1 hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
14.7.2 H_{2}O . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
14.7.3 CO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
14.7.4 CO_{2} . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
14.7.5 Standard state heat of reaction . . . . . . . . . . . . . . . 278
14.7.6 Non-standard state ∆H and ∆G . . . . . . . . . . . . . . 278
14.7.7 Plot how the ∆G varies with temperature . . . . . . . . . 279
14.7.8 Equilibrium constant calculation . . . . . . . . . . . . . . 279
14.7.9 Equilibrium yield of WGS . . . . . . . . . . . . . . . . . . 280
14.7.10 Compute gas phase pressures of each species . . . . . . . 281
14.7.11 Compare the equilibrium constants . . . . . . . . . . . . . 281
14.7.12 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
14.8 Constrained minimization to find equilibrium compositions . . . 282
14.8.1 summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
14.9 Using constrained optimization to find the amount of each phase
present . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
14.10Conservation of mass in chemical reactions . . . . . . . . . . . . 288
14.11Numerically calculating an effectiveness factor for a porous cata-
lyst bead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
14.12Computing a pipe diameter . . . . . . . . . . . . . . . . . . . . . 291
14.13Reading parameter database text files in python . . . . . . . . . 293
14.14Calculating a bubble point pressure of a mixture . . . . . . . . . 296
14.15The equal area method for the van der Waals equation . . . . . . 297
14.15.1 Compute areas . . . . . . . . . . . . . . . . . . . . . . . . 300
14.16Time dependent concentration in a first order reversible reaction
in a batch reactor . . . . . . . . . . . . . . . . . . . . . . . . . . . 302
14.17Finding equilibrium conversion . . . . . . . . . . . . . . . . . . . 303
14.18Integrating a batch reactor design equation . . . . . . . . . . . . 304
14.19Integrating the batch reactor mole balance . . . . . . . . . . . . . 304
14.20Plug flow reactor with a pressure drop . . . . . . . . . . . . . . . 306
14.21Solving CSTR design equations . . . . . . . . . . . . . . . . . . . 307
14.22Meet the steam tables . . . . . . . . . . . . . . . . . . . . . . . . 308
14.22.1 Starting point in the Rankine cycle in condenser. . . . . . 308
14.22.2 Isentropic compression of liquid to point 2 . . . . . . . . . 308
14.22.3 Isobaric heating to T3 in boiler where we make steam . . 309
14.22.4 Isentropic expansion through turbine to point 4 . . . . . . 309
14.22.5 To get from point 4 to point 1 . . . . . . . . . . . . . . . 309
14.22.6 Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . 310
14.22.7 Entropy-temperature chart . . . . . . . . . . . . . . . . . 310
14.22.8 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
14.23What region is a point in . . . . . . . . . . . . . . . . . . . . . . 312

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 15 Units 318
15.1 Using units in python . . . . . . . . . . . . . . . . . . . . . . . . 318
15.2 Handling units with the quantities module . . . . . . . . . . . . . 320
15.3 Units in ODEs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324
15.4 Handling units with dimensionless equations . . . . . . . . . . . . 328

16 GNU Free Documentation License 329

17 References 339

18 Index 339

1 Overview
This is a collection of examples of using python in the kinds of scientific and en-
gineering computations I have used in classes and research. They are organized
by topics.
I recommend the Enthought python distribution (http://www.enthought.
com). This distribution is free for academic use, and cheap otherwise. It is pretty
complete in terms of mathematical, scientific and plotting modules. All of the
examples in this book were created with the Enthought python distribution.

2 Basic python usage

2.1 Basic math
Python is a basic calculator out of the box. Here we consider the most basic
mathematical operations: addition, subtraction, multiplication, division and
exponenetiation. we use the print to get the output. For now we consider
integers and float numbers. An integer is a plain number like 0, 10 or -2345. A
float number has a decimal in it. The following are all floats: 1.0, -9., and 3.56.
Note the trailing zero is not required, although it is good style.

1 print 2 + 4
2 print 8.1 - 5

Multiplication is equally straightforward.

1 print 5 * 4
2 print 3.1 * 2

8
 20
6.2

Division is almost as straightforward, but we have to remember that integer

division is not the same as float division. Let us consider float division first.

1 print 4.0 / 2.0

2 print 1.0/3.1

2.0
0.322580645161

Now, consider the integer versions:

1 print 4 / 2
2 print 1/3

2
0

The first result is probably what you expected, but the second may come as
a surprise. In integer division the remainder is discarded, and the result is an
integer.
Exponentiation is also a basic math operation that python supports directly.

1 print 3.**2
2 print 3**2
3 print 2**0.5

9.0
9
1.41421356237

Other types of mathematical operations require us to import functionality

from python libraries. We consider those in the next section.

2.2 Advanced mathematical operators

The primary library we will consider is numpy, which provides many mathemat-
ical functions, statistics as well as support for linear algebra. For a complete
listing of the functions available, see http://docs.scipy.org/doc/numpy/
reference/routines.math.html. We begin with the simplest functions.

1 import numpy as np
2 print np.sqrt(2)

1.41421356237

9
 2.2.1 Exponential and logarithmic functions
Here is the exponential function.

1 import numpy as np
2 print np.exp(1)

2.71828182846

There are two logarithmic functions commonly used, the natural log function
numpy.log and the base10 logarithm numpy.log10.

1 import numpy as np
2 print np.log(10)
3 print np.log10(10) # base10

2.30258509299
1.0

There are many other intrinsic functions available in numpy which we will
eventually cover. First, we need to consider how to create our own functions.

2.3 Creating your own functions

We can combine operations to evaluate complex equations. Consider the value
of the equation x3 − log(x) for the value x = 4.1.

1 import numpy as np
2 x = 3
3 print x**3 - np.log(x)

25.9013877113

It would be tedious to type this out each time. Next, we learn how to express
this equation as a new function, which we can call with different values.

1 import numpy as np
2 def f(x):
3 return x**3 - np.log(x)
4
5 print f(3)
6 print f(5.1)

25.9013877113
131.02175946

It may not seem like we did much there, but this is the foundation for solving
equations in the future. Before we get to solving equations, we have a few more
details to consider. Next, we consider evaluating functions on arrays of values.

10
 2.4 Defining functions in python
Compare what’s here to the Matlab implementation.
We often need to make functions in our codes to do things.

1 def f(x):
2 "return the inverse square of x"
3 return 1.0 / x**2
4
5 print f(3)
6 print f([4,5])

... ... >>> 0.111111111111

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<stdin>", line 3, in f
TypeError: unsupported operand type(s) for ** or pow(): ’list’ and ’int’

Note that functions are not automatically vectorized. That is why we see the
error above. There are a few ways to achieve that. One is to "cast" the input
variables to objects that support vectorized operations, such as numpy.array
objects.

1 import numpy as np
2
3 def f(x):
4 "return the inverse square of x"
5 x = np.array(x)
6 return 1.0 / x**2
7
8 print f(3)
9 print f([4,5])

>>> ... ... ... ... >>> 0.111111111111

[ 0.0625 0.04 ]

It is possible to have more than one variable.

1 import numpy as np
2
3 def func(x, y):
4 "return product of x and y"
5 return x * y
6
7 print func(2, 3)
8 print func(np.array([2, 3]), np.array([3, 4]))

6
[ 6 12]

11
 You can define "lambda" functions, which are also known as inline or anony-
mous functions. The syntax is lambda var:f(var). I think these are hard to
read and discourage their use. Here is a typical usage where you have to define
a simple function that is passed to another function, e.g. scipy.integrate.quad
to perform an integral.

1 from scipy.integrate import quad

2 print quad(lambda x:x**3, 0 ,2)

(4.0, 4.440892098500626e-14)
It is possible to nest functions inside of functions like this.

1 def wrapper(x):
2 a = 4
3 def func(x, a):
4 return a * x
5
6 return func(x, a)
7
8 print wrapper(4)

16
An alternative approach is to "wrap" a function, say to fix a parameter. You
might do this so you can integrate the wrapped function, which depends on only
a single variable, whereas the original function depends on two variables.

1 def func(x, a):

2 return a * x
3
4 def wrapper(x):
5 a = 4
6 return func(x, a)
7
8 print wrapper(4)

16
Last example, defining a function for an ode

1 from scipy.integrate import odeint

2 import numpy as np
3 import matplotlib.pyplot as plt
4
5 k = 2.2
6 def myode(t,y):
7 "ode defining exponential growth"
8 return k * t
9
10 y0 = 3
11 tspan = np.linspace(0,1)
12 y = odeint(myode, y0, tspan)
13
14 plt.plot(tspan, y)
15 plt.xlabel(’Time’)
16 plt.ylabel(’y’)
17 plt.savefig(’images/funcs-ode.png’)

12
 2.5 Advanced function creation
Python has some nice features in creating functions. You can create default
values for variables, have optional variables and optional keyword variables.
In this function f(a,b), a and b are called positional arguments, and they are
required, and must be provided in the same order as the function defines.
If we provide a default value for an argument, then the argument is called
a keyword argument, and it becomes optional. You can combine positional
arguments and keyword arguments, but positional arguments must come first.
Here is an example.

1 def func(a, n=2):

2 "compute the nth power of a"
3 return a**n
4
5 # three different ways to call the function
6 print func(2)
7 print func(2, 3)
8 print func(2, n=4)

4
8
16

In the first call to the function, we only define the argument a, which is a
mandatory, positional argument. In the second call, we define a and n, in the
order they are defined in the function. Finally, in the third call, we define a as
a positional argument, and n as a keyword argument.

13
 If all of the arguments are optional, we can even call the function with no
arguments. If you give arguments as positional arguments, they are used in
the order defined in the function. If you use keyword arguments, the order is
arbitrary.

1 def func(a=1, n=2):

2 "compute the nth power of a"
3 return a**n
4
5 # three different ways to call the function
6 print func()
7 print func(2, 4)
8 print func(n=4, a=2)

1
16
16

It is occasionally useful to allow an arbitrary number of arguments in a

function. Suppose we want a function that can take an arbitrary number of
positional arguments and return the sum of all the arguments. We use the
syntax *args to indicate arbitrary positional arguments. Inside the function the
variable args is a tuple containing all of the arguments passed to the function.

1 def func(*args):
2 sum = 0
3 for arg in args:
4 sum += arg
5 return sum
6
7 print func(1, 2, 3, 4)

10

A more "functional programming" version of the last function is given here.

This is an advanced approach that is less readable to new users, but more
compact and likely more efficient for large numbers of arguments.

1 import operator
2 def func(*args):
3 return reduce(operator.add, args)
4 print func(1, 2, 3, 4)

10

It is possible to have arbitrary keyword arguments. This is a common pat-

tern when you call another function within your function that takes keyword
arguments. We use **kwargs to indicate that arbitrary keyword arguments can
be given to the function. Inside the function, kwargs is variable containing a
dictionary of the keywords and values passed in.

14
1 def func(**kwargs):
2 for kw in kwargs:
3 print ’{0} = {1}’.format(kw, kwargs[kw])
4
5 func(t1=6, color=’blue’)

color = blue
t1 = 6
A typical example might be:

1 import matplotlib.pyplot as plt

2
3 def myplot(x, y, fname=None, **kwargs):
4 "make plot of x,y. save to fname if not None. provide kwargs to plot"
5 plt.plot(x, y, **kwargs)
6 plt.xlabel(’X’)
7 plt.ylabel(’Y’)
8 plt.title(’My plot’)
9 if fname:
10 plt.savefig(fname)
11 else:
12 plt.show()
13
14 x = [1, 3, 4, 5]
15 y = [3, 6, 9, 12]
16
17 myplot(x, y, ’images/myfig.png’, color=’orange’, marker=’s’)
18
19 # you can use a dictionary as kwargs
20 d = {’color’:’magenta’,
21 ’marker’:’d’}
22
23 myplot(x, y, ’images/myfig2.png’, **d)

15
 In that example we wrap the matplotlib plotting commands in a function,
which we can call the way we want to, with arbitrary optional arguments. In
this example, you cannot pass keyword arguments that are illegal to the plot
command or you will get an error.
It is possible to combine all the options at once. I admit it is hard to imagine
where this would be really useful, but it can be done!

1 import numpy as np
2
3 def func(a, b=2, *args, **kwargs):
4 "return a**b + sum(args) and print kwargs"
5 for kw in kwargs:
6 print ’kw: {0} = {1}’.format(kw, kwargs[kw])
7
8 return a**b + np.sum(args)
9
10 print func(2, 3, 4, 5, mysillykw=’hahah’)

kw: mysillykw = hahah

17

2.6 Lambda Lambda Lambda

Is that some kind of fraternity? of anonymous functions? What is that!? There
are many times where you need a callable, small function in python, and it is
inconvenient to have to use def to create a named function. Lambda functions
solve this problem. Let us look at some examples. First, we create a lambda
function, and assign it to a variable. Then we show that variable is a function,
and that we can call it with an argument.

16
1 f = lambda x: 2*x
2 print f
3 print f(2)

<function <lambda> at 0x0000000001E6AAC8>

4

We can have more than one argument:

1 f = lambda x,y: x + y
2 print f
3 print f(2, 3)

<function <lambda> at 0x0000000001E3AAC8>

5

And default arguments:

1 f = lambda x, y=3: x + y
2 print f
3 print f(2)
4 print f(4, 1)

<function <lambda> at 0x0000000001E9AAC8>

5
5

It is also possible to have arbitrary numbers of positional arguments. Here

is an example that provides the sum of an arbitrary number of arguments.

1 import operator
2 f = lambda *x: reduce(operator.add, x)
3 print f
4
5 print f(1)
6 print f(1, 2)
7 print f(1, 2, 3)

<function <lambda> at 0x0000000001DFAAC8>

1
3
6

You can also make arbitrary keyword arguments. Here we make a function
that simply returns the kwargs as a dictionary. This feature may be helpful in
passing kwargs to other functions.

1 f = lambda **kwargs: kwargs

2
3 print f(a=1, b=3)

17
 {’a’: 1, ’b’: 3}

Of course, you can combine these options. Here is a function with all the
options.

1 f = lambda a, b=4, *args, **kwargs: (a, b, args, kwargs)

2
3 print f(’required’, 3, ’optional-positional’, g=4)

(’required’, 3, (’optional-positional’,), {’g’: 4})

One of the primary limitations of lambda functions is they are limited to

single expressions. They also do not have documentation strings, so it can be
difficult to understand what they were written for later.

2.6.1 Applications of lambda functions

Lambda functions are used in places where you need a function, but may not
want to define
√ one using def. For example, say you want to solve the nonlinear
equation x = 2.5.

1 from scipy.optimize import fsolve

2 import numpy as np
3
4 sol, = fsolve(lambda x: 2.5 - np.sqrt(x), 8)
5 print sol

6.25

Another time to use lambda functions is if you want to set a particular value
of a parameter in a function. Say we have a function with an independent
variable, x and a parameter a, i.e. f (x; a). If we want to find a solution
f (x; a) = 0 for some value of a, we can use a lambda function to make a
function of the single variable x. Here is a example.

1 from scipy.optimize import fsolve

2 import numpy as np
3
4 def func(x, a):
5 return a * np.sqrt(x) - 4.0
6
7 sol, = fsolve(lambda x: func(x, 3.2), 3)
8 print sol

1.5625

Any function that takes a function as an argument can use lambda functions.
Here we use a lambda function that adds two numbers in the reduce function
to sum a list of numbers.

1 print reduce(lambda x, y: x + y, [0, 1, 2, 3, 4])

18
 10
R2
We can evaluate the integral 0
x2 dx with a lambda function.
1 from scipy.integrate import quad
2
3 print quad(lambda x: x**2, 0, 2)

(2.666666666666667, 2.960594732333751e-14)

2.6.2 Summary
Lambda functions can be helpful. They are never necessary. You can always
define a function using def, but for some small, single-use functions, a lambda
function could make sense. Lambda functions have some limitations, including
that they are limited to a single expression, and they lack documentation strings.

2.7 Creating arrays in python

Often, we will have a set of 1-D arrays, and we would like to construct a 2D array
with those vectors as either the rows or columns of the array. This may happen
because we have data from different sources we want to combine, or because
we organize the code with variables that are easy to read, and then want to
combine the variables. Here are examples of doing that to get the vectors as
the columns.
1 import numpy as np
2
3 a = np.array([1, 2, 3])
4 b = np.array([4, 5, 6])
5
6 print np.column_stack([a, b])
7
8 # this means stack the arrays vertically, e.g. on top of each other
9 print np.vstack([a, b]).T

[[1 4]
[2 5]
[3 6]]
[[1 4]
[2 5]
[3 6]]
Or rows:

1 import numpy as np
2
3 a = np.array([1, 2, 3])
4 b = np.array([4, 5, 6])
5
6 print np.row_stack([a, b])
7
8 # this means stack the arrays vertically, e.g. on top of each other
9 print np.vstack([a, b])

19
 [[1 2 3]
[4 5 6]]
[[1 2 3]
[4 5 6]]

The opposite operation is to extract the rows or columns of a 2D array into

smaller arrays. We might want to do that to extract a row or column from
a calculation for further analysis, or plotting for example. There are splitting
functions in numpy. They are somewhat confusing, so we examine some ex-
amples. The numpy.hsplit command splits an array "horizontally". The best
way to think about it is that the "splits" move horizontally across the array.
In other words, you draw a vertical split, move over horizontally, draw another
vertical split, etc. . . You must specify the number of splits that you want, and
the array must be evenly divisible by the number of splits.

1 import numpy as np
2
3 A = np.array([[1, 2, 3, 5],
4 [4, 5, 6, 9]])
5
6 # split into two parts
7 p1, p2 = np.hsplit(A, 2)
8 print p1
9 print p2
10
11 #split into 4 parts
12 p1, p2, p3, p4 = np.hsplit(A, 4)
13 print p1
14 print p2
15 print p3
16 print p4

[[1 2]
[4 5]]
[[3 5]
[6 9]]
[[1]
[4]]
[[2]
[5]]
[[3]
[6]]
[[5]
[9]]

In the numpy.vsplit command the "splits" go "vertically" down the array.

Note that the split commands return 2D arrays.

1 import numpy as np
2
3 A = np.array([[1, 2, 3, 5],
4 [4, 5, 6, 9]])

20
5
6 # split into two parts
7 p1, p2 = np.vsplit(A, 2)
8 print p1
9 print p2
10 print p2.shape

[[1 2 3 5]]
[[4 5 6 9]]
(1, 4)

An alternative approach is array unpacking. In this example, we unpack the

array into two variables. The array unpacks by row.

1 import numpy as np
2
3 A = np.array([[1, 2, 3, 5],
4 [4, 5, 6, 9]])
5
6 # split into two parts
7 p1, p2 = A
8 print p1
9 print p2

[1 2 3 5]
[4 5 6 9]

To get the columns, just transpose the array.

1 import numpy as np
2
3 A = np.array([[1, 2, 3, 5],
4 [4, 5, 6, 9]])
5
6 # split into two parts
7 p1, p2, p3, p4 = A.T
8 print p1
9 print p2
10 print p3
11 print p4
12 print p4.shape

[1 4]
[2 5]
[3 6]
[5 9]
(2,)

Note that now, we have 1D arrays.

You can also access rows and columns by indexing. We index an array by
[row, column]. To get a row, we specify the row number, and all the columns in
that row like this [row, :]. Similarly, to get a column, we specify that we want
all rows in that column like this: [:, column]. This approach is useful when you
only want a few columns or rows.

21
1 import numpy as np
2
3 A = np.array([[1, 2, 3, 5],
4 [4, 5, 6, 9]])
5
6 # get row 1
7 print A[1]
8 print A[1, :] # row 1, all columns
9
10 print A[:, 2] # get third column
11 print A[:, 2].shape

[4 5 6 9]
[4 5 6 9]
[3 6]
(2,)

Note that even when we specify a column, it is returned as a 1D array.

2.8 Functions on arrays of values

It is common to evaluate a function for a range of values. Let us consider the
value of the function f (x) = cos(x) over the range of 0 < x < π. We cannot
consider every value in that range, but we can consider say 10 points in the
range. The numpy.linspace conveniently creates an array of values.

1 import numpy as np
2 print np.linspace(0, np.pi, 10)

[ 0. 0.34906585 0.6981317 1.04719755 1.3962634 1.74532925

2.0943951 2.44346095 2.7925268 3.14159265]

The main point of using the numpy functions is that they work element-wise
on elements of an array. In this example, we compute the cos(x) for each element
of x.

1 import numpy as np
2 x = np.linspace(0, np.pi, 10)
3 print np.cos(x)

[ 1. 0.93969262 0.76604444 0.5 0.17364818 -0.17364818

-0.5 -0.76604444 -0.93969262 -1. ]

You can already see from this output that there is a root to the equation
cos(x) = 0, because there is a change in sign in the output. This is not a very
convenient way to view the results; a graph would be better. We use matplotlib
to make figures. Here is an example.

22
1 import matplotlib.pyplot as plt
2 import numpy as np
3
4 x = np.linspace(0, np.pi, 10)
5 plt.plot(x, np.cos(x))
6 plt.xlabel(’x’)
7 plt.ylabel(’cos(x)’)
8 plt.savefig(’images/plot-cos.png’)

This figure illustrates graphically what the numbers above show. The
function crosses zero at approximately x = 1.5. To get a more precise
value, we must actually solve the function numerically. We use the function
scipy.optimize.fsolve to do that. More precisely, we want to solve the equa-
tion f (x) = cos(x) = 0. We create a function that defines that equation, and
then use scipy.optimize.fsolve to solve it.

1 from scipy.optimize import fsolve

2 import numpy as np
3
4 def f(x):
5 return np.cos(x)
6
7 sol, = fsolve(f, x0=1.5) # the comma after sol makes it return a float
8 print sol
9 print np.pi / 2

1.57079632679
1.57079632679

We know the solution is π/2.

23
 2.9 Some basic data structures in python
Matlab post
We often have a need to organize data into structures when solving problems.

2.9.1 the list

A list in python is data separated by commas in square brackets. Here, we
might store the following data in a variable to describe the Antoine coefficients
for benzene and the range they are relevant for [Tmin Tmax]. Lists are flexible,
you can put anything in them, including other lists. We access the elements of
the list by indexing:

1 c = [’benzene’, 6.9056, 1211.0, 220.79, [-16, 104]]

2 print c[0]
3 print c[-1]
4
5 a,b = c[0:2]
6 print a,b
7
8 name, A, B, C, Trange = c
9 print Trange

benzene
[-16, 104]
benzene 6.9056
[-16, 104]

Lists are "mutable", which means you can change their values.

1 a = [3, 4, 5, [7, 8], ’cat’]

2 print a[0], a[-1]
3 a[-1] = ’dog’
4 print a

3 cat
>>> [3, 4, 5, [7, 8], ’dog’]

2.9.2 tuples
Tuples are immutable; you cannot change their values. This is handy in cases
where it is an error to change the value. A tuple is like a list but it is enclosed
in parentheses.

1 a = (3, 4, 5, [7, 8], ’cat’)

2 print a[0], a[-1]
3 a[-1] = ’dog’

24
 3 cat
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: ’tuple’ object does not support item assignment

2.9.3 struct
Python does not exactly have the same thing as a struct in Matlab. You can
achieve something like it by defining an empty class and then defining attributes
of the class. You can check if an object has a particular attribute using hasattr.

1 class Antoine:
2 pass
3
4 a = Antoine()
5 a.name = ’benzene’
6 a.Trange = [-16, 104]
7
8 print a.name
9 print hasattr(a, ’Trange’)
10 print hasattr(a, ’A’)

benzene
True
False

2.9.4 dictionaries
The analog of the containers.Map in Matlab is the dictionary in python. Dic-
tionaries are enclosed in curly brackets, and are composed of key:value pairs.

1 s = {’name’:’benzene’,
2 ’A’:6.9056,
3 ’B’:1211.0}
4
5 s[’C’] = 220.79
6 s[’Trange’] = [-16, 104]
7
8 print s
9 print s[’Trange’]

{’A’: 6.9056, ’C’: 220.79, ’B’: 1211.0, ’name’: ’benzene’, ’Trange’: [-16, 104]}
[-16, 104]

1 s = {’name’:’benzene’,
2 ’A’:6.9056,
3 ’B’:1211.0}
4
5 print ’C’ in s
6 # default value for keys not in the dictionary
7 print s.get(’C’, None)
8
9 print s.keys()
10 print s.values()

25
 False
None
[’A’, ’B’, ’name’]
[6.9056, 1211.0, ’benzene’]

2.9.5 Summary
We have examined four data structures in python. Note that none of these types
are arrays/vectors with defined mathematical operations. For those, you need
to consider numpy.array.

2.10 Indexing vectors and arrays in Python

Matlab post There are times where you have a lot of data in a vector or array
and you want to extract a portion of the data for some analysis. For example,
maybe you want to plot column 1 vs column 2, or you want the integral of data
between x = 4 and x = 6, but your vector covers 0 < x < 10. Indexing is the
way to do these things.
A key point to remember is that in python array/vector indices start at
0. Unlike Matlab, which uses parentheses to index a array, we use brackets in
python.

1 import numpy as np
2
3 x = np.linspace(-np.pi, np.pi, 10)
4 print x
5
6 print x[0] # first element
7 print x[2] # third element
8 print x[-1] # last element
9 print x[-2] # second to last element

>>> >>> [-3.14159265 -2.44346095 -1.74532925 -1.04719755 -0.34906585 0.34906585

1.04719755 1.74532925 2.44346095 3.14159265]
>>> -3.14159265359
-1.74532925199
3.14159265359
2.44346095279

We can select a range of elements too. The syntax a:b extracts the aˆ{th}
to (b-1)ˆ{th} elements. The syntax a:b:n starts at a, skips nelements up to the
index b.

1 print x[1:4] # second to fourth element. Element 5 is not included

2 print x[0:-1:2] # every other element
3 print x[:] # print the whole vector
4 print x[-1:0:-1] # reverse the vector!

26
 [-2.44346095 -1.74532925 -1.04719755]
[-3.14159265 -1.74532925 -0.34906585 1.04719755 2.44346095]
[-3.14159265 -2.44346095 -1.74532925 -1.04719755 -0.34906585 0.34906585
1.04719755 1.74532925 2.44346095 3.14159265]
[ 3.14159265 2.44346095 1.74532925 1.04719755 0.34906585 -0.34906585
-1.04719755 -1.74532925 -2.44346095]

Suppose we want the part of the vector where x > 2. We could do that by
inspection, but there is a better way. We can create a mask of boolean (0 or 1)
values that specify whether x > 2 or not, and then use the mask as an index.

1 print x[x > 2]

[ 2.44346095 3.14159265]

You can use this to analyze subsections of data, for example to integrate the
function y = sin(x) where x > 2.

1 y = np.sin(x)
2
3 print np.trapz( x[x > 2], y[x > 2])

>>> -1.79500162881

2.10.1 2d arrays
In 2d arrays, we use row, column notation. We use a : to indicate all rows or
all columns.

1 a = np.array([[1, 2, 3],
2 [4, 5, 6],
3 [7, 8, 9]])
4
5 print a[0, 0]
6 print a[-1, -1]
7
8 print a[0, :] # row one
9 print a[:, 0] # column one
10 print a[:]

... >>> >>> 1

9
>>> [1 2 3]
[1 4 7]
[[1 2 3]
[4 5 6]
[7 8 9]]

27
 2.10.2 Using indexing to assign values to rows and columns

1 b = np.zeros((3, 3))
2 print b
3
4 b[:, 0] = [1, 2, 3] # set column 0
5 b[2, 2] = 12 # set a single element
6 print b
7
8 b[2] = 6 # sets everything in row 2 to 6!
9 print b

[[ 0. 0. 0.]
[ 0. 0. 0.]
[ 0. 0. 0.]]
>>> >>> >>> [[ 1. 0. 0.]
[ 2. 0. 0.]
[ 3. 0. 12.]]
>>> >>> [[ 1. 0. 0.]
[ 2. 0. 0.]
[ 6. 6. 6.]]

Python does not have the linear assignment method like Matlab does. You
can achieve something like that as follows. We flatten the array to 1D, do the
linear assignment, and reshape the result back to the 2D array.

1 c = b.flatten()
2 c[2] = 34
3 b[:] = c.reshape(b.shape)
4 print b

>>> >>> [[ 1. 0. 34.]

[ 2. 0. 0.]
[ 6. 6. 6.]]

2.10.3 3D arrays
The 3d array is like book of 2D matrices. Each page has a 2D matrix on it.
think about the indexing like this: (row, column, page)

1 M = np.random.uniform(size=(3,3,3)) # a 3x3x3 array

2 print M

[[[ 0.78557795 0.36454381 0.96090072]

[ 0.76133373 0.03250485 0.08517174]
[ 0.96007909 0.08654002 0.29693648]]

[[ 0.58270738 0.60656083 0.47703339]

[ 0.62551477 0.62244626 0.11030327]

28
 [ 0.2048839 0.83081982 0.83660668]]

[[ 0.12489176 0.20783996 0.38481792]

[ 0.05234762 0.03989146 0.09731516]
[ 0.67427208 0.51793637 0.89016255]]]

1 print M[:, :, 0] # 2d array on page 0

2 print M[:, 0, 0] # column 0 on page 0
3 print M[1, :, 2] # row 1 on page 2

[[ 0.78557795 0.76133373 0.96007909]

[ 0.58270738 0.62551477 0.2048839 ]
[ 0.12489176 0.05234762 0.67427208]]
[ 0.78557795 0.58270738 0.12489176]
[ 0.47703339 0.11030327 0.83660668]

2.10.4 Summary
The most common place to use indexing is probably when a function returns an
array with the independent variable in column 1 and solution in column 2, and
you want to plot the solution. Second is when you want to analyze one part of
the solution. There are also applications in numerical methods, for example in
assigning values to the elements of a matrix or vector.

2.11 Controlling the format of printed variables

This was first worked out in this original Matlab post.
Often you will want to control the way a variable is printed. You may want
to only show a few decimal places, or print in scientific notation, or embed the
result in a string. Here are some examples of printing with no control over the
format.

1 a = 2./3
2 print a
3 print 1/3
4 print 1./3.
5 print 10.1
6 print "Avogadro’s number is ", 6.022e23,’.’

0.666666666667
0
0.333333333333
10.1
Avogadro’s number is 6.022e+23 .

There is no control over the number of decimals, or spaces around a printed

number.

29
 In python, we use the format function to control how variables are printed.
With the format function you use codes like {n:format specifier} to indicate
that a formatted string should be used. n is the nˆ{th} argument passed to
format, and there are a variety of format specifiers. Here we examine how to
format float numbers. The specifier has the general form "w.df" where w is
the width of the field, and d is the number of decimals, and f indicates a float
number. "1.3f" means to print a float number with 3 decimal places. Here is
an example.

1 print ’The value of 1/3 to 3 decimal places is {0:1.3f}’.format(1./3.)

The value of 1/3 to 3 decimal places is 0.333

In that example, the 0 in {0:1.3f} refers to the first (and only) argument to
the format function. If there is more than one argument, we can refer to them
like this:

1 print ’Value 0 = {0:1.3f}, value 1 = {1:1.3f}, value 0 = {0:1.3f}’.format(1./3., 1./6.)

Value 0 = 0.333, value 1 = 0.167, value 0 = 0.333

Note you can refer to the same argument more than once, and in arbitrary
order within the string.
Suppose you have a list of numbers you want to print out, like this:

1 for x in [1./3., 1./6., 1./9.]:

2 print ’The answer is {0:1.2f}’.format(x)

The answer is 0.33

The answer is 0.17
The answer is 0.11

The "g" format specifier is a general format that can be used to indicate
a precision, or to indicate significant digits. To print a number with a specific
number of significant digits we do this:

1 print ’{0:1.3g}’.format(1./3.)
2 print ’{0:1.3g}’.format(4./3.)

0.333
1.33

We can also specify plus or minus signs. Compare the next two outputs.

1 for x in [-1., 1.]:

2 print ’{0:1.2f}’.format(x)

30
 -1.00
1.00

You can see the decimals do not align. That is because there is a minus sign
in front of one number. We can specify to show the sign for positive and negative
numbers, or to pad positive numbers to leave space for positive numbers.

1 for x in [-1., 1.]:

2 print ’{0:+1.2f}’.format(x) # explicit sign
3
4 for x in [-1., 1.]:
5 print ’{0: 1.2f}’.format(x) # pad positive numbers

-1.00
+1.00
-1.00
1.00

We use the "e" or "E" format modifier to specify scientific notation.

1 import numpy as np
2 eps = np.finfo(np.double).eps
3 print eps
4 print ’{0}’.format(eps)
5 print ’{0:1.2f}’.format(eps)
6 print ’{0:1.2e}’.format(eps) #exponential notation
7 print ’{0:1.2E}’.format(eps) #exponential notation with capital E

2.22044604925e-16
2.22044604925e-16
0.00
2.22e-16
2.2E-16

As a float with 2 decimal places, that very small number is practically equal
to 0.
We can even format percentages. Note you do not need to put the % in your
string.

1 print ’the fraction {0} corresponds to {0:1.0%}’.format(0.78)

the fraction 0.78 corresponds to 78%

There are many other options for formatting strings. See http://docs.
python.org/2/library/string.html#formatstrings for a full specification
of the options.

31
 2.12 Advanced string formatting
There are several more advanced ways to include formatted values in a string.
In the previous case we examined replacing format specifiers by positional ar-
guments in the format command. We can instead use keyword arguments.

1 s = ’The {speed} {color} fox’.format(color=’brown’, speed=’quick’)

2 print s

The quick brown fox

If you have a lot of variables already defined in a script, it is convenient to

use them in string formatting with the locals command:

1 speed = ’slow’
2 color= ’blue’
3
4 print ’The {speed} {color} fox’.format(**locals())

The slow blue fox

If you want to access attributes on an object, you can specify them directly
in the format identifier.

1 class A:
2 def __init__(self, a, b, c):
3 self.a = a
4 self.b = b
5 self.c = c
6
7 mya = A(3,4,5)
8
9 print ’a = {obj.a}, b = {obj.b}, c = {obj.c:1.2f}’.format(obj=mya)

a = 3, b = 4, c = 5.00

You can access values of a dictionary:

1 d = {’a’: 56, "test":’woohoo!’}

2
3 print "the value of a in the dictionary is {obj[a]}. It works {obj[test]}".format(obj=d)

the value of a in the dictionary is 56. It works woohoo!.

And, you can access elements of a list. Note, however you cannot use -1 as
an index in this case.

1 L = [4, 5, ’cat’]
2
3 print ’element 0 = {obj[0]}, and the last element is {obj[2]}’.format(obj=L)

32
 element 0 = 4, and the last element is cat

There are three different ways to "print" an object. If an object has a format
function, that is the default used in the format command. It may be helpful to
use the str or repr of an object instead. We get this with !s for str and !r for
repr.

1 class A:
2 def __init__(self, a, b):
3 self.a = a; self.b = b
4
5 def __format__(self, format):
6 s = ’a={{0:{0}}} b={{1:{0}}}’.format(format)
7 return s.format(self.a, self.b)
8
9 def __str__(self):
10 return ’str: class A, a={0} b={1}’.format(self.a, self.b)
11
12 def __repr__(self):
13 return ’representing: class A, a={0}, b={1}’.format(self.a, self.b)
14
15 mya = A(3, 4)
16
17 print ’{0}’.format(mya) # uses __format__
18 print ’{0!s}’.format(mya) # uses __str__
19 print ’{0!r}’.format(mya) # uses __repr__

a=3 b=4
str: class A, a=3 b=4
representing: class A, a=3, b=4

This covers the majority of string formatting requirements I have come

across. If there are more sophisticated needs, they can be met with various
string templating python modules. the one I have used most is Cheetah.

3 Math
3.1 Numeric derivatives by differences
numpy has a function called numpy.diff() that is similar to the one found in
matlab. It calculates the differences between the elements in your list, and
returns a list that is one element shorter, which makes it unsuitable for plotting
the derivative of a function.
Loops in python are pretty slow (relatively speaking) but they are usually
trivial to understand. In this script we show some simple ways to construct
derivative vectors using loops. It is implied in these formulas that the data
points are equally spaced. If they are not evenly spaced, you need a different
approach.

1 import numpy as np
2 from pylab import *
3 import time

33
4
5 ’’’
6 These are the brainless way to calculate numerical derivatives. They
7 work well for very smooth data. they are surprisingly fast even up to
8 10000 points in the vector.
9 ’’’
10
11 x = np.linspace(0.78,0.79,100)
12 y = np.sin(x)
13 dy_analytical = np.cos(x)
14 ’’’
15 lets use a forward difference method:
16 that works up until the last point, where there is not
17 a forward difference to use. there, we use a backward difference.
18 ’’’
19
20 tf1 = time.time()
21 dyf = [0.0]*len(x)
22 for i in range(len(y)-1):
23 dyf[i] = (y[i+1] - y[i])/(x[i+1]-x[i])
24 #set last element by backwards difference
25 dyf[-1] = (y[-1] - y[-2])/(x[-1] - x[-2])
26
27 print ’ Forward difference took %1.1f seconds’ % (time.time() - tf1)
28
29 ’’’and now a backwards difference’’’
30 tb1 = time.time()
31 dyb = [0.0]*len(x)
32 #set first element by forward difference
33 dyb[0] = (y[0] - y[1])/(x[0] - x[1])
34 for i in range(1,len(y)):
35 dyb[i] = (y[i] - y[i-1])/(x[i]-x[i-1])
36
37 print ’ Backward difference took %1.1f seconds’ % (time.time() - tb1)
38
39 ’’’and now, a centered formula’’’
40 tc1 = time.time()
41 dyc = [0.0]*len(x)
42 dyc[0] = (y[0] - y[1])/(x[0] - x[1])
43 for i in range(1,len(y)-1):
44 dyc[i] = (y[i+1] - y[i-1])/(x[i+1]-x[i-1])
45 dyc[-1] = (y[-1] - y[-2])/(x[-1] - x[-2])
46
47 print ’ Centered difference took %1.1f seconds’ % (time.time() - tc1)
48
49 ’’’
50 the centered formula is the most accurate formula here
51 ’’’
52
53 plt.plot(x,dy_analytical,label=’analytical derivative’)
54 plt.plot(x,dyf,’--’,label=’forward’)
55 plt.plot(x,dyb,’--’,label=’backward’)
56 plt.plot(x,dyc,’--’,label=’centered’)
57
58 plt.legend(loc=’lower left’)
59 plt.savefig(’images/simple-diffs.png’)
60 plt.show()

Forward difference took 0.0 seconds

Backward difference took 0.0 seconds
Centered difference took 0.0 seconds

34
 3.2 Vectorized numeric derivatives
Loops are usually not great for performance. Numpy offers some vectorized
methods that allow us to compute derivatives without loops, although this comes
at the mental cost of harder to understand syntax

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(0, 2 * np.pi, 100)
5 y = np.sin(x)
6 dy_analytical = np.cos(x)
7
8
9 # we need to specify the size of dy ahead because diff returns
10 #an array of n-1 elements
11 dy = np.zeros(y.shape, np.float) #we know it will be this size
12 dy[0:-1] = np.diff(y) / np.diff(x)
13 dy[-1] = (y[-1] - y[-2]) / (x[-1] - x[-2])
14
15
16 ’’’
17 calculate dy by center differencing using array slices
18 ’’’
19
20 dy2 = np.zeros(y.shape,np.float) #we know it will be this size
21 dy2[1:-1] = (y[2:] - y[0:-2]) / (x[2:] - x[0:-2])
22
23 # now the end points
24 dy2[0] = (y[1] - y[0]) / (x[1] - x[0])
25 dy2[-1] = (y[-1] - y[-2]) / (x[-1] - x[-2])
26
27 plt.plot(x,y)
28 plt.plot(x,dy_analytical,label=’analytical derivative’)
29 plt.plot(x,dy,label=’forward diff’)

35
30 plt.plot(x,dy2,’k--’,lw=2,label=’centered diff’)
31 plt.legend(loc=’lower left’)
32 plt.savefig(’images/vectorized-diffs.png’)
33 plt.show()

3.3 2-point vs. 4-point numerical derivatives

If your data is very noisy, you will have a hard time getting good derivatives;
derivatives tend to magnify noise. In these cases, you have to employ smoothing
techniques, either implicitly by using a multipoint derivative formula, or explic-
itly by smoothing the data yourself, or taking the derivative of a function that
has been fit to the data in the neighborhood you are interested in.
Here is an example of a 4-point centered difference of some noisy data:

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(0, 2*np.pi, 100)
5 y = np.sin(x) + 0.1 * np.random.random(size=x.shape)
6 dy_analytical = np.cos(x)
7
8 #2-point formula
9 dyf = [0.0] * len(x)
10 for i in range(len(y)-1):
11 dyf[i] = (y[i+1] - y[i])/(x[i+1]-x[i])
12 #set last element by backwards difference
13 dyf[-1] = (y[-1] - y[-2])/(x[-1] - x[-2])
14
15 ’’’
16 calculate dy by 4-point center differencing using array slices
17
18 \frac{y[i-2] - 8y[i-1] + 8[i+1] - y[i+2]}{12h}

36
19
20 y[0] and y[1] must be defined by lower order methods
21 and y[-1] and y[-2] must be defined by lower order methods
22 ’’’
23
24 dy = np.zeros(y.shape, np.float) #we know it will be this size
25 h = x[1] - x[0] #this assumes the points are evenely spaced!
26 dy[2:-2] = (y[0:-4] - 8 * y[1:-3] + 8 * y[3:-1] - y[4:]) / (12.0 * h)
27
28 # simple differences at the end-points
29 dy[0] = (y[1] - y[0])/(x[1] - x[0])
30 dy[1] = (y[2] - y[1])/(x[2] - x[1])
31 dy[-2] = (y[-2] - y[-3]) / (x[-2] - x[-3])
32 dy[-1] = (y[-1] - y[-2]) / (x[-1] - x[-2])
33
34
35 plt.plot(x, y)
36 plt.plot(x, dy_analytical, label=’analytical derivative’)
37 plt.plot(x, dyf, ’r-’, label=’2pt-forward diff’)
38 plt.plot(x, dy, ’k--’, lw=2, label=’4pt-centered diff’)
39 plt.legend(loc=’lower left’)
40 plt.savefig(’images/multipt-diff.png’)
41 plt.show()

3.4 Derivatives by polynomial fitting

One way to reduce the noise inherent in derivatives of noisy data is to fit a
smooth function through the data, and analytically take the derivative of the
curve. Polynomials are especially convenient for this. The challenge is to fig-
ure out what an appropriate polynomial order is. This requires judgment and
experience.

37
1 import numpy as np
2 import matplotlib.pyplot as plt
3 from pycse import deriv
4
5 tspan = [0, 0.1, 0.2, 0.4, 0.8, 1]
6 Ca_data = [2.0081, 1.5512, 1.1903, 0.7160, 0.2562, 0.1495]
7
8 p = np.polyfit(tspan, Ca_data, 3)
9 plt.figure()
10 plt.plot(tspan, Ca_data)
11 plt.plot(tspan, np.polyval(p, tspan), ’g-’)
12 plt.savefig(’images/deriv-fit-1.png’)
13
14 # compute derivatives
15 dp = np.polyder(p)
16
17 dCdt_fit = np.polyval(dp, tspan)
18
19 dCdt_numeric = deriv(tspan, Ca_data) # 2-point deriv
20
21 plt.figure()
22 plt.plot(tspan, dCdt_numeric, label=’numeric derivative’)
23 plt.plot(tspan, dCdt_fit, label=’fitted derivative’)
24
25 t = np.linspace(min(tspan), max(tspan))
26 plt.plot(t, np.polyval(dp, t), label=’resampled derivative’)
27 plt.legend(loc=’best’)
28 plt.savefig(’images/deriv-fit-2.png’)

You can see a third order polynomial is a reasonable fit here. There are only
6 data points here, so any higher order risks overfitting. Here is the comparison
of the numerical derivative and the fitted derivative. We have "resampled" the
fitted derivative to show the actual shape. Note the derivative appears to go
through a maximum near t = 0.9. In this case, that is probably unphysical as
the data is related to the consumption of species A in a reaction. The derivative

38
 should increase monotonically to zero. The increase is an artefact of the fitting
process. End points are especially sensitive to this kind of error.

3.5 Derivatives by fitting a function and taking the ana-

lytical derivative
A variation of a polynomial fit is to fit a model with reasonable physics. Here
we fit a nonlinear function to the noisy data. The model is for the concentration
vs. time in a batch reactor for a first order irreversible reaction. Once we fit
the data, we take the analytical derivative of the fitted function.

1 import numpy as np
2 import matplotlib.pyplot as plt
3 from scipy.optimize import curve_fit
4 from pycse import deriv
5
6 tspan = np.array([0, 0.1, 0.2, 0.4, 0.8, 1])
7 Ca_data = np.array([2.0081, 1.5512, 1.1903, 0.7160, 0.2562, 0.1495])
8
9 def func(t, Ca0, k):
10 return Ca0 * np.exp(-k * t)
11
12
13 pars, pcov = curve_fit(func, tspan, Ca_data, p0=[2, 2.3])
14
15 plt.plot(tspan, Ca_data)
16 plt.plot(tspan, func(tspan, *pars), ’g-’)
17 plt.savefig(’images/deriv-funcfit-1.png’)
18
19 # analytical derivative
20 k, Ca0 = pars
21 dCdt = -k * Ca0 * np.exp(-k * tspan)
22 t = np.linspace(0, 2)

39
23 dCdt_res = -k * Ca0 * np.exp(-k * t)
24
25 plt.figure()
26 plt.plot(tspan, deriv(tspan, Ca_data), label=’numerical derivative’)
27 plt.plot(tspan, dCdt, label=’analytical derivative of fit’)
28 plt.plot(t, dCdt_res, label=’extrapolated’)
29 plt.legend(loc=’best’)
30 plt.savefig(’images/deriv-funcfit-2.png’)

Visually this fit is about the same as a third order polynomial. Note the dif-
ference in the derivative though. We can readily extrapolate this derivative and
get reasonable predictions of the derivative. That is true in this case because we
fitted a physically relevant model for concentration vs. time for an irreversible,
first order reaction.

40
 3.6 Derivatives by FFT
1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 N = 101 #number of points
5 L = 2 * np.pi #interval of data
6
7 x = np.arange(0.0, L, L/float(N)) #this does not include the endpoint
8
9 #add some random noise
10 y = np.sin(x) + 0.05 * np.random.random(size=x.shape)
11 dy_analytical = np.cos(x)
12
13 ’’’
14 http://sci.tech-archive.net/Archive/sci.math/2008-05/msg00401.html
15
16 you can use fft to calculate derivatives!
17 ’’’
18
19 if N % 2 == 0:
20 k = np.asarray(range(0, N / 2) + [0] + range(-N / 2 + 1,0))
21 else:
22 k = np.asarray(range(0,(N - 1) / 2) + [0] + range(-(N - 1) / 2, 0))
23
24 k *= 2 * np.pi / L
25
26 fd = np.real(np.fft.ifft(1.0j * k * np.fft.fft(y)))
27
28 plt.plot(x, y, label=’function’)
29 plt.plot(x,dy_analytical,label=’analytical der’)
30 plt.plot(x,fd,label=’fft der’)
31 plt.legend(loc=’lower left’)
32
33 plt.savefig(’images/fft-der.png’)
34 plt.show()

41
 3.7 A novel way to numerically estimate the derivative of
a function - complex-step derivative approximation
Matlab post
Adapted from http://biomedicalcomputationreview.org/2/3/8.pdf and
http://dl.acm.org/citation.cfm?id=838250.838251
This posts introduces a novel way to numerically estimate the derivative
of a function that does not involve finite difference schemes. Finite difference
schemes are approximations to derivatives that become more and more accurate
as the step size goes to zero, except that as the step size approaches the limits
of machine accuracy, new errors can appear in the approximated results. In the
references above, a new way to compute the derivative is presented that does
not rely on differences!
The new way is: f 0 (x) = imag(f(x + i∆x)/∆x) where the function f is eval-
uated in imaginary space with a small ∆x in the complex plane. The derivative
is miraculously equal to the imaginary part of the result in the limit of $∆ x →
0$!
This example comes from the first link. The derivative must be evaluated
using the chain rule. We compare a forward difference, central difference and
complex-step derivative approximations.

1 import numpy as np
2 import matplotlib.pyplot as plt
3

42
4 def f(x): return np.sin(3*x)*np.log(x)
5
6 x = 0.7
7 h = 1e-7
8
9 # analytical derivative
10 dfdx_a = 3 * np.cos( 3*x)*np.log(x) + np.sin(3*x) / x
11
12 # finite difference
13 dfdx_fd = (f(x + h) - f(x))/h
14
15 # central difference
16 dfdx_cd = (f(x+h)-f(x-h))/(2*h)
17
18 # complex method
19 dfdx_I = np.imag(f(x + np.complex(0, h))/h)
20
21 print dfdx_a
22 print dfdx_fd
23 print dfdx_cd
24 print dfdx_cd

1.77335410624
1.7733539398
1.77335410523
1.77335410523

These are all the same to 4 decimal places. The simple finite difference is the
least accurate, and the central differences is practically the same as the complex
number approach.
Let us use this method to verify the fundamental Theorem of Calculus, i.e.
2
Rx
to evaluate the derivative of an integral function. Let f (x) = tan(t3 )dt, and
1
we now want to compute df/dx. Of course, this can be done analytically, but
it is not trivial!

1 import numpy as np
2 from scipy.integrate import quad
3
4 def f_(z):
5 def integrand(t):
6 return np.tan(t**3)
7 return quad(integrand, 0, z**2)
8
9 f = np.vectorize(f_)
10
11 x = np.linspace(0, 1)
12
13 h = 1e-7
14
15 dfdx = np.imag(f(x + complex(0, h)))/h
16 dfdx_analytical = 2 * x * np.tan(x**6)
17
18 import matplotlib.pyplot as plt
19
20 plt.plot(x, dfdx, x, dfdx_analytical, ’r--’)
21 plt.show()

>>> >>> ... ... ... ... >>> >>> >>> >>> >>> >>> >>> c:\Python27\lib\site-packages\scipy\inte

43
 return _quadpack._qagse(func,a,b,args,full_output,epsabs,epsrel,limit)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "c:\Python27\lib\site-packages\numpy\lib\function_base.py", line 1885, in __call__
for x, c in zip(self.ufunc(*newargs), self.otypes)])
File "<stdin>", line 4, in f_
File "c:\Python27\lib\site-packages\scipy\integrate\quadpack.py", line 247, in quad
retval = _quad(func,a,b,args,full_output,epsabs,epsrel,limit,points)
File "c:\Python27\lib\site-packages\scipy\integrate\quadpack.py", line 312, in _quad
return _quadpack._qagse(func,a,b,args,full_output,epsabs,epsrel,limit)
TypeError: can’t convert complex to float
>>> >>> >>> >>> Traceback (most recent call last):
File "<stdin>", line 1, in <module>
NameError: name ’dfdx’ is not defined

Interesting this fails.

3.8 Vectorized piecewise functions

Matlab post Occasionally we need to define piecewise functions, e.g.

f (x) = 0, x < 0 (1)

= x, 0 <= x < 1 (2)
= 2 − x, 1 < x <= 2 (3)
= 0, x > 2 (4)

Today we examine a few ways to define a function like this. A simple way
is to use conditional statements.

1 def f1(x):
2 if x < 0:
3 return 0
4 elif (x >= 0) & (x < 1):
5 return x
6 elif (x >= 1) & (x < 2):
7 return 2.0 - x
8 else:
9 return 0
10
11 print f1(-1)
12 print f1([0, 1, 2, 3]) # does not work!

... ... ... ... ... ... ... ... >>> 0

0

This works, but the function is not vectorized, i.e. f([-1 0 2 3]) does not
evaluate properly (it should give a list or array). You can get vectorized behavior
by using list comprehension, or by writing your own loop. This does not fix all

44
 limitations, for example you cannot use the f1 function in the quad function to
integrate it.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(-1, 3)
5 y = [f1(xx) for xx in x]
6
7 plt.plot(x, y)
8 plt.savefig(’images/vector-piecewise.png’)

>>> >>> >>> >>> >>> [<matplotlib.lines.Line2D object at 0x048D6790>]

Neither of those methods is convenient. It would be nicer if the function was

vectorized, which would allow the direct notation f1([0, 1, 2, 3, 4]). A simple
way to achieve this is through the use of logical arrays. We create logical arrays
from comparison statements.

1 def f2(x):
2 ’fully vectorized version’
3 x = np.asarray(x)
4 y = np.zeros(x.shape)
5 y += ((x >= 0) & (x < 1)) * x
6 y += ((x >= 1) & (x < 2)) * (2 - x)
7 return y
8
9 print f2([-1, 0, 1, 2, 3, 4])
10 x = np.linspace(-1,3);
11 plt.plot(x,f2(x))
12 plt.savefig(’images/vector-piecewise-2.png’)

45
 ... ... ... ... ... ... >>> [ 0. 0. 1. 0. 0. 0.]
>>> [<matplotlib.lines.Line2D object at 0x043A4910>]

A third approach is to use Heaviside functions. The Heaviside function is

defined to be zero for x less than some value, and 0.5 for x=0, and 1 for x >=
0. If you can live with y=0.5 for x=0, you can define a vectorized function in
terms of Heaviside functions like this.

1 def heaviside(x):
2 x = np.array(x)
3 if x.shape != ():
4 y = np.zeros(x.shape)
5 y[x > 0.0] = 1
6 y[x == 0.0] = 0.5
7 else: # special case for 0d array (a number)
8 if x > 0: y = 1
9 elif x == 0: y = 0.5
10 else: y = 0
11 return y
12
13 def f3(x):
14 x = np.array(x)
15 y1 = (heaviside(x) - heaviside(x - 1)) * x # first interval
16 y2 = (heaviside(x - 1) - heaviside(x - 2)) * (2 - x) # second interval
17 return y1 + y2
18
19 from scipy.integrate import quad
20 print quad(f3, -1, 3)

... ... ... ... ... ... ... ... ... ... >>> ... ... ... ... ... >>> >>> (1.0, 1.110223024625

46
1 plt.plot(x, f3(x))
2 plt.savefig(’images/vector-piecewise-3.png’)

[<matplotlib.lines.Line2D object at 0x048F96F0>]

There are many ways to define piecewise functions, and vectorization is not
always necessary. The advantages of vectorization are usually notational sim-
plicity and speed; loops in python are usually very slow compared to vectorized
functions.

3.9 Smooth transitions between discontinuous functions

original post
In Post 1280 we used a correlation for the Fanning friction factor for turbu-
lent flow in a pipe. For laminar flow (Re < 3000), there is another correlation
that is commonly used: fF = 16/Re. Unfortunately, the correlations for lami-
nar flow and turbulent flow have different values at the transition that should
occur at Re = 3000. This discontinuity can cause a lot of problems for numerical
solvers that rely on derivatives.
Today we examine a strategy for smoothly joining these two functions. First
we define the two functions.

1 import numpy as np
2 from scipy.optimize import fsolve
3 import matplotlib.pyplot as plt
4
5 def fF_laminar(Re):

47
6 return 16.0 / Re
7
8 def fF_turbulent_unvectorized(Re):
9 # Nikuradse correlation for turbulent flow
10 # 1/np.sqrt(f) = (4.0*np.log10(Re*np.sqrt(f))-0.4)
11 # we have to solve this equation to get f
12 def func(f):
13 return 1/np.sqrt(f) - (4.0*np.log10(Re*np.sqrt(f))-0.4)
14 fguess = 0.01
15 f, = fsolve(func, fguess)
16 return f
17
18 # this enables us to pass vectors to the function and get vectors as
19 # solutions
20 fF_turbulent = np.vectorize(fF_turbulent_unvectorized)

Now we plot the correlations.

1 Re1 = np.linspace(500, 3000)

2 f1 = fF_laminar(Re1)
3
4 Re2 = np.linspace(3000, 10000)
5 f2 = fF_turbulent(Re2)
6
7 plt.figure(1); plt.clf()
8 plt.plot(Re1, f1, label=’laminar’)
9 plt.plot(Re2, f2, label=’turbulent’)
10 plt.xlabel(’Re’)
11 plt.ylabel(’$f_F$’)
12 plt.legend()
13 plt.savefig(’images/smooth-transitions-1.png’)

>>> >>> >>> >>> >>> <matplotlib.figure.Figure object at 0x051FF630>

[<matplotlib.lines.Line2D object at 0x05963C10>]
[<matplotlib.lines.Line2D object at 0x0576DD70>]
<matplotlib.text.Text object at 0x0577CFF0>
<matplotlib.text.Text object at 0x05798790>
<matplotlib.legend.Legend object at 0x05798030>

48
 You can see the discontinuity at Re = 3000. What we need is a method
to join these two functions smoothly. We can do that with a sigmoid function.
Sigmoid functions
A sigmoid function smoothly varies from 0 to 1 according to the equation:
1
σ(x) = 1+e−(x−x0)/α . The transition is centered on x0, and α determines the
width of the transition.

1 x = np.linspace(-4,4);
2 y = 1.0 / (1 + np.exp(-x / 0.1))
3 plt.figure(2); plt.clf()
4 plt.plot(x, y)
5 plt.xlabel(’x’); plt.ylabel(’y’); plt.title(’$\sigma(x)$’)
6 plt.savefig(’images/smooth-transitions-sigma.png’)

>>> <matplotlib.figure.Figure object at 0x0596CF10>

[<matplotlib.lines.Line2D object at 0x05A26D90>]
<matplotlib.text.Text object at 0x059A6050>
<matplotlib.text.Text object at 0x059AF0D0>
<matplotlib.text.Text object at 0x059BEA30>

49
 If we have two functions, f1 (x) and f2 (x) we want to smoothly join, we do it
like this: f (x) = (1−σ(x))f1 (x)+σ(x)f2 (x). There is no formal justification for
this form of joining, it is simply a mathematical convenience to get a numerically
smooth function. Other functions besides the sigmoid function could also be
used, as long as they smoothly transition from 0 to 1, or from 1 to zero.

1 def fanning_friction_factor(Re):
2 ’’’combined, continuous correlation for the fanning friction factor.
3 the alpha parameter is chosen to provide the desired smoothness.
4 The transition region is about +- 4*alpha. The value 450 was
5 selected to reasonably match the shape of the correlation
6 function provided by Morrison (see last section of this file)’’’
7 sigma = 1. / (1 + np.exp(-(Re - 3000.0) / 450.0));
8 f = (1-sigma) * fF_laminar(Re) + sigma * fF_turbulent(Re)
9 return f
10
11 Re = np.linspace(500,10000);
12 f = fanning_friction_factor(Re);
13
14 # add data to figure 1
15 plt.figure(1)
16 plt.plot(Re,f, label=’smooth transition’)
17 plt.xlabel(’Re’)
18 plt.ylabel(’$f_F$’)
19 plt.legend()
20 plt.savefig(’images/smooth-transitions-3.png’)

... ... ... ... ... ... ... ... >>> >>> >>> >>> ... <matplotlib.figure.Figure object at 0x05
[<matplotlib.lines.Line2D object at 0x05786310>]
<matplotlib.text.Text object at 0x0577CFF0>
<matplotlib.text.Text object at 0x05798790>
<matplotlib.legend.Legend object at 0x05A302B0>

50
 You can see that away from the transition the combined function is practi-
cally equivalent to the original two functions. That is because away from the
transition the sigmoid function is 0 or 1. Near Re = 3000 is a smooth transition
from one curve to the other curve.
Morrison derived a single function for the friction factor correlation over all
0.165
0.0076( 3170
Re )
Re: f = 7.0
16
+ Re . Here we show the comparison with the approach
1+( 3171
Re )
used above. The friction factor differs slightly at high Re, because Morrison’s is
based on the Prandlt correlation, while the work here is based on the Nikuradse
correlation. They are similar, but not the same.

1 # add this correlation to figure 1

2 h, = plt.plot(Re, 16.0/Re + (0.0076 * (3170 / Re)**0.165) / (1 + (3170.0 / Re)**7))
3
4 ax = plt.gca()
5 handles, labels = ax.get_legend_handles_labels()
6
7 handles.append(h)
8 labels.append(’Morrison’)
9 ax.legend(handles, labels)
10 plt.savefig(’images/smooth-transitions-morrison.png’)

>>> >>> >>> >>> >>> >>> >>> <matplotlib.legend.Legend object at 0x05A5AEB0>

51
 3.9.1 Summary
The approach demonstrated here allows one to smoothly join two discontinuous
functions that describe physics in different regimes, and that must transition
over some range of data. It should be emphasized that the method has no
physical basis, it simply allows one to create a mathematically smooth function,
which could be necessary for some optimizers or solvers to work.

3.10 Smooth transitions between two constants

Suppose we have a parameter that has two different values depending on the
value of a dimensionless number. For example when the dimensionless number is
much less than 1, x = 2/3, and when x is much greater than 1, x = 1. We desire
a smooth transition from 2/3 to 1 as a function of x to avoid discontinuities in
functions of x. We will adapt the smooth transitions between functions to be a
smooth transition between constants.
We define our function as x(D) = x0 + (x1 − x0) ∗ (1 − sigma(D, w). We
control the rate of the transition by the variable w

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x0 = 2.0 / 3.0
5 x1 = 1.5
6
7 w = 0.05
8
9 D = np.linspace(0,2, 500)

52
10
11 sigmaD = 1.0 / (1.0 + np.exp(-(1 - D) / w))
12
13 x = x0 + (x1 - x0)*(1 - sigmaD)
14
15 plt.plot(D, x)
16 plt.xlabel(’D’); plt.ylabel(’x’)
17 plt.savefig(’images/smooth-transitions-constants.png’)

This is a nice trick to get an analytical function with continuous derivatives

for a transition between two constants. You could have the transition occur at
a value other than D = 1, as well by changing the argument to the exponential
function.

3.11 On the quad or trapz’d in ChemE heaven

Matlab post
What is the difference between quad and trapz? The short answer is that
quad integrates functions (via a function handle) using numerical quadrature,
and trapz performs integration of arrays of data using the trapezoid method.
R 2 Let us look at some examples. We consider the example of computing
0
x 3
dx. the analytical integral is 1/4x4 , so we know the integral evaluates
to 16/4 = 4. This will be our benchmark for comparison to the numerical
methods. R2
We use the scipy.integrate.quad command to evaluate this 0 x3 dx.

1 from scipy.integrate import quad

2

53
3 ans, err = quad(lambda x: x**3, 0, 2)
4 print ans

4.0

you can also define a function for the integrand.

1 from scipy.integrate import quad

2
3 def integrand(x):
4 return x**3
5
6 ans, err = quad(integrand, 0, 2)
7 print ans

4.0

3.11.1 Numerical data integration

if we had numerical data like this, we use trapz to integrate it

1 import numpy as np
2
3 x = np.array([0, 0.5, 1, 1.5, 2])
4 y = x**3
5
6 i2 = np.trapz(y, x)
7
8 error = (i2 - 4)/4
9
10 print i2, error

4.25 0.0625

Note the integral of these vectors is greater than 4! You can see why here.

1 import numpy as np
2 import matplotlib.pyplot as plt
3 x = np.array([0, 0.5, 1, 1.5, 2])
4 y = x**3
5
6 x2 = np.linspace(0, 2)
7 y2 = x2**3
8
9 plt.plot(x, y, label=’5 points’)
10 plt.plot(x2, y2, label=’50 points’)
11 plt.legend()
12 plt.savefig(’images/quad-1.png’)

54
 The trapezoid method is overestimating the area significantly. With more
points, we get much closer to the analytical value.

1 import numpy as np
2
3 x2 = np.linspace(0, 2, 100)
4 y2 = x2**3
5
6 print np.trapz(y2, x2)

4.00040812162

3.11.2 Combining numerical data with quad

You might want to combine numerical data with the quad function if you want
to perform integrals easily. Let us say you are given this data:
x = [0 0.5 1 1.5 2]; y = [0 0.1250 1.0000 3.3750 8.0000];
and you want to integrate this from x = 0.25 to 1.75. We do not have data in
those regions, so some interpolation is going to be needed. Here is one approach.

1 from scipy.interpolate import interp1d

2 from scipy.integrate import quad
3 import numpy as np
4
5 x = [0, 0.5, 1, 1.5, 2]
6 y = [0, 0.1250, 1.0000, 3.3750, 8.0000]
7
8 f = interp1d(x, y)
9
10 # numerical trapezoid method
11 xfine = np.linspace(0.25, 1.75)

55
12 yfine = f(xfine)
13 print np.trapz(yfine, xfine)
14
15 # quadrature with interpolation
16 ans, err = quad(f, 0.25, 1.75)
17 print ans

2.53199187838
2.53125
These approaches are very similar, and both rely on linear interpolation.
The second approach is simpler, and uses fewer lines of code.

3.11.3 Summary
trapz and quad are functions for getting integrals. Both can be used with
numerical data if interpolation is used. The syntax for the quad and trapz
function is different in scipy than in Matlab.
Finally, see this post for an example of solving an integral equation using
quad and fsolve.

3.12 Polynomials in python

Matlab post
Polynomials can be represented as a list of coefficients. For example, the
polynomial 4 ∗ x3 + 3 ∗ x2 − 2 ∗ x + 10 = 0 can be represented as [4, 3, -2, 10].
Here are some ways to create a polynomial object, and evaluate it.

1 import numpy as np
2
3 ppar = [4, 3, -2, 10]
4 p = np.poly1d(ppar)
5
6 print p(3)
7 print np.polyval(ppar, 3)
8
9 x = 3
10 print 4*x**3 + 3*x**2 -2*x + 10

139
139
139
numpy makes it easy to get the derivative and integral of a polynomial.
Consider: y = 2x2 − 1. We know the derivative is 4x. Here we compute the
derivative and evaluate it at x=4.

1 import numpy as np
2
3 p = np.poly1d([2, 0, -1])
4 p2 = np.polyder(p)
5 print p2
6 print p2(4)

56
 4 x
16
The integral of the previous polynomial is 23 x3 − x + c. We assume C = 0.
R4
Let us compute the integral 2 2x2 − 1dx.

1 import numpy as np
2
3 p = np.poly1d([2, 0, -1])
4 p2 = np.polyint(p)
5 print p2
6 print p2(4) - p2(2)

3
0.6667 x - 1 x
35.3333333333
One reason to use polynomials is the ease of finding all of the roots using
numpy.roots.

1 import numpy as np
2 print np.roots([2, 0, -1]) # roots are +- sqrt(2)
3
4 # note that imaginary roots exist, e.g. x^2 + 1 = 0 has two roots, +-i
5 p = np.poly1d([1, 0, 1])
6 print np.roots(p)

[ 0.70710678 -0.70710678]
[ 0.+1.j 0.-1.j]
There are applications of polynomials in thermodynamics. The van der waal
2 3
equation is a cubic polynomial f (V ) = V 3 − pnb+nRT
p V 2 + npa V − n pab = 0,
where a and b are constants, p is the pressure, R is the gas constant, T is an
absolute temperature and n is the number of moles. The roots of this equation
tell you the volume of the gas at those conditions.

1 import numpy as np
2 # numerical values of the constants
3 a = 3.49e4
4 b = 1.45
5 p = 679.7 # pressure in psi
6 T = 683 # T in Rankine
7 n = 1.136 # lb-moles
8 R = 10.73 # ft^3 * psi /R / lb-mol
9
10 ppar = [1.0, -(p*n*b+n*R*T)/p, n**2*a/p, -n**3*a*b/p];
11 print np.roots(ppar)

[ 5.09432376+0.j 4.40066810+1.43502848j 4.40066810-1.43502848j]

Note that only one root is real (and even then, we have to interpet 0.j as not
being imaginary. Also, in a cubic polynomial, there can only be two imaginary
roots). In this case that means there is only one phase present.

57
 3.12.1 Summary
Polynomials in numpy are even better than in Matlab, because you get a poly-
nomial object that acts just like a function. Otherwise, they are functionally
equivalent.

3.13 The trapezoidal method of integration

Matlab post See http://en.wikipedia.org/wiki/Trapezoidal_rule
Z b N
1X
f (x)dx ≈ (xk+1 − xk )(f (xk+1 ) + f (xk ))
a 2
k=1
Let us compute the integral of sin(x) from x=0 to π. To approximate the
integral, we need to divide the interval from a to b into N intervals. The
analytical answer is 2.0.
We will use this example to illustrate the difference in performance between
loops and vectorized operations in python.

1 import numpy as np
2 import time
3
4 a = 0.0; b = np.pi;
5 N = 1000; # this is the number of intervals
6
7 h = (b - a)/N; # this is the width of each interval
8 x = np.linspace(a, b, N)
9 y = np.sin(x); # the sin function is already vectorized
10
11 t0 = time.time()
12 f = 0.0
13 for k in range(len(x) - 1):
14 f += 0.5 * ((x[k+1] - x[k]) * (y[k+1] + y[k]))
15
16 tf = time.time() - t0
17 print ’time elapsed = {0} sec’.format(tf)
18
19 print f

>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ... ... >>> >>> time elapsed = 0.0780000686646 s
>>> 1.99999835177

1 t0 = time.time()
2 Xk = x[1:-1] - x[0:-2] # vectorized version of (x[k+1] - x[k])
3 Yk = y[1:-1] + y[0:-2] # vectorized version of (y[k+1] + y[k])
4
5 f = 0.5 * np.sum(Xk * Yk) # vectorized version of the loop above
6 tf = time.time() - t0
7 print ’time elapsed = {0} sec’.format(tf)
8
9 print f

>>> >>> >>> >>> >>> time elapsed = 0.077999830246 sec

>>> 1.99999340709

58
 In the last example, there may be loop buried in the sum command. Let us do
one final method, using linear algebra, in a single line. The key to understanding
this is to recognize the sum is just the result of a dot product of the x differences
and y sums.

1 t0 = time.time()
2 f = 0.5 * np.dot(Xk, Yk)
3 tf = time.time() - t0
4 print ’time elapsed = {0} sec’.format(tf)
5
6 print f

>>> >>> time elapsed = 0.0310001373291 sec

>>> 1.99999340709
The loop method is straightforward to code, and looks alot like the formula
that defines the trapezoid method. the vectorized methods are not as easy to
read, and take fewer lines of code to write. However, the vectorized methods
are much faster than the loop, so the loss of readability could be worth it for
very large problems.
The times here are considerably slower than in Matlab. I am not sure if that
is a totally fair comparison. Here I am running python through emacs, which
may result in slower performance. I also used a very crude way of timing the
performance which lumps some system performance in too.

3.14 Numerical Simpsons rule

A more accurate numerical integration than the trapezoid method is Simpson’s
rule. The syntax is similar to trapz, but the method is in scipy.integrate.

1 import numpy as np
2 from scipy.integrate import simps, romb
3
4 a = 0.0; b = np.pi / 4.0;
5 N = 10 # this is the number of intervals
6
7 x = np.linspace(a, b, N)
8 y = np.cos(x)
9
10 t = np.trapz(y, x)
11 s = simps(y, x)
12 a = np.sin(b) - np.sin(a)
13
14 print
15 print ’trapz = {0} ({1:%} error)’.format(t, (t - a)/a)
16 print ’simps = {0} ({1:%} error)’.format(s, (s - a)/a)
17 print ’analy = {0}’.format(a)

>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>>
trapz = 0.70665798038 (-0.063470% error)
simps = 0.707058914216 (-0.006769% error)
analy = 0.707106781187

59
 You can see the Simpson’s method is more accurate than the trapezoid
method.

3.15 Integrating functions in python

Matlab post
Problem statement
find the integral of a function f(x) from a to b i.e.
Z b
f (x)dx
a
In python we use numerical quadrature to achieve this with the scipy.integrate.quad
command.
as a specific example, lets integrate

y = x2
from x=0 to x=1. You should be able to work out that the answer is 1/3.

1 from scipy.integrate import quad

2
3 def integrand(x):
4 return x**2
5
6 ans, err = quad(integrand, 0, 1)
7 print ans

0.333333333333

3.15.1 double integrals

we use the scipy.integrate.dblquad command
Integrate f (x, y) = ysin(x) + xcos(y) over
π <= x <= 2π
0 <= y <= π
i.e.
R 2π R π
x=π y=0
ysin(x) + xcos(y)dydx
The syntax in dblquad is a bit more complicated than in Matlab. We have
to provide callable functions for the range of the y-variable. Here they are
constants, so we create lambda functions that return the constants. Also, note
that the order of arguments in the integrand is different than in Matlab.

1 from scipy.integrate import dblquad

2 import numpy as np
3
4 def integrand(y, x):
5 ’y must be the first argument, and x the second.’
6 return y * np.sin(x) + x * np.cos(y)
7
8 ans, err = dblquad(integrand, np.pi, 2*np.pi,
9 lambda x: 0,

60
10 lambda x: np.pi)
11 print ans

-9.86960440109
we use the tplquad command to integrate f (x, y, z) = ysin(x) + zcos(x) over
the region
0 <= x <= π
0 <= y <= 1
−1 <= z <= 1

1 from scipy.integrate import tplquad

2 import numpy as np
3
4 def integrand(z, y, x):
5 return y * np.sin(x) + z * np.cos(x)
6
7 ans, err = tplquad(integrand,
8 0, np.pi, # x limits
9 lambda x: 0,
10 lambda x: 1, # y limits
11 lambda x,y: -1,
12 lambda x,y: 1) # z limits
13
14 print ans

2.0

3.15.2 Summary
scipy.integrate offers the same basic functionality as Matlab does. The syntax
differs significantly for these simple examples, but the use of functions for the
limits enables freedom to integrate over non-constant limits.

3.16 Integrating equations in python

A common need in engineering calculations is to integrate an equation over some
range to determine the total change. For example, say we know the volumetric
flow changes with time according to dν/dt = αt, where α = 1 L/min and we
want to know how much liquid flows into a tank over 10 minutes if the volumetric
flowrate is ν0 = 5 L/min at t = 0. The answer to that question is the value of
R 10
this integral: V = 0 ν0 + αtdt.

1 import scipy
2 from scipy.integrate import quad
3
4 nu0 = 5 # L/min
5 alpha = 1.0 # L/min
6 def integrand(t):
7 return nu0 + alpha * t
8
9 t0 = 0.0
10 tfinal = 10.0
11 V, estimated_error = quad(integrand, t0, tfinal)
12 print(’{0:1.2f} L flowed into the tank over 10 minutes’.format(V))

61
 100.00 L flowed into the tank over 10 minutes

That is all there is too it!

3.17 Function integration by the Romberg method

An alternative to the scipy.integrate.quad function is the Romberg method. This
method is not likely to be more accurate than quad, and it does not give you
an error estimate.

1 import numpy as np
2
3 from scipy.integrate import quad, romberg
4
5 a = 0.0
6 b = np.pi / 4.0
7
8 print quad(np.sin, a, b)
9 print romberg(np.sin, a, b)

(0.2928932188134524, 3.2517679528326894e-15)
0.292893218813

3.18 Symbolic math in python

Matlab post Python has capability to do symbolic math through the sympy
package.

3.18.1 Solve the quadratic equation

1 from sympy import solve, symbols, pprint

2
3 a,b,c,x = symbols(’a,b,c,x’)
4
5 f = a*x**2 + b*x + c
6
7 solution = solve(f, x)
8 print solution
9 pprint(solution)

>>> >>> >>> >>> >>> >>> [(-b + (-4*a*c + b**2)**(1/2))/(2*a), -(b + (-4*a*c + b**2)**(1/2))/
_____________ / _____________\
/ 2 | / 2 |
-b + \/ -4*a*c + b -\b + \/ -4*a*c + b /
[---------------------, -----------------------]
2*a 2*a
√
The solution you should recognize in the form of b± b2 −4ac
2a although python
does not print it this nicely!

62
 3.18.2 differentiation
you might find this helpful!

1 from sympy import diff

2
3 print diff(f, x)
4 print diff(f, x, 2)
5
6 print diff(f, a)

>>> 2*a*x + b
2*a
>>> x**2

3.18.3 integration

1 from sympy import integrate

2
3 print integrate(f, x) # indefinite integral
4 print integrate(f, (x, 0, 1)) # definite integral from x=0..1

>>> a*x**3/3 + b*x**2/2 + c*x

a/3 + b/2 + c

3.18.4 Analytically solve a simple ODE

1 from sympy import Function, Symbol, dsolve

2 f = Function(’f’)
3 x = Symbol(’x’)
4 fprime = f(x).diff(x) - f(x) # f’ = f(x)
5
6 y = dsolve(fprime, f(x))
7
8 print y
9 print y.subs(x,4)
10 print [y.subs(x, X) for X in [0, 0.5, 1]] # multiple values

>>> >>> >>> >>> >>> >>> f(x) == exp(C1 + x)

f(4) == exp(C1 + 4)
[f(0) == exp(C1), f(0.5) == exp(C1 + 0.5), f(1) == exp(C1 + 1)]

It is not clear you can solve the initial value problem to get C1.
The symbolic math in sympy is pretty good. It is not up to the capability of
Maple or Mathematica, (but neither is Matlab) but it continues to be developed,
and could be helpful in some situations.

63
 3.19 Is your ice cream float bigger than mine
Float numbers (i.e. the ones with decimals) cannot be perfectly represented in
a computer. This can lead to some artifacts when you have to compare float
numbers that on paper should be the same, but in silico are not. Let us look at
some examples. In this example, we do some simple math that should result in
an answer of 1, and then see if the answer is "equal" to one.

1 print 3.0 * (1.0/3.0)

2 print 1.0 == 3.0 * (1.0/3.0)

1.0
True

Everything looks fine. Now, consider this example.

1 print 49.0 * (1.0/49.0)

2 print 1.0 == 49.0 * (1.0/49.0)

1.0
False

The first line looks like everything is find, but the equality fails!

1.0
False

You can see here why the equality statement fails. We will print the two
numbers to sixteen decimal places.

1 print ’{0:1.16f}’.format(49.0 * (1.0/49.0) )

2 print ’{0:1.16f}’.format(1.0)
3 print 1 - 49.0 * (1.0/49.0)

0.9999999999999999
1.0000000000000000
1.11022302463e-16

The two numbers actually are not equal to each other because of float math.
They are very, very close to each other, but not the same.
This leads to the idea of asking if two numbers are equal to each other within
some tolerance. The question of what tolerance to use requires thought. Should
it be an absolute tolerance? a relative tolerance? How large should the tolerance
be? We will use the distance between 1 and the nearest floating point number
(this is eps in Matlab). numpy can tell us this number with the np.spacing
command.
Below, we implement a comparison function from 10.1107/S010876730302186X
that allows comparisons with tolerance.

64
1 # Implemented from Acta Crystallographica A60, 1-6 (2003). doi:10.1107/S010876730302186X
2
3 import numpy as np
4 print np.spacing(1)
5
6 def feq(x, y, epsilon):
7 ’x == y’
8 return not((x < (y - epsilon)) or (y < (x - epsilon)))
9
10 print feq(1.0, 49.0 * (1.0/49.0), np.spacing(1))

2.22044604925e-16
True
For completeness, here are the other float comparison operators from that
paper. We also show a few examples.
1 import numpy as np
2
3 def flt(x, y, epsilon):
4 ’x < y’
5 return x < (y - epsilon)
6
7 def fgt(x, y, epsilon):
8 ’x > y’
9 return y < (x - epsilon)
10
11 def fle(x, y, epsilon):
12 ’x <= y’
13 return not(y < (x - epsilon))
14
15 def fge(x, y, epsilon):
16 ’x >= y’
17 return not(x < (y - epsilon))
18
19 print fge(1.0, 49.0 * (1.0/49.0), np.spacing(1))
20 print fle(1.0, 49.0 * (1.0/49.0), np.spacing(1))
21
22 print fgt(1.0 + np.spacing(1), 49.0 * (1.0/49.0), np.spacing(1))
23 print flt(1.0 - 2 * np.spacing(1), 49.0 * (1.0/49.0), np.spacing(1))

True
True
True
True
As you can see, float comparisons can be tricky. You have to give a lot of
thought to how to make the comparisons, and the functions shown above are
not the only way to do it. You need to build in testing to make sure your
comparisons are doing what you want.

4 Linear algebra
4.1 Potential gotchas in linear algebra in numpy
Numpy has some gotcha features for linear algebra purists. The first is that a
1d array is neither a row, nor a column vector. That is, a = aT if a is a 1d array.

65
 That means you can take the dot product of a with itself, without transposing
the second argument. This would not be allowed in Matlab.

1 import numpy as np
2
3 a = np.array([0, 1, 2])
4 print a.shape
5 print a
6 print a.T
7
8 print
9 print np.dot(a, a)
10 print np.dot(a, a.T)

>>> >>> (3L,)

[0 1 2]
[0 1 2]
>>>
5
5
Compare the previous behavior with this 2d array. In this case, you cannot
take the dot product of b with itself, because the dimensions are incompatible.
You must transpose the second argument to make it dimensionally consistent.
Also, the result of the dot product is not a simple scalar, but a 1 × 1 array.

1 b = np.array([[0, 1, 2]])
2 print b.shape
3 print b
4 print b.T
5
6 print np.dot(b, b) # this is not ok, the dimensions are wrong.
7 print np.dot(b, b.T)
8 print np.dot(b, b.T).shape

(1L, 3L)
[[0 1 2]]
[[0]
[1]
[2]]
>>> Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: objects are not aligned
[[5]]
(1L, 1L)
Try to figure this one out! x is a column vector, and y is a 1d vector. Just
by adding them you get a 2d array.

1 x = np.array([[2], [4], [6], [8]])

2 y = np.array([1, 1, 1, 1, 1, 2])
3 print x + y

66
 >>> [[ 3 3 3 3 3 4]
[ 5 5 5 5 5 6]
[ 7 7 7 7 7 8]
[ 9 9 9 9 9 10]]

Or this crazy alternative way to do the same thing.

1 x = np.array([2, 4, 6, 8])
2 y = np.array([1, 1, 1, 1, 1, 1, 2])
3
4 print x[:, np.newaxis] + y

>>> >>> [[ 3 3 3 3 3 3 4]
[ 5 5 5 5 5 5 6]
[ 7 7 7 7 7 7 8]
[ 9 9 9 9 9 9 10]]

In the next example, we have a 3 element vector and a 4 element vector. We

convert b to a 2D array with np.newaxis, and compute the outer product of the
two arrays. The result is a 4 × 3 array.

1 a = np.array([1, 2, 3])
2 b = np.array([10, 20, 30, 40])
3
4 print a * b[:, np.newaxis]

>>> >>> [[ 10 40 90]

[ 20 80 180]
[ 30 120 270]
[ 40 160 360]]

These concepts are known in numpy as array broadcasting. See http://www.

scipy.org/EricsBroadcastingDoc and http://docs.scipy.org/doc/numpy/
user/basics.broadcasting.html for more details.
These are points to keep in mind, as the operations do not strictly follow
the conventions of linear algebra, and may be confusing at times.

4.2 Solving linear equations

Given these equations, find [x1, x2, x3]

x1 − x2 + x3 = 0 (5)
10x2 + 25x3 = 90 (6)
20x1 + 10x2 = 80 (7)

reference: Kreysig, Advanced Engineering Mathematics, 9th ed. Sec. 7.3

67
 When solving linear equations, we can represent them in matrix form. The
we simply use numpy.linalg.solve to get the solution.

1 import numpy as np
2 A = np.array([[1, -1, 1],
3 [0, 10, 25],
4 [20, 10, 0]])
5
6 b = np.array([0, 90, 80])
7
8 x = np.linalg.solve(A, b)
9 print x
10 print np.dot(A,x)
11
12 # Let us confirm the solution.
13 # this shows one element is not equal because of float tolerance
14 print np.dot(A,x) == b
15
16 # here we use a tolerance comparison to show the differences is less
17 # than a defined tolerance.
18 TOLERANCE = 1e-12
19 print np.abs((np.dot(A, x) - b)) <= TOLERANCE

[ 2. 4. 2.]
[ 2.66453526e-15 9.00000000e+01 8.00000000e+01]
[False True True]
[ True True True]

It can be useful to confirm there should be a solution, e.g. that the equations
are all independent. The matrix rank will tell us that. Note that numpy:rank
does not give you the matrix rank, but rather the number of dimensions of the
array. We compute the rank by computing the number of singular values of
the matrix that are greater than zero, within a prescribed tolerance. We use
the numpy.linalg.svd function for that. In Matlab you would use the rref
command to see if there are any rows that are all zero, but this command does
not exist in numpy. That command does not have practical use in numerical
linear algebra and has not been implemented.

1 import numpy as np
2 A = np.array([[1, -1, 1],
3 [0, 10, 25],
4 [20, 10, 0]])
5
6 b = np.array([0, 90, 80])
7
8 # determine number of independent rows in A we get the singular values
9 # and count the number greater than 0.
10 TOLERANCE = 1e-12
11 u, s, v = np.linalg.svd(A)
12 print ’Singular values: {0}’.format(s)
13 print ’# of independent rows: {0}’.format(np.sum(np.abs(s) > TOLERANCE))
14
15 # to illustrate a case where there are only 2 independent rows
16 # consider this case where row3 = 2*row2.
17 A = np.array([[1, -1, 1],
18 [0, 10, 25],
19 [0, 20, 50]])
20

68
21 u, s, v = np.linalg.svd(A)
22
23 print ’Singular values: {0}’.format(s)
24 print ’# of independent rows: {0}’.format(np.sum(np.abs(s) > TOLERANCE))

Singular values: [ 27.63016717 21.49453733 1.5996022 ]

# of independent rows: 3
Singular values: [ 60.21055203 1.63994657 -0. ]
# of independent rows: 2

Matlab comparison

4.3 Rules for transposition

Matlab comparison
Here are the four rules for matrix multiplication and transposition

1. (AT )T = A
2. (A + B)T = AT + BT
3. (cA)T = cAT

4. (AB)T = BT AT

reference: Chapter 7.2 in Advanced Engineering Mathematics, 9th edition.

by E. Kreyszig.

4.3.1 The transpose in Python

There are two ways to get the transpose of a matrix: with a notation, and with
a function.

1 import numpy as np
2 A = np.array([[5, -8, 1],
3 [4, 0, 0]])
4
5 # function
6 print np.transpose(A)
7
8
9 # notation
10 print A.T

[[ 5 4]
[-8 0]
[ 1 0]]
[[ 5 4]
[-8 0]
[ 1 0]]

69
 4.3.2 Rule 1

1 import numpy as np
2
3 A = np.array([[5, -8, 1],
4 [4, 0, 0]])
5
6 print np.all(A == (A.T).T)

True

4.3.3 Rule 2

1 import numpy as np
2 A = np.array([[5, -8, 1],
3 [4, 0, 0]])
4
5 B = np.array([[3, 4, 5], [1, 2,3]])
6
7 print np.all( A.T + B.T == (A + B).T)

True

4.3.4 Rule 3

1 import numpy as np
2 A = np.array([[5, -8, 1],
3 [4, 0, 0]])
4
5 c = 2.1
6
7 print np.all( (c*A).T == c*A.T)

True

4.3.5 Rule 4

1 import numpy as np
2 A = np.array([[5, -8, 1],
3 [4, 0, 0]])
4
5 B = np.array([[0, 2],
6 [1, 2],
7 [6, 7]])
8
9 print np.all(np.dot(A, B).T == np.dot(B.T, A.T))

True

4.3.6 Summary
That wraps up showing numerically the transpose rules work for these examples.

70
 4.4 Sums products and linear algebra notation - avoiding
loops where possible
Matlab comparison
Today we examine some methods of linear algebra that allow us to avoid
writing explicit loops in Matlab for some kinds of mathematical operations.
Consider the operation on two vectors a and b.
n
X
y= ai bi
i=1
a = [1 2 3 4 5]
b = [3 6 8 9 10]

4.4.1 Old-fashioned way with a loop

We can compute this with a loop, where you initialize y, and then add the
product of the ith elements of a and b to y in each iteration of the loop. This
is known to be slow for large vectors

1 a = [1, 2, 3, 4, 5]
2 b = [3, 6, 8, 9, 10]
3
4 sum = 0
5 for i in range(len(a)):
6 sum = sum + a[i] * b[i]
7 print sum

125
This is an old fashioned style of coding. A more modern, pythonic approach
is:
1 a = [1, 2, 3, 4, 5]
2 b = [3, 6, 8, 9, 10]
3
4 sum = 0
5 for x,y in zip(a,b):
6 sum += x * y
7 print sum

125

4.4.2 The numpy approach

The most compact method is to use the methods in numpy.
1 import numpy as np
2
3 a = np.array([1, 2, 3, 4, 5])
4 b = np.array([3, 6, 8, 9, 10])
5
6 print np.sum(a * b)

125

71
 4.4.3 Matrix algebra approach.
The operation defined above is actually a dot product. We an directly compute
the dot product in numpy. Note that with 1d arrays, python knows what to do
and does not require any transpose operations.

1 import numpy as np
2
3 a = np.array([1, 2, 3, 4, 5])
4 b = np.array([3, 6, 8, 9, 10])
5
6 print np.dot(a, b)

125

4.4.4 Another example

n
Consider y = wi x2i . This operation is like a weighted sum of squares. The
P
i=1
old-fashioned way to do this is with a loop.

1 w = [0.1, 0.25, 0.12, 0.45, 0.98];

2 x = [9, 7, 11, 12, 8];
3 y = 0
4 for wi, xi in zip(w,x):
5 y += wi * xi**2
6 print y

162.39
Compare this to the more modern numpy approach.

1 import numpy as np
2 w = np.array([0.1, 0.25, 0.12, 0.45, 0.98])
3 x = np.array([9, 7, 11, 12, 8])
4 y = np.sum(w * x**2)
5 print y

162.39
We can also express this in matrix algebra form. The operation is equivalent
to y = ~x · Dw · ~xT where Dw is a diagonal matrix with the weights on the
diagonal.

1 import numpy as np
2 w = np.array([0.1, 0.25, 0.12, 0.45, 0.98])
3 x = np.array([9, 7, 11, 12, 8])
4 y = np.dot(x, np.dot(np.diag(w), x))
5 print y

162.39
This last form avoids explicit loops and sums, and relies on fast linear algebra
routines.

72
 4.4.5 Last example
n
Consider the sum of the product of three vectors. Let y = wi xi yi . This is
P
i=1
like a weighted sum of products.

1 import numpy as np
2
3 w = np.array([0.1, 0.25, 0.12, 0.45, 0.98])
4 x = np.array([9, 7, 11, 12, 8])
5 y = np.array([2, 5, 3, 8, 0])
6
7 print np.sum(w * x * y)
8 print np.dot(w, np.dot(np.diag(x), y))

57.71
57.71

4.4.6 Summary
We showed examples of the following equalities between traditional sum nota-
tions and linear algebra
n
X
ab = ai bi
i=1
n
X
xDw xT = wi x2i
i=1
n
X
T
xDw y = wi x i y i
i=1

These relationships enable one to write the sums as a single line of python
code, which utilizes fast linear algebra subroutines, avoids the construction of
slow loops, and reduces the opportunity for errors in the code. Admittedly, it
introduces the opportunity for new types of errors, like using the wrong rela-
tionship, or linear algebra errors due to matrix size mismatches.

4.5 Determining linear independence of a set of vectors

Matlab post Occasionally we have a set of vectors and we need to determine
whether the vectors are linearly independent of each other. This may be neces-
sary to determine if the vectors form a basis, or to determine how many inde-
pendent equations there are, or to determine how many independent reactions
there are.
Reference: Kreysig, Advanced Engineering Mathematics, sec. 7.4
Matlab provides a rank command which gives you the number of singular
values greater than some tolerance. The numpy.rank function, unfortunately,

73
 does not do that. It returns the number of dimensions in the array. We will
just compute the rank from singular value decomposition.
The default tolerance used in Matlab is max(size(A))*eps(norm(A)). Let us
break that down. eps(norm(A)) is the positive distance from abs(X) to the next
larger in magnitude floating point number of the same precision as X. Basically,
the smallest significant number. We multiply that by the size of A, and take
the largest number. We have to use some judgment in what the tolerance is,
and what "zero" means.

1 import numpy as np
2 v1 = [6, 0, 3, 1, 4, 2];
3 v2 = [0, -1, 2, 7, 0, 5];
4 v3 = [12, 3, 0, -19, 8, -11];
5
6 A = np.row_stack([v1, v2, v3])
7
8 # matlab definition
9 eps = np.finfo(np.linalg.norm(A).dtype).eps
10 TOLERANCE = max(eps * np.array(A.shape))
11
12 U, s, V = np.linalg.svd(A)
13 print s
14 print np.sum(s > TOLERANCE)
15
16 TOLERANCE = 1e-14
17 print np.sum(s > TOLERANCE)

>>> >>> >>> >>> >>> >>> ... >>> >>> >>> >>> [ 2.75209239e+01 9.30584482e+00 1.42425400e
3
>>> >>> 2

You can see if you choose too small a TOLERANCE, nothing looks like
zero. the result with TOLERANCE=1e-14 suggests the rows are not linearly
independent. Let us show that one row can be expressed as a linear combination
of the other rows.
The number of rows is greater than the rank, so these vectors are not inde-
pendent. Let’s demonstrate that one vector can be defined as a linear combina-
tion of the other two vectors. Mathematically we represent this as:
x1 v1 + x2 v2 = v3
or
[x1 x2 ][v1; v2] = v3
This is not the usual linear algebra form of Ax = b. To get there, we
transpose each side of the equation to get:
[v1.T v2.T][x_1; x_2] = v3.T
which is the form Ax = b. We solve it in a least-squares sense.

1 A = np.column_stack([v1, v2])
2 x = np.linalg.lstsq(A, v3)
3 print x[0]

74
 >>> [ 2. -3.]

This shows that v3 = 2*v1 - 3*v2

4.5.1 another example

1 #Problem set 7.4 #17

2 import numpy as np
3
4 v1 = [0.2, 1.2, 5.3, 2.8, 1.6]
5 v2 = [4.3, 3.4, 0.9, 2.0, -4.3]
6
7 A = np.row_stack([v1, v2])
8 U, s, V = np.linalg.svd(A)
9 print s

[ 7.57773162 5.99149259]

You can tell by inspection the rank is 2 because there are no near-zero
singular values.

4.5.2 Near deficient rank

the rank command roughly works in the following way: the matrix is converted
to a reduced row echelon form, and then the number of rows that are not all
equal to zero are counted. Matlab uses a tolerance to determine what is equal to
zero. If there is uncertainty in the numbers, you may have to define what zero
is, e.g. if the absolute value of a number is less than 1e-5, you may consider that
close enough to be zero. The default tolerance is usually very small, of order
1e-15. If we believe that any number less than 1e-5 is practically equivalent to
zero, we can use that information to compute the rank like this.

1 import numpy as np
2
3 A = [[1, 2, 3],
4 [0, 2, 3],
5 [0, 0, 1e-6]]
6
7 U, s, V = np.linalg.svd(A)
8 print s
9 print np.sum(np.abs(s) > 1e-15)
10 print np.sum(np.abs(s) > 1e-5)

[ 5.14874857e+00 7.00277208e-01 5.54700196e-07]

3
2

4.5.3 Application to independent chemical reactions.

reference: Exercise 2.4 in Chemical Reactor Analysis and Design Fundamentals
by Rawlings and Ekerdt.

75
 The following reactions are proposed in the hydrogenation of bromine:
Let this be our species vector: v = [H2 H Br2 Br HBr].T
the reactions are then defined by M*v where M is a stoichometric matrix in
which each row represents a reaction with negative stoichiometric coefficients for
reactants, and positive stoichiometric coefficients for products. A stoichiometric
coefficient of 0 is used for species not participating in the reaction.

1 import numpy as np
2
3 # [H2 H Br2 Br HBr]
4 M = [[-1, 0, -1, 0, 2], # H2 + Br2 == 2HBR
5 [ 0, 0, -1, 2, 0], # Br2 == 2Br
6 [-1, 1, 0, -1, 1], # Br + H2 == HBr + H
7 [ 0, -1, -1, 1, 1], # H + Br2 == HBr + Br
8 [ 1, -1, 0, 1, -1], # H + HBr == H2 + Br
9 [ 0, 0, 1, -2, 0]] # 2Br == Br2
10
11 U, s, V = np.linalg.svd(M)
12 print s
13 print np.sum(np.abs(s) > 1e-15)
14
15 import sympy
16 M = sympy.Matrix(M)
17 reduced_form, inds = M.rref()
18
19 print reduced_form
20
21 labels = [’H2’, ’H’, ’Br2’, ’Br’, ’HBr’]
22 for row in reduced_form.tolist():
23 s = ’0 = ’
24 for nu,species in zip(row,labels):
25 if nu != 0:
26
27 s += ’ {0:+d}{1}’.format(int(nu), species)
28 if s != ’0 = ’: print s

[ 3.84742803e+00 3.32555975e+00 1.46217301e+00 1.73313660e-16

8.57422679e-17]
3
[1, 0, 0, 2, -2]
[0, 1, 0, 1, -1]
[0, 0, 1, -2, 0]
[0, 0, 0, 0, 0]
[0, 0, 0, 0, 0]
[0, 0, 0, 0, 0]
0 = +1H2 +2Br -2HBr
0 = +1H +1Br -1HBr
0 = +1Br2 -2Br

6 reactions are given, but the rank of the matrix is only 3. so there are only
three independent reactions. You can see that reaction 6 is just the opposite of
reaction 2, so it is clearly not independent. Also, reactions 3 and 5 are just the
reverse of each other, so one of them can also be eliminated. finally, reaction 4
is equal to reaction 1 minus reaction 3.

76
 There are many possible independent reactions. In the code above, we use
sympy to put the matrix into reduced row echelon form, which enables us to
identify three independent reactions, and shows that three rows are all zero, i.e.
they are not independent of the other three reactions. The choice of independent
reactions is not unique.

4.6 Reduced row echelon form

There is a nice discussion here on why there is not a rref command in numpy,
primarily because one rarely actually needs it in linear algebra. Still, it is so
often taught, and it helps visually see what the rank of a matrix is that I wanted
to examine ways to get it.

1 import numpy as np
2 from sympy import Matrix
3
4 A = np.array([[3, 2, 1],
5 [2, 1, 1],
6 [6, 2, 4]])
7
8 rA, pivots = Matrix(A).rref()
9 print rA

[1, 0, 1]
[0, 1, -1]
[0, 0, 0]

This rref form is a bit different than you might get from doing it by hand.
The rows are also normalized.
Based on this, we conclude the A matrix has a rank of 2 since one row of
the reduced form contains all zeros. That means the determinant will be zero,
and it should not be possible to compute the inverse of the matrix, and there
should be no solution to linear equations of Ax = b. Let us check it out.

1 import numpy as np
2 from sympy import Matrix
3
4 A = np.array([[3, 2, 1],
5 [2, 1, 1],
6 [6, 2, 4]])
7
8 print np.linalg.det(A)
9 print np.linalg.inv(A)
10
11 b = np.array([3, 0, 6])
12
13 print np.linalg.solve(A, b)

>>> >>> ... ... >>> >>> 6.66133814775e-16

[[ 3.00239975e+15 -9.00719925e+15 1.50119988e+15]
[ -3.00239975e+15 9.00719925e+15 -1.50119988e+15]

77
 [ -3.00239975e+15 9.00719925e+15 -1.50119988e+15]]
>>> >>> >>> [ 1.80143985e+16 -1.80143985e+16 -1.80143985e+16]
There are "solutions", but there are a couple of red flags that should catch
your eye. First, the determinant is within machine precision of zero. Second
the elements of the inverse are all "large". Third, the solutions are all "large".
All of these are indications of or artifacts of numerical imprecision.

4.7 Computing determinants from matrix decompositions

There are a few properties of a matrix that can make it easy to compute deter-
minants.
1. The determinant of a triangular matrix is the product of the elements on
the diagonal.
2. The determinant of a permutation matrix is (-1)**n where n is the number
of permutations. Recall a permutation matrix is a matrix with a one in
each row, and column, and zeros everywhere else.
3. The determinant of a product of matrices is equal to the product of the
determinant of the matrices.
The LU decomposition computes three matrices such that A = P LU . Thus,
det A = det P det L det U . L and U are triangular, so we just need to compute
the product of the diagonals. P is not triangular, but if the elements of the
diagonal are not 1, they will be zero, and then there has been a swap. So we
simply subtract the sum of the diagonal from the length of the diagonal and
then subtract 1 to get the number of swaps.

1 import numpy as np
2 from scipy.linalg import lu
3
4 A = np.array([[6, 2, 3],
5 [1, 1, 1],
6 [0, 4, 9]])
7
8 P, L, U = lu(A)
9
10 nswaps = len(np.diag(P)) - np.sum(np.diag(P)) - 1
11
12 detP = (-1)**nswaps
13 detL = np.prod(np.diag(L))
14 detU = np.prod(np.diag(U))
15
16 print detP * detL * detU
17
18 print np.linalg.det(A)

24.0
24.0
According to the numpy documentation, a method similar to this is used to
compute the determinant.

78
 4.8 Calling lapack directly from scipy
If the built in linear algebra functions in numpy and scipy do not meet your
needs, it is often possible to directly call lapack functions. Here we call a
function to solve a set of complex linear equations. The lapack function for this
is ZGBSV. The description of this function (http://linux.die.net/man/l/
zgbsv) is:
ZGBSV computes the solution to a complex system of linear equations A *
X = B, where A is a band matrix of order N with KL subdiagonals and KU
superdiagonals, and X and B are N-by-NRHS matrices. The LU decomposition
with partial pivoting and row interchanges is used to factor A as A = L * U,
where L is a product of permutation and unit lower triangular matrices with
KL subdiagonals, and U is upper triangular with KL+KU superdiagonals. The
factored form of A is then used to solve the system of equations A * X = B.
The python signature is (http://docs.scipy.org/doc/scipy/reference/
generated/scipy.linalg.lapack.zgbsv.html#scipy.linalg.lapack.zgbsv):
lub,piv,x,info = zgbsv(kl,ku,ab,b,[overwrite_ab,overwrite_b])
We will look at an example from http://www.nag.com/lapack-ex/node22.
html.
We solve Ax = b with

 
−1.65 + 2.26i −2.05 − 0.85i 0.97 − 2.84i 0
 6.30i −1.48 − 1.75i −3.99 + 4.01i 0.59 − 0.48i 
 (8)
A=
 0 −0.77 + 2.83i −1.06 + 1.94i 3.33 − 1.04i 
0 0 4.48 − 1.09i −0.46 − 1.72i

and
 
−1.06 + 21.50i
 −22.72 − 53.90i 
 28.24 − 38.60i  .
b=  (9)
−34.56 + 16.73i
The A matrix has one lower diagonal (kl = 1) and two upper diagonals (ku
= 2), four equations (n = 4) and one right-hand side.

1 import scipy.linalg.lapack as la
2
3 # http://www.nag.com/lapack-ex/node22.html
4 import numpy as np
5 A = np.array([[-1.65 + 2.26j, -2.05 - 0.85j, 0.97 - 2.84j, 0.0 ],
6 [6.30j, -1.48 - 1.75j, -3.99 + 4.01j, 0.59 - 0.48j],
7 [0.0, -0.77 + 2.83j, -1.06 + 1.94j, 3.33 - 1.04j],
8 [0.0, 0.0, 4.48 - 1.09j, -0.46 - 1.72j]])
9
10 # construction of Ab is tricky. Fortran indexing starts at 1, not
11 # 0. This code is based on the definition of Ab at
12 # http://linux.die.net/man/l/zgbsv. First, we create the Fortran
13 # indices based on the loops, and then subtract one from them to index
14 # the numpy arrays.
15 Ab = np.zeros((5,4),dtype=np.complex)
16 n, kl, ku = 4, 1, 2

79
17
18 for j in range(1, n + 1):
19 for i in range(max(1, j - ku), min(n, j + kl) + 1):
20 Ab[kl + ku + 1 + i - j - 1, j - 1] = A[i-1, j-1]
21
22 b = np.array([[-1.06 + 21.50j],
23 [-22.72 - 53.90j],
24 [28.24 - 38.60j],
25 [-34.56 + 16.73j]])
26
27 lub, piv, x, info = la.flapack.zgbsv(kl, ku, Ab, b)
28
29 # compare to results at http://www.nag.com/lapack-ex/examples/results/zgbsv-ex.r
30 print ’x = ’,x
31 print ’info = ’,info
32
33 # check solution
34 print ’solved: ’,np.all(np.dot(A,x) - b < 1e-12)
35
36 # here is the easy way!!!
37 print ’\n\nbuilt-in solver’
38 print np.linalg.solve(A,b)

x = [[-3.+2.j]
[ 1.-7.j]
[-5.+4.j]
[ 6.-8.j]]
info = 0
solved: True

built-in solver
[[-3.+2.j]
[ 1.-7.j]
[-5.+4.j]
[ 6.-8.j]]

Some points of discussion.

1. Kind of painful! but, nevertheless, possible. You have to do a lot more

work figuring out the dimensions of the problem, how to setup the problem,
keeping track of indices, etc. . .

But, one day it might be helpful to know this can be done, e.g. to debug an
installation, to validate an approach against known results, etc. . .

5 Nonlinear algebra
Nonlinear algebra problems are typically solved using an iterative process that
terminates when the solution is found within a specified tolerance. This process
is hidden from the user. The canonical standard form to solve is f (X) = 0.

80
 5.1 Know your tolerance
Matlab post
ν(CAo − CA )
V = 2
kCA
with the information given below, solve for the exit concentration. This
should be simple.

Cao = 2*u.mol/u.L;
V = 10*u.L;
nu = 0.5*u.L/u.s;
k = 0.23 * u.L/u.mol/u.s;

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 # unit definitions
6 m = 1.0
7 L = m**3 / 1000.0
8 mol = 1.0
9 s = 1.0
10
11 # provide data
12 Cao = 2.0 * mol / L
13 V = 10.0 * L
14 nu = 0.5 * L / s
15 k = 0.23 * L / mol / s
16
17 def func(Ca):
18 return V - nu * (Cao - Ca)/(k * Ca**2)

Let us plot the function to estimate the solution.

1 c = np.linspace(0.001, 2) * mol / L
2
3 plt.plot(c, func(c))
4 plt.xlabel(’C (mol/m^3)’)
5 plt.ylim([-0.1, 0.1])
6 plt.savefig(’images/nonlin-tolerance.png’)

>>> [<matplotlib.lines.Line2D object at 0x000000000832A6A0>]

<matplotlib.text.Text object at 0x00000000083012E8>
(-0.1, 0.1)

81
 Now let us solve the equation. It looks like an answer is near C=500.

1 from scipy.optimize import fsolve

2
3 cguess = 500
4 c, = fsolve(func, cguess)
5 print c
6 print func(c)
7 print func(c) / (mol / L)

>>> >>> >>> 559.583745606

-1.73472347598e-18
-1.73472347598e-21

Interesting. In Matlab, the default tolerance was not sufficient to get a good
solution. Here it is.

5.2 Solving integral equations with fsolve

Original post in Matlab
Occasionally we have integral equations we need to solve in engineering prob-
lems, for example, the volume of plug flow reactor can be defined by this equa-
R Fa
tion: V = F a(V =0) r1a dF a where ra is the rate law. Suppose we know the
reactor volume is 100 L, the inlet molar flow of A is 1 mol/L, the volumetric
flow is 10 L/min, and ra = −kCa, with k = 0.23 1/min. What is the exit molar
flow rate? We need to solve the following equation:

82
 Z Fa
1
100 = dF a
F a(V =0) −kF a/ν
We start by creating a function handle that describes the integrand. We can
use this function in the quad command to evaluate the integral.

1 import numpy as np
2 from scipy.integrate import quad
3 from scipy.optimize import fsolve
4
5 k = 0.23
6 nu = 10.0
7 Fao = 1.0
8
9 def integrand(Fa):
10 return -1.0 / (k * Fa / nu)
11
12 def func(Fa):
13 integral,err = quad(integrand, Fao, Fa)
14 return 100.0 - integral
15
16 vfunc = np.vectorize(func)

We will need an initial guess, so we make a plot of our function to get an

idea.

1 import matplotlib.pyplot as plt

2
3 f = np.linspace(0.01, 1)
4 plt.plot(f, vfunc(f))
5 plt.xlabel(’Molar flow rate’)
6 plt.savefig(’images/integral-eqn-guess.png’)
7 plt.show()

>>> >>> [<matplotlib.lines.Line2D object at 0x964a910>]

<matplotlib.text.Text object at 0x961fe50>

83
 Now we can see a zero is near Fa = 0.1, so we proceed to solve the equation.

1 Fa_guess = 0.1
2 Fa_exit, = fsolve(vfunc, Fa_guess)
3 print ’The exit concentration is {0:1.2f} mol/L’.format(Fa_exit / nu)

>>> The exit concentration is 0.01 mol/L

5.2.1 Summary notes

This example seemed a little easier in Matlab, where the quad function seemed
to get automatically vectorized. Here we had to do it by hand.

5.3 Method of continuity for nonlinear equation solving

Matlab post Adapted from Perry’s Chemical Engineers Handbook, 6th edition
2-63.
We seek the solution to the following nonlinear equations:
2 + x + y − x2 + 8xy + y 3 = 0
1 + 2x − 3y + x2 + xy − yex = 0
In principle this is easy, we simply need some initial guesses and a nonlinear
solver. The challenge here is what would you guess? There could be many
solutions. The equations are implicit, so it is not easy to graph them, but let
us give it a shot, starting on the x range -5 to 5. The idea is set a value for x,
and then solve for y in each equation.

84
1 import numpy as np
2 from scipy.optimize import fsolve
3
4 import matplotlib.pyplot as plt
5
6 def f(x, y):
7 return 2 + x + y - x**2 + 8*x*y + y**3;
8
9 def g(x, y):
10 return 1 + 2*x - 3*y + x**2 + x*y - y*np.exp(x)
11
12 x = np.linspace(-5, 5, 500)
13
14 @np.vectorize
15 def fy(x):
16 x0 = 0.0
17 def tmp(y):
18 return f(x, y)
19 y1, = fsolve(tmp, x0)
20 return y1
21
22 @np.vectorize
23 def gy(x):
24 x0 = 0.0
25 def tmp(y):
26 return g(x, y)
27 y1, = fsolve(tmp, x0)
28 return y1
29
30
31 plt.plot(x, fy(x), x, gy(x))
32 plt.xlabel(’x’)
33 plt.ylabel(’y’)
34 plt.legend([’fy’, ’gy’])
35 plt.savefig(’images/continuation-1.png’)

>>> >>> >>> >>> ... ... >>> ... ... >>> >>> >>> ... ... ... ... ... ... ... >>> ... ... ...
improvement from the last ten iterations.
warnings.warn(msg, RuntimeWarning)
/opt/kitchingroup/enthought/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/scipy/optimize/
improvement from the last five Jacobian evaluations.
warnings.warn(msg, RuntimeWarning)
[<matplotlib.lines.Line2D object at 0x1a0c4990>, <matplotlib.lines.Line2D object at 0x1a0c4a
<matplotlib.text.Text object at 0x19d5e390>
<matplotlib.text.Text object at 0x19d61d90>
<matplotlib.legend.Legend object at 0x189df850>

85
 You can see there is a solution near x = -1, y = 0, because both functions
equal zero there. We can even use that guess with fsolve. It is disappointly
easy! But, keep in mind that in 3 or more dimensions, you cannot perform this
visualization, and another method could be required.

1 def func(X):
2 x,y = X
3 return [f(x, y), g(x, y)]
4
5 print fsolve(func, [-2, -2])

... ... >>> [ -1.00000000e+00 1.28730858e-15]

We explore a method that bypasses this problem today. The principle is to

introduce a new variable, λ, which will vary from 0 to 1. at λ = 0 we will have a
simpler equation, preferrably a linear one, which can be easily solved, or which
can be analytically solved. At λ = 1, we have the original equations. Then,
we create a system of differential equations that start at the easy solution, and
integrate from λ = 0 to λ = 1, to recover the final solution.
We rewrite the equations as:
f (x, y) = (2 + x + y) + λ(−x2 + 8xy + y 3 ) = 0
g(x, y) = (1 + 2x − 3y) + λ(x2 + xy − yex ) = 0
Now, at λ = 0 we have the simple linear equations:
x + y = −2
2x − 3y = −1
These equations are trivial to solve:

86
1 x0 = np.linalg.solve([[1., 1.], [2., -3.]],[ -2, -1])
2 print x0

[-1.4 -0.6]

We form the system of ODEs by differentiating the new equations with

respect to λ. Why do we do that? The solution, (x,y) will be a function of λ.
From calculus, you can show that:
∂f ∂x ∂f ∂y ∂f
∂x ∂λ + ∂y ∂λ = − ∂λ
∂g ∂x ∂g ∂y ∂g
∂x ∂λ + ∂y ∂λ = − ∂λ
Now, solve this for ∂x
∂λ and ∂λ .
∂y
You can use Cramer’s rule to solve for these
to yield:

∂x ∂f /∂y∂g/∂λ − ∂f /∂λ∂g/∂y
= (10)
∂λ ∂f /∂x∂g/∂y − ∂f /∂y∂g/∂x
(11)
∂y ∂f /∂λ∂g/∂x − ∂f /∂x∂g/∂λ
= (12)
∂λ ∂f /∂x∂g/∂y − ∂f /∂y∂g/∂x
For this set of equations:

∂f /∂x = 1 − 2λx + 8λy (13)

(14)
∂f /∂y = 1 + 8λx + 3λy 2 (15)
(16)
∂g/∂x = 2 + 2λx + λy − λye x
(17)
(18)
∂g/∂y = −3 + λx − λex (19)

Now, we simply set up those two differential equations on ∂λ ∂x

and ∂λ
∂y
, with
the initial conditions at λ = 0 which is the solution of the simpler linear equa-
tions, and integrate to λ = 1, which is the final solution of the original equations!

1 def ode(X, LAMBDA):

2 x,y = X
3 pfpx = 1.0 - 2.0 * LAMBDA * x + 8 * LAMBDA * y
4 pfpy = 1.0 + 8.0 * LAMBDA * x + 3.0 * LAMBDA * y**2
5 pfpLAMBDA = -x**2 + 8.0 * x * y + y**3;
6 pgpx = 2. + 2. * LAMBDA * x + LAMBDA * y - LAMBDA * y * np.exp(x)
7 pgpy = -3. + LAMBDA * x - LAMBDA * np.exp(x)
8 pgpLAMBDA = x**2 + x * y - y * np.exp(x);
9 dxdLAMBDA = (pfpy * pgpLAMBDA - pfpLAMBDA * pgpy) / (pfpx * pgpy - pfpy * pgpx)
10 dydLAMBDA = (pfpLAMBDA * pgpx - pfpx * pgpLAMBDA) / (pfpx * pgpy - pfpy * pgpx)
11 dXdLAMBDA = [dxdLAMBDA, dydLAMBDA]
12 return dXdLAMBDA

87
13
14
15 from scipy.integrate import odeint
16
17 lambda_span = np.linspace(0, 1, 100)
18
19 X = odeint(ode, x0, lambda_span)
20
21 xsol, ysol = X[-1]
22 print ’The solution is at x={0:1.3f}, y={1:1.3f}’.format(xsol, ysol)
23 print f(xsol, ysol), g(xsol, ysol)

... ... ... ... ... ... ... ... ... >>> >>> >>> >>> >>> >>> >>> The solution is at x=-1.000,
-1.27746598808e-06 -1.15873819107e-06

You can see the solution is somewhat approximate; the true solution is x
= -1, y = 0. The approximation could be improved by lowering the tolerance
on the ODE solver. The functions evaluate to a small number, close to zero.
You have to apply some judgment to determine if that is sufficiently accurate.
For instance if the units on that answer are kilometers, but you need an answer
accurate to a millimeter, this may not be accurate enough.
This is a fair amount of work to get a solution! The idea is to solve a simple
problem, and then gradually turn on the hard part by the lambda parameter.
What happens if there are multiple solutions? The answer you finally get will
depend on your λ = 0 starting point, so it is possible to miss solutions this way.
For problems with lots of variables, this would be a good approach if you can
identify the easy problem.

5.4 Method of continuity for solving nonlinear equations

- Part II
Matlab post Yesterday in Post 1324 we looked at a way to solve nonlinear
equations that takes away some of the burden of initial guess generation. The
idea was to reformulate the equations with a new variable λ, so that at λ = 0
we have a simpler problem we know how to solve, and at λ = 1 we have the
original set of equations. Then, we derive a set of ODEs on how the solution
changes with λ, and solve them.
Today we look at a simpler example and explain a little more about what is
going on. Consider the equation: f (x) = x2 − 5x + 6 = 0, which has two roots,
x = 2 and x = 3. We will use the method of continuity to solve this equation
to illustrate a few ideas. First, we introduce a new variable λ as: f (x; λ) = 0.
For example, we could write f (x; λ) = λx2 − 5x + 6 = 0. Now, when λ = 0, we
hve the simpler equation −5x + 6 = 0, with the solution x = 6/5. The question
now is, how does x change as λ changes? We get that from the total derivative
of how f (x, λ) changes with λ. The total derivative is:
df ∂f ∂f ∂x
= + =0
dλ ∂λ ∂x ∂λ

88
 We can calculate two of those quantities: ∂f
∂λ and ∂f
∂x analytically from our
equation and solve for ∂λ
∂x
as
∂x ∂f ∂f
=− /
∂λ ∂λ ∂x
That defines an ordinary differential equation that we can solve by integrat-
ing from λ = 0 where we know the solution to λ = 1 which is the solution to
the real problem. For this problem: ∂λ
∂f
= x2 and ∂f
∂x = −5 + 2λx.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 def dxdL(x, Lambda):
6 return -x**2 / (-5.0 + 2 * Lambda * x)
7
8 x0 = 6.0/5.0
9 Lspan = np.linspace(0, 1)
10 x = odeint(dxdL, x0, Lspan)
11
12 plt.plot(Lspan, x)
13 plt.xlabel(’$\lambda$’)
14 plt.ylabel(’x’)
15 plt.savefig(’images/nonlin-contin-II-1.png’)

We found one solution at x=2. What about the other solution? To get
that we have to introduce λ into the equations in another way. We could try:
f (x; λ) = x2 + λ(−5x + 6), but this leads to an ODE that is singular at the
initial starting point. Another approach is f (x; λ) = x2 + 6 + λ(−5x), but now
the solution at λ = 0 is imaginary, and we do not have a way to integrate that!
What we can do instead is add and subtract a number like this: f (x; λ) =

89
 x2 − 4 + λ(−5x + 6 + 4). Now at λ = 0, we have a simple equation with roots
at ±2, and we already know that x = 2 is a solution. So, we create our ODE
on dx/dλ with initial condition x(0) = −2.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 def dxdL(x, Lambda):
6 return (5 * x - 10) / (2 * x - 5 * Lambda)
7
8 x0 = -2
9 Lspan = np.linspace(0, 1)
10 x = odeint(dxdL, x0, Lspan)
11
12 plt.plot(Lspan, x)
13 plt.xlabel(’$\lambda$’)
14 plt.ylabel(’x’)
15 plt.savefig(’images/nonlin-contin-II-2.png’)

Now we have the other solution. Note if you choose the other root, x = 2,
you find that 2 is a root, and learn nothing new. You could choose other values
to add, e.g., if you chose to add and subtract 16, then you would find that one
starting point leads to one root, and the other starting point leads to the other
root. This method does not solve all problems associated with nonlinear root
solving, namely, how many roots are there, and which one is "best" or physically
reasonable? But it does give a way to solve an equation where you have no idea
what an initial guess should be. You can see, however, that just like you can
get different answers from different initial guesses, here you can get different
answers by setting up the equations differently.

90
 5.5 Counting roots
Matlab post The goal here is to determine how many roots there are in a non-
linear function we are interested in solving. For this example, we use a cubic
polynomial because we know there are three roots.

f (x) = x3 + 6x2 − 4x − 24

5.5.1 Use roots for this polynomial

This ony works for a polynomial, it does not work for any other nonlinear
function.

1 import numpy as np
2 print np.roots([1, 6, -4, -24])

[-6. 2. -2.]
Let us plot the function to see where the roots are.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(-8, 4)
5 y = x**3 + 6 * x**2 - 4*x - 24
6 plt.plot(x, y)
7 plt.savefig(’images/count-roots-1.png’)

Now we consider several approaches to counting the number of roots in this

interval. Visually it is pretty easy, you just look for where the function crosses
zero. Computationally, it is tricker.

91
 5.5.2 method 1
Count the number of times the sign changes in the interval. What we have to do
is multiply neighboring elements together, and look for negative values. That
indicates a sign change. For example the product of two positive or negative
numbers is a positive number. You only get a negative number from the product
of a positive and negative number, which means the sign changed.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(-8, 4)
5 y = x**3 + 6 * x**2 - 4*x - 24
6
7 print np.sum(y[0:-2] * y[1:-1] < 0)

This method gives us the number of roots, but not where the roots are.

5.5.3 Method 2
Using events in an ODE solver python can identify events in the solution to
an ODE, for example, when a function has a certain value, e.g. f(x) = 0. We
can take advantage of this to find the roots and number of roots in this case.
We take the derivative of our function, and integrate it from an initial starting
point, and define an event function that counts zeros.

f 0 (x) = 3x2 + 12x − 4

with f(-8) = -120

1 import numpy as np
2 from pycse import odelay
3
4 def fprime(f, x):
5 return 3.0 * x**2 + 12.0*x - 4.0
6
7 def event(f, x):
8 value = f # we want f = 0
9 isterminal = False
10 direction = 0
11 return value, isterminal, direction
12
13 xspan = np.linspace(-8, 4)
14 f0 = -120
15
16 X, F, TE, YE, IE = odelay(fprime, f0, xspan, events=[event])
17 for te, ye in zip(TE, YE):
18 print ’root found at x = {0: 1.3f}, f={1: 1.3f}’.format(te, ye)

root found at x = -6.000, f=-0.000

root found at x = -2.000, f=-0.000
root found at x = 2.000, f= 0.000

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 5.6 Finding the nth root of a periodic function
There is a heat transfer problem where one needs to find the nˆth root of
the following equation: xJ1 (x) − BiJ0 (x) = 0 where J0 and J1 are the Bessel
functions of zero and first order, and Bi is the Biot number. We examine an
approach to finding these roots.
First, we plot the function.

1 from scipy.special import jn, jn_zeros

2 import matplotlib.pyplot as plt
3 import numpy as np
4
5 Bi = 1
6
7 def f(x):
8 return x * jn(1, x) - Bi * jn(0, x)
9
10 X = np.linspace(0, 30, 200)
11 plt.plot(X, f(X))
12 plt.savefig(’images/heat-transfer-roots-1.png’)

You can see there are many roots to this equation, and we want to be sure we
get the nˆ{th} root. This function is pretty well behaved, so if you make a good
guess about the solution you will get an answer, but if you make a bad guess, you
may get the wrong root. We examine next a way to do it without guessing the
solution. What we want is the solution to f (x) = 0, but we want all the solutions
in a given interval. We derive a new equation, f 0 (x) = 0, with initial condition
f (0) = f 0, and integrate the ODE with an event function that identifies all
zeros of f for us. The derivative of our function is df /dx = d/dx(xJ1 (x)) −
BiJ00 (x). It is known (http://www.markrobrien.com/besselfunct.pdf) that

93
 d/dx(xJ1 (x)) = xJ0 (x), and J00 (x) = −J1 (x). All we have to do now is set up
the problem and run it.

1 from pycse import * # contains the ode integrator with events

2
3 from scipy.special import jn, jn_zeros
4 import matplotlib.pyplot as plt
5 import numpy as np
6
7 Bi = 1
8
9 def f(x):
10 "function we want roots for"
11 return x * jn(1, x) - Bi * jn(0, x)
12
13 def fprime(f, x):
14 "df/dx"
15 return x * jn(0, x) - Bi * (-jn(1, x))
16
17 def e1(f, x):
18 "event function to find zeros of f"
19 isterminal = False
20 value = f
21 direction = 0
22 return value, isterminal, direction
23
24 f0 = f(0)
25 xspan = np.linspace(0, 30, 200)
26
27 x, fsol, XE, FE, IE = odelay(fprime, f0, xspan, events=[e1])
28
29 plt.plot(x, fsol, ’.-’, label=’Numerical solution’)
30 plt.plot(xspan, f(xspan), ’--’, label=’Analytical function’)
31 plt.plot(XE, FE, ’ro’, label=’roots’)
32 plt.legend(loc=’best’)
33 plt.savefig(’images/heat-transfer-roots-2.png’)
34
35 for i, root in enumerate(XE):
36 print ’root {0} is at {1}’.format(i, root)
37
38 plt.show()

root 0 is at 1.25578377377
root 1 is at 4.07947743741
root 2 is at 7.15579904465
root 3 is at 10.2709851256
root 4 is at 13.3983973869
root 5 is at 16.5311587137
root 6 is at 19.6667276775
root 7 is at 22.8039503455
root 8 is at 25.9422288192
root 9 is at 29.081221492

94
 You can work this out once, and then you have all the roots in the interval
and you can select the one you want.

6 Statistics
6.1 Introduction to statistical data analysis
Matlab post
Given several measurements of a single quantity, determine the average value
of the measurements, the standard deviation of the measurements and the 95%
confidence interval for the average.

1 import numpy as np
2
3 y = [8.1, 8.0, 8.1]
4
5 ybar = np.mean(y)
6 s = np.std(y, ddof=1)
7
8 print ybar, s

>>> >>> >>> >>> >>> >>> 8.06666666667 0.057735026919

Interesting, we have to specify the divisor in numpy.std by the ddof argu-

ment. The default for this in Matlab is 1, the default for this function is 0.
Here is the principle of computing a confidence interval.

1. compute the average

95
 2. Compute the standard deviation of your data
3. Define the confidence interval, e.g. 95% = 0.95
4. compute the student-t multiplier. This is a function of the confidence
interval you specify, and the number of data points you have minus 1.
You subtract 1 because one degree of freedom is lost from calculating the
average.

The confidence interval is defined as ybar +- T_multiplier*std/sqrt(n).

1 from scipy.stats.distributions import t

2 ci = 0.95
3 alpha = 1.0 - ci
4
5 n = len(y)
6 T_multiplier = t.ppf(1.0 - alpha / 2.0, n - 1)
7
8 ci95 = T_multiplier * s / np.sqrt(n)
9
10 print ’T_multiplier = {0}’.format(T_multiplier)
11 print ’ci95 = {0}’.format(ci95)
12 print ’The true average is between {0} and {1} at a 95% confidence level’.format(ybar - ci95, ybar + ci95)

>>> >>> >>> >>> >>> >>> >>> >>> T_multiplier = 4.30265272991
ci95 = 0.143421757664
The true average is between 7.923244909 and 8.21008842433 at a 95% confidence level

6.2 Basic statistics

Given several measurements of a single quantity, determine the average value
of the measurements, the standard deviation of the measurements and the 95%
confidence interval for the average.
This is a recipe for computing the confidence interval. The strategy is:
1. compute the average
2. Compute the standard deviation of your data
3. Define the confidence interval, e.g. 95% = 0.95
4. compute the student-t multiplier. This is a function of the confidence
interval you specify, and the number of data points you have minus 1. You
subtract 1 because one degree of freedom is lost from calculating the average.
The confidence interval is defined as ybar +- T_multiplier*std/sqrt(n).

1 import numpy as np
2 from scipy.stats.distributions import t
3
4 y = [8.1, 8.0, 8.1]
5
6 ybar = np.mean(y)

96
7 s = np.std(y)
8
9 ci = 0.95
10 alpha = 1.0 - ci
11
12 n = len(y)
13 T_multiplier = t.ppf(1-alpha/2.0, n-1)
14
15 ci95 = T_multiplier * s / np.sqrt(n-1)
16
17 print [ybar - ci95, ybar + ci95]

[7.9232449090029595, 8.210088424330376]

We are 95% certain the next measurement will fall in the interval above.

6.3 Confidence interval on an average

scipy has a statistical package available for getting statistical distributions.
This is useful for computing confidence intervals using the student-t tables. Here
is an example of computing a 95% confidence interval on an average.

1 import numpy as np
2 from scipy.stats.distributions import t
3
4 n = 10 # number of measurements
5 dof = n - 1 # degrees of freedom
6 avg_x = 16.1 # average measurement
7 std_x = 0.01 # standard deviation of measurements
8
9 # Find 95% prediction interval for next measurement
10
11 alpha = 1.0 - 0.95
12
13 pred_interval = t.ppf(1-alpha/2.0, dof) * std_x / np.sqrt(n)
14
15 s = [’We are 95% confident the next measurement’,
16 ’ will be between {0:1.3f} and {1:1.3f}’]
17 print ’’.join(s).format(avg_x - pred_interval, avg_x + pred_interval)

We are 95% confident the next measurement will be between 16.093 and 16.107

6.4 Are averages different

Matlab post
Adapted from http://stattrek.com/ap-statistics-4/unpaired-means.
aspx
Class A had 30 students who received an average test score of 78, with
standard deviation of 10. Class B had 25 students an average test score of 85,
with a standard deviation of 15. We want to know if the difference in these
averages is statistically relevant. Note that we only have estimates of the true
average and standard deviation for each class, and there is uncertainty in those
estimates. As a result, we are unsure if the averages are really different. It could
have just been luck that a few students in class B did better.

97
 The hypothesis:
the true averages are the same. We need to perform a two-sample t-test of
the hypothesis that µ1 − µ2 = 0 (this is often called the null hypothesis). we use
a two-tailed test because we do not care if the difference is positive or negative,
either way means the averages are not the same.

1 import numpy as np
2
3 n1 = 30 # students in class A
4 x1 = 78.0 # average grade in class A
5 s1 = 10.0 # std dev of exam grade in class A
6
7 n2 = 25 # students in class B
8 x2 = 85.0 # average grade in class B
9 s2 = 15.0 # std dev of exam grade in class B
10
11 # the standard error of the difference between the two averages.
12 SE = np.sqrt(s1**2 / n1 + s2**2 / n2)
13
14 # compute DOF
15 DF = (n1 - 1) + (n2 - 1)

see the discussion at http://stattrek.com/Help/Glossary.aspx?Target=

Two-sample%20t-test for a more complex definition of degrees of freedom.
Here we simply subtract one from each sample size to account for the estimation
of the average of each sample.
compute the t-score for our data
The difference between two averages determined from small sample numbers
follows the t-distribution. the t-score is the difference between the difference
of the means and the hypothesized difference of the means, normalized by the
standard error. we compute the absolute value of the t-score to make sure it is
positive for convenience later.

1 tscore = np.abs(((x1 - x2) - 0) / SE)

2 print tscore

1.99323179108

Interpretation
A way to approach determinining if the difference is significant or not is to
ask, does our computed average fall within a confidence range of the hypothe-
sized value (zero)? If it does, then we can attribute the difference to statistical
variations at that confidence level. If it does not, we can say that statistical
variations do not account for the difference at that confidence level, and hence
the averages must be different.
Let us compute the t-value that corresponds to a 95% confidence level for
a mean of zero with the degrees of freedom computed earlier. This means that
95% of the t-scores we expect to get will fall within ± t95.

98
1 from scipy.stats.distributions import t
2
3 ci = 0.95;
4 alpha = 1 - ci;
5 t95 = t.ppf(1.0 - alpha/2.0, DF)
6
7 print t95

>>> >>> >>> >>> >>> 2.00574599354

since tscore < t95, we conclude that at the 95% confidence level we cannot
say these averages are statistically different because our computed t-score falls
in the expected range of deviations. Note that our t-score is very close to the
95% limit. Let us consider a smaller confidence interval.

1 ci = 0.94
2 alpha = 1 - ci;
3 t95 = t.ppf(1.0 - alpha/2.0, DF)
4
5 print t95

>>> >>> >>> 1.92191364181

at the 94% confidence level, however, tscore > t94, which means we can
say with 94% confidence that the two averages are different; class B performed
better than class A did. Alternatively, there is only about a 6% chance we are
wrong about that statement. another way to get there
An alternative way to get the confidence that the averages are different is to
directly compute it from the cumulative t-distribution function. We compute
the difference between all the t-values less than tscore and the t-values less than
-tscore, which is the fraction of measurements that are between them. You can
see here that we are practically 95% sure that the averages are different.

1 f = t.cdf(tscore, DF) - t.cdf(-tscore, DF)

2 print f

0.948605075732

6.5 Model selection

Matlab post
adapted from http://www.itl.nist.gov/div898/handbook/pmd/section4/
pmd44.htm
In this example, we show some ways to choose which of several models fit
data the best. We have data for the total pressure and temperature of a fixed

99
 amount of a gas in a tank that was measured over the course of several days.
We want to select a model that relates the pressure to the gas temperature.
The data is stored in a text file download PT.txt , with the following struc-
ture:

Run Ambient Fitted

Order Day Temperature Temperature Pressure Value Residual
1 1 23.820 54.749 225.066 222.920 2.146
...

We need to read the data in, and perform a regression analysis on P vs. T.
In python we start counting at 0, so we actually want columns 3 and 4.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 data = np.loadtxt(’data/PT.txt’, skiprows=2)
5 T = data[:, 3]
6 P = data[:, 4]
7
8 plt.plot(T, P, ’k.’)
9 plt.xlabel(’Temperature’)
10 plt.ylabel(’Pressure’)
11 plt.savefig(’images/model-selection-1.png’)

>>> >>> >>> >>> >>> >>> [<matplotlib.lines.Line2D object at 0x00000000084398D0>]

<matplotlib.text.Text object at 0x000000000841F6A0>
<matplotlib.text.Text object at 0x0000000008423DD8>

100
 It appears the data is roughly linear, and we know from the ideal gas law that
PV = nRT, or P = nR/V*T, which says P should be linearly correlated with
V. Note that the temperature data is in degC, not in K, so it is not expected
that P=0 at T = 0. We will use linear algebra to compute the line coefficients.

1 A = np.vstack([T**0, T]).T
2 b = P
3
4 x, res, rank, s = np.linalg.lstsq(A, b)
5 intercept, slope = x
6 print ’b, m =’, intercept, slope
7
8 n = len(b)
9 k = len(x)
10
11 sigma2 = np.sum((b - np.dot(A,x))**2) / (n - k)
12
13 C = sigma2 * np.linalg.inv(np.dot(A.T, A))
14 se = np.sqrt(np.diag(C))
15
16 from scipy.stats.distributions import t
17 alpha = 0.05
18
19 sT = t.ppf(1-alpha/2., n - k) # student T multiplier
20 CI = sT * se
21
22 print ’CI = ’,CI
23 for beta, ci in zip(x, CI):
24 print ’[{0} {1}]’.format(beta - ci, beta + ci)

>>> >>> >>> >>> b, m = 7.74899739238 3.93014043824

>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> CI = [ 4.76511545 0.1026405 ]
... ... [2.98388194638 12.5141128384]
[3.82749994079 4.03278093569]
The confidence interval on the intercept is large, but it does not contain zero
at the 95% confidence level.
The Rˆ2 value accounts roughly for the fraction of variation in the data that
can be described by the model. Hence, a value close to one means nearly all the
variations are described by the model, except for random variations.

1 ybar = np.mean(P)
2 SStot = np.sum((P - ybar)**2)
3 SSerr = np.sum((P - np.dot(A, x))**2)
4 R2 = 1 - SSerr/SStot
5 print R2

>>> >>> >>> 0.993715411798

1 plt.figure(); plt.clf()
2 plt.plot(T, P, ’k.’, T, np.dot(A, x), ’b-’)
3 plt.xlabel(’Temperature’)
4 plt.ylabel(’Pressure’)
5 plt.title(’R^2 = {0:1.3f}’.format(R2))
6 plt.savefig(’images/model-selection-2.png’)

101
 <matplotlib.figure.Figure object at 0x0000000008423860>
[<matplotlib.lines.Line2D object at 0x00000000085BE780>, <matplotlib.lines.Line2D object at
<matplotlib.text.Text object at 0x0000000008449898>
<matplotlib.text.Text object at 0x000000000844CCF8>
<matplotlib.text.Text object at 0x000000000844ED30>

The fit looks good, and Rˆ2 is near one, but is it a good model? There are
a few ways to examine this. We want to make sure that there are no systematic
trends in the errors between the fit and the data, and we want to make sure
there are not hidden correlations with other variables. The residuals are the
error between the fit and the data. The residuals should not show any patterns
when plotted against any variables, and they do not in this case.

1 residuals = P - np.dot(A, x)
2
3 plt.figure()
4
5 f, (ax1, ax2, ax3) = plt.subplots(3)
6
7 ax1.plot(T,residuals,’ko’)
8 ax1.set_xlabel(’Temperature’)
9
10
11 run_order = data[:, 0]
12 ax2.plot(run_order, residuals,’ko ’)
13 ax2.set_xlabel(’run order’)
14
15 ambientT = data[:, 2]
16 ax3.plot(ambientT, residuals,’ko’)
17 ax3.set_xlabel(’ambient temperature’)
18
19 plt.tight_layout() # make sure plots do not overlap

102
20
21 plt.savefig(’images/model-selection-3.png’)

>>> <matplotlib.figure.Figure object at 0x00000000085C21D0>

>>> >>> >>> [<matplotlib.lines.Line2D object at 0x0000000008861CC0>]
<matplotlib.text.Text object at 0x00000000085D3A58>
>>> >>> >>> [<matplotlib.lines.Line2D object at 0x0000000008861E80>]
<matplotlib.text.Text object at 0x00000000085EC5F8>
>>> >>> [<matplotlib.lines.Line2D object at 0x0000000008861C88>]
<matplotlib.text.Text object at 0x0000000008846828>

There may be some correlations in the residuals with the run order. That
could indicate an experimental source of error.
We assume all the errors are uncorrelated with each other. We can use a
lag plot to assess this, where we plot residual[i] vs residual[i-1], i.e. we look for
correlations between adjacent residuals. This plot should look random, with no
correlations if the model is good.

1 plt.figure(); plt.clf()
2 plt.plot(residuals[1:-1], residuals[0:-2],’ko’)
3 plt.xlabel(’residual[i]’)
4 plt.ylabel(’residual[i-1]’)
5 plt.savefig(’images/model-selection-correlated-residuals.png’)

<matplotlib.figure.Figure object at 0x000000000886EB00>

[<matplotlib.lines.Line2D object at 0x0000000008A02908>]

103
 <matplotlib.text.Text object at 0x00000000089E8198>
<matplotlib.text.Text object at 0x00000000089EB908>

It is hard to argue there is any correlation here.

Lets consider a quadratic model instead.

1 A = np.vstack([T**0, T, T**2]).T
2 b = P;
3
4 x, res, rank, s = np.linalg.lstsq(A, b)
5 print x
6
7 n = len(b)
8 k = len(x)
9
10 sigma2 = np.sum((b - np.dot(A,x))**2) / (n - k)
11
12 C = sigma2 * np.linalg.inv(np.dot(A.T, A))
13 se = np.sqrt(np.diag(C))
14
15 from scipy.stats.distributions import t
16 alpha = 0.05
17
18 sT = t.ppf(1-alpha/2., n - k) # student T multiplier
19 CI = sT * se
20
21 print ’CI = ’,CI
22 for beta, ci in zip(x, CI):
23 print ’[{0} {1}]’.format(beta - ci, beta + ci)
24
25
26 ybar = np.mean(P)
27 SStot = np.sum((P - ybar)**2)
28 SSerr = np.sum((P - np.dot(A,x))**2)
29 R2 = 1 - SSerr/SStot
30 print ’R^2 = {0}’.format(R2)

104
 >>> >>> >>> [ 9.00353031e+00 3.86669879e+00 7.26244301e-04]
>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> CI = [ 1.38030344e+01 6.6210
... ... [-4.79950412123 22.8065647329]
[3.20459813681 4.52879944409]
[-0.00675892296907 0.00821141157035]
>>> >>> >>> >>> >>> R^2 = 0.993721969407

You can see that the confidence interval on the constant and Tˆ2 term
includes zero. That is a good indication this additional parameter is not signif-
icant. You can see also that the Rˆ2 value is not better than the one from a
linear fit, so adding a parameter does not increase the goodness of fit. This is an
example of overfitting the data. Since the constant in this model is apparently
not significant, let us consider the simplest model with a fixed intercept of zero.
Let us consider a model with intercept = 0, P = alpha*T.

1 A = np.vstack([T]).T
2 b = P;
3
4 x, res, rank, s = np.linalg.lstsq(A, b)
5
6 n = len(b)
7 k = len(x)
8
9 sigma2 = np.sum((b - np.dot(A,x))**2) / (n - k)
10
11 C = sigma2 * np.linalg.inv(np.dot(A.T, A))
12 se = np.sqrt(np.diag(C))
13
14 from scipy.stats.distributions import t
15 alpha = 0.05
16
17 sT = t.ppf(1-alpha/2.0, n - k) # student T multiplier
18 CI = sT * se
19
20 for beta, ci in zip(x, CI):
21 print ’[{0} {1}]’.format(beta - ci, beta + ci)
22
23 plt.figure()
24 plt.plot(T, P, ’k. ’, T, np.dot(A, x))
25 plt.xlabel(’Temperature’)
26 plt.ylabel(’Pressure’)
27 plt.legend([’data’, ’fit’])
28
29 ybar = np.mean(P)
30 SStot = np.sum((P - ybar)**2)
31 SSerr = np.sum((P - np.dot(A,x))**2)
32 R2 = 1 - SSerr/SStot
33 plt.title(’R^2 = {0:1.3f}’.format(R2))
34 plt.savefig(’images/model-selection-no-intercept.png’)

>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ... ... [4.056801244
<matplotlib.figure.Figure object at 0x0000000008870BE0>
[<matplotlib.lines.Line2D object at 0x00000000089F4550>, <matplotlib.lines.Line2D object at
<matplotlib.text.Text object at 0x0000000008A13630>
<matplotlib.text.Text object at 0x0000000008A16DA0>

105
 <matplotlib.legend.Legend object at 0x00000000089EFD30>
>>> >>> >>> >>> >>> <matplotlib.text.Text object at 0x000000000B26C0B8>

The
fit is visually still pretty good, and the Rˆ2 value is only slightly worse. Let us
examine the residuals again.

1 residuals = P - np.dot(A,x)
2
3 plt.figure()
4 plt.plot(T,residuals,’ko’)
5 plt.xlabel(’Temperature’)
6 plt.ylabel(’residuals’)
7 plt.savefig(’images/model-selection-no-incpt-resid.png’)

>>> <matplotlib.figure.Figure object at 0x0000000008A0F5C0>

[<matplotlib.lines.Line2D object at 0x000000000B29B0F0>]
<matplotlib.text.Text object at 0x000000000B276FD0>
<matplotlib.text.Text object at 0x000000000B283780>

106
 You can see a slight trend of decreasing value of the residuals as the Temper-
ature increases. This may indicate a deficiency in the model with no intercept.
For the ideal gas law in degC: P V = nR(T +273) or P = nR/V ∗T +273∗nR/V ,
so the intercept is expected to be non-zero in this case. Specifically, we expect
the intercept to be 273*R*n/V. Since the molar density of a gas is pretty small,
the intercept may be close to, but not equal to zero. That is why the fit still
looks ok, but is not as good as letting the intercept be a fitting parameter. That
is an example of the deficiency in our model.
In the end, it is hard to justify a model more complex than a line in this
case.

6.6 Numerical propagation of errors

Matlab post
Propagation of errors is essential to understanding how the uncertainty in
a parameter affects computations that use that parameter. The uncertainty
propagates by a set of rules into your solution. These rules are not easy to
remember, or apply to complicated situations, and are only approximate for
equations that are nonlinear in the parameters.
We will use a Monte Carlo simulation to illustrate error propagation. The
idea is to generate a distribution of possible parameter values, and to evaluate
your equation for each parameter value. Then, we perform statistical analysis
on the results to determine the standard error of the results.
We will assume all parameters are defined by a normal distribution with
known mean and standard deviation.

107
 6.6.1 Addition and subtraction

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 N = 1e6 # number of samples of parameters
5
6 A_mu = 2.5; A_sigma = 0.4
7 B_mu = 4.1; B_sigma = 0.3
8
9 A = np.random.normal(A_mu, A_sigma, size=(1, N))
10 B = np.random.normal(B_mu, B_sigma, size=(1, N))
11
12 p = A + B
13 m = A - B
14
15 plt.hist(p)
16 plt.show()
17
18 print np.std(p)
19 print np.std(m)
20
21 print np.sqrt(A_sigma**2 + B_sigma**2) # the analytical std dev

>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> 0.500505424616
0.500113385681
>>> 0.5

6.6.2 Multiplication

1 F_mu = 25.0; F_sigma = 1;

2 x_mu = 6.4; x_sigma = 0.4;
3
4 F = np.random.normal(F_mu, F_sigma, size=(1, N))
5 x = np.random.normal(x_mu, x_sigma, size=(1, N))
6
7 t = F * x
8 print np.std(t)
9 print np.sqrt((F_sigma / F_mu)**2 + (x_sigma / x_mu)**2) * F_mu * x_mu

>>> >>> >>> >>> >>> >>> 11.8900166284

11.8726576637

6.6.3 Division
This is really like multiplication: F / x = F * (1 / x).

1 d = F / x
2 print np.std(d)
3 print np.sqrt((F_sigma / F_mu)**2 + (x_sigma / x_mu)**2) * F_mu / x_mu

0.293757533168
0.289859806243

108
 6.6.4 exponents
This rule is different than multiplication (Aˆ2 = A*A) because in the previous
examples we assumed the errors in A and B for A*B were uncorrelated. in A*A,
the errors are not uncorrelated, so there is a different rule for error propagation.

1 t_mu = 2.03; t_sigma = 0.01*t_mu; # 1% error

2 A_mu = 16.07; A_sigma = 0.06;
3
4 t = np.random.normal(t_mu, t_sigma, size=(1, N))
5 A = np.random.normal(A_mu, A_sigma, size=(1, N))
6
7 # Compute t^5 and sqrt(A) with error propagation
8 print np.std(t**5)
9 print (5 * t_sigma / t_mu) * t_mu**5

>>> >>> >>> >>> >>> ... 1.72454836176

1.72365440621

1 print np.std(np.sqrt(A))
2 print 1.0 / 2.0 * A_sigma / A_mu * np.sqrt(A_mu)

0.00748903477329
0.00748364738749

6.6.5 the chain rule in error propagation

let v = v0 + a*t, with uncertainties in vo,a and t

1 vo_mu = 1.2; vo_sigma = 0.02;

2 a_mu = 3.0; a_sigma = 0.3;
3 t_mu = 12.0; t_sigma = 0.12;
4
5 vo = np.random.normal(vo_mu, vo_sigma, (1, N))
6 a = np.random.normal(a_mu, a_sigma, (1, N))
7 t = np.random.normal(t_mu, t_sigma, (1, N))
8
9 v = vo + a*t
10
11 print np.std(v)
12 print np.sqrt(vo_sigma**2 + t_mu**2 * a_sigma**2 + a_mu**2 * t_sigma**2)

>>> >>> >>> >>> >>> >>> >>> >>> >>> 3.62232509326
3.61801050303

6.6.6 Summary
You can numerically perform error propagation analysis if you know the under-
lying distribution of errors on the parameters in your equations. One benefit of
the numerical propogation is you do not have to remember the error propaga-
tion rules, and you directly look at the distribution in nonlinear cases. Some
limitations of this approach include

109
 1. You have to know the distribution of the errors in the parameters
2. You have to assume the errors in parameters are uncorrelated.

6.7 Another approach to error propagation

In the previous section we examined an analytical approach to error propa-
gation, and a simulation based approach. There is another approach to er-
ror propagation, using the uncertainties module (https://pypi.python.org/
pypi/uncertainties/). You have to install this package, e.g. pip install
uncertainties. After that, the module provides new classes of numbers and
functions that incorporate uncertainty and propagate the uncertainty through
the functions. In the examples that follow, we repeat the calculations from the
previous section using the uncertainties module.
Addition and subtraction

1 import uncertainties as u
2
3 A = u.ufloat((2.5, 0.4))
4 B = u.ufloat((4.1, 0.3))
5 print A + B
6 print A - B

>>> >>> >>> 6.6+/-0.5

-1.6+/-0.5

Multiplication and division

1 F = u.ufloat((25, 1))
2 x = u.ufloat((6.4, 0.4))
3
4 t = F * x
5 print t
6
7 d = F / x
8 print d

>>> >>> >>> 160.0+/-11.8726576637

>>> >>> 3.90625+/-0.289859806243

Exponentiation

1 t = u.ufloat((2.03, 0.0203))
2 print t**5
3
4 from uncertainties.umath import sqrt
5 A = u.ufloat((16.07, 0.06))
6 print sqrt(A)
7 # print np.sqrt(A) # this does not work
8
9 from uncertainties import unumpy as unp
10 print unp.sqrt(A)

110
 34.4730881243+/-1.72365440621
>>> >>> >>> >>> 4.00874045057+/-0.00748364738749
... >>> >>> 4.00874045057+/-0.00748364738749

Note in the last example, we had to either import a function from uncertain-
ties.umath or import a special version of numpy that handles uncertainty. This
may be a limitation of teh uncertainties package as not all functions in arbitrary
modules can be covered. Note, however, that you can wrap a function to make
it handle uncertainty like this.

1 import numpy as np
2
3 wrapped_sqrt = u.wrap(np.sqrt)
4 print wrapped_sqrt(A)

>>> >>> 4.00874045057+/-0.00748364738774

Propagation of errors in an integral

1 import numpy as np
2 import uncertainties as u
3
4 x = np.array([u.ufloat((1, 0.01)),
5 u.ufloat((2, 0.1)),
6 u.ufloat((3, 0.1))])
7
8 y = 2 * x
9
10 print np.trapz(x, y)

>>> >>> ... ... >>> >>> >>> >>> 8.0+/-0.600333240792

Chain rule in error propagation

1 v0 = u.ufloat((1.2, 0.02))
2 a = u.ufloat((3.0, 0.3))
3 t = u.ufloat((12.0, 0.12))
4
5 v = v0 + a * t
6 print v

>>> >>> >>> >>> 37.2+/-3.61801050303

A real example? This is what I would setup for a real working example.
We try to compute the exit concentration from a CSTR. The idea is to wrap
the "external" fsolve function using the uncertainties.wrap function, which
handles the units. Unfortunately, it does not work, and it is not clear why. But
see the following discussion for a fix.

111
1 from scipy.optimize import fsolve
2
3 Fa0 = u.ufloat((5.0, 0.05))
4 v0 = u.ufloat((10., 0.1))
5
6 V = u.ufloat((66000.0, 100)) # reactor volume L^3
7 k = u.ufloat((3.0, 0.2)) # rate constant L/mol/h
8
9 def func(Ca):
10 "Mole balance for a CSTR. Solve this equation for func(Ca)=0"
11 Fa = v0 * Ca # exit molar flow of A
12 ra = -k * Ca**2 # rate of reaction of A L/mol/h
13 return Fa0 - Fa + V * ra
14
15 # CA guess that that 90 % is reacted away
16 CA_guess = 0.1 * Fa0 / v0
17
18 wrapped_fsolve = u.wrap(fsolve)
19 CA_sol = wrapped_fsolve(func, CA_guess)
20
21 print ’The exit concentration is {0} mol/L’.format(CA_sol)

>>> >>> >>> >>> >>> >>> >>> ... ... ... ... ... >>> ... >>> >>> >>> <function fsolve at 0x14
>>> >>> The exit concentration is NotImplemented mol/L

I got a note from the author of the uncertainties package explaining the
cryptic error above, and a solution for it. The error arises because fsolve does
not know how to deal with uncertainties. The idea is to create a function that
returns a float, when everything is given as a float. Then, we wrap the fsolve
call, and finally wrap the wrapped fsolve call!

• Step 1. Write the function to solve with arguments for all unitted quan-
tities. This function may be called with uncertainties, or with floats.
• Step 2. Wrap the call to fsolve in a function that takes all the parameters
as arguments, and that returns the solution.
• Step 3. Use uncertainties.wrap to wrap the function in Step 2 to get the
answer with uncertainties.

Here is the code that does work:

1 import uncertainties as u
2 from scipy.optimize import fsolve
3
4 Fa0 = u.ufloat((5.0, 0.05))
5 v0 = u.ufloat((10., 0.1))
6
7 V = u.ufloat((66000.0, 100.0)) # reactor volume L^3
8 k = u.ufloat((3.0, 0.2)) # rate constant L/mol/h
9
10 # Step 1
11 def func(Ca, v0, k, Fa0, V):
12 "Mole balance for a CSTR. Solve this equation for func(Ca)=0"
13 Fa = v0 * Ca # exit molar flow of A
14 ra = -k * Ca**2 # rate of reaction of A L/mol/h
15 return Fa0 - Fa + V * ra

112
16
17 # Step 2
18 def Ca_solve(v0, k, Fa0, V):
19 ’wrap fsolve to pass parameters as float or units’
20 # this line is a little fragile. You must put [0] at the end or
21 # you get the NotImplemented result
22 sol = fsolve(func, 0.1 * Fa0 / v0, args=(v0, k, Fa0, V))[0]
23 return sol
24
25 # Step 3
26 print u.wrap(Ca_solve)(v0, k, Fa0, V)

0.005+/-0.000167764327667

It would take some practice to get used to this, but the payoff is that you
have an "automatic" error propagation method.
Being ever the skeptic, let us compare the result above to the Monte Carlo
approach to error estimation below.

1 import numpy as np
2 from scipy.optimize import fsolve
3
4 N = 10000
5 Fa0 = np.random.normal(5, 0.05, (1, N))
6 v0 = np.random.normal(10.0, 0.1, (1, N))
7 V = np.random.normal(66000, 100, (1,N))
8 k = np.random.normal(3.0, 0.2, (1, N))
9
10 SOL = np.zeros((1, N))
11
12 for i in range(N):
13 def func(Ca):
14 return Fa0[0,i] - v0[0,i] * Ca + V[0,i] * (-k[0,i] * Ca**2)
15 SOL[0,i] = fsolve(func, 0.1 * Fa0[0,i] / v0[0,i])[0]
16
17 print ’Ca(exit) = {0}+/-{1}’.format(np.mean(SOL), np.std(SOL))

Ca(exit) = 0.00500829453185+/-0.000169103578901

I am pretty content those are the same!

6.7.1 Summary
The uncertainties module is pretty amazing. It automatically propagates errors
through a pretty broad range of computations. It is a little tricky for third-party
packages, but it seems doable.
Read more about the package at http://pythonhosted.org/uncertainties/
index.html.

6.8 Random thoughts

Matlab post
Random numbers are used in a variety of simulation methods, most notably
Monte Carlo simulations. In another later example, we will see how we can
use random numbers for error propagation analysis. First, we discuss two types

113
 of pseudorandom numbers we can use in python: uniformly distributed and
normally distributed numbers.
Say you are the gambling type, and bet your friend $5 the next random
number will be greater than 0.49. Let us ask Python to roll the random number
generator for us.

1 import numpy as np
2
3 n = np.random.uniform()
4 print ’n = {0}’.format(n)
5
6 if n > 0.49:
7 print ’You win!’
8 else:
9 print ’you lose.’

n = 0.381896986693
you lose.

The odds of you winning the last bet are slightly stacked in your favor. There
is only a 49% chance your friend wins, but a 51% chance that you win. Lets
play the game a lot of times times and see how many times you win, and your
friend wins. First, lets generate a bunch of numbers and look at the distribution
with a histogram.

1 import numpy as np
2
3 N = 10000
4 games = np.random.uniform(size=(1,N))
5
6 wins = np.sum(games > 0.49)
7 losses = N - wins
8
9 print ’You won {0} times ({1:%})’.format(wins, float(wins) / N)
10
11 import matplotlib.pyplot as plt
12 count, bins, ignored = plt.hist(games)
13 plt.savefig(’images/random-thoughts-1.png’)

You won 5090 times (50.900000%)

114
 As you can see you win slightly more than you lost.
It is possible to get random integers. Here are a few examples of getting a
random integer between 1 and 100. You might do this to get random indices of
a list, for example.

1 import numpy as np
2
3 print np.random.random_integers(1, 100)
4 print np.random.random_integers(1, 100, 3)
5 print np.random.random_integers(1, 100, (2,2))

96
[ 95 49 100]
[[69 54]
[41 93]]
2
The normal distribution is defined by f (x) = √2πσ
1
2
exp(− (x−µ)
2σ 2 ) where µ is
the mean value, and σ is the standard deviation. In the standard distribution,
µ = 0 and σ = 1.

1 import numpy as np
2
3 mu = 1
4 sigma = 0.5
5 print np.random.normal(mu, sigma)
6 print np.random.normal(mu, sigma, 2)

1.04225842065
[ 0.58105204 0.64853157]

115
 Let us compare the sampled distribution to the analytical distribution. We
generate a large set of samples, and calculate the probability of getting each
value using the matplotlib.pyplot.hist command.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 mu = 0; sigma = 1
5
6 N = 5000
7 samples = np.random.normal(mu, sigma, N)
8
9 counts, bins, ignored = plt.hist(samples, 50, normed=True)
10
11 plt.plot(bins, 1.0/np.sqrt(2 * np.pi * sigma**2)*np.exp(-((bins - mu)**2)/(2*sigma**2)))
12 plt.savefig(’images/random-thoughts-2.png’)

What fraction of points lie between plus and minus one standard deviation
of the mean?
samples >= mu-sigma will return a vector of ones where the inequality
is true, and zeros where it is not. (samples >= mu-sigma) & (samples <=
mu+sigma) will return a vector of ones where there is a one in both vectors,
and a zero where there is not. In other words, a vector where both inequalities
are true. Finally, we can sum the vector to get the number of elements where the
two inequalities are true, and finally normalize by the total number of samples
to get the fraction of samples that are greater than -sigma and less than sigma.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 mu = 0; sigma = 1

116
5
6 N = 5000
7 samples = np.random.normal(mu, sigma, N)
8
9 a = np.sum((samples >= (mu - sigma)) & (samples <= (mu + sigma))) / float(N)
10 b = np.sum((samples >= (mu - 2*sigma)) & (samples <= (mu + 2*sigma))) / float(N)
11 print ’{0:%} of samples are within +- standard deviations of the mean’.format(a)
12 print ’{0:%} of samples are within +- 2standard deviations of the mean’.format(b)

67.500000% of samples are within +- standard deviations of the mean

95.580000% of samples are within +- 2standard deviations of the mean

6.8.1 Summary
We only considered the numpy.random functions here, and not all of them.
There are many distributions of random numbers to choose from. There are
also random numbers in the python random module. Remember these are only
pseudorandom numbers, but they are still useful for many applications.

7 Data analysis
7.1 Fit a line to numerical data
Matlab post
We want to fit a line to this data:

1 x = [0, 0.5, 1, 1.5, 2.0, 3.0, 4.0, 6.0, 10]

2 y = [0, -0.157, -0.315, -0.472, -0.629, -0.942, -1.255, -1.884, -3.147]

We use the polyfit(x, y, n) command where n is the polynomial order, n=1

for a line.

1 import numpy as np
2
3 p = np.polyfit(x, y, 1)
4 print p
5 slope, intercept = p
6 print slope, intercept

>>> >>> [-0.31452218 0.00062457]

>>> -0.3145221843 0.00062457337884

To show the fit, we can use numpy.polyval to evaluate the fit at many points.

1 import matplotlib.pyplot as plt

2
3 xfit = np.linspace(0, 10)
4 yfit = np.polyval(p, xfit)
5
6 plt.plot(x, y, ’bo’, label=’raw data’)

117
7 plt.plot(xfit, yfit, ’r-’, label=’fit’)
8 plt.xlabel(’x’)
9 plt.ylabel(’y’)
10 plt.legend()
11 plt.savefig(’images/linefit-1.png’)

>>> >>> >>> >>> [<matplotlib.lines.Line2D object at 0x053C1790>]

[<matplotlib.lines.Line2D object at 0x0313C610>]
<matplotlib.text.Text object at 0x052A4950>
<matplotlib.text.Text object at 0x052B9A10>
<matplotlib.legend.Legend object at 0x053C1CD0>

7.2 Linear least squares fitting with linear algebra

Matlab post
The idea here is to formulate a set of linear equations that is easy to solve.
We can express the equations in terms of our unknown fitting parameters pi as:

x1^0*p0 + x1*p1 = y1
x2^0*p0 + x2*p1 = y2
x3^0*p0 + x3*p1 = y3
etc...

Which we write in matrix form as Ap = y where A is a matrix of column

vectors, e.g. [1, x_i]. A is not a square matrix, so we cannot solve it as written.
Instead, we form AT Ap = AT y and solve that set of equations.

118
1 import numpy as np
2 x = np.array([0, 0.5, 1, 1.5, 2.0, 3.0, 4.0, 6.0, 10])
3 y = np.array([0, -0.157, -0.315, -0.472, -0.629, -0.942, -1.255, -1.884, -3.147])
4
5 A = np.column_stack([x**0, x])
6
7 M = np.dot(A.T, A)
8 b = np.dot(A.T, y)
9
10 i1, slope1 = np.dot(np.linalg.inv(M), b)
11 i2, slope2 = np.linalg.solve(M, b) # an alternative approach.
12
13 print i1, slope1
14 print i2, slope2
15
16 # plot data and fit
17 import matplotlib.pyplot as plt
18
19 plt.plot(x, y, ’bo’)
20 plt.plot(x, np.dot(A, [i1, slope1]), ’r--’)
21 plt.xlabel(’x’)
22 plt.ylabel(’y’)
23 plt.savefig(’images/la-line-fit.png’)

0.00062457337884 -0.3145221843
0.00062457337884 -0.3145221843

This method can be readily extended to fitting any polynomial model, or

other linear model that is fit in a least squares sense. This method does not
provide confidence intervals.

7.3 Linear regression with confidence intervals.

Matlab post Fit a fourth order polynomial to this data and determine the con-

119
 fidence interval for each parameter. Data from example 5-1 in Fogler, Elements
of Chemical Reaction Engineering.
We want the equation Ca(t) = b0 + b1 ∗ t + b2 ∗ t2 + b3 ∗ t3 + b4 ∗ t4 fit to the
data in the least squares sense. We can write this in a linear algebra form as:
T*p = Ca where T is a matrix of columns [1 t tˆ2 tˆ3 tˆ4], and p is a column
vector of the fitting parameters. We want to solve for the p vector and estimate
the confidence intervals.

1 import numpy as np
2 from scipy.stats.distributions import t
3
4 time = np.array([0.0, 50.0, 100.0, 150.0, 200.0, 250.0, 300.0])
5 Ca = np.array([50.0, 38.0, 30.6, 25.6, 22.2, 19.5, 17.4])*1e-3
6
7 T = np.column_stack([time**0, time, time**2, time**3, time**4])
8
9 p, res, rank, s = np.linalg.lstsq(T, Ca)
10 # the parameters are now in p
11
12 # compute the confidence intervals
13 n = len(Ca)
14 k = len(p)
15
16 sigma2 = np.sum((Ca - np.dot(T, p))**2) / (n - k) # RMSE
17
18 C = sigma2 * np.linalg.inv(np.dot(T.T, T)) # covariance matrix
19 se = np.sqrt(np.diag(C)) # standard error
20
21 alpha = 0.05 # 100*(1 - alpha) confidence level
22
23 sT = t.ppf(1.0 - alpha/2.0, n - k) # student T multiplier
24 CI = sT * se
25
26 for beta, ci in zip(p, CI):
27 print ’{2: 1.2e} [{0: 1.4e} {1: 1.4e}]’.format(beta - ci, beta + ci, beta)
28
29 SS_tot = np.sum((Ca - np.mean(Ca))**2)
30 SS_err = np.sum((np.dot(T, p) - Ca)**2)
31
32 # http://en.wikipedia.org/wiki/Coefficient_of_determination
33 Rsq = 1 - SS_err/SS_tot
34 print ’R^2 = {0}’.format(Rsq)
35
36 # plot fit
37 import matplotlib.pyplot as plt
38 plt.plot(time, Ca, ’bo’, label=’raw data’)
39 plt.plot(time, np.dot(T, p), ’r-’, label=’fit’)
40 plt.xlabel(’Time’)
41 plt.ylabel(’Ca (mol/L)’)
42 plt.legend(loc=’best’)
43 plt.savefig(’images/linregress-conf.png’)

5.00e-02 [ 4.9680e-02 5.0300e-02]

-2.98e-04 [-3.1546e-04 -2.8023e-04]
1.34e-06 [ 1.0715e-06 1.6155e-06]
-3.48e-09 [-4.9032e-09 -2.0665e-09]
3.70e-12 [ 1.3501e-12 6.0439e-12]
R^2 = 0.999986967246

120
 A fourth order polynomial fits the data well, with a good Rˆ2 value. All of
the parameters appear to be significant, i.e. zero is not included in any of the
parameter confidence intervals. This does not mean this is the best model for
the data, just that the model fits well.

7.4 Nonlinear curve fitting

Here is a typical nonlinear function fit to data. you need to provide an initial
guess. In this example we fit the Birch-Murnaghan equation of state to energy
vs. volume data from density functional theory calculations.

1 from scipy.optimize import leastsq

2 import numpy as np
3
4 vols = np.array([13.71, 14.82, 16.0, 17.23, 18.52])
5
6 energies = np.array([-56.29, -56.41, -56.46, -56.463, -56.41])
7
8 def Murnaghan(parameters, vol):
9 ’From Phys. Rev. B 28, 5480 (1983)’
10 E0, B0, BP, V0 = parameters
11
12 E = E0 + B0 * vol / BP * (((V0 / vol)**BP) / (BP - 1) + 1) - V0 * B0 / (BP - 1.0)
13
14 return E
15
16 def objective(pars, y, x):
17 #we will minimize this function
18 err = y - Murnaghan(pars, x)
19 return err
20
21 x0 = [ -56.0, 0.54, 2.0, 16.5] #initial guess of parameters
22
23 plsq = leastsq(objective, x0, args=(energies, vols))

121
24
25 print ’Fitted parameters = {0}’.format(plsq[0])
26
27 import matplotlib.pyplot as plt
28 plt.plot(vols,energies, ’ro’)
29
30 #plot the fitted curve on top
31 x = np.linspace(min(vols), max(vols), 50)
32 y = Murnaghan(plsq[0], x)
33 plt.plot(x, y, ’k-’)
34 plt.xlabel(’Volume’)
35 plt.ylabel(’Energy’)
36 plt.savefig(’images/nonlinear-curve-fitting.png’)

Fitted parameters = [-56.46839641 0.57233217 2.7407944 16.55905648]

Figure 1: Example of least-squares non-linear curve fitting.

See additional examples at http://docs.scipy.org/doc/scipy/reference/

tutorial/optimize.html.

7.5 Nonlinear curve fitting by direct least squares mini-

mization
Here is an example of fitting a nonlinear function to data by direct minimization
of the summed squared error.

1 from scipy.optimize import fmin

2 import numpy as np

122
3
4 volumes = np.array([13.71, 14.82, 16.0, 17.23, 18.52])
5
6 energies = np.array([-56.29, -56.41, -56.46, -56.463,-56.41])
7
8 def Murnaghan(parameters,vol):
9 ’From PRB 28,5480 (1983’
10 E0 = parameters[0]
11 B0 = parameters[1]
12 BP = parameters[2]
13 V0 = parameters[3]
14
15 E = E0 + B0*vol/BP*(((V0/vol)**BP)/(BP-1)+1) - V0*B0/(BP-1.)
16
17 return E
18
19 def objective(pars,vol):
20 #we will minimize this function
21 err = energies - Murnaghan(pars,vol)
22 return np.sum(err**2) #we return the summed squared error directly
23
24 x0 = [ -56., 0.54, 2., 16.5] #initial guess of parameters
25
26 plsq = fmin(objective,x0,args=(volumes,)) #note args is a tuple
27
28 print ’parameters = {0}’.format(plsq)
29
30 import matplotlib.pyplot as plt
31 plt.plot(volumes,energies,’ro’)
32
33 #plot the fitted curve on top
34 x = np.linspace(min(volumes),max(volumes),50)
35 y = Murnaghan(plsq,x)
36 plt.plot(x,y,’k-’)
37 plt.xlabel(’Volume ($\AA^3$)’)
38 plt.ylabel(’Total energy (eV)’)
39 plt.savefig(’images/nonlinear-fitting-lsq.png’)

Optimization terminated successfully.

Current function value: 0.000020
Iterations: 137
Function evaluations: 240
parameters = [-56.46932645 0.59141447 1.9044796 16.59341303]

7.6 Parameter estimation by directly minimizing summed

squared errors
Matlab post

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.array([0.0, 1.1, 2.3, 3.1, 4.05, 6.0])
5 y = np.array([0.0039, 1.2270, 5.7035, 10.6472, 18.6032, 42.3024])
6
7 plt.plot(x, y)
8 plt.xlabel(’x’)
9 plt.ylabel(’y’)
10 plt.savefig(’images/nonlin-minsse-1.png’)

123
 Figure 2: Fitting a nonlinear function.

>>> >>> >>> >>> >>> [<matplotlib.lines.Line2D object at 0x000000000733D898>]

<matplotlib.text.Text object at 0x00000000071EC5C0>
<matplotlib.text.Text object at 0x00000000071EED30>

124
 We are going to fit the function y = xa to the data. The best a will minimize
the summed squared error between the model and the fit.

1 def errfunc_(a):
2 return np.sum((y - x**a)**2)
3
4 errfunc = np.vectorize(errfunc_)
5
6 arange = np.linspace(1, 3)
7 sse = errfunc(arange)
8
9 plt.figure()
10 plt.plot(arange, sse)
11 plt.xlabel(’a’)
12 plt.ylabel(’$\Sigma (y - y_{pred})^2$’)
13 plt.savefig(’images/nonlin-minsse-2.png’)

... >>> >>> >>> >>> >>> >>> <matplotlib.figure.Figure object at 0x000000000736DBA8>
[<matplotlib.lines.Line2D object at 0x00000000075CBEF0>]
<matplotlib.text.Text object at 0x00000000076B8C18>
<matplotlib.text.Text object at 0x0000000007698BE0>

125
 Based on the graph above, you can see a minimum in the summed squared
error near a = 2.1. We use that as our initial guess. Since we know the answer
is bounded, we use scipy.optimize.fminbound

1 from scipy.optimize import fminbound

2
3 amin = fminbound(errfunc, 1.0, 3.0)
4
5 print amin
6
7 plt.figure()
8 plt.plot(x, y, ’bo’, label=’data’)
9 plt.plot(x, x**amin, ’r-’, label=’fit’)
10 plt.xlabel(’x’)
11 plt.ylabel(’y’)
12 plt.legend(loc=’best’)
13 plt.savefig(’images/nonlin-minsse-3.png’)

>>> >>> >>> 2.09004838933

>>> <matplotlib.figure.Figure object at 0x00000000075D8470>
[<matplotlib.lines.Line2D object at 0x0000000007BDFA20>]
[<matplotlib.lines.Line2D object at 0x0000000007BDFC18>]
<matplotlib.text.Text object at 0x0000000007BC6828>
<matplotlib.text.Text object at 0x0000000007BCAF98>
<matplotlib.legend.Legend object at 0x0000000007BE3128>

126
 We can do nonlinear fitting by directly minimizing the summed squared
error between a model and data. This method lacks some of the features of other
methods, notably the simple ability to get the confidence interval. However, this
method is flexible and may offer more insight into how the solution depends on
the parameters.

7.7 Nonlinear curve fitting with parameter confidence in-

tervals
Matlab post
We often need to estimate parameters from nonlinear regression of data. We
should also consider how good the parameters are, and one way to do that is to
consider the confidence interval. A confidence interval tells us a range that we
are confident the true parameter lies in.
In this example we use a nonlinear curve-fitting function: scipy.optimize.curve_-
fit to give us the parameters in a function that we define which best fit the data.
The scipy.optimize.curve_fit function also gives us the covariance matrix which
we can use to estimate the standard error of each parameter. Finally, we modify
the standard error by a student-t value which accounts for the additional un-
certainty in our estimates due to the small number of data points we are fitting
to.
We will fit the function y = ax/(b + x) to some data, and compute the 95%
confidence intervals on the parameters.

1 # Nonlinear curve fit with confidence interval

2 import numpy as np
3 from scipy.optimize import curve_fit

127
4 from scipy.stats.distributions import t
5
6 x = np.array([0.5, 0.387, 0.24, 0.136, 0.04, 0.011])
7 y = np.array([1.255, 1.25, 1.189, 1.124, 0.783, 0.402])
8
9 # this is the function we want to fit to our data
10 def func(x, a, b):
11 ’nonlinear function in a and b to fit to data’
12 return a * x / (b + x)
13
14 initial_guess = [1.2, 0.03]
15 pars, pcov = curve_fit(func, x, y, p0=initial_guess)
16
17 alpha = 0.05 # 95% confidence interval = 100*(1-alpha)
18
19 n = len(y) # number of data points
20 p = len(pars) # number of parameters
21
22 dof = max(0, n - p) # number of degrees of freedom
23
24 # student-t value for the dof and confidence level
25 tval = t.ppf(1.0-alpha/2., dof)
26
27 for i, p,var in zip(range(n), pars, np.diag(pcov)):
28 sigma = var**0.5
29 print ’p{0}: {1} [{2} {3}]’.format(i, p,
30 p - sigma*tval,
31 p + sigma*tval)
32
33 import matplotlib.pyplot as plt
34 plt.plot(x,y,’bo ’)
35 xfit = np.linspace(0,1)
36 yfit = func(xfit, pars[0], pars[1])
37 plt.plot(xfit,yfit,’b-’)
38 plt.legend([’data’,’fit’],loc=’best’)
39 plt.savefig(’images/nonlin-curve-fit-ci.png’)

p0: 1.32753141454 [1.3005365922 1.35452623688]

p1: 0.0264615569701 [0.0236076538292 0.0293154601109]
(array([ 1.32753141, 0.02646156]), [[1.3005365921998688, 1.3545262368760884], [0.0236076538

128
 You can see by inspection that the fit looks pretty reasonable. The parameter
confidence intervals are not too big, so we can be pretty confident of their values.

7.8 Nonlinear curve fitting with confidence intervals

Our goal is to fit this equation to data y = c1exp(−x) + c2 ∗ x and compute the
confidence intervals on the parameters.
This is actually could be a linear regression problem, but it is convenient
to illustrate the use the nonlinear fitting routine because it makes it easy to
get confidence intervals for comparison. The basic idea is to use the covariance
matrix returned from the nonlinear fitting routine to estimate the student-t
corrected confidence interval.

1 # Nonlinear curve fit with confidence interval

2 import numpy as np
3 from scipy.optimize import curve_fit
4 from scipy.stats.distributions import t
5
6 x = np.array([ 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. ])
7 y = np.array([ 4.70192769, 4.46826356, 4.57021389, 4.29240134, 3.88155125,
8 3.78382253, 3.65454727, 3.86379487, 4.16428541, 4.06079909])
9
10 # this is the function we want to fit to our data
11 def func(x,c0, c1):
12 return c0 * np.exp(-x) + c1*x
13
14 pars, pcov = curve_fit(func, x, y, p0=[4.96, 2.11])
15
16 alpha = 0.05 # 95% confidence interval
17
18 n = len(y) # number of data points
19 p = len(pars) # number of parameters
20

129
21 dof = max(0, n-p) # number of degrees of freedom
22
23 tval = t.ppf(1.0 - alpha / 2.0, dof) # student-t value for the dof and confidence level
24
25 for i, p,var in zip(range(n), pars, np.diag(pcov)):
26 sigma = var**0.5
27 print ’c{0}: {1} [{2} {3}]’.format(i, p,
28 p - sigma*tval,
29 p + sigma*tval)
30
31 import matplotlib.pyplot as plt
32 plt.plot(x,y,’bo ’)
33 xfit = np.linspace(0,1)
34 yfit = func(xfit, pars[0], pars[1])
35 plt.plot(xfit,yfit,’b-’)
36 plt.legend([’data’,’fit’],loc=’best’)
37 plt.savefig(’images/nonlin-fit-ci.png’)

c0: 4.96713966439 [4.62674476567 5.30753456311]

c1: 2.10995112628 [1.76711622427 2.45278602828]

Figure 3: Nonlinear fit to data.

7.9 Graphical methods to help get initial guesses for mul-

tivariate nonlinear regression
Matlab post
Fit the model f(x1,x2; a,b) = a*x1 + x2ˆb to the data given below. This
model has two independent variables, and two parameters.

130
 We want to do a nonlinear fit to find a and b that minimize the summed
squared errors between the model predictions and the data. With only two vari-
ables, we can graph how the summed squared error varies with the parameters,
which may help us get initial guesses. Let us assume the parameters lie in a
range, here we choose 0 to 5. In other problems you would adjust this as needed.

1 import numpy as np
2 from mpl_toolkits.mplot3d import Axes3D
3 import matplotlib.pyplot as plt
4
5 x1 = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0]
6 x2 = [0.2, 0.4, 0.8, 0.9, 1.1, 2.1]
7 X = np.column_stack([x1, x2]) # independent variables
8
9 f = [ 3.3079, 6.6358, 10.3143, 13.6492, 17.2755, 23.6271]
10
11 fig = plt.figure()
12 ax = fig.gca(projection = ’3d’)
13
14 ax.plot(x1, x2, f)
15 ax.set_xlabel(’x1’)
16 ax.set_ylabel(’x2’)
17 ax.set_zlabel(’f(x1,x2)’)
18
19 plt.savefig(’images/graphical-mulvar-1.png’)
20
21
22 arange = np.linspace(0,5);
23 brange = np.linspace(0,5);
24
25 A,B = np.meshgrid(arange, brange)
26
27 def model(X, a, b):
28 ’Nested function for the model’
29 x1 = X[:, 0]
30 x2 = X[:, 1]
31
32 f = a * x1 + x2**b
33 return f
34
35 @np.vectorize
36 def errfunc(a, b):
37 # function for the summed squared error
38 fit = model(X, a, b)
39 sse = np.sum((fit - f)**2)
40 return sse
41
42 SSE = errfunc(A, B)
43
44 plt.clf()
45 plt.contourf(A, B, SSE, 50)
46 plt.plot([3.2], [2.1], ’ro’)
47 plt.figtext( 3.4, 2.2, ’Minimum near here’, color=’r’)
48
49 plt.savefig(’images/graphical-mulvar-2.png’)
50
51 guesses = [3.18, 2.02]
52
53 from scipy.optimize import curve_fit
54
55 popt, pcov = curve_fit(model, X, f, guesses)
56 print popt
57
58 plt.plot([popt[0]], [popt[1]], ’r*’)
59 plt.savefig(’images/graphical-mulvar-3.png’)

131
60
61 print model(X, *popt)
62
63 fig = plt.figure()
64 ax = fig.gca(projection = ’3d’)
65
66 ax.plot(x1, x2, f, ’ko’, label=’data’)
67 ax.plot(x1, x2, model(X, *popt), ’r-’, label=’fit’)
68 ax.set_xlabel(’x1’)
69 ax.set_ylabel(’x2’)
70 ax.set_zlabel(’f(x1,x2)’)
71
72 plt.savefig(’images/graphical-mulvar-4.png’)

[ 3.21694798 1.9728254 ]
[ 3.25873623 6.59792994 10.29473657 13.68011436 17.29161001
23.62366445]

132
133
 It can be difficult to figure out initial guesses for nonlinear fitting problems.
For one and two dimensional systems, graphical techniques may be useful to
visualize how the summed squared error between the model and data depends
on the parameters.

7.10 Fitting a numerical ODE solution to data

Matlab post
Suppose we know the concentration of A follows this differential equation:
dt = −kCA , and we have data we want to fit to it. Here is an example of
dCA

doing that.

1 import numpy as np
2 from scipy.optimize import curve_fit
3 from scipy.integrate import odeint
4
5 # given data we want to fit
6 tspan = [0, 0.1, 0.2, 0.4, 0.8, 1]
7 Ca_data = [2.0081, 1.5512, 1.1903, 0.7160, 0.2562, 0.1495]
8
9 def fitfunc(t, k):
10 ’Function that returns Ca computed from an ODE for a k’
11 def myode(Ca, t):
12 return -k * Ca
13
14 Ca0 = Ca_data[0]
15 Casol = odeint(myode, Ca0, t)
16 return Casol[:,0]
17
18 k_fit, kcov = curve_fit(fitfunc, tspan, Ca_data, p0=1.3)
19 print k_fit
20
21 tfit = np.linspace(0,1);

134
22 fit = fitfunc(tfit, k_fit)
23
24 import matplotlib.pyplot as plt
25 plt.plot(tspan, Ca_data, ’ro’, label=’data’)
26 plt.plot(tfit, fit, ’b-’, label=’fit’)
27 plt.legend(loc=’best’)
28 plt.savefig(’images/ode-fit.png’)

[ 2.58893455]

7.11 Reading in delimited text files

Matlab post
sometimes you will get data in a delimited text file format, .e.g. separated
by commas or tabs. Matlab can read these in easily. Suppose we have a file
containing this data:
1 3
3 4
5 6
4 8
It is easy to read this directly into variables like this:
1 import numpy as np
2
3 x,y = np.loadtxt(’data/testdata.txt’, unpack=True)
4
5 print x,y

[ 1. 3. 5. 4.] [ 3. 4. 6. 8.]

135
 8 Interpolation
8.1 Better interpolate than never
Matlab post
We often have some data that we have obtained in the lab, and we want
to solve some problem using the data. For example, suppose we have this data
that describes the value of f at time t.

1 import matplotlib.pyplot as plt

2
3 t = [0.5, 1, 3, 6]
4 f = [0.6065, 0.3679, 0.0498, 0.0025]
5 plt.plot(t,f)
6 plt.xlabel(’t’)
7 plt.ylabel(’f(t)’)
8 plt.savefig(’images/interpolate-1.png’)

>>> >>> >>> [<matplotlib.lines.Line2D object at 0x04D18730>]

<matplotlib.text.Text object at 0x04BEE8B0>
<matplotlib.text.Text object at 0x04C03970>

8.1.1 Estimate the value of f at t=2.

This is a simple interpolation problem.

1 from scipy.interpolate import interp1d

2

136
3 g = interp1d(t, f) # default is linear interpolation
4
5 print g(2)
6 print g([2, 3, 4])

>>> >>> >>> 0.20885

[ 0.20885 0.0498 0.03403333]

The function we sample above is actually f(t) = exp(-t). The linearly inter-
polated example is not too accurate.

1 import numpy as np
2 print np.exp(-2)

0.135335283237

8.1.2 improved interpolation?

we can tell interp1d to use a different interpolation scheme such as cubic poly-
nomial splines like this. For nonlinear functions, this may improve the accuracy
of the interpolation, as it implicitly includes information about the curvature
by fitting a cubic polynomial over neighboring points.

1 g2 = interp1d(t, f, ’cubic’)
2 print g2(2)
3 print g2([2, 3, 4])

0.108481818182
[ 0.10848182 0.0498 0.08428727]

Interestingly, this is a different value than Matlab’s cubic interpolation. Let

us show the cubic spline fit.

1 plt.figure()
2 plt.plot(t,f)
3 plt.xlabel(’t’)
4 plt.ylabel(’f(t)’)
5
6 x = np.linspace(0.5, 6)
7 fit = g2(x)
8 plt.plot(x, fit, label=’fit’)
9 plt.savefig(’images/interpolation-2.png’)

<matplotlib.figure.Figure object at 0x04EF2430>

[<matplotlib.lines.Line2D object at 0x04F20ED0>]
<matplotlib.text.Text object at 0x04EF2FF0>
<matplotlib.text.Text object at 0x04F060D0>
>>> >>> >>> [<matplotlib.lines.Line2D object at 0x04F17570>]

137
 Wow. That is a weird looking fit. Very different from what Matlab produces.
This is a good teaching moment not to rely blindly on interpolation! We will
rely on the linear interpolation from here out which behaves predictably.

8.1.3 The inverse question

It is easy to interpolate a new value of f given a value of t. What if we want to
know the time that f=0.2? We can approach this a few ways.

method 1 We setup a function that we can use fsolve on. The function will
be equal to zero at the time. The second function will look like 0 = 0.2 - f(t).
The answer for 0.2=exp(-t) is t = 1.6094. Since we use interpolation here, we
will get an approximate answer.

1 from scipy.optimize import fsolve

2
3 def func(t):
4 return 0.2 - g(t)
5
6 initial_guess = 2
7 ans, = fsolve(func, initial_guess)
8 print ans

>>> ... ... >>> >>> >>> 2.0556428796

method 2: switch the interpolation order We can switch the order of the
interpolation to solve this problem. An issue we have to address in this method

138
 is that the "x" values must be monotonically increasing. It is somewhat subtle
to reverse a list in python. I will use the cryptic syntax of [::-1] instead of the
list.reverse() function or reversed() function. list.reverse() actually reverses the
list "in place", which changes the contents of the variable. That is not what I
want. reversed() returns an iterator which is also not what I want. [::-1] is a
fancy indexing trick that returns a reversed list.

1 g3 = interp1d(f[::-1], t[::-1])
2
3 print g3(0.2)

>>> 2.0556428796

8.1.4 A harder problem

Suppose we want to know at what time is 1/f = 100? Now we have to decide
what do we interpolate: f(t) or 1/f(t). Let us look at both ways and decide
what is best. The answer to 1/exp(−t) = 100 is 4.6052

interpolate on f(t) then invert the interpolated number

1 def func(t):
2 ’objective function. we do some error bounds because we cannot interpolate out of the range.’
3 if t < 0.5: t=0.5
4 if t > 6: t = 6
5 return 100 - 1.0 / g(t)
6
7 initial_guess = 4.5
8 a1, = fsolve(func, initial_guess)
9 print a1
10 print ’The %error is {0:%}’.format((a1 - 4.6052)/4.6052)

... ... ... ... >>> >>> >>> 5.52431289641

The %error is 19.958154%

invert f(t) then interpolate on 1/f

1 ig = interp1d(t, 1.0 / np.array(f))
2
3 def ifunc(t):
4 if t < 0.5: t=0.5
5 if t > 6: t = 6
6 return 100 - ig(t)
7
8 initial_guess = 4.5
9 a2, = fsolve(ifunc, initial_guess)
10 print a2
11 print ’The %error is {0:%}’.format((a2 - 4.6052)/4.6052)

>>> ... ... ... ... >>> >>> >>> 3.6310782241

The %error is -21.152649%

139
 8.1.5 Discussion
In this case you get different errors, one overestimates and one underestimates
the answer, and by a lot: ± 20%. Let us look at what is happening.

1 import matplotlib.pyplot as plt

2 import numpy as np
3 from scipy.interpolate import interp1d
4
5 t = [0.5, 1, 3, 6]
6 f = [0.6065, 0.3679, 0.0498, 0.0025]
7
8 x = np.linspace(0.5, 6)
9
10
11 g = interp1d(t, f) # default is linear interpolation
12 ig = interp1d(t, 1.0 / np.array(f))
13
14 plt.figure()
15 plt.plot(t, 1 / np.array(f), ’ko ’, label=’data’)
16 plt.plot(x, 1 / g(x), label=’1/interpolated f(x)’)
17 plt.plot(x, ig(x), label=’interpolate on 1/f(x)’)
18 plt.plot(x, 1 / np.exp(-x), ’k--’, label=’1/exp(-x)’)
19 plt.xlabel(’t’)
20 plt.ylabel(’1/f(t)’)
21 plt.legend(loc=’best’)
22 plt.savefig(’images/interpolation-3.png’)

You can see that the 1/interpolated f(x) underestimates the value, while
interpolated (1/f(x)) overestimates the value. This is an example of where
you clearly need more data in that range to make good estimates. Neither
interpolation method is doing a great job. The trouble in reality is that you
often do not know the real function to do this analysis. Here you can say the
time is probably between 3.6 and 5.5 where 1/f(t) = 100, but you can not read

140
 much more than that into it. If you need a more precise answer, you need better
data, or you need to use an approach other than interpolation. For example,
you could fit an exponential function to the data and use that to estimate values
at other times.
So which is the best to interpolate? I think you should interpolate the
quantity that is linear in the problem you want to solve, so in this case I think
interpolating 1/f(x) is better. When you use an interpolated function in a
nonlinear function, strange, unintuitive things can happen. That is why the
blue curve looks odd. Between data points are linear segments in the original
interpolation, but when you invert them, you cause the curvature to form.

8.2 Interpolation of data

Matlab post
When we have data at two points but we need data in between them we
use interpolation. Suppose we have the points (4,3) and (6,2) and we want to
know the value of y at x=4.65, assuming y varies linearly between these points.
we use the interp1d command to achieve this. The syntax in python is slightly
different than in matlab.

1 from scipy.interpolate import interp1d

2
3 x = [4, 6]
4 y = [3, 2]
5
6 ifunc = interp1d(x, y)
7
8 print ifunc(4.65)
9
10
11 ifunc = interp1d(x, y, bounds_error=False) # do not raise error on out of bounds
12 print ifunc([4.65, 5.01, 4.2, 9])

2.675
[ 2.675 2.495 2.9 nan]
The default interpolation method is simple linear interpolation between
points. Other methods exist too, such as fitting a cubic spline to the data
and using the spline representation to interpolate from.

1 from scipy.interpolate import interp1d

2
3 x = [1, 2, 3, 4];
4 y = [1, 4, 9, 16]; # y = x^2
5
6 xi = [ 1.5, 2.5, 3.5]; # we want to interpolate on these values
7 y1 = interp1d(x,y)
8
9 print y1(xi)
10
11 y2 = interp1d(x,y,’cubic’)
12 print y2(xi)
13
14 import numpy as np
15 print np.array(xi)**2

141
 [ 2.5 6.5 12.5]
[ 2.25 6.25 12.25]
[ 2.25 6.25 12.25]
In this case the cubic spline interpolation is more accurate than the linear
interpolation. That is because the underlying data was polynomial in nature,
and a spline is like a polynomial. That may not always be the case, and you
need some engineering judgement to know which method is best.

8.3 Interpolation with splines

When you do not know the functional form of data to fit an equation, you can
still fit/interpolate with splines.

1 # use splines to fit and interpolate data

2 from scipy.interpolate import interp1d
3 from scipy.optimize import fmin
4 import numpy as np
5 import matplotlib.pyplot as plt
6
7 x = np.array([ 0, 1, 2, 3, 4 ])
8 y = np.array([ 0., 0.308, 0.55, 0.546, 0.44 ])
9
10 # create the interpolating function
11 f = interp1d(x, y, kind=’cubic’, bounds_error=False)
12
13 # to find the maximum, we minimize the negative of the function. We
14 # cannot just multiply f by -1, so we create a new function here.
15 f2 = interp1d(x, -y, kind=’cubic’)
16 xmax = fmin(f2, 2.5)
17
18 xfit = np.linspace(0,4)
19
20 plt.plot(x,y,’bo’)
21 plt.plot(xfit, f(xfit),’r-’)
22 plt.plot(xmax, f(xmax),’g*’)
23 plt.legend([’data’,’fit’,’max’], loc=’best’, numpoints=1)
24 plt.xlabel(’x data’)
25 plt.ylabel(’y data’)
26 plt.title(’Max point = ({0:1.2f}, {1:1.2f})’.format(float(xmax),
27 float(f(xmax))))
28 plt.savefig(’images/splinefit.png’)

Optimization terminated successfully.

Current function value: -0.575712
Iterations: 12
Function evaluations: 24
There are other good examples at http://docs.scipy.org/doc/scipy/
reference/tutorial/interpolate.html

9 Optimization
9.1 Constrained optimization
Matlab post

142
 Figure 4: Illustration of a spline fit to data and finding the maximum point.

adapted from http://en.wikipedia.org/wiki/Lagrange_multipliers.

Suppose we seek to minimize the function f (x, y) = x + y subject to the
constraint that x2 + y 2 = 1. The function we seek to maximize is an unbounded
plane, while the constraint is a unit circle. We could setup a Lagrange multiplier
approach to solving this problem, but we will use a constrained optimization
approach instead.

1 from scipy.optimize import fmin_slsqp

2
3 def objective(X):
4 x, y = X
5 return x + y
6
7 def eqc(X):
8 ’equality constraint’
9 x, y = X
10 return x**2 + y**2 - 1.0
11
12 X0 = [-1, -1]
13 X = fmin_slsqp(objective, X0, eqcons=[eqc])
14 print X

Optimization terminated successfully. (Exit mode 0)

Current function value: -1.41421356237
Iterations: 5
Function evaluations: 20
Gradient evaluations: 5

143
 [-0.70710678 -0.70710678]

9.2 Using Lagrange multipliers in optimization

Matlab post (adapted from http://en.wikipedia.org/wiki/Lagrange_multipliers.)
Suppose we seek to maximize the function f (x, y) = x + y subject to the
constraint that x2 + y 2 = 1. The function we seek to maximize is an unbounded
plane, while the constraint is a unit circle. We want the maximum value of the
circle, on the plane. We plot these two functions here.

1 import numpy as np
2
3 x = np.linspace(-1.5, 1.5)
4
5 [X, Y] = np.meshgrid(x, x)
6
7 import matplotlib as mpl
8 from mpl_toolkits.mplot3d import Axes3D
9 import matplotlib.pyplot as plt
10
11 fig = plt.figure()
12 ax = fig.gca(projection=’3d’)
13
14 ax.plot_surface(X, Y, X + Y)
15
16 theta = np.linspace(0,2*np.pi);
17 R = 1.0
18 x1 = R * np.cos(theta)
19 y1 = R * np.sin(theta)
20
21 ax.plot(x1, y1, x1 + y1, ’r-’)
22 plt.savefig(’images/lagrange-1.png’)

144
 9.2.1 Construct the Lagrange multiplier augmented function
To find the maximum, we construct the following function: Λ(x, y; λ) = f (x, y)+
λg(x, y) where g(x, y) = x2 + y 2 − 1 = 0, which is the constraint function. Since
g(x, y) = 0, we are not really changing the original function, provided that the
constraint is met!

1 import numpy as np
2
3 def func(X):
4 x = X[0]
5 y = X[1]
6 L = X[2] # this is the multiplier. lambda is a reserved keyword in python
7 return x + y + L * (x**2 + y**2 - 1)

9.2.2 Finding the partial derivatives

The minima/maxima of the augmented function are located where all of the
partial derivatives of the augmented function are equal to zero, i.e. ∂Λ/∂x =
0, ∂Λ/∂y = 0, and ∂Λ/∂λ = 0. the process for solving this is usually to
analytically evaluate the partial derivatives, and then solve the unconstrained
resulting equations, which may be nonlinear.
Rather than perform the analytical differentiation, here we develop a way to
numerically approximate the partial derivatives.

1 def dfunc(X):
2 dLambda = np.zeros(len(X))
3 h = 1e-3 # this is the step size used in the finite difference.
4 for i in range(len(X)):
5 dX = np.zeros(len(X))
6 dX[i] = h
7 dLambda[i] = (func(X+dX)-func(X-dX))/(2*h);
8 return dLambda

9.2.3 Now we solve for the zeros in the partial derivatives

The function we defined above (dfunc) will equal zero at a maximum or min-
imum. It turns out there are two solutions to this problem, but only one of
them is the maximum value. Which solution you get depends on the initial
guess provided to the solver. Here we have to use some judgement to identify
the maximum.

1 from scipy.optimize import fsolve

2
3 # this is the max
4 X1 = fsolve(dfunc, [1, 1, 0])
5 print X1, func(X1)
6
7 # this is the min
8 X2 = fsolve(dfunc, [-1, -1, 0])
9 print X2, func(X2)

145
 >>> ... >>> [ 0.70710678 0.70710678 -0.70710678] 1.41421356237
>>> ... >>> [-0.70710678 -0.70710678 0.70710678] -1.41421356237

9.2.4 Summary
Three dimensional plots in matplotlib are a little more difficult than in Matlab
(where the code is almost the same as 2D plots, just different commands, e.g.
plot vs plot3). In Matplotlib you have to import additional modules in the right
order, and use the object oriented approach to plotting as shown here.

9.3 Linear programming example with inequality con-

straints
Matlab post
adapted from http://www.matrixlab-examples.com/linear-programming.
html which solves this problem with fminsearch.
Let us suppose that a merry farmer has 75 roods (4 roods = 1 acre) on
which to plant two crops: wheat and corn. To produce these crops, it costs the
farmer (for seed, water, fertilizer, etc. ) $120 per rood for the wheat, and $210
per rood for the corn. The farmer has $15,000 available for expenses, but after
the harvest the farmer must store the crops while awaiting favorable or good
market conditions. The farmer has storage space for 4,000 bushels. Each rood
yields an average of 110 bushels of wheat or 30 bushels of corn. If the net profit
per bushel of wheat (after all the expenses) is $1.30 and for corn is $2.00, how
should the merry farmer plant the 75 roods to maximize profit?
Let x be the number of roods of wheat planted, and y be the number of roods
of corn planted. The profit function is: P = (110)(1.3)x + (30)(2)y = 143x+60y
There are some constraint inequalities, specified by the limits on expenses,
storage and roodage. They are:
$120x + $210y <= $15000 (The total amount spent cannot exceed the
amount the farm has)
110x + 30y <= 4000 (The amount generated should not exceed storage
space.)
x + y <= 75 (We cannot plant more space than we have.)
0 <= xand0 <= y (all amounts of planted land must be positive.)
To solve this problem, we cast it as a linear programming problem, which
minimizes a function f(X) subject to some constraints. We create a proxy func-
tion for the negative of profit, which we seek to minimize.
f = -(143*x + 60*y)

1 from scipy.optimize import fmin_cobyla

2
3 def objective(X):
4 ’’’objective function to minimize. It is the negative of profit,
5 which we seek to maximize.’’’
6 x, y = X
7 return -(143*x + 60*y)

146
8
9 def c1(X):
10 ’Ensure 120x + 210y <= 15000’
11 x,y = X
12 return 15000 - 120 * x - 210*y
13
14 def c2(X):
15 ’ensure 110x + 30y <= 4000’
16 x,y = X
17 return 4000 - 110*x - 30 * y
18
19 def c3(X):
20 ’Ensure x + y is less than or equal to 75’
21 x,y = X
22 return 75 - x - y
23
24 def c4(X):
25 ’Ensure x >= 0’
26 return X[0]
27
28 def c5(X):
29 ’Ensure y >= 0’
30 return X[1]
31
32 X = fmin_cobyla(objective, x0=[20, 30], cons=[c1, c2, c3, c4, c5])
33
34 print ’We should plant {0:1.2f} roods of wheat.’.format(X[0])
35 print ’We should plant {0:1.2f} roods of corn’.format(X[1])
36 print ’The maximum profit we can earn is ${0:1.2f}.’.format(-objective(X))

Normal return from subroutine COBYLA

NFVALS = 40 F =-6.315625E+03 MAXCV = 4.547474E-13

X = 2.187500E+01 5.312500E+01
We should plant 21.88 roods of wheat.
We should plant 53.12 roods of corn
The maximum profit we can earn is $6315.62.

This code is not exactly the same as the original post, but we get to the
same answer. The linear programming capability in scipy is currently somewhat
limited in 0.10. It is a little better in 0.11, but probably not as advanced as
Matlab. There are some external libraries available:

1. http://abel.ee.ucla.edu/cvxopt/
2. http://openopt.org/LP

9.4 Find the minimum distance from a point to a curve.

A problem that can be cast as a constrained minimization problem is to find
the minimum distance from a point to a curve. Suppose we have f (x) = x2 ,
and the point (0.5, 2). what is the minimum distance from that point to f (x)?

1 import numpy as np
2 import matplotlib.pyplot as plt

147
3 from scipy.optimize import fmin_cobyla
4
5 P = (0.5, 2)
6
7 def f(x):
8 return x**2
9
10 def objective(X):
11 x,y = X
12 return np.sqrt((x - P[0])**2 + (y - P[1])**2)
13
14 def c1(X):
15 x,y = X
16 return f(x) - y
17
18 X = fmin_cobyla(objective, x0=[0.5,0.5], cons=[c1])
19
20 print ’The minimum distance is {0:1.2f}’.format(objective(X))
21
22 # Verify the vector to this point is normal to the tangent of the curve
23 # position vector from curve to point
24 v1 = np.array(P) - np.array(X)
25 # position vector
26 v2 = np.array([1, 2.0 * X[0]])
27 print ’dot(v1, v2) = ’,np.dot(v1, v2)
28
29 x = np.linspace(-2, 2, 100)
30
31 plt.plot(x, f(x), ’r-’, label=’f(x)’)
32 plt.plot(P[0], P[1], ’bo’, label=’point’)
33 plt.plot([P[0], X[0]], [P[1], X[1]], ’b-’, label=’shortest distance’)
34 plt.plot([X[0], X[0] + 1], [X[1], X[1] + 2.0 * X[0]], ’g-’, label=’tangent’)
35 plt.axis(’equal’)
36 plt.xlabel(’x’)
37 plt.ylabel(’y’)
38 plt.legend(loc=’best’)
39 plt.savefig(’images/min-dist-p-func.png’)

The minimum distance is 0.86

dot(v1, v2) = 0.000336477214214

Normal return from subroutine COBYLA

NFVALS = 44 F = 8.579598E-01 MAXCV = 0.000000E+00

X = 1.300793E+00 1.692061E+00

148
 In the code above, we demonstrate that the point we find on the curve that
minimizes the distance satisfies the property that a vector from that point to our
other point is normal to the tangent of the curve at that point. This is shown
by the fact that the dot product of the two vectors is very close to zero. It is
not zero because of the accuracy criteria that is used to stop the minimization
is not high enough.

10 Differential equations
The key to successfully solving many differential equations is correctly classi-
fying the equations, putting them into a standard form and then picking the
appropriate solver. You must be able to determine if an equation is:

• An ordinary differential equation Y 0 = f (x, Y ) with

– initial values (good support in python/numpy/scipy)

– boundary values (not difficult to write code for simple cases)
• Delay differential equation
• Differential algebraic equations

• A partial differential equation

The following sections will illustrate the methods for solving these kinds of
equations.

149
 10.1 Ordinary differential equations
10.1.1 Numerical solution to a simple ode
Matlab post
Integrate this ordinary differential equation (ode):
dy
= y(t)
dt
over the time span of 0 to 2. The initial condition is y(0) = 1.
to solve this equation, you need to create a function of the form: dydt = f(y,
t) and then use one of the odesolvers, e.g. odeint.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 def fprime(y,t):
6 return y
7
8 tspan = np.linspace(0, 2)
9 y0 = 1
10 ysol = odeint(fprime, y0, tspan)
11 plt.figure(figsize=(4,3))
12 plt.plot(tspan, ysol, label=’numerical solution’)
13 plt.plot(tspan, np.exp(tspan), ’r--’, label=’analytical solution’)
14 plt.xlabel(’time’)
15 plt.ylabel(’y(t)’)
16 plt.legend(loc=’best’)
17 plt.savefig(’images/simple-ode.png’)

The numerical and analytical solutions agree.

150
 Now, suppose you want to know at what time is the solution equal to 3?
There are several approaches to this, including setting up a solver, or using an
event like approach to stop integration at y=3. A simple approach is to use
reverse interpolation. We simply reverse the x and y vectors so that y is the
independent variable, and we interpolate the corresponding x-value.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 def fprime(y,t):
6 return y
7
8 tspan = np.linspace(0, 2)
9 y0 = 1
10 ysol = odeint(fprime, y0, tspan)
11
12 from scipy.interpolate import interp1d
13
14 ip = interp1d(ysol[:,0], tspan) # reverse interpolation
15 print ’y = 3 at x = {0}’.format(ip(3))

y = 3 at x = 1.09854780564

10.1.2 Plotting ODE solutions in cylindrical coordinates

Matlab post
It is straightforward to plot functions in Cartesian coordinates. It is less
convenient to plot them in cylindrical coordinates. Here we solve an ODE in
cylindrical coordinates, and then convert the solution to Cartesian coordinates
for simple plotting.

1 import numpy as np
2 from scipy.integrate import odeint
3
4 def dfdt(F, t):
5 rho, theta, z = F
6 drhodt = 0 # constant radius
7 dthetadt = 1 # constant angular velocity
8 dzdt = -1 # constant dropping velocity
9 return [drhodt, dthetadt, dzdt]
10
11 # initial conditions
12 rho0 = 1
13 theta0 = 0
14 z0 = 100
15
16 tspan = np.linspace(0, 50, 500)
17 sol = odeint(dfdt, [rho0, theta0, z0], tspan)
18
19 rho = sol[:,0]
20 theta = sol[:,1]
21 z = sol[:,2]
22
23 # convert cylindrical coords to cartesian for plotting.
24 X = rho * np.cos(theta)
25 Y = rho * np.sin(theta)
26
27 from mpl_toolkits.mplot3d import Axes3D

151
28 import matplotlib.pyplot as plt
29 fig = plt.figure()
30 ax = fig.gca(projection=’3d’)
31 ax.plot(X, Y, z)
32 plt.savefig(’images/ode-cylindrical.png’)

10.1.3 ODEs with discontinuous forcing functions

Matlab post
Adapted from http://archives.math.utk.edu/ICTCM/VOL18/S046/paper.
pdf
A mixing tank initially contains 300 g of salt mixed into 1000 L of water.
At t=0 min, a solution of 4 g/L salt enters the tank at 6 L/min. At t=10 min,
the solution is changed to 2 g/L salt, still entering at 6 L/min. The tank is well
stirred, and the tank solution leaves at a rate of 6 L/min. Plot the concentration
of salt (g/L) in the tank as a function of time.
A mass balance on the salt in the tank leads to this differential equation:
dt = νCS,in (t) − νMS /V with the initial condition that MS (t = 0) = 300.
dMS

The wrinkle is that the inlet conditions are not constant.

0 t ≤ 0,
CS,in (t) = 4 0 < t ≤ 10,
2 t > 10.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4

152
5 V = 1000.0 # L
6 nu = 6.0 # L/min
7
8 def Cs_in(t):
9 ’inlet concentration’
10 if t < 0:
11 Cs = 0.0 # g/L
12 elif (t > 0) and (t <= 10):
13 Cs = 4.0
14 else:
15 Cs = 2.0
16 return Cs
17
18 def mass_balance(Ms, t):
19 ’$\frac{dM_S}{dt} = \nu C_{S,in}(t) - \nu M_S/V$’
20 dMsdt = nu * Cs_in(t) - nu * Ms / V
21 return dMsdt
22
23 tspan = np.linspace(0.0, 15.0, 50)
24
25 M0 = 300.0 # gm salt
26 Ms = odeint(mass_balance, M0, tspan)
27
28 plt.plot(tspan, Ms/V, ’b.-’)
29 plt.xlabel(’Time (min)’)
30 plt.ylabel(’Salt concentration (g/L)’)
31 plt.savefig(’images/ode-discont.png’)

You can see the discontinuity in the salt concentration at 10 minutes due to
the discontinous change in the entering salt concentration.

10.1.4 Simulating the events feature of Matlab’s ode solvers

The ode solvers in Matlab allow you create functions that define events that can
stop the integration, detect roots, etc. . . We will explore how to get a similar

153
 effect in python. Here is an example that somewhat does this, but it is only an
approximation. We will manually integrate the ODE, adjusting the time step in
each iteration to zero in on the solution. When the desired accuracy is reached,
we stop the integration.
It does not appear that events are supported in scipy. A solution is at http:
//mail.scipy.org/pipermail/scipy-dev/2005-July/003078.html, but it does
not appear integrated into scipy yet (8 years later ;).

1 import numpy as np
2 from scipy.integrate import odeint
3
4 def dCadt(Ca, t):
5 "the ode function"
6 k = 0.23
7 return -k * Ca**2
8
9 Ca0 = 2.3
10
11 # create lists to store time span and solution
12 tspan = [0, ]
13 sol = [Ca0,]
14 i = 0
15
16 while i < 100: # take max of 100 steps
17 t1 = tspan[i]
18 Ca = sol[i]
19
20 # pick the next time using a Newton-Raphson method
21 # we want f(t, Ca) = (Ca(t) - 1)**2 = 0
22 # df/dt = df/dCa dCa/dt
23 # = 2*(Ca - 1) * dCadt
24 t2 = t1 - (Ca - 1.0)**2 / (2 * (Ca - 1) *dCadt(Ca, t1))
25
26 f = odeint(dCadt, Ca, [t1, t2])
27
28 if np.abs(Ca - 1.0) <= 1e-4:
29 print ’Solution reached at i = {0}’.format(i)
30 break
31
32 tspan += [t2]
33 sol.append(f[-1][0])
34 i += 1
35
36 print ’At t={0:1.2f} Ca = {1:1.3f}’.format(tspan[-1], sol[-1])
37
38 import matplotlib.pyplot as plt
39 plt.plot(tspan, sol, ’bo’)
40 plt.show()

Solution reached at i = 15
At t=2.46 Ca = 1.000

This particular solution works for this example, probably because it is well
behaved. It is "downhill" to the desired solution. It is not obvious this would
work for every example, and it is certainly possible the algorithm could go
"backward" in time. A better approach might be to integrate forward until you
detect a sign change in your event function, and then refine it in a separate loop.
I like the events integration in Matlab better, but this is actually pretty
functional. It should not be too hard to use this for root counting, e.g. by

154
 counting sign changes. It would be considerably harder to get the actual roots.
It might also be hard to get the positions of events that include the sign or value
of the derivatives at the event points.
ODE solving in Matlab is considerably more advanced in functionality than
in scipy. There do seem to be some extra packages, e.g. pydstools, scikits.odes
that add extra ode functionality.

10.1.5 Mimicking ode events in python

The ODE functions in scipy.integrate do not directly support events like the
functions in Matlab do. We can achieve something like it though, by digging
into the guts of the solver, and writing a little code. In previous example I used
an event to count the number of roots in a function by integrating the derivative
of the function.

1 import numpy as np
2 from scipy.integrate import odeint
3
4 def myode(f, x):
5 return 3*x**2 + 12*x -4
6
7 def event(f, x):
8 ’an event is when f = 0’
9 return f
10
11 # initial conditions
12 x0 = -8
13 f0 = -120
14
15 # final x-range and step to integrate over.
16 xf = 4 #final x value
17 deltax = 0.45 #xstep
18
19 # lists to store the results in
20 X = [x0]
21 sol = [f0]
22 e = [event(f0, x0)]
23 events = []
24 x2 = x0
25 # manually integrate at each time step, and check for event sign changes at each step
26 while x2 <= xf: #stop integrating when we get to xf
27 x1 = X[-1]
28 x2 = x1 + deltax
29 f1 = sol[-1]
30
31 f2 = odeint(myode, f1, [x1, x2]) # integrate from x1,f1 to x2,f2
32 X += [x2]
33 sol += [f2[-1][0]]
34
35 # now evaluate the event at the last position
36 e += [event(sol[-1], X[-1])]
37
38 if e[-1] * e[-2] < 0:
39 # Event detected where the sign of the event has changed. The
40 # event is between xPt = X[-2] and xLt = X[-1]. run a modified bisect
41 # function to narrow down to find where event = 0
42 xLt = X[-1]
43 fLt = sol[-1]
44 eLt = e[-1]
45
46 xPt = X[-2]

155
47 fPt = sol[-2]
48 ePt = e[-2]
49
50 j = 0
51 while j < 100:
52 if np.abs(xLt - xPt) < 1e-6:
53 # we know the interval to a prescribed precision now.
54 # print ’Event found between {0} and {1}’.format(x1t, x2t)
55 print ’x = {0}, event = {1}, f = {2}’.format(xLt, eLt, fLt)
56 events += [(xLt, fLt)]
57 break # and return to integrating
58
59 m = (ePt - eLt)/(xPt - xLt) #slope of line connecting points
60 #bracketing zero
61
62 #estimated x where the zero is
63 new_x = -ePt / m + xPt
64
65 # now get the new value of the integrated solution at that new x
66 f = odeint(myode, fPt, [xPt, new_x])
67 new_f = f[-1][-1]
68 new_e = event(new_f, new_x)
69
70 # now check event sign change
71 if eLt * new_e > 0:
72 xPt = new_x
73 fPt = new_f
74 ePt = new_e
75 else:
76 xLt = new_x
77 fLt = new_f
78 eLt = new_e
79
80 j += 1
81
82
83 import matplotlib.pyplot as plt
84 plt.plot(X, sol)
85
86 # add event points to the graph
87 for x,e in events:
88 plt.plot(x,e,’bo ’)
89 plt.savefig(’images/event-ode-1.png’)

x = -6.00000006443, event = -4.63518112781e-15, f = -4.63518112781e-15

x = -1.99999996234, event = -1.40512601554e-15, f = -1.40512601554e-15
x = 1.99999988695, event = -1.11022302463e-15, f = -1.11022302463e-15

156
 That was a lot of programming to do something like find the roots of the
function! Below is an example of using a function coded into pycse to solve the
same problem. It is a bit more sophisticated because you can define whether an
event is terminal, and the direction of the approach to zero for each event.

1 from pycse import *

2 import numpy as np
3
4 def myode(f, x):
5 return 3*x**2 + 12*x -4
6
7 def event1(f, x):
8 ’an event is when f = 0 and event is decreasing’
9 isterminal = True
10 direction = -1
11 return f, isterminal, direction
12
13 def event2(f, x):
14 ’an event is when f = 0 and increasing’
15 isterminal = False
16 direction = 1
17 return f, isterminal, direction
18
19 f0 = -120
20
21 xspan = np.linspace(-8, 4)
22 X, F, TE, YE, IE = odelay(myode, f0, xspan, events=[event1, event2])
23
24 import matplotlib.pyplot as plt
25 plt.plot(X, F, ’.-’)
26
27 # plot the event locations.use a different color for each event
28 colors = ’rg’
29
30 for x,y,i in zip(TE, YE, IE):
31 plt.plot([x], [y], ’o’, color=colors[i])
32

157
33 plt.savefig(’images/event-ode-2.png’)
34 plt.show()
35 print TE, YE, IE

[-6.0000001083101306, -1.9999999635550625] [-3.0871138978483259e-14, -7.7715611723760958e-16

10.1.6 Solving an ode for a specific solution value

Matlab post The analytical solution to an ODE is a function, which can be
solved to get a particular value, e.g. if the solution to an ODE is y(x) = exp(x),
you can solve the solution to find the value of x that makes y(x) = 2. In a
numerical solution to an ODE we get a vector of independent variable values,
and the corresponding function values at those values. To solve for a particular
function value we need a different approach. This post will show one way to do
that in python.
Given that the concentration of a species A in a constant volume, batch
reactor obeys this differential equation dC dt = −kCA with the initial condition
A 2

CA (t = 0) = 2.3 mol/L and k = 0.23 L/mol/s, compute the time it takes for
CA to be reduced to 1 mol/L.
We will get a solution, then create an interpolating function and use fsolve
to get the answer.

1 from scipy.integrate import odeint

2 from scipy.interpolate import interp1d
3 from scipy.optimize import fsolve
4 import numpy as np
5 import matplotlib.pyplot as plt
6

158
7 k = 0.23
8 Ca0 = 2.3
9
10 def dCadt(Ca, t):
11 return -k * Ca**2
12
13 tspan = np.linspace(0, 10)
14
15 sol = odeint(dCadt, Ca0, tspan)
16 Ca = sol[:,0]
17
18 plt.plot(tspan, Ca)
19 plt.xlabel(’Time (s)’)
20 plt.ylabel(’$C_A$ (mol/L)’)
21 plt.savefig(’images/ode-specific-1.png’)

>>> >>> >>> >>> ... >>> [<matplotlib.lines.Line2D object at 0x1b710d50>]

<matplotlib.text.Text object at 0x1b2f8410>
<matplotlib.text.Text object at 0x1b2fae10>

You can see the solution is near two seconds. Now we create an interpolating
function to evaluate the solution. We will plot the interpolating function on a
finer grid to make sure it seems reasonable.

1 ca_func = interp1d(tspan, Ca, ’cubic’)

2
3 itime = np.linspace(0, 10, 200)
4
5 plt.figure()
6 plt.plot(tspan, Ca, ’.’)
7 plt.plot(itime, ca_func(itime), ’b-’)
8

159
9 plt.xlabel(’Time (s)’)
10 plt.ylabel(’$C_A$ (mol/L)’)
11 plt.legend([’solution’,’interpolated’])
12 plt.savefig(’images/ode-specific-2.png’)
13 plt.show()

>>> >>> >>> <matplotlib.figure.Figure object at 0x1b2dfed0>

[<matplotlib.lines.Line2D object at 0x1c103b90>]
[<matplotlib.lines.Line2D object at 0x1c107050>]
>>> <matplotlib.text.Text object at 0x1c0e65d0>
<matplotlib.text.Text object at 0x1b95bfd0>
<matplotlib.legend.Legend object at 0x1c107550>

that loos pretty reasonable. Now we solve the problem.

1 tguess = 2.0
2 tsol, = fsolve(lambda t: 1.0 - ca_func(t), tguess)
3 print tsol
4
5 # you might prefer an explicit function
6 def func(t):
7 return 1.0 - ca_func(t)
8
9 tsol2, = fsolve(func, tguess)
10 print tsol2

>>> 2.4574668235
>>> ... ... >>> 2.4574668235

160
 That is it. Interpolation can provide a simple way to evaluate the numerical
solution of an ODE at other values.
For completeness we examine a final way to construct the function. We can
actually integrate the ODE in the function to evaluate the solution at the point
of interest. If it is not computationally expensive to evaluate the ODE solution
this works fine. Note, however, that the ODE will get integrated from 0 to the
value t for each iteration of fsolve.

1 def func(t):
2 tspan = [0, t]
3 sol = odeint(dCadt, Ca0, tspan)
4 return 1.0 - sol[-1]
5
6 tsol3, = fsolve(func, tguess)
7 print tsol3

... ... ... >>> >>> 2.45746688202

10.1.7 A simple first order ode evaluated at specific points

Matlab post
We have integrated an ODE over a specific time span. Sometimes it is
desirable to get the solution at specific points, e.g. at t = [0 0.2 0.4 0.8]; This
could be desirable to compare with experimental measurements at those time
points. This example demonstrates how to do that.
dy
= y(t)
dt
The initial condition is y(0) = 1.

1 from scipy.integrate import odeint

2
3 y0 = 1
4 tspan = [0, 0.2, 0.4, 0.8]
5
6 def dydt(y, t):
7 return y
8
9 Y = odeint(dydt, y0, tspan)
10 print Y[:,0]

[ 1. 1.22140275 1.49182469 2.22554103]

10.1.8 Stopping the integration of an ODE at some condition

Matlab post In Post 968 we learned how to get the numerical solution to an
ODE, and then to use the deval function to solve the solution for a particular
value. The deval function uses interpolation to evaluate the solution at other
valuse. An alternative approach would be to stop the ODE integration when
the solution has the value you want. That can be done in Matlab by using an

161
 "event" function. You setup an event function and tell the ode solver to use it
by setting an option.
Given that the concentration of a species A in a constant volume, batch
dt = −kCA with the initial condition
reactor obeys this differential equation dC A 2

CA (t = 0) = 2.3 mol/L and k = 0.23 L/mol/s, compute the time it takes for
CA to be reduced to 1 mol/L.

1 from pycse import *

2 import numpy as np
3
4 k = 0.23
5 Ca0 = 2.3
6
7 def dCadt(Ca, t):
8 return -k * Ca**2
9
10 def stop(Ca, t):
11 isterminal = True
12 direction = 0
13 value = 1.0 - Ca
14 return value, isterminal, direction
15
16 tspan = np.linspace(0.0, 10.0)
17
18 t, CA, TE, YE, IE = odelay(dCadt, Ca0, tspan, events=[stop], full_output=1)
19
20 print ’At t = {0:1.2f} seconds the concentration of A is {1:1.2f} mol/L.’.format(t[-1], CA[-1])

At t = 2.46 seconds the concentration of A is 1.00 mol/L.

10.1.9 Finding minima and maxima in ODE solutions with events

Matlab post Today we look at another way to use events in an ode solver. We
use an events function to find minima and maxima, by evaluating the ODE
in the event function to find conditions where the first derivative is zero, and
approached from the right direction. A maximum is when the fisrt derivative
is zero and increasing, and a minimum is when the first derivative is zero and
decreasing.
We use a simple ODE, y 0 = sin(x) ∗ e−0.05x , which has minima and maxima.

1 from pycse import *

2 import numpy as np
3
4 def ode(y, x):
5 return np.sin(x) * np.exp(-0.05 * x)
6
7 def minima(y, x):
8 ’’’Approaching a minumum, dydx is negatime and going to zero. our event function is increasing’’’
9 value = ode(y, x)
10 direction = 1
11 isterminal = False
12 return value, isterminal, direction
13
14 def maxima(y, x):
15 ’’’Approaching a maximum, dydx is positive and going to zero. our event function is decreasing’’’
16 value = ode(y, x)
17 direction = -1
18 isterminal = False

162
19 return value, isterminal, direction
20
21 xspan = np.linspace(0, 20, 100)
22
23 y0 = 0
24
25 X, Y, XE, YE, IE = odelay(ode, y0, xspan, events=[minima, maxima])
26 print IE
27 import matplotlib.pyplot as plt
28 plt.plot(X, Y)
29
30 # blue is maximum, red is minimum
31 colors = ’rb’
32 for xe, ye, ie in zip(XE, YE, IE):
33 plt.plot([xe], [ye], ’o’, color=colors[ie])
34
35 plt.savefig(’./images/ode-events-min-max.png’)
36 plt.show()

[1, 0, 1, 0, 1, 0]

10.1.10 Error tolerance in numerical solutions to ODEs

Matlab post Usually, the numerical ODE solvers in python work well with the
standard settings. Sometimes they do not, and it is not always obvious they
have not worked! Part of using a tool like python is checking how well your
solution really worked. We use an example of integrating an ODE that defines
the van der Waal equation of an ideal gas here.
we plot the analytical solution to the van der waal equation in reduced form
here.

163
1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 Tr = 0.9
5 Vr = np.linspace(0.34,4,1000)
6
7 #analytical equation for Pr
8 Prfh = lambda Vr: 8.0 / 3.0 * Tr / (Vr - 1.0 / 3.0) - 3.0 / (Vr**2)
9 Pr = Prfh(Vr) # evaluated on our reduced volume vector.
10
11 # Plot the EOS
12 plt.plot(Vr,Pr)
13 plt.ylim([0, 2])
14 plt.xlabel(’$V_R$’)
15 plt.ylabel(’$P_R$’)
16 plt.savefig(’images/ode-vw-1.png’)
17 plt.show()

>>> >>> >>> >>> >>> ... >>> >>> >>> ... [<matplotlib.lines.Line2D object at 0x1c5a3550>]
(0, 2)
<matplotlib.text.Text object at 0x1c22f750>
<matplotlib.text.Text object at 0x1d4e0750>

we want an equation for dPdV, which we will integrate we use symbolic

math to do the derivative for us.

1 from sympy import diff, Symbol

2 Vrs = Symbol(’Vrs’)
3
4 Prs = 8.0 / 3.0 * Tr / (Vrs - 1.0/3.0) - 3.0/(Vrs**2)
5 print diff(Prs,Vrs)

164
 >>> -2.4/(Vrs - 0.333333333333333)**2 + 6.0/Vrs**3

Now, we solve the ODE. We will specify a large relative tolerance criteria
(Note the default is much smaller than what we show here).

1 from scipy.integrate import odeint

2
3 def myode(Pr, Vr):
4 dPrdVr = -2.4/(Vr - 0.333333333333333)**2 + 6.0/Vr**3
5 return dPrdVr
6
7 Vspan = np.linspace(0.334, 4)
8 Po = Prfh(Vspan[0])
9 P = odeint(myode, Po, Vspan, rtol=1e-4)
10
11 # Plot the EOS
12 plt.plot(Vr,Pr) # analytical solution
13 plt.plot(Vspan, P[:,0], ’r.’)
14 plt.ylim([0, 2])
15 plt.xlabel(’$V_R$’)
16 plt.ylabel(’$P_R$’)
17 plt.savefig(’images/ode-vw-2.png’)
18 plt.show()

... >>> >>> >>> >>> ... [<matplotlib.lines.Line2D object at 0x1d4f3b90>]

[<matplotlib.lines.Line2D object at 0x2ac47518e710>]
(0, 2)
<matplotlib.text.Text object at 0x1c238fd0>
<matplotlib.text.Text object at 0x1c22af10>

165
 You can see there is disagreement between the analytical solution and nu-
merical solution. The origin of this problem is accuracy at the initial condition,
where the derivative is extremely large.

1 print myode(Po, 0.34)

-53847.3437818
We can increase the tolerance criteria to get a better answer. The defaults
in odeint are actually set to 1.49012e-8.

1 Vspan = np.linspace(0.334, 4)
2 Po = Prfh(Vspan[0])
3 P = odeint(myode, Po, Vspan)
4
5 # Plot the EOS
6 plt.plot(Vr,Pr) # analytical solution
7 plt.plot(Vspan, P[:,0], ’r.’)
8 plt.ylim([0, 2])
9 plt.xlabel(’$V_R$’)
10 plt.ylabel(’$P_R$’)
11 plt.savefig(’images/ode-vw-3.png’)
12 plt.show()

>>> ... [<matplotlib.lines.Line2D object at 0x1d4dbf10>]

[<matplotlib.lines.Line2D object at 0x1c6e5550>]
(0, 2)
<matplotlib.text.Text object at 0x1d4e31d0>
<matplotlib.text.Text object at 0x1d9d3710>

166
 The problem here was the derivative value varied by four orders of magni-
tude over the integration range, so the default tolerances were insufficient to
accurately estimate the numerical derivatives over that range. Tightening the
tolerances helped resolve that problem. Another approach might be to split the
integration up into different regions. For instance, if instead of starting at Vr
= 0.34, which is very close to a sigularity in the van der waal equation at Vr =
1/3, if you start at Vr = 0.5, the solution integrates just fine with the standard
tolerances.

10.1.11 Solving parameterized ODEs over and over conveniently

Matlab post Sometimes we have an ODE that depends on a parameter, and we
want to solve the ODE for several parameter values. It is inconvenient to write
an ode function for each parameter case. Here we examine a convenient way to
solve this problem; we pass the parameter to the ODE at runtime. We consider
the following ODE:
dCa
= −kCa(t)
dt
where k is a parameter, and we want to solve the equation for a couple of
values of k to test the sensitivity of the solution on the parameter. Our question
is, given Ca(t = 0) = 2, how long does it take to get Ca = 1, and how sensitive
is the answer to small variations in k?

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 def myode(Ca, t, k):
6 ’ODE definition’
7 dCadt = -k * Ca
8 return dCadt
9
10 tspan = np.linspace(0, 0.5)
11 k0 = 2
12 Ca0 = 2
13
14 plt.figure(); plt.clf()
15
16 for k in [0.95 * k0, k0, 1.05 * k0]:
17 sol = odeint(myode, Ca0, tspan, args=(k,))
18 plt.plot(tspan, sol, label=’k={0:1.2f}’.format(k))
19 print ’At t=0.5 Ca = {0:1.2f} mol/L’.format(sol[-1][0])
20
21 plt.legend(loc=’best’)
22 plt.xlabel(’Time’)
23 plt.ylabel(’$C_A$ (mol/L)’)
24 plt.savefig(’images/parameterized-ode1.png’)

At t=0.5 Ca = 0.77 mol/L

At t=0.5 Ca = 0.74 mol/L
At t=0.5 Ca = 0.70 mol/L

167
 You can see there are some variations in the concentration at t = 0.5. You
could over or underestimate the concentration if you have the wrong estimate
of $k$! You have to use some judgement here to decide how long to run the
reaction to ensure a target goal is met.

10.1.12 Yet another way to parameterize an ODE

Matlab post We previously examined a way to parameterize an ODE. In those
methods, we either used an anonymous function to parameterize an ode func-
tion, or we used a nested function that used variables from the shared workspace.
We want a convenient way to solve dCa/dt = −kCa for multiple values
of k. Here we use a trick to pass a parameter to an ODE through the initial
conditions. We expand the ode function definition to include this parameter,
and set its derivative to zero, effectively making it a constant.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 def ode(F, t):
6 Ca, k = F
7 dCadt = -k * Ca
8 dkdt = 0.0
9 return [dCadt, dkdt]
10
11 tspan = np.linspace(0, 4)
12
13 Ca0 = 1;
14 K = [2.0, 3.0]
15 for k in K:
16 F = odeint(ode, [Ca0, k], tspan)
17 Ca = F[:,0]

168
18 plt.plot(tspan, Ca, label=’k={0}’.format(k))
19 plt.xlabel(’time’)
20 plt.ylabel(’$C_A$’)
21 plt.legend(loc=’best’)
22 plt.savefig(’images/ode-parameterized-1.png’)
23 plt.show()

I do not think this is a very elegant way to pass parameters around compared
to the previous methods, but it nicely illustrates that there is more than one
way to do it. And who knows, maybe it will be useful in some other context
one day!

10.1.13 Another way to parameterize an ODE - nested function

Matlab post We saw one method to parameterize an ODE, by creating an ode
function that takes an extra parameter argument, and then making a function
handle that has the syntax required for the solver, and passes the parameter
the ode function.
Here we define the ODE function in a loop. Since the nested function is in
the namespace of the main function, it can "see" the values of the variables in
the main function. We will use this method to look at the solution to the van
der Pol equation for several different values of mu.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 MU = [0.1, 1, 2, 5]
6 tspan = np.linspace(0, 100, 5000)
7 Y0 = [0, 3]

169
8
9 for mu in MU:
10 # define the ODE
11 def vdpol(Y, t):
12 x,y = Y
13 dxdt = y
14 dydt = -x + mu * (1 - x**2) * y
15 return [dxdt, dydt]
16
17 Y = odeint(vdpol, Y0, tspan)
18
19 x = Y[:,0]; y = Y[:,1]
20 plt.plot(x, y, label=’mu={0:1.2f}’.format(mu))
21
22 plt.axis(’equal’)
23 plt.legend(loc=’best’)
24 plt.savefig(’images/ode-nested-parameterization.png’)
25 plt.savefig(’images/ode-nested-parameterization.svg’)
26 plt.show()

You can see the solution changes dramatically for different values of mu.
The point here is not to understand why, but to show an easy way to study a
parameterize ode with a nested function. Nested functions can be a great way to
"share" variables between functions especially for ODE solving, and nonlinear
algebra solving, or any other application where you need a lot of parameters
defined in one function in another function.

10.1.14 Solving a second order ode

Matlab post
The odesolvers in scipy can only solve first order ODEs, or systems of first
order ODES. To solve a second order ODE, we must convert it by changes of

170
 variables to a system of first order ODES. We consider the Van der Pol oscillator
here:

d2 x dx
2
− µ(1 − x2 ) +x=0
dt dt
µ is a constant. If we let y = x − x3 /3 http://en.wikipedia.org/wiki/
Van_der_Pol_oscillator, then we arrive at this set of equations:
dx
= µ(x − 1/3x3 − y)
dt
dy
= µ/x
dt
here is how we solve this set of equations. Let µ = 1.

1 from scipy.integrate import odeint

2 import numpy as np
3
4 mu = 1.0
5
6 def vanderpol(X, t):
7 x = X[0]
8 y = X[1]
9 dxdt = mu * (x - 1./3.*x**3 - y)
10 dydt = x / mu
11 return [dxdt, dydt]
12
13 X0 = [1, 2]
14 t = np.linspace(0, 40, 250)
15
16 sol = odeint(vanderpol, X0, t)
17
18 import matplotlib.pyplot as plt
19 x = sol[:, 0]
20 y = sol[:, 1]
21
22 plt.plot(t,x, t, y)
23 plt.xlabel(’t’)
24 plt.legend((’x’, ’y’))
25 plt.savefig(’images/vanderpol-1.png’)
26
27 # phase portrait
28 plt.figure()
29 plt.plot(x,y)
30 plt.plot(x[0], y[0], ’ro’)
31 plt.xlabel(’x’)
32 plt.ylabel(’y’)
33 plt.savefig(’images/vanderpol-2.png’)

171
 Here is the phase portrait. You can see that a limit cycle is approached,
indicating periodicity in the solution.

10.1.15 Solving Bessel’s Equation numerically

Matlab post
Reference Ch 5.5 Kreysig, Advanced Engineering Mathematics, 9th ed.

172
 Bessel’s equation x2 y 00 + xy 0 + (x2 − ν 2 )y = 0 comes up often in engineering
problems such as heat transfer. The solutions to this equation are the Bessel
functions. To solve this equation numerically, we must convert it to a system of
first order ODEs. This can be done by letting z = y 0 and z 0 = y 00 and performing
the change of variables:

y0 = z

1
z0 =
(−xz − (x2 − ν 2 )y
x2
if we take the case where ν = 0, the solution is known to be the Bessel func-
tion J0 (x), which is represented in Matlab as besselj(0,x). The initial conditions
for this problem are: y(0) = 1 and y 0 (0) = 0.
There is a problem with our system of ODEs at x=0. Because of the 1/x2
term, the ODEs are not defined at x=0. If we start very close to zero instead,
we avoid the problem.

1 import numpy as np
2 from scipy.integrate import odeint
3 from scipy.special import jn # bessel function
4 import matplotlib.pyplot as plt
5
6 def fbessel(Y, x):
7 nu = 0.0
8 y = Y[0]
9 z = Y[1]
10
11 dydx = z
12 dzdx = 1.0 / x**2 * (-x * z - (x**2 - nu**2) * y)
13 return [dydx, dzdx]
14
15 x0 = 1e-15
16 y0 = 1
17 z0 = 0
18 Y0 = [y0, z0]
19
20 xspan = np.linspace(1e-15, 10)
21 sol = odeint(fbessel, Y0, xspan)
22
23 plt.plot(xspan, sol[:,0], label=’numerical soln’)
24 plt.plot(xspan, jn(0, xspan), ’r--’, label=’Bessel’)
25 plt.legend()
26 plt.savefig(’images/bessel.png’)

173
 You can see the numerical and analytical solutions overlap, indicating they
are at least visually the same.

10.1.16 Phase portraits of a system of ODEs

Matlab post An undamped pendulum with no driving force is described by

y 00 + sin(y) = 0
We reduce this to standard matlab form of a system of first order ODEs by
letting y1 = y and y2 = y10 . This leads to:
y10 = y2
y20 = −sin(y1 )
The phase portrait is a plot of a vector field which qualitatively shows how
the solutions to these equations will go from a given starting point. here is our
definition of the differential equations:
To generate the phase portrait, we need to compute the derivatives y10 and
y2 at t = 0 on a grid over the range of values for y1 and y2 we are interested in.
0

We will plot the derivatives as a vector at each (y1, y2) which will show us the
initial direction from each point. We will examine the solutions over the range
-2 < y1 < 8, and -2 < y2 < 2 for y2, and create a grid of 20 x 20 points.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 def f(Y, t):
5 y1, y2 = Y
6 return [y2, -np.sin(y1)]
7

174
8 y1 = np.linspace(-2.0, 8.0, 20)
9 y2 = np.linspace(-2.0, 2.0, 20)
10
11 Y1, Y2 = np.meshgrid(y1, y2)
12
13 t = 0
14
15 u, v = np.zeros(Y1.shape), np.zeros(Y2.shape)
16
17 NI, NJ = Y1.shape
18
19 for i in range(NI):
20 for j in range(NJ):
21 x = Y1[i, j]
22 y = Y2[i, j]
23 yprime = f([x, y], t)
24 u[i,j] = yprime[0]
25 v[i,j] = yprime[1]
26
27
28 Q = plt.quiver(Y1, Y2, u, v, color=’r’)
29
30 plt.xlabel(’$y_1$’)
31 plt.ylabel(’$y_2$’)
32 plt.xlim([-2, 8])
33 plt.ylim([-4, 4])
34 plt.savefig(’images/phase-portrait.png’)

>>> >>> ... ... ... >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ... ... ... ... ... ...
<matplotlib.text.Text object at 0x00000000075CACF8>
(-2, 8)
(-4, 4)

Let us plot a few solutions on the vector field. We will consider the solutions

175
 where y1(0)=0, and values of y2(0) = [0 0.5 1 1.5 2 2.5], in otherwords we start
the pendulum at an angle of zero, with some angular velocity.

1 from scipy.integrate import odeint

2
3 for y20 in [0, 0.5, 1, 1.5, 2, 2.5]:
4 tspan = np.linspace(0, 50, 200)
5 y0 = [0.0, y20]
6 ys = odeint(f, y0, tspan)
7 plt.plot(ys[:,0], ys[:,1], ’b-’) # path
8 plt.plot([ys[0,0]], [ys[0,1]], ’o’) # start
9 plt.plot([ys[-1,0]], [ys[-1,1]], ’s’) # end
10
11
12 plt.xlim([-2, 8])
13 plt.savefig(’images/phase-portrait-2.png’)
14 plt.savefig(’images/phase-portrait-2.svg’)
15 plt.show()

>>> ... ... ... [<matplotlib.lines.Line2D object at 0xbc0dbd0>]

[<matplotlib.lines.Line2D object at 0xc135050>]
[<matplotlib.lines.Line2D object at 0xbd1a450>]
[<matplotlib.lines.Line2D object at 0xbd1a1d0>]
[<matplotlib.lines.Line2D object at 0xb88aa10>]
[<matplotlib.lines.Line2D object at 0xb88a5d0>]
[<matplotlib.lines.Line2D object at 0xc14e410>]
[<matplotlib.lines.Line2D object at 0xc14ed90>]
[<matplotlib.lines.Line2D object at 0xc2c5290>]
[<matplotlib.lines.Line2D object at 0xbea4bd0>]
[<matplotlib.lines.Line2D object at 0xbea4d50>]
[<matplotlib.lines.Line2D object at 0xbc401d0>]
[<matplotlib.lines.Line2D object at 0xc2d1190>]
[<matplotlib.lines.Line2D object at 0xc2f3e90>]
[<matplotlib.lines.Line2D object at 0xc2f3bd0>]
[<matplotlib.lines.Line2D object at 0xc2e4790>]
[<matplotlib.lines.Line2D object at 0xc2e0a90>]
[<matplotlib.lines.Line2D object at 0xc2c7390>]
(-2, 8)

176
 What do these figures mean? For starting points near the origin, and small
velocities, the pendulum goes into a stable limit cycle. For others, the trajectory
appears to fly off into y1 space. Recall that y1 is an angle that has values from
−π to π. The y1 data in this case is not wrapped around to be in this range.

10.1.17 Linear algebra approaches to solving systems of constant

coefficient ODEs
Matlab post Today we consider how to solve a system of first order, constant
coefficient ordinary differential equations using linear algebra. These equations
could be solved numerically, but in this case there are analytical solutions that
can be derived. The equations we will solve are:
y10 = −0.02y1 + 0.02y2
y20 = 0.02y1 − 0.02y2  0 
y1
We can express this set of equations in matrix form as: =
y20
  
−0.02 0.02 y1
0.02 −0.02 y2
The
 general
 solution to this setof equations
 is   
y1   c1 0 λ1 0 t
= v1 v2 exp
y2 0 c2 0 λ2 t
 
λ1 0
where is a diagonal matrix of the eigenvalues of the constant
0 λ2
coefficient matrix, v1 v2 is a matrix of eigenvectorswhere the ith column
 

c1 0
corresponds to the eigenvector of the ith eigenvalue, and is a matrix
0 c2

177
 determined by the initial conditions.
In this example, we evaluate the solution using linear algebra. The initial
conditions we will consider are y1 (0) = 0 and y2 (0) = 150.

1 import numpy as np
2
3 A = np.array([[-0.02, 0.02],
4 [ 0.02, -0.02]])
5
6 # Return the eigenvalues and eigenvectors of a Hermitian or symmetric matrix.
7 evals, evecs = np.linalg.eigh(A)
8 print evals
9 print evecs

>>> ... >>> >>> ... >>> [-0.04 0. ]

[[ 0.70710678 0.70710678]
[-0.70710678 0.70710678]]

The eigenvectors are the columns of evecs.

Compute the c matrix
V*c = Y0

1 Y0 = [0, 150]
2
3 c = np.diag(np.linalg.solve(evecs, Y0))
4 print c

>>> >>> [[-106.06601718 0. ]

[ 0. 106.06601718]]

Constructing the solution

We will create a vector of time values, and stack them for each solution,
y1 (t) and Y2 (t).

1 import matplotlib.pyplot as plt

2
3 t = np.linspace(0, 100)
4 T = np.row_stack([t, t])
5
6 D = np.diag(evals)
7
8 # y = V*c*exp(D*T);
9 y = np.dot(np.dot(evecs, c), np.exp(np.dot(D, T)))
10
11 # y has a shape of (2, 50) so we have to transpose it
12 plt.plot(t, y.T)
13 plt.xlabel(’t’)
14 plt.ylabel(’y’)
15 plt.legend([’$y_1$’, ’$y_2$’])
16 plt.savefig(’images/ode-la.png’)
17 plt.show()

178
>>> >>> >>> >>> ... >>> >>> ... [<matplotlib.lines.Line2D object at 0x1d4db950>, <matplotlib
<matplotlib.text.Text object at 0x1d35fbd0>
<matplotlib.text.Text object at 0x1c222390>
<matplotlib.legend.Legend object at 0x1d34ee90>

10.2 Delay Differential Equations

In Matlab you can solve Delay Differential equations (DDE) (Matlab post). I
do not know of a solver in scipy at this time that can do this.

10.3 Differential algebraic systems of equations

There is not a builtin solver for DAE systems in scipy. It looks like pysundials
may do it, but it must be compiled and installed.

10.4 Boundary value equations

I am unaware of dedicated BVP solvers in scipy. In the following examples we
implement some approaches to solving certain types of linear BVPs.

10.4.1 Plane Poiseuille flow - BVP solve by shooting method

Matlab post
One approach to solving BVPs is to use the shooting method. The reason
we cannot use an initial value solver for a BVP is that there is not enough

179
 information at the initial value to start. In the shooting method, we take the
function value at the initial point, and guess what the function derivatives are
so that we can do an integration. If our guess was good, then the solution will
go through the known second boundary point. If not, we guess again, until we
get the answer we need. In this example we repeat the pressure driven flow
example, but illustrate the shooting method.
In the pressure driven flow of a fluid with viscosity µ between two stationary
plates separated by distance d and driven by a pressure drop ∆P/∆x, the
governing equations on the velocity u of the fluid are (assuming flow in the
x-direction with the velocity varying only in the y-direction):

∆P d2 u
=µ 2
∆x dy
with boundary conditions u(y = 0) = 0 and u(y = d) = 0, i.e. the no-slip
condition at the edges of the plate.
we convert this second order BVP to a system of ODEs by letting u1 = u,
u2 = u01 and then u02 = u001 . This leads to:
du1
dy = u2
du2 1 ∆P
dy = µ ∆x
with boundary conditions u1 (y = 0) = 0 and u1 (y = d) = 0.
for this problem we let the plate separation be d=0.1, the viscosity µ = 1,
and ∆P
∆x = −100.

First guess We need u_1(0) and u_2(0), but we only have u_1(0). We need
to guess a value for u_2(0) and see if the solution goes through the u_2(d)=0
boundary value.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 d = 0.1 # plate thickness
6
7 def odefun(U, y):
8 u1, u2 = U
9 mu = 1
10 Pdrop = -100
11 du1dy = u2
12 du2dy = 1.0 / mu * Pdrop
13 return [du1dy, du2dy]
14
15 u1_0 = 0 # known
16 u2_0 = 1 # guessed
17
18 dspan = np.linspace(0, d)
19
20 U = odeint(odefun, [u1_0, u2_0], dspan)
21
22 plt.plot(dspan, U[:,0])
23 plt.plot([d],[0], ’ro’)
24 plt.xlabel(’d’)
25 plt.ylabel(’$u_1$’)
26 plt.savefig(’images/bvp-shooting-1.png’)

180
 Here we have undershot the boundary condition. Let us try a larger guess.

Second guess

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 d = 0.1 # plate thickness
6
7 def odefun(U, y):
8 u1, u2 = U
9 mu = 1
10 Pdrop = -100
11 du1dy = u2
12 du2dy = 1.0 / mu * Pdrop
13 return [du1dy, du2dy]
14
15 u1_0 = 0 # known
16 u2_0 = 10 # guessed
17
18 dspan = np.linspace(0, d)
19
20 U = odeint(odefun, [u1_0, u2_0], dspan)
21
22 plt.plot(dspan, U[:,0])
23 plt.plot([d],[0], ’ro’)
24 plt.xlabel(’d’)
25 plt.ylabel(’$u_1$’)
26 plt.savefig(’images/bvp-shooting-2.png’)

181
 Now we have clearly overshot. Let us now make a function that will iterate
for us to find the right value.

Let fsolve do the work

1 import numpy as np
2 from scipy.integrate import odeint
3 from scipy.optimize import fsolve
4 import matplotlib.pyplot as plt
5
6 d = 0.1 # plate thickness
7 Pdrop = -100
8 mu = 1
9
10 def odefun(U, y):
11 u1, u2 = U
12 du1dy = u2
13 du2dy = 1.0 / mu * Pdrop
14 return [du1dy, du2dy]
15
16 u1_0 = 0 # known
17 dspan = np.linspace(0, d)
18
19 def objective(u2_0):
20 dspan = np.linspace(0, d)
21 U = odeint(odefun, [u1_0, u2_0], dspan)
22 u1 = U[:,0]
23 return u1[-1]
24
25 u2_0, = fsolve(objective, 1.0)
26
27 # now solve with optimal u2_0
28 U = odeint(odefun, [u1_0, u2_0], dspan)
29
30 plt.plot(dspan, U[:,0], label=’Numerical solution’)
31 plt.plot([d],[0], ’ro’)

182
32
33 # plot an analytical solution
34 u = -(Pdrop) * d**2 / 2 / mu * (dspan / d - (dspan / d)**2)
35 plt.plot(dspan, u, ’r--’, label=’Analytical solution’)
36
37
38 plt.xlabel(’d’)
39 plt.ylabel(’$u_1$’)
40 plt.legend(loc=’best’)
41 plt.savefig(’images/bvp-shooting-3.png’)

You can see the agreement is excellent!

This also seems like a useful bit of code to not have to reinvent regularly, so
it has been added to pycse as BVP_sh. Here is an example usage.

1 from pycse import BVP_sh

2 import matplotlib.pyplot as plt
3
4 d = 0.1 # plate thickness
5 Pdrop = -100
6 mu = 1
7
8 def odefun(U, y):
9 u1, u2 = U
10 du1dy = u2
11 du2dy = 1.0 / mu * Pdrop
12 return [du1dy, du2dy]
13
14 x1 = 0.0; alpha = 0.0
15 x2 = 0.1; beta = 0.0
16 init = 2.0 # initial guess of slope at x=0
17
18 X,Y = BVP_sh(odefun, x1, x2, alpha, beta, init)
19 plt.plot(X, Y[:,0])
20 plt.ylim([0, 0.14])
21

183
22 # plot an analytical solution
23 u = -(Pdrop) * d**2 / 2 / mu * (X / d - (X / d)**2)
24 plt.plot(X, u, ’r--’, label=’Analytical solution’)
25 plt.savefig(’images/bvp-shooting-4.png’)
26 plt.show()

10.4.2 Plane poiseuelle flow solved by finite difference

Matlab post
Adapted from http://www.physics.arizona.edu/~restrepo/475B/Notes/
sourcehtml/node24.html
We want to solve a linear boundary value problem of the form: y” = p(x)y’
+ q(x)y + r(x) with boundary conditions y(x1) = alpha and y(x2) = beta.
For this example, we solve the plane poiseuille flow problem using a finite
difference approach. An advantage of the approach we use here is we do not
have to rewrite the second order ODE as a set of coupled first order ODEs,
nor do we have to provide guesses for the solution. We do, however, have to
discretize the derivatives and formulate a linear algebra problem.
we want to solve u” = 1/mu*DPDX with u(0)=0 and u(0.1)=0. for this
problem we let the plate separation be d=0.1, the viscosity µ = 1, and ∆P ∆x =
−100.
The idea behind the finite difference method is to approximate the deriva-
tives by finite differences on a grid. See here for details. By discretizing the
ODE, we arrive at a set of linear algebra equations of the form Ay = b, where
A and b are defined as follows.

184
 2 + h2 q1 −1 + h2 p1
 
0 0 0
 −1 − h p2 2 + h2 q2 −1 + h2 p2 0 0 
2
.. .. ..
 
A= . . .
 
 0 0 

 0 0 −1 − h2 pN −1 2 + h2 qN −1 −1 + h2 pN −1 
0 0 0 −1 − h2 pN 2 + h2 qN

 
yi
y =  ... 
 

yN

−h2 r1 + (1 + h2 p1 )α
 
 −h2 r2 
..
 
b= .
 

 
 −h2 rN −1 
−h rN + (1 − h2 pN )β
2

1 import numpy as np
2
3 # we use the notation for y’’ = p(x)y’ + q(x)y + r(x)
4 def p(x): return 0
5 def q(x): return 0
6 def r(x): return -100
7
8 #we use the notation y(x1) = alpha and y(x2) = beta
9
10 x1 = 0; alpha = 0.0
11 x2 = 0.1; beta = 0.0
12
13 npoints = 100
14
15 # compute interval width
16 h = (x2-x1)/npoints;
17
18 # preallocate and shape the b vector and A-matrix
19 b = np.zeros((npoints - 1, 1));
20 A = np.zeros((npoints - 1, npoints - 1));
21 X = np.zeros((npoints - 1, 1));
22
23 #now we populate the A-matrix and b vector elements
24 for i in range(npoints - 1):
25 X[i,0] = x1 + (i + 1) * h
26
27 # get the value of the BVP Odes at this x
28 pi = p(X[i])
29 qi = q(X[i])
30 ri = r(X[i])
31
32 if i == 0:
33 # first boundary condition
34 b[i] = -h**2 * ri + (1 + h / 2 * pi)*alpha;
35 elif i == npoints - 1:
36 # second boundary condition
37 b[i] = -h**2 * ri + (1 - h / 2 * pi)*beta;
38 else:

185
39 b[i] = -h**2 * ri # intermediate points
40
41 for j in range(npoints - 1):
42 if j == i: # the diagonal
43 A[i,j] = 2 + h**2 * qi
44 elif j == i - 1: # left of the diagonal
45 A[i,j] = -1 - h / 2 * pi
46 elif j == i + 1: # right of the diagonal
47 A[i,j] = -1 + h / 2 * pi
48 else:
49 A[i,j] = 0 # off the tri-diagonal
50
51 # solve the equations A*y = b for Y
52 Y = np.linalg.solve(A,b)
53
54 x = np.hstack([x1, X[:,0], x2])
55 y = np.hstack([alpha, Y[:,0], beta])
56
57 import matplotlib.pyplot as plt
58
59 plt.plot(x, y)
60
61 mu = 1
62 d = 0.1
63 x = np.linspace(0,0.1);
64 Pdrop = -100 # this is DeltaP/Deltax
65 u = -(Pdrop) * d**2 / 2.0 / mu * (x / d - (x / d)**2)
66 plt.plot(x,u,’r--’)
67
68 plt.xlabel(’distance between plates’)
69 plt.ylabel(’fluid velocity’)
70 plt.legend((’finite difference’, ’analytical soln’))
71 plt.savefig(’images/pp-bvp-fd.png’)
72 plt.show()

You can see excellent agreement here between the numerical and analytical
solution.

186
 10.4.3 Boundary value problem in heat conduction
Matlab post
For steady state heat conduction the temperature distribution in one-
dimension is governed by the Laplace equation:

∇2 T = 0
with boundary conditions that at T (x = a) = TA and T (x = L) = TB .
The analytical solution is not difficult here: T = TA − TA −T
L
B
x, but we will
solve this by finite differences.
For this problem, lets consider a slab that is defined by x=0 to x=L, with
T (x = 0) = 100, and T (x = L) = 200. We want to find the function T(x) inside
the slab.
We approximate the second derivative by finite differences as
f 00 (x) ≈ f (x−h)−2fh(x)+f
2
(x+h)

Since the second derivative in this case is equal to zero, we have at each
discretized node 0 = Ti−1 − 2Ti + Ti+1 . We know the values of Tx=0 = α and
Tx=L = β.
 
−2 1 0 0 0
 1 −2 1 0 0 
.. .. ..
 
A= 0 . . .
 
 0 

 0 0 1 −2 1 
0 0 0 1 −2

 
T1
x =  ... 
 

TN

 
−T (x = 0)
 0 
..
 
b= .
 

 
 0 
−T (x = L)

These are linear equations in the unknowns x that we can easily solve. Here,
we evaluate the solution.

1 import numpy as np
2
3 #we use the notation T(x1) = alpha and T(x2) = beta
4 x1 = 0; alpha = 100
5 x2 = 5; beta = 200
6
7 npoints = 100

187
8
9 # preallocate and shape the b vector and A-matrix
10 b = np.zeros((npoints, 1));
11 b[0] = -alpha
12 b[-1] = -beta
13
14 A = np.zeros((npoints, npoints));
15
16 #now we populate the A-matrix and b vector elements
17 for i in range(npoints ):
18 for j in range(npoints):
19 if j == i: # the diagonal
20 A[i,j] = -2
21 elif j == i - 1: # left of the diagonal
22 A[i,j] = 1
23 elif j == i + 1: # right of the diagonal
24 A[i,j] = 1
25
26 # solve the equations A*y = b for Y
27 Y = np.linalg.solve(A,b)
28
29 x = np.linspace(x1, x2, npoints + 2)
30 y = np.hstack([alpha, Y[:,0], beta])
31
32 import matplotlib.pyplot as plt
33
34 plt.plot(x, y)
35
36 plt.plot(x, alpha + (beta - alpha)/(x2 - x1) * x, ’r--’)
37
38 plt.xlabel(’X’)
39 plt.ylabel(’T(X)’)
40 plt.legend((’finite difference’, ’analytical soln’), loc=’best’)
41 plt.savefig(’images/bvp-heat-conduction-1d.png’)

188
 10.4.4 BVP in pycse
I thought it was worthwhile coding a BVP solver into pycse. This function
(bvp_L0) solves y 00 (x)+p(x)y 0 (x)+q(x)y(x) = r(x) with constant value bound-
ary conditions y(x0 ) = α and y(xL ) = β.
Fluids example for Plane poiseuelle flow (y 00 (x) = constant, y(0) = 0 and
y(L) = 0:

1 from pycse import bvp_L0

2
3 # we use the notation for y’’ = p(x)y’ + q(x)y + r(x)
4 def p(x): return 0
5 def q(x): return 0
6 def r(x): return -100
7
8 #we use the notation y(x1) = alpha and y(x2) = beta
9
10 x1 = 0; alpha = 0.0
11 x2 = 0.1; beta = 0.0
12
13 npoints = 100
14
15 x, y = bvp_L0(p, q, r, x1, x2, alpha, beta, npoints=100)
16 print len(x)
17
18 import matplotlib.pyplot as plt
19 plt.plot(x, y)
20 plt.show()

100

Heat transfer example y 00 (x) = 0, y(0) = 100 and y(L) = 200.

1 from pycse import bvp_L0

2
3 # we use the notation for y’’ = p(x)y’ + q(x)y + r(x)
4 def p(x): return 0
5 def q(x): return 0
6 def r(x): return 0
7
8 #we use the notation y(x1) = alpha and y(x2) = beta
9
10 x1 = 0; alpha = 100
11 x2 = 1; beta = 200
12
13 npoints = 100
14
15 x, y = bvp_L0(p, q, r, x1, x2, alpha, beta, npoints=100)
16 print len(x)
17
18 import matplotlib.pyplot as plt
19 plt.plot(x, y)
20 plt.xlabel(’X’)
21 plt.ylabel(’T’)
22 plt.show()

100

189
 10.4.5 A nonlinear BVP
Adapted from Example 8.7 in Numerical Methods in Engineering with Python
by Jaan Kiusalaas.
We want to solve y 00 (x) = −3y(x)y 0 (x) with $y(0) = 0 and y(2) = 1 us-
ing a finite difference method. We discretize the region and approximate the
derivatives as:
y 00 (x) ≈ yi−1 −2y
h2
i +yi+1

0 yi+1 −yi−1
y (x) ≈ 2h
We define a function y 00 (x) = F (x, y, y 0 ). At each node in our discretized
region, we will have an equation that looks like y 00 (x) − F (x, y, y 0 ) = 0, which
will be nonlinear in the unknown solution y. The set of equations to solve is:

y0 − α = 0 (20)
yi−1 − 2yi + yi+1 yi+1 − yi−1
+ (3yi )( ) = 0 (21)
h2 2h
yL − β = 0 (22)

Since we use a nonlinear solver, we will have to provide an initial guess to

the solution. We will in this case assume a line. In other cases, a bad initial
guess may lead to no solution.

1 import numpy as np
2 from scipy.optimize import fsolve
3 import matplotlib.pyplot as plt
4
5 x1 = 0.0
6 x2 = 2.0
7
8 alpha = 0.0
9 beta = 1.0
10
11 N = 11
12 X = np.linspace(x1, x2, N)
13 h = (x2 - x1) / (N - 1)
14
15 def Ypp(x, y, yprime):
16 ’’’define y’’ = 3*y*y’ ’’’
17 return -3.0 * y * yprime
18
19 def residuals(y):
20 ’’’When we have the right values of y, this function will be zero.’’’
21
22 res = np.zeros(y.shape)
23
24 res[0] = y[0] - alpha
25
26 for i in range(1, N - 1):
27 x = X[i]
28 YPP = (y[i - 1] - 2 * y[i] + y[i + 1]) / h**2
29 YP = (y[i + 1] - y[i - 1]) / (2 * h)
30 res[i] = YPP - Ypp(x, y[i], YP)
31
32 res[-1] = y[-1] - beta
33 return res
34
35 # we need an initial guess

190
36 init = alpha + (beta - alpha) / (x2 - x1) * X
37
38 Y = fsolve(residuals, init)
39
40 plt.plot(X, Y)
41 plt.savefig(’images/bvp-nonlinear-1.png’)

That code looks useful, so I put it in the pycse module in the function
BVP_nl. Here is an example usage. We have to create two functions, one for
the differential equation, and one for the initial guess.

1 from pycse import BVP_nl

2 import matplotlib.pyplot as plt
3
4 def Ypp(x, y, yprime):
5 ’’’define y’’ = 3*y*y’ ’’’
6 return -3.0 * y * yprime
7
8 def init(x):
9 return alpha + (beta - alpha) / (x2 - x1) * x
10
11 x1 = 0.0
12 x2 = 2.0
13
14 alpha = 0.0
15 beta = 1.0
16
17 N = 11
18 x, y = BVP_nl(Ypp, x1, x2, alpha, beta, init, N)
19
20 plt.plot(x, y)
21 plt.savefig(’images/bvp-nonlinear-2.png’)

191
 The results are the same.

10.4.6 Another look at nonlinear BVPs

Adapted from http://www.mathworks.com/help/matlab/ref/bvp4c.html
Boundary value problems may have more than one solution. Let us consider
the BVP:

y 00 + |y| = 0 (23)
y(0) = 0 (24)
y(4) = −2 (25)

We will see this equation has two answers, depending on your initial guess.
We convert this to the following set of coupled equations:

y10 = y2 (26)
y20 = −|y1 | (27)
y1 (0) = 0 (28)
y1 (4) = −2 (29)

This BVP is nonlinear because of the absolute value. We will have to guess
solutions to get started. We will guess two different solutions, both of which
will be constant values. We will use pycse.bvp to solve the equation.

192
1 import numpy as np
2 from pycse import bvp
3 import matplotlib.pyplot as plt
4
5 def odefun(Y, x):
6 y1, y2 = Y
7 dy1dx = y2
8 dy2dx = -np.abs(y1)
9 return [dy1dx, dy2dx]
10
11 def bcfun(Ya, Yb):
12 y1a, y2a = Ya
13 y1b, y2b = Yb
14
15 return [y1a, -2 - y1b]
16
17 x = np.linspace(0, 4, 100)
18
19 y1 = 1.0 * np.ones(x.shape)
20 y2 = 0.0 * np.ones(x.shape)
21
22 Yinit = np.vstack([y1, y2])
23
24 sol = bvp(odefun, bcfun, x, Yinit)
25
26 plt.plot(x, sol[0])
27
28 # another initial guess
29 y1 = -1.0 * np.ones(x.shape)
30 y2 = 0.0 * np.ones(x.shape)
31
32 Yinit = np.vstack([y1, y2])
33
34 sol = bvp(odefun, bcfun, x, Yinit)
35
36 plt.plot(x, sol[0])
37 plt.legend([’guess 1’, ’guess 2’])
38 plt.savefig(’images/bvp-another-nonlin-1.png’)
39 plt.show()

193
 This example shows that a nonlinear BVP may have different solutions, and
which one you get depends on the guess you make for the solution. This is
analogous to solving nonlinear algebraic equations (which is what is done in
solving this problem!).

10.4.7 Solving the Blasius equation

In fluid mechanics the Blasius equation comes up (http://en.wikipedia.org/
wiki/Blasius_boundary_layer) to describe the boundary layer that forms
near a flat plate with fluid moving by it. The nonlinear differential equation is:

1
f 000 + f f 00 = 0 (30)
2
f (0) = 0 (31)
f (0)0
= 0 (32)
0
f (∞) = 1 (33)

This is a nonlinear, boundary value problem. The point of solving this

equation is to get the value of f 00 (0) to evaluate the shear stress at the plate.
We have to convert this to a system of first-order differential equations. Let
f1 = f , f2 = f10 and f3 = f20 . This leads to:

f10 = f2 (34)
f20 = f3 (35)

194
 1
f30 = − f1 f3 (36)
2
f1 (0) = 0 (37)
f2 (0) = 0 (38)
f2 (∞) = 1 (39)

It is not possible to specify a boundary condition at ∞ numerically, so we

will have to use a large number, and verify it is "large enough". From the
solution, we evaluate the derivatives at η = 0, and we have f 00 (0) = f3 (0).
We have to provide initial guesses for f_1, f_2 and f_3. This is the hardest
part about this problem. We know that f_1 starts at zero, and is flat there
(f’(0)=0), but at large eta, it has a constant slope of one. We will guess a
simple line of slope = 1 for f_1. That is correct at large eta, and is zero at
η=0. If the slope of the function is constant at large η, then the values of higher
derivatives must tend to zero. We choose an exponential decay as a guess.
Finally, we let a solver iteratively find a solution for us, and find the answer
we want. The solver is in the pycse module.

1 import numpy as np
2 from pycse import bvp
3
4 def odefun(F, x):
5 f1, f2, f3 = F
6 return [f2,
7 f3,
8 -0.5 * f1 * f3]
9
10 def bcfun(Fa, Fb):
11 return [Fa[0], # f1(0) = 0
12 Fa[1], # f2(0) = 0
13 1.0 - Fb[1]] # f2(inf) = 1
14
15 eta = np.linspace(0, 6, 100)
16 f1init = eta
17 f2init = np.exp(-eta)
18 f3init = np.exp(-eta)
19
20 Finit = np.vstack([f1init, f2init, f3init])
21
22 sol = bvp(odefun, bcfun, eta, Finit)
23
24 print "f’’(0) = f_3(0) = {0}".format(sol[2, 0])
25
26 import matplotlib.pyplot as plt
27 plt.plot(eta, sol[0])
28 plt.xlabel(’$\eta$’)
29 plt.ylabel(’$f(\eta)$’)
30 plt.savefig(’images/blasius.png’)

f’’(0) = f_3(0) = 0.332491109552

195
10.5 Partial differential equations
10.5.1 Modeling a transient plug flow reactor
Matlab post
The PDE that describes the transient behavior of a plug flow reactor with
constant volumetric flow rate is:
∂dt = −ν0 ∂dV + rA .
∂CA ∂CA

To solve this numerically in python, we will utilize the method of lines.

The idea is to discretize the reactor in volume, and approximate the spatial
derivatives by finite differences. Then we will have a set of coupled ordinary
differential equations that can be solved in the usual way. Let us simplify the
notation with C = CA , and let rA = −kC 2 . Graphically this looks like this:

This leads to the following set of equations:

dC0
= 0 (entrance concentration never changes) (40)
dt
dC1 C1 − C0
= −ν0 − kC12 (41)
dt V1 − V0

196
 dC2 C2 − C1
= −ν0 − kC22 (42)
dt V2 − V1
..
. (43)
dC4 C4 − C3
= −ν0 − kC42 (44)
dt V4 − V3
Last, we need initial conditions for all the nodes in the discretization. Let
us assume the reactor was full of empty solvent, so that Ci = 0 at t = 0. In
the next block of code, we get the transient solutions, and the steady state
solution.

1 import numpy as np
2 from scipy.integrate import odeint
3
4 Ca0 = 2 # Entering concentration
5 vo = 2 # volumetric flow rate
6 volume = 20 # total volume of reactor, spacetime = 10
7 k = 1 # reaction rate constant
8
9 N = 100 # number of points to discretize the reactor volume on
10
11 init = np.zeros(N) # Concentration in reactor at t = 0
12 init[0] = Ca0 # concentration at entrance
13
14 V = np.linspace(0, volume, N) # discretized volume elements
15 tspan = np.linspace(0, 25) # time span to integrate over
16
17 def method_of_lines(C, t):
18 ’coupled ODES at each node point’
19 D = -vo * np.diff(C) / np.diff(V) - k * C[1:]**2
20 return np.concatenate([[0], #C0 is constant at entrance
21 D])
22
23
24 sol = odeint(method_of_lines, init, tspan)
25
26 # steady state solution
27 def pfr(C, V):
28 return 1.0 / vo * (-k * C**2)
29
30 ssol = odeint(pfr, Ca0, V)

The transient solution contains the time dependent behavior of each node
in the discretized reactor. Each row contains the concentration as a function of
volume at a specific time point. For example, we can plot the concentration of
A at the exit vs. time (that is, the last entry of each row) as:

1 import matplotlib.pyplot as plt

2 plt.plot(tspan, sol[:, -1])
3 plt.xlabel(’time’)
4 plt.ylabel(’$C_A$ at exit’)
5 plt.savefig(’images/transient-pfr-1.png’)

[<matplotlib.lines.Line2D object at 0x05A18830>]

<matplotlib.text.Text object at 0x059FE1D0>
<matplotlib.text.Text object at 0x05A05270>

197
 After approximately one space time, the steady state solution is reached at
the exit. For completeness, we also examine the steady state solution.

1 plt.figure()
2 plt.plot(V, ssol, label=’Steady state’)
3 plt.plot(V, sol[-1], label=’t = {}’.format(tspan[-1]))
4 plt.xlabel(’Volume’)
5 plt.ylabel(’$C_A$’)
6 plt.legend(loc=’best’)
7 plt.savefig(’images/transient-pfr-2.png’)

198
 There is some minor disagreement between the final transient solution and
the steady state solution. That is due to the approximation in discretizing the
reactor volume. In this example we used 100 nodes. You get better agreement
with a larger number of nodes, say 200 or more. Of course, it takes slightly longer
to compute then, since the number of coupled odes is equal to the number of
nodes.
We can also create an animated gif to show how the concentration of A
throughout the reactor varies with time. Note, I had to install ffmpeg (http:
//ffmpeg.org/) to save the animation.

1 from matplotlib import animation

2
3 # make empty figure
4 fig = plt.figure()
5 ax = plt.axes(xlim=(0, 20), ylim=(0, 2))
6 line, = ax.plot(V, init, lw=2)
7
8 def animate(i):
9 line.set_xdata(V)
10 line.set_ydata(sol[i])
11 ax.set_title(’t = {0}’.format(tspan[i]))
12 ax.figure.canvas.draw()
13 return line,
14
15
16 anim = animation.FuncAnimation(fig, animate, frames=50, blit=True)
17
18 anim.save(’images/transient_pfr.mp4’, fps=10)

http://jkitchin.github.com/media/transient_pfr.mp4
You can see from the animation that after about 10 time units, the solution
is not changing further, suggesting steady state has been reached.

199
 10.5.2 Transient heat conduction - partial differential equations
Matlab post adapated from http://msemac.redwoods.edu/~darnold/math55/
DEproj/sp02/AbeRichards/slideshowdefinal.pdf
We solved a steady state BVP modeling heat conduction. Today we examine
the transient behavior of a rod at constant T put between two heat reservoirs
at different temperatures, again T1 = 100, and T2 = 200. The rod will start at
150. Over time, we should expect a solution that approaches the steady state
solution: a linear temperature profile from one side of the rod to the other.
∂u ∂2u
∂t = k ∂x2
at t = 0, in this example we have u0 (x) = 150 as an initial condition. with
boundary conditions u(0, t) = 100 and u(L, t) = 200.
In Matlab there is the pdepe command. There is not yet a PDE solver in
scipy. Instead, we will utilze the method of lines to solve this problem. We
discretize the rod into segments, and approximate the second derivative in the
2
spatial dimension as ∂∂xu2 = (u(x + h) − 2u(x) + u(x − h))/h2 at each node. This
leads to a set of coupled ordinary differential equations that is easy to solve.
Let us say the rod has a length of 1, k = 0.02, and solve for the time-
dependent temperature profiles.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 N = 100 # number of points to discretize
6 L = 1.0
7 X = np.linspace(0, L, N) # position along the rod
8 h = L / (N - 1)
9
10 k = 0.02
11
12 def odefunc(u, t):
13 dudt = np.zeros(X.shape)
14
15 dudt[0] = 0 # constant at boundary condition
16 dudt[-1] = 0
17
18 # now for the internal nodes
19 for i in range(1, N-1):
20 dudt[i] = k * (u[i + 1] - 2*u[i] + u[i - 1]) / h**2
21
22 return dudt
23
24 init = 150.0 * np.ones(X.shape) # initial temperature
25 init[0] = 100.0 # one boundary condition
26 init[-1] = 200.0 # the other boundary condition
27
28 tspan = np.linspace(0.0, 5.0, 100)
29 sol = odeint(odefunc, init, tspan)
30
31
32 for i in range(0, len(tspan), 5):
33 plt.plot(X, sol[i], label=’t={0:1.2f}’.format(tspan[i]))
34
35 # put legend outside the figure
36 plt.legend(loc=’center left’, bbox_to_anchor=(1, 0.5))
37 plt.xlabel(’X position’)
38 plt.ylabel(’Temperature’)
39

200
40 # adjust figure edges so the legend is in the figure
41 plt.subplots_adjust(top=0.89, right=0.77)
42 plt.savefig(’images/pde-transient-heat-1.png’)
43
44
45 # Make a 3d figure
46 from mpl_toolkits.mplot3d import Axes3D
47 fig = plt.figure()
48 ax = fig.add_subplot(111, projection=’3d’)
49
50 SX, ST = np.meshgrid(X, tspan)
51 ax.plot_surface(SX, ST, sol, cmap=’jet’)
52 ax.set_xlabel(’X’)
53 ax.set_ylabel(’time’)
54 ax.set_zlabel(’T’)
55 ax.view_init(elev=15, azim=-124) # adjust view so it is easy to see
56 plt.savefig(’images/pde-transient-heat-3d.png’)
57
58 # animated solution. We will use imagemagick for this
59
60 # we save each frame as an image, and use the imagemagick convert command to
61 # make an animated gif
62 for i in range(len(tspan)):
63 plt.clf()
64 plt.plot(X, sol[i])
65 plt.xlabel(’X’)
66 plt.ylabel(’T(X)’)
67 plt.title(’t = {0}’.format(tspan[i]))
68 plt.savefig(’___t{0:03d}.png’.format(i))
69
70 import commands
71 print commands.getoutput(’convert -quality 100 ___t*.png images/transient_heat.gif’)
72 print commands.getoutput(’rm ___t*.png’) #remove temp files

This version of the graphical solution is not that easy to read, although
with some study you can see the solution evolves from the initial condition
which is flat, to the steady state solution which is a linear temperature ramp.

201
 The 3d version may be easier to interpret. The temperature profile starts out

flat, and gradually changes to the linear ramp.

Finally, the animated solution.
./images/transient_heat.gif

202
 10.5.3 Transient diffusion - partial differential equations
We want to solve for the concentration profile of component that diffuses into
a 1D rod, with an impermeable barrier at the end. The PDE governing this
situation is:
∂C ∂2C
∂t = D ∂x2
at t = 0, in this example we have C0 (x) = 0 as an initial condition, with
boundary conditions C(0, t) = 0.1 and ∂C/∂x(L, t) = 0.
We are going to discretize this equation in both time and space to arrive at
the solution. We will let i be the index for the spatial discretization, and j be
the index for the temporal discretization. The discretization looks like this.

Note that we cannot use the method of lines as we did before because we
have the derivative-based boundary condition at one of the boundaries.
We approximate the time derivative as:
∂C 
 C −Ci,j
∂t  ≈ i,j+1
∆t
i,j

∂2C  C −2C +C

∂x2  ≈ i+1,j h2i,j i−1,j
i,j
We define α = D∆th2 , and from these two approximations and the PDE, we
solve for the unknown solution at a later time step as:
Ci,j+1 = αCi+1,j + (1 − 2α)Ci,j + αCi−1,j
We know Ci,j=0 from the initial conditions, so we simply need to iterate to
evaluate Ci,j , which is the solution at each time step.
See also: http://www3.nd.edu/~jjwteach/441/PdfNotes/lecture16.pdf

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 N = 20 # number of points to discretize
5 L = 1.0
6 X = np.linspace(0, L, N) # position along the rod
7 h = L / (N - 1) # discretization spacing
8
9 C0t = 0.1 # concentration at x = 0
10 D = 0.02
11
12 tfinal = 50.0

203
13 Ntsteps = 1000
14 dt = tfinal / (Ntsteps - 1)
15 t = np.linspace(0, tfinal, Ntsteps)
16
17 alpha = D * dt / h**2
18 print alpha
19
20 C_xt = [] # container for all the time steps
21
22 # initial condition at t = 0
23 C = np.zeros(X.shape)
24 C[0] = C0t
25
26 C_xt += [C]
27
28 for j in range(1, Ntsteps):
29 N = np.zeros(C.shape)
30 N[0] = C0t
31 N[1:-1] = alpha*C[2:] + (1 - 2 * alpha) * C[1:-1] + alpha * C[0:-2]
32 N[-1] = N[-2] # derivative boundary condition flux = 0
33 C[:] = N
34 C_xt += [N]
35
36 # plot selective solutions
37 if j in [1,2,5,10,20,50,100,200,500]:
38 plt.plot(X, N, label=’t={0:1.2f}’.format(t[j]))
39
40 plt.xlabel(’Position in rod’)
41 plt.ylabel(’Concentration’)
42 plt.title(’Concentration at different times’)
43 plt.legend(loc=’best’)
44 plt.savefig(’images/transient-diffusion-temporal-dependence.png’)
45
46 C_xt = np.array(C_xt)
47 plt.figure()
48 plt.plot(t, C_xt[:,5], label=’x={0:1.2f}’.format(X[5]))
49 plt.plot(t, C_xt[:,10], label=’x={0:1.2f}’.format(X[10]))
50 plt.plot(t, C_xt[:,15], label=’x={0:1.2f}’.format(X[15]))
51 plt.plot(t, C_xt[:,19], label=’x={0:1.2f}’.format(X[19]))
52 plt.legend(loc=’best’)
53 plt.xlabel(’Time’)
54 plt.ylabel(’Concentration’)
55 plt.savefig(’images/transient-diffusion-position-dependence.png’)
56
57 plt.show()

0.361361361361

204
 The solution is somewhat sensitive to the choices of time step and spatial
discretization. If you make the time step too big, the method is not stable, and
large oscillations may occur.

205
 11 Plotting
11.1 Plot customizations - Modifying line, text and figure
properties
Matlab post
Here is a vanilla plot.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(0, 2 * np.pi)
5 plt.plot(x, np.sin(x))
6 plt.savefig(’images/plot-customization-1.png’)

>>> >>> >>> [<matplotlib.lines.Line2D object at 0x000000000771D860>]

Lets increase the line thickness, change the line color to red, and make the
markers red circles with black outlines. I also like figures in presentations to be
6 inches high, and 4 inches wide.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(0, 2 * np.pi)
5
6 plt.figure(figsize=(4, 6))
7 plt.plot(x, np.sin(x), lw=2, color=’r’, marker=’o’, mec=’k’, mfc=’b’)
8
9 plt.xlabel(’x data’, fontsize=12, fontweight=’bold’)

206
10 plt.ylabel(’y data’, fontsize=12, fontstyle=’italic’, color=’b’)
11 plt.tight_layout() # auto-adjust position of axes to fit figure.
12 plt.savefig(’images/plot-customization-2.png’)
13 plt.show()

11.1.1 setting all the text properties in a figure.

You may notice the axis tick labels are not consistent with the labels now. If
you have many plots it can be tedious to try setting each text property. Python
to the rescue! With these commands you can find all the text instances, and
change them all at one time! Likewise, you can change all the lines, and all the
axes.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(0, 2 * np.pi)
5
6 plt.figure(figsize=(4, 6))
7 plt.plot(x, np.sin(x), lw=2, color=’r’, marker=’o’, mec=’k’, mfc=’b’)
8
9 plt.xlabel(’x data’, fontsize=12, fontweight=’bold’)
10 plt.ylabel(’y data’, fontsize=12, fontstyle=’italic’, color=’b’)
11
12 # set all font properties
13 fig = plt.gcf()
14 for o in fig.findobj(lambda x:hasattr(x, ’set_fontname’)
15 or hasattr(x, ’set_fontweight’)
16 or hasattr(x, ’set_fontsize’)):
17 o.set_fontname(’Arial’)
18 o.set_fontweight(’bold’)
19 o.set_fontsize(14)
20
21 # make anything you can set linewidth to be lw=2
22 def myfunc(x):
23 return hasattr(x, ’set_linewidth’)
24
25 for o in fig.findobj(myfunc):
26 o.set_linewidth(2)
27
28 plt.tight_layout() # auto-adjust position of axes to fit figure.
29 plt.savefig(’images/plot-customization-3.png’)
30 plt.show()

207
 There are many other things you can do!

11.2 Plotting two datasets with very different scales

Matlab plot
Sometimes you will have two datasets you want to plot together, but the
scales will be so different it is hard to seem them both in the same plot. Here

208
 we examine a few strategies to plotting this kind of data.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(0, 2*np.pi)
5 y1 = np.sin(x);
6 y2 = 0.01 * np.cos(x);
7
8 plt.plot(x, y1, x, y2)
9 plt.legend([’y1’, ’y2’])
10 plt.savefig(’images/two-scales-1.png’)
11 # in this plot y2 looks almost flat!

>>> >>> >>> >>> >>> >>> [<matplotlib.lines.Line2D object at 0x0000000006089128>, <matplotlib
<matplotlib.legend.Legend object at 0x0000000007661668>

11.2.1 Make two plots!

this certainly solves the problem, but you have two full size plots, which can
take up a lot of space in a presentation and report. Often your goal in plotting
both data sets is to compare them, and it is easiest to compare plots when they
are perfectly lined up. Doing that manually can be tedious.

1 plt.figure()
2 plt.plot(x,y1)
3 plt.legend([’y1’])
4 plt.savefig(’images/two-scales-2.png’)
5

209
6 plt.figure()
7 plt.plot(x,y2)
8 plt.legend([’y2’])
9 plt.savefig(’images/two-scales-3.png’)

<matplotlib.figure.Figure object at 0x0000000007D45438>

[<matplotlib.lines.Line2D object at 0x00000000081C61D0>]
<matplotlib.legend.Legend object at 0x0000000007FA1CF8>
>>> >>> <matplotlib.figure.Figure object at 0x00000000081C63C8>
[<matplotlib.lines.Line2D object at 0x00000000081C8F60>]
<matplotlib.legend.Legend object at 0x00000000081D7278>

210
 11.2.2 Scaling the results
Sometimes you can scale one dataset so it has a similar magnitude as the other
data set. Here we could multiply y2 by 100, and then it will be similar in size
to y1. Of course, you need to indicate that y2 has been scaled in the graph
somehow. Here we use the legend.

1 plt.figure()
2 plt.plot(x, y1, x, 100 * y2)
3 plt.legend([’y1’, ’100*y2’])
4 plt.savefig(’images/two-scales-4.png’)

<matplotlib.figure.Figure object at 0x0000000007FA7908>

[<matplotlib.lines.Line2D object at 0x000000000B0285C0>, <matplotlib.lines.Line2D object at
<matplotlib.legend.Legend object at 0x000000000B028C88>

211
 11.2.3 Double-y axis plot
Using two separate y-axes can solve your scaling problem. Note that each y-axis
is color coded to the data. It can be difficult to read these graphs when printed
in black and white

1 fig = plt.figure()
2 ax1 = fig.add_subplot(111)
3 ax1.plot(x, y1)
4 ax1.set_ylabel(’y1’)
5
6 ax2 = ax1.twinx()
7 ax2.plot(x, y2, ’r-’)
8 ax2.set_ylabel(’y2’, color=’r’)
9 for tl in ax2.get_yticklabels():
10 tl.set_color(’r’)
11
12 plt.savefig(’images/two-scales-5.png’)

>>> [<matplotlib.lines.Line2D object at 0x000000000BA34208>]

<matplotlib.text.Text object at 0x000000000BA37C50>
>>> >>> [<matplotlib.lines.Line2D object at 0x000000000BA4DEF0>]
<matplotlib.text.Text object at 0x000000000BA594A8>

212
 11.2.4 Subplots
An alternative approach to double y axes is to use subplots.

1 plt.figure()
2 f, axes = plt.subplots(2, 1)
3 axes[0].plot(x, y1)
4 axes[0].set_ylabel(’y1’)
5
6 axes[1].plot(x, y2)
7 axes[1].set_ylabel(’y2’)
8 plt.savefig(’images/two-scales-6.png’)

<matplotlib.figure.Figure object at 0x000000000BDC47B8>

>>> [<matplotlib.lines.Line2D object at 0x000000000BDE2F28>]
<matplotlib.text.Text object at 0x000000000BDD74E0>
>>> [<matplotlib.lines.Line2D object at 0x000000000D05E748>]
<matplotlib.text.Text object at 0x000000000BDEC438>

213
 11.3 Customizing plots after the fact
Matlab post Sometimes it is desirable to make a plot that shows the data you
want to present, and to customize the details, e.g. font size/type and line
thicknesses afterwards. It can be tedious to try to add the customization code
to the existing code that makes the plot. Today, we look at a way to do the
customization after the plot is created.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 x = np.linspace(0,2)
5 y1 = x
6 y2 = x**2
7 y3 = x**3
8
9 plt.plot(x, y1, x, y2, x, y3)
10 xL = plt.xlabel(’x’)
11 yL = plt.ylabel(’f(x)’)
12 plt.title(’plots of y = x^n’)
13 plt.legend([’x’, ’x^2’, ’x^3’], loc=’best’)
14 plt.savefig(’images/after-customization-1.png’)
15
16 fig = plt.gcf()
17
18 plt.setp(fig, ’size_inches’, (4, 6))
19 plt.savefig(’images/after-customization-2.png’)
20
21
22 # set lines to dashed
23 from matplotlib.lines import Line2D
24 for o in fig.findobj(Line2D):
25 o.set_linestyle(’--’)
26

214
27 #set(allaxes,’FontName’,’Arial’,’FontWeight’,’Bold’,’LineWidth’,2,’FontSize’,14);
28
29 import matplotlib.text as text
30 for o in fig.findobj(text.Text):
31 plt.setp(o, ’fontname’,’Arial’, ’fontweight’,’bold’, ’fontsize’, 14)
32
33 plt.setp(xL, ’fontstyle’, ’italic’)
34 plt.setp(yL, ’fontstyle’, ’italic’)
35 plt.savefig(’images/after-customization-3.png’)
36 plt.show()

215
216
11.4 Fancy, built-in colors in Python
Matlab post
Matplotlib has a lot of built-in colors. Here is a list of them, and an example
of using them.

217
1 import matplotlib.pyplot as plt
2 from matplotlib.colors import cnames
3 print cnames.keys()
4
5 plt.plot([1, 2, 3, 4], lw=2, color=’moccasin’, marker=’o’, mfc=’lightblue’, mec=’seagreen’)
6 plt.savefig(’images/fall-colors.png’)

[’indigo’, ’gold’, ’hotpink’, ’firebrick’, ’indianred’, ’yellow’, ’mistyrose’, ’darkolivegre

11.5 Picasso’s short lived blue period with Python

Matlab post
It is an unknown fact that Picasso had a brief blue plotting period with
Matlab before moving on to his more famous paintings. It started from irritation
with the default colors available in Matlab for plotting. After watching his friend
van Gogh cut off his own ear out of frustration with the ugly default colors,
Picasso had to do something different.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4
5 #this plots horizontal lines for each y value of m.
6 for m in np.linspace(1, 50, 100):
7 plt.plot([0, 50], [m, m])
8
9 plt.savefig(’images/blues-1.png’)

218
 Picasso copied the table availabe at http://en.wikipedia.org/wiki/
List_of_colors and parsed it into a dictionary of hex codes for new colors.
That allowed him to specify a list of beautiful blues for his graph. Picasso
eventually gave up on python as an artform, and moved on to painting.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 c = {}
5 with open(’color.table’) as f:
6 for line in f:
7 fields = line.split(’\t’)
8 colorname = fields[0].lower()
9 hexcode = fields[1]
10 c[colorname] = hexcode
11
12 names = c.keys()
13 names.sort()
14 print names
15
16 blues = [c[’alice blue’],
17 c[’light blue’],
18 c[’baby blue’],
19 c[’light sky blue’],
20 c[’maya blue’],
21 c[’cornflower blue’],
22 c[’bleu de france’],
23 c[’azure’],
24 c[’blue sapphire’],
25 c[’cobalt’],
26 c[’blue’],
27 c[’egyptian blue’],
28 c[’duke blue’]]
29
30 ax = plt.gca()
31 ax.set_color_cycle(blues)
32

219
33 #this plots horizontal lines for each y value of m.
34 for i, m in enumerate(np.linspace(1, 50, 100)):
35 plt.plot([0, 50], [m, m])
36
37 plt.savefig(’images/blues-2.png’)
38 plt.show()

[’aero’, ’aero blue’, ’african violet’, ’air force blue (raf)’, ’air force blue (usaf)’, ’ai

11.6 Interactive plotting

11.6.1 Basic mouse clicks
One basic event a figure can react to is a mouse click. Let us make a graph
with a parabola in it, and draw the shortest line from a point clicked on to the
graph. Here is an example of doing that.

1 import matplotlib.pyplot as plt

2 import numpy as np
3 from scipy.optimize import fmin_cobyla
4
5 fig = plt.figure()
6
7 def f(x):
8 return x**2
9
10 x = np.linspace(-2, 2)
11 y = f(x)
12
13 ax = fig.add_subplot(111)
14 ax.plot(x, y)
15 ax.set_title(’Click somewhere’)

220
16
17 def onclick(event):
18 ax = plt.gca()
19
20 P = (event.xdata, event.ydata)
21
22 def objective(X):
23 x,y = X
24 return np.sqrt((x - P[0])**2 + (y - P[1])**2)
25
26 def c1(X):
27 x,y = X
28 return f(x) - y
29
30 X = fmin_cobyla(objective, x0=[P[0], f(P[0])], cons=[c1])
31
32 ax.set_title(’x={0:1.2f} y={1:1.2f}’.format(event.xdata, event.ydata))
33 ax.plot([event.xdata, X[0]], [event.ydata, X[1]], ’ro-’)
34 ax.figure.canvas.draw() # this line is critical to change the title
35 plt.savefig(’images/interactive-basic-click.png’)
36
37 cid = fig.canvas.mpl_connect(’button_press_event’, onclick)
38 plt.show()

Normal return from subroutine COBYLA

NFVALS = 43 F = 4.598867E-01 MAXCV = 0.000000E+00

X =-1.467536E+00 2.153663E+00

Normal return from subroutine COBYLA

NFVALS = 47 F = 4.913005E-01 MAXCV = 0.000000E+00

X = 5.251398E-01 2.757718E-01

Here is the result from two clicks. For some reason, this only works when
you click inside the parabola. It does not work outside the parabola.

221
 We can even do different things with different mouse clicks. A left click
corresponds to event.button = 1, a middle click is event.button = 2, and a right
click is event.button = 3. You can detect if a double click occurs too. Here is
an example of these different options.

1 import matplotlib.pyplot as plt

2 import numpy as np
3
4 fig = plt.figure()
5
6 ax = fig.add_subplot(111)
7 ax.plot(np.random.rand(10))
8 ax.set_title(’Click somewhere’)
9
10 def onclick(event):
11 ax.set_title(’x={0:1.2f} y={1:1.2f} button={2}’.format(event.xdata, event.ydata, event.button))
12 colors = ’ rbg’
13 print ’button={0} (dblclick={2}). making a {1} dot’.format(event.button,
14 colors[event.button],
15 event.dblclick)
16
17 ms=5 # marker size
18 if event.dblclick: #make marker bigger
19 ms = 10
20
21 ax.plot([event.xdata], [event.ydata], ’o’, color=colors[event.button], ms=ms)
22 ax.figure.canvas.draw() # this line is critical to change the title
23 plt.savefig(’images/interactive-button-click.png’)
24
25 cid = fig.canvas.mpl_connect(’button_press_event’, onclick)
26 plt.show()

button=1 (dblclick=False). making a r dot

button=1 (dblclick=False). making a r dot

222
 button=1 (dblclick=True). making a r dot
button=2 (dblclick=False). making a b dot
button=2 (dblclick=False). making a b dot
button=2 (dblclick=True). making a b dot
button=3 (dblclick=False). making a g dot
button=3 (dblclick=False). making a g dot
button=3 (dblclick=True). making a g dot

Finally, you may want to have key modifiers for your clicks, e.g. Ctrl-click
is different than a click.

1 import matplotlib.pyplot as plt

2 import numpy as np
3
4 fig = plt.figure()
5
6 ax = fig.add_subplot(111)
7 ax.plot(np.random.rand(10))
8 ax.set_title(’Click somewhere’)
9
10 def onclick(event):
11 print event.key
12 ax = plt.gca()
13 ax.set_title(’x={0:1.2f} y={1:1.2f}’.format(event.xdata, event.ydata))
14 if event.key == ’ctrl+control’:
15 color = ’red’
16 elif event.key == ’shift’:
17 color = ’yellow’
18 else:
19 color = ’blue’
20
21 ax.plot([event.xdata], [event.ydata], ’o’, color=color)
22 ax.figure.canvas.draw() # this line is critical to change the title
23 plt.savefig(’images/interactive-button-key-click.png’)

223
24
25 cid = fig.canvas.mpl_connect(’button_press_event’, onclick)
26 plt.show()

ctrl+control
shift
alt+alt

You can have almost every key-click combination imaginable. This allows
you to have many different things that can happen when you click on a graph.
With this method, you can get the coordinates close to a data point, but you
do not get the properties of the point. For that, we need another mechanism.

11.6.2 Mouse movement

In this example, we will let the mouse motion move a point up and down a
curve. This might be helpful to explore a function graph, for example. We use
interpolation to estimate the curve between data points.

1 import matplotlib.pyplot as plt

2 import numpy as np
3 from scipy.interpolate import interp1d
4
5 # the "data"
6 x = np.linspace(0, np.pi)
7 y = np.sin(x)
8
9 # interpolating function between points
10 p = interp1d(x, y, ’cubic’)
11
12 # make the figure

224
13 fig = plt.figure()
14
15 ax = fig.add_subplot(111)
16 line, = ax.plot(x, y, ’ro-’)
17 marker, = ax.plot([0.5], [0.5],’go’, ms=15)
18
19 ax.set_title(’Move the mouse around’)
20
21 def onmove(event):
22
23 xe = event.xdata
24 ye = event.ydata
25
26 ax.set_title(’at x={0} y={1}’.format(xe, p(xe)))
27 marker.set_xdata(xe)
28 marker.set_ydata(p(xe))
29
30 ax.figure.canvas.draw() # this line is critical to change the title
31
32 cid = fig.canvas.mpl_connect(’motion_notify_event’, onmove)
33 plt.show()

11.6.3 key press events

Pressing a key is different than pressing a mouse button. We can do different
things with different key presses. You can access the coordinates of the mouse
when you press a key.

1 import matplotlib.pyplot as plt

2 import numpy as np
3
4 fig = plt.figure()
5
6 ax = fig.add_subplot(111)
7 ax.plot(np.random.rand(10))
8 ax.set_title(’Move the mouse somewhere and press a key’)
9
10 def onpress(event):
11 print event.key
12 ax = plt.gca()
13 ax.set_title(’key={2} at x={0:1.2f} y={1:1.2f}’.format(event.xdata, event.ydata, event.key))
14 if event.key == ’r’:
15 color = ’red’
16 elif event.key == ’y’:
17 color = ’yellow’
18 else:
19 color = ’blue’
20
21 ax.plot([event.xdata], [event.ydata], ’o’, color=color)
22 ax.figure.canvas.draw() # this line is critical to change the title
23 plt.savefig(’images/interactive-key-press.png’)
24
25 cid = fig.canvas.mpl_connect(’key_press_event’, onpress)
26 plt.show()

r
t
y

225
 11.6.4 Picking lines
Instead of just getting the points in a figure, let us interact with lines on the
graph. We want to make the line we click on thicker. We use a "pick_event"
event and bind a function to that event that does something.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 fig = plt.figure()
5 ax = fig.add_subplot(111)
6 ax.set_title(’click on a line’)
7
8 x = np.linspace(0, 2*np.pi)
9
10 L1, = ax.plot(x, np.sin(x), picker=5)
11 L2, = ax.plot(x, np.cos(x), picker=5)
12
13 def onpick(event):
14 thisline = event.artist
15
16 # reset all lines to thin
17 for line in [L1, L2]:
18 line.set_lw(1)
19
20 thisline.set_lw(5) # make selected line thick
21 ax.figure.canvas.draw() # this line is critical to change the linewidth
22
23 fig.canvas.mpl_connect(’pick_event’, onpick)
24
25 plt.show()

11.6.5 Picking data points

In this example we show how to click on a data point, and show which point
was selected with a transparent marker, and show a label which refers to the
point.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 fig = plt.figure()
5 ax = fig.add_subplot(111)
6 ax.set_title(’click on a point’)
7
8 x = [0, 1, 2, 3, 4, 5]
9 labels = [’a’, ’b’, ’c’, ’d’, ’e’, ’f’]
10 ax.plot(x, ’bo’, picker=5)
11
12 # this is the transparent marker for the selected data point
13 marker, = ax.plot([0], [0], ’yo’, visible=False, alpha=0.8, ms=15)
14
15 def onpick(event):
16 ind = event.ind
17 ax.set_title(’Data point {0} is labeled "{1}"’.format(ind, labels[ind]))
18
19 marker.set_visible(True)
20 marker.set_xdata(x[ind])
21 marker.set_ydata(x[ind])
22
23 ax.figure.canvas.draw() # this line is critical to change the linewidth
24 plt.savefig(’images/interactive-labeled-points.png’)

226
25
26 fig.canvas.mpl_connect(’pick_event’, onpick)
27
28 plt.show()

12 Programming
12.1 Some of this, sum of that
Matlab plot
Python provides a sum function to compute the sum of a list. However, the
sum function does not work on every arrangement of numbers, and it certainly
does not work on nested lists. We will solve this problem with recursion.
Here is a simple example.

1 v = [1, 2, 3, 4, 5, 6, 7, 8, 9] # a list
2 print sum(v)
3
4 v = (1, 2, 3, 4, 5, 6, 7, 8, 9) # a tuple
5 print sum(v)

45
45

If you have data in a dictionary, sum works by default on the keys. You can
give the sum function the values like this.

227
1 v = {’a’:1, ’b’:3, ’c’:4}
2 print sum(v.values())

12.1.1 Nested lists

Suppose now we have nested lists. This kind of structured data might come up
if you had grouped several things together. For example, suppose we have 5
departments, with 1, 5, 15, 7 and 17 people in them, and in each department
they are divided into groups.
Department 1: 1 person Department 2: group of 2 and group of 3 Depart-
ment 3: group of 4 and 11, with a subgroups of 5 and 6 making up the group of
11. Department 4: 7 people Department 5: one group of 8 and one group of 9.
We might represent the data like this nested list. Now, if we want to compute
the total number of people, we need to add up each group. We cannot simply
sum the list, because some elements are single numbers, and others are lists,
or lists of lists. We need to recurse through each entry until we get down to a
number, which we can add to the running sum.

1 v = [1,
2 [2, 3],
3 [4, [5, 6]],
4 7,
5 [8,9]]
6
7 def recursive_sum(X):
8 ’compute sum of arbitrarily nested lists’
9 s = 0 # initial value of the sum
10
11 for i in range(len(X)):
12 import types # we use this to test if we got a number
13 if isinstance(X[i], (types.IntType,
14 types.LongType,
15 types.FloatType,
16 types.ComplexType)):
17 # this is the terminal step
18 s += X[i]
19 else:
20 # we did not get a number, so we recurse
21 s += recursive_sum(X[i])
22 return s
23
24 print recursive_sum(v)
25 print recursive_sum([1,2,3,4,5,6,7,8,9]) # test on non-nested list

45
45

In Post 1970 we examined recursive functions that could be replaced by

loops. Here we examine a function that can only work with recursion because
the nature of the nested data structure is arbitrary. There are arbitary branches
and depth in the data structure. Recursion is nice because you do not have to
define that structure in advance.

228
 12.2 Sorting in python
Matlab post
Occasionally it is important to have sorted data. Python has a few sorting
options.

1 a = [4, 5, 1, 6, 8, 3, 2]
2 print a
3 a.sort() # inplace sorting
4 print a
5
6 a.sort(reverse=True)
7 print a

[4, 5, 1, 6, 8, 3, 2]
[1, 2, 3, 4, 5, 6, 8]
[8, 6, 5, 4, 3, 2, 1]

If you do not want to modify your list, but rather get a copy of a sorted list,
use the sorted command.

1 a = [4, 5, 1, 6, 8, 3, 2]
2 print ’sorted a = ’,sorted(a) # no change to a
3 print ’sorted a = ’,sorted(a, reverse=True) # no change to a
4 print ’a = ’,a

sorted a = [1, 2, 3, 4, 5, 6, 8]
sorted a = [8, 6, 5, 4, 3, 2, 1]
a = [4, 5, 1, 6, 8, 3, 2]

This works for strings too:

1 a = [’b’, ’a’, ’c’, ’tree’]

2 print sorted(a)

[’a’, ’b’, ’c’, ’tree’]

Here is a subtle point though. A capitalized letter comes before a lowercase

letter. We can pass a function to the sorted command that is called on each
element prior to the sort. Here we make each word lower case before sorting.

1 a = [’B’, ’a’, ’c’, ’tree’]

2 print sorted(a)
3
4 # sort by lower case letter
5 print sorted(a, key=str.lower)

[’B’, ’a’, ’c’, ’tree’]

[’a’, ’B’, ’c’, ’tree’]

229
 Here is a more complex sorting problem. We have a list of tuples with group
names and the letter grade. We want to sort the list by the letter grades. We
do this by creating a function that maps the letter grades to the position of the
letter grades in a sorted list. We use the list.index function to find the index of
the letter grade, and then sort on that.

1 groups = [(’group1’, ’B’),

2 (’group2’, ’A+’),
3 (’group3’, ’A’)]
4
5 def grade_key(gtup):
6 ’’’gtup is a tuple of (’groupname’, ’lettergrade’)’’’
7 lettergrade = gtup[1]
8
9 grades = [’A++’, ’A+’, ’A’, ’A-’, ’A/B’
10 ’B+’, ’B’, ’B-’, ’B/C’,
11 ’C+’, ’C’, ’C-’, ’C/D’,
12 ’D+’, ’D’, ’D-’, ’D/R’,
13 ’R+’, ’R’, ’R-’, ’R--’]
14
15 return grades.index(lettergrade)
16
17 print sorted(groups, key=grade_key)

[(’group2’, ’A+’), (’group3’, ’A’), (’group1’, ’B’)]

12.3 Unique entries in a vector

Matlab post
It is surprising how often you need to know only the unique entries in a
vector of entries. In python, we create a "set" from a list, which only contains
unique entries. Then we convert the set back to a list.

1 a = [1, 1, 2, 3, 4, 5, 3, 5]
2
3 b = list(set(a))
4 print b

[1, 2, 3, 4, 5]

1 a = [’a’,
2 ’b’,
3 ’abracadabra’,
4 ’b’,
5 ’c’,
6 ’d’,
7 ’b’]
8
9 print list(set(a))

[’a’, ’c’, ’b’, ’abracadabra’, ’d’]

230
 12.4 Lather, rinse and repeat
Matlab post
Recursive functions are functions that call themselves repeatedly until some
exit condition is met. Today we look at a classic example of recursive function
for computing a factorial. The factorial of a non-negative integer n is denoted
n!, and is defined as the product of all positive integers less than or equal to n.
The key ideas in defining a recursive function is that there needs to be some
logic to identify when to terminate the function. Then, you need logic that calls
the function again, but with a smaller part of the problem. Here we recursively
call the function with n-1 until it gets called with n=0. 0! is defined to be 1.

1 def recursive_factorial(n):
2 ’’’compute the factorial recursively. Note if you put a negative
3 number in, this function will never end. We also do not check if
4 n is an integer.’’’
5 if n == 0:
6 return 1
7 else:
8 return n * recursive_factorial(n - 1)
9
10 print recursive_factorial(5)

120

1 from scipy.misc import factorial

2 print factorial(5)

120.0

Compare to a loop solution This example can also be solved by a loop.

This loop is easier to read and understand than the recursive function. Note
the recursive nature of defining the variable as itself times a number.

1 n = 5
2 factorial_loop = 1
3 for i in range(1, n + 1):
4 factorial_loop *= i
5
6 print factorial_loop

120

There are some significant differences in this example than in Matlab.

1. the syntax of the for loop is quite different with the use of the in operator.
2. python has the nice *= operator to replace a = a * i
3. We have to loop from 1 to n+1 because the last number in the range is
not returned.

231
 12.4.1 Conclusions
Recursive functions have a special niche in mathematical programming. There
is often another way to accomplish the same goal. That is not always true
though, and in a future post we will examine cases where recursion is the only
way to solve a problem.

12.5 Brief intro to regular expressions

Matlab post
This example shows how to use a regular expression to find strings matching
the pattern :cmd:‘datastring‘. We want to find these strings, and then replace
them with something that depends on what cmd is, and what datastring is.
Let us define some commands that will take datasring as an argument, and
return the modified text. The idea is to find all the cmds, and then run them.
We use python’s eval command to get the function handle from a string, and
the cmd functions all take a datastring argument (we define them that way).
We will create commands to replace :cmd:‘datastring‘ with html code for a light
gray background, and :red:‘some text‘ with html code making the text red.

1 text = r’’’Here is some text. use the :cmd:‘open‘ to get the text into
2 a variable. It might also be possible to get a multiline
3 :red:‘line
4 2‘ directive.’’’
5
6 print text
7 print ’---------------------------------’

... ... >>> >>> Here is some text. use the :cmd:‘open‘ to get the text into
a variable. It might also be possible to get a multiline
:red:‘line
2‘ directive.
---------------------------------

Now, we define our functions.

1 def cmd(datastring):
2 ’ replace :cmd:‘datastring‘ with html code with light gray background’
3 s = ’<FONT style="BACKGROUND-COLOR: LightGray">%{0}</FONT>’;
4 html = s.format(datastring)
5 return html
6
7 def red(datastring):
8 ’replace :red:‘datastring‘ with html code to make datastring in red font’
9 html = ’<font color=red>{0}</font>’.format(datastring)
10 return html

Finally, we do the regular expression. Regular expressions are hard. There

are whole books on them. The point of this post is to alert you to the possibili-
ties. I will break this regexp down as follows. 1. we want everything between :*:

232
 as the directive. ([^:]*) matches everything not a :. :([^:]*): matches the
stuff between two :. 2. then we want everything between ‘*‘. ([^‘]*) matches
everything not a ‘. 3. The () makes a group that python stores so we can refer
to them later.

1 import re
2 regex = ’:([^:]*):‘([^‘]*)‘’
3 matches = re.findall(regex, text)
4 for directive, datastring in matches:
5 directive = eval(directive) # get the function
6 text = re.sub(regex, directive(datastring), text)
7
8 print ’Modified text:’
9 print text

>>> >>> ... ... ... >>> Modified text:

Here is some text. use the <FONT style="BACKGROUND-COLOR: LightGray">%open</FONT> to get the
a variable. It might also be possible to get a multiline
<FONT style="BACKGROUND-COLOR: LightGray">%open</FONT> directive.

12.6 Working with lists

It is not too uncommon to have a list of data, and then to apply a function to
every element, to filter the list, or extract elements that meet some criteria. In
this example, we take a string and split it into words. Then, we will examine
several ways to apply functions to the words, to filter the list to get data that
meets some criteria. Here is the string splitting.

1 text = ’’’
2 As we have seen, handling units with third party functions is fragile, and often requires additional code to wrap the function to
3
4 Before doing the examples, let us consider how the quantities package handles dimensionless numbers.
5
6 import quantities as u
7
8 a = 5 * u.m
9 L = 10 * u.m # characteristic length
10
11 print a/L
12 print type(a/L)
13
14 ’’’
15
16 words = text.split()
17 print words

... ... ... ... ... ... ... ... ... ... ... ... >>> >>> >>> [’As’, ’we’, ’have’, ’seen,’, ’h

Let us get the length of each word.

1 print [len(word) for word in words]

2

233
3 # functional approach with a lambda function
4 print map(lambda word: len(word), words)
5
6 # functional approach with a builtin function
7 print map(len, words)
8
9 # functional approach with a user-defined function
10 def get_length(word):
11 return len(word)
12
13 print map(get_length, words)

[2, 2, 4, 5, 8, 5, 4, 5, 5, 9, 2, 8, 3, 5, 8, 10, 4, 2, 4, 3, 8, 2, 6, 3, 6, 2, 11, 8, 4, 6,

>>> ... [2, 2, 4, 5, 8, 5, 4, 5, 5, 9, 2, 8, 3, 5, 8, 10, 4, 2, 4, 3, 8, 2, 6, 3, 6, 2, 11,
>>> [2, 2, 4, 5, 8, 5, 4, 5, 5, 9, 2, 8, 3, 5, 8, 10, 4, 2, 4, 3, 8, 2, 6, 3, 6, 2, 11, 8, 4
>>> ... ... ... >>> [2, 2, 4, 5, 8, 5, 4, 5, 5, 9, 2, 8, 3, 5, 8, 10, 4, 2, 4, 3, 8, 2, 6, 3

Now let us get all the words that start with the letter "a". This is sometimes
called filtering a list. We use a string function startswith to check for upper
and lower-case letters. We will use list comprehension with a condition.

1 print [word for word in words if word.startswith(’a’) or word.startswith(’A’)]

2
3 # make word lowercase to simplify the conditional statement
4 print [word for word in words if word.lower().startswith(’a’)]

[’As’, ’and’, ’additional’, ’An’, ’alternative’, ’approach’, ’avoids’, ’are’, ’able’, ’all’,
[’As’, ’and’, ’additional’, ’An’, ’alternative’, ’approach’, ’avoids’, ’are’, ’able’, ’all’,

A slightly harder example is to find all the words that are actually numbers.
We could use a regular expression for that, but we will instead use a function
we create. We use a function that tries to cast a word as a float. If this fails,
we know the word is not a float, so we return False.

1 def float_p(word):
2 try:
3 float(word)
4 return True
5 except ValueError:
6 return False
7
8 print [word for word in words if float_p(word)]
9
10 # here is a functional approach
11 print filter(float_p, words)

... ... ... ... ... >>> [’5’, ’10’]

[’5’, ’10’]

Finally, we consider filtering the list to find all words that contain certain
symbols, say any character in this string "./=*#". Any of those characters will
do, so we search each word for one of them, and return True if it contains it,
and False if none are contained.

234
1 def punctuation_p(word):
2 S = ’./=*#’
3 for s in S:
4 if s in word:
5 return True
6 return False
7
8 print [word for word in words if punctuation_p(word)]
9 print filter(punctuation_p, words)

... ... ... ... ... >>> [’units.’, ’dimensionless.’, ’modification.’, ’want.’, ’numbers.’, ’
[’units.’, ’dimensionless.’, ’modification.’, ’want.’, ’numbers.’, ’=’, ’*’, ’u.m’, ’=’, ’*’

In this section we examined a few ways to interact with lists using list com-
prehension and functional programming. These approaches make it possible to
work on arbitrary size lists, without needing to know in advance how big the
lists are. New lists are automatically generated as results, without the need to
preallocate lists, i.e. you do not need to know the size of the output. This can
be handy as it avoids needing to write loops in some cases and leads to more
compact code.

12.7 Making word files in python

Matlab post
We can use COM automation in python to create Microsoft Word documents.
This only works on windows, and Word must be installed.

1 from win32com.client import constants, Dispatch

2 import os
3
4 word = Dispatch(’Word.Application’)
5 word.Visible = True
6
7 document = word.Documents.Add()
8 selection = word.Selection
9
10 selection.TypeText(’Hello world. \n’)
11 selection.TypeText(’My name is Professor Kitchin\n’)
12 selection.TypeParagraph
13 selection.TypeText(’How are you today?\n’)
14 selection.TypeParagraph
15 selection.Style=’Normal’
16
17
18 selection.TypeText(’Big Finale\n’)
19 selection.Style=’Heading 1’
20 selection.TypeParagraph
21
22 H1 = document.Styles.Item(’Heading 1’)
23 H1.Font.Name = ’Garamond’
24 H1.Font.Size = 20
25 H1.Font.Bold = 1
26 H1.Font.TextColor.RGB=60000 # some ugly color green
27
28 selection.TypeParagraph
29 selection.TypeText(’That is all for today!’)
30

235
31
32 document.SaveAs2(os.getcwd() + ’/test.docx’)
33 word.Quit()

./test.docx
That is it! I would not call this extra convenient, but if you have a need
to automate the production of Word documents from a program, this is an ap-
proach that you can use. You may find http://msdn.microsoft.com/en-us/
library/kw65a0we%28v=vs.80%29.aspx a helpful link for documentation of
what you can do.
I was going to do this by docx, which does not require windows, but it
appears broken. It is missing a template directory, and it does not match the
github code. docx is not actively maintained anymore either.

1 from docx import *

2
3 # Make a new document tree - this is the main part of a Word document
4 document = Docx()
5
6 document.append(paragraph(’Hello world. ’
7 ’My name is Professor Kitchin’
8 ’How are you today?’))
9
10 document.append(heading("Big Finale", 1))
11
12 document.append(paragraph(’That is all for today.’))
13
14 document.save(’test.doc’)

12.8 Interacting with Excel in python

Matlab post
There will be times it is convenient to either read data from Excel, or write
data to Excel. This is possible in python (http://www.python-excel.org/).
You may also look at (https://bitbucket.org/ericgazoni/openpyxl/wiki/
Home).

1 import xlrd
2
3 wb = xlrd.open_workbook(’data/example.xlsx’)
4 sh1 = wb.sheet_by_name(u’Sheet1’)
5
6 print sh1.col_values(0) # column 0
7 print sh1.col_values(1) # column 1
8
9 sh2 = wb.sheet_by_name(u’Sheet2’)
10
11 x = sh2.col_values(0) # column 0
12 y = sh2.col_values(1) # column 1
13
14 import matplotlib.pyplot as plt
15 plt.plot(x, y)
16 plt.savefig(’images/excel-1.png’)

[u’value’, u’function’]
[2.0, 3.0]

236
 12.8.1 Writing Excel workbooks
Writing data to Excel sheets is pretty easy. Note, however, that this overwrites
the worksheet if it already exists.

1 import xlwt
2 import numpy as np
3
4 x = np.linspace(0, 2)
5 y = np.sqrt(x)
6
7 # save the data
8 book = xlwt.Workbook()
9
10 sheet1 = book.add_sheet(’Sheet 1’)
11
12 for i in range(len(x)):
13 sheet1.write(i, 0, x[i])
14 sheet1.write(i, 1, y[i])
15
16 book.save(’data/example2.xls’) # maybe can only write .xls format

12.8.2 Updating an existing Excel workbook

It turns out you have to make a copy of an existing workbook, modify the copy
and then write out the results using the xlwt module.

1 from xlrd import open_workbook

2
3 from xlutils.copy import copy
4

237
5 rb = open_workbook(’data/example2.xls’,formatting_info=True)
6 rs = rb.sheet_by_index(0)
7
8 wb = copy(rb)
9
10 ws = wb.add_sheet(’Sheet 2’)
11 ws.write(0, 0, "Appended")
12
13 wb.save(’data/example2.xls’)

12.8.3 Summary
Matlab has better support for interacting with Excel than python does right
now. You could get better Excel interaction via COM, but that is Windows
specific, and requires you to have Excel installed on your computer. If you only
need to read or write data, then xlrd/xlwt or the openpyxl modules will server
you well.

12.9 Using Excel in Python

, There may be a time where you have an Excel sheet that already has a model
built into it, and you normally change cells in the sheet, and it solves the model.
It can be tedious to do that a lot, and we can use python to do that. Python has
a COM interface that can communicate with Excel (and many other windows
programs. see http://my.safaribooksonline.com/1565926218 for Python
Programming on Win32). In this example, we will use a very simple Excel
sheet that calculates the volume of a CSTR that runs a zeroth order reaction
(−rA = k) for a particular conversion. You set the conversion in the cell B1,
and the volume is automatically computed in cell B6. We simply need to set the
value of B1, and get the value of B6 for a range of different conversion values.
In this example, the volume is returned in Liters.

1 import win32com.client as win32

2 excel = win32.Dispatch(’Excel.Application’)
3
4 wb = excel.Workbooks.Open(’c:/Users/jkitchin/Dropbox/pycse/data/cstr-zeroth-order.xlsx’)
5 ws = wb.Worksheets(’Sheet1’)
6
7 X = [0.1, 0.5, 0.9]
8 for x in X:
9 ws.Range("B1").Value = x
10 V = ws.Range("B6").Value
11 print ’at X = {0} V = {1:1.2f} L’.format(x, V)
12
13 # we tell Excel the workbook is saved, even though it is not, so it
14 # will quit without asking us to save.
15 excel.ActiveWorkbook.Saved = True
16 excel.Application.Quit()

at X = 0.1 V = 22.73 L
at X = 0.5 V = 113.64 L
at X = 0.9 V = 204.55 L

238
 This was a simple example (one that did not actually need Excel at all) that
illustrates the feasibility of communicating with Excel via a COM interface.
Some links I have found that help figure out how to do this are:
• http://www.numbergrinder.com/2008/11/pulling-data-from-excel-using-python-com/

• http://www.numbergrinder.com/2008/11/closing-excel-using-python/
• http://www.dzone.com/snippets/script-excel-python

12.10 Running Aspen via Python

Aspen is a process modeling tool that simulates industrial processes. It has a
GUI for setting up the flowsheet, defining all the stream inputs and outputs,
and for running the simulation. For single calculations it is pretty convenient.
For many calculations, all the pointing and clicking to change properties can
be tedious, and difficult to reproduce. Here we show how to use Python to
automate Aspen using the COM interface.
We have an Aspen flowsheet setup for a flash operation. The feed consists of
91.095 mol% water and 8.905 mol% ethanol at 100 degF and 50 psia. 48.7488
lbmol/hr of the mixture is fed to the flash tank which is at 150 degF and 20
psia. We want to know the composition of the VAPOR and LIQUID streams.
The simulation has been run once.

This is an example that just illustrates it is possible to access data from a

simulation that has been run. You have to know quite a bit about the Aspen
flowsheet before writing this code. Particularly, you need to open the Variable
Explorer to find the "path" to the variables that you want, and to know what
the units are of those variables are.

1 import os
2 import win32com.client as win32
3 aspen = win32.Dispatch(’Apwn.Document’)
4
5 aspen.InitFromArchive2(os.path.abspath(’data\Flash_Example.bkp’))
6

239
7 ## Input variables
8 feed_temp = aspen.Tree.FindNode(’\Data\Streams\FEED\Input\TEMP\MIXED’).Value
9 print ’Feed temperature was {0} degF’.format(feed_temp)
10
11 ftemp = aspen.Tree.FindNode(’\Data\Blocks\FLASH\Input\TEMP’).Value
12 print ’Flash temperature = {0}’.format(ftemp)
13
14 ## Output variables
15 eL_out = aspen.Tree.FindNode("\Data\Streams\LIQUID\Output\MOLEFLOW\MIXED\ETHANOL").Value
16 wL_out = aspen.Tree.FindNode("\Data\Streams\LIQUID\Output\MOLEFLOW\MIXED\WATER").Value
17
18 eV_out = aspen.Tree.FindNode("\Data\Streams\VAPOR\Output\MOLEFLOW\MIXED\ETHANOL").Value
19 wV_out = aspen.Tree.FindNode("\Data\Streams\VAPOR\Output\MOLEFLOW\MIXED\WATER").Value
20
21 tot = aspen.Tree.FindNode("\Data\Streams\FEED\Input\TOTFLOW\MIXED").Value
22
23 print ’Ethanol vapor mol flow: {0} lbmol/hr’.format(eV_out)
24 print ’Ethanol liquid mol flow: {0} lbmol/hr’.format(eL_out)
25
26 print ’Water vapor mol flow: {0} lbmol/hr’.format(wV_out)
27 print ’Water liquid mol flow: {0} lbmol/hr’.format(wL_out)
28
29 print ’Total = {0}. Total in = {1}’.format(eV_out + eL_out + wV_out + wL_out,
30 tot)
31
32 aspen.Close()

Feed temperature was 100.0 degF

Flash temperature = 150.0
Ethanol vapor mol flow: 3.89668323 lbmol/hr
Ethanol liquid mol flow: 0.444397241 lbmol/hr
Water vapor mol flow: 0.774592763 lbmol/hr
Water liquid mol flow: 43.6331268 lbmol/hr
Total = 48.748800034. Total in = 48.7488

It is nice that we can read data from a simulation, but it would be helpful if
we could change variable values and to rerun the simulations. That is possible.
We simply set the value of the variable, and tell Aspen to rerun. Here, we will
change the temperature of the Flash tank and plot the composition of the outlet
streams as a function of that temperature.

1 import os
2 import numpy as np
3 import matplotlib.pyplot as plt
4 import win32com.client as win32
5
6 aspen = win32.Dispatch(’Apwn.Document’)
7 aspen.InitFromArchive2(os.path.abspath(’data\Flash_Example.bkp’))
8
9 T = np.linspace(150, 200, 10)
10
11 x_ethanol, y_ethanol = [], []
12
13 for temperature in T:
14 aspen.Tree.FindNode(’\Data\Blocks\FLASH\Input\TEMP’).Value = temperature
15 aspen.Engine.Run2()
16
17 x_ethanol.append(aspen.Tree.FindNode(’\Data\Streams\LIQUID\Output\MOLEFRAC\MIXED\ETHANOL’).Value)
18 y_ethanol.append(aspen.Tree.FindNode(’\Data\Streams\VAPOR\Output\MOLEFRAC\MIXED\ETHANOL’).Value)
19

240
20 plt.plot(T, y_ethanol, T, x_ethanol)
21 plt.legend([’vapor’, ’liquid’])
22 plt.xlabel(’Flash Temperature (degF)’)
23 plt.ylabel(’Ethanol mole fraction’)
24 plt.savefig(’images/aspen-water-ethanol-flash.png’)
25 aspen.Close()

It takes about 30 seconds to run the previous example. Unfortunately, the

way it is written, if you want to change anything, you have to run all of the
calculations over again. How to avoid that is moderately tricky, and will be the
subject of another example.
In summary, it seems possible to do a lot with Aspen automation via
python. This can also be done with Matlab, Excel, and other program-
ming languages where COM automation is possible. The COM interface is
not especially well documented, and you have to do a lot of digging to fig-
ure out some things. It is not clear how committed Aspen is to maintaining
or improving the COM interface (http://www.chejunkie.com/aspen-plus/
aspen-plus-activex-automation-server/). Hopefully they can keep it alive
for power users who do not want to program in Excel!

12.11 Using an external solver with Aspen

One reason to interact with Aspen via python is to use external solvers to
drive the simulations. Aspen has some built-in solvers, but it does not have
everything. You may also want to integrate additional calculations, e.g. capital
costs, water usage, etc. . . and integrate those results into a report.
Here is a simple example where we use fsolve to find the temperature of the
flash tank that will give a vapor phase mole fraction of ethanol of 0.8. It is a

241
 simple example, but it illustrates the possibility.

1 import os
2 import win32com.client as win32
3 aspen = win32.Dispatch(’Apwn.Document’)
4
5 aspen.InitFromArchive2(os.path.abspath(’data\Flash_Example.bkp’))
6
7 from scipy.optimize import fsolve
8
9 def func(flashT):
10 flashT = float(flashT) # COM objects do not understand numpy types
11 aspen.Tree.FindNode(’\Data\Blocks\FLASH\Input\TEMP’).Value = flashT
12 aspen.Engine.Run2()
13 y = aspen.Tree.FindNode(’\Data\Streams\VAPOR\Output\MOLEFRAC\MIXED\ETHANOL’).Value
14 return y - 0.8
15
16 sol, = fsolve(func, 150.0)
17 print ’A flash temperature of {0:1.2f} degF will have y_ethanol = 0.8’.format(sol)

A flash temperature of 157.38 degF will have y_ethanol = 0.8

One unexpected detail was that the Aspen COM objects cannot be assigned
numpy number types, so it was necessary to recast the argument as a float.
Otherwise, this worked about as expected for an fsolve problem.

12.12 Redirecting the print function

Ordinarily a print statement prints to stdout, or your terminal/screen. You
can redirect this so that printing is done to a file, for example. This might be
helpful if you use print statements for debugging, and later want to save what
is printed to a file. Here we make a simple function that prints some things.

1 def debug():
2 print ’step 1’
3 print 3 + 4
4 print ’finished’
5
6 debug()

... ... ... >>> step 1

7
finished

Now, let us redirect the printed lines to a file. We create a file object, and
set sys.stdout equal to that file object.

1 import sys
2 print >> sys.__stdout__, ’__stdout__ before = ’, sys.__stdout__
3 print >> sys.__stdout__, ’stdout before = ’, sys.stdout
4
5 f = open(’data/debug.txt’, ’w’)
6 sys.stdout = f
7

242
8 # note that sys.__stdout__ does not change, but stdout does.
9 print >> sys.__stdout__, ’__stdout__ after = ’, sys.__stdout__
10 print >> sys.__stdout__, ’stdout after = ’, sys.stdout
11
12 debug()
13
14 # reset stdout back to console
15 sys.stdout = sys.__stdout__
16
17 print f
18 f.close() # try to make it a habit to close files
19 print f

__stdout__ before = <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>

stdout before = <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
>>> >>> >>> >>> ... __stdout__ after = <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
stdout after = <open file ’data/debug.txt’, mode ’w’ at 0x2ae7dbcbbb70>
>>> >>> >>> ... >>> >>> >>> <open file ’data/debug.txt’, mode ’w’ at 0x2ae7dbcbbb70>
>>> <closed file ’data/debug.txt’, mode ’w’ at 0x2ae7dbcbbb70>

Note it can be important to close files. If you are looping through large
numbers of files, you will eventually run out of file handles, causing an error.
We can use a context manager to automatically close the file like this

1 import sys
2
3 # use the open context manager to automatically close the file
4 with open(’data/debug.txt’, ’w’) as f:
5 sys.stdout = f
6 debug()
7 print >> sys.__stdout__, f
8
9 # reset stdout
10 sys.stdout = sys.__stdout__
11 print f

>>> ... ... ... ... ... <open file ’data/debug.txt’, mode ’w’ at 0x0000000002071C00>
... >>> <closed file ’data/debug.txt’, mode ’w’ at 0x0000000002071C00>

See, the file is closed for us! We can see the contents of our file like
this.

1 cat data/debug.txt

step 1
7
finished

The approaches above are not fault safe. Suppose our debug function raised
an exception. Then, it could be possible the line to reset the stdout would not
be executed. We can solve this with try/finally code.

243
1 import sys
2
3 print ’before: ’, sys.stdout
4 try:
5 with open(’data/debug-2.txt’, ’w’) as f:
6 sys.stdout = f
7 # print to the original stdout
8 print >> sys.__stdout__, ’during: ’, sys.stdout
9 debug()
10 raise Exception(’something bad happened’)
11 finally:
12 # reset stdout
13 sys.stdout = sys.__stdout__
14
15 print ’after: ’, sys.stdout
16 print f # verify it is closed
17 print sys.stdout # verify this is reset

>>> before: <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>

... ... ... ... ... ... ... ... ... ... during: <open file ’data/debug-2.txt’, mode ’w’ at
Traceback (most recent call last):
File "<stdin>", line 7, in <module>
Exception: something bad happened
after: <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
<closed file ’data/debug-2.txt’, mode ’w’ at 0x2ae7dbcbbf60>
<open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>

1 cat data/debug-2.txt

step 1
7
finished

This is the kind of situation where a context manager is handy. Context

managers are typically a class that executes some code when you "enter" the
context, and then execute some code when you "exit" the context. Here we
want to change sys.stdout to a new value inside our context, and change it back
when we exit the context. We will store the value of sys.stdout going in, and
restore it on the way out.

1 import sys
2
3 class redirect:
4 def __init__(self, f=sys.stdout):
5 "redirect print statement to f. f must be a file-like object"
6 self.f = f
7 self.stdout = sys.stdout
8 print >> sys.__stdout__, ’init stdout: ’, sys.stdout
9 def __enter__(self):
10 sys.stdout = self.f
11 print >> sys.__stdout__, ’stdout in context-manager: ’,sys.stdout
12 def __exit__(self, *args):
13 sys.stdout = self.stdout

244
14 print ’__stdout__ at exit = ’,sys.__stdout__
15
16 # regular printing
17 with redirect():
18 debug()
19
20 # write to a file
21 with open(’data/debug-3.txt’, ’w’) as f:
22 with redirect(f):
23 debug()
24
25 # mixed regular and
26 with open(’data/debug-4.txt’, ’w’) as f:
27 with redirect(f):
28 print ’testing redirect’
29 with redirect():
30 print ’temporary console printing’
31 debug()
32 print ’Now outside the inner context. this should go to data/debug-4.txt’
33 debug()
34 raise Exception(’something else bad happened’)
35
36 print sys.stdout

>>> ... ... ... ... ... ... ... ... ... ... ... ... >>> ... ... ... init stdout: <open file
stdout in context-manager: <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
step 1
7
finished
__stdout__ at exit = <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
... ... ... ... init stdout: <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
stdout in context-manager: <open file ’data/debug-3.txt’, mode ’w’ at 0x2ae7dbcbbb70>
__stdout__ at exit = <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
... ... ... ... ... ... ... ... ... ... init stdout: <open file ’<stdout>’, mode ’w’ at 0x2
stdout in context-manager: <open file ’data/debug-4.txt’, mode ’w’ at 0x2ae7dca4d030>
init stdout: <open file ’data/debug-4.txt’, mode ’w’ at 0x2ae7dca4d030>
stdout in context-manager: <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
temporary console printing
step 1
7
finished
__stdout__ at exit = <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
Traceback (most recent call last):
File "<stdin>", line 10, in <module>
Exception: something else bad happened
<open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
Here are the contents of the debug file.

1 cat data/debug-3.txt

step 1
7
finished

245
 The contents of the other debug file have some additional lines, because we
printed some things while in the redirect context.

1 cat data/debug-4.txt

testing redirect
__stdout__ at exit = <open file ’<stdout>’, mode ’w’ at 0x2ae7d70e01e0>
Now outside the inner context. this should go to data/debug-4.txt
step 1
7
finished

See http://www.python.org/dev/peps/pep-0343/ (number 5) for another

example of redirecting using a function decorator. I think it is harder to under-
stand, because it uses a generator.
There were a couple of points in this section:

1. You can control where things are printed in your programs by modifying
the value of sys.stdout
2. You can use try/except/finally blocks to make sure code gets executed in
the event an exception is raised

3. You can use context managers to make sure files get closed, and code gets
executed if exceptions are raised.

12.13 Modifying functions with decorators

Sometimes, it is useful to modify an existing function, without changing the
original definition of the function.

12.14 Getting a dictionary of counts

I frequently want to take a list and get a dictionary of keys that have the count
of each element in the list. Here is how I have typically done this countless times
in the past.

1 L = [’a’, ’a’, ’b’,’d’, ’e’, ’b’, ’e’, ’a’]

2
3 d = {}
4 for el in L:
5 if el in d:
6 d[el] += 1
7 else:
8 d[el] = 1
9
10 print d

{’a’: 3, ’b’: 2, ’e’: 2, ’d’: 1}

246
 That seems like too much code, and that there must be a list comprehension
approach combined with a dictionary constructor.

1 L = [’a’, ’a’, ’b’,’d’, ’e’, ’b’, ’e’, ’a’]

2
3 print dict((el,L.count(el)) for el in L)

{’a’: 3, ’b’: 2, ’e’: 2, ’d’: 1}

Wow, that is a lot simpler! I suppose for large lists this might be slow, since
count must look through the list for each element, whereas the longer code looks
at each element once, and does one conditional analysis.
Here is another example of much shorter and cleaner code.

1 from collections import Counter

2 L = [’a’, ’a’, ’b’,’d’, ’e’, ’b’, ’e’, ’a’]
3 print Counter(L)
4 print Counter(L)[’a’]

Counter({’a’: 3, ’b’: 2, ’e’: 2, ’d’: 1})

3

12.15 About your python

1 import sys
2
3 print sys.version
4
5 print sys.executable
6
7 print sys.getwindowsversion()
8
9 print sys.platform
10
11 # where the platform independent Python files are installed
12 print sys.prefix

2.7.3 | 64-bit | (default, Mar 25 2013, 15:41:53) [MSC v.1500 64 bit (AMD64)]
C:\Users\jkitchin\AppData\Local\Enthought\Canopy\User\Scripts\python.exe
sys.getwindowsversion(major=6, minor=1, build=7601, platform=2, service_pack=’Service Pack 1
win32
C:\Users\jkitchin\AppData\Local\Enthought\Canopy\User

The platform module provides similar, complementary information.

1 import platform
2
3 print platform.uname()
4 print platform.system()
5 print platform.architecture()
6 print platform.machine()
7 print platform.node()
8 print platform.platform()

247
9 print platform.processor()
10 print platform.python_build()
11 print platform.python_version()

(’Windows’, ’jkitchin-2012’, ’7’, ’6.1.7601’, ’AMD64’, ’Intel64 Family 6 Model 58 Stepping 9

Windows
(’64bit’, ’WindowsPE’)
AMD64
jkitchin-2012
Windows-7-6.1.7601-SP1
Intel64 Family 6 Model 58 Stepping 9, GenuineIntel
(’default’, ’Mar 25 2013 15:41:53’)
2.7.3

12.16 Automatic, temporary directory changing

If you are doing some analysis that requires you to change directories, e.g. to
read a file, and then change back to another directory to read another file, you
have probably run into problems if there is an error somewhere. You would like
to make sure that the code changes back to the original directory after each
error. We will look at a few ways to accomplish that here.
The try/except/finally method is the traditional way to handle exceptions,
and make sure that some code "finally" runs. Let us look at two examples here.
In the first example, we try to change into a directory that does not exist.

1 import os, sys

2
3 CWD = os.getcwd() # store initial position
4 print ’initially inside {0}’.format(os.getcwd())
5 TEMPDIR = ’data/run1’ # this does not exist
6
7 try:
8 os.chdir(TEMPDIR)
9 print ’inside {0}’.format(os.getcwd())
10 except:
11 print ’Exception caught: ’,sys.exc_info()[0]
12 finally:
13 print ’Running final code’
14 os.chdir(CWD)
15 print ’finally inside {0}’.format(os.getcwd())

initially inside c:\users\jkitchin\Dropbox\pycse

Exception caught: <type ’exceptions.WindowsError’>
Running final code
finally inside c:\users\jkitchin\Dropbox\pycse

Now, let us look at an example where the directory does exist. We will
change into the directory, run some code, and then raise an Exception.

1 import os, sys

2

248
3 CWD = os.getcwd() # store initial position
4 print ’initially inside {0}’.format(os.getcwd())
5 TEMPDIR = ’data’
6
7 try:
8 os.chdir(TEMPDIR)
9 print ’inside {0}’.format(os.getcwd())
10 print os.listdir(’.’)
11 raise Exception(’boom’)
12 except:
13 print ’Exception caught: ’,sys.exc_info()[0]
14 finally:
15 print ’Running final code’
16 os.chdir(CWD)
17 print ’finally inside {0}’.format(os.getcwd())

initially inside c:\users\jkitchin\Dropbox\pycse

inside c:\users\jkitchin\Dropbox\pycse\data
[’antoine_data.dat’, ’antoine_database.mat’, ’commonshellsettings.xml’, ’cstr-zeroth-order.x
Exception caught: <type ’exceptions.Exception’>
Running final code
finally inside c:\users\jkitchin\Dropbox\pycse

You can see that we changed into the directory, ran some code, and then
caught an exception. Afterwards, we changed back to our original directory.
This code works fine, but it is somewhat verbose, and tedious to write over
and over. We can get a cleaner syntax with a context manager. The context
manager uses the with keyword in python. In a context manager some code is
executed on entering the "context", and code is run on exiting the context. We
can use that to automatically change directory, and when done, change back to
the original directory. We use the contextlib.contextmanager decorator on a
function. With a function, the code up to a yield statement is run on entering
the context, and the code after the yield statement is run on exiting. We wrap
the yield statement in try/except/finally block to make sure our final code gets
run.

1 import contextlib
2 import os, sys
3
4 @contextlib.contextmanager
5 def cd(path):
6 print ’initially inside {0}’.format(os.getcwd())
7 CWD = os.getcwd()
8
9 os.chdir(path)
10 print ’inside {0}’.format(os.getcwd())
11 try:
12 yield
13 except:
14 print ’Exception caught: ’,sys.exc_info()[0]
15 finally:
16 print ’finally inside {0}’.format(os.getcwd())
17 os.chdir(CWD)
18
19 # Now we use the context manager
20 with cd(’data’):
21 print os.listdir(’.’)

249
22 raise Exception(’boom’)
23
24 print
25 with cd(’data/run2’):
26 print os.listdir(’.’)

One case that is not handled well with this code is if the directory you want
to change into does not exist. In that case an exception is raised on entering the
context when you try change into a directory that does not exist. An alternative
class based context manager can be found here.

12.17 multiprocessing
1 import multiprocessing
2
3 cpus = multiprocessing.cpu_count()
4 print cpus

13 Miscellaneous
13.1 Mail merge with python
Suppose you are organizing some event, and you have a mailing list of email
addresses and people you need to send a mail to telling them what room they
will be in. You would like to send a personalized email to each person, and you
do not want to type each one by hand. Python can automate this for you. All
you need is the mailing list in some kind of structured format, and then you can
go through it line by line to create and send emails.
We will use an org-table to store the data in.
First name Last name email address Room number
Jane Doe [email protected] 1
John Doe [email protected] 2
Jimmy John [email protected] 3
We pass that table into an org-mode source block as a variable called data,
which will be a list of lists, one for each row of the table. You could alternatively
read these from an excel spreadsheet, a csv file, or some kind of python data
structure.
We do not actually send the emails in this example. To do that you need to
have access to a mail server, which could be on your own machine, or it could
be a relay server you have access to.
We create a string that is a template with some fields to be substituted, e.g.
the firstname and room number in this case. Then we loop through each row
of the table, and format the template with those values, and create an email
message to the person. First we print each message to check that they are
correct.

250
1 import smtplib
2 from email.MIMEMultipart import MIMEMultipart
3 from email.MIMEText import MIMEText
4 from email.Utils import formatdate
5
6 template = ’’’
7 Dear {firstname:s},
8
9 I am pleased to inform you that your talk will be in room {roomnumber:d}.
10
11 Sincerely,
12 John
13 ’’’
14
15 for firstname, lastname, emailaddress, roomnumber in data:
16 msg = MIMEMultipart()
17 msg[’From’] = "[email protected]"
18 msg[’To’] = emailaddress
19 msg[’Date’] = formatdate(localtime=True)
20
21 msgtext = template.format(**locals())
22 print msgtext
23
24 msg.attach(MIMEText(msgtext))
25
26 ## Uncomment these lines and fix
27 #server = smtplib.SMTP(’your.relay.server.edu’)
28 #server.sendmail(’[email protected]’, # from
29 # emailaddress,
30 # msg.as_string())
31 #server.quit()
32
33 print msg.as_string()
34 print ’------------------------------------------------------------------’

Dear Jane,

I am pleased to inform you that your talk will be in room 1.

Sincerely,
John

Content-Type: multipart/mixed; boundary="===============1191311863=="

MIME-Version: 1.0
From: [email protected]
To: [email protected]
Date: Tue, 16 Apr 2013 16:10:23 -0400

--===============1191311863==
Content-Type: text/plain; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit

Dear Jane,

251
I am pleased to inform you that your talk will be in room 1.

Sincerely,
John

--===============1191311863==--
------------------------------------------------------------------

Dear John,

I am pleased to inform you that your talk will be in room 2.

Sincerely,
John

Content-Type: multipart/mixed; boundary="===============1713881863=="

MIME-Version: 1.0
From: [email protected]
To: [email protected]
Date: Tue, 16 Apr 2013 16:10:23 -0400

--===============1713881863==
Content-Type: text/plain; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit

Dear John,

I am pleased to inform you that your talk will be in room 2.

Sincerely,
John

--===============1713881863==--
------------------------------------------------------------------

Dear Jimmy,

I am pleased to inform you that your talk will be in room 3.

Sincerely,
John

Content-Type: multipart/mixed; boundary="===============0696685580=="

MIME-Version: 1.0

252
 From: [email protected]
To: [email protected]
Date: Tue, 16 Apr 2013 16:10:23 -0400

--===============0696685580==
Content-Type: text/plain; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit

Dear Jimmy,

I am pleased to inform you that your talk will be in room 3.

Sincerely,
John

--===============0696685580==--
------------------------------------------------------------------

14 Worked examples
14.1 Peak finding in Raman spectroscopy
Raman spectroscopy is a vibrational spectroscopy. The data typically comes
as intensity vs. wavenumber, and it is discrete. Sometimes it is necessary to
identify the precise location of a peak. In this post, we will use spline smoothing
to construct an interpolating function of the data, and then use fminbnd to
identify peak positions.
This example was originally worked out in Matlab at http://matlab.
cheme.cmu.edu/2012/08/27/peak-finding-in-raman-spectroscopy/
numpy:loadtxt
Let us take a look at the raw data.

1 import os
2 print os.getcwd()
3 print os.environ[’HOME’]

/home/jkitchin/Dropbox/intro-python
/home/jkitchin

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 w, i = np.loadtxt(’data/raman.txt’, usecols=(0, 1), unpack=True)
5

253
6 plt.plot(w, i)
7 plt.xlabel(’Raman shift (cm$^{-1}$)’)
8 plt.ylabel(’Intensity (counts)’)
9 plt.savefig(’images/raman-1.png’)
10 plt.show()

>>> >>> >>> >>> [<matplotlib.lines.Line2D object at 0x1d372810>]

<matplotlib.text.Text object at 0x1d48df90>
<matplotlib.text.Text object at 0x1d356a10>

The next thing to do is narrow our focus to the region we are interested in
between 1340 cmˆ{-1} and 1360 cmˆ{-1}.

1 ind = (w > 1340) & (w < 1360)

2 w1 = w[ind]
3 i1 = i[ind]
4
5 plt.plot(w1, i1, ’b. ’)
6 plt.xlabel(’Raman shift (cm$^{-1}$)’)
7 plt.ylabel(’Intensity (counts)’)
8 plt.savefig(’images/raman-2.png’)
9 plt.show()

>>> [<matplotlib.lines.Line2D object at 0x1d5005d0>]

<matplotlib.text.Text object at 0x1d37a650>
<matplotlib.text.Text object at 0x1d3809d0>

254
 Next we consider a scipy:UnivariateSpline. This function "smooths" the
data.

1 from scipy.interpolate import UnivariateSpline

2
3 # s is a "smoothing" factor
4 sp = UnivariateSpline(w1, i1, s=3000)
5
6 plt.plot(w1, i1, ’b. ’)
7 plt.plot(w1, sp(w1), ’r-’)
8 plt.xlabel(’Raman shift (cm$^{-1}$)’)
9 plt.ylabel(’Intensity (counts)’)
10 plt.savefig(’images/raman-3.png’)
11 plt.show()

... [<matplotlib.lines.Line2D object at 0x1dd35e90>]

[<matplotlib.lines.Line2D object at 0x2ab334a3d510>]
<matplotlib.text.Text object at 0x1d49bad0>
<matplotlib.text.Text object at 0x1dd3b950>

255
 Note that the UnivariateSpline function returns a "callable" function! Our
next goal is to find the places where there are peaks. This is defined by the first
derivative of the data being equal to zero. It is easy to get the first derivative
of a UnivariateSpline with a second argument as shown below.

1 # get the first derivative evaluated at all the points

2 d1 = sp(w1, 1)
3 plt.plot(w1, d1, label=’first derivative’)
4 plt.xlabel(’Raman shift (cm$^{-1}$)’)
5 plt.ylabel(’First derivative’)
6
7 # find the places where the first derivative crosses zero
8 s = np.zeros(d1.shape)
9 s[d1 >= 0] = 1
10 s[d1 < 0] = 0
11
12 initial_guesses = w1[np.diff(s) == -1]
13 plt.plot(initial_guesses, 0*initial_guesses, ’ro ’, label=’Guesses of zeros’)
14 plt.legend(loc=’best’)
15 plt.savefig(’images/raman-4.png’
16 plt.show()

>>> [<matplotlib.lines.Line2D object at 0x1d9eaad0>]

<matplotlib.text.Text object at 0x1d4f2210>
<matplotlib.text.Text object at 0x1d9e6910>
>>> ... >>> >>> >>> >>> >>> [<matplotlib.lines.Line2D object at 0x1d4f3250>]
<matplotlib.legend.Legend object at 0x1d839510>

256
 Now, we can use these initial guesses to solve for the actual values.

1 from scipy.optimize import fminbound

2
3 def func(w):
4 ’function to minimize’
5 return -sp(w)
6
7 for value in initial_guesses:
8 sol = fminbound(func, value - 1, value + 1)
9 plt.plot(sol, sp(sol), ’ro ’, ms=8)
10 print ’Peak found at {0} cm^{{-1}}’.format(sol)
11
12 plt.plot(w1, i1, ’b. ’)
13 plt.plot(w1, sp(w1), ’r-’)
14 plt.xlabel(’Raman shift (cm$^{-1}$)’)
15 plt.ylabel(’Intensity (counts)’)
16 plt.savefig(’images/raman-5.png’)
17 plt.show()

... ... ... >>> ... [<matplotlib.lines.Line2D object at 0x1da00510>]

Peak found at 1346.50980295 cm^{-1}
[<matplotlib.lines.Line2D object at 0x1d4c0110>]
Peak found at 1348.11261373 cm^{-1}
[<matplotlib.lines.Line2D object at 0x1da02b90>]
[<matplotlib.lines.Line2D object at 0x1da02750>]
<matplotlib.text.Text object at 0x1da01850>
<matplotlib.text.Text object at 0x1d9d4110>

In the end, we have illustrated how to construct a spline smoothing interpo-

lation function and to find maxima in the function, including generating some

257
 initial guesses. There is more art to this than you might like, since you have to
judge how much smoothing is enough or too much. With too much, you may
smooth peaks out. With too little, noise may be mistaken for peaks.

14.1.1 Summary notes

Using org-mode with :session allows a large script to be broken up into mini
sections. However, it only seems to work with the default python mode in
Emacs, and it does not work with emacs-for-python or the latest python-mode.
I also do not really like the output style, e.g. the output from the plotting
commands.

14.2 Curve fitting to get overlapping peak areas

Today we examine an approach to fitting curves to overlapping peaks to decon-
volute them so we can estimate the area under each curve. We have a text file
that contains data from a gas chromatograph with two peaks that overlap. We
want the area under each peak to estimate the gas composition. You will see
how to read the text file in, parse it to get the data for plotting and analysis,
and then how to fit it.
A line like "# of Points 9969" tells us the number of points we have to read.
The data starts after a line containing "R.Time Intensity". Here we read the
number of points, and then get the data into arrays.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 datafile = ’data/gc-data-21.txt’
5
6 i = 0
7 with open(datafile) as f:
8 lines = f.readlines()
9
10 for i,line in enumerate(lines):
11 if ’# of Points’ in line:
12 npoints = int(line.split()[-1])
13 elif ’R.Time Intensity’ in line:
14 i += 1
15 break
16
17 # now get the data
18 t, intensity = [], []
19 for j in range(i, i + npoints):
20 fields = lines[j].split()
21 t += [float(fields[0])]
22 intensity += [int(fields[1])]
23
24 t = np.array(t)
25 intensity = np.array(intensity)
26
27 # now plot the data in the relevant time frame
28 plt.plot(t, intensity)
29 plt.xlim([4, 6])
30 plt.xlabel(’Time (s)’)
31 plt.ylabel(’Intensity (arb. units)’)
32 plt.savefig(’images/deconvolute-1.png’)

258
 >>> >>> >>> >>> >>> ... ... >>> ... ... ... ... ... ... >>> ... >>> ... ... ... ... >>> >>>
(4, 6)
<matplotlib.text.Text object at 0x04BBB950>
<matplotlib.text.Text object at 0x04BD0A10>

You can see there is a non-zero baseline. We will normalize that by the
average between 4 and 4.4 seconds.

1 intensity -= np.mean(intensity[(t> 4) & (t < 4.4)])

2 plt.figure()
3 plt.plot(t, intensity)
4 plt.xlim([4, 6])
5 plt.xlabel(’Time (s)’)
6 plt.ylabel(’Intensity (arb. units)’)
7 plt.savefig(’./images/deconvolute-2.png’)

<matplotlib.figure.Figure object at 0x04CF7950>

[<matplotlib.lines.Line2D object at 0x04DF5C30>]
(4, 6)
<matplotlib.text.Text object at 0x04DDB690>
<matplotlib.text.Text object at 0x04DE3630>

259
 The peaks are asymmetric, decaying gaussian functions. We define a function
for this

1 from scipy.special import erf

2
3 def asym_peak(t, pars):
4 ’from Anal. Chem. 1994, 66, 1294-1301’
5 a0 = pars[0] # peak area
6 a1 = pars[1] # elution time
7 a2 = pars[2] # width of gaussian
8 a3 = pars[3] # exponential damping term
9 f = (a0/2/a3*np.exp(a2**2/2.0/a3**2 + (a1 - t)/a3)
10 *(erf((t-a1)/(np.sqrt(2.0)*a2) - a2/np.sqrt(2.0)/a3) + 1.0))
11 return f

To get two peaks, we simply add two peaks together.

1 def two_peaks(t, *pars):

2 ’function of two overlapping peaks’
3 a10 = pars[0] # peak area
4 a11 = pars[1] # elution time
5 a12 = pars[2] # width of gaussian
6 a13 = pars[3] # exponential damping term
7 a20 = pars[4] # peak area
8 a21 = pars[5] # elution time
9 a22 = pars[6] # width of gaussian
10 a23 = pars[7] # exponential damping term
11 p1 = asym_peak(t, [a10, a11, a12, a13])
12 p2 = asym_peak(t, [a20, a21, a22, a23])
13 return p1 + p2

To show the function is close to reasonable, we plot the fitting function with
an initial guess for each parameter. The fit is not good, but we have only guessed
the parameters for now.

260
1 parguess = (1500, 4.85, 0.05, 0.05, 5000, 5.1, 0.05, 0.1)
2 plt.figure()
3 plt.plot(t, intensity)
4 plt.plot(t,two_peaks(t, *parguess),’g-’)
5 plt.xlim([4, 6])
6 plt.xlabel(’Time (s)’)
7 plt.ylabel(’Intensity (arb. units)’)
8 plt.savefig(’images/deconvolution-3.png’)

<matplotlib.figure.Figure object at 0x04FEF690>

[<matplotlib.lines.Line2D object at 0x05049870>]
[<matplotlib.lines.Line2D object at 0x04FEFA90>]
(4, 6)
<matplotlib.text.Text object at 0x0502E210>
<matplotlib.text.Text object at 0x050362B0>

Next, we use nonlinear curve fitting from scipy.optimize.curve_fit

1 from scipy.optimize import curve_fit

2
3 popt, pcov = curve_fit(two_peaks, t, intensity, parguess)
4 print popt
5
6 plt.plot(t, two_peaks(t, *popt), ’r-’)
7 plt.legend([’data’, ’initial guess’,’final fit’])
8
9 plt.savefig(’images/deconvolution-4.png’)

261
 >>> >>> [ 1.31039283e+03 4.87474330e+00 5.55414785e-02 2.50610175e-02
5.32556821e+03 5.14121507e+00 4.68236129e-02 1.04105615e-01]
>>> [<matplotlib.lines.Line2D object at 0x0505BA10>]
<matplotlib.legend.Legend object at 0x05286270>

The fits are not perfect. The small peak is pretty good, but there is an
unphysical tail on the larger peak, and a small mismatch at the peak. There is
not much to do about that, it means the model peak we are using is not a good
model for the peak. We will still integrate the areas though.

1 pars1 = popt[0:4]
2 pars2 = popt[4:8]
3
4 peak1 = asym_peak(t, pars1)
5 peak2 = asym_peak(t, pars2)
6
7 area1 = np.trapz(peak1, t)
8 area2 = np.trapz(peak2, t)
9
10 print ’Area 1 = {0:1.2f}’.format(area1)
11 print ’Area 2 = {0:1.2f}’.format(area2)
12
13 print ’Area 1 is {0:1.2%} of the whole area’.format(area1/(area1 + area2))
14 print ’Area 2 is {0:1.2%} of the whole area’.format(area2/(area1 + area2))
15
16 plt.figure()
17 plt.plot(t, intensity)
18 plt.plot(t, peak1, ’r-’)
19 plt.plot(t, peak2, ’g-’)
20 plt.xlim([4, 6])
21 plt.xlabel(’Time (s)’)
22 plt.ylabel(’Intensity (arb. units)’)
23 plt.legend([’data’, ’peak 1’, ’peak 2’])
24 plt.savefig(’images/deconvolution-5.png’)

262
>>> >>> >>> >>> >>> >>> >>> >>> Area 1 = 1310.39
Area 2 = 5325.57
>>> Area 1 is 19.75% of the whole area
Area 2 is 80.25% of the whole area
>>> <matplotlib.figure.Figure object at 0x05286ED0>
[<matplotlib.lines.Line2D object at 0x053A5AB0>]
[<matplotlib.lines.Line2D object at 0x05291D30>]
[<matplotlib.lines.Line2D object at 0x053B9810>]
(4, 6)
<matplotlib.text.Text object at 0x0529C4B0>
<matplotlib.text.Text object at 0x052A3450>
<matplotlib.legend.Legend object at 0x053B9ED0>

This sample was air, and the first peak is oxygen, and the second peak is
nitrogen. we come pretty close to the actual composition of air, although it is
low on the oxygen content. To do better, one would have to use a calibration
curve.
In the end, the overlap of the peaks is pretty small, but it is still difficult
to reliably and reproducibly deconvolute them. By using an algorithm like
we have demonstrated here, it is possible at least to make the deconvolution
reproducible.

14.2.1 Notable differences from Matlab

1. The order of arguments to np.trapz is reversed.
2. The order of arguments to the fitting function scipy.optimize.curve_fit is

263
 different than in Matlab.
3. The scipy.optimize.curve_fit function expects a fitting function that has
all parameters as arguments, where Matlab expects a vector of parameters.

14.3 Estimating the boiling point of water

Matlab post
I got distracted looking for Shomate parameters for ethane today, and came
across this website on predicting the boiling point of water using the Shomate
equations. The basic idea is to find the temperature where the Gibbs energy of
water as a vapor is equal to the Gibbs energy of the liquid.

1 import matplotlib.pyplot as plt

Liquid water (http://webbook.nist.gov/cgi/cbook.cgi?ID=C7732185&Units=

SI&Mask=2#Thermo-Condensed)

1 # valid over 298-500

2
3 Hf_liq = -285.830 # kJ/mol
4 S_liq = 0.06995 # kJ/mol/K
5 shomateL = [-203.6060,
6 1523.290,
7 -3196.413,
8 2474.455,
9 3.855326,
10 -256.5478,
11 -488.7163,
12 -285.8304]

Gas phase water (http://webbook.nist.gov/cgi/cbook.cgi?ID=C7732185&Units=

SI&Mask=1&Type=JANAFG&Table=on#JANAFG)
Interestingly, these parameters are listed as valid only above 500K. That
means we have to extrapolate the values down to 298K. That is risky for poly-
nomial models, as they can deviate substantially outside the region they were
fitted to.

1 Hf_gas = -241.826 # kJ/mol

2 S_gas = 0.188835 # kJ/mol/K
3
4 shomateG = [30.09200,
5 6.832514,
6 6.793435,
7 -2.534480,
8 0.082139,
9 -250.8810,
10 223.3967,
11 -241.8264]

Now, we wan to compute G for each phase as a function of T

264
1 import numpy as np
2
3 T = np.linspace(0, 200) + 273.15
4 t = T / 1000.0
5
6 sTT = np.vstack([np.log(t),
7 t,
8 (t**2) / 2.0,
9 (t**3) / 3.0,
10 -1.0 / (2*t**2),
11 0 * t,
12 t**0,
13 0 * t**0]).T / 1000.0
14
15 hTT = np.vstack([t,
16 (t**2)/2.0,
17 (t**3)/3.0,
18 (t**4)/4.0,
19 -1.0 / t,
20 1 * t**0,
21 0 * t**0,
22 -1 * t**0]).T
23
24 Gliq = Hf_liq + np.dot(hTT, shomateL) - T*(np.dot(sTT, shomateL))
25 Ggas = Hf_gas + np.dot(hTT, shomateG) - T*(np.dot(sTT, shomateG))
26
27 from scipy.interpolate import interp1d
28 from scipy.optimize import fsolve
29
30 f = interp1d(T, Gliq - Ggas)
31 bp, = fsolve(f, 373)
32 print ’The boiling point is {0} K’.format(bp)

>>> >>> >>> >>> ... ... ... ... ... ... ... >>> >>> ... ... ... ... ... ... ... >>> >>> >>>

1 plt.figure(); plt.clf()
2 plt.plot(T-273.15, Gliq, T-273.15, Ggas)
3 plt.legend([’liquid water’, ’steam’])
4
5 plt.xlabel(’Temperature $^\circ$C’)
6 plt.ylabel(’$\Delta G$ (kJ/mol)’)
7 plt.title(’The boiling point is approximately {0:1.2f} $^\circ$C’.format(bp-273.15))
8 plt.savefig(’images/boiling-water.png’)

<matplotlib.figure.Figure object at 0x050D2E30>

[<matplotlib.lines.Line2D object at 0x051AB610>, <matplotlib.lines.Line2D object at 0x051B4C
<matplotlib.legend.Legend object at 0x051B9030>
>>> <matplotlib.text.Text object at 0x0519E390>
<matplotlib.text.Text object at 0x050FB390>
<matplotlib.text.Text object at 0x050FBFB0>

265
 14.3.1 Summary
The answer we get us 0.05 K too high, which is not bad considering we estimated
it using parameters that were fitted to thermodynamic data and that had finite
precision and extrapolated the steam properties below the region the parameters
were stated to be valid for.

14.4 Gibbs energy minimization and the NIST webbook

Matlab post In Post 1536 we used the NIST webbook to compute a temperature
dependent Gibbs energy of reaction, and then used a reaction extent variable to
compute the equilibrium concentrations of each species for the water gas shift
reaction.
Today, we look at the direct minimization of the Gibbs free energy of the
species, with no assumptions about stoichiometry of reactions. We only apply
the constraint of conservation of atoms. We use the NIST Webbook to provide
the data for the Gibbs energy of each species.
As a reminder we consider equilibrium between the species CO, H2 O, CO2
and H2 , at 1000K, and 10 atm total pressure with an initial equimolar molar
flow rate of CO and H2 O.

1 import numpy as np
2
3 T = 1000 # K
4 R = 8.314e-3 # kJ/mol/K
5
6 P = 10.0 # atm, this is the total pressure in the reactor
7 Po = 1.0 # atm, this is the standard state pressure

266
 We are going to store all the data and calculations in vectors, so we need to
assign each position in the vector to a species. Here are the definitions we use
in this work.

1 CO
2 H2O
3 CO2
4 H2

1 species = [’CO’, ’H2O’, ’CO2’, ’H2’]

2
3 # Heats of formation at 298.15 K
4
5 Hf298 = [
6 -110.53, # CO
7 -241.826, # H2O
8 -393.51, # CO2
9 0.0] # H2
10
11 # Shomate parameters for each species
12 # A B C D E F G H
13 WB = [[25.56759, 6.096130, 4.054656, -2.671301, 0.131021, -118.0089, 227.3665, -110.5271], # CO
14 [30.09200, 6.832514, 6.793435, -2.534480, 0.082139, -250.8810, 223.3967, -241.8264], # H2O
15 [24.99735, 55.18696, -33.69137, 7.948387, -0.136638, -403.6075, 228.2431, -393.5224], # CO2
16 [33.066178, -11.363417, 11.432816, -2.772874, -0.158558, -9.980797, 172.707974, 0.0]] # H2
17
18 WB = np.array(WB)
19
20 # Shomate equations
21 t = T/1000
22 T_H = np.array([t, t**2 / 2.0, t**3 / 3.0, t**4 / 4.0, -1.0 / t, 1.0, 0.0, -1.0])
23 T_S = np.array([np.log(t), t, t**2 / 2.0, t**3 / 3.0, -1.0 / (2.0 * t**2), 0.0, 1.0, 0.0])
24
25 H = np.dot(WB, T_H) # (H - H_298.15) kJ/mol
26 S = np.dot(WB, T_S/1000.0) # absolute entropy kJ/mol/K
27
28 Gjo = Hf298 + H - T*S # Gibbs energy of each component at 1000 K

Now, construct the Gibbs free energy function, accounting for the change in
activity due to concentration changes (ideal mixing).

1 def func(nj):
2 nj = np.array(nj)
3 Enj = np.sum(nj);
4 Gj = Gjo / (R * T) + np.log(nj / Enj * P / Po)
5 return np.dot(nj, Gj)

We impose the constraint that all atoms are conserved from the initial con-
ditions to the equilibrium distribution of species. These constraints are in the
form of Aeq n = beq , where n is the vector of mole numbers for each species.

1 Aeq = np.array([[ 1, 0, 1, 0], # C balance

2 [ 1, 1, 2, 0], # O balance
3 [ 0, 2, 0, 2]]) # H balance
4

267
5 # equimolar feed of 1 mol H2O and 1 mol CO
6 beq = np.array([1, # mol C fed
7 2, # mol O fed
8 2]) # mol H fed
9
10 def ec1(nj):
11 ’conservation of atoms constraint’
12 return np.dot(Aeq, nj) - beq

Now we are ready to solve the problem.

1 from scipy.optimize import fmin_slsqp

2
3 n0 = [0.5, 0.5, 0.5, 0.5] # initial guesses
4 N = fmin_slsqp(func, n0, f_eqcons=ec1)
5 print N

>>> >>> Optimization terminated successfully. (Exit mode 0)

Current function value: -91.204832308
Iterations: 2
Function evaluations: 13
Gradient evaluations: 2
[ 0.45502309 0.45502309 0.54497691 0.54497691]

14.4.1 Compute mole fractions and partial pressures

The pressures here are in good agreement with the pressures found by other
methods. The minor disagreement (in the third or fourth decimal place) is
likely due to convergence tolerances in the different algorithms used.

1 yj = N / np.sum(N)
2 Pj = yj * P
3
4 for s, y, p in zip(species, yj, Pj):
5 print ’{0:10s}: {1:1.2f} {2:1.2f}’.format(s, y, p)

>>> >>> ... ... CO : 0.23 2.28

H2O : 0.23 2.28
CO2 : 0.27 2.72
H2 : 0.27 2.72

14.4.2 Computing equilibrium constants

We can compute the equilibrium constant for the reaction CO + H2 O
CO2 +
H2 . Compared to the value of K = 1.44 we found at the end of Post 1536 ,
the agreement is excellent. Note, that to define an equilibrium constant it is
necessary to specify a reaction, even though it is not necessary to even consider
a reaction to obtain the equilibrium distribution of species!

268
1 nuj = np.array([-1, -1, 1, 1]) # stoichiometric coefficients of the reaction
2 K = np.prod(yj**nuj)
3 print K

>>> 1.43446295961

14.5 Finding equilibrium composition by direct minimiza-

tion of Gibbs free energy on mole numbers
Matlab post Adapted from problem 4.5 in Cutlip and Shacham Ethane and
steam are fed to a steam cracker at a total pressure of 1 atm and at 1000K at
a ratio of 4 mol H2O to 1 mol ethane. Estimate the equilibrium distribution of
products (CH4, C2H4, C2H2, CO2, CO, O2, H2, H2O, and C2H6).
Solution method: We will construct a Gibbs energy function for the mixture,
and obtain the equilibrium composition by minimization of the function subject
to elemental mass balance constraints.

1 import numpy as np
2
3 R = 0.00198588 # kcal/mol/K
4 T = 1000 # K
5
6 species = [’CH4’, ’C2H4’, ’C2H2’, ’CO2’, ’CO’, ’O2’, ’H2’, ’H2O’, ’C2H6’]
7
8 # $G_^\circ for each species. These are the heats of formation for each
9 # species.
10 Gjo = np.array([4.61, 28.249, 40.604, -94.61, -47.942, 0, 0, -46.03, 26.13]) # kcal/mol

14.5.1 The Gibbs energy of a mixture

We start with G = nj µj . Recalling that we define µj = G◦j + RT ln aj , and
P
j
n
in the ideal gas limit, aj = yj P/P ◦ , and that yj = P nj j . Since in this problem,
n  ◦
G

n
P = 1 atm, this leads to the function RT G
nj RTj + ln P nj j .
P
=
j=1

1 import numpy as np
2
3 def func(nj):
4 nj = np.array(nj)
5 Enj = np.sum(nj);
6 G = np.sum(nj * (Gjo / R / T + np.log(nj / Enj)))
7 return G

14.5.2 Linear equality constraints for atomic mass conservation

The total number of each type of atom must be the same as what entered the
reactor. These form equality constraints on the equilibrium composition. We
express these constraints as: Aeq n = b where n is a vector of the moles of each
species present in the mixture. CH4 C2H4 C2H2 CO2 CO O2 H2 H2O C2H6

269
1 Aeq = np.array([[0, 0, 0, 2, 1, 2, 0, 1, 0], # oxygen balance
2 [4, 4, 2, 0, 0, 0, 2, 2, 6], # hydrogen balance
3 [1, 2, 2, 1, 1, 0, 0, 0, 2]]) # carbon balance
4
5 # the incoming feed was 4 mol H2O and 1 mol ethane
6 beq = np.array([4, # moles of oxygen atoms coming in
7 14, # moles of hydrogen atoms coming in
8 2]) # moles of carbon atoms coming in
9
10 def ec1(n):
11 ’equality constraint’
12 return np.dot(Aeq, n) - beq

Now we solve the problem.

1 # initial guess suggested in the example

2 n0 = [1e-3, 1e-3, 1e-3, 0.993, 1.0, 1e-4, 5.992, 1.0, 1e-3]
3
4 from scipy.optimize import fmin_slsqp
5
6 X = fmin_slsqp(func, n0, f_eqcons=ec1, iter=300, acc=1e-12)
7
8 for s,x in zip(species, X):
9 print ’{0:10s} {1:1.4g}’.format(s, x)
10
11 # check that constraints were met
12 print np.dot(Aeq, X) - beq
13 print np.all( np.abs( np.dot(Aeq, X) - beq) < 1e-12)

>>> >>> >>> >>> Optimization terminated successfully. (Exit mode 0)

Current function value: -104.403947663
Iterations: 217
Function evaluations: 2937
Gradient evaluations: 217
>>> ... ... CH4 0.06694
C2H4 8.108e-08
C2H2 5.174e-08
CO2 0.5441
CO 1.389
O2 1.222e-14
H2 5.343
H2O 1.523
C2H6 8.44e-08
... [ -1.66977543e-13 1.77635684e-15 4.44089210e-16]
True

I found it necessary to tighten the accuracy parameter to get pretty good

matches to the solutions found in Matlab. It was also necessary to increase the
number of iterations. Even still, not all of the numbers match well, especially the
very small numbers. You can, however, see that the constraints were satisfied
pretty well.
Interestingly there is a distribution of products! That is interesting because
only steam and ethane enter the reactor, but a small fraction of methane is

270
 formed! The main product is hydrogen. The stoichiometry of steam reforming
is ideally C2 H6 + 4H2 O → 2CO2 + 7H2. Even though nearly all the ethane
is consumed, we do not get the full yield of hydrogen. It appears that another
equilibrium, one between CO, CO2, H2O and H2, may be limiting that, since
the rest of the hydrogen is largely in the water. It is also of great importance
that we have not said anything about reactions, i.e. how these products were
formed.
The water gas shift reaction is: CO + H2 O
CO2 + H2 . We can compute
the Gibbs free energy of the reaction from the heats of formation of each species.
Assuming these are the formation energies at 1000K, this is the reaction free
energy at 1000K.

1 G_wgs = Gjo[3] + Gjo[6] - Gjo[4] - Gjo[7]

2 print G_wgs
3
4 K = np.exp(-G_wgs / (R*T))
5 print K

-0.638
>>> >>> 1.37887528109

14.5.3 Equilibrium constant based on mole numbers

One normally uses activities to define the equilibrium constant. Since there are
the same number of moles on each side of the reaction all factors that convert
mole numbers to activity, concentration or pressure cancel, so we simply consider
the ratio of mole numbers here.

1 print (X[3] * X[6]) / (X[4] * X[7])

1.37450039394

This is close, but not exactly the same as the equilibrium constant computed
above. I think they should be exactly the same, and the difference is due to
convergence errors in the solution to the problem.
Clearly, there is an equilibrium between these species that prevents the com-
plete reaction of steam reforming.

14.5.4 Summary
This is an appealing way to minimize the Gibbs energy of a mixture. No as-
sumptions about reactions are necessary, and the constraints are easy to identify.
The Gibbs energy function is especially easy to code.

271
14.6 The Gibbs free energy of a reacting mixture and the
equilibrium composition
Matlab post
In this post we derive the equations needed to find the equilibrium compo-
sition of a reacting mixture. We use the method of direct minimization of the
Gibbs free energy of the reacting mixture.
The Gibbs free energy of a mixture is defined as G = µj nj where µj is the
P
j
chemical potential of species j, and it is temperature and pressure dependent,
and nj is the number of moles of species j.
We define the chemical potential as µj = G◦j + RT ln aj , where G◦j is the
Gibbs energy in a standard state, and aj is the activity of species j if the pressure
and temperature are not at standard state conditions.
If a reaction is occurring, then the number of moles of each species are related
to each other through the reaction extent  and stoichiometric coefficients: nj =
nj0 + νj . Note that the reaction extent has units of moles.
Combining these three equations and expanding the terms leads to:
X X X
G= nj0 G◦j + νj G◦j  + RT (nj0 + νj ) ln aj
j j j

The first term is simply the initial Gibbs free energy that is present before
any reaction begins, and it is a constant. It is difficult to evaluate, so we will
move it to the left side of the equation in the next step, because it does not
matter what its value is since it is a constant. The second term is related to
the Gibbs free energy of reaction: ∆r G = νj G◦j . With these observations we
P
j
rewrite the equation as:
X X
G− nj0 G◦j = ∆r G + RT (nj0 + νj ) ln aj
j j

Now, we have an equation that allows us to compute the change in Gibbs

free energy as a function of the reaction extent, initial number of moles of each
species, and the activities of each species. This difference in Gibbs free energy
has no natural scale, and depends on the size of the system, i.e. on nj0 . It is
desirable to avoid this, so we now rescale the equation by the total initial moles
present, nT 0 and define a new variable 0 = /nT 0 , which is dimensionless. This
leads to:

G − nj0 G◦j
P
j X
= ∆r G0 + RT (yj0 + νj 0 ) ln aj
nT 0 j

where yj0 is the initial mole fraction of species j present. The mole fractions
are intensive properties that do not depend on the system size. Finally, we need
y P
to address aj . For an ideal gas, we know that Aj = Pj ◦ , where the numerator

272
 is the partial pressure of species j computed from the mole fraction of species j
times the total pressure. To get the mole fraction we note:

nj nj0 + νj  y + ν 0
yj = = P = j0 0 Pj
nT nT 0 +  νj 1+ νj
j j

This finally leads us to an equation that we can evaluate as a function of

reaction extent:

nj0 G◦j
P  
G− 0
j X  yj0 +P νj  P 
=G = ∆r G0 + RT (yj0 + νj 0 ) ln 
ee
nT 0 1 +  0 νj P ◦

j
j

we use a double tilde notation to distinguish this quantity from the quantity
derived by Rawlings and Ekerdt which is further normalized by a factor of
RT . This additional scaling makes the quantities dimensionless, and makes the
quantity have a magnitude of order unity, but otherwise has no effect on the
shape of the graph.
Finally, if we know the initial mole fractions, the initial total pressure, the
Gibbs energy of reaction, and the stoichiometric coefficients, we can plot the
scaled reacting mixture energy as a function of reaction extent. At equilibrium,
this energy will be a minimum. We consider the example in Rawlings and Ekerdt
where isobutane (I) reacts with 1-butene (B) to form 2,2,3-trimethylpentane (P).
The reaction occurs at a total pressure of 2.5 atm at 400K, with equal molar
amounts of I and B. The standard Gibbs free energy of reaction at 400K is -3.72
kcal/mol. Compute the equilibrium composition.

1 import numpy as np
2
3 R = 8.314
4 P = 250000 # Pa
5 P0 = 100000 # Pa, approximately 1 atm
6 T = 400 # K
7
8 Grxn = -15564.0 #J/mol
9 yi0 = 0.5; yb0 = 0.5; yp0 = 0.0; # initial mole fractions
10
11 yj0 = np.array([yi0, yb0, yp0])
12 nu_j = np.array([-1.0, -1.0, 1.0]) # stoichiometric coefficients
13
14 def Gwigglewiggle(extentp):
15 diffg = Grxn * extentp
16 sum_nu_j = np.sum(nu_j)
17 for i,y in enumerate(yj0):
18 x1 = yj0[i] + nu_j[i] * extentp
19 x2 = x1 / (1.0 + extentp*sum_nu_j)
20 diffg += R * T * x1 * np.log(x2 * P / P0)
21 return diffg

There are bounds on how large 0 can be. Recall that nj = nj0 + νj , and
that nj ≥ 0. Thus, max = −nj0 /νj , and the maximum value that 0 can have

273
 is therefore −yj0 /νj where yj0 > 0. When there are multiple species, you need
the smallest epsilon0max to avoid getting negative mole numbers.

1 epsilonp_max = min(-yj0[yj0 > 0] / nu_j[yj0 > 0])

2 epsilonp = np.linspace(1e-6, epsilonp_max, 1000);
3
4 import matplotlib.pyplot as plt
5
6 plt.plot(epsilonp,Gwigglewiggle(epsilonp))
7 plt.xlabel(’$\epsilon$’)
8 plt.ylabel(’Gwigglewiggle’)
9 plt.savefig(’images/gibbs-minim-1.png’)

>>> [<matplotlib.lines.Line2D object at 0x10a8bf50>]

<matplotlib.text.Text object at 0x10608190>
<matplotlib.text.Text object at 0x10609d10>

Now we simply minimize our Gwigglewiggle function. Based on the figure

above, the miminum is near 0.45.

1 from scipy.optimize import fminbound

2
3 epsilonp_eq = fminbound(Gwigglewiggle, 0, 0.45)
4
5 plt.plot([extmin], [Gwigglewiggle(epsilonp_eq)], ’ro’)
6 plt.savefig(’images/gibbs-minim-2.png’)

>>> >>> [<matplotlib.lines.Line2D object at 0x10a8b5d0>]

274
 To compute equilibrium mole fractions we do this:

1 yi = (yi0 + nu_j[0]*epsilonp_eq) / (1.0 + epsilonp_eq*np.sum(nu_j))

2 yb = (yb0 + nu_j[1]*epsilonp_eq) / (1.0 + epsilonp_eq*np.sum(nu_j))
3 yp = (yp0 + nu_j[2]*epsilonp_eq) / (1.0 + epsilonp_eq*np.sum(nu_j))
4
5 print yi, yb, yp
6
7 # or this
8 y_j = (yj0 + np.dot(nu_j, epsilonp_eq)) / (1.0 + epsilonp_eq*np.sum(nu_j))
9 print y_j

>>> >>> >>> 0.0573226598476 0.0573226598476 0.885354680305

>>> >>> >>> [ 0.05732266 0.05732266 0.88535468]
y P/P ◦ ◦
K = aaI aPB = yi P/Pp ◦ yb P/P ◦ = yyiPyb PP .
Q ν
We can express the equilibrium constant like this :K = aj j , and compute
j
it with a single line of code.

1 K = np.exp(-Grxn/R/T)
2 print K
3 print yp / (yi * yb) * P0 / P
4
5 print np.prod((y_j * P / P0)**nu_j)

107.776294742
107.776632714
>>> 107.776632714

275
 These results are very close, and only disagree because of the default toler-
ance used in identifying the minimum of our function. you could tighten the
tolerances by setting options to the fminbnd function.

14.6.1 Summary
In this post we derived an equation for the Gibbs free energy of a reacting
mixture and used it to find the equilibrium composition. In future posts we will
examine some alternate forms of the equations that may be more useful in some
circumstances.

14.7 Water gas shift equilibria via the NIST Webbook

Matlab post
The NIST webbook provides parameterized models of the enthalpy, entropy
and heat capacity of many molecules. In this example, we will examine how to
use these to compute the equilibrium constant for the water gas shift reaction
CO + H2 O
CO2 + H2 in the temperature range of 500K to 1000K.
Parameters are provided for:
Cp = heat capacity (J/mol*K) H = standard enthalpy (kJ/mol) S = stan-
dard entropy (J/mol*K)
with models in the form: Cp◦ = A + B ∗ t + C ∗ t2 + D ∗ t3 + E/t2
H ◦ − H298.15
◦
= A ∗ t + B ∗ t2 /2 + C ∗ t3 /3 + D ∗ t4 /4 − E/t + F − H
◦
S = A ∗ ln(t) + B ∗ t + C ∗ t2 /2 + D ∗ t3 /3 − E/(2 ∗ t2 ) + G
where t = T /1000, and T is the temperature in Kelvin. We can use this
data to calculate equilibrium constants in the following manner. First, we have
heats of formation at standard state for each compound; for elements, these
are zero by definition, and for non-elements, they have values available from
the NIST webbook. There are also values for the absolute entropy at standard
state. Then, we have an expression for the change in enthalpy from standard
state as defined above, as well as the absolute entropy. From these we can derive
the reaction enthalpy, free energy and entropy at standard state, as well as at
other temperatures.
We will examine the water gas shift enthalpy, free energy and equilibrium
constant from 500K to 1000K, and finally compute the equilibrium composition
of a gas feed containing 5 atm of CO and H_2 at 1000K.

1 import numpy as np
2
3 T = np.linspace(500,1000) # degrees K
4 t = T/1000;

14.7.1 hydrogen
http://webbook.nist.gov/cgi/cbook.cgi?ID=C1333740&Units=SI&Mask=1#
Thermo-Gas

276
1 # T = 298-1000K valid temperature range
2 A = 33.066178
3 B = -11.363417
4 C = 11.432816
5 D = -2.772874
6 E = -0.158558
7 F = -9.980797
8 G = 172.707974
9 H = 0.0
10
11 Hf_29815_H2 = 0.0 # kJ/mol
12 S_29815_H2 = 130.68 # J/mol/K
13
14 dH_H2 = A*t + B*t**2/2 + C*t**3/3 + D*t**4/4 - E/t + F - H;
15 S_H2 = (A*np.log(t) + B*t + C*t**2/2 + D*t**3/3 - E/(2*t**2) + G);

14.7.2 H_{2}O
http://webbook.nist.gov/cgi/cbook.cgi?ID=C7732185&Units=SI&Mask=1#
Thermo-Gas
Note these parameters limit the temperature range we can examine, as these
parameters are not valid below 500K. There is another set of parameters for
lower temperatures, but we do not consider them here.

1 # 500-1700 K valid temperature range

2 A = 30.09200
3 B = 6.832514
4 C = 6.793435
5 D = -2.534480
6 E = 0.082139
7 F = -250.8810
8 G = 223.3967
9 H = -241.8264
10
11 Hf_29815_H2O = -241.83 #this is Hf.
12 S_29815_H2O = 188.84
13
14 dH_H2O = A*t + B*t**2/2 + C*t**3/3 + D*t**4/4 - E/t + F - H;
15 S_H2O = (A*np.log(t) + B*t + C*t**2/2 + D*t**3/3 - E/(2*t**2) + G);

14.7.3 CO
http://webbook.nist.gov/cgi/cbook.cgi?ID=C630080&Units=SI&Mask=1#Thermo-Gas

1 # 298. - 1300K valid temperature range

2 A = 25.56759
3 B = 6.096130
4 C = 4.054656
5 D = -2.671301
6 E = 0.131021
7 F = -118.0089
8 G = 227.3665
9 H = -110.5271
10
11 Hf_29815_CO = -110.53 #this is Hf kJ/mol.
12 S_29815_CO = 197.66
13
14 dH_CO = A*t + B*t**2/2 + C*t**3/3 + D*t**4/4 - E/t + F - H;
15 S_CO = (A*np.log(t) + B*t + C*t**2/2 + D*t**3/3 - E/(2*t**2) + G);

277
 14.7.4 CO_{2}
http://webbook.nist.gov/cgi/cbook.cgi?ID=C124389&Units=SI&Mask=1#Thermo-Gas

1 # 298. - 1200.K valid temperature range

2 A = 24.99735
3 B = 55.18696
4 C = -33.69137
5 D = 7.948387
6 E = -0.136638
7 F = -403.6075
8 G = 228.2431
9 H = -393.5224
10
11 Hf_29815_CO2 = -393.51 # this is Hf.
12 S_29815_CO2 = 213.79
13
14 dH_CO2 = A*t + B*t**2/2 + C*t**3/3 + D*t**4/4 - E/t + F - H;
15 S_CO2 = (A*np.log(t) + B*t + C*t**2/2 + D*t**3/3 - E/(2*t**2) + G);

14.7.5 Standard state heat of reaction

We compute the enthalpy and free energy of reaction at 298.15 K for the fol-
lowing reaction CO + H2O
H2 + CO2.

1 Hrxn_29815 = Hf_29815_CO2 + Hf_29815_H2 - Hf_29815_CO - Hf_29815_H2O;

2 Srxn_29815 = S_29815_CO2 + S_29815_H2 - S_29815_CO - S_29815_H2O;
3 Grxn_29815 = Hrxn_29815 - 298.15*(Srxn_29815)/1000;
4
5 print(’deltaH = {0:1.2f}’.format(Hrxn_29815))
6 print(’deltaG = {0:1.2f}’.format(Grxn_29815))

>>> >>> >>> deltaH = -41.15

deltaG = -28.62

14.7.6 Non-standard state ∆H and ∆G

We have to correct for temperature change away from standard state. We only
correct the enthalpy for this temperature change. The correction looks like this:
X
∆Hrxn (T ) = ∆Hrxn (Tref ) + νi (Hi (T ) − Hi (Tref ))
i

Where νi are the stoichiometric coefficients of each species, with appropriate

sign for reactants and products, and (Hi (T ) − Hi (Tref ) is precisely what is
calculated for each species with the equations
The entropy is on an absolute scale, so we directly calculate entropy at each
temperature. Recall that H is in kJ/mol and S is in J/mol/K, so we divide S
by 1000 to make the units match.

1 Hrxn = Hrxn_29815 + dH_CO2 + dH_H2 - dH_CO - dH_H2O

2 Grxn = Hrxn - T*(S_CO2 + S_H2 - S_CO - S_H2O)/1000

278
 14.7.7 Plot how the ∆G varies with temperature

1 import matplotlib.pyplot as plt

2 plt.figure(); plt.clf()
3 plt.plot(T,Grxn, label=’$\Delta G_{rxn}$’)
4 plt.plot(T,Hrxn, label=’$\Delta H_{rxn}$’)
5 plt.xlabel(’Temperature (K)’)
6 plt.ylabel(’(kJ/mol)’)
7 plt.legend( loc=’best’)
8 plt.savefig(’images/wgs-nist-1.png’)

<matplotlib.figure.Figure object at 0x04199CF0>

[<matplotlib.lines.Line2D object at 0x0429BF30>]
[<matplotlib.lines.Line2D object at 0x0427DFB0>]
<matplotlib.text.Text object at 0x041B79F0>
<matplotlib.text.Text object at 0x040CEF70>
<matplotlib.legend.Legend object at 0x043CB5F0>

Over this temperature range the reaction is exothermic, although near 1000K
it is just barely exothermic. At higher temperatures we expect the reaction to
become endothermic.

14.7.8 Equilibrium constant calculation

Note the equilibrium constant starts out high, i.e. strongly favoring the forma-
tion of products, but drops very quicky with increasing temperature.

279
1 R = 8.314e-3 # kJ/mol/K
2 K = np.exp(-Grxn/R/T);
3
4 plt.figure()
5 plt.plot(T,K)
6 plt.xlim([500, 1000])
7 plt.xlabel(’Temperature (K)’)
8 plt.ylabel(’Equilibrium constant’)
9 plt.savefig(’images/wgs-nist-2.png’)

>>> >>> <matplotlib.figure.Figure object at 0x044DBE90>

[<matplotlib.lines.Line2D object at 0x045A53F0>]
(500, 1000)
<matplotlib.text.Text object at 0x04577470>
<matplotlib.text.Text object at 0x0457F410>

14.7.9 Equilibrium yield of WGS

Now let us suppose we have a reactor with a feed of H_2O and CO at 10atm at
1000K. What is the equilibrium yield of H_2? Let  be the extent of reaction,
so that Fi = Fi,0 + νi . For reactants, νi is negative, and for products, νi is
positive. We have to solve for the extent of reaction that satisfies the equilibrium
condition.

1 from scipy.interpolate import interp1d

2 from scipy.optimize import fsolve
3
4 #

280
5 # A = CO
6 # B = H2O
7 # C = H2
8 # D = CO2
9
10 Pa0 = 5; Pb0 = 5; Pc0 = 0; Pd0 = 0; # pressure in atm
11 R = 0.082;
12 Temperature = 1000;
13
14 # we can estimate the equilibrium like this. We could also calculate it
15 # using the equations above, but we would have to evaluate each term. Above
16 # we simply computed a vector of enthalpies, entropies, etc... Here we interpolate
17 K_func = interp1d(T,K);
18 K_Temperature = K_func(1000)
19
20
21 # If we let X be fractional conversion then we have $C_A = C_{A0}(1-X)$,
22 # $C_B = C_{B0}-C_{A0}X$, $C_C = C_{C0}+C_{A0}X$, and $C_D =
23 # C_{D0}+C_{A0}X$. We also have $K(T) = (C_C C_D)/(C_A C_B)$, which finally
24 # reduces to $0 = K(T) - Xeq^2/(1-Xeq)^2$ under these conditions.
25
26 def f(X):
27 return K_Temperature - X**2/(1-X)**2;
28
29 x0 = 0.5
30 Xeq, = fsolve(f, x0)
31
32 print(’The equilibrium conversion for these feed conditions is: {0:1.2f}’.format(Xeq))

>>> >>> ... ... ... ... ... >>> >>> >>> >>> >>> ... ... ... >>> >>> >>> >>> ... ... ... ...
The equilibrium conversion for these feed conditions is: 0.55

14.7.10 Compute gas phase pressures of each species

Since there is no change in moles for this reaction, we can directly calculation the
pressures from the equilibrium conversion and the initial pressure of gases. you
can see there is a slightly higher pressure of H_2 and CO_2 than the reactants,
consistent with the equilibrium constant of about 1.44 at 1000K. At a lower
temperature there would be a much higher yield of the products. For example,
at 550K the equilibrium constant is about 58, and the pressure of H_2 is 4.4
atm due to a much higher equilibrium conversion of 0.88.

1 P_CO = Pa0*(1-Xeq)
2 P_H2O = Pa0*(1-Xeq)
3 P_H2 = Pa0*Xeq
4 P_CO2 = Pa0*Xeq
5
6 print P_CO,P_H2O, P_H2, P_CO2

>>> >>> >>> >>> 2.2747854428 2.2747854428 2.7252145572 2.7252145572

14.7.11 Compare the equilibrium constants

We can compare the equilibrium constant from the Gibbs free energy and the
one from the ratio of pressures. They should be the same!

281
1 print K_Temperature
2 print (P_CO2*P_H2)/(P_CO*P_H2O)

1.43522674762
1.43522674762

They are the same.

14.7.12 Summary
The NIST Webbook provides a plethora of data for computing thermodynamic
properties. It is a little tedious to enter it all into Matlab, and a little tricky to
use the data to estimate temperature dependent reaction energies. A limitation
of the Webbook is that it does not tell you have the thermodynamic properties
change with pressure. Luckily, those changes tend to be small.
I noticed a different behavior in interpolation between scipy.interpolate.interp1d
and Matlab’s interp1. The scipy function returns an interpolating function,
whereas the Matlab function directly interpolates new values, and returns the
actual interpolated data.

14.8 Constrained minimization to find equilibrium com-

positions
adapated from Chemical Reactor analysis and design fundamentals, Rawlings
and Ekerdt, appendix A.2.3.
Matlab post
The equilibrium composition of a reaction is the one that minimizes the total
Gibbs free energy. The Gibbs free energy of a reacting ideal gas mixture depends
on the mole fractions of each species, which are determined by the initial mole
fractions of each species, the extent of reactions that convert each species, and
the equilibrium constants.
Reaction 1: I + B
P 1
Reaction 2: I + B
P 2
Here we define the Gibbs free energy of the mixture as a function of the
reaction extents.

1 import numpy as np
2
3 def gibbs(E):
4 ’function defining Gibbs free energy as a function of reaction extents’
5 e1 = E[0]
6 e2 = E[1]
7 # known equilibrium constants and initial amounts
8 K1 = 108; K2 = 284; P = 2.5;
9 yI0 = 0.5; yB0 = 0.5; yP10 = 0.0; yP20 = 0.0;
10 # compute mole fractions
11 d = 1 - e1 - e2;
12 yI = (yI0 - e1 - e2) / d;
13 yB = (yB0 - e1 - e2) / d;
14 yP1 = (yP10 + e1) / d;

282
15 yP2 = (yP20 + e2) / d;
16 G = (-(e1 * np.log(K1) + e2 * np.log(K2)) +
17 d * np.log(P) + yI * d * np.log(yI) +
18 yB * d * np.log(yB) + yP1 * d * np.log(yP1) + yP2 * d * np.log(yP2))
19 return G

The equilibrium constants for these reactions are known, and we seek to find
the equilibrium reaction extents so we can determine equilibrium compositions.
The equilibrium reaction extents are those that minimize the Gibbs free energy.
We have the following constraints, written in standard less than or equal to
form:
−1 ≤ 0
−2 ≤ 0
1 + 2 ≤ 0.5
In Matlab we express this in matrix form as Ax=b where
 
−1 0
A =  0 −1  (45)
1 1

and
 
0
b= 0  (46)
0.5
Unlike in Matlab, in python we construct the inequality constraints as func-
tions that are greater than or equal to zero when the constraint is met.

1 def constraint1(E):
2 e1 = E[0]
3 return e1
4
5 def constraint2(E):
6 e2 = E[1]
7 return e2
8
9 def constraint3(E):
10 e1 = E[0]
11 e2 = E[1]
12 return 0.5 - (e1 + e2)

Now, we minimize.

1 from scipy.optimize import fmin_slsqp

2
3 X0 = [0.133, 0.351]
4 X = fmin_slsqp(gibbs, X0, ieqcons=[constraint1, constraint2, constraint3])
5 print X
6
7 print gibbs(X)

283
 >>> >>> Optimization terminated successfully. (Exit mode 0)
Current function value: -2.55942338611
Iterations: 1
Function evaluations: 8
Gradient evaluations: 1
[ 0.1330313 0.35101555]
>>> -2.55942338611

One way we can verify our solution is to plot the gibbs function and see
where the minimum is, and whether there is more than one minimum. We start
by making grids over the range of 0 to 0.5. Note we actually start slightly above
zero because at zero there are some numerical imaginary elements of the gibbs
function or it is numerically not defined since there are logs of zero there. We
also set all elements where the sum of the two extents is greater than 0.5 to near
zero, since those regions violate the constraints.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 def gibbs(E):
5 ’function defining Gibbs free energy as a function of reaction extents’
6 e1 = E[0]
7 e2 = E[1]
8 # known equilibrium constants and initial amounts
9 K1 = 108; K2 = 284; P = 2.5;
10 yI0 = 0.5; yB0 = 0.5; yP10 = 0.0; yP20 = 0.0;
11 # compute mole fractions
12 d = 1 - e1 - e2;
13 yI = (yI0 - e1 - e2)/d;
14 yB = (yB0 - e1 - e2)/d;
15 yP1 = (yP10 + e1)/d;
16 yP2 = (yP20 + e2)/d;
17 G = (-(e1 * np.log(K1) + e2 * np.log(K2)) +
18 d * np.log(P) + yI * d * np.log(yI) +
19 yB * d * np.log(yB) + yP1 * d * np.log(yP1) + yP2 * d * np.log(yP2))
20 return G
21
22
23 a = np.linspace(0.001, 0.5, 100)
24 E1, E2 = np.meshgrid(a,a)
25
26 sumE = E1 + E2
27 E1[sumE >= 0.5] = 0.00001
28 E2[sumE >= 0.5] = 0.00001
29
30 # now evaluate gibbs
31 G = np.zeros(E1.shape)
32 m,n = E1.shape
33
34 G = gibbs([E1, E2])
35
36 CS = plt.contour(E1, E2, G, levels=np.linspace(G.min(),G.max(),100))
37 plt.xlabel(’$\epsilon_1$’)
38 plt.ylabel(’$\epsilon_2$’)
39 plt.colorbar()
40
41 plt.plot([ 0.1330313], [0.35101555], ’ro’)
42
43 plt.savefig(’images/gibbs-minimization-1.png’)
44 plt.savefig(’images/gibbs-minimization-1.svg’)
45 plt.show()

284
 You can see we found the minimum. We can compute the mole fractions
pretty easily.

1 e1 = X[0];
2 e2 = X[1];
3
4 yI0 = 0.5; yB0 = 0.5; yP10 = 0; yP20 = 0; #initial mole fractions
5
6 d = 1 - e1 - e2;
7 yI = (yI0 - e1 - e2)/d;
8 yB = (yB0 - e1 - e2)/d;
9 yP1 = (yP10 + e1)/d;
10 yP2 = (yP20 + e2)/d;
11
12 print(’y_I = {0:1.3f} y_B = {1:1.3f} y_P1 = {2:1.3f} y_P2 = {3:1.3f}’.format(yI,yB,yP1,yP2))

>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> y_I = 0.031 y_B = 0.031 y_P1 = 0.258 y_P2 = 0.680

14.8.1 summary
I found setting up the constraints in this example to be more confusing than
the Matlab syntax.

14.9 Using constrained optimization to find the amount

of each phase present
The problem we solve here is that we have several compounds containing Ni and
Al, and a bulk mixture of a particular composition of Ni and Al. We want to

285
 know which mixture of phases will minimize the total energy. The tricky part
is that the optimization is constrained because the mixture of phases must have
the overall stoichiometry we want. We formulate the problem like this.
Basically, we want to minimize the function E = wi Ei , where wi is the
P
mass of phase i, and Ei is the energy per unit mass of phase i. There are
some constraints to ensure conservation of mass. Let us consider the following
compounds: Al, NiAl, Ni3Al, and Ni, and consider a case where the bulk com-
position of our alloy is 93.8% Ni and balance Al. We want to know which phases
are present, and in what proportions. There are some subtleties in considering
the formula and molecular weight of an alloy. We consider the formula with
each species amount normalized so the fractions all add up to one. For exam-
ple, Ni_3Al is represented as Ni_{0.75}Al_{0.25}, and the molecular weight
is computed as 0.75*MW_{Ni} + 0.25*MW_{Al}.
We use scipy.optimize.fmin_slsqp to solve this problem, and define two
equality constraint functions, and the bounds on each weight fraction.
Note: the energies in this example were computed by density functional
theory at 0K.

1 import numpy as np
2 from scipy.optimize import fmin_slsqp
3
4 # these are atomic masses of each species
5 Ni = 58.693
6 Al = 26.982
7
8 COMPOSITIONS = [’Al’, ’NiAl’, ’Ni3Al’, ’Ni’]
9 MW = np.array( [Al, (Ni + Al)/2.0, (3*Ni + Al)/4.0, Ni])
10
11 xNi = np.array([0.0, 0.5, 0.75, 1.0]) # mole fraction of nickel in each compd
12 WNi = xNi*Ni / MW # weight fraction of Ni in each cmpd
13
14 ENERGIES = np.array([0.0, -0.7, -0.5, 0.0])
15
16 BNi = 0.938
17
18 def G(w):
19 ’function to minimize. w is a vector of weight fractions, ENERGIES is defined above.’
20 return np.dot(w, ENERGIES)
21
22 def ec1(w):
23 ’conservation of Ni constraint’
24 return BNi - np.dot(w, WNi)
25
26 def ec2(w):
27 ’weight fractions sum to one constraint’
28 return 1 - np.sum(w)
29
30 w0 = np.array([0.0, 0.0, 0.5, 0.5]) # guess weight fractions
31
32 y = fmin_slsqp(G,
33 w0,
34 eqcons=[ec1, ec2],
35 bounds=[(0,1)]*len(w0))
36
37 for ci, wi in zip(COMPOSITIONS, y):
38 print ’{0:8s} {1:+8.2%}’.format(ci, wi)

Optimization terminated successfully. (Exit mode 0)

286
 Current function value: -0.233299644373
Iterations: 2
Function evaluations: 12
Gradient evaluations: 2
Al -0.00%
NiAl +0.00%
Ni3Al +46.66%
Ni +53.34%

So, the sample will be about 47% by weight of Ni3Al, and 53% by weight of
pure Ni.
It may be convenient to formulate this in terms of moles.

1 import numpy as np
2 from scipy.optimize import fmin_slsqp
3
4 COMPOSITIONS = [’Al’, ’NiAl’, ’Ni3Al’, ’Ni’]
5 xNi = np.array([0.0, 0.5, 0.75, 1.0]) # define this in mole fractions
6
7 ENERGIES = np.array([0.0, -0.7, -0.5, 0.0])
8
9 xNiB = 0.875 # bulk Ni composition
10
11 def G(n):
12 ’function to minimize’
13 return np.dot(n, ENERGIES)
14
15 def ec1(n):
16 ’conservation of Ni’
17 Ntot = np.sum(n)
18 return (Ntot * xNiB) - np.dot(n, xNi)
19
20 def ec2(n):
21 ’mole fractions sum to one’
22 return 1 - np.sum(n)
23
24 n0 = np.array([0.0, 0.0, 0.45, 0.55]) # initial guess of mole fractions
25
26 y = fmin_slsqp(G,
27 n0,
28 eqcons=[ec1, ec2],
29 bounds=[(0, 1)]*(len(n0)))
30
31 for ci, xi in zip(COMPOSITIONS, y):
32 print ’{0:8s} {1:+8.2%}’.format(ci, xi)

Optimization terminated successfully. (Exit mode 0)

Current function value: -0.25
Iterations: 2
Function evaluations: 12
Gradient evaluations: 2
Al +0.00%
NiAl -0.00%
Ni3Al +50.00%
Ni +50.00%

287
 This means we have a 1:1 molar ratio of Ni and Ni_{0.75}Al_{0.25}. That
works out to the overall bulk composition in this particular problem.
Let us verify that these two approaches really lead to the same conclusions.
On a weight basis we estimate 53.3%wt Ni and 46.7%wt Ni3Al, whereas we
predict an equimolar mixture of the two phases. Below we compute the mole
fraction of Ni in each case.

1 # these are atomic masses of each species

2 Ni = 58.693
3 Al = 26.982
4
5 # Molar case
6 # 1 mol Ni + 1 mol Ni_{0.75}Al_{0.25}
7 N1 = 1.0; N2 = 1.0
8 mol_Ni = 1.0 * N1 + 0.75 * N2
9 xNi = mol_Ni / (N1 + N2)
10 print xNi
11
12 # Mass case
13 M1 = 0.533; M2 = 0.467
14 MW1 = Ni; MW2 = 0.75*Ni + 0.25*Al
15
16 xNi2 = (1.0 * M1/MW1 + 0.75 * M2 / MW2) / (M1/MW1 + M2/MW2)
17 print xNi2

0.875
0.874192746385

You can see the overall mole fraction of Ni is practically the same in each
case.

14.10 Conservation of mass in chemical reactions

Matlab post
Atoms cannot be destroyed in non-nuclear chemical reactions, hence it fol-
lows that the same number of atoms entering a reactor must also leave the
reactor. The atoms may leave the reactor in a different molecular configuration
due to the reaction, but the total mass leaving the reactor must be the same.
Here we look at a few ways to show this.
We consider the water gas shift reaction : CO + H2 O
H2 + CO2 . We
can illustrate the conservation of mass with the following equation: νM = 0.
Where ν is the stoichiometric coefficient vector and M is a column vector of
molecular weights. For simplicity, we use pure isotope molecular weights, and
not the isotope-weighted molecular weights. This equation simply examines the
mass on the right side of the equation and the mass on left side of the equation.

1 import numpy as np
2 nu = [-1, -1, 1, 1];
3 M = [28, 18, 2, 44];
4 print np.dot(nu, M)

288
 You can see that sum of the stoichiometric coefficients times molecular
weights is zero. In other words a CO and H_2O have the same mass as H_2
and CO_2.
For any balanced chemical equation, there are the same number of each kind
of atom on each side of the equation. Since the mass of each atom is unchanged
with reaction, that means the mass of all the species that are reactants must
equal the mass of all the species that are products! Here we look at the number
of C, O, and H on each side of the reaction. Now if we add the mass of atoms
in the reactants and products, it should sum to zero (since we used the negative
sign for stoichiometric coefficients of reactants).

1 import numpy as np
2 # C O H
3 reactants = [-1, -2, -2]
4 products = [ 1, 2, 2]
5
6 atomic_masses = [12.011, 15.999, 1.0079] # atomic masses
7
8 print np.dot(reactants, atomic_masses) + np.dot(products, atomic_masses)

>>> ... >>> >>> >>> >>> >>> 0.0

That is all there is to mass conservation with reactions. Nothing changes if

there are lots of reactions, as long as each reaction is properly balanced, and
none of them are nuclear reactions!

14.11 Numerically calculating an effectiveness factor for

a porous catalyst bead
Matlab post
If reaction rates are fast compared to diffusion in a porous catalyst pellet,
then the observed kinetics will appear to be slower than they really are because
not all of the catalyst surface area will be effectively used. For example, the
reactants may all be consumed in the near surface area of a catalyst bead, and
the inside of the bead will be unutilized because no reactants can get in due to
the high reaction rates.
References: Ch 12. Elements of Chemical Reaction Engineering, Fogler, 4th
edition.
A mole balance on the particle volume in spherical coordinates with a first
2
order reaction leads to: ddrCa2 dr − De CA = 0 with boundary conditions
+ 2r dCa k

CA (R) = CAs and dr = 0 at r = 0. We convert this equation to a system of

dCa

first order ODEs by letting WA = dCa dr .

We have a condition of no flux at r=0 and Ca(R) = CAs, which makes this
a boundary value problem. We use the shooting method here, and guess what
Ca(0) is and iterate the guess to get Ca(R) = CAs.

289
1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 De = 0.1 # diffusivity cm^2/s
6 R = 0.5 # particle radius, cm
7 k = 6.4 # rate constant (1/s)
8 CAs = 0.2 # concentration of A at outer radius of particle (mol/L)
9
10 def ode(Y, r):
11 Wa = Y[0] # molar rate of delivery of A to surface of particle
12 Ca = Y[1] # concentration of A in the particle at r
13
14 if r == 0:
15 dWadr = 0 #this solves the singularity at r = 0
16 else:
17 dWadr = -2*Wa/r + k/De*Ca
18
19 dCadr = Wa
20
21 return [dWadr, dCadr]
22
23 # Initial conditions
24 Ca0 = 0.029315 # Ca(0) (mol/L) guessed to satisfy Ca(R) = CAs
25 Wa0 = 0 # no flux at r=0 (mol/m^2/s)
26
27 rspan = np.linspace(0, R, 500)
28
29 Y = odeint(ode, [Wa0, Ca0], rspan)
30
31 Ca = Y[:,1]
32
33 # here we check that Ca(R) = Cas
34 print ’At r={0} Ca={1}’.format(rspan[-1],Ca[-1])
35
36 plt.plot(rspan, Ca)
37 plt.xlabel(’Particle radius’)
38 plt.ylabel(’$C_A$’)
39 plt.savefig(’images/effectiveness-factor.png’)
40
41 r = rspan
42 eta_numerical = np.trapz(k*Ca*4*np.pi*(r**2), r)/np.trapz(k*CAs*4*np.pi*(r**2), r)
43 print eta_numerical
44
45 phi = R*np.sqrt(k/De);
46 eta_analytical = (3/phi**2)*(phi*(1.0 / np.tanh(phi))-1)
47 print eta_analytical

At r=0.5 Ca=0.200001488652
0.563011348314
0.563003362801

290
 You can see the concentration of A inside the particle is significantly lower
than outside the particle. That is because it is reacting away faster than it can
diffuse into the particle. Hence, the overall reaction rate in the particle is lower
than it would be without the diffusion limit.
The effectiveness factor is the ratio of the actual reaction rate in the par-
ticle with diffusion limitation to the ideal rate in the particle if there was no
concentration gradient:
RR
k 00 aCA (r)4πr2 dr
η = R0 R
0
k 00 aCAs 4πr2 dr
We will evaluate this numerically from our solution and compare it to the
analytical solution. The results are in good agreement, and you can make the
numerical estimate better by increasing the number of points in the solution so
that the numerical integration is more accurate.
Why go through the numerical solution when an analytical solution exists?
The analytical solution here is only good for 1st order kinetics in a sphere.
What would you do for a complicated rate law? You might be able to find some
limiting conditions where the analytical equation above is relevant, and if you
are lucky, they are appropriate for your problem. If not, it is a good thing you
can figure this out numerically!

14.12 Computing a pipe diameter

Matlab post A heat exchanger must handle 2.5 L/s of water through a smooth
pipe with length of 100 m. The pressure drop cannot exceed 103 kPa at 25
degC. Compute the minimum pipe diameter required for this application.

291
 Adapted from problem 8.8 in Problem solving in chemical and Biochemical
Engineering with Polymath, Excel, and Matlab. page 303.
We need to estimate the Fanning friction factor for these conditions so we can
estimate the frictional losses that result in a pressure drop for a uniform, circular
2
pipe. The frictional forces are given by Ff = 2fF ∆Lv D , and the corresponding
pressure drop is given by ∆P = ρFf . In these equations, ρ is the fluid density,
v is the fluid velocity, D is the pipe diameter, and fF is the Fanning friction
factor. The average fluid velocity is given by v = πDq2 /4 .
For laminar flow, we estimate fF = 16/Re, which is a linear equation,
and for turbulent flow (Re > 2100) we have the implicit equation √1f =
√ F

4.0 log(Re fF ) − 0.4. Of course, we define Re = Dvρ µ where µ is the viscosity

of the fluid.
It is known that ρ(T 2 −5
 ) = 46.048 + 9.418T− 0.0329T + 4.882 × 10 − 2.895 ×
10−8 T 4 and µ = exp −10.547 + T −144.53
541.69
where ρ is in kg/mˆ3 and µ is in
kg/(m*s).
2
The aim is to find D that solves: ∆p = ρ2fF ∆Lv D . This is a nonlinear
equation in D, since D affects the fluid velocity, the Re, and the Fanning friction
factor. Here is the solution

1 import numpy as np
2 from scipy.optimize import fsolve
3 import matplotlib.pyplot as plt
4
5 T = 25 + 273.15
6 Q = 2.5e-3 # m^3/s
7 deltaP = 103000 # Pa
8 deltaL = 100 # m
9
10 #Note these correlations expect dimensionless T, where the magnitude
11 # of T is in K
12
13 def rho(T):
14 return 46.048 + 9.418 * T -0.0329 * T**2 +4.882e-5 * T**3 - 2.895e-8 * T**4
15
16 def mu(T):
17 return np.exp(-10.547 + 541.69 / (T - 144.53))
18
19 def fanning_friction_factor_(Re):
20 if Re < 2100:
21 raise Exception(’Flow is probably not turbulent, so this correlation is not appropriate.’)
22 # solve the Nikuradse correlation to get the friction factor
23 def fz(f): return 1.0/np.sqrt(f) - (4.0*np.log10(Re*np.sqrt(f))-0.4)
24 sol, = fsolve(fz, 0.01)
25 return sol
26
27 fanning_friction_factor = np.vectorize(fanning_friction_factor_)
28
29 Re = np.linspace(2200, 9000)
30 f = fanning_friction_factor(Re)
31
32 plt.plot(Re, f)
33 plt.xlabel(’Re’)
34 plt.ylabel(’fanning friction factor’)
35 # You can see why we use 0.01 as an initial guess for solving for the
36 # Fanning friction factor; it falls in the middle of ranges possible
37 # for these Re numbers.
38 plt.savefig(’images/pipe-diameter-1.png’)

292
39
40 def objective(D):
41 v = Q / (np.pi * D**2 / 4)
42 Re = D * v * rho(T) / mu(T)
43
44 fF = fanning_friction_factor(Re)
45
46 return deltaP - 2 * fF * rho(T) * deltaL * v**2 / D
47
48 D, = fsolve(objective, 0.04)
49
50 print(’The minimum pipe diameter is {0} m\n’.format(D))

The minimum pipe diameter is 0.0389653369531 m

Any pipe diameter smaller than that value will result in a larger pressure drop
at the same volumetric flow rate, or a smaller volumetric flowrate at the same
pressure drop. Either way, it will not meet the design specification.

14.13 Reading parameter database text files in python

Matlab post
The datafile at http://terpconnect.umd.edu/~nsw/ench250/antoine.
dat (dead link) contains data that can be used to estimate the vapor pressure
of about 700 pure compounds using the Antoine equation
The data file has the following contents:

Antoine Coefficients
log(P) = A-B/(T+C) where P is in mmHg and T is in Celsius
Source of data: Yaws and Yang (Yaws, C. L. and Yang, H. C.,
"To estimate vapor pressure easily. antoine coefficients relate vapor pressure to temperatur

ID formula compound name A B C Tmin Tmax ?? ?

-----------------------------------------------------------------------------------
1 CCL4 carbon-tetrachloride 6.89410 1219.580 227.170 -20 101 Y2 0
2 CCL3F trichlorofluoromethane 6.88430 1043.010 236.860 -33 27 Y2 0
3 CCL2F2 dichlorodifluoromethane 6.68619 782.072 235.377 -119 -30 Y6 0

To use this data, you find the line that has the compound you want, and
read off the data. You could do that manually for each component you want
but that is tedious, and error prone. Today we will see how to retrieve the file,
then read the data into python to create a database we can use to store and
retrieve the data.
We will use the data to find the temperature at which the vapor pressure of
acetone is 400 mmHg.
We use numpy.loadtxt to read the file, and tell the function the format of
each column. This creates a special kind of record array which we can access
data by field name.

293
1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 data = np.loadtxt(’data/antoine_data.dat’,
5 dtype=[(’id’, np.int),
6 (’formula’, ’S8’),
7 (’name’, ’S28’),
8 (’A’, np.float),
9 (’B’, np.float),
10 (’C’, np.float),
11 (’Tmin’, np.float),
12 (’Tmax’, np.float),
13 (’??’, ’S4’),
14 (’?’, ’S4’)],
15 skiprows=7)
16
17 names = data[’name’]
18
19 acetone, = data[names == ’acetone’]
20
21 # for readability we unpack the array into variables
22 id, formula, name, A, B, C, Tmin, Tmax, u1, u2 = acetone
23
24 T = np.linspace(Tmin, Tmax)
25 P = 10**(A - B / ( T + C))
26 plt.plot(T, P)
27 plt.xlabel(’T ($^\circ$C)’)
28 plt.ylabel(’P$_{vap}$ (mmHg)’)
29
30 # Find T at which Pvap = 400 mmHg
31 # from our graph we might guess T ~ 40 ^{\circ}C
32
33 def objective(T):
34 return 400 - 10**(A - B / (T + C))
35
36 from scipy.optimize import fsolve
37 Tsol, = fsolve(objective, 40)
38 print Tsol
39 print ’The vapor pressure is 400 mmHg at T = {0:1.1f} degC’.format(Tsol)
40
41 #Plot CRC data http://en.wikipedia.org/wiki/Acetone_%28data_page%29#Vapor_pressure_of_liquid
42 # We only include the data for the range where the Antoine fit is valid.
43
44 Tcrc = [-59.4, -31.1, -9.4, 7.7, 39.5, 56.5]
45 Pcrc = [ 1, 10, 40, 100, 400, 760]
46
47 plt.plot(Tcrc, Pcrc, ’bo’)
48 plt.legend([’Antoine’,’CRC Handbook’], loc=’best’)
49 plt.savefig(’images/antoine-2.png’)

38.6138198197
The vapor pressure is 400 mmHg at T = 38.6 degC

294
 This result is close to the value reported here (39.5 degC), from the CRC
Handbook. The difference is probably that the value reported in the CRC is an
actual experimental number.

295
 14.14 Calculating a bubble point pressure of a mixture
Matlab post
Adapted from http://terpconnect.umd.edu/~nsw/ench250/bubpnt.htm
(dead link)
We previously learned to read a datafile containing lots of Antoine coeffi-
cients into a database, and use the coefficients to estimate vapor pressure of
a single compound. Here we use those coefficents to compute a bubble point
pressure of a mixture.
The bubble point is the temperature at which the sum of the component
vapor pressures is equal to the the total pressure. This is where a bubble of
vapor will first start forming, and the mixture starts to boil.
Consider an equimolar mixture of benzene, toluene, chloroform, acetone and
methanol. Compute the bubble point at 760 mmHg, and the gas phase compo-
sition. The gas phase composition is given by: yi = xi ∗ Pi /PT .

1 import numpy as np
2 from scipy.optimize import fsolve
3
4 # load our thermodynamic data
5 data = np.loadtxt(’data/antoine_data.dat’,
6 dtype=[(’id’, np.int),
7 (’formula’, ’S8’),
8 (’name’, ’S28’),
9 (’A’, np.float),
10 (’B’, np.float),
11 (’C’, np.float),
12 (’Tmin’, np.float),
13 (’Tmax’, np.float),
14 (’??’, ’S4’),
15 (’?’, ’S4’)],
16 skiprows=7)
17
18 compounds = [’benzene’, ’toluene’, ’chloroform’, ’acetone’, ’methanol’]
19
20 # extract the data we want
21 A = np.array([data[data[’name’] == x][’A’][0] for x in compounds])
22 B = np.array([data[data[’name’] == x][’B’][0] for x in compounds])
23 C = np.array([data[data[’name’] == x][’C’][0] for x in compounds])
24 Tmin = np.array([data[data[’name’] == x][’Tmin’][0] for x in compounds])
25 Tmax = np.array([data[data[’name’] == x][’Tmax’][0] for x in compounds])
26
27
28 # we have an equimolar mixture
29 x = np.array([0.2, 0.2, 0.2, 0.2, 0.2])
30
31 # Given a T, we can compute the pressure of each species like this:
32
33 T = 67 # degC
34 P = 10**(A - B / (T + C))
35 print P
36 print np.dot(x, P) # total mole-fraction weighted pressure
37
38 Tguess = 67
39 Ptotal = 760
40
41 def func(T):
42 P = 10**(A - B / (T + C))
43 return Ptotal - np.dot(x, P)
44
45 Tbubble, = fsolve(func, Tguess)

296
46
47 print ’The bubble point is {0:1.2f} degC’.format(Tbubble)
48
49 # double check answer is in a valid T range
50 if np.any(Tbubble < Tmin) or np.any(Tbubble > Tmax):
51 print ’T_bubble is out of range!’
52
53 # print gas phase composition
54 y = x * 10**(A - B / (Tbubble + C))/Ptotal
55
56 for cmpd, yi in zip(compounds, y):
57 print ’y_{0:<10s} = {1:1.3f}’.format(cmpd, yi)

[ 498.4320267 182.16010994 898.31061294 1081.48181768 837.88860027]

699.654633507
The bubble point is 69.46 degC
y_benzene = 0.142
y_toluene = 0.053
y_chloroform = 0.255
y_acetone = 0.308
y_methanol = 0.242

14.15 The equal area method for the van der Waals equa-
tion
Matlab post
When a gas is below its Tc the van der Waal equation oscillates. In the
portion of the isotherm where ∂PR /∂Vr > 0, the isotherm fails to describe real
materials, which phase separate into a liquid and gas in this region.
Maxwell proposed to replace this region by a flat line, where the area above
and below the curves are equal. Today, we examine how to identify where that
line should be.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 Tr = 0.9 # A Tr below Tc: Tr = T/Tc
5 # analytical equation for Pr. This is the reduced form of the van der Waal
6 # equation.
7 def Prfh(Vr):
8 return 8.0 / 3.0 * Tr / (Vr - 1.0 / 3.0) - 3.0 / (Vr**2)
9
10 Vr = np.linspace(0.5, 4, 100) # vector of reduced volume
11 Pr = Prfh(Vr) # vector of reduced pressure
12
13 plt.plot(Vr,Pr)
14 plt.ylim([0, 2])
15 plt.xlabel(’$V_R$’)
16 plt.ylabel(’$P_R$’)
17 plt.savefig(’images/maxwell-eq-area-1.png’)

>>> >>> >>> ... ... ... ... >>> >>> >>> >>> [<matplotlib.lines.Line2D object at 0x0000000007
(0, 2)

297
 <matplotlib.text.Text object at 0x00000000075C8630>
<matplotlib.text.Text object at 0x00000000075CADA0>

The idea is to pick a Pr and draw a line through the EOS. We want the areas
between the line and EOS to be equal on each side of the middle intersection.

1 y = 0.65
2
3 plt.plot([0.5, 4.0], [y, y], ’k--’)
4 plt.savefig(’images/maxwell-eq-area-2.png’)

>>> [<matplotlib.lines.Line2D object at 0x0000000007720048>]

298
 To find the areas, we need to know where the intersection of the vdW eqn
with the horizontal line. This is the same as asking what are the roots of the
vdW equation at that Pr. We need all three intersections so we can integrate
from the first root to the middle root, and then the middle root to the third
root. We take advantage of the polynomial nature of the vdW equation, which
allows us to use the roots command to get all the roots at once. The polynomial
is VR3 − 13 (1 + 8TR /PR ) + 3/PR − 1/PR = 0. We use the coefficients t0 get the
roots like this.

1 vdWp = [1.0, -1. / 3.0 * (1.0 + 8.0 * Tr / y), 3.0 / y, - 1.0 / y]

2 v = np.roots(vdWp)
3 v.sort()
4 print v
5
6 plt.plot(v[0], y, ’bo’, v[1], y, ’bo’, v[2], y, ’bo’)
7 plt.savefig(’images/maxwell-eq-area-3.png’)

>>> >>> [ 0.60286812 1.09743234 2.32534056]

>>> [<matplotlib.lines.Line2D object at 0x0000000007728630>, <matplotlib.lines.Line2D object

299
 14.15.1 Compute areas
for A1, we need the area under the line minus the area under the vdW curve.
That is the area between the curves. For A2, we want the area under the vdW
curve minus the area under the line. The area under the line between root 2
and root 1 is just the width (root2 - root1)*y

1 from scipy.integrate import quad

2
3 A1, e1 = (v[1] - v[0]) * y - quad(Prfh, v[0], v[1])
4 A2, e2 = quad(Prfh, v[1], v[2]) - (v[2] - v[1]) * y
5
6 print A1, A2
7 print e1, e2 # interesting these look so large

>>> >>> >>> >>> 0.063225945606 0.0580212098122

0.321466743765 -0.798140339268

1 from scipy.optimize import fsolve

2
3 def equal_area(y):
4 Tr = 0.9
5 vdWp = [1, -1.0 / 3 * ( 1.0 + 8.0 * Tr / y), 3.0 / y, -1.0 / y]
6 v = np.roots(vdWp)
7 v.sort()
8 A1 = (v[1] - v[0]) * y - quad(Prfh, v[0], v[1])
9 A2 = quad(Prfh, v[1], v[2]) - (v[2] - v[1]) * y
10 return A1 - A2
11
12 y_eq, = fsolve(equal_area, 0.65)

300
13 print y_eq
14
15 A1, e1 = (v[1] - v[0]) * y_eq - quad(Prfh, v[0], v[1])
16 A2, e2 = quad(Prfh, v[1], v[2]) - (v[2] - v[1]) * y_eq
17
18 vdWp = [1.0, -1.0 / 3.0 * (1.0 + 8.0 * Tr / y_eq), 3.0 / y_eq, -1.0 / y_eq]
19 v = np.roots(vdWp)
20 v.sort()
21
22 print v

>>> ... ... ... ... ... ... ... ... >>> >>> 0.646998351872
>>> >>> >>> >>> >>> >>> >>> >>> [ 0.6034019 1.09052663 2.34884238]

Now let us plot the equal areas and indicate them by shading.

1 ax = fig.add_subplot(111)
2
3 ax.plot(Vr,Pr)
4
5 hline = np.ones(Vr.size) * y_eq
6
7 ax.plot(Vr, hline)
8 ax.fill_between(Vr, hline, Pr, where=(Vr >= v[0]) & (Vr <= v[1]), facecolor=’gray’)
9 ax.fill_between(Vr, hline, Pr, where=(Vr >= v[1]) & (Vr <= v[2]), facecolor=’gray’)
10
11 plt.text(v[0], 1, ’A1 = {0}’.format(A1))
12 plt.text(v[2], 1, ’A2 = {0}’.format(A2))
13 plt.xlabel(’$V_R$’)
14 plt.ylabel(’$P_R$’)
15 plt.title(’$T_R$ = 0.9’)
16
17 plt.savefig(’images/maxwell-eq-area-4.png’)
18 plt.savefig(’images/maxwell-eq-area-4.svg’)

>>> >>> >>> [<matplotlib.lines.Line2D object at 0x0000000007CD0D68>]

>>> >>> >>> [<matplotlib.lines.Line2D object at 0x00000000075B14E0>]
<matplotlib.collections.PolyCollection object at 0x0000000007CF3D68>
<matplotlib.collections.PolyCollection object at 0x0000000007CF9C88>
>>> <matplotlib.text.Text object at 0x0000000007CFE0F0>
<matplotlib.text.Text object at 0x0000000007CFE208>
<matplotlib.text.Text object at 0x0000000007CD89E8>
<matplotlib.text.Text object at 0x0000000007CE1198>
<matplotlib.text.Text object at 0x0000000007CEC470>

301
 14.16 Time dependent concentration in a first order re-
versible reaction in a batch reactor
Matlab post
Given this reaction A
B, with these rate laws:
forward rate law: −ra = k1 CA
backward rate law: −rb = k−1 CB
plot the concentration of A vs. time. This example illustrates a set of
coupled first order ODES.

1 from scipy.integrate import odeint

2 import numpy as np
3
4 def myode(C, t):
5 # ra = -k1*Ca
6 # rb = -k_1*Cb
7 # net rate for production of A: ra - rb
8 # net rate for production of B: -ra + rb
9
10 k1 = 1 # 1/min;
11 k_1 = 0.5 # 1/min;
12
13 Ca = C[0]
14 Cb = C[1]
15
16 ra = -k1 * Ca
17 rb = -k_1 * Cb
18
19 dCadt = ra - rb
20 dCbdt = -ra + rb
21
22 dCdt = [dCadt, dCbdt]

302
23 return dCdt
24
25 tspan = np.linspace(0, 5)
26
27 init = [1, 0] # mol/L
28 C = odeint(myode, init, tspan)
29
30 Ca = C[:,0]
31 Cb = C[:,1]
32
33 import matplotlib.pyplot as plt
34 plt.plot(tspan, Ca, tspan, Cb)
35 plt.xlabel(’Time (min)’)
36 plt.ylabel(’C (mol/L)’)
37 plt.legend([’$C_A$’, ’$C_B$’])
38 plt.savefig(’images/reversible-batch.png’)

That is it. The main difference between this and Matlab is the order of
arguments in odeint is different, and the ode function has differently ordered
arguments.

14.17 Finding equilibrium conversion

A common problem to solve in reaction engineering is finding the equilibrium
conversion.1 A typical problem to solve is the following nonlinear equation:
X2
1.44 = (1−Xee )2
To solve this we create a2 function:
X
f (Xe ) = 0 = 1.44 − (1−Xee )2
and use a nonlinear solver to find the value of Xe that makes this function
equal to zero. We have to provide an initial guess. Chemical intuition suggests
1 See Fogler, 4th ed. page 1025 for the setup of this equation.

303
 that the solution must be between 0 and 1, and mathematical intuition suggests
the solution might be near 0.5 (which would give a ratio near 1).
Here is our solution.

1 from scipy.optimize import fsolve

2
3 def func(Xe):
4 z = 1.44 - (Xe**2)/(1-Xe)**2
5 return z
6
7 X0 = 0.5
8 Xe, = fsolve(func, X0)
9 print(’The equilibrium conversion is X = {0:1.2f}’.format(Xe))

The equilibrium conversion is X = 0.55

14.18 Integrating a batch reactor design equation

For a constant volume batch reactor where A → B at a rate of −rA = kCA 2
, we
derive the following design equation for the length of time required to achieve
a particular level of conversion :
RX
t(X) = kC1A0 X=0 (1−X)dX
2

if k = 10 L/mol/s and CA0 = 1 mol/L, estimate the time to achieve 90%

−3

conversion.
We could analytically solve the integral and evaluate it, but instead we will
numerically evaluate it using scipy.integrate.quad. This function returns two
values: the evaluated integral, and an estimate of the absolute error in the
answer.

1 from scipy.integrate import quad

2
3 def integrand(X):
4 k = 1.0e-3
5 Ca0 = 1.0 # mol/L
6 return 1./(k*Ca0)*(1./(1-X)**2)
7
8 sol, abserr = quad(integrand, 0, 0.9)
9 print ’t = {0} seconds ({1} hours)’.format(sol, sol/3600)
10 print ’Estimated absolute error = {0}’.format(abserr)

t = 9000.0 seconds (2.5 hours)

Estimated absolute error = 2.12203274482e-07

You can see the estimate error is very small compared to the solution.

14.19 Integrating the batch reactor mole balance

An alternative approach of evaluating an integral is to integrate a differential
equation. For the batch reactor, the differential equation that describes conver-
sion as a function of time is:
dt = −rA V /NA0 .
dX

304
 Given a value of initial concentration, or volume and initial number of moles
of A, we can integrate this ODE to find the conversion at some later time. We
assume that X(t = 0) = 0. We will integrate the ODE over a time span of 0 to
10,000 seconds.

1 from scipy.integrate import odeint

2 import numpy as np
3 import matplotlib.pyplot as plt
4
5 k = 1.0e-3
6 Ca0 = 1.0 # mol/L
7
8 def func(X, t):
9 ra = -k * (Ca0 * (1 - X))**2
10 return -ra / Ca0
11
12 X0 = 0
13 tspan = np.linspace(0,10000)
14
15 sol = odeint(func, X0, tspan)
16 plt.plot(tspan,sol)
17 plt.xlabel(’Time (sec)’)
18 plt.ylabel(’Conversion’)
19 plt.savefig(’images/2013-01-06-batch-conversion.png’)

You can read off of this figure to find the time required to achieve a particular
conversion.

305
 14.20 Plug flow reactor with a pressure drop
If there is a pressure drop in a plug flow reactor, 2 there are two equations
needed to determine the exit conversion: one for the conversion, and one from
the pressure drop.

k0
 
dX 1−X
= y (47)
dW FA 0 1 + X
dX α(1 + X)
= − (48)
dy 2y
Here is how to integrate these equations numerically in python.

1 import numpy as np
2 from scipy.integrate import odeint
3 import matplotlib.pyplot as plt
4
5 kprime = 0.0266
6 Fa0 = 1.08
7 alpha = 0.0166
8 epsilon = -0.15
9
10 def dFdW(F, W):
11 ’set of ODEs to integrate’
12 X = F[0]
13 y = F[1]
14 dXdW = kprime / Fa0 * (1-X) / (1 + epsilon*X) * y
15 dydW = -alpha * (1 + epsilon * X) / (2 * y)
16 return [dXdW, dydW]
17
18 Wspan = np.linspace(0,60)
19 X0 = 0.0
20 y0 = 1.0
21 F0 = [X0, y0]
22 sol = odeint(dFdW, F0, Wspan)
23
24 # now plot the results
25 plt.plot(Wspan, sol[:,0], label=’Conversion’)
26 plt.plot(Wspan, sol[:,1], ’g--’, label=’y=$P/P_0$’)
27 plt.legend(loc=’best’)
28 plt.xlabel(’Catalyst weight (lb_m)’)
29 plt.savefig(’images/2013-01-08-pdrop.png’)

Here is the resulting figure.

2 Fogler, 4th edition. page 193.

306
 14.21 Solving CSTR design equations
Given a continuously stirred tank reactor with a volume of 66,000 dmˆ3 where
the reaction A → B occurs, at a rate of −rA = kCA 2
(k = 3 L/mol/h), with an
entering molar flow of F_{A0} = 5 mol/h and a volumetric flowrate of 10 L/h,
what is the exit concentration of A?
From a mole balance we know that at steady state 0 = FA0 − FA + V rA .
That equation simply states the sum of the molar flow of A in in minus the
molar flow of A out plus the molar rate A is generated is equal to zero at steady
state. This is directly the equation we need to solve. We need the following
relationship:

1. FA = v0CA

1 from scipy.optimize import fsolve

2
3 Fa0 = 5.0
4 v0 = 10.
5
6 V = 66000.0 # reactor volume L^3
7 k = 3.0 # rate constant L/mol/h
8
9 def func(Ca):
10 "Mole balance for a CSTR. Solve this equation for func(Ca)=0"
11 Fa = v0 * Ca # exit molar flow of A
12 ra = -k * Ca**2 # rate of reaction of A L/mol/h
13 return Fa0 - Fa + V * ra
14
15 # CA guess that that 90 % is reacted away
16 CA_guess = 0.1 * Fa0 / v0
17 CA_sol, = fsolve(func, CA_guess)

307
18
19 print ’The exit concentration is {0} mol/L’.format(CA_sol)

The exit concentration is 0.005 mol/L

It is a little confusing why it is necessary to put a comma after the CA_sol

in the fsolve command. If you do not put it there, you get brackets around the
answer.

14.22 Meet the steam tables

Matlab post
We will use the iapws module. Install it like this:

1 pip install iapws

Problem statement: A Rankine cycle operates using steam with the con-
denser at 100 degC, a pressure of 3.0 MPa and temperature of 600 degC in the
boiler. Assuming the compressor and turbine operate reversibly, estimate the
efficiency of the cycle.
Starting point in the Rankine cycle in condenser.
we have saturated liquid here, and we get the thermodynamic properties
for the given temperature. In this python module, these properties are all in
attributes of an IAPWS object created at a set of conditions.

14.22.1 Starting point in the Rankine cycle in condenser.

We have saturated liquid here, and we get the thermodynamic properties for
the given temperature.

1 from iapws import IAPWS97

2
3 T1 = 100 + 273.15 #in K
4
5 sat_liquid1 = IAPWS97(T=T1, x=0) # x is the steam quality. 0 = liquid
6
7 P1 = sat_liquid1.P
8 s1 = sat_liquid1.s
9 h1 = sat_liquid1.h
10 v1 = sat_liquid1.v

14.22.2 Isentropic compression of liquid to point 2

The final pressure is given, and we need to compute the new temperatures, and
enthalpy.

1 P2 = 3.0 # MPa
2 s2 = s1 # this is what isentropic means
3
4 sat_liquid2 = IAPWS97(P=P2, s=s1)

308
5 T2, = sat_liquid2.T
6 h2 = sat_liquid2.h
7
8 # work done to compress liquid. This is an approximation, since the
9 # volume does change a little with pressure, but the overall work here
10 # is pretty small so we neglect the volume change.
11 WdotP = v1*(P2 - P1);
12 print
13 print(’The compressor work is: {0:1.4f} kJ/kg’.format(WdotP))

>>> >>> >>> >>> >>> >>> ... ... ... >>>
The compressor work is: 0.0030 kJ/kg
The compression work is almost negligible. This number is 1000 times
smaller than we computed with Xsteam. I wonder what the units of v1 ac-
tually are.

14.22.3 Isobaric heating to T3 in boiler where we make steam

1 T3 = 600 + 273.15 # K
2 P3 = P2 # definition of isobaric
3 steam = IAPWS97(P=P3, T=T3)
4
5 h3 = steam.h
6 s3 = steam.s
7
8 Qb, = h3 - h2 # heat required to make the steam
9
10 print
11 print ’The boiler heat duty is: {0:1.2f} kJ/kg’.format(Qb)

>>> >>> >>> >>> >>> >>> >>> >>>

The boiler heat duty is: 3260.69 kJ/kg

14.22.4 Isentropic expansion through turbine to point 4

1 steam = IAPWS97(P=P1, s=s3)

2 T4, = steam.T
3 h4 = steam.h
4 s4 = s3 # isentropic
5 Qc, = h4 - h1 # work required to cool from T4 to T1
6 print
7 print ’The condenser heat duty is {0:1.2f} kJ/kg’.format(Qc)

>>> >>> >>> >>>

The condenser heat duty is 2317.00 kJ/kg

14.22.5 To get from point 4 to point 1

1 WdotTurbine, = h4 - h3 # work extracted from the expansion

2 print(’The turbine work is: {0:1.2f} kJ/kg’.format(WdotTurbine))

309
 The turbine work is: -946.71 kJ/kg

14.22.6 Efficiency
This is a ratio of the work put in to make the steam, and the net work obtained
from the turbine. The answer here agrees with the efficiency calculated in
Sandler on page 135.

1 eta = -(WdotTurbine - WdotP) / Qb

2 print(’The overall efficiency is {0:1.2%}.’.format(eta))

The overall efficiency is 29.03%.

14.22.7 Entropy-temperature chart

The IAPWS module makes it pretty easy to generate figures of the steam tables.
Here we generate an entropy-Temperature graph. We do this to illustrate the
path of the Rankine cycle. We need to compute the values of steam entropy for
a range of pressures and temperatures.

1 import numpy as np
2 import matplotlib.pyplot as plt
3
4 plt.figure()
5 plt.clf()
6 T = np.linspace(300, 372+273, 200) # range of temperatures
7 for P in [0.1, 1, 2, 5, 10, 20]: #MPa
8 steam = [IAPWS97(T=t, P=P) for t in T]
9 S = [s.s for s in steam]
10 plt.plot(S, T, ’k-’)
11
12 # saturated vapor and liquid entropy lines
13 svap = [s.s for s in [IAPWS97(T=t, x=1) for t in T]]
14 sliq = [s.s for s in [IAPWS97(T=t, x=0) for t in T]]
15
16 plt.plot(svap, T, ’r-’)
17 plt.plot(sliq, T, ’b-’)
18
19 plt.xlabel(’Entropy (kJ/(kg K)’)
20 plt.ylabel(’Temperature (K)’)
21 plt.savefig(’images/iawps-steam.png’)

>>> >>> <matplotlib.figure.Figure object at 0x000000000638BC18>

>>> >>> ... ... ... ... [<matplotlib.lines.Line2D object at 0x0000000007F9C208>]
[<matplotlib.lines.Line2D object at 0x0000000007F9C400>]
[<matplotlib.lines.Line2D object at 0x0000000007F9C8D0>]
[<matplotlib.lines.Line2D object at 0x0000000007F9CD30>]
[<matplotlib.lines.Line2D object at 0x0000000007F9E1D0>]
[<matplotlib.lines.Line2D object at 0x0000000007F9E630>]
... >>> >>> >>> [<matplotlib.lines.Line2D object at 0x0000000001FDCEB8>]
[<matplotlib.lines.Line2D object at 0x0000000007F9EA90>]

310
 >>> <matplotlib.text.Text object at 0x0000000007F7BE48>
<matplotlib.text.Text object at 0x0000000007F855F8>

We can plot our Rankine cycle path like this. We compute the entropies
along the non-isentropic paths.

1 T23 = np.linspace(T2, T3)

2 S23 = [s.s for s in [IAPWS97(P=P2, T=t) for t in T23]]
3
4 T41 = np.linspace(T4, T1 - 0.01) # subtract a tiny bit to make sure we get a liquid
5 S41 = [s.s for s in [IAPWS97(P=P1, T=t) for t in T41]]

And then we plot the paths.

1 plt.plot([s1, s2], [T1, T2], ’r-’, lw=4) # Path 1 to 2

2 plt.plot(S23, T23, ’b-’, lw=4) # path from 2 to 3 is isobaric
3 plt.plot([s3, s4], [T3, T4], ’g-’, lw=4) # path from 3 to 4 is isentropic
4 plt.plot(S41, T41, ’k-’, lw=4) # and from 4 to 1 is isobaric
5 plt.savefig(’images/iawps-steam-2.png’)
6 plt.savefig(’images/iawps-steam-2.svg’)

[<matplotlib.lines.Line2D object at 0x0000000008350908>]

[<matplotlib.lines.Line2D object at 0x00000000083358D0>]
[<matplotlib.lines.Line2D object at 0x000000000835BEB8>]
[<matplotlib.lines.Line2D object at 0x0000000008357160>]

311
 14.22.8 Summary
This was an interesting exercise. On one hand, the tedium of interpolating the
steam tables is gone. On the other hand, you still have to know exactly what to
ask for to get an answer that is correct. The iapws interface is a little clunky,
and takes some getting used to. It does not seem as robust as the Xsteam
module I used in Matlab.

14.23 What region is a point in

Suppose we have a space that is divided by a boundary into two regions, and
we want to know if an arbitrary point is on one region or the other. One way
to figure this out is to pick a point that is known to be in a region, and then
draw a line to the arbitrary point counting the number of times it crosses the
boundary. If the line crosses an even number of times, then the point is in the
same region and if it crosses an odd number of times, then the point is in the
other region.
Here is the boundary and region we consider in this example:

1 boundary = [[0.1, 0],

2 [0.25, 0.1],
3 [0.3, 0.2],
4 [0.35, 0.34],
5 [0.4, 0.43],
6 [0.51, 0.47],
7 [0.48, 0.55],
8 [0.44, 0.62],
9 [0.5, 0.66],

312
10 [0.55,0.57],
11 [0.556, 0.48],
12 [0.63, 0.43],
13 [0.70, 0.44],
14 [0.8, 0.51],
15 [0.91, 0.57],
16 [1.0, 0.6]]
17
18 import matplotlib.pyplot as plt
19
20 plt.plot([p[0] for p in boundary],
21 [p[1] for p in boundary])
22 plt.ylim([0, 1])
23 plt.savefig(’images/boundary-1.png’)

... ... ... ... ... ... ... ... ... ... ... ... ... ... >>> >>> >>> >>> >>> ... [<matplotlib
(0, 1)

In this example, the boundary is complicated, and not described by a simple

function. We will check for intersections of the line from the arbitrary point
to the reference point with each segment defining the boundary. If there is an
intersection in the boundary, we count that as a crossing. We choose the origin
(0, 0) in this case for the reference point. For an arbitrary point (x1, y1), the
equation of the line is therefore (provided x1 !=0):
y1
y = x1 x.
Let the points defining a boundary segment be (bx1, by1) and (bx2, by2).
The equation for the line connecting these points (provided bx1 != bx2) is:
by2−by1
y = by1 + bx2−bx1 (x − bx1)
Setting these two equations equal to each other, we can solve for the value
of x, and if bx1 <= x <= bx2 then we would say there is an intersection with

313
that segment. The solution for x is:
x = mbx1−by1
m−y1/x1
This can only fail if m = y1/x1 which means the segments are parallel and
either do not intersect or go through each other. One issue we have to resolve
is what to do when the intersection is at the boundary. In that case, we would
see an intersection with two segments since bx1 of one segment is also bx2 of
another segment. We resolve the issue by only counting intersections with bx1.
Finally, there may be intersections at values of x greater than the point, and we
are not interested in those because the intersections are not between the point
and reference point.
Here are all of the special cases that we have to handle:

314
 We will have to do float comparisons, so we will define tolerance functions
for all of these. I tried this previously with regular comparison operators, and
there were many cases that did not work because of float comparisons. In the
code that follows, we define the tolerance functions, the function that handles
almost all the special cases, and show that it almost always correctly identifies
the region a point is in.

1 import numpy as np
2

315
3 TOLERANCE = 2 * np.spacing(1)
4
5 def feq(x, y, epsilon=TOLERANCE):
6 ’x == y’
7 return not((x < (y - epsilon)) or (y < (x - epsilon)))
8
9 def flt(x, y, epsilon=TOLERANCE):
10 ’x < y’
11 return x < (y - epsilon)
12
13 def fgt(x, y, epsilon=TOLERANCE):
14 ’x > y’
15 return y < (x - epsilon)
16
17 def fle(x, y, epsilon=TOLERANCE):
18 ’x <= y’
19 return not(y < (x - epsilon))
20
21 def fge(x, y, epsilon=TOLERANCE):
22 ’x >= y’
23 return not(x < (y - epsilon))
24
25 boundary = [[0.1, 0],
26 [0.25, 0.1],
27 [0.3, 0.2],
28 [0.35, 0.34],
29 [0.4, 0.43],
30 [0.51, 0.47],
31 [0.48, 0.55],
32 [0.44, 0.62],
33 [0.5, 0.66],
34 [0.55,0.57],
35 [0.556, 0.48],
36 [0.63, 0.43],
37 [0.70, 0.44],
38 [0.8, 0.51],
39 [0.91, 0.57],
40 [1.0, 0.6]]
41
42 def intersects(p, isegment):
43 ’p is a point (x1, y1), isegment is an integer indicating which segment starting with 0’
44 x1, y1 = p
45 bx1, by1 = boundary[isegment]
46 bx2, by2 = boundary[isegment + 1]
47
48 # outline cases to handle
49 if feq(bx1, bx2) and feq(x1, 0.0): # both segments are vertical
50 if feq(bx1, x1):
51 return True
52 else:
53 return False
54 elif feq(bx1, bx2): # segment is vertical
55 m1 = y1 / x1 # slope of reference line
56 y = m1 * bx1 # value of reference line at bx1
57 if ((fge(y, by1) and flt(y, by2))
58 or (fle(y, by1) and fgt(y,by2))):
59 # reference line intersects the segment
60 return True
61 else:
62 return False
63 else: # neither reference line nor segment is vertical
64 m = (by2 - by1) / (bx2 - bx1) # segment slope
65 m1 = y1 / x1
66 if feq(m, m1): # line and segment are parallel
67 if feq(y1, m * bx1):
68 return True
69 else:
70 return False

316
71 else: # lines are not parallel
72 x = (m * bx1 - by1) / (m - m1) # x at intersection
73
74 if ((fge(x, bx1) and flt(x, bx2))
75 or (fle(x, bx1) and fgt(x, bx2))) and fle(x, x1):
76 return True
77 else:
78 return False
79
80 raise Exception(’you should not get here’)
81
82 import matplotlib.pyplot as plt
83
84 plt.plot([p[0] for p in boundary],
85 [p[1] for p in boundary], ’go-’)
86 plt.ylim([0, 1])
87
88 N = 100
89
90 X = np.linspace(0, 1, N)
91
92 for x in X:
93 for y in X:
94 p = (x, y)
95
96 nintersections = sum([intersects(p, i) for i in range(len(boundary) - 1)])
97
98 if nintersections % 2 == 0:
99 plt.plot(x, y, ’r.’)
100 else:
101 plt.plot(x, y, ’b.’)
102
103 plt.savefig(’images/boundary-2.png’)
104 plt.show()

If you look carefully, there are two blue points in the red region, which means
there is some edge case we do not capture in our function. Kudos to the person

317
 who figures it out.

15 Units
15.1 Using units in python
Units in Matlab
I think an essential feature in an engineering computational environment is
properly handling units and unit conversions. Mathcad supports that pretty
well. I wrote a package for doing it in Matlab. Today I am going to explore
units in python. Here are some of the packages that I have found which support
units to some extent

1. http://pypi.python.org/pypi/units/

2. http://packages.python.org/quantities/user/tutorial.html
3. http://dirac.cnrs-orleans.fr/ScientificPython/ScientificPythonManual/
Scientific.Physics.PhysicalQuantities-module.html
4. http://home.scarlet.be/be052320/Unum.html

5. https://simtk.org/home/python_units
6. http://docs.enthought.com/scimath/units/intro.html

The last one looks most promising.

1 import numpy as np
2 from scimath.units.volume import liter
3 from scimath.units.substance import mol
4
5 q = np.array([1, 2, 3]) * mol
6 print q
7
8 P = q / liter
9 print P

[1.0*mol 2.0*mol 3.0*mol]

[1000.0*m**-3*mol 2000.0*m**-3*mol 3000.0*m**-3*mol]

That doesn’t look too bad. It is a little clunky to have to import every unit,
and it is clear the package is saving everything in SI units by default. Let us
try to solve an equation.
Find the time that solves this equation.
0.01 = CA0 e−kt
First we solve without units. That way we know the answer.

318
1 import numpy as np
2 from scipy.optimize import fsolve
3
4 CA0 = 1.0 # mol/L
5 CA = 0.01 # mol/L
6 k = 1.0 # 1/s
7
8 def func(t):
9 z = CA - CA0 * np.exp(-k*t)
10 return z
11
12 t0 = 2.3
13
14 t, = fsolve(func, t0)
15 print ’t = {0:1.2f} seconds’.format(t)

t = 4.61 seconds

Now, with units. I note here that I tried the obvious thing of just importing
the units, and adding them on, but the package is unable to work with floats
that have units. For some functions, there must be an ndarray with units which
is practically what the UnitScalar code below does.

1 import numpy as np
2 from scipy.optimize import fsolve
3 from scimath.units.volume import liter
4 from scimath.units.substance import mol
5 from scimath.units.time import second
6 from scimath.units.api import has_units, UnitScalar
7
8 CA0 = UnitScalar(1.0, units = mol / liter)
9 CA = UnitScalar(0.01, units = mol / liter)
10 k = UnitScalar(1.0, units = 1 / second)
11
12 @has_units(inputs="t::units=s",
13 outputs="result::units=mol/liter")
14 def func(t):
15 z = CA - CA0 * float(np.exp(-k*t))
16 return z
17
18 t0 = UnitScalar(2.3, units = second)
19
20 t, = fsolve(func, t0)
21 print ’t = {0:1.2f} seconds’.format(t)
22 print type(t)

t = 4.61 seconds
<type ’numpy.float64’>

This is some heavy syntax that in the end does not preserve the units. In
my Matlab package, we had to "wrap" many functions like fsolve so they would
preserve units. Clearly this package will need that as well. Overall, in its current
implementation this package does not do what I would expect all the time.3
3 Then again no package does yet!

319
 15.2 Handling units with the quantities module
The quantities module (https://pypi.python.org/pypi/quantities) is an-
other option for handling units in python. We are going to try the previous
example. It does not work, because scipy.optimize.fsolve is not designed to
work with units.

1 import quantities as u
2 import numpy as np
3
4 from scipy.optimize import fsolve
5 CA0 = 1 * u.mol / u.L
6 CA = 0.01 * u.mol / u.L
7 k = 1.0 / u.s
8
9 def func(t):
10 return CA - CA0 * np.exp(-k * t)
11
12 tguess = 4 * u.s
13
14 print func(tguess)
15
16 print fsolve(func, tguess)

>>> >>> >>> >>> >>> >>> >>> ... ... >>> >>> >>> -0.00831563888873 mol/L
>>> Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "c:\Python27\lib\site-packages\scipy\optimize\minpack.py", line 115, in fsolve
_check_func(’fsolve’, ’func’, func, x0, args, n, (n,))
File "c:\Python27\lib\site-packages\scipy\optimize\minpack.py", line 13, in _check_func
res = atleast_1d(thefunc(*((x0[:numinputs],) + args)))
File "<stdin>", line 2, in func
File "c:\Python27\lib\site-packages\quantities-0.10.1-py2.7.egg\quantities\quantity.py", l
res._dimensionality = p_dict[uf](*objs)
File "c:\Python27\lib\site-packages\quantities-0.10.1-py2.7.egg\quantities\dimensionality.
raise ValueError("quantity must be dimensionless")
ValueError: quantity must be dimensionless

Our function works fine with units, but fsolve does not pass numbers with
units back to the function, so this function fails because the exponential function
gets an argument with dimensions in it. We can create a new function that solves
this problem. We need to "wrap" the function we want to solve to make sure
that it uses units, but returns a float number. Then, we put the units back onto
the final solved value. Here is how we do that.

1 import quantities as u
2 import numpy as np
3
4 from scipy.optimize import fsolve as _fsolve
5
6 CA0 = 1 * u.mol / u.L
7 CA = 0.01 * u.mol / u.L
8 k = 1.0 / u.s
9

320
10 def func(t):
11 return CA - CA0 * np.exp(-k * t)
12
13 def fsolve(func, t0):
14 ’wrapped fsolve command to work with units’
15 tU = t0 / float(t0) # units on initial guess, normalized
16 def wrapped_func(t):
17 ’t will be unitless, so we add unit to it. t * tU has units.’
18 return float(func(t * tU))
19
20 sol, = _fsolve(wrapped_func, t0)
21 return sol * tU
22
23 tguess = 4 * u.s
24
25 print fsolve(func, tguess)

4.60517018599 s

It is a little tedious to do this, but we might only have to do it once if we store

the new fsolve command in a module. You might notice the wrapped function
we wrote above only works for one dimensional problems. If there are multiple
dimensions, we have to be a little more careful. In the next example, we expand
the wrapped function definition to do both one and multidimensional problems.
It appears we cannot use numpy.array element-wise multiplication because you
cannot mix units in an array. We will use lists instead. When the problem is
one-dimensional, the function will take a scalar, but when it is multidimensional
it will take a list or array. We will use try/except blocks to handle these two
cases. We will assume multidimensional cases, and if that raises an exception
because the argument is not a list, we assume it is scalar. Here is the more
robust code example.

1 import quantities as u
2 import numpy as np
3
4 from scipy.optimize import fsolve as _fsolve
5
6 def fsolve(func, t0):
7 ’’’wrapped fsolve command to work with units. We get the units on
8 the function argument, then wrap the function so we can add units
9 to the argument and return floats. Finally we call the original
10 fsolve from scipy. Note: this does not support all of the options
11 to fsolve.’’’
12
13 try:
14 tU = [t / float(t) for t in t0] # units on initial guess, normalized
15 except TypeError:
16 tU = t0 / float(t0)
17
18 def wrapped_func(t):
19 ’t will be unitless, so we add unit to it. t * tU has units.’
20 try:
21 T = [x1 * x2 for x1,x2 in zip(t, tU)]
22 except TypeError:
23 T = t * tU
24
25 try:
26 return [float(x) for x in func(T)]
27 except TypeError:
28 return float(func(T))

321
29
30 sol = _fsolve(wrapped_func, t0)
31 try:
32 return [x1 * x2 for x1,x2 in zip(sol, tU)]
33 except TypeError:
34 return sol * tU
35
36 ### Problem 1
37 CA0 = 1 * u.mol / u.L
38 CA = 0.01 * u.mol / u.L
39 k = 1.0 / u.s
40
41 def func(t):
42 return CA - CA0 * np.exp(-k * t)
43
44
45 tguess = 4 * u.s
46 sol1, = fsolve(func, tguess)
47 print ’sol1 = ’,sol1
48
49 ### Problem 2
50 def func2(X):
51 a,b = X
52 return [a**2 - 4*u.kg**2,
53 b**2 - 25*u.J**2]
54
55 Xguess = [2.2*u.kg, 5.2*u.J]
56 s2a, s2b = fsolve(func2, Xguess)
57 print ’s2a = {0}\ns2b = {1}’.format(s2a, s2b)

sol1 = 4.60517018599 s
s2a = 2.0 kg
s2b = 5.0 J

That is pretty good. There is still room for improvement in the wrapped
function, as it does not support all of the options that scipy.optimize.fsolve
supports. Here is a draft of a function that does that. We have to return
different numbers of arguments depending on the value of full_output. This
function works, but I have not fully tested all the options. Here are three
examples that work, including one with an argument.

1 import quantities as u
2 import numpy as np
3
4 from scipy.optimize import fsolve as _fsolve
5
6 def fsolve(func, t0, args=(),
7 fprime=None, full_output=0, col_deriv=0,
8 xtol=1.49012e-08, maxfev=0, band=None,
9 epsfcn=0.0, factor=100, diag=None):
10 ’’’wrapped fsolve command to work with units. We get the units on
11 the function argument, then wrap the function so we can add units
12 to the argument and return floats. Finally we call the original
13 fsolve from scipy. ’’’
14
15 try:
16 tU = [t / float(t) for t in t0] # units on initial guess, normalized
17 except TypeError:
18 tU = t0 / float(t0)
19
20 def wrapped_func(t, *args):
21 ’t will be unitless, so we add unit to it. t * tU has units.’

322
22 try:
23 T = [x1 * x2 for x1,x2 in zip(t, tU)]
24 except TypeError:
25 T = t * tU
26
27 try:
28 return [float(x) for x in func(T, *args)]
29 except TypeError:
30 return float(func(T))
31
32 sol = _fsolve(wrapped_func, t0, args,
33 fprime, full_output, col_deriv,
34 xtol, maxfev, band,
35 epsfcn, factor, diag)
36
37 if full_output:
38 x, infodict, ier, mesg = sol
39 try:
40 x = [x1 * x2 for x1,x2 in zip(x, tU)]
41 except TypeError:
42 x = x * tU
43 return x, infodict, ier, mesg
44 else:
45 try:
46 x = [x1 * x2 for x1,x2 in zip(sol, tU)]
47 except TypeError:
48 x = sol * tU
49 return x
50
51 ### Problem 1
52 CA0 = 1 * u.mol / u.L
53 CA = 0.01 * u.mol / u.L
54 k = 1.0 / u.s
55
56 def func(t):
57 return CA - CA0 * np.exp(-k * t)
58
59
60 tguess = 4 * u.s
61 sol1, = fsolve(func, tguess)
62 print ’sol1 = ’,sol1
63
64 ### Problem 2
65 def func2(X):
66 a,b = X
67 return [a**2 - 4*u.kg**2,
68 b**2 - 25*u.J**2]
69
70 Xguess = [2.2*u.kg, 5.2*u.J]
71 sol, infodict, ier, mesg = fsolve(func2, Xguess, full_output=1)
72 s2a, s2b = sol
73 print ’s2a = {0}\ns2b = {1}’.format(s2a, s2b)
74
75 ### Problem 3 - with an arg
76 def func3(a, arg):
77 return a**2 - 4*u.kg**2 + arg**2
78
79 Xguess = 1.5 * u.kg
80 arg = 0.0* u.kg
81
82 sol3, = fsolve(func3, Xguess, args=(arg,))
83 print’sol3 = ’, sol3

sol1 = 4.60517018599 s
s2a = 2.0 kg
s2b = 5.0 J

323
 sol3 = 2.0 kg

The only downside I can see in the quantities module is that it only handle
temperature differences, and not absolute temperatures. If you only use absolute
temperatures, this would not be a problem I think. But, if you have mixed
temperature scales, the quantities module does not convert them on an absolute
scale.

1 import quantities as u
2
3 T = 20 * u.degC
4
5 print T.rescale(u.K)
6 print T.rescale(u.degF)

20.0 K
36.0 degF

Nevertheless, this module seems pretty promising, and there are a lot
more features than shown here. Some documentation can be found at http:
//pythonhosted.org/quantities/.

15.3 Units in ODEs

We reconsider a simple ODE but this time with units. We will use the quantities
package again.
Here is the ODE, dCadt = −kCa with CA (0) = 1.0 mol/L and k = 0.23 1/s.
Compute the concentration after 5 s.

1 import quantities as u
2
3 k = 0.23 / u.s
4 Ca0 = 1 * u.mol / u.L
5
6 def dCadt(Ca, t):
7 return -k * Ca
8
9 import numpy as np
10 from scipy.integrate import odeint
11
12 tspan = np.linspace(0, 5) * u.s
13
14 sol = odeint(dCadt, Ca0, tspan)
15
16 print sol[-1]

[ 0.31663678]

No surprise, the units are lost. Now we start wrapping odeint. We wrap
everything, and then test two examples including a single ODE, and a coupled
set of ODEs with mixed units.

324
1 import quantities as u
2 import matplotlib.pyplot as plt
3
4 import numpy as np
5 from scipy.integrate import odeint as _odeint
6
7 def odeint(func, y0, t, args=(),
8 Dfun=None, col_deriv=0, full_output=0,
9 ml=None, mu=None, rtol=None, atol=None,
10 tcrit=None, h0=0.0, hmax=0.0, hmin=0.0,
11 ixpr=0, mxstep=0, mxhnil=0, mxordn=12,
12 mxords=5, printmessg=0):
13
14 def wrapped_func(Y0, T, *args):
15 # put units on T if they are on the original t
16 # check for units so we don’t put them on twice
17 if not hasattr(T, ’units’) and hasattr(t, ’units’):
18 T = T * t.units
19 # now for the dependent variable units. Y0 may be a scalar or
20 # a list or an array. we want to check each element of y0 for
21 # units, and add them to the corresponding element of Y0 if we
22 # need to.
23 try:
24 uY0 = [x for x in Y0] # a list copy of contents of Y0
25 # this works if y0 is an iterable, eg. a list or array
26 for i, yi in enumerate(y0):
27 if not hasattr(uY0[i],’units’) and hasattr(yi, ’units’):
28
29 uY0[i] = uY0[i] * yi.units
30
31 except TypeError:
32 # we have a scalar
33 if not hasattr(Y0, ’units’) and hasattr(y0, ’units’):
34 uY0 = Y0 * y0.units
35
36 val = func(uY0, t, *args)
37
38 try:
39 return np.array([float(x) for x in val])
40 except TypeError:
41 return float(val)
42
43 if full_output:
44 y, infodict = _odeint(wrapped_func, y0, t, args,
45 Dfun, col_deriv, full_output,
46 ml, mu, rtol, atol,
47 tcrit, h0, hmax, hmin,
48 ixpr, mxstep, mxhnil, mxordn,
49 mxords, printmessg)
50 else:
51 y = _odeint(wrapped_func, y0, t, args,
52 Dfun, col_deriv, full_output,
53 ml, mu, rtol, atol,
54 tcrit, h0, hmax, hmin,
55 ixpr, mxstep, mxhnil, mxordn,
56 mxords, printmessg)
57
58 # now we need to put units onto the solution units should be the
59 # same as y0. We cannot put mixed units in an array, so, we return a list
60 m,n = y.shape # y is an ndarray, so it has a shape
61 if n > 1: # more than one equation, we need a list
62 uY = [0 for yi in range(n)]
63
64 for i, yi in enumerate(y0):
65 if not hasattr(uY[i],’units’) and hasattr(yi, ’units’):
66 uY[i] = y[:,i] * yi.units
67 else:

325
68 uY[i] = y[:,i]
69
70 else:
71 uY = y * y0.units
72
73 y = uY
74
75
76 if full_output:
77 return y, infodict
78 else:
79 return y
80
81 ##################################################################
82 # test a single ODE
83 k = 0.23 / u.s
84 Ca0 = 1 * u.mol / u.L
85
86 def dCadt(Ca, t):
87 return -k * Ca
88
89 tspan = np.linspace(0, 5) * u.s
90 sol = odeint(dCadt, Ca0, tspan)
91
92 print sol[-1]
93
94 plt.plot(tspan, sol)
95 plt.xlabel(’Time ({0})’.format(tspan.dimensionality.latex))
96 plt.ylabel(’$C_A$ ({0})’.format(sol.dimensionality.latex))
97 plt.savefig(’images/ode-units-ca.png’)
98
99 ##################################################################
100 # test coupled ODEs
101 lbmol = 453.59237*u.mol
102
103 kprime = 0.0266 * lbmol / u.hr / u.lb
104 Fa0 = 1.08 * lbmol / u.hr
105 alpha = 0.0166 / u.lb
106 epsilon = -0.15
107
108 def dFdW(F, W, alpha0):
109 X, y = F
110 dXdW = kprime / Fa0 * (1.0 - X)/(1.0 + epsilon * X) * y
111 dydW = - alpha0 * (1.0 + epsilon * X) / (2.0 * y)
112 return [dXdW, dydW]
113
114 X0 = 0.0 * u.dimensionless
115 y0 = 1.0
116
117 # initial conditions
118 F0 = [X0, y0] # one without units, one with units, both are dimensionless
119
120 wspan = np.linspace(0,60) * u.lb
121
122 sol = odeint(dFdW, F0, wspan, args=(alpha,))
123 X, y = sol
124
125 print ’Test 2’
126 print X[-1]
127 print y[-1]
128
129 plt.figure()
130 plt.plot(wspan, X, wspan, y)
131 plt.legend([’X’,’$P/P_0$’])
132 plt.xlabel(’Catalyst weight ({0})’.format(wspan.dimensionality.latex))
133 plt.savefig(’images/ode-coupled-units-pdrpo.png’)

326
[ 0.31663678] mol/L
Test 2
0.665569578156 dimensionless
0.263300470681

That is not too bad. This is another example of a function you would want
to save in a module for reuse. There is one bad feature of the wrapped odeint

327
 function, and that is that it changes the solution for coupled ODEs from an
ndarray to a list. That is necessary because you apparently cannot have mixed
units in an ndarray. It is fine, however, to have a list of mixed units. This is not
a huge problem, but it changes the syntax for plotting results for the wrapped
odeint function compared to the unwrapped function without units.

15.4 Handling units with dimensionless equations

As we have seen, handling units with third party functions is fragile, and often
requires additional code to wrap the function to handle the units. An alter-
native approach that avoids the wrapping is to rescale the equations so they
are dimensionless. Then, we should be able to use all the standard external
functions without modification. We obtain the final solutions by rescaling back
to the answers we want.
Before doing the examples, let us consider how the quantities package han-
dles dimensionless numbers.

1 import quantities as u
2
3 a = 5 * u.m
4 L = 10 * u.m # characteristic length
5
6 print a/L
7 print type(a/L)

0.5 dimensionless
<class ’quantities.quantity.Quantity’>

As you can see, the dimensionless number is scaled properly, and is listed
as dimensionless. The result is still an instance of a quantities object though.
That is not likely to be a problem.
Now, we consider using fsolve with dimensionless equations. Our goal is to
solve CA = CA0 exp(−kt) for the time required to reach a desired CA . We let
X = Ca/Ca0 and τ = t ∗ k, which leads to X = exp −τ in dimensionless terms.

1 import quantities as u
2 import numpy as np
3 from scipy.optimize import fsolve
4
5 CA0 = 1 * u.mol / u.L
6 CA = 0.01 * u.mol / u.L # desired exit concentration
7 k = 1.0 / u.s
8
9 # we need new dimensionless variables
10 # let X = Ca / Ca0
11 # so, Ca = Ca0 * X
12
13 # let tau = t * k
14 # so t = tau / k
15
16 X = CA / CA0 # desired exit dimensionless concentration
17
18 def func(tau):
19 return X - np.exp(-tau)

328
20
21 tauguess = 2
22
23 print func(tauguess) # confirm we have a dimensionless function
24
25 tau_sol, = fsolve(func, tauguess)
26 t = tau_sol / k
27 print t

-0.125335283237 dimensionless
4.60517018599 s

Now consider the ODE dCa dt = −kCa. We let X = Ca/Ca0, so Ca0dX =

dCa. Let τ = t ∗ k which in this case is dimensionless. That means dτ = kdt.
Substitution of these new variables leads to:
Ca0 ∗ k dX
dτ = −kCa0X
or equivalently: dX
dτ = −X

1 import quantities as u
2
3 k = 0.23 / u.s
4 Ca0 = 1 * u.mol / u.L
5
6 # Let X = Ca/Ca0 -> Ca = Ca0 * X dCa = dX/Ca0
7 # let tau = t * k -> dt = 1/k dtau
8
9
10 def dXdtau(X, tau):
11 return -X
12
13 import numpy as np
14 from scipy.integrate import odeint
15
16 tspan = np.linspace(0, 5) * u.s
17 tauspan = tspan * k
18
19 X0 = 1
20 X_sol = odeint(dXdtau, X0, tauspan)
21
22 print ’Ca at t = {0} = {1}’.format(tspan[-1], X_sol.flatten()[-1] * Ca0)

Ca at t = 5.0 s = 0.316636777351 mol/L

That is pretty much it. Using dimensionless quantities simplifies the need
to write wrapper code, although it does increase the effort to rederive your
equations (with corresponding increased opportunities to make mistakes). Using
units to confirm your dimensionless derivation reduces those opportunities.

16 GNU Free Documentation License

GNU Free Documentation License
Version 1.3, 3 November 2008

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17 References
http://scipy-lectures.github.com/index.html

18 Index

339
Index
animation, 196 ODE, 158
reverse, 151
BVP, 192
LU decomposition,determinant, 78
COM, 238
Continuation, 84 ODE
coupled, 177
derivative event, 161, 162
4 point formula, 36 parameterized, 167–169
backward difference, 33 second order, 170
centered difference, 33 tolerance, 163
complex step, 42 optimization
FFT, 41 constrained, 142, 147
fitting, 39 Lagrange multipliers, 144
forward difference, 33 linear programming, 146
numerical, 33
polynomial, 37 PDE
vectorized, 35 method of lines, 196, 200
nonlinear, 190
Excel, 238 pde, 203
plot
fmin_slsqp, 142 double y-axis, 212
fsolve, 144 subplot, 213
plotting
integration animation, 196
quad, 53 interactive key press, 220
Simpson’s rule, 59 interactive mouse click, 220
trapezoid , 53
integration:trapz, 58 sort, 229
interpolation, 136
cubic, 137 transpose, 69

340