Adding a GSL integration function to Emacs with a dynamic module

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Here we work out how to run this program: in a dynamic module in emacs. The goal is to be able to evaluate \(\int_0^1 x^{-1/2} \log(x) dx\). According to the example page the answer is -4. We will define an integration function that takes at least a function and integration bounds as arguments, and several optional arguments to specify tolerances and limits. In other words we want to evaluate integrals of the form:

\(\int_a^b f(x; params) dx\)

I want that to happen in an elisp function with a signature like:

(gsl-integration-qags (lambda (x params) body) a b &optional params epsabs epsrel limit)

And that function will return a list containing (result error-estimate). Here is the C-code that makes this happen. It is more complex that the last example, and only compiles with gcc that allows nested functions. I don't know how to write this without that feature. This is more complex also because you have to create a workspace to do the integration inside the function that does the integration. The C-module also has extra code in it to allow for optional arguments.

#include <gsl/gsl_integration.h>
#include "emacs-module.h"

int plugin_is_GPL_compatible;

static emacs_value F_gsl_integrate (emacs_env *env, ptrdiff_t nargs, emacs_value args[], void *data)
  // nested function - only supported as an extension in gcc
  double f (double x, void *params) 
    emacs_value fn = args[0];  // function we will integrate
    emacs_value x2[] = { env->make_float(env, x), params };
    emacs_value y = env->funcall(env, fn, 2, &x2);   
    return env->extract_float (env, y);

  double a = env->extract_float (env, args[1]);
  double b = env->extract_float (env, args[2]);

  // default values for optional arguments
  double epsabs = 0.0;
  double epsrel = 1e-7;
  size_t limit = 1000;
  double result, error; 

  // Here is how I handle the optional arguments
  // (gsl-integrate func a b params epsabs epsrel limit)
  gsl_function F;
  F.function = &f;
  if (nargs >= 4) {F.params = args[3];}
  if (nargs >= 5 && env->is_not_nil(env, args[4])) {epsabs = env->extract_float(env, args[4]);}
  if (nargs >= 6 && env->is_not_nil(env, args[5])) {epsrel = env->extract_float(env, args[5]);}
  if (nargs >= 7 && env->is_not_nil(env, args[6])) {limit = env->extract_integer(env, args[6]);}

  gsl_integration_workspace * w = gsl_integration_workspace_alloc (limit);

  gsl_integration_qags (&F, // gsl_function pointer
                        a, // lower integration bound
                        b, // upper integration bound
                        epsabs, // absolute error tolerance
                        epsrel, // relative error tolerance
                        limit, // max number of subintervals for integration
                        w, // the workspace
                        // pointers to put results and error in
                        &result, &error);

  gsl_integration_workspace_free (w);
  // make a list of (result error) to return
  emacs_value Qlist = env->intern(env, "list");
  emacs_value Qresult = env->make_float (env, result);
  emacs_value Qerror = env->make_float (env, error);
  emacs_value list_args[] = { Qresult, Qerror };
  return env->funcall(env, Qlist, 2, list_args);

int emacs_module_init(struct emacs_runtime *ert)
  emacs_env *env = ert->get_environment(ert);
  // Here we create the function.
  emacs_value fset = env->intern(env, "fset");
  emacs_value args[2];
  args[0] = env->intern(env, "gsl-integration-qags"); // symbol to create for function
  // The function we set that symbol to.
  args[1] = env->make_function(env,
                               3, // min nargs
                               7, // max nargs
                               "(gsl-integration-qags F A B &optional PARAMS EPSABS EPSREL LIMIT)\n" \
                               "Integrate F(x; params) from A to B.\n" \
                               "F is a function of a single variable and parameters.\n" \
                               "A is the lower bound of integration\n"  \
                               "B is the upper bound of integration.\n" \
                               "Optional parameters:\n"\
                               "PARAMS is a list of params to pass to F.\n" \
                               "EPSABS is a float (default 0.0) and is the absolute error tolerance.\n" \
                               "EPSREL is a float (default 1e-7) and is the relative error tolerance.\n" \
                               "LIMIT is the maximum number of subintervals for the integration (default 1000).\n" \
                               "Returns (list result error-estimate).\n" \
  // This is basically (fset 'gsl-integration-qags (lambda func))
  env->funcall(env, fset, 2, args);
  // This is what allows the shared library to provide a feature 
  emacs_value provide = env->intern(env, "provide");
  emacs_value provide_args[] = { env->intern(env, "gsl-integration") };
  env->funcall(env, provide, 1, provide_args);
  return 0;

Building this was moderately tricky. It appears the first gcc on my path uses clang which does not support nested functions in C. I don't know enough C to figure out how to do this without a nested function though, since the function has to be defined at run-time based on the emacs env and args. gcc does support inline functions, so the code below uses a gcc that does compile it.

rm -f gsl-integration.o
/usr/local/Cellar/gcc/6.1.0/bin/gcc-6 -Wall -I/usr/local/include -fPIC -c gsl-integration.c
/usr/local/Cellar/gcc/6.1.0/bin/gcc-6  -shared -L/usr/local/include -lgsl -o gsl-integration.o

Now we add this directory to our path since it is not on it and require our new module.

(add-to-list 'load-path "/Users/jkitchin/vc/")
(require 'gsl-integration)

Let us see our new function in action. We evaluate \(\int_0^1 x^{-1/2} \log(x) dx\). According to the example page the answer is -4. Here is an example where we ignore the parameters. You have to be careful; Emacs sometimes segfaults and crashes if you use an integer or float argument when it expects the other type.

(gsl-integration-qags (lambda (x params) (/ (log x) (sqrt x))) 0.0 1.0)
-4.000000000000085 1.354472090042691e-13

Here are some optional arguments.

(gsl-integration-qags (lambda (x params) (/ (log x) (sqrt x))) 0.0 1.0 nil nil 0.01)
-4.000000000000075 0.019526557540360034

Nice, with a larger epsrel argument we get a larger error. Note the arguments are positional, so we have to include them all just to set the epsrel argument. How about an easier example with parameters that we actually use. Here we integrate a constant, and set the value of the constant from the params arg. The integral should be the area of a rectangle of length 1 and width of the param we use.

 (gsl-integration-qags (lambda (x params) (first params)) 0.0 1.0 '(1.0))
 (gsl-integration-qags (lambda (x params) (first params)) 0.0 1.0 '(0.5)))
1.0 1.1102230246251565e-14
0.5 5.551115123125783e-15

Wow! It actually works!!! That was harder won success than usual for me. I am claiming victory for now and leaving the following notes to future me:

  1. It would be nice to have optional keyword arguments. This would take some handling of the arguments beyond what I know how to do for now, unless it is possible to pull in something like plist-get the way we pull in fset, provide and list in this example.
  2. Error checking on types would be helpful. It is not good for Emacs to crash because 0 is not 0.0!
  3. In numpy there is often a feature to get full_output. Here, the workspace created in the function has more information available in a struct that might be helpful to have access to at times. It seems like it might be possible to get that here too.

Copyright (C) 2017 by John Kitchin. See the License for information about copying.

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Numerical Simpsons rule

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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.

import numpy as np
from scipy.integrate import simps, romb

a = 0.0; b = np.pi / 4.0;
N = 10  # this is the number of intervals

x = np.linspace(a, b, N)
y = np.cos(x)

t = np.trapz(y, x)
s = simps(y, x)
a = np.sin(b) - np.sin(a)

print 'trapz = {0} ({1:%} error)'.format(t, (t - a)/a)
print 'simps = {0} ({1:%} error)'.format(s, (s - a)/a)
print 'analy = {0}'.format(a)
>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>>
trapz = 0.70665798038 (-0.063470% error)
simps = 0.707058914216 (-0.006769% error)
analy = 0.707106781187

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

Copyright (C) 2013 by John Kitchin. See the License for information about copying.

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Integrating the Fermi distribution to compute entropy

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The Fermi distribution is defined by \(f(\epsilon) = \frac{1}{e^{(\epsilon - \mu)/(k T)} + 1}\). This function describes the occupation of energy levels at temperatures above absolute zero. We use this function to compute electronic entropy in a metal, which contains an integral of \(\int n(\epsilon) (f \ln f + (1 - f) \ln (1-f)) d\epsilon\), where \(n(\epsilon)\) is the electronic density of states. Here we plot the Fermi distribution function. It shows that well below the Fermi level the states are fully occupied, and well above the Fermi level, they are unoccupied. Near the Fermi level, the states go from occupied to unoccupied smoothly.

import numpy as np
import matplotlib.pyplot as plt

mu = 0
k = 8.6e-5
T = 1000

def f(e):
    return 1.0 / (np.exp((e - mu)/(k*T)) + 1)

espan = np.linspace(-10, 10, 200)
plt.plot(espan, f(espan))
plt.ylim([-0.1, 1.1])

Let us consider a simple density of states function, just a parabola. This could represent a s-band for example. We will use this function to explore the integral.

import numpy as np
import matplotlib.pyplot as plt

mu = 0
k = 8.6e-5
T = 1000

def f(e):
    return 1.0 / (np.exp((e - mu)/(k*T)) + 1)

def dos(e):
    d = (np.ones(e.shape) - 0.03 * e**2) 
    return d * (d > 0)
espan = np.linspace(-10, 10)

plt.plot(espan, dos(espan), label='Total dos')
plt.plot(espan, f(espan) * dos(espan), label='Occupied states')

Now, we consider the integral to compute the electronic entropy. The entropy is proportional to this integral.

\( \int n(\epsilon) (f \ln f + (1 - f) \ln (1-f)) d\epsilon \)

It looks straightforward to compute, but it turns out there is a wrinkle. Evaluating the integrand leads to nan elements because the ln(0) is -∞.

import numpy as np
mu = 0
k = 8.6e-5
T = 100

def fermi(e):
    return 1.0 / (np.exp((e - mu)/(k*T)) + 1)

espan = np.array([-20, -10, -5, 0.0, 5, 10])
f = fermi(espan)

print f * np.log(f)
print (1 - f) * np.log(1 - f)
[  0.00000000e+000   0.00000000e+000   0.00000000e+000  -3.46573590e-001
  -1.85216532e-250               nan]
[        nan         nan         nan -0.34657359  0.          0.        ]

In this case, these nan elements should be equal to zero (x ln(x) goes to zero as x goes to zero). So, we can just ignore those elements in the integral. Here is how to do that.

import numpy as np
import matplotlib.pyplot as plt

mu = 0
k = 8.6e-5
T = 1000

def fermi(e):
    return 1.0 / (np.exp((e - mu)/(k*T)) + 1)

def dos(e):
    d = (np.ones(e.shape) - 0.03 * e**2) 
    return d * (d > 0)

espan = np.linspace(-20, 10)
f = fermi(espan)
n = dos(espan)

g = n * (f * np.log(f) + (1 - f) * np.log(1 - f))

print np.trapz(espan, g) # nan because of the nan in the g vector
print g

plt.plot(espan, g)

# find the elements that are not nan
ind = np.logical_not(np.isnan(g))

# evaluate the integrand for only those points
print np.trapz(espan[ind], g[ind])
[             nan              nan              nan              nan
              nan              nan              nan              nan
              nan              nan              nan              nan
              nan              nan              nan              nan
              nan              nan              nan              nan
              nan              nan              nan              nan
              nan              nan              nan              nan
  -9.75109643e-14  -1.05987106e-10  -1.04640574e-07  -8.76265644e-05
  -4.92684641e-02  -2.91047740e-01  -7.75652579e-04  -1.00962241e-06
  -1.06972936e-09  -1.00527877e-12  -8.36436686e-16  -6.48930917e-19
  -4.37946336e-22  -2.23285389e-25  -1.88578082e-29   0.00000000e+00
   0.00000000e+00   0.00000000e+00   0.00000000e+00   0.00000000e+00
   0.00000000e+00   0.00000000e+00]

The integrand is pretty well behaved in the figure above. You do not see the full range of the x-axis, because the integrand evaluates to nan for very negative numbers. This causes the trapz function to return nan also. We can solve the problem by only integrating the parts that are not nan. We have to use numpy.logicalnot to get an element-wise array of which elements are not nan. In this example, the integrand is not well sampled, so the area under that curve may not be very accurate.

Copyright (C) 2013 by John Kitchin. See the License for information about copying.

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The trapezoidal method of integration

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Matlab post See

$$\int_a^b f(x) dx \approx \frac{1}{2}\displaystyle\sum\limits_{k=1}^N(x_{k+1}-x_k)(f(x_{k+1}) + f(x_k))$$

Let us compute the integral of sin(x) from x=0 to \(\pi\). 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.

import numpy as np
import time

a = 0.0; b = np.pi;
N = 1000; # this is the number of intervals

h = (b - a)/N; # this is the width of each interval
x = np.linspace(a, b, N) 
y = np.sin(x); # the sin function is already vectorized

t0 = time.time()
f = 0.0
for k in range(len(x) - 1):
    f += 0.5 * ((x[k+1] - x[k]) * (y[k+1] + y[k]))

tf = time.time() - t0
print 'time elapsed = {0} sec'.format(tf)

print f
>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ... ... >>> >>> time elapsed = 0.0780000686646 sec
>>> 1.99999835177
t0 = time.time()
Xk = x[1:-1] - x[0:-2] # vectorized version of (x[k+1] - x[k])
Yk = y[1:-1] + y[0:-2] # vectorized version of (y[k+1] + y[k])

f = 0.5 * np.sum(Xk * Yk) # vectorized version of the loop above
tf = time.time() - t0
print 'time elapsed = {0} sec'.format(tf)

print f
>>> >>> >>> >>> >>> time elapsed = 0.077999830246 sec
>>> 1.99999340709

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.

t0 = time.time()
f = 0.5 *, Yk)
tf = time.time() - t0
print 'time elapsed = {0} sec'.format(tf)

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.

Copyright (C) 2013 by John Kitchin. See the License for information about copying.

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On the quad or trapz'd in ChemE heaven

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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.

Let us look at some examples. We consider the example of computing \(\int_0^2 x^3 dx\). the analytical integral is \(1/4 x^4\), so we know the integral evaluates to 16/4 = 4. This will be our benchmark for comparison to the numerical methods.

We use the scipy.integrate.quad command to evaluate this \(\int_0^2 x^3 dx\).

from scipy.integrate import quad

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

you can also define a function for the integrand.

from scipy.integrate import quad

def integrand(x):
    return x**3

ans, err = quad(integrand, 0, 2)
print ans

1 Numerical data integration

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

import numpy as np

x = np.array([0, 0.5, 1, 1.5, 2])
y = x**3

i2 = np.trapz(y, x)

error = (i2 - 4)/4

print i2, error
4.25 0.0625

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

import numpy as np
import matplotlib.pyplot as plt
x = np.array([0, 0.5, 1, 1.5, 2])
y = x**3

x2 = np.linspace(0, 2)
y2 = x2**3

plt.plot(x, y, label='5 points')
plt.plot(x2, y2, label='50 points')

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

import numpy as np

x2 = np.linspace(0, 2, 100)
y2 = x2**3

print np.trapz(y2, x2)

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.

from scipy.interpolate import interp1d
from scipy.integrate import quad
import numpy as np

x = [0, 0.5, 1, 1.5, 2]
y = [0,    0.1250,    1.0000,    3.3750,    8.0000]

f = interp1d(x, y)

# numerical trapezoid method
xfine = np.linspace(0.25, 1.75)
yfine = f(xfine)
print np.trapz(yfine, xfine)

# quadrature with interpolation
ans, err = quad(f, 0.25, 1.75)
print ans

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

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.

Copyright (C) 2013 by John Kitchin. See the License for information about copying.

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