# Source code for pycalphad.core.polytope

```
"""
This module provides functions to uniformly sample points subject to a system of linear
inequality constraints, :math:`Ax <= b` (convex polytope), and linear equality
constraints, :math:`Ax = b` (affine projection).
A comparison of MCMC algorithms to generate uniform samples over a convex polytope is
given in [Chen2018]_. Here, we use the Hit & Run algorithm described in [Smith1984]_.
The R-package `hitandrun`_ provides similar functionality to this module.
Based on https://github.com/DavidWalz/polytope-sampling
Used under the terms of the MIT license. License information can be found in the pycalphad LICENSE.txt.
References
----------
.. [Chen2018] Chen Y., Dwivedi, R., Wainwright, M., Yu B. (2018) Fast MCMC Sampling
Algorithms on Polytopes. JMLR, 19(55):1−86
https://arxiv.org/abs/1710.08165
.. [Smith1984] Smith, R. (1984). Efficient Monte Carlo Procedures for Generating
Points Uniformly Distributed Over Bounded Regions. Operations Research,
32(6), 1296-1308.
www.jstor.org/stable/170949
.. _`hitandrun`: https://cran.r-project.org/web/packages/hitandrun/index.html
"""
import numpy as np
import scipy.linalg
import scipy.optimize
[docs]
def check_Ab(A, b):
"""Check if matrix equation Ax=b is well defined.
Parameters
----------
A : 2d-array of shape (n_constraints, dimension)
Left-hand-side of Ax <= b.
b : 1d-array of shape (n_constraints)
Right-hand-side of Ax <= b.
"""
assert A.ndim == 2
assert b.ndim == 1
assert A.shape[0] == b.shape[0]
[docs]
def chebyshev_center(A, b):
"""Find the center of the polytope Ax <= b.
Parameters
----------
A : 2d-array of shape (n_constraints, dimension)
Left-hand-side of Ax <= b.
b : 1d-array of shape (n_constraints)
Right-hand-side of Ax <= b.
Returns
-------
1d-array of shape (dimension)
Chebyshev center of the polytope
"""
res = scipy.optimize.linprog(
np.r_[np.zeros(A.shape[1]), -1],
A_ub=np.hstack([A, np.linalg.norm(A, axis=1, keepdims=True)]),
b_ub=b,
bounds=(None, None),
)
if not res.success:
raise Exception("Unable to find Chebyshev center")
return res.x[:-1]
[docs]
def constraints_from_bounds(lower, upper):
"""Construct the inequality constraints Ax <= b that correspond to the given
lower and upper bounds.
Parameters
----------
lower : array-like
lower bound in each dimension
upper : array-like
upper bound in each dimension
Returns
-------
A: 2d-array of shape (2 * dimension, dimension)
Left-hand-side of Ax <= b.
b: 1d-array of shape (2 * dimension)
Right-hand-side of Ax <= b.
"""
n = len(lower)
A = np.vstack([-np.eye(n), np.eye(n)])
b = np.r_[-np.array(lower), np.array(upper)]
return A, b
[docs]
def affine_subspace(A, b):
"""Compute a basis of the nullspace of A, and a particular solution to Ax = b.
This allows to to construct arbitrary solutions as the sum of any vector in the
nullspace, plus the particular solution.
Parameters
----------
A : 2d-array of shape (n_constraints, dimension)
Left-hand-side of Ax <= b.
b : 1d-array of shape (n_constraints)
Right-hand-side of Ax <= b.
Returns
-------
N: 2d-array of shape (dimension, dimension)
Orthonormal basis of the nullspace of A.
xp: 1d-array of shape (dimension)
Particular solution to Ax = b.
"""
N = scipy.linalg.null_space(A)
xp = np.linalg.pinv(A) @ b
return N, xp
[docs]
def sample(n_points, lower, upper, A1=None, b1=None, A2=None, b2=None):
"""Sample a number of points from a convex polytope A1 x <= b1 using the Hit & Run
algorithm.
Lower and upper bounds need to be provided to ensure that the polytope is bounded.
Equality constraints A2 x = b2 may be optionally provided.
Parameters
----------
n_points : int
Number of samples to generate.
lower: 1d-array of shape (dimension)
Lower bound in each dimension. If not wanted set to -np.inf.
upper: 1d-array of shape (dimension)
Upper bound in each dimension. If not wanted set to np.inf.
A1 : 2d-array of shape (n_constraints, dimension)
Left-hand-side of A1 x <= b1.
b1 : 1d-array of shape (n_constraints)
Right-hand-side of A1 x <= b1.
A2 : 2d-array of shape (n_constraints, dimensions), optional
Left-hand-side of A2 x = b2.
b2 : 1d-array of shape (n_constraints), optional
Right-hand-side of A2 x = b2.
Returns
-------
2d-array of shape (n_points)
Points sampled from the polytope.
"""
A, b = constraints_from_bounds(lower, upper)
if (A1 is not None) and (b1 is not None):
A1 = np.r_[A, A1]
b1 = np.r_[b, b1]
else:
A1, b1 = A, b
if (A2 is not None) and (b2 is not None):
check_Ab(A2, b2)
N, xp = affine_subspace(A2, b2)
else:
N = np.eye(A1.shape[1])
xp = np.zeros(A1.shape[1])
# Do not allow particular solutions to fall outside of bounds
# This operation helps with numerical robustness
xp = np.clip(xp, lower+1e-14, upper-1e-14)
if N.shape[1] == 0:
# zero-dimensional polytope, return unique solution
# Use lstsq instead of solve, to allow for redundant constraints (non-square constraint matrix)
solution = np.linalg.lstsq(A2, b2, rcond=None)
X = np.atleast_2d(solution[0])
# Check residuals to ensure system was fully determined, or constraints were redundant
if solution[1].size > 0:
residual = float(solution[1])
if residual > 1e-10:
# Starting point is not feasible
return np.empty((0, A1.shape[1]))
return X
# project to the affine subspace of the equality constraints
At = A1 @ N
bt = b1 - A1 @ xp
try:
x0 = chebyshev_center(At, bt)
except:
# Unable to find center
return np.empty((0, A1.shape[1]))
test_point = x0[np.newaxis, :] @ N.T + xp
if np.any(test_point < lower-1e-10) or np.any(test_point > upper+1e-10):
# Starting point is not feasible
return np.empty((0, A1.shape[1]))
X = np.empty((n_points, At.shape[1]))
x = x0
rng = np.random.RandomState(1769)
with np.errstate(divide='ignore', invalid='ignore'):
directions = rng.randn(n_points, At.shape[1])
directions /= np.linalg.norm(directions, axis=0)
for i in range(n_points):
# sample random direction from unit hypersphere
direction = directions[i]
# distances to each face from the current point in the sampled direction
D = (bt - x @ At.T) / (direction @ At.T)
# distance to the closest face in and opposite to direction
lo = max(D[D < 1e-10])
hi = min(D[D > -1e-10])
if hi < lo:
# Amount of 'wiggle room' is down in the numerical noise
lo = 0.0
hi = 0.0
# make random step
x += rng.uniform(lo, hi) * direction
X[i] = x
# project back
X = X @ N.T + xp
X = np.clip(X, lower, upper)
return X
```