Global Optimization

The main algorithm for global optimization is basin hopping. The core object for a basin hopping run is a BasinHopping object. The step taking and various other customization routines (e.g. storage, acceptance criterion, ...) can be attached to this object to customize the behaviour of the basin hopping procedure.

BasinHopping(coords, potential, takeStep[, ...]) A class to run the basin hopping algorithm
import numpy as np
import pele.potentials.lj as lj
import pele.basinhopping as bh
from pele.takestep import displace

natoms = 12

# random initial coordinates
potential = lj.LJ()

step = displace.RandomDisplacement(stepsize=0.5)

opt = bh.BasinHopping(coords, potential, takeStep=step)

Step Taking (pele.takestep)

The performance of the basin hopping critically depends on the step taking algorithm. pele comes with a set of basic takestep routines. For anything non-standard, the user is encouraged to implement a custom takestep routine.

Basic steptaking

RandomDisplacement([stepsize]) Random displacement on each individual coordinate
UniformDisplacement([srange, stepsize]) Displace each atom be a uniform random vector
RotationalDisplacement([srange, stepsize]) Random rotation for angle axis vector
ParticleExchange(Alist, Blist[, verbose]) Implement a takestep move which swaps two un-like atoms

Grouping moves + adaptive steptaking

AdaptiveStepsize(stepclass[, acc_ratio, ...]) Adaptive stepsize adjustment
AdaptiveStepsizeTemperature(stepclass[, ...]) adjust both the stepsize and the temperature adaptively
GroupSteps(steptakers) group several takestep objects
BlockMoves() block based step taking
Reseeding(takestep, reseed[, maxnoimprove, ...]) Reseeding if energy did not improve

Writing custom steptaking routines

pele makes it very simple to design custom takestep routines. Any takestep class should have TakestepInterface as a parent class (directly derived from that or a child class of TakestepInterface).

from pele.takestep import TakestepInterface
from pele.takestep import buildingblocks as bb

class MyStep(TakestepInterface):
    def takeStep(self, coords, **kwargs):
        # create an rigid body coordinate interface for coordinates array
        ca = CoordsAdapter(nrigid=GMIN.getNRigidBody(), nlattice=6, coords=coords)
        # rotate one random rigid body
        select = [np.random.randint(0,nrigid)]
        bb.rotate(1.6, ca.rotRigid, indices = select)

Building blocks to design custom takestep routines

uniform_displace(stepsize, coords[, indices]) uniform random displacement
rotate(stepsize, coords[, indices]) uniform random rotation of angle axis vector
reduced_coordinates_displace(stepsize, ...) uniform random displacement of reduced coordinates

The takestep interface

TakestepInterface Interface for step taking classes ..
Takestep([stepsize]) basic takestep interface which stores the stepsize
TakestepSlice([srange, stepsize]) basic takestep interface on slice of coordinates array