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

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