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