Commit e9f52417 authored by Malthe Kjær Bisbo's avatar Malthe Kjær Bisbo
Browse files

Cleaned up cand_opp and missing missing wrap() calls

parent 531b2f5e
gofee.surrogate package
=======================
Submodules
----------
gofee.surrogate.custom\_calculators module
------------------------------------------
.. automodule:: gofee.surrogate.custom_calculators
:members:
:undoc-members:
:show-inheritance:
gofee.surrogate.gpr module
--------------------------
.. automodule:: gofee.surrogate.gpr
:members:
:undoc-members:
:show-inheritance:
gofee.surrogate.gpr\_calculator module
--------------------------------------
.. automodule:: gofee.surrogate.gpr_calculator
:members:
:undoc-members:
:show-inheritance:
gofee.surrogate.gpr\_old module
-------------------------------
.. automodule:: gofee.surrogate.gpr_old
:members:
:undoc-members:
:show-inheritance:
gofee.surrogate.kernel module
-----------------------------
.. automodule:: gofee.surrogate.kernel
:members:
:undoc-members:
:show-inheritance:
gofee.surrogate.test\_descriptor module
---------------------------------------
.. automodule:: gofee.surrogate.test_descriptor
:members:
:undoc-members:
:show-inheritance:
gofee.surrogate.test\_gpr module
--------------------------------
.. automodule:: gofee.surrogate.test_gpr
:members:
:undoc-members:
:show-inheritance:
gofee.surrogate.test\_kernel module
-----------------------------------
.. automodule:: gofee.surrogate.test_kernel
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: gofee.surrogate
:members:
:undoc-members:
:show-inheritance:
.. GOFEE documentation master file, created by
sphinx-quickstart on Wed Jan 22 20:36:44 2020.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to GOFEE's documentation!
=================================
.. toctree::
:maxdepth: 2
:caption: Contents:
#modules
test
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
gofee
=====
.. toctree::
:maxdepth: 4
gofee
================
GOFEE
================
The following is an introduction to the structure determination method
:class:`GOFEE`, which relies on Gaussian Process Regression model to
more efficiently explore the configurational search space.
When initializing the search, the two most important pieces of
information, is what system to optimize and what energy expression
(in the form of an ase.calculator) to optimize with respect to.
There two ways of supplying the information of what system to optimize.
1) The search can be initialized with one or more :class:`ase.Atoms`
objects, and the search will optimize all non-fixed atoms in the
system.
2) By defining a :class:`StartGenerator`, that randomly initializes
the atoms, to be optimized, within a user-specified box. Using this
box, the atoms ate placed within the cell of a supplied
:class:`ase.Atoms` objects, which potentially contains fixed slab
atoms.
Initializing the search with just a structure and a calculator looks
like this::
# Creates: structures.traj
import numpy as np
from ase import Atoms
from gpaw import GPAW, FermiDirac, PoissonSolver, Mixer, PW
from gpaw import extra_parameters
extra_parameters['blacs'] = True
from gpaw.utilities import h2gpts
from gofee import GOFEE
# Define calculator
calc=GPAW(poissonsolver = PoissonSolver(relax = 'GS',eps = 1.0e-7),
mode = 'lcao',
basis = 'dzp',
xc='PBE',
gpts = h2gpts(0.2, slab.get_cell(), idiv = 8),
occupations=FermiDirac(0.1),
maxiter=99,
mixer=Mixer(nmaxold=5, beta=0.05, weight=75),
nbands=-50,
kpts=(1,1,1))
# Load structure to initialise search
positions = np.random.uniform(8.5,11.5,36).reshape(-1,3)
a = Atoms('C6H6',
positions=positions,
cell=(20,20,20))
# Initialize and run search
search = GOFEE(structures=a,
calc=calc,
trajectory='structures.traj',
max_steps=200)
search.run()
Specifying the system - supplying Structures
============================================
Specifying the system - supplying StartGenerator
================================================
Basic settings
==============
CandidateGenerator
==================
Gaussian Process Regression (GPR) model
=======================================
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