Commit b5c348c0 authored by Malthe Kjær Bisbo's avatar Malthe Kjær Bisbo
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Added further documentation, fixed problem with restart option, added gauss_kernel hessian

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\ No newline at end of file
......@@ -35,6 +35,7 @@
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="next" title="GOFEE" href="../../GOFEE/GOFEE.html" />
<link rel="prev" title="Searching for the TiO2(001)-(1x4) reconstruction" href="../tio2_reconstruction/tio2_reconstruction.html" />
</head>
......@@ -80,12 +81,15 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="../../installation/installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../getting_started/getting_started.html">Getting started</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../tutorial.html">Tutorial</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../tio_clusters/tio_clusters.html">Searching for TiO clusters</a></li>
<li class="toctree-l2"><a class="reference internal" href="../tio2_reconstruction/tio2_reconstruction.html">Searching for the TiO2(001)-(1x4) reconstruction</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Modifying surrogate model</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......@@ -196,6 +200,8 @@ to the GPR model, the code will look like this:</p>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="../../GOFEE/GOFEE.html" class="btn btn-neutral float-right" title="GOFEE" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="../tio2_reconstruction/tio2_reconstruction.html" class="btn btn-neutral float-left" title="Searching for the TiO2(001)-(1x4) reconstruction" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
......
......@@ -81,6 +81,8 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="../../installation/installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../getting_started/getting_started.html">Getting started</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../tutorial.html">Tutorial</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../tio_clusters/tio_clusters.html">Searching for TiO clusters</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Searching for the TiO2(001)-(1x4) reconstruction</a><ul>
......@@ -90,6 +92,7 @@
<li class="toctree-l2"><a class="reference internal" href="../modifying_surrogate_model/modifying_surrogate_model.html">Modifying surrogate model</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......
......@@ -81,6 +81,8 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="../../installation/installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../getting_started/getting_started.html">Getting started</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../tutorial.html">Tutorial</a><ul class="current">
<li class="toctree-l2 current"><a class="current reference internal" href="#">Searching for TiO clusters</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#setting-up-the-system">Setting up the system</a></li>
......@@ -93,6 +95,7 @@
<li class="toctree-l2"><a class="reference internal" href="../modifying_surrogate_model/modifying_surrogate_model.html">Modifying surrogate model</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......@@ -159,8 +162,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="id1">
<h1>Searching for TiO clusters<a class="headerlink" href="#id1" title="Permalink to this headline"></a></h1>
<div class="section" id="searching-for-tio-clusters">
<span id="id1"></span><h1>Searching for TiO clusters<a class="headerlink" href="#searching-for-tio-clusters" title="Permalink to this headline"></a></h1>
<p>For this tutorial we will use the dftb-calculator with
the tiorg parameters.</p>
<p>In this tutorial we carry out a search for titanium-oxide clusters using
......
......@@ -36,7 +36,7 @@
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Searching for TiO clusters" href="tio_clusters/tio_clusters.html" />
<link rel="prev" title="Welcome to the documentation for GOFEE!" href="../index.html" />
<link rel="prev" title="Getting started" href="../getting_started/getting_started.html" />
</head>
<body class="wy-body-for-nav">
......@@ -81,12 +81,15 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="../installation/installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../getting_started/getting_started.html">Getting started</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Tutorial</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tio_clusters/tio_clusters.html">Searching for TiO clusters</a></li>
<li class="toctree-l2"><a class="reference internal" href="tio2_reconstruction/tio2_reconstruction.html">Searching for the TiO2(001)-(1x4) reconstruction</a></li>
<li class="toctree-l2"><a class="reference internal" href="modifying_surrogate_model/modifying_surrogate_model.html">Modifying surrogate model</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......@@ -152,7 +155,7 @@
<div itemprop="articleBody">
<div class="section" id="tutorial">
<h1>Tutorial<a class="headerlink" href="#tutorial" title="Permalink to this headline"></a></h1>
<span id="id1"></span><h1>Tutorial<a class="headerlink" href="#tutorial" title="Permalink to this headline"></a></h1>
<p>This is the turorial for the GOFEE structure search.</p>
<div class="toctree-wrapper compound">
<ul>
......@@ -174,7 +177,7 @@
<a href="tio_clusters/tio_clusters.html" class="btn btn-neutral float-right" title="Searching for TiO clusters" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
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</div>
......
......@@ -12,7 +12,16 @@
#
import os
import sys
#sys.path.insert(0, os.path.abspath('/home/mkb/GOFEE/'))
sys.path.remove(os.path.abspath('..'))
#sys.path.remove(os.path.abspath('../..'))
print('SYS.PATH :', sys.path)
sys.path.insert(0, os.path.abspath('..'))
print('SYS.PATH :', sys.path)
#sys.path.insert(0, os.path.abspath('../../..'))
#sys.path.append(os.path.abspath('..'))
#sys.path.append(os.path.abspath('../..'))
#sys.path.append(os.path.abspath('../../..'))
# -- Project information -----------------------------------------------------
......@@ -27,7 +36,8 @@ author = 'Malthe Kjær Bisbo, Bjørk Hammer'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.autodoc']
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
autoclass_content = 'both'
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
......
===============
Getting started
===============
GOFEE is implemented in python, so a basic understanding of python
is neccisary to use the program.
In addition it relies heavily on the python library ASE
(Atomic Simulation Environment). In particular, some ASE methods
are used to set up the atomistic system of interest, prior to a
GOFEE search. It is therefore a prerequisite to also have basic
experience with especially the :class:`Atoms` object of ASE as well as
trajectory files.
Before continuing complete the :ref:`installation guide <installation>`,
if you have not done it already.
Otherwise you can start getting familiar with GOFEE by going through
some of the examples in the :ref:`tutorial <tutorial>`.
.. 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 the documentation for GOFEE!
=================================
=======================================
The global optimization with first-principles energy expression (GOFEE) is
a global optimization method used to optimize the geometry of atomistic
systems.
......@@ -12,5 +8,8 @@ systems.
.. toctree::
:maxdepth: 2
installation/installation
getting_started/getting_started
tutorial/tutorial
GOFEE/GOFEE
.. _installation:
============
Installation
============
=====
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.
The calculator is supplied using the ``calc`` keyword.
One way of supplying what system to optimize (although not the typically
recomended one) is to use the ``structures`` keyword to supply
:class:`GOFEE` with a number of pre-prepared ASE :class:`Atoms` objects.
Initializing the search with just a structure and a calculator, and running
the search for 200 iterations using ``max_steps``, can then look 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()
The search must be run in parallel using MPI. To run the code in
parallel on grendel, use a .job script like the following::
#!/bin/bash
#SBATCH --job-name=C6H6_0
#SBATCH --partition=q12,q16,q16l,q20
#SBATCH --mem=30G
#SBATCH --nodes=1
#SBATCH --time=6:00:00
##SBATCH --exclusive
#SBATCH --ntasks-per-node=10
#SBATCH --cpus-per-task=1
#SBATCH --no-requeue
#SBATCH --array=0-2%3
echo "========= Job started at `date` =========="
# Go to the directory where this job was submitted
cd $SLURM_SUBMIT_DIR
source /home/mkb/.gpaw_py3
source /home/mkb/.GOFEE
# Setup directories to run the search in
base_path=$SLURM_SUBMIT_DIR/runs0/run$SLURM_ARRAY_TASK_ID
mkdir $base_path
# Copy files
cp run_search.py $base_path
cp slab.traj $base_path