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 \ No newline at end of file
...@@ -35,6 +35,7 @@ ...@@ -35,6 +35,7 @@
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../../genindex.html" /> <link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" /> <link rel="search" title="Search" href="../../search.html" />
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</head> </head>
...@@ -80,12 +81,15 @@ ...@@ -80,12 +81,15 @@
<ul class="current"> <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-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="../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="../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> <li class="toctree-l2 current"><a class="current reference internal" href="#">Modifying surrogate model</a></li>
</ul> </ul>
</li> </li>
<li class="toctree-l1"><a class="reference internal" href="../../GOFEE/GOFEE.html">GOFEE</a></li>
</ul> </ul>
...@@ -196,6 +200,8 @@ to the GPR model, the code will look like this:</p> ...@@ -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"> <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> <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 @@ ...@@ -81,6 +81,8 @@
<ul class="current"> <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-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="../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> <li class="toctree-l2 current"><a class="current reference internal" href="#">Searching for the TiO2(001)-(1x4) reconstruction</a><ul>
...@@ -90,6 +92,7 @@ ...@@ -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> <li class="toctree-l2"><a class="reference internal" href="../modifying_surrogate_model/modifying_surrogate_model.html">Modifying surrogate model</a></li>
</ul> </ul>
</li> </li>
<li class="toctree-l1"><a class="reference internal" href="../../GOFEE/GOFEE.html">GOFEE</a></li>
</ul> </ul>
......
...@@ -81,6 +81,8 @@ ...@@ -81,6 +81,8 @@
<ul class="current"> <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-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-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> <li class="toctree-l3"><a class="reference internal" href="#setting-up-the-system">Setting up the system</a></li>
...@@ -93,6 +95,7 @@ ...@@ -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> <li class="toctree-l2"><a class="reference internal" href="../modifying_surrogate_model/modifying_surrogate_model.html">Modifying surrogate model</a></li>
</ul> </ul>
</li> </li>
<li class="toctree-l1"><a class="reference internal" href="../../GOFEE/GOFEE.html">GOFEE</a></li>
</ul> </ul>
...@@ -159,8 +162,8 @@ ...@@ -159,8 +162,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody"> <div itemprop="articleBody">
<div class="section" id="id1"> <div class="section" id="searching-for-tio-clusters">
<h1>Searching for TiO clusters<a class="headerlink" href="#id1" title="Permalink to this headline"></a></h1> <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 <p>For this tutorial we will use the dftb-calculator with
the tiorg parameters.</p> the tiorg parameters.</p>
<p>In this tutorial we carry out a search for titanium-oxide clusters using <p>In this tutorial we carry out a search for titanium-oxide clusters using
......
...@@ -36,7 +36,7 @@ ...@@ -36,7 +36,7 @@
<link rel="index" title="Index" href="../genindex.html" /> <link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.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="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> </head>
<body class="wy-body-for-nav"> <body class="wy-body-for-nav">
...@@ -81,12 +81,15 @@ ...@@ -81,12 +81,15 @@
<ul class="current"> <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-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="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="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> <li class="toctree-l2"><a class="reference internal" href="modifying_surrogate_model/modifying_surrogate_model.html">Modifying surrogate model</a></li>
</ul> </ul>
</li> </li>
<li class="toctree-l1"><a class="reference internal" href="../GOFEE/GOFEE.html">GOFEE</a></li>
</ul> </ul>
...@@ -152,7 +155,7 @@ ...@@ -152,7 +155,7 @@
<div itemprop="articleBody"> <div itemprop="articleBody">
<div class="section" id="tutorial"> <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> <p>This is the turorial for the GOFEE structure search.</p>
<div class="toctree-wrapper compound"> <div class="toctree-wrapper compound">
<ul> <ul>
...@@ -174,7 +177,7 @@ ...@@ -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> <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> </div>
......
...@@ -12,7 +12,16 @@ ...@@ -12,7 +12,16 @@
# #
import os import os
import sys 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('..')) 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 ----------------------------------------------------- # -- Project information -----------------------------------------------------
...@@ -27,7 +36,8 @@ author = 'Malthe Kjær Bisbo, Bjørk Hammer' ...@@ -27,7 +36,8 @@ author = 'Malthe Kjær Bisbo, Bjørk Hammer'
# Add any Sphinx extension module names here, as strings. They can be # Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones. # 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. # Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates'] 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! Welcome to the documentation for GOFEE!
================================= =======================================
The global optimization with first-principles energy expression (GOFEE) is The global optimization with first-principles energy expression (GOFEE) is
a global optimization method used to optimize the geometry of atomistic a global optimization method used to optimize the geometry of atomistic
systems. systems.
...@@ -12,5 +8,8 @@ systems. ...@@ -12,5 +8,8 @@ systems.
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
installation/installation
getting_started/getting_started
tutorial/tutorial