Commit 83773159 authored by Malthe Kjær Bisbo's avatar Malthe Kjær Bisbo
Browse files

fixed dublicate initial structures in output trajectory

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<div class="section" id="slurm-job-examples">
<span id="slurm"></span><h1>SLURM job examples<a class="headerlink" href="#slurm-job-examples" title="Permalink to this headline"></a></h1>
<p>If you are running your calculations on a cluster using
SLURM for job management, you can use a jobscript like
this (propperly modified for your setup):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>#!/bin/bash
#SBATCH --job-name=GOFEE_test
#SBATCH --partition=&lt;desired partitions&gt;
#SBATCH --mem=30G
#SBATCH --nodes=1
#SBATCH --time=2:00:00
##SBATCH --exclusive
#SBATCH --ntasks-per-node=10
#SBATCH --cpus-per-task=1
echo &quot;========= Job started at `date` ==========&quot;
# Go to the directory where this job was submitted
cd $SLURM_SUBMIT_DIR
export PYTHONPATH=&lt;path to GOFEE code&gt;:$PYTHONPATH
source &lt;python stuff&gt;
source &lt;GPAW stuff&gt;
source &lt;DFTB stuff&gt; # if running DFTB
mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py &gt; search.log
echo &quot;========= Job finished at `date` ==========&quot;
</pre></div>
</div>
<p>This job will be run locally in the submission folder on 10 cpu cores.</p>
<p>NOTE: for this jobscript, the submission folder must contain a file
“run_search.py”, which runs GOFEE as described in the
<a class="reference internal" href="../tutorial/tutorial.html#tutorial"><span class="std std-ref">tutorial</span></a>.</p>
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&copy; Copyright 2020, Malthe Kjær Bisbo, Bjørk Hammer
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\ No newline at end of file
......@@ -2,30 +2,57 @@
=====
GOFEE
=====
Below an overview of the inputs to GOFEE is shown. Many of the inputs
can be safely kept at default settings. However ``calc``, defining the
calculator, as well as either ``startgenerator`` or ``structures``,
defining the system, must always be set.
In addition it is recomended to also set the ``candidate_generatior``.
.. autoclass:: gofee.GOFEE
:members:
Surrogate
=========
.. .. autoclass:: surrogate.gpr.GPR
:members:
Kernel
======
:members: run
StartGenerator
==============
The :class:`StartGenerator` is used to generate initial structures for
the search. In addition it can be used to generate new candidates during
the search, if it is included as an operation in the
:class:`CandidateGenerator`.
.. autoclass:: candidate_operations.candidate_generation.StartGenerator
:exclude-members:
CandidateGenerator
==================
The :class:`CandidateGenerator` is used in each iteration in the GOFEE search
to generate new candidates based on a list on operations to use. Possible
operation can be found below under the "Mutations" section.
.. autoclass:: candidate_operations.candidate_generation.CandidateGenerator
:members: get_new_candidate
.. .. autoclass:: candidate_operations.CandidateGenerator
:members: get_new_candidate
Mutations
=========
The mutations to chose from are listed below.
RattleMutation
==============
--------------
.. autoclass:: candidate_operations.basic_mutations.RattleMutation
:exclude-members:
RattleMutation2
---------------
.. autoclass:: candidate_operations.basic_mutations.RattleMutation2
:exclude-members:
PermutationMutation
===================
\ No newline at end of file
-------------------
.. autoclass:: candidate_operations.basic_mutations.PermutationMutation
:exclude-members:
\ No newline at end of file
.. _slurm:
==================
SLURM job examples
==================
If you are running your calculations on a cluster using
SLURM for job management, you can use a jobscript like
this (propperly modified for your setup)::
#!/bin/bash
#SBATCH --job-name=GOFEE_test
#SBATCH --partition=<desired partitions>
#SBATCH --mem=30G
#SBATCH --nodes=1
#SBATCH --time=2:00:00
##SBATCH --exclusive
#SBATCH --ntasks-per-node=10
#SBATCH --cpus-per-task=1
echo "========= Job started at `date` =========="
# Go to the directory where this job was submitted
cd $SLURM_SUBMIT_DIR
export PYTHONPATH=<path to GOFEE code>:$PYTHONPATH
source <python stuff>
source <GPAW stuff>
source <DFTB stuff> # if running DFTB
mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py > search.log
echo "========= Job finished at `date` =========="
This job will be run locally in the submission folder on 10 cpu cores.
NOTE: for this jobscript, the submission folder must contain a file
"run_search.py", which runs GOFEE as described in the
:ref:`tutorial <tutorial>`.
\ No newline at end of file
......@@ -10,6 +10,7 @@ systems.
installation/installation
getting_started/getting_started
SLURM/SLURM
tutorial/tutorial
GOFEE/GOFEE
......@@ -82,6 +82,7 @@
<ul>
<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"><a class="reference internal" href="SLURM/SLURM.html">SLURM job examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial/tutorial.html">Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......@@ -151,40 +152,16 @@
<div class="genindex-jumpbox">
<a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#W"><strong>W</strong></a>
</div>
<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.certainty_filter">certainty_filter() (gofee.GOFEE method)</a>
</li>
</ul></td>
</tr></table>
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.dump">dump() (gofee.GOFEE method)</a>
</li>
</ul></td>
</tr></table>
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.evaluate">evaluate() (gofee.GOFEE method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.evaluate_initial_structures">evaluate_initial_structures() (gofee.GOFEE method)</a>
<li><a href="GOFEE/GOFEE.html#candidate_operations.candidate_generation.CandidateGenerator">CandidateGenerator (class in candidate_operations.candidate_generation)</a>
</li>
</ul></td>
</tr></table>
......@@ -192,65 +169,41 @@
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.generate_candidate">generate_candidate() (gofee.GOFEE method)</a>
</li>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.get_dualpoint">get_dualpoint() (gofee.GOFEE method)</a>
<li><a href="GOFEE/GOFEE.html#candidate_operations.candidate_generation.CandidateGenerator.get_new_candidate">get_new_candidate() (candidate_operations.candidate_generation.CandidateGenerator method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.get_initial_structures">get_initial_structures() (gofee.GOFEE method)</a>
</li>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.get_surrogate_relaxed_candidates">get_surrogate_relaxed_candidates() (gofee.GOFEE method)</a>
</li>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE">GOFEE (class in gofee)</a>
</li>
</ul></td>
</tr></table>
<h2 id="R">R</h2>
<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.read">read() (gofee.GOFEE method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.run">run() (gofee.GOFEE method)</a>
<li><a href="GOFEE/GOFEE.html#candidate_operations.basic_mutations.PermutationMutation">PermutationMutation (class in candidate_operations.basic_mutations)</a>
</li>
</ul></td>
</tr></table>
<h2 id="S">S</h2>
<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.select_with_acquisition">select_with_acquisition() (gofee.GOFEE method)</a>
<li><a href="GOFEE/GOFEE.html#candidate_operations.basic_mutations.RattleMutation">RattleMutation (class in candidate_operations.basic_mutations)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.surrogate_relaxation">surrogate_relaxation() (gofee.GOFEE method)</a>
<li><a href="GOFEE/GOFEE.html#candidate_operations.basic_mutations.RattleMutation2">RattleMutation2 (class in candidate_operations.basic_mutations)</a>
</li>
</ul></td>
</tr></table>
<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.train_surrogate">train_surrogate() (gofee.GOFEE method)</a>
</li>
</ul></td>
</tr></table>
<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.update_population">update_population() (gofee.GOFEE method)</a>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.run">run() (gofee.GOFEE method)</a>
</li>
</ul></td>
</tr></table>
<h2 id="W">W</h2>
<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.write">write() (gofee.GOFEE method)</a>
<li><a href="GOFEE/GOFEE.html#candidate_operations.candidate_generation.StartGenerator">StartGenerator (class in candidate_operations.candidate_generation)</a>
</li>
</ul></td>
</tr></table>
......
......@@ -35,7 +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" />
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<link rel="prev" title="Installation" href="../installation/installation.html" />
</head>
......@@ -83,6 +83,7 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="../installation/installation.html">Installation</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Getting started</a></li>
<li class="toctree-l1"><a class="reference internal" href="../SLURM/SLURM.html">SLURM job examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial/tutorial.html">Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="../GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......@@ -173,7 +174,7 @@ some of the examples in the <a class="reference internal" href="../tutorial/tuto
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="../tutorial/tutorial.html" class="btn btn-neutral float-right" title="Tutorial" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="../installation/installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
......
......@@ -82,6 +82,7 @@
<ul>
<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"><a class="reference internal" href="SLURM/SLURM.html">SLURM job examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial/tutorial.html">Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......@@ -157,6 +158,7 @@ systems.</p>
<ul>
<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"><a class="reference internal" href="SLURM/SLURM.html">SLURM job examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial/tutorial.html">Tutorial</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial/tio_clusters/tio_clusters.html">Searching for TiO clusters</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/tio2_reconstruction/tio2_reconstruction.html">Searching for the TiO2(001)-(1x4) reconstruction</a></li>
......@@ -164,12 +166,9 @@ systems.</p>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="GOFEE/GOFEE.html">GOFEE</a><ul>
<li class="toctree-l2"><a class="reference internal" href="GOFEE/GOFEE.html#surrogate">Surrogate</a></li>
<li class="toctree-l2"><a class="reference internal" href="GOFEE/GOFEE.html#kernel">Kernel</a></li>
<li class="toctree-l2"><a class="reference internal" href="GOFEE/GOFEE.html#startgenerator">StartGenerator</a></li>
<li class="toctree-l2"><a class="reference internal" href="GOFEE/GOFEE.html#candidategenerator">CandidateGenerator</a></li>
<li class="toctree-l2"><a class="reference internal" href="GOFEE/GOFEE.html#rattlemutation">RattleMutation</a></li>
<li class="toctree-l2"><a class="reference internal" href="GOFEE/GOFEE.html#permutationmutation">PermutationMutation</a></li>
<li class="toctree-l2"><a class="reference internal" href="GOFEE/GOFEE.html#mutations">Mutations</a></li>
</ul>
</li>
</ul>
......
......@@ -83,6 +83,7 @@
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">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"><a class="reference internal" href="../SLURM/SLURM.html">SLURM job examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial/tutorial.html">Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="../GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......
......@@ -82,6 +82,7 @@
<ul>
<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"><a class="reference internal" href="SLURM/SLURM.html">SLURM job examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial/tutorial.html">Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="GOFEE/GOFEE.html">GOFEE</a></li>
</ul>
......
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