Commit 06721060 authored by Malthe Kjær Bisbo's avatar Malthe Kjær Bisbo
Browse files

modified moduse structure, added test of imports and changed documentation...

modified moduse structure, added test of imports and changed documentation accordingly as some import statements have changed as a result
parent 752fd85b
......@@ -19,7 +19,7 @@ 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
.. autoclass:: gofee.candidates.StartGenerator
:exclude-members:
CandidateGenerator
......@@ -28,7 +28,7 @@ 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
.. autoclass:: gofee.candidates.CandidateGenerator
:members: get_new_candidate
......@@ -42,17 +42,17 @@ The mutations to chose from are listed below.
RattleMutation
--------------
.. autoclass:: candidate_operations.basic_mutations.RattleMutation
.. autoclass:: gofee.candidates.RattleMutation
:exclude-members:
RattleMutation2
---------------
.. autoclass:: candidate_operations.basic_mutations.RattleMutation2
.. autoclass:: gofee.candidates.RattleMutation2
:exclude-members:
PermutationMutation
-------------------
.. autoclass:: candidate_operations.basic_mutations.PermutationMutation
.. autoclass:: gofee.candidates.PermutationMutation
:exclude-members:
\ No newline at end of file
......@@ -27,7 +27,7 @@ this (propperly modified for your setup)::
source <GPAW stuff>
source <DFTB stuff> # if running DFTB
mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py > search.log
mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py
echo "========= Job finished at `date` =========="
This job will be run locally in the submission folder on 10 cpu cores.
......
.. _au_on_cu_search:
=======================
Au7 in Cu(111) with EMT
=======================
In this tutorial we carry out a search for Au7-clusters on
the Cu(111) surface.
In this search we will utilize an :class:`OperationConstraint`
to constraint the :class:`RattleMutation` to only rattle the
atoms within a certain box in space that we define.
......@@ -23,8 +23,8 @@ One can for example apply a GPR model with another degree of regularization
in the search. As the regularization is a parameter of the *kernel*, passed
to the GPR model, the code will look like this::
from surrogate.gpr import GPR
from surrogate.kernel import double_gauss_kernel
from gofee.surrogate.gpr import GPR
from gofee.surrogate.kernel import double_gauss_kernel
kernel = double_gauss_kernel(noise=1e-6)
gpr = GPR(kernel=kernel)
......
......@@ -21,7 +21,7 @@ following code :download:`TiO2.py` is used to carry out the search:
If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as::
mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py
mpiexec --mca mpi_warn_on_fork 0 gpaw-python TiO2.py
Setting up the system - atoms in template
=========================================
......
......@@ -18,7 +18,7 @@ explainted further below):
If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as::
mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py
mpiexec --mca mpi_warn_on_fork 0 gpaw-python Ti5O10.py
What follows is a description of the python script above.
......
......@@ -161,7 +161,7 @@
<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#candidate_operations.candidate_generation.CandidateGenerator">CandidateGenerator (class in candidate_operations.candidate_generation)</a>
<li><a href="GOFEE/GOFEE.html#gofee.candidates.CandidateGenerator">CandidateGenerator (class in gofee.candidates)</a>
</li>
</ul></td>
</tr></table>
......@@ -169,7 +169,7 @@
<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#candidate_operations.candidate_generation.CandidateGenerator.get_new_candidate">get_new_candidate() (candidate_operations.candidate_generation.CandidateGenerator method)</a>
<li><a href="GOFEE/GOFEE.html#gofee.candidates.CandidateGenerator.get_new_candidate">get_new_candidate() (gofee.candidates.CandidateGenerator method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
......@@ -181,7 +181,7 @@
<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#candidate_operations.basic_mutations.PermutationMutation">PermutationMutation (class in candidate_operations.basic_mutations)</a>
<li><a href="GOFEE/GOFEE.html#gofee.candidates.PermutationMutation">PermutationMutation (class in gofee.candidates)</a>
</li>
</ul></td>
</tr></table>
......@@ -189,11 +189,11 @@
<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#candidate_operations.basic_mutations.RattleMutation">RattleMutation (class in candidate_operations.basic_mutations)</a>
<li><a href="GOFEE/GOFEE.html#gofee.candidates.RattleMutation">RattleMutation (class in gofee.candidates)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="GOFEE/GOFEE.html#candidate_operations.basic_mutations.RattleMutation2">RattleMutation2 (class in candidate_operations.basic_mutations)</a>
<li><a href="GOFEE/GOFEE.html#gofee.candidates.RattleMutation2">RattleMutation2 (class in gofee.candidates)</a>
</li>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.run">run() (gofee.GOFEE method)</a>
</li>
......@@ -203,7 +203,7 @@
<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#candidate_operations.candidate_generation.StartGenerator">StartGenerator (class in candidate_operations.candidate_generation)</a>
<li><a href="GOFEE/GOFEE.html#gofee.candidates.StartGenerator">StartGenerator (class in gofee.candidates)</a>
</li>
</ul></td>
</tr></table>
......
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<div class="section" id="au7-in-cu-111-with-emt">
<span id="au-on-cu-search"></span><h1>Au7 in Cu(111) with EMT<a class="headerlink" href="#au7-in-cu-111-with-emt" title="Permalink to this headline"></a></h1>
<p>In this tutorial we carry out a search for Au7-clusters on
the Cu(111) surface.</p>
<p>In this search we will utilize an <code class="xref py py-class docutils literal notranslate"><span class="pre">OperationConstraint</span></code>
to constraint the <code class="xref py py-class docutils literal notranslate"><span class="pre">RattleMutation</span></code> to only rattle the
atoms within a certain box in space that we define.</p>
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......@@ -177,8 +177,8 @@ during the search and used for cheap optimization of new candidates.</p>
<p>One can for example apply a GPR model with another degree of regularization
in the search. As the regularization is a parameter of the <em>kernel</em>, passed
to the GPR model, the code will look like this:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">surrogate.gpr</span> <span class="k">import</span> <span class="n">GPR</span>
<span class="kn">from</span> <span class="nn">surrogate.kernel</span> <span class="k">import</span> <span class="n">double_gauss_kernel</span>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">gofee.surrogate.gpr</span> <span class="k">import</span> <span class="n">GPR</span>
<span class="kn">from</span> <span class="nn">gofee.surrogate.kernel</span> <span class="k">import</span> <span class="n">double_gauss_kernel</span>
<span class="n">kernel</span> <span class="o">=</span> <span class="n">double_gauss_kernel</span><span class="p">(</span><span class="n">noise</span><span class="o">=</span><span class="mf">1e-6</span><span class="p">)</span>
<span class="n">gpr</span> <span class="o">=</span> <span class="n">GPR</span><span class="p">(</span><span class="n">kernel</span><span class="o">=</span><span class="n">kernel</span><span class="p">)</span>
......
......@@ -177,8 +177,8 @@ following code <a class="reference download internal" download="" href="../../_d
<span class="kn">from</span> <span class="nn">ase.calculators.dftb</span> <span class="k">import</span> <span class="n">Dftb</span>
<span class="kn">from</span> <span class="nn">ase.io</span> <span class="k">import</span> <span class="n">read</span>
<span class="kn">from</span> <span class="nn">candidate_operations.candidate_generation</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span>
<span class="kn">from</span> <span class="nn">candidate_operations.basic_mutations</span> <span class="k">import</span> <span class="n">RattleMutation</span><span class="p">,</span> <span class="n">PermutationMutation</span>
<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span>
<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">RattleMutation</span><span class="p">,</span> <span class="n">PermutationMutation</span>
<span class="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>
<span class="c1">### Define calculator ###</span>
......@@ -227,7 +227,7 @@ following code <a class="reference download internal" download="" href="../../_d
</div>
<p>If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">run_search</span><span class="o">.</span><span class="n">py</span>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">TiO2</span><span class="o">.</span><span class="n">py</span>
</pre></div>
</div>
<div class="section" id="setting-up-the-system-atoms-in-template">
......
......@@ -177,8 +177,7 @@ explainted further below):</p>
<span class="kn">from</span> <span class="nn">ase</span> <span class="k">import</span> <span class="n">Atoms</span>
<span class="kn">from</span> <span class="nn">ase.calculators.dftb</span> <span class="k">import</span> <span class="n">Dftb</span>
<span class="kn">from</span> <span class="nn">candidate_operations.candidate_generation</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span>
<span class="kn">from</span> <span class="nn">candidate_operations.basic_mutations</span> <span class="k">import</span> <span class="n">RattleMutation</span>
<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span><span class="p">,</span> <span class="n">RattleMutation</span>
<span class="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>
<span class="c1">### Define calculator ###</span>
......@@ -228,7 +227,7 @@ explainted further below):</p>
</div>
<p>If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">run_search</span><span class="o">.</span><span class="n">py</span>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">Ti5O10</span><span class="o">.</span><span class="n">py</span>
</pre></div>
</div>
<p>What follows is a description of the python script above.</p>
......
......@@ -23,8 +23,8 @@ One can for example apply a GPR model with another degree of regularization
in the search. As the regularization is a parameter of the *kernel*, passed
to the GPR model, the code will look like this::
from surrogate.gpr import GPR
from surrogate.kernel import double_gauss_kernel
from gofee.surrogate.gpr import GPR
from gofee.surrogate.kernel import double_gauss_kernel
kernel = double_gauss_kernel(noise=1e-6)
gpr = GPR(kernel=kernel)
......
......@@ -3,8 +3,8 @@ import numpy as np
from ase.calculators.dftb import Dftb
from ase.io import read
from candidate_operations.candidate_generation import CandidateGenerator, StartGenerator
from candidate_operations.basic_mutations import RattleMutation, PermutationMutation
from gofee.candidates import CandidateGenerator, StartGenerator
from gofee.candidates import RattleMutation, PermutationMutation
from gofee import GOFEE
### Define calculator ###
......
......@@ -21,7 +21,7 @@ following code :download:`TiO2.py` is used to carry out the search:
If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as::
mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py
mpiexec --mca mpi_warn_on_fork 0 gpaw-python TiO2.py
Setting up the system - atoms in template
=========================================
......
......@@ -4,8 +4,7 @@ import numpy as np
from ase import Atoms
from ase.calculators.dftb import Dftb
from candidate_operations.candidate_generation import CandidateGenerator, StartGenerator
from candidate_operations.basic_mutations import RattleMutation
from gofee.candidates import CandidateGenerator, StartGenerator, RattleMutation
from gofee import GOFEE
### Define calculator ###
......
......@@ -18,7 +18,7 @@ explainted further below):
If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as::
mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py
mpiexec --mca mpi_warn_on_fork 0 gpaw-python Ti5O10.py
What follows is a description of the python script above.
......
from gofee.gofee import GOFEE
__all__ = ['GOFEE']
\ No newline at end of file
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