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 ...@@ -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 the search, if it is included as an operation in the
:class:`CandidateGenerator`. :class:`CandidateGenerator`.
.. autoclass:: candidate_operations.candidate_generation.StartGenerator .. autoclass:: gofee.candidates.StartGenerator
:exclude-members: :exclude-members:
CandidateGenerator CandidateGenerator
...@@ -28,7 +28,7 @@ The :class:`CandidateGenerator` is used in each iteration in the GOFEE search ...@@ -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 to generate new candidates based on a list on operations to use. Possible
operation can be found below under the "Mutations" section. operation can be found below under the "Mutations" section.
.. autoclass:: candidate_operations.candidate_generation.CandidateGenerator .. autoclass:: gofee.candidates.CandidateGenerator
:members: get_new_candidate :members: get_new_candidate
...@@ -42,17 +42,17 @@ The mutations to chose from are listed below. ...@@ -42,17 +42,17 @@ The mutations to chose from are listed below.
RattleMutation RattleMutation
-------------- --------------
.. autoclass:: candidate_operations.basic_mutations.RattleMutation .. autoclass:: gofee.candidates.RattleMutation
:exclude-members: :exclude-members:
RattleMutation2 RattleMutation2
--------------- ---------------
.. autoclass:: candidate_operations.basic_mutations.RattleMutation2 .. autoclass:: gofee.candidates.RattleMutation2
:exclude-members: :exclude-members:
PermutationMutation PermutationMutation
------------------- -------------------
.. autoclass:: candidate_operations.basic_mutations.PermutationMutation .. autoclass:: gofee.candidates.PermutationMutation
:exclude-members: :exclude-members:
\ No newline at end of file
...@@ -27,7 +27,7 @@ this (propperly modified for your setup):: ...@@ -27,7 +27,7 @@ this (propperly modified for your setup)::
source <GPAW stuff> source <GPAW stuff>
source <DFTB stuff> # if running DFTB 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` ==========" echo "========= Job finished at `date` =========="
This job will be run locally in the submission folder on 10 cpu cores. 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 ...@@ -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 in the search. As the regularization is a parameter of the *kernel*, passed
to the GPR model, the code will look like this:: to the GPR model, the code will look like this::
from surrogate.gpr import GPR from gofee.surrogate.gpr import GPR
from surrogate.kernel import double_gauss_kernel from gofee.surrogate.kernel import double_gauss_kernel
kernel = double_gauss_kernel(noise=1e-6) kernel = double_gauss_kernel(noise=1e-6)
gpr = GPR(kernel=kernel) gpr = GPR(kernel=kernel)
......
...@@ -21,7 +21,7 @@ following code :download:`TiO2.py` is used to carry out the search: ...@@ -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 If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as:: 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 Setting up the system - atoms in template
========================================= =========================================
......
...@@ -18,7 +18,7 @@ explainted further below): ...@@ -18,7 +18,7 @@ explainted further below):
If ASE, GPAW and dftb are set up and sourced propperly, you can run If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as:: 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. What follows is a description of the python script above.
......
...@@ -161,7 +161,7 @@ ...@@ -161,7 +161,7 @@
<h2 id="C">C</h2> <h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr> <table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul> <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> </li>
</ul></td> </ul></td>
</tr></table> </tr></table>
...@@ -169,7 +169,7 @@ ...@@ -169,7 +169,7 @@
<h2 id="G">G</h2> <h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr> <table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul> <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> </li>
</ul></td> </ul></td>
<td style="width: 33%; vertical-align: top;"><ul> <td style="width: 33%; vertical-align: top;"><ul>
...@@ -181,7 +181,7 @@ ...@@ -181,7 +181,7 @@
<h2 id="P">P</h2> <h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr> <table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul> <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> </li>
</ul></td> </ul></td>
</tr></table> </tr></table>
...@@ -189,11 +189,11 @@ ...@@ -189,11 +189,11 @@
<h2 id="R">R</h2> <h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr> <table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul> <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> </li>
</ul></td> </ul></td>
<td style="width: 33%; vertical-align: top;"><ul> <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>
<li><a href="GOFEE/GOFEE.html#gofee.GOFEE.run">run() (gofee.GOFEE method)</a> <li><a href="GOFEE/GOFEE.html#gofee.GOFEE.run">run() (gofee.GOFEE method)</a>
</li> </li>
...@@ -203,7 +203,7 @@ ...@@ -203,7 +203,7 @@
<h2 id="S">S</h2> <h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr> <table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul> <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> </li>
</ul></td> </ul></td>
</tr></table> </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> ...@@ -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 <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 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> 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> <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">surrogate.kernel</span> <span class="k">import</span> <span class="n">double_gauss_kernel</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">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> <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 ...@@ -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.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">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">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">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">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="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>
<span class="c1">### Define calculator ###</span> <span class="c1">### Define calculator ###</span>
...@@ -227,7 +227,7 @@ following code <a class="reference download internal" download="" href="../../_d ...@@ -227,7 +227,7 @@ following code <a class="reference download internal" download="" href="../../_d
</div> </div>
<p>If ASE, GPAW and dftb are set up and sourced propperly, you can run <p>If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as:</p> 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> </pre></div>
</div> </div>
<div class="section" id="setting-up-the-system-atoms-in-template"> <div class="section" id="setting-up-the-system-atoms-in-template">
......
...@@ -177,8 +177,7 @@ explainted further below):</p> ...@@ -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</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">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">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">candidate_operations.basic_mutations</span> <span class="k">import</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="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>
<span class="c1">### Define calculator ###</span> <span class="c1">### Define calculator ###</span>
...@@ -228,7 +227,7 @@ explainted further below):</p> ...@@ -228,7 +227,7 @@ explainted further below):</p>
</div> </div>
<p>If ASE, GPAW and dftb are set up and sourced propperly, you can run <p>If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as:</p> 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> </pre></div>
</div> </div>
<p>What follows is a description of the python script above.</p>