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...@@ -4,4 +4,44 @@ ...@@ -4,4 +4,44 @@
Installation Installation
============ ============
Most code is written in python, however timecritical parts such as descriptor
and prior-mean evaluations are implemented using cython (and cymem), and need
be compiled for your particular setup.
Requirements
------------
* Python (only tested with 3.6.3)
* ASE (tested with 3.17 and newer)
* Cython (tested with 0.28 and newer)
* cymem (tested with 1.31.2 and newer)
* mpi4py (tested with 3.0 and newer)
* GPAW
Install from source
-------------------
The code is avaliable as a tar-file :download:`gofee.tar.gz`.
After downloading the tar-file, unpack it using::
tar -zxvf gofee.tar.gz
Then run the build_code file inside the gofee-folder, to compile descriptor
and prior-function, both used in the surrogate model. Do this using::
./build_code
This will compile the mentioned files for the python setup used
at the time of compiling.
Finally when using the code, you need to have the gofee-folder in
the PYTHONPATH. This is achieved using::
export PYTHONPATH=<path-to-folder>/gofee:$PYTHONPATH
When this is done, and assuming you have a working GPAW installation, you
can run python scripts calling GOFFE using::
mpiexec --mca mpi_warn_on_fork 0 gpaw-python script_calling_GOFEE.py
...@@ -156,7 +156,11 @@ a global optimization method used to optimize the geometry of atomistic ...@@ -156,7 +156,11 @@ a global optimization method used to optimize the geometry of atomistic
systems.</p> systems.</p>
<div class="toctree-wrapper compound"> <div class="toctree-wrapper compound">
<ul> <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="installation/installation.html">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="installation/installation.html#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation/installation.html#install-from-source">Install from source</a></li>
</ul>
</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="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="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-l1"><a class="reference internal" href="tutorial/tutorial.html">Tutorial</a><ul>
......
...@@ -81,7 +81,11 @@ ...@@ -81,7 +81,11 @@
<ul class="current"> <ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a></li> <li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="#install-from-source">Install from source</a></li>
</ul>
</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="../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="../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="../tutorial/tutorial.html">Tutorial</a></li>
...@@ -152,6 +156,45 @@ ...@@ -152,6 +156,45 @@
<div class="section" id="installation"> <div class="section" id="installation">
<span id="id1"></span><h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h1> <span id="id1"></span><h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h1>
<p>Most code is written in python, however timecritical parts such as descriptor
and prior-mean evaluations are implemented using cython (and cymem), and need
be compiled for your particular setup.</p>
<div class="section" id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline"></a></h2>
<ul class="simple">
<li><p>Python (only tested with 3.6.3)</p></li>
<li><p>ASE (tested with 3.17 and newer)</p></li>
<li><p>Cython (tested with 0.28 and newer)</p></li>
<li><p>cymem (tested with 1.31.2 and newer)</p></li>
<li><p>mpi4py (tested with 3.0 and newer)</p></li>
<li><p>GPAW</p></li>
</ul>
</div>
<div class="section" id="install-from-source">
<h2>Install from source<a class="headerlink" href="#install-from-source" title="Permalink to this headline"></a></h2>
<p>The code is avaliable as a tar-file <a class="reference download internal" download="" href="../_downloads/920d389b1e05cf17f747d8e1eb83f642/gofee.tar.gz"><code class="xref download docutils literal notranslate"><span class="pre">gofee.tar.gz</span></code></a>.</p>
<p>After downloading the tar-file, unpack it using:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">tar</span> <span class="o">-</span><span class="n">zxvf</span> <span class="n">gofee</span><span class="o">.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
</pre></div>
</div>
<p>Then run the build_code file inside the gofee-folder, to compile descriptor
and prior-function, both used in the surrogate model. Do this using:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">build_code</span>
</pre></div>
</div>
<p>This will compile the mentioned files for the python setup used
at the time of compiling.</p>
<p>Finally when using the code, you need to have the gofee-folder in
the PYTHONPATH. This is achieved using:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>export PYTHONPATH=&lt;path-to-folder&gt;/gofee:$PYTHONPATH
</pre></div>
</div>
<p>When this is done, and assuming you have a working GPAW installation, you
can run python scripts calling GOFFE using:</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">script_calling_GOFEE</span><span class="o">.</span><span class="n">py</span>
</pre></div>
</div>
</div>
</div> </div>
......
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\ No newline at end of file \ No newline at end of file
...@@ -12,17 +12,9 @@ ...@@ -12,17 +12,9 @@
# #
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('..'))
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('../../..'))
# Set path to module
sys.path.insert(0, os.path.abspath('..'))
# -- Project information ----------------------------------------------------- # -- Project information -----------------------------------------------------
...@@ -55,6 +47,9 @@ exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] ...@@ -55,6 +47,9 @@ exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# #
html_theme = 'sphinx_rtd_theme' html_theme = 'sphinx_rtd_theme'
# Change the encoding language of the HTML output files.
#html_output_encoding = 'iso-8859-1' # default 'utf-8'
# Add any paths that contain custom static files (such as style sheets) here, # Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files, # relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css". # so a file named "default.css" will overwrite the builtin "default.css".
......
...@@ -4,32 +4,35 @@ ...@@ -4,32 +4,35 @@
Installation Installation
============ ============
Most code is written in python, however timecritical parts such as descriptor
and prior-mean evaluations are implemented using cython (and cymem), and need
be compiled for your particular setup.
Requirements Requirements
------------ ------------
Python (only tested with 3.6.3) * Python (only tested with 3.6.3)
ASE (tested with 3.17 and newer) * ASE (tested with 3.17 and newer)
Cython (tested with 0.28 and newer) * Cython (tested with 0.28 and newer)
cymem (tested with 1.31.2 and newer) * cymem (tested with 1.31.2 and newer)
mpi4py (tested with 3.0 and newer) * mpi4py (tested with 3.0 and newer)
GPAW * GPAW
Install from source Install from source
------------------- -------------------
The code is avaliable as a tar-file here (you can get it using wget). The code is avaliable as a tar-file :download:`gofee.tar.gz`.
After downloading the tar-file, unpack it using:: After downloading the tar-file, unpack it using::
tar -xvf yourfile.tar tar -zxvf gofee.tar.gz
tar -zxvf yourfile.tar.gz
Then run the build_code file inside the gofee-folder, to compile descriptor Then run the build_code file inside the gofee-folder, to compile descriptor
and prior-function, both used in the surrogate model. Do this using:: and prior-function, both used in the surrogate model. Do this using::
./build_code ./build_code
This will compile the mentioned files for the python setup sources This will compile the mentioned files for the python setup used
at the time of compiling. at the time of compiling.
Finally when using the code, you need to have the gofee-folder in Finally when using the code, you need to have the gofee-folder in
......
...@@ -234,16 +234,6 @@ class GPR(): ...@@ -234,16 +234,6 @@ class GPR():
return -lml return -lml
def constrained_optimization(self, theta_initial): def constrained_optimization(self, theta_initial):
"""
result = minimize(self.neg_log_marginal_likelihood,
x0=theta_initial,
bounds=self.kernel.theta_bounds,
method='L-BFGS-B',
jac=True)
if not result.success:
warnings.warn(f"L_BFGS_B terminated with state: {result.message}")
return result.x, result.fun
"""
theta_opt, func_min, convergence_dict = \ theta_opt, func_min, convergence_dict = \
fmin_l_bfgs_b(self.neg_log_marginal_likelihood, fmin_l_bfgs_b(self.neg_log_marginal_likelihood,
theta_initial, theta_initial,
......
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