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Update to 7.8 #50

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merged 12 commits into from
Sep 12, 2024
Merged

Update to 7.8 #50

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e06e234
Fix COSMO results parsing.
davidwaroquiers Sep 6, 2024
eb0c81e
Checked unit and integration tests. Updated reference files to 7.8.1.
davidwaroquiers Sep 6, 2024
123cee9
Fixed linting.
davidwaroquiers Sep 6, 2024
b711bf9
Changed documentation.
davidwaroquiers Sep 6, 2024
ab1217a
Fixed epsilon type in cosmo.
davidwaroquiers Sep 10, 2024
f986005
Fixed lowercase for solvents.
davidwaroquiers Sep 10, 2024
33c2c21
Updated reference files for integration tests.
davidwaroquiers Sep 10, 2024
92e24dc
Added test for bad solvent name.
davidwaroquiers Sep 10, 2024
583d15d
Added test for cosmo predefined solvent.
davidwaroquiers Sep 10, 2024
ca52f14
Added deps for docs generation.
davidwaroquiers Sep 10, 2024
44607de
Updated documentation.
davidwaroquiers Sep 10, 2024
77eca6e
Fixed missing data file (added __init__.py in the directory).
davidwaroquiers Sep 10, 2024
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75 changes: 69 additions & 6 deletions dev_scripts/generate_output_files.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -476,6 +476,7 @@ def compare_to_reference_files(
all_diffs,
tm_exec,
ref_fname="ref_output.json",
dryrun=False,
):
"""
Generate the output object and compare it to the reference one.
Expand All @@ -495,6 +496,7 @@ def compare_to_reference_files(
the reference log files.
tm_exec: Turbomole executable being tested.
ref_fname: Filename of the json-serialized reference output object.
dryrun: Whether in dryrun mode.

Returns:
tuple: Output object and serialized Output object.
Expand All @@ -520,13 +522,34 @@ def compare_to_reference_files(
)
for idiff, diff in enumerate(out_diffs, start=1):
print(f"#{idiff} {diff[0]}\n {diff[1]}")
all_diffs[f"{tm_exec}_{out_cls.__name__}"] = out_diffs
test_name = f"{tm_exec}_{out_cls.__name__}"
all_diffs[test_name] = out_diffs
if dryrun:
dumpfn(
ref_out,
os.path.join(ref_test_dirpath, f"{test_name}_REF.json"),
indent=2,
sort_keys=True,
)
dumpfn(
gen_out_dict,
os.path.join(ref_test_dirpath, f"{test_name}_NEW.json"),
indent=2,
sort_keys=True,
)

return gen_out, gen_out_dict


def compare_to_reference_parser(
log_fpath, ref_test_dirpath, rtol, atol, print_diffs, all_diffs, tm_exec
log_fpath,
ref_test_dirpath,
rtol,
atol,
print_diffs,
all_diffs,
tm_exec,
dryrun,
):
"""
Generate all results of parser methods and compare to the reference parser file.
Expand All @@ -541,6 +564,7 @@ def compare_to_reference_parser(
updated if differences are found between the new and the reference
parser files.
tm_exec: Turbomole executable being tested.
dryrun: Whether in dryrun mode.

Returns:
dict: Dictionary mapping each parser method with it's resulting parsed data.
Expand Down Expand Up @@ -568,13 +592,34 @@ def compare_to_reference_parser(
print("There are differences in the parsed methods:")
for idiff, diff in enumerate(parser_diffs, start=1):
print(f"#{idiff} {diff[0]}\n {diff[1]}")
all_diffs[f"{tm_exec}_Parser"] = parser_diffs
test_name = f"{tm_exec}_Parser"
all_diffs[test_name] = parser_diffs
if dryrun:
dumpfn(
ref_parser_methods,
os.path.join(ref_test_dirpath, f"{test_name}_REF.json"),
indent=2,
sort_keys=True,
)
dumpfn(
parsed_data,
os.path.join(ref_test_dirpath, f"{test_name}_NEW.json"),
indent=2,
sort_keys=True,
)

return parsed_data


def get_outputs_and_parser_objects_and_compare(
log_fpath, ref_test_dirpath, rtol, atol, print_diffs, all_diffs, tm_exec
log_fpath,
ref_test_dirpath,
rtol,
atol,
print_diffs,
all_diffs,
tm_exec,
dryrun,
):
"""
Get the serialized output and parser objects and compare them to the reference.
Expand All @@ -589,6 +634,7 @@ def get_outputs_and_parser_objects_and_compare(
Will be updated if differences are found
between the new and the reference parser and/or output files.
tm_exec: Turbomole executable being tested.
dryrun: Whether in dryrun mode.

Returns:
dict: Dictionary mapping the reference outputs and parser filenames
Expand All @@ -605,6 +651,7 @@ def get_outputs_and_parser_objects_and_compare(
all_diffs,
tm_exec,
ref_fname="ref_output.json",
dryrun=dryrun,
)
outputs_parser_dicts = {"ref_output.json": output_dict}
if tm_exec == "escf":
Expand All @@ -618,11 +665,19 @@ def get_outputs_and_parser_objects_and_compare(
all_diffs,
tm_exec,
ref_fname="ref_escf_output.json",
dryrun=dryrun,
)
outputs_parser_dicts["ref_escf_output.json"] = escf_output_dict

outputs_parser_dicts["ref_parser.json"] = compare_to_reference_parser(
log_fpath, ref_test_dirpath, rtol, atol, print_diffs, all_diffs, tm_exec
log_fpath,
ref_test_dirpath,
rtol,
atol,
print_diffs,
all_diffs,
tm_exec,
dryrun=dryrun,
)

return outputs_parser_dicts
Expand Down Expand Up @@ -656,7 +711,14 @@ def update_json_files(dryrun, rtol, atol, print_diffs):
# to the old ones.
log_fpath = get_log_fpath(test_dirpath, tm_exec)
outputs_parser_dicts = get_outputs_and_parser_objects_and_compare(
log_fpath, test_dirpath, rtol, atol, print_diffs, all_diffs, tm_exec
log_fpath,
test_dirpath,
rtol,
atol,
print_diffs,
all_diffs,
tm_exec,
dryrun=dryrun,
)

# Dump the new json-serialized reference output and parser objects.
Expand Down Expand Up @@ -761,6 +823,7 @@ def main():
args.print_diffs,
all_diffs,
tm_exec,
dryrun=dryrun,
)

# Dump the new json-serialized reference output and parser objects.
Expand Down
11 changes: 6 additions & 5 deletions docs/_modules/index.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &mdash; turbomoleio 1.5.0 documentation</title>
<title>Overview: module code &mdash; turbomoleio 1.6.0 documentation</title>
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />

Expand All @@ -14,8 +14,8 @@

<script src="../_static/jquery.js?v=5d32c60e"></script>
<script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="../_static/documentation_options.js?v=e0a75244"></script>
<script src="../_static/doctools.js?v=888ff710"></script>
<script src="../_static/documentation_options.js?v=72d88caf"></script>
<script src="../_static/doctools.js?v=9a2dae69"></script>
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
Expand All @@ -34,7 +34,7 @@
turbomoleio
</a>
<div class="version">
1.5.0
1.6.0
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
Expand Down Expand Up @@ -105,6 +105,7 @@ <h1>All modules for which code is available</h1>
<li><a href="turbomoleio/output/files.html">turbomoleio.output.files</a></li>
<li><a href="turbomoleio/output/parser.html">turbomoleio.output.parser</a></li>
<li><a href="turbomoleio/output/states.html">turbomoleio.output.states</a></li>
<li><a href="turbomoleio/testing.html">turbomoleio.testing</a></li>
</ul>

</div>
Expand All @@ -114,7 +115,7 @@ <h1>All modules for which code is available</h1>
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2018-2022 BASF SE, Matgenix SRL.</p>
<p>&#169; Copyright 2018-2024 BASF SE, Matgenix SRL.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
Expand Down
10 changes: 5 additions & 5 deletions docs/_modules/turbomoleio/core/base.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>turbomoleio.core.base &mdash; turbomoleio 1.5.0 documentation</title>
<title>turbomoleio.core.base &mdash; turbomoleio 1.6.0 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />

Expand All @@ -14,8 +14,8 @@

<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="../../../_static/documentation_options.js?v=e0a75244"></script>
<script src="../../../_static/doctools.js?v=888ff710"></script>
<script src="../../../_static/documentation_options.js?v=72d88caf"></script>
<script src="../../../_static/doctools.js?v=9a2dae69"></script>
<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../../genindex.html" />
Expand All @@ -34,7 +34,7 @@
turbomoleio
</a>
<div class="version">
1.5.0
1.6.0
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
Expand Down Expand Up @@ -430,7 +430,7 @@ <h1>Source code for turbomoleio.core.base</h1><div class="highlight"><pre>
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2018-2022 BASF SE, Matgenix SRL.</p>
<p>&#169; Copyright 2018-2024 BASF SE, Matgenix SRL.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
Expand Down
35 changes: 29 additions & 6 deletions docs/_modules/turbomoleio/core/control.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>turbomoleio.core.control &mdash; turbomoleio 1.5.0 documentation</title>
<title>turbomoleio.core.control &mdash; turbomoleio 1.6.0 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />

Expand All @@ -14,8 +14,8 @@

<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="../../../_static/documentation_options.js?v=e0a75244"></script>
<script src="../../../_static/doctools.js?v=888ff710"></script>
<script src="../../../_static/documentation_options.js?v=72d88caf"></script>
<script src="../../../_static/doctools.js?v=9a2dae69"></script>
<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../../genindex.html" />
Expand All @@ -34,7 +34,7 @@
turbomoleio
</a>
<div class="version">
1.5.0
1.6.0
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
Expand Down Expand Up @@ -122,6 +122,7 @@ <h1>Source code for turbomoleio.core.control</h1><div class="highlight"><pre>
<span class="sd">energy, etc ...</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">importlib.resources</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">re</span>
<span class="kn">import</span> <span class="nn">shutil</span>
Expand All @@ -139,6 +140,11 @@ <h1>Source code for turbomoleio.core.control</h1><div class="highlight"><pre>
<span class="kn">from</span> <span class="nn">turbomoleio.core.periodic</span> <span class="kn">import</span> <span class="n">PeriodicSystem</span>
<span class="kn">from</span> <span class="nn">turbomoleio.core.symmetry</span> <span class="kn">import</span> <span class="n">irrep_size</span>

<span class="k">with</span> <span class="n">importlib</span><span class="o">.</span><span class="n">resources</span><span class="o">.</span><span class="n">open_text</span><span class="p">(</span>
<span class="s2">&quot;turbomoleio.core.data&quot;</span><span class="p">,</span> <span class="s2">&quot;available_solvents.txt&quot;</span>
<span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">available_solvents</span> <span class="o">=</span> <span class="p">[</span><span class="n">solvent</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">for</span> <span class="n">solvent</span> <span class="ow">in</span> <span class="n">f</span><span class="o">.</span><span class="n">readlines</span><span class="p">()]</span>


<div class="viewcode-block" id="Defaults">
<a class="viewcode-back" href="../../../api/turbomoleio.core.html#turbomoleio.core.control.Defaults">[docs]</a>
Expand Down Expand Up @@ -791,7 +797,9 @@ <h1>Source code for turbomoleio.core.control</h1><div class="highlight"><pre>
<a class="viewcode-back" href="../../../api/turbomoleio.core.html#turbomoleio.core.control.Control.add_cosmo">[docs]</a>
<span class="k">def</span> <span class="nf">add_cosmo</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">solvent</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">epsilon</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">refind</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">nppa</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">nspa</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">disex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
Expand All @@ -807,7 +815,11 @@ <h1>Source code for turbomoleio.core.control</h1><div class="highlight"><pre>
<span class="sd"> If None all the options will not be written to the control file.</span>

<span class="sd"> Args:</span>
<span class="sd"> solvent (str): name of solvent used. This sets the values of epsilon and</span>
<span class="sd"> refind below from predefined solvents.</span>
<span class="sd"> epsilon (float): permittivity used for scaling of the screening charges.</span>
<span class="sd"> refind (float): refractive index used for the calculation of vertical</span>
<span class="sd"> excitations and numerical frequencies.</span>
<span class="sd"> nppa (int): number of basis grid points per atom.</span>
<span class="sd"> nspa (int): number of segments per atom.</span>
<span class="sd"> disex (float): distance threshold for A matrix elements (Angstrom).</span>
Expand All @@ -825,8 +837,19 @@ <h1>Source code for turbomoleio.core.control</h1><div class="highlight"><pre>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">cosmo_lines</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;&quot;</span><span class="p">]</span>

<span class="k">if</span> <span class="n">solvent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">solvent_lower</span> <span class="o">=</span> <span class="n">solvent</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
<span class="k">if</span> <span class="n">solvent_lower</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">available_solvents</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
<span class="sa">f</span><span class="s2">&quot;Solvent with name </span><span class="si">{</span><span class="n">solvent</span><span class="si">}</span><span class="s2"> is not available. &quot;</span>
<span class="sa">f</span><span class="s2">&quot;See turbomoleio/core/data/available_solvents.txt for available &quot;</span>
<span class="sa">f</span><span class="s2">&quot;solvents.&quot;</span>
<span class="p">)</span>
<span class="n">cosmo_lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot; solvent=</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">solvent_lower</span><span class="p">))</span>
<span class="k">if</span> <span class="n">epsilon</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">cosmo_lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot; epsilon=</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">epsilon</span><span class="p">))</span>
<span class="k">if</span> <span class="n">refind</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">cosmo_lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot; refind=</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">refind</span><span class="p">))</span>
<span class="k">if</span> <span class="n">nppa</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">cosmo_lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot; nppa=</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">nppa</span><span class="p">))</span>
<span class="k">if</span> <span class="n">nspa</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
Expand Down Expand Up @@ -920,7 +943,7 @@ <h1>Source code for turbomoleio.core.control</h1><div class="highlight"><pre>

<span class="k">if</span> <span class="n">dispersion_correction</span> <span class="o">==</span> <span class="s2">&quot;dft-d1&quot;</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
<span class="s2">&quot;D1 dispersion correction is not working anymore in &quot;</span> <span class="s2">&quot;Turbomole v7.5.&quot;</span>
<span class="s2">&quot;D1 dispersion correction is not working anymore in Turbomole v7.5.&quot;</span>
<span class="p">)</span>
<span class="c1"># self.add_data_group(&quot;olddisp&quot;, &quot;&quot;)</span>
<span class="k">elif</span> <span class="n">dispersion_correction</span> <span class="o">==</span> <span class="s2">&quot;dft-d2&quot;</span><span class="p">:</span>
Expand Down Expand Up @@ -1398,7 +1421,7 @@ <h1>Source code for turbomoleio.core.control</h1><div class="highlight"><pre>
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2018-2022 BASF SE, Matgenix SRL.</p>
<p>&#169; Copyright 2018-2024 BASF SE, Matgenix SRL.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
Expand Down
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