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daavid00 merged 1 commit into from
Apr 11, 2026
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Code quality fixes suggested by copilot #16

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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -5,7 +5,8 @@

# pofff: An open-source image-based history-matching framework for the FluidFlower benchmark study using OPM Flow

<img src="docs/text/figs/pofff.png" width="830" height="247">
<center><img src="docs/text/figs/pofff+plopm_xco2l.gif" width="830" height="auto" /></center>
<center><img src="docs/text/figs/pofff.png" width="830" height="auto"></center>

This repository contains runscripts to simulate CO2 injection in the
[_fluidflower benchmark system_](https://fluidflower.w.uib.no) using the
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10 changes: 7 additions & 3 deletions docs/_sources/examples.rst.txt
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Expand Up @@ -105,9 +105,13 @@ Then the following GIF is generated by:

.. code-block:: bash

pofff -i appendixb.toml -o plopm -m single -c '5e-2' -f none
plopm -v xco2l -i plopm/PLOPM -d 8,2.5 -mask satnum -m gif -dpi 1000 -f 12 -loop 1 -cformat .2f -cbsfax 0.30,0.01,0.4,0.02 -remove 0,0,1,0 -interval 437.5 -maskthr 1e-5 -tunits h
pofff -i appendixb.toml -o plopm+pofff -m single -c '5e-2' -f none
plopm -v xco2l -i 'pofff+plopm/POFFF+PLOPM' -d 16,5 -mask satnum -m gif -dpi 1000 -f 20 -loop 1 -cformat .1e -cbsfax 0.30,0.01,0.4,0.02 -interval 437.5 -maskthr 1e-5 -tunits h -cnum 5 -clabel 'CO$_2$ mass fraction in liquid [-]' -t 'FluidFlower simulation (GitHub/cssr-tools/pofff),'

.. image:: ./figs/plopm_xco2l.gif
.. figure:: figs/pofff+plopm_xco2l.gif

The total simulation time for this GIF (five days of experiment) using eight CPUs for OPM Flow in a Mac is **LESS THAN TWO MINUTES!!!**



See the `plopm online docmunetation <https://cssr-tools.github.io/plopm/>`_ for additional information of supported flag parameters to generate customized PNGs and GIFs.
11 changes: 8 additions & 3 deletions docs/examples.html
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Expand Up @@ -173,12 +173,17 @@ <h2>Visualization<a class="headerlink" href="#visualization" title="Link to this
</div>
<p>Then the following GIF is generated by:</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pofff<span class="w"> </span>-i<span class="w"> </span>appendixb.toml<span class="w"> </span>-o<span class="w"> </span>plopm<span class="w"> </span>-m<span class="w"> </span>single<span class="w"> </span>-c<span class="w"> </span><span class="s1">&#39;5e-2&#39;</span><span class="w"> </span>-f<span class="w"> </span>none
plopm<span class="w"> </span>-v<span class="w"> </span>xco2l<span class="w"> </span>-i<span class="w"> </span>plopm/PLOPM<span class="w"> </span>-d<span class="w"> </span><span class="m">8</span>,2.5<span class="w"> </span>-mask<span class="w"> </span>satnum<span class="w"> </span>-m<span class="w"> </span>gif<span class="w"> </span>-dpi<span class="w"> </span><span class="m">1000</span><span class="w"> </span>-f<span class="w"> </span><span class="m">12</span><span class="w"> </span>-loop<span class="w"> </span><span class="m">1</span><span class="w"> </span>-cformat<span class="w"> </span>.2f<span class="w"> </span>-cbsfax<span class="w"> </span><span class="m">0</span>.30,0.01,0.4,0.02<span class="w"> </span>-remove<span class="w"> </span><span class="m">0</span>,0,1,0<span class="w"> </span>-interval<span class="w"> </span><span class="m">437</span>.5<span class="w"> </span>-maskthr<span class="w"> </span>1e-5<span class="w"> </span>-tunits<span class="w"> </span>h
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pofff<span class="w"> </span>-i<span class="w"> </span>appendixb.toml<span class="w"> </span>-o<span class="w"> </span>plopm+pofff<span class="w"> </span>-m<span class="w"> </span>single<span class="w"> </span>-c<span class="w"> </span><span class="s1">&#39;5e-2&#39;</span><span class="w"> </span>-f<span class="w"> </span>none
plopm<span class="w"> </span>-v<span class="w"> </span>xco2l<span class="w"> </span>-i<span class="w"> </span><span class="s1">&#39;pofff+plopm/POFFF+PLOPM&#39;</span><span class="w"> </span>-d<span class="w"> </span><span class="m">16</span>,5<span class="w"> </span>-mask<span class="w"> </span>satnum<span class="w"> </span>-m<span class="w"> </span>gif<span class="w"> </span>-dpi<span class="w"> </span><span class="m">1000</span><span class="w"> </span>-f<span class="w"> </span><span class="m">20</span><span class="w"> </span>-loop<span class="w"> </span><span class="m">1</span><span class="w"> </span>-cformat<span class="w"> </span>.1e<span class="w"> </span>-cbsfax<span class="w"> </span><span class="m">0</span>.30,0.01,0.4,0.02<span class="w"> </span>-interval<span class="w"> </span><span class="m">437</span>.5<span class="w"> </span>-maskthr<span class="w"> </span>1e-5<span class="w"> </span>-tunits<span class="w"> </span>h<span class="w"> </span>-cnum<span class="w"> </span><span class="m">5</span><span class="w"> </span>-clabel<span class="w"> </span><span class="s1">&#39;CO$_2$ mass fraction in liquid [-]&#39;</span><span class="w"> </span>-t<span class="w"> </span><span class="s1">&#39;FluidFlower simulation (GitHub/cssr-tools/pofff),&#39;</span>
</pre></div>
</div>
</div></blockquote>
<img alt="_images/plopm_xco2l.gif" src="_images/plopm_xco2l.gif" />
<figure class="align-default" id="id3">
<img alt="_images/pofff%2Bplopm_xco2l.gif" src="_images/pofff%2Bplopm_xco2l.gif" />
<figcaption>
<p><span class="caption-text">The total simulation time for this GIF (five days of experiment) using eight CPUs for OPM Flow in a Mac is <strong>LESS THAN TWO MINUTES!!!</strong></span><a class="headerlink" href="#id3" title="Link to this image"></a></p>
</figcaption>
</figure>
<p>See the <a class="reference external" href="https://cssr-tools.github.io/plopm/">plopm online docmunetation</a> for additional information of supported flag parameters to generate customized PNGs and GIFs.</p>
</section>
</section>
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2 changes: 1 addition & 1 deletion docs/genindex.html
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Expand Up @@ -634,7 +634,7 @@ <h2 id="P">P</h2>
</ul></li>
<li><a href="pofff.visualization.everert.html#pofff.visualization.everert.plot_cumulative_misfit">plot_cumulative_misfit() (in module pofff.visualization.everert)</a>
</li>
<li><a href="pofff.visualization.everert.html#pofff.visualization.everert.plot_hm_missmatch">plot_hm_missmatch() (in module pofff.visualization.everert)</a>
<li><a href="pofff.visualization.everert.html#pofff.visualization.everert.plot_hm_mismatch">plot_hm_mismatch() (in module pofff.visualization.everert)</a>
</li>
<li><a href="pofff.visualization.everert.html#pofff.visualization.everert.plot_misfit">plot_misfit() (in module pofff.visualization.everert)</a>
</li>
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2 changes: 1 addition & 1 deletion docs/pofff.html
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Expand Up @@ -223,7 +223,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
<li class="toctree-l4"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.parse_args"><code class="docutils literal notranslate"><span class="pre">parse_args()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_cumulative_misfit"><code class="docutils literal notranslate"><span class="pre">plot_cumulative_misfit()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_hm_missmatch"><code class="docutils literal notranslate"><span class="pre">plot_hm_missmatch()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_hm_mismatch"><code class="docutils literal notranslate"><span class="pre">plot_hm_mismatch()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_misfit"><code class="docutils literal notranslate"><span class="pre">plot_misfit()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_observable_distribution"><code class="docutils literal notranslate"><span class="pre">plot_observable_distribution()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_optimization"><code class="docutils literal notranslate"><span class="pre">plot_optimization()</span></code></a></li>
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4 changes: 2 additions & 2 deletions docs/pofff.visualization.everert.html
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Expand Up @@ -303,8 +303,8 @@
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="pofff.visualization.everert.plot_hm_missmatch">
<span class="sig-prename descclassname"><span class="pre">pofff.visualization.everert.</span></span><span class="sig-name descname"><span class="pre">plot_hm_missmatch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cfg</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pofff.visualization.everert.Config" title="pofff.visualization.everert.Config"><span class="pre">Config</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">state</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pofff.visualization.everert.EnsembleState" title="pofff.visualization.everert.EnsembleState"><span class="pre">EnsembleState</span></a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pofff.visualization.everert.plot_hm_missmatch" title="Link to this definition"></a></dt>
<dt class="sig sig-object py" id="pofff.visualization.everert.plot_hm_mismatch">
<span class="sig-prename descclassname"><span class="pre">pofff.visualization.everert.</span></span><span class="sig-name descname"><span class="pre">plot_hm_mismatch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cfg</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pofff.visualization.everert.Config" title="pofff.visualization.everert.Config"><span class="pre">Config</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">state</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pofff.visualization.everert.EnsembleState" title="pofff.visualization.everert.EnsembleState"><span class="pre">EnsembleState</span></a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pofff.visualization.everert.plot_hm_mismatch" title="Link to this definition"></a></dt>
<dd><p>Plot ensemble-mean misfit per iteration.</p>
</dd></dl>

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2 changes: 1 addition & 1 deletion docs/pofff.visualization.html
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Expand Up @@ -148,7 +148,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
<li class="toctree-l2"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.parse_args"><code class="docutils literal notranslate"><span class="pre">parse_args()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_cumulative_misfit"><code class="docutils literal notranslate"><span class="pre">plot_cumulative_misfit()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_hm_missmatch"><code class="docutils literal notranslate"><span class="pre">plot_hm_missmatch()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_hm_mismatch"><code class="docutils literal notranslate"><span class="pre">plot_hm_mismatch()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_misfit"><code class="docutils literal notranslate"><span class="pre">plot_misfit()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_observable_distribution"><code class="docutils literal notranslate"><span class="pre">plot_observable_distribution()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="pofff.visualization.everert.html#pofff.visualization.everert.plot_optimization"><code class="docutils literal notranslate"><span class="pre">plot_optimization()</span></code></a></li>
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10 changes: 7 additions & 3 deletions docs/text/examples.rst
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Expand Up @@ -105,9 +105,13 @@ Then the following GIF is generated by:

.. code-block:: bash

pofff -i appendixb.toml -o plopm -m single -c '5e-2' -f none
plopm -v xco2l -i plopm/PLOPM -d 8,2.5 -mask satnum -m gif -dpi 1000 -f 12 -loop 1 -cformat .2f -cbsfax 0.30,0.01,0.4,0.02 -remove 0,0,1,0 -interval 437.5 -maskthr 1e-5 -tunits h
pofff -i appendixb.toml -o plopm+pofff -m single -c '5e-2' -f none
plopm -v xco2l -i 'pofff+plopm/POFFF+PLOPM' -d 16,5 -mask satnum -m gif -dpi 1000 -f 20 -loop 1 -cformat .1e -cbsfax 0.30,0.01,0.4,0.02 -interval 437.5 -maskthr 1e-5 -tunits h -cnum 5 -clabel 'CO$_2$ mass fraction in liquid [-]' -t 'FluidFlower simulation (GitHub/cssr-tools/pofff),'

.. image:: ./figs/plopm_xco2l.gif
.. figure:: figs/pofff+plopm_xco2l.gif

The total simulation time for this GIF (five days of experiment) using eight CPUs for OPM Flow in a Mac is **LESS THAN TWO MINUTES!!!**



See the `plopm online docmunetation <https://cssr-tools.github.io/plopm/>`_ for additional information of supported flag parameters to generate customized PNGs and GIFs.
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2 changes: 1 addition & 1 deletion examples/ert.toml
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Expand Up @@ -30,7 +30,7 @@ krn="(max(0, (1 - sw - sni) / (1 - sni))) ** nkrn" #Non-wetting rel perm
cap="pen * ((sw-swi) / (1-swi)) ** (-(1.0 / npen))" #Capillary pressure saturation function [Pa]

# Ert
ertargs = "test_run" # Command line for Ert: gui, test_run, ensemble_experiment, ensemble_smoother, iterative_ensemble_smoother, and es_mda
ertargs = "es_mda --weights 1" # Command line for Ert: gui, test_run, ensemble_experiment, ensemble_smoother, iterative_ensemble_smoother, and es_mda
min_realizations_success = 0 # Minimum number of simulations that must have succeeded for the simulation to be regarded as a success.
ensembles = 8 # Number of members in each ensemble
random_seed = 7 # Set a specific seed for reproducibility; a value of 0 means no seed (rng for everest and random_seed for ert)
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2 changes: 1 addition & 1 deletion examples/everest.toml
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Expand Up @@ -31,7 +31,7 @@ cap="pen * ((sw-swi) / (1-swi)) ** (-(1.0 / npen))" #Capillary pressure s

# Everest
min_realizations_success = 0 # Minimum number of simulations that must have succeeded for the simulation to be regarded as a success
max_function_evaluations = 2 # Maximum number of simulations
max_function_evaluations = 20 # Maximum number of simulations
rng = 7 # Set a specific seed for reproducibility; a value of 0 means no seed (rng for everest and random_seed for ert)
cores = 8 # Maximum number of simulations running in parallel
maxtime = 120 # Maximum runtime in seconds of a realization; a value of 0 means unlimited runtime
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -23,7 +23,7 @@ classifiers = [
]
dependencies = [
"alive-progress",
"ert<=21.0.6",
"ert<=21.0.7",
"iterative_ensemble_smoother",
"mako",
"matplotlib",
Expand All @@ -36,7 +36,7 @@ dependencies = [
"scipy",
"shapely"
]
requires-python = ">=3.11"
requires-python = ">=3.12"

[project.scripts]
pofff = "pofff.core.pofff:main"
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4 changes: 0 additions & 4 deletions src/pofff/fluidflower/general/evaluation/emd.py
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Expand Up @@ -43,10 +43,6 @@ def calculateEMD(inFileName1, inFileName2):
a_flat = a.flatten(order="F")
b_flat = b.flatten(order="F")

# Cell centers of all cells - x and y coordinates.
cc_x = np.zeros((Nx, Ny), dtype=float).flatten("F")
cc_y = np.zeros((Nx, Ny), dtype=float).flatten("F")

cc_x, cc_y = np.meshgrid(np.arange(Nx), np.arange(Ny), indexing="ij")

cc_x_flat = cc_x.flatten("F") / Nx * 2.8 + 5e-3 * 280 / Nx
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4 changes: 0 additions & 4 deletions src/pofff/jobs/metric.py
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Expand Up @@ -49,10 +49,6 @@ def calculate_emd(file_1, file_2):
a_flat = a_1.flatten(order="F")
b_flat = b_1.flatten(order="F")

# --- Cell center coordinates (fixed definition) ---
cc_x = np.zeros((n_x, n_z), dtype=float).flatten("F")
cc_y = np.zeros((n_x, n_z), dtype=float).flatten("F")

cc_x, cc_y = np.meshgrid(np.arange(n_x), np.arange(n_z), indexing="ij")

cc_x_flat = cc_x.flatten("F") / n_x * 2.8 + 5e-3 * 280 / n_x
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8 changes: 4 additions & 4 deletions src/pofff/visualization/everert.py
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Expand Up @@ -296,7 +296,7 @@ def plot_misfit(cfg: Config, state: EnsembleState):
ax.set_title(
r"$O_{i,j}=\frac{1}{2N_{obs}}\sum_n^{N_{obs}}((d^{n}_{i,j}-d^{n})/\sigma_n)^2$"
)
save_figure(fig, cfg.path / "figures/dist_missmatch.png")
save_figure(fig, cfg.path / "figures/dist_mismatch.png")


def plot_parameter_distributions(cfg: Config, state: EnsembleState):
Expand Down Expand Up @@ -542,7 +542,7 @@ def plot_observable_distribution(cfg: Config, state: EnsembleState):
save_figure(fig, cfg.path / "figures/dist_observable.png")


def plot_hm_missmatch(cfg: Config, state: EnsembleState):
def plot_hm_mismatch(cfg: Config, state: EnsembleState):
"""Plot ensemble-mean misfit per iteration."""
fig, ax = plt.subplots()

Expand All @@ -561,7 +561,7 @@ def plot_hm_missmatch(cfg: Config, state: EnsembleState):
ax.set_xticks(range(state.n_i))
ax.legend()

save_figure(fig, cfg.path / "figures/hm_missmatch.png")
save_figure(fig, cfg.path / "figures/hm_mismatch.png")


def plot_cumulative_misfit(cfg: Config, state: EnsembleState, tab20):
Expand Down Expand Up @@ -670,7 +670,7 @@ def main():
read_realisation(cfg, state, i, j)

plot_simulation_ensemble(cfg, state, tab20)
plot_hm_missmatch(cfg, state)
plot_hm_mismatch(cfg, state)
plot_misfit(cfg, state)
plot_observable_distribution(cfg, state)
plot_parameter_distributions(cfg, state)
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2 changes: 1 addition & 1 deletion tests/test_2_ert.py
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Expand Up @@ -27,5 +27,5 @@ def test_ert(tmp_path, monkeypatch):
check=True,
)
base = tmp_path / "ert" / "figures"
assert (base / "hm_missmatch.png").is_file()
assert (base / "hm_mismatch.png").is_file()
assert (base / "best_simulation" / "spatial_map_0.25h.csv").is_file()
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