Merge pull request #23 from fusion-energy/develop

reproducing basic plots

.github/workflows/ci.yml

@@ -0,0 +1,32 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    container:
+      image: openmc/openmc:v0.13.1
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: install package
+        run: |
+          pip install .
+          python -c "import openmc_depletion_plotter"
+      - name: run examples
+        run: |
+          python examples/plot_activity_vs_time.py
+          python examples/plot_isotope_charts.py
+          python examples/plot_multiple_isotope_charts.py
+          python examples/plot_pulse_schedule.py
+      - name: run tests
+        run: |
+          pip install .[tests]
+          pytest tests -v

README.md

@@ -1,2 +1,55 @@
-# openmc_depletion_plotter
-Plot the atoms present during depletion steps on an isotope chart.
+Extends OpenMC to provides convienent plotting methods.
+This is done by Monkey Patching OpenMC to provide additional functionality to the base classes.
+One benefit of this is the user can continue to work with the familiar OpenMC classes and they simply get additional functionality.
+Another benefit is that if any of these functions ever become popular enough to include in OpenMC then it could be done with a simple copy paste into the existing class structure.
+Plotly figures or MatPlotLib figures are returned for user customization.
+
+# Plotting pulse schedule
+
+All the Integrator classes have been extended to include a ```.plot_pulse_schedule()``` method.
+
+This method plots the source rate as a function of time.
+
+This is useful when wanting to visually display a pulse schedule used in an depletion / activation study.
+
+Additional methods provided
+
+```python
+openmc.deplete.PredictorIntegrator.plot_pulse_schedule()
+openmc.deplete.CECMIntegrator.plot_pulse_schedule()
+openmc.deplete.CF4Integrator.plot_pulse_schedule()
+openmc.deplete.CELIIntegrator.plot_pulse_schedule()
+openmc.deplete.EPCRK4Integrator.plot_pulse_schedule()
+openmc.deplete.LEQIIntegrator.plot_pulse_schedule()
+openmc.deplete.SICELIIntegrator.plot_pulse_schedule()
+openmc.deplete.SILEQIIntegrator.plot_pulse_schedule()
+```
+
+# Plotting activation or atoms as a function of time
+
+The ```openmc.deplete.Results()``` class has been extended to include a ```plot_atoms_vs_time()``` method and a ```plot_activity_vs_time``` method.
+
+These methods plot atoms or activity as a function of time.
+These plots optionally include a breakdown of the dominant nuclides.
+
+Additional methods provided
+
+```python
+openmc.deplete.Results.plot_atoms_vs_time()
+openmc.deplete.Results.plot_activity_vs_time()
+```
+
+# Plotting activation or atoms on an isotope chart
+
+The ```openmc.Material()``` class has been extended to include a ```plot_isotope_chart_of_activity()``` method and  ```plot_isotope_chart_of_atoms()``` method.
+
+This method plots the material atoms or the material activity on an isotope chart.
+
+I started making isotope plots back in 2010 so nice to finally distribute this :smile:
+
+Additional methods provided
+
+```python
+openmc.Material.plot_isotope_chart_of_atoms()
+openmc.Material.plot_isotope_chart_of_activity()
+```

examples/plot_activity_vs_time.py

@@ -0,0 +1,35 @@
+import openmc
+import openmc.deplete
+import openmc_depletion_plotter
+from pathlib import Path
+
+
+output_dir = "/home/jshimwell/activation_example/outputs_Aluminum_maintenance"
+results = openmc.deplete.Results.from_hdf5(Path(output_dir) / "depletion_results.h5")
+
+# plot = results.plot_activity_vs_time()
+# plot.show()
+plot = results.plot_atoms_vs_time()
+plot.show()
+
+
+# def load_data(output_dir, time_units="d"):
+
+#     results = openmc.deplete.Results.from_hdf5(Path(output_dir) / "depletion_results.h5")
+#     time_steps = results.get_times(time_units=time_units)
+
+#     unirradiated_material = openmc.Summary(str(Path(output_dir) / "summary.h5")).materials[0]
+
+#     all_materials = []
+#     for counter, step in enumerate(time_steps):
+#         materials = results.export_to_materials(counter)[
+#             0
+#         ]  # zero index as one material in problem
+#         all_materials.append(materials)
+#     openmc_materials = openmc.Materials(all_materials)
+
+#     return openmc_materials, time_steps, unirradiated_material
+
+# openmc_materials, time_steps, unirradiated_material = load_data("/home/jshimwell/activation_example/outputs_Aluminum_maintenance")
+
+# openmc_materials[0].plot_isotope_atom_chart()

examples/plot_isotope_charts.py

@@ -0,0 +1,26 @@
+import openmc
+import openmc_depletion_plotter  # adds plotting methods to the material class
+
+my_mat = openmc.Material()
+my_mat.add_element("Fe", 1)
+my_mat.add_element("Li", 0.5)
+my_mat.add_element("Be", 0.5)
+my_mat.add_element("Al", 0.5)
+my_mat.add_element("B", 0.5)
+my_mat.add_element("Co", 0.5)
+my_mat.add_element("Cs", 0.5)
+my_mat.add_nuclide("Fe60", 0.1)
+my_mat.add_nuclide("Fe61", 0.2)
+my_mat.add_nuclide("Fe62", 0.3)
+my_mat.set_density("g/cm3", 7.7)
+my_mat.volume = 1
+
+plotly_figure = my_mat.plot_isotope_chart_of_activity(my_mat)
+plotly_figure.write_html("my_mat_activity_on_isotope_chart.html")
+plotly_figure.write_image("my_mat_activity_on_isotope_chart.png")
+plotly_figure.show()
+
+plotly_figure_2 = my_mat.plot_isotope_chart_of_atoms(my_mat)
+plotly_figure_2.write_html("my_mat_atoms_on_isotope_chart.html")
+plotly_figure_2.write_image("my_mat_atoms_on_isotope_chart.png")
+plotly_figure_2.show()

examples/plot_multiple_isotope_charts.py

@@ -0,0 +1,26 @@
+import openmc
+import openmc_depletion_plotter  # adds plotting methods to the material class
+
+my_mat = openmc.Material()
+my_mat.add_element("Fe", 1)
+my_mat.add_element("Li", 0.5)
+my_mat.add_element("Be", 0.5)
+my_mat.add_element("Al", 0.5)
+my_mat.add_element("B", 0.5)
+my_mat.add_element("Co", 0.5)
+my_mat.set_density("g/cm3", 7.7)
+my_mat.volume = 1
+
+my_mat_2 = openmc.Material()
+my_mat_2.add_element("Fe", 1)
+my_mat_2.add_element("Li", 0.5)
+my_mat_2.add_element("C", 0.5)
+my_mat_2.add_element("Al", 0.5)
+my_mat_2.add_element("Ni", 0.5)
+my_mat_2.add_element("Co", 0.5)
+my_mat_2.set_density("g/cm3", 7.7)
+my_mat_2.volume = 1
+
+for mat, filename in zip([my_mat, my_mat_2], ["my_mat_1.png", "my_mat_2.png"]):
+    plotly_figure = mat.plot_isotope_chart_of_atoms()
+    plotly_figure.write_image(filename)

examples/plot_pulse_schedule.py

@@ -1,13 +1,12 @@
-
 import openmc
 import openmc.deplete
-from openmc_depletion_plotter import IntegratorWithPlotting  # class extends openmc depletion classes
+import openmc_depletion_plotter
 import matplotlib.pyplot as plt
 
 
 # a minimal material is needed to pass to the model
 material = openmc.Material()
-material.add_nuclide('Fe59', 1)
+material.add_nuclide("Fe59", 1)
 material.volume = 100
 material.depletable = True
 materials = openmc.Materials([material])
@@ -18,21 +17,20 @@
 
 # a minimal operator is needed to pass to the integrator
 operator = openmc.deplete.Operator(
-        model=model,
-        chain_file="chain-nndc-b7.1.xml",
-        normalization_mode="source-rate"
-    )
+    model=model, chain_file="chain-nndc-b7.1.xml", normalization_mode="source-rate"
+)
 
 
 # arbitrary lists provided here, but this would be defined by the the pulse schedule (maintenance, waste, single shot)
 source_rates = [1e21] + [0] * 24  # single pulse followed by 0 neutrons
-time_steps = [1] + [3600] * 24   # one second followed by 1 hour periods for 24 hours
+time_steps = [1] + [3600] * 24  # one second followed by 1 hour periods for 24 hours
 
-integrator = IntegratorWithPlotting(
+integrator = openmc.deplete.PredictorIntegrator(
     operator=operator,
     timesteps=time_steps,
     source_rates=source_rates,
-    timestep_units='d',
+    timestep_units="d",
 )
-integrator.plot()
-plt.savefig('pulse_single_shot.png')
+integrator.plot_pulse_schedule()
+plt.savefig("pulse_single_shot.png")
+plt.show()

openmc_depletion_plotter/__init__.py

@@ -13,11 +13,11 @@
 
 __all__ = ["__version__"]
 
-from .core import plot_isotope_chart_of_atoms
-from .core import plot_isotope_chart_of_activity
-from .core import plot_activity_vs_time
-from .core import plot_specific_activity_vs_time
-from .core import plot_atoms_vs_time
+# from .core import plot_isotope_chart_of_atoms
+# from .core import plot_isotope_chart_of_activity
+# from .core import plot_activity_vs_time
+# from .core import plot_specific_activity_vs_time
+# from .core import plot_atoms_vs_time
 from .utils import get_atoms_activity_from_material
 from .utils import find_most_abundant_nuclides_in_material
 from .utils import find_most_abundant_nuclides_in_materials
@@ -32,4 +32,7 @@
 from .utils import update_axis_range_full_chart
 from .utils import add_scale_buttons
 
-from .integrators import IntegratorWithPlotting
+
+from .materials import *
+from .integrators import *
+from .results import *