From 3e295b25fa2c6bcba11735c9c7557c88a69aab5f Mon Sep 17 00:00:00 2001 From: Arun Persaud Date: Sun, 17 Nov 2024 09:07:23 -0800 Subject: [PATCH] docs: updated docs, added roadmap and more examples --- docs/source/conf.py | 2 +- docs/source/examples.md | 130 ++++++++++++++++++++++- docs/source/index.rst | 4 + examples/example_read_F1F8out.py | 2 + examples/example_read_energy_and_time.py | 1 + examples/example_read_meshtal.py | 2 +- 6 files changed, 138 insertions(+), 3 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index ab22c02..23aa0cc 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -14,7 +14,7 @@ project = 'PyMCNP' copyright = '2024, The Regents of the University of California, through Lawrence Berkeley National Laboratory ' '(subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.' -author = 'Devin Pease, Arun Persaud' +author = 'Devin Pease, Arun Persaud, Mauricio Ayllon Unzueta' # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration diff --git a/docs/source/examples.md b/docs/source/examples.md index 5e9c50f..a0e4c38 100644 --- a/docs/source/examples.md +++ b/docs/source/examples.md @@ -11,7 +11,8 @@ For examples using the command line, see the [Comand Line Interface](cli.rst). ## Loading a file, modyfing it and saving it again -We load a file and change the number of particles to 100,000. +We load a file and change the number of particles to 100,000. Here, we +use the universal `modify` function. import pymcnp @@ -22,3 +23,130 @@ We load a file and change the number of particles to 100,000. data.to_mcnp_file('/path/to/data/new_file_name.i') + +However, dor common operations, we have specific helper functions, so +the above can also be done using: + + import pymcnp + + filename = "/path/to/data/input.i' + data = pymcnp.read_input(filename) + + data = data.set_nps(100_000) + + data.to_mcnp_file('/path/to/data/new_file_name.i') + + +## Creating materials using chemical formula + +Creating a material input for water: + + water = pymcnp.inp.Material.from_formula( + 0, + {'H2O': 1}, + atomic_or_weight=True, + ) + print(water.to_mcnp()) + +Will result in: + + m0 001001 -0.1118855432927602 $ H-001 + 001002 -1.2868317335160966e-05 $ H-002 + 008016 -0.8859435015301171 $ O-016 + 008017 -0.00033747860358816377 $ O-017 + 008018 -0.0018206082561993046 $ O-018 + + +Using a combination of more complicated materials: + + clinker_concrete = pymcnp.inp.Material.from_formula( + 1, + { + 'Ca3Al2O6': 0.100, + 'Ca4Al2Fe2O10': 0.080, + 'Ca2SiO5': 0.200, + 'Ca3SiO4': 0.550, + 'Na2O': 0.010, + 'K2O': 0.010, + 'CaSO4H4O2': 0.050, + }, + atomic_or_weight=False, + ) + print(clinker_concrete.to_mcnp()) + +Will result in: + + m1 013027 0.01997201102245584 $ Al-027 + 020040 0.043137987745945364 $ Ca-040 + 020042 0.00028790994596328333 $ Ca-042 + 020043 6.007394544828941e-05 $ Ca-043 + 020044 0.0009282537052231979 $ Ca-044 + 020046 1.77996875402339e-06 $ Ca-046 + 020048 8.321353925059347e-05 $ Ca-048 + 008016 0.03544243521555091 $ O-016 + 008017 1.3500932648244581e-05 $ O-017 + ... + + +## Reading output files + +The following examples are also provided as python files in the git +repo 'example' folder. + +### F1 and F8 tallies + +To read tally data, we read in the output file. This creates a data +frame that tells us how many tallies are available. We can then load +the data of a specific one and easily plot it. + + file = "data/output_files/F1F8.o" + out = pymcnp.outp.ReadOutput(file) + print(out.get_runtime()) + + # store tally information + df_info = out.df_info + print(df_info.head(5)) + + # Based on df_info, choose desired tally + df1 = out.read_tally(n=1) + print(df1.head(5)) + + df8 = out.read_tally(n=6) + df18 = out.read_tally(n=7) + + plt.figure() + plt.plot(df1["energy"], df1["cts"], label="F1") + plt.plot(df18["energy"], df18["cts"], label="F8") + plt.plot(df8["energy"], df8["cts"], label="F8 + GEB") + plt.xlabel("Energy (MeV)") + plt.ylabel("Counts") + plt.yscale("log") + plt.legend() + plt.show() + +Creates the following image: +![F1F8 Tally plot](./images/Example-F1F8-tally.png) + + +### Energy and time + + + file = "data/output_files/png_e.o" + out = pymcnp.outp.ReadOutput(file) + + # information about tallies found + dfi = out.df_info + df_err, df = out.read_tally(n=0, mode="te") + + df5 = df.loc[1][1:] # between 0-5 MeV + df14 = df.loc[2][1:] # between 5-14 MeV + plt.figure() + plt.plot(df5.index, df5, label="0-5 MeV") + plt.plot(df14.index, df14, label="5-14 MeV") + plt.xlabel("Time (us)") + plt.ylabel("counts") + plt.legend() + plt.show() + +Creates the following image: +![Time plot](./images/Example-energy-and-time.png) diff --git a/docs/source/index.rst b/docs/source/index.rst index 63f9f70..d197f9e 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -12,6 +12,9 @@ PyMCNP allows to automate parameter scans, split long runs in many smaller runs for easy parallelization, automated optimization of parameters. +**Note: PyMCNP is still in beta and not everything is fully implemented** +See: :doc:`roadmap`. + Table of Contents ----------------- @@ -23,3 +26,4 @@ Table of Contents cli.rst pymcnp.rst examples.md + roadmap.md diff --git a/examples/example_read_F1F8out.py b/examples/example_read_F1F8out.py index 72e0725..7aa9ad0 100644 --- a/examples/example_read_F1F8out.py +++ b/examples/example_read_F1F8out.py @@ -27,4 +27,6 @@ plt.plot(df8['energy'], df8['cts'], label='F8 + GEB') plt.xlabel('Energy (MeV)') plt.ylabel('Counts') +plt.yscale('log') plt.legend() +plt.show() diff --git a/examples/example_read_energy_and_time.py b/examples/example_read_energy_and_time.py index 8bde86b..d8043bd 100644 --- a/examples/example_read_energy_and_time.py +++ b/examples/example_read_energy_and_time.py @@ -20,3 +20,4 @@ plt.xlabel('Time (us)') plt.ylabel('counts') plt.legend() +plt.show() diff --git a/examples/example_read_meshtal.py b/examples/example_read_meshtal.py index a62214e..1e0568a 100644 --- a/examples/example_read_meshtal.py +++ b/examples/example_read_meshtal.py @@ -5,7 +5,7 @@ import pymcnp import matplotlib.pyplot as plt -file_fmesh = 'data/meshtal' +file_fmesh = 'data/output_files/meshtal' df = pymcnp.outp.output.read_fmesh(file_fmesh) dfz = df[(df.Z > -1) & (df.Z < 1)] # central slice xx, mat = pymcnp.outp.output.griddata(dfz.X, dfz.Y, dfz.Result, nbins=100)