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Added some example notebooks #40

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merged 48 commits into from
Feb 22, 2025
+1,327 −332
Merged

Added some example notebooks #40

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f2e4015
adding ex012 example in notebook format.
alexmlongLANL Feb 18, 2025
907d17d
fixed bug with reading in isotope header for card 10 in the parfile
alexmlongLANL Feb 18, 2025
a01df6b
added some print statements for errors from_string that prints the ac…
alexmlongLANL Feb 18, 2025
8fe77d5
cut out print statements I added into wrong error message.
alexmlongLANL Feb 19, 2025
3f3fd8c
added repo map (not complete)
alexmlongLANL Feb 19, 2025
be1d4f8
adding notebooks.
alexmlongLANL Feb 19, 2025
b060098
deleted notebook
alexmlongLANL Feb 19, 2025
2fb392d
made fudge card optional
alexmlongLANL Feb 19, 2025
7cca3dd
updated repo.map
alexmlongLANL Feb 19, 2025
21fc928
got rid off le=1.0 for abundances in Isotope class.
alexmlongLANL Feb 19, 2025
124fb1d
modified isotope.py to not use extended format and git rid of validat…
alexmlongLANL Feb 19, 2025
472889e
added a fudge factor line
alexmlongLANL Feb 19, 2025
1b9d628
modified print_parameters function.
alexmlongLANL Feb 19, 2025
f0c01b1
modified notebook ex012a.ipynb
alexmlongLANL Feb 20, 2025
c67acab
modified notebook
alexmlongLANL Feb 21, 2025
e4fa46c
adding logger for debugging issues
alexmlongLANL Feb 21, 2025
359ab09
adding os and logger imports to parfile.py
alexmlongLANL Feb 21, 2025
d80ef6b
moved _log_and_raise_error() to logger.py
alexmlongLANL Feb 21, 2025
260c4e3
implemented logging in parfile.py for most functions.
alexmlongLANL Feb 21, 2025
dc780be
adding more logging functionality.
alexmlongLANL Feb 21, 2025
b0be537
added class and function finder.
alexmlongLANL Feb 21, 2025
d8f0420
reorged radius.py
alexmlongLANL Feb 21, 2025
32cd3c4
got rid of logger functionality to find class and function being called
alexmlongLANL Feb 21, 2025
3d8d65a
got rid of get_current_class_and_function()
alexmlongLANL Feb 22, 2025
51d2df7
using where_am_i strings for debugging
alexmlongLANL Feb 22, 2025
f505fd6
idk!
alexmlongLANL Feb 22, 2025
eba8fd9
debugging default card reading
alexmlongLANL Feb 22, 2025
e4e7ea4
fixed bug to allow RadiusCard to handle multiple RadiusParameters ent…
alexmlongLANL Feb 22, 2025
7860595
deleted example.
alexmlongLANL Feb 22, 2025
d528bc1
added attribustes in doc string of ResonanceEntry
alexmlongLANL Feb 22, 2025
d128137
finally fixed bugs in radius with printing to file!
alexmlongLANL Feb 22, 2025
e71c678
expanded print function for parameters
alexmlongLANL Feb 22, 2025
f305335
added notes on parameter libraries.
alexmlongLANL Feb 22, 2025
842af1f
updated debug to info for logging
alexmlongLANL Feb 22, 2025
b7b6bf4
added loggign
alexmlongLANL Feb 22, 2025
4294188
got rid of RadiusParametersContainer class.
alexmlongLANL Feb 22, 2025
40068a6
adding more detials to parfile_notes.md
alexmlongLANL Feb 22, 2025
c25dc03
updated notebook for example 12.
alexmlongLANL Feb 22, 2025
75f9c51
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 22, 2025
c4d7cb5
got rid of testing abundance validation, since this is no longer true…
alexmlongLANL Feb 22, 2025
b0d97d8
Fixed bug in IsotopeCard.is_header_line(). Can now identify both "ISO…
alexmlongLANL Feb 22, 2025
2599a4f
Merge branch '39-v20-examples' of github.com:lanl/PLEIADES into 39-v2…
alexmlongLANL Feb 22, 2025
1528139
adjusted functions test_radius.py for new list object for RadiusCard.
alexmlongLANL Feb 22, 2025
9cd9253
adjusted test_full_roundtrip to handle list of radiusParameters
alexmlongLANL Feb 22, 2025
fa9bd68
fixed bug in reading in parFile strings.
alexmlongLANL Feb 22, 2025
aeecdb8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 22, 2025
3b589a6
using unused variables in RadiusCardKeyword class to make overlord "p…
alexmlongLANL Feb 22, 2025
b48eed1
more making overlord happy
alexmlongLANL Feb 22, 2025
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77 changes: 77 additions & 0 deletions docs/repo.map
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@@ -0,0 +1,77 @@
PLEIADES
├── .readthedocs.yaml
├── .gitignore
├── .pre-commit-config.yaml
├── pyproject.toml
├── poetry.lock
├── LICENSE
├── environment.yaml
├── pleiades.egg-info
├── README.rst
├── src/
│ └── pleiades
| ├── __init__.py
| ├── __main__.py
| ├── utils/
| ├── data/
| | ├── cross-sections/
| | ├── isotopes/
| | └── resonances/
| ├── core/
| │ ├── transmission.py
| │ ├── constants.py
| │ ├── __init__.py
| │ ├── models.py
| │ └── data_manager.py
| └── sammy/
| ├── interface.py
| ├── config.py
| ├── __init__.py
| ├── factory.py
| ├── parfile.py
| ├── backends/
| │ ├── nova_ornl.py
| │ ├── __init__.py
| │ ├── local.py
| │ └── docker.py
| └── parameters/
| ├── unused_var.py
| ├── paramagnetic.py
| ├── orres.py
| ├── normalization.py
| ├── misc.py
| ├── helper.py
| ├── external_r.py
| ├── data_reduction.py
| ├── user_resolution.py
| ├── resonance.py
| ├── resolution.py
| ├── radius.py
| ├── last.py
| ├── det_efficiency.py
| ├── broadening.py
| ├── background.py
| ├── __init__.py
| └── isotope.py
├── examples/
├── scripts/
├── docs/
│ └── repo.map
├── legacy/
├── paper/
├── tests/
│ ├── unit/
│ │ ├── pleiades
│ │ └── conftest.py
│ └── data/
│ ├── config
│ └── ex012
└── notebook/
├── sammy.param/
│ └── example.ipynb
└── samexm/
├── ex012/
│ ├── ex012.ipynb
│ └── ex012a.par
└── ex027/
└── ex027a.endf
75 changes: 75 additions & 0 deletions notebook/samexm/ex012/ex012a.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This notebook is based on example 12 from the SAMMY repo. "
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"# Importing specific classes from the pleiades.sammy module\n",
"from pleiades.sammy.parfile import SammyParameterFile"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we want to load SAMMY parameters based on a given parameter file. "
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"# reading in SAMMY parameters from a parameter file \"./ex012a.par\"\n",
"sammy_params = SammyParameterFile.from_file(\"./ex012a.par\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Write the parameters to an output file \"ex012b.par\". "
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"sammy_params.to_file(\"./ex012b.par\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "pleiades",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.9"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
177 changes: 177 additions & 0 deletions notebook/samexm/ex012/ex012a.par
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0.1

RADIUS PARAMETERS FOLLOW
4.13642 4.13642 0-1 1 4 5
4.94372 4.94372 0-1 2 3 6 7
4.40000 4.40000 0-1 8 91011121314151617
4.20000 4.20000 0-11819202122
4.20000 4.20000 0-123242526272829

ISOTOPIC MASSES AND ABUNDANCES FOLLOW
27.976929 1.0000000 .9200 1 1 2 3 4 5 6 7
28.976496 .0467000 .0500 1 8 91011121314151617
29.973772 .0310000 .0200 11819202122
16.000000 1.0000000 .0100000 023242526272829
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2 changes: 1 addition & 1 deletion src/pleiades/core/models.py
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Expand Up @@ -178,7 +178,7 @@ class Isotope(BaseModel):
atomic_mass: Mass
thickness: NonNegativeFloat
thickness_unit: str = Field(pattern=r"^(cm|mm|atoms/cm2)$")
abundance: float = Field(ge=0.0, le=1.0)
abundance: float = Field(ge=0.0)
density: NonNegativeFloat
density_unit: str = Field(default="g/cm3", pattern=r"^g/cm3$")

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