started big cleanup
This commit is contained in:
Benoît Sierro
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include src/scgenerator/data/*
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@@ -1,3 +1,5 @@
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# THIS README IS NOT UP TO DATE
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It is recommended to import scgenerator in the following manner :
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`import scgenerator as sc`
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@@ -1,34 +0,0 @@
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\documentclass[preview]{standalone}
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\usepackage{siunitx}
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\usepackage{tikz}
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\usepackage[siunitx]{circuitikz}
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\usepackage{babel}
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\usepackage{acronym}
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\newcommand{\At}{A(z, t)}
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\newcommand{\Et}{E(z, t)}
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\newcommand{\Ew}{\tilde{E}(z, \omega)}
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\newcommand{\PNL}{\tilde{\mathrm{P}}^\mathrm{NL}}
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\begin{document}
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Complex envelope such that $|A|^2$ is in W with E in V/m~:
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\begin{equation}
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\At = \sqrt{\frac12 \epsilon_0 c n A_\mathrm{eff}} \Et
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\end{equation}
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Equations with E in V/m
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\begin{equation}
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\frac{\partial \Ew}{\partial z} = i\left(\beta(\omega) - \frac{\omega}{\nu} \right)\Ew + i \frac{\omega^2}{2c\epsilon_0 \beta(\omega)}\PNL(z, \omega)
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\end{equation}
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\begin{equation}
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\tau = t - \frac{z}{\nu}
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\,, \quad \xi = z
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\,, \quad \frac{\partial}{\partial z} = -\frac1{\nu}\frac{\partial}{\partial \tau} + \frac{\partial}{\partial \xi} = -\frac{i \omega}{\nu} + \frac{\partial}{\partial \xi}
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\,, \quad \frac{\partial}{\partial t} = \frac{\partial}{\partial \tau}
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\end{equation}
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$\Rightarrow$
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\begin{equation}
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\frac{\partial \Ew}{\partial z} = i\beta(\omega)\Ew + i \frac{\omega^2}{2c\epsilon_0 \beta(\omega)}\PNL(z, \omega)
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\end{equation}
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\end{document}
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26
pyproject.toml
Normal file
26
pyproject.toml
Normal file
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[build-system]
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requires = ["setuptools"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "scgenerator"
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version = "0.3.0"
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description = "Simulate nonlinear pulse propagation in optical fibers"
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readme = "README.md"
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authors = [{ name = "Benoit Sierro", email = "benoit.sierro@iap.unibe.ch" }]
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license = "MIT"
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classifiers = [
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"License :: OSI Approved :: MIT",
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"Programming Language :: Python :: 3",
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]
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requires-python = ">=3.10"
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keywords = ["nonlinear", "fiber optics", "simulation", "runge-kutta"]
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dependencies = ["numpy >= 1.23", "tomli", "numba", "pydantic", "tqdm"]
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[tool.ruff]
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line-length = 100
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[tool.ruff.pydocstyle]
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convention = "numpy"
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[tool.black]
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line-length = 100
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@@ -1,6 +0,0 @@
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numpy
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matplotlib
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scipy
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tomli
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tomli-w
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tqdm
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42
setup.cfg
42
setup.cfg
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[metadata]
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name = scgenerator
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version = 0.2.8dev
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description = Simulated PCFs and supercontinuum generation !
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author = Benoit Sierro
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author_email = benoit.sierro@iap.unibe.ch
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long_description = file: README.md
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long_description_content_type = text/markdown
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keywords = supercontinuum, nonlinear optics, GNLSE
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license = MIT
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classifiers =
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License :: OSI Approved :: MIT
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Programming Language :: Python :: 3
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[options]
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zip_safe = False
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include_package_data = True
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packages = find:
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package_dir =
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= src
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install_requires =
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numpy
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numba
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matplotlib
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scipy
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tomli
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tomli-w
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tqdm
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[options.package_data]
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scgenerator =
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data/hr_t.npz
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data/materials.toml
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[options.packages.find]
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where = src
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[options.entry_points]
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console_scripts =
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scgenerator = scgenerator.cli.cli:main
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sc-submit = scgenerator.scripts.slurm_submit:main
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7
setup.py
7
setup.py
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from setuptools import setup
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#!/usr/bin/env python
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setup()
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import setuptools
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if __name__ == "__main__":
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setuptools.setup()
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@@ -1,4 +0,0 @@
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from .cli import main
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if __name__ == "__main__":
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main()
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@@ -1,248 +0,0 @@
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import argparse
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import os
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import re
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from collections import ChainMap
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from pathlib import Path
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import matplotlib.pyplot as plt
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import numpy as np
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from .. import const, env, scripts, utils
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from ..logger import get_logger
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from ..physics.fiber import dispersion_coefficients
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from ..physics.simulate import SequencialSimulations, run_simulation
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try:
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import ray
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except ImportError:
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ray = None
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def set_env_variables(cmd_line_args: dict[str, str]):
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cm = ChainMap(cmd_line_args, os.environ)
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for env_key in env.global_config:
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k = env_key.replace(env.ENVIRON_KEY_BASE, "").lower()
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v = cm.get(k)
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if v is not None:
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os.environ[env_key] = str(v)
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def create_parser():
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parser = argparse.ArgumentParser(description="scgenerator command", prog="scgenerator")
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subparsers = parser.add_subparsers(help="sub-command help")
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for key, args in env.global_config.items():
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names = ["--" + key.replace(env.ENVIRON_KEY_BASE, "").replace("_", "-").lower()]
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if "short_name" in args:
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names.append(args["short_name"])
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parser.add_argument(
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*names, **{k: v for k, v in args.items() if k not in {"short_name", "type"}}
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)
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parser.add_argument("--version", action="version", version=const.__version__)
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run_parser = subparsers.add_parser("run", help="run a simulation from a config file")
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run_parser.add_argument("config", help="path(s) to the toml configuration file(s)")
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run_parser.set_defaults(func=run_sim)
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merge_parser = subparsers.add_parser("merge", help="merge simulation results")
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merge_parser.add_argument(
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"path", help="path to the final simulation folder containing 'initial_config.toml'"
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)
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merge_parser.set_defaults(func=merge)
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plot_parser = subparsers.add_parser("plot", help="generate basic plots of a simulation")
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plot_parser.add_argument(
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"sim_dir",
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help="path to the root directory of the simulation (i.e. the "
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"directory directly containing 'initial_config0.toml'",
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)
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plot_parser.add_argument(
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"spectrum_limits",
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nargs=argparse.REMAINDER,
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help="comma-separated list of left limit, right limit and unit. "
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"One plot is made for each limit set provided. Example : 600,1200,nm or -2,2,ps",
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)
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plot_parser.add_argument("--options", "-o", default=None)
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plot_parser.add_argument(
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"--show", action="store_true", help="show the plots instead of saving them"
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)
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plot_parser.set_defaults(func=plot_all)
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dispersion_parser = subparsers.add_parser(
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"dispersion", help="show the dispersion of the given config"
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)
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dispersion_parser.add_argument("config", help="path to the config file")
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dispersion_parser.add_argument(
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"--limits", "-l", default=None, type=float, nargs=2, help="left and right limits in nm"
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)
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dispersion_parser.set_defaults(func=plot_dispersion)
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init_pulse_plot_parser = subparsers.add_parser(
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"plot-spec-field", help="plot the initial field and spectrum"
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)
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init_pulse_plot_parser.add_argument("config", help="path to the config file")
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init_pulse_plot_parser.add_argument(
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"--wavelength-limits",
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"-l",
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default=None,
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type=float,
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nargs=2,
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help="left and right limits in nm",
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)
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init_pulse_plot_parser.add_argument(
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"--time-limit", "-t", default=None, type=float, help="time axis limit in fs"
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)
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init_pulse_plot_parser.set_defaults(func=plot_init_field_spec)
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init_plot_parser = subparsers.add_parser("plot-init", help="plot initial values")
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init_plot_parser.add_argument("config", help="path to the config file")
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init_plot_parser.add_argument(
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"--dispersion-limits",
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"-d",
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default=None,
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type=float,
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nargs=2,
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help="left and right limits for dispersion plots in nm",
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)
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init_plot_parser.add_argument(
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"--time-limit", "-t", default=None, type=float, help="time axis limit in fs"
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)
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init_plot_parser.add_argument(
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"--wavelength-limits",
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"-l",
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default=None,
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nargs=2,
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type=float,
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help="wavelength axis limit in nm",
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)
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init_plot_parser.set_defaults(func=plot_init)
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preview_parser = subparsers.add_parser("preview", help="preview a currently running simulation")
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plc_hld = "XX"
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preview_parser.add_argument(
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"path", help=f"path to the directory containing {const.SPEC1_FN.format(plc_hld)!r}"
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)
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preview_parser.add_argument(
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"spectrum_limits",
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nargs=argparse.REMAINDER,
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help="comma-separated list of left limit, right limit and unit. "
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"One plot is made for each limit set provided. Example : 600,1200,nm or -2,2,ps",
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)
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preview_parser.set_defaults(func=preview)
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return parser
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def main():
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parser = create_parser()
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args = parser.parse_args()
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set_env_variables({k: v for k, v in vars(args).items() if v is not None})
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args.func(args)
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logger = get_logger(__name__)
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logger.info(f"dispersion cache : {dispersion_coefficients.cache_info()}")
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def run_sim(args):
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method = prep_ray()
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run_simulation(args.config, method=method)
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# if sys.platform == "darwin" and sys.stdout.isatty():
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# subprocess.run(
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# [
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# "osascript",
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# "-e",
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# 'tell app "System Events" to display dialog "simulation finished !"',
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# ],
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# stdout=subprocess.DEVNULL,
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# stderr=subprocess.DEVNULL,
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# )
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def merge(args):
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path_trees = utils.build_path_trees(Path(args.path))
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output = env.output_path()
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if output is None:
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output = path_trees[0][-1][0].parent.name + " merged"
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utils.merge(output, path_trees)
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def preview(args):
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for path in utils.simulations_list(args.path):
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lims = args.spectrum_limits or [None, "-10,10,ps"]
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for lim in lims:
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scripts.partial_plot(path, lim)
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plt.show()
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plt.close()
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def prep_ray():
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logger = get_logger(__name__)
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if ray:
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if env.get(env.START_RAY):
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init_str = ray.init()
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elif not env.get(env.NO_RAY):
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try:
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init_str = ray.init(
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address="auto",
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_redis_password=os.environ.get("redis_password", "caco1234"),
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)
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logger.info(init_str)
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except ConnectionError as e:
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logger.warning(e)
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return SequencialSimulations if env.get(env.NO_RAY) else None
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def plot_all(args):
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opts = {}
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if args.options is not None:
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opts |= dict([o.split("=")[:2] for o in re.split("[, ]+", args.options)])
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root = Path(args.sim_dir).resolve()
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scripts.plot_all(root, args.spectrum_limits, show=args.show, **opts)
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def plot_init_field_spec(args):
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if args.wavelength_limits is None:
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l = None
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else:
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l = list(args.wavelength_limits)
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if args.time_limit is None:
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t = None
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else:
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t = [-args.time_limit, args.time_limit]
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scripts.plot_init_field_spec(args.config, t, l)
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def plot_init(args):
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if args.wavelength_limits is None:
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l = None
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else:
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l = list(args.wavelength_limits)
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if args.dispersion_limits is None:
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d = None
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else:
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d = list(args.dispersion_limits)
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if args.time_limit is None:
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t = None
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else:
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t = [-args.time_limit, args.time_limit]
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scripts.plot_init(args.config, t, l, d)
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def plot_dispersion(args):
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if args.limits is None:
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lims = None
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else:
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lims = 1e-9 * np.array(args.limits, dtype=float)
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scripts.plot_dispersion(args.config, lims)
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if __name__ == "__main__":
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main()
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