ascl_id stringclasses 752
values | repo_url stringclasses 737
values | file_path stringlengths 4 194 | content large_stringlengths 1 1M | language stringclasses 29
values | license_type stringclasses 24
values | size int64 1 1M |
|---|---|---|---|---|---|---|
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/conf.py | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup ------------------------------------------------------------... | Python | MIT | 5,545 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/index.rst | RascalC: Fast Estimation of Galaxy Covariance Matrices
=======================================================
Overview
----------
RascalC is a code to quickly estimate covariance matrices for two- or three-point galaxy correlation functions, written in C++ and Python.
Given an input set of random particle locations ... | reStructuredText | MIT | 3,116 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/requirements.txt | recommonmark
sphinx-rtd-theme
graphviz
git+https://github.com/cosmodesi/pycorr
sphinxext-rediraffe | Text | MIT | 102 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/main-code.rst | Covariance Matrix Estimation
=============================
**NB**: This documentation page is about the legacy/command-line usage. We believe it is much easier to learn the Python library, please see its :doc:`../library/fundamentals` and :doc:`../library/installation`.
Overview
----------
This is the main section o... | reStructuredText | MIT | 18,282 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/tutorial_periodic.rst | Tutorial: Periodic Data and Legendre Multipoles
================================================
We present a basic example of the use of the RascalC code on a periodic dataset, such as the output of an N-body simulation. Here we'll restrict to a single-field analysis (using only a single set of tracer galaxies), but ... | reStructuredText | MIT | 12,762 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/geometry-correction.rst | Computing Random Counts and Survey Correction Functions
========================================================
Here, we describe the scripts provided to compute RR and RRR random counts, in addition to the *survey correction functions*, defined as the ratio of ideal to true RR (RRR) counts for the 2PCF (3PCF). The R... | reStructuredText | MIT | 11,162 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/installation.rst | Installation
============
**NB**: This documentation page is about the legacy/command-line usage. We believe it is much easier to learn the Python library, please see its :doc:`../library/fundamentals` and :doc:`../library/installation`.
To install RascalC, simply clone the Github repository and compile the C++ code ... | reStructuredText | MIT | 2,386 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/tutorial.rst | Tutorial: Aperiodic Data and Jackknives
=======================================
**NB**: This tutorial has been adapted as a Jupyter notebook (:root:`tutorial.ipynb`) using the newer RascalC Python library and we believe it is more user-friendly this way.
We present a basic example of the use of the RascalC code for a... | reStructuredText | MIT | 15,600 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/getting-started.rst | Getting Started
================
**NB**: This documentation page is about the legacy/command-line usage. We believe it is much easier to learn the Python library, please see its :doc:`../library/fundamentals` and :doc:`../library/installation`.
RascalC computes covariance matrix estimates from a given correlation fun... | reStructuredText | MIT | 12,257 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/pre-processing.rst | Pre-Processing
===============
We provide a suite of Python scripts to create input files for the RascalC code. These are found in the ``scripts/`` directory.
.. _coord-conversion:
Coordinate Conversion
----------------------
This converts a set of input particles (either random particle or galaxy positions) in the ... | reStructuredText | MIT | 4,417 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/post-processing.rst | Post-Processing & Reconstruction
=================================
These scripts post-process the single- or multi-field integrals computed by the C++ code described in :doc:`main-code`. For the DEFAULT, LEGENDRE and 3PCF modes, the output covariance matrix products (as well as precision matrices and effective number ... | reStructuredText | MIT | 11,714 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/correlation-functions.rst |
Correlation Functions
=======================
The scripts described below are wrappers of the `Corrfunc <https://corrfunc.readthedocs.io>`_ code (Sinha & Garrison 2017), used to create full-survey and jackknife correlation functions. The former are used in the computation of the Gaussian covariance matrices, and the ... | reStructuredText | MIT | 14,426 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/legacy/jackknife-weights.rst | Computing Jackknife Weights
=============================
**NB**: This is *only* required when running the RascalC code in the JACKKNIFE mode.
Here, we compute the weights assigned to each jackknife region for each bin. This is done using the `Corrfunc <https://corrfunc.readthedocs.io>`_ code of Sinha & Garrison to c... | reStructuredText | MIT | 4,837 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/library/tutorials-examples.rst | Practical examples
==================
Tutorials
---------
- Aperiodic data (realistic survey geometry) with jackknife shot-noise tuning: :root:`tutorial.ipynb`
- Uses a BOSS DR12 FastPM mock
- This tutorial is also available as scripts (which seem more practical to run) in :root:`tutorial/`. `The Jupyter not... | reStructuredText | MIT | 1,529 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/library/fundamentals.rst | Fundamentals
============
Introduction
------------
Here we strive to provide a practical summary.
We also recommend reading a theoretical overview of the RascalC methodology in Sections 2.1 and 3 of `Rashkovetskyi et al 2025 <https://arxiv.org/abs/2404.03007>`_, or Section 2.2 of `Rashkovetskyi 2025 dissertation <ht... | reStructuredText | MIT | 31,914 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/library/installation.rst | Package installation
====================
.. highlight:: bash
Simplified way for DESI members at NERSC
----------------------------------------
Recommended to use with `cosmodesi` environment.
In particular, load it before installing::
source /global/common/software/desi/users/adematti/cosmodesi_environment.sh ... | reStructuredText | MIT | 2,901 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | docs/library/advanced-functions.rst | Advanced functions
==================
This list is not complete, but aims to provide references for the more used/useful extended features.
Covariance comparison functions
-------------------------------
.. automodule:: RascalC.cov_comparison
:members:
:member-order: bysource
Extra convergence check funct... | reStructuredText | MIT | 1,772 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | ransampl/ransampl.h | /*
* Library: ransampl (random number sampling)
*
* File: ransampl.h
*
* Contents: Random-number sampling using the Walker-Vose alias method
*
* Copyright: Joachim Wuttke, Forschungszentrum Juelich GmbH (2013)
*
* License: see ../COPYING (FreeBSD)
*
* Homepage: apps.jcns.fz-juelich.de/ransampl
*... | C/C++ Header | MIT | 883 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | ransampl/ransampl.c | /*
* Library: ransampl (random number sampling)
*
* File: ransampl.c
*
* Contents: Random-number sampling using the Walker-Vose alias method,
* as described by Keith Schwarz (2011)
* [http://www.keithschwarz.com/darts-dice-coins]
*
* Copyright: Joachim Wuttke, Forschungszentrum Ju... | C | MIT | 3,014 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | cubature/vwrapper.h | /* vectorized wrapper around non-vectorized integrands */
typedef struct fv_data_s { integrand f; void *fdata; } fv_data;
static int fv(unsigned ndim, size_t npt,
const double *x, void *d_,
unsigned fdim, double *fval)
{
fv_data *d = (fv_data *) d_;
integrand f = d->f;
void *fdata = d->fdat... | C/C++ Header | MIT | 513 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | cubature/cubature.h | /* Adaptive multidimensional integration of a vector of integrands.
*
* Copyright (c) 2005-2013 Steven G. Johnson
*
* Portions (see comments) based on HIntLib (also distributed under
* the GNU GPL, v2 or later), copyright (c) 2002-2005 Rudolf Schuerer.
* (http://www.cosy.sbg.ac.at/~rschuer/hintlib/)
*
* Por... | C/C++ Header | MIT | 5,337 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | cubature/converged.h | /* Body of convergence test, shared between hcubature.c and
pcubature.c. We use an #include file because the two routines use
somewhat different data structures, and define macros ERR(j) and
VAL(j) to get the error and value estimates, respectively, for
integrand j. */
{
unsigned j;
# define SQR(x)... | C/C++ Header | MIT | 2,399 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | cubature/hcubature.c | /* Adaptive multidimensional integration of a vector of integrands.
*
* Copyright (c) 2005-2013 Steven G. Johnson
*
* Portions (see comments) based on HIntLib (also distributed under
* the GNU GPL, v2 or later), copyright (c) 2002-2005 Rudolf Schuerer.
* (http://www.cosy.sbg.ac.at/~rschuer/hintlib/)
*
* Por... | C | MIT | 34,031 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | power_spectra/power_mod/kernel_interp.h | // kernel_interp.h - Interpolator for kernel functions for power spectrum computation
#ifndef KERNEL_INTERP_H
#define KERNEL_INTERP_H
class KernelInterp{
// Compute a interpolation kernel function
private:
Float R0, k_min, k_max;
public:
int npoint=100000;
Float min_val,max_val;
double *sep, *ker... | C/C++ Header | MIT | 7,236 |
[ascl:1909.008] | https://github.com/oliverphilcox/RascalC | power_spectra/power_mod/survey_correction_legendre.h | // survey_correction_legendre.h - This contains utility functions for computing Legendre moments etc
// NB: This is a trivial function (unity for ell=0) if we have periodic boundary conditions
#ifndef SURVEY_CORRECTION_LEGENDRE_H
#define SURVEY_CORRECTION_LEGENDRE_H
class SurveyCorrection{
// this class stores th... | C/C++ Header | MIT | 5,395 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Rassine_multiprocessed.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri May 17 10:41:21 2019
@author: cretignier
"""
from __future__ import print_function
import getopt
import glob as glob
import multiprocessing as multicpu
import os
import platform
import sys
import threading
import numpy as np
import pandas as pd
from... | Python | null | 12,119 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Rassine_trigger.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 22 11:50:04 2019
@author: cretignier
"""
from __future__ import print_function
import matplotlib
matplotlib.use('Qt5Agg',force=True)
import getopt
import glob as glob
import os
import sys
import matplotlib.pylab as plt
import numpy as np
import ... | Python | null | 6,446 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Rassine.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
r"""
Created on Thu Feb 7 16:34:29 2019
19.04.19
@author: michael cretignier & jémémie francfort
# =====================================================================================
# Rolling Alpha Shape for a Spectral Improved Normalisation Estimator (RASSINE)
# ====... | Python | null | 82,499 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | CONTRIBUTING.md | RASSINE is for the moment able to read HARPS/HARPN/CORALIE/ESPRESSO 1d fits spectra before to convert them in a pickle format with the preprocessing function.
If a user is using another instrument, I will be very happy to include their preprocessing into the main code.
| Markdown | null | 272 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | README.md | # RASSINE
<p align="center">
<img src="logo.png" alt="Project logo" width="750">
</p>
# Contact Me
If you have any problem, please contact me at:
michael.cretignier@physics.ox.ac.uk
# Description
————————
NEWS :
————————
For a Python version below 3.7, replace the five codes with the ones stored in the Python<... | Markdown | null | 5,383 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Rassine_functions.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 7 16:34:29 2019
@author: cretignier
"""
from __future__ import print_function
import matplotlib
matplotlib.use('Qt5Agg',force=True)
import glob as glob
import multiprocessing as multicpu
import os
import pickle
import platform
import sys
#from ... | Python | null | 74,827 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Rassine_config.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
r"""
Created on Thu Feb 7 16:34:29 2019
19.04.19
@author: michael cretignier & jémémie francfort
# =====================================================================================
# Rolling Alpha Shape for a Spectral Improved Normalisation Estimator (RASSINE)
# ====... | Python | null | 5,924 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python<3.7/Rassine_config.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
r"""
Created on Thu Feb 7 16:34:29 2019
19.04.19
@author: michael cretignier & jémémie francfort
# =====================================================================================
# Rolling Alpha Shape for a Spectral Improved Normalisation Estimator (RASSINE)
# ====... | Python | null | 5,926 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python<3.7/Rassine_trigger.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 22 11:50:04 2019
@author: cretignier
"""
from __future__ import print_function
import matplotlib
matplotlib.use('Qt5Agg',force=True)
import getopt
import glob as glob
import os
import sys
import matplotlib.pylab as plt
import numpy as np
import ... | Python | null | 6,284 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python<3.7/Rassine_multiprocessed.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri May 17 10:41:21 2019
@author: cretignier
"""
from __future__ import print_function
import multiprocessing as multicpu
import os
import numpy as np
import threading
import pandas as pd
import getopt
import sys
import glob as glob
from Rassine_functions... | Python | null | 8,375 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python<3.7/Rassine_functions.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 7 16:34:29 2019
@author: cretignier
"""
from __future__ import print_function
import matplotlib
matplotlib.use('Qt5Agg',force=True)
import glob as glob
import multiprocessing as multicpu
import os
import pickle
import sys
#from tqdm import tqdm... | Python | null | 70,445 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python<3.7/Rassine.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
r"""
Created on Thu Feb 7 16:34:29 2019
19.04.19
@author: michael cretignier & jémémie francfort
# =====================================================================================
# Rolling Alpha Shape for a Spectral Improved Normalisation Estimator (RASSINE)
# ====... | Python | null | 82,449 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python_3.8/Rassine_multiprocessed.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri May 17 10:41:21 2019
@author: cretignier
"""
from __future__ import print_function
import getopt
import glob as glob
import multiprocessing as multicpu
import os
import platform
import sys
import threading
import numpy as np
import pandas as pd
from... | Python | null | 12,119 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python_3.8/Rassine_trigger.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 22 11:50:04 2019
@author: cretignier
"""
from __future__ import print_function
import matplotlib
matplotlib.use('Qt5Agg',force=True)
import getopt
import glob as glob
import os
import sys
import matplotlib.pylab as plt
import numpy as np
import ... | Python | null | 6,446 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python_3.8/Rassine_functions.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 7 16:34:29 2019
@author: cretignier
"""
from __future__ import print_function
import matplotlib
matplotlib.use('Qt5Agg',force=True)
import glob as glob
import multiprocessing as multicpu
import os
import pickle
import platform
import sys
#from ... | Python | null | 74,825 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python_3.8/Rassine_config.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
r"""
Created on Thu Feb 7 16:34:29 2019
19.04.19
@author: michael cretignier & jémémie francfort
# =====================================================================================
# Rolling Alpha Shape for a Spectral Improved Normalisation Estimator (RASSINE)
# ====... | Python | null | 5,924 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python_3.8/README.txt | The multiprocessing seems to be broken with the old version of the files since Python 3.8 producing a typical error :
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork ... | Text | null | 777 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | Python_3.8/Rassine.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
r"""
Created on Thu Feb 7 16:34:29 2019
19.04.19
@author: michael cretignier & jémémie francfort
# =====================================================================================
# Rolling Alpha Shape for a Spectral Improved Normalisation Estimator (RASSINE)
# ====... | Python | null | 82,499 |
[ascl:2102.022] | https://github.com/MichaelCretignier/Rassine_public | .github/ISSUE_TEMPLATE/bug_report.md | ---
name: Bug report
about: Create a report to help us improve
title: ''
labels: ''
assignees: ''
---
**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error
**Expected behavior... | Markdown | null | 834 |
[ascl:1904.014] | https://github.com/pcubillos/rate | README.md | # rate:
## Reliable Analytic Thermochemical Equilibrium
This code computes thermochemical-equilibrium abundances for a H-C-N-O system with known pressure, temperature, and elemental abundances. The output abundances are H2O, CH4, CO, CO2, NH3, C2H2, C2H4, HCN, and N2, H2, H, and He.
These calculations are valid over... | Markdown | MIT | 3,998 |
[ascl:1904.014] | https://github.com/pcubillos/rate | rate/VERSION.py | # Copyright (c) 2018-2019 Patricio Cubillos and contributors.
# rate is open-source software under the MIT license (see LICENSE).
# rate version:
rate_VER = 1 # Major version
rate_MIN = 0 # Minor version
rate_REV = 0 # Revision
| Python | MIT | 235 |
[ascl:1904.014] | https://github.com/pcubillos/rate | rate/__init__.py | # Copyright (c) 2018-2019 Patricio Cubillos and contributors.
# rate is open-source software under the MIT license (see LICENSE).
from . import VERSION as ver
from .rate import *
from .rate import __all__
__version__ = "{:d}.{:d}.{:d}".format(ver.rate_VER,
ver.rate_MIN, ver.rate_... | Python | MIT | 636 |
[ascl:1904.014] | https://github.com/pcubillos/rate | rate/rate.py | # Copyright (c) 2018-2019 Patricio Cubillos and contributors.
# rate is open-source software under the MIT license (see LICENSE).
__all__ = ["gRT", "newton_raphson", "bound_nr", "top", "Rate"]
import os
import numpy as np
import scipy.constants as sc
import scipy.interpolate as si
rootdir = os.path.realpath(os.pa... | Python | MIT | 27,366 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/C2H4_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 252.466 58.194
200 222.975 55.542
250 220.011 54.002
298.15 219.330 52.467
300 219.331 52.408 ... | Text | MIT | 3,577 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/C2H2_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 234.338 227.078
200 204.720 226.911
298.15 200.958 226.731
300 200.959 226.728
400 202.774 226.527 ... | Text | MIT | 3,412 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/H2_ref.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 155.408 0.
200 133.284 0.
250 131.152 0.
298.15 130.680 0.
300 130.680 0. ... | Text | MIT | 3,577 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/H_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 133.197 216.614
200 116.618 217.346
250 115.059 217.687
298.15 114.716 217.999
300 114.717 218.011 ... | Text | MIT | 3,577 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/CO_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 223.539 -112.415
200 200.317 -111.286
298.15 197.653 -110.527
300 197.653 -110.516
400 198.798 -110.102 ... | Text | MIT | 3,412 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/N2_ref.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 217.490 0.
200 194.272 0.
250 192.088 0.
298.15 191.609 0.
300 191.610 0. ... | Text | MIT | 3,577 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/CO2_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 243.568 -393.208
200 217.046 -393.404
298.15 213.795 -393.522
300 213.795 -393.523
400 215.307 -393.583 ... | Text | MIT | 3,412 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/CH4_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 216.485 -69.644
200 189.418 -72.027
250 186.829 -73.426
298.15 186.251 -74.873
300 186.252 -74.929 ... | Text | MIT | 3,577 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/NH3_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 223.211 -41.550
200 195.962 -43.703
298.15 192.774 -45.898
300 192.775 -45.939
400 194.209 -48.041 ... | Text | MIT | 3,412 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/HCN_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 230.911 135.422
200 204.966 135.306
298.15 201.828 135.143
300 201.829 135.140
400 203.281 134.972 ... | Text | MIT | 3,412 |
[ascl:1904.014] | https://github.com/pcubillos/rate | inputs/H2O_g.txt | # T (K) -[G-H(Tr)]/T (J/K/mol) delta-f H (kJ/mol)
100 218.534 -240.083
200 191.896 -240.900
298.15 188.834 -241.826
300 188.835 -241.844
400 190.159 -242.846 ... | Text | MIT | 3,412 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | CHANGELOG.md | # Changelog
All notable changes **following the 1.0.0 release** of *Rayleigh* will be documented in this file. Changes in 1.0.0 and prior versions are summarized. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
with the addition of author(s), date of change and optionally the relevant... | Markdown | Unknown | 16,824 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | README.md |
# Rayleigh - dynamo in spherical geometry #
[](https://github.com/geodynamics/Rayleigh/blob/main/LICENSE)
[](https://doi.org/10.5281/zenodo.11391213)
[ equations, in a rotating frame, within spherical shells,
using the anelastic or Boussinesq approximations.
Derivatives in Rayleigh are calculated using a spectral transform scheme.
Spherical ha... | reStructuredText | Unknown | 947 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | CMakeLists.txt | #
# Copyright (C) 2024 by the authors of the RAYLEIGH code.
#
# This file is part of RAYLEIGH.
#
# RAYLEIGH is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3, or (at your option)
# any lat... | Text | Unknown | 2,377 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | .readthedocs.yaml | # .readthedocs.yml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
# Required
version: 2
#Use Mamba instead of Conda to avoid running into memory limits (recommended by ReadtheDocs)
build:
os: "ubuntu-20.04"
tools:
python: "mambaforge-4.10"
# Bui... | YAML | Unknown | 539 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | environment_doc.yml | # Rayleigh documentation environment.
#
# If you change this file make sure to also update
# environment.yml.
name: radoc
channels:
- conda-forge
dependencies:
- python=3.9
- matplotlib=3.4
- jupyter=1.0
- scipy=1.10
- sphinx=4.0
- sphinxcontrib-bibtex=2.2
- nbsphinx=0.8
- pandoc=3.2
- recommonmark... | YAML | Unknown | 376 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | conf.py | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup --------------------------------------------------------------
# If extensions (or module... | Python | Unknown | 6,297 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | .zenodo.json | {
"creators": [
{
"name": "Nicholas Featherstone",
"affiliation": "University of Colorado",
"orcid": "0000-0002-2256-5884"
}
]
}
| JSON | Unknown | 154 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | CONTRIBUTING.md | # Contributing to Rayleigh
Rayleigh is a community project that lives by the participation of its
members — i.e., including you! It is our goal to build an inclusive
and participatory community so we are happy that you are interested in
participating!
## Getting started with git and GitHub
GitHub provides a helpful
g... | Markdown | Unknown | 5,954 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | pre_processing/rayleigh_spectral_input.py | #!/usr/bin/env python3
#
# Copyright (C) 2018 by the authors of the RAYLEIGH code.
#
# This file is part of RAYLEIGH.
#
# RAYLEIGH is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3, or (at... | Python | Unknown | 41,307 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/main_input_class/jobinfo.txt |
===========================================================================
Job Information
===========================================================================
Date = 2021-08-25
Time = 15:55:51
Path =
===========================================================================
Compiler Information
=========... | Text | Unknown | 11,707 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/main_input_class/main_input_demo.ipynb | {
"cells": [
{
"cell_type": "markdown",
"id": "0d34e892",
"metadata": {},
"source": [
"# The Main_Input Class \n",
"\n",
"This notebook demonstrates how to use the main_input class. The main_input class was developed primarily to assist with parameter-space studies, but it may be useful in ... | Jupyter Notebook | Unknown | 12,054 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/custom_thermal_profile/custom_thermal_profile.ipynb | {
"cells": [
{
"cell_type": "markdown",
"id": "edca7fc5",
"metadata": {},
"source": [
"### Custom Thermal Profile Creation\n",
"\n",
"While Rayleigh can define an initial, conductive thermal profile based on the details of internal heating and boundary conditions, alternative ell=0 initial pr... | Jupyter Notebook | Unknown | 5,852 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/ultraspherical_polynomials/Scalar_Diffusion.ipynb | {
"cells": [
{
"cell_type": "markdown",
"id": "be00a73f",
"metadata": {},
"source": [
"Let's solve the scalar diffusion equation on $(t,x)\\in[0,\\infty)\\times[-1,1]$,\n",
"\n",
"$$\\partial_t q(t,x) - \\nu \\partial_{xx} q(t,x) = 0.$$\n",
"\n",
"Starting with a constant $\\nu$, usin... | Jupyter Notebook | Unknown | 19,984 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/ultraspherical_polynomials/Reaction_Diffusion.ipynb | {
"cells": [
{
"cell_type": "markdown",
"id": "be00a73f",
"metadata": {},
"source": [
"Let's solve the scalar Newell–Whitehead-Segel reaction-diffusion equation on $(t,x)\\in[0,\\infty)\\times[-1,1]$,\n",
"\n",
"$$\\partial_t q(t,x) - \\nu(x) \\partial_{xx} q(t,x) - \\partial_x\\nu(x)\\partia... | Jupyter Notebook | Unknown | 12,090 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/custom_reference_states/mesa.py | import numpy as np
G = 6.67428e-8 # dyne cm^2 / g^2
clight = 2.9979246e+10 # cm / s
arad = 7.5657e-15 # erg cm^-3 K^-4
msol = 1.9891e+33 # g
rsol = 6.9598e10 # cm
kb = 1.3806503e-16 # g cm^2 / K s^2
Na = 6.022142e+23 # 1 / mol
Rgas = 83144621.0 # erg / mol K
solarlum = 3.846e33 # erg / s
umass = 1.660538921e-24 # g
hp... | Python | Unknown | 1,480 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/custom_reference_states/Boussinesq_CZ.ipynb | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Custom reference state for a non-dimensional Boussinesq MHD setup in a convective spherical shell "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Custom reference state for a Boussinesq convective s... | Jupyter Notebook | Unknown | 9,978 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/custom_reference_states/Anelastic_Dim_CZ.ipynb | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Custom reference state for the dimensional anelastic MHD formulation in a convective spherical shell based on polytropes"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Problem Setup\n",
"\n"... | Jupyter Notebook | Unknown | 15,428 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/custom_reference_states/Anelastic_NonDim_CZ.ipynb | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Custom reference state for non-dimensional anelastic MHD formulation in a convective spherical shell\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We non-dimensionalize the dimensional anelastic... | Jupyter Notebook | Unknown | 21,077 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/custom_reference_states/Boussinesq_Dynamo_Viscous.ipynb | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Boussinesq dynamo: nondimensionalized using viscous timescale"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"'''\n",
"\n",
"This code provides an ex... | Jupyter Notebook | Unknown | 5,672 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | examples/custom_reference_states/MESA-input-1Msun-ZAMS.ipynb | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# An example for custom reference states from MESA\n",
"\n",
"This script will take a MESA stellar evolution profile and convert it into a format that can be read in as a custom reference state in Rayleigh. You will need the `r... | Jupyter Notebook | Unknown | 10,099 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/CMakeLists.txt | #
# Copyright (C) 2024 by the authors of the RAYLEIGH code.
#
# This file is part of RAYLEIGH.
#
# RAYLEIGH is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3, or (at your option)
# any lat... | Text | Unknown | 2,073 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/build_menu_pdf.py | #
# Copyright (C) 2018 by the authors of the RAYLEIGH code.
#
# This file is part of RAYLEIGH.
#
# RAYLEIGH is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3, or (at your option)
# any lat... | Python | Unknown | 8,643 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/video_gallery.rst | .. raw:: latex
\clearpage
.. |nbspc| unicode:: U+00A0 .. non-breaking space
.. ADDING YOUR VIDEOS
.. Embed YouTube videos changing the width to 30% and deleting the height
.. Follow the format below creating a unique alias for your video
.. |Feathern1| raw:: html
<iframe width="30%" src="https://www.youtub... | reStructuredText | Unknown | 1,377 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/research_projects.rst | Research Projects
*****************
Under construction.
One of the research projects using Rayleigh: https://geodynamics.org/groups/dynamo/frontiers.
| reStructuredText | Unknown | 152 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/citing_rayleigh.rst | .. _citing_rayleigh:
Citing Rayleigh
===============
We ask that you cite the appropriate references if you publish results that were obtained in some
part using Rayleigh. Receiving citations for Rayleigh is important to demonstrate the relevance of our work to our funding agencies and is a matter of fairness to all... | reStructuredText | Unknown | 7,098 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/getting_help.rst | Getting Help
============
For questions on the source code of Rayleigh, portability, installation, new or existing features, etc., use the `Rayleigh forum <https://community.geodynamics.org/c/rayleigh/5>`_. This is also the place where we announce our regular user calls. For a more direct contact you can also join our... | reStructuredText | Unknown | 434 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/accessing_and_sharing_data.rst | Accessing and Sharing Model Data
***********************************
Accessing Available Datasets
----------------------------
Rayleigh model configurations and checkpoint data of several publications can be accessed here:
- https://osf.io/j275z/
- https://osf.io/qbt32/
- https://doi.org/10.5281/zenodo.7117668
A la... | reStructuredText | Unknown | 891 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/research_enabled_by_rayleigh.rst | Research Enabled by Rayleigh
********************
.. toctree::
:maxdepth: 1
research_projects
video_gallery
images/image_gallery
publications/publications
| reStructuredText | Unknown | 172 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/quick_reference.rst | Quick Reference
********************
.. toctree::
:maxdepth: 1
Namelist_Definitions/Namelist_Variables.rst
diagnostic_codes/qcodes
| reStructuredText | Unknown | 142 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/images/image_gallery.rst |
Image Gallery
=============
.. figure:: fig7_hindman2020.jpg
:width: 85%
:align: center
Radial velocity profiles near the top of shell for stellar-like convection that is sufficiently supercritical :cite:`Hindman_2020`
.. figure:: fig3_Duer_2023.jpg
:width: 85%
:align: center
Zonal velocity near t... | reStructuredText | Unknown | 1,373 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/transport_namelist.txt | **{nu,kappa,eta}_type**
Determines the radial profile of the associated diffusion coefficient.
* type 1 : no radial variation
* type 2 : diffusivity profile varies as :math:`\rho^{n}` for some real number *n*.
* type 3 : diffusivity profile is read from a custom-reference-state file
**{nu,kappa,eta}_top*... | Text | Unknown | 1,590 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/physical_controls_namelist.txt | **magnetism**
When set to .true., the MHD approximation is employed. The default (magnetism=.false.) is to omit the effects of magnetism.
**nonlinear**
When set to .false., all nonlinear terms are omitted in the model. The default (nonlinear=.true.) is to include those terms.
**momentum_advection**
... | Text | Unknown | 2,669 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/problemsize_namelist.txt | **n_r**
Number of radial points in model grid
**rmin**
Radius of the inner domain boundary, :math:`r_\mathrm{min}`
**rmax**
Radius of the outer domain boundary, :math:`r_\mathrm{max}`
**aspect_ratio**
:math:`{r_\mathrm{min}}/{r_\mathrm{max}}`
**shell_depth**
:math:`r_\mathrm{max}-r_\mathrm{min}`
**... | Text | Unknown | 2,640 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/reference_namelist.txt | **reference_type**
Determines the fluid approximation and background state used by Rayleigh.
* type 1: Boussinesq + nondimensional
* type 2: Anelastic + polytropic background state (dimensional)
* type 3: Anelastic + polytropic background state (non-dimensional)
* type 4: Custom reference-state (read ... | Text | Unknown | 4,296 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/initial_conditions_namelist.txt | **init_type**
Integer value indicating how nonmagnetic variables should be initialized.
* type -1: Restart from a checkpoint
* type 1: Hydro Boussinesq benchmark init (Christensen et al. 2001). The temperature field is initialized with an :math:`\ell=4` , m=4 perturbation on top of a conductive profile. ... | Text | Unknown | 3,438 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/Namelist_Variables.rst |
.. _namelists:
Input parameters
==============================================
This page provides a quick reference for all supported namelist variables in the main_input file.
Problemsize
-------------------------
This namelist is used to specify the grid.
.. include:: ../Namelist_Definitions/problemsize_nameli... | reStructuredText | Unknown | 2,168 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/boundary_conditions_namelist.txt | **fix_tvar_top**
Logical flag indicating whether thermal variable (T,S) should be fixed on the upper boundary. Default = .false.
**fix_tvar_bottom**
Logical flag indicating whether thermal variable (T,S) should be fixed on the lower boundary. Default = .false.
**fix_dtdr_top**
Logical flag indicating whethe... | Text | Unknown | 3,393 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/temporal_controls_namelist.txt | **alpha_implicit**
Determines the value of :math:`\alpha` used in the Crank-Nicolson semi-implicit time-stepping scheme employed for linear terms. The default value is 0.5, which ensures second-order accuracy of the algorithm. A value of 1 (0) describes a fully implicit (explicit) algorithm.
**max_iterations**
... | Text | Unknown | 3,445 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | doc/source/Namelist_Definitions/io_controls_namelist.txt | **stdout_file**
If desired, set this variable to the name of a file to which Rayleigh's text output is redirected. This can be useful for monitoring run progress and time-step size on systems that otherwise don't produce the text output until a run has complete. The default value is 'nofile,' which indicates that ... | Text | Unknown | 2,114 |
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