diff --git a/burnman/__init__.py b/burnman/__init__.py index 5373e9201..64d707380 100644 --- a/burnman/__init__.py +++ b/burnman/__init__.py @@ -98,7 +98,7 @@ 2. Clone the BurnMan repository ``git clone https://github.com/geodynamics/burnman.git`` 3. Go to the Burnman examples directory and type: ``python example_beginner.py`` -Figures should show up, indicating that it is working. + Figures should show up, indicating that it is working. Install on a Mac @@ -114,7 +114,7 @@ 4. Install the latest Sympy from http://sourceforge.net/projects/sympy/files/ 5. Install the latest Matplotlib from http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.1.1/ 6. Clone the BurnMan repository ``git clone https://github.com/geodynamics/burnman.git`` -7. Go to the Burnman examples directory and type `python example_beginner.py` +7. Go to the Burnman examples directory and type ``python example_beginner.py`` Figures should show up, indicating that it is working. Install under Windows @@ -140,11 +140,12 @@ - Cottaar, S., Heister, T., Myhill, R., Rose, I., and Unterborn, C. (2017): BurnMan v0.10.0 [Software]. Computational Infrastructure for Geodynamics. Zenodo. - `(link) `_ + `(https://doi.org/10.5281/zenodo.546210) `_ - Cottaar S., Heister, T., Rose, I., and Unterborn, C., 2014, BurnMan: A lower mantle mineral physics toolkit, Geochemistry, Geophysics, and - Geosystems, 15(4), 1164-1179 `(link) `_ + Geosystems, 15(4), 1164-1179 `(https://doi.org/10.1002/2013GC005122) + `_ Contributing to BurnMan ----------------------- diff --git a/burnman/minerals/DKS_2013_liquids.py b/burnman/minerals/DKS_2013_liquids.py index 086f5b9a5..b6313b254 100644 --- a/burnman/minerals/DKS_2013_liquids.py +++ b/burnman/minerals/DKS_2013_liquids.py @@ -3,8 +3,10 @@ # Released under GPL v2 or later. """ -DKS_2013 -Liquids from de Koker and Stixrude (2013) FPMD simulations +DKS_2013_liquids +^^^^^^^^^^^^^^^^ + +Liquids from de Koker and Stixrude (2013) FPMD simulations. """ from ..mineral import Mineral diff --git a/burnman/minerals/DKS_2013_solids.py b/burnman/minerals/DKS_2013_solids.py index 94411e709..8a4546b99 100644 --- a/burnman/minerals/DKS_2013_solids.py +++ b/burnman/minerals/DKS_2013_solids.py @@ -4,6 +4,8 @@ """ DKS_2013_solids +^^^^^^^^^^^^^^^ + Solids from de Koker and Stixrude (2013) FPMD simulations """ diff --git a/burnman/minerals/HHPH_2013.py b/burnman/minerals/HHPH_2013.py index 2c8ca14a7..caddcf283 100644 --- a/burnman/minerals/HHPH_2013.py +++ b/burnman/minerals/HHPH_2013.py @@ -5,10 +5,12 @@ """ HHPH_2013 -Minerals from Holland et al 2013 and references therein +^^^^^^^^^ + +Minerals from Holland et al. (2013) and references therein. The values in this document are all in S.I. units, -unlike those in the original paper -File autogenerated using HHPHdata_to_burnman.py +unlike those in the original paper. +File autogenerated using HHPHdata_to_burnman.py. """ from __future__ import absolute_import diff --git a/burnman/minerals/HP_2011_ds62.py b/burnman/minerals/HP_2011_ds62.py index 94f0136c1..657c73f0c 100644 --- a/burnman/minerals/HP_2011_ds62.py +++ b/burnman/minerals/HP_2011_ds62.py @@ -5,11 +5,13 @@ """ HP_2011 (ds-62) -Endmember minerals from Holland and Powell 2011 and references therein -Update to dataset version 6.2 +^^^^^^^^^^^^^^^ + +Endmember minerals from Holland and Powell 2011 and references therein. +Update to dataset version 6.2. The values in this document are all in S.I. units, -unlike those in the original tc-ds62.txt -File autogenerated using HPdata_to_burnman.py +unlike those in the original tc-ds62.txt. +File autogenerated using HPdata_to_burnman.py. """ from ..mineral import Mineral diff --git a/burnman/minerals/HP_2011_fluids.py b/burnman/minerals/HP_2011_fluids.py index 6c5e49786..60bbe3d56 100644 --- a/burnman/minerals/HP_2011_fluids.py +++ b/burnman/minerals/HP_2011_fluids.py @@ -6,28 +6,38 @@ """ HP_2011_fluids -^^^^^^^^ +^^^^^^^^^^^^^^ Fluids from Holland and Powell 2011 and references therein. -CORK parameters: -CHO gases from Holland and Powell, 1991. ["CO2",304.2,0.0738],["CH4",190.6,0.0460],["H2",41.2,0.0211],["CO",132.9,0.0350] -H2O and S2 from Wikipedia, 2012/10/23. ["H2O",647.096,0.22060],["S2",1314.00,0.21000] -H2S from ancyclopedia.airliquide.com, 2012/10/23. ["H2S",373.15,0.08937] - -NB: Units for cork[i] in Holland and Powell datasets are -a = kJ^2/kbar*K^(1/2)/mol^2 -> multiply by 1e-2 -b = kJ/kbar/mol -> multiply by 1e-5 -c = kJ/kbar^1.5/mol -> multiply by 1e-9 -d = kJ/kbar^2/mol -> multiply by 1e-13 - -Individual terms are divided through by P, P, P^1.5, P^2, so -[0][j] -> multiply by 1e6 -[1][j] -> multiply by 1e3 -[2][j] -> multiply by 1e3 -[3][j] -> multiply by 1e3 - -cork_P: kbar -> multiply by 1e8 +CORK parameters are taken from various sources. + +CHO gases from Holland and Powell, 1991: + - ["CO2",304.2,0.0738] + - ["CH4",190.6,0.0460] + - ["H2",41.2,0.0211] + - ["CO",132.9,0.0350] + +H2O and S2 from Wikipedia, 2012/10/23: + - ["H2O",647.096,0.22060] + - ["S2",1314.00,0.21000] + +H2S from ancyclopedia.airliquide.com, 2012/10/23: + - ["H2S",373.15,0.08937] + +NB: Units for cork[i] in Holland and Powell datasets are: + - a = kJ^2/kbar*K^(1/2)/mol^2: multiply by 1e-2 + - b = kJ/kbar/mol: multiply by 1e-5 + - c = kJ/kbar^1.5/mol: multiply by 1e-9 + - d = kJ/kbar^2/mol: multiply by 1e-13 + +Individual terms are divided through by P, P, P^1.5, P^2, so: + - [0][j]: multiply by 1e6 + - [1][j]: multiply by 1e3 + - [2][j]: multiply by 1e3 + - [3][j]: multiply by 1e3 + - cork_P is given in kbar: multiply by 1e8 """ + from __future__ import absolute_import from ..mineral import Mineral diff --git a/burnman/minerals/JH_2015.py b/burnman/minerals/JH_2015.py index 0767527de..3022655c3 100644 --- a/burnman/minerals/JH_2015.py +++ b/burnman/minerals/JH_2015.py @@ -5,6 +5,8 @@ """ JH_2015 +^^^^^^^ + Solid solutions from Jennings and Holland, 2015 and references therein (10.1093/petrology/egv020). The values in this document are all in S.I. units, diff --git a/burnman/minerals/RS_2014_liquids.py b/burnman/minerals/RS_2014_liquids.py index f1ccd8a4e..edee7bdf2 100644 --- a/burnman/minerals/RS_2014_liquids.py +++ b/burnman/minerals/RS_2014_liquids.py @@ -3,8 +3,10 @@ # Released under GPL v2 or later. """ -RS_2014 -Liquids from Ramo and Stixrude (2014) FPMD simulations +RS_2014_liquids +^^^^^^^^^^^^^^^ + +Liquids from Ramo and Stixrude (2014) FPMD simulations. There are some typos in the article which have been corrected where marked with the help of David Munoz Ramo. """ diff --git a/burnman/minerals/SLB_2011.py b/burnman/minerals/SLB_2011.py index 81bb3f97e..e6039b5cf 100644 --- a/burnman/minerals/SLB_2011.py +++ b/burnman/minerals/SLB_2011.py @@ -5,8 +5,10 @@ """ SLB_2011 -Minerals from Stixrude & Lithgow-Bertelloni 2011 and references therein -File autogenerated using SLBdata_to_burnman.py +^^^^^^^^ + +Minerals from Stixrude & Lithgow-Bertelloni 2011 and references therein. +File autogenerated using SLBdata_to_burnman.py. """ from __future__ import absolute_import diff --git a/burnman/tools.py b/burnman/tools.py index 37d0bf44e..76b257f3e 100644 --- a/burnman/tools.py +++ b/burnman/tools.py @@ -882,9 +882,6 @@ def compare_l2(depth, calc, obs): """ Computes the L2 norm for N profiles at a time (assumed to be linear between points). - .. math:: math does not work yet... - \sum_{i=1}^{\\infty} x_{i} - :type depths: array of float :param depths: depths. :math:`[m]` :type calc: list of arrays of float diff --git a/sphinx/api.rst b/sphinx/api.rst index e7308cfea..cb966f0c0 100644 --- a/sphinx/api.rst +++ b/sphinx/api.rst @@ -3,7 +3,6 @@ Autogenerated Full API .. toctree:: - main materials eos solution_models diff --git a/sphinx/averaging.rst b/sphinx/averaging.rst index 5aca3cc44..90c0988e6 100644 --- a/sphinx/averaging.rst +++ b/sphinx/averaging.rst @@ -1,38 +1,44 @@ Averaging Schemes ================= -Given a set of mineral physics parameters and an equation of state we can calculate the density, bulk, and shear modulus for a given phase. -However, as soon as we have a composite material (e.g., a rock), the determination of elastic properties become more complicated. -The bulk and shear modulus of a rock are dependent on the specific geometry of the grains in the rock, so there is no general -formula for its averaged elastic properties. Instead, we must choose from a number of averaging schemes if we want a single value, -or use bounding methods to get a range of possible values. The module :mod:`burnman.averaging_schemes` provides a number of different +Given a set of mineral physics parameters and an equation of state we can calculate the density, bulk, and shear modulus for a given phase. +However, as soon as we have a composite material (e.g., a rock), the determination of elastic properties become more complicated. +The bulk and shear modulus of a rock are dependent on the specific geometry of the grains in the rock, so there is no general +formula for its averaged elastic properties. Instead, we must choose from a number of averaging schemes if we want a single value, +or use bounding methods to get a range of possible values. The module :mod:`burnman.averaging_schemes` provides a number of different average and bounding schemes for determining a composite rock's physical parameters. Base class ----------- + .. autoclass:: burnman.averaging_schemes.AveragingScheme Voigt bound ----------- + .. autoclass:: burnman.averaging_schemes.Voigt Reuss bound ----------- + .. autoclass:: burnman.averaging_schemes.Reuss Voigt-Reuss-Hill average ------------------------ + .. autoclass:: burnman.averaging_schemes.VoigtReussHill Hashin-Shtrikman upper bound ---------------------------- + .. autoclass:: burnman.averaging_schemes.HashinShtrikmanUpper Hashin-Shtrikman lower bound ---------------------------- + .. autoclass:: burnman.averaging_schemes.HashinShtrikmanLower Hashin-Shtrikman arithmetic average ----------------------------------- -.. autoclass:: burnman.averaging_schemes.HashinShtrikmanAverage +.. autoclass:: burnman.averaging_schemes.HashinShtrikmanAverage diff --git a/sphinx/composites.rst b/sphinx/composites.rst index 14d289d07..5c05de494 100644 --- a/sphinx/composites.rst +++ b/sphinx/composites.rst @@ -5,4 +5,3 @@ Base class ---------- .. autoclass:: burnman.composite.Composite - diff --git a/sphinx/conf.py b/sphinx/conf.py index 8d3761c7b..cca71e59d 100644 --- a/sphinx/conf.py +++ b/sphinx/conf.py @@ -1,45 +1,56 @@ -# -*- coding: utf-8 -*- +# Configuration file for the Sphinx documentation builder. # -# BurnMan documentation build configuration file, created by -# sphinx-quickstart on Mon Apr 21 16:47:58 2014. -# -# This file is execfile()d with the current directory set to its containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html -import sys -import os +# -- Path setup -------------------------------------------------------------- +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import os +import sys sys.path.insert(0, os.path.abspath('..')) +sys.path.insert(0, os.path.abspath('../examples')) + import burnman import burnman.version -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# sys.path.insert(0, os.path.abspath('.')) +# -- Project information ----------------------------------------------------- -# -- General configuration ----------------------------------------------- +project = 'BurnMan' +copyright = '2021, Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn' +author = 'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn' -# If your documentation needs a minimal Sphinx version, state it here. -# needs_sphinx = '1.0' +# The short X.Y version. +version = burnman.version.short_version +# The full version, including alpha/beta/rc tags +release = burnman.__version__ + + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary', + 'sphinx.ext.mathjax', 'numpydoc', 'sphinx.ext.intersphinx', + 'sphinx.ext.ifconfig', 'sphinx.ext.inheritance_diagram', + 'sphinx.ext.viewcode', 'sphinxcontrib.bibtex'] +bibtex_bibfiles = ['ref.bib'] -# Add any Sphinx extension module names here, as strings. They can be extensions -# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = [ - 'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.mathjax', - 'numpydoc', 'sphinx.ext.intersphinx', 'sphinx.ext.ifconfig', 'sphinx.ext.inheritance_diagram', - 'sphinx.ext.viewcode', 'sphinxcontrib.bibtex'] numpydoc_show_class_members = False -autodoc_default_flags = [ - 'members', 'undoc-members', 'show-inheritance', 'inherited-members'] +autodoc_default_options = {'members': True, + 'undoc-members': True, + 'show-inheritance': True, + 'inherited-members': True} + autodoc_member_order = 'bysource' + # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] @@ -52,42 +63,10 @@ # The master toctree document. master_doc = 'index' -# General information about the project. -project = u'BurnMan' -copyright = u'2014, Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = burnman.version.short_version -# The full version, including alpha/beta/rc tags. -release = burnman.__version__ - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build'] - -# The reST default role (used for this markup: `text`) to use for all documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. @@ -99,87 +78,21 @@ # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] - -# -- Options for HTML output --------------------------------------------- +# -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'default' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = None +# +html_theme = 'alabaster' -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None +# Output file base name for HTML help builder. +htmlhelp_basename = 'BurnMandoc' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -# html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = 'BurnMandoc' - - # -- Options for LaTeX output -------------------------------------------- preamble1 = ''' @@ -191,7 +104,12 @@ \newcommand{\burnman}{\texttt{\bf BurnMan}} -\renewcommand{\maketitle}{ + ''' + +latex_maketitle = r''' +\begin{titlepage} + +{ \definecolor{dark_grey}{gray}{0.3} \definecolor{aspect_blue}{rgb}{0.9,0.35,0.3} @@ -277,25 +195,31 @@ \pagebreak } - ''' +\end{titlepage} +''' + +language='en' + +latex_logo='burnjack-small.png' latex_elements = { + 'sphinxsetup': '', + 'passoptionstopackages': r'\PassOptionsToPackage{table}{xcolor}', # The paper size ('letterpaper' or 'a4paper'). 'papersize': 'letterpaper', - 'babel': '\usepackage[english]{babel}', # The font size ('10pt', '11pt' or '12pt'). 'pointsize': '11pt', - 'classoptions': ',openany', - 'preamble': preamble + 'preamble': preamble, + 'maketitle': latex_maketitle } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('index_pdf', 'BurnMan.tex', u'BurnMan Documentation', - u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn', 'manual'), + ('index_pdf', 'BurnMan.tex', u'BurnMan Documentation', author, 'manual'), ] + # The name of an image file (relative to this directory) to place at the top of # the title page. # latex_logo = None @@ -322,8 +246,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - ('index', 'burnman', u'BurnMan Documentation', - [u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn'], 1) + ('index', 'burnman', u'BurnMan Documentation', [author], 1) ] # If true, show URL addresses after external links. @@ -337,7 +260,7 @@ # dir menu entry, description, category) texinfo_documents = [ ('index', 'BurnMan', u'BurnMan Documentation', - u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn', 'BurnMan', 'One line description of project.', + author, 'BurnMan', 'One line description of project.', 'Miscellaneous'), ] @@ -350,6 +273,5 @@ # How to display URL addresses: 'footnote', 'no', or 'inline'. # texinfo_show_urls = 'footnote' - # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/sphinx/eos.rst b/sphinx/eos.rst index 03979a131..71eed5fb8 100644 --- a/sphinx/eos.rst +++ b/sphinx/eos.rst @@ -30,7 +30,7 @@ Reciprocal K-prime ------------------ .. autoclass:: burnman.eos.RKprime - + Stixrude and Lithgow-Bertelloni Formulation ------------------------------------------- @@ -69,4 +69,3 @@ Anderson and Ahrens (1994) CoRK ---- .. autoclass:: burnman.eos.CORK - diff --git a/sphinx/examples.rst b/sphinx/examples.rst index 38b363e52..dabd12403 100644 --- a/sphinx/examples.rst +++ b/sphinx/examples.rst @@ -63,7 +63,7 @@ The following is a list of simple examples: .. image:: figures/example_seismic2.png -.. automodule:: examples.example_composition +.. automodule:: examples.example_composition *Resulting figure:* @@ -93,31 +93,36 @@ Advanced examples: - :mod:`~examples.example_compare_all_methods`. .. automodule:: examples.example_spintransition + *Resulting figure:* .. image:: figures/example_spintransition.png - + .. automodule:: examples.example_user_input_material .. automodule:: examples.example_optimize_pv + *Resulting figure:* .. image:: figures/example_opt_pv.png .. automodule:: examples.example_build_planet + *Resulting figure:* .. image:: figures/example_build_planet.png -.. automodule:: examples.example_compare_all_methods +.. automodule:: examples.example_compare_all_methods + *Resulting figure:* .. image:: figures/example_compare_all_methods.png .. automodule:: examples.example_anisotropy + *Resulting figure:* .. image:: figures/example_anisotropy.png @@ -126,6 +131,7 @@ Advanced examples: .. automodule:: examples.example_fit_data + *Resulting figures:* .. image:: figures/example_fit_data1.png @@ -137,24 +143,25 @@ Advanced examples: .. automodule:: examples.example_fit_eos + *Last seven resulting figures:* .. image:: figures/example_fit_eos11.png - + .. image:: figures/example_fit_eos12.png .. image:: figures/example_fit_eos13.png .. image:: figures/example_fit_eos14.png - + .. image:: figures/example_fit_eos15.png .. image:: figures/example_fit_eos16.png .. image:: figures/example_fit_eos17.png - + .. _ref-example-paper: Reproducing Cottaar, Heister, Rose and Unterborn (2014) @@ -184,7 +191,6 @@ figures in the 2014 BurnMan paper: Cottaar, Heister, Rose & Unterborn (2014) :ci Misc or work in progress ======================== - -.. automodule:: examples.example_grid -.. automodule:: examples.example_woutput +.. automodule:: examples.example_grid +.. automodule:: examples.example_woutput diff --git a/sphinx/geotherms.rst b/sphinx/geotherms.rst index cbb67d7eb..486105f6a 100644 --- a/sphinx/geotherms.rst +++ b/sphinx/geotherms.rst @@ -3,6 +3,3 @@ Geotherms ========= .. automodule:: burnman.geotherm - :members: - :undoc-members: - diff --git a/sphinx/index.rst b/sphinx/index.rst index 52c167e24..553202ea3 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,5 +1,5 @@ .. BurnMan documentation master file, created by - sphinx-quickstart on Mon Apr 21 16:47:58 2014. + sphinx-quickstart on Sun Aug 1 20:20:43 2021. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. @@ -8,64 +8,64 @@ BurnMan: a thermodynamic and geophysics toolkit for the Earth and planetary scie .. image:: burnjack-bar.png - + BurnMan is a Python library for computing the thermodynamic and thermoelastic properties of geological materials from simple mineral endmembers to complex multilayered planetary interiors. BurnMan is released under the GNU GPL v2 or newer. It relies heavily on numpy, scipy, and matplotlib. - - Homepage: http://burnman.org - - Documentation: http://burnman.readthedocs.io - - Source code: https://github.com/geodynamics/burnman + - Homepage: http://burnman.org + - Documentation: http://burnman.readthedocs.io + - Source code: https://github.com/geodynamics/burnman If you haven't yet installed BurnMan, you can go straight to :ref:`ref-installation` for detailed instructions. After that, you might want to try out our :ref:`ref-example-tutorial` or the other :ref:`ref-examples`. Finally, and most importantly, have fun! - + Citing BurnMan -------------- If you use BurnMan in your work, we ask that you cite the following publications: - - Cottaar, S., Heister, T., Myhill, R., Rose, I., and Unterborn, C. (2017): - BurnMan v0.10.0 [Software]. Computational Infrastructure for Geodynamics. Zenodo. - `(link) `_ + - Cottaar, S., Heister, T., Myhill, R., Rose, I., and Unterborn, C. (2017): + BurnMan v0.10.0 [Software]. Computational Infrastructure for Geodynamics. Zenodo. + `(https://doi.org/10.5281/zenodo.546210) `_ - - Cottaar S., Heister, T., Rose, I., and Unterborn, C., 2014, BurnMan: A - lower mantle mineral physics toolkit, Geochemistry, Geophysics, and - Geosystems, 15(4), 1164-1179 `(link) `_ + - Cottaar S., Heister, T., Rose, I., and Unterborn, C., 2014, BurnMan: A + lower mantle mineral physics toolkit, Geochemistry, Geophysics, and + Geosystems, 15(4), 1164-1179 `(https://doi.org/10.1002/2013GC005122) `_ -Contributing to BurnMan +Contributing to BurnMan ----------------------- -We welcome the submission of scripts used to create published results. If you +We welcome the submission of scripts used to create published results. If you have any scripts that you would like to contribute, please contact us at info@burnman.org or make a pull request at `https://github.com/geodynamics/burnman `_ Acknowledgement and Support --------------------------- - - This project was initiated at, and follow-up research support was received - through, Cooperative Institute of Deep Earth Research, CIDER (NSF FESD - grant 1135452) -- see `www.deep-earth.org `_ + - This project was initiated at, and follow-up research support was received + through, Cooperative Institute of Deep Earth Research, CIDER (NSF FESD + grant 1135452) -- see `www.deep-earth.org `_ + + - We thank all the members of the CIDER Mg/Si team for their input: + Valentina Magni, Yu Huang, JiaChao Liu, Marc Hirschmann, and Barbara + Romanowicz. We also thank Lars Stixrude for providing benchmarking calculations + and Zack Geballe, Motohiko Murakami, Bill McDonough, Quentin Williams, + Wendy Panero, and Wolfgang Bangerth for helpful discussions. + + - We thank CIG (`www.geodynamics.org `_) for support + and accepting our donation of BurnMan as an official project. - - We thank all the members of the CIDER Mg/Si team for their input: - Valentina Magni, Yu Huang, JiaChao Liu, Marc Hirschmann, and Barbara - Romanowicz. We also thank Lars Stixrude for providing benchmarking calculations - and Zack Geballe, Motohiko Murakami, Bill McDonough, Quentin Williams, - Wendy Panero, and Wolfgang Bangerth for helpful discussions. - - We thank CIG (`www.geodynamics.org `_) for support - and accepting our donation of BurnMan as an official project. - - .. toctree:: - :maxdepth: 4 - - introduction - background - tutorial - examples - api - zreferences + :maxdepth: 4 + + introduction + background + tutorial + examples + api + zreferences diff --git a/sphinx/main.rst b/sphinx/main.rst deleted file mode 100644 index a87d3a14b..000000000 --- a/sphinx/main.rst +++ /dev/null @@ -1,4 +0,0 @@ -Main module -=========== - -.. automodule:: burnman.main diff --git a/sphinx/materials.rst b/sphinx/materials.rst index fdc9210df..859fd9d7c 100644 --- a/sphinx/materials.rst +++ b/sphinx/materials.rst @@ -13,9 +13,8 @@ Material Base Class .. autoclass:: burnman.material.Material - -PerpleX Class -------------- +Perple_X Class +-------------- .. autoclass:: burnman.perplex.PerplexMaterial @@ -41,4 +40,3 @@ Composites ---------- .. autoclass:: burnman.composite.Composite - diff --git a/sphinx/mineral_database.rst b/sphinx/mineral_database.rst index 5ec618247..2959a2db8 100644 --- a/sphinx/mineral_database.rst +++ b/sphinx/mineral_database.rst @@ -1,19 +1,47 @@ -Mineral database ----------------- +Mineral databases +----------------- .. automodule:: burnman.minerals - -.. automodule:: burnman.minerals.Murakami_2013 - :no-inherited-members: -.. automodule:: burnman.minerals.SLB_2011 :no-inherited-members: + .. automodule:: burnman.minerals.Matas_etal_2007 :no-inherited-members: + .. automodule:: burnman.minerals.Murakami_etal_2012 :no-inherited-members: + +.. automodule:: burnman.minerals.Murakami_2013 + :no-inherited-members: + .. automodule:: burnman.minerals.SLB_2005 :no-inherited-members: + +.. automodule:: burnman.minerals.SLB_2011 + :no-inherited-members: + .. automodule:: burnman.minerals.SLB_2011_ZSB_2013 :no-inherited-members: + +.. automodule:: burnman.minerals.DKS_2013_solids + :no-inherited-members: + +.. automodule:: burnman.minerals.DKS_2013_liquids + :no-inherited-members: + +.. automodule:: burnman.minerals.RS_2014_liquids + :no-inherited-members: + +.. automodule:: burnman.minerals.HP_2011_ds62 + :no-inherited-members: + +.. automodule:: burnman.minerals.HP_2011_fluids + :no-inherited-members: + +.. automodule:: burnman.minerals.HHPH_2013 + :no-inherited-members: + +.. automodule:: burnman.minerals.JH_2015 + :no-inherited-members: + .. automodule:: burnman.minerals.other :no-inherited-members: diff --git a/sphinx/ref.bib b/sphinx/ref.bib index 24097fd52..2ed8d0a4b 100644 --- a/sphinx/ref.bib +++ b/sphinx/ref.bib @@ -51,16 +51,16 @@ @article{Trampert2004 } @article{Lin2007, -author = {Lin, Jung-Fu and Vankó, György and Jacobsen, Steven D. and Iota, Valentin and Struzhkin, Viktor V. and Prakapenka, Vitali B. and Kuznetsov, Alexei and Yoo, Choong-Shik}, +author = {Lin, Jung-Fu and Vankó, György and Jacobsen, Steven D. and Iota, Valentin and Struzhkin, Viktor V. and Prakapenka, Vitali B. and Kuznetsov, Alexei and Yoo, Choong-Shik}, title = {{Spin transition zone in Earth's lower mantle}}, -volume = {317}, -number = {5845}, -pages = {1740--1743}, -year = {2007}, -abstract ={Mineral properties in Earth's lower mantle are affected by iron electronic states, but representative pressures and temperatures have not yet been probed. Spin states of iron in lower-mantle ferropericlase have been measured up to 95 gigapascals and 2000 kelvin with x-ray emission in a laser-heated diamond cell. A gradual spin transition of iron occurs over a pressure-temperature range extending from about 1000 kilometers in depth and 1900 kelvin to 2200 kilometers and 2300 kelvin in the lower mantle. Because low-spin ferropericlase exhibits higher density and faster sound velocities relative to the high-spin ferropericlase, the observed increase in low-spin (Mg,Fe)O at mid-lower mantle conditions would manifest seismically as a lower-mantle spin transition zone characterized by a steeper-than-normal density gradient.}, -URL = {http://www.sciencemag.org/content/317/5845/1740.abstract}, -eprint = {http://www.sciencemag.org/content/317/5845/1740.full.pdf}, -journal = {Science} +volume = {317}, +number = {5845}, +pages = {1740--1743}, +year = {2007}, +abstract ={Mineral properties in Earth's lower mantle are affected by iron electronic states, but representative pressures and temperatures have not yet been probed. Spin states of iron in lower-mantle ferropericlase have been measured up to 95 gigapascals and 2000 kelvin with x-ray emission in a laser-heated diamond cell. A gradual spin transition of iron occurs over a pressure-temperature range extending from about 1000 kilometers in depth and 1900 kelvin to 2200 kilometers and 2300 kelvin in the lower mantle. Because low-spin ferropericlase exhibits higher density and faster sound velocities relative to the high-spin ferropericlase, the observed increase in low-spin (Mg,Fe)O at mid-lower mantle conditions would manifest seismically as a lower-mantle spin transition zone characterized by a steeper-than-normal density gradient.}, +URL = {http://www.sciencemag.org/content/317/5845/1740.abstract}, +eprint = {http://www.sciencemag.org/content/317/5845/1740.full.pdf}, +journal = {Science} } @article{Brown1981, @@ -74,14 +74,14 @@ @article{Brown1981 year = {1981} } @article{anderson1982earth, -author = {Anderson, O. L.}, +author = {Anderson, O. L.}, title = "{The Earth's Core and the Phase Diagram of Iron}", -volume = {306}, -number = {1492}, -pages = {21--35}, -year = {1982}, -URL = {http://rsta.royalsocietypublishing.org/content/306/1492/21.abstract}, -journal = {Philos. T. Roy. Soc. A} +volume = {306}, +number = {1492}, +pages = {21--35}, +year = {1982}, +URL = {http://rsta.royalsocietypublishing.org/content/306/1492/21.abstract}, +journal = {Philos. T. Roy. Soc. A} } @article{Murakami2012, author = {Murakami, M and Ohishi, Y and Hirao, N and Hirose, K}, @@ -444,13 +444,7 @@ @article{Watson2007 issn = "0012-821X", doi = "https://doi.org/10.1016/j.epsl.2006.11.015", url = "http://www.sciencedirect.com/science/article/pii/S0012821X06008168", -author = "E. Bruce Watson and Ethan F. Baxter", -keywords = "diffusion", -keywords = "solid Earth", -keywords = "chemical transport", -keywords = "thermochronology", -keywords = "geochronology", -keywords = "diffusive closure " +author = "E. Bruce Watson and Ethan F. Baxter" } @article{Deschamps2012, author = {Deschamps, F and Cobden, L and Tackley, PJ}, @@ -679,35 +673,35 @@ @article{Ita1992 } @article{PH1999, -author = {Powell, Roger and Holland, Tim}, +author = {Powell, Roger and Holland, Tim}, title = {Relating formulations of the thermodynamics of mineral solid solutions; activity modeling of pyroxenes, amphiboles, and micas}, -volume = {84}, -number = {1-2}, -pages = {1-14}, +volume = {84}, +number = {1-2}, +pages = {1-14}, year = {1999}, -URL = {http://ammin.geoscienceworld.org/content/84/1-2/1.abstract}, -eprint = {http://ammin.geoscienceworld.org/content/84/1-2/1.full.pdf+html}, -journal = {American Mineralogist} +URL = {http://ammin.geoscienceworld.org/content/84/1-2/1.abstract}, +eprint = {http://ammin.geoscienceworld.org/content/84/1-2/1.full.pdf+html}, +journal = {American Mineralogist} } @article{HHPH2013, -author = {Holland, Tim J.B. and Hudson, Neil F.C. and Powell, Roger and Harte, Ben}, +author = {Holland, Tim J.B. and Hudson, Neil F.C. and Powell, Roger and Harte, Ben}, title = "{New thermodynamic models and calculated phase equilibria in NCFMAS for basic and ultrabasic compositions through the transition zone into the uppermost lower mantle}", -volume = {54}, -number = {9}, -pages = {1901-1920}, -year = {2013}, -doi = {10.1093/petrology/egt035}, -URL = {http://petrology.oxfordjournals.org/content/54/9/1901.abstract}, -eprint = {http://petrology.oxfordjournals.org/content/54/9/1901.full.pdf+html}, -journal = {Journal of Petrology} +volume = {54}, +number = {9}, +pages = {1901-1920}, +year = {2013}, +doi = {10.1093/petrology/egt035}, +URL = {http://petrology.oxfordjournals.org/content/54/9/1901.abstract}, +eprint = {http://petrology.oxfordjournals.org/content/54/9/1901.full.pdf+html}, +journal = {Journal of Petrology} } @article{Schreinemakers1916, author={Schreinemakers, F. A. H.}, title="{In-, mono-, and di-variant equilibria. VIII. Further consideration of the bivariant regions; the turning lines}", journal="{Proc. K. Akad. Wet. (Netherlands)}", -volume=18, +volume=18, pages={1539-1552}, year={1916} } @@ -804,18 +798,18 @@ @ARTICLE{Darken1967 volume={239}, issue={1}, pages={80-89}, -year=1967 +year=1967 } @article{Pow1987, -author = {Powell, Roger}, -title = {Darken's quadratic formalism and the thermodynamics of minerals}, -volume = {72}, -number = {1-2}, -pages = {1-11}, -year = {1987}, -URL = {http://ammin.geoscienceworld.org/content/72/1-2/1.short}, -journal = {American Mineralogist} +author = {Powell, Roger}, +title = {Darken's quadratic formalism and the thermodynamics of minerals}, +volume = {72}, +number = {1-2}, +pages = {1-11}, +year = {1987}, +URL = {http://ammin.geoscienceworld.org/content/72/1-2/1.short}, +journal = {American Mineralogist} } @BOOK{AC1989, @@ -845,14 +839,14 @@ @ARTICLE{HP2003 } @article{PH1993, -author = {Powell, Roger and Holland, Tim}, -title = {On the formulation of simple mixing models for complex phases}, -volume = {78}, -number = {11-12}, -pages = {1174-1180}, -year = {1993}, -URL = {http://ammin.geoscienceworld.org/content/78/11-12/1174.short}, -journal = {American Mineralogist} +author = {Powell, Roger and Holland, Tim}, +title = {On the formulation of simple mixing models for complex phases}, +volume = {78}, +number = {11-12}, +pages = {1174-1180}, +year = {1993}, +URL = {http://ammin.geoscienceworld.org/content/78/11-12/1174.short}, +journal = {American Mineralogist} } @ARTICLE{HP1998, @@ -1016,8 +1010,8 @@ @BOOK{Putnis1992 } @ARTICLE{NissenMeyer2014, - author = {{Nissen-Meyer}, T. and {van Driel}, M. and {St{\"a}hler}, S.~C. and - {Hosseini}, K. and {Hempel}, S. and {Auer}, L. and {Colombi}, A. and + author = {{Nissen-Meyer}, T. and {van Driel}, M. and {St{\"a}hler}, S.~C. and + {Hosseini}, K. and {Hempel}, S. and {Auer}, L. and {Colombi}, A. and {Fournier}, A.}, title = "{AxiSEM: broadband 3-D seismic wavefields in axisymmetric media}", journal = {Solid Earth}, diff --git a/sphinx/seismic.rst b/sphinx/seismic.rst index a26b704cd..4c0ba6ab2 100644 --- a/sphinx/seismic.rst +++ b/sphinx/seismic.rst @@ -7,7 +7,6 @@ Base class for all seismic models .. autoclass:: burnman.seismic.Seismic1DModel - Class for 1D Models ------------------- .. autoclass:: burnman.seismic.SeismicTable @@ -34,4 +33,3 @@ Attenuation Correction ----------------------- .. autofunction:: burnman.seismic.attenuation_correction - diff --git a/sphinx/solution_models.rst b/sphinx/solution_models.rst index e52f3d061..37c1827ed 100644 --- a/sphinx/solution_models.rst +++ b/sphinx/solution_models.rst @@ -4,18 +4,30 @@ Solution models Base class ---------- .. autoclass:: burnman.solidsolution.SolidSolution - + .. autoclass:: burnman.solutionmodel.SolutionModel -Solution models ---------------- +Mechanical solution +------------------- .. autoclass:: burnman.solutionmodel.MechanicalSolution +Ideal solution +-------------- + .. autoclass:: burnman.solutionmodel.IdealSolution +Asymmetric regular solution +--------------------------- + .. autoclass:: burnman.solutionmodel.AsymmetricRegularSolution +Symmetric regular solution +-------------------------- + .. autoclass:: burnman.solutionmodel.SymmetricRegularSolution +Subregular solution +------------------- + .. autoclass:: burnman.solutionmodel.SubregularSolution diff --git a/sphinx/thermodynamics.rst b/sphinx/thermodynamics.rst index 10680f91f..a907a0851 100644 --- a/sphinx/thermodynamics.rst +++ b/sphinx/thermodynamics.rst @@ -9,28 +9,18 @@ Lattice Vibrations Debye model ^^^^^^^^^^^ -.. automodule:: burnman.debye + +.. automodule:: burnman.eos.debye Einstein model ^^^^^^^^^^^^^^ -.. automodule:: burnman.eos.einstein - -Solution models ---------------- - -.. automodule:: burnman.solutionmodel +.. automodule:: burnman.eos.einstein Chemistry parsing ----------------- -.. autofunction:: burnman.processchemistry.read_masses -.. autofunction:: burnman.processchemistry.dictionarize_formula -.. autofunction:: burnman.processchemistry.formula_mass -.. autofunction:: burnman.processchemistry.dictionarize_site_formula -.. autofunction:: burnman.processchemistry.process_solution_chemistry -.. autofunction:: burnman.processchemistry.compositional_array -.. autofunction:: burnman.processchemistry.ordered_compositional_array +.. automodule:: burnman.processchemistry Chemical potentials