diff --git a/.coverage b/.coverage new file mode 100644 index 0000000..c9a1e04 Binary files /dev/null and b/.coverage differ diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7c038d8 --- /dev/null +++ b/.gitignore @@ -0,0 +1,21 @@ +__pycache__ + +# Build +build +dist +**/*.egg-info + +# VSCode settings +.vscode +.conda +.pytest_cache + +# Docs +docs/make.bat +docs/build +docs/source/api/generated +*generated + + +# Debug +tmp* diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..8969772 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,37 @@ +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks +repos: +- repo: https://github.com/adrybakov/pre-commit-hooks + rev: 0.2.0 + hooks: + - id: license-headers + args: + - --license-file + - L-HEADER + - --update-year + - --verbose +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-yaml + - id: check-added-large-files +- repo: https://github.com/pycqa/isort + rev: 5.13.2 + hooks: + - id: isort + args: ["--profile", "black", "--filter-files"] +- repo: https://github.com/psf/black-pre-commit-mirror + rev: 24.4.2 + hooks: + - id: black + language_version: python3.11 +- repo: local + hooks: + - id: pytest-check + name: pytest-check + entry: pytest + language: system + pass_filenames: false + always_run: true diff --git a/L-HEADER b/L-HEADER new file mode 100644 index 0000000..2c1c62f --- /dev/null +++ b/L-HEADER @@ -0,0 +1,19 @@ +Copyright (c) [2024] [Daniel Pozsar] + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..00582b3 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) [2024] [Daniel Pozsar] + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md index e69de29..5e1a4b7 100644 --- a/README.md +++ b/README.md @@ -0,0 +1 @@ +# Relativistic magnetic interactions from non-orthogonal basis sets diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..1422923 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,4 @@ +sphinx +sphinx_rtd_theme +numpydoc +doctest diff --git a/docs/source/.coverage b/docs/source/.coverage new file mode 100644 index 0000000..4ce7682 Binary files /dev/null and b/docs/source/.coverage differ diff --git a/docs/source/Makefile b/docs/source/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/docs/source/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/source/_build/doctrees/environment.pickle b/docs/source/_build/doctrees/environment.pickle new file mode 100644 index 0000000..74e6848 Binary files /dev/null and b/docs/source/_build/doctrees/environment.pickle differ diff --git a/docs/source/_build/doctrees/grogu.doctree b/docs/source/_build/doctrees/grogu.doctree new file mode 100644 index 0000000..a099c16 Binary files /dev/null and b/docs/source/_build/doctrees/grogu.doctree differ diff --git a/docs/source/_build/doctrees/index.doctree b/docs/source/_build/doctrees/index.doctree new file mode 100644 index 0000000..e84e375 Binary files /dev/null and b/docs/source/_build/doctrees/index.doctree differ diff --git a/docs/source/_build/doctrees/modules.doctree b/docs/source/_build/doctrees/modules.doctree new file mode 100644 index 0000000..93edda6 Binary files /dev/null and b/docs/source/_build/doctrees/modules.doctree differ diff --git a/docs/source/_build/html/.buildinfo b/docs/source/_build/html/.buildinfo new file mode 100644 index 0000000..ed21c1e --- /dev/null +++ b/docs/source/_build/html/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 0f8ff1598a5b65221fc2ef8f29fdbeac +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/source/_build/html/_modules/grogu/useful.html b/docs/source/_build/html/_modules/grogu/useful.html new file mode 100644 index 0000000..15af420 --- /dev/null +++ b/docs/source/_build/html/_modules/grogu/useful.html @@ -0,0 +1,282 @@ + + + + + + + + grogu.useful — Grogu 0.0.1 documentation + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +

Source code for grogu.useful

+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import numpy as np
+from scipy.special import roots_legendre
+from itertools import permutations, product
+
+
+# define some useful functions
+

+[docs]
+def hsk(dh, k=(0, 0, 0)):
+    """
+    One way to speed up Hk and Sk generation
+    """
+    k = np.asarray(k, np.float64)  # this two conversion lines
+    k.shape = (-1,)  # are from the sisl source
+
+    # this generates the list of phases
+    phases = np.exp(-1j * np.dot(np.dot(np.dot(dh.rcell, k), dh.cell), dh.sc.sc_off.T))
+
+    HKU = np.einsum("abc,c->ab", dh.hup, phases)
+    HKD = np.einsum("abc,c->ab", dh.hdo, phases)
+    SK = np.einsum("abc,c->ab", dh.sov, phases)
+
+    return HKU, HKD, SK

+
+
+
+

+[docs]
+def make_contour(emin=-20, emax=0.0, enum=42, p=150):
+    """
+    A more sophisticated contour generator
+    """
+
+    x, wl = roots_legendre(enum)
+    R = (emax - emin) / 2
+    z0 = (emax + emin) / 2
+    y1 = -np.log(1 + np.pi * p)
+    y2 = 0
+
+    y = (y2 - y1) / 2 * x + (y2 + y1) / 2
+    phi = (np.exp(-y) - 1) / p
+    ze = z0 + R * np.exp(1j * phi)
+    we = -(y2 - y1) / 2 * np.exp(-y) / p * 1j * (ze - z0) * wl
+
+    class ccont:
+        # just an empty container class
+        pass
+
+    cont = ccont()
+    cont.R = R
+    cont.z0 = z0
+    cont.ze = ze
+    cont.we = we
+    cont.enum = enum
+
+    return cont

+
+
+
+

+[docs]
+def make_kset(dirs="xyz", NUMK=20):
+    """
+    Simple k-grid generator. Depending on the value of the dirs
+    argument k sampling in 1,2 or 3 dimensions is generated.
+    If dirs argument does not contain either of x,y or z
+    a kset of a single k-pont at the origin is returend.
+    """
+    if not (sum([d in dirs for d in "xyz"])):
+        return np.array([[0, 0, 0]])
+
+    kran = len(dirs) * [np.linspace(0, 1, NUMK, endpoint=False)]
+    mg = np.meshgrid(*kran)
+    dirsdict = dict()
+
+    for d in enumerate(dirs):
+        dirsdict[d[1]] = mg[d[0]].flatten()
+    for d in "xyz":
+        if not (d in dirs):
+            dirsdict[d] = 0 * dirsdict[dirs[0]]
+    kset = np.array([dirsdict[d] for d in "xyz"]).T
+
+    return kset

+
+
+
+

+[docs]
+def make_atran(nauc, dirs="xyz", dist=1):
+    """
+    Simple pair generator. Depending on the value of the dirs
+    argument sampling in 1,2 or 3 dimensions is generated.
+    If dirs argument does not contain either of x,y or z
+    a single pair is returend.
+    """
+    if not (sum([d in dirs for d in "xyz"])):
+        return (0, 0, [1, 0, 0])
+
+    dran = len(dirs) * [np.arange(-dist, dist + 1)]
+    mg = np.meshgrid(*dran)
+    dirsdict = dict()
+
+    for d in enumerate(dirs):
+        dirsdict[d[1]] = mg[d[0]].flatten()
+    for d in "xyz":
+        if not (d in dirs):
+            dirsdict[d] = 0 * dirsdict[dirs[0]]
+
+    ucran = np.array([dirsdict[d] for d in "xyz"]).T
+    atran = []
+    for i, j in list(product(range(nauc), repeat=2)):
+        for u in ucran:
+            if (abs(i - j) + sum(abs(u))) > 0:
+                atran.append((i, j, list(u)))
+
+    return atran

+
+
+
+

+[docs]
+def add(x, y):
+    """The sum of two numbers for testing.
+
+    This function adds to numbers together. I only created this for testing documentation and examples.
+
+    Parameters
+    ----------
+    x : float
+        First number
+    y : float
+        Second number added to `x`
+
+    Returns
+    -------
+    sum : int
+        The sum of the inputs
+
+    See Also
+    --------
+    numpy.add : Adds more than two numbers.
+
+    Notes
+    -----
+    We can create some latex notes here [1]_ :
+
+    .. math:: a + b = c
+
+    References
+    ----------
+    .. [1] https://numpydoc.readthedocs.io/en/latest/format.html
+
+
+    Examples
+    --------
+    >>> add(1, 2)
+    3
+
+    """
+    return x + y

+
+
+ +
+
+ +
+
+
+
+ + + + diff --git a/docs/source/_build/html/_modules/index.html b/docs/source/_build/html/_modules/index.html new file mode 100644 index 0000000..85e47e5 --- /dev/null +++ b/docs/source/_build/html/_modules/index.html @@ -0,0 +1,101 @@ + + + + + + + + Overview: module code — Grogu 0.0.1 documentation + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Overview: module code
    • +
  • +
    • +
+
+
+
+
+ +

All modules for which code is available

+ + +
+
+ +
+
+
+
+ + + + diff --git a/docs/source/_build/html/_sources/grogu.rst.txt b/docs/source/_build/html/_sources/grogu.rst.txt new file mode 100644 index 0000000..e8b3bc1 --- /dev/null +++ b/docs/source/_build/html/_sources/grogu.rst.txt @@ -0,0 +1,37 @@ +grogu package +============= + +Submodules +---------- + +grogu.example module +-------------------- + +.. automodule:: grogu.example + :members: + :undoc-members: + :show-inheritance: + +grogu.jij module +---------------- + +.. automodule:: grogu.jij + :members: + :undoc-members: + :show-inheritance: + +grogu.useful module +------------------- + +.. automodule:: grogu.useful + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: grogu + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/_build/html/_sources/index.rst.txt b/docs/source/_build/html/_sources/index.rst.txt new file mode 100644 index 0000000..7b9c75d --- /dev/null +++ b/docs/source/_build/html/_sources/index.rst.txt @@ -0,0 +1,25 @@ +.. asd documentation master file, created by + sphinx-quickstart on Thu Oct 10 17:10:03 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +asd documentation +================= + +Add your content using ``reStructuredText`` syntax. See the +`reStructuredText `_ +documentation for details. + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + modules + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/source/_build/html/_sources/modules.rst.txt b/docs/source/_build/html/_sources/modules.rst.txt new file mode 100644 index 0000000..34386df --- /dev/null +++ b/docs/source/_build/html/_sources/modules.rst.txt @@ -0,0 +1,7 @@ +src +=== + +.. toctree:: + :maxdepth: 4 + + grogu diff --git a/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js b/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/docs/source/_build/html/_static/basic.css b/docs/source/_build/html/_static/basic.css new file mode 100644 index 0000000..93a4776 --- /dev/null +++ b/docs/source/_build/html/_static/basic.css @@ -0,0 +1,914 @@ +/* + * Sphinx stylesheet -- basic theme. + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin-top: 10px; +} + +ul.search li { + padding: 5px 0; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + 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+ document.dispatchEvent(event); + }); +}); diff --git a/docs/source/_build/html/_static/language_data.js b/docs/source/_build/html/_static/language_data.js new file mode 100644 index 0000000..a5ea78e --- /dev/null +++ b/docs/source/_build/html/_static/language_data.js @@ -0,0 +1,191 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; 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+ } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); 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font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #BA2121 } /* Literal.String.Double */ +.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ diff --git a/docs/source/_build/html/_static/searchtools.js b/docs/source/_build/html/_static/searchtools.js new file mode 100644 index 0000000..2c774d1 --- /dev/null +++ b/docs/source/_build/html/_static/searchtools.js @@ -0,0 +1,632 @@ +/* + * Sphinx JavaScript utilities for the full-text search. + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/docs/source/_build/html/_static/sphinx_highlight.js b/docs/source/_build/html/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/docs/source/_build/html/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/docs/source/_build/html/genindex.html b/docs/source/_build/html/genindex.html new file mode 100644 index 0000000..112bda8 --- /dev/null +++ b/docs/source/_build/html/genindex.html @@ -0,0 +1,186 @@ + + + + + + + + Index — Grogu 0.0.1 documentation + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ A + | G + | H + | M + +
+

A

+ + +
+ +

G

+ + + +
    +
  • + grogu + +
    • +
  • + grogu.example + +
    • +
    +
  • + grogu.jij + +
    • +
  • + grogu.useful + +
    • +
+ +

H

+ + +
+ +

M

+ + +
+ + + +
+
+ +
+
+
+
+ + + + diff --git a/docs/source/_build/html/grogu.html b/docs/source/_build/html/grogu.html new file mode 100644 index 0000000..23c92ec --- /dev/null +++ b/docs/source/_build/html/grogu.html @@ -0,0 +1,215 @@ + + + + + + + + + grogu package — Grogu 0.0.1 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

grogu package

+
+

Submodules

+
+
+

grogu.example module

+
+
+

grogu.jij module

+
+
+

grogu.useful module

+
+
+grogu.useful.add(x, y)[source]
+

The sum of two numbers for testing.

+

This function adds to numbers together. I only created this for testing documentation and examples.

+
+
Parameters:
+
    +

  • x (float) – First number

    • +

  • y (float) – Second number added to x

    • +
+
+
Returns:
+

sum – The sum of the inputs

+
+
Return type:
+

int

+
+
+
+

See also

+
+
numpy.add

Adds more than two numbers.

+
+
+
+

Notes

+

We can create some latex notes here [1] :

+
+\[a + b = c\]
+

References

+ +

Examples

+
>>> add(1, 2)
+3
+
+
+
+ +
+
+grogu.useful.hsk(dh, k=(0, 0, 0))[source]
+

One way to speed up Hk and Sk generation

+
+ +
+
+grogu.useful.make_atran(nauc, dirs='xyz', dist=1)[source]
+

Simple pair generator. Depending on the value of the dirs +argument sampling in 1,2 or 3 dimensions is generated. +If dirs argument does not contain either of x,y or z +a single pair is returend.

+
+ +
+
+grogu.useful.make_contour(emin=-20, emax=0.0, enum=42, p=150)[source]
+

A more sophisticated contour generator

+
+ +
+
+grogu.useful.make_kset(dirs='xyz', NUMK=20)[source]
+

Simple k-grid generator. Depending on the value of the dirs +argument k sampling in 1,2 or 3 dimensions is generated. +If dirs argument does not contain either of x,y or z +a kset of a single k-pont at the origin is returend.

+
+ +
+
+

Module contents

+
+
+ + +
+
+ +
+
+
+
+ + + + diff --git a/docs/source/_build/html/index.html b/docs/source/_build/html/index.html new file mode 100644 index 0000000..6708b9c --- /dev/null +++ b/docs/source/_build/html/index.html @@ -0,0 +1,128 @@ + + + + + + + + + asd documentation — Grogu 0.0.1 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

asd documentation

+

Add your content using reStructuredText syntax. See the +reStructuredText +documentation for details.

+
+

Contents:

+ +
+
+
+

Indices and tables

+ +
+ + +
+
+ +
+
+
+
+ + + + diff --git a/docs/source/_build/html/modules.html b/docs/source/_build/html/modules.html new file mode 100644 index 0000000..68a6a30 --- /dev/null +++ b/docs/source/_build/html/modules.html @@ -0,0 +1,132 @@ + + + + + + + + + src — Grogu 0.0.1 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+ +
+ +
+
+
+
+ + + + diff --git a/docs/source/_build/html/objects.inv b/docs/source/_build/html/objects.inv new file mode 100644 index 0000000..45e7134 --- /dev/null +++ b/docs/source/_build/html/objects.inv @@ -0,0 +1,7 @@ +# Sphinx inventory version 2 +# Project: Grogu +# Version: +# The remainder of this file is compressed using zlib. +xڕM +@ =E@z$Ķv~3MՊv^TV~` UVVujZ`nD_ltj&B)5>ڷ3h-084sMš`kk=2tV Ձ].9}L:-VTGr^BR&0TC|٠G{!İw$>N6:QYcϑ; + \ No newline at end of file diff --git a/docs/source/_build/html/py-modindex.html b/docs/source/_build/html/py-modindex.html new file mode 100644 index 0000000..afa884e --- /dev/null +++ b/docs/source/_build/html/py-modindex.html @@ -0,0 +1,135 @@ + + + + + + + + Python Module Index — Grogu 0.0.1 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Python Module Index
    • +
  • +
    • +
+
+
+
+
+ + +

Python Module Index

+ +
+ g +
+ + + + + + + + + + + + + + + + +
 
+ g
+ grogu +
    + grogu.example +
    + grogu.jij +
    + grogu.useful +
+ + +
+
+ +
+
+
+
+ + + + diff --git a/docs/source/_build/html/search.html b/docs/source/_build/html/search.html new file mode 100644 index 0000000..61399b5 --- /dev/null +++ b/docs/source/_build/html/search.html @@ -0,0 +1,120 @@ + + + + + + + + Search — Grogu 0.0.1 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
+ + + + + + + + + diff --git a/docs/source/_build/html/searchindex.js b/docs/source/_build/html/searchindex.js new file mode 100644 index 0000000..3d96987 --- /dev/null +++ b/docs/source/_build/html/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"Contents:": [[1, null]], "Indices and tables": [[1, "indices-and-tables"]], "Module contents": [[0, "module-grogu"]], "Submodules": [[0, "submodules"]], "asd documentation": [[1, null]], "grogu package": [[0, null]], "grogu.example module": [[0, "module-grogu.example"]], "grogu.jij module": [[0, "module-grogu.jij"]], "grogu.useful module": [[0, "module-grogu.useful"]], "src": [[2, null]]}, "docnames": ["grogu", "index", "modules"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["grogu.rst", "index.rst", "modules.rst"], "indexentries": {"add() (in module grogu.useful)": [[0, "grogu.useful.add", false]], "grogu": [[0, "module-grogu", false]], "grogu.example": [[0, "module-grogu.example", false]], "grogu.jij": [[0, "module-grogu.jij", false]], "grogu.useful": [[0, "module-grogu.useful", false]], "hsk() (in module grogu.useful)": [[0, "grogu.useful.hsk", false]], "make_atran() (in module grogu.useful)": [[0, "grogu.useful.make_atran", false]], "make_contour() (in module grogu.useful)": [[0, "grogu.useful.make_contour", false]], "make_kset() (in module grogu.useful)": [[0, "grogu.useful.make_kset", false]], "module": [[0, "module-grogu", false], [0, "module-grogu.example", false], [0, "module-grogu.jij", false], [0, "module-grogu.useful", false]]}, "objects": {"": [[0, 0, 0, "-", "grogu"]], "grogu": [[0, 0, 0, "-", "example"], [0, 0, 0, "-", "jij"], [0, 0, 0, "-", "useful"]], "grogu.useful": [[0, 1, 1, "", "add"], [0, 1, 1, "", "hsk"], [0, 1, 1, "", "make_atran"], [0, 1, 1, "", "make_contour"], [0, 1, 1, "", "make_kset"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:function"}, "terms": {"0": 0, "1": 0, "150": 0, "2": 0, "20": 0, "3": 0, "42": 0, "A": 0, "If": 0, "One": 0, "The": 0, "ad": 0, "add": [0, 1, 2], "argument": 0, "b": 0, "c": 0, "can": 0, "contain": 0, "content": 2, "contour": 0, "creat": 0, "depend": 0, "detail": 1, "dh": 0, "dimens": 0, "dir": 0, "dist": 0, "document": 0, "doe": 0, "either": 0, "emax": 0, "emin": 0, "en": 0, "enum": 0, "exampl": 2, "first": 0, "float": 0, "format": 0, "function": 0, "gener": 0, "grid": 0, "grogu": [1, 2], "here": 0, "hk": 0, "hsk": [0, 2], "html": 0, "http": 0, "i": 0, "index": 1, "input": 0, "int": 0, "io": 0, "jij": 2, "k": 0, "kset": 0, "latest": 0, "latex": 0, "make_atran": [0, 2], "make_contour": [0, 2], "make_kset": [0, 2], "modul": [1, 2], "more": 0, "nauc": 0, "note": 0, "number": 0, "numk": 0, "numpi": 0, "numpydoc": 0, "onli": 0, "origin": 0, "p": 0, "packag": [1, 2], "page": 1, "pair": 0, "paramet": 0, "pont": 0, "readthedoc": 0, "refer": 0, "restructuredtext": 1, "returend": 0, "return": 0, "sampl": 0, "search": 1, "second": 0, "see": 1, "simpl": 0, "singl": 0, "sk": 0, "some": 0, "sophist": 0, "sourc": 0, "speed": 0, "src": 1, "submodul": 2, "sum": 0, "syntax": 1, "test": 0, "than": 0, "thi": 0, "togeth": 0, "two": 0, "type": 0, "up": 0, "us": [1, 2], "valu": 0, "wai": 0, "we": 0, "x": 0, "xyz": 0, "y": 0, "your": 1, "z": 0}, "titles": ["grogu package", "asd documentation", "src"], "titleterms": {"asd": 1, "content": [0, 1], "document": 1, "exampl": 0, "grogu": 0, "indic": 1, "jij": 0, "modul": 0, "packag": 0, "src": 2, "submodul": 0, "tabl": 1, "us": 0}}) diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..e36971e --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,52 @@ +# Copyright (c) [2024] [Daniel Pozsar] +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. + +import os +import sys + +sys.path.insert(0, os.path.abspath("../../src")) + + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = "Grogu" +copyright = "2024, Grogu" +author = "Laszlo Oroszlany, Daniel Pozsar" +release = "0.0.1" + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.viewcode", + "sphinx.ext.napoleon", +] + +templates_path = ["_templates"] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = "sphinx_rtd_theme" +html_static_path = ["_static"] diff --git a/docs/source/grogu.rst b/docs/source/grogu.rst new file mode 100644 index 0000000..e8b3bc1 --- /dev/null +++ b/docs/source/grogu.rst @@ -0,0 +1,37 @@ +grogu package +============= + +Submodules +---------- + +grogu.example module +-------------------- + +.. automodule:: grogu.example + :members: + :undoc-members: + :show-inheritance: + +grogu.jij module +---------------- + +.. automodule:: grogu.jij + :members: + :undoc-members: + :show-inheritance: + +grogu.useful module +------------------- + +.. automodule:: grogu.useful + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: grogu + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..7b9c75d --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,25 @@ +.. asd documentation master file, created by + sphinx-quickstart on Thu Oct 10 17:10:03 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +asd documentation +================= + +Add your content using ``reStructuredText`` syntax. See the +`reStructuredText `_ +documentation for details. + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + modules + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/source/make.bat b/docs/source/make.bat new file mode 100644 index 0000000..32bb245 --- /dev/null +++ b/docs/source/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/modules.rst b/docs/source/modules.rst new file mode 100644 index 0000000..34386df --- /dev/null +++ b/docs/source/modules.rst @@ -0,0 +1,7 @@ +src +=== + +.. toctree:: + :maxdepth: 4 + + grogu diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..8668515 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,52 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "grogu" +version = "0.0.1" +authors = [ + { name="Laszlo Oroszlany", email="laszlo.oroszlany@ttk.elte.hu" }, + { name="Daniel Pozsar", email="danielpozsar@student.elte.hu" }, +] +description = "Relativistic magnetic interactions from non-orthogonal basis sets" +readme = "README.md" +kewords = [ + "DFT", + "physics", +] +requires-python = ">=3.8" +dependencies = [ + "numpy", + "scipy", + "sisl", + "mpi4py", + "argparse", +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Programming Language :: Python", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3 :: Only", + "Topic :: Scientific/Engineering :: Physics", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", +] + +[project.urls] +Homepage = "https://github.com/pypa/sampleproject" +Documentation = "https://readthedocs.org" +Repository = "https://github.com/me/spam.git" +Issues = "https://github.com/pypa/sampleproject/issues" + +[tool.pytest.ini_options] +addopts = [ + "--import-mode=importlib", +# "--cov", + "--doctest-modules", +] +pythonpath = [ + "src/grogu/", +] diff --git a/requirements-dev.txt b/requirements-dev.txt new file mode 100644 index 0000000..bd831e6 --- /dev/null +++ b/requirements-dev.txt @@ -0,0 +1,17 @@ +# PyPI +wheel +setuptools +build + +# code-linters +black +license-headers + +# dev-tools +pre-commit +pytest +pytest-randomly +pytest-cov +doctest +sphinx +git diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..539e9e5 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,6 @@ +# Package dependencies +numpy +scipy +sisl +mpi4py +argparse diff --git a/src/grogu/__init__.py b/src/grogu/__init__.py new file mode 100644 index 0000000..39a4a19 --- /dev/null +++ b/src/grogu/__init__.py @@ -0,0 +1,22 @@ +# Copyright (c) [2024] [Daniel Pozsar] +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. + +from jij import * +from useful import * diff --git a/src/grogu/example.py b/src/grogu/example.py new file mode 100644 index 0000000..93d0ca4 --- /dev/null +++ b/src/grogu/example.py @@ -0,0 +1,19 @@ +# Copyright (c) [2024] [Daniel Pozsar] +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. diff --git a/src/grogu/jij.py b/src/grogu/jij.py new file mode 100644 index 0000000..3de5d32 --- /dev/null +++ b/src/grogu/jij.py @@ -0,0 +1,294 @@ +# Copyright (c) [2024] [Daniel Pozsar] +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. + +if __name__ == "__main__": + import argparse + import sys + from itertools import permutations, product + from timeit import default_timer as timer + + import numpy as np + import numpy.linalg as nl + import sisl + import tqdm + from mpi4py import MPI + from scipy.special import roots_legendre + + from grogu.useful import hsk, make_atran, make_contour, make_kset + + start = timer() + + # Some input parsing + parser = argparse.ArgumentParser() + parser.add_argument( + "--kset", + dest="kset", + default=2, + type=int, + help="k-space resolution of Jij calculation", + ) + parser.add_argument( + "--kdirs", + dest="kdirs", + default="xyz", + help="Definition of k-space dimensionality", + ) + parser.add_argument( + "--eset", + dest="eset", + default=42, + type=int, + help="Number of energy points on the contour", + ) + parser.add_argument( + "--eset-p", + dest="esetp", + default=10, + type=int, + help="Parameter tuning the distribution on the contour", + ) + parser.add_argument("--input", dest="infile", required=True, help="Input file name") + parser.add_argument( + "--output", dest="outfile", required=True, help="Output file name" + ) + parser.add_argument( + "--Ebot", + dest="Ebot", + default=-20.0, + type=float, + help="Bottom energy of the contour", + ) + parser.add_argument( + "--npairs", + dest="npairs", + default=1, + type=int, + help="Number of unitcell pairs in each direction for Jij calculation", + ) + parser.add_argument( + "--adirs", dest="adirs", default=False, help="Definition of pair directions" + ) + parser.add_argument( + "--use-tqdm", + dest="usetqdm", + default="not", + help="Use tqdm for progressbars or not", + ) + parser.add_argument( + "--cutoff", + dest="cutoff", + default=100.0, + type=float, + help="Real space cutoff for pair generation in Angs", + ) + parser.add_argument( + "--pairfile", + dest="pairfile", + default=False, + help="File to read pair information", + ) + args = parser.parse_args() + # ---------------------------------------------------------------------- + + # MPI init + comm = MPI.COMM_WORLD + size = comm.Get_size() + rank = comm.Get_rank() + root_node = 0 + if rank == root_node: + print("Number of nodes in the parallel cluster: ", size) + # ---------------------------------------------------------------------- + + # importing the necessary structures from SIESTA output + dat = sisl.get_sile(args.infile) + dh = dat.read_hamiltonian() + # update datastructure of the hamiltonian + # this is needed for quick Hk building + dh.hup = ( + dh.tocsr(0) + .toarray() + .reshape(dh.no, dh.n_s, dh.no) + .transpose(0, 2, 1) + .astype("complex128") + ) + dh.hdo = ( + dh.tocsr(1) + .toarray() + .reshape(dh.no, dh.n_s, dh.no) + .transpose(0, 2, 1) + .astype("complex128") + ) + dh.sov = ( + dh.tocsr(2) + .toarray() + .reshape(dh.no, dh.n_s, dh.no) + .transpose(0, 2, 1) + .astype("complex128") + ) + # ---------------------------------------------------------------------- + + # generate k space sampling + kset = make_kset(dirs=args.kdirs, NUMK=args.kset) + wk = 1 / len(kset) # weight of a kpoint in BZ integral + kpcs = np.array_split(kset, size) + if "k" in args.usetqdm: + kpcs[root_node] = tqdm.tqdm(kpcs[root_node], desc="k loop") + # ---------------------------------------------------------------------- + # define pairs + + if args.pairfile: + # if pair file is specified read in pair information from pairfile + if rank == root_node: + # read in pair on root node file in a format of five integer columns + # first two integers define sublattice + # second three define distance vectors of unitcells + dummy = np.loadtxt(args.pairfile, dtype=int) + atran = [ + (dummy[p, 0], dummy[p, 1], [dummy[p, 2], dummy[p, 3], dummy[p, 4]]) + for p in range(len(dummy)) + ] + else: + atran = None + # syncronize atran over all nodes + atran = comm.bcast(atran, root=root_node) + else: + # if pairfile is not specified generate pair as defined by npairs and adirs + # Take pair directions for k directions if adirs is not set + args.adirs = args.adirs if args.adirs else args.kdirs + # definition of pairs in terms of integer coordinates refering + # to unicell distances and atomic positions + atran = make_atran(len(dh.atoms), args.adirs, dist=args.npairs) + pairs = [] + for i, j, uc in atran: + if nl.norm(np.dot(uc, dh.cell)) < args.cutoff: + pairs.append( + dict( + offset=uc, # lattice vector offset between the unitcells the two atoms are + aiij=[i, j], # indecies of the atoms in the unitcell + noij=[ + dh.atoms.orbitals[i], + dh.atoms.orbitals[j], + ], # number of orbitals on the appropriate atoms + slij=[ + slice( + *(lambda x: [min(x), max(x) + 1])(dh.a2o(i, all=True)) + ), # slices for + slice(*(lambda x: [min(x), max(x) + 1])(dh.a2o(j, all=True))), + ], # appropriate orbitals + rirj=[ + dh.axyz()[i], + dh.axyz()[j], + ], # real space vectors of atoms in the unit cell + Rij=np.dot( + uc, dh.cell + ), # real space distance vector between unit cells + rij=np.dot(uc, dh.cell) + - dh.axyz()[i] + + dh.axyz()[j], # real space vector between atoms + Jijz=[], # in this empty list are we going to gather the integrad of the energy integral + Jij=0, # the final results of the calculation are going to be here on the root node + ) + ) + + if rank == root_node: + print("Number of pairs beeing calculated: ", len(pairs)) + + comm.Barrier() + # ---------------------------------------------------------------------- + + # make energy contour + # we are working in eV now ! + # and sisil shifts E_F to 0 ! + cont = make_contour(emin=args.Ebot, enum=args.eset, p=args.esetp) + eran = cont.ze + # ---------------------------------------------------------------------- + + # generating onsite matrix and overalp elements of all the atoms in the unitcell + # onsite of the origin supercell + orig_indx = np.arange(0, dh.no) + dh.sc_index([0, 0, 0]) * dh.no + # spin up + uc_up = dh.tocsr(dh.UP)[:, orig_indx].toarray() + # spin down + uc_down = dh.tocsr(dh.DOWN)[:, orig_indx].toarray() + Hs = [] + # get number of atoms in the unit cell + for i in range(len(dh.atoms)): + at_indx = dh.a2o(i, all=True) + Hs.append(uc_up[:, at_indx][at_indx, :] - uc_down[:, at_indx][at_indx, :]) + + # ---------------------------------------------------------------------- + + # sampling the integrand on the contour and the BZ + + for pair in pairs: + noi, noj = pair["noij"] + pair["Guij"] = np.zeros((args.eset, noi, noj), dtype="complex128") + pair["Gdji"] = np.zeros((args.eset, noj, noi), dtype="complex128") + pair["Guij_tmp"] = np.zeros((args.eset, noi, noj), dtype="complex128") + pair["Gdji_tmp"] = np.zeros((args.eset, noj, noi), dtype="complex128") + + for k in kpcs[rank]: + HKU, HKD, SK = hsk(dh, k) + Gku = nl.inv(SK * eran.reshape(args.eset, 1, 1) - HKU) + Gkd = nl.inv(SK * eran.reshape(args.eset, 1, 1) - HKD) + for pair in pairs: + phase = np.exp(1j * np.dot(np.dot(k, dh.rcell), pair["Rij"])) + si, sj = pair["slij"] + pair["Guij_tmp"] += Gku[:, si, sj] * phase * wk + pair["Gdji_tmp"] += Gkd[:, sj, si] / phase * wk + + # summ reduce partial results of mpi nodes + for pair in pairs: + comm.Reduce(pair["Guij_tmp"], pair["Guij"], root=root_node) + comm.Reduce(pair["Gdji_tmp"], pair["Gdji"], root=root_node) + + if rank == root_node: + for pair in pairs: + i, j = pair["aiij"] + # The Szunyogh-Lichtenstein formula + pair["Jijz"] = np.trace( + (Hs[i] @ pair["Guij"]) @ (Hs[j] @ pair["Gdji"]), axis1=1, axis2=2 + ) + # evaluation of the contour integral + pair["Jij"] = np.trapz(np.imag(pair["Jijz"] * cont.we) / (2 * np.pi)) + end = timer() + + # ---------------------------------------------------------------------- + # and saveing output of the calculation + np.savetxt( + args.outfile, + np.array( + [ + [nl.norm(p["rij"]), p["Jij"] * sisl.unit_convert("eV", "Ry") * 1000] + + p["aiij"] + + list(p["offset"]) + + list(p["rij"]) + for p in pairs + ], + dtype=object, + ), + header=str(args) + + "\nnumber of cores = " + + str(size) + + "\ntime of calculation = " + + str(end - start) + + "\nnorm(rij),Jij[mRy],aiij,offset,rij", + fmt="%s", + ) diff --git a/src/grogu/useful.py b/src/grogu/useful.py new file mode 100644 index 0000000..a898a7e --- /dev/null +++ b/src/grogu/useful.py @@ -0,0 +1,167 @@ +# Copyright (c) [2024] [Daniel Pozsar] +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. + +from itertools import permutations, product + +import numpy as np +from scipy.special import roots_legendre + + +# define some useful functions +def hsk(dh, k=(0, 0, 0)): + """ + One way to speed up Hk and Sk generation + """ + k = np.asarray(k, np.float64) # this two conversion lines + k.shape = (-1,) # are from the sisl source + + # this generates the list of phases + phases = np.exp(-1j * np.dot(np.dot(np.dot(dh.rcell, k), dh.cell), dh.sc.sc_off.T)) + + HKU = np.einsum("abc,c->ab", dh.hup, phases) + HKD = np.einsum("abc,c->ab", dh.hdo, phases) + SK = np.einsum("abc,c->ab", dh.sov, phases) + + return HKU, HKD, SK + + +def make_contour(emin=-20, emax=0.0, enum=42, p=150): + """ + A more sophisticated contour generator + """ + + x, wl = roots_legendre(enum) + R = (emax - emin) / 2 + z0 = (emax + emin) / 2 + y1 = -np.log(1 + np.pi * p) + y2 = 0 + + y = (y2 - y1) / 2 * x + (y2 + y1) / 2 + phi = (np.exp(-y) - 1) / p + ze = z0 + R * np.exp(1j * phi) + we = -(y2 - y1) / 2 * np.exp(-y) / p * 1j * (ze - z0) * wl + + class ccont: + # just an empty container class + pass + + cont = ccont() + cont.R = R + cont.z0 = z0 + cont.ze = ze + cont.we = we + cont.enum = enum + + return cont + + +def make_kset(dirs="xyz", NUMK=20): + """ + Simple k-grid generator. Depending on the value of the dirs + argument k sampling in 1,2 or 3 dimensions is generated. + If dirs argument does not contain either of x,y or z + a kset of a single k-pont at the origin is returend. + """ + if not (sum([d in dirs for d in "xyz"])): + return np.array([[0, 0, 0]]) + + kran = len(dirs) * [np.linspace(0, 1, NUMK, endpoint=False)] + mg = np.meshgrid(*kran) + dirsdict = dict() + + for d in enumerate(dirs): + dirsdict[d[1]] = mg[d[0]].flatten() + for d in "xyz": + if not (d in dirs): + dirsdict[d] = 0 * dirsdict[dirs[0]] + kset = np.array([dirsdict[d] for d in "xyz"]).T + + return kset + + +def make_atran(nauc, dirs="xyz", dist=1): + """ + Simple pair generator. Depending on the value of the dirs + argument sampling in 1,2 or 3 dimensions is generated. + If dirs argument does not contain either of x,y or z + a single pair is returend. + """ + if not (sum([d in dirs for d in "xyz"])): + return (0, 0, [1, 0, 0]) + + dran = len(dirs) * [np.arange(-dist, dist + 1)] + mg = np.meshgrid(*dran) + dirsdict = dict() + + for d in enumerate(dirs): + dirsdict[d[1]] = mg[d[0]].flatten() + for d in "xyz": + if not (d in dirs): + dirsdict[d] = 0 * dirsdict[dirs[0]] + + ucran = np.array([dirsdict[d] for d in "xyz"]).T + atran = [] + for i, j in list(product(range(nauc), repeat=2)): + for u in ucran: + if (abs(i - j) + sum(abs(u))) > 0: + atran.append((i, j, list(u))) + + return atran + + +def add(x, y): + """The sum of two numbers for testing. + + This function adds to numbers together. I only created this for testing documentation and examples. + + Parameters + ---------- + x : float + First number + y : float + Second number added to `x` + + Returns + ------- + sum : int + The sum of the inputs + + See Also + -------- + numpy.add : Adds more than two numbers. + + Notes + ----- + We can create some latex notes here [1]_ : + + .. math:: a + b = c + + References + ---------- + .. [1] https://numpydoc.readthedocs.io/en/latest/format.html + + + Examples + -------- + >>> add(1, 2) + 3 + + """ + return x + y diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..93d0ca4 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,19 @@ +# Copyright (c) [2024] [Daniel Pozsar] +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. diff --git a/tests/test_jij.py b/tests/test_jij.py new file mode 100644 index 0000000..93d0ca4 --- /dev/null +++ b/tests/test_jij.py @@ -0,0 +1,19 @@ +# Copyright (c) [2024] [Daniel Pozsar] +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. diff --git a/tests/test_useful.py b/tests/test_useful.py new file mode 100644 index 0000000..56c5d99 --- /dev/null +++ b/tests/test_useful.py @@ -0,0 +1,29 @@ +# Copyright (c) [2024] [Daniel Pozsar] +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. + +import pytest +from useful import add + + +@pytest.mark.parametrize( + "a, b, c, expected_out", [(1, 2, 3, True), (6, 7, 13, True), (1, 2, 10, False)] +) +def test_add(a, b, c, expected_out): + assert (add(a, b) == c) == expected_out