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High level specifications of the environments are given in ``stardis_env3.yml`` and ``stardis_env3_cuda.yml``, and then ``conda-lock`` is used to create the corresponding lockfile. The steps are as follow. + +.. note:: + These steps are only tested using `miniconda `__. + +.. note:: + Both sets of steps below assume that all commands are being run from your local STARDIS git repository, which can be obtained using the developer installation instructions. + +Without CUDA Support +^^^^^^^^^^^^^^^^^^^^ + +#. Activate the Conda virtual environment: + + .. code-block:: bash + + $ conda activate stardis + +#. `Create a lockfile `__ using conda-lock's `unified lockfile format `__: + + .. code-block:: bash + + $ conda-lock -f stardis_env3.yml --conda $(which conda) --strip-auth + +#. `Render `__ platform-specific lockfiles: + + .. code-block:: bash + + $ conda-lock render conda-lock.yml + +With CUDA Support +^^^^^^^^^^^^^^^^^^^^ + +#. Activate the Conda virtual environment: + + .. code-block:: bash + + $ conda activate stardis-cuda + +#. `Create a lockfile `__ using conda-lock's `unified lockfile format `__: + + .. code-block:: bash + + $ conda-lock -f stardis_env3_cuda.yml --conda $(which conda) --strip-auth --lockfile conda-lock-cuda.yml + +#. `Render `__ platform-specific lockfiles: + + .. code-block:: bash + + $ conda-lock render --filename-template conda-{platform}-cuda.lock conda-lock-cuda.yml diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/index.rst.txt b/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/index.rst.txt new file mode 100644 index 00000000..8c3d43be --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/index.rst.txt @@ -0,0 +1,22 @@ +stardis Documentation +----------------------- + +This is the documentation for stardis. + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + Quickstart + Downloading and Installation + Physics of STARDIS + Running the Code + Contributing + Bibliography + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/installation.rst.txt b/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/installation.rst.txt new file mode 100644 index 00000000..52df6e36 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/installation.rst.txt @@ -0,0 +1,73 @@ +.. + This file was converted from MarkDown using pandoc 2.19.2, Compiled with pandoc-types 1.22.2.1, texmath 0.12.5.2, skylighting 0.13, citeproc 0.8.0.1, ipynb 0.2, hslua 2.2.1, Scripting engine: Lua 5.4 + The command was `$ pandoc -t rst installation.md -o installation.rst`__ + +Downloading and Installation +============================ + +Setting Up the Environment +-------------------------- + +.. note:: + * STARDIS is only supported on macOS and GNU/Linux. Windows users can run STARDIS on a virtual machine. + + * STARDIS packages and dependencies are distributed only through the `conda `__ package management system, therefore installation requires a conda distribution to be installed on your system. STARDIS uses `Miniconda `__ or `Mamba `__ by default. Other distributions are untested. + +STARDIS uses exclusively the packages in the TARDIS enviroment, as well +as using the TARDIS code itself. However, since STARDIS can be sensitive +to changes in TARDIS, we strongly suggest that users create a separate +environment for STARDIS that pins the TARDIS version. To do this, run +the following in the terminal (replacing ``{platform}`` with +``linux-64``, ``linux-64-cuda``, or ``osx-64`` as applicable). + +.. code-block:: bash + + $ cd + $ conda create --name stardis --file conda-{platform}.lock + $ conda activate stardis + $ pip install git+https://github.com/tardis-sn/tardis.git@release-2023.04.16 + +The third command (``conda activate stardis``) activates the +environment, which is necessary to correctly install STARDIS using the directions below. + +If you are using Mamba, the steps are similar: + +.. code-block:: bash + + $ cd + $ mamba create --name stardis --file conda-{platform}.lock + $ mamba activate stardis + $ pip install git+https://github.com/tardis-sn/tardis.git@release-2023.04.16 + +Downloading and Installing STARDIS +---------------------------------- + +For Non-Developers +^^^^^^^^^^^^^^^^^^ + +STARDIS can be downloaded by **non-developers** by running + +:: + + $ pip install git+https://github.com/tardis-sn/stardis.git@main + +in the terminal with your STARDIS environment activated. + +For Developers +^^^^^^^^^^^^^^ + +Developers should fork and clone the STARDIS repository. +First, `fork the +repository `__ and `configure +GitHub to work with SSH +keys `__, +and then run the following in the terminal: + +:: + + $ git clone git@github.com:/stardis.git + $ cd stardis + $ git remote add upstream git@github.com:tardis-sn/stardis.git + $ git fetch upstream + $ git checkout upstream/main + $ pip install -e .[test,docs] diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/physics/physics_of_stardis.rst.txt b/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/physics/physics_of_stardis.rst.txt new file mode 100644 index 00000000..8431d02a --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/physics/physics_of_stardis.rst.txt @@ -0,0 +1,143 @@ +****************** +Physics of STARDIS +****************** + +================ +Model and Plasma +================ + +STARDIS breaks down the stellar atmosphere into spherical shells as shown below and approximates that the plasma state is uniform throughout each shell. We rely on the MARCS code, a code that generates models of stellar atmospheres, to determine the temperatures, elemental abundances, and densities in each shell. The existing TARDIS plasma infrastructure determines the rest of the plasma state, namely the excitation and ionization properties and transition rates. + +.. image:: media/model_and_plasma-1.png + :width: 500 px + :alt: Diagram showing inner and outer boundaries of the stellar atmosphere + +========= +Opacities +========= + +To determine an output spectrum, we need to understand how photons of light move through the atmosphere and what interactions they experience. Opacity is a measure of how likely it is that light will be scattered or absorbed by some material, like the stellar plasma, per unit distance it travels. This is contributed to by several mechanisms, which are described :ref:`below`. + +--------------- +Opacity Sources +--------------- + +The first four of these interactions are called continuum interactions, as they affect light at a large range of frequencies. Line interactions, on the other hand, only occur with light around specific frequencies, corresponding to the electron’s jump in energy. These are called *resonant frequencies*. + +^^^^^^^^^^^^^^^^^^^^^ +Bound-Free Absorbtion +^^^^^^^^^^^^^^^^^^^^^ + +.. math:: + \alpha = \frac{64 \pi^4 e^{10} m_e Z^4}{3 \sqrt 3 h^6 c n_{\text{eff}}^5} n + +.. image:: media/bound_free_absorbtion-1.png + :width: 500 px + :alt: Diagram of bound-free absorbtion + + +^^^^^^^^^^^^^^^^^^^^ +Free-Free Absorbtion +^^^^^^^^^^^^^^^^^^^^ + +.. math:: + \alpha = \frac{4 e^6 Z^2 n}{3 h c v^3} \sqrt{\frac{2 \pi}{3 m_e^3 k_B T}} + +.. image:: media/free_free_absorbtion-1.png + :width: 500 px + :alt: Diagram of free-free absorbtion + + +^^^^^^^^^^^^^^^^^^^ +Rayleigh Scattering +^^^^^^^^^^^^^^^^^^^ + +.. math:: + \alpha = \sigma_T n \left ( c_4 \left ( \frac{v}{2 v_H} \right )^4 + c_6 \left ( \frac{v}{2 v_H} \right )^6 + c_8 \left ( \frac{v}{2 v_H} \right )^8 \right ) + +.. image:: media/rayleigh_scattering-1.png + :width: 500 px + :alt: Diagram of Rayleigh scattering + + +^^^^^^^^^^^^^^^^^^^ +Electron Scattering +^^^^^^^^^^^^^^^^^^^ + +.. math:: + \alpha = \sigma_T n_E + +.. image:: media/electron_scattering-1.png + :width: 500 px + :alt: Diagram of electron scattering + + +^^^^^^^^^^^^^^^^ +Line Interaction +^^^^^^^^^^^^^^^^ + +.. math:: + \alpha = \frac{\pi e^2}{m_e c} n_l f_{lu} \left (1 - \frac{g_l n_u}{g_u n_l} \right ) \phi(v) + +.. image:: media/line_interaction-1.png + :width: 500 px + :alt: Diagram of line interaction + +---------- +Broadening +---------- + +Line interaction opacity does not occur only at the exact resonant frequencies; lines are broadened to reach other nearby frequencies. Thus, the line interaction opacity is the total line opacity + +.. math:: + \alpha_{lu} = \frac{\pi e^2}{m_e c} n_l f_{lu} \left ( 1 - \frac{g_l n_u}{g_u n_l} \right ) + +times the *line profile* :math:`\phi(v)` which describes the broadening. + +.. + The below was taken from https://stackoverflow.com/a/42522042 + +|wide_line_profile| vs. |narrow_line_profile| + +.. |wide_line_profile| image:: media/wide_line_profile.png + :width: 45 % + :alt: Broad line profile + +.. |narrow_line_profile| image:: media/narrow_line_profile.png + :width: 45 % + :alt: Less broad line profile + +Above are examples of line profiles, the left being very broadened and the right being less broadened. + +The line profile uses the following parameters for determining how much the line is broadened: + +- The Einstein coefficient :math:`A_{ul}`, describing the line’s natural acceptance of non-resonant frequencies. +- The doppler width :math:`\Delta v_D`, the range of frequencies that are doppler shifted to be the resonant frequency due to the movement of ions in the plasma. +- The collisional broadening parameter :math:`\gamma_{\text{col}}`, describing the effects of forces between ions or ions and electrons which shift the resonant frequency. + +The line profile centered at the resonant frequency :math:`v_{lu}` is then: + +.. math:: + \phi(v) = \frac{\gamma_{\text{col}}}{4 \pi^{\frac{5}{2}} \Delta v_D} \int_{-\infty}^{\infty} \frac{\exp \left ( -\frac{y^2}{\Delta v_D^2} \right )}{\left (v - v_{lu} - y \right )^2 + \left ( \frac{\gamma_{\text{col}} + A_{ul}}{4 \pi} \right )^2} \, d y + +========= +Transport +========= + +Finally, we use the opacity information to trace beams of light coming from the photosphere at different angles and frequencies to find the final intensity. We use the equation + +.. math:: + I_{N + 1}(v, \theta) = I_N(v, \theta) e^{-\tau} + (1 - e^{- \tau}) B_{N + 1} (v) + (1 - e^{-\tau} - \tau e^{-\tau}) \frac{\Delta B_{N + 1}(v)}{\tau} + +where :math:`\tau = \frac{\alpha l}{\cos \theta}` is the *optical depth*, :math:`l` is the depth of each shell, and :math:`B(v)` is the blackbody distribution. + +.. image:: media/transport.png + :width: 500 px + :alt: A diagram of how the opacity is a function of the angle and frequency of a location in the photosphere + + +The flux density (the desired spectrum) is then: + +.. math:: + F(v) = 2 \pi \int_0^{\frac{\pi}{2}} I(v, \theta) \sin \theta \cos \theta \, d \theta. + diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/quickstart/quickstart.ipynb.txt b/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/quickstart/quickstart.ipynb.txt new file mode 100644 index 00000000..b4d9e247 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/_sources/quickstart/quickstart.ipynb.txt @@ -0,0 +1,365 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# STARDIS" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "ExecuteTime": { + "end_time": "2022-01-12T00:13:43.539653Z", + "start_time": "2022-01-12T00:13:40.679189Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Iterations: 0/? 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The main function, ``run_stardis()``, +requires as its first argument the name of a configuration file, which +will be described below. The second argument is an array of the +frequencies or wavelengths for which you are requesting the flux +density, times an appropriate astropy quantity (such as Hertz or +Angstroms). Note that this must be an array times a quantity, **not** an +array of astropy quantities. + +The STARDIS Configuration +------------------------- + +STARDIS uses `YAML `__ files for the configuration. +The `Quickstart notebook `__ uses an example configuration called ``stardis_example.yml``, which can be found `here `__, along with any other files from the Quickstart. +Below, we present an example for instructions for customizing the +configuration for your needs. + +.. code:: yaml + + stardis_config_version: 1.0 + atom_data: + model: + type: marcs # more options will be available in the future + fname: + final_atomic_number: # may be up to 30 + opacity: + file: # reads a bound-free or free-free opacity file, omit if none + _: + _: + ... + bf: # uses the hydrogenic approximation for bound-free opacity, omit if none + : {} # there will eventually be options to include files with gaunt factors or departure coefficients + : {} + ... + ff: # uses the hydrogenic approximation for free-free opacity, omit if none + : {} # there will eventually be options to include files with gaunt factors or departure coefficients + : {} + ... + rayleigh: # may include H, He, and/or H2, omit or use [] for none + disable_electron_scattering: + line: # settings for line interaction opacity, at least one subfield is required + disable: + broadening: # may include radiation, linear_stark, quadratic_stark, and/or van_der_waals, omit or use [] for none + min: # must have units, such as Hz or AA + max: # must have units, such as Hz or AA + broadening_range: # necessary for computational efficiency and must have units, 1e13 Hz recommended + no_of_thetas: + +In fields where an atomic species is requested, the species must be in +the form ``_``. For example, +``H_I`` for neutral hydrogen, or ``Si_III`` for twice-ionized silicon. + +Additionally, in the opacity file section, the following entries are +valid: + +* ``Hminus_bf`` +* ``Hminus_ff`` +* ``Heminus_ff`` +* ``H2minus_ff`` +* ``H2plus_ff`` + +Opacity File Format +------------------- + +STARDIS can read and interpolate continuum opacity cross-section files +for bound-free or free-free absorption (technically, for free-free +absorption the files would provide the cross-section per electron +density). The files must be one of the following formats: + +.. code:: csv + + wavelength_1, cross-section_1 + wavelength_2, cross-section_2 + wavelength_3, cross-section_3 + ... + +or + +.. code:: csv + + , temperature_1, temperature_2, temperature_3, ... + wavelength_1, cross-section_11, cross-section_12, cross-section_13, ... + wavelength_2, cross-section_21, cross-section_22, cross-section_23, ... + wavelength_3, cross-section_31, cross-section_32, cross-section_33, ... + ... + +Note the leading comma in the latter format. Temperatures must be in +Kelvin, wavelengths in Angstroms, and cross-sections in cm\ :sup:`2`\ for +bound-free or cm\ :sup:`5`\ for free-free (once again because free-free opacity +files provide the cross-section per electron density). diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/_static/_sphinx_javascript_frameworks_compat.js b/branch/gpu/broadening/calc_doppler_width/add-cuda/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/_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")) { + 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+ +/** + * 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] = 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, + }; +} + +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, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = docUrlRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = docUrlRoot + 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 + ")"; + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + }); + 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 = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms +) => { + // 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); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * 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) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you 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.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); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + 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; + + // 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]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // 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] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((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; + }); + + // 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; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms); + }, + + /** + * 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]], + ]); + }; + 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); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], 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.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [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], + ]); + } + 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) => { + const text = Search.htmlToText(htmlText); + 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/branch/gpu/broadening/calc_doppler_width/add-cuda/_static/sphinx_highlight.js b/branch/gpu/broadening/calc_doppler_width/add-cuda/_static/sphinx_highlight.js new file mode 100644 index 00000000..aae669d7 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/_static/sphinx_highlight.js @@ -0,0 +1,144 @@ +/* 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))); + parent.insertBefore( + span, + parent.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + + 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(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/bibliography.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/bibliography.html new file mode 100644 index 00000000..a23237e1 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/bibliography.html @@ -0,0 +1,208 @@ + + + + + + + Bibliography — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Bibliography

+

The following are references used for the development of STARDIS.

+
+
+[Bel80] +

K. L. Bell. The free-free absorption coefficient of the negative pion of molecular hydrogen. Journal of Physics B: Atomic and Molecular Physics, 13(9):1859, May 1980. URL: https://dx.doi.org/10.1088/0022-3700/13/9/016, doi:10.1088/0022-3700/13/9/016.

+
+
+[CKM+16] +

J. Colgan, D. P. Kilcrease, N. H. Magee, M. E. Sherrill, J. Abdallah Jr, P. Hakel, C. J. Fontes, J. A. Guzik, and K. A. Mussack. A NEW GENERATION OF LOS ALAMOS OPACITY TABLES. The Astrophysical Journal, 817(2):116, January 2016. Publisher: The American Astronomical Society. URL: https://dx.doi.org/10.3847/0004-637X/817/2/116, doi:10.3847/0004-637X/817/2/116.

+
+
+[DW62] +

A. Dalgarno and D. A. Williams. Rayleigh Scattering by Molecular Hydrogen. \apj, 136:690–692, September 1962. doi:10.1086/147428.

+
+
+[Gra15] +

David F. Gray. The observation and analysis of stellar photospheres. Cambridge University Press, Cambridge, third edition edition, 2015. ISBN 978-1-316-03657-0. OCLC: 1050543949.

+
+
+[HM14] +

Ivan Hubeny and Dimitri Mihalas. Theory of Stellar Atmospheres. 2014.

+
+
+[Joh94] +

T. L. John. Absorption coefficients of the negative helium ion. Monthly Notices of the Royal Astronomical Society, 269(4):871–878, August 1994. _eprint: https://academic.oup.com/mnras/article-pdf/269/4/871/3046750/mnras269-0871.pdf. URL: https://doi.org/10.1093/mnras/269.4.871, doi:10.1093/mnras/269.4.871.

+
+
+[KL61] +

W. J. Karzas and R. Latter. Electron Radiative Transitions in a Coulomb Field. \apjs, 6:167, May 1961. doi:10.1086/190063.

+
+
+[KS14] +

Wolfgang E. Kerzendorf and Stuart A. Sim. A spectral synthesis code for rapid modelling of supernovae. Monthly Notices of the Royal Astronomical Society, 440:387–404, May 2014. tex.ids: kerzendorf_spectral_2014-1, kerzendorf_spectral_2014-2. URL: http://adsabs.harvard.edu/abs/2014MNRAS.440..387K (visited on 2020-09-01), doi:10.1093/mnras/stu055.

+
+
+[KK] +

Charles Kittel and Herbert Kroemer. Thermal Physics. W. H. Freeman and Company, New York, 2nd edition. ISBN 978-0-7167-1088-2.

+
+
+[Kur70] +

R. L. Kurucz. Atlas: a Computer Program for Calculating Model Stellar Atmospheres. SAO Special Report, February 1970.

+
+
+[Pea70] +

G. Peach. Continuous absorption coefficients for non-hydrogenic atoms. \memras, 73:1, January 1970. URL: https://ui.adsabs.harvard.edu/abs/1970MmRAS..73....1P/abstract.

+
+
+[Rut03] +

Robert J. Rutten. Radiative Transfer in Stellar Atmospheres. May 2003. Publication Title: Radiative Transfer in Stellar Atmospheres ADS Bibcode: 2003rtsa.book.....R. URL: https://ui.adsabs.harvard.edu/abs/2003rtsa.book.....R (visited on 2022-01-10).

+
+
+[SYMP94] +

M. J. Seaton, Yu Yan, D. Mihalas, and Anil K. Pradhan. Opacities for stellar envelopes. Monthly Notices of the Royal Astronomical Society, 266(4):805–828, February 1994. _eprint: https://academic.oup.com/mnras/article-pdf/266/4/805/3050789/mnras266-0805.pdf. URL: https://doi.org/10.1093/mnras/266.4.805, doi:10.1093/mnras/266.4.805.

+
+
+[Sta94] +

P. C. Stancil. Continuous Absorption by He + 2 and H + 2 in Cool White Dwarfs. \apj, 430:360, July 1994. doi:10.1086/174411.

+
+
+[Sut78] +

Kenneth Sutton. Approximate line shapes for hydrogen. Journal of Quantitative Spectroscopy and Radiative Transfer, 20(4):333–343, 1978. URL: https://www.sciencedirect.com/science/article/pii/0022407378901024, doi:https://doi.org/10.1016/0022-4073(78)90102-4.

+
+
+[vHWV+14] +

P. A. M. van Hoof, R. J. R. Williams, K. Volk, M. Chatzikos, G. J. Ferland, M. Lykins, R. L. Porter, and Y. Wang. Accurate determination of the free–free Gaunt factor – I. Non-relativistic Gaunt factors. Monthly Notices of the Royal Astronomical Society, 444(1):420–428, August 2014. _eprint: https://academic.oup.com/mnras/article-pdf/444/1/420/18753385/stu1438.pdf. URL: https://doi.org/10.1093/mnras/stu1438, doi:10.1093/mnras/stu1438.

+
+
+[vNHL02] +

Michiel van Noort, Ivan Hubeny, and Thierry Lanz. Multidimensional Non-LTE Radiative Transfer. I. A Universal Two-dimensional Short-Characteristics Scheme for Cartesian, Spherical, and Cylindrical Coordinate Systems. \apj, 568(2):1066–1094, April 2002. doi:10.1086/338949.

+
+
+[War67] +

Brian Warner. Some Effects of Pressure Broadening in Solar and Stellar Curves of Growth. Monthly Notices of the Royal Astronomical Society, 136(4):381–388, August 1967. _eprint: https://academic.oup.com/mnras/article-pdf/136/4/381/8078683/mnras136-0381.pdf. URL: https://doi.org/10.1093/mnras/136.4.381, doi:10.1093/mnras/136.4.381.

+
+
+[WACN23] +

Adam J. Wheeler, Matthew W. Abruzzo, Andrew R. Casey, and Melissa K. Ness. KORG: A Modern 1D LTE Spectral Synthesis Package. \aj, 165(2):68, February 2023. _eprint: 2211.00029. doi:10.3847/1538-3881/acaaad.

+
+
+[Wis79] +

A. W. Wishart. The bound-free photo-detachment cross-section of H-. \mnras, 187:59P–61, May 1979. doi:10.1093/mnras/187.1.59P.

+
+
+[GustafssonBEdvardssonBErikssonK+08] +

Gustafsson, B., Edvardsson, B., Eriksson, K., Jørgensen, U. G., Nordlund, Å., and Plez, B. A grid of MARCS model atmospheres for late-type stars - I. Methods and general properties. A&A, 486(3):951–970, 2008. URL: https://doi.org/10.1051/0004-6361:200809724, doi:10.1051/0004-6361:200809724.

+
+
+[HusserTOWendevBergSDreizlerS+13] +

Husser, T.-O., Wende-von Berg, S., Dreizler, S., Homeier, D., Reiners, A., Barman, T., and Hauschildt, P. H. A new extensive library of PHOENIX stellar atmospheres and synthetic spectra. A&A, 553:A6, 2013. URL: https://doi.org/10.1051/0004-6361/201219058, doi:10.1051/0004-6361/201219058.

+
+
+
+
+ + +
+ + + + + + + + + + \ No newline at end of file diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/contributing.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/contributing.html new file mode 100644 index 00000000..03fbeb09 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/contributing.html @@ -0,0 +1,177 @@ + + + + + + + Contributing — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Contributing

+
+

Generating Conda Lockfiles

+

In the interest of reproducibility, STARDIS uses conda-lock files to keep the virtual environment consistent across similar machines and installations. High level specifications of the environments are given in stardis_env3.yml and stardis_env3_cuda.yml, and then conda-lock is used to create the corresponding lockfile. The steps are as follow.

+
+

Note

+

These steps are only tested using miniconda.

+
+
+

Note

+

Both sets of steps below assume that all commands are being run from your local STARDIS git repository, which can be obtained using the developer installation instructions.

+
+
+

Without CUDA Support

+
    +

  1. Activate the Conda virtual environment:

    +
    $ conda activate stardis
+
    +
    +
    2. +

  2. Create a lockfile using conda-lock’s unified lockfile format:

    +
    $ conda-lock -f stardis_env3.yml --conda $(which conda) --strip-auth
+
    +
    +
    3. +

  3. Render platform-specific lockfiles:

    +
    $ conda-lock render conda-lock.yml
+
    +
    +
    4. +
+
+
+

With CUDA Support

+
    +

  1. Activate the Conda virtual environment:

    +
    $ conda activate stardis-cuda
+
    +
    +
    2. +

  2. Create a lockfile using conda-lock’s unified lockfile format:

    +
    $ conda-lock -f stardis_env3_cuda.yml --conda $(which conda) --strip-auth --lockfile conda-lock-cuda.yml
+
    +
    +
    3. +

  3. Render platform-specific lockfiles:

    +
    $ conda-lock render --filename-template conda-{platform}-cuda.lock conda-lock-cuda.yml
+
    +
    +
    4. +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/genindex.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/genindex.html new file mode 100644 index 00000000..19adf850 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/genindex.html @@ -0,0 +1,114 @@ + + + + + + Index — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+
+ +
+ +
+

© Copyright 2022, TARDIS Collaboration.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/index.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/index.html new file mode 100644 index 00000000..b0006d5a --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/index.html @@ -0,0 +1,153 @@ + + + + + + + stardis Documentation — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+ +
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/installation.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/installation.html new file mode 100644 index 00000000..603ab3ce --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/installation.html @@ -0,0 +1,185 @@ + + + + + + + Downloading and Installation — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Downloading and Installation

+
+

Setting Up the Environment

+
+

Note

+
    +

  • STARDIS is only supported on macOS and GNU/Linux. Windows users can run STARDIS on a virtual machine.

    • +

  • STARDIS packages and dependencies are distributed only through the conda package management system, therefore installation requires a conda distribution to be installed on your system. STARDIS uses Miniconda or Mamba by default. Other distributions are untested.

    • +
+
+

STARDIS uses exclusively the packages in the TARDIS enviroment, as well +as using the TARDIS code itself. However, since STARDIS can be sensitive +to changes in TARDIS, we strongly suggest that users create a separate +environment for STARDIS that pins the TARDIS version. To do this, run +the following in the terminal (replacing {platform} with +linux-64, linux-64-cuda, or osx-64 as applicable).

+
$ cd <path-to-stardis-directory>
+$ conda create --name stardis --file conda-{platform}.lock
+$ conda activate stardis
+$ pip install git+https://github.com/tardis-sn/tardis.git@release-2023.04.16
+
+
+

The third command (conda activate stardis) activates the +environment, which is necessary to correctly install STARDIS using the directions below.

+

If you are using Mamba, the steps are similar:

+
$ cd <path-to-stardis-directory>
+$ mamba create --name stardis --file conda-{platform}.lock
+$ mamba activate stardis
+$ pip install git+https://github.com/tardis-sn/tardis.git@release-2023.04.16
+
+
+
+
+

Downloading and Installing STARDIS

+
+

For Non-Developers

+

STARDIS can be downloaded by non-developers by running

+
$ pip install git+https://github.com/tardis-sn/stardis.git@main
+
+
+

in the terminal with your STARDIS environment activated.

+
+
+

For Developers

+

Developers should fork and clone the STARDIS repository. +First, fork the +repository and configure +GitHub to work with SSH +keys, +and then run the following in the terminal:

+
$ git clone git@github.com:<username>/stardis.git
+$ cd stardis
+$ git remote add upstream git@github.com:tardis-sn/stardis.git
+$ git fetch upstream
+$ git checkout upstream/main
+$ pip install -e .[test,docs]
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/objects.inv b/branch/gpu/broadening/calc_doppler_width/add-cuda/objects.inv new file mode 100644 index 00000000..e9a54d7d Binary files /dev/null and b/branch/gpu/broadening/calc_doppler_width/add-cuda/objects.inv differ diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/physics/physics_of_stardis.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/physics/physics_of_stardis.html new file mode 100644 index 00000000..996bb780 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/physics/physics_of_stardis.html @@ -0,0 +1,208 @@ + + + + + + + Physics of STARDIS — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Physics of STARDIS

+
+

Model and Plasma

+

STARDIS breaks down the stellar atmosphere into spherical shells as shown below and approximates that the plasma state is uniform throughout each shell. We rely on the MARCS code, a code that generates models of stellar atmospheres, to determine the temperatures, elemental abundances, and densities in each shell. The existing TARDIS plasma infrastructure determines the rest of the plasma state, namely the excitation and ionization properties and transition rates.

+Diagram showing inner and outer boundaries of the stellar atmosphere +
+
+

Opacities

+

To determine an output spectrum, we need to understand how photons of light move through the atmosphere and what interactions they experience. Opacity is a measure of how likely it is that light will be scattered or absorbed by some material, like the stellar plasma, per unit distance it travels. This is contributed to by several mechanisms, which are described below.

+
+

Opacity Sources

+

The first four of these interactions are called continuum interactions, as they affect light at a large range of frequencies. Line interactions, on the other hand, only occur with light around specific frequencies, corresponding to the electron’s jump in energy. These are called resonant frequencies.

+
+

Bound-Free Absorbtion

+
+\[\alpha = \frac{64 \pi^4 e^{10} m_e Z^4}{3 \sqrt 3 h^6 c n_{\text{eff}}^5} n\]
+Diagram of bound-free absorbtion +
+
+

Free-Free Absorbtion

+
+\[\alpha = \frac{4 e^6 Z^2 n}{3 h c v^3} \sqrt{\frac{2 \pi}{3 m_e^3 k_B T}}\]
+Diagram of free-free absorbtion +
+
+

Rayleigh Scattering

+
+\[\alpha = \sigma_T n \left ( c_4 \left ( \frac{v}{2 v_H} \right )^4 + c_6 \left ( \frac{v}{2 v_H} \right )^6 + c_8 \left ( \frac{v}{2 v_H} \right )^8 \right )\]
+Diagram of Rayleigh scattering +
+
+

Electron Scattering

+
+\[\alpha = \sigma_T n_E\]
+Diagram of electron scattering +
+
+

Line Interaction

+
+\[\alpha = \frac{\pi e^2}{m_e c} n_l f_{lu} \left (1 - \frac{g_l n_u}{g_u n_l} \right ) \phi(v)\]
+Diagram of line interaction +
+
+
+

Broadening

+

Line interaction opacity does not occur only at the exact resonant frequencies; lines are broadened to reach other nearby frequencies. Thus, the line interaction opacity is the total line opacity

+
+\[\alpha_{lu} = \frac{\pi e^2}{m_e c} n_l f_{lu} \left ( 1 - \frac{g_l n_u}{g_u n_l} \right )\]
+

times the line profile \(\phi(v)\) which describes the broadening.

+

Broad line profile vs. Less broad line profile

+

Above are examples of line profiles, the left being very broadened and the right being less broadened.

+

The line profile uses the following parameters for determining how much the line is broadened:

+
    +

  • The Einstein coefficient \(A_{ul}\), describing the line’s natural acceptance of non-resonant frequencies.

    • +

  • The doppler width \(\Delta v_D\), the range of frequencies that are doppler shifted to be the resonant frequency due to the movement of ions in the plasma.

    • +

  • The collisional broadening parameter \(\gamma_{\text{col}}\), describing the effects of forces between ions or ions and electrons which shift the resonant frequency.

    • +
+

The line profile centered at the resonant frequency \(v_{lu}\) is then:

+
+\[\phi(v) = \frac{\gamma_{\text{col}}}{4 \pi^{\frac{5}{2}} \Delta v_D} \int_{-\infty}^{\infty} \frac{\exp \left ( -\frac{y^2}{\Delta v_D^2} \right )}{\left (v - v_{lu} - y \right )^2 + \left ( \frac{\gamma_{\text{col}} + A_{ul}}{4 \pi} \right )^2} \, d y\]
+
+
+
+

Transport

+

Finally, we use the opacity information to trace beams of light coming from the photosphere at different angles and frequencies to find the final intensity. We use the equation

+
+\[I_{N + 1}(v, \theta) = I_N(v, \theta) e^{-\tau} + (1 - e^{- \tau}) B_{N + 1} (v) + (1 - e^{-\tau} - \tau e^{-\tau}) \frac{\Delta B_{N + 1}(v)}{\tau}\]
+

where \(\tau = \frac{\alpha l}{\cos \theta}\) is the optical depth, \(l\) is the depth of each shell, and \(B(v)\) is the blackbody distribution.

+A diagram of how the opacity is a function of the angle and frequency of a location in the photosphere +

The flux density (the desired spectrum) is then:

+
+\[F(v) = 2 \pi \int_0^{\frac{\pi}{2}} I(v, \theta) \sin \theta \cos \theta \, d \theta.\]
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/quickstart/quickstart.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/quickstart/quickstart.html new file mode 100644 index 00000000..7d84ca33 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/quickstart/quickstart.html @@ -0,0 +1,210 @@ + + + + + + + STARDIS — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

STARDIS

+
+
[1]:
+
+
+
# Import necessary code
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+from tardis.io.atom_data.util import download_atom_data
+
+from stardis.base import run_stardis
+
+from astropy import units as u, constants as const
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
[2]:
+
+
+
# Download atomic data
+
+download_atom_data('kurucz_cd23_chianti_H_He')
+
+
+
+
+
[3]:
+
+
+
# Create array of wavelengths and run STARDIS
+
+tracing_lambdas = np.arange(6540, 6590, .01) * u.Angstrom
+
+sim = run_stardis('stardis_example.yml', tracing_lambdas)
+
+
+
+
+
+
+
+
+/home/smithis7/anaconda3/envs/stardis/lib/python3.8/site-packages/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in true_divide
+  (g_lower * n_upper) / (g_upper * n_lower)
+
+
+
+
[4]:
+
+
+
# Plot spectra
+
+#%matplotlib notebook
+
+plt.figure(figsize=(10,6))
+plt.plot(sim.lambdas, sim.spectrum_lambda)
+
+plt.xlim((6540,6590))
+plt.title("STARDIS Solar Spectrum")
+plt.xlabel("Wavelength [$\AA$]")
+plt.ylabel("Flux density [erg/s/cm$^2$/$\AA$]")
+
+plt.show()
+
+
+
+
+
+
+
+../_images/quickstart_quickstart_4_0.png +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/quickstart/quickstart.ipynb b/branch/gpu/broadening/calc_doppler_width/add-cuda/quickstart/quickstart.ipynb new file mode 100644 index 00000000..b4d9e247 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/quickstart/quickstart.ipynb @@ -0,0 +1,365 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# STARDIS" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "ExecuteTime": { + "end_time": "2022-01-12T00:13:43.539653Z", + "start_time": "2022-01-12T00:13:40.679189Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Iterations: 0/? [00:00" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Plot spectra\n", + "\n", + "#%matplotlib notebook\n", + "\n", + "plt.figure(figsize=(10,6))\n", + "plt.plot(sim.lambdas, sim.spectrum_lambda)\n", + "\n", + "plt.xlim((6540,6590))\n", + "plt.title(\"STARDIS Solar Spectrum\")\n", + "plt.xlabel(\"Wavelength [$\\AA$]\")\n", + "plt.ylabel(\"Flux density [erg/s/cm$^2$/$\\AA$]\")\n", + "\n", + "plt.show()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python [conda env:anaconda3-stardis]", + "language": "python", + "name": "conda-env-anaconda3-stardis-py" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.16" + }, + "toc": { + "base_numbering": 1, + "nav_menu": {}, + "number_sections": true, + "sideBar": true, + "skip_h1_title": false, + "title_cell": "Table of Contents", + "title_sidebar": "Contents", + "toc_cell": false, + "toc_position": {}, + "toc_section_display": true, + "toc_window_display": false + }, + "vscode": { + "interpreter": { + "hash": "fa8628d2318bd99a3d47e52206e03625a3fa16b2b0ce3640eae09b1452043fd1" + } + }, + "widgets": { + "application/vnd.jupyter.widget-state+json": { + "state": { + "00f819ed799047a5906a7d5e61c7f216": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "DescriptionStyleModel", + "state": { + "description_width": "" + } + }, + "15e49533d7ac4a2d96ea59e47e3f4a07": { + "model_module": "@jupyter-widgets/base", + "model_module_version": "1.2.0", + "model_name": "LayoutModel", + "state": {} + }, + "2018d7f561e74bc98e0446b10b4840c3": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "HTMLModel", + "state": { + "layout": "IPY_MODEL_40cefbf886cf43f0ac75d3b2e715e14b", + "style": 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[00:00<?, ?it/s]" + } + }, + "e6c5089217494a3c9e38d393f4844273": { + "model_module": "@jupyter-widgets/output", + "model_module_version": "1.0.0", + "model_name": "OutputModel", + "state": { + "layout": "IPY_MODEL_8381733a4c7d40919c4b499ae4ea7176" + } + }, + "f138d85378eb4aa9870eb7fe83adb223": { + "model_module": "@jupyter-widgets/base", + "model_module_version": "1.2.0", + "model_name": "LayoutModel", + "state": {} + } + }, + "version_major": 2, + "version_minor": 0 + } + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/running_the_code.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/running_the_code.html new file mode 100644 index 00000000..0e97a9a3 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/running_the_code.html @@ -0,0 +1,208 @@ + + + + + + + Running the Code — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Running the Code

+
+

The run_stardis() Function

+

In the Quickstart, there is a basic notebook that +runs STARDIS and plots a spectrum. The main function, run_stardis(), +requires as its first argument the name of a configuration file, which +will be described below. The second argument is an array of the +frequencies or wavelengths for which you are requesting the flux +density, times an appropriate astropy quantity (such as Hertz or +Angstroms). Note that this must be an array times a quantity, not an +array of astropy quantities.

+
+
+

The STARDIS Configuration

+

STARDIS uses YAML files for the configuration. +The Quickstart notebook uses an example configuration called stardis_example.yml, which can be found here, along with any other files from the Quickstart. +Below, we present an example for instructions for customizing the +configuration for your needs.

+
stardis_config_version: 1.0
+atom_data: <filepath to atomic data file>
+model:
+    type: marcs # more options will be available in the future
+    fname: <filepath to MARCS model file>
+    final_atomic_number: <atomic number of largest element considered> # may be up to 30
+opacity:
+    file: # reads a bound-free or free-free opacity file, omit if none
+        <species1>_<either bf for bound-free or ff for free-free>: <filepath to opacity file>
+        <species2>_<either bf for bound-free or ff for free-free>: <filepath to opacity file>
+        ...
+    bf: # uses the hydrogenic approximation for bound-free opacity, omit if none
+        <species1>: {} # there will eventually be options to include files with gaunt factors or departure coefficients
+        <species2>: {}
+        ...
+    ff: # uses the hydrogenic approximation for free-free opacity, omit if none
+        <species1>: {} # there will eventually be options to include files with gaunt factors or departure coefficients
+        <species2>: {}
+        ...
+    rayleigh: <list of species considered for rayleigh scattering> # may include H, He, and/or H2, omit or use [] for none
+    disable_electron_scattering: <True or False>
+    line: # settings for line interaction opacity, at least one subfield is required
+        disable: <True or False>
+        broadening: <list of non-thermal broadening sources considered> # may include radiation, linear_stark, quadratic_stark, and/or van_der_waals, omit or use [] for none
+        min: <minimum resonance frequency or wavelength of lines considered> # must have units, such as Hz or AA
+        max: <maximum resonance frequency or wavelength of lines considered> # must have units, such as Hz or AA
+        broadening_range: <maximum distance in frquency space to the resonant frequency for line broadening to be considered> # necessary for computational efficiency and must have units, 1e13 Hz recommended
+no_of_thetas: <number of angles to sample for raytracing>
+
+
+

In fields where an atomic species is requested, the species must be in +the form <atomic symbol>_<ionization roman numeral>. For example, +H_I for neutral hydrogen, or Si_III for twice-ionized silicon.

+

Additionally, in the opacity file section, the following entries are +valid:

+
    +

  • Hminus_bf

    • +

  • Hminus_ff

    • +

  • Heminus_ff

    • +

  • H2minus_ff

    • +

  • H2plus_ff

    • +
+
+
+

Opacity File Format

+

STARDIS can read and interpolate continuum opacity cross-section files +for bound-free or free-free absorption (technically, for free-free +absorption the files would provide the cross-section per electron +density). The files must be one of the following formats:

+
wavelength_1, cross-section_1
+wavelength_2, cross-section_2
+wavelength_3, cross-section_3
+...
+
+
+

or

+
, temperature_1, temperature_2, temperature_3, ...
+wavelength_1, cross-section_11, cross-section_12, cross-section_13, ...
+wavelength_2, cross-section_21, cross-section_22, cross-section_23, ...
+wavelength_3, cross-section_31, cross-section_32, cross-section_33, ...
+...
+
+
+

Note the leading comma in the latter format. Temperatures must be in +Kelvin, wavelengths in Angstroms, and cross-sections in cm2 for +bound-free or cm5 for free-free (once again because free-free opacity +files provide the cross-section per electron density).

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/gpu/broadening/calc_doppler_width/add-cuda/search.html b/branch/gpu/broadening/calc_doppler_width/add-cuda/search.html new file mode 100644 index 00000000..8ce52422 --- /dev/null +++ b/branch/gpu/broadening/calc_doppler_width/add-cuda/search.html @@ -0,0 +1,129 @@ + + + + + + Search — stardis 0.1.dev1+g5ef48ee documentation + + + + + + + + + + + + + + + + + + + + + + +
+ + +
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+
+
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