diff --git a/README.md b/README.md index 48dd72b..706890d 100644 --- a/README.md +++ b/README.md @@ -52,6 +52,10 @@ Run `pycopm --help` to see all possible command line argument options. ## Getting started See the [_examples_](https://cssr-tools.github.io/pycopm/examples.html) in the [_documentation_](https://cssr-tools.github.io/pycopm/introduction.html). +## Citing + +* Landa-Marbán, D. 2024. pycopm: An open-source coarsening framework for OPM Flow geological models. V2024.04. https://doi.org/10.5281/zenodo.12740838. + ## Publications The following is a list of manuscripts in which _pycopm_ is used: @@ -59,6 +63,6 @@ The following is a list of manuscripts in which _pycopm_ is used: ## About pycopm The _pycopm_ package is being funded by the [_Center for Sustainable Subsurface Resources (CSSR)_](https://cssr.no) -[project no. 331841]. +[project no. 331841] and by [_Expansion of Resources for CO2 Storage on the Horda Platform (ExpReCCS)_](https://www.norceresearch.no/en/projects/expansion-of-resources-for-co2-storage-on-the-horda-platform-expreccs) [project no. 336294]. This is work in progress. Contributions are more than welcome using the fork and pull request approach. \ No newline at end of file diff --git a/docs/_sources/about.rst.txt b/docs/_sources/about.rst.txt index 9ea1f09..a66ddfc 100644 --- a/docs/_sources/about.rst.txt +++ b/docs/_sources/about.rst.txt @@ -5,6 +5,7 @@ About pycopm .. image:: ./figs/droganim.gif :scale: 65% -**pycopm**, a tool for coarsening OPM Flow geological models, is being funded by the `Center for Sustainable Subsurface Resources (CSSR) `_ [project no. 331841]. +**pycopm**, a tool for coarsening OPM Flow geological models, is being funded by the `Center for Sustainable Subsurface Resources (CSSR) `_ [project no. 331841] +and by `Expansion of Resources for CO2 Storage on the Horda Platform (ExpReCCS) `_ [project no. 336294]. This is work in progress. Contributions are more than welcome using the fork and pull request approach. \ No newline at end of file diff --git a/docs/_sources/introduction.rst.txt b/docs/_sources/introduction.rst.txt index f7c7199..d53410e 100644 --- a/docs/_sources/introduction.rst.txt +++ b/docs/_sources/introduction.rst.txt @@ -40,11 +40,11 @@ where -y Vector of y-coarsening, see the description for -x ('' by default). -z Vector of z-coarsening, see the description for -x ('' by default). -a Use `min`, `max`, or `mode` to scale the actnum, e.g., min makes the new coarser cell inactive if at least one cell is inactive, while max makes it active it at least one cell is active (`mode` by default). --n Use `min`, `max`, or `mode` to scale endnum, eqlnum, fipnum, fluxnum, imbnum, miscnum, multnum, pvtnum, rocknum, and satnum (`mode` by default). +-n Use `min`, `max`, or `mode` to scale endnum, eqlnum, fipnum, fluxnum, imbnum, miscnum, multnum, opernum, pvtnum, rocknum, and satnum (`mode` by default). -s Use `min`, `max`, or `mean` to scale permx, permy, permz, poro, swatinit, and all mult(-)xyz ('' by default, i.e., using the arithmetic average for permx/permy, harmonic average for permz, volume weighted mean for mult(-)xyz, and the pore volume weighted mean for the rest). -p Add the removed pore volume to the closest coarser cells (`0` by default, `1` to enable). --q Adjust the pv to the initial FGIP and FOIP from the input deck (`0` by default, `1` to enable). --t Write and use upscaled transmissibilities (`0` by default, it is advice to use only with z-coarsening). +-q Adjust the pv to the initial FGIP and FOIP from the input deck; use this option only for systems with initial oil, gas, and water, e.g., norne or drogon, but no in Smeaheia (`0` by default, `1` to enable). +-t Write and use upscaled transmissibilities by (`1`) armonic averaging and summing the transmissibilities in the corresponding coarsening direction and (`2`) scaling the face transmissibily on the coarse faces (`0` by default). -r Remove CONFACT and KH from COMPDAT (`1`) and also remove PEQVR (`2`) (ITEM 13, the last entry) to compute the well transmisibility connections internally in OPM Flow using the grid properties (`2` by default; `0` to not remove). -j Tuning parameter to avoid creation of neighbouring connections in the coarser model where there are discontinuities between cells along the z direction, e.g., around faults ('' by default, i.e., nothing corrected; if need it, try with values of the order of 1). -m Execute a dry run on the input deck to generate the static properties ('prep'), generate only the coarse files ('deck'), only exectute a dry run on the generated coarse model ('dry'), 'prep_deck', 'deck_dry', or do all ('all') (`prep_deck` by default). diff --git a/docs/_static/basic.css b/docs/_static/basic.css index 30fee9d..7ebbd6d 100644 --- a/docs/_static/basic.css +++ b/docs/_static/basic.css @@ -1,12 +1,5 @@ /* - * basic.css - * ~~~~~~~~~ - * * Sphinx stylesheet -- basic 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module&&module.exports&&(module.exports=t)}("undefined"!=typeof window?window:this,document); \ No newline at end of file diff --git a/docs/_static/js/versions.js b/docs/_static/js/versions.js new file mode 100644 index 0000000..818bc99 --- /dev/null +++ b/docs/_static/js/versions.js @@ -0,0 +1,224 @@ +const themeFlyoutDisplay = "hidden"; +const themeVersionSelector = "True"; +const themeLanguageSelector = "True"; + +if (themeFlyoutDisplay === "attached") { + function renderLanguages(config) { + if (!config.projects.translations.length) { + return ""; + } + + const languagesHTML = ` +
+
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+ ${config.projects.translations + .map( + (translation) => ` +
+ ${translation.language.code} +
+ `, + ) + .join("\n")} +
+ `; + return languagesHTML; + } + + function renderVersions(config) { + if (!config.versions.active.length) { + return ""; + } + const versionsHTML = ` +
+
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+ ${config.versions.active + .map( + (version) => ` +
+ ${version.slug} +
+ `, + ) + .join("\n")} +
+ `; + return versionsHTML; + } + + function renderDownloads(config) { + if (!Object.keys(config.versions.current.downloads).length) { + return ""; + } + const downloadsNameDisplay = { + pdf: "PDF", + epub: "Epub", + htmlzip: "HTML", + }; + + const downloadsHTML = ` +
+
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+ ${Object.entries(config.versions.current.downloads) + .map( + ([name, url]) => ` +
+ ${downloadsNameDisplay[name]} +
+ `, + ) + .join("\n")} +
+ `; + return downloadsHTML; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const flyout = ` +
+ + Read the Docs + v: ${config.versions.current.slug} + + +
+
+ ${renderLanguages(config)} + ${renderVersions(config)} + ${renderDownloads(config)} +
+
On Read the Docs
+
+ Project Home +
+
+ Builds +
+
+ Downloads +
+
+
+
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+
+
+ +
+
+
+
+ + Hosted by Read the Docs + +
+
+ `; + + // Inject the generated flyout into the body HTML element. + document.body.insertAdjacentHTML("beforeend", flyout); + + // Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout. + document + .querySelector("#flyout-search-form") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); + }) +} + +if (themeLanguageSelector || themeVersionSelector) { + function onSelectorSwitch(event) { + const option = event.target.selectedIndex; + const item = event.target.options[option]; + window.location.href = item.dataset.url; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const versionSwitch = document.querySelector( + "div.switch-menus > div.version-switch", + ); + if (themeVersionSelector) { + let versions = config.versions.active; + if (config.versions.current.hidden || config.versions.current.type === "external") { + versions.unshift(config.versions.current); + } + const versionSelect = ` + + `; + + versionSwitch.innerHTML = versionSelect; + versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + + const languageSwitch = document.querySelector( + "div.switch-menus > div.language-switch", + ); + + if (themeLanguageSelector) { + if (config.projects.translations.length) { + // Add the current language to the options on the selector + let languages = config.projects.translations.concat( + config.projects.current, + ); + languages = languages.sort((a, b) => + a.language.name.localeCompare(b.language.name), + ); + + const languageSelect = ` + + `; + + languageSwitch.innerHTML = languageSelect; + languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + else { + languageSwitch.remove(); + } + } + }); +} + +document.addEventListener("readthedocs-addons-data-ready", function (event) { + // Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav. + document + .querySelector("[role='search'] input") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); +}); \ No newline at end of file diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js index 250f566..c7fe6c6 100644 --- a/docs/_static/language_data.js +++ b/docs/_static/language_data.js @@ -1,19 +1,12 @@ /* - * language_data.js - * ~~~~~~~~~~~~~~~~ - * * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ 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, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Porter Stemmer diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js index 7918c3f..2c774d1 100644 --- a/docs/_static/searchtools.js +++ b/docs/_static/searchtools.js @@ -1,12 +1,5 @@ /* - * searchtools.js - * ~~~~~~~~~~~~~~~~ - * * Sphinx JavaScript utilities for the full-text search. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ "use strict"; @@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") { // and returns the new score. /* score: result => { - const [docname, title, anchor, descr, score, filename] = result + const [docname, title, anchor, descr, score, filename, kind] = result return score }, */ @@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") { }; } +// 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); }; @@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => { const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; const contentRoot = document.documentElement.dataset.content_root; - const [docName, title, anchor, descr, score, _filename] = item; + 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") { @@ -99,7 +104,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -115,9 +120,11 @@ const _finishSearch = (resultCount) => { "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.` - ); + 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, @@ -137,6 +144,22 @@ const _displayNextItem = ( // 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 @@ -160,13 +183,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + 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 !== undefined) return docContent.textContent; + if (docContent) 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." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -219,6 +255,7 @@ const Search = { 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"); @@ -239,16 +276,7 @@ const Search = { 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; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,22 +312,40 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + 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(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { - let score = Math.round(100 * queryLower.length / title.length) - results.push([ + 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, + score + boost, filenames[file], + SearchResultKind.title, ]); } } @@ -308,46 +354,48 @@ const Search = { // 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([ + 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) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.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; - }); + 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 @@ -361,7 +409,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + 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 @@ -432,6 +485,7 @@ const Search = { descr, score, filenames[match[0]], + SearchResultKind.object, ]); }; Object.keys(objects).forEach((prefix) => @@ -466,14 +520,18 @@ const Search = { // 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 }); - }); + 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 @@ -496,9 +554,8 @@ const Search = { // 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]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -539,6 +596,7 @@ const Search = { null, score, filenames[file], + SearchResultKind.text, ]); } return results; @@ -549,8 +607,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/docs/about.html b/docs/about.html index a4336c7..856af75 100644 --- a/docs/about.html +++ b/docs/about.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ About pycopm — pycopm documentation - + - - - - - - - + + + + + @@ -82,8 +80,10 @@

About pycopm

-_images/droganim.gif -

pycopm, a tool for coarsening OPM Flow geological models, is being funded by the Center for Sustainable Subsurface Resources (CSSR) [project no. 331841]. +_images/droganim.gif + +

pycopm, a tool for coarsening OPM Flow geological models, is being funded by the Center for Sustainable Subsurface Resources (CSSR) [project no. 331841] +and by Expansion of Resources for CO2 Storage on the Horda Platform (ExpReCCS) [project no. 336294]. This is work in progress. Contributions are more than welcome using the fork and pull request approach.

diff --git a/docs/api.html b/docs/api.html index cef6b5d..9283f9a 100644 --- a/docs/api.html +++ b/docs/api.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm Python API — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/configuration_file.html b/docs/configuration_file.html index 675c7ce..7adbfac 100644 --- a/docs/configuration_file.html +++ b/docs/configuration_file.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ Configuration file — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/examples.html b/docs/examples.html index 3cd9046..80862ca 100644 --- a/docs/examples.html +++ b/docs/examples.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ Examples — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/genindex.html b/docs/genindex.html index 4d01dd5..d26a2b9 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -1,3 +1,5 @@ + + @@ -5,18 +7,14 @@ Index — pycopm documentation - + - - - - - - - + + + + + @@ -120,12 +118,14 @@

A

C

  • handle_mapaxes() (in module pycopm.utils.generate_coarser_files) +
    • +
  • handle_multflt() (in module pycopm.utils.generate_coarser_files)
  • handle_oper() (in module pycopm.utils.generate_coarser_files)
    • diff --git a/docs/index.html b/docs/index.html index d2e2a42..da0a195 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ Welcome to pycopm’s documentation! — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/installation.html b/docs/installation.html index 972d34d..3517e1e 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ Installation — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/introduction.html b/docs/introduction.html index 2f36409..675f59f 100644 --- a/docs/introduction.html +++ b/docs/introduction.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ Introduction — pycopm documentation - + - - - - - - - + + + + + @@ -136,7 +134,7 @@

    Roadmap

    Use min, max, or mode to scale the actnum, e.g., min makes the new coarser cell inactive if at least one cell is inactive, while max makes it active it at least one cell is active (mode by default).

    -n
    -

    Use min, max, or mode to scale endnum, eqlnum, fipnum, fluxnum, imbnum, miscnum, multnum, pvtnum, rocknum, and satnum (mode by default).

    +

    Use min, max, or mode to scale endnum, eqlnum, fipnum, fluxnum, imbnum, miscnum, multnum, opernum, pvtnum, rocknum, and satnum (mode by default).

    -s

    Use min, max, or mean to scale permx, permy, permz, poro, swatinit, and all mult(-)xyz (’’ by default, i.e., using the arithmetic average for permx/permy, harmonic average for permz, volume weighted mean for mult(-)xyz, and the pore volume weighted mean for the rest).

    @@ -145,10 +143,10 @@

    Roadmap

    Add the removed pore volume to the closest coarser cells (0 by default, 1 to enable).

    -q
    -

    Adjust the pv to the initial FGIP and FOIP from the input deck (0 by default, 1 to enable).

    +

    Adjust the pv to the initial FGIP and FOIP from the input deck; use this option only for systems with initial oil, gas, and water, e.g., norne or drogon, but no in Smeaheia (0 by default, 1 to enable).

    -t
    -

    Write and use upscaled transmissibilities (0 by default, it is advice to use only with z-coarsening).

    +

    Write and use upscaled transmissibilities by (1) armonic averaging and summing the transmissibilities in the corresponding coarsening direction and (2) scaling the face transmissibily on the coarse faces (0 by default).

    -r

    Remove CONFACT and KH from COMPDAT (1) and also remove PEQVR (2) (ITEM 13, the last entry) to compute the well transmisibility connections internally in OPM Flow using the grid properties (2 by default; 0 to not remove).

    diff --git a/docs/modules.html b/docs/modules.html index 100e7e9..c599be3 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/objects.inv b/docs/objects.inv index 7d1a96f..002aaa6 100644 Binary files a/docs/objects.inv and b/docs/objects.inv differ diff --git a/docs/output_folder.html b/docs/output_folder.html index 17af0bd..eeae5f5 100644 --- a/docs/output_folder.html +++ b/docs/output_folder.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ Output folder — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/py-modindex.html b/docs/py-modindex.html index 6dea9eb..b79635a 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -1,3 +1,5 @@ + + @@ -5,18 +7,14 @@ Python Module Index — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/pycopm.core.html b/docs/pycopm.core.html index 6fef77c..1b193fc 100644 --- a/docs/pycopm.core.html +++ b/docs/pycopm.core.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.core package — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/pycopm.core.pycopm.html b/docs/pycopm.core.pycopm.html index fe5d64b..748e98c 100644 --- a/docs/pycopm.core.pycopm.html +++ b/docs/pycopm.core.pycopm.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.core.pycopm module — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/pycopm.html b/docs/pycopm.html index 97b87b3..795a7bb 100644 --- a/docs/pycopm.html +++ b/docs/pycopm.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm package — pycopm documentation - + - - - - - - - + + + + + @@ -112,6 +110,7 @@

    Subpackagespycopm.utils.generate_coarser_files module
      +
    • coarsening_dir()
    • create_deck()
    • find_neighbors()
    • get_ijk()
      • @@ -120,6 +119,7 @@

      Subpackageshandle_fault()
    • handle_grid_props()
    • handle_mapaxes()
      • +
    • handle_multflt()
    • handle_oper()
    • handle_props()
    • handle_pv()
      • diff --git a/docs/pycopm.utils.files_writer.html b/docs/pycopm.utils.files_writer.html index df6fecf..aee39d9 100644 --- a/docs/pycopm.utils.files_writer.html +++ b/docs/pycopm.utils.files_writer.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.utils.files_writer module — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/pycopm.utils.generate_coarser_files.html b/docs/pycopm.utils.generate_coarser_files.html index 5a5fb59..6b87f47 100644 --- a/docs/pycopm.utils.generate_coarser_files.html +++ b/docs/pycopm.utils.generate_coarser_files.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.utils.generate_coarser_files module — pycopm documentation - + - - - - - - - + + + + + @@ -87,6 +85,18 @@

      pycopm.utils.generate_coarser_files module

      Utiliy methods to only create the coarser files by pycopm.

      +
      +
      +pycopm.utils.generate_coarser_files.coarsening_dir(dic)
      +

      Get the coarsenign directions

      +
      +
      Args:

      dic (dict): Global dictionary

      +
      +
      Returns:

      dic (dict): Modified global dictionary

      +
      +
      +
      +
      pycopm.utils.generate_coarser_files.create_deck(dic)
      @@ -192,6 +202,19 @@

    +
    +
    +pycopm.utils.generate_coarser_files.handle_multflt(dic, nrwo)
    +

    Handle the fault multipliers

    +
    +
    Args:

    dic (dict): Global dictionary

    +

    nrwo (list): Splited row from the input deck

    +
    +
    Returns:

    dic (dict): Modified global dictionary

    +
    +
    +
    +
    pycopm.utils.generate_coarser_files.handle_oper(dic, nrwo)
    @@ -312,12 +335,11 @@
    -pycopm.utils.generate_coarser_files.map_properties(dic, actnum, d_z, z_t, z_b, z_b_t, v_c, d_az)
    +pycopm.utils.generate_coarser_files.map_properties(dic, actnum, z_t, z_b, z_b_t, v_c)

    Mapping to the coarse properties

    Args:

    dic (dict): Global dictionary

    actnum (array): Integers with the active cells

    -

    d_z (array): Floats with the corresponding grid DZ

    z_t (array): Floats with the top cell z-center position

    z_b (array): Floats with the bottom cell z-center position

    diff --git a/docs/pycopm.utils.grid_builder.html b/docs/pycopm.utils.grid_builder.html index 3665e16..ee6c74c 100644 --- a/docs/pycopm.utils.grid_builder.html +++ b/docs/pycopm.utils.grid_builder.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.utils.grid_builder module — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/pycopm.utils.html b/docs/pycopm.utils.html index d058cbd..a7d92c1 100644 --- a/docs/pycopm.utils.html +++ b/docs/pycopm.utils.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.utils package — pycopm documentation - + - - - - - - - + + + + + @@ -98,6 +96,7 @@

    Submodulespycopm.utils.generate_coarser_files module
      +
    • coarsening_dir()
    • create_deck()
    • find_neighbors()
    • get_ijk()
      • @@ -106,6 +105,7 @@

      Submoduleshandle_fault()
    • handle_grid_props()
    • handle_mapaxes()
      • +
    • handle_multflt()
    • handle_oper()
    • handle_props()
    • handle_pv()
      • diff --git a/docs/pycopm.utils.input_values.html b/docs/pycopm.utils.input_values.html index 293d472..8d45e57 100644 --- a/docs/pycopm.utils.input_values.html +++ b/docs/pycopm.utils.input_values.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.utils.input_values module — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/pycopm.utils.properties_builder.html b/docs/pycopm.utils.properties_builder.html index b47de14..c9243f3 100644 --- a/docs/pycopm.utils.properties_builder.html +++ b/docs/pycopm.utils.properties_builder.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.utils.properties_builder module — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/pycopm.utils.runs_executer.html b/docs/pycopm.utils.runs_executer.html index 5a14139..37b4b53 100644 --- a/docs/pycopm.utils.runs_executer.html +++ b/docs/pycopm.utils.runs_executer.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ pycopm.utils.runs_executer module — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/related.html b/docs/related.html index 9515e03..7ccafb9 100644 --- a/docs/related.html +++ b/docs/related.html @@ -1,3 +1,5 @@ + + @@ -6,18 +8,14 @@ Related — pycopm documentation - + - - - - - - - + + + + + @@ -94,12 +92,14 @@

      Related

      Below are some tools that might be of interest; check them out 🙂.

      pyopmspe11

      -_images/pyopmspe11.gif +_images/pyopmspe11.gif +

      A Python framework using OPM Flow for the CSP SPE11 benchmark project.

      pyopmnearwell

      -_images/pyopmnearwell.gif +_images/pyopmnearwell.gif +

      A framework to simulate near well dynamics using OPM Flow.

      @@ -109,17 +109,20 @@

      plopm

      expreccs

      -_images/expreccs.gif +_images/expreccs.gif +

      Expansion of ResourCes for CO2 Storage on the Horda Platform.

      ad-micp

      -_images/ad-micp.gif +_images/ad-micp.gif +

      A module to study CO2 leakage remediation by microbially induced calcite precipitation (MICP).

      pymm

      -_images/pymm.gif +_images/pymm.gif +

      An open-source image-based framework for CFD in microsystems.

      diff --git a/docs/search.html b/docs/search.html index d0e73c9..6b0127c 100644 --- a/docs/search.html +++ b/docs/search.html @@ -1,3 +1,5 @@ + + @@ -5,19 +7,15 @@ Search — pycopm documentation - + - - - - - - - + + + + + diff --git a/docs/searchindex.js b/docs/searchindex.js index 3ca3adf..2314ce6 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["about", "api", "configuration_file", "examples", "index", "installation", "introduction", "modules", "output_folder", "pycopm", "pycopm.core", "pycopm.core.pycopm", "pycopm.utils", "pycopm.utils.files_writer", "pycopm.utils.generate_coarser_files", "pycopm.utils.grid_builder", "pycopm.utils.input_values", "pycopm.utils.properties_builder", "pycopm.utils.runs_executer", "related"], "filenames": ["about.rst", "api.rst", "configuration_file.rst", "examples.rst", "index.rst", "installation.rst", "introduction.rst", "modules.rst", "output_folder.rst", "pycopm.rst", "pycopm.core.rst", 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"Welcome to pycopm\u2019s documentation!", "Installation", "Introduction", "pycopm", "Output folder", "pycopm package", "pycopm.core package", "pycopm.core.pycopm module", "pycopm.utils package", "pycopm.utils.files_writer module", "pycopm.utils.generate_coarser_files module", "pycopm.utils.grid_builder module", "pycopm.utils.input_values module", "pycopm.utils.properties_builder module", "pycopm.utils.runs_executer module", "Related"], "titleterms": {"": 4, "about": 0, "ad": 19, "an": 8, "api": 1, "build": 5, "concept": 6, "configur": [2, 3, 8], "content": [9, 10, 12], "core": [10, 11], "deck": [3, 8], "document": 4, "drogon": 3, "exampl": 3, "exprecc": 19, "file": [2, 3, 8], "files_writ": 13, "flow": [3, 5, 8], "folder": 8, "generate_coarser_fil": 14, "grid_build": 15, "hello": 3, "indic": 4, "input": 8, "input_valu": 16, "instal": 5, "introduct": 6, "linux": 5, "maco": 5, "micp": 19, "modul": [9, 10, 11, 12, 13, 14, 15, 16, 17, 18], "norn": 3, "opm": [3, 5, 8], "output": 8, "overview": 6, "packag": [5, 9, 10, 12], "plopm": 19, "properties_build": 17, "pycopm": [0, 1, 4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], "pymm": 19, "pyopmnearwel": 19, "pyopmspe11": 19, "python": [1, 5], "relat": 19, "roadmap": 6, "runs_execut": 18, "smeaheia": 3, "sourc": 5, "spe10": 3, "submodul": [10, 12], "subpackag": 9, "tabl": 4, "util": [12, 13, 14, 15, 16, 17, 18], "via": [3, 8], "welcom": 4, "window": 5, "world": 3}}) \ No newline at end of file diff --git a/docs/text/about.rst b/docs/text/about.rst index 9ea1f09..a66ddfc 100644 --- a/docs/text/about.rst +++ b/docs/text/about.rst @@ -5,6 +5,7 @@ About pycopm .. image:: ./figs/droganim.gif :scale: 65% -**pycopm**, a tool for coarsening OPM Flow geological models, is being funded by the `Center for Sustainable Subsurface Resources (CSSR) `_ [project no. 331841]. +**pycopm**, a tool for coarsening OPM Flow geological models, is being funded by the `Center for Sustainable Subsurface Resources (CSSR) `_ [project no. 331841] +and by `Expansion of Resources for CO2 Storage on the Horda Platform (ExpReCCS) `_ [project no. 336294]. This is work in progress. Contributions are more than welcome using the fork and pull request approach. \ No newline at end of file diff --git a/docs/text/introduction.rst b/docs/text/introduction.rst index f7c7199..d53410e 100644 --- a/docs/text/introduction.rst +++ b/docs/text/introduction.rst @@ -40,11 +40,11 @@ where -y Vector of y-coarsening, see the description for -x ('' by default). -z Vector of z-coarsening, see the description for -x ('' by default). -a Use `min`, `max`, or `mode` to scale the actnum, e.g., min makes the new coarser cell inactive if at least one cell is inactive, while max makes it active it at least one cell is active (`mode` by default). --n Use `min`, `max`, or `mode` to scale endnum, eqlnum, fipnum, fluxnum, imbnum, miscnum, multnum, pvtnum, rocknum, and satnum (`mode` by default). +-n Use `min`, `max`, or `mode` to scale endnum, eqlnum, fipnum, fluxnum, imbnum, miscnum, multnum, opernum, pvtnum, rocknum, and satnum (`mode` by default). -s Use `min`, `max`, or `mean` to scale permx, permy, permz, poro, swatinit, and all mult(-)xyz ('' by default, i.e., using the arithmetic average for permx/permy, harmonic average for permz, volume weighted mean for mult(-)xyz, and the pore volume weighted mean for the rest). -p Add the removed pore volume to the closest coarser cells (`0` by default, `1` to enable). --q Adjust the pv to the initial FGIP and FOIP from the input deck (`0` by default, `1` to enable). --t Write and use upscaled transmissibilities (`0` by default, it is advice to use only with z-coarsening). +-q Adjust the pv to the initial FGIP and FOIP from the input deck; use this option only for systems with initial oil, gas, and water, e.g., norne or drogon, but no in Smeaheia (`0` by default, `1` to enable). +-t Write and use upscaled transmissibilities by (`1`) armonic averaging and summing the transmissibilities in the corresponding coarsening direction and (`2`) scaling the face transmissibily on the coarse faces (`0` by default). -r Remove CONFACT and KH from COMPDAT (`1`) and also remove PEQVR (`2`) (ITEM 13, the last entry) to compute the well transmisibility connections internally in OPM Flow using the grid properties (`2` by default; `0` to not remove). -j Tuning parameter to avoid creation of neighbouring connections in the coarser model where there are discontinuities between cells along the z direction, e.g., around faults ('' by default, i.e., nothing corrected; if need it, try with values of the order of 1). -m Execute a dry run on the input deck to generate the static properties ('prep'), generate only the coarse files ('deck'), only exectute a dry run on the generated coarse model ('dry'), 'prep_deck', 'deck_dry', or do all ('all') (`prep_deck` by default). diff --git a/src/pycopm/core/pycopm.py b/src/pycopm/core/pycopm.py index af4588a..9fc7c27 100644 --- a/src/pycopm/core/pycopm.py +++ b/src/pycopm/core/pycopm.py @@ -25,10 +25,12 @@ def pycopm(): dic["pat"] = os.path.dirname(__file__)[:-5] # Path to the pycopm folder dic["exe"] = os.getcwd() # Path to the folder of the input.txt file dic["flow"] = cmdargs["flow"].strip() # Path to flow - dic["how"] = cmdargs["how"].strip() # Max, min, or mode for satnum + dic["how"] = (cmdargs["how"].strip()).split(",") # Max, min, or mode for actnum dic["nhow"] = cmdargs["nhow"].strip() # Max, min, or mode for other nums dic["show"] = cmdargs["show"].strip() # Max, min, or mean for static props - dic["jump"] = cmdargs["jump"].strip() # Tuning parameter to remove nnc + dic["jump"] = (cmdargs["jump"].strip()).split( + "," + ) # Tuning parameters to remove nnc dic["write"] = cmdargs["write"].strip() # Name of the generated deck dic["mode"] = cmdargs["mode"].strip() # What to run dic["label"] = cmdargs["label"].strip() # Prefix to the generted inc files @@ -172,7 +174,7 @@ def load_parser(): "--nhow", default="mode", help="Use 'min', 'max', or 'mode' to scale endnum, eqlnum, fipnum, fluxnum, imbnum, " - "miscnum, multnum, pvtnum, rocknum, and satnum ('mode' by default).", + "miscnum, multnum, opernum, pvtnum, rocknum, and satnum ('mode' by default).", ) parser.add_argument( "-s", @@ -193,14 +195,17 @@ def load_parser(): "-q", "--fipcorr", default=0, - help="Adjust the pv to the initial FGIP and FOIP from the input deck ('0' by default).", + help="Adjust the pv to the initial FGIP and FOIP from the input deck; use this option " + "only for systems with initial oil, gas, and water, e.g., norne or drogon, but " + "no in Smeaheia ('0' by default, '1' to enable).", ) parser.add_argument( "-t", "--trans", default=0, - help="Write and use upscaled transmissibilities ('0' by default, it is advice to use " - "only with z-coarsening).", + help="Write and use upscaled transmissibilities by ('1') armonic averaging and summing " + "the transmissibilities in the corresponding coarsening direction and ('2') scaling " + "the face transmissibily on the coarse faces ('0' by default).", ) parser.add_argument( "-r", diff --git a/src/pycopm/utils/generate_coarser_files.py b/src/pycopm/utils/generate_coarser_files.py index eec3b78..a1c4379 100644 --- a/src/pycopm/utils/generate_coarser_files.py +++ b/src/pycopm/utils/generate_coarser_files.py @@ -1,6 +1,6 @@ # SPDX-FileCopyrightText: 2024 NORCE # SPDX-License-Identifier: GPL-3.0 -# pylint: disable=R0912,R0913,R0914,R0915,C0302,R0917 +# pylint: disable=R0912,R0913,R0914,R0915,C0302,R0917,R1702 """ Utiliy methods to only create the coarser files by pycopm. @@ -47,7 +47,8 @@ def create_deck(dic): f"{dic['flow']} {dic['deck']}_PREP_PYCOPM_DRYRUN.DATA {dic['flags']} " f"--output-dir={dic['fol']}" ) - os.system(f"mv {dic['deck']}_PREP_PYCOPM_DRYRUN.DATA " + f"{dic['fol']}") + if dic["fol"] != ".": + os.system(f"mv {dic['deck']}_PREP_PYCOPM_DRYRUN.DATA " + f"{dic['fol']}") for name in [".INIT", ".EGRID"]: files = f"{dic['fol']}/{dic['deck']}_PREP_PYCOPM_DRYRUN" + name if not os.path.isfile(files): @@ -65,6 +66,7 @@ def create_deck(dic): print("\nThe dry run succeeded") if dic["mode"] in ["prep_deck", "deck", "deck_dry", "all"]: + coarsening_dir(dic) dic["deck"] = f"{dic['fol']}/{dic['deck']}_PREP_PYCOPM_DRYRUN" for name in [".INIT", ".EGRID"]: files = dic["deck"] + name @@ -101,7 +103,7 @@ def create_deck(dic): if dic["ini"].has_kw(name.upper()): if max(dic["ini"].iget_kw(name.upper())[0]) > 1: dic["grids"] += [name] - if dic["trans"] == 1: + if dic["trans"] > 0: for name in ["tranx", "trany", "tranz"]: dic["props"] += [name] for name in [ @@ -110,6 +112,7 @@ def create_deck(dic): "fipnum", "imbnum", "miscnum", + "opernum", "pvtnum", "rocknum", "satnum", @@ -121,8 +124,9 @@ def create_deck(dic): dic["con"] = np.array([0 for _ in range(nc)]) dic["porv"] = np.array(dic["ini"].iget_kw("PORV")[0]) actnum = np.array([0 for _ in range(nc)]) - d_z = np.array([np.nan for _ in range(nc)]) - d_az = np.array([np.nan for _ in range(nc)]) + for i in ["x", "y", "z"]: + dic[f"d_{i}"] = np.array([np.nan for _ in range(nc)]) + dic[f"d_a{i}"] = np.array([np.nan for _ in range(nc)]) v_c = np.array([np.nan for _ in range(nc)]) z_t = np.array([np.nan for _ in range(nc)]) z_b = np.array([np.nan for _ in range(nc)]) @@ -134,17 +138,27 @@ def create_deck(dic): zbi = [14, 17, 20, 23] cxyz = dic["grid"].export_corners(dic["grid"].export_index()) for cell in dic["grid"].cells(): + dic["d_x"][cell.global_index] = dic["grid"].get_cell_dims( + ijk=(cell.i, cell.j, cell.k) + )[0] + dic["d_y"][cell.global_index] = dic["grid"].get_cell_dims( + ijk=(cell.i, cell.j, cell.k) + )[1] actnum[cell.global_index] = cell.active z_t[cell.global_index] = min(cxyz[cell.global_index][i] for i in zti) z_b[cell.global_index] = max(cxyz[cell.global_index][i] for i in zti) tmp = max(cxyz[cell.global_index][i] for i in zbi) z_b_t[cell.global_index] = tmp - z_t[cell.global_index] - d_z[cell.global_index] = dic["grid"].cell_dz(ijk=(cell.i, cell.j, cell.k)) + dic["d_z"][cell.global_index] = dic["grid"].cell_dz( + ijk=(cell.i, cell.j, cell.k) + ) v_c[cell.global_index] = dic["grid"].cell_volume( ijk=(cell.i, cell.j, cell.k) ) if cell.active == 1: - d_az[cell.global_index] = dic["grid"].cell_dz( + dic["d_ax"][cell.global_index] = dic["d_x"][cell.global_index] + dic["d_ay"][cell.global_index] = dic["d_y"][cell.global_index] + dic["d_az"][cell.global_index] = dic["grid"].cell_dz( ijk=(cell.i, cell.j, cell.k) ) for name in dic["props"] + dic["regions"] + dic["grids"]: @@ -152,11 +166,12 @@ def create_deck(dic): n ] if not dic["show"]: - dic["permx"][cell.global_index] *= d_z[cell.global_index] - dic["permy"][cell.global_index] *= d_z[cell.global_index] + dic["permx"][cell.global_index] *= dic["d_z"][cell.global_index] + dic["permy"][cell.global_index] *= dic["d_z"][cell.global_index] if dic["permz"][cell.global_index] != 0: dic["permz"][cell.global_index] = ( - d_z[cell.global_index] / dic["permz"][cell.global_index] + dic["d_z"][cell.global_index] + / dic["permz"][cell.global_index] ) dic["poro"][cell.global_index] *= dic["porv"][cell.global_index] if "swatinit" in dic["props"]: @@ -165,6 +180,12 @@ def create_deck(dic): ] for name in dic["mults"]: dic[name][cell.global_index] *= v_c[cell.global_index] + if len(dic["coardir"]) == 1 and dic["trans"] == 1: + drc = dic["coardir"][0] + if dic[f"tran{drc}"][cell.global_index] != 0: + dic[f"tran{drc}"][cell.global_index] = ( + 1.0 / dic[f"tran{drc}"][cell.global_index] + ) n += 1 # Coarsening @@ -177,15 +198,13 @@ def create_deck(dic): dic["kc"][dic["ijk"][2]], ) sys.exit() - clusmin, clusmax, rmv = map_properties( - dic, actnum, d_z, z_t, z_b, z_b_t, v_c, d_az - ) + process_the_deck(dic) + clusmin, clusmax, rmv = map_properties(dic, actnum, z_t, z_b, z_b_t, v_c) if dic["pvcorr"] == 1: handle_pv(dic, clusmin, clusmax, rmv) handle_cp_grid(dic) write_grid(dic) write_props(dic) - process_the_deck(dic) with open( f"{dic['exe']}/{dic['fol']}/{dic['write']}.DATA", "w", @@ -269,14 +288,13 @@ def create_deck(dic): print("\nThe dry run of the coarse model succeeded\n") -def map_properties(dic, actnum, d_z, z_t, z_b, z_b_t, v_c, d_az): +def map_properties(dic, actnum, z_t, z_b, z_b_t, v_c): """ Mapping to the coarse properties Args: dic (dict): Global dictionary\n actnum (array): Integers with the active cells\n - d_z (array): Floats with the corresponding grid DZ\n z_t (array): Floats with the top cell z-center position\n z_b (array): Floats with the bottom cell z-center position @@ -285,59 +303,200 @@ def map_properties(dic, actnum, d_z, z_t, z_b, z_b_t, v_c, d_az): """ clusmax = pd.Series(actnum).groupby(dic["con"]).max() + clusming = pd.Series(actnum).groupby(dic["con"]).min() + clusmode = ( + pd.Series(actnum).groupby(dic["con"]).agg(lambda x: pd.Series.mode(x).iat[0]) + ) freq = pd.Series(actnum).groupby(dic["con"]).sum() dz_c = pd.Series(z_b_t).groupby(dic["con"]).mean() - h_tot = pd.Series(d_z).groupby(dic["con"]).sum() - ha_tot = pd.Series(d_az).groupby(dic["con"]).sum() + for i in ["x", "y", "z"]: + dic[f"{i}_tot"] = pd.Series(dic[f"d_{i}"]).groupby(dic["con"]).sum() + dic[f"{i}a_tot"] = pd.Series(dic[f"d_a{i}"]).groupby(dic["con"]).sum() v_tot = pd.Series(v_c).groupby(dic["con"]).sum() - if dic["how"] == "min": - clusmin = pd.Series(actnum).groupby(dic["con"]).min() - clust = clusmin - elif dic["how"] == "mode": - clusmin = ( - pd.Series(actnum) - .groupby(dic["con"]) - .agg(lambda x: pd.Series.mode(x).iat[0]) - ) - clust = clusmin + if len(dic["how"]) == 1: + if dic["how"][0] == "min": + clusmin = clusming + clust = clusmin + elif dic["how"][0] == "mode": + clusmin = clusmode + clust = clusmin + else: + clusmin = clusmax + clust = clusmax else: - clusmin = clusmax - clust = clusmax - if dic["jump"]: - rmv = 1 * ( - ( + clusmin = 1 * freq + clust = 1 * freq + for k, val in enumerate(dic["how"]): + if val == "min": + clusmin[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] = clusming[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] + clust[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] = clusming[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] + elif val == "mode": + clusmin[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] = clusmode[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] + clust[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] = clusmode[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] + else: + clusmin[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] = clusmax[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] + clust[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] = clusmax[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] + if dic["jump"][0]: + if len(dic["jump"]) == 1: + rmv = 1 * ( + ( + pd.Series(z_b).groupby(dic["con"]).max() + - pd.Series(z_t).groupby(dic["con"]).min() + ) + < float(dic["jump"][0]) * dz_c + ) + else: + rmv = 0.0 * freq + deltaz = ( pd.Series(z_b).groupby(dic["con"]).max() - pd.Series(z_t).groupby(dic["con"]).min() ) - < float(dic["jump"]) * dz_c - ) + for k, val in enumerate(dic["jump"]): + rmv[ + k * dic["nx"] * dic["ny"] + 1 : (k + 1) * dic["nx"] * dic["ny"] + 2 + ] = ( + 1 + * (deltaz < float(val) * dz_c)[ + k * dic["nx"] * dic["ny"] + + 1 : (k + 1) * dic["nx"] * dic["ny"] + + 2 + ] + ) dic["actnum_c"] = [int(val * r_m) for val, r_m in zip(clust, rmv)] else: rmv = 0 * dz_c + 1 dic["actnum_c"] = [int(val) for val in clust] p_vs = pd.Series(dic["porv"]).groupby(dic["con"]).sum() dic["porv_c"] = [f"{val}" for val in p_vs] + drc = dic["coardir"][0] for name in dic["props"]: if not dic["show"]: c_c = pd.Series(dic[name]).groupby(dic["con"]).sum() if name in ["permx", "permy"]: dic[f"{name}_c"] = [ f"{val/h_t}" if h_t * val > 0 else "0" - for val, h_t in zip(c_c, h_tot) + for val, h_t in zip(c_c, dic["z_tot"]) ] - elif name in ["tranx", "trany"]: - dic[f"{name}_c"] = [f"{val}" if val > 0 else "0" for val in c_c] + elif name == "tranx": + if "x" in dic["coardir"]: + if dic["trans"] == 1: + c_m = pd.Series(dic[name]).groupby(dic["con"]).min() + dic[f"{name}_c"] = [ + f"{l_t/val}" if m_v * val > 0 else "0" + for val, m_v, l_t in zip(c_c, c_m, dic[f"{drc}_tot"]) + ] + else: + # conxs = pd.Series(dic[name]).groupby(dic["con"]).agg(lambda x: + # sum(max(list(x)[i],np.roll(x, 2)[i])>0 for i in + # range(int(len(x)/2))) == int(len(x)/2)) + # conys = pd.Series(dic["trany"]).groupby(dic["con"]).agg(lambda x: + # sum(max(list(x)[2*i],list(x)[2*i+1])>0 for i in range(int(len(x)/2)-1)) + # == int(len(x)/2)-1) + c_ls = pd.Series(dic[name]).groupby(dic["con"]).mean() + d_ls = pd.Series(dic[name]).groupby(dic["con"]).min() + # d_ls = pd.Series(dic[f"d_x"]).groupby(dic["con"]).mean() + # dic[f"{name}_c"] = [f"{val*d_l/l_t}" if val*conx*cony > 0 else "0" for + # val, d_l, l_t, conx, cony in zip(c_ls, d_ls, dic[f"x_tot"], conxs, conys)] + dic[f"{name}_c"] = [ + f"{val}" if d_l > 0 else "0" for val, d_l in zip(c_ls, d_ls) + ] + else: + dic[f"{name}_c"] = [ + f"{val*l_a/l_t}" if val > 0 else "0" + for val, l_a, l_t in zip( + c_c, dic[f"{drc}a_tot"], dic[f"{drc}_tot"] + ) + ] + elif name == "trany": + if "y" in dic["coardir"]: + if dic["trans"] == 1: + c_m = pd.Series(dic[name]).groupby(dic["con"]).min() + dic[f"{name}_c"] = [ + f"{l_t/val}" if m_v * val > 0 else "0" + for val, m_v, l_t in zip(c_c, c_m, dic[f"{drc}_tot"]) + ] + else: + # conxs = pd.Series(dic["tranx"]).groupby(dic["con"]).agg(lambda + # x: sum(max(list(x)[i],np.roll(x, 2)[i])>0 for i in + # range(int(len(x)/2)-1)) == int(len(x)/2)-1) + # conys = pd.Series(dic[name]).groupby(dic["con"]).agg(lambda + # x: sum(max(list(x)[2*i],list(x)[2*i+1])>0 for i in + # range(int(len(x)/2))) == int(len(x)/2)) + c_ls = pd.Series(dic[name]).groupby(dic["con"]).mean() + d_ls = pd.Series(dic[name]).groupby(dic["con"]).min() + # d_ls = pd.Series(dic[f"d_y"]).groupby(dic["con"]).mean() + # dic[f"{name}_c"] = [f"{val*d_l/l_t}" if val*conx*cony > 0 + # else "0" for val, d_l, l_t, conx, cony in zip(c_ls, d_ls, + # dic[f"y_tot"], conxs, conys)] + dic[f"{name}_c"] = [ + f"{val}" if d_l > 0 else "0" for val, d_l in zip(c_ls, d_ls) + ] + else: + dic[f"{name}_c"] = [ + f"{val*l_a/l_t}" if val > 0 else "0" + for val, l_a, l_t in zip( + c_c, dic[f"{drc}a_tot"], dic[f"{drc}_tot"] + ) + ] elif name == "tranz": - d_l = pd.Series(d_z).groupby(dic["con"]).last() - c_c = pd.Series(dic[name]).groupby(dic["con"]).last() - dic["tranz_c"] = [ - f"{val*d_h/h_t}" if h_t * val > 0 else "0" - for val, h_t, d_h in zip(c_c, h_tot, d_l) - ] + if "z" in dic["coardir"]: + if dic["trans"] == 1: + c_m = pd.Series(dic[name]).groupby(dic["con"]).min() + l_as = pd.Series(dic["d_az"]).groupby(dic["con"]).mean() + c_c[: -dic["nx"] * dic["ny"]] = ( + ( + np.array(c_c[: -dic["nx"] * dic["ny"]]) + + np.array(c_c[dic["nx"] * dic["ny"] :]) + ) + * (np.array(c_m[: -dic["nx"] * dic["ny"]] > 0)) + * (np.array(c_m[dic["nx"] * dic["ny"] :] > 0)) + ) + dic[f"{name}_c"] = [ + f"{1.*l_a/(val * l_t)}" if val > 0 else "0" + for val, l_t, l_a in zip(c_c, dic[f"{drc}_tot"], l_as) + ] + else: + c_ls = pd.Series(dic[name]).groupby(dic["con"]).last() + d_ls = pd.Series(dic["d_z"]).groupby(dic["con"]).last() + dic[f"{name}_c"] = [ + f"{val*d_l/l_t}" if val > 0 else "0" + for val, d_l, l_t in zip(c_ls, d_ls, dic[f"{drc}_tot"]) + ] + else: + dic[f"{name}_c"] = [ + f"{val*l_a/l_t}" if val > 0 else "0" + for val, l_a, l_t in zip( + c_c, dic[f"{drc}a_tot"], dic[f"{drc}_tot"] + ) + ] elif name == "permz": dic["permz_c"] = [ f"{h_t/val}" if h_t * val > 0 else "0" - for val, h_t in zip(c_c, ha_tot) + for val, h_t in zip(c_c, dic["za_tot"]) ] elif name in ["poro", "swatinit"]: dic[f"{name}_c"] = [ @@ -486,6 +645,28 @@ def get_ijk(dic, i_d): return i, j, k +def coarsening_dir(dic): + """ + Get the coarsenign directions + + Args: + dic (dict): Global dictionary + + Returns: + dic (dict): Modified global dictionary + + """ + dic["coardir"] = "" + if len(dic["cijk"]) > 2: + for i, drc in enumerate(["x", "y", "z"]): + if dic["cijk"][i] > 1: + dic["coardir"] += drc + else: + for drc in ["x", "y", "z"]: + if dic[f"{drc}coar"]: + dic["coardir"] += drc + + def write_grid(dic): """ Write the corner-point grid @@ -712,19 +893,20 @@ def process_the_deck(dic): dic (dict): Modified global dictionary """ - dic["lol"], dic["lolc"] = [], [] + dic["lol"], dic["lolc"], dic["flts"] = [], [], [] dic["dimens"] = False dic["removeg"] = False dic["welspecs"] = False dic["compdat"] = False dic["compsegs"] = False dic["mapaxes"] = False - dic["props"] = False + dic["prop"] = False dic["oper"] = False dic["region"] = False dic["schedule"] = False dic["fault"] = False dic["rptsrt"] = False + dic["multflt"] = False with open(dic["deck"] + ".DATA", "r", encoding=dic["encoding"]) as file: for row in csv.reader(file): nrwo = str(row)[2:-2].strip() @@ -773,15 +955,15 @@ def handle_props(dic, nrwo): dic (dict): Modified global dictionary """ - if nrwo == "PROPS" and not dic["props"]: - dic["props"] = True + if nrwo == "PROPS" and not dic["prop"]: + dic["prop"] = True dic["lol"].append(nrwo + "\n") return True - if dic["props"]: + if dic["prop"]: if handle_oper(dic, nrwo): return True if nrwo in ["REGIONS", "SOLUTION"]: - dic["props"] = False + dic["prop"] = False return False @@ -798,7 +980,7 @@ def handle_oper(dic, nrwo): """ if nrwo in ["EQUALS", "COPY", "ADD", "MULTIPLY"]: - if not dic["props"] and nrwo == "COPY": + if not dic["prop"] and nrwo == "COPY": return False dic["oper"] = True dic["lol"].append(nrwo) @@ -820,7 +1002,7 @@ def handle_oper(dic, nrwo): edit[7] = str(dic["kc"][int(edit[7])]) dic["lol"].append(" ".join(edit)) return True - if not dic["props"]: + if not dic["prop"]: dic["lol"].append(nrwo) return False @@ -914,6 +1096,8 @@ def handle_grid_props(dic, nrwo): return True if handle_mapaxes(dic, nrwo): return True + if handle_multflt(dic, nrwo): + return True # if handle_oper(dic, nrwo): # return True if nrwo == "PROPS": @@ -921,7 +1105,7 @@ def handle_grid_props(dic, nrwo): dic["lol"].append("EDIT\n") dic["lol"].append("INCLUDE") dic["lol"].append(f"'{dic['label']}PORV.INC' /\n") - if dic["trans"] == 1: + if dic["trans"] > 0: for name in ["tranx", "trany", "tranz"]: dic["lol"].append("INCLUDE") dic["lol"].append(f"'{dic['label']}{name.upper()}.INC' /\n") @@ -930,6 +1114,35 @@ def handle_grid_props(dic, nrwo): return False +def handle_multflt(dic, nrwo): + """ + Handle the fault multipliers + + Args: + dic (dict): Global dictionary\n + nrwo (list): Splited row from the input deck + + Returns: + dic (dict): Modified global dictionary + + """ + if "MULTFLT" in nrwo: + edit = nrwo.split() + if edit[0] != "MULTFLT": + return False + dic["multflt"] = True + dic["lol"].append(edit[0]) + return True + if dic["multflt"]: + edit = nrwo.split() + if edit: + dic["lol"].append(nrwo) + if edit[0] == "/": + dic["multflt"] = False + return True + return False + + def handle_mapaxes(dic, nrwo): """ Keep the mapping so the grids have the same view @@ -974,6 +1187,7 @@ def handle_fault(dic, nrwo): if nrwo == "FAULTS": dic["fault"] = True dic["lol"].append(nrwo) + dic["afault"] = [] return True if dic["fault"]: edit = nrwo.split() diff --git a/tests/test_generic_deck.py b/tests/test_generic_deck.py index c92551a..c3b919c 100644 --- a/tests/test_generic_deck.py +++ b/tests/test_generic_deck.py @@ -67,7 +67,7 @@ def test_generic_deck(): "coarser", "-m", "deck_dry", - "p", + "-p", "1", "-n", "mode", @@ -100,4 +100,24 @@ def test_generic_deck(): ) assert os.path.exists(f"{cwd}/tests/decks/coarser/TRANS.INIT") assert os.path.exists(f"{cwd}/tests/decks/coarser/TRANS.EGRID") + subprocess.run( + [ + "pycopm", + "-i", + "HELLO_WORLD.DATA", + "-o", + "coarser", + "-c", + "5,4,1", + "-m", + "deck_dry", + "-t", + "2", + "-w", + "TRANS2", + ], + check=True, + ) + assert os.path.exists(f"{cwd}/tests/decks/coarser/TRANS2.INIT") + assert os.path.exists(f"{cwd}/tests/decks/coarser/TRANS2.EGRID") os.chdir(cwd)