From 00282c53c32bde171a8ac838771a2b88a219103d Mon Sep 17 00:00:00 2001 From: Anubhav Jain Date: Fri, 15 Feb 2019 11:32:50 -0800 Subject: [PATCH] Update to v0.8.6 --- atomate/__init__.py | 2 +- ...4b629275000c607845a73db48e6ac7f90e2c66.png | Bin 0 -> 524 bytes ...bf7e6d55dfb97d60bdb21b0339d8b343f3ba84.png | Bin 0 -> 469 bytes ...4bfec245799ab29aace193d2a6a9ca12c107b0.png | Bin 0 -> 308 bytes ...66981dc77862de77b6ecfcb64aad59b425cbaf.png | Bin 0 -> 221 bytes ...a97789fe1a1365e5a6db0b58fc1abec5dfeb46.png | Bin 0 -> 471 bytes ...ebfcff6eadbfdcfbed124f9584df0c3570dc8a.png | Bin 0 -> 467 bytes ...be806f44b78982eb821332699a2c84e086485d.png | Bin 0 -> 384 bytes ...9a37bbd7b0416548ee19df7cf0858bb9ec46b1.png | Bin 0 -> 303 bytes ...763521c82d5102be5a3f148fe107a4705627c7.png | Bin 0 -> 460 bytes ...28b83e95abf8aa59bcd91638cd7497b0045c5f.png | Bin 0 -> 395 bytes ...af98f30bcea97cee6215f77d3f45e87073d56d.png | Bin 0 -> 966 bytes docs/_sources/changelog.rst.txt | 4 + docs/_sources/contributors.rst.txt | 2 +- docs/_static/basic.css | 11 + docs/_static/doctools.js | 10 +- docs/_static/documentation_options.js | 295 +++- docs/_static/searchtools.js | 351 +--- docs/atomate.common.firetasks.html | 14 +- docs/atomate.common.firetasks.tests.html | 68 +- docs/atomate.common.html | 14 +- docs/atomate.feff.firetasks.html | 12 +- docs/atomate.feff.firetasks.tests.html | 12 +- docs/atomate.feff.fireworks.html | 12 +- docs/atomate.feff.fireworks.tests.html | 12 +- docs/atomate.feff.html | 12 +- docs/atomate.feff.workflows.html | 12 +- docs/atomate.feff.workflows.tests.html | 12 +- docs/atomate.html | 94 +- docs/atomate.lammps.firetasks.html | 12 +- docs/atomate.lammps.fireworks.html | 12 +- docs/atomate.lammps.html | 14 +- docs/atomate.lammps.workflows.html | 12 +- docs/atomate.qchem.firetasks.html | 12 +- docs/atomate.qchem.firetasks.tests.html | 12 +- docs/atomate.qchem.fireworks.html | 12 +- docs/atomate.qchem.html | 22 +- 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docs/contributors.html | 12 +- docs/creating_workflows.html | 24 +- docs/customizing_workflows.html | 14 +- docs/developer_installation.html | 12 +- docs/genindex.html | 704 +++++++- docs/gibbs_workflow_tutorial.html | 30 +- docs/index.html | 12 +- docs/installation.html | 12 +- docs/license.html | 10 +- docs/modules.html | 14 +- docs/objects.inv | Bin 5211 -> 7477 bytes docs/py-modindex.html | 215 ++- docs/running_workflows.html | 18 +- docs/search.html | 11 +- docs/searchindex.js | 2 +- docs/workflow_yaml_reference.html | 14 +- docs_rst/changelog.rst | 4 + docs_rst/contributors.rst | 2 +- setup.py | 2 +- 80 files changed, 5380 insertions(+), 946 deletions(-) create mode 100644 docs/_images/math/1a4b629275000c607845a73db48e6ac7f90e2c66.png create mode 100644 docs/_images/math/21bf7e6d55dfb97d60bdb21b0339d8b343f3ba84.png create mode 100644 docs/_images/math/294bfec245799ab29aace193d2a6a9ca12c107b0.png create mode 100644 docs/_images/math/3666981dc77862de77b6ecfcb64aad59b425cbaf.png 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!jQuery(node.parentNode).hasClass(className)) { + 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) { @@ -148,7 +150,9 @@ var Documentation = { this.fixFirefoxAnchorBug(); this.highlightSearchWords(); this.initIndexTable(); - + if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) { + this.initOnKeyListeners(); + } }, /** @@ -308,4 +312,4 @@ _ = Documentation.gettext; $(document).ready(function() { Documentation.init(); -}); \ No newline at end of file +}); diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index bdc4c35e9..147685d35 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,9 +1,296 @@ var DOCUMENTATION_OPTIONS = { - URL_ROOT: '', - VERSION: '0.8.5', + URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), + VERSION: '0.8.6', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', HAS_SOURCE: true, - SOURCELINK_SUFFIX: '.txt' -}; \ No newline at end of file + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SEARCH_LANGUAGE_STOP_WORDS: ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"] +}; + + + +/* Non-minified version JS is _stemmer.js if file is provided */ +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + + + + +var splitChars = (function() { + var result = {}; + var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, + 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, + 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, + 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, + 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, + 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, + 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, + 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, + 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, + 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; + var i, j, start, end; + for (i = 0; i < singles.length; i++) { + result[singles[i]] = true; + } + var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], + [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], + [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], + [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], + [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], + [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], + [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], + [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], + [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], + [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], + [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], + [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], + [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], + [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], + [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], + [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], + [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], + [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], + [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], + [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], + [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], + [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], + [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], + [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], + [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], + [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], + [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], + [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], + [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], + [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], + [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], + [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], + [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], + [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], + [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], + [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], + [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], + [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], + [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], + [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], + [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], + [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], + [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], + [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], + [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], + [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], + [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], + [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], + [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; + for (i = 0; i < ranges.length; i++) { + start = ranges[i][0]; + end = ranges[i][1]; + for (j = start; j <= end; j++) { + result[j] = true; + } + } + return result; +})(); + +function splitQuery(query) { + var result = []; + var start = -1; + for (var i = 0; i < query.length; i++) { + if (splitChars[query.charCodeAt(i)]) { + if (start !== -1) { + result.push(query.slice(start, i)); + start = -1; + } + } else if (start === -1) { + start = i; + } + } + if (start !== -1) { + result.push(query.slice(start)); + } + return result; +} + + diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js index 41b833677..7473859b2 100644 --- a/docs/_static/searchtools.js +++ b/docs/_static/searchtools.js @@ -1,5 +1,5 @@ /* - * searchtools.js_t + * searchtools.js * ~~~~~~~~~~~~~~~~ * * Sphinx JavaScript utilities for the full-text search. @@ -9,323 +9,44 @@ * */ - -/* Non-minified version JS is _stemmer.js if file is provided */ -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' +if (!Scorer) { + /** + * Simple result scoring code. + */ + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [filename, title, anchor, descr, score] + // and returns the new score. + /* + score: function(result) { + return result[4]; + }, + */ + + // 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, + // query found in terms + term: 5 }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } } - - -/** - * Simple result scoring code. - */ -var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [filename, title, anchor, descr, score] - // and returns the new score. - /* - score: function(result) { - return result[4]; - }, - */ - - // 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, - // query found in terms - term: 5 -}; - - - - - -var splitChars = (function() { - var result = {}; - var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, - 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, - 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, - 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, - 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, - 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, - 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, - 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, - 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, - 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; - var i, j, start, end; - for (i = 0; i < singles.length; i++) { - result[singles[i]] = true; - } - var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], - [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], - [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], - [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], - [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], - [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], - [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], - [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], - [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], - [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], - [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], - [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], - [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], - [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], - [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], - [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], - [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], - [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], - [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], - [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], - [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], - [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], - [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], - [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], - [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], - [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], - [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], - [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], - [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], - [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], - [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], - [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], - [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], - [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], - [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], - [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], - [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], - [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], - [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], - [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], - [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], - [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], - [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], - [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], - [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], - [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], - [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], - [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], - [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; - for (i = 0; i < ranges.length; i++) { - start = ranges[i][0]; - end = ranges[i][1]; - for (j = start; j <= end; j++) { - result[j] = true; - } - } - return result; -})(); - -function splitQuery(query) { - var result = []; - var start = -1; - for (var i = 0; i < query.length; i++) { - if (splitChars[query.charCodeAt(i)]) { - if (start !== -1) { - result.push(query.slice(start, i)); - start = -1; - } - } else if (start === -1) { - start = i; - } - } - if (start !== -1) { - result.push(query.slice(start)); - } - return result; +if (!splitQuery) { + function splitQuery(query) { + return query.split(/\s+/); + } } - - - /** * Search Module */ @@ -417,7 +138,7 @@ var Search = { */ query : function(query) { var i; - 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"]; + var stopwords = DOCUMENTATION_OPTIONS.SEARCH_LANGUAGE_STOP_WORDS; // stem the searchterms and add them to the correct list var stemmer = new Stemmer(); @@ -758,4 +479,4 @@ var Search = { $(document).ready(function() { Search.init(); -}); \ No newline at end of file +}); diff --git a/docs/atomate.common.firetasks.html b/docs/atomate.common.firetasks.html index a60568e23..9378b7802 100644 --- a/docs/atomate.common.firetasks.html +++ b/docs/atomate.common.firetasks.html @@ -6,10 +6,10 @@ - atomate.common.firetasks package — atomate 0.8.5 documentation + atomate.common.firetasks package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -45,7 +45,7 @@

    Subpackagesatomate.common.firetasks.tests package @@ -632,7 +632,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.common.firetasks.tests.html b/docs/atomate.common.firetasks.tests.html index 83fad6666..de5f94c7d 100644 --- a/docs/atomate.common.firetasks.tests.html +++ b/docs/atomate.common.firetasks.tests.html @@ -6,10 +6,10 @@ - atomate.common.firetasks.tests package — atomate 0.8.5 documentation + atomate.common.firetasks.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -42,8 +42,58 @@

    atomate.common.firetasks.tests package

    Submodules

    -
    -

    atomate.common.firetasks.tests.test_glue_tasks module

    +
    +

    atomate.common.firetasks.tests.test_glue_tasks module

    +
    +
    +class atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +classmethod setUpClass()
    +

    Hook method for setting up class fixture before running tests in the class.

    +
    + +
    +
    +test_copyfilesfromcalcloc()
    +
    + +
    + +
    +
    +class atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +test_createfolder()
    +
    + +
    + +
    +
    +class atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +test_cleanupfiles()
    +
    + +
    + +
    +
    +class atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +test_passcalclocs()
    +
    + +
    +

    atomate.common.firetasks.tests.test_parse_outputs module

    @@ -118,11 +168,11 @@

    atomate.common.firetasks.tests.test_glue_tasks module @@ -47,7 +47,7 @@

    SubpackagesSubpackages

    @@ -406,7 +406,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.feff.firetasks.tests.html b/docs/atomate.feff.firetasks.tests.html index 3eae05c68..c176448d8 100644 --- a/docs/atomate.feff.firetasks.tests.html +++ b/docs/atomate.feff.firetasks.tests.html @@ -6,10 +6,10 @@ - atomate.feff.firetasks.tests package — atomate 0.8.5 documentation + atomate.feff.firetasks.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -79,7 +79,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.feff.fireworks.html b/docs/atomate.feff.fireworks.html index 2e2ec99cb..95766b5ee 100644 --- a/docs/atomate.feff.fireworks.html +++ b/docs/atomate.feff.fireworks.html @@ -6,10 +6,10 @@ - atomate.feff.fireworks package — atomate 0.8.5 documentation + atomate.feff.fireworks package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -169,7 +169,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.feff.fireworks.tests.html b/docs/atomate.feff.fireworks.tests.html index ce6be0047..696dd7449 100644 --- a/docs/atomate.feff.fireworks.tests.html +++ b/docs/atomate.feff.fireworks.tests.html @@ -6,10 +6,10 @@ - atomate.feff.fireworks.tests package — atomate 0.8.5 documentation + atomate.feff.fireworks.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -74,7 +74,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.feff.html b/docs/atomate.feff.html index ac16f39f2..7ed884e1d 100644 --- a/docs/atomate.feff.html +++ b/docs/atomate.feff.html @@ -6,10 +6,10 @@ - atomate.feff package — atomate 0.8.5 documentation + atomate.feff package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -142,7 +142,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.feff.workflows.html b/docs/atomate.feff.workflows.html index 4e2c4419b..1471b78da 100644 --- a/docs/atomate.feff.workflows.html +++ b/docs/atomate.feff.workflows.html @@ -6,10 +6,10 @@ - atomate.feff.workflows package — atomate 0.8.5 documentation + atomate.feff.workflows package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -207,7 +207,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.feff.workflows.tests.html b/docs/atomate.feff.workflows.tests.html index 9238bf6c8..fadb3c6a9 100644 --- a/docs/atomate.feff.workflows.tests.html +++ b/docs/atomate.feff.workflows.tests.html @@ -6,10 +6,10 @@ - atomate.feff.workflows.tests package — atomate 0.8.5 documentation + atomate.feff.workflows.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -145,7 +145,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.html b/docs/atomate.html index 5b3ca3b26..236f438ad 100644 --- a/docs/atomate.html +++ b/docs/atomate.html @@ -6,10 +6,10 @@ - atomate package — atomate 0.8.5 documentation + atomate package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -49,7 +49,7 @@

    SubpackagesSubpackages
  • atomate.vasp.fireworks package
  • atomate.vasp.tests package
    • @@ -318,42 +318,42 @@

    SubpackagesSubpackages -
  • Module contents
    • +
  • Module contents
    • @@ -362,10 +362,10 @@

    Subpackagesatomate.vasp.config module
  • atomate.vasp.database module
  • atomate.vasp.drones module
    • -
  • atomate.vasp.powerups module
    • +
  • atomate.vasp.powerups module
  • atomate.vasp.submission_filter module
  • atomate.vasp.vasp_config module
    • -
  • atomate.vasp.vasp_powerups module
    • +
  • atomate.vasp.vasp_powerups module
  • Module contents
    • @@ -383,7 +383,7 @@

    Subpackages
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.lammps.firetasks.html b/docs/atomate.lammps.firetasks.html index f6eb9246b..9887a6d42 100644 --- a/docs/atomate.lammps.firetasks.html +++ b/docs/atomate.lammps.firetasks.html @@ -6,10 +6,10 @@ - atomate.lammps.firetasks package — atomate 0.8.5 documentation + atomate.lammps.firetasks package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -426,7 +426,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.lammps.fireworks.html b/docs/atomate.lammps.fireworks.html index 9f6d0eea0..1d3eb3e4f 100644 --- a/docs/atomate.lammps.fireworks.html +++ b/docs/atomate.lammps.fireworks.html @@ -6,10 +6,10 @@ - atomate.lammps.fireworks package — atomate 0.8.5 documentation + atomate.lammps.fireworks package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -155,7 +155,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.lammps.html b/docs/atomate.lammps.html index ff33f9bad..a33e4d54e 100644 --- a/docs/atomate.lammps.html +++ b/docs/atomate.lammps.html @@ -6,10 +6,10 @@ - atomate.lammps package — atomate 0.8.5 documentation + atomate.lammps package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -198,7 +198,7 @@

    Submodules
    -schema = {'root': {'input', 'output', 'state', 'dir_name', 'completed_at', 'last_updated', 'schema'}}
    +schema = {'root': {'completed_at', 'dir_name', 'input', 'last_updated', 'output', 'schema', 'state'}}
    @@ -223,7 +223,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.lammps.workflows.html b/docs/atomate.lammps.workflows.html index 7e1b495f4..87eda42db 100644 --- a/docs/atomate.lammps.workflows.html +++ b/docs/atomate.lammps.workflows.html @@ -6,10 +6,10 @@ - atomate.lammps.workflows package — atomate 0.8.5 documentation + atomate.lammps.workflows package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -119,7 +119,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.qchem.firetasks.html b/docs/atomate.qchem.firetasks.html index 38d036633..fc4e9e571 100644 --- a/docs/atomate.qchem.firetasks.html +++ b/docs/atomate.qchem.firetasks.html @@ -6,10 +6,10 @@ - atomate.qchem.firetasks package — atomate 0.8.5 documentation + atomate.qchem.firetasks package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -502,7 +502,7 @@

    atomate.qchem.firetasks.run_calc module
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.qchem.firetasks.tests.html b/docs/atomate.qchem.firetasks.tests.html index 20f93f1a2..2b9cc08bd 100644 --- a/docs/atomate.qchem.firetasks.tests.html +++ b/docs/atomate.qchem.firetasks.tests.html @@ -6,10 +6,10 @@ - atomate.qchem.firetasks.tests package — atomate 0.8.5 documentation + atomate.qchem.firetasks.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -255,7 +255,7 @@

    atomate.qchem.firetasks.tests.test_run_calc module @@ -56,7 +56,7 @@

    atomate.qchem.fireworks.core module
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.qchem.html b/docs/atomate.qchem.html index 80a512a75..14a629e05 100644 --- a/docs/atomate.qchem.html +++ b/docs/atomate.qchem.html @@ -6,10 +6,10 @@ - atomate.qchem package — atomate 0.8.5 documentation + atomate.qchem package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -193,7 +193,7 @@

    Submodules
    -static get_valid_paths(path)
    +static get_valid_paths(self, path)

    Checks if path contains valid data for assimilation, and then returns the valid paths. The paths returned can be a list of directory or file paths, depending on what kind of data you are assimilating. For @@ -215,27 +215,27 @@

    Submodules
    -static post_process(d)
    +static post_process(dir_name, d)

    Post-processing for various files other than the QChem input and output files. Currently only looks for custodian.json. Modify this if other files need to be processed.

    -static process_qchem_multirun(input_files, output_files)
    +static process_qchem_multirun(dir_name, input_files, output_files)

    Process a QChem run which is known to include multiple calculations in a single input/output pair.

    -static process_qchemrun(taskname, input_file, output_file)
    +static process_qchemrun(dir_name, taskname, input_file, output_file)

    Process a QChem calculation, aka an input/output pair.

    -schema = {'input': {'job_type', 'initial_molecule'}, 'output': {'job_type', 'initial_molecule'}, 'root': {'chemsys', 'cputime', 'input', 'output', 'dir_name', 'smiles', 'calcs_reversed', 'walltime', 'pointgroup', 'formula_anonymous', 'formula_pretty'}}
    +schema = {'input': {'initial_molecule', 'job_type'}, 'output': {'initial_molecule', 'job_type'}, 'root': {'calcs_reversed', 'chemsys', 'cputime', 'dir_name', 'formula_anonymous', 'formula_pretty', 'input', 'output', 'pointgroup', 'smiles', 'walltime'}}
    @@ -262,7 +262,7 @@

    atomate.qchem.powerups module
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.qchem.workflows.base.html b/docs/atomate.qchem.workflows.base.html index 313bbd646..4de33ce13 100644 --- a/docs/atomate.qchem.workflows.base.html +++ b/docs/atomate.qchem.workflows.base.html @@ -6,10 +6,10 @@ - atomate.qchem.workflows.base package — atomate 0.8.5 documentation + atomate.qchem.workflows.base package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -62,7 +62,7 @@

    atomate.qchem.workflows.base.torsion_potential module @@ -74,7 +74,7 @@

    Subpackages
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.qchem.workflows.tests.html b/docs/atomate.qchem.workflows.tests.html index dcf7de642..c7010b9c9 100644 --- a/docs/atomate.qchem.workflows.tests.html +++ b/docs/atomate.qchem.workflows.tests.html @@ -6,10 +6,10 @@ - atomate.qchem.workflows.tests package — atomate 0.8.5 documentation + atomate.qchem.workflows.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -93,7 +93,7 @@

    atomate.qchem.workflows.tests.test_torsion_potential module
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.tools.html b/docs/atomate.tools.html index ed576e200..243579d6f 100644 --- a/docs/atomate.tools.html +++ b/docs/atomate.tools.html @@ -6,10 +6,10 @@ - atomate.tools package — atomate 0.8.5 documentation + atomate.tools package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -70,7 +70,7 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.tools.post_process.html b/docs/atomate.tools.post_process.html index ab46d81a1..8abcf18ae 100644 --- a/docs/atomate.tools.post_process.html +++ b/docs/atomate.tools.post_process.html @@ -6,10 +6,10 @@ - atomate.tools.post_process package — atomate 0.8.5 documentation + atomate.tools.post_process package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -59,7 +59,7 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.tools.tests.html b/docs/atomate.tools.tests.html index a92296fb2..a9224fc52 100644 --- a/docs/atomate.tools.tests.html +++ b/docs/atomate.tools.tests.html @@ -6,10 +6,10 @@ - atomate.tools.tests package — atomate 0.8.5 documentation + atomate.tools.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -56,7 +56,7 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.utils.html b/docs/atomate.utils.html index e54f5beda..6f3b2eb6c 100644 --- a/docs/atomate.utils.html +++ b/docs/atomate.utils.html @@ -6,10 +6,10 @@ - atomate.utils package — atomate 0.8.5 documentation + atomate.utils package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -159,7 +159,7 @@

    Submodules
    -static exists(path)
    +static exists(sftp, path)

    os.path.exists() for paramiko’s SCP object

    Args:
    @@ -170,7 +170,7 @@

    Submodules
    -static get_ssh_connection(host, private_key)
    +static get_ssh_connection(username, host, private_key)

    Connect to the remote host via paramiko using the private key. If the host key is not present it will be added automatically.

    @@ -467,7 +467,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.utils.tests.html b/docs/atomate.utils.tests.html index cf4c4604a..a6f772a8b 100644 --- a/docs/atomate.utils.tests.html +++ b/docs/atomate.utils.tests.html @@ -6,10 +6,10 @@ - atomate.utils.tests package — atomate 0.8.5 documentation + atomate.utils.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -188,7 +188,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.vasp.analysis.html b/docs/atomate.vasp.analysis.html index 01c8067a1..4bbda7722 100644 --- a/docs/atomate.vasp.analysis.html +++ b/docs/atomate.vasp.analysis.html @@ -6,10 +6,10 @@ - atomate.vasp.analysis package — atomate 0.8.5 documentation + atomate.vasp.analysis package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -128,7 +128,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.vasp.builders.examples.html b/docs/atomate.vasp.builders.examples.html index 0929114fb..709f10ae5 100644 --- a/docs/atomate.vasp.builders.examples.html +++ b/docs/atomate.vasp.builders.examples.html @@ -6,10 +6,10 @@ - atomate.vasp.builders.examples package — atomate 0.8.5 documentation + atomate.vasp.builders.examples package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -58,7 +58,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.vasp.builders.html b/docs/atomate.vasp.builders.html index 004af9f50..6ef1b370b 100644 --- a/docs/atomate.vasp.builders.html +++ b/docs/atomate.vasp.builders.html @@ -6,10 +6,10 @@ - atomate.vasp.builders package — atomate 0.8.5 documentation + atomate.vasp.builders package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -75,7 +75,7 @@

    Submodules
    -static from_file(m='materials', **kwargs)
    +static from_file(db_file, m='materials', **kwargs)

    Get builder using only a db file.

    Args:
    @@ -192,7 +192,7 @@

    Submodules
    -static from_file(m='materials', **kwargs)
    +static from_file(db_file, m='materials', **kwargs)

    Get a MaterialsEhullBuilder using only a db file.

    Args:
    @@ -533,7 +533,7 @@

    Submodules
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.vasp.examples.html b/docs/atomate.vasp.examples.html index d1a344708..fda762124 100644 --- a/docs/atomate.vasp.examples.html +++ b/docs/atomate.vasp.examples.html @@ -6,10 +6,10 @@ - atomate.vasp.examples package — atomate 0.8.5 documentation + atomate.vasp.examples package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -56,7 +56,7 @@

    atomate.vasp.examples.builders_example module
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.vasp.firetasks.html b/docs/atomate.vasp.firetasks.html index 34097cf00..04d00a021 100644 --- a/docs/atomate.vasp.firetasks.html +++ b/docs/atomate.vasp.firetasks.html @@ -6,10 +6,10 @@ - atomate.vasp.firetasks package — atomate 0.8.5 documentation + atomate.vasp.firetasks package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -45,12 +45,12 @@

    Subpackagesatomate.vasp.firetasks.tests package @@ -578,17 +578,1489 @@

    Submodules -

    atomate.vasp.firetasks.parse_outputs module

    +
    +

    atomate.vasp.firetasks.parse_outputs module

    +
    +
    +class atomate.vasp.firetasks.parse_outputs.BoltztrapToDBTask(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.parse_outputs.BoltztrapToDb

    +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.BoltztrapToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Enter a BoltzTraP run into the database. Note that this assumes you are in a current dir +that has the uniform band structure data with a sub-directory called “boltztrap” containing +the BoltzTraP information.

    +
    +
    Optional params:
    +
    +
    db_file (str): path to file containing the database credentials.
    +
    Supports env_chk. Default: write data to JSON file.
    +
    +

    hall_doping (bool): set True to retain hall_doping in dict +additional_fields (dict): fields added to the document such as user-defined tags or name, ids, etc

    +
    +
    +
    +
    +optional_params = ['db_file', 'hall_doping', 'additional_fields']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.ElasticTensorToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Analyzes the stress/strain data of an elastic workflow to produce +an elastic tensor and various other quantities.

    +
    +
    Required params:
    +
    +
    structure (Structure): structure to use for symmetrization,
    +
    input structure. If an optimization was used, will +look for relaxed structure in calc locs
    +
    +
    +
    Optional params:
    +
    +
    db_file (str): path to file containing the database credentials.
    +
    Supports env_chk. Default: write data to JSON file.
    +
    +

    order (int): order of fit to perform +fw_spec_field (str): if set, will update the task doc with the contents

    +
    +
    of this key in the fw_spec.
    +
    +
    fitting_method (str): if set, will use one of the specified
    +
    fitting methods from pymatgen. Supported methods are +“independent”, “pseudoinverse”, and “finite_difference.” +Note that order 3 and higher required finite difference +fitting, and will override.
    +
    +
    +
    +
    +
    +optional_params = ['db_file', 'order', 'fw_spec_field', 'fitting_method']
    +
    + +
    +
    +required_params = ['structure']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.ElasticTensorToDbTask(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.parse_outputs.ElasticTensorToDb

    +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.FitEOSToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Retrieve the energy and volume data and fit it to the given equation of state. The summary dict +is written to ‘bulk_modulus.json’ file.

    +
    +
    Required parameters:
    +
    +
    tag (str): unique tag appended to the task labels in other fireworks so that all the
    +
    required data can be queried directly from the database.
    +
    +

    db_file (str): path to the db file

    +
    +
    Optional parameters:
    +

    to_db (bool): if True, the data will be inserted to “eos” collection; otherwise, dumped to a .json file. +eos (str): equation of state used for fitting the energies and the volumes.

    +
    +
    options supported by pymatgen: “quadratic”, “murnaghan”, “birch”, “birch_murnaghan”, +“pourier_tarantola”, “vinet”, “deltafactor”. Default: “vinet”
    +
    +
    +
    +
    +optional_params = ['to_db', 'eos']
    +
    + +
    +
    +required_params = ['tag', 'db_file']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.FitEquationOfStateTask(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.parse_outputs.FitEOSToDb

    +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.GibbsAnalysisToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Compute the quasi-harmonic gibbs free energy. There are 2 options available for the +quasi-harmonic approximation (set via ‘qha_type’ parameter): +1. use the phonopy package quasi-harmonic approximation interface or +2. use the debye model. +Note: Instead of relying on fw_spec, this task gets the required data directly from the +tasks collection for processing. The summary dict is written to ‘gibbs.json’ file.

    +
    +
    required_params:
    +
    +
    tag (str): unique tag appended to the task labels in other fireworks so that all the
    +
    required data can be queried directly from the database.
    +
    +

    db_file (str): path to the db file

    +
    +
    optional_params:
    +
    +
    qha_type(str): quasi-harmonic approximation type: “debye_model” or “phonopy”,
    +
    default is “debye_model”
    +
    +

    t_min (float): min temperature +t_step (float): temperature step +t_max (float): max temperature +mesh (list/tuple): reciprocal space density +eos (str): equation of state used for fitting the energies and the volumes.

    +
    +
    options supported by phonopy: “vinet”, “murnaghan”, “birch_murnaghan”.
    +

    pressure (float): in GPa, optional. +poisson (float): poisson ratio. Defaults to 0.25. +anharmonic_contribution (bool): consider anharmonic contributions to

    +
    +
    Gibbs energy from the Debye model. Defaults to False.
    +

    pressure (float): in GPa, optional. +metadata (dict): meta data

    +
    +
    +
    +
    +optional_params = ['qha_type', 't_min', 't_step', 't_max', 'mesh', 'eos', 'pressure', 'poisson', 'anharmonic_contribution', 'metadata']
    +
    + +
    +
    +required_params = ['tag', 'db_file']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.GibbsFreeEnergyTask(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.parse_outputs.GibbsAnalysisToDb

    +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.JsonToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Insert the a JSON file (default: task.json) directly into the tasks database. +Note that if the JSON file contains a “task_id” key, that task_id must not already be present +in the tasks collection.

    +
    +
    Optional params:
    +

    json_filename (str): name of the JSON file to insert (default: “task.json”) +db_file (str): path to file containing the database credentials. Supports env_chk. +calc_dir (str): path to dir (on current filesystem) that contains VASP output files.

    +
    +
    Default: use current working directory.
    +
    +
    +
    +
    +optional_params = ['json_filename', 'db_file', 'calc_dir']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.JsonToDbTask(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.parse_outputs.JsonToDb

    +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.PolarizationToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Recovers the same branch polarization and spontaneous polarization +for a ferroelectric workflow.

    +
    +
    +optional_params = ['db_file']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.RamanSusceptibilityTensorToDbTask(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.parse_outputs.RamanTensorToDb

    +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.RamanTensorToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +
    +
    Raman susceptibility tensor for each mode = Finite difference derivative of the dielectric
    +
    tensor wrt the displacement along that mode.
    +
    +

    See: 10.1103/PhysRevB.73.104304. +The frequencies are in the units of cm^-1. To convert the frequency to THz: multiply by 0.1884.

    +
    +
    optional_params:
    +
    db_file (str): path to the db file
    +
    +
    +
    +optional_params = ['db_file']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffTask(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffToDb

    +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Compute the quasi-harmonic thermal expansion coefficient using phonopy.

    +
    +
    required_params:
    +
    +
    tag (str): unique tag appended to the task labels in other fireworks so that all the
    +
    required data can be queried directly from the database.
    +
    +

    db_file (str): path to the db file

    +
    +
    optional_params:
    +

    t_min (float): min temperature +t_step (float): temperature step +t_max (float): max temperature +mesh (list/tuple): reciprocal space density +eos (str): equation of state used for fitting the energies and the volumes.

    +
    +
    options supported by phonopy: “vinet” (default), “murnaghan”, “birch_murnaghan”.
    +

    pressure (float): in GPa, optional.

    +
    +
    +
    +
    +optional_params = ['t_min', 't_step', 't_max', 'mesh', 'eos', 'pressure']
    +
    + +
    +
    +required_params = ['tag', 'db_file']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.VaspToDb(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Enter a VASP run into the database. Uses current directory unless you +specify calc_dir or calc_loc.

    +
    +
    Optional params:
    +
    +
    calc_dir (str): path to dir (on current filesystem) that contains VASP
    +
    output files. Default: use current working directory.
    +
    calc_loc (str OR bool): if True will set most recent calc_loc. If str
    +
    search for the most recent calc_loc with the matching name
    +
    parse_dos (bool): whether to parse the DOS and store in GridFS.
    +
    Defaults to False.
    +
    bandstructure_mode (str): Set to “uniform” for uniform band structure.
    +
    Set to “line” for line mode. If not set, band structure will not +be parsed.
    +
    +

    additional_fields (dict): dict of additional fields to add +db_file (str): path to file containing the database credentials.

    +
    +
    Supports env_chk. Default: write data to JSON file.
    +
    +
    fw_spec_field (str): if set, will update the task doc with the contents
    +
    of this key in the fw_spec.
    +
    defuse_unsuccessful (bool): this is a three-way toggle on what to do if
    +
    your job looks OK, but is actually unconverged (either electronic or +ionic). True -> mark job as COMPLETED, but defuse children. +False –> do nothing, continue with workflow as normal. “fizzle” +–> throw an error (mark this job as FIZZLED)
    +
    task_fields_to_push (dict): if set, will update the next Firework/Firetask
    +
    spec using fields from the task document. +Format: {key : path} -> fw.spec[key] = task_doc[path] +The path is a full mongo-style path so subdocuments can be referneced +using dot notation and array keys can be referenced using the index. +E.g “calcs_reversed.0.output.outar.run_stats”
    +
    +
    +
    +
    +
    +optional_params = ['calc_dir', 'calc_loc', 'parse_dos', 'bandstructure_mode', 'additional_fields', 'db_file', 'fw_spec_field', 'defuse_unsuccessful', 'task_fields_to_push', 'parse_chgcar', 'parse_aeccar']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.VaspToDbTask(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.parse_outputs.VaspToDb

    +
    +
    -
    -

    atomate.vasp.firetasks.run_calc module

    +
    +

    atomate.vasp.firetasks.run_calc module

    +
    +
    +class atomate.vasp.firetasks.run_calc.RunBoltztrap(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Run Boltztrap directly. Requires vasprun.xml and OUTCAR to be in current dir.

    +
    +
    Required params:
    +
    (none)
    +
    Optional params:
    +
    scissor: (float) scissor band gap amount in eV (i.e. new gap == scissor) +tmax: (float) max temperature to evaluate (default = 1300K) +tgrid: (float) temperature interval (default = 50K) +doping: ([float]) doping levels you want to compute +soc: (bool) whether the band structure is calculated with spin-orbit coupling or not
    +
    +
    +
    +optional_params = ['scissor', 'tmax', 'tgrid', 'doping', 'soc']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.run_calc.RunNoVasp(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Do NOT run vasp. Do nothing.

    +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.run_calc.RunVaspCustodian(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Run VASP using custodian “on rails”, i.e. in a simple way that supports most common options.

    +
    +
    Required params:
    +
    vasp_cmd (str): the name of the full executable for running VASP. Supports env_chk.
    +
    Optional params:
    +
    +
    job_type: (str) - choose from “normal” (default), “double_relaxation_run” (two consecutive
    +
    jobs), “full_opt_run” (multiple optimizations), and “neb”
    +
    handler_group: (str or [ErrorHandler]) - group of handlers to use. See handler_groups dict in the code for
    +
    the groups and complete list of handlers in each group. Alternatively, you can +specify a list of ErrorHandler objects.
    +
    max_force_threshold: (float) - if >0, adds MaxForceErrorHandler. Not recommended for
    +
    nscf runs.
    +
    scratch_dir: (str) - if specified, uses this directory as the root scratch dir.
    +
    Supports env_chk.
    +
    +

    gzip_output: (bool) - gzip output (default=T) +max_errors: (int) - maximum # of errors to fix before giving up (default=5) +ediffg: (float) shortcut for setting EDIFFG in special custodian jobs +auto_npar: (bool) - use auto_npar (default=F). Recommended set to T

    +
    +
    for single-node jobs only. Supports env_chk.
    +
    +
    gamma_vasp_cmd: (str) - cmd for Gamma-optimized VASP compilation.
    +
    Supports env_chk.
    +
    +

    wall_time (int): Total wall time in seconds. Activates WalltimeHandler if set. +half_kpts_first_relax (bool): Use half the k-points for the first relaxation

    +
    +
    +
    +
    +optional_params = ['job_type', 'handler_group', 'max_force_threshold', 'scratch_dir', 'gzip_output', 'max_errors', 'ediffg', 'auto_npar', 'gamma_vasp_cmd', 'wall_time', 'half_kpts_first_relax']
    +
    + +
    +
    +required_params = ['vasp_cmd']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.run_calc.RunVaspDirect(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Execute a command directly (no custodian).

    +
    +
    Required params:
    +
    cmd (str): the name of the full executable to run. Supports env_chk.
    +
    Optional params:
    +
    expand_vars (str): Set to true to expand variable names in the cmd.
    +
    +
    +
    +optional_params = ['expand_vars']
    +
    + +
    +
    +required_params = ['vasp_cmd']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.run_calc.RunVaspFake(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Vasp Emulator

    +
    +
    Required params:
    +
    +
    ref_dir (string): Path to reference vasp run directory with input files in the folder
    +
    named ‘inputs’ and output files in the folder named ‘outputs’.
    +
    +
    +
    Optional params:
    +
    params_to_check (list): optional list of incar parameters to check. +check_incar (bool): whether to confirm the INCAR params (default: True) +check_kpoints (bool): whether to confirm the KPOINTS params (default: True) +check_poscar (bool): whether to confirm the POSCAR params (default: True) +check_potcar (bool): whether to confirm the POTCAR params (default: True)
    +
    +
    +
    +optional_params = ['params_to_check', 'check_incar', 'check_kpoints', 'check_poscar', 'check_potcar']
    +
    + +
    +
    +required_params = ['ref_dir']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    +
    -
    -

    atomate.vasp.firetasks.write_inputs module

    +
    +

    atomate.vasp.firetasks.write_inputs module

    +
    +
    +class atomate.vasp.firetasks.write_inputs.ModifyIncar(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Modify an INCAR file.

    +
    +
    Required params:
    +
    (none)
    +
    Optional params:
    +

    incar_update (dict): overwrite Incar dict key. Supports env_chk. +incar_multiply ([{<str>:<float>}]) - multiply Incar key by a constant

    +
    +
    factor. Supports env_chk.
    +
    +
    incar_dictmod ([{}]): use DictMod language to change Incar.
    +
    Supports env_chk.
    +
    +

    input_filename (str): Input filename (if not “INCAR”) +output_filename (str): Output filename (if not “INCAR”)

    +
    +
    +
    +
    +optional_params = ['incar_update', 'incar_multiply', 'incar_dictmod', 'input_filename', 'output_filename']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.ModifyPotcar(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Modify Potcar file.

    +
    +
    Required params:
    +
    potcar_symbols (dict): overwrite potcar with symbol. Supports env_chk.
    +
    Optional params:
    +
    functional (dict): functional to use, e.g. PBE, PBE_52, LDA_US, PW91 +input_filename (str): Input filename (if not “INCAR”) +output_filename (str): Output filename (if not “INCAR”)
    +
    +
    +
    +optional_params = ['functional', 'input_filename', 'output_filename']
    +
    + +
    +
    +required_params = ['potcar_symbols']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteNormalmodeDisplacedPoscar(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Displace the structure from the previous calculation along the provided normal mode by the +given amount and write the corresponding Poscar file. The fw_spec must contain a “normalmodes” +key with “eigenvecs” sub-key that is likely produced by a previous calc.

    +
    +
    Required params:
    +
    mode (int): normal mode index +displacement (float): displacement along the normal mode in Angstroms
    +
    +
    +
    +required_params = ['mode', 'displacement']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteTransmutedStructureIOSet(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Apply the provided transformations to the input structure and write the +input set for that structure. Reads structure from POSCAR if no structure provided. Note that +if a transformation yields many structures from one, only the last structure in the list is +used.

    +
    +
    Required params:
    +

    structure (Structure): input structure +transformations (list): list of names of transformation classes as defined in

    +
    +
    the modules in pymatgen.transformations
    +

    vasp_input_set (VaspInputSet): VASP input set.

    +
    +
    Optional params:
    +
    +
    transformation_params (list): list of dicts where each dict specifies the input parameters
    +
    to instantiate the transformation class in the transformations list.
    +
    +

    override_default_vasp_params (dict): additional user input settings. +prev_calc_dir: path to previous calculation if using structure from another calculation.

    +
    +
    +
    +
    +optional_params = ['prev_calc_dir', 'transformation_params', 'override_default_vasp_params']
    +
    + +
    +
    +required_params = ['structure', 'transformations', 'vasp_input_set']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Create VASP input files using implementations of pymatgen’s AbstractVaspInputSet. An input set +can be provided as an object or as a String/parameter combo.

    +
    +
    Required params:
    +

    structure (Structure): structure +vasp_input_set (AbstractVaspInputSet or str): Either a VaspInputSet object or a string

    +
    +
    name for the VASP input set (e.g., “MPRelaxSet”).
    +
    +
    Optional params:
    +
    +
    vasp_input_params (dict): When using a string name for VASP input set, use this as a dict
    +
    to specify kwargs for instantiating the input set parameters. For example, if you want +to change the user_incar_settings, you should provide: {“user_incar_settings”: …}. +This setting is ignored if you provide the full object representation of a VaspInputSet +rather than a String.
    +
    +
    +
    +
    +
    +optional_params = ['vasp_input_params']
    +
    + +
    +
    +required_params = ['structure', 'vasp_input_set']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSetFromInterpolatedPOSCAR(*args, **kwargs)
    +

    Bases: atomate.vasp.firetasks.glue_tasks.GetInterpolatedPOSCAR

    +

    Grabs CONTCARS from two previous calculations to create interpolated +structure. Create VASP input files using implementations of pymatgen’s +AbstractVaspInputSet. An input set can be provided as String/parameter +combo.

    +
    +
    Required params:
    +

    start (str): name of fw for start of interpolation. +end (str): name of fw for end of interpolation. +this_image (int): which interpolation this is. +nimages (int) : number of interpolations. +autosort_tol (float): a distance tolerance in angstrom in which

    +
    +
    to automatically sort end_structure to match to the closest +points in this particular structure.
    +

    vasp_input_set (str): a string name for the VASP input set (e.g., “MPRelaxSet”).

    +
    +
    Optional params:
    +
    +
    vasp_input_params (dict): When using a string name for VASP input set, use this as a dict
    +
    to specify kwargs for instantiating the input set parameters. For example, if you want +to change the user_incar_settings, you should provide: {“user_incar_settings”: …}. +This setting is ignored if you provide the full object representation of a VaspInputSet +rather than a String.
    +
    +
    +
    +
    +
    +optional_params = ['vasp_input_params', 'autosort_tol']
    +
    + +
    +
    +required_params = ['start', 'end', 'this_image', 'nimages', 'vasp_input_set']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteVaspFromPMGObjects(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Write VASP files using pymatgen objects.

    +
    +
    Required params:
    +
    (none) - although non-functional unless you set one or more optional params
    +
    Optional params:
    +
    incar (Incar): pymatgen Incar object +poscar (Poscar): pymatgen Poscar object +kpoints (Kpoints): pymatgen Kpoints object +potcar (Potcar): pymatgen Potcar object
    +
    +
    +
    +optional_params = ['incar', 'poscar', 'kpoints', 'potcar']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteVaspHSEBSFromPrev(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Writes input files for HSE band structure run. Assumes that output files from a +a previous job can be accessed. Since HSE always re-optimizes the charge density (no nSCF mode), +the previous job is used to get the location of VBM/CBM for mode=”gap” (otherwise just used to +get the structure / starting charge density).

    +
    +
    Required params:
    +
    (none)
    +
    Optional params:
    +
    (documentation for all other optional params can be found in +MPHSEBSSet)
    +
    +
    +
    +optional_params = ['prev_calc_dir', 'mode', 'reciprocal_density', 'kpoints_line_density']
    +
    + +
    +
    +required_params = []
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteVaspNMRFromPrev(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Writes input files for a NMR calculation

    +
    +
    Optional params::
    +

    prev_calc_dir: path to previous calculation, else current directory +mode (str): the NMR calculation type: cs or efg, default is cs +isotopes (list): list of isotopes to include, default is to include the

    +
    +
    lowest mass quadrupolar isotope for all applicable elements
    +

    reciprocol_density (int): the reciprocol density for the kpoint mesh, defaults to 100 +other_aprams (dict) : any other params passsed to MPNMRSet as a dictionary

    +
    +
    +
    +
    +optional_params = ['mode', 'isotopes', 'reciprocal_density', 'other_params']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteVaspNSCFFromPrev(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Writes input files for an NSCF static run. Assumes that output files from an +scf job can be accessed. There are many options, e.g. uniform mode, +line mode, adding the optical properties, etc.

    +
    +
    Required params:
    +
    (none)
    +
    Optional params:
    +
    (documentation for all optional params can be found in +NonSCFVaspInputSet)
    +
    +
    +
    +optional_params = ['prev_calc_dir', 'copy_chgcar', 'nbands_factor', 'reciprocal_density', 'kpoints_line_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'mode', 'nedos', 'optics', 'other_params']
    +
    + +
    +
    +required_params = []
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteVaspSOCFromPrev(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Writes input files for a spinorbit coupling calculation.

    +
    +
    Required params:
    +
    magmom (list): magnetic moment values for each site in the structure. +saxis (list): magnetic field direction
    +
    +
    +
    +optional_params = ['prev_calc_dir', 'copy_chgcar', 'nbands_factor', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'other_params']
    +
    + +
    +
    +required_params = ['magmom', 'saxis']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.write_inputs.WriteVaspStaticFromPrev(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Writes input files for a static run. Assumes that output files from a previous +(e.g., optimization) run can be accessed in current dir or prev_calc_dir. Also allows +lepsilon (dielectric constant) calcs.

    +
    +
    Required params:
    +
    (none)
    +
    Optional params:
    +
    (documentation for all other optional params can be found in +MPStaticSet)
    +
    +
    +
    +optional_params = ['prev_calc_dir', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'lepsilon', 'other_params']
    +
    + +
    +
    +run_task(fw_spec)
    +

    This method gets called when the Firetask is run. It can take in a +Firework spec, perform some task using that data, and then return an +output in the form of a FWAction.

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    +
    -
    -

    Module contents

    +
    +

    Module contents

    @@ -598,17 +2070,17 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    @@ -645,13 +2117,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • diff --git a/docs/atomate.vasp.firetasks.tests.html b/docs/atomate.vasp.firetasks.tests.html index 8114b5527..a05b875fc 100644 --- a/docs/atomate.vasp.firetasks.tests.html +++ b/docs/atomate.vasp.firetasks.tests.html @@ -6,10 +6,10 @@ - atomate.vasp.firetasks.tests package — atomate 0.8.5 documentation + atomate.vasp.firetasks.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -42,23 +42,160 @@

    atomate.vasp.firetasks.tests package

    Submodules

    -
    -

    atomate.vasp.firetasks.tests.test_copy module

    +
    +

    atomate.vasp.firetasks.tests.test_copy module

    +
    +
    +class atomate.vasp.firetasks.tests.test_copy.TestCopyVaspOutputs(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +classmethod setUpClass()
    +

    Hook method for setting up class fixture before running tests in the class.

    +
    + +
    +
    +test_gzip_copy()
    +
    + +
    +
    +test_plain_copy()
    +
    + +
    +
    +test_plain_copy_more()
    +
    + +
    +
    +test_relax2_copy()
    +
    + +
    +
    +test_unittestsetup()
    +
    + +
    +
    -
    -

    atomate.vasp.firetasks.tests.test_get_interpolated_poscar module

    +
    +

    atomate.vasp.firetasks.tests.test_get_interpolated_poscar module

    +
    +
    +class atomate.vasp.firetasks.tests.test_get_interpolated_poscar.TestGetInterpolatedPOSCAR(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +classmethod setUpClass()
    +

    Hook method for setting up class fixture before running tests in the class.

    +
    + +
    +
    +test_getinterpolatedposcar()
    +
    + +
    +
    -
    -

    atomate.vasp.firetasks.tests.test_polarization_to_db module

    +
    +

    atomate.vasp.firetasks.tests.test_polarization_to_db module

    +
    +
    +class atomate.vasp.firetasks.tests.test_polarization_to_db.TestFerroelectricWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +test_polarizationtodb()
    +
    + +
    +
    -
    -

    atomate.vasp.firetasks.tests.test_write_vasp module

    +
    +

    atomate.vasp.firetasks.tests.test_write_vasp module

    +
    +
    +class atomate.vasp.firetasks.tests.test_write_vasp.TestWriteVasp(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp()
    +

    Create scratch directory(removes the old one if there is one) and change to it. +Also initialize launchpad.

    +
    + +
    +
    +classmethod setUpClass()
    +

    Hook method for setting up class fixture before running tests in the class.

    +
    + +
    +
    +tearDown()
    +

    Remove the scratch directory and teardown the test db.

    +
    + +
    +
    +test_ioset_explicit()
    +
    + +
    +
    +test_ioset_implicit()
    +
    + +
    +
    +test_ioset_params()
    +
    + +
    +
    +test_modify_incar()
    +
    + +
    +
    +test_modify_potcar()
    +
    + +
    +
    +test_pmgobjects()
    +
    + +
    +
    -
    -

    atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar module

    +
    +

    atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar module

    +
    +
    +class atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar.TestWriteVaspFromInterpolatedPOSCAR(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +classmethod setUpClass()
    +

    Hook method for setting up class fixture before running tests in the class.

    +
    + +
    +
    +test_writevaspfrominterpolatedposcar()
    +
    + +
    +
    -
    -

    Module contents

    +
    +

    Module contents

    @@ -68,16 +205,16 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    @@ -114,13 +251,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • diff --git a/docs/atomate.vasp.fireworks.html b/docs/atomate.vasp.fireworks.html index f86785737..14b2e27de 100644 --- a/docs/atomate.vasp.fireworks.html +++ b/docs/atomate.vasp.fireworks.html @@ -6,10 +6,10 @@ - atomate.vasp.fireworks package — atomate 0.8.5 documentation + atomate.vasp.fireworks package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -42,17 +42,567 @@

    atomate.vasp.fireworks package

    Submodules

    -
    -

    atomate.vasp.fireworks.core module

    +
    +

    atomate.vasp.fireworks.core module

    +
    +
    +class atomate.vasp.fireworks.core.BoltztrapFW(parents=None, structure=None, name='boltztrap', db_file=None, scissor=0.0, doping=None, tmax=1300, tgrid=50, prev_calc_dir=None, soc=False, additional_fields=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(parents=None, structure=None, name='boltztrap', db_file=None, scissor=0.0, doping=None, tmax=1300, tgrid=50, prev_calc_dir=None, soc=False, additional_fields=None, **kwargs)
    +

    Run Boltztrap (which includes writing bolztrap input files and parsing outputs). Assumes +you have a previous FW with the calc_locs passed into the current FW.

    +
    +
    Args:
    +

    structure (Structure): - only used for setting name of FW +name (str): name of this FW +db_file (str): path to the db file +parents (Firework): Parents of this particular Firework. FW or list of FWS. +prev_calc_dir (str): Path to a previous calculation to copy from +scissor (float): if scissor > 0, apply scissor on the band structure so that new

    +
    +
    band gap = scissor (in eV)
    +

    doping: ([float]) doping levels you want to compute +tmax: (float) max temperature to evaluate +tgrid: (float) temperature interval +soc (bool): whether the band structure is calculated with spin-orbit coupling +additional_fields (dict): fields added to the document such as user-defined tags or name, ids, etc +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.DFPTFW(structure=None, prev_calc_dir=None, name='static dielectric', vasp_cmd='vasp', copy_vasp_outputs=True, lepsilon=True, db_file=None, parents=None, user_incar_settings=None, pass_nm_results=False, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure=None, prev_calc_dir=None, name='static dielectric', vasp_cmd='vasp', copy_vasp_outputs=True, lepsilon=True, db_file=None, parents=None, user_incar_settings=None, pass_nm_results=False, **kwargs)
    +
    +
    Static DFPT calculation Firework
    +
    +
    Args:
    +
    +
    structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
    +
    name of the FW.
    +
    +

    name (str): Name for the Firework. +lepsilon (bool): Turn on LEPSILON to calculate polar properties +vasp_cmd (str): Command to run vasp. +copy_vasp_outputs (str or bool): Whether to copy outputs from previous

    +
    +
    run. Defaults to True.
    +

    prev_calc_dir (str): Path to a previous calculation to copy from +db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework.

    +
    +
    FW or list of FWS.
    +

    user_incar_settings (dict): Parameters in INCAR to override +pass_nm_results (bool): if true the normal mode eigen vals and vecs are passed so that

    +
    +
    next firework can use it.
    +

    **kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.HSEBSFW(parents=None, prev_calc_dir=None, structure=None, mode='gap', name=None, vasp_cmd='vasp', db_file=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(parents=None, prev_calc_dir=None, structure=None, mode='gap', name=None, vasp_cmd='vasp', db_file=None, **kwargs)
    +

    For getting a more accurate band gap or a full band structure with HSE - requires previous +calculation that gives VBM/CBM info or the high-symmetry kpoints.

    +
    +
    Args:
    +

    parents (Firework): Parents of this particular Firework. FW or list of FWS. +prev_calc_dir (str): Path to a previous calculation to copy from +structure (Structure): Input structure - used only to set the name of the FW. +mode (string): options:

    +
    +
    “line” to get a full band structure along symmetry lines or +“uniform” for uniform mesh band structure or +“gap” to get the energy at the CBM and VBM
    +

    name (str): Name for the Firework. +vasp_cmd (str): Command to run vasp. +db_file (str): Path to file specifying db credentials. +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.LepsFW(structure, name='static dielectric', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, phonon=False, mode=None, displacement=None, user_incar_settings=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure, name='static dielectric', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, phonon=False, mode=None, displacement=None, user_incar_settings=None, **kwargs)
    +

    Standard static calculation Firework for dielectric constants using DFPT.

    +
    +
    Args:
    +
    +
    structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
    +
    name of the FW.
    +
    +

    name (str): Name for the Firework. +vasp_cmd (str): Command to run vasp. +copy_vasp_outputs (bool): Whether to copy outputs from previous

    +
    +
    run. Defaults to True.
    +

    db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework.

    +
    +
    FW or list of FWS.
    +
    +
    phonon (bool): Whether or not to extract normal modes and pass it. This argument along
    +
    with the mode and displacement arguments must be set for the calculation of +dielectric constant in the Raman tensor workflow.
    +
    +

    mode (int): normal mode index. +displacement (float): displacement along the normal mode in Angstroms. +user_incar_settings (dict): Parameters in INCAR to override +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.MDFW(structure, start_temp, end_temp, nsteps, name='molecular dynamics', vasp_input_set=None, vasp_cmd='vasp', override_default_vasp_params=None, wall_time=19200, db_file=None, parents=None, copy_vasp_outputs=True, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure, start_temp, end_temp, nsteps, name='molecular dynamics', vasp_input_set=None, vasp_cmd='vasp', override_default_vasp_params=None, wall_time=19200, db_file=None, parents=None, copy_vasp_outputs=True, **kwargs)
    +

    Standard firework for a single MD run.

    +
    +
    Args:
    +

    structure (Structure): Input structure. +start_temp (float): Start temperature of MD run. +end_temp (float): End temperature of MD run. +nsteps (int): Number of MD steps +name (string): Name for the Firework. +vasp_input_set (string): string name for the VASP input set (e.g.,

    +
    +
    “MITMDVaspInputSet”).
    +

    vasp_cmd (string): Command to run vasp. +override_default_vasp_params (dict): If this is not None,

    +
    +
    these params are passed to the default vasp_input_set, i.e., +MITMDSet. This allows one to easily override some +settings, e.g., user_incar_settings, etc. Particular to MD, +one can control time_step and all other settings of the input set.
    +

    wall_time (int): Total wall time in seconds before writing STOPCAR. +copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True. +db_file (string): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework. FW or list of FWS. +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.NEBFW(spec, neb_label, from_images=True, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +

    CI-NEB Firework in NEB Workflow.

    +
    +
    Task 1) Read in image structures from spec and generates input sets.
    +
    The group of structures are labeled with neb_label (1, 2…)
    +
    +

    Task 2) Run NEB VASP using Custodian +Task 3) Update structure to spec +Task 4) Pass CalcLocs named “neb_{}”.format(neb_label)

    +
    +
    +__init__(spec, neb_label, from_images=True, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)
    +
    +
    Args:
    +

    spec (dict): Specification of the job to run. +neb_label (str): “1”, “2”…, label neb run. +from_images (bool): Set True to initialize from image structures, False starting

    +
    +
    from relaxed endpoint structures.
    +

    user_incar_settings (dict): Additional INCAR settings. +user_kpoints_settings (dict): Additional KPOINTS settings. +additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian. +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.NEBRelaxationFW(spec, label, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +

    Relaxation Firework in NEB Workflow.

    +

    Task 1) Read in a structure with “st_label” (“rlx”, “ep0” or “ep1”) and generates input sets. +Task 2) Run VASP using Custodian +Task 3) Update structure to spec +Task 4) Pass CalcLocs named “{}_dir”.format(st_label)

    +
    +
    +__init__(spec, label, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)
    +
    +
    Args:
    +
    spec (dict): Specification of the job to run. +label (str): “parent”, “ep0” or “ep1” +vasp_input_set (VaspInputSet): Input set to use. +user_kpoints_settings (dict): Additional KPOINTS settings. +additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian. +**kwargs: Other kwargs that are passed to Firework.__init__.
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.NonSCFFW(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, **kwargs)
    +

    Standard NonSCF Calculation Firework supporting both +uniform and line modes.

    +
    +
    Args:
    +

    structure (Structure): Input structure - used only to set the name of the FW. +name (str): Name for the Firework. +mode (str): “uniform” or “line” mode. +vasp_cmd (str): Command to run vasp. +copy_vasp_outputs (bool): Whether to copy outputs from previous

    +
    +
    run. Defaults to True.
    +

    prev_calc_dir (str): Path to a previous calculation to copy from +db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework.

    +
    +
    FW or list of FWS.
    +

    **kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.OptimizeFW(structure, name='structure optimization', vasp_input_set=None, vasp_cmd='vasp', override_default_vasp_params=None, ediffg=None, db_file=None, force_gamma=True, job_type='double_relaxation_run', max_force_threshold=0.25, auto_npar='>>auto_npar<<', half_kpts_first_relax=False, parents=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure, name='structure optimization', vasp_input_set=None, vasp_cmd='vasp', override_default_vasp_params=None, ediffg=None, db_file=None, force_gamma=True, job_type='double_relaxation_run', max_force_threshold=0.25, auto_npar='>>auto_npar<<', half_kpts_first_relax=False, parents=None, **kwargs)
    +

    Optimize the given structure.

    +
    +
    Args:
    +

    structure (Structure): Input structure. +name (str): Name for the Firework. +vasp_input_set (VaspInputSet): input set to use. Defaults to MPRelaxSet() if None. +override_default_vasp_params (dict): If this is not None, these params are passed to

    +
    +
    the default vasp_input_set, i.e., MPRelaxSet. This allows one to easily override +some settings, e.g., user_incar_settings, etc.
    +

    vasp_cmd (str): Command to run vasp. +ediffg (float): Shortcut to set ediffg in certain jobs +db_file (str): Path to file specifying db credentials to place output parsing. +force_gamma (bool): Force gamma centered kpoint generation +job_type (str): custodian job type (default “double_relaxation_run”) +max_force_threshold (float): max force on a site allowed at end; otherwise, reject job +auto_npar (bool or str): whether to set auto_npar. defaults to env_chk: “>>auto_npar<<” +half_kpts_first_relax (bool): whether to use half the kpoints for the first relaxation +parents ([Firework]): Parents of this particular Firework. +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.RamanFW(mode, displacement, prev_calc_dir=None, structure=None, name='raman', vasp_cmd='vasp', db_file=None, parents=None, user_incar_settings=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(mode, displacement, prev_calc_dir=None, structure=None, name='raman', vasp_cmd='vasp', db_file=None, parents=None, user_incar_settings=None, **kwargs)
    +

    Static calculation Firework that computes the DFPT dielectric constant for +structure displaced along the given normal mode direction.

    +
    +
    Args:
    +
    +
    structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
    +
    name of the FW.
    +
    +

    mode (int): normal mode index. +displacement (float): displacement along the normal mode in Angstroms. +name (str): Name for the Firework. +prev_calc_dir (str): Path to a previous calculation to copy from +vasp_cmd (str): Command to run vasp. +db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework.

    +
    +
    FW or list of FWS.
    +

    user_incar_settings (dict): Parameters in INCAR to override +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.SOCFW(magmom, structure=None, name='spin-orbit coupling', saxis=(0, 0, 1), prev_calc_dir=None, vasp_cmd='vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(magmom, structure=None, name='spin-orbit coupling', saxis=(0, 0, 1), prev_calc_dir=None, vasp_cmd='vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)
    +

    Firework for spin orbit coupling calculation.

    +
    +
    Args:
    +
    +
    structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
    +
    name of the FW.
    +
    +

    name (str): Name for the Firework. +prev_calc_dir (str): Path to a previous calculation to copy from +vasp_cmd (str): Command to run vasp. +copy_vasp_outputs (bool): Whether to copy outputs from previous

    +
    +
    run. Defaults to True.
    +

    db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework.

    +
    +
    FW or list of FWS.
    +

    **kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.StaticFW(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='vasp', prev_calc_loc=True, prev_calc_dir=None, db_file=None, vasptodb_kwargs={}, parents=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='vasp', prev_calc_loc=True, prev_calc_dir=None, db_file=None, vasptodb_kwargs={}, parents=None, **kwargs)
    +

    Standard static calculation Firework - either from a previous location or from a structure.

    +
    +
    Args:
    +
    +
    structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
    +
    is only used to set the name of the FW and any structure with the same composition +can be used.
    +
    +

    name (str): Name for the Firework. +vasp_input_set (VaspInputSet): input set to use (for jobs w/no parents)

    +
    +
    Defaults to MPStaticSet() if None.
    +

    vasp_input_set_params (dict): Dict of vasp_input_set kwargs. +vasp_cmd (str): Command to run vasp. +prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If

    +
    +
    a str value, retrieves a previous calculation output by name. If False/None, will create +new static calculation using the provided structure.
    +

    prev_calc_dir (str): Path to a previous calculation to copy from +db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework. FW or list of FWS. +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.StaticInterpolateFW(structure, start, end, name='static', vasp_input_set='MPStaticSet', vasp_input_set_params=None, vasp_cmd='vasp', db_file=None, parents=None, this_image=None, nimages=None, autosort_tol=0, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure, start, end, name='static', vasp_input_set='MPStaticSet', vasp_input_set_params=None, vasp_cmd='vasp', db_file=None, parents=None, this_image=None, nimages=None, autosort_tol=0, **kwargs)
    +

    Standard static calculation Firework that interpolates structures from two previous calculations.

    +
    +
    Args:
    +

    structure (Structure): Input structure used to name FireWork. +start (str): PassCalcLoc name of StaticFW or RelaxFW run of starting structure. +end (str): PassCalcLoc name of StaticFW or RelaxFW run of ending structure. +name (str): Name for the Firework. +vasp_input_set (str): Input set to use. Defaults to MPStaticSet. +vasp_input_set_params (dict): Dict of vasp_input_set_kwargs. +vasp_cmd (str): Command to run vasp. +copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True. +db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework. FW or list of FWS. +this_image (int): which interpolation to use for this run +nimages (int): number of interpolations +autosort_tol (float): a distance tolerance in angstrom in which

    +
    +
    to automatically sort end_structure to match to the closest +points in this particular structure.
    +

    **kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.core.TransmuterFW(structure, transformations, transformation_params=None, vasp_input_set=None, prev_calc_dir=None, name='structure transmuter', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, override_default_vasp_params=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure, transformations, transformation_params=None, vasp_input_set=None, prev_calc_dir=None, name='structure transmuter', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, override_default_vasp_params=None, **kwargs)
    +

    Apply the transformations to the input structure, write the input set corresponding +to the transformed structure, and run vasp on them. Note that if a transformation yields +many structures from one, only the last structure in the list is used.

    +
    +
    Args:
    +

    structure (Structure): Input structure. +transformations (list): list of names of transformation classes as defined in

    +
    +
    the modules in pymatgen.transformations. +eg: transformations=[‘DeformStructureTransformation’, ‘SupercellTransformation’]
    +
    +
    transformation_params (list): list of dicts where each dict specify the input
    +
    parameters to instantiate the transformation class in the transformations list.
    +
    vasp_input_set (VaspInputSet): VASP input set, used to write the input set for the
    +
    transmuted structure.
    +
    +

    name (string): Name for the Firework. +vasp_cmd (string): Command to run vasp. +copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True. +prev_calc_dir (str): Path to a previous calculation to copy from +db_file (string): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework. FW or list of FWS. +override_default_vasp_params (dict): additional user input settings for vasp_input_set. +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    +
    -
    -

    atomate.vasp.fireworks.nmr module

    +
    +

    atomate.vasp.fireworks.nmr module

    +
    +
    +class atomate.vasp.fireworks.nmr.NMRFW(structure=None, mode='cs', isotopes=None, name='nmr tensor', prev_calc_dir=None, vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure=None, mode='cs', isotopes=None, name='nmr tensor', prev_calc_dir=None, vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)
    +

    Firework for NMR tensor calculations

    +
    +
    Args:
    +
    +
    structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
    +
    name of the FW.
    +
    +

    mode (str): the NMR calculation type: cs or efg, default is cs +isotopes (list): list of isotopes to include, default is to include the

    +
    +
    lowest mass quadrupolar isotope for all applicable elements
    +

    name (str): Name for the Firework. +prev_calc_dir (str): Path to a previous calculation to copy from +vasp_cmd (str): Command to run vasp. +copy_vasp_outputs (bool): Whether to copy outputs from previous

    +
    +
    run. Defaults to True.
    +

    db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework.

    +
    +
    FW or list of FWS.
    +

    kwargs: Other kwargs that are passed to Firework.__init__.

    +
    +
    +
    + +
    +
    -
    -

    atomate.vasp.fireworks.polarization module

    +
    +

    atomate.vasp.fireworks.polarization module

    +
    +
    +class atomate.vasp.fireworks.polarization.LcalcpolFW(structure, name='static dipole moment', static_name='static', vasp_cmd='vasp', vasp_input_set=None, vasp_input_set_params=None, db_file=None, parents=None, gap_threshold=0.01, interpolate=False, start=None, end=None, this_image=0, nimages=5, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure, name='static dipole moment', static_name='static', vasp_cmd='vasp', vasp_input_set=None, vasp_input_set_params=None, db_file=None, parents=None, gap_threshold=0.01, interpolate=False, start=None, end=None, this_image=0, nimages=5, **kwargs)
    +

    Static Firework that calculates the dipole moment of structure or a single interpolated image of structures +output by two calculations specified by PassCalcLoc names start and end.

    +

    This Firework uses three steps to calculate the dipole moment. +1. A StaticFW or StaticInterpolatFW calculation is performed to compute the band gap of the structure. +2. Because VASP cannot compute the dipole moment of metallic structures, CheckBandgap checks that the structure +has a band gap greater than gap_threshold. If the structure has a band gap less than gap_threshold, +the Firework defuses. Otherwise, +3. a polarization calculation (LCALCPOL=TRUE) is performed to calculate the dipole moment.

    +

    If interpolate is equal to True, the keywords start and end are PassCalcLoc names used to locate the output +structures (CONTCAR) of two previous calculations. These two structures must have the same number and +type of atoms given in identical order in the structures. These structures are used to create nimages structures +interpolations.

    +

    this_image specifies which of the interpolated structures to use in this Firework. For example in the +ferroelectric workflow, two structures that can be distorted into one another (a +high-symmetry nonpolar structure and a low-symmetry polar structure) are relaxed using OptimizeFW. Then the +dipole moment is calculated for nimages intermediate structures generated by interpolating between these two +relaxed structures.

    +
    +
    Args:
    +
    +
    structure (Structure): Input structure. For an interpolation, this is a dummy structure. See interpolate arg
    +
    description.
    +
    +

    name (str): Name for the polarization FireWork. +static_name (str): Name for the SCF run to be used in PassCalcLoc if copy_vasp_outputs != True. +vasp_cmd (str): Command to run vasp. +vasp_input_set (str): string name for the VASP input set (e.g., “MITMDVaspInputSet”). +vasp_input_set_params (dict): Dict of vasp_input_set_kwargs. +db_file (str): Path to file specifying db credentials. +parents (Firework): Parents of this particular Firework. FW or list of FWS. +gap_threshold: Band gap cutoff for determining whether polarization calculation will proceed from

    +
    +
    SCF band gap.
    +
    +
    interpolate (bool): use structure created by interpolating CONTCAR structure from calculations indicated by
    +
    start and end PassCalcLoc names. If interpolate is False, start and end do not need to be set.
    +
    +

    start (str): PassCalcLoc name of StaticFW or RelaxFW run of starting structure +end (str): PassCalcLoc name of StaticFW or RelaxFW run of ending structure +this_image (int): which interpolation to use for this run of the nimage interpolations. +nimages (int): number of interpolations between CONTCAR structures from calculations indicated by start and

    +
    +
    end args.
    +
    +
    +
    + +
    +
    -
    -

    Module contents

    +
    +

    Module contents

    @@ -62,14 +612,14 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    @@ -106,13 +656,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • diff --git a/docs/atomate.vasp.html b/docs/atomate.vasp.html index 8b05f4e1c..ce023df96 100644 --- a/docs/atomate.vasp.html +++ b/docs/atomate.vasp.html @@ -6,10 +6,10 @@ - atomate.vasp package — atomate 0.8.5 documentation + atomate.vasp package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -78,12 +78,12 @@

    SubpackagesSubpackages @@ -91,25 +91,25 @@

    SubpackagesSubmodules
  • atomate.vasp.firetasks.glue_tasks module
  • atomate.vasp.firetasks.neb_tasks module
    • -
  • atomate.vasp.firetasks.parse_outputs module
    • -
  • atomate.vasp.firetasks.run_calc module
    • -
  • atomate.vasp.firetasks.write_inputs module
    • -
  • Module contents
    • +
  • atomate.vasp.firetasks.parse_outputs module
    • +
  • atomate.vasp.firetasks.run_calc module
    • +
  • atomate.vasp.firetasks.write_inputs module
    • +
  • Module contents
  • atomate.vasp.fireworks package
  • atomate.vasp.tests package
    • @@ -117,42 +117,42 @@

    SubpackagesSubpackages -
  • Module contents
    • +
  • Module contents
    • @@ -452,12 +452,12 @@

    Submodules
    -schema = {'analysis': {'delta_volume_as_percent', 'warnings', 'delta_volume', 'errors', 'max_force'}, 'calcs_reversed': {'input', 'nsites', 'formula_reduced_abc', 'vasp_version', 'task', 'dir_name', 'output', 'has_vasp_completed', 'nelements', 'elements', 'composition_reduced', 'composition_unit_cell', 'completed_at', 'formula_anonymous', 'run_type', 'formula_pretty'}, 'input': {'pseudo_potential', 'is_hubbard', 'potcar_spec', 'structure', 'is_lasph', 'hubbards', 'xc_override'}, 'output': {'bandgap', 'cbm', 'vbm', 'energy', 'density', 'spacegroup', 'is_gap_direct', 'is_metal', 'structure', 'forces', 'stress', 'energy_per_atom'}, 'root': {'chemsys', 'input', 'nsites', 'formula_reduced_abc', 'output', 'state', 'dir_name', 'run_stats', 'nelements', 'elements', 'composition_reduced', 'analysis', 'calcs_reversed', 'completed_at', 'formula_anonymous', 'composition_unit_cell', 'schema', 'formula_pretty'}}
    +schema = {'analysis': {'delta_volume', 'delta_volume_as_percent', 'errors', 'max_force', 'warnings'}, 'calcs_reversed': {'completed_at', 'composition_reduced', 'composition_unit_cell', 'dir_name', 'elements', 'formula_anonymous', 'formula_pretty', 'formula_reduced_abc', 'has_vasp_completed', 'input', 'nelements', 'nsites', 'output', 'run_type', 'task', 'vasp_version'}, 'input': {'hubbards', 'is_hubbard', 'is_lasph', 'potcar_spec', 'pseudo_potential', 'structure', 'xc_override'}, 'output': {'bandgap', 'cbm', 'density', 'energy', 'energy_per_atom', 'forces', 'is_gap_direct', 'is_metal', 'spacegroup', 'stress', 'structure', 'vbm'}, 'root': {'analysis', 'calcs_reversed', 'chemsys', 'completed_at', 'composition_reduced', 'composition_unit_cell', 'dir_name', 'elements', 'formula_anonymous', 'formula_pretty', 'formula_reduced_abc', 'input', 'nelements', 'nsites', 'output', 'run_stats', 'schema', 'state'}}

    -static set_analysis(max_force_threshold=0.5, volume_change_threshold=0.2)
    +static set_analysis(d, max_force_threshold=0.5, volume_change_threshold=0.2)

    Adapted from matgendb.creator

    set the ‘analysis’ key

    @@ -472,8 +472,372 @@

    Submodules -

    atomate.vasp.powerups module

    +
    +

    atomate.vasp.powerups module

    +
    +
    +atomate.vasp.powerups.add_additional_fields_to_taskdocs(original_wf, update_dict=None, task_name_constraint='VaspToDb')
    +

    For all VaspToDbTasks in a given workflow, add information to “additional_fields” to be +placed in the task doc.

    +
    +
    Args:
    +
    original_wf (Workflow) +update_dict (Dict): dictionary to add additional_fields
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_bandgap_check(original_wf, check_bandgap_params=None, fw_name_constraint=None)
    +

    Every FireWork that enters into the Db has a band gap check afterwards, e.g. min_gap and max_gap

    +
    +
    Args:
    +
    original_wf (Workflow) +check_bandgap_params (dict): a kwargs style dict of params, e.g. min_gap or max_gap +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_common_powerups(wf, c=None)
    +

    Apply the common powerups such as add_namefile, use_scratch_dir etc. from the given config dict.

    +
    +
    Args:
    +
    wf (Workflow) +c (dict): Config dict
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_modify_incar(original_wf, modify_incar_params=None, fw_name_constraint=None)
    +

    Every FireWork that runs VASP has a ModifyIncar task just beforehand. For example, allows +you to modify the INCAR based on the Worker using env_chk or using hard-coded changes.

    +
    +
    Args:
    +
    original_wf (Workflow) +modify_incar_params (dict) - dict of parameters for ModifyIncar. +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_modify_incar_envchk(original_wf, fw_name_constraint=None)
    +

    If you set the “incar_update” parameter in the Worker env, the INCAR will update this +parameter for all matching VASP runs

    +
    +
    Args:
    +
    original_wf (Workflow) +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_modify_potcar(original_wf, modify_potcar_params=None, fw_name_constraint=None)
    +

    Every FireWork that runs VASP has a ModifyIncar task just beforehand. For example, allows +you to modify the INCAR based on the Worker using env_chk or using hard-coded changes.

    +
    +
    Args:
    +
    original_wf (Workflow) +modify_incar_params (dict) - dict of parameters for ModifyIncar. +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_namefile(original_wf, use_slug=True)
    +

    Every FireWork begins by writing an empty file with the name +“FW–<fw.name>”. This makes it easy to figure out what jobs are in what +launcher directories, e.g. “ls -l launch*/FW–*” from within a “block” dir.

    +
    +
    Args:
    +
    original_wf (Workflow) +use_slug (bool): whether to replace whitespace-type chars with a slug
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_priority(original_wf, root_priority, child_priority=None)
    +

    Adds priority to a workflow

    +
    +
    Args:
    +
    original_wf (Workflow): original WF +root_priority (int): priority of first (root) job(s) +child_priority(int): priority of all child jobs. Defaults to root_priority
    +
    Returns:
    +
    Workflow: priority-decorated workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_small_gap_multiply(original_wf, gap_cutoff, density_multiplier, fw_name_constraint=None)
    +

    In all FWs with specified name constraints, add a ‘small_gap_multiply’ parameter that +multiplies the k-mesh density of compounds with gap < gap_cutoff by density multiplier. +Useful for increasing the k-point mesh for metallic or small gap systems. +Note that this powerup only works on FireWorks with the appropriate WriteVasp* tasks that +accept the small_gap_multiply argument…

    +
    +
    Args:
    +
    original_wf (Workflow) +gap_cutoff (float): Only multiply k-points for materials with gap < gap_cutoff (eV) +density_multiplier (float): Multiply k-point density by this amount +fw_name_constraint (str): Only apply changes to FWs where fw_name contains this substring.
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_stability_check(original_wf, check_stability_params=None, fw_name_constraint=None)
    +

    Every FireWork that enters into the Db has a CheckStability task afterward. This +allows defusing jobs that are not stable. In practice, you might want +to set the fw_name_constraint so that the stability is only checked at the +beginning of the workflow

    +
    +
    Args:
    +
    original_wf (Workflow) +check_stability_params (dict): a kwargs style dict of params +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_tags(original_wf, tags_list)
    +

    Adds tags to all Fireworks in the Workflow, WF metadata, as well as additional_fields for +the VaspDrone to track them later (e.g. all fireworks and vasp tasks related to a research project)

    +
    +
    Args:
    +
    original_wf (Workflow) +tags_list: list of tags parameters (list of strings)
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_trackers(original_wf, tracked_files=None, nlines=25)
    +

    Every FireWork that runs VASP also tracks the OUTCAR, OSZICAR, etc using FWS Trackers.

    +
    +
    Args:
    +
    original_wf (Workflow) +tracked_files (list) : list of files to be tracked +nlines (int): number of lines at the end of files to be tracked
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.add_wf_metadata(original_wf, structure)
    +

    Adds structure metadata to a workflow

    +
    +
    Args:
    +
    original_wf: (Workflow) +structure: (Structure) the structure being run by this workflow
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.clean_up_files(original_wf, files=('WAVECAR*', ), fw_name_constraint=None, task_name_constraint='RunVasp')
    +

    Cleans up files after another fireworks. Default behavior is to remove WAVECAR after running VASP

    +
    +
    Args:
    +
    original_wf (Workflow) +files (list): list of patterns to match for files to clean up +fw_name_constraint (str): pattern for firetask to clean up files after
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.clear_modify(original_wf, fw_name_constraint=None)
    +

    Simple powerup that clears the modifications to a workflow.

    +
    +
    Args:
    +
    +
    fw_name_constraint (str): name constraint for fireworks to
    +
    have their modification tasks removed
    +
    +
    +
    +
    + +
    +
    +atomate.vasp.powerups.modify_to_soc(original_wf, nbands, structure=None, modify_incar_params=None, fw_name_constraint=None)
    +

    Takes a regular workflow and transforms its VASP fireworkers that are specified with +fw_name_constraints to non-collinear calculations taking spin orbit coupling into account.

    +
    +
    Args:
    +
    original_wf (Workflow) +nbands (int): number of bands selected by the user (for now) +structure (Structure) +modify_incar_params ({}): a dictionary containing the setting for modyfining the INCAR (e.g. {“ICHARG”: 11}) +fw_name_constraint (string): name of the fireworks to be modified (all if None is passed)
    +
    Returns:
    +
    Workflow: modified with SOC
    +
    +
    + +
    +
    +atomate.vasp.powerups.preserve_fworker(original_wf, fw_name_constraint=None)
    +

    set _preserve_fworker spec of Fireworker(s) of a Workflow. Can be used to pin a workflow to +the first fworker it is run with. Very useful when running on multiple machines that can’t +share files. fw_name_constraint can be used to only preserve fworker after a certain point +where file passing becomes important

    +
    +
    Args:
    +
    original_wf (Workflow): +fw_name_constraint (str): name of the Fireworks to be tagged (all if None is passed)
    +
    Returns:
    +
    Workflow: modified workflow with specified Fireworkers tagged
    +
    +
    + +
    +
    +atomate.vasp.powerups.remove_custodian(original_wf, fw_name_constraint=None)
    +

    Replaces all tasks with “RunVasp*” (e.g. RunVaspCustodian) to be RunVaspDirect.

    +
    +
    Args:
    +
    original_wf (Workflow): original workflow +fw_name_constraint (str): Only apply changes to FWs where fw_name contains this substring.
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.set_execution_options(original_wf, fworker_name=None, category=None, fw_name_constraint=None, task_name_constraint=None)
    +

    set _fworker spec of Fireworker(s) of a Workflow. It can be used to specify a queue; +e.g. run large-memory jobs on a separate queue.

    +
    +
    Args:
    +

    original_wf (Workflow): +fworker_name (str): user-defined tag to be added under fw.spec._fworker

    +
    +
    e.g. “large memory”, “big”, etc
    +

    category (str): category of FWorker that should pul job +fw_name_constraint (str): name of the Fireworks to be tagged (all if None is passed) +task_name_constraint (str): name of the Firetasks to be tagged (e.g. None or ‘RunVasp’)

    +
    +
    Returns:
    +
    Workflow: modified workflow with specified Fireworkers tagged
    +
    +
    + +
    +
    +atomate.vasp.powerups.use_custodian(original_wf, fw_name_constraint=None, custodian_params=None)
    +

    Replaces all tasks with “RunVasp*” (e.g. RunVaspDirect) to be RunVaspCustodian. Thus, this +powerup adds error correction into VASP runs if not originally present and/or modifies +the correction behavior.

    +
    +
    Args:
    +

    original_wf (Workflow): original workflow +fw_name_constraint (str): Only apply changes to FWs where fw_name contains this substring.

    +
    +
    For example, use custodian only for certain runs, or set job_type to +“double_relaxation_run” only for structure optimization run, or set different +handler_group for different runs.
    +
    +
    custodian_params (dict): A dict of parameters for RunVaspCustodian. e.g., use it to set
    +
    a “scratch_dir” or “handler_group”.
    +
    +
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.use_fake_vasp(original_wf, ref_dirs, params_to_check=None)
    +

    Replaces all tasks with “RunVasp” (e.g. RunVaspDirect) to be RunVaspFake. Thus, we do not +actually run VASP but copy pre-determined inputs and outputs.

    +
    +
    Args:
    +
    original_wf (Workflow) +ref_dirs (dict): key=firework name, value=path to the reference vasp calculation directory +params_to_check (list): optional list of incar parameters to check.
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.use_gamma_vasp(original_wf, gamma_vasp_cmd)
    +

    For all RunVaspCustodian tasks, add the desired scratch dir.

    +
    +
    Args:
    +
    original_wf (Workflow) +gamma_vasp_cmd (str): path to gamma_vasp_cmd. Supports env_chk
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.use_no_vasp(original_wf, ref_dirs)
    +

    Instead of running VASP, does nothing and pass task documents from task.json files in ref_dirs +to task database.

    +
    +
    Args:
    +
    original_wf (Workflow) +ref_dirs(dict): key=firework name, value=path to the reference vasp calculation directory
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.powerups.use_scratch_dir(original_wf, scratch_dir)
    +

    For all RunVaspCustodian tasks, add the desired scratch dir.

    +
    +
    Args:
    +
    original_wf (Workflow) +scratch_dir (path): Path to the scratch dir to use. Supports env_chk
    +
    Returns:
    +
    Workflow
    +
    +
    +

    atomate.vasp.submission_filter module

    @@ -530,8 +894,8 @@

    atomate.vasp.powerups module

    atomate.vasp.vasp_config module

    -
    -

    atomate.vasp.vasp_powerups module

    +
    +

    atomate.vasp.vasp_powerups module

    Module contents

    @@ -544,7 +908,7 @@

    atomate.vasp.vasp_powerups module
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.vasp.tests.html b/docs/atomate.vasp.tests.html index 543813983..dbe2ffb8e 100644 --- a/docs/atomate.vasp.tests.html +++ b/docs/atomate.vasp.tests.html @@ -6,10 +6,10 @@ - atomate.vasp.tests package — atomate 0.8.5 documentation + atomate.vasp.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -119,8 +119,70 @@

    Submodules -

    atomate.vasp.tests.test_vasp_powerups module

    +
    +

    atomate.vasp.tests.test_vasp_powerups module

    +
    +
    +class atomate.vasp.tests.test_vasp_powerups.TestVaspPowerups(methodName='runTest')
    +

    Bases: unittest.case.TestCase

    +
    +
    +classmethod setUpClass()
    +

    Hook method for setting up class fixture before running tests in the class.

    +
    + +
    +
    +test_add_clean_up()
    +
    + +
    +
    +test_add_priority()
    +
    + +
    +
    +test_add_small_gap_multiply()
    +
    + +
    +
    +test_add_tags()
    +
    + +
    +
    +test_add_trackers()
    +
    + +
    +
    +test_add_wf_metadata()
    +
    + +
    +
    +test_custodian_powerups()
    +
    + +
    +
    +test_modify_incar()
    +
    + +
    +
    +test_modify_potcar()
    +
    + +
    +
    +test_use_scratch_dir()
    +
    + +
    +

    Module contents

    @@ -133,13 +195,13 @@

    atomate.vasp.tests.test_vasp_powerups module
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.vasp.workflows.base.html b/docs/atomate.vasp.workflows.base.html index c04242463..202e2b772 100644 --- a/docs/atomate.vasp.workflows.base.html +++ b/docs/atomate.vasp.workflows.base.html @@ -6,10 +6,10 @@ - atomate.vasp.workflows.base package — atomate 0.8.5 documentation + atomate.vasp.workflows.base package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -42,38 +42,551 @@

    atomate.vasp.workflows.base package

    Submodules

    -
    -

    atomate.vasp.workflows.base.adsorption module

    +
    +

    atomate.vasp.workflows.base.adsorption module

    +
    +
    +class atomate.vasp.workflows.base.adsorption.MPSurfaceSet(structure, bulk=False, auto_dipole=None, **kwargs)
    +

    Bases: pymatgen.io.vasp.sets.MVLSlabSet

    +

    Input class for MP slab calcs, mostly to change parameters +and defaults slightly

    +
    +
    +__init__(structure, bulk=False, auto_dipole=None, **kwargs)
    +

    Initialize self. See help(type(self)) for accurate signature.

    +
    + +
    +
    +incar
    +

    Incar object

    +
    + +
    + +
    +
    +atomate.vasp.workflows.base.adsorption.get_slab_fw(slab, transmuter=False, db_file=None, vasp_input_set=None, parents=None, vasp_cmd='vasp', name='', add_slab_metadata=True)
    +

    Function to generate a a slab firework. Returns a TransmuterFW if +bulk_structure is specified, constructing the necessary transformations +from the slab and slab generator parameters, or an OptimizeFW if only a +slab is specified.

    +
    +
    Args:
    +
    +
    slab (Slab or Structure): structure or slab corresponding
    +
    to the slab to be calculated
    +
    transmuter (bool): whether or not to use a TransmuterFW based
    +
    on slab params, if this option is selected, input slab must +be a Slab object (as opposed to Structure)
    +
    vasp_input_set (VaspInputSet): vasp_input_set corresponding to
    +
    the slab calculation
    +
    +

    parents (Fireworks or list of ints): parent FWs +db_file (string): path to database file +vasp_cmd (string): vasp command +name (string): name of firework +add_slab_metadata (bool): whether to add slab metadata to task doc

    +
    +
    Returns:
    +
    Firework corresponding to slab calculation
    +
    +
    + +
    +
    +atomate.vasp.workflows.base.adsorption.get_slab_trans_params(slab)
    +

    Gets a set of slab transformation params

    +
    +
    Args:
    +
    slab (Slab): slab to find transformation params from
    +
    Returns (SlabTransformation):
    +
    Transformation for a transformation that will transform +the oriented unit cell to the slab
    +
    +
    + +
    +
    +atomate.vasp.workflows.base.adsorption.get_wf_molecules(molecules, vasp_input_set=None, db_file=None, vasp_cmd='vasp', name='')
    +
    +
    Args:
    +
    molecules (Molecules): list of molecules to calculate +vasp_input_set (DictSet): VaspInputSet for molecules +db_file (string): database file path +vasp_cmd (string): VASP command +name (string): name for workflow
    +
    Returns:
    +
    workflow consisting of molecule calculations
    +
    +
    + +
    +
    +atomate.vasp.workflows.base.adsorption.get_wf_slab(slab, include_bulk_opt=False, adsorbates=None, ads_structures_params=None, vasp_cmd='vasp', db_file=None, add_molecules_in_box=False)
    +

    Gets a workflow corresponding to a slab calculation along with optional +adsorbate calcs and precursor oriented unit cell optimization

    +
    +
    Args:
    +

    slabs (list of Slabs or Structures): slabs to calculate +include_bulk_opt (bool): whether to include bulk optimization,

    +
    +
    this flag sets the slab fireworks to be TransmuterFWs based +on bulk optimization of oriented unit cells
    +

    adsorbates ([Molecule]): list of molecules to place as adsorbates +ads_structures_params (dict): parameters to be supplied as

    +
    +
    kwargs to AdsorbateSiteFinder.generate_adsorption_structures
    +
    +
    add_molecules_in_box (boolean): flag to add calculation of
    +
    adsorbate molecule energies to the workflow
    +
    +

    db_file (string): path to database file +vasp_cmd (string): vasp command

    +
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.workflows.base.adsorption.get_wfs_all_slabs(bulk_structure, include_bulk_opt=False, adsorbates=None, max_index=1, slab_gen_params=None, ads_structures_params=None, vasp_cmd='vasp', db_file=None, add_molecules_in_box=False)
    +

    Convenience constructor that allows a user to construct a workflow +that finds all adsorption configurations (or slabs) for a given +max miller index.

    +
    +
    Args:
    +

    bulk_structure (Structure): bulk structure from which to construct slabs +include_bulk_opt (bool): whether to include bulk optimization

    +
    +
    of oriented unit cells
    +

    adsorbates ([Molecule]): adsorbates to place on surfaces +max_index (int): max miller index +slab_gen_params (dict): dictionary of kwargs for generate_all_slabs +ads_structures_params (dict): dictionary of kwargs for generating

    +
    +
    of adsorption structures via AdsorptionSiteFinder
    +

    vasp_cmd (str): vasp command +db_file (str): location of db file +add_molecules_in_box (bool): whether to add molecules in a box

    +
    +
    for the entire workflow
    +
    +
    Returns:
    +
    list of slab-specific Workflows
    +
    +
    +
    -
    -

    atomate.vasp.workflows.base.bulk_modulus module

    +
    +

    atomate.vasp.workflows.base.bulk_modulus module

    +
    +
    +atomate.vasp.workflows.base.bulk_modulus.get_wf_bulk_modulus(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, eos='vinet', tag=None, user_incar_settings=None)
    +

    Returns the workflow that computes the bulk modulus by fitting to the given equation of state.

    +
    +
    Args:
    +

    structure (Structure): input structure. +deformations (list): list of deformation matrices(list of lists). +vasp_input_set (VaspInputSet): for the static deformation calculations +vasp_cmd (str): vasp command to run. +db_file (str): path to the db file. +user_kpoints_settings (dict): example: {“grid_density”: 7000} +eos (str): equation of state used for fitting the energies and the volumes.

    +
    +
    supported equation of states: “quadratic”, “murnaghan”, “birch”, “birch_murnaghan”, +“pourier_tarantola”, “vinet”, “deltafactor”. See pymatgen.analysis.eos.py
    +
    +
    tag (str): something unique to identify the tasks in this workflow. If None a random uuid
    +
    will be assigned.
    +
    +

    user_incar_settings (dict):

    +
    +
    Returns:
    +
    Workflow
    +
    +
    +
    -
    -

    atomate.vasp.workflows.base.core module

    +
    +

    atomate.vasp.workflows.base.core module

    +
    +
    +atomate.vasp.workflows.base.core.get_wf(structure, wf_filename, params=None, common_params=None, vis=None, wf_metadata=None)
    +

    Get a workflow given a structure and a name of file from the workflow library.

    +

    Possible options for wf_filename are listed in: atomate.vasp.workflows.base.library and +include band structure, dielectric constant, NEB, and more.

    +

    You can also override some of the parameters via the function arguments.

    +
    +
    Args:
    +

    structure: (Structure) structure to run +wf_filename: filename in library subdir, e.g. “band_structure.yaml” +params: (list of dicts) set params for each Firework; format is list

    +
    +
    that is same length as # of fws in the workflow
    +

    common_params: (dict) set common params +vis: (VaspInputSet) A VaspInputSet to use for the first FW +wf_metadata: (dict) workflow metadata

    +
    +
    Returns:
    +
    A Workflow
    +
    +
    +
    -
    -

    atomate.vasp.workflows.base.deformations module

    +
    +

    atomate.vasp.workflows.base.deformations module

    +
    +
    +atomate.vasp.workflows.base.deformations.get_wf_deformations(structure, deformations, name='deformation', vasp_input_set=None, vasp_cmd='vasp', db_file=None, tag='', copy_vasp_outputs=True, metadata=None)
    +

    Returns a structure deformation workflow.

    +

    Firework 1 : structural relaxation +Firework 2 - len(deformations): Deform the optimized structure and run static calculations.

    +
    +
    Args:
    +

    structure (Structure): input structure to be optimized and run +deformations (list of 3x3 array-likes): list of deformations +name (str): some appropriate name for the transmuter fireworks. +vasp_input_set (DictVaspInputSet): vasp input set for static deformed structure calculation. +vasp_cmd (str): command to run +db_file (str): path to file containing the database credentials. +tag (str): some unique string that will be appended to the names of the fireworks so that

    +
    +
    the data from those tagged fireworks can be queried later during the analysis.
    +
    +
    copy_vasp_outputs (bool): whether or not copy the outputs from the previous calc(usually
    +
    structure optimization) before the transmuter fireworks.
    +
    +

    metadata (dict): meta data

    +
    +
    Returns:
    +
    Workflow
    +
    +
    +
    -
    -

    atomate.vasp.workflows.base.elastic module

    +
    +

    atomate.vasp.workflows.base.elastic module

    +
    +
    +atomate.vasp.workflows.base.elastic.get_default_strain_states(order=2)
    +

    Generates a list of “strain-states”

    +
    + +
    +
    +atomate.vasp.workflows.base.elastic.get_wf_elastic_constant(structure, strain_states=None, stencils=None, db_file=None, conventional=False, order=2, vasp_input_set=None, analysis=True, sym_reduce=False, tag='elastic', copy_vasp_outputs=False, **kwargs)
    +

    Returns a workflow to calculate elastic constants.

    +
    +
    Firework 1 : write vasp input set for structural relaxation,
    +
    run vasp, +pass run location, +database insertion.
    +
    +

    Firework 2 - number of total deformations: Static runs on the deformed structures

    +

    last Firework : Analyze Stress/Strain data and fit the elastic tensor

    +
    +
    Args:
    +

    structure (Structure): input structure to be optimized and run. +strain_states (list of Voigt-notation strains): list of ratios of nonzero elements

    +
    +
    of Voigt-notation strain, e. g. [(1, 0, 0, 0, 0, 0), (0, 1, 0, 0, 0, 0), etc.].
    +
    +
    stencils (list of floats, or list of list of floats): values of strain to multiply
    +
    by for each strain state, i. e. stencil for the perturbation along the strain +state direction, e. g. [-0.01, -0.005, 0.005, 0.01]. If a list of lists, +stencils must correspond to each strain state provided.
    +
    +

    db_file (str): path to file containing the database credentials. +conventional (bool): flag to convert input structure to conventional structure,

    +
    +
    defaults to False.
    +
    +
    order (int): order of the tensor expansion to be determined. Defaults to 2 and
    +
    currently supports up to 3.
    +
    vasp_input_set (VaspInputSet): vasp input set to be used. Defaults to static
    +
    set with ionic relaxation parameters set. Take care if replacing this, +default ensures that ionic relaxation is done and that stress is calculated +for each vasp run.
    +
    analysis (bool): flag to indicate whether analysis task should be added
    +
    and stresses and strains passed to that task
    +
    +

    sym_reduce (bool): Whether or not to apply symmetry reductions +tag (str): +copy_vasp_outputs (bool): whether or not to copy previous vasp outputs. +kwargs (keyword arguments): additional kwargs to be passed to get_wf_deformations

    +
    +
    Returns:
    +
    Workflow
    +
    +
    +
    -
    -

    atomate.vasp.workflows.base.ferroelectric module

    +
    +

    atomate.vasp.workflows.base.ferroelectric module

    +
    +
    +atomate.vasp.workflows.base.ferroelectric.get_wf_ferroelectric(polar_structure, nonpolar_structure, vasp_cmd='vasp', db_file=None, vasp_input_set_polar='MPStaticSet', vasp_input_set_nonpolar='MPStaticSet', relax=False, vasp_relax_input_set_polar=None, vasp_relax_input_set_nonpolar=None, nimages=9, hse=False, add_analysis_task=False, wfid=None, tags=None)
    +

    Returns a workflow to calculate the spontaneous polarization of polar_structure using +a nonpolar reference phase structure and linear interpolations between the polar and +nonpolar structure.

    +

    The nonpolar and polar structures must be in the same space group setting and atoms ordered +such that a linear interpolation can be performed to create intermediate structures along +the distortion.

    +

    For example, to calculate the polarization of orthorhombic BaTiO3 (space group 38) using +the cubic structure (space group 221) as the nonpolar reference phase, we must transform +the cubic to the orthorhombic setting. This can be accomplished using Bilbao Crystallographic +Server’s Structure Relations tool. (http://www.cryst.ehu.es/cryst/rel.html)

    +
    +
    Args:
    +

    polar_structure (Structure): polar structure of candidate ferroelectric +nonpolar_structure (Structure): nonpolar reference structure in polar setting +vasp_input_set_polar (DictVaspInputSet): VASP polar input set. Defaults to MPStaticSet. +vasp_input_set_nonpolar (DictVaspInputSet): VASP nonpolar input set. Defaults to MPStaticSet. +vasp_relax_input_set_polar (DictVaspInputSet): VASP polar input set. Defaults to MPRelaxSet. +vasp_relax_input_set_nonpolar (DictVaspInputSet): VASP nonpolar input set. Defaults to MPRelaxSet. +vasp_cmd (str): command to run +db_file (str): path to file containing the database credentials. +nimages: Number of interpolations calculated from polar to nonpolar structures, including the nonpolar.

    +
    +
    For example, nimages = 9 will calculate 8 interpolated structures. 8 interpolations + nonpolar = 9.
    +

    add_analysis_task: Analyze polarization and energy trends as part of workflow. Default False. +wfid (string): Unique worfklow id starting with “wfid_”. If None this is atomatically generated (recommended). +tags (list of strings): Additional tags to add such as identifiers for structures.

    +
    +
    +

    Returns:

    +
    +
    -
    -

    atomate.vasp.workflows.base.gibbs module

    +
    +

    atomate.vasp.workflows.base.gibbs module

    +
    +
    +atomate.vasp.workflows.base.gibbs.get_wf_gibbs_free_energy(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000, mesh=(20, 20, 20), eos='vinet', qha_type='debye_model', pressure=0.0, poisson=0.25, anharmonic_contribution=False, metadata=None, tag=None)
    +

    Returns quasi-harmonic gibbs free energy workflow. +Note: phonopy package is required for the final analysis step if qha_type=”phonopy”

    +
    +
    Args:
    +

    structure (Structure): input structure. +deformations (list): list of deformation matrices(list of lists). +vasp_input_set (VaspInputSet) +vasp_cmd (str): vasp command to run. +db_file (str): path to the db file. +user_kpoints_settings (dict): example: {“grid_density”: 7000} +t_step (float): temperature step (in K) +t_min (float): min temperature (in K) +t_max (float): max temperature (in K) +mesh (list/tuple): reciprocal space density +eos (str): equation of state used for fitting the energies and the volumes.

    +
    +
    options supported by phonopy: “vinet”, “murnaghan”, “birch_murnaghan”. +Note: pymatgen supports more options than phonopy. see pymatgen.analysis.eos.py
    +
    +
    qha_type(str): quasi-harmonic approximation type: “debye_model” or “phonopy”,
    +
    default is “debye_model”
    +
    +

    pressure (float): in GPa +poisson (float): poisson ratio +anharmonic_contribution (bool): consider anharmonic contributions to

    +
    +
    Gibbs energy from the Debye model. Defaults to False.
    +

    metadata (dict): meta data +tag (str): something unique to identify the tasks in this workflow. If None a random uuid

    +
    +
    will be assigned.
    +
    +
    Returns:
    +
    Workflow
    +
    +
    +
    -
    -

    atomate.vasp.workflows.base.neb module

    +
    +

    atomate.vasp.workflows.base.neb module

    +

    This module defines the Nudged Elastic Band (NEB) workflow.

    +
    +
    +atomate.vasp.workflows.base.neb.get_wf_neb_from_endpoints(parent, endpoints, user_incar_settings=None, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)
    +

    Get a CI-NEB workflow from given endpoints. +Workflow: (Endpoints relax – ) NEB_1 – NEB_2 - … - NEB_r

    +
    +
    endpoints not optimized: ep–neb(r) +endpoints are optimized: neb(r)
    +
    +
    Args:
    +

    parent (Structure): parent structure. +endpoints (list[Structure]): The endpoint structures. +user_incar_settings([dict]): Additional user_incar_settings. Note that the order of the

    +
    +
    list is set as: “parent”, “ep_relax”, “neb1”, “neb2” etc., which contains +at least three elements. The first dict is for parent structure relaxation, +the second dict is for endpoints relaxation, and the rest are for NEB +calculations. For example, [{}, {}, {“IOPT”: 7}, {“IOPT”: 1}]. Besides, +user_incar_settings is used to determine how many NEB rounds will be. Default +is [{}, {}, {}].
    +

    additional_spec (dict): User spec settings to overwrite default_spec. +user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at

    +
    +
    least three elements, which is similar to user_incar_settings. For example, +[{}, {}, {“grid_density”: 100}] for the workflow from the parent structure +relaxation, then the endpoint relaxation followed by one-round NEB simulation. +Default values depend on the selected VaspInputSet.
    +
    +
    additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure
    +
    with user_incar_settings and user_kpoints_settings.
    +
    +
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.workflows.base.neb.get_wf_neb_from_images(parent, images, user_incar_settings, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)
    +

    Get a CI-NEB workflow from given images. +Workflow: NEB_1 – NEB_2 - … - NEB_n

    +
    +
    Args:
    +

    parent (Structure): parent structure. +images ([Structure]): All images and two endpoints. +user_incar_settings([dict]): Additional user_incar_settings. Note that the order of the

    +
    +
    list is set as: “parent”, “ep_relax”, “neb1”, “neb2” etc., which contains +at least three elements. The first dict is for parent structure relaxation, +the second dict is for endpoints relaxation, and the rest are for NEB +calculations. For example, [{}, {}, {“IOPT”: 7}, {“IOPT”: 1}]. Besides, +user_incar_settings is used to determine how many NEB rounds will be. Default +is [{}, {}, {}].
    +

    additional_spec (dict): User spec settings to overwrite default_spec. +user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at

    +
    +
    least three elements, which is similar to user_incar_settings. For example, +[{}, {}, {“grid_density”: 100}] for the workflow from the parent structure +relaxation, then the endpoint relaxation followed by one-round NEB simulation. +Default values depend on the selected VaspInputSet.
    +
    +
    additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure
    +
    with user_incar_settings and user_kpoints_settings.
    +
    +
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.workflows.base.neb.get_wf_neb_from_structure(structure, user_incar_settings=None, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)
    +

    Obtain the CI-NEB workflow staring with a parent structure. This works only under the single +vacancy diffusion mechanism.

    +
    +
    Workflow: (parent relaxation) –> Endpoints relaxation –> NEB_1 –> NEB_2 –> … –> NEB_r
    +
      +
    1. +
      If parent is not relaxed: then parent relaxation–ep–neb(r)
      +
      (r rounds of NEB)
      +
      +
      2. +
    2. If parent is relaxed: ep–neb(r) (r rounds of NEB)
      3. +
    +
    +
    Args:
    +

    structure (Structure): The parent structure. +user_incar_settings([dict]): Additional user_incar_settings. Note that the order of the

    +
    +
    list is set as: “parent”, “ep_relax”, “neb1”, “neb2” etc., which contains +at least three elements. The first dict is for parent structure relaxation, +the second dict is for endpoints relaxation, and the rest are for NEB +calculations. For example, [{}, {}, {“IOPT”: 7}, {“IOPT”: 1}]. Besides, +user_incar_settings is used to determine how many NEB rounds will be. Default +is [{}, {}, {}].
    +

    additional_spec (dict): User spec settings to overwrite default_spec. +user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at

    +
    +
    least three elements, which is similar to user_incar_settings. For example, +[{}, {}, {“grid_density”: 100}] for the workflow from the parent structure +relaxation, then the endpoint relaxation followed by one-round NEB simulation. +Default values depend on the selected VaspInputSet.
    +
    +
    additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure
    +
    with user_incar_settings and user_kpoints_settings.
    +
    +
    +
    Returns:
    +
    Workflow
    +
    +
    +
    -
    -

    atomate.vasp.workflows.base.raman module

    +
    +

    atomate.vasp.workflows.base.raman module

    +
    +
    +atomate.vasp.workflows.base.raman.get_wf_raman_spectra(structure, modes=None, step_size=0.005, vasp_cmd='vasp', db_file=None)
    +
    +
    Raman susceptibility tensor workflow:
    +
    Calculation of phonon normal modes followed by the computation of dielectric tensor for +structures displaced along the normal modes. Finally the dielectric tensors corresponding +to each mode are used to compute the Raman susceptibility tensor using finite difference +(central difference scheme).
    +
    Args:
    +

    structure (Structure): Input structure. +modes (tuple/list): list of modes for which the Raman spectra need to be calculated.

    +
    +
    The default is to use all the 3N modes.
    +
    +
    step_size (float): site displacement along the normal mode in Angstroms. Used to compute
    +
    the finite difference(central difference scheme) first derivative of the dielectric +constant along the normal modes.
    +
    +

    vasp_cmd (str): vasp command to run. +db_file (str): path to file containing the database credentials.

    +
    +
    Returns:
    +
    Workflow
    +
    +
    +
    -
    -

    atomate.vasp.workflows.base.thermal_expansion module

    +
    +

    atomate.vasp.workflows.base.thermal_expansion module

    +
    +
    +atomate.vasp.workflows.base.thermal_expansion.get_wf_thermal_expansion(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000, mesh=(20, 20, 20), eos='vinet', pressure=0.0, tag=None)
    +

    Returns quasi-harmonic thermal expansion workflow. +Note: phonopy package is required for the final analysis step.

    +
    +
    Args:
    +

    structure (Structure): input structure. +deformations (list): list of deformation matrices(list of lists). +vasp_input_set (VaspInputSet) +vasp_cmd (str): vasp command to run. +db_file (str): path to the db file. +user_kpoints_settings (dict): example: {“grid_density”: 7000} +t_step (float): temperature step (in K) +t_min (float): min temperature (in K) +t_max (float): max temperature (in K) +mesh (list/tuple): reciprocal space density +eos (str): equation of state used for fitting the energies and the volumes.

    +
    +
    options supported by phonopy: “vinet”, “murnaghan”, “birch_murnaghan”. +Note: pymatgen supports more options than phonopy. see pymatgen.analysis.eos.py
    +

    pressure (float): in GPa +tag (str): something unique to identify the tasks in this workflow. If None a random uuid

    +
    +
    will be assigned.
    +
    +
    Returns:
    +
    Workflow
    +
    +
    +
    -
    -

    Module contents

    +
    +

    Module contents

    @@ -83,21 +596,21 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    @@ -134,13 +647,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • diff --git a/docs/atomate.vasp.workflows.html b/docs/atomate.vasp.workflows.html index ee8240942..eaa2d5e9d 100644 --- a/docs/atomate.vasp.workflows.html +++ b/docs/atomate.vasp.workflows.html @@ -6,10 +6,10 @@ - atomate.vasp.workflows package — atomate 0.8.5 documentation + atomate.vasp.workflows package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -45,44 +45,44 @@

    Subpackagesatomate.vasp.workflows.base package
  • atomate.vasp.workflows.presets package
  • atomate.vasp.workflows.tests package

    • -
    -

    Module contents

    +
    +

    Module contents

    @@ -92,11 +92,11 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    @@ -133,13 +133,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • diff --git a/docs/atomate.vasp.workflows.presets.html b/docs/atomate.vasp.workflows.presets.html index 1e24e33d8..7f068857e 100644 --- a/docs/atomate.vasp.workflows.presets.html +++ b/docs/atomate.vasp.workflows.presets.html @@ -6,10 +6,10 @@ - atomate.vasp.workflows.presets package — atomate 0.8.5 documentation + atomate.vasp.workflows.presets package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -42,11 +42,177 @@

    atomate.vasp.workflows.presets package

    Submodules

    -
    -

    atomate.vasp.workflows.presets.core module

    +
    +

    atomate.vasp.workflows.presets.core module

    +
    +
    +atomate.vasp.workflows.presets.core.wf_bandstructure(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_bandstructure_hse(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_bandstructure_no_opt(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_bandstructure_plus_boltztrap(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_bandstructure_plus_hse(structure, gap_only=True, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_bulk_modulus(structure, c=None)
    +

    Bulk modulus workflow from the given structure and config dict.

    +
    +
    Args:
    +
    structure (Structure): input structure +c (dict): workflow config dict
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_dielectric_constant(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_dielectric_constant_no_opt(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_elastic_constant(structure, c=None, order=2, sym_reduce=False)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_elastic_constant_minimal(structure, c=None, order=2, sym_reduce=True)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_gibbs_free_energy(structure, c=None)
    +

    Gibbs free energy workflow from the given structure and config dict.

    +
    +
    Args:
    +
    structure (Structure): input structure +c (dict): workflow config dict
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_nmr(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_nudged_elastic_band(structures, parent, c=None)
    +

    Nudged elastic band (NEB) workflow from the given structures and config dict.

    +

    ‘is_optimized’ default False +‘neb_round’ default 1

    +
    +
    Notes:
    +

    Length of Structure list and “is_optimized” are used to determine the workflow: +1 structure # The parent structure & two endpoint indexes provided; need relaxation.

    +
    +
    # The parent structure & two endpoint indexes provided; no need to relax.
    +
    +
    2 structures # Two endpoints provided; need to relax two endpoints.
    +
    # Two relaxed endpoints provided; no need to relax two endpoints.
    +
    +

    >=3 structures # All images including two endpoints are provided.

    +
    +
    Args:
    +
    +
    structures ([Structure]):
    +
      +
    1. The parent structure
      2. +
    2. Two endpoint structures
      3. +
    3. An initial NEB path that comprises both images and endpoints
      4. +
    +
    +
    +

    parent (Structure): parent structure used to get two endpoints. +c (dict): workflow config dict, basic format:

    +
    +
    +
    {“fireworks”: [], “common_params”: {}, “additional_ep_params”: {},
    +
    “additional_neb_params”: {}}. When the length of structures is 1, “site_indices” key +must be included in c. Note that “fireworks” is a list corresponding to the order of +execution.
    +
    +
    +
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_piezoelectric_constant(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_raman_spectra(structure, c=None)
    +

    Raman spectra workflow from the given structure and config dict

    +
    +
    Args:
    +
    structure (Structure): input structure +c (dict): workflow config dict
    +
    Returns:
    +
    Workflow
    +
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_static(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_structure_optimization(structure, c=None)
    +
    + +
    +
    +atomate.vasp.workflows.presets.core.wf_thermal_expansion(structure, c=None)
    +

    Thermal expansion coefficient workflow from the given structure and config dict.

    +
    +
    Args:
    +
    structure (Structure): input structure +c (dict): workflow config dict
    +
    Returns:
    +
    Workflow
    +
    +
    +
    -
    -

    atomate.vasp.workflows.presets.scan module

    +
    +

    atomate.vasp.workflows.presets.scan module

    +
    +
    +atomate.vasp.workflows.presets.scan.wf_scan_opt(structure, c=None)
    +
    +

    Module contents

    @@ -59,12 +225,12 @@

    atomate.vasp.workflows.presets.scan module
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/atomate.vasp.workflows.tests.html b/docs/atomate.vasp.workflows.tests.html index ff0142652..ea4de24ea 100644 --- a/docs/atomate.vasp.workflows.tests.html +++ b/docs/atomate.vasp.workflows.tests.html @@ -6,10 +6,10 @@ - atomate.vasp.workflows.tests package — atomate 0.8.5 documentation + atomate.vasp.workflows.tests package — atomate 0.8.6 documentation - + @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -42,32 +42,251 @@

    atomate.vasp.workflows.tests package

    Submodules

    -
    -

    atomate.vasp.workflows.tests.test_adsorbate_workflow module

    +
    +

    atomate.vasp.workflows.tests.test_adsorbate_workflow module

    +
    +
    +class atomate.vasp.workflows.tests.test_adsorbate_workflow.TestAdsorptionWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp()
    +

    Create scratch directory(removes the old one if there is one) and change to it. +Also initialize launchpad.

    +
    + +
    +
    +test_input_sets()
    +
    + +
    +
    +test_wf()
    +
    + +
    +
    +test_wf_functions()
    +
    + +
    +
    -
    -

    atomate.vasp.workflows.tests.test_bulk_modulus_workflow module

    +
    +

    atomate.vasp.workflows.tests.test_bulk_modulus_workflow module

    +
    +
    +class atomate.vasp.workflows.tests.test_bulk_modulus_workflow.TestBulkModulusWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +

    This test will either actually run VASP (if VASP_CMD is set) or artificially pass on outputs +(if not VASP_CMD) and test the whole bulk modulus workflow and its implementation and outputs +for an example calculation for silicon.

    +

    note for the developer of the test: +This tests can be run in two modes if not VASP_CMD: +1. first all inputs and outputs of all deformations are present in which case

    +
    +
    in each folder a trimmed version of task.json will be generated so that
    +
      +
    1. +
      once task.json is present, VaspRun can be skipped where task.json is
      +
      available and their “inputs” and “outputs” folders can be removed
      +
      +
      2. +
    +
    +
    +setUp()
    +

    Create scratch directory(removes the old one if there is one) and change to it. +Also initialize launchpad.

    +
    + +
    +
    +setup_task_docs()
    +
    + +
    +
    +test_wf()
    +
    + +
    +
    +write_task_docs()
    +
    + +
    +
    -
    -

    atomate.vasp.workflows.tests.test_elastic_workflow module

    +
    +

    atomate.vasp.workflows.tests.test_elastic_workflow module

    +
    +
    +class atomate.vasp.workflows.tests.test_elastic_workflow.TestElasticWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp()
    +

    Create scratch directory(removes the old one if there is one) and change to it. +Also initialize launchpad.

    +
    + +
    +
    +test_wf()
    +
    + +
    +
    -
    -

    atomate.vasp.workflows.tests.test_ferroelectric_workflow module

    +
    +

    atomate.vasp.workflows.tests.test_ferroelectric_workflow module

    +
    +
    +class atomate.vasp.workflows.tests.test_ferroelectric_workflow.TestFerroelectricWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp()
    +

    Create scratch directory(removes the old one if there is one) and change to it. +Also initialize launchpad.

    +
    + +
    +
    +test_wf()
    +
    + +
    +
    +untarTestFiles()
    +
    + +
    +
    -
    -

    atomate.vasp.workflows.tests.test_neb_workflow module

    +
    +

    atomate.vasp.workflows.tests.test_neb_workflow module

    +
    +
    +class atomate.vasp.workflows.tests.test_neb_workflow.TestNudgedElasticBandWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp()
    +
      +
    1. Basic check for pymatgen configurations.
      2. +
    2. Setup all test workflow.
      3. +
    +
    + +
    +
    +test_wf()
    +
    + +
    +
    -
    -

    atomate.vasp.workflows.tests.test_nmr module

    +
    +

    atomate.vasp.workflows.tests.test_nmr module

    +
    +
    +class atomate.vasp.workflows.tests.test_nmr.TestNMRWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +

    This test will either actually run VASP (if VASP_CMD is set) or artificially pass on outputs +(if not VASP_CMD) and test the NMR workflow and its implementation and outputs +for an example calculation for LiAlSiO4.

    +
    +
    +setUp()
    +

    Create scratch directory(removes the old one if there is one) and change to it. +Also initialize launchpad.

    +
    + +
    +
    +test_wf()
    +
    + +
    +
    -
    -

    atomate.vasp.workflows.tests.test_raman_workflow module

    +
    +

    atomate.vasp.workflows.tests.test_raman_workflow module

    +
    +
    +class atomate.vasp.workflows.tests.test_raman_workflow.TestRamanWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp()
    +

    Create scratch directory(removes the old one if there is one) and change to it. +Also initialize launchpad.

    +
    + +
    +
    +test_wf()
    +
    + +
    +
    -
    -

    atomate.vasp.workflows.tests.test_vasp_workflows module

    +
    +

    atomate.vasp.workflows.tests.test_vasp_workflows module

    +
    +
    +class atomate.vasp.workflows.tests.test_vasp_workflows.TestVaspWorkflows(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp()
    +

    Create scratch directory(removes the old one if there is one) and change to it. +Also initialize launchpad.

    +
    + +
    +
    +test_bandgap_check_Vasp()
    +
    + +
    +
    +test_bandstructure_Vasp()
    +
    + +
    +
    +test_chgcar_db_read()
    +
    + +
    +
    +test_chgcar_db_read_write()
    +
    + +
    +
    +test_single_Vasp()
    +
    + +
    +
    +test_single_Vasp_dbinsertion()
    +
    + +
    +
    +test_trackers()
    +
    + +
    +
    -
    -

    Module contents

    +
    +

    Module contents

    @@ -77,19 +296,19 @@

    Module contents
    -

    Table Of Contents

    +

    Table of Contents

    @@ -126,13 +345,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • diff --git a/docs/builders.html b/docs/builders.html index 5fbb609c6..5c584e46d 100644 --- a/docs/builders.html +++ b/docs/builders.html @@ -6,10 +6,10 @@ - Builders — atomate 0.8.5 documentation + Builders — atomate 0.8.6 documentation - + @@ -36,7 +36,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -97,7 +97,7 @@

    Running builders
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/changelog.html b/docs/changelog.html index aa21a4a1d..70bf5f6f8 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -6,10 +6,10 @@ - atomate Changelog — atomate 0.8.5 documentation + atomate Changelog — atomate 0.8.6 documentation - + @@ -36,7 +36,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -47,6 +47,10 @@

    Navigation

    atomate Changelog

    +

    v0.8.6

    +
      +
    • add bandstructure no-opt workflow preset (A. Ganose)
      • +

    v0.8.5

    diff --git a/docs/concepts.html b/docs/concepts.html index ec4ee7ac1..6ebefd7bf 100644 --- a/docs/concepts.html +++ b/docs/concepts.html @@ -6,10 +6,10 @@ - Atomate concepts — atomate 0.8.5 documentation + Atomate concepts — atomate 0.8.6 documentation - + @@ -32,7 +32,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -103,7 +103,7 @@

    Tuning performance on different machines
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/contributors.html b/docs/contributors.html index 383caa297..f4cb4cb7d 100644 --- a/docs/contributors.html +++ b/docs/contributors.html @@ -6,10 +6,10 @@ - Contributors — atomate 0.8.5 documentation + Contributors — atomate 0.8.6 documentation - + @@ -36,7 +36,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -50,10 +50,10 @@

    Contributors +
  • Alireza Faghaninia, Alex Dunn, Alex Ganose, and Evan Spotte-Smith through the research group of A. Jain at LBNL.
  • Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, and Anne Rutt through the research group of Prof. Kristin Persson at UC Berkeley.
  • Hanmei Tang, Prof. Shyue Ping Ong, and the Materials Virtual Lab research group at UC San Diego.
  • Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State.
    • -
  • Alireza Faghaninia, Alex Dunn, and Evan Spotte-Smith through the research group of A. Jain at LBNL.
  • Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley.
  • Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley.
  • External contributors: specter119, M. Dias Costa, S. Torrisi
    • @@ -110,13 +110,13 @@

    Navigation

  • previous |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »

    • diff --git a/docs/creating_workflows.html b/docs/creating_workflows.html index 228af0734..fa67a4872 100644 --- a/docs/creating_workflows.html +++ b/docs/creating_workflows.html @@ -6,10 +6,10 @@ - Creating workflows — atomate 0.8.5 documentation + Creating workflows — atomate 0.8.6 documentation - + @@ -36,7 +36,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -103,7 +103,7 @@

    Sketch the workflow

    Finding Fireworks

    -

    Once you have identified each calculation or analysis step as a Firework in our graph, we must determine which Fireworks correspond to each node in our graph. The full Python documentation for each of the atomate Fireworks can be found in the atomate.vasp.fireworks module documentation or the corresponding documentation page for the software you want to use. Currently FEFF, LAMMPS, and VASP are supported. Some available VASP Fireworks are

    +

    Once you have identified each calculation or analysis step as a Firework in our graph, we must determine which Fireworks correspond to each node in our graph. The full Python documentation for each of the atomate Fireworks can be found in the atomate.vasp.fireworks module documentation or the corresponding documentation page for the software you want to use. Currently FEFF, LAMMPS, and VASP are supported. Some available VASP Fireworks are

    • OptimizeFW
    • StaticFW
      • @@ -132,12 +132,12 @@

      Finding Fireworksatomate.common.firetasks module for software-agnostic tasks such as PassCalcLocs or atomate.vasp.firetasks package <atomate.vasp.firetasks for some VASP specific ones, including the analysis tasks usually found in atomate.vasp.firetasks.parse_outputs.

      +

      You’ll notice that more generic Fireworks and Fireworks for analysis tasks are not in this list. Because they are intended to be simple and modular, these Fireworks are actually written as plain Firetasks that will get wrapped into a Firework when the Workflow is constructed. We’ll cover how to use them as Fireworks in the next section, but know that they can be found at places like atomate.common.firetasks module for software-agnostic tasks such as PassCalcLocs or atomate.vasp.firetasks package <atomate.vasp.firetasks for some VASP specific ones, including the analysis tasks usually found in atomate.vasp.firetasks.parse_outputs.

    Creating the workflow

    With each of the Fireworks identified for our sketched workflow, they can assemble them into a complete atomate Workflow in Python. In order to understand what’s going on here, you should be comfortable with creating instances of classes and using functions. To demonstrate how to assemble and use a workflow, we will use a slightly modified version of the Gibbs Free Energy Workflow and step through each line of code to explain what is going on.

    -

    For context, the Gibbs Free Energy Workflow calculates G(P,T) for a structure. Two methods for doing this are using the Debye model (see Blanco et al. Comput. Phys. Commun., 158, (2004)) or through vibration frequencies of atoms (see Togo and Tanaka, Scr. Mater., 108 (2015). It does this by first optimizing the desired structure. Next, that optimized structure has its volume scaled and a VASP calculation that is either a static calculation or calculation with density functional perturbation theory (the IBRION = 7 or 8 INCAR setting) is performed depending on what type of analysis is used. In the analysis, the Debye model or a phonon calculation is used to extrapolate the from 0K to finite temperatures using the harmonic approximation, giving each structure an F(T) dependence. Then each of these structures are considered together and fit to an equation of state which allows us express F(V,T) for this structure, which we can transform to G(P,T) to get the Gibbs free energy of that structure. The phonopy website has a good visualization for Helmholtz energies and volumes with increasing temperature.

    +

    For context, the Gibbs Free Energy Workflow calculates G(P,T) for a structure. Two methods for doing this are using the Debye model (see Blanco et al. Comput. Phys. Commun., 158, (2004)) or through vibration frequencies of atoms (see Togo and Tanaka, Scr. Mater., 108 (2015). It does this by first optimizing the desired structure. Next, that optimized structure has its volume scaled and a VASP calculation that is either a static calculation or calculation with density functional perturbation theory (the IBRION = 7 or 8 INCAR setting) is performed depending on what type of analysis is used. In the analysis, the Debye model or a phonon calculation is used to extrapolate the from 0K to finite temperatures using the harmonic approximation, giving each structure an F(T) dependence. Then each of these structures are considered together and fit to an equation of state which allows us express F(V,T) for this structure, which we can transform to G(P,T) to get the Gibbs free energy of that structure. The phonopy website has a good visualization for Helmholtz energies and volumes with increasing temperature.

    The Python implementation of the modified Gibbs Free Energy Workflow is:

     1
  2
@@ -314,7 +314,7 @@ 
    Creating the workflow

    Note

    -

    The documentation and source for the actual Gibbs Free Energy Workflow is found at atomate.vasp.workflows.base.gibbs. Here we have simplified some of the options and explicitly added each Firework.

    +

    The documentation and source for the actual Gibbs Free Energy Workflow is found at atomate.vasp.workflows.base.gibbs. Here we have simplified some of the options and explicitly added each Firework.

    In the above code example, we start by importing the classes and functions we’ll be using and defining our wf_gibbs_free_energy function with all of the parameters we’d like to control from a workflow level and the documentation for those parameters. Running the function will return a FireWorks Workflow to add to the LaunchPad.

    Lines 41-51 is where we define the optimization Firework. First we check if a vasp_input_set_relax parameter was passed, if not we default to MPRelaxSet and update that set if the user_kpoints_settings parameter was passed. It’s common to see a similar parameter for user_incar_settings. On line 49 we create our list of Fireworks (fws) with the OptimizeFW that we imported. Take note that this is the only Firework we pass our structure to, which allows for more flexibility. More on this later.

    @@ -325,7 +325,7 @@

    Creating the workflow

    More help

      -
    • Reading the source the base Workflows (atomate.vasp.workflows.base) would be a good place to find functional examples with reasonable parameters
      • +
    • Reading the source the base Workflows (atomate.vasp.workflows.base) would be a good place to find functional examples with reasonable parameters
    • Creating workflows can also be done to some extent in YAML files. You can adapt the example along with a short explanation of the Workflow YAML Reference.

    @@ -335,7 +335,7 @@

    Modifying workflows

    Powerups

    -

    Powerups (atomate.vasp.powerups) enable modifications to be made to workflows after they have been created. The benefit of these is that you can apply powerups conditionally in code or to a large list of Workflows that you’ll later add to your LaunchPad. Some powerups affect the behavior of your calculations, others simply add metadata or change how the individual Fireworks interact with the database under the hood.

    +

    Powerups (atomate.vasp.powerups) enable modifications to be made to workflows after they have been created. The benefit of these is that you can apply powerups conditionally in code or to a large list of Workflows that you’ll later add to your LaunchPad. Some powerups affect the behavior of your calculations, others simply add metadata or change how the individual Fireworks interact with the database under the hood.

    Some useful powerups that affect the behavior of VASP are

    @@ -50,7 +50,7 @@

    Navigation

    Introduction

    The Creating Workflows guide gave details on constructing workflows. This group of tutorials will give specific examples for customizations to workflows as you create them.

    -

    For some of these customizations, preset workflows cannot be used. Preset workflows are designed to give generically reasonable options. More full access for customizing the workflows can be achieved by using the atomate.vasp.workflows.base workflows instead of the presets.

    +

    For some of these customizations, preset workflows cannot be used. Preset workflows are designed to give generically reasonable options. More full access for customizing the workflows can be achieved by using the atomate.vasp.workflows.base workflows instead of the presets.

    Objectives

    @@ -244,7 +244,7 @@

    Use a different POTCAR @@ -112,7 +112,7 @@

    (optional) Run unit tests
    -

    Table Of Contents

    +

    Table of Contents

    diff --git a/docs/genindex.html b/docs/genindex.html index 127579109..8aede77f5 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -7,10 +7,10 @@ - Index — atomate 0.8.5 documentation + Index — atomate 0.8.6 documentation - + @@ -29,7 +29,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.8.5 documentation »
    • +
  • atomate 0.8.6 documentation »
    • @@ -50,7 +50,9 @@

    Index

    | E | F | G + | H | I + | J | L | M | N @@ -119,8 +121,42 @@

    _

  • (atomate.vasp.database.VaspCalcDb method)
  • (atomate.vasp.drones.VaspDrone method) +
    • +
  • (atomate.vasp.fireworks.core.BoltztrapFW method) +
    • +
  • (atomate.vasp.fireworks.core.DFPTFW method) +
    • +
  • (atomate.vasp.fireworks.core.HSEBSFW method) +
    • +
  • (atomate.vasp.fireworks.core.LepsFW method) +
    • +
  • (atomate.vasp.fireworks.core.MDFW method) +
    • +
  • (atomate.vasp.fireworks.core.NEBFW method) +
    • +
  • (atomate.vasp.fireworks.core.NEBRelaxationFW method) +
    • +
  • (atomate.vasp.fireworks.core.NonSCFFW method) +
    • +
  • (atomate.vasp.fireworks.core.OptimizeFW method) +
    • +
  • (atomate.vasp.fireworks.core.RamanFW method) +
    • +
  • (atomate.vasp.fireworks.core.SOCFW method) +
    • +
  • (atomate.vasp.fireworks.core.StaticFW method) +
    • +
  • (atomate.vasp.fireworks.core.StaticInterpolateFW method) +
    • +
  • (atomate.vasp.fireworks.core.TransmuterFW method) +
    • +
  • (atomate.vasp.fireworks.nmr.NMRFW method) +
    • +
  • (atomate.vasp.fireworks.polarization.LcalcpolFW method)
  • (atomate.vasp.submission_filter.SubmissionFilter method) +
    • +
  • (atomate.vasp.workflows.base.adsorption.MPSurfaceSet method)
    • @@ -132,6 +168,32 @@

    A

  • abspath() (atomate.utils.fileio.FileClient method)
  • AbstractBuilder (class in atomate.vasp.builders.base) +
    • +
  • add_additional_fields_to_taskdocs() (in module atomate.vasp.powerups) +
    • +
  • add_bandgap_check() (in module atomate.vasp.powerups) +
    • +
  • add_common_powerups() (in module atomate.vasp.powerups) +
    • +
  • add_modify_incar() (in module atomate.vasp.powerups) +
    • +
  • add_modify_incar_envchk() (in module atomate.vasp.powerups) +
    • +
  • add_modify_potcar() (in module atomate.vasp.powerups) +
    • +
  • add_namefile() (in module atomate.vasp.powerups) +
    • +
  • add_priority() (in module atomate.vasp.powerups) +
    • +
  • add_small_gap_multiply() (in module atomate.vasp.powerups) +
    • +
  • add_stability_check() (in module atomate.vasp.powerups) +
    • +
  • add_tags() (in module atomate.vasp.powerups) +
    • +
  • add_trackers() (in module atomate.vasp.powerups) +
    • +
  • add_wf_metadata() (in module atomate.vasp.powerups)
  • AddPathsToFilepadTask (class in atomate.feff.firetasks.parse_outputs)
    • @@ -166,6 +228,8 @@

    A

  • atomate.common.firetasks.run_calc (module)
  • atomate.common.firetasks.tests (module) +
    • +
  • atomate.common.firetasks.tests.test_glue_tasks (module)
  • atomate.common.firetasks.tests.test_parse_outputs (module)
    • @@ -239,8 +303,6 @@

    A

  • atomate.qchem.database (module)
    • - - +
    • atomate.qchem.workflows.tests (module)
    • atomate.qchem.workflows.tests.test_parse_pass_write (module) @@ -328,10 +392,40 @@

      A

    • atomate.vasp.drones (module)
    • atomate.vasp.examples (module) +
      • +
    • atomate.vasp.firetasks (module)
    • atomate.vasp.firetasks.glue_tasks (module)
    • atomate.vasp.firetasks.neb_tasks (module) +
      • +
    • atomate.vasp.firetasks.parse_outputs (module) +
      • +
    • atomate.vasp.firetasks.run_calc (module) +
      • +
    • atomate.vasp.firetasks.tests (module) +
      • +
    • atomate.vasp.firetasks.tests.test_copy (module) +
      • +
    • atomate.vasp.firetasks.tests.test_get_interpolated_poscar (module) +
      • +
    • atomate.vasp.firetasks.tests.test_polarization_to_db (module) +
      • +
    • atomate.vasp.firetasks.tests.test_write_vasp (module) +
      • +
    • atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar (module) +
      • +
    • atomate.vasp.firetasks.write_inputs (module) +
      • +
    • atomate.vasp.fireworks (module) +
      • +
    • atomate.vasp.fireworks.core (module) +
      • +
    • atomate.vasp.fireworks.nmr (module) +
      • +
    • atomate.vasp.fireworks.polarization (module) +
      • +
    • atomate.vasp.powerups (module)
    • atomate.vasp.submission_filter (module)
      • @@ -340,10 +434,60 @@

      A

    • atomate.vasp.tests.test_drones (module)
    • atomate.vasp.tests.test_setup (module) +
      • +
    • atomate.vasp.tests.test_vasp_powerups (module)
    • atomate.vasp.vasp_config (module) +
      • +
    • atomate.vasp.vasp_powerups (module) +
      • +
    • atomate.vasp.workflows (module) +
      • +
    • atomate.vasp.workflows.base (module) +
      • +
    • atomate.vasp.workflows.base.adsorption (module) +
      • +
    • atomate.vasp.workflows.base.bulk_modulus (module) +
      • +
    • atomate.vasp.workflows.base.core (module) +
      • +
    • atomate.vasp.workflows.base.deformations (module) +
      • +
    • atomate.vasp.workflows.base.elastic (module) +
      • +
    • atomate.vasp.workflows.base.ferroelectric (module) +
      • +
    • atomate.vasp.workflows.base.gibbs (module) +
      • +
    • atomate.vasp.workflows.base.neb (module) +
      • +
    • atomate.vasp.workflows.base.raman (module) +
      • +
    • atomate.vasp.workflows.base.thermal_expansion (module)
    • atomate.vasp.workflows.presets (module) +
      • +
    • atomate.vasp.workflows.presets.core (module) +
      • +
    • atomate.vasp.workflows.presets.scan (module) +
      • +
    • atomate.vasp.workflows.tests (module) +
      • +
    • atomate.vasp.workflows.tests.test_adsorbate_workflow (module) +
      • +
    • atomate.vasp.workflows.tests.test_bulk_modulus_workflow (module) +
      • +
    • atomate.vasp.workflows.tests.test_elastic_workflow (module) +
      • +
    • atomate.vasp.workflows.tests.test_ferroelectric_workflow (module) +
      • +
    • atomate.vasp.workflows.tests.test_neb_workflow (module) +
      • +
    • atomate.vasp.workflows.tests.test_nmr (module) +
      • +
    • atomate.vasp.workflows.tests.test_raman_workflow (module) +
      • +
    • atomate.vasp.workflows.tests.test_vasp_workflows (module)
    • AtomateTest (class in atomate.utils.testing)
      • @@ -354,9 +498,17 @@

      B

      + - +
      +
    • FitEOSToDb (class in atomate.vasp.firetasks.parse_outputs) +
      • +
    • FitEquationOfStateTask (class in atomate.vasp.firetasks.parse_outputs) +
    • FixTasksBuilder (class in atomate.vasp.builders.fix_tasks)
    • FragmentMolecule (class in atomate.qchem.firetasks.fragmenter) @@ -522,6 +688,8 @@

      G

    • get_chgcar_string() (atomate.vasp.database.VaspCalcDb method)
    • get_database() (in module atomate.utils.utils) +
      • +
    • get_default_strain_states() (in module atomate.vasp.workflows.base.elastic)
    • get_dos() (atomate.vasp.database.VaspCalcDb method)
      • @@ -537,13 +705,15 @@

      G

    • get_packmol_wf() (in module atomate.lammps.workflows.core)
      • -       		+
    • get_wf() (in module atomate.vasp.workflows.base.core) +
    • get_wf_basic() (in module atomate.lammps.workflows.core) +
      • +
    • get_wf_bulk_modulus() (in module atomate.vasp.workflows.base.bulk_modulus) +
      • +
    • get_wf_deformations() (in module atomate.vasp.workflows.base.deformations)
    • get_wf_eels() (in module atomate.feff.workflows.core) +
      • +
    • get_wf_elastic_constant() (in module atomate.vasp.workflows.base.elastic)
    • get_wf_exafs_paths() (in module atomate.feff.workflows.core) +
      • +
    • get_wf_ferroelectric() (in module atomate.vasp.workflows.base.ferroelectric)
    • get_wf_from_spec_dict() (in module atomate.utils.utils) +
      • +
    • get_wf_gibbs_free_energy() (in module atomate.vasp.workflows.base.gibbs) +
      • +
    • get_wf_molecules() (in module atomate.vasp.workflows.base.adsorption) +
      • +
    • get_wf_neb_from_endpoints() (in module atomate.vasp.workflows.base.neb) +
      • +
    • get_wf_neb_from_images() (in module atomate.vasp.workflows.base.neb) +
      • +
    • get_wf_neb_from_structure() (in module atomate.vasp.workflows.base.neb) +
      • +
    • get_wf_raman_spectra() (in module atomate.vasp.workflows.base.raman) +
      • +
    • get_wf_slab() (in module atomate.vasp.workflows.base.adsorption) +
      • +
    • get_wf_thermal_expansion() (in module atomate.vasp.workflows.base.thermal_expansion)
    • get_wf_xas() (in module atomate.feff.workflows.core) +
      • +
    • get_wfs_all_slabs() (in module atomate.vasp.workflows.base.adsorption)
    • GetInterpolatedPOSCAR (class in atomate.vasp.firetasks.glue_tasks) +
      • +
    • GibbsAnalysisToDb (class in atomate.vasp.firetasks.parse_outputs) +
      • +
    • GibbsFreeEnergyTask (class in atomate.vasp.firetasks.parse_outputs)
    • glob() (atomate.utils.fileio.FileClient method)
      • +

      H

      + + +
      +

      I

      +

      J

      + + + +
      +

      L

      - +
      diff --git a/docs/running_workflows.html b/docs/running_workflows.html index 03a76ac90..5d4823774 100644 --- a/docs/running_workflows.html +++ b/docs/running_workflows.html @@ -6,10 +6,10 @@ - Running workflows tutorial — atomate 0.8.5 documentation + Running workflows tutorial — atomate 0.8.6 documentation - + @@ -36,7 +36,7 @@

      Navigation

    • previous |
      • -
    • atomate 0.8.5 documentation »
      • +
    • atomate 0.8.6 documentation »
      • @@ -142,9 +142,9 @@

      Option 3: use Python to generate and add the workflowThe YAML version above is more efficient and clear to read and modify than a typical shell script to set up and run these calculations by hand. Even so, this workflow would have been tedious to type out rather than copy-paste. There must be a better way! Enter Python.

      -

      In the installation tutorial, you set up your FW_config.yaml, you indicated the atomate Fireworks can be found at atomate.vasp.fireworks. -Similarly, atomate preset workflows can be imported from atomate.vasp.workflows.presets.core, -which thinly wraps the base workflows (atomate.vasp.workflows.base) allowing for common settings to be changed with configuration dictionaries. +

      In the installation tutorial, you set up your FW_config.yaml, you indicated the atomate Fireworks can be found at atomate.vasp.fireworks. +Similarly, atomate preset workflows can be imported from atomate.vasp.workflows.presets.core, +which thinly wraps the base workflows (atomate.vasp.workflows.base) allowing for common settings to be changed with configuration dictionaries. We can setup the workflow and add it to our LaunchPad ready to run in just a few lines of Python.

      Create the workflow script

      In the same directory as the POSCAR, create a Python script named mgo_bandstructure.py with the following contents:

      @@ -249,7 +249,7 @@

      Conclusion
      -

      Table Of Contents

      +

      Table of Contents

      diff --git a/docs/search.html b/docs/search.html index 0d259b2bf..39fcae64b 100644 --- a/docs/search.html +++ b/docs/search.html @@ -6,10 +6,11 @@ - Search — atomate 0.8.5 documentation + Search — atomate 0.8.6 documentation - + + @@ -36,7 +37,7 @@

      Navigation

    • modules |
      • -
    • atomate 0.8.5 documentation »
      • +
    • atomate 0.8.6 documentation »
      • @@ -87,13 +88,13 @@

      Navigation

    • modules |
      • -
    • atomate 0.8.5 documentation »
      • +
    • atomate 0.8.6 documentation »
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\ No newline at end of file diff --git a/docs/workflow_yaml_reference.html b/docs/workflow_yaml_reference.html index 80f434fe6..5fe5f1822 100644 --- a/docs/workflow_yaml_reference.html +++ b/docs/workflow_yaml_reference.html @@ -6,10 +6,10 @@ - Workflow YAML Reference — atomate 0.8.5 documentation + Workflow YAML Reference — atomate 0.8.6 documentation - + @@ -36,7 +36,7 @@

      Navigation

    • previous |
      • -
    • atomate 0.8.5 documentation »
      • +
    • atomate 0.8.6 documentation »
      • @@ -173,7 +173,7 @@

      EOS Workflow Example
      atwf add POSCAR -s eos.yaml
      -

      The YAML file format is typically considered easy to read, but it is less practical for more complicated workflows. The Python implementation of the EOS workflow is at atomate.vasp.workflows.base.bulk_modulus and it uses the existing deformation workflow to express the same as the above YAML file in less than 20 lines of Python code, including imports. Another advantage of using Python is being able to have more control over Fireworks and create them from Firetasks in the workflow, like the FitEOSToDb Firetask.

      +

      The YAML file format is typically considered easy to read, but it is less practical for more complicated workflows. The Python implementation of the EOS workflow is at atomate.vasp.workflows.base.bulk_modulus and it uses the existing deformation workflow to express the same as the above YAML file in less than 20 lines of Python code, including imports. Another advantage of using Python is being able to have more control over Fireworks and create them from Firetasks in the workflow, like the FitEOSToDb Firetask.

      @@ -183,7 +183,7 @@

      EOS Workflow Example