Skip to content

Commit

Permalink
update candela
Browse files Browse the repository at this point in the history
  • Loading branch information
@Chentao168
Chentao168 committed Aug 23, 2023
1 parent f9db28c commit e035267
Show file tree
Hide file tree
Showing 23 changed files with 251 additions and 33 deletions.
12 changes: 6 additions & 6 deletions _book/abacus-candela.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -399,7 +399,7 @@ <h1>
<h1 id="abacuscandela-&#x4F7F;&#x7528;&#x6559;&#x7A0B;"><a name="abacuscandela-&#x4F7F;&#x7528;&#x6559;&#x7A0B;" class="plugin-anchor" href="#abacuscandela-&#x4F7F;&#x7528;&#x6559;&#x7A0B;"><i class="fa fa-link" aria-hidden="true"></i></a>ABACUS+Candela &#x4F7F;&#x7528;&#x6559;&#x7A0B;</h1>
<p><strong>&#x4F5C;&#x8005;&#xFF1A;&#x9648;&#x6D9B;&#xFF0C;&#x90AE;&#x7BB1;&#xFF1A;[email protected]</strong></p>
<p><strong>&#x5BA1;&#x6838;&#xFF1A;&#x9648;&#x9ED8;&#x6DB5;&#xFF0C;&#x90AE;&#x7BB1;&#xFF1A;[email protected]</strong></p>
<p><strong>&#x6700;&#x540E;&#x66F4;&#x65B0;&#x65F6;&#x95F4;&#xFF1A;2023/08/02</strong></p>
<p><strong>&#x6700;&#x540E;&#x66F4;&#x65B0;&#x65F6;&#x95F4;&#xFF1A;2023/08/23</strong></p>
<h1 id="&#x4E00;&#x3001;&#x4ECB;&#x7ECD;"><a name="&#x4E00;&#x3001;&#x4ECB;&#x7ECD;" class="plugin-anchor" href="#&#x4E00;&#x3001;&#x4ECB;&#x7ECD;"><i class="fa fa-link" aria-hidden="true"></i></a>&#x4E00;&#x3001;&#x4ECB;&#x7ECD;</h1>
<p>&#x672C;&#x6559;&#x7A0B;&#x65E8;&#x5728;&#x4ECB;&#x7ECD;&#x91C7;&#x7528; Candela &#x5206;&#x6790; ABACUS&#xFF08;&#x57FA;&#x4E8E; 3.2.4 &#x7248;&#x672C;&#xFF09;&#x5206;&#x5B50;&#x52A8;&#x529B;&#x5B66;&#x8F68;&#x8FF9;&#xFF0C;&#x8BA1;&#x7B97;&#x5F84;&#x5411;&#x5206;&#x5E03;&#x51FD;&#x6570;&#xFF08;Radial Distribution Function&#xFF0C;&#x7B80;&#x79F0; RDF&#xFF09;&#xFF0C;&#x9759;&#x6001;&#x7ED3;&#x6784;&#x56E0;&#x5B50;&#xFF08;Static Structure Factor&#xFF0C;&#x7B80;&#x79F0; SSF&#xFF09;&#xFF0C;&#x79BB;&#x5B50;-&#x79BB;&#x5B50;&#x52A8;&#x6001;&#x7ED3;&#x6784;&#x56E0;&#x5B50;&#xFF08;Ion-ion Dynamic Structure Factor&#xFF0C;&#x7B80;&#x79F0; DSF&#xFF09;&#x4EE5;&#x53CA;&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;&#xFF08;Mean Square Displacement&#xFF0C;&#x7B80;&#x79F0; MSD&#xFF09;&#x6D41;&#x7A0B;&#x3002;</p>
<p>&#x4E0A;&#x8FF0;&#x6027;&#x8D28;&#x7684;&#x5177;&#x4F53;&#x63CF;&#x8FF0;&#x53EF;&#x4EE5;&#x53C2;&#x8003;&#xFF1A;<a href="https://iopscience.iop.org/article/10.1088/1361-648X/ab5890" target="_blank">Qianrui Liu <em>et al</em> 2020 <em>J. Phys.: Condens. Matter</em> <strong>32</strong> 144002</a>&#xFF0C;&#x5F84;&#x5411;&#x5206;&#x5E03;&#x51FD;&#x6570;&#xFF08;RDF&#xFF09;&#x89C1;&#x6587;&#x4E2D;&#x516C;&#x5F0F;&#xFF08;12&#xFF09;&#xFF0C;&#x9759;&#x6001;&#x7ED3;&#x6784;&#x56E0;&#x5B50;&#xFF08;SSF&#xFF09;&#x89C1;&#x516C;&#x5F0F;&#xFF08;13&#xFF09;&#xFF0C;&#x79BB;&#x5B50;-&#x79BB;&#x5B50;&#x52A8;&#x6001;&#x7ED3;&#x6784;&#x56E0;&#x5B50;&#xFF08;DSF&#xFF09;&#x89C1;&#x516C;&#x5F0F;&#xFF08;15&#xFF0C;16&#xFF0C;17&#xFF09;&#x4EE5;&#x53CA;&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;&#xFF08;MSD&#xFF09;&#x89C1;&#x516C;&#x5F0F;&#xFF08;18&#xFF09;&#x3002;</p>
Expand Down Expand Up @@ -431,7 +431,7 @@ <h2 id="1-&#x8BA1;&#x7B97;&#x5F84;&#x5411;&#x5206;&#x5E03;&#x51FD;&#x6570;"><a n

ntype <span class="token number">1</span>
natom <span class="token number">32</span>
rcut <span class="token number">1.2</span>
rcut <span class="token number">2.3</span>
dr <span class="token number">0.01</span>
</code></pre>
<p>&#x4EE5;&#x4E0A;&#x53C2;&#x6570;&#x5728; Candela &#x7684;<a href="https://candela-docs.readthedocs.io/en/latest/" target="_blank">&#x7EBF;&#x4E0A;&#x6587;&#x6863;</a>&#x4E2D;&#x5747;&#x6709;&#x8BE6;&#x7EC6;&#x8BF4;&#x660E;&#xFF0C;&#x8FD9;&#x91CC;&#x518D;&#x8FDB;&#x884C;&#x7B80;&#x5355;&#x6982;&#x8FF0;&#xFF1A;</p>
Expand Down Expand Up @@ -527,10 +527,10 @@ <h2 id="3-&#x79BB;&#x5B50;-&#x79BB;&#x5B50;&#x52A8;&#x6001;&#x7ED3;&#x6784;&#x56
<pre class="language-"><code class="lang-bash">mpirun <span class="token parameter variable">-n</span> <span class="token number">2</span> candela
</code></pre>
<p>&#x5373;&#x53EF;&#x5F97;&#x5230; ISF&#xFF0C;&#x8F93;&#x51FA;&#x5230; <code>isf.txt</code>&#xFF0C;&#x5176;&#x4E2D;&#x7B2C;&#x4E00;&#x5217;&#x4E3A;&#x65F6;&#x95F4;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps&#xFF0C;&#x7B2C;&#x4E8C;&#x5217;&#x5373;&#x4E3A;&#x5BF9;&#x5E94;&#x7684; ISF&#x3002;</p>
<p>&#x63A5;&#x7740;&#x6267;&#x884C;&#x5982;&#x4E0B;&#x547D;&#x4EE4;&#x5F97;&#x5230;&#x79BB;&#x5B50;-&#x79BB;&#x5B50;&#x52A8;&#x6001;&#x7ED3;&#x6784;&#x56E0;&#x5B50;&#xFF1A;</p>
<p>&#x63A5;&#x7740;&#x6267;&#x884C;&#x5982;&#x4E0B;&#x547D;&#x4EE4;&#x5F97;&#x5230;&#x79BB;&#x5B50;-&#x79BB;&#x5B50;&#x52A8;&#x6001;&#x7ED3;&#x6784;&#x56E0;&#x5B50;&#xFF0C;&#x5176;&#x4E2D;<code>PathtoCandela</code>&#x6307;&#x7684;&#x662F;Candela&#x7684;&#x4E0B;&#x8F7D;&#x76EE;&#x5F55;&#xFF1A;</p>
<pre class="language-"><code class="lang-bash">python PathtoCandela/examples/e3_dsf/onedsf.py <span class="token number">0.00006</span> <span class="token number">0.0006</span>
</code></pre>
<p>&#x5176;&#x4E2D;&#x7B2C;&#x4E00;&#x4E2A;&#x53C2;&#x6570; 0.00006=dt_snapshots*geo_interval&#xFF0C;&#x4E3A; ISF &#x7684;&#x65F6;&#x95F4;&#x6B65;&#x957F;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps&#xFF1B;&#x7B2C;&#x4E8C;&#x4E2A;&#x53C2;&#x6570; 0.0006&#xFF0C;&#x4E3A;&#x5BF9; ISF &#x505A;&#x5085;&#x91CC;&#x53F6;&#x53D8;&#x6362;&#x7684;&#x603B;&#x65F6;&#x957F;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps&#x3002;&#x8FD9;&#x91CC; <code>onedsf.py</code> &#x9ED8;&#x8BA4;&#x8BFB;&#x53D6; <code>isf.txt</code>&#xFF0C;&#x5E76;&#x8F93;&#x51FA;&#x5230; <code>dsf.txt</code>&#xFF0C;&#x5176;&#x4E2D;&#x7B2C;&#x4E00;&#x5217;&#x4E3A;<script type="math/tex; ">\hbar \omega</script>&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; meV&#xFF0C;&#x7B2C;&#x4E8C;&#x5217;&#x5373;&#x4E3A;&#x5BF9;&#x5E94;&#x7684; DSF&#x3002;</p>
<p>&#x5176;&#x4E2D;&#x7B2C;&#x4E00;&#x4E2A;&#x53C2;&#x6570; 0.00006 = dt_snapshots * geo_interval&#xFF0C;&#x4E3A; ISF &#x7684;&#x65F6;&#x95F4;&#x6B65;&#x957F;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps&#xFF1B;&#x7B2C;&#x4E8C;&#x4E2A;&#x53C2;&#x6570; 0.0006&#xFF0C;&#x4E3A;&#x5BF9; ISF &#x505A;&#x5085;&#x91CC;&#x53F6;&#x53D8;&#x6362;&#x7684;&#x603B;&#x65F6;&#x957F;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps&#x3002;&#x8FD9;&#x91CC; <code>onedsf.py</code> &#x9ED8;&#x8BA4;&#x8BFB;&#x53D6; <code>isf.txt</code>&#xFF0C;&#x5E76;&#x8F93;&#x51FA;&#x5230; <code>dsf.txt</code>&#xFF0C;&#x5176;&#x4E2D;&#x7B2C;&#x4E00;&#x5217;&#x4E3A;<script type="math/tex; ">\hbar \omega</script>&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; meV&#xFF0C;&#x7B2C;&#x4E8C;&#x5217;&#x5373;&#x4E3A;&#x5BF9;&#x5E94;&#x7684; DSF&#x3002;</p>
<h2 id="4-&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;"><a name="4-&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;" class="plugin-anchor" href="#4-&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;"><i class="fa fa-link" aria-hidden="true"></i></a>4 &#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;</h2>
<p>&#x8FDB;&#x5165; <code>MSD</code> &#x6587;&#x4EF6;&#x5939;&#xFF0C;<code>INPUT</code> &#x6587;&#x4EF6;&#x5177;&#x4F53;&#x5982;&#x4E0B;&#xFF1A;</p>
<pre class="language-"><code class="lang-bash">calculation msd_multiple
Expand All @@ -557,7 +557,7 @@ <h2 id="4-&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;"><a name="4-&#x5747;&#x65B9;&
<li>msd_t0&#xFF1A;&#x8BA1;&#x7B97;&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;&#x7684;&#x8D77;&#x59CB;&#x65F6;&#x95F4;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps</li>
<li>msd_t&#xFF1A;&#x6BCF;&#x6BB5;&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;&#x7684;&#x65F6;&#x957F;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps</li>
<li>msd_dt0&#xFF1A;&#x4E24;&#x6BB5;&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;&#x8D77;&#x59CB;&#x4F4D;&#x7F6E;&#x7684;&#x95F4;&#x9694;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps&#x3002;&#x82E5;&#x8BBE;&#x7F6E;&#x7B49;&#x4E8E; msd_t&#xFF0C;&#x5219;&#x6BCF;&#x6BB5;&#x5747;&#x65B9;&#x5DEE;&#x4F4D;&#x79FB;&#x4E4B;&#x95F4;&#x7684;&#x65F6;&#x95F4;&#x8DDD;&#x79BB;&#x4E3A; 0</li>
<li>msd_dt&#xFF1A;&#x83B7;&#x53D6;&#x7684; MD &#x8F68;&#x8FF9;&#x6BCF;&#x4E00;&#x5E27;&#x4E4B;&#x95F4;&#x7684;&#x65F6;&#x95F4;&#x6B65;&#x957F;&#xFF08;=geo_interval*dt&#xFF0C;&#x5176;&#x4E2D; dt &#x4E3A; MD &#x8F68;&#x8FF9;&#x6BCF;&#x4E00;&#x5E27;&#x4E4B;&#x95F4;&#x7684;&#x65F6;&#x95F4;&#x6B65;&#x957F;&#xFF09;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps</li>
<li>msd_dt&#xFF1A;&#x83B7;&#x53D6;&#x7684; MD &#x8F68;&#x8FF9;&#x6BCF;&#x4E00;&#x5E27;&#x4E4B;&#x95F4;&#x7684;&#x65F6;&#x95F4;&#x6B65;&#x957F;&#xFF08;&#x7B49;&#x4E8E;geo_interval * dt&#xFF0C;&#x5176;&#x4E2D; dt &#x4E3A; MD &#x8F68;&#x8FF9;&#x6BCF;&#x4E00;&#x5E27;&#x4E4B;&#x95F4;&#x7684;&#x65F6;&#x95F4;&#x6B65;&#x957F;&#xFF09;&#xFF0C;&#x5355;&#x4F4D;&#x4E3A; ps</li>
<li>msd_natom&#xFF1A;&#x9700;&#x8981;&#x8BBE;&#x7F6E;&#x4E3A;&#x8BA1;&#x7B97;&#x7684;&#x539F;&#x5B50;&#x6570;</li>
</ul>
<p>&#x6267;&#x884C;&#x5982;&#x4E0B;&#x547D;&#x4EE4;&#xFF1A;</p>
Expand Down Expand Up @@ -607,7 +607,7 @@ <h1 class="search-results-title">No results matching "<span class='search-query'
<script>
var gitbook = gitbook || [];
gitbook.push(function() {
gitbook.page.hasChanged({"page":{"title":"ABACUS+Candela 使用教程","level":"1.1.13","depth":2,"next":{"title":"ABACUS 新闻稿整理","level":"1.2","depth":1,"path":"abacus-news.md","ref":"abacus-news.md","articles":[]},"previous":{"title":"ABACUS+LibRI 做杂化泛函计算教程","level":"1.1.12","depth":2,"path":"abacus-libri.md","ref":"abacus-libri.md","articles":[]},"dir":"ltr"},"config":{"plugins":["disqus","3-ba","pageview-count","theme-comscore","insert-logo","custom-favicon","intopic-toc","anchors","chapter-fold","expandable-chapters","-lunr","-search","search-plus","prism","-highlight","code","mathjax-pro","hide-element","github-buttons","sharing-plus","-sharing","livereload"],"styles":{"website":"styles/website.css","pdf":"styles/pdf.css","epub":"styles/epub.css","mobi":"styles/mobi.css","ebook":"styles/ebook.css","print":"styles/print.css"},"pluginsConfig":{"page-treeview":{"copyright":"Copyright &#169; aleen42","minHeaderCount":"2","minHeaderDeep":"2"},"chapter-fold":{},"prism":{},"disqus":{"useIdentifier":false,"shortName":"abacus-user-guide"},"intopic-toc":{"isCollapsed":true,"isScrollspyActive":true,"label":"In this article","maxDepth":6,"mode":"nested","selector":".markdown-section h1, .markdown-section h2, .markdown-section h3, .markdown-section h4, .markdown-section h5, .markdown-section h6","visible":true},"livereload":{},"sharing-plus":{"qq":false,"all":["facebook","google","twitter","instapaper","linkedin","pocket","stumbleupon"],"douban":false,"facebook":true,"weibo":false,"instapaper":false,"whatsapp":false,"hatenaBookmark":false,"twitter":true,"messenger":false,"line":false,"vk":false,"pocket":true,"google":false,"viber":false,"stumbleupon":false,"qzone":false,"linkedin":false},"code":{"copyButtons":true},"hide-element":{"elements":[".gitbook-link"]},"fontsettings":{"theme":"white","family":"sans","size":2},"favicon":"./picture/abacus-logo.jpg","theme-comscore":{},"page-toc-button":{"maxTocDepth":2,"minTocSize":2},"pageview-count":{},"github-buttons":{"buttons":[{"user":"MCresearch","repo":"abacus-user-guide","type":"star","size":"middle","count":true}]},"custom-favicon":{},"3-ba":{"configuration":"auto","token":"25153cb8bd9a872cfec60b4b23ac0176"},"mathjax-pro":{"forceSVG":false,"version":"2.7.7"},"sharing":{"weibo":false},"theme-default":{"styles":{"website":"styles/website.css","pdf":"styles/pdf.css","epub":"styles/epub.css","mobi":"styles/mobi.css","ebook":"styles/ebook.css","print":"styles/print.css"},"showLevel":false},"anchors":{},"insert-logo":{"style":"background: none;max-height: 70px;width: -webkit-fill-available;max-width: 180px;","url":"./picture/abacus-logo.svg"},"expandable-chapters":{},"search-plus":{}},"theme":"default","name":"abacus-user-guide","pdf":{"pageNumbers":true,"fontSize":12,"fontFamily":"Arial","paperSize":"a4","chapterMark":"pagebreak","pageBreaksBefore":"/","margin":{"right":62,"left":62,"top":56,"bottom":56}},"structure":{"langs":"LANGS.md","readme":"README.md","glossary":"GLOSSARY.md","summary":"SUMMARY.md"},"variables":{},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"abacus-candela.md","mtime":"2023-08-10T11:41:19.916Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-08-21T09:48:51.933Z"},"basePath":".","book":{"language":""}});
gitbook.page.hasChanged({"page":{"title":"ABACUS+Candela 使用教程","level":"1.1.13","depth":2,"next":{"title":"ABACUS 新闻稿整理","level":"1.2","depth":1,"path":"abacus-news.md","ref":"abacus-news.md","articles":[]},"previous":{"title":"ABACUS+LibRI 做杂化泛函计算教程","level":"1.1.12","depth":2,"path":"abacus-libri.md","ref":"abacus-libri.md","articles":[]},"dir":"ltr"},"config":{"plugins":["disqus","3-ba","pageview-count","theme-comscore","insert-logo","custom-favicon","intopic-toc","anchors","chapter-fold","expandable-chapters","-lunr","-search","search-plus","prism","-highlight","code","mathjax-pro","hide-element","github-buttons","sharing-plus","-sharing","livereload"],"styles":{"website":"styles/website.css","pdf":"styles/pdf.css","epub":"styles/epub.css","mobi":"styles/mobi.css","ebook":"styles/ebook.css","print":"styles/print.css"},"pluginsConfig":{"page-treeview":{"copyright":"Copyright &#169; aleen42","minHeaderCount":"2","minHeaderDeep":"2"},"chapter-fold":{},"prism":{},"disqus":{"useIdentifier":false,"shortName":"abacus-user-guide"},"intopic-toc":{"isCollapsed":true,"isScrollspyActive":true,"label":"In this article","maxDepth":6,"mode":"nested","selector":".markdown-section h1, .markdown-section h2, .markdown-section h3, .markdown-section h4, .markdown-section h5, .markdown-section h6","visible":true},"livereload":{},"sharing-plus":{"qq":false,"all":["facebook","google","twitter","instapaper","linkedin","pocket","stumbleupon"],"douban":false,"facebook":true,"weibo":false,"instapaper":false,"whatsapp":false,"hatenaBookmark":false,"twitter":true,"messenger":false,"line":false,"vk":false,"pocket":true,"google":false,"viber":false,"stumbleupon":false,"qzone":false,"linkedin":false},"code":{"copyButtons":true},"hide-element":{"elements":[".gitbook-link"]},"fontsettings":{"theme":"white","family":"sans","size":2},"favicon":"./picture/abacus-logo.jpg","theme-comscore":{},"page-toc-button":{"maxTocDepth":2,"minTocSize":2},"pageview-count":{},"github-buttons":{"buttons":[{"user":"MCresearch","repo":"abacus-user-guide","type":"star","size":"middle","count":true}]},"custom-favicon":{},"3-ba":{"configuration":"auto","token":"25153cb8bd9a872cfec60b4b23ac0176"},"mathjax-pro":{"forceSVG":false,"version":"2.7.7"},"sharing":{"weibo":false},"theme-default":{"styles":{"website":"styles/website.css","pdf":"styles/pdf.css","epub":"styles/epub.css","mobi":"styles/mobi.css","ebook":"styles/ebook.css","print":"styles/print.css"},"showLevel":false},"anchors":{},"insert-logo":{"style":"background: none;max-height: 70px;width: -webkit-fill-available;max-width: 180px;","url":"./picture/abacus-logo.svg"},"expandable-chapters":{},"search-plus":{}},"theme":"default","name":"abacus-user-guide","pdf":{"pageNumbers":true,"fontSize":12,"fontFamily":"Arial","paperSize":"a4","chapterMark":"pagebreak","pageBreaksBefore":"/","margin":{"right":62,"left":62,"top":56,"bottom":56}},"structure":{"langs":"LANGS.md","readme":"README.md","glossary":"GLOSSARY.md","summary":"SUMMARY.md"},"variables":{},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"abacus-candela.md","mtime":"2023-08-23T07:57:18.023Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-08-23T07:59:18.754Z"},"basePath":".","book":{"language":""}});
});
</script>
</div>
Expand Down
Loading

0 comments on commit e035267

Please sign in to comment.