{"id":602,"date":"2022-03-06T11:09:41","date_gmt":"2022-03-06T03:09:41","guid":{"rendered":"https:\/\/rayray.moe\/?p=602"},"modified":"2026-02-21T19:12:20","modified_gmt":"2026-02-21T11:12:20","slug":"raspa-%e8%ae%be%e7%bd%ae%e6%94%bb%e7%95%a5-%e7%ae%80%e4%bb%8b","status":"publish","type":"post","link":"https:\/\/rayray.moe\/?p=602","title":{"rendered":"RASPA \u8bbe\u7f6e\u653b\u7565 &#8211; \u7b80\u4ecb"},"content":{"rendered":"<p><img decoding=\"async\" src=\"https:\/\/s2.loli.net\/2022\/03\/06\/7ZxsyGO1A6oV8dm.jpg\" alt=\"IMG_6713\" \/><\/p>\n<p>@tkaray RASPA \u76f8\u5173\u5185\u5bb9\u9075\u5faa\u539f\u4f5c\u8005\u6388\u6743\u534f\u8bae, \u672c\u6587\u7b80\u8bd1\u548c\u6ce8\u91ca\u5185\u5bb9\u9075\u5faa CC-BY-NC 4.0 \u534f\u8bae\u5171\u4eab.<\/p>\n<p>\u672c\u6587\u662f RASPA manual \u7684\u4e2d\u6587\u7b80\u8bd1, \u5e26\u6709\u4e00\u4e9b\u4e2a\u4eba\u8865\u5145\u7684\u6ce8\u91ca\u5185\u5bb9. \u90e8\u5206\u5185\u5bb9\u6ca1\u6709\u7279\u522b\u5408\u9002\u7684\u7ffb\u8bd1\u5219\u4f1a\u4f7f\u7528\u82f1\u6587\u539f\u6587. \u9650\u4e8e\u80fd\u529b\u6240\u9650\u672c\u6587\u7684\u5185\u5bb9\u53ef\u80fd\u6709\u90e8\u5206\u7eb0\u6f0f, \u8bf7\u914c\u60c5\u53c2\u8003. \u6240\u6709\u8865\u5145\u7684\u6ce8\u91ca\u5185\u5bb9\u5747\u4f7f\u7528\u4ee5\u4e0b\u65b9\u6cd5\u6807\u8bb0:<\/p>\n<blockquote>\n<p>Note: \u5efa\u8bae\u4f7f\u7528 Linux \u548c macOS \u5b89\u88c5.<\/p>\n<\/blockquote>\n<h2><a id=\"part-1%E7%AE%80%E4%BB%8B\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>Part 1. \u7b80\u4ecb<\/h2>\n<p>RASPA\u662f\u7531 Randall Q. Snurr, Sofia Calero, David Dubbeldam, T.J.H. Vlugt \u7b49\u7814\u7a76\u8005\u5f00\u53d1\u7684\u7ecf\u5178\u6a21\u62df\u8f6f\u4ef6\u5305, \u53ef\u4ee5\u7528\u4e8e\u6a21\u62df\u6c14\u4f53, \u6d41\u4f53, \u6cb8\u77f3, \u7845\u94dd\u9178\u76d0, MOF, \u78b3\u7eb3\u7c73\u7ba1\u7b49\u6750\u6599.<\/p>\n<p>\u5f15\u7528\u6587\u732e: (\u6765\u81ea\u4e8e GitHub \u7684\u4ecb\u7ecd\u9875)<\/p>\n<ul>\n<li>D. Dubbeldam, S. Calero, D.E. Ellis, and R.Q. Snurr, &quot;RASPA: Molecular Simulation Software for Adsorption and Diffusion in Flexible Nanoporous Materials&quot;,<br \/>\nMol. Sim., 42 (2), 81-101, 2016.<br \/>\n<a href=\"https:\/\/www.tandfonline.com\/doi\/full\/10.1080\/08927022.2015.1010082\">link to article<\/a><\/li>\n<li>D. Dubbeldam, A. Torres-Knoop, and K.S. Walton,  &quot;On the Inner Workings of Monte Carlo Codes&quot;,<br \/>\nMol. Sim. (special issue on Monte Carlo) 39(14-15), 1253-1292, 2013.<br \/>\n<a href=\"http:\/\/www.tandfonline.com\/doi\/full\/10.1080\/08927022.2013.819102\">link to article<\/a><\/li>\n<li>D. Dubbeldam and R.Q. Snurr, &quot;Recent developments in the molecular modeling of diffusion in nanoporous materials&quot;,<br \/>\nMol. Sim., 33 (4-5), 305-325, 2007.<br \/>\n<a href=\"http:\/\/www.tandfonline.com\/doi\/abs\/10.1080\/08927020601156418\">link to article<\/a><\/li>\n<li>D. Dubbeldam, K.S. Walton, T.J.H. Vlugt, and S. Calero, &quot;Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials&quot;,<br \/>\nAdv. Theory Simulat., 2(11), 1900135, 2019.<br \/>\n<a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/adts.201900135\">link to article<\/a><\/li>\n<\/ul>\n<h2><a id=\"%E5%AE%89%E8%A3%85%E7%BC%96%E8%AF%91%E4%B8%8E%E8%BF%90%E8%A1%8C\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>\u5b89\u88c5, \u7f16\u8bd1\u4e0e\u8fd0\u884c<\/h2>\n<h3><a id=\"%E8%87%AA%E8%A1%8C%E7%BC%96%E8%AF%91\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>\u81ea\u884c\u7f16\u8bd1<\/h3>\n<p>RASPA \u662f\u7531 C \u8bed\u8a00\u5199\u6210\u7684, \u56e0\u6b64\u9700\u8981\u4e00\u4e2a gcc \u6216 icc \u7f16\u8bd1\u5668.<\/p>\n<blockquote>\n<p>Note: \u5efa\u8bae\u4f7f\u7528 Linux \/ macOS \u7cfb\u7edf\u8fd0\u884c()<\/p>\n<\/blockquote>\n<pre><code class=\"language-BASH\">export RASPA_DIR=\/path\/to\/environment\/root\nrm -rf autom4te.cache  \nmkdir m4  \naclocal  \nautoreconf -i  \nautomake --add-missing  \nautoconf  \n.\/configure --prefix=${RASPA_DIR}  \n# or .\/scripts\/CompileScript\/make-gcc-local  \nmake  \nmake install  \n<\/code><\/pre>\n<blockquote>\n<p>Note: cd \u5230\u5bf9\u5e94\u76ee\u5f55\u540e\u76f4\u63a5\u8fd0\u884c\u5373\u53ef. RASPA_DIR \u4e3a\u76ee\u6807\u5b89\u88c5\u4f4d\u7f6e.<\/p>\n<\/blockquote>\n<h3><a id=\"%E4%BD%BF%E7%94%A8conda-forge%E6%BA%90\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>\u4f7f\u7528 Conda-forge \u6e90<\/h3>\n<p>\u4e5f\u53ef\u4ee5\u4f7f\u7528 Anaconda \u7684\u65b9\u5f0f\u5b89\u88c5\u9884\u7f16\u8bd1\u7248\u672c.<\/p>\n<pre><code class=\"language-BASH\">conda install -c conda-forge raspa2\nexport RASPA_DIR=\/path\/to\/environment\/root\n# e.g. export RASPA_DIR=\/Users\/leopold\/Applications\/miniconda3\/envs\/raspa-env\n<\/code><\/pre>\n<blockquote>\n<p>Note: Conda-forge \u7248\u672c\u7684\u8f6f\u4ef6\u672c\u4f53\u5728 \/path\/to\/anaconda3\/envs\/envs-name\/bin\/simulate, \u652f\u6301\u6587\u4ef6\u5728 \/path\/to\/anaconda3\/envs\/envs-name\/share\/raspa\u4e0b.  \u56e0\u6b64, RASPA_DIR \u73af\u5883\u53d8\u91cf\u8bbe\u7f6e\u4f4d\u7f6e\u5e94\u5f53\u4f4d\u4e8e\u865a\u62df\u73af\u5883\u76ee\u5f55\u5904, \u6b64\u65f6\u548c\u81ea\u884c\u7f16\u8bd1\u7684\u60c5\u51b5\u76f8\u540c.<\/p>\n<\/blockquote>\n<blockquote>\n<p>Note: (2022\u5e743\u67085\u65e5\u8bb0) \u5373\u4f7f\u4f7f\u7528 conda-forge \u6e90\u7684\u9884\u7f16\u8bd1\u65b9\u6cd5\u5b89\u88c5, \u4e5f\u5e94\u8be5\u4e0b\u8f7d GitHub \u7248\u672c, \u56e0\u4e3a\u5176\u4e2d\u6709\u4e00\u4e9b\u6559\u5b66\u793a\u4f8b demo \u662f\u9884\u7f16\u8bd1\u65b9\u6cd5\u672a\u63d0\u4f9b\u7684. \u6b64\u5916, GitHub \u6e90\u76ee\u524d\u4ec5\u542b\u6709\u90e8\u5206 example forcefield &amp; molecules, \u4f46 conda-forge \u6e90\u6709\u66f4\u591a\u793a\u4f8b\u7528\u7684\u529b\u573a\u548c\u5c0f\u5206\u5b50\u6587\u4ef6. \u56e0\u6b64, \u5efa\u8bae\u4e24\u4e2a\u90fd\u88c5, \u7136\u540e\u5408\u5e76\u5230\u4e00\u5904.<\/p>\n<\/blockquote>\n<blockquote>\n<p>Note: \u8fd8\u9700\u8981\u6ce8\u610f\u7684\u662f, \u6240\u6709\u7684\u6559\u5b66\u793a\u4f8b demo \u5747\u6307\u5b9a\u4e86~\u76ee\u5f55\u4e0b\u7684\u6587\u4ef6\u5939, \u5982\u679c\u4e0d\u60f3\u6bcf\u6b21\u8fd0\u884c\u793a\u4f8b\u90fd\u6539\u63d0\u4ea4\u6587\u4ef6, \u8bf7\u5728\u5bb6\u76ee\u5f55\u5bf9\u5bf9\u5e94\u4f4d\u7f6e\u4f7f\u7528 ln -s \u5efa\u7acb\u8f6f\u94fe\u63a5.<\/p>\n<\/blockquote>\n<h3><a id=\"%E6%96%87%E6%A1%A3%E7%BC%96%E8%AF%91%E4%B8%8E%E4%B8%8B%E8%BD%BD\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>\u6587\u6863\u7f16\u8bd1\u4e0e\u4e0b\u8f7d<\/h3>\n<p>\u867d\u7136 GitHub \u4e2d\u63d0\u4f9b\u4e86 tex \u7f16\u8bd1\u7684\u9009\u9879, \u4f46\u662f\u6709\u5df2\u7ecf\u7f16\u8bd1\u597d\u7684\u7248\u672c\u5728 iRASPA \u7684\u4e3b\u9875: <a href=\"https:\/\/iraspa.org\/raspa\/\">Link<\/a><\/p>\n<h3><a id=\"%E8%BF%90%E8%A1%8C\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>\u8fd0\u884c<\/h3>\n<blockquote>\n<p>Note: RASPA\u7684\u8fd0\u884c\u9700\u8981\u591a\u4e2a\u6587\u4ef6. \u5176\u4e2d, simulation.input \u6587\u4ef6\u63a7\u5236\u8fd0\u884c\u8fc7\u7a0b, \u4e00\u4e2a\u8fd0\u884c\u811a\u672c\u8d1f\u8d23\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf\u548c\u8c03\u7528\u4e3b\u7a0b\u5e8f simulate. \u5177\u4f53\u5185\u5bb9\u53ef\u4ee5\u67e5\u770b\u793a\u4f8b. \u8fd0\u884c\u8fc7\u7a0b\u5982\u679c\u9700\u8981\u4f7f\u7528 mpi, \u5219\u5e94\u5f53\u5728\u8fd0\u884c\u524d\u6dfb\u52a0 mpirun \u6307\u4ee4. \u6682\u4e0d\u6e05\u695a\u5f00\u542f openMPI \u7f16\u8bd1\u540e\u4f7f\u7528 intelMPI \u8fd0\u884c\u662f\u5426\u4f1a\u62a5\u9519, \u548c\u5b89\u88c5\u65f6\u4fdd\u6301\u4e00\u81f4\u5c31\u597d\u4e86.<\/p>\n<\/blockquote>\n<h3><a id=\"%E4%BD%BF%E7%94%A8aiida%E8%B0%83%E7%94%A8\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>\u4f7f\u7528 AiiDA \u8c03\u7528<\/h3>\n<blockquote>\n<p>Note: \u901a\u8fc7\u5b89\u88c5 AiiDA \u6846\u67b6\u548c\u4ea4\u4e92\u7ec4\u4ef6 aiida-raspa \u53ef\u4ee5\u5b9e\u73b0\u57fa\u4e8e Python \u7684\u63a7\u5236. \u5177\u4f53\u65b9\u6cd5\u53ef\u4ee5\u67e5\u770b aiida-raspa \u7684 GitHub repo \u7684 demo.<\/p>\n<\/blockquote>\n<h2><a id=\"part-2%E6%96%87%E4%BB%B6%E8%AE%BE%E7%BD%AE\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>Part 2. \u6587\u4ef6\u8bbe\u7f6e<\/h2>\n<h3><a id=\"%E5%B7%A5%E7%A8%8B%E6%96%87%E4%BB%B6%E7%9A%84%E7%A7%8D%E7%B1%BB\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>\u5de5\u7a0b\u6587\u4ef6\u7684\u79cd\u7c7b<\/h3>\n<ul>\n<li>\n<p>simulation.input<\/p>\n<p>\u5305\u542b\u6a21\u62df\u7c7b\u578b, \u6a21\u62df\u7684\u6b65\u6570, \u9aa8\u67b6\u540d\u5b57, \u6676\u80de\u6570\u76ee, \u4f7f\u7528\u7684\u5c0f\u5206\u5b50, Monte-Carlo \u884c\u52a8 (move) \u7c7b\u578b\u7b49\u63a7\u5236\u8bcd\u6761.<\/p>\n<\/li>\n<li>\n<p>structure-name.cif<\/p>\n<p>\u5982\u679c\u4f7f\u7528\u4e86\u4e00\u4e2a\u9aa8\u67b6 (\u5982\u6cb8\u77f3\u548c MOF), \u5219\u9700\u8981\u63d0\u4f9b\u4e00\u4e2a CIF \u6587\u4ef6, \u8be5\u6587\u4ef6\u540d\u7684\u524d\u534a\u90e8\u5206\u9700\u8981\u5728 simulation.input \u4e2d\u8fdb\u884c\u6307\u5b9a.<\/p>\n<\/li>\n<li>\n<p>pseudo_atoms.def<\/p>\n<p>\u5217\u4e3e\u4f7f\u7528\u7684\u8d5d\u539f\u5b50\u7684\u4fe1\u606f, \u5305\u62ec\u7535\u8377\u548c\u8d28\u91cf\u7b49. \u4e00\u822c\u60c5\u51b5\u4e0b\u8d5d\u539f\u5b50\u4ee3\u8868\u4e00\u4e2a\u539f\u5b50, \u4f46\u4e5f\u53ef\u80fd\u4ee3\u8868\u4e00\u4e2a\u5c0f\u57fa\u56e2 (\u6bd4\u5982 -CH3). \u7531\u4e8e CIF \u6587\u4ef6\u4f1a\u63d0\u4f9b\u539f\u5b50\u4fe1\u606f, \u56e0\u6b64\u5728 CIF \u4e2d\u5217\u4e3e\u7684\u539f\u5b50\u5e76\u4e0d\u9700\u8981\u5728\u8d5d\u539f\u5b50\u5217\u8868\u4e2d\u8fdb\u884c\u89c4\u5b9a, \u5f53\u8bfb\u53d6 CIF \u6587\u4ef6\u65f6\u539f\u5b50\u4fe1\u606f\u5c06\u81ea\u52a8\u52a0\u5165\u5230\u8be5\u5217\u8868\u4e2d. \u5982\u679c\u5728\u8d5d\u539f\u5b50\u4e2d\u4e5f\u63d0\u4f9b\u4e86\u539f\u5b50\u4fe1\u606f, \u90a3\u4e48\u8be5\u6587\u4ef6\u4e2d\u7684\u6570\u636e\u5c06\u88ab\u4f18\u5148\u8bfb\u53d6.<\/p>\n<\/li>\n<li>\n<p>force_field_mixing_rules.def \u548c force_field.def<\/p>\n<p>\u8d5d\u539f\u5b50\u5217\u8868\u4e2d\u6bcf\u4e2a\u539f\u5b50\u6240\u4f7f\u7528\u7684\u529b\u573a\u53c2\u6570. \u8fd9\u4e9b\u53c2\u6570\u5305\u62ec Van der Waals potential \u7c7b\u578b\u548c\u5176\u4ed6\u53c2\u6570, \u5982\u662f\u5426\u4f7f\u7528\u5c3e\u90e8\u6821\u6b63 (tail correction), \u662f\u5426\u5728 cutoff \u4e4b\u540e\u5c06\u4f5c\u7528\u7f6e\u96f6, \u8fd8\u6709 mixing rule \u7684\u7c7b\u578b\u7b49.<\/p>\n<p>\u5728\u6587\u732e\u4e2d\u62a5\u9053\u7684\u529b\u573a\u53c2\u6570\u4e3b\u8981\u5305\u62ec\u4e24\u79cd\u7c7b\u578b, \u7b2c\u4e00\u79cd\u4f1a\u63d0\u4f9b\u6bcf\u4e2a\u539f\u5b50\u7684\u52bf\u80fd\u53c2\u6570\u548c mixing rule \u7684\u5217\u8868, \u7b2c\u4e8c\u79cd\u5219\u4f1a\u63d0\u4f9b\u539f\u5b50\u5bf9\u548c\u53c2\u6570. \u7b2c\u4e00\u79cd\u5bf9\u5e94 force_field_mixing_rules.def, \u7b2c\u4e8c\u79cd\u5219\u5bf9\u5e94 force_field.def. \u5176\u4e2d, force_field.def \u7684\u4f18\u5148\u7ea7\u9ad8\u4e8e force_field_mixing_rules.def.<\/p>\n<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>@tkaray RASPA \u76f8\u5173\u5185\u5bb9\u9075\u5faa\u539f\u4f5c\u8005\u6388\u6743\u534f\u8bae, \u672c\u6587\u7b80\u8bd1\u548c\u6ce8 &hellip;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[30],"tags":[35],"class_list":["post-602","post","type-post","status-publish","format-standard","hentry","category-notes","tag-35"],"_links":{"self":[{"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/posts\/602","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/rayray.moe\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=602"}],"version-history":[{"count":2,"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/posts\/602\/revisions"}],"predecessor-version":[{"id":604,"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/posts\/602\/revisions\/604"}],"wp:attachment":[{"href":"https:\/\/rayray.moe\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=602"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/rayray.moe\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=602"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/rayray.moe\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=602"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}