{"id":2060,"date":"2019-01-18T15:35:10","date_gmt":"2019-01-18T15:35:10","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=2060"},"modified":"2019-02-21T11:23:38","modified_gmt":"2019-02-21T11:23:38","slug":"votca","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/votca\/","title":{"rendered":"Votca"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge transport in disordered semiconductors.<br \/>\nThe following versions are installed on the CSF:<\/p>\n<ul>\n<li>Votca 1.5.2 &#8211; includes Gromacs 2016.4 (multi-threaded single precision only) in the VOTCA directory.<\/li>\n<li>Votca 1.2.3 &#8211; includes Gromacs 4.6.1 (multi-threaded single precision only) in the VOTCA directory.<\/li>\n<\/ul>\n<h2>Restrictions on use<\/h2>\n<p>All users may use the software. All users should cite their use of the software as per the <a href=\"http:\/\/www.votca.org\/citations\">VOTCA Citations<\/a> webpage.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the executables please load <em>one<\/em> of the appropriate modulefiles:<\/p>\n<pre>\r\nmodule load apps\/intel-17.0\/votca\/1.5.2\r\nmodule load apps\/intel-17.0\/votca\/1.2.3\r\n<\/pre>\n<p>NOTE we now recommend loading module files in your job script rather than on the login node.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run VOTCA on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h2>Serial batch job submission<\/h2>\n<p>VOTCA is not suitable for serial jobs. Some components default to using all the cores available on a compute node and can therefore cause issues to other running jobs.<\/p>\n<h2>Parallel batch job submission<\/h2>\n<ul>\n<li>It is recommended that you request a whole node for your job. There are a number of node types to choose from &#8211; please see the examples below.<\/li>\n<li>smp.pe is the only suitable parallel environment, VOTCA cannot run on more than one node.<\/li>\n<\/ul>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe smp.pe 12\r\n\r\nmodule load apps\/intel-17.0\/votca\/1.5.2\r\n\r\ncsg_inverse --nt $NSLOTS --options settings.xml\r\n<\/pre>\n<h2>Further info<\/h2>\n<ul>\n<li>Documentation: <a href=\"https:\/\/sites.google.com\/a\/votca.org\/main\/\">VOTCA Website<\/a><\/li>\n<li>Manpages, e.g. <code>man votcha-csg<\/code><\/li>\n<li>Tutorials\/examples are available in <code>$VOTCA_HOME\/csg-tutorials<\/code><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge transport in disordered semiconductors. The following versions are installed on the CSF: Votca 1.5.2 &#8211; includes Gromacs 2016.4 (multi-threaded single precision only) in the VOTCA directory. Votca 1.2.3 &#8211; includes Gromacs 4.6.1 (multi-threaded single precision only) in the VOTCA directory. Restrictions on use All users.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/votca\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2060","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2060","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=2060"}],"version-history":[{"count":10,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2060\/revisions"}],"predecessor-version":[{"id":2380,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2060\/revisions\/2380"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=2060"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}