Amsterdam Density Functional (ADF) is a computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT).<\/p>\n
Versions 2016.107, 2016.101 and 2014.10 are installed on the CSF. This is a pre-compiled binary install, no source code is available.<\/p>\n
Only members of Research Groups licensed to use this software may access it. All users of the software need to be in the Visitor\/collaborators are not permitted to access the software.<\/p>\n License holders: The Research Group leader holds a copy of the license terms and conditions for this software and all users must abide by it. Some guidance, which is not intended as a replacement for the license, is given below.<\/p>\n The license stipulates that:<\/p>\n Please see clause 6 of the license for further details.<\/p>\n You MUST not:<\/p>\n Please see clause 6 of the license for further details.<\/p>\n Please see the citation requirements<\/a> on the vendor website.<\/p>\n You must comply with all United States and United Kingdom export control laws and regulations controlling the export of the software, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.<\/p>\n Please be aware that allowing remote access from outside the United Kingdom may constitute an export.<\/p>\n To access the software you must first load the modulefile for the version you wish to use:<\/p>\n Prof. Nik Kaltsoyannis’ group:<\/p>\n Prof. Steve Liddle’s group:<\/p>\n Please do not<\/strong> submit any work to the system using the ADF GUI application. Use the jobscript methods shown below instead.<\/p>\n It is not recommended that you run adf in serial, it performs well on multiple cores. If you really feel you need to run it in serial please ask for advice via its-ri-team@manchester.ac.uk<\/a> before trying it.<\/p>\n The maximum number of cores that may be used by all users and all jobs at any one time is 64 (license restriction).<\/p>\n or<\/p>\n Please refer to the ADF manual<\/a> for further details about setting up input files.<\/p>\n Note:<\/strong> The variable where Please follow the same steps as for single node jobs, but the job submission script at step 4 should be:<\/p>\n You may run the ADF jobs GUI on the login node for very short periods of time to view your output. Please do not<\/strong> submit any work to the system via this GUI – it is not configured to do this and doing so will lead to running compute work on the login node which the CSF sysadmins will kill. <\/p>\n You must be correctly logged in to the CSF for the GUI to work – see the note displayed when you load the modulefile – and you need to have X11 tunnelling enabled<\/a> at connection time. <\/p>\n To start the GUI use the command:<\/p>\n If you do not log in correctly you will be asked for license information. Close the license window that appears and use the command:<\/p>\n for a reminder of the login requirements.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Amsterdam Density Functional (ADF) is a computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT). Versions 2016.107, 2016.101 and 2014.10 are installed on the CSF. This is a pre-compiled binary install, no source code is available. Restrictions on use Only members of Research Groups licensed to use this software may access it. All users of the software need to be in the adf unix group and all.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2254","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2254","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=2254"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2254\/revisions"}],"predecessor-version":[{"id":3774,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2254\/revisions\/3774"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=2254"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}adf<\/code> unix group and all additions to the group must be approved by the Research Group leader (please copy them on your request to us).<\/p>\n
\nProf. Nik Kaltsoyannis (adf<\/code> unix group)
\nProf Steve Liddle (adf-liddle<\/code> unix group)<\/p>\nWhat may ADF be used for?<\/h3>\n
\n
What may ADF not be used for?<\/h3>\n
\n
How should the program be cited?<\/h3>\n
Export regulations including remote access<\/h3>\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/binapps\/adf\/2017.103\r\nmodule load apps\/binapps\/adf\/2016.107\r\nmodule load apps\/binapps\/adf\/2016.101\r\nmodule load apps\/binapps\/adf\/2014.10\r\n<\/pre>\n
\r\nmodule load apps\/binapps\/adf\/liddle-rg\/2017.101\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
Parallel batch job submission<\/h3>\n
Jobs of 2 to 24 cores on a single compute node<\/h3>\n
\n
\r\nend\r\n<\/pre>\n
\r\neof\r\n<\/pre>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd\r\n#$ -V\r\n#$ -pe adf-smp.pe 4\r\n\r\n$ADFBIN\/adf -n $NSLOTS < input.in > output.out\r\n<\/pre>\n
$NSLOTS<\/code> ensures that the number of cores ADF uses matched the number requested in your job submission script. This also means that if you want to submit again and use a different number of cores you only need to make a change in the submission script.
\nNote:<\/strong> The normal smp.pe<\/code> must not be used – jobs will fail, but they also do not exit the batch system and cause problems to the scheduler. The pe adf-smp.pe<\/code> has been set up specifically to run single node ADF single jobs.<\/p>\n\r\nqsub adf-submit.txt\r\n<\/pre>\n
adf-submit.txt<\/code> is the name of your submission script.\n<\/li>\n<\/ol>\nJobs of 48 cores or more in multiples of 24 (multi-node jobs on Infiniband connected nodes)<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd\r\n#$ -V\r\n#$ -pe orte-24-ib.pe 48\r\n\r\n$ADFBIN\/adf -n $NSLOTS < input.in > output.out\r\n<\/pre>\n
The ADF jobs GUI<\/h2>\n
\r\nadfjobs &\r\n<\/pre>\n
\r\nmodule help apps\/binapps\/adf\/2014.10\r\n<\/pre>\n
Further info<\/h2>\n
\n
Updates<\/h2>\n