{"id":6126,"date":"2024-04-25T15:46:33","date_gmt":"2024-04-25T06:46:33","guid":{"rendered":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/?page_id=6126"},"modified":"2024-04-25T15:46:33","modified_gmt":"2024-04-25T06:46:33","slug":"openmx_guide","status":"publish","type":"page","link":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/en\/system\/openmx_guide","title":{"rendered":"OpenMX (Open source package for Material eXplorer)"},"content":{"rendered":"

OpenMX (Open source package for Material eXplorer)<\/h2>\r\n

OpenMX\uff08Open source package for Material eXplorer\uff09is a density functional theory (DFT) software package based on the pseudo atomic basis with norm-conserved pseudopotentials.<\/span><\/p>\r\n

Webpages<\/span><\/h3>\r\n

\u516c\u5f0fOfficial page: http:\/\/www.openmx-square.org\/<\/a>
\r\nMateriApps: https:\/\/ma.issp.u-tokyo.ac.jp\/en\/app\/649<\/a><\/p>\r\n

Official Documents<\/span><\/h3>\r\n

Version 3.9<\/a><\/p>\r\n

Installed versions (2023-05-22)<\/span><\/h3>\r\n

3.9.9<\/p>\r\n\r\n

How to use OpenMX on ISSP Supercomputer System B<\/span><\/h3>\r\n

Executable binary file<\/p>\r\n

\r\n
\/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/openmx-3.9.9-1\/bin\/openmx<\/code><\/pre>\r\n<\/div>\r\n
Directory where VPS and PAO (pseudopotentials and atomic basis) are installed<\/p>\r\n
\r\n
\/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/openmx-3.9.9-1\/DFT_DATA19\/<\/code><\/pre>\r\n<\/div>\r\n
Add the following line to the input file of openmx<\/code> to use VPS and PAO.<\/p>\r\n
\r\n
data.path \/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/openmx-3.9.9-1\/DFT_DATA19\/<\/code><\/pre>\r\n<\/div>\r\n
Sample input files<\/span><\/h4>\r\n
\r\n
\/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/sample_script\/openmx.sh\r\n\r\n\/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/openmx-3.9.9-1\/work\/<\/code><\/pre>\r\n<\/div>\r\n
How to use OpenMX on System B<\/span><\/h3>\r\n
Copy a sample job script and an input file (e.g., Methane.dat<\/code>) to the working directory (in this case, the current directory)<\/p>\r\n
\r\n
$ cp \/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/sample_jobscript\/openmx.sh .\r\n\r\n$ cp \/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/openmx-3.9.9-1\/work\/Methane.dat .<\/code><\/pre>\r\n<\/div>\r\n
Add the following line to the end of the input file (Methane.dat<\/code>)<\/p>\r\n
\r\n
data.path \/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/openmx-3.9.9-1\/DFT_DATA19\/<\/code><\/pre>\r\n<\/div>\r\n
Submit a job<\/span><\/h3>\r\n
Replace input.dat<\/code> in the last line of the job script file, openmx.sh<\/code>, with Methane.dat<\/code>, and then run the following command<\/p>\r\n
\r\n
$ sbatch openmx.sh<\/code><\/pre>\r\n<\/div>\r\n
For details of compilation options, see<\/p>\r\n
\r\n
\/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5\/openmx\/openmx-3.9.9-1.log<\/code><\/pre>\r\n<\/div>\r\n
How to use OpenMX on SystemC<\/span><\/h3>\r\n
There are two differences from usage on SystemB<\/p>\r\n
    \r\n\t
  • Replace oneapi_compiler_classic-2023.0.0--openmpi-4.1.5<\/code>with PrgEnv-intel_8.3.3<\/code><\/li>\r\n\t
  • Use qsub<\/code> command instead of sbatch<\/code> command.<\/li>\r\n<\/ul>","protected":false},"excerpt":{"rendered":"OpenMX (Open source package for Material eXplorer) OpenMX\uff08Open source package for Material eXplorer\uff09is a density functional theory (DFT) software package based on the pseudo atomic basis with norm-conserved pseudopotentials. Webpages \u516c\u5f0fOfficial page: http:\/\/www.openmx-square.org\/ MateriApps: https:\/\/ma.issp.u-tokyo.ac.jp\/en\/app\/649 Official Documents Version 3.9 Installed versions (2023-05-22) 3.9.9 How to use OpenMX on ISSP Supercomputer System B Executable binary file […]","protected":false},"author":19,"featured_media":0,"parent":4479,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"_locale":"en_US","_original_post":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/?page_id=3153","footnotes":""},"class_list":["post-6126","page","type-page","status-publish","hentry","en-US"],"acf":[],"_links":{"self":[{"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/6126","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/users\/19"}],"replies":[{"embeddable":true,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/comments?post=6126"}],"version-history":[{"count":1,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/6126\/revisions"}],"predecessor-version":[{"id":6128,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/6126\/revisions\/6128"}],"up":[{"embeddable":true,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/4479"}],"wp:attachment":[{"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/media?parent=6126"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}