{"id":6119,"date":"2024-04-25T15:02:46","date_gmt":"2024-04-25T06:02:46","guid":{"rendered":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/?page_id=6119"},"modified":"2024-04-25T15:20:23","modified_gmt":"2024-04-25T06:20:23","slug":"salmon-guide","status":"publish","type":"page","link":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/en\/system\/salmon-guide","title":{"rendered":"SALMON"},"content":{"rendered":"

SALMON<\/h2>\r\n

Photo-excited electron dynamics simulator based on time-dependent density functional theory using real-time, real-space grids. It can perform calculations of linear photo-response and nonlinear photo-response to pulse radiation in a variety of systems including isolated systems, periodic systems, interfaces\/surfaces, etc. It can perform massively parallel calculations in systems consisting of thousands of atoms, and it can also perform multiscale simulation of electron-electromagnetic field-coupled dynamics.<\/span><\/p>\r\n

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

Official home Page:\u00a0<\/span>https:\/\/salmon-tddft.jp\/index.html<\/a>
\r\nOfficial Document:\u00a0<\/span>https:\/\/salmon-tddft.jp\/documents.html<\/a>
\r\nLAMMPS on MateriApps:\u00a0<\/span>https:\/\/ma.issp.u-tokyo.ac.jp\/en\/app\/326<\/a><\/p>\r\n

Installed versions (2024-04-25)<\/span><\/h3>\r\n

SALMON<\/span>
\r\nv2.2.0<\/span><\/p>\r\n

How to use SALMON on ISSP Supercomputers<\/span><\/h3>\r\n

Hereafter, please replace $MA_ROOT<\/code> with the following directory:<\/p>\r\n

System B: \/home\/issp\/materiapps\/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5<\/code>
\r\nSystem C: \/home\/issp\/materiapps\/PrgEnv-intel_8.3.3<\/code><\/p>\r\n

Preparation<\/span><\/h4>\r\n

SALMON is installed under<\/p>\r\n

\r\n
$MA_ROOT\/salmon\/<\/code><\/pre>\r\n<\/div>\r\n
The following command<\/p>\r\n
\r\n
$ source $MA_ROOT\/salmon\/salmonvars.sh<\/span><\/code><\/pre>\r\n<\/div>\r\n
sets the root directory of the latest installed version of SALMON as an environment variable SALMON_ROOT<\/code> , and adds the directory including the executable binary file,\u00a0 $SALMON_ROOT\/bin<\/code> , to the environment variable PATH<\/code>\u00a0 . <\/span><\/p>\r\n
The latest version of SALMON may be updated without announcement. If you want to fix the version, please source<\/code> the configuration file with the version number.\u00a0<\/span><\/p>\r\n
Executable binary file<\/span><\/h4>\r\n
The executable binary file is salmon<\/code> . On ISSP supercomputer, srun<\/code> (ohtaka) or mpiexec<\/code> (kugui) is required even if run as a single process.<\/span><\/p>\r\n
Directories of sample files<\/span><\/h4>\r\n
Official sample files are available from<\/p>\r\n
\r\n
$SALMON_ROOT\/samples<\/span><\/code><\/pre>\r\n<\/div>\r\n
Use them after copying into your space:<\/span><\/p>\r\n
\r\n
$ cp -r $SALMON_ROOT\/samples .<\/span><\/code><\/pre>\r\n<\/div>\r\n
How to run SALMON jobs<\/span><\/h4>\r\n
A sample job script file, salmon.sh<\/code>, is available from<\/p>\r\n
\r\n
$MA_ROOT\/salmon\/sample_jobscript\/<\/code><\/pre>\r\n<\/div>\r\n
Copy salmon.sh<\/code> to the working directory, then rename the input file name in salmon.sh<\/code>, C2H2_gs.inp<\/code><\/span>, as necessary, and finally submit the job script file as follows:<\/span><\/p>\r\n
\r\n
$ cp $MA_ROOT\/salmon\/sample_jobscript\/salmon.sh .\r\n\r\n# System B\r\n$ sbatch salmon.sh\r\n# System C\r\n$ qsub salmon.sh<\/code><\/pre>\r\n<\/div>","protected":false},"excerpt":{"rendered":"SALMON Photo-excited electron dynamics simulator based on time-dependent density functional theory using real-time, real-space grids. It can perform calculations of linear photo-response and nonlinear photo-response to pulse radiation in a variety of systems including isolated systems, periodic systems, interfaces\/surfaces, etc. It can perform massively parallel calculations in systems consisting of thousands of atoms, and it […]","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=6116","footnotes":""},"class_list":["post-6119","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\/6119","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=6119"}],"version-history":[{"count":4,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/6119\/revisions"}],"predecessor-version":[{"id":6127,"href":"https:\/\/mdcl.issp.u-tokyo.ac.jp\/scc\/wp-json\/wp\/v2\/pages\/6119\/revisions\/6127"}],"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=6119"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}