{"id":5719,"date":"2012-01-24T12:52:09","date_gmt":"2012-01-24T10:52:09","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/?p=5719"},"modified":"2019-07-08T14:23:18","modified_gmt":"2019-07-08T12:23:18","slug":"lammps-3","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/biokimika\/lammps-3","title":{"rendered":"LAMMPS"},"content":{"rendered":"<p>LAMMPS\u00a0(\u00abLarge-scale Atomic\/Molecular Massively Parallel Simulator\u00bb) \u00a0Sandia\u00a0National Laborategiak garatutako dinamika\u00a0molekular programa bat da.\u00a0LAMMPS-ek \u00a0MPI\u00a0komunikazioa erabiltzen du kalkulu paraleloentzat. Kode \u00a0irekia\u00a0da eta GNU\u00a0General\u00a0Public\u00a0License\u00a0baldintzapean\u00a0banatzen da. 2019ko Ekainare 5eko bertsioa.<\/p>\n<h2>Informazio orokorra<\/h2>\n<p>LAMMPS \u00a0dinamika\u00a0molekular\u00a0klasikoak egiteko \u00a0kodea da. Egoera likido, solido\u00a0edo gaseosoan dauden partikula\u00a0multzoak simula ditzake. Sistemak\u00a0atomikoak,\u00a0polimerikok, biologikoak, metalikoak\u00a0sistemak granularrak ,\u00a0eta \u00abcoarse grined\u00bb direlakoak aztertu ditzake\u00a0indar-eremu eta\u00a0muga-baldintza\u00a0barietate\u00a0desberdinak erabiliz.<\/p>\n<p>Zentzu\u00a0orokorrean,\u00a0LAMMPS-ek hedapen laburreko edo luzeko indarrekin elkar-interakzionatzen duten atomo-bilduma, molekula\u00a0edo part\u00edkula makroskopikoen Newtonen\u00a0mugimenduaren\u00a0ekuazioak integratzen ditu\u00a0hasierako edo inguruneko\u00a0baldintza desberdinak erabiliz.<\/p>\n<h2 id=\"comousar\">Nola erabili<\/h2>\n<p><strong>send_lmp<\/strong><\/p>\n<ul>\n<li>LAMMPS\u00a0ilarara bidaltzeko \u00a0 send_lmp\u00a0tresna sortu dugu. Komando\u00a0sintaxia,\u00a0honakoa da:<\/li>\n<li><tt>send_lmp JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]<\/tt><\/li>\n<\/ul>\n<table cellpadding=\"3\">\n<tbody>\n<tr>\n<td align=\"LEFT\"><tt><strong>JOBNAME<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\">Is the \u00a0name of the input with extension.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt><strong>NODES<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\">Number of nodes.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt><strong>PROCS<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\">Number of \u00a0processors.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt><strong>TIME<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\">Time requested to the queue system, format\u00a0<tt>hh:mm:ss.<\/tt><\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt><strong>MEM<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\"><strong>Optional<\/strong>. Memory in Gb ( It will used 1GB\/core if not set).<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><strong><tt>[``Other Torque Options'' ]<\/tt><\/strong><\/td>\n<td align=\"LEFT\"><strong>Optional<\/strong>. There is\u00a0the possibility to pass\u00a0more variables\u00a0to the\u00a0queuing system.<br \/>\nSee examples\u00a0below.\u00a0\u00a0<a href=\"http:\/\/www.ehu.es\/sgi\/mandar-trabajos\/comandos-de-interes-del-sistema-de-colas\"> More information about this options<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3 id=\"ejemplos\">Adibideak<\/h3>\n<ul>\n<li>Job1 \u00a0lana nodo batera eta 4 prozesagailuetara bidali dugu, 4 ordutarako:<\/li>\n<\/ul>\n<pre><code>send_lmp job1.in 1 4 04:00:00<\/code><\/pre>\n<ul>\n<li>Lana \u00a02 nodo eta 8 prozesagailutara \u00a0eskatutako denbora \u00a0192\u00a0ordutakoa izanik. Memoria ere adierazi dugu, \u00a08 GB, eta lana ez da 1234. \u00a0lana amaitu aurretik martxan jarriko.<\/li>\n<\/ul>\n<pre><code>send_lmp job2.inp 2 8 192:00:00 8 ``-W depend=afterany:1234'<\/code><\/pre>\n<ul>\n<li>Lana 4\u00a0nodo eta 4 prozesagailuetara bidali dugu. 200 ordu eta 2 GB-etako RAM-a askatu dugu. Gainera, kalkulua hasi eta amaitzean email bat bidaliko digu adierazitako emailera .<\/li>\n<\/ul>\n<pre><code>send_lmp job.inp 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''<\/code><\/pre>\n<h2 id=\"jobsmonitoring\">Lanen Monitorizazioa<\/h2>\n<p>LAMMPS lanaen jarraipena egiteko \u00a0remote_vi tresna erabili daiteke.<\/p>\n<pre>remote_vi JOBID<\/pre>\n<p>*. out fitxategia erakutsiko digu. \u00a0(Lana send_lmp-rekin bidali bada soilik).<\/p>\n<div>\n<h2 id=\"masinformacin\">Informazio gehiago<\/h2>\n<p><a href=\"http:\/\/lammps.sandia.gov\/\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/lammps.sandia.gov<\/a><\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>LAMMPS\u00a0(\u00abLarge-scale Atomic\/Molecular Massively Parallel Simulator\u00bb) \u00a0Sandia\u00a0National Laborategiak garatutako dinamika\u00a0molekular programa bat da.\u00a0LAMMPS-ek \u00a0MPI\u00a0komunikazioa erabiltzen du kalkulu paraleloentzat. Kode \u00a0irekia\u00a0da eta GNU\u00a0General\u00a0Public\u00a0License\u00a0baldintzapean\u00a0banatzen da. 2019ko Ekainare 5eko bertsioa. Informazio orokorra LAMMPS \u00a0dinamika\u00a0molekular\u00a0klasikoak egiteko \u00a0kodea da. Egoera likido, solido\u00a0edo gaseosoan dauden partikula\u00a0multzoak simula ditzake. Sistemak\u00a0atomikoak,\u00a0polimerikok, biologikoak, metalikoak\u00a0sistemak granularrak ,\u00a0eta \u00abcoarse grined\u00bb direlakoak aztertu ditzake\u00a0indar-eremu eta\u00a0muga-baldintza\u00a0barietate\u00a0desberdinak erabiliz. Zentzu\u00a0orokorrean,\u00a0LAMMPS-ek hedapen &hellip; <a href=\"https:\/\/www.ehu.eus\/sgi\/biokimika\/lammps-3\" class=\"more-link\">Seguir leyendo <span class=\"screen-reader-text\">LAMMPS<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_links_to":"","_links_to_target":""},"categories":[144,156],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5719"}],"collection":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/comments?post=5719"}],"version-history":[{"count":15,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5719\/revisions"}],"predecessor-version":[{"id":8901,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5719\/revisions\/8901"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=5719"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=5719"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=5719"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}