{"id":5739,"date":"2012-01-24T14:53:28","date_gmt":"2012-01-24T12:53:28","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/?p=5739"},"modified":"2012-01-25T10:20:40","modified_gmt":"2012-01-25T08:20:40","slug":"gulp-4-0","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/biochemistry\/gulp-4-0","title":{"rendered":"Gulp 4.0"},"content":{"rendered":"<h2>General Information<\/h2>\n<p>\ufeff\ufeff\ufeffGULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.<\/p>\n<h2>How to Use<\/h2>\n<p>First, before you use it,\u00a0be aware of its <a href=\"http:\/\/projects.ivec.org\/gulp\/downloads.html\" target=\"_blank\">usage conditions<\/a>.<\/p>\n<p><strong>send_gulp<\/strong><\/p>\n<ul>\n<li>\ufeffTo send GULP to the queue\u00a0system \u00a0use the send_gulp utility.\u00a0When\u00a0executed,<br \/>\nshows\u00a0the\u00a0command\u00a0syntax,\u00a0which is\u00a0summarized\u00a0below:<\/li>\n<li><tt>send_gulp 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\ufeff\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>Examples<\/h3>\n<p>We send\u00a0the GULP input\u00a0job1\u00a0to\u00a01 node,\u00a04\u00a0processors\u00a0on that node,\u00a0with\u00a0a\u00a0requested time\u00a0of 4\u00a0hours :<\/p>\n<pre><tt>send_gulp job1.gin 1 4 04:00:00<\/tt><\/pre>\n<p>We send job2 \u00a0to 2\u00a0compuation nodes,\u00a08\u00a0processors\u00a0on each\u00a0node,\u00a0with\u00a0a requested time\u00a0of 192\u00a0hours,\u00a08\u00a0GB\u00a0of\u00a0RAM\u00a0and to start running\u00a0after\u00a0work\u00a01234.arinab is finished:<\/p>\n<pre><tt>send_gulp job2.gin 2 8 192:00:00 8 ``-W depend=afterany:1234'<\/tt><\/pre>\n<p>We \u00a0send\u00a0the\u00a0input\u00a0job3\u00a0to\u00a04\u00a0nodes\u00a0and\u00a04\u00a0processors\u00a0on\u00a0each\u00a0node,\u00a0with\u00a0arequested time\u00a0of\u00a0200:00:00\u00a0hours,\u00a02\u00a0GB\u00a0of\u00a0RAM\u00a0and\u00a0we request to be\u00a0send an\u00a0email\u00a0at the beginning\u00a0and\u00a0end of the\u00a0calculation\u00a0to the direction\u00a0specified.<\/p>\n<pre><tt>send_gulp job.gin 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''<\/tt><\/pre>\n<p>\ufeffsend_gulp command\u00a0copies\u00a0the\u00a0contents\u00a0of the\u00a0directory\u00a0from\u00a0which the job is sent to\u00a0\/scratch\u00a0or\u00a0\/\u00a0gscratch,\u00a0if\u00a0we use 2\u00a0or more\u00a0nodes.\u00a0And\u00a0there is where\u00a0the calculation is done.<\/p>\n<h2>Jobs Monitoring<\/h2>\n<p>\ufeffTo\u00a0facilitate monitoring and\/or\u00a0control\u00a0of the GULP calculations, you can use\u00a0<strong>remote_vi<\/strong><\/p>\n<pre>remote_vi JOBID<\/pre>\n<p>It show us\u00a0the *.out file \u00a0(only\u00a0if it was\u00a0sent\u00a0using\u00a0send_lmp).<\/p>\n<div>\n<h2>More information<\/h2>\n<p>\ufeff<a href=\"http:\/\/projects.ivec.org\/gulp\/\">http:\/\/projects.ivec.org\/gulp\/<\/a><\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>General Information \ufeff\ufeff\ufeffGULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than &hellip; <a href=\"https:\/\/www.ehu.eus\/sgi\/biochemistry\/gulp-4-0\" class=\"more-link\">Seguir leyendo <span class=\"screen-reader-text\">Gulp 4.0<\/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":[212],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5739"}],"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=5739"}],"version-history":[{"count":7,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5739\/revisions"}],"predecessor-version":[{"id":5743,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5739\/revisions\/5743"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=5739"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=5739"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=5739"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}