CASTEPconv<\/a> Python script designed to automate the process of calculating system convergence with cutoff energy and kpoints against final energy, forces, and stresses.<\/p>\n Versions 0.9.5, 1.0.1 and 1.0.2 are installed on the CSF.<\/p>\n There are no restrictions on accessing this software.<\/p>\n To access the software you must first load the modulefile:<\/p>\n This will automatically load the python 2.7.1 modulefile.<\/p>\n It is strongly recommended that you read the short user guide by running the following command on the login node:<\/p>\n The CASTEPconv command is a python script that is run using:<\/p>\n The following file must be present in the directory where you run the script:<\/p>\n Additional optional files can also be present in the directory:<\/p>\n The You can change this if your castep command is different – here we use An alternative method of running the The optional Make sure you have the castepconv modulefile loaded AND<\/strong> the CASTEP modulefile for the version of CASTEP you wish to use. Then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n The User Guide contains a simple tutorial. The example files for the tutorial are available by running the following command on the login node:<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview CASTEPconv Python script designed to automate the process of calculating system convergence with cutoff energy and kpoints against final energy, forces, and stresses. Versions 0.9.5, 1.0.1 and 1.0.2 are installed on the CSF. Restrictions on use There are no restrictions on accessing this software. Set up procedure To access the software you must first load the modulefile: module load apps\/binapps\/castepconv\/1.0.2 module load apps\/binapps\/castepconv\/1.0.1 module load apps\/binapps\/castepconv\/0.9.5 This will automatically load the python 2.7.1 modulefile… 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-2668","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2668","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=2668"}],"version-history":[{"count":13,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2668\/revisions"}],"predecessor-version":[{"id":4864,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2668\/revisions\/4864"}],"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=2668"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/binapps\/castepconv\/1.0.2\r\nmodule load apps\/binapps\/castepconv\/1.0.1\r\nmodule load apps\/binapps\/castepconv\/0.9.5\r\n<\/pre>\n
Running the application<\/h2>\n
\r\nevince $CASTEPCONV_HOME\/doc\/user_guide.pdf\r\n<\/pre>\n
\r\ncastepconv.py options<\/em> seedname<\/em>\r\n<\/pre>\n
\n
seedname<\/em>.cell<\/code><\/li>\n<\/ul>\n\n
seedname<\/em>.param<\/code> – specify additional parameters (e.g., redefined convergence criteria for SCF iterations, add dispersion correction etc.)<\/li>\nseedname<\/em>.conv<\/code> – to control the convergence of the job itself.<\/li>\n<\/ul>\ncastepconv.py<\/code> script can be run from within your own jobscript. It will eventually run CASTEP and so you must<\/em> have loaded the appropriate CASTEP modulefile<\/a> so that CASTEP will run correctly. The CASTEP command executed by the castepconv.py script is defined in the seedname<\/em>.conv file by the line:<\/p>\n\r\nrunning_command: castep.serial <seedname>\r\n<\/pre>\n
castep.serial<\/code>. But you must<\/em> keep the <seedname><\/code> keyword exactly as written. Do not<\/em> replace it with your own filename. We will let the castepconv.py script do the replacement instead. It won’t work if you enter your own filename here!<\/p>\ncastepconv.py<\/code> script is to allow it to submit jobs to the batch queues. This means that the castepconv.py script should be run on the login node. You must still write a jobscript in the usual manner for CASTEP and copy it to the directory from where you will be running the python script. Any instances of the string <seedname><\/code> in your jobscript will be replaced with the seedname specified on the castepconv.py command-line. You should then edit your seedname<\/em>.conv<\/code> file and set the following parameters<\/p>\n\r\nrunning_command: qsub <seedname>\r\nsubmission script: my_jobscript\r\n<\/pre>\n
options<\/em><\/code> before the seedname can be used to override settings in the seedname<\/em>.conv<\/code> file (currently only the convergence_task<\/code> keyword can be overridden).<\/p>\nSerial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\ncastepconv.py seedname<\/em>\r\n #\r\n # Ensure you have written a seedname<\/em>.conv file\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Tutorial<\/h3>\n
\r\ncp $CASTEPCONV_HOME\/example\/* . # The . at the end is important\r\n<\/pre>\n
Further info<\/h2>\n
\n
\r\nevince $CASTEPCONV_HOME\/doc\/user_guide.pdf\r\n<\/pre>\n<\/li>\n<\/ul>\n
Updates<\/h2>\n