{"id":258,"date":"2016-11-22T13:16:56","date_gmt":"2016-11-22T18:16:56","guid":{"rendered":"http:\/\/williamkennerly.com\/blog\/?p=258"},"modified":"2016-11-30T14:06:30","modified_gmt":"2016-11-30T19:06:30","slug":"running-the-newtonx-tutorial","status":"publish","type":"post","link":"http:\/\/williamkennerly.com\/blog\/running-the-newtonx-tutorial\/","title":{"rendered":"Running the NewtonX Tests"},"content":{"rendered":"

First you need to install NewtonX. \u00a0To do this, you request a download link from the NewtonX site, follow the link, and download the binary file recommended (it will be called something like “NX-1.4.0-3-source+binary.tgz”). \u00a0Then copy the file to comet, and untar and unzip it by typing tar -zxf NX-1.4.0-3-source+binary.tgz<\/code>. \u00a0This corresponds to section 9.1 in the documentation. \u00a0Do not go further and do 9.2; 9.2 is only for if you want to install the program manually.<\/p>\n

After installing NewtonX, I spent a while trying to get the built in tests to run. \u00a0Eventually I came up with this procedure:<\/p>\n

First we have to set up the variables so NewtonX can find Gaussian. \u00a0We do this through the following lines of code:<\/p>\n

export NX=\/home\/kvorwerk\/NX-1.4.0-2\/bin
\nexport g09root=\/share\/apps\/compute\/gaussian\/09.E.01\/g09
\nsource $g09root\/bsd\/g09.profile
\nexport g09root=\/share\/apps\/compute\/gaussian\/09.E.01
\n<\/code><\/p>\n

The last line is necessary to avoid an error by which NewtonX adds an extra \/g09\/ into the path where it searches for gaussian. \u00a0Also note the line setting the NX variable would need to be modified to match the path where you installed NewtonX.<\/p>\n

Next we make a directory to run the tests in. \u00a0This can be anywhere. \u00a0Then we select the tests to run by typing:<\/p>\n

$NX\/inp-testnx.pl<\/code><\/p>\n

This shows a list of tests. \u00a0We want to run the gaussian09 one and the NewtonX ones; that is, 18, 19, 24, and 25. \u00a0To actually run the tests we type:<\/p>\n

$NX\/test-nx.pl >test.log<\/code><\/p>\n

This creates a bunch of subdirectories and a file called test.log. \u00a0The test.log file contains basic output, and more output is in the sub directories. \u00a0When I ran the tests, the test.log file told me that:<\/p>\n

18 finished, but with a message saying:<\/p>\n

Files \/home\/kvorwerk\/nx_test\/TEST_NX\/MD-SICH4-G09-TDDFT-NAD\/RESULTS\/dyn.out\u00a0and\u00a0\u00a0 \/home\/kvorwerk\/NX-1.4.0-2\/bin\/..\/test-nx\/STANDARD-RESULTS\/MD-SICH4-G0\u00a0\u00a0\u00a0 9-TDDFT-NAD\/RESULTS\/dyn.out differ. \u00a0It seems to be important differences. Something may be wrong in the installation.<\/code><\/p>\n

The files it refers to are easy to find. \u00a0However, I have been unable to find the file or script which compared them.<\/p>\n

19 finished normally<\/p>\n

24 finished with a message saying:<\/p>\n

Files \/home\/kvorwerk\/nx_test\/TEST_NX\/MD-ANALYTICAL-MODEL1\/RESULTS\/dyn.out\u00a0and\u00a0\u00a0 \/home\/kvorwerk\/NX-1.4.0-2\/bin\/..\/test-nx\/STANDARD-RESULTS\/MD-ANALYTIC\u00a0\u00a0\u00a0 AL-MODEL1\/RESULTS\/dyn.out differ. \u00a0It seems to be only minor numerical differences. Probably installation is OK.<\/code><\/p>\n

I do not think this error is worth worrying about.<\/p>\n

25 finished normally.<\/p>\n

The issue with test 18 may be due to us using a more recent version of gaussian (09.E) than the developers used to create the test. \u00a0Hopefully we will be able to find the comparisson they use and learn if this is indeed the case.<\/p>\n

-Kristine<\/p>\n","protected":false},"excerpt":{"rendered":"

First you need to install NewtonX. \u00a0To do this, you request a download link from the NewtonX site, follow the link, and download the binary file recommended (it will be called something like “NX-1.4.0-3-source+binary.tgz”). \u00a0Then copy the file to comet, … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":5,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[25],"class_list":["post-258","post","type-post","status-publish","format-standard","hentry","category-computing","tag-newtonx"],"_links":{"self":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/258","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/comments?post=258"}],"version-history":[{"count":10,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/258\/revisions"}],"predecessor-version":[{"id":269,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/258\/revisions\/269"}],"wp:attachment":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/media?parent=258"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/categories?post=258"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/tags?post=258"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}