Differences

This shows you the differences between two versions of the page.

--- howto:gaussian [2019/10/16 10:26]
kgovender
+++ howto:gaussian [2025/10/17 09:51] (current)
alopis [Easy Gaussian09 and Gaussian16 PBS creation and submission]
@@ Line 1: / Line 1: @@
 ====== Gaussian at CHPC ======
-Gaussian can be run over single nodes or more than one node (see examples below), with an example input file below these.
+This license can only be used by CHPC registered users, which are associated with either **South African** or **SKA partner** higher education institutions
+Gaussian can be run over 1 or 2 nodes (see example below)
 ====Easy Gaussian09 and Gaussian16 PBS creation and submission====
-Execute **qg09_E01** or **qg16_A03**
+In order to see all available Easy Scripts, first include/load this module - even better if your add this line to your .bashrc:
+  module load chpc/easy_scripts
+Execute **qg09_E01** or **qg16_A03** or **qg16_B01** or **qg16_C01**
 This script handles PBS setup and submission.
@@ Line 40: / Line 47: @@
   y
-====Easy Gaussian16 PBS creation and submission====
-Execute **qg16_A03** or **qg16_B01**
+If you wish to use the utility **formchk** (to create readable format files for visualisers) please do the following.
-This script handles PBS setup and submission.
-Also takes care of jobs running over more than one node with LINDA and does cleanup of temporary GAU files when job is completed/killed. Examples of these scripts are provided below.
+  module load chpc/gaussian16/C01
+  source $g16root/g16/bsd/g16.profile
+Then the command **formcheck** should be available for use. Other Gaussian commands should also be available, such as **freqchk** and **chkchk**.
-              EXAMPLE1
-  Enter project name/shortname
-  CHEM0100
-  Enter input file (with .com or .gjf extension)
-  test.gjf
-  Enter number of nodes on which to run job
-  Enter total walltime (hour:minute)
-:00
-  Enter email address
-  testing@gmail.com
-  Generated pbs file for test
-  Do you wish to submit job to cluster (y/n)
-  y
-    EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
+You can use a **checkpoint file (.chk)** which will allow you to continue with a 2nd (or subsequent) calculation from close to where the initial/previous calculation ended. This is especially helpful for jobs which exceed walltime limits or have stopped for another reason. There is info online including from Gaussian website, these links may be helpful too:
-  Enter project name/shortname
-  CHEM0100
+https://gaussian.com/faq2/
-  Enter input file (with .com or .gjf extension)
-  test.gjf
+https://gaussian.com/restart/
-  Enter number of nodes on which to run job
+https://gaussian.com/tip4/
-  Enter total walltime (hour:minute)
+https://www.researchgate.net/post/How-can-I-res...
-  Enter email address
-  testing@gmail.com
+Very occassionally  a checkpoint file may be corrupted, so keeping the most recent backup copy of a good checkpoint (.chk) file can be helpful. Otherwise in these circumstances the calculation may need to be started from scratch - or the most recent molecular geometry (the coordinated of all the atoms) could be used from the Gaussian output (.log) file.
-  Generated pbs file for test
-  Do you wish to submit job to cluster (y/n)
+Please **recheck** your molecular **geometry very carefully** to ensure there are no issues - this will result in calculations which take much longer than necessary.
-  y

wiki.chpc.ac.za

User Tools

Site Tools

Differences

Page Tools