Skip to content

Running Gaussian by Command Lines

Here we are going to do an geometry optimization calculation on a simple molecule Formamide (HCONH2). Users can use the Gaussian input file g16.com :

g16.com

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
%NProcShared=4
%Mem=5GB
%NoSave
%chk=g16.chk
# opt freq b3lyp/cc-pvdz

Title Card: Single Molecule Formamide

0 1
 C                  3.89594917   -4.10509404   -0.06119675
 O                  5.13960552   -4.14687675    0.12626969
 H                  3.41099598   -3.16562892   -0.22589552
 N                  3.10941607   -5.34695260   -0.05391726
 H                  2.79423275   -5.53644967    0.87600227
 H                  2.31994463   -5.24505745   -0.65918762

In the file, the % lines (Link 0 section) specify the system resources. %NprocShared gives how many CPUs to use in a node and %Mem indicates how much memory to use. If any file specified before the %NoSave line, it will not be saved once Gaussian finishes the calculation normally.  %chk specify a check point file name to save and # line (Route section) specify the methods of Gaussian calculations. You can give this Gaussian input a title name in Title Card section. After that, use Molecule Specification section to assign the coordinates of the atoms with the charge and spin multiplicity of the system in the first line. Please make sure there is at least one empty line in the end of file.

By logging into HPCC and ssh to a dev node, users can find Gaussian program installed in HPCC with the module commands:

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
$ module spider Gaussian

----------------------------
  Gaussian:
----------------------------
 Versions:
        Gaussian/g16_AVX
        Gaussian/g16-AVX2
        Gaussian/g16

----------------------------
  For detailed information about a specific "Gaussian" module (including how to load the modules) use the module's full name.
  For example:

     $ module spider Gaussian/g16
----------------------------

Please load Gaussian module with g16 version:

1
2
3
$ module load Gaussian/g16
$ which g16
/opt/software/Gaussian/g16-AVX/g16/g16

and the Gaussian command "g16" can be used. Simply run the command by giving the input and output file names:

1
$ g16 < g16.com > g16.log

and it starts to calculate the system on the node. It will take about 2 minutes to complete the calculation. After it is finished, you can check the output file g16.log. All dev nodes have 2-hour CPU limit. Please restrict your resource usage on them.

GaussView

Users can also use GaussView to create their molecular system and do calculations. To use GaussView, just run the command gview.sh after loading the Gaussian module.