Building with GaussView:.Instead of typing all the coordinates, theory, basis set, etc., we can use GaussView.The calculation is specified by pointing and clicking to build the molecule, and using pull-down menus to select the calculation type, level of theory and basis set.GaussView generates the Gaussian input file,. GAUSSIAN 09W TUTORIAL AN INTRODUCTION TO COMPUTATIONAL CHEMISTRY USING G09W AND AVOGADRO SOFTWARE Anna Tomberg anna.tomberg@mail.mcgill.com This is a quick tutorial that will help you to make your way through the.
Table of Content
Versions and Availability
▶ Display Softenv Keys for gaussview on all clusters
| Machine | Version | Softenv Key |
|---|---|---|
| supermike2 | 5.0.8 | +gaussview-5.0.8 |
▶ Softenv FAQ?
Since Fall 2018, SoftEnv has no longer been supported by HPC@LSU,and it is very unlikely that it will be brought back in the future. Therefore,all HPC users should use Modules to add/remove softwarepackages in their work environment from now on. For advice or additional information,contactsys-help@loni.org
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Shells
A user may choose between using /bin/bashand /bin/tcsh. Details about each shell follows.
/bin/bash
System resource file: /etc/profile
When one access the shell, the following user files are read in ifthey exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.profile
When a user logs out of an interactive session, thefile ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, isset automatically using SoftEnv. See below for moreinformation.
/bin/tcsh
The file ~/.cshrc is used to customize the user'senvironment if his login shell is /bin/tcsh.
SoftEnv
SoftEnv is a utility that is supposed to help users manage complexuser environments with potentially conflicting application versionsand libraries.
System Default Path
When a user logs in, the system /etc/profileor /etc/csh.cshrc (depending on login shell, and mirroredfrom csm:/cfmroot/etc/profile)calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh toset up the default path via the SoftEnv database.
SoftEnv looks for a user's ~/.soft file and updates thevariables and paths accordingly.
Viewing Available Packages
The command softenv will provide a list ofavailable packages. The listing will look something like:
Managing SoftEnv
The file ~/.soft in the user's home directory is wherethe different packages are managed. Add the +keyword into your .softfile. For instance, ff one wants to add the Amber Molecular Dynamicspackage into their environment, the end of the .soft file should looklike this:
+amber-8
@default
To update the environment after modifying this file, one simplyuses the resoft command:
The command soft can be used to manipulate the environmentfrom the command line. It takes the form:
Using this method of adding or removing keywords requires the userto pay attention to possible order dependencies. That is, best resultsrequire the user to remove keywords in the reverse order in which theywere added. It is handy to test out individual keys, but can lead totrouble if changing multiple keys. Changing the .soft file andissuing the resoft is the recommended way of dealing withmultiple changes.
▶ Display Module Names for gaussview on all clusters.
| Machine | Version | Module |
|---|---|---|
| supermike2 | 5.0.8 | gaussview/5.0.8 |
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
h4
Shells
A user may choose between using /bin/bashand /bin/tcsh. Details about each shell follows.
/bin/bash
System resource file: /etc/profile
When one access the shell, the following user files are read in ifthey exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.profile
When a user logs out of an interactive session, thefile ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, isset automatically using Modules. See below for moreinformation.
/bin/tcsh
Gaussview 5
The file ~/.cshrc is used to customize the user'senvironment if his login shell is /bin/tcsh.
Modules
Modules is a utility which helps users manage the complex businessof setting up their shell environment in the face of potentiallyconflicting application versions and libraries.
Default Setup
When a user logs in, the system looks for a file named .modulesin their home directory. This file contains module commands toset up the initial shell environment.
Viewing Available Modules
The command
displays a list of all the modules available. The list will looksomething like:
The module names take the form appname/version/compiler,providing the application name, the version, and information about howit was compiled (if needed).
Managing Modules
Besides avail, there are other basic module commands to use formanipulating the environment. These include:
The -h option to module will list all available commands.
▶ Did not find the version you want to use??
If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.
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Types of request
Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:
- The user's home directory
- Software packages installed here will be accessible only to the user.
- It is suitable for software packages that will be used by a single user.
- Python, Perl and R modules should be installed here.
- /project
- Software packages installed in /project can be accessed by a group of users.
- It is suitable for software packages that
- Need to be shared by users from the same research group, or
- are bigger than the quota on the home file syste.
- This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.
- /usr/local/packages
- Software packages installed under /usr/local/packages can be accessed by all users.
- It is suitable for software packages that will be used by users from multiple research groups.
- This type of request must be sent by the PI of a research group.
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How to request
Please send an email to sys-help@loni.org with the following information:
- Your user name
- The name of cluster where you want to use the requested software
- The name, version and download link of the software
- Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
- Why the software is needed
- Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.
Please note that, once the software is installed, testing and validation are users' responsibility.
About the Software
A graphical user interface designed to help prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces.
Usage
Gaussview must be run in an X-windows session. Details for controlling the application are provided in the materials found in the Resources section.
▶ X11 FAQ?
From *nix
Since ssh and X11 are already on most client machines running somesort of unix (Linux, FreeBSD, etc), one would simply use the followingcommand:
Once successfully logged in, the following command should open anew terminal window on the local host:
An xterm window should appear. If this is not thecase, emailus.
From Mac OS X
An X11 service is not installed by default, but one is availablefor installation on the OS distribution disks as an add-on. Analternative would be to install the XQuartz version. Make sure the X11application is running and connect to the cluster using:
From Windows
Microsoft Windows does not provide an X11 server, but there areboth open source and commercial versions available. You also need toinstall an SSH client. Recommended applications are:
- MobaXterm - a Windows ssh client with X11 server integrated (recommended)
- Xming - a Windows X11 server
- PuTTY - a Windows ssh client
When a PuTTY session is created, make sure the 'X11 ForwardingEnabled' option is set, and that the X11 server is running beforestarting the session.
Testing
Once Xming and puTTY have been set up and in stalled, the followingwill provide a simple test for success:
- start Xming
- start puTTY
- connect to the remote host (make sure puTTY knows about Xming for this host)
Once successfully logged in, the following command should open anew terminal window on the local host:
An xterm window should appear. If this is not the case, referto 'Trouble with Xming?'or emailus.
Note About Cygwin
Cygwin is still a useful environment, but is too complicated andcontains too many unnecessary parts when all one wants is to interfacewith remote X11 sessions.
Advanced Usage
The most important connection that is made is from the user'sclient machine to the first remote host. One may 'nest' X11forwarding by using the ssh -XY commandto jump to other remote hosts.
For example:
1. on client PC (*nix or Windows), ssh to remotehost1
2. on remotehost1 (presumably a *nix machine), ssh -XY to remotehost2
3. on remotehost2 (presumably a *nix machine), ssh -XY to remotehost3
Gaussview 6 Linux Download
...
8. on remotehost8 (presumably a *nix machine), ssh -XY to remotehost9
9. on remotehost9, running an X11 application like xtermshould propagate the remote window back to the initial client PC through all of the additional remote connects.
Resources
Last modified: September 10 2020 11:58:50.
Installation Of Gaussview 6 Free
About
GaussView is the latest iteration of a graphical interface used with Gaussian. It aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output (e.g., you can use it to plot properties, animate vibrations, visualize computed spectra, etc.).
an electronic structure package capable of predicting many properties of atoms, molecules, and reactive systems e.g.
• Energies
• Structures
• Vibrational frequencies
utilizing ab initio, density functional theory, semi-empirical, molecular mechanics, and hybrid methods.
Types of Calculations
• single point energy and properties (electron density, dipole moment, …).
• geometry optimization.
• frequency.
• reaction path following
Building with GaussView
• Instead of typing all the coordinates, theory, basis set, etc., we can use GaussView.
• The calculation is specified by pointing and clicking to build the molecule, and using pull-down menus to select the calculation type, level of theory and basis set.
• GaussView generates the Gaussian input file, and can run Gaussian without ever returning to the Unix prompt.
• GaussView can also be used to read Gaussian output files and visualize the results.
Download
GaussView Software is distributed as a free software under the terms of the GPL. The current version for Windows operating systems can be downloaded here.
Citation
The preferred way to cite GaussView software is :
GaussView, Version 6.1, Roy Dennington, Todd A. Keith, and John M. Millam, Semichem Inc., Shawnee Mission, KS, 2016.