Difference between revisions of "IQmol"

Latest revision as of 21:43, 20 February 2017

Description

From the IQmol web site: IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).

Version

2.2

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

IQmol requires the following module file to run:

apps/iqmol/2.2

See Modules for more information.

Running IQmol on CIRCE/SC

The IQmol user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Starting the Application

Establishing a GUI connection to CIRCE/SC

To use IQmol, you will need to connect to CIRCE/SC with GUI redirection, either using:

CIRCE/SC Desktop Environment
SSH with X11 redirection
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
  - ```
  [user@localhost ~]$ ssh -X circe.rc.usf.edu
```
  or
- ```
[user@localhost ~]$ ssh -X sc.rc.usf.edu
```

Once connected to CIRCE/SC, you can open IQmol using the steps below:

[user@login0 ~]$ module add apps/iqmol/2.2
[user@login0 ~]$ iqmol

Finally, go to File->Open and open your molecule file.

Documentation

Home Page, User Guides, and Manuals

IQmol Home Page
- http://iqmol.org/index.html
IQmol Documentation
- http://iqmol.org/documentation.php

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

IQmol Known Sample inputs
- /apps/iqmol/2.2/samples

Reporting Bugs

Report bugs with IQmol to the IT Help Desk: rc-help@usf.edu

@@ Line 3: / Line 3: @@
 ''From the IQmol web site:'' IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).
-*[http://iqmol.org/index.html IQmol Home Page]
+{{AppStandardHeader|2.2|iqmol}}
-{{AppVersion| 2.2}}
+{{AppRunningOnAll}}
-{{AuthorizedUsers}}
-{{Platforms}}
-== Running IQmol on CIRCE ==
-{{AppModule| apps/iqmol/2.2}}
 === Starting the Application ===
-First, you will need to have properly configured an X11 session. This can be accomplished using an “ssh -Y” connection from a Linux box or an SSH client in Windows. Alternatively, a CIRCE Desktop Environment session can also be used. For more information about the CIRCE Desktop Environment, please see our [[CIRCE Desktop|CIRCE Desktop Environment]] documentation.
+{{X11Connection}}
-Below is an example for using an ssh connection from the command line.
+Once connected to CIRCE/SC, you can open IQmol using the steps below:
-<pre style="white-space:pre-wrap; width:35%; border:1px solid lightgrey; background:#000000; color:white;">
+<pre style="white-space:pre-wrap; width:35%; border:1px solid lightgrey; background:#000000; color:white;">[user@login0 ~]$ module add apps/iqmol/2.2
-[user@localhost ~]$ ssh -Y circe.rc.usf.edu
+[user@login0 ~]$ iqmol</pre>
-[user@circe ~]$ module add apps/iqmol/2.2
-[user@circe ~]$ iqmol</pre>
 Finally, go to '''File-&gt;Open''' and open your molecule file.
-=== Manuals and Test Data ===
+{{Documentation}}
+*IQmol Home Page
+**http://iqmol.org/index.html
+*IQmol Documentation
+**http://iqmol.org/documentation.php
-* Official IQmol Documentation
+{{BKETOR}}
-** [http://iqmol.org/documentation.php http://iqmol.org/documentation.php]
+* IQmol Known Sample inputs
-* Known IQmol sample inputs
 ** /apps/iqmol/2.2/samples
 {{ReportingBugs}}