Tutorial I - Job Submission & Monitoring
- Job Submission is available through desktop application and web application.
- Download the Desktop application
- Job submission steps from web portal
- Job submission steps from desktop client
- Job monitoring can be done using both desktop application and web portal.
- Steps for desktop application based monitoring:
- In desktop home screen → 'Recent Experiment' panel will provide the statuses for the recent experiments.
- Or use 'Filter Experiments and filter using the name, application, host, etc..., and monitor the experiment in Experiment Summary.
- Select the project from left hand side drop down and search for the experiment.
- Steps for web portal based monitoring
- In order to monitor the progress navigate to experiment's summary page. for navigation use
- Project → Browse →Select Project and click 'View' → Click on experiment name to monitor → Opens Experiment Summary
- Experiment →Browse → Click on experiment name or status →Opens Experiment Summary
- In order to monitor the progress navigate to experiment's summary page. for navigation use
- Steps for desktop application based monitoring:
- Experiment Summary page in both web and desktop portal provide with clone, edit, launch and cancel functions.
Tutorial II - Sharing Experiments
- Sharing is available only from SEAGrid web portal.
- Users can share experiments and projects with other gateway users.
- More sharing details.
Tutorial III - SEAGrid Data Portal
- login at data.seagrid.org
- click on "search" menu item
- A list of experiments that have been parsed by the default parser ( gaussian) should appear
- click on the experiment - A page with Metadata should appear for the experiment chosen
- Use the Filters to search for specific experiments
- Select Formula and type N to select for Molecular Formula Containing N atoms and enter search
- Change the N to O atoms
- Click on Add Group and set additional selection on Formula and set N and enter search such that Formula Containing both N and O are selected.
- Select Calculation Method and type B3LYP and enter search
- Add a new group and select Basis Set and type 6-31 and enter search
- There is a link to make the results public should be present along with links for different information related to the experiment.
- Click on the "make public" on an experiment
- Now this experiment/result is shared and should be available for everybody in their search table
- Make private makes the data private again
Tutorial IV - Post Processing
Post Processing is done by internal Jamberoo as well as external tools such as Avagadro, Molden,
Please download Avagadro from https://avogadro.cc/ Download link
Please download http://www.cmbi.ru.nl/molden/platforms.html
Let us first look at Jamberoo which is available from the SEAGrid Rich Client
- Go to Recent Experiments
- Select an experiment that has a "Complete" under Experiment Status
- Scroll Down and click on the output "Gaussian.log" file and it should download the file
- Under the "Molecular Editors" menu select Jamberoo
- Under "File" menu in Jamberoo Choose "Open As" → Gaussian→ Gaussian (03) Output
- From the file browser chose one of the logfiles from recent runs
available in SEAGrid → Experiment Data → Experiment Folder→ gaussian.log file - Depending on the run you have one or more choices ( for example opt freq runs result in two choices )
- For choice #2 corresponding to Freq run select this and
- Select OK
- Select OK again for the vibrational modes and Infrared spectrum
- A vibrational control panel should appear
- Select a Frequency of interest (highest)
- checkbox before "Animate Vibrations"
this should show vibrational mode - select displacement vectors and this should add displacement vector lines on atoms
- From the file browser chose one of the logfiles from recent runs
Under