Job Submission, Monitoring, Sharing and Post Processing

Owned by Eroma Abeysinghe
Last updated: May 08, 2017 by Sudhakar Pamidighantam
3 min read

Tutorial I - Job Submission & Monitoring

  1. Job Submission is available through desktop application and web application.
    1. Download the Desktop application
    2. Job submission steps from web portal
    3. Job submission steps from desktop client
  2. Job monitoring can be done using both desktop application and web portal.
    1. Steps for desktop application based monitoring:
      1. In desktop home screen → 'Recent Experiment' panel will provide the statuses for the recent experiments.
      2. Or use 'Filter Experiments and filter using the name, application, host, etc..., and monitor the experiment in Experiment Summary.
      3. Select the project from left hand side drop down and search for the experiment.
    2. Steps for web portal based monitoring
      1. In order to monitor the progress navigate to experiment's summary page. for navigation use
        1. Project → Browse →Select Project and click 'View' → Click on experiment name to monitor → Opens Experiment Summary
        2. Experiment →Browse →  Click on experiment name or status →Opens Experiment Summary
  3. Experiment Summary page in both web and desktop portal provide with clone, edit, launch and cancel functions.


Tutorial II - Sharing Experiments

  1. Sharing is available only from SEAGrid web portal.
  2. Users can share experiments and projects with other gateway users.
  3. More sharing details.

Tutorial III - SEAGrid Data Portal

  1. login at data.seagrid.org
  2. click on "search" menu item 
  3. A list of experiments that have been parsed by the default parser ( gaussian) should appear
  4. click on the experiment - A page with Metadata should appear for the experiment chosen
  5. Use the Filters to search for specific experiments
    1. Select Formula and type N to select for Molecular Formula Containing N atoms and enter search
    2. Change the N to O atoms
    3. 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.
    4. Select Calculation Method and type B3LYP and enter search
    5. Add a new group and select Basis Set and type 6-31 and enter search 
  6. There is a link to make the results public should be present along with links for different information related to the experiment. 
  7. Click on the "make public" on an experiment 
  8. Now this experiment/result is shared and should be available for everybody in their search table
  9. 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

  1. Go to Recent Experiments
  2. Select an experiment that has a "Complete" under Experiment Status
  3. Scroll Down and click on the output "Gaussian.log" file and it should download the file 
  4. Under the "Molecular Editors" menu select Jamberoo
  5. Under "File" menu in Jamberoo Choose "Open As" →  Gaussian→ Gaussian (03) Output
    1. From the file browser chose one of the logfiles from recent runs 
      available in SEAGrid → Experiment Data → Experiment Folder→ gaussian.log file
    2. Depending on the run you have one or more choices ( for example opt freq runs result in two choices )
    3. For choice #2 corresponding to Freq run select this and 
      1. Select OK 
      2.  Select OK again for the vibrational modes and Infrared spectrum 
      3. A vibrational control panel should appear
        1. Select a Frequency of interest (highest) 
        2. checkbox before "Animate Vibrations"
          this should show vibrational mode
        3. select displacement vectors and this should add displacement vector lines on atoms

Under 

Avagadro Based post Processing

  1. Start Avagadro by running the Avagadro Application
  2. Under File menu Open the previous log file from SEAGrid → Experiment Data → Experiment Folder→ gaussian.log
  3. Under Extension Select Spectra 
    1. One can change the Gaussian widths and other plot variables under Advanced setting

      Molden Post Processing
      execute molden with the gaussian log file
      (

      ~/Applications/gmolden5.1.macosX.64 gaussian.log  on  a Mac)

    2. Use the density mode and set the space for contour to .06 

    3. Select Orbital to open the orbital selection panel

    4. adjust the space for contour until the desired contour is plotted

    5. Chose Geom Conv to plot optimization convergence plots.

    6. Click on the skull and confirm exit to quit molden program.



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