Restarting ABINIT calculation from Checkpoint

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smithsc
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Restarting ABINIT calculation from Checkpoint

Post by smithsc » Fri Jul 31, 2015 7:43 pm

I am trying to run DFT calculations using ABINIT on systems with a large number of atoms (1200), however the Westgrid computer system that I am using doesn't have a long enough wall time for me to complete this calculation in one run. Therefore, is there anyway of restarting the calculation from a previous run? Essentially, I would like to know if there is a method for restarting the calculation multiple times from where the calculation stopped in a previous run, in order to complete a calculation? Any help or suggestions would be greatly appreciated.

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jzwanzig
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Re: Restarting ABINIT calculation from Checkpoint

Post by jzwanzig » Sun Aug 02, 2015 5:37 pm

1200 atoms is big. How are you handling parallelization? How many kpts, bands, etc do you have?
Josef W. Zwanziger
Professor, Department of Chemistry
Canada Research Chair in NMR Studies of Materials
Dalhousie University
Halifax, NS B3H 4J3 Canada
jzwanzig@gmail.com

Jordan
Posts: 282
Joined: Tue May 07, 2013 9:47 am

Re: Restarting ABINIT calculation from Checkpoint

Post by Jordan » Mon Aug 03, 2015 8:30 am

If you cannot terminate a full SCF calculation because of time issue, you can check the input variable chkexit ifyou want to kill a job properly by hand (meaning writing the WFK and DEN files before termination)
Or you can also make use of prtden with a negative value (-1) to print after each SCF step the current DEN file (Only two files are written no matter the number of steps). You can then use the last DEN file to restart the calculation.

Jordan

smithsc
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Joined: Fri Jul 31, 2015 7:39 pm

Re: Restarting ABINIT calculation from Checkpoint

Post by smithsc » Tue Aug 04, 2015 5:38 pm

Jordan,

Thank you for your suggestion. What is the procedure for restarting the calculation from the last DEN file?

Silvija

Jordan
Posts: 282
Joined: Tue May 07, 2013 9:47 am

Re: Restarting ABINIT calculation from Checkpoint

Post by Jordan » Wed Aug 05, 2015 8:31 am

if you use the prtden -1 option,
you should have 2 files named logprefix_DEN_0000 and _DEN_0001
in a script you can find the last one with

Code: Select all

ls -rt logprefix_DEN_0* | tail -n 1

then you move or better make a symbolic link from you inputprefix_DEN to this file whith

Code: Select all

ln -s inputprefix_DEN "your last DEN file"


And finally, just add irdden 1 in your input file.

Jordan

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