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QuantumATK => General Questions and Answers => Topic started by: njuxyh_1 on May 20, 2022, 16:06

Title: how to continue the MD calculation for the PBS: job killed: walltime 604832
Post by: njuxyh_1 on May 20, 2022, 16:06

Hi support:

i have an MD job stopped for job killed: walltime 60482, i do not want to restart the MD calculation from begin, for it lasted one week and has finished 7000 steps
so i want to continue the stopped MD calculation.  how to perform the continued job.

thanks very much

Title: Re: how to continue the MD calculation for the PBS: job killed: walltime 604832
Post by: filipr on May 23, 2022, 09:04

If you read the documentation for MolecularDynamics: https://docs.quantumatk.com/manual/Types/MolecularDynamics/MolecularDynamics.html#moleculardynamics-f you'll see that you can pass a previously calculated trajectory as input to the 'configuration' parameter in which case it will continue the calculation. So you can write a script like this:

Code

old_trajectory = nlread('my_trajectory_file.hdf5', MDTrajectory)[-1]
new_trajectory = MolecularDynamics(old_trajectory, <other arguments>)

and it should continue the MD calculation.