[CP2K-user] [CP2K:20200] Re: Computing FES from multiple RESTART files

[David M. Sherman]

Perhaps I'm misreading your post, but I have a horrible feeling that, every 
3 days, you are simply restarting the whole metadynamics simulation from 
the very beginning!  As such, you will never get a converged FES.

Just to clarify: you simply need to restart the job using the the *.restart 
file from the previous 3 day run as the input file for the next 3 day run 
(that's why it's called a "restart" file...).  Cp2k reads a *.restart file 
as an input file.  Maybe that's obvious; if so, forgive me.  Note, however, 
that the restart file (as it evolves) will keep accumulating all of the 
HILLS that were generated during the whole metadynamics run, not just the 
HILLS generated over the past 3 days.  There is no need to move things to a 
new folder (directory); again, you simply restart the job using the 
*.restart file as the input file.  You don't need the previous *.restart 
files to generate the FES. Indeed, the latest *.restart file actually 
contains a record of the time-evolution of the FES that you can generate 
using the -span argument to the "graph" program. The only thing that you 
need to be careful about is if your job stops during an update of the 
restart file.  That's why you should always have your input file generate a 
few *restart.bak files so that, if necessary,  you can copy the last 
*restart.bak-1 to *.restart.

On Tuesday, May 7, 2024 at 7:55:00 PM UTC+1 Diana Marlén Castañeda 
Bagatella wrote:

> Hello everyone,
> I hope you are doing well.
>
> I am running calculations in a cluster that constrains them to 3 days per 
> job; after these 3 days, I need to rerun the simulation from their last 
> checkpoint.
>
> CP2K generates a restart file during the simulation process, which is used 
> by the graph.popt program (included in the CP2K module) to save the free 
> energy surface (FES) path in a file called fes.dat. Likewise, the same 
> restart file can be used to continue the simulation from its last 
> interruption (checkpoint).
>
> The inconvenience happens when the simulation is interrupted as the 
> restart file only saves the simulation progress during the 3-day wall time. 
> Hence, graph.popt can only save the fes path of the last piece of 
> simulation. To avoid losing information, I copy the restart of the 
> interrupted simulation to a new folder and continue the simulation in this 
> new folder. However, graph.popt can read only one restart file, and I 
> cannot find any way to create a restart file containing the information of 
> the simulation (which is split into several pieces) and make it readable 
> for graph.popt.
>
> I would greatly appreciate it if someone could advise me on how to compute 
> the FES of the whole simulation properly. 
>
> I wish you a great day, and thanks for your time,
> Diana.
>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/12e606d3-04eb-4f41-bfe5-cf92874281fdn%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20240509/0444e4f1/attachment.htm>