[ase-users] Asking for Help

[Firas Shuaib]

 Hi Adam,
Thank you for your email. Actually the problem not in writing data on a file, I did your suggestions and i got 4 files but all of then start from scratch not from the last point of the previous MD run. That can be seen when plot the Thermal cycle.

The problem is I get a data for the run at 1000K then, when the loop move on and start the run at 700K it starts from scratch not from the restart file. I do not know how to let the MD run starts from the last point of the previous run not from scratch.

Thank you in Advance,
Firas

*****************************************
Firas Shuaib, PHD Researcher.
Institut de Recherche sur les Céramiques
IRCER CNRS UMR 7315
Centre Européen de la Céramique
12 Rue Atlantis, 87068 Limoges, France
Tel: +33751084024
E-mail: firasshuaib at yahoo.com, firas.shuaib at etu.unilim.fr
*****************************************

     On Tuesday, February 22, 2022, 06:02:26 PM GMT+2, Adam Jackson <a.j.jackson at physics.org> wrote:  
 
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Hi Firas,
 
  
 
Something like that should indeed be possible. What errors are you encountering?
 
  
 
One possible issue I see in your code is that you create a new Trajectory with the same name in ‘w’ mode inside the loop. This means that each iteration will overwrite the last one, which is probably not what you intended. Perhaps it would be a good idea to e.g. include the temperature in the filename with
 
  
 
traj_writer = Trajectory(f‘md_runs_si/si_traj_{T}K.traj’, ‘w’, si)
 
  
 
Or you could append to the existing trajectory with ‘a’ mode, leaving existing steps intact. Or you could set up the trajectory writer outside the loop, and only update the dynamics.
 
  
 
Regards,
 
Adam
 

Date: Mon, 21 Feb 2022 15:37:50 +0000 (UTC)
From: Firas Shuaib <firasshuaib at yahoo.com>
To: ase-users at listserv.fysik.dtu.dk
Subject: [ase-users] Asking for Help
Message-ID: <828946716.1074470.1645457870610 at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Dear All,
Hope this email finds you well. This Firas SHUAIB. I am a master holder of Condensed matter physics. Recently, I am trying to learn how to use ASE to train a gap model. I have a problem in creating a dateset. I want to run Molecular dynamics for a simple NVT system? Si? at different temperature [1000, 700, 500, 300]. I have a problem in restarting the simulation, I want when the simulation is done at 1000 to restart from the last point and just the change the temperature. I have tried different ways but non of them worked. Please find attached screenshot. could you guide me with this ?

 Thank you in advance,
 Firas

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