[CP2K-user] [CP2K:19337] Extracting Atomic Forces from XYZ Trajectories in CP2K

[Jürg Hutter]

Hi

in this case you want forces from uncorrelated configurations. Depending on your system and the ML algorithm you probably need about 1000 learning points.
I would run a REFTRAJ run with about 1000 points along your full trajectory
and recalculate the forces (NO Langevin!).
You will have the additional benefit, that your forces are more accurate
then in the original run.

regards
JH

________________________________________
From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of riccardo piombo <riccardo.piombo at gmail.com>
Sent: Tuesday, October 10, 2023 11:19 AM
To: cp2k
Subject: Re: [CP2K:19337] Extracting Atomic Forces from XYZ Trajectories in CP2K

In particular, the goal is to obtain a file like an extended xyz one and try training a machine learing potential.

Best regards,
Riccardo Piombo

Il giorno martedì 10 ottobre 2023 alle 10:37:48 UTC+2 riccardo piombo ha scritto:
Hi Prof. Hutter,
my simulations are also based on the Langevin ensamble.
do we have to give up on calculating atomic forces from the xyz trajectory?

Kind regards,
Riccardo Piombo

Il giorno martedì 10 ottobre 2023 alle 10:17:17 UTC+2 Simone Ritarossi ha scritto:
Hi users,
I have the same problem and I used Langevin (second-generation Car-Parrinello). In this case?

Simone Ritarossi

Il Mar 10 Ott 2023, 08:58 Jürg Hutter <hut... at chem.uzh.ch> ha scritto:
Hi

all integrators in CP2K are based on the Velocity Verlet algorithm.
The different routines can be found in the src/motion directory.

If your trajectory was generated for a NVE ensemble without any
constraints, you can easily extract the forces from inverting the
Velocity Verlet algorithm.
If you were using any type of thermostat or any geometrical constraints
it will be very difficult or impossible. At least I don't see a straightforward
way.
Depending on you final goal, recalculating the forces at a subset of your
trajectory will be your only option.

regards
JH

________________________________________
From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of riccardo piombo <riccard... at gmail.com>
Sent: Monday, October 9, 2023 5:54 PM
To: cp2k
Subject: [CP2K:19326] Extracting Atomic Forces from XYZ Trajectories in CP2K

Dear CP2K Community,

We have encountered a challenge while working with MD trajectories in XYZ format. Specifically, we have trajectories containing atomic positions and velocities for each frame, but unfortunately, we do not have the corresponding atomic forces.

In theory, it is possible to calculate atomic forces based on atomic positions and velocities. However, we are unsure about the specific algorithm and where it can be found within the CP2K codebase.

We are reaching out to the community to inquire if anyone can provide guidance on:

  1.  1. Locating the algorithm or module responsible for calculating atomic forces within CP2K.
  2.  2. Assessing the feasibility of extracting atomic forces from our XYZ trajectories in a reasonably short amount of time.

Any assistance or insights on this matter would be greatly appreciated. We understand that this may be a non-trivial task, but we are hopeful that the CP2K community's expertise can help us navigate this challenge.

Thank you in advance for your support and expertise.

Best regards Riccardo Piombo

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