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

[riccardo piombo]

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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>>

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