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[Feature Request] We need another `LabeledSystem` input and output format, such as extxyz

Open QuantumMisaka opened this issue 5 months ago • 14 comments

Summary

We wanna transform a training set stored by deepmd/raw and deepmd/npy format to another format which can be parsed by ASE or Ovito. and we need Energy/Force label in the same time.

We've tried all output in dpdata, but there're no another output for LabeledSystem valid but only deepmd/npy and deepmd/raw, only system without label can be output in xyz format and another format which only include coordinates, but not label information.

I do consider that dpdata need another io-format for LabeledSystem (not just read-in, but alos write-out),

Extxyz format is a widely used LabeledSystem and MultiSystems format, which I do think dpdata should include

Detailed Description

extxyz format information: https://wiki.fysik.dtu.dk/ase/ase/io/formatoptions.html#extxyz

Further Information, Files, and Links

ABACUS MD_dump file and another trajectory output will also transform to extxyz format, see https://github.com/deepmodeling/abacus-develop/issues/5022

QuantumMisaka avatar Aug 31 '24 08:08 QuantumMisaka