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Can trajectory files, such as MD_dump, be converted to the .xyz format? #5022
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I recommend extxyz format to store energy ,atom force, stress, atom velocity and other information, and which can be viewed in ASE and Ovito Introduction to extxyz Also, if extxyz is too large, we can consider an binary format (like .npy in dpdata ?) |
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@YuLiu98 @kirk0830 @pxlxingliang Any comments ? |
We should be careful about changing the format of MD output files. We have changed it many times in the past few versions, which often leads to incompatibility of post-processing software such as dpdata. I agree with changing the format, but the premise is that everyone can reach a consensus before doing so. |
@YuLiu98 I think so, so change its format to a usually used format may help. |
@qinrui-oss ase can deal with extxyz format originally, but ASE-ABACUS cannot deal with MD_dump file. ASE-ABACUS interface have a very weird way to deal with MD data:
I think that some change is needed @1041176461 any comments ? |
I have read above discussion. I think a better idea is to give freedom to user to select format of file he/she wants, instead of changing one again and again. So in principle we can support extxyz, xyz, cif, md_dump, etc. |
@QuantumMisaka ASE-ABACUS has already supported MD_dump 2 month ago, please see this issue(https://gitlab.com/1041176461/ase-abacus/-/issues/31) |
We can conveniently convert ABACUS MD output files to XYZ, VASP, or LAMMPS format by very few Python codes using dpdata. Also, a number of codes dealing with ABACUS MD output rely on the format of MD output. If we change the format, all the codes have to be modified accordingly. In case of these issues, we think it better to keep the MD format unchanged at the current time. |
@Liu-RX I consider a extxyz-like trajectory format for store energy, force, virial (and even velocity) is needed in every task of ABACUS calculation. which means the MD_dump file will keep, but add a well-recognized trajectory output for trans-platform usage. which is surely needed |
Background
After running a Molecular Dynamics (MD) simulation, it is often necessary to parse the output files to calculate the Mean Square Displacement (MSD). The output file, MD_dump, contains essential information such as time, position, and velocity. However, most post-processing tools, such as VMD, GROMACS, and Python MDAnalysis, cannot directly read the MD_dump file, which makes further analysis inconvenient.
Describe the solution you'd like
It would be more convenient if the trajectory file could be generated in the .xyz format after the MD simulation. The .xyz file can be read by VMD and Python MDAnalysis, and it can be converted to the g96 format using ASE. This g96 format can then be further converted to the trr format using GROMACS for calculating the MSD.
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