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abelcarreras / DynaPhoPy

Phonon anharmonicity analysis from molecular dynamics
http://abelcarreras.github.io/DynaPhoPy/
MIT License
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size is increased, after trajectory in the format of lammps is transfered to the format of hdf5 #26

Closed XIANG-Xing closed 8 months ago

XIANG-Xing commented 11 months ago

Hi,

When I change the format of trajectory from lammpstrj to hdf5, the size is increased from 13.5 MB to 53.1 MB. It is quite wired because the file in hdf5 is expected to be smaller. Could you give me some helps?

The command for trajectory production is: dump dynaphopypos all custom 100 LiSi${t}_pos.lammpstrj x y z dump_modify dynaphopy_pos sort id

The format transfer is conducted following: dynaphopy input LiSi_300_pos.lammpstrj -ts 0.001 -sv LiSi_300_pos.hdf5

abelcarreras commented 10 months ago

Hi,

-sv tag saves additional data aside from the trajectory (including lattice info, velocity and projected velocities). If you want to reduce the file size I recommend to use --velocity-only tag to save only the velocity or use --save_vc_hdf5 to save only the velocity projected onto a wave vector.

XiangXing96 commented 10 months ago

Ok. Thank you very much.