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ASE Toolkit

ai2-kit tool ase

This toolkit is a command line wrapper of ASE to allow user to process trajectory via command line.

Usage

This toolkit include the following commands:

Command Description Example Reference
read Read trajectory files into memory. This command by itself is useless, you should chain other command after reading data into memory. ai2-kit tool ase read ./path/to/traj.xyz ase.io.read, support wildcard, can be call multiple times
write Write all frame of a trajectory into a single file. ai2-kit tool ase read ./path/to/traj.xyz - write ./path/to/output.xyz ase.io.write
write_each_frame Write each frame of a trajectory into a separated file. The file name should include {i} or other valid Python str.format to indicate the frame number ai2-kit tool ase read ./path/to/traj.xyz - write_each_frame ./path/to/POSCAR-{i:04d} --format vasp ase.io.write
set_cell Set the cell of all frames in the trajectory. ai2-kit tool ase read ./path/to/traj.xyz - set_cell "[10,10,10,90,90,90]" ase.Atoms.set_cell
set_pbc Set the periodic boundary condition of all frames in the trajectory. ai2-kit tool ase read ./path/to/traj.xyz - set_pbc "[True,True,True]" ase.Atoms.set_pbc
delete_atoms Delete atoms from all frames in the trajectory. ai2-kit tool ase read ./path/to/traj.xyz - delete_atoms "[1,2,3]"

Those commands are chainable and can be used to process trajectory in a pipeline fashion (separated by -). For more information, please refer to the following examples.

Example

# Convert every frame in xyz trajectory to a POSCAR file
ai2-kit tool ase read ./path/to/traj.xyz - write_each_frame "POSCAR-{i:04d}" --format vasp

# Convert every 20th frame in xyz trajectory to a POSCAR file
# For more information about the index syntax, please refer to https://wiki.fysik.dtu.dk/ase/ase/io/io.html#ase.io.read
ai2-kit tool ase read ./path/to/traj.xyz --index '::20' - write_each_frame "POSCAR-{i:04d}" --format vasp 

# Convert lammps dump data to a POSCAR file
ai2-kit tool ase read ./path/to/lammp-dump.data --format lammps-dump-text --specorder "['O','H']" - write "POSCAR" --format vasp

# Delete atoms from a trajectory
ai2-kit tool ase read lammps.data --format lammps-data --style atomic - delete_atoms "[10, 12]" - write lammps-fin.data --format lammps-data

# Read multiple files and write them into a single file
ai2-kit tool ase read ./path/to/data1/*.xyz - read ./path/to/data2/*.xyz - write all.xyz

# Read all `good` structures generate by CLL training workflow
ai2-kit tool ase read ./workdir/iters-*/selector*/model-devi/*/good.xyz  - write all-good.syz

# Convert xyz file to cp2k-inc file
ai2-kit tool ase read coord.xyz - set_cell "[10,10,10,90,90,90]" - write coord_n_cell.inc --format cp2k-inc