shnitsel-tools documentation¶
Getting started¶
First install,
pip install shnitsel-tools
then import.
import shnitsel as st
import shnitsel.xarray # Activate accessors
Reading data from…¶
…trajectories:
# One of the following:
ds = st.read_trajs('path/to/Singlet_1/', kind='sharc')
ds = st.read_trajs('path/to/Newton-X/', kind='nx')
ds = st.read_trajs('path/to/PyRAI2MD/', kind='pyrai2md')
# And then:
ds = ds.sh.setup_frames()
…ASE databases:
# One of the following:
ds = st.read_ase('path/to/ase.db', kind='spainn')
ds = st.read_ase('path/to/ase.db', kind='schnet')
ds = st.read_ase('path/to/geometries_only.db', kind=None)
…SHNITSEL-style NetCDF4:
ds = st.open_frames('path/to/dataset.nc')
Saving data to…¶
…NetCDF4:
ds.sh.save_frames('path/to/dataset.nc')
…ASE:
ds = st.write_ase('path/to/ase.db', kind='spainn')
# see above for other kinds
Select…¶
…a variable:
ds['energy'] # ...or:
ds.energy
…a trajectory:
ds.sel(trajid=1)
…a point in time:
ds.sel(time=1)
Derive…¶
…bond lengths: TODO