Manipulating data formats of DeePMD-kit, VASP, QE, and LAMMPS, etc.
Project description
dpdata is a python package for manipulating DeePMD-kit, VASP, LAMMPS data formats. dpdata only works with python 3.x.
Installation
One can download the source code of dpdata by
git clone https://github.com/deepmodeling/dpdata.git dpdata
then use setup.py to install the module
cd dpdata
python setup.py install
dpdata can also by install via pip
pip3 install dpdata
Quick start
This section gives some examples on how dpdata works. Firstly one needs to import the module in a python 3.x compatible code.
import dpdata
The typicall workflow of dpdata is
Load data from vasp or lammps or deepmd-kit data files.
Manipulate data
Dump data to in a desired format
Load data
d_poscar = dpdata.System('POSCAR', fmt = 'vasp/poscar')
or let dpdata infer the format (vasp/poscar) of the file from the file name extension
d_poscar = dpdata.System('my.POSCAR')
The number of atoms, atom types, coordinates are loaded from the POSCAR and stored to a data System called d_poscar. A data System (a concept used by deepmd-kit) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one System. It is noted that POSCAR only contains one frame. If the multiple frames stored in, for example, a OUTCAR is wanted,
d_outcar = dpdata.LabeledSystem('OUTCAR')
The labels provided in the OUTCAR, i.e. energies, forces and virials (if any), are loaded by LabeledSystem. It is noted that the forces of atoms are always assumed to exist. LabeledSystem is a derived class of System.
The System or LabeledSystem can be constructed from the following file formats with the format key in the table passed to argument fmt:
The Class dpdata.MultiSystems can read data from a dir which may contains many files of different systems, or from single xyz file which contains different systems.
Use dpdata.MultiSystems.from_dir to read from a directory, dpdata.MultiSystems will walk in the directory Recursively and find all file with specific file_name. Supports all the file formats that dpdata.LabeledSystem supports.
Use dpdata.MultiSystems.from_file to read from single file. Now only support quip/gap/xyz format file.
For example, for quip/gap xyz files, single .xyz file may contain many different configurations with different atom numbers and atom type.
The following commands relating to Class dpdata.MultiSystems may be useful.
# load data
xyz_multi_systems = dpdata.MultiSystems.from_file(file_name='tests/xyz/xyz_unittest.xyz',fmt='quip/gap/xyz')
vasp_multi_systems = dpdata.MultiSystems.from_dir(dir_name='./mgal_outcar', file_name='OUTCAR', fmt='vasp/outcar')
# use wildcard
vasp_multi_systems = dpdata.MultiSystems.from_dir(dir_name='./mgal_outcar', file_name='*OUTCAR', fmt='vasp/outcar')
# print the multi_system infomation
print(xyz_multi_systems)
print(xyz_multi_systems.systems) # return a dictionaries
# print the system infomation
print(xyz_multi_systems.systems['B1C9'].data)
# dump a system's data to ./my_work_dir/B1C9_raw folder
xyz_multi_systems.systems['B1C9'].to_deepmd_raw('./my_work_dir/B1C9_raw')
# dump all systems
xyz_multi_systems.to_deepmd_raw('./my_deepmd_data/')
Software |
format |
multi frames |
labeled |
class |
format key |
---|---|---|---|---|---|
vasp |
poscar |
False |
False |
System |
‘vasp/poscar’ |
vasp |
outcar |
True |
True |
LabeledSystem |
‘vasp/outcar’ |
vasp |
xml |
True |
True |
LabeledSystem |
‘vasp/xml’ |
lammps |
lmp |
False |
False |
System |
‘lammps/lmp’ |
lammps |
dump |
True |
False |
System |
‘lammps/dump’ |
deepmd |
raw |
True |
False |
System |
‘deepmd/raw’ |
deepmd |
npy |
True |
False |
System |
‘deepmd/npy’ |
deepmd |
raw |
True |
True |
LabeledSystem |
‘deepmd/raw’ |
deepmd |
npy |
True |
True |
LabeledSystem |
‘deepmd/npy’ |
gaussian |
log |
False |
True |
LabeledSystem |
‘gaussian/log’ |
gaussian |
log |
True |
True |
LabeledSystem |
‘gaussian/md’ |
siesta |
output |
False |
True |
LabeledSystem |
‘siesta/output’ |
siesta |
aimd_output |
True |
True |
LabeledSystem |
‘siesta/aimd_output’ |
cp2k |
output |
False |
True |
LabeledSystem |
‘cp2k/output’ |
QE |
log |
False |
True |
LabeledSystem |
‘qe/pw/scf’ |
QE |
log |
True |
False |
System |
‘qe/cp/traj’ |
QE |
log |
True |
True |
LabeledSystem |
‘qe/cp/traj’ |
quip/gap |
xyz |
True |
True |
MultiSystems |
‘quip/gap/xyz’ |
Access data
These properties stored in System and LabeledSystem can be accessed by operator [] with the key of the property supplied, for example
coords = d_outcar['coords']
Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)
key |
type |
dimension |
are labels |
description |
---|---|---|---|---|
‘atom_names’ |
list of str |
ntypes |
False |
The name of each atom type |
‘atom_numbs’ |
list of int |
ntypes |
False |
The number of atoms of each atom type |
‘atom_types’ |
np.ndarray |
natoms |
False |
Array assigning type to each atom |
‘cells’ |
np.ndarray |
nframes x 3 x 3 |
False |
The cell tensor of each frame |
‘coords’ |
np.ndarray |
nframes x natoms x 3 |
False |
The atom coordinates |
‘energies’ |
np.ndarray |
nframes |
True |
The frame energies |
‘forces’ |
np.ndarray |
nframes x natoms x 3 |
True |
The atom forces |
‘virials’ |
np.ndarray |
nframes x 3 x 3 |
True |
The virial tensor of each frame |
Dump data
The data stored in System or LabeledSystem can be dumped in ‘lammps/lmp’ or ‘vasp/poscar’ format, for example:
d_outcar.to_lammps_lmp('conf.lmp', frame_idx=0)
The first frames of d_outcar will be dumped to ‘conf.lmp’
d_outcar.to_vasp_poscar('POSCAR', frame_idx=-1)
The last frames of d_outcar will be dumped to ‘POSCAR’.
The data stored in LabeledSystem can be dumped to deepmd-kit raw format, for example
d_outcar.to_deepmd_raw('dpmd_raw')
Or a simpler command:
dpdata.LabeledSystem('OUTCAR').to_deepmd_raw('dpmd_raw')
Frame selection can be implemented by
dpdata.LabeledSystem('OUTCAR').sub_system([0,-1]).to_deepmd_raw('dpmd_raw')
by which only the first and last frames are dumped to dpmd_raw.
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