https://github.com/unkcpz/pniggli
Pure python niggli cell
https://github.com/unkcpz/pniggli
Last synced: 6 months ago
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Pure python niggli cell
- Host: GitHub
- URL: https://github.com/unkcpz/pniggli
- Owner: unkcpz
- License: mit
- Created: 2019-04-24T02:37:22.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2019-04-25T10:57:45.000Z (about 6 years ago)
- Last Synced: 2024-12-03T20:57:33.257Z (6 months ago)
- Language: Python
- Size: 47.9 KB
- Stars: 5
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
pniggli
========================================
This is a (P)ure python implementation of algorithm to determin Niggli cell.
The library supports both 2D and 3D niggli transformations.
Rows of list or rows of `numpy.ndarray` correspond basis vectors, a, b, c or a, b
They are input to niggli_reduce as a row with three colum matrices,
same as most DFT softwares' lattice inputs.
In the implementation details, since the lattice is represented by a row vector,
the transformation operation on the lattice is left-multiplied, such as:
.. code-block:: python
import numpy as np
# TMatrix is the transform matrix
new_Lattice = np.matmul(TMatrix, old_Lattice)
For details of the algorithm, see [[Niggli for 2d and 3d]](http://)
Install
----------
.. code-block:: shell
$ pip install pniggli
Usage
----------
.. code-block:: python
from pniggli import niggli_reduce, niggli_check
lattice_3D = [4.912, 0.000, 0.000,
-2.456, 4.254, 0.000,
0.000, 0.000, 0.000]
niggli_lattice = niggli_reduce(lattice_3D)
print(niggli_lattice)
# Out:
# array([[ 4.912, 0. , 0. ],
# [-2.456, 4.254, 0. ],
# [ 0. , 0. , 16. ]])
print(niggli_check(niggli_lattice)) # True
lattice_2D = [2.4560000896, 0.0000000000,
11.0520002567, 2.1269502021]
niggli_lattice = niggli_reduce(lattice_2D)
print(niggli_lattice)
# Out[6]:
# array([[-1.2279999 , -2.1269502 ],
# [-1.22800019, 2.1269502 ]])
The 2D example is a triangle motif.
Version
----------
v0.1.2
########
+ 2D and 3D niggli reduce support
+ niggli_check for 3D lattice
v0.1.0
#######
+ 3D niggli reduce support
+ niggli_check for 3D lattice