pymsym's Introduction

pymsym

libmsym is a C library dealing with point group symmetry in molecules. pymsym is its python interface.

about

this library was originally developed by Marcus Johansson. the original library can be found here and seems unmaintained - after reaching out to the initial authors, i've decided to fork this so i can maintain it.

for more info, read the blog post.

installation

use pip:

pip install pymsym

api

there are two high-level functions, pymsym.get_point_group() and pymsym.get_symmetry_number().

here's a simple introduction:

import pymsym

# water
atomic_numbers = [8, 1, 1]
positions = [
  [0.007544053252786398, 0.39774343371391296, 0.0],
  [-0.7671031355857849, -0.18439316749572754, 0.0],
  [0.7595590949058533, -0.21335026621818542, 0.0]
 ]

pymsym.get_point_group(atomic_numbers, positions) # returns C2v
print(pymsym.get_symmetry_number(atomic_numbers, positions) # returns 2

the original lower-level classes from libmsym can also be accessed (pymsym.Element, etc).

point groups

here's all the point groups that pymsym can handle. some of these haven't been tested very well, please let me know if there are issues.

point_groups = [
    "C1", "Cs", "Ci", "C2", "C3", "C4", "C5", "C6", "C7", "C8",
    "D2", "D3", "D4", "D5", "D6", "D7", "D8", "C2v", "C3v", "C4v",
    "C5v", "C6v", "C7v", "C8v", "C2h", "C3h", "C4h", "C5h", "C6h",
    "C7h", "C8h", "D2h", "D3h", "D4h", "D5h", "D6h", "D7h", "D8h",
    "D2d", "D3d", "D4d", "D5d", "D6d", "D7d", "D8d", "S4", "S6",
    "S8", "T", "Th", "Td", "O", "Oh", "Cinfv", "Dinfh", "I", "Kh"
]

Corin Wagen, 2024

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