sagar.molecule package

Subpackages

• sagar.molecule.tests package
  • Submodules
  • sagar.molecule.tests.test_derive module
  • sagar.molecule.tests.test_structure module
  • Module contents

Submodules

sagar.molecule.derive module

class sagar.molecule.derive.ConfigurationGenerator(mol, symprec=0.001)

基类：object

这个类用于产生各种替换原子的需求

get_configurations(sites, e_num)

get_configurations output specific molecule for specific concentration.

parameters: sites: list of (lists or tuples), represent element disorder of each sites e_num: tuple, number of atoms in disorderd sites.

yield:

a tuple tuple[0]: Cell object, a list of non-redundant configurations of certain volume supercell. tuple[1]: int object, degeneracy of the configuration in all configurations of this volume.

sagar.molecule.structure module

Created on Sat Aug 25 16:41:45 2018 @author: hecc

Modified by: Jason Yu

class sagar.molecule.structure.Molecule(positions, atoms)

基类：object

Molecule object represent a 1D Molecule structure.

parameters:

positions: n tuples(x,y,z) in fraction. 可多态初始化 atoms: list of atoms, can be atomic number (int), can be atomic symbol (string), represent atom in periodic table. (用全称初始化？？谁TM会这么用？)

atoms

check(elements=None, limit=0.1, warn=False)

该方法用于自查对象中的位点是否过近 若过近则抛出一个warning

get_symmetry_permutation(symprec=0.001)

positions

sagar.molecule.symmetry module

Created on Sat Aug 25 16:02:21 2018

@author: hecc

sagar.molecule.symmetry.get_distance_matrix(pos)

sagar.molecule.symmetry.get_new_symm(d, origin_d, tri_symm, atoms, pres=0.001)

sagar.molecule.symmetry.get_permutations(pos, atoms, pres=0.001)

This algorithm are mainly derived by Chaobin Qiu

sagar.molecule.symmetry.get_three_permutation(d, atoms, pres=0.001)

Module contents