pyxtal().from_random fails to generate a crystal from Materials Project

[kazeevn]

Hello! I'm trying to generate a crystal according to the following Materials Project entry: Nd(Al2Cu)4, space group I4/mmm [139]. However, PyXtal declares the space group and composition incomparable:

my_crystal = pyxtal()
my_crystal.from_random(dim=3, group="I4/mmm", species=['Nd', 'Al', 'Cu'], numIons=[1, 8, 4])

...
Comp_CompatibilityError: Compoisition [1 8 4] not compatible with symmetry 139

I've also tried to pass the sites:

sites = [
        {'1a': [0., 0., 0.]},
        {'4j': [0.721222, 0.778778, 0.778778],
        '4i': [0.34894, 0.65106, 0.65106]},
        {'4f': [0.5, 0.5, 0. ]}
]
my_crystal.from_random(dim=3, group="I4/mmm", species=['Nd', 'Al', 'Cu'], numIons=[1, 8, 4], sites=sites)

It didn't help with a similar message. Is there some nuance in PyXtal's definition of symmetries I'm not aware of? Any advice would be much appreciated!

PyXtal version is 0.6.1

[kazeevn]

Here is an experiment. I doubled the number of atoms, and PyXtal successfully generated the structure Nd2Cu16Al8. Then I used pymatgen to get the primitive cell, and it returned Nd1Cu8Al4:

my_crystal = pyxtal()
my_crystal.from_random(dim=3, group="I4/mmm", species=['Nd', 'Al', 'Cu'], numIons=[2, 16, 8])
my_crystal_pymatgen = my_crystal.to_pymatgen()
analyzer = SpacegroupAnalyzer(my_crystal_pymatgen)
analyzer.get_symmetrized_structure()

SymmetrizedStructure
Full Formula (Nd2 Al16 Cu8)
Reduced Formula: Nd(Al2Cu)4
Spacegroup: I4/mmm (139)
abc   :   6.471440   6.471440  11.870218
angles:  90.000000  90.000000  90.000000
Sites (26)
  #  SP           a         b          c  Wyckoff
---  ----  --------  --------  ---------  ---------
  0  Al    0         0.5       -0         4c
  1  Al    0         0          0.149988  4e
  2  Al    0.25      0.25       0.25      8f
  3  Cu    0.668589  0.668589  -0         8h
  4  Nd    0         0          0         2a

Naively this suggests that there is no substantial disagreement between the libraries (good!), just some convention difference.

[qzhu2017]

Thanks. It is difference between Primitive unit cell and I/A/B/C/F centered cell.