pyxtal.build() function

[XinYu73]

In the build() function, we have following code: wp0 = self.group[0] for sp, wps in zip(species, sites): for wp in wps: if type(wp) is dict: #dict for pair in wp.items(): (key, pos) = pair if we pass species as ['H','H'], and sites :[{'4a': [0.0,0.0,0.0]},{'4b':[0.5,0.5,0.5]}] then we have wps as {'4b':[0.5,0.5,0.5]} and wp as '4b' which will lead to the error that numpy cannot convert string to float

[qzhu2017]

What's the space group number in your input? Can you post the full input script?

[XinYu73]

from pyxtal import pyxtal
from pyxtal.lattice import Lattice
import numpy as np

# def build(self, group, species, numIons, lattice, sites):
#         """
#         Build a atomic crystal based on the necessary input

#         Args:
#             group: 225
#             species: ['Na', 'Cl']
#             numIons: [4, 4]
#             lattice: lattice object
#             sites: [{"4a": [0.0, 0.0, 0.0]}, {"4b": [0.5, 0.5, 0.5]}]
#         """
xtal = pyxtal()
xtal.build(
    group=225,
    species=["Na", "Cl"],
    numIons=[4, 4],
    lattice=Lattice.from_matrix(np.diag([2, 2, 2])),
    sites=[{"4a": [0.0, 0.0, 0.0]}, {"4b": [0.5, 0.5, 0.5]}],
)

[XinYu73]

the error

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[8], line 16
      4 # def build(self, group, species, numIons, lattice, sites):
      5 #         """
      6 #         Build a atomic crystal based on the necessary input
   (...)
     13 #             sites: [{"4a": [0.0, 0.0, 0.0]}, {"4b": [0.5, 0.5, 0.5]}]
     14 #         """
     15 xtal = pyxtal()
---> 16 xtal.build(group = 225,species = ['Na','Cl'],numIons = [4,4],lattice = Lattice.from_matrix(np.diag([2,2,2])),sites = [{"4a": [0.0, 0.0, 0.0]}, {"4b": [0.5, 0.5, 0.5]}])

File [~/workplace/PyXtal/pyxtal/__init__.py:1511](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241494c6561726e227d.vscode-resource.vscode-cdn.net/home/xinyu/workplace/high_symmetry_derivative_structure/draft/XXXX_build_database/~/workplace/PyXtal/pyxtal/__init__.py:1511), in pyxtal.build(self, group, species, numIons, lattice, sites)
   1509                 raise RuntimeError("Cannot interpret site", key)
   1510         else: # List of atomic coordinates
-> 1511             pt, _wp, _ = wp0.merge(wp, lattice.matrix, tol=0.1)
   1512             _sites.append(atom_site(_wp, pt, sp))
   1514 self.atom_sites = _sites

File [~/workplace/PyXtal/pyxtal/symmetry.py:2062](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241494c6561726e227d.vscode-resource.vscode-cdn.net/home/xinyu/workplace/high_symmetry_derivative_structure/draft/XXXX_build_database/~/workplace/PyXtal/pyxtal/symmetry.py:2062), in Wyckoff_position.merge(self, pt, lattice, tol, orientations)
   2060 PBC = wp.PBC
   2061 group = Group(wp.number, wp.dim)
-> 2062 pt = self.project(pt, lattice, PBC)
   2063 coor = apply_ops(pt, wp)
   2064 if orientations is None:
...
   2288 def project_single(point, rot, trans):
   2289     # move the point in the opposite direction of the translation
   2290     point -= trans

ValueError: could not convert string to float: '4a'

[XinYu73]

a simple fix is to pass the sites argument as "sites=[[{"4a": [0.0, 0.0, 0.0]}], [{"4b": [0.5, 0.5, 0.5]}]],"

[qzhu2017]

Yes, you are right. Thanks.