Specify custom tolerance matrix in from_random()

[Evmoerman]

Dear ladies and gentlemen,

I would like to generate random 3D-bulk crystals using custom inter-atomic distances for the distance-check.
In the documentation under "Optional parameters",
it is explained that that can be achieved by defining a new Tol_matrix object and passing it to from_random() for example via:

crystal = pyxtal()
crystal.from_random(3, 12, ['C','N'], [2,4], tm=tol_m_1)

However, when trying this, I receive an error, stating that tm is not an existing keyword of from_random().
TypeError: from_random() got an unexpected keyword argument 'tm'

Is that part of the documentation outdated?
Is there actually a possibility to pass a tolerance matrix to from_random()?

Thanks in advance.

Kind regards,
Evgeny

[qzhu2017]

@Evmoerman
This issue has been resolved. Please try to update the code and reinstall it.

Run the following script:

from pyxtal import pyxtal
from pyxtal.tolerance import Tol_matrix
xtal = pyxtal()
xtal.from_random(3, 12, ['C','N'], [2,4])
print(xtal)

xtal = pyxtal()
tol_m = Tol_matrix()
tol_m.set_tol('C', 'N', 2.0)
print(tol_m)
xtal.from_random(3, 12, ['C','N'], [2,4], tm=tol_m)
print(xtal)

You will see the following output:

------Crystal from random------
Dimension: 3
Composition: C2N4
Group: C2/m (12)
monoclinic lattice:   5.7468   2.1158   3.7166  90.0000  84.8496  90.0000
Wyckoff sites:
	 C @ [ 0.0000  0.0000  0.0000], WP [2a] Site [.2/m.]
	 N @ [ 0.6692  0.0000  0.5282], WP [4i] Site [.m.]

--Tol_matrix class object--
Prototype: atomic
Atomic radius type: covalent
Radius scaling factor: 0.5
Custom tolerance values:
C-N:  2.000

------Crystal from random------
Dimension: 3
Composition: C2N4
Group: C2/m (12)
monoclinic lattice:   5.1097   2.6992   4.0948  90.0000  80.2407  90.0000
Wyckoff sites:
	 C @ [ 0.0000  0.5000  0.5000], WP [2d] Site [.2/m.]
	 N @ [ 0.2476  0.0000  0.9665], WP [4i] Site [.m.]