r2stanton / pyrovskite Goto Github PK

Hi, I am very excited to read the paper from arXiv and then tried this package. However, I could not repeat the example in your paper (on page 4) as follows.

from pyrovskite.builder import make_2drp
A = "./methylammonium.xyz"
Ap = "./butylammonium.xyz"
org_A_2drp = make_2drp (Ap , A, "Pb", "I", 2, 3)
in_A_2drp = make_2drp (Ap , "Cs", "Pb", "I", 2, 3)

I was in the directory of /public/home/clxy_wh/BACKUP/pyrovskite/tests/data .

There are many .cif and .xyz files, shown below.

(pyrovskite) [clxy_wh@login data]$ ls
3AMP_CsInSbI_dj.cif  mapbi3_2x2x2.cif   methylammonium.xyz     test_bulk.json    test_mono.json         testvcopt_fcopt.cif  testvcopt_vcopt.inp
benzylammonium.xyz   mapbi3.cif         test_2ddouble_dj.json  test_dj.json      test_perovskite_1.cif  testvcopt_fcopt.py
mapbi_2d_diag.cif    mapbi_3d_diag.cif  test_2ddouble_rp.json  test_double.json  test_rp.json           testvcopt_vcopt.cif

I can find the methylammonium.xyz file as demonstrated in the paper, but there is only benzylammonium.xyz instead of butylammonium.xyz.

The codes below were what I tried. (I installed the Pyrovskite package in the virtual environment via Anaconda 3).

(pyrovskite) [clxy_wh@login data]$ python
Python 3.10.11 (main, Apr 20 2023, 19:02:41) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pyrovskite.builder import make_2drp
>>>
>>> Ap = "./benzylammonium.xyz"
>>> in_A_2drp = make_2drp(Ap, "Cs", "Pb", "I", 2, 3)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/public/home/clxy_wh/BACKUP/pyrovskite/pyrovskite/builder.py", line 278, in make_2drp
    raise ValueError("Ap must be a molecule in the form of an Atoms "
ValueError: Ap must be a molecule in the form of an Atoms object, not a single atom as a string.
>>> 

I also tried to use the methylammonium.xyz as Ap, however, the same ValueError appeared.
Could you please kindly help me to fix it? Thanks a lot.

Hi,
I am sorry that I don't find The_Lambda_parameters.ipynb notebook in the package. Could you please upload it or share it with me?

Thank you very much

Hi Robert,
I found that the structures generated by pyrovskite are (0,0) positions with the interlayer octahedrons top-to-top stacked. Is it possible to generate the (0, 1/2) shift between the octahedron interlayers, as shown in panels (b) and (d) of the figure below?