montoyjh
commented
6 years ago Hi Gerry, try
CifWriter(struct=material, symprec=1e-5).write_file('Li_Test.cif')
Also, just FYI, be a bit careful when interpreting the elastic constants of materials with non-empty "warnings" fields. The elastic analysis of this particularly material strongly suggests it is mechanically unstable, which may mean that its suggested predicted auxetic behavior is the consequence of a bad linear fit.
Best, Joey
On Fri, Mar 23, 2018 at 11:45 AM, GerardMattei notifications@github.com wrote:
System
- Pymatgen version: 2017.8.21
- Python version: 3.6
Summary
Hello, I'm currently searching through the Materials Project's auxetic materials and I'm having difficulty ensuring that pymatgen generates cif files with the correct structures/properties. I have an example below using lithium metal. mp-567337 is the lithium polymorph I'm interested in with a Poisson's ratio of 0.
I'm using the MPRester method to load mp-567337 as a pymatgen structure object from its material ID which appears to produce the correct space group, sites, etc. However when I output the structure object with CifWriter and symprec, the output is of the corresponding Li subcell, mp-135, which exhibits a positive Poisson's ratio of 0.36. Is there a way to ensure that pymatgen outputs a Cif file using the exact structure object I'm observing in my code? Example code
import json from pymatgen.matproj.rest import MPRester from pymatgen.io.cif import CifWriter
with MPRester(matproj_key) as m: mat_id = 'mp-567337' material = m.get_structure_by_material_id(mat_id) print(mat_id, material.composition, material.get_space_group_info(), material.sites)
This outputs the correct material ID and spacegroup of mp-567337 lithium
with a negative poisson's ratio.
CifWriter(struct=material, symprec=True).write_file('Li_Test.cif')
This instead appears to output the subcell of the desired structure,
mp-135 lithium with a positive poisson's ratio.
Thank you, -Gerry
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/materialsproject/pymatgen/issues/1078, or mute the thread https://github.com/notifications/unsubscribe-auth/AGMZNNEzVNv0rd4_BLnR6aTqGMH-BI7uks5thULQgaJpZM4S5NZS .
GerardMattei
System
Summary
Hello, I'm currently searching through the Materials Project's auxetic materials and I'm having difficulty ensuring that pymatgen generates cif files with the correct structures/properties. I have an example below using lithium metal. mp-567337 is the lithium polymorph I'm interested in with a Poisson's ratio of 0.
I'm using the MPRester method to load mp-567337 as a pymatgen structure object from its material ID which appears to produce the correct space group, sites, etc. However when I output the structure object with CifWriter and symprec, the output is of the corresponding Li subcell, mp-135, which exhibits a positive Poisson's ratio of 0.36. Is there a way to ensure that pymatgen outputs a Cif file using the exact structure object I'm observing in my code?
Example code
import json from pymatgen.matproj.rest import MPRester from pymatgen.io.cif import CifWriter
with MPRester(matproj_key) as m: mat_id = 'mp-567337' material = m.get_structure_by_material_id(mat_id) print(mat_id, material.composition, material.get_space_group_info(), material.sites)
This outputs the correct material ID and spacegroup of mp-567337 lithium with a negative poisson's ratio.
CifWriter(struct=material, symprec=True).write_file('Li_Test.cif')
This instead appears to output the subcell of the desired structure, mp-135 lithium with a positive poisson's ratio.
Thank you, -Gerry