On Ubuntu 20.04.3 LTS, I try to install and test ifermi as follows:
$ pyenv shell datasci
$ git clone https://github.com/fermisurfaces/IFermi.git IFermi.git
$ cd IFermi.git
$ pip install -r requirements.txt
$ pip install -e .
$ cd examples/MgB2
$ ifermi plot --output fermi-surface.jpg
WARNING: Structure does not match expected primitive cell
Saving plot to fermi-surface.jpg
As you can see, there is a warning triggered. Any hints for fixing it?
Regards,
HZ
Did you find a resolution to this? I am getting the same warning.
I am trying to visualize the fermi surface for a body-centered unit cell from a VASP 5 calculation. The band structure from my calculation is as expected but I’m not sure if the Fermi surface is being generated correctly since I am using a centered cell.
I should mention that the program crashes and does not generate a surface at all unless I specify the --no-wigner option.
Below is the testing results now:
$ pyenv shell datasci
$ git clone https://github.com/fermisurfaces/IFermi.git IFermi.git
$ cd IFermi.git
$ pip install .[tests]
$ pytest
========================================= test session starts =========================================
platform linux -- Python 3.11.1, pytest-7.4.4, pluggy-1.4.0
rootdir: /home/werner/Public/repo/github.com/fermisurfaces/IFermi.git
configfile: pyproject.toml
plugins: anyio-3.7.1
collected 13 items
tests/test_brillouin_zone.py .. [ 15%]
tests/test_fermi_surface.py s.. [ 38%]
tests/test_integration.py ...... [ 84%]
tests/test_plot.py .. [100%]
========================================== warnings summary ===========================================
tests/test_integration.py::IntegrationTest::test_integration_reciprocal
tests/test_integration.py::IntegrationTest::test_integration_spin
tests/test_integration.py::IntegrationTest::test_integration_wigner_seitz
/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/ifermi/plot.py:168: UserWarning: Structure does not match expected primitive cell
self._symmetry_pts = self.get_symmetry_points(fermi_surface, symprec=symprec)
tests/test_integration.py::EmptySurfaceIntegrationTest::test_integration_reciprocal
/home/werner/Public/repo/github.com/fermisurfaces/IFermi.git/tests/test_integration.py:84: UserWarning: Fermi level does not cross any bands. Fermi surface will be empty.
fs = FermiSurface.from_band_structure(new_bs, wigner_seitz=False)
tests/test_integration.py::EmptySurfaceIntegrationTest::test_integration_spin
/home/werner/Public/repo/github.com/fermisurfaces/IFermi.git/tests/test_integration.py:94: UserWarning: Fermi level does not cross any bands. Fermi surface will be empty.
fs = FermiSurface.from_band_structure(new_bs, wigner_seitz=False)
tests/test_integration.py::EmptySurfaceIntegrationTest::test_integration_wigner_seitz
/home/werner/Public/repo/github.com/fermisurfaces/IFermi.git/tests/test_integration.py:74: UserWarning: Fermi level does not cross any bands. Fermi surface will be empty.
fs = FermiSurface.from_band_structure(new_bs)
tests/test_plot.py::FermiSurfaceTest::test_plot_slice
/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/ifermi/plot.py:822: UserWarning: Structure does not match expected primitive cell
self._symmetry_pts = self.get_symmetry_points(fermi_slice, symprec=symprec)
tests/test_plot.py::FermiSurfaceTest::test_plot_surface
/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/ifermi/plot.py:168: UserWarning:
Structure does not match expected primitive cell
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================== 12 passed, 1 skipped, 8 warnings in 136.16s (0:02:16) ========================
But the previous warning is still the same:
$ pip install -U kaleido
$ cd examples/MgB2
$ ifermi plot --output fermi-surface.jpg
WARNING: Structure does not match expected primitive cell
Saving plot to fermi-surface.jpg