Comments (5)
I'm a bit confused with the errors there, my guess is that your pip is a different version of python than when you run python (i.e. the difference between running pip
and python -m pip
.
I'd double check this with seeing if which pip
and which python
point within the same conda environment
More broadly my apologies, I haven't updated the wheels on pypi yet as I've been rewriting the build system after there were changes with python 3.12.
Installing from the repository should work i.e.:
pip install git+https://github.com/peterspackman/chmpy
I'll get onto uploading the latest wheels when I can.
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- I'll try and figure out why those dependencies aren't resolved properly. My guess is it's to do with packages that are already installed.
- I have updated the README to point to the correct file location.
- I'm not quite sure what you exactly mean here. So I'll break down as I think there's been some confusion:
Are you trying to generate fingerprint plots? I think you may have some wires crossed between what a Hirshfeld surface is as they are not the same thing (though they are related).
I'm going to assume this is the case as that's very likely. There's no builtin single method to do it, but an example is here:
from chmpy import Crystal
from chmpy.crystal.fingerprint import fingerprint_histogram, plot_fingerprint_histogram
# change to your crystal structure file
c = Crystal.load("src/chmpy/tests/test_files/acetic_acid.cif")
# the default separation is only 0.2, but for a histogram this is a bit sparse
# obviousl you can tweak it depending on your use case
surfaces = c.hirshfeld_surfaces(separation=0.1)
for i, surf in enumerate(surfaces):
hist = fingerprint_histogram(surf)
plot_fingerprint_histogram(hist, filename=f"surface_{i}.png")
Should look something like the below:
Naturally you can tweak this however you want with number of bins, etc. just take a look at the code in src/chmpy/crystal/fingerpint.png
it's pretty straightforward
If you're trying to generate an actual 2D Hirshfeld surface (more of an isoline) then there's no built in code to do that, but you'd just have to evaluate the StockholderWeight
function along the plane of interest.
As for the second part, there is no QM engine scripted in here? There's nothing really QM about the Hirshfeld surface,
Also keep in mind if you're not doing this for molecules (or molecular crystals) you'll have to dig into the machinery a bit more as the convenience methods are only available for atomic environments or molecular environments.
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Also just saw you specifically wanted atom type breakdowns. There's no built in code to do that easily, but it's not too hard so if it's important I can make it easier when I get time.
It's completely possible to do with the existing code, you'd just have to dig in a bit beyond the convenience methods.
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