fable-3dxrd / xrd_simulator Goto Github PK

Tools for simulating x-ray diffraction. Detailed documentation is found at the below link.

Home Page: https://fable-3dxrd.github.io/xrd_simulator/

License: MIT License

Python 100.00%

xrd diffraction diffraction-analysis diffraction-pattern polycrystal xray-images xray-diffraction xray-crystallography xray-diffraction-analysis

xrd_simulator's People

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ravipurohit1991 haoz3 wangvei jonwright axelhenningsson marcraven

xrd_simulator's Issues

Struggling to run any .cif files

Hi Alex,

First off, thank you so much for supporting this code base! I'm a computer scientist attempting to learn about x-ray diffraction and being able to step through this code has been a godsend. A lot of topics that were very confusing to me in the textbook now make perfect sense.

I'm working on a research project around finding new (and hopefully more accurate) ways of doing molecule structure prediction using diffraction data. On that note, I'd like to run a .cif file through the simulator and get intensity values that I can hopefully try to invert using my method.

I am however having an issue getting .cif files taken randomly from the Crystallography Open Database to run. Specifically, the .cif files I'm finding on the internet contain isotopes and it seems the atomlib.py file does not support that? In any case, I'm getting errors that the program does not recognize the atom's name (for example, "SR2+" is the current error I'm getting from a random .cif file).

By chance am I misunderstanding something?

I couldn't find much documentation recommending how to properly use .cif files. By chance would you happen to have any .cif files to share which you know will work? For my purposes I don't really care what the molecule is, as long as its sufficiently large and complex that finding its structure is non-trivial.

Many Thanks!
Eric

H5 broken on linux

Something seems to be broken with the H5 libs on linux, see job fail:

https://github.com/FABLE-3DXRD/xrd_simulator/actions/runs/3311789179/jobs/5468121970

Pinned versions?

Hi Axel,
I just tried to install with a draft environment for the ESRF site conda and I got an error with the version on pip (below). With a git checkout I just needed to bump to allow python 3.11 and then pytest in xrd_simulator/tests is passing.

Shall I send a pull request or is there a reason to avoid python 3.11?

Thanks!

Jon

(jupy2023) hpc5-0301:~/git/PolyXSim/test % pip install xrd-simulator
DEPRECATION: Loading egg at /gpfs/easy/data/id11/jon/mamba/envs/jupy2023/lib/python3.11/site-packages/cctbx_base-2023.8-py3.11.egg is deprecated. pip 23.3 will enforce this behaviour change. A possible replacement is to use pip for package installation..
Collecting xrd-simulator
  Downloading xrd_simulator-0.1.1-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.4/80.4 kB 6.9 MB/s eta 0:00:00
Collecting matplotlib==3.3.1 (from xrd-simulator)
  Downloading matplotlib-3.3.1.tar.gz (38.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.8/38.8 MB 223.7 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
INFO: pip is looking at multiple versions of xrd-simulator to determine which version is compatible with other requirements. This could take a while.
Collecting xrd-simulator
  Downloading xrd_simulator-0.0.9-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.3/80.3 kB 105.1 MB/s eta 0:00:00
  Downloading xrd_simulator-0.0.8-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.3/80.3 kB 105.4 MB/s eta 0:00:00
  Downloading xrd_simulator-0.0.7-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.3/80.3 kB 104.6 MB/s eta 0:00:00
  Downloading xrd_simulator-0.0.6-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.3/80.3 kB 111.4 MB/s eta 0:00:00
  Downloading xrd_simulator-0.0.5-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.3/80.3 kB 110.0 MB/s eta 0:00:00
  Downloading xrd_simulator-0.0.4-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.3/80.3 kB 113.1 MB/s eta 0:00:00
  Downloading xrd_simulator-0.0.3-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.3/80.3 kB 111.3 MB/s eta 0:00:00
INFO: pip is still looking at multiple versions of xrd-simulator to determine which version is compatible with other requirements. This could take a while.
  Downloading xrd_simulator-0.0.2-py3-none-any.whl (44 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.1/44.1 kB 79.3 MB/s eta 0:00:00
Collecting miniball==1.1.0 (from xrd-simulator)
  Downloading miniball-1.1.0.tar.gz (6.3 kB)
  Preparing metadata (setup.py) ... done
Collecting xrd-simulator
  Downloading xrd_simulator-0.0.1-py3-none-any.whl (44 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.0/44.0 kB 97.2 MB/s eta 0:00:00
ERROR: Cannot install xrd-simulator==0.0.1, xrd-simulator==0.0.2, xrd-simulator==0.0.3, xrd-simulator==0.0.4, xrd-simulator==0.0.5, xrd-simulator==0.0.6, xrd-simulator==0.0.7, xrd-simulator==0.0.8, xrd-simulator==0.0.9 and xrd-simulator==0.1.1 because these package versions have conflicting dependencies.

The conflict is caused by:
    xrd-simulator 0.1.1 depends on numpy==1.21.4
    xrd-simulator 0.0.9 depends on numpy==1.21.4
    xrd-simulator 0.0.8 depends on numpy==1.21.4
    xrd-simulator 0.0.7 depends on numpy==1.21.4
    xrd-simulator 0.0.6 depends on numpy==1.21.4
    xrd-simulator 0.0.5 depends on numpy==1.21.4
    xrd-simulator 0.0.4 depends on numpy==1.21.4
    xrd-simulator 0.0.3 depends on numpy==1.21.4
    xrd-simulator 0.0.2 depends on numpy==1.21.4
    xrd-simulator 0.0.1 depends on miniball==1.1.0matplotlib==3.3.1numpy==1.21.4meshio==5.0.2pygalmesh==0.10.6scipy==1.6.1xfab==0.0.4numba

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

Reflection mode is possible?

Hello,
Thank you for this nice library. I had a question, I haven't explored deeply the code yet and was wondering does the code also simulates reflection geometry or is it transmission alone?
Thanks,
Cheers,
Ravi.

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