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Introduction of pfcc-ase-extras

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Summary

pfcc-ase-extras is a library package that offers more convenient tools by modifying the source code used internally by ASE.
Since ASE is licensed under the GNU Lesser General Public License v2.1+ (link), it is required to inherit the license when redistributing. Therefore, it is provided separately from pfcc-extras.

Please note that since this is provided as an experimental library package, compatibility with new features is not guaranteed and may be changed or removed without prior notice.

 

Introduction to pfcc-ase-extras features here

2024.9 note:

ASE 3.23 was released in May 2024. pfcc-ase-extras version 0.3.0 and later are compatible only with ASE 3.23. If you are using ASE 3.22, please use pfcc-ase-extras version 0.2.0 or earlier.

 

The functions in pfcc and the path to sample scripts were summarized as below.

Category Functions Scripts  Ver
file IO structure with charge IO
(for ASE 3.22)
  • ase_io/ase_read.ipynb
 >0.1.0
file IO LAMMPS file IO
(for ASE 3.22)
  • io_lammpsdata/io_lammpsdata.ipynb
 >0.2.0
Calculation

RDFAnalyzer
  • geometry/rdf_example.ipynb
 >0.2.0

* The all script paths only represents the relative path after "/pfcc-extras-v0.x.0/examples/"

 

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How to Install

  1. Open Package Launcher and move to the bottom to find pfcc-ase-extras package.



  2.  Copy to the directry as zip format



  3. Right click the file and select “Extract Archive”



  4. Open /pfcc-extras-v0.x.0/examples/install.ipynb, and run the cell below
    !pip install ..
    If you add -e option, the package will be installed in editable mode.
  5. After install command, please restart the kernel.


  6. Please confirm the completion of the installation as below.

    • How to restart kernel
      • Kernel > Restart Kernel...


      • Click "Restart the kernel" button


    • Output example in v0.6.0
      import pfcc_ase_extras

      print("pfcc_ase_extras version: ", pfcc_extras.__version__)
      pfcc_ase_extras version: 0.3.0

 

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Introduction of major functions

■ RDFAnalyzer

The function added and modified from rdf calculation in ASE version.

  • Addition
    • RDF calculation between molecules
  • Improve efficiency
    • calculation in low memory
    • cache of distance calculation

With this extension, it is possible to perform RDF calculations on large systems that cannot be computed due to memory constraints in the ASE version of Matlantis. By specifying the molecular species, RDF calculations can also be performed targeting the centers of those molecules.

 

 

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