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QuantumMisaka / ATST-Tools

Advanced ASE Transition State Tools for ABACUS
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Update the neb_make_pymatgen.py #13

Closed MoseyQAQ closed 5 months ago

MoseyQAQ commented 5 months ago

I have updated the neb_make_pymatgen.py

Example:

python .\neb_make_pymatgen.py -i .\0\OUT.ABACUS\running_scf.log .\9\OUT.ABACUS\running_scf.log -n 8
MoseyQAQ commented 5 months ago

@QuantumMisaka Dear Developer, I have updated the script to generate the initial neb chain file using Pymatgen + ASE, and made some modifications to make the script more easy to read and use.

QuantumMisaka commented 5 months ago

@MoseyQAQ Sorry to notice your PR too late, I'll have a look in convenient time

QuantumMisaka commented 5 months ago

@MoseyQAQ Thanks for your PR!

Could you add some function like that in the existing neb_make.py which allows users to

  1. set initial magnetic moment
  2. set constraints (by certain direction and certain height) Since the running*.log by ABACUS do not have these information
MoseyQAQ commented 5 months ago

@QuantumMisaka OK, I will update the code. Thanks for your feedback!

MoseyQAQ commented 5 months ago

@QuantumMisaka The new functions have been added, please check.

QuantumMisaka commented 5 months ago

@MoseyQAQ Thanks a lot!

For dependencies, in my recollection the installation method for pymatgen is recommended to be conda install -c conda-forge ?

MoseyQAQ commented 5 months ago

@MoseyQAQ Thanks a lot!

For dependencies, in my recollection the installation method for pymatgen is recommended to be conda install -c conda-forge ?

yes. More detailed information can be seen at: https://pymatgen.org/installation.html

QuantumMisaka commented 5 months ago

@MoseyQAQ Thanks! You're welcome to have my contact: QQ 948967102