A robust code for assigning REPEAT outputs to MOFs. Different checks are implemented to ensure the provided files refers to the same structure; if not, AssertError will arise with the appropriate information.

This code is tested with the following packages (just use the latest version you can find):

• Python 3.8+
• pymatgen 2022+

Directories storing the related MOF files should follow the below structure:

src/path/to/MOFs/
├── MOF1
│   ├── MOF1.cif
│   ├── POSCAR
│   └── repeat.output
├── MOF2
│   ├── MOF2.cif
│   ├── POSCAR
│   └── repeat.output
└── MOF3
    ├── MOF3.cif
    ├── POSCAR
    └── repeat.output

Checkout example_MOFs for example INPUTs, and assigned_MOFs for example OUTPUTs.

1. Set up a Python environment based on the prerequisites
2. Prepare new folders for receiving assigned CIFs and problematic MOFs, e.g.:

mkdir dst/path/to/assigned/CIFs
mkdir dst/path/to/problematic/MOFs

3. Modify batch_assignment.py to set up the appropriate paths, e.g.:

# The number of parallel jobs
n_procs = 2
# The source directory for the REPEAT outputs as shown above
src_path = Path("src/path/to/MOFs")
# The destination directory for receiving the assigned CIFs
dst_path = Path("dst/path/to/assigned/CIFs")
# The destination directory for receiving the problematic MOFs
problem_path = Path("dst/path/to/problematic/MOFs")

4. Simply run the batch_assignment.py script under an appropriate Python environment:

python batch_assignment.py

5. If everything is fine, there will be no outputs in the terminal. If any necessary files are missing or problematic, the MOF name alongside an error message will be displayed, e.g.:

[DIMKAN] has no CIF
[QARQAF] has no POSCAR
[BIBTEP] has no REPEAT output
[ILECEH] has empty CIF
[FIHJEO] has empty POSCAR
[HALZAW] has different cell vectors in CIF and POSCAR
[IWASOR] has has different cell angles in CIF and POSCAR
[DEVNIF] has different different number of atoms in CIF and POSCAR
[IQIPIH] has has different number of atoms in POSCAR and REPEAT output
[GAXTIM] has different ordering in POSCAR and REPEAT output

NOTE : If you want to change any options when doing batch processing, you can modify the main function in the batch_assignment.py script.

Simply only pass the path to the CIF file:

python repeat_assigner.py path/to/MOFs/MOF1.cif

The above command will result in:

path/to/MOFs/
├── MOF1
│   ├── MOF1.cif
│   ├── MOF1_repeat.cif
│   ├── POSCAR
│   └── repeat.output
├── ...

Use the -o or --outdir option:

python repeat_assigner.py path/to/MOFs/MOF2.cif -o path/to/new/cifs
python repeat_assigner.py path/to/MOFs/MOF2.cif --outdir path/to/new/cifs

The above command will result in:

path/to/new/cifs/
└── MOF2_repeat.cif
path/to/MOFs/
├── MOF2
│   ├── MOF2.cif
│   ├── POSCAR
│   └── repeat.output
├── ...

To specify a different filename for POSCAR, use the -p or --poscar option; for REPEAT output, use the -r or --repeat option. For example, if your MOFs files are:

path/to/MOFs/
├── MOF3
│   ├── MOF3.cif
│   ├── vasp.poscar
│   └── output.repeat
├── ...

You can use the following command:

python repeat_assigner.py path/to/MOFs/MOF3.cif --poscar vasp.poscar --repeat output.repeat