sdfm

Spatial Disorder Framework Manipulation
(working title)

Basic functionality to deconstruct (metal-organic) frameworks into building blocks, manipulate structures and extract finite molecular clusters.

See the notebook for a limited tutorial.

TODO

general

• type hints are wack
• combine separate selection objects?
• maybe store blocks in a numbered dict? Then the CG graph also contains numbers
• SelectLoop containing specific ids?
• SelectClosest to get the block closest to the center of the selection?

template

• what for nonperiodic structures?
• find a consistent way to order blocks - currently it is random after size (supposedly only after merging)
• block.mic() call fails if not periodic
• merge_blocks does weird things for UiO-68

cluster

• allow option to focus on elements?
• some easy way to define templates

modify

• fix dangling bond problem
• modification reorders blocks, so that repeated identical function calls (swapping blocks) will have a different effect every time..

termination

• redo this fully

tools

• duplicated code
• get_distance that automatically does PBC

tests

• where are they

OPEN BUGS

Traceback (most recent call last): File "/home/pieter/PycharmProjects/Research/workdir/2024_07_09_krause/generate_clusters.py", line 108, in main() File "/home/pieter/PycharmProjects/Research/workdir/2024_07_09_krause/generate_clusters.py", line 83, in main cluster = extract_cluster(template, recipe, at) File "/home/pieter/PycharmProjects/Research/code/sdfm/sdfm/cluster.py", line 153, in extract_cluster unite_blocks(template, blocks, blocks_core[0]) # TODO: this will not work for disconnected clusters File "/home/pieter/PycharmProjects/Research/code/sdfm/sdfm/cluster.py", line 186, in unite_blocks block = check.popleft() IndexError: pop from an empty deque