molmod/copacof

COPACOF: a computational protocol for the assignment of NMR resonances in covalent organic frameworks

This repository contains data related to the following publication in ACS-JCTC: https://doi.org/10.1021/acs.jctc.3c01414. The folder vasp/ contains input files for the structural optimization and NMR calculations of the covalent organic framework materials studied. The folder spectrum/ contains the following Python scripts and files, which may be used to produce a computational NMR spectrum based on theoretical shielding data using the gs model as described in the main text:
(a) classify_carbon.py
(b) gs_model.py
(c) Input and output files as an example of the usage of the scripts.

(a) classify_carbon.py Based on connectivity (using graphs), classify the carbon atoms in the COF into classes.
input files:
system.extxyz -- periodic COF material
node.xyz -- TAPD node that will be searched for in the material
linker.xyz -- Me linker that will be searched for in the material
output files: txt files where the first column is the number of the carbon atom, which is a label derived from the index in the node/linker xyz. Next columns are the indices of the carbon atom in the COF material xyz that belong to that class. One class per row.
linkers_classified.dat
nodes_classified.dat

(b) gs_model.py
input files:
shieldings -- all shieldings in the COF system
linkers_classified.dat
nodes_classified.dat
nodes_colordef.dat -- color choice specific to example case. Change to whatever color codes desired.
linkers_colordef.dat
spectrum.dat -- the experimental spectrum to fit to

Run: python classify_carbon.py
python gs_model.py mse

where mse is the choice for the residual function (others are implemented as well, see script). Additionally, boxplots (and other indicators) may be plotted for the data on the spectrum, which may be switched on in the script setting boxplot_on to value of 1.