File Structure¶

It is very important to me that humans can understand my code and how to get what they want from it. As LLMs get better at parsing codebases, human understanding and decent documentation can seem less important. But in my experiance, predominately using LLMs makes gaining an intutive sense for code structure much harder. Then, when you want just one thing from a complicated codebase (or heaven forbid nosense bugs happen), things get messy and LLMs often solve nonoptimally. (That said, I did use LLMs to help build this website and still expect others to use them to understand/use COGITO.)

To try and achieve this goal, I have created this interactive visualization of different file inputs and outputs of my different COGITO modules. I hope you enjoy clicking through them and this proves to be a handy reference for understanding the various files of COGITO.

The boxes are bolded if the input/output file is required. The boxes are colored red for quality accessment files and yellow for debug/developer files. More tags and colors will be added when I get more time for it. This is still a bit underdevelopment and as such there may be small errors here and there. For some ridiculous rendering go click ‘bond_cohp_plot.html’ in the COGITOpost output section (it may take a second to load).

COGITOpost¶

requiredinput

Used by:COGITO_TB_Model.__init__() [api]

Description

Structural input file for the TB model. Written by COGITO. Contains lattice vectors, atom positions and types, orbital positions and types, spherical harmonic combination vectors, Fermi energy, and energy shift. Read first on initialization of any COGITOpost class.

tb_input.txt

TBparams.npy

overlaps.npy

TBparams.txt

overlaps.txt

EIGENVAL

orbitals.npy

orb_converg_info.json

→

COGITOpost

→

all_unique_bonds.json

all_bonds.json

all_atoms.json

bond_info.txt

ICOHP.npy

ICOOP.npy

bond_occup.npy

small_ham.npy

small_over.npy

DFT_band_error.txt

compareDFT.png

tbparams_decay.png

overlaps_decay.png

crystal_bonds.html

bond_cohp_plot.html

crystal_bond_density.html

COHP_DOS.png

COOP_DOS.png

projectedDOS.png

bandstruc.png

COHP_BS.html

COOP_BS.html

projectedBS.html

field_splitting.png

COGITOanalyze¶

orb_converg_info.jsonerror_output.txtDFT_band_error.txt

optionalinputquality

Used by:analyze_orb_converg_info() [api]
analyze_all() [api]

Description

JSON file tracking orbital convergence across outer loops. Written by COGITO. Read to check radial change per iteration, orbital radius change, Bloch NRMSE/NME, and Gaussian fit error. Required for analyze_orb_converg_info(); if missing, analyze_all() catches the error and skips.

root
├── orb_type
├── orb_rad
├── orb_change
├── orb_change_periter
├── radial_change_periter
├── bloch_nrmse_iter
└── ...

orb_converg_info.json

error_output.txt

DFT_band_error.txt

→

COGITOanalyze

→

orb_change.png

analysis.txt

orb_change.pnganalysis.txt

optionaloutput

Made by:analyze_orb_converg_info() [api]
analyze_all() [api]
Requires:make_change_plot=True (default) Make in CLI:COGITOanalyze.py --dir DIR Skip in CLI:COGITOanalyze.py --dir DIR --no_make_change_plot

Description

Bar chart of percent orbital radius change from the initial POTCAR value to the converged COGITO value, grouped by element and orbital type (s/p/d indicated by bar hatch). Useful for quickly seeing which orbitals changed the most during convergence and whether the changes are chemically reasonable.

COGITOico¶

requiredinput

Used by:COGITO_ICO.__init__() [api]

Description

lattice_vecs
    4.05505270     0.00000000     0.00000000
    0.00000000     4.05505270     0.00000000
    0.00000000     0.00000000     5.47357943
atoms
    0.50000000     0.00000000     0.21770996 Pb 14.0000
   -0.00000000     0.50000000     0.78229004 Pb 14.0000
    0.50000000     0.50000000     0.00000000 O  6.0000
    0.00000000     0.00000000    -0.00000000 O  6.0000
orbitals
    0.50000000     0.00000000     0.21770996 0 d
    0.50000000     0.00000000     0.21770996 0 d
    0.50000000     0.00000000     0.21770996 0 d
    0.50000000     0.00000000     0.21770996 0 d
    0.50000000     0.00000000     0.21770996 0 d
    0.50000000     0.00000000     0.21770996 0 s
    0.50000000     0.00000000     0.21770996 0 p
    0.50000000     0.00000000     0.21770996 0 p
    0.50000000     0.00000000     0.21770996 0 p
   -0.00000000     0.50000000     0.78229004 1 d
   -0.00000000     0.50000000     0.78229004 1 d
   -0.00000000     0.50000000     0.78229004 1 d
   -0.00000000     0.50000000     0.78229004 1 d
   -0.00000000     0.50000000     0.78229004 1 d
   -0.00000000     0.50000000     0.78229004 1 s
   -0.00000000     0.50000000     0.78229004 1 p
   -0.00000000     0.50000000     0.78229004 1 p
   -0.00000000     0.50000000     0.78229004 1 p
    0.50000000     0.50000000     0.00000000 2 s
    0.50000000     0.50000000     0.00000000 2 p

...

tb_input.txt

ICOHP.npy

ICOOP.npy

bond_occup.npy

orbitals.npy

→

COGITOico

→

ICOHP.npy / ICOOP.npy

crystal_bonds.html

crystal_bond_density.html

ICOHP.npy / ICOOP.npycrystal_bonds.htmlcrystal_bond_density.html

optionaloutput

Made by:COGITO_ICO.save_ICOnpy() [api]

Description

Re-saves the ICOHP and ICOOP matrices loaded into COGITO_ICO, one file per spin channel. Useful for converting from the legacy txt format to the faster .npy format, or after any in-place modification of the matrices. Overwrites files with the same name.

File Structure¶

COGITO¶

COGITOpost¶

COGITOanalyze¶

COGITOico¶