qstack.spahm.rho.bond_selected¶

Representation for a specific bond in a molecule.

qstack.spahm.rho.bond_selected.get_spahm_b_selected(mols, bondidx, xyzlist, readdm=None, guess='LB', xc='hf', spin=None, cutoff=5.0, printlevel=0, omods=['alpha', 'beta'], bpath='/home/runner/work/Q-stack/Q-stack/qstack/spahm/rho/basis_opt', only_m0=False, same_basis=False)[source]¶

Compute SPAHM(b) representations for specific bonds in molecules.

Generates bond-centered representations for user-specified atom pairs across a dataset of molecules, useful for targeted bond analysis.

Parameters:

mols (list) – List of pyscf Mole objects.
bondidx (numpy ndarray) – 2D array (nmols, 2) of 0-indexed atom pairs defining bonds.
xyzlist (list) – List of XYZ filenames corresponding to mols.
readdm (str, optional) – Directory to load pre-computed density matrices. Defaults to None.
guess (str) – Guess Hamiltonian method name. Defaults to defaults.guess.
xc (str) – Exchange-correlation functional. Defaults to defaults.xc.
spin (numpy ndarray, optional) – Array of numbers of unpaired electrons per molecule. Defaults to None.
cutoff (float) – Maximum bond distance in Å. Defaults to defaults.cutoff.
printlevel (int) – Verbosity level. Defaults to 0.
omods (list) – Open-shell modes (e.g. ‘alpha’, ‘beta’). Defaults to defaults.omod.
bpath (str) – Path to bond basis set directory. Defaults to defaults.bpath.
only_m0 (bool) – Use only m=0 basis functions. Defaults to False.
same_basis (bool) – Use generic CC.bas for all pairs. Defaults to False.

Returns:

List of (filename, representation) tuples for each specified bond.

Return type:

list

qstack.spahm.rho.bond_selected.main()[source]¶

Command-line interface for computing SPAHM(b) representations for specific bonds.

Reads a file listing XYZ structures and bond indices, computes representations for each specified bond, and saves them to individual files. The input file format is: XYZ_path atom1_index atom2_index (1-indexed).

Parameters:: None – Parses command-line arguments.

Output:: Saves bond representations to numpy files in specified directory.

Command-line use¶

This program computes the SPAHM(b) representation for a list of bonds

usage: python3 -m qstack.spahm.rho.bond_selected [-h]
                                                 [--guess {core,sad,sap,gwh,lb,huckel,lb-hfs}]
                                                 [--basis BASIS] [--xc XC]
                                                 [--ecp ECP] [--readdm READDM]
                                                 [--units {Angstrom,Bohr}]
                                                 [--omod {sum,diff,alpha,beta} [{sum,diff,alpha,beta} ...]]
                                                 [--print PRINT]
                                                 [--cutoff CUTOFF]
                                                 [--bpath BPATH] [--onlym0]
                                                 [--same_basis] --mol FILENAME
                                                 [--charge CHARGE]
                                                 [--spin SPIN] [--dir DIR]

Named Arguments¶

--guess

Possible choices: core, sad, sap, gwh, lb, huckel, lb-hfs

the initial guess Hamiltonian to be used

Default: 'LB'

--basis

basis set for computing density matrix

Default: 'minao'

--xc

DFT functional for the SAD guess

Default: 'hf'

--ecp

effective core potential to use

--readdm

directory to read density matrices from

--units

Possible choices: Angstrom, Bohr

the units of the input coordinates

Default: 'Angstrom'

--omod

Possible choices: sum, diff, alpha, beta

model(s) for open-shell systems (alpha, beta, sum, diff

Default: ['alpha', 'beta']

--print

printing level

Default: 0

--cutoff

bond length cutoff in Å

Default: 5.0

--bpath

directory with basis sets

Default: '/home/runner/work/Q-stack/Q-stack/qstack/spahm/rho/basis_opt'

--onlym0

use only functions with m=0

Default: False

--same_basis

if to use generic CC.bas basis file for all atom pairs (Default: uses pair-specific basis, if exists)

Default: False

--mol

path to a list of molecular structures in xyz format and indices of bonds in question

--charge

file with a list of charges

--spin

file with a list of numbers of unpaired electrons

--dir

directory to save the output in

Default: './'

Note

If you built those docs yourself and the command-line section is empty, please make sure you have installed the right components of qstack.