qstack.spahm.rho.bond

Legacy command-line entry point for SPAHM(b) computations.

qstack.spahm.rho.bond.main(args=None)

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

Computes bond-centered SPAHM representations for molecules or molecular datasets. Representations capture chemical bonding information using density fitting on bond centers.

Parameters:

args (list, optional) – Command-line arguments. If None, uses sys.argv. Defaults to None.

Output:

Saves representations to numpy files with names based on –name argument.

Command-line use

This program computes the SPAHM(b) representation for a given molecular system or a list of thereof

usage: python3 -m qstack.spahm.rho.bond [-h] --mol FILENAME [--charge CHARGE]
                                        [--spin SPIN]
                                        [--guess {core,sad,sap,gwh,lb,huckel,lb-hfs}]
                                        [--basis BASIS] [--xc XC] [--ecp ECP]
                                        [--readdm READDM]
                                        [--units {Angstrom,Bohr}]
                                        [--elements ELEMENTS [ELEMENTS ...]]
                                        [--only-z ONLY_Z [ONLY_Z ...]]
                                        [--omod {sum,diff,alpha,beta} [{sum,diff,alpha,beta} ...]]
                                        [--name NAME_OUT] [--split]
                                        [--nomerge] [--symbols]
                                        [--print PRINT] [--cutoff CUTOFF]
                                        [--bpath BPATH] [--zeros] [--onlym0]
                                        [--pairfile PAIRFILE]
                                        [--dump_and_exit] [--same_basis]

Named Arguments

--mol

path to an xyz file / to a list of molecular structures in xyz format

--charge

charge / path to a file with a list of thereof

Default: 'None'

--spin

number of unpaired electrons / path to a file with a list of thereof

Default: 'None'

--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'

--elements

the elements contained in the database

--only-z

restrict the representation to one or several atom types

--omod

Possible choices: sum, diff, alpha, beta

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

Default: ['alpha', 'beta']

--name

name of the output representations file.

--split

split into molecules (use twice to also split the output in one file per molecule)

Default: 0

--nomerge

merge different omods

Default: True

--symbols

if save tuples with (symbol, vec) for all atoms

Default: False

--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'

--zeros

use a version with more padding zeros

Default: False

--onlym0

use only functions with m=0

Default: False

--pairfile

path to the atom pair file

--dump_and_exit

write the atom pair file and exit if –pairfile is set

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

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.