qstack.spahm.rho.main¶

Command-line entry point for SPAHM(a,b) computation.

Main executable script for ρ-SPAHM, also found in qstack.spahm.rho.compute_rho_spahm

Command-line use¶

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

usage: python3 -m qstack.spahm.rho [-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]
                                   [--aux-basis AUXBASIS]
                                   [--model {pure,sad-diff,occup,lowdin-short,lowdin-long,lowdin-short-x,lowdin-long-x,mr2021}]
                                   [--cutoff CUTOFF] [--bpath BPATH] [--zeros]
                                   [--onlym0] [--pairfile PAIRFILE]
                                   [--dump_and_exit] [--same_basis]
                                   --rep {atom,bond}

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

--aux-basis

auxiliary basis set for density fitting

Default: 'ccpvdzjkfit'

--model

Possible choices: pure, sad-diff, occup, lowdin-short, lowdin-long, lowdin-short-x, lowdin-long-x, mr2021

model for the atomic density fitting

Default: 'Lowdin-long-x'

--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

--rep

Possible choices: atom, bond

the type of representation

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.

qstack.spahm.rho.__main__¶

Command-line use¶

Named Arguments¶

qstack.spahm.rho.main¶