qstack.spahm.rho.atom¶

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

qstack.spahm.rho.atom.main(args=None)[source]¶

Command-line interface for computing SPAHM(a) atomic representations.

Computes atom-centered SPAHM representations for a single molecule from an XYZ file. The representation is based on fitted atomic densities from a guess Hamiltonian.

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

Output:: Saves representation to numpy file specified by –name argument.

Command-line use¶

This program computes the SPAHM(a) representation for a given molecular system

usage: python3 -m qstack.spahm.rho.atom [-h]
                                        [--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}]
                                        --mol MOL [--charge CHARGE]
                                        [--spin SPIN]

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'

--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'

--mol

the path to the xyz file with the molecular structure

--charge

total charge of the system (default: 0)

Default: 0

--spin

number of unpaired electrons (default: None) (use 0 to treat a closed-shell system in a UHF manner)

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.