AQME.qprep

Parameters

filesmol object, str or list of str, default=None

This module prepares input QM file(s). Formats accepted: mol object(s), Gaussian or ORCA LOG/OUT output files, JSON, XYZ, SDF, PDB. Also, lists can be used (i.e. [FILE1.log, FILE2.log] or *.FORMAT such as *.json).

atom_typeslist of str, default=[]

(If files is None) List containing the atoms of the system

cartesianslist of str, default=[]

(If files is None) Cartesian coordinates used for further processing

w_dir_mainstr, default=os.getcwd()

Working directory

destinationstr, default=None,

Directory to create the input file(s)

varfilestr, default=None

Option to parse the variables using a yaml file (specify the filename)

programstr, default=None

Program required to create the new input files. Current options: 'gaussian', 'orca'

qm_inputstr, default=''

Keywords line for new input files (i.e. 'B3LYP/6-31G opt freq')

qm_endstr, default=''

Final line(s) in the new input files

chargeint, default=None

Charge of the calculations used in the following input files. If charge isn't defined, it defaults to 0

multint, default=None

Multiplicity of the calculations used in the following input files. If mult isn't defined, it defaults to 1

suffixstr, default=''

Suffix for the new input files (i.e. FILENAME_SUFFIX.com for FILENAME.log)

prefixstr, default=''

Prefix added to all the names

chkbool, default=False

Include the chk input line in new input files for Gaussian calculations

chk_pathstr, default=''

PATH to store CHK files. For example, if chk_path='root/user, the chk line of the input file would be %chk=root/user/FILENAME.chk

memstr, default='4GB'

Memory for the QM calculations (i) Gaussian: total memory; (ii) ORCA: memory per processor

nprocsint, default=2

Number of processors used in the QM calculations

gen_atomslist of str, default=[]

Atoms included in the gen(ECP) basis set (i.e. ['I','Pd'])

bs_genstr, default=''

Basis set used for gen(ECP) atoms (i.e. 'def2svp')

bs_nogenstr, default=''

Basis set used for non gen(ECP) atoms in gen(ECP) calculations (i.e. '6-31G*')

lowest_onlybool, default=False

Only create input for the conformer with lowest energy of the SDF file

lowest_nint, default=None

Only create inputs for the n conformers with lowest energy of the SDF file

e_threshold_qprepfloat, default=None

Only create inputs for conformers below the energy threshold (to the lowest conformer) of the SDF file

freeze_atomslist of int, default=[]

Atom indices (zero indexed) to be constrained during optimization. This adds the -1 frozen flag if program=gaussian, or a %geom Constraints section if program=orca