compechem.engines.xtb
sub-module#
XtbInput
class#
- class compechem.engines.xtb.XtbInput(method='gfn2', solvent=None, optionals='', XTBPATH=None)#
Interface for running xTB calculations
- Parameters:
method (str, optional) – level of theory, by default “gfn2”
solvent (str, optional) – ALPB solvent, by default no solvent (vacuum)
optionals (str, optional) – optional keywords/flags, by default “”
XTBPATH (str, optional) – the path to the xtb executable. If set to None (default) the xtb executable will be loaded automatically.
- freq(mol, ncores=None, maxcore=None, save_cubes=False, cube_step=0.1, inplace=False, remove_tdir=True)#
Frequency analysis.
- Parameters:
mol (System object) – input system to use in the calculation
ncores (int, optional) – number of cores, by default all available cores
maxcore (dummy variable) – dummy variable used for compatibility with Orca calculations
save_cubes (bool, optional) – if set to True, will save a cube file containing electronic and spin densities, by default False.
cube_step (int, optional) – grid spacing for cube files, in Bohrs (default 0.4)
inplace (bool, optional) – updates info for the input system instead of outputting a new system object, by default False
remove_tdir (bool, optional) – temporary work directory will be removed, by default True
- Returns:
newmol – Output system containing the new energies.
- Return type:
System object
- opt(mol, ncores=None, maxcore=None, save_cubes=False, cube_step=0.1, inplace=False, remove_tdir=True)#
Geometry optimization + frequency analysis.
- Parameters:
mol (System object) – Input system to use in the calculation
ncores (int, optional) – number of cores, by default all available cores
maxcore (dummy variable) – dummy variable used for compatibility with Orca calculations
save_cubes (bool, optional) – if set to True, will save a cube file containing electronic and spin densities, by default False.
cube_step (int, optional) – grid spacing for cube files, in Bohrs (default 0.4)
inplace (bool, optional) – updates info for the input system instead of outputting a new system object, by default False
remove_tdir (bool, optional) – Temporary work directory will be removed, by default True
- Returns:
newmol (System object) – Output system containing the new geometry and energies.
If a dissociation or a cyclization is observed, ignore the calculation and return the
original “mol” system.
- property output_suffix: str#
Suffix used to compose the name of calculation output files
- Returns:
The output suffix string
- Return type:
str
- parse_output(mol)#
The function will parse an xTB output file automatically looking for all the relevant numerical properties derived form a calculation. All the properties of the given molecule will be set or updated.
- Parameters:
mol (System) – The System to which the properties must be written to.
- Raises:
RuntimeError – Exception raised if the given path to the output file is not valid.
- Return type:
None
- spe(mol, ncores=None, maxcore=None, save_cubes=False, cube_step=0.1, inplace=False, remove_tdir=True)#
Single point energy calculation.
- Parameters:
mol (System object) – Input system to use in the calculation.
ncores (int, optional) – number of cores, by default all available cores
maxcore (dummy variable) – dummy variable used for compatibility with Orca calculations
save_cubes (bool, optional) – if set to True, will save a cube file containing electronic and spin densities, by default False.
cube_step (int, optional) – grid spacing for cube files, in Bohrs (default 0.4)
inplace (bool, optional) – updates info for the input system instead of outputting a new system object, by default False
remove_tdir (bool, optional) – Temporary work directory will be removed, by default True
- Returns:
newmol – Output system containing the new energies.
- Return type:
System object