QMMM¶
There are three QM/MM calculators native to ASE:
Explicit Interaction QMMM 

Simple, subtrative QMMM 

Forcebased qmmm 
Explicit Interaction QMMM¶
In Explicit Interaction QMMM, the QM and MM regions are explicitly coupled with an electrostatic interaction term. This requires that the electrostatic potential from the classical charges of the MM subsystem is fed into the QM calculator. This is built into GPAW. More info in this paper, which should be cited if the method is used.
Other ASEcalculators that currently support EIQMMM:
See also
The ASE for QM/MM Simulations tutorial, on how to use the Explicit Interaction QMMM calculator
 class ase.calculators.qmmm.EIQMMM(selection, qmcalc, mmcalc, interaction, vacuum=None, embedding=None, output=None)[source]¶
Explicit interaction QMMM calculator.
EIQMMM object.
The energy is calculated as:
_ _ _ _ E = E (R ) + E (R ) + E (R , R ) QM QM MM MM I QM MM
parameters:
 selection: list of int, slice object or list of bool
Selection out of all the atoms that belong to the QM part.
 qmcalc: Calculator object
QMcalculator.
 mmcalc: Calculator object
MMcalculator.
 interaction: Interaction object
Interaction between QM and MM regions.
 vacuum: float or None
Amount of vacuum to add around QM atoms. Use None if QM calculator doesn’t need a box.
 embedding: Embedding object or None
Specialized embedding object. Use None in order to use the default one.
 output: None, ‘‘, str or filedescriptor.
File for logging information  default is no logging (None).
Here, you need to specify the interaction:
from ase.calculators.qmmm import EIQMMM, LJInteraction
from ase.calculators.tip3p import epsilon0, sigma0
lj = LJInteraction({'OO': (epsilon0, sigma0)})
atoms.calc = EIQMMM([0, 1, 2],
QMCalculator(...),
MMCalculator(...),
interaction=lj)
For LennardJones type of interactions you can use:
 class ase.calculators.qmmm.LJInteractions(parameters)[source]¶
LennardJones type explicit interaction.
 parameters: dict
Mapping from pair of atoms to tuple containing epsilon and sigma for that pair.
Example
lj = LJInteractions({(‘O’, ‘O’): (eps, sigma)})
Or, for couplings requiring more generality, you should use:
 class ase.calculators.qmmm.LJInteractionsGeneral(sigmaqm, epsilonqm, sigmamm, epsilonmm, qm_molecule_size, mm_molecule_size=3, rc=inf, width=1.0)[source]¶
General LennardJones type explicit interaction.
 sigmaqm: array
Array of sigmaparameters which should have the length of the QM subsystem
 epsilonqm: array
As sigmaqm, but for epsilonparamaters
 sigmamm: Either array (A) or tuple (B)
 A (no counterions):
Array of sigmaparameters with the length of the smallests repeating atomsgroup (i.e. molecule) of the MM subsystem
 B (counterions):
Tuple: (arr1, arr2), where arr1 is an array of sigmas with the length of counterions in the MM subsystem, and arr2 is the array from A.
 epsilonmm: array or tuple
As sigmamm but for epsilonparameters.
 qm_molecule_size: int
number of atoms of the smallest repeating atomsgroup (i.e. molecule) in the QM subsystem (often just the number of atoms in the QM subsystem)
 mm_molecule_size: int
as qm_molecule_size but for the MM subsystem. Will be overwritten if counterions are present in the MM subsystem (via the CombineMM calculator)
You can control how the QM part is embedded in the MM part by supplying your
own embedding object when you construct the EIQMMM
instance. The
Embedding object will be specific to the QM calculator you want to use. The
default is this one:
Simple, subtractive QMMM calculations¶
This QM/MM calculator is similar to the original ONIOM model, doing simple, subtractive QM/MM between any two calculators.
 class ase.calculators.qmmm.SimpleQMMM(selection, qmcalc, mmcalc1, mmcalc2, vacuum=None)[source]¶
Simple QMMM calculator.
SimpleQMMM object.
The energy is calculated as:
_ _ _ E = E (R )  E (R ) + E (R ) QM QM MM QM MM all
parameters:
 selection: list of int, slice object or list of bool
Selection out of all the atoms that belong to the QM part.
 qmcalc: Calculator object
QMcalculator.
 mmcalc1: Calculator object
MMcalculator used for QM region.
 mmcalc2: Calculator object
MMcalculator used for everything.
 vacuum: float or None
Amount of vacuum to add around QM atoms. Use None if QM calculator doesn’t need a box.
This type of QMMM can combine any pair of ASE calculators:
from ase.calculators.qmmm import SimpleQMMM
atoms = ...
atoms.calc = SimpleQMMM([0, 1, 2],
QMCalculator(...),
MMCalculator(...))
where [0, 1, 2]
would select the first three atoms for the QMpart.
Forcebased QM/MM¶
This QM/MM calculator mixes forces from any pair of ASE calculators. A finite buffer is added around the core QM region to ensure accurate forces; careful testing of the required buffer size is required. See N. Bernstein, J. R. Kermode, and G. Csányi, Rep. Prog. Phys. 72, 026501 (2009) for a review of forcebased QM/MM approaches, which should be cited if this method is used, and T. D. Swinburne and J. R. Kermode, Phys. Rev. B 96, 144102 (2017) for an application which used this implementation.
 class ase.calculators.qmmm.ForceQMMM(atoms, qm_selection_mask, qm_calc, mm_calc, buffer_width, vacuum=5.0, zero_mean=True, qm_cell_round_off=3, qm_radius=None)[source]¶
Forcebased QM/MM calculator
QM forces are computed using a buffer region and then mixed abruptly with MM forces:
 F^i_QMMM = { F^i_QM if i in QM region
{ F^i_MM otherwise
cf. N. Bernstein, J. R. Kermode, and G. Csanyi, Rep. Prog. Phys. 72, 026501 (2009) and T. D. Swinburne and J. R. Kermode, Phys. Rev. B 96, 144102 (2017).
ForceQMMM calculator
Parameters:
 qm_selection_mask: list of ints, slice object or bool list/array
Selection out of atoms that belong to the QM region.
 qm_calc: Calculator object
QMcalculator.
 mm_calc: Calculator object
MMcalculator (should be scaled, see
RescaledCalculator
) Can use \(ForceConstantCalculator\) based on QM force constants, if available. vacuum: float or None
Amount of vacuum to add around QM atoms.
 zero_mean: bool
If True, add a correction to zero the mean force in each direction
 qm_cell_round_off: float
Tolerance value in Angstrom to round the qm cluster cell
 qm_radius: 3x1 array of floats qm_radius for [x, y, z]
3d qm radius for calculation of qm cluster cell. default is None and the radius is estimated from maximum distance between the atoms in qm region.
Basic usage is as follows:
from ase.calculators.qmmm import ForceQMMM
atoms = ...
qm_mask = ...
atoms.calc = ForceQMMM(qm_mask,
QMCalculator(...),
MMCalculator(...),
buffer_width=...)
See ase/test/forcefields/test_forceqmmm.py testcase for a complete example.