Keywords¶

Engine Hybrid¶

AllowSanityCheckWarnings

Type:

Bool

Default value:

No

Description:

Sanity checks will be performed on the setup. If this option is on, only warnings are printed. If not the program will stop on warnings.

Capping

Type:

Block

Description:

This block is about capping details. Capping occurs with hydrogen atoms when a bond is broken between an atom inside the region and one outside.

AllowHighBondOrders

Type:

Bool

Default value:

No

Description:

Allows capping of interregional aromatic, double and triple bonds. This is normally not a good idea, since the capping is done with hydrogen atoms.

AtomicInfoForCappingAtom

Type:

String

Default value:

ForceField.Type=H_ ForceField.Charge=0.0

Description:

The AtomicInfo for the capping atoms. Typically a string like ForceField.Type=X much like forcefield info is entered in the System block for normal atoms.

CappingElement

Type:

String

Default value:

H

Description:

The element to be used for capping. The hydrogen atom has the advantage that it is very small.

CheckCapping

Type:

Bool

Default value:

Yes

Description:

The same outside atom can be involved in multiple capping coordinate definitions. This is not a good idea, and this will not be accepted by using this check.

Distance

Type:

Float

Default value:

-1.0

Description:

A negative value means automatic. In that case the sum of covalent radii is used

Option

Type:

Multiple Choice

Default value:

Fixed

Options:

[Fractional, Fixed]

GUI name:

Capping option

Description:

The capping atom is always along the broken bond vector. The bond distance between the capping atom and the two atoms are obtained from covalent radii, let us call them D1H and D2H. With option=Fractional the capping is on the bond vector with the fraction D1H/(D1H+D2H). With the Fixed option it at the distance D1H from atom 1. A distance of zero always means the coordinate of the inside atom.

Committee

Type:

Block

Description:

Settings for using the hybrid engine as a committee. The factors and region for each engine must be the same. When committee is enabled the standard deviation is also reported as the uncertainty.

Enabled

Type:

Bool

Default value:

No

Description:

Enable committee

Energy

Type:

Block

Description:

This block is there to construct the energy.

DynamicFactors

Type:

Multiple Choice

Default value:

Default

Options:

[Default, UseLowestEnergy, UseHighestEnergy]

GUI name:

Adjust factors

Description:

Default - use factors as set in the corresponding Term blocks; UseLowestEnergy - set all factors to 0 except for that of the engine with the lowest energy, which is set to 1; UseHighestEnergy - set all factors to 0 except for that of the engine with the highest energy, which is set to 1. The last two options make sense only for non-QMMM hybrid calculation (that is, if the QMMM block is not present) and only when using engines whose energies can be compared directly.

Term

Type:

Block

Recurring:

True

Description:

This block is there to construct the energy term. Can have multiple occurrences

Charge

Type:

Float

Default value:

0.0

Description:

Net charge to be used for this energy term.

EngineID

Type:

String

Description:

Identifier for the engine

Factor

Type:

Float

Default value:

1.0

Description:

Region

Type:

String

Description:

Identifier for the region

UseCappingAtoms

Type:

Bool

Default value:

Yes

Description:

Whether to use capping for broken bonds

Engine

Type:

Block

Recurring:

True

Description:

The input for the computational (sub) engine. The header of the block determines the type of the engine. An optional second word in the header serves as the EngineID, if not present it defaults to the engine name. Currently it is not allowed to have a Hybrid engine as a sub engine.

GuessAttributesOnce

Type:

Bool

Default value:

Yes

Description:

If any ForceField subengines are defined, and if automatic atom typing is possible, then the atom typing is done at the level of the Hybrid engine, and not of the ForceField subengines. This ensures that the same atom types and charges are used in each subsystem, so that pair energy terms that should cancel, will cancel. If set to False, then for each energy term the atom types and charges of the subsystem will be determined separately.

QMMM

Type:

Block

Description:

This block is there to identify the QMMM engines.

Embedding

Type:

Multiple Choice

Default value:

Electrostatic

Options:

[Mechanical, Electrostatic]

Description:

Determines how the QM region is embedded into the MM region. Mechanical embedding embedding can also be achieved using the Energy%Terms keywords, but the common case of a two region mechanical QM/MM embedding is easier to set up using this keyword.

MMCharge

Type:

Float

Default value:

0.0

Description:

Net charge to be used for the MM region.

MMEngineID

Type:

String

Description:

Identifier for the MM engine

QMCharge

Type:

Float

Default value:

0.0

Description:

Net charge to be used for the QM region.

QMEngineID

Type:

String

Description:

Identifier for the QM engine

QMRegion

Type:

String

Description:

Identifier for the QM region. The rest of the system is considered the MM region.

UseCappingAtoms

Type:

Bool

Default value:

Yes

Description:

Whether to use capping for broken bonds.

RestartSubEngines

Type:

Bool

Default value:

Yes

Description:

Save all the results of the subengines and pass those in a next geometry step or MD step.

TweakRequestForSubEngines

Type:

Bool

Default value:

Yes

Description:

Only request what is really needed, gradients and charges.