Appendices

Extended XYZ file format

The .xyz file format is a simple text based format for molecular geometries. .xyz files have the number of atoms in the first line, followed by a comment line, followed by one line per atom, specifying the element as well as the x, y, and z coordinates of this atom.

However, the standard .xyz file format does not include lattice vectors. AMS therefore uses an extended .xyz file format which is also suitable for periodic systems. In this extended format the lattice vectors are specified at the end of the .xyz file via the keys VEC1, VEC2 and VEC3. For 1D periodic systems (chains) only VEC1 is needed. For 2D periodic systems (slabs) only VEC1 and VEC2 are needed. An example extended .xyz for graphene looks like this:

2

C     0.0   0.0      0.0
C     1.23  0.71014  0.0
VEC1  2.46  0.0      0.0
VEC2  1.23  2.13042  0.0

Note that the extended .xyz format is also understood by the AMS GUI for importing and exporting geometries from/to .xyz files.

Developer options

Print
   Timers [None | Normal | Detail | TooMuchDetail]
End
Print
Type

Block

Description

This block controls the printing of additional information to stdout.

Timers
Type

Multiple Choice

Default value

None

Options

[None, Normal, Detail, TooMuchDetail]

Description

Printing timing details to see how much time is spend in which part of the code.

EngineDebugging
   AlwaysClaimSuccess Yes/No
   CheckInAndOutput Yes/No
   ForceContinousPES Yes/No
   IgnoreGradientsRequest Yes/No
   IgnorePreviousResults Yes/No
   IgnoreStressTensorRequest Yes/No
   NeverQuiet Yes/No
   RandomFailureChance float
   RandomNoiseInEnergy float
   RandomNoiseInGradients float
   RandomStopChance float
End
EngineDebugging
Type

Block

Description

This block contains some options useful for debugging the computational engines.

AlwaysClaimSuccess
Type

Bool

Default value

No

Description

If an engine fails, pretend that it worked. This can be useful when you know that an SCF might fail.

CheckInAndOutput
Type

Bool

Default value

No

Description

Enables some additional checks on the input and output of an engine, e.g. for NaN values.

ForceContinousPES
Type

Bool

Default value

No

Description

If this option is set, the engine will always run in continuous PES mode. For many engines this disables the use of symmetry, as this one always leads to a discontinuous PES around the symmetric points: Basically there is jump in the PES at the point where the symmetry detection starts classifying the system as symmetric. Normally the continuous PES mode of the engine (often disabling the symmetry) is only used when doing numerical derivatives, but this flag forces the engine to continuously run in this mode.

IgnoreGradientsRequest
Type

Bool

Default value

No

Description

If this option is set, the engine will not do analytical gradients if asked for it, so that gradients will have to be evaluated numerically by AMS.

IgnorePreviousResults
Type

Bool

Default value

No

Description

If this option is set, the engine will not receive information from previous calculations. Typically this information is used to restart the self consistent procedure of the engine.

IgnoreStressTensorRequest
Type

Bool

Default value

No

Description

If this option is set, the engine will not calculate an analytical stress tensor if asked for it, so that the stress tensor will have to be evaluated numerically by AMS.

NeverQuiet
Type

Bool

Default value

No

Description

Makes the engine ignore the request to work quietly.

RandomFailureChance
Type

Float

Default value

0.0

Description

Makes the engine randomly report failures, even though the results are actually fine. Useful for testing error handling on the application level.

RandomNoiseInEnergy
Type

Float

Default value

0.0

Unit

Hartree

Description

Adds a random noise to the energy returned by the engine. The random contribution is drawn from [-r,r] where r is the value of this keyword.

RandomNoiseInGradients
Type

Float

Default value

0.0

Unit

Hartree/Angstrom

Description

Adds a random noise to the gradients returned by the engine. A random number in the range [-r,r] (where r is the value of this keyword) is drawn and added separately to each component of the gradient.

RandomStopChance
Type

Float

Default value

0.0

Description

Makes the engine randomly stop. Can be used to simulate crashes.

Symmetry

Schönfliess symbols and symmetry labels

A survey of all molecular point groups that are recognized by AMS is given below. The table contains the Schönfliess symbols together with the names of the subspecies of the irreducible representations as they are used by AMS to label normal modes.

Table 6 Schönfliess symbols and the labels of the irreducible representations.

Point

Schönfliess

Irreducible representations

Group

Symbol in AMS

C1

NOSYM

A

C∞v

C(LIN)

Sigma Pi

D∞h

D(LIN)

Sigma.g Sigma.u Pi.g Pi.u

I

I

A T1 T2 G H

Ih

I(H)

A.g A.u T1.g T1.u T2.g T2.u G.g G.u H.g H.u

O

O

A1 A2 E T1 T2

Oh

O(H)

A1.g A1.u A2.g A2.u E.g E.u T1.g T1.u T2.g T2.u

T

T

A E T

Th

T(H)

A.g A.u E.g E.u T.g T.u

Td

T(D)

A1 A2 E T1 T2

Ci

C(I)

A.g A.u

Sn

S(N)

n=4: A B E

n=6: A.g A.u E.g E.u

n=8: A B E1 E2 E3

Cn

C(N)

n=2: A B

n=4: A B E

even n: A B E1 E2 …

n=3: A E

odd n: A E1 E2 …

Cnv

C(NV)

n=2: A1 A2 B1 B2

n=4: A1 A2 B1 B2 E

even n: A1 A2 B1 B2 E1 E2 …

n=3: A1 A2 E

odd n: A1 A2 E1 E2 …

Cs

C(S)

A’ A’’

Cnh

C(NH)

n=2: A.g A.u B.g B.u

n=4: A.g A.u B.g B.u E.g E.u

even n: A.g A.u B.g B.u E1.g E1.u E2.g E2.u …

n=3: A’ A’’ E’ E’’

odd n: A’ A’’ E1’ E1’’ E2’ E2’’ …

Dn

D(N)

n=2: A B1 B2 B3

n=4: A1 A2 B1 B2 E

even n A1 A2 B1 B2 E1 E2 …

n=3: A1 A2 E

odd n: A1 A2 E1 E2 …

Dnd

D(ND)

n=2: A1 A2 B1 B2 E

even n: A1 A2 B1 B2 E1 E2 …

n=3: A1.g A1.u A2.g A2.u E.g E.u

odd n: A1.g A1.u A2.g A2.u E1.g E1.u E2.g E2.u …

Dnh

D(NH)

n=2: A.g A.u B1.g B1.u B2.g B2.u B3.g B3.u

n=4: A.g A.u B1.g B1.u B2.g B2.u B3.g B3.u E.g E.u

even n: A.g A.u B1.g B1.u B2.g B2.u B3.g B3.u E1.g E1.u E2.g E2.u …

n=3: A1’ A1’’ A2’ A2’’ E’ E’’

odd n: A1’ A1’’ A2’ A2’’ E1’ E1’’ E2’ E2’’ …

The symmetry labeling may depend on the choice of coordinate system. For instance, B1 and B2 representations in Cnv are interchanged when you rotate the system by 90 degrees around the z-axis so that x-axis becomes y-axis and vice-versa (apart from sign).

Molecular orientation requirements

In order that AMS recognizes the (sub)symmetry of a molecule, the molecule has to have a specific orientation in space.

  • The origin is a fixed point of the symmetry group.

  • The z-axis is the main rotation axis.

  • xy is the \(\sigma\)h -plane (axial groups, C(s)).

  • The x-axis is a C2 axis (D symmetries).

  • The xz-plane is a \(\sigma\)v -plane (Cnv symmetries).

  • In Td and Oh the z-axis is a fourfold axis (S4 and C4 , respectively) and the (111)-direction is a threefold axis.

If the system is symmetrized (and no symmetry is given in the System block key) the molecular structure is rotranslated into this standard orientation.

Molecular orientation conventions

The molecular requirements for AMS may not fully determine the orientation of the molecule, like for D2h molecules. See Mulliken 1 for standard conventions on the molecular orientation and notation. A few of these conventions are listed below:

  • in planar C2v molecules the x axis is perpendicular to the plane of the molecule.

  • in planar D2h molecules the x axis is perpendicular to the plane of the molecule and the z-axis passes through the greatest number of atoms. If the last condition is not decisive, the z-axis should pass through the greatest number of bonds.

  • in planar D4h and D6h molecules the C2-axis passes through the greatest number of atoms. If the last condition is not decisive, the C2-axis should pass through the greatest number of bonds.

1

R.S Mulliken, Report on Notation for the Spectra of Polyatomic Molecules, Journal of Chemical Physics 23, 1997 (1955)