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
   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.
CheckInAndOutput
Type:Bool
Default value:No
Description:Enables some additional checks on the input and output of and 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.