# 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 This block controls the printing of additional information to stdout.
Timers
Type: Multiple Choice None [None, Normal, Detail, TooMuchDetail] Printing timing details to see how much time is spend in which part of the code.
EngineDebugging
CheckInAndOutput Yes/No
ForceContinousPES Yes/No
IgnorePreviousResults Yes/No
IgnoreStressTensorRequest Yes/No
NeverQuiet Yes/No
RandomFailureChance float
RandomNoiseInEnergy float
RandomStopChance float
End

EngineDebugging
Type: Block This block contains some options useful for debugging the computational engines.
CheckInAndOutput
Type: Bool No Enables some additional checks on the input and output of and engine, e.g. for NaN values.
ForceContinousPES
Type: Bool No 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 No 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 No 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 No 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 No Makes the engine ignore the request to work quietly.
RandomFailureChance
Type: Float 0.0 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 0.0 Hartree 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 0.0 Hartree/Angstrom 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 0.0 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.

 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.