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.
Point 
Schönfliess 
Irreducible representations 
Group 
Symbol in AMS 

C_{1} 
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 
I_{h} 
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 
O_{h} 
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 
T_{h} 
T(H) 
A.g A.u E.g E.u T.g T.u 
T_{d} 
T(D) 
A1 A2 E T1 T2 
C_{i} 
C(I) 
A.g A.u 
S_{n} 
S(N) 
n=4: A B E 
n=6: A.g A.u E.g E.u 

n=8: A B E1 E2 E3 

C_{n} 
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 … 

C_{nv} 
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 … 

C_{s} 
C(S) 
A’ A’’ 
C_{nh} 
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’’ … 

D_{n} 
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 … 

D_{nd} 
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 … 

D_{nh} 
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 C_{nv} are interchanged when you rotate the system by 90 degrees around the zaxis so that xaxis becomes yaxis and viceversa (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 zaxis is the main rotation axis.
xy is the \(\sigma\)_{h} plane (axial groups, C(s)).
The xaxis is a C_{2} axis (D symmetries).
The xzplane is a \(\sigma\)_{v} plane (C_{nv} symmetries).
In T_{d} and O_{h} the zaxis is a fourfold axis (S_{4} and C_{4} , 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 D_{2h} molecules. See Mulliken 1 for standard conventions on the molecular orientation and notation. A few of these conventions are listed below:
in planar C_{2v} molecules the x axis is perpendicular to the plane of the molecule.
in planar D_{2h} molecules the x axis is perpendicular to the plane of the molecule and the zaxis passes through the greatest number of atoms. If the last condition is not decisive, the zaxis should pass through the greatest number of bonds.
in planar D_{4h} and D_{6h} molecules the C_{2}axis passes through the greatest number of atoms. If the last condition is not decisive, the C_{2}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)