Turbomole's coordinate data group

Specification

Note

Reference

The Turbomole format mainly builds around the control file. The control file contains several data groups which are delimited by their identifier, groups are either present in the control file or references from the control file. This format is defined by the geometry related information from the control file, mainly the:

  • coord data group
  • lattice data group
  • cell data group
  • periodic data group
  • eht data group

For simplicity file references are not allowed and all data groups should be in the same file. The data groups are not required to be in any particular order.

A group is started by a $ symbol and accept modifiers. It is terminated by another group or the end group which stops the scanning for further groups:

$group1 [modifier]...
[entries]...
$group2 [modifier]...
[entries]...
$end

The coord data group contains the cartesian coordinates of all atoms and their element symbols at the end of each line. Atomic coordinates can either be specified in Bohr, by default or with the bohr modifier on the coord data group, in Ångström with the modifier angs or as fractions of the lattice vectors with the modifier frac. Fractional coordinates can only be present for periodicities greater than zero.

The periodicity of the system is specified as modifier to the periodic data group, the group itself is empty.

The lattice parameters can either be specified in the lattice or the cell data group, which require different amounts of entries depending on the systems periodicity. Both data groups are either given in atomic units (Bohr) or in Ångström with the angs modifier.

For 3D periodic systems three lines with each three reals are required in the lattice data group. For a 2D periodic system two lines with each two reals are required and the aperiodic direction is the z-axis. Finally, for 1D periodic systems one real is required, giving the translation vector in the x-direction. The periodic directions are fixed in this format.

Similarly, the cell data groups allows for six, three, and one entries for 3D, 2D, and 1D periodic systems, respectively. The cell parameters are given as the length of the lattice vectors and their angles, with the angles given in degrees.

Charge and spin can be given in the eht data group with

$eht charge=<int> unpaired=<int>

The format is identified by coord or tmol extension or by using coord as basename.

Example

Caffeine molecule in Turbomole’s coord format

$coord
    2.02799694102955E+00    9.23131009712288E-02   -1.43108928076789E-01      C
    4.75010903288289E+00    2.37349549273006E-02   -1.43241208876543E-01      N
    6.33434168525178E+00    2.07098820094962E+00   -1.42353037792480E-01      C
    8.72860526354322E+00    1.38002889206282E+00   -1.42655393906204E-01      N
    8.65318631042630E+00   -1.19324840281009E+00   -1.42315243278265E-01      C
    6.23857038622984E+00   -2.08353597966915E+00   -1.42182962478511E-01      C
    5.63266763158490E+00   -4.69950217834841E+00   -1.39405065683676E-01      C
    3.44931633987275E+00   -5.48092265700988E+00   -1.43184517105220E-01      O
    7.77508746440172E+00   -6.24427735787637E+00   -1.31071375299170E-01      N
    1.03022932464460E+01   -5.39739678059374E+00   -1.36721655174379E-01      C
    1.20741000728661E+01   -6.91573469742800E+00   -1.36664963403056E-01      O
    1.07003828646773E+01   -2.79078472418281E+00   -1.41483763965525E-01      N
    1.32459756778874E+01   -1.76969033362408E+00   -1.42182962478511E-01      C
    7.40891531342536E+00   -8.95905731397191E+00   -1.16369309269361E-01      C
    1.38702087719268E+00    2.05575701172080E+00   -1.41786120079249E-01      H
    1.34622169909711E+00   -8.63566855308744E-01    1.55590566396441E+00      H
    1.34624059635422E+00   -8.61336978970033E-01   -1.84340853360131E+00      H
    5.65596794959872E+00    4.00172095964572E+00   -1.41313688651556E-01      H
    1.46743059591176E+01   -3.26230908353472E+00   -1.43449078704728E-01      H
    1.35089688050556E+01   -6.08151528240755E-01    1.54898926786298E+00      H
    1.35077971751149E+01   -6.06148418987336E-01   -1.83214576836511E+00      H
    5.41408305861986E+00   -9.49239460132319E+00   -1.10227700709351E-01      H
    8.31919618830440E+00   -9.74947288701666E+00    1.56539208703248E+00      H
    8.31511438076913E+00   -9.76854021943835E+00   -1.79108202867002E+00      H
$end

Ammonia molecular crystal:

$coord
    4.15467326939489E+00    3.33328828180759E+00    1.66323354579962E+00      H
    3.33328828180759E+00    1.66323354579962E+00    4.15467326939489E+00      H
    1.66323354579962E+00    4.15467326939489E+00    3.33328828180759E+00      H
    9.14844767316819E+00    3.06025119596830E+00    9.33489353886275E+00      H
    8.23222919393441E+00    4.72395843553239E+00    6.86439107965696E+00      H
    6.65103940814062E+00    2.17993870408119E+00    7.71770302696940E+00      H
    7.71770302696940E+00    6.65103940814062E+00    2.17993870408119E+00      H
    9.33489353886275E+00    9.14844767316819E+00    3.06025119596830E+00      H
    6.86439107965696E+00    8.23222919393441E+00    4.72395843553239E+00      H
    4.72395843553239E+00    6.86439107965696E+00    8.23222919393441E+00      H
    2.17993870408119E+00    7.71770302696940E+00    6.65103940814062E+00      H
    3.06025119596830E+00    9.33489353886275E+00    9.14844767316819E+00      H
    2.59764186558897E+00    2.59764186558897E+00    2.59764186558897E+00      N
    7.55541554326270E+00    3.76254957116838E+00    8.43506486387956E+00      N
    8.43506486387956E+00    7.55541554326270E+00    3.76254957116838E+00      N
    3.76254957116838E+00    8.43506486387956E+00    7.55541554326270E+00      N
$periodic 3
$lattice
    9.47387528935762    0.00000000000000    0.00000000000000
    0.00000000000000    9.47387528935762    0.00000000000000
    0.00000000000000    0.00000000000000    9.47387528935762
$end

Extensions

The original format does only allow for the periodic or eht group to appear in the control file, to make the format self-contained, all groups must appear in the same file.

The coord group only supports the frac modifier in Turbomole, but this reader also allows angs and bohr.

Missing Features

The following features are currently not supported:

  • Preserving information about frozen atoms from coord data group

Note

Feel free to contribute support for missing features or bring missing features to our attention by opening an issue.