Turbomole Coordinate Format

Overview

Property Value
File extensions .tmol, .coord
Coordinate units Bohr (default), Ångström (angs), or fractional (frac)
Supports periodicity Yes (0D, 1D, 2D, 3D)
Supports charge/spin Yes (via $eht data group)
Format hints tmol, coord

Specification

Note

Reference

The Turbomole coordinate format uses data groups delimited by $ identifiers. This format supports molecules and periodic systems (1D, 2D, 3D).

Format Detection

The format is identified by: - File extension: .tmol, .coord - Basename: coord (case-insensitive)

Data Groups

Data Group Purpose
$coord Cartesian or fractional atomic coordinates
$lattice Lattice vectors (Bohr or Ångström)
$cell Cell parameters (lengths and angles)
$periodic Periodicity (0, 1, 2, or 3)
$eht Charge and unpaired electrons
$end End of file marker

Coordinate Data Group

$coord [bohr|angs|frac]
   x1   y1   z1   element1
   x2   y2   z2   element2
   ...
  • Default: Bohr (atomic units)
  • angs: Ångström
  • frac: Fractional coordinates (periodic systems only)

Lattice Specification

Lattice vectors via $lattice data group: - 3D: Three lines, three values each (3×3 matrix) - 2D: Two lines, two values each (z-axis is aperiodic) - 1D: One value (translation in x-direction)

Cell parameters via $cell data group: - 3D: a, b, c, α, β, γ (lengths in Bohr/Å, angles in degrees) - 2D: a, b, γ - 1D: a

Charge and Spin

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

Examples

Molecular System

Caffeine molecule:

$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

3D Periodic System

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

This implementation extends the original Turbomole format:

  • All data groups can appear in the same file (original format requires some groups in separate control file)
  • The $coord group supports angs and bohr modifiers (original only supports frac)

Limitations

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.