Geometry Input
Supported Geometry Formats
Currently the following input formats are supported by xtb.
Format |
Basename |
Suffix |
molecular |
periodic |
|---|---|---|---|---|
Turbomole |
coord |
coord, tmol |
x |
3D |
xyz file |
xyz |
x |
||
mol file |
mol |
x |
||
Structure-Data file |
sdf |
x |
||
Protein Database file |
pdb |
x |
||
Vasp’s POSCAR/CONTCAR |
poscar, contcar |
vasp, poscar, contcar |
3D |
|
genFormat |
gen |
x |
3D |
|
Gaussian external |
ein |
x |
Note
The default format is always Turbomole and neither the suffix nor the base name is case-sensitive for file type detection.
Turbomole Coordinate Input
The default input format is the Turbomole coordinate file as a $coord data
group.
$coord
0.00000000000000 0.00000000000000 -0.73578586109551 o
1.44183152868459 0.00000000000000 0.36789293054775 h
-1.44183152868459 0.00000000000000 0.36789293054775 h
$end
Like in Turbomole the coordinates can be given in Bohr (default)
or Ångström ($coord angs) or fractional coordinates ($coord frac).
Optional data groups like the systems periodicity ($periodic),
lattice parameters ($lattice [bohr|angs]) and cell parameters
($cell [bohr|angs]) can be provided as well.
The following input for a MgO crystal utilize this data groups:
$coord frac
0.00 0.00 0.00 mg
0.50 0.50 0.50 o
$periodic 3
$cell
5.798338236 5.798338236 5.798338236 60. 60. 60.
$end
Note
crest only supporting a plain coord data group without modifiers.
xyz Input
The well-known xyz or xmol format is supported by xtb as well.
The atom is identified by its element symbol and followed by its cartesian
coordinates in Ångström.
An example for caffeine is given with:
24
C 1.07317 0.04885 -0.07573
N 2.51365 0.01256 -0.07580
C 3.35199 1.09592 -0.07533
N 4.61898 0.73028 -0.07549
C 4.57907 -0.63144 -0.07531
C 3.30131 -1.10256 -0.07524
C 2.98068 -2.48687 -0.07377
O 1.82530 -2.90038 -0.07577
N 4.11440 -3.30433 -0.06936
C 5.45174 -2.85618 -0.07235
O 6.38934 -3.65965 -0.07232
N 5.66240 -1.47682 -0.07487
C 7.00947 -0.93648 -0.07524
C 3.92063 -4.74093 -0.06158
H 0.73398 1.08786 -0.07503
H 0.71239 -0.45698 0.82335
H 0.71240 -0.45580 -0.97549
H 2.99301 2.11762 -0.07478
H 7.76531 -1.72634 -0.07591
H 7.14864 -0.32182 0.81969
H 7.14802 -0.32076 -0.96953
H 2.86501 -5.02316 -0.05833
H 4.40233 -5.15920 0.82837
H 4.40017 -5.16929 -0.94780
mol and sdf Input
The mol and sdf format of the ct-file formats are partly supported in xtb.
Some limitations apply to those input formats are applied to those formats to
make them play nicely together with QM nature of the xTB methods.
This means not any mol or sdf input will be accepted as geometry input.
A valid sdf input is given for the water molecule with
Water
xtb 11041909383D
Comment line
3 2 0 0 0 999 V2000
-0.2191 -0.3098 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7400 -0.2909 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5210 0.6007 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
M END
> <Formula>
H2 O
> <Mw>
18.01528
> <SMILES>
O([H])[H]
> <CSID>
937
$$$$
The input reader is strict in differentiating mol and sdf input, mol input with the sdf extension will be rejected by the reader. The topology and the sdf key-value pairs will be preserved and printed again in the final optimized geometry.
Multiple entries in an sdf input will be ignored by the reader.
Protein Database Input
The input reader supports parts of the pdb-format for reading single PDB file. Minimal sanity checks on the PDB input will be performed, i.e. the reader will outright reject any geometry without hydrogen atoms.
An valid example input (with hydrogen atoms and partial occupied sides removed) is given here:
ATOM 1 N GLY Z 1 -0.821 -2.072 16.609 1.00 9.93 N
ATOM 2 CA GLY Z 1 -1.705 -2.345 15.487 1.00 7.38 C
ATOM 3 C GLY Z 1 -0.968 -3.008 14.344 1.00 4.89 C
ATOM 4 O GLY Z 1 0.258 -2.982 14.292 1.00 5.05 O
ATOM 5 HA2 GLY Z 1 -2.130 -1.405 15.135 1.00 0.00 H
ATOM 6 HA3 GLY Z 1 -2.511 -2.999 15.819 1.00 0.00 H
ATOM 7 H1 GLY Z 1 -1.364 -1.742 17.394 1.00 0.00 H
ATOM 8 H2 GLY Z 1 -0.150 -1.365 16.344 1.00 0.00 H
ATOM 9 H3 GLY Z 1 -0.334 -2.918 16.868 1.00 0.00 H
ATOM 10 N ASN Z 2 -1.721 -3.603 13.425 1.00 3.53 N
ATOM 11 CA ASN Z 2 -1.141 -4.323 12.291 1.00 1.85 C
ATOM 12 C ASN Z 2 -1.748 -3.900 10.968 1.00 3.00 C
ATOM 13 O ASN Z 2 -2.955 -3.683 10.873 1.00 3.99 O
ATOM 14 CB ASN Z 2 -1.353 -5.827 12.446 1.00 5.03 C
ATOM 15 CG ASN Z 2 -0.679 -6.391 13.683 1.00 5.08 C
ATOM 16 OD1 ASN Z 2 0.519 -6.202 13.896 1.00 6.10 O
ATOM 17 ND2 ASN Z 2 -1.448 -7.087 14.506 1.00 8.41 N
ATOM 18 H ASN Z 2 -2.726 -3.557 13.512 1.00 0.00 H
ATOM 19 HA ASN Z 2 -0.070 -4.123 12.263 1.00 0.00 H
ATOM 20 HB2 ASN Z 2 -0.945 -6.328 11.568 1.00 0.00 H
ATOM 21 HB3 ASN Z 2 -2.423 -6.029 12.503 1.00 0.00 H
ATOM 22 HD21 ASN Z 2 -2.427 -7.218 14.293 1.00 0.00 H
ATOM 23 HD22 ASN Z 2 -1.056 -7.487 15.346 1.00 0.00 H
ATOM 24 N LEU Z 3 -0.907 -3.803 9.944 1.00 3.47 N
ATOM 25 CA LEU Z 3 -1.388 -3.576 8.586 1.00 3.48 C
ATOM 26 C LEU Z 3 -0.783 -4.660 7.709 1.00 3.29 C
ATOM 27 O LEU Z 3 0.437 -4.788 7.643 1.00 3.80 O
ATOM 28 CB LEU Z 3 -0.977 -2.185 8.081 1.00 3.88 C
ATOM 29 CG LEU Z 3 -1.524 -1.669 6.736 1.00 8.66 C
ATOM 30 CD1 LEU Z 3 -1.225 -0.191 6.570 1.00 9.89 C
ATOM 31 CD2 LEU Z 3 -0.962 -2.409 5.541 1.00 13.56 C
ATOM 32 H LEU Z 3 0.086 -3.888 10.109 1.00 0.00 H
ATOM 33 HA LEU Z 3 -2.475 -3.661 8.568 1.00 0.00 H
ATOM 34 HB2 LEU Z 3 -1.284 -1.469 8.843 1.00 0.00 H
ATOM 35 HB3 LEU Z 3 0.111 -2.162 8.026 1.00 0.00 H
ATOM 36 HG LEU Z 3 -2.606 -1.798 6.737 1.00 0.00 H
ATOM 37 HD11 LEU Z 3 -1.623 0.359 7.423 1.00 0.00 H
ATOM 38 HD12 LEU Z 3 -1.691 0.173 5.654 1.00 0.00 H
ATOM 39 HD13 LEU Z 3 -0.147 -0.043 6.513 1.00 0.00 H
ATOM 40 HD21 LEU Z 3 -1.168 -3.475 5.643 1.00 0.00 H
ATOM 41 HD22 LEU Z 3 -1.429 -2.035 4.630 1.00 0.00 H
ATOM 42 HD23 LEU Z 3 0.115 -2.250 5.489 1.00 0.00 H
ATOM 43 N VAL Z 4 -1.635 -5.424 7.029 1.00 3.17 N
ATOM 44 CA VAL Z 4 -1.165 -6.460 6.119 1.00 3.61 C
ATOM 45 C VAL Z 4 -1.791 -6.230 4.755 1.00 5.31 C
ATOM 46 O VAL Z 4 -3.014 -6.209 4.620 1.00 7.31 O
ATOM 47 CB VAL Z 4 -1.567 -7.872 6.593 1.00 5.31 C
ATOM 48 CG1 VAL Z 4 -1.012 -8.934 5.633 1.00 6.73 C
ATOM 49 CG2 VAL Z 4 -1.083 -8.120 8.018 1.00 5.48 C
ATOM 50 H VAL Z 4 -2.628 -5.282 7.146 1.00 0.00 H
ATOM 51 HA VAL Z 4 -0.080 -6.402 6.034 1.00 0.00 H
ATOM 52 HB VAL Z 4 -2.655 -7.939 6.585 1.00 0.00 H
ATOM 53 HG11 VAL Z 4 -1.303 -9.926 5.980 1.00 0.00 H
ATOM 54 HG12 VAL Z 4 -1.414 -8.766 4.634 1.00 0.00 H
ATOM 55 HG13 VAL Z 4 0.075 -8.864 5.603 1.00 0.00 H
ATOM 56 HG21 VAL Z 4 -1.377 -9.121 8.333 1.00 0.00 H
ATOM 57 HG22 VAL Z 4 0.003 -8.032 8.053 1.00 0.00 H
ATOM 58 HG23 VAL Z 4 -1.529 -7.383 8.686 1.00 0.00 H
ATOM 59 N SER Z 5 -0.966 -6.052 3.736 1.00 7.53 N
ATOM 60 CA SER Z 5 -1.526 -5.888 2.407 1.00 11.48 C
ATOM 61 C SER Z 5 -1.207 -7.085 1.529 1.00 16.35 C
ATOM 62 O SER Z 5 -0.437 -7.976 1.902 1.00 14.00 O
ATOM 63 CB SER Z 5 -1.031 -4.596 1.767 1.00 13.36 C
ATOM 64 OG SER Z 5 0.361 -4.652 1.540 1.00 15.80 O
ATOM 65 OXT SER Z 5 -1.737 -7.178 0.429 1.00 17.09 O
ATOM 66 H SER Z 5 0.033 -6.031 3.880 1.00 0.00 H
ATOM 67 HA SER Z 5 -2.610 -5.822 2.504 1.00 0.00 H
ATOM 68 HB2 SER Z 5 -1.543 -4.449 0.816 1.00 0.00 H
ATOM 69 HB3 SER Z 5 -1.254 -3.759 2.428 1.00 0.00 H
ATOM 70 HG SER Z 5 0.653 -3.831 1.137 1.00 0.00 H
TER 71 SER Z 5
HETATM 72 O HOH Z 101 0.935 -5.175 16.502 1.00 18.83 O
HETATM 73 H1 HOH Z 101 0.794 -5.522 15.621 1.00 0.00 H
HETATM 74 H2 HOH Z 101 1.669 -4.561 16.489 1.00 0.00 H
HETATM 75 O HOH Z 102 0.691 -8.408 17.879 1.00 56.55 O
HETATM 76 H1 HOH Z 102 1.392 -8.125 18.466 1.00 0.00 H
HETATM 77 H2 HOH Z 102 0.993 -8.356 16.972 1.00 0.00 H
CONECT 73 72
CONECT 74 72
CONECT 72 73 74
CONECT 76 75
CONECT 77 75
CONECT 75 76 77
END
Vasp’s POSCAR/CONTCAR Input
For periodic input Vasp’s POSCAR / CONTCAR input files are supported, for more information on the format visit the vasp-wiki.
For a molecular crystal of ammonia the input would look like:
H N
1.0000000000000000
5.0133599999999996 0.0000000000000000 0.0000000000000000
0.0000000000000000 5.0133599999999996 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.0133599999999996
12 4
Cartesian
2.1985588943999996 1.7639005823999998 0.8801454815999999
1.7639005823999998 0.8801454815999999 2.1985588943999996
0.8801454815999999 2.1985588943999996 1.7639005823999998
4.8411510839999998 1.6194155471999998 4.9398140088000000
4.3563090384000001 2.4998116967999997 3.6324801215999996
3.5195792543999995 1.1535741359999998 4.0840334567999994
4.0840334567999994 3.5195792543999995 1.1535741359999998
4.9398140088000000 4.8411510839999998 1.6194155471999998
3.6324801215999996 4.3563090384000001 2.4998116967999997
2.4998116967999997 3.6324801215999996 4.3563090384000001
1.1535741359999998 4.0840334567999994 3.5195792543999995
1.6194155471999998 4.9398140088000000 4.8411510839999998
1.3746131783999997 1.3746131783999997 1.3746131783999997
3.9981545999999994 1.9910559239999999 4.4636450759999997
4.4636450759999997 3.9981545999999994 1.9910559239999999
1.9910559239999999 4.4636450759999997 3.9981545999999994
genFormat Input
The DFTB+ genFormat is supported for molecular and 3D periodic systems.
A valid input file for a molecular system is given here:
9 C
C Br H O
1 1 -8.9147060000E-02 -6.6786080000E-02 -1.0432907000E-01
2 2 1.7639746700E+00 2.6771621000E-01 4.2178865000E-01
3 3 -2.6325805000E-01 -1.1300550700E+00 -1.3052621000E-01
4 3 -7.4963702000E-01 3.9302570000E-01 6.1238499000E-01
5 3 -2.6130022000E-01 3.5462634000E-01 -1.0812232600E+00
6 4 4.7684499800E+00 7.6734388000E-01 1.2078966200E+00
7 1 5.5165496700E+00 2.5437564000E-01 4.3331738000E-01
8 3 6.6378745000E+00 3.1585526000E-01 5.3760272000E-01
9 3 5.1708208600E+00 -3.3263252000E-01 -4.6451965000E-01
For a periodic system the input would look like
2 F
Ga As
1 1 0.00 0.00 0.00
2 2 0.25 0.25 0.25
0.0000000E+00 0.0000000E+00 0.0000000E+00
0.2713546E+01 0.2713546E+01 0.0000000E+00
0.0000000E+00 0.2713546E+01 0.2713546E+01
0.2713546E+01 0.0000000E+00 0.2713546E+01
Gaussian External Input
The Gaussian external format is supported to use xtb with the Gaussian
program. A thin wrapper around the xtb binary is required to convert the
external call to a valid xtb program call.
An example input file is given here:
4 1 0 1
7 0.000000000000 0.000000000000 -0.114091591161 0.000000000000
1 -1.817280998039 0.000000000000 0.528409372569 0.000000000000
1 0.908640499019 -1.573811509290 0.528409372569 0.000000000000
1 0.908640499019 1.573811509290 0.528409372569 0.000000000000
Custom Annotations in Geometries
The element type is detected by the element symbol, xtb filters the input
string in the respective format for letters and uses them to figure out the
element type in a case-insensitive way.
While reading the geometry input the actual element symbol will be preserved
and not normalized, a buffer of four characters is available to hold the symbol
which will be used when referring to the element and printing the final geometry.
Note
Prior to version 6.3 only a two character buffer was available.
This allows to add annotations to the geometry input which will not affect the calculation, but show up in the output, log files and the final geometry printout. Consider the following xyz example:
24
13C 1.07317 0.04885 -0.07573
N 2.51365 0.01256 -0.07580
C* 3.35199 1.09592 -0.07533
N 4.61898 0.73028 -0.07549
C 4.57907 -0.63144 -0.07531
C 3.30131 -1.10256 -0.07524
C 2.98068 -2.48687 -0.07377
O(1) 1.82530 -2.90038 -0.07577
N 4.11440 -3.30433 -0.06936
C 5.45174 -2.85618 -0.07235
O 6.38934 -3.65965 -0.07232
N 5.66240 -1.47682 -0.07487
C 7.00947 -0.93648 -0.07524
C 3.92063 -4.74093 -0.06158
H 0.73398 1.08786 -0.07503
D 0.71239 -0.45698 0.82335
D 0.71240 -0.45580 -0.97549
D 2.99301 2.11762 -0.07478
H 7.76531 -1.72634 -0.07591
2H 7.14864 -0.32182 0.81969
3H 7.14802 -0.32076 -0.96953
H 2.86501 -5.02316 -0.05833
H 4.40233 -5.15920 0.82837
H 4.40017 -5.16929 -0.94780
Which is a valid input for xtb. Note that D and T can be used as synonyms
for hydrogen (H).
Note
Mangled names are not supported with crest and must be normalized.