Single point calculations#
Evaluating the tight-binding methods is possible using the tblite-run command.
Calculating with the standalone#
The tblite standalone allows to perform single point calculations with the built-in methods and parameter files.
Energy evaluation with different methods#
To run a first calculation we only need a geometry input in one of the supported formats.
As a simple example we choose the caffeine molecule and save it as struc.xyz:
24
# caffeine
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
To perform a single point calculation we use the tblite-run subcommand:
tblite run struc.xyz
The output is written to the standard output, no further files are produced at this point. By default the GFN2-xTB method is used.
repulsion energy 4.9222938485600E-01 Eh
dispersion energy 9.6582008183032E-05 Eh
number of electrons 7.4000000000000E+01 e
integral cutoff 1.7347787504999E+01 bohr
------------------------------------------------------------
cycle total energy energy error density error
------------------------------------------------------------
1 -41.75569301832 -4.2248019E+01 1.9479952E-01
2 -42.10609780052 -3.5040478E-01 7.5972187E-02
3 -42.14069903418 -3.4601234E-02 4.6343369E-02
4 -42.14507107704 -4.3720429E-03 1.2550655E-02
5 -42.14724061029 -2.1695333E-03 6.1305110E-03
6 -42.14770623967 -4.6562938E-04 2.4358040E-03
7 -42.14738299681 3.2324286E-04 1.0726483E-03
8 -42.14747017326 -8.7176447E-05 3.6117531E-04
9 -42.14746157709 8.5961684E-06 1.6698164E-04
10 -42.14746263709 -1.0599990E-06 5.4777834E-05
11 -42.14746337487 -7.3778077E-07 2.5306995E-05
12 -42.14746403618 -6.6130801E-07 8.2333411E-06
------------------------------------------------------------
electronic energy -4.2639790003039E+01 Eh
total energy -4.2147464036175E+01 Eh
------------------------------------------------------------------
# Occupation Energy/Eh Energy/eV
------------------------------------------------------------------
1 2.0000 -0.7201238 -19.5956
... ... ... ...
29 2.0000 -0.4792385 -13.0407
30 2.0000 -0.4764138 -12.9639
31 2.0000 -0.4564304 -12.4201
32 2.0000 -0.4379226 -11.9165
33 2.0000 -0.4264752 -11.6050
34 2.0000 -0.4193573 -11.4113
35 2.0000 -0.4148063 -11.2875
36 2.0000 -0.4035253 -10.9805
37 2.0000 -0.3892737 -10.5927 (HOMO)
38 -0.2657013 -7.2301 (LUMO)
39 -0.2265846 -6.1657
40 -0.2098114 -5.7093
41 -0.1225595 -3.3350
42 -0.0559053 -1.5213
43 -0.0080016 -0.2177
44 0.0133961 0.3645
... ... ...
66 0.6592542 17.9392
------------------------------------------------------------------
HL-Gap 0.1235725 Eh 3.3626 eV
------------------------------------------------------------------
We can select a method by adding the --method argument to the command line and rerun
tblite run --method gfn1 struc.xyz
This will perform the calculation again using the GFN1-xTB method.
Calculating derivatives#
So far only energies are calculated, to enable the evaluation of molecular gradients we add the --grad keyword to the command line for our GFN1-xTB calculation
tblite run --grad --method gfn1 struc.xyz
Note
The gradient option takes one optional argument, make sure to separate the geometry input file by the -- separator in case you do not provide the output file for the derivatives:
tblite run --grad -- struc.xyz
The output will show that the gradient output has been written to a file
[Info] Tight-binding results written to 'tblite.txt'
Tip
Generally, tblite will never write to a file without explicitly stating it in the standard output.
We can inspect the result using a pager like less or any text editor of your choice, the output should look similar to this:
energy :real:0:
-4.4509702550094509E+01
gradient :real:2:3,24
3.8751207233845646E-03 1.0589576505981196E-03 4.0101833008853537E-06
-6.8197644662543388E-03 -2.5469121433516095E-02 -4.7470927704034663E-05
1.0648728891662693E-02 8.8366335898543858E-03 4.7996917287539728E-05
3.1902722527341862E-04 7.4242248622642722E-03 -2.8496918953763304E-05
-2.6208973446986007E-02 -9.0131378921360604E-03 -3.8669871255270171E-05
-1.7509318247989529E-03 3.6705299785918994E-03 3.4118097773531792E-05
1.9484148290568090E-02 4.7415207908131207E-03 4.0471496678204742E-05
-1.1722356880465069E-02 7.4828408528079754E-03 -1.1612153192208481E-04
-1.2241607563977187E-03 -1.9132992220688570E-02 1.2461589545076379E-04
-1.6766717498318165E-02 1.2103660828186829E-02 -3.4573645420344302E-05
2.4844203069064843E-02 -1.9287321306216326E-02 -4.9197479201307158E-05
1.1084471631753511E-02 1.7004159137354469E-02 -3.2214753172841759E-06
-6.4592191454479423E-03 -4.2860776915391351E-03 -4.0858618678683595E-06
-6.5899183170761598E-03 1.3221070732562403E-02 -9.0165446293088262E-05
-1.3268732296168747E-03 2.1245633439957766E-03 4.0929253563542303E-06
1.7227511511327858E-03 1.1717306153688867E-03 2.6844186750092148E-03
1.7254183949399506E-03 1.1710614866087398E-03 -2.6879103256391306E-03
-1.5499406234334675E-03 3.9313477434577580E-03 2.5224714308249690E-05
6.3570530436816057E-03 2.2899202031480908E-03 3.4807215781027190E-06
5.1739877369726952E-04 -5.0616912429584586E-04 1.9423398812888478E-03
5.4061192657724807E-04 -4.8581923304342556E-04 -1.9455409758072379E-03
-1.2675930676672822E-03 -7.6587507428546708E-03 8.4916914284767576E-05
2.7792577845120209E-04 -1.8293010741325709E-04 1.4003154522332375E-03
2.8959035627490622E-04 -2.0990206390925764E-04 -1.3505474151682963E-03
virial :real:2:3,3
7.8713512660909479E-02 -3.0635463233997452E-02 -1.6134089053178151E-04
-3.0635463233997452E-02 8.4807095398895124E-02 -1.1909491256157945E-04
-1.6134089053176757E-04 -1.1909491256159344E-04 2.0323518845924864E-02
The ASCII output format is adopted from the DFTB+ project and called tagged output (see tblite-tag). It has the advantage of being easily human-readable and a custom parser is straight-forward to write.
Instead of relying on a custom parser, a more standardized format like JSON might be preferable for automating calculations with tblite.
We can request to create to use JSON to store the results with the --json argument.
tblite run --grad --json --method gfn1 struc.xyz
In the output we will now find
[Info] JSON dump of results written to 'tblite.json'
Note
The tagged output file will not be written by default when requesting a JSON output, to enable both provide the name of the output files in the command line
tblite run --grad caffeine.txt --json caffeine.json struc.xyz
The output will show that both output are now available
[Info] Tight-binding results written to 'caffeine.txt'
[Info] JSON dump of results written to 'caffeine.json'
We find that tblite also included meta data like the version number of the program in the JSON dump, which can be useful when automatically processing the data later.