PTB
Introducing PTB
PTB stands for density (P) tight-binding (TB), a method that emulates the density matrix of a \({\omega}\)B97X-3c range-separated hybrid DFT calculation (see also below).
PTB can be used out-of-the-box to various electronic structure properties for molecules composed of all spd-block elements up to Z=86. The key improvement is the substitution of commonly used minimal atomic orbital basis sets with an extended and properly polarized basis set (vDZP). Its main purpose is to provide extremely fast the one-particle electronic density matrix P and derived properties, such as atomic charges, shell populations, dipole moments, and geometric derivatives as well as static dipole polarizabilities. For a wide range of molecules from various chemical compound classes (organic, inorganic, transition metal complexes, clusters, and aggregates), including multiple anions/cations, excellent agreement between PTB and \({\omega}\)B97X-3c computed properties is obtained. Typical RMSDs are 0.02 e- for atomic charges or shell populations, with deviations of approximately 5% to 10% for dipole moments and polarizabilities. Artificial charge transfer, such as in zwitterions, or SCF convergence issues in electronically challenging small-gap systems is largely avoided, which also results from the applied non-iterative, two-step diagonalization scheme. No energy expression is available currently, and the entire development was focused on reproducing the DFT density matrix and some of its response features as accurately as possible.
PTB has been published in The Journal of Chemical Physics:
Grimme, S.; Müller, M.; Hansen, A. A Non-Self-Consistent Tight-Binding Electronic Structure Potential in a Polarized Double-ζ Basis Set for All spd-Block Elements up to Z = 86. J. Chem. Phys. 2023, 158 (12), 124111. DOI: 10.1063/5.0137838
For further information on \({\omega}\)B97X-3c, see: Müller, M.; Hansen, A.; Grimme, S. J. Chem. Phys. 2023, 158 (1), 014103.
Basic usage
PTB is implemented in the xtb program.
It extends the portfolio of the package by the non-self-consistent density tight-binding method PTB. It is invoked with the keyword --ptb as shown in the example below.
> xtb coord.xyz --ptb --json
A cofacial NCI complex of benzene and nitrobenzene for testing PTB.
26
C -1.20618 0.69599 1.75211
C -1.20379 -0.70017 1.75215
C 0.00616 -1.39690 1.75210
C 1.21824 -0.70002 1.75171
C 1.23033 0.70989 1.75117
C 0.00125 1.40067 1.75172
H 2.14504 -1.25925 1.74975
H -0.02278 2.48280 1.74976
H -2.14520 1.23405 1.75041
H -2.14028 -1.24255 1.75044
H 0.00554 -2.47919 1.75040
C -1.21072 0.69984 -1.75114
C -1.21074 -0.69902 -1.75149
C 0.00072 -1.39843 -1.75114
C 1.21220 -0.69897 -1.75037
C 1.21222 0.69988 -1.74995
C 0.00077 1.39929 -1.75036
H 2.14941 -1.24008 -1.74839
H 2.14945 1.24099 -1.74755
H 0.00077 2.48148 -1.74837
H -2.14799 1.24091 -1.74971
H -2.14800 -1.24014 -1.75028
H 0.00066 -2.48066 -1.74972
N 2.46723 1.42685 1.74737
O 2.47280 2.62117 1.74468
O 3.50640 0.83800 1.74471
-------------------------------------------------
| P T B |
-------------------------------------------------
Reference 10.1063/5.0137838
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@,,,,,,,,,,,,,,,,,,,,,,,,,,,,@@
@,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,@
@,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,*
@,,,,,,,,@///////////////#,,,,,,,,,@
@,,,,,,,,@/////////////////,,,,,,,,(
@,,,,,,,,@/////////////////,,,,,,,,(
@,,,,,,,,@/////////////////,,,,,,,,(
@,,,,,,,,@/////////////////,,,,,,,,(
@,,,,,,,,@/////////////////,,,,,,,,(
@,,,,,,,,@/////////////////,,,,,,,,(
@,,,,,,,,@////////////////@,,,,,,,,@
@,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,% @@@@@@@@@@@@@@@@@@ @@@@@@@@@@@@@@
@,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,&////@,,,,,,,,,,,,,,,,,///@,,,,,,,,,,,,,,@
@,,,,,,,,,,,,,,,,,,,,,,,,,,,,,@///////@,,,,,,,,,,,,,,,,,,//@,,,,,,,,,,,,,,,,@
@,,,,,,,,@///////////////////////////////////@,,,#/////////@,,,@////////*,,,@
@,,,,,,,,@/////////@ ////////////////////////@,,,#/////////@,,,@////////*,,,@
@,,,,,,,,@///// %@@ ( @@@ (@ @@@ @//////////@,,,#/////////@,,,@////////*,,,@
@,,,,,,,,@////( @//@ ( @@@ @@ @//.@//////////@,,,#/////////@,,,,,,,,,,,,,,,*
@,,,,,,,,@///// @//@ ( @////@ @//.@//////////@,,,#/////////@,,,,,,,,,,,,,,,,@
@,,,,,,,,@//////@@@@@/(@@@@/@@@//@@//////////@,,,#/////////@,,,@////////(,,,,@
@,,,,,,,,@///////////#@@/ @//////////////////@,,,#/////////@,,,@/////////,,,,@
@,,,,,,,,@//// .@@/(/# @@ @@/@ /// @/////////@,,,#/////////@,,,@/////////,,,,@
@,,,,,,,,@////% @/# @/ @//@ /// @/////////@,,,#/////////@,,,@////////@,,,,@
@,,,,,,,,@////////@ /# @/ @//@ /// @/////////@,,,#/////////@,,,,,,,,,,,,,,,,@
&@@@@@@@@@/////@@@@//(@@/#@@(/#@@@ @
@@@ @
...................................................
: SETUP :
:.................................................:
: # atomic orbitals 250 :
: # shells 108 :
: # electrons 76 :
: # open shells 0 :
: max. iterations 2 :
: Hamiltonian PTB :
: PC potential false :
: electronic temp. 300.0000000 K :
: -> integral cutoff 0.2500000E+02 :
: verbosity level 2 :
...................................................
--- Calculation progress: ---
1st iteration...
2nd iteration...
--- Two-step SCF done. ---
-------------------------------------------------
| Property Printout |
-------------------------------------------------
* Orbital Energies and Occupations
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -1.4335353 -39.0085
... ... ... ...
26 2.0000 -0.5045711 -13.7301
27 2.0000 -0.5040396 -13.7156
28 2.0000 -0.4808924 -13.0857
29 2.0000 -0.4722708 -12.8511
30 2.0000 -0.4561747 -12.4131
31 2.0000 -0.4557899 -12.4027
32 2.0000 -0.4309614 -11.7271
33 2.0000 -0.4259563 -11.5909
34 2.0000 -0.4044794 -11.0064
35 2.0000 -0.3964229 -10.7872
36 2.0000 -0.3947316 -10.7412
37 2.0000 -0.3670100 -9.9869
38 2.0000 -0.3665408 -9.9741 (HOMO)
39 -0.0239028 -0.6504 (LUMO)
40 0.0361502 0.9837
41 0.0638157 1.7365
42 0.0661394 1.7997
43 0.1022883 2.7834
44 0.1226305 3.3369
45 0.1550123 4.2181
46 0.2012073 5.4751
47 0.2105286 5.7288
48 0.2372001 6.4545
49 0.2389287 6.5016
... ... ...
250 1880.0926856 51159.9260
-------------------------------------------------------------
HL-Gap 0.3426379 Eh 9.3237 eV
Fermi-level 0.0000000 Eh 0.0000 eV
* Atomic partial charges (q) Shell populations (p)
------------------------------------------------------------------------------------
# sym q 1 2 3 4 5
------------------------------------------------------------------------------------
1 C -0.02580 0.56624 0.25826 2.14868 0.77647 0.27615
2 C -0.01955 0.56946 0.25888 2.13958 0.76848 0.28315
3 C -0.02579 0.56627 0.25829 2.14863 0.77652 0.27608
4 C -0.00674 0.57136 0.26101 2.13410 0.76488 0.27539
5 C -0.01140 0.56315 0.24359 2.13512 0.71189 0.35765
6 C -0.00687 0.57136 0.26099 2.13427 0.76482 0.27544
7 H 0.05450 0.66023 0.14231 0.14297
8 H 0.05446 0.66025 0.14231 0.14298
9 H 0.05064 0.66417 0.14119 0.14400
10 H 0.04931 0.66558 0.14146 0.14366
11 H 0.05064 0.66417 0.14120 0.14399
12 C -0.04504 0.56668 0.25975 2.14638 0.78730 0.28493
13 C -0.04650 0.56670 0.25972 2.14711 0.78765 0.28531
14 C -0.04508 0.56668 0.25975 2.14641 0.78730 0.28493
15 C -0.03969 0.56642 0.25979 2.14367 0.78616 0.28365
16 C -0.03467 0.56633 0.25982 2.14085 0.78496 0.28271
17 C -0.03968 0.56643 0.25979 2.14367 0.78616 0.28363
18 H 0.04302 0.66835 0.14362 0.14502
19 H 0.04581 0.66728 0.14289 0.14402
20 H 0.04301 0.66836 0.14361 0.14502
21 H 0.04078 0.66938 0.14399 0.14585
22 H 0.04037 0.66955 0.14405 0.14602
23 H 0.04076 0.66940 0.14399 0.14585
24 N 0.09115 0.72096 0.24406 2.47323 0.78151 0.68909
25 O -0.12891 1.16607 0.40893 3.39118 1.05904 0.10369
26 O -0.12874 1.16608 0.40896 3.39091 1.05912 0.10367
------------------------------------------------------------------------------------
total: 0.00000
Wiberg/Mayer (AO) data.
largest (>0.10) Wiberg bond orders for each atom
---------------------------------------------------------------------------
# Z sym total # sym WBO # sym WBO # sym WBO
---------------------------------------------------------------------------
1 6 C 3.965 -- 6 C 1.445 2 C 1.429 9 H 0.989
2 6 C 3.977 -- 1 C 1.429 3 C 1.429 10 H 0.993
3 6 C 3.965 -- 4 C 1.445 2 C 1.429 11 H 0.989
4 6 C 3.967 -- 3 C 1.445 5 C 1.403 7 H 0.982
5 6 C 4.006 -- 4 C 1.403 6 C 1.403 24 N 1.052
6 6 C 3.967 -- 1 C 1.445 5 C 1.403 8 H 0.982
7 1 H 1.016 -- 4 C 0.982
8 1 H 1.016 -- 6 C 0.982
9 1 H 1.035 -- 1 C 0.989
10 1 H 1.038 -- 2 C 0.993
11 1 H 1.035 -- 3 C 0.989
12 6 C 3.992 -- 13 C 1.441 17 C 1.440 21 H 0.993
13 6 C 3.994 -- 12 C 1.441 14 C 1.441 22 H 0.994
14 6 C 3.992 -- 13 C 1.441 15 C 1.440 23 H 0.993
15 6 C 3.987 -- 14 C 1.440 16 C 1.439 18 H 0.991
16 6 C 3.980 -- 15 C 1.439 17 C 1.439 19 H 0.988
17 6 C 3.987 -- 12 C 1.440 16 C 1.439 20 H 0.991
18 1 H 1.038 -- 15 C 0.991
19 1 H 1.033 -- 16 C 0.988
20 1 H 1.038 -- 17 C 0.991
21 1 H 1.041 -- 12 C 0.993
22 1 H 1.042 -- 13 C 0.994
23 1 H 1.041 -- 14 C 0.993
24 7 N 4.311 -- 26 O 1.621 25 O 1.621 5 C 1.052
25 8 O 1.880 -- 24 N 1.621 26 O 0.198
26 8 O 1.880 -- 24 N 1.621 25 O 0.198
---------------------------------------------------------------------------
Topologies differ in total number of bonds
Writing topology from bond orders to xtbtopo.mol
--------------------------------------
Molecular dipole moment (a.u.)
X Y Z
--------------------------------------
-1.6560 -0.9605 0.0032
--------------------------------------
Total dipole moment (a.u. / Debye):
1.9144 4.8658
--------------------------------------
Molecular quadrupole tensor: (a.u.)
X Y Z
X -4.6099
Y -18.7964 6.5225
Z -17.6585 -10.2393 -1.9126
{
"total energy": 0.00000000,
"HOMO-LUMO gap / eV": 9.32365300,
"electronic energy": 0.00000000,
"dipole / a.u.": [ -1.65595034, -0.96050070, 0.00324936],
"partial charges": [
-0.02580418,
-0.01955062,
-0.02578955,
-0.00673978,
-0.01139657,
-0.00687004,
0.05449601,
0.05446298,
0.05064076,
0.04930957,
0.05064248,
-0.04504331,
-0.04650347,
-0.04507944,
-0.03968609,
-0.03467388,
-0.03967838,
0.04301740,
0.04581142,
0.04301236,
0.04078359,
0.04037447,
0.04075952,
0.09114600,
-0.12890616,
-0.12873510],
"shell charges": [
[ -0.00957618, -0.00706229, -0.04112235, -0.01900655, 0.05096319],
[ -0.01279822, -0.00767786, -0.03201783, -0.01101893, 0.04396222],
[ -0.00960229, -0.00708624, -0.04107428, -0.01905729, 0.05103056],
[ -0.01469682, -0.00980551, -0.02654501, -0.00741039, 0.05171796],
[ -0.00648151, 0.00761632, -0.02756281, 0.04557390, -0.03054247],
[ -0.01469601, -0.00978240, -0.02671271, -0.00735074, 0.05167182],
[ 0.03241257, -0.00070811, 0.02279154],
[ 0.03239064, -0.00070551, 0.02277785],
[ 0.02847477, 0.00040602, 0.02175998],
[ 0.02706603, 0.00014321, 0.02210034],
[ 0.02847696, 0.00040179, 0.02176373],
[ -0.01001242, -0.00854798, -0.03882204, -0.02983659, 0.04217572],
[ -0.01003868, -0.00851992, -0.03955334, -0.03018934, 0.04179781],
[ -0.01001808, -0.00854912, -0.03885175, -0.02983662, 0.04217614],
[ -0.00975838, -0.00858791, -0.03610517, -0.02869582, 0.04346118],
[ -0.00966665, -0.00861631, -0.03329379, -0.02749367, 0.04439655],
[ -0.00976372, -0.00858896, -0.03610916, -0.02869079, 0.04347425],
[ 0.02429422, -0.00201553, 0.02073871],
[ 0.02536325, -0.00128692, 0.02173510],
[ 0.02428199, -0.00201121, 0.02074158],
[ 0.02325873, -0.00238696, 0.01991182],
[ 0.02308916, -0.00245145, 0.01973676],
[ 0.02324259, -0.00239520, 0.01991213],
[ 0.07527729, 0.07343734, 0.26312472, 0.19945280, -0.52014616],
[ -0.08146427, -0.02758942, -0.06355142, 0.07033950, -0.02664057],
[ -0.08147586, -0.02761816, -0.06328206, 0.07026077, -0.02661980]],
"bond orders": [
,
[ 1, 2, 1.4289],
[ 1, 4, 0.0771],
[ 1, 6, 1.4452],
[ 1, 9, 0.9892],
[ 1, 11, 0.0135],
[ 2, 3, 1.4289],
[ 2, 5, 0.0709],
[ 2, 7, 0.0135],
[ 2, 8, 0.0135],
[ 2, 10, 0.9926],
[ 3, 4, 1.4452],
[ 3, 6, 0.0771],
[ 3, 9, 0.0135],
[ 3, 11, 0.9892],
[ 4, 5, 1.4031],
[ 4, 7, 0.9819],
[ 4, 8, 0.0135],
[ 4, 10, 0.0135],
[ 4, 25, 0.0298],
[ 5, 6, 1.4030],
[ 5, 9, 0.0133],
[ 5, 11, 0.0133],
[ 5, 24, 1.0518],
[ 5, 25, 0.0195],
[ 5, 26, 0.0195],
[ 6, 7, 0.0135],
[ 6, 8, 0.9819],
[ 6, 10, 0.0135],
[ 6, 26, 0.0298],
[ 12, 13, 1.4414],
[ 12, 15, 0.0823],
[ 12, 17, 1.4404],
[ 12, 19, 0.0136],
[ 12, 21, 0.9934],
[ 12, 23, 0.0138],
[ 13, 14, 1.4414],
[ 13, 16, 0.0823],
[ 13, 18, 0.0137],
[ 13, 20, 0.0137],
[ 13, 22, 0.9937],
[ 14, 15, 1.4405],
[ 14, 17, 0.0823],
[ 14, 19, 0.0136],
[ 14, 21, 0.0138],
[ 14, 23, 0.9934],
[ 15, 16, 1.4389],
[ 15, 18, 0.9908],
[ 15, 20, 0.0137],
[ 15, 22, 0.0138],
[ 16, 17, 1.4389],
[ 16, 19, 0.9881],
[ 16, 21, 0.0138],
[ 16, 23, 0.0138],
[ 17, 18, 0.0137],
[ 17, 20, 0.9908],
[ 17, 22, 0.0138],
[ 24, 25, 1.6205],
[ 24, 26, 1.6207],
[ 25, 26, 0.1977]],
"atomic dipole moments": [
[ 0.17817237, -0.08486467, -0.04392900],
[ 0.14540861, 0.08417827, -0.04278264],
[ 0.01511332, 0.19675971, -0.04389043],
[ -0.13312254, 0.12935626, -0.04018292],
[ 0.19288286, 0.11173317, -0.03496594],
[ 0.04602572, -0.17971285, -0.04021404],
[ 0.20153653, -0.11378295, 0.01052811],
[ 0.00160042, 0.23134930, 0.01053943],
[ -0.21014330, 0.11689540, 0.01051611],
[ -0.20767197, -0.12027608, 0.01047094],
[ -0.00330039, -0.24047911, 0.01050497],
[ 0.14364790, -0.09442200, 0.04646228],
[ 0.14775082, 0.08525506, 0.04574296],
[ -0.00988717, 0.17152388, 0.04651218],
[ -0.16085752, 0.07853975, 0.04618875],
[ -0.15928291, -0.09201357, 0.04788960],
[ -0.01237952, -0.17861850, 0.04614049],
[ 0.20393913, -0.11931464, -0.00923317],
[ 0.20084041, 0.11598812, -0.00705150],
[ -0.00132604, 0.23622454, -0.00922251],
[ -0.20820109, 0.11939647, -0.00910789],
[ -0.20838147, -0.12034087, -0.00917493],
[ -0.00072895, -0.23997078, -0.00911999],
[ 0.08511339, 0.04958329, -0.01580055],
[ 0.02008492, -0.59870284, 0.00147451],
[ -0.50942425, 0.31508169, 0.00145541]],
"atomic quadrupole moments": [
[ -0.23483260, 0.35458689, 0.08721839, 0.00404713, -0.00221582, 0.14761421],
[ -0.31404269, -0.32538294, 0.07534445, -0.00036567, -0.00033284, 0.23869824],
[ 0.32466627, 0.04769748, -0.47213648, 0.00021495, 0.00440101, 0.14747021],
[ -0.20137605, 0.26534859, -0.05158060, 0.00369766, 0.01287493, 0.25295665],
[ 0.07557700, 0.10609333, -0.02576532, 0.01046279, 0.00595898, -0.04981168],
[ 0.14900317, 0.06774764, -0.40152994, 0.01311216, -0.00339044, 0.25252677],
[ 0.01254889, 0.09029415, 0.04976636, -0.02624647, 0.01511978, -0.06231526],
[ 0.11602428, 0.02847786, -0.05355800, 0.00002533, -0.03028812, -0.06246627],
[ -0.02997061, 0.08898874, 0.07958685, 0.02520322, -0.01434626, -0.04961624],
[ -0.02365008, -0.08660731, 0.07219455, 0.02550166, 0.01477689, -0.04854447],
[ 0.12662694, -0.00399738, -0.07710619, 0.00009921, 0.02900232, -0.04952076],
[ -0.30006940, 0.30202639, 0.09376142, -0.00114705, 0.00264928, 0.20630798],
[ -0.28880250, -0.30941643, 0.08581319, 0.00000131, -0.00012030, 0.20298930],
[ 0.26998302, -0.01227972, -0.47633316, 0.00185920, -0.00253625, 0.20635014],
[ -0.27412905, 0.31742810, 0.07440885, 0.00468830, 0.00165078, 0.19972020],
[ -0.28631949, -0.30807791, 0.08539979, 0.01417986, 0.00809755, 0.20091970],
[ 0.27510342, 0.01535060, -0.47444771, 0.00389347, 0.00302610, 0.19934429],
[ -0.02455963, 0.08953758, 0.07142463, 0.01809144, -0.01319294, -0.04686500],
[ -0.02258736, -0.08556863, 0.07278918, 0.01619300, 0.00935858, -0.05020182],
[ 0.12238760, 0.00168068, -0.07550214, -0.00241218, 0.02224940, -0.04688547],
[ -0.03381135, 0.09231522, 0.07534668, -0.02181480, 0.01271313, -0.04153533],
[ -0.03241315, -0.09470785, 0.07339190, -0.02201384, -0.01270961, -0.04097875],
[ 0.12541539, -0.00265213, -0.08381623, 0.00011766, -0.02524766, -0.04159916],
[ -0.02351376, -0.17170182, 0.20003381, 0.02815354, 0.01628303, -0.17652005],
[ -0.68178231, -0.07559419, 1.00107233, -0.00398393, -0.00629851, -0.31929002],
[ 0.52214226, -0.59650562, -0.20281034, -0.00741448, -0.00034301, -0.31933192]],
"number of molecular orbitals": 250,
"number of electrons": 76,
"number of unpaired electrons": 0,
"orbital energies / eV": [
-39.00848045,
-30.92408173,
-29.27753379,
-27.99909431,
-25.90152418,
-24.80824514,
-23.90248768,
-23.87258388,
-23.05138303,
-20.97789424,
-20.48867211,
-20.12048257,
-20.11544364,
-18.76695942,
-17.47736764,
-17.34381024,
-17.20541071,
-17.07185189,
-16.08872553,
-15.84927455,
-15.84807800,
-15.65614615,
-15.21613067,
-14.56330637,
-14.54742452,
-13.73007911,
-13.71561491,
-13.08574752,
-12.85114162,
-12.41314585,
-12.40267379,
-11.72705663,
-11.59086129,
-11.00644510,
-10.78721567,
-10.74119348,
-9.98685133,
-9.97408150,
-0.65042850,
0.98369714,
1.73651469,
1.79974353,
2.78340727,
3.33694685,
4.21809892,
5.47513054],
"fractional occupation": [
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
2.00000000,
0.00000000,
0.00000000,
0.00000000,
0.00000000,
0.00000000,
0.00000000,
0.00000000,
0.00000000],
"program call": "xtb_dev benzene_dimer.xyz --ptb --json",
"method": "PTB",
"xtb version": "6.7.1 (1779d8a)"
}
The output as well as the JSON file contain the following properties:
orbital energies and occupations
atomic partial charges
shell populations
Wiberg bond orders
molecular dipole moment
molecular quadrupole tensor
Vibrational spectroscopy
Infrared and Raman intensity calculations for vibrational spectroscopy are additional applications of PTB. An example is the spectrum of endothelin (1EDN).
In all spectra, the notation “MethodX [MethodY]” indicates that frequencies were computed with Method Y and intensities with MethodX. Within
xtb, this procedure is fully automated and requires no additional user input when using the CLI command below.
![Raman activities of the polypeptide endothelin (327 atoms) computed by :math:`{\omega}`\ B97X-3c [GFN2-xTB] and PTB [GFN2-xTB]. The notation indicates that intensities were calculated with PTB or :math:`{\omega}`\ B97X-3c, while frequencies were computed with GFN2-xTB. In this example, Raman activities instead of Raman scattering cross-sections (== intensities) are plotted.](_images/ptb_raman_1edn.png)
Raman activities of the polypeptide endothelin (327 atoms) computed by \({\omega}\)B97X-3c [GFN2-xTB] and PTB [GFN2-xTB]. The notation indicates that intensities were calculated with PTB or \({\omega}\)B97X-3c, while frequencies were computed with GFN2-xTB. In this example, Raman activities instead of Raman scattering cross-sections (= intensities) are plotted.
Note
Vibrational frequencies are not available with PTB! Instead, mixed GFNn-xTB and PTB spectra can be calculated.
The following example shows the output of a vibrational spectrum calculation utilizing GFN2-xTB frequencies and PTB intensities.
> xtb coord.xyz --ptb --hess --raman
12
C -1.21072 0.69984 -1.75114
C -1.21074 -0.69902 -1.75149
C 0.00072 -1.39843 -1.75114
C 1.21220 -0.69897 -1.75037
C 1.21222 0.69988 -1.74995
C 0.00077 1.39929 -1.75036
H 2.14941 -1.24008 -1.74839
H 2.14945 1.24099 -1.74755
H 0.00077 2.48148 -1.74837
H -2.14799 1.24091 -1.74971
H -2.14800 -1.24014 -1.75028
H 0.00066 -2.48066 -1.74972
$vibrational spectrum
# mode symmetry wave number IR intensity Raman activity Raman scatt. cross-section selection rules
# (cm⁻¹) (km*mol⁻¹) (Å⁴*amu⁻¹) (Ų*sr⁻¹) IR RAMAN
1 -0.00 0.00000 0.00000 0.00000E+00 - -
2 -0.00 0.00000 0.00000 0.00000E+00 - -
3 -0.00 0.00000 0.00000 0.00000E+00 - -
4 -0.00 0.00000 0.00000 0.00000E+00 - -
5 0.00 0.00000 0.00000 0.00000E+00 - -
6 0.00 0.00000 0.00000 0.00000E+00 - -
7 a 396.50 0.00000 0.00000 0.18961E-20 NO NO
8 a 396.53 0.00000 0.00000 0.33360E-20 NO NO
9 a 579.98 0.00000 1.54626 0.20949E-14 NO YES
10 a 580.02 0.00000 1.54429 0.20921E-14 NO YES
11 a 670.85 0.00000 0.00000 0.12043E-21 NO NO
12 a 701.48 126.55730 0.00015 0.16106E-18 YES NO
13 a 893.74 0.00061 0.23750 0.18585E-15 NO YES
14 a 893.79 0.00069 0.23627 0.18488E-15 NO YES
15 a 930.33 0.00000 0.00004 0.29258E-19 NO NO
16 a 930.39 0.00001 0.00004 0.31197E-19 NO NO
17 a 935.21 0.00000 0.00000 0.39056E-21 NO NO
18 a 954.09 0.00000 0.00000 0.18351E-22 NO NO
19 a 1025.26 0.00007 79.02989 0.52065E-13 NO YES
20 a 1070.03 15.31859 0.00001 0.35843E-20 YES NO
21 a 1070.11 15.26901 0.00001 0.40505E-20 YES NO
22 a 1170.72 0.00001 0.00004 0.21074E-19 NO NO
23 a 1186.56 0.00000 9.41232 0.51526E-14 NO YES
24 a 1186.60 0.00000 9.41073 0.51516E-14 NO YES
25 a 1233.84 0.00001 0.00000 0.93316E-21 NO NO
26 a 1305.43 0.00000 0.00001 0.72249E-20 NO NO
27 a 1431.72 18.20659 0.00001 0.28783E-20 YES NO
28 a 1431.79 18.18773 0.00001 0.28429E-20 YES NO
29 a 1542.28 0.00000 10.20802 0.39632E-14 NO YES
30 a 1542.41 0.00000 10.21628 0.39659E-14 NO YES
31 a 3048.92 0.00061 0.17889 0.24697E-16 NO YES
32 a 3052.31 0.00041 85.12880 0.11730E-13 NO YES
33 a 3052.40 0.00541 85.28612 0.11751E-13 NO YES
34 a 3063.56 22.28601 0.13306 0.18217E-16 YES YES
35 a 3063.68 22.38385 0.02186 0.29920E-17 YES YES
36 a 3071.51 0.00809 358.17986 0.48815E-13 NO YES
$end
In the shown example, omitting the --raman flag would result in a pure IR spectrum calculation (examples below).
Similar to the basic usage example, also here, --json can be used to obtain the output (all components of the vibrational spectrum) in JSON format.
![IR spectra of 3-pentenenitrile and 1-nitrosopyrrolidine. The experimental gas phase spectra and the spectra calculated with :math:`{\omega}`\ B97X-3c [GFN2-xTB], full GFN2-xTB, and PTB [GFN2-xTB] are shown.](_images/ptb_ir_spectra.png)
IR spectra of 3-pentenenitrile and 1-nitrosopyrrolidine. The experimental gas phase spectra and the spectra calculated with \({\omega}\)B97X-3c [GFN2-xTB], full GFN2-xTB, and PTB [GFN2-xTB] are shown.