Properties¶
In this chapter, all necessary information about the properties of xTB will be given. Description of how to acquire different output information will be provided. Calculation of FOD will be described.
Contents
General printout¶
First the orbital energies and occupation are printed, where the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are marked. The HOMO-LUMO gap and the Fermi-level are summed up.
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| Property Printout |
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* Orbital Energies and Occupations
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.6801050 -18.5066
2 2.0000 -0.5683264 -15.4649
3 2.0000 -0.5108650 -13.9013
4 2.0000 -0.4463919 -12.1469 (HOMO)
5 0.0826818 2.2499 (LUMO)
6 0.2518567 6.8534
-------------------------------------------------------------
HL-Gap 0.5290737 Eh 14.3968 eV
Fermi-level -0.1818551 Eh -4.9485 eV
The information provided by the printout can be modified and extended. This can be done either by using the option-flags when calling the program (Commandline Usage), or by editing the input file (Detailed Input). The kind of default information given is determined by the GFN-xTB version used. The default values called by the program are given:
- --pop
requests printout of Mulliken population analysis
- --molden
requests printout of molden file
- --dipole
requests printout of dipole moments
- --wbo
requests Wiberg bond order printout
GFN1-xTB¶
Default settings for GFN1-xTB first prints the Mulliken and CM5 charges. n(x) denotes the population partioned to the x = s/p/d shells:
Mulliken/CM5 charges n(s) n(p) n(d)
1 O 0.67569 0.33312 1.682 4.994 0.000
2 H -0.33784 -0.16656 0.662 0.000 0.000
3 H -0.33784 -0.16656 0.662 0.000 0.000
Wiberg bond orders describe the partial bond orders and their disposition onto the atoms:
Wiberg/Mayer (AO) data.
largest (>0.10) Wiberg bond orders for each atom
total WBO WBO to atom ...
1 O 1.782 H 2 0.891 H 3 0.891
2 H 0.892 O 1 0.891
3 H 0.892 O 1 0.891
The molecular dipole moment and its cartesian components calculated from the electron density. The components are given in atomic units while the total dipole moment is given in Debye, to convert from atomic units to Debye multiply by 2.5417 D/au.
dipole moment from electron density (au)
X Y Z
0.8659 0.0000 0.6123 total (Debye): 2.696
GFN2-xTB¶
Default settings for GFN2-xTB first prints populations and coefficients. From left to right, these are the atomic number Z, Coordination number CN, Atomic partial charge q, Dispersion coefficient C6, Polarizability alpha:
# Z covCN q C6AA α(0)
1 8 O 1.613 -0.568 24.435 6.672
2 1 H 0.806 0.284 0.771 1.379
3 1 H 0.806 0.284 0.771 1.379
The C6, C8 and alpha coefficients are denoted explicitly in a.u.:
Mol. C6AA /au·bohr⁶ : 44.553640
Mol. C8AA /au·bohr⁸ : 796.459844
Mol. α(0) /au : 9.429351
Wiberg bond orders:
Wiberg/Mayer (AO) data.
largest (>0.10) Wiberg bond orders for each atom
total WBO WBO to atom ...
1 O 1.839 H 3 0.919 H 2 0.919
2 H 0.919 O 1 0.919
3 H 0.919 O 1 0.919
Molecular dipole and quadropole moments. The contributions are seperated into their respective cartesian dimensions. ‘Full’ represents the corresponding contributions of the molecular dipole or quadropole moments.
molecular dipole:
x y z tot (Debye)
q only: 0.481 0.000 0.340
full: 0.696 0.000 0.492 2.167
molecular quadrupole (traceless):
xx xy yy xz yz zz
q only: 0.305 0.000 -0.916 -0.432 0.000 0.610
q+dip: 0.390 0.000 -1.177 -0.563 0.000 0.787
full: 0.495 -0.000 -1.436 -0.632 -0.000 0.942
All is summed up in the end in both GFN-xTB versions:
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| TOTAL ENERGY -5.070322476938 Eh |
| GRADIENT NORM 0.019484395925 Eh/α |
| HOMO-LUMO GAP 14.652302902752 eV |
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Density Properties¶
Cube Files¶
The xtb
program is able to calculate the density, spin-density and the fractional occupation number weighted density (FOD).
For these caclualtions, the program first creates a proper cube grid. The corresponding file is created in your working directory and marked as .cub
file.
It provides density and step size informations. An overview is already given in the printout:
cube file module (SG, 7/16)
cube_pthr : 0.050
cube_step : 0.400
non-zero P (%): 76.190 nmat: 16
Grid Boundaries (x y z) :
4.69257109135830 3.00000000000000 4.79524030780751
-3.00000000000000 -3.00000000000000 -3.59840693802375
Total # of points 6720
writing density.cub
cpu time for cube 0.01 s
wall time for cube 0.01 s
Here, various information are provided, like the density matrix neglect threshold cube_pthr
and the grid step size cube_step
(in Bohr). These values can be changed in the input (xcontrol) file (Detailed Input).
For visualization, programs like chimera can be used, for which the .cub
file can be loaded as volume data.
Density and Spin-Density¶
To calculate the density or the spin denisty, the input (xcontrol) file has to be manipulated. Here, the bools density='bool'
or respectively spin density='bool'
have to be set to 'true'
. This will create a .cub
cube file, where the corresponding information is gathered.
For visualization, programs like chimera can be used, for which the .cub
file can be loaded as volume data.
Fractional Occupation Density (FOD) calculation¶
The fractional occupation density analysis (FOD) is a diagnostic scheme that displays the static electron correlation localized on a molecule. The density is hereby obtained by performing a computationally cheap Finite-Temperature DFT computation. The electrons are therefore self-consistenly smeared over the molecular orbitals according to a Fermi-Dirac distribution. For a more detailed insight and the theory behind the FOD analytics, please see the original publication. To use FOD for selecting active spaces in CASSCF calculations, refer to our later work on this topic.
To access the FOD analysis, simply use the flag --fod
or set fod='true'
in the input (xcontrol) file. This will create a fod.cub
file and calculate the FOD on the cube grid.
Be sure to set the electronic temperature to a higher value, e.g. 5000 K (--etemp 5000
). The FOD population will be displayed in the printout section as:
NFOD : 0.6698
Loewdin FODpop n(s) n(p) n(d)
1 C 0.1924 0.018 0.175 0.000
2 C 0.0673 0.003 0.064 0.000
3 C 0.0673 0.003 0.064 0.000
4 C 0.1924 0.018 0.175 0.000
5 C 0.0673 0.003 0.064 0.000
6 C 0.0673 0.003 0.064 0.000
7 H 0.0039 0.004 0.000 0.000
8 H 0.0039 0.004 0.000 0.000
9 H 0.0039 0.004 0.000 0.000
10 H 0.0039 0.004 0.000 0.000
The NFOD number indicates the static electon correlation
If you do not want to write a full fod.cub
file, but still want to analyse the FOD population at least qualitatively, change the fod population ='bool'
in the input (xcontrol) file to true
. This will display the fractional loewdin
population of the system (see above) and only writes the fod
file, where this information is stored.
Redirecting Property Printout¶
For large systems the property printout can become quite lenghty and will
clutter maybe thousands of lines in the standard output.
One possibility is to rigourously deactivate all printouts using the
$write
instruction in the input file,
but if one might need this information later it is hard to recover,
as an alternative the property printout can be redirected.
Simply add
$write
output file=properties.out
to your input and specify the name for the redirection. The calculations of the properties are performed as usual but the standard output will show something like
Property printout bound to 'properties.out'
instead of the header, the usual printout can be found in properties.out
.
In the file the command line call and current time is saved additionally to
ensure that the printout is reproducable.
Machine Readable Data Dump¶
xtb
is able to dump parts of the calculated data in a machine-readable way
using the json-format. To activate the dump into a json file use the input
$write
json=true
which will write a xtbout.json
file containing partial charges,
cumulative atomic multipole moments, occupation number and orbtial energies
for single point calculations or frequencies, reduced masses and IR intensities
from hessian calculations.