xtb - Man Page

performs semiempirical quantummechanical calculations, for version 6.0 and newer

Synopsis

xtb [Options] FILE [Options]

Description

The xtb(1) program performs semiempirical quantummechanical calculations. The underlying effective Hamiltonian is derived from density functional tight binding (DFTB). This implementation of the xTB Hamiltonian is currently compatible with the zeroth (6.1 only), first and second level parametrisation for geometries, frequencies and non-covalent interactions (GFN) as well as with the ionisation potential and electron affinity (IPEA) parametrisation of the GFN1 Hamiltonian. The generalized born (GB) model with solvent accessable surface area (SASA) is also available available in this version. Ground state calculations for the simplified Tamm-Danceoff approximation (sTDA) with the vTB model are currently not implemented.

Geometry Input

The input coordinates can be presented in XMOL format and in Turbomole format. For most calculations no specific changes to these formats have to be made. The file type is determined automatically and the file extension can be freely chosen. XMOL coordinates must be given in Ångström, while in Turbomole format they can be given in Ångström as well as in Bohr (default). The corresponding keyword is given in the first line as ang or bohr instead of the $coord keyword.

Note

This implementation of xtb(1) can only identify and read coordinate files in Turbomole, if the $coord is in the first line of the file, valid Turbomole coordinate files with the $coord datagroup elsewhere will not be read in correctly and lead to abnormal termination of the program.

xtb(1) reads additionally .CHRG and .UHF files if present.

Input Sources

xtb(1) gets its information from different sources. The one with highest priority is the commandline with all allowed flags and arguments described below. The secondary source is the xcontrol(7) system, which can in principle use as many input files as wished. The xcontrol(7) system is the successor of the set-block as present in version 5.8.2 and earlier. This implementation of xtb(1) reads the xcontrol(7) from two of three possible sources, the local xcontrol file or the FILE used to specify the geometry and the global configuration file found in the XTBPATH.

Options

-c, --chrg INT

specify molecular charge as INT, overrides .CHRG file and xcontrol option

-u, --uhf INT

specify Nalpha-Nbeta as INT, overrides .UHF file and xcontrol option

--gfn INT

specify parametrisation of GFN-xTB (default = 2)

--gfnff, --gff

specify parametrisation of GFN-FF

--etemp REAL

electronic temperature (default = 300K)

--esp

calculate electrostatic potential on VdW-grid

--stm

calculate STM image

-a, --acc REAL

accuracy for SCC calculation, lower is better (default = 1.0)

--vparam FILE

Parameter file for vTB calculation

--xparam FILE

Parameter file for xTB calculation (not used)

--alpb SOLVENT [STATE]

analytical linearized Poisson-Boltzmann (ALPB) model, available solvents are acetone, acetonitrile, aniline, benzaldehyde, benzene, ch2cl2, chcl3, cs2, dioxane, dmf, dmso, ether, ethylacetate, furane, hexandecane, hexane, methanol, nitromethane, octanol, woctanol, phenol, toluene, thf, water. The solvent input is not case-sensitive. The Gsolv reference state can be chosen as reference or bar1M (default).

-g, --gbsa SOLVENT [STATE]

generalized born (GB) model with solvent accessable surface (SASA) model, available solvents are acetone, acetonitrile, benzene (only GFN1-xTB), CH2Cl2, CHCl3, CS2, DMF (only GFN2-xTB), DMSO, ether, H2O, methanol, n-hexane (only GFN2-xTB), THF and toluene. The solvent input is not case-sensitive. The Gsolv reference state can be chosen as reference or bar1M (default).

--cma

shifts molecule to center of mass and transforms cartesian coordinates into the coordinate system of the principle axis (not affected by ‘isotopes’-file).

--pop

requests printout of Mulliken population analysis

--molden

requests printout of molden file

--dipole

requests dipole printout

--wbo

requests Wiberg bond order printout

--lmo

requests localization of orbitals

--fod

requests FOD calculation

Runtyps

Note

You can only select one runtyp, only the first runtyp will be used from the program, use implemented composite runtyps to perform several operations at once.

--scc, --sp

performs a single point calculation

--vip

performs calculation of ionisation potential. This needs the .param_ipea.xtb parameters and a GFN1 Hamiltonian.

--vea

performs calculation of electron affinity. This needs the .param_ipea.xtb parameters and a GFN1 Hamiltonian.

--vipea

performs calculation of electron affinity and ionisation potential. This needs the .param_ipea.xtb parameters and a GFN1 Hamiltonian.

--vfukui

performs calculation of Fukui indices.

--vomega

performs calculation of electrophilicity index. This needs the .param_ipea.xtb parameters and a GFN1 Hamiltonian.

--grad

performs a gradient calculation

-o, --opt [LEVEL]

call ancopt(3) to perform a geometry optimization, levels from crude, sloppy, loose, normal (default), tight, verytight to extreme can be chosen

--optts [LEVEL] [ROOT]

call ancopt(3) to perform a transition state optimization, may need to perform a hessian calculation first

--hess

perform a numerical hessian calculation on input geometry

--ohess [LEVEL]

perform a numerical hessian calculation on an ancopt(3) optimized geometry

--bhess [LEVEL]

perform a biased numerical hessian calculation on an ancopt(3) optimized geometry

--md

molecular dynamics simulation on start geometry

--metadyn [int]

meta dynamics simulation on start geometry, saving int snapshots of the trajectory to bias the simulation (6.1 only)

--omd

molecular dynamics simulation on ancopt(3) optimized geometry, a loose optimization level will be chosen

--metaopt [LEVEL]

call ancopt(3) to perform a geometry optimization, then try to find other minimas by meta dynamics (6.1 only)

--path [FILE]

use meta dynamics to calculate a path from the input geometry to the given product structure (6.1 only)

--reactor

experimental (6.1 only)

--siman

conformational search by simulated annealing based on molecular dynamics. Conformers are optimized with ancopt(3).

--modef INT

modefollowing algorithm. INT specifies the mode that should be used for the modefollowing.

General

-I, --input FILE

use FILE as input source for xcontrol(7) instructions

--namespace STRING

give this xtb(1) run a namespace. All files, even temporary ones, will be named according to STRING (might not work everywhere).

--[no]copy

copies the xcontrol file at startup (default = true)

--[no]restart

restarts calculation from xtbrestart (default = true)

-P, --parallel INT

number of parallel processes

--define

performs automatic check of input and terminate

--json

write xtbout.json file

--citation

print citation and terminate

--license

print license and terminate

-v, --verbose

be more verbose (not supported in every unit)

-s, --silent

clutter the screen less (not supported in every unit)

--ceasefiles

reduce the amount of output and files written

--strict

turns all warnings into hard errors

-h, --help

show help page

Environment Variables

xtb(1) accesses a path-like variable to determine the location of its parameter files, you have to provide the XTBPATH variable in the same syntax as the system PATH variable. If this variable is not set, xtb(1) will try to generate the XTBPATH from the deprecated XTBHOME variable. In case the XTBHOME variable is not set it will be generated from the HOME variable. So in principle storing the parameter files in the users home directory is suffient but might lead to come cluttering.

Since the XTBHOME variable is deprecated with version 6.0 and newer xtb(1) will issue a warning if XTBHOME is not part of the XTBPATH since the XTBHOME variable is not used in production runs.

Local Files

xtb(1) accesses a number of local files in the current working directory and also writes some output in specific files. Note that not all input and output files allow the --namespace option.

Input

.CHRG

molecular charge as int

.UHF

Nalpha-Nbeta as int

mdrestart

contains restart information for MD, --namespace compatible.

pcharge

point charge input, format is real real real real [int]. The first real is used as partial charge, the next three entries are the cartesian coordinates and the last is an optional atom type. Note that the point charge input is not affected by a CMA transformation. Also parallel Hessian calculations will fail due to I/O errors when using point charge embedding.

solvent

qmdff(1) input file

xcontrol

default input file in --copy mode, see xcontrol(7) for details, set by --input.

xtbrestart

contains restart information for SCC, --namespace compatible.

Output

charges

contains Mulliken partial charges calculated in SCC

wbo

contains Wiberg bond order calculated in SCC, --namespace compatible.

energy

total energy in Turbomole format

gradient

geometry, energy and gradient in Turbomole format

hessian

contains the (not mass weighted) cartesian Hessian, --namespace compatible.

xtbopt.xyz, xtbopt.coord

optimized geometry in the same format as the input geometry.

xtbhess.coord

distorted geometry if imaginary frequency was found

xtbopt.log

contains all structures obtained in the geometry optimization with the respective energy in the comment line in a XMOL formatted trajectory

xtbsiman.log,xtb.trj.int

trajectories from MD

scoord.int

coordinate dump of MD

fod.cub

FOD on a cube-type grid

spindensity.cub

spindensity on a cube-type grid

density.cub

density on a cube-type grid

molden.input

MOs and occupation for visualisation and sTDA-xTB calculations

pcgrad

gradient of the point charges

xtb_esp.cosmo

ESP fake cosmo output

xtb_esp_profile.dat

ESP histogramm data

vibspectrum

Turbomole style vibrational spectrum data group

g98.out, g98l.out, g98_canmode.out, g98_locmode.out

g98 fake output with normal or local modes

.tmpxtbmodef

input for mode following

coordprot.0

protonated species

xtblmoinfo

centers of the localized molecular orbitals

lmocent.coord

centers of the localized molecular orbitals

tmpxx

number of recommended modes for mode following

xtb_normalmodes, xtb_localmodes

binary dump for mode following

Touch

xtbmdok

generated by successful MD

.xtbok

generated after each successful xtb(1) run

.sccnotconverged

generated after failed SCC with printlevel=2

Warnings

xtb(1) can generate the two types of warnings, the first warning section is printed immediately after the normal banner at startup, summing up the evaluation of all input sources (commandline, xcontrol, xtbrc). To check this warnings exclusively before running an expensive calculation a input check is implemented via the --define flag. Please, study this warnings carefully!

After xtb(1) has evaluated the all input sources it immediately enters the production mode. Severe errors will lead to an abnormal termination which is signalled by the printout to STDERR and a non-zero return value (usually 128). All non-fatal errors are summerized in the end of the calculation in one block, right bevor the timing analysis.

To aid the user to fix the problems generating these warnings a brief summary of each warning with its respective string representation in the output will be shown here:

ANCopt failed to converge the optimization

geometry optimization has failed to converge in the given number optimization cycles. This is not neccessary a problem if only a small number of cycles was given for the optimization on purpose. All further calculations are done on the last geometry of the optimization.

Hessian on incompletely optimized geometry!

This warning will be issued twice, once before the Hessian, calculations starts (it would otherwise take some time before this this warning could be detected) and in the warning block in the end. The warning will be generated if the gradient norm on the given geometry is higher than a certain threshold.

Exit Status

0

normal termination of xtb(1)

128

Failure (termination via error stop generates 128 as return value)

Bugs

please report all bugs with an example input, --copy dump of internal settings and the used geometry, as well as the --verbose output to xtb@thch.uni-bonn.de

Resources

Main web site: http://grimme.uni-bonn.de/software/xtb

Copying

Copyright (C) 2015-2018 S. Grimme. For non-commerical, academia use only.

Referenced By

xcontrol(7).

2020-09-17