xtb - Man Page

performs semiempirical quantummechanical calculations, for version 6.0 and newer

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, 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 in this version. Ground state calculations for the simplified Tamm-Dancoff approximation (sTDA) with the vTB model are currently not implemented.

Geometry Input

The wide variety of input formats for the geometry are supported by using the mctc-lib. Supported formats are:

Xmol/xyz files (xyz, log)
Turbomole’s coord, riper’s periodic coord (tmol, coord)
DFTB+ genFormat geometry inputs as cluster, supercell or fractional (gen)
VASP’s POSCAR/CONTCAR input files (vasp, poscar, contcar)
Protein Database files, only single files (pdb)
Connection table files, molfile (mol) and structure data format (sdf)
Gaussian’s external program input (ein)
JSON input with qcschema_molecule or qcschema_input structure (json)
FHI-AIMS' input files (geometry.in)
Q-Chem molecule block inputs (qchem)

For a full list visit: https://grimme-lab.github.io/mctc-lib/page/index.html

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
-c, --chrg INT:INT: specify charges for inner region:outer region for oniom calculation, overrides .CHRG file and xcontrol option
-u, --uhf INT: specify number of unpaired electrons as INT, overrides .UHF file and xcontrol option
--gfn INT: specify parametrisation of GFN-xTB (default = 2)
--gfnff, --gff: specify parametrisation of GFN-FF
--tblite: use tblite library as implementation for xTB
--ceh*: calculate CEH (Charge-Extended Hückel model) charges and write them to ceh.charges file
--ptb: performs single-point calculation with the density tight-binding method PTB. Provides electronic structure and properties, such as, e.g., atomic charges, bond orders, and dipole moments, but does not provide any energy-related properties, such as, e.g., total energy, nuclear gradients, or vibrational frequencies.
--spinpol: enables spin-polarization for xTB methods (tblite required)
--oniom METHOD LIST: use subtractive embedding via ONIOM method. METHOD is given as high:low where high can be orca, turbomole, gfn2, gfn1, or gfnff and low can be gfn2, gfn1, or gfnff. The inner region is given as comma-separated indices directly in the commandline or in a file with each index on a separate line.
--etemp, --temp REAL: electronic temperature for SCC (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)
--iterations, --maxiterations INT: maximum number of SCC iterations per single point calculation (default = 250)
--vparam FILE: Parameter file for xTB calculation
--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, bar1M, or gsolv (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, bar1M, or gsolv (default).
--cosmo SOLVENT/EPSILON: domain decomposition conductor-like screening model (ddCOSMO) available solvents are all solvents that are available for alpb. Additionally, the dielectric constant can be set manually or an ideal conductor can be chosen by setting epsilon to infinity.
--tmcosmo SOLVENT/EPSILON: same as --cosmo, but uses TM convention for writing the .cosmo files.
--cpcmx SOLVENT: extended conduction-like polarizable continuum solvation model (CPCM-X), available solvents are all solvents included in the Minnesota Solvation Database.
--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
--alpha: requests the extension of electrical properties to static molecular dipole polarizabilities
--raman: requests Raman spectrum calculation via combination of GFN2-xTB and PTB using the temperature REAL (default 298.15 K) and the wavelength of the incident laser which must be given in nm REAL (default 514 nm)
--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
--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
--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
--path [FILE]: use meta dynamics to calculate a path from the input geometry to the given product structure
--reactor: experimental
--modef INT: modefollowing algorithm. INT specifies the mode that should be used for the modefollowing.
--dipro [REAL]: the dimer projection method for the calculation of electronic coupling integrals between two fragments. REAL sets the threshold for nearly degenerate orbitals to still be considered (default = 0.1 eV).

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 (e.g. xtbtopo.mol)
--strict: turns all warnings into hard errors
-h, --help: show help page
--cut: create inner region for oniom calculation without performing any calcultion

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: Number of unpaired electrons 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.
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
ceh.charges: contains CEH (Charge-Extended Hückel) charges
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.
xtbtopo.mol: topology information written in molfile format.
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 before 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)

You should have received a copy of the GNU Lesser General Public License along with xtb. If not, see https://www.gnu.org/licenses/.

Referenced By

crest(1), xcontrol(7).

2024-09-13