1XTB(1) XTB(1)
2
6 xtb - performs semiempirical quantummechanical calculations, for
7 version 6.0 and newer
8
10 xtb [OPTIONS] FILE [OPTIONS]
11
13 The xtb(1) program performs semiempirical quantummechanical
14 calculations. The underlying effective Hamiltonian is derived from
15 density functional tight binding (DFTB). This implementation of the xTB
16 Hamiltonian is currently compatible with the zeroth, first and second
17 level parametrisation for geometries, frequencies and non-covalent
18 interactions (GFN) as well as with the ionisation potential and
19 electron affinity (IPEA) parametrisation of the GFN1 Hamiltonian. The
20 generalized born (GB) model with solvent accessable surface area (SASA)
21 is also available available in this version. Ground state calculations
22 for the simplified Tamm-Danceoff approximation (sTDA) with the vTB
23 model are currently not implemented.
24 GEOMETRY INPUT
26 The wide variety of input formats for the geometry are supported by
27 using the mctc-lib. Supported formats are:
28 • Xmol/xyz files (xyz, log)
30 • Turbomole’s coord, riper’s periodic coord (tmol, coord)
32 • DFTB+ genFormat geometry inputs as cluster, supercell or fractional
34 (gen)
35 • VASP’s POSCAR/CONTCAR input files (vasp, poscar, contcar)
37 • Protein Database files, only single files (pdb)
39 • Connection table files, molfile (mol) and structure data format
41 (sdf)
42 • Gaussian’s external program input (ein)
44 • JSON input with qcschema_molecule or qcschema_input structure
46 (json)
47 • FHI-AIMS' input files (geometry.in)
49 • Q-Chem molecule block inputs (qchem)
51 For a full list visit:
53 https://grimme-lab.github.io/mctc-lib/page/index.html
54 xtb(1) reads additionally .CHRG and .UHF files if present.
56
58 xtb(1) gets its information from different sources. The one with
59 highest priority is the commandline with all allowed flags and
60 arguments described below. The secondary source is the xcontrol(7)
61 system, which can in principle use as many input files as wished. The
62 xcontrol(7) system is the successor of the set-block as present in
63 version 5.8.2 and earlier. This implementation of xtb(1) reads the
64 xcontrol(7) from two of three possible sources, the local xcontrol file
65 or the FILE used to specify the geometry and the global configuration
66 file found in the XTBPATH.
67
69 -c, --chrg INT
70 specify molecular charge as INT, overrides .CHRG file and xcontrol
71 option
72 -u, --uhf INT
74 specify number of unpaired electrons as INT, overrides .UHF file
75 and xcontrol option
76 --gfn INT
78 specify parametrisation of GFN-xTB (default = 2)
79 --gfnff, --gff
81 specify parametrisation of GFN-FF
82 --oniom METHOD LIST
84 use subtractive embedding via ONIOM method. METHOD is given as
85 inner:outer where inner can be orca, turbomole, gfn2, gfn1, or
86 gfnff and outer can be gfn2, gfn1, or gfnff. The inner region is
87 given as a comma separated indices directly in the commandline or
88 in a file with each index on a separate line.
89 --etemp REAL
91 electronic temperature (default = 300K)
92 --esp
94 calculate electrostatic potential on VdW-grid
95 --stm
97 calculate STM image
98 -a, --acc REAL
100 accuracy for SCC calculation, lower is better (default = 1.0)
101 --vparam FILE
103 Parameter file for vTB calculation
104 --xparam FILE
106 Parameter file for xTB calculation (not used)
107 --alpb SOLVENT [STATE]
109 analytical linearized Poisson-Boltzmann (ALPB) model, available
110 solvents are acetone, acetonitrile, aniline, benzaldehyde, benzene,
111 ch2cl2, chcl3, cs2, dioxane, dmf, dmso, ether, ethylacetate,
112 furane, hexandecane, hexane, methanol, nitromethane, octanol,
113 woctanol, phenol, toluene, thf, water. The solvent input is not
114 case-sensitive. The Gsolv reference state can be chosen as
115 reference or bar1M (default).
116 -g, --gbsa SOLVENT [STATE]
118 generalized born (GB) model with solvent accessable surface (SASA)
119 model, available solvents are acetone, acetonitrile, benzene (only
120 GFN1-xTB), CH2Cl2, CHCl3, CS2, DMF (only GFN2-xTB), DMSO, ether,
121 H2O, methanol, n-hexane (only GFN2-xTB), THF and toluene. The
122 solvent input is not case-sensitive. The Gsolv reference state can
123 be chosen as reference or bar1M (default).
124 --cma
126 shifts molecule to center of mass and transforms cartesian
127 coordinates into the coordinate system of the principle axis (not
128 affected by ‘isotopes’-file).
129 --pop
131 requests printout of Mulliken population analysis
132 --molden
134 requests printout of molden file
135 --dipole
137 requests dipole printout
138 --wbo
140 requests Wiberg bond order printout
141 --lmo
143 requests localization of orbitals
144 --fod
146 requests FOD calculation
147 RUNTYPS
149 Note
150 You can only select one runtyp, only the first runtyp will be used
151 from the program, use implemented composite runtyps to perform
152 several operations at once.
153 --scc, --sp
155 performs a single point calculation
156 --vip
158 performs calculation of ionisation potential. This needs the
159 .param_ipea.xtb parameters and a GFN1 Hamiltonian.
160 --vea
162 performs calculation of electron affinity. This needs the
163 .param_ipea.xtb parameters and a GFN1 Hamiltonian.
164 --vipea
166 performs calculation of electron affinity and ionisation potential.
167 This needs the .param_ipea.xtb parameters and a GFN1 Hamiltonian.
168 --vfukui
170 performs calculation of Fukui indices.
171 --vomega
173 performs calculation of electrophilicity index. This needs the
174 .param_ipea.xtb parameters and a GFN1 Hamiltonian.
175 --grad
177 performs a gradient calculation
178 -o, --opt [LEVEL]
180 call ancopt(3) to perform a geometry optimization, levels from
181 crude, sloppy, loose, normal (default), tight, verytight to extreme
182 can be chosen
183 --hess
185 perform a numerical hessian calculation on input geometry
186 --ohess [LEVEL]
188 perform a numerical hessian calculation on an ancopt(3) optimized
189 geometry
190 --bhess [LEVEL]
192 perform a biased numerical hessian calculation on an ancopt(3)
193 optimized geometry
194 --md
196 molecular dynamics simulation on start geometry
197 --metadyn [int]
199 meta dynamics simulation on start geometry, saving int snapshots of
200 the trajectory to bias the simulation
201 --omd
203 molecular dynamics simulation on ancopt(3) optimized geometry, a
204 loose optimization level will be chosen
205 --metaopt [LEVEL]
207 call ancopt(3) to perform a geometry optimization, then try to find
208 other minimas by meta dynamics
209 --path [FILE]
211 use meta dynamics to calculate a path from the input geometry to
212 the given product structure
213 --reactor
215 experimental
216 --modef INT
218 modefollowing algorithm. INT specifies the mode that should be used
219 for the modefollowing.
220 GENERAL
222 -I, --input FILE
223 use FILE as input source for xcontrol(7) instructions
224 --namespace STRING
226 give this xtb(1) run a namespace. All files, even temporary ones,
227 will be named according to STRING (might not work everywhere).
228 --[no]copy
230 copies the xcontrol file at startup (default = true)
231 --[no]restart
233 restarts calculation from xtbrestart (default = true)
234 -P, --parallel INT
236 number of parallel processes
237 --define
239 performs automatic check of input and terminate
240 --json
242 write xtbout.json file
243 --citation
245 print citation and terminate
246 --license
248 print license and terminate
249 -v, --verbose
251 be more verbose (not supported in every unit)
252 -s, --silent
254 clutter the screen less (not supported in every unit)
255 --ceasefiles
257 reduce the amount of output and files written
258 --strict
260 turns all warnings into hard errors
261 -h, --help
263 show help page
264
266 xtb(1) accesses a path-like variable to determine the location of its
267 parameter files, you have to provide the XTBPATH variable in the same
268 syntax as the system PATH variable. If this variable is not set, xtb(1)
269 will try to generate the XTBPATH from the deprecated XTBHOME variable.
270 In case the XTBHOME variable is not set it will be generated from the
271 HOME variable. So in principle storing the parameter files in the users
272 home directory is suffient but might lead to come cluttering.
273 Since the XTBHOME variable is deprecated with version 6.0 and newer
275 xtb(1) will issue a warning if XTBHOME is not part of the XTBPATH since
276 the XTBHOME variable is not used in production runs.
277
279 xtb(1) accesses a number of local files in the current working
280 directory and also writes some output in specific files. Note that not
281 all input and output files allow the --namespace option.
282 INPUT
284 .CHRG
285 molecular charge as int
286 .UHF
288 Number of unpaired electrons as int
289 mdrestart
291 contains restart information for MD, --namespace compatible.
292 pcharge
294 point charge input, format is real real real real [int]. The first
295 real is used as partial charge, the next three entries are the
296 cartesian coordinates and the last is an optional atom type. Note
297 that the point charge input is not affected by a CMA
298 transformation. Also parallel Hessian calculations will fail due to
299 I/O errors when using point charge embedding.
300 xcontrol
302 default input file in --copy mode, see xcontrol(7) for details, set
303 by --input.
304 xtbrestart
306 contains restart information for SCC, --namespace compatible.
307 OUTPUT
309 charges
310 contains Mulliken partial charges calculated in SCC
311 wbo
313 contains Wiberg bond order calculated in SCC, --namespace
314 compatible.
315 energy
317 total energy in Turbomole format
318 gradient
320 geometry, energy and gradient in Turbomole format
321 hessian
323 contains the (not mass weighted) cartesian Hessian, --namespace
324 compatible.
325 xtbopt.xyz, xtbopt.coord
327 optimized geometry in the same format as the input geometry.
328 xtbhess.coord
330 distorted geometry if imaginary frequency was found
331 xtbopt.log
333 contains all structures obtained in the geometry optimization with
334 the respective energy in the comment line in a XMOL formatted
335 trajectory
336 xtbsiman.log,xtb.trj.int
338 trajectories from MD
339 scoord.int
341 coordinate dump of MD
342 fod.cub
344 FOD on a cube-type grid
345 spindensity.cub
347 spindensity on a cube-type grid
348 density.cub
350 density on a cube-type grid
351 molden.input
353 MOs and occupation for visualisation and sTDA-xTB calculations
354 pcgrad
356 gradient of the point charges
357 xtb_esp.cosmo
359 ESP fake cosmo output
360 xtb_esp_profile.dat
362 ESP histogramm data
363 vibspectrum
365 Turbomole style vibrational spectrum data group
366 g98.out, g98l.out, g98_canmode.out, g98_locmode.out
368 g98 fake output with normal or local modes
369 .tmpxtbmodef
371 input for mode following
372 coordprot.0
374 protonated species
375 xtblmoinfo
377 centers of the localized molecular orbitals
378 lmocent.coord
380 centers of the localized molecular orbitals
381 tmpxx
383 number of recommended modes for mode following
384 xtb_normalmodes, xtb_localmodes
386 binary dump for mode following
387 TOUCH
389 xtbmdok
390 generated by successful MD
391 .xtbok
393 generated after each successful xtb(1) run
394 .sccnotconverged
396 generated after failed SCC with printlevel=2
397
399 xtb(1) can generate the two types of warnings, the first warning
400 section is printed immediately after the normal banner at startup,
401 summing up the evaluation of all input sources (commandline, xcontrol,
402 xtbrc). To check this warnings exclusively before running an expensive
403 calculation a input check is implemented via the --define flag. Please,
404 study this warnings carefully!
405 After xtb(1) has evaluated the all input sources it immediately enters
407 the production mode. Severe errors will lead to an abnormal termination
408 which is signalled by the printout to STDERR and a non-zero return
409 value (usually 128). All non-fatal errors are summerized in the end of
410 the calculation in one block, right bevor the timing analysis.
411 To aid the user to fix the problems generating these warnings a brief
413 summary of each warning with its respective string representation in
414 the output will be shown here:
415 ANCopt failed to converge the optimization
417 geometry optimization has failed to converge in the given number
418 optimization cycles. This is not neccessary a problem if only a
419 small number of cycles was given for the optimization on purpose.
420 All further calculations are done on the last geometry of the
421 optimization.
422 Hessian on incompletely optimized geometry!
424 This warning will be issued twice, once before the Hessian,
425 calculations starts (it would otherwise take some time before this
426 this warning could be detected) and in the warning block in the
427 end. The warning will be generated if the gradient norm on the
428 given geometry is higher than a certain threshold.
429
431 0
432 normal termination of xtb(1)
433 128
435 Failure (termination via error stop generates 128 as return value)
436
438 please report all bugs with an example input, --copy dump of internal
439 settings and the used geometry, as well as the --verbose output to
440 xtb@thch.uni-bonn.de
441
443 Main web site: http://grimme.uni-bonn.de/software/xtb
444
446 Copyright (C) 2015-2018 S. Grimme. For non-commerical, academia use
447 only.
448 2023-01-21 XTB(1)