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 (6.1 only), first
17 and second level parametrisation for geometries, frequencies and
18 non-covalent interactions (GFN) as well as with the ionisation
19 potential and electron affinity (IPEA) parametrisation of the GFN1
20 Hamiltonian. The generalized born (GB) model with solvent accessable
21 surface area (SASA) is also available available in this version. Ground
22 state calculations for the simplified Tamm-Danceoff approximation
23 (sTDA) with the vTB model are currently not implemented.
24 GEOMETRY INPUT
26 The input coordinates can be presented in XMOL format and in Turbomole
27 format. For most calculations no specific changes to these formats have
28 to be made. The file type is determined automatically and the file
29 extension can be freely chosen. XMOL coordinates must be given in
30 Ångström, while in Turbomole format they can be given in Ångström as
31 well as in Bohr (default). The corresponding keyword is given in the
32 first line as ang or bohr instead of the $coord keyword.
33 Note
35 This implementation of xtb(1) can only identify and read coordinate
36 files in Turbomole, if the $coord is in the first line of the file,
37 valid Turbomole coordinate files with the $coord datagroup
38 elsewhere will not be read in correctly and lead to abnormal
39 termination of the program.
40 xtb(1) reads additionally .CHRG and .UHF files if present.
42
44 xtb(1) gets its information from different sources. The one with
45 highest priority is the commandline with all allowed flags and
46 arguments described below. The secondary source is the xcontrol(7)
47 system, which can in principle use as many input files as wished. The
48 xcontrol(7) system is the successor of the set-block as present in
49 version 5.8.2 and earlier. This implementation of xtb(1) reads the
50 xcontrol(7) from two of three possible sources, the local xcontrol file
51 or the FILE used to specify the geometry and the global configuration
52 file found in the XTBPATH.
53
55 -c, --chrg INT
56 specify molecular charge as INT, overrides .CHRG file and xcontrol
57 option
58 -u, --uhf INT
60 specify Nalpha-Nbeta as INT, overrides .UHF file and xcontrol
61 option
62 --gfn INT
64 specify parametrisation of GFN-xTB (default = 2)
65 --gfnff, --gff
67 specify parametrisation of GFN-FF
68 --etemp REAL
70 electronic temperature (default = 300K)
71 --esp
73 calculate electrostatic potential on VdW-grid
74 --stm
76 calculate STM image
77 -a, --acc REAL
79 accuracy for SCC calculation, lower is better (default = 1.0)
80 --vparam FILE
82 Parameter file for vTB calculation
83 --xparam FILE
85 Parameter file for xTB calculation (not used)
86 --alpb SOLVENT [STATE]
88 analytical linearized Poisson-Boltzmann (ALPB) model, available
89 solvents are acetone, acetonitrile, aniline, benzaldehyde, benzene,
90 ch2cl2, chcl3, cs2, dioxane, dmf, dmso, ether, ethylacetate,
91 furane, hexandecane, hexane, methanol, nitromethane, octanol,
92 woctanol, phenol, toluene, thf, water. The solvent input is not
93 case-sensitive. The Gsolv reference state can be chosen as
94 reference or bar1M (default).
95 -g, --gbsa SOLVENT [STATE]
97 generalized born (GB) model with solvent accessable surface (SASA)
98 model, available solvents are acetone, acetonitrile, benzene (only
99 GFN1-xTB), CH2Cl2, CHCl3, CS2, DMF (only GFN2-xTB), DMSO, ether,
100 H2O, methanol, n-hexane (only GFN2-xTB), THF and toluene. The
101 solvent input is not case-sensitive. The Gsolv reference state can
102 be chosen as reference or bar1M (default).
103 --cma
105 shifts molecule to center of mass and transforms cartesian
106 coordinates into the coordinate system of the principle axis (not
107 affected by ‘isotopes’-file).
108 --pop
110 requests printout of Mulliken population analysis
111 --molden
113 requests printout of molden file
114 --dipole
116 requests dipole printout
117 --wbo
119 requests Wiberg bond order printout
120 --lmo
122 requests localization of orbitals
123 --fod
125 requests FOD calculation
126 RUNTYPS
128 Note
129 You can only select one runtyp, only the first runtyp will be used
130 from the program, use implemented composite runtyps to perform
131 several operations at once.
132 --scc, --sp
134 performs a single point calculation
135 --vip
137 performs calculation of ionisation potential. This needs the
138 .param_ipea.xtb parameters and a GFN1 Hamiltonian.
139 --vea
141 performs calculation of electron affinity. This needs the
142 .param_ipea.xtb parameters and a GFN1 Hamiltonian.
143 --vipea
145 performs calculation of electron affinity and ionisation potential.
146 This needs the .param_ipea.xtb parameters and a GFN1 Hamiltonian.
147 --vfukui
149 performs calculation of Fukui indices.
150 --vomega
152 performs calculation of electrophilicity index. This needs the
153 .param_ipea.xtb parameters and a GFN1 Hamiltonian.
154 --grad
156 performs a gradient calculation
157 -o, --opt [LEVEL]
159 call ancopt(3) to perform a geometry optimization, levels from
160 crude, sloppy, loose, normal (default), tight, verytight to extreme
161 can be chosen
162 --hess
164 perform a numerical hessian calculation on input geometry
165 --ohess [LEVEL]
167 perform a numerical hessian calculation on an ancopt(3) optimized
168 geometry
169 --bhess [LEVEL]
171 perform a biased numerical hessian calculation on an ancopt(3)
172 optimized geometry
173 --md
175 molecular dynamics simulation on start geometry
176 --metadyn [int]
178 meta dynamics simulation on start geometry, saving int snapshots of
179 the trajectory to bias the simulation (6.1 only)
180 --omd
182 molecular dynamics simulation on ancopt(3) optimized geometry, a
183 loose optimization level will be chosen
184 --metaopt [LEVEL]
186 call ancopt(3) to perform a geometry optimization, then try to find
187 other minimas by meta dynamics (6.1 only)
188 --path [FILE]
190 use meta dynamics to calculate a path from the input geometry to
191 the given product structure (6.1 only)
192 --reactor
194 experimental (6.1 only)
195 --modef INT
197 modefollowing algorithm. INT specifies the mode that should be used
198 for the modefollowing.
199 GENERAL
201 -I, --input FILE
202 use FILE as input source for xcontrol(7) instructions
203 --namespace STRING
205 give this xtb(1) run a namespace. All files, even temporary ones,
206 will be named according to STRING (might not work everywhere).
207 --[no]copy
209 copies the xcontrol file at startup (default = true)
210 --[no]restart
212 restarts calculation from xtbrestart (default = true)
213 -P, --parallel INT
215 number of parallel processes
216 --define
218 performs automatic check of input and terminate
219 --json
221 write xtbout.json file
222 --citation
224 print citation and terminate
225 --license
227 print license and terminate
228 -v, --verbose
230 be more verbose (not supported in every unit)
231 -s, --silent
233 clutter the screen less (not supported in every unit)
234 --ceasefiles
236 reduce the amount of output and files written
237 --strict
239 turns all warnings into hard errors
240 -h, --help
242 show help page
243
245 xtb(1) accesses a path-like variable to determine the location of its
246 parameter files, you have to provide the XTBPATH variable in the same
247 syntax as the system PATH variable. If this variable is not set, xtb(1)
248 will try to generate the XTBPATH from the deprecated XTBHOME variable.
249 In case the XTBHOME variable is not set it will be generated from the
250 HOME variable. So in principle storing the parameter files in the users
251 home directory is suffient but might lead to come cluttering.
252 Since the XTBHOME variable is deprecated with version 6.0 and newer
254 xtb(1) will issue a warning if XTBHOME is not part of the XTBPATH since
255 the XTBHOME variable is not used in production runs.
256
258 xtb(1) accesses a number of local files in the current working
259 directory and also writes some output in specific files. Note that not
260 all input and output files allow the --namespace option.
261 INPUT
263 .CHRG
264 molecular charge as int
265 .UHF
267 Nalpha-Nbeta as int
268 mdrestart
270 contains restart information for MD, --namespace compatible.
271 pcharge
273 point charge input, format is real real real real [int]. The first
274 real is used as partial charge, the next three entries are the
275 cartesian coordinates and the last is an optional atom type. Note
276 that the point charge input is not affected by a CMA
277 transformation. Also parallel Hessian calculations will fail due to
278 I/O errors when using point charge embedding.
279 solvent
281 qmdff(1) input file
282 xcontrol
284 default input file in --copy mode, see xcontrol(7) for details, set
285 by --input.
286 xtbrestart
288 contains restart information for SCC, --namespace compatible.
289 OUTPUT
291 charges
292 contains Mulliken partial charges calculated in SCC
293 wbo
295 contains Wiberg bond order calculated in SCC, --namespace
296 compatible.
297 energy
299 total energy in Turbomole format
300 gradient
302 geometry, energy and gradient in Turbomole format
303 hessian
305 contains the (not mass weighted) cartesian Hessian, --namespace
306 compatible.
307 xtbopt.xyz, xtbopt.coord
309 optimized geometry in the same format as the input geometry.
310 xtbhess.coord
312 distorted geometry if imaginary frequency was found
313 xtbopt.log
315 contains all structures obtained in the geometry optimization with
316 the respective energy in the comment line in a XMOL formatted
317 trajectory
318 xtbsiman.log,xtb.trj.int
320 trajectories from MD
321 scoord.int
323 coordinate dump of MD
324 fod.cub
326 FOD on a cube-type grid
327 spindensity.cub
329 spindensity on a cube-type grid
330 density.cub
332 density on a cube-type grid
333 molden.input
335 MOs and occupation for visualisation and sTDA-xTB calculations
336 pcgrad
338 gradient of the point charges
339 xtb_esp.cosmo
341 ESP fake cosmo output
342 xtb_esp_profile.dat
344 ESP histogramm data
345 vibspectrum
347 Turbomole style vibrational spectrum data group
348 g98.out, g98l.out, g98_canmode.out, g98_locmode.out
350 g98 fake output with normal or local modes
351 .tmpxtbmodef
353 input for mode following
354 coordprot.0
356 protonated species
357 xtblmoinfo
359 centers of the localized molecular orbitals
360 lmocent.coord
362 centers of the localized molecular orbitals
363 tmpxx
365 number of recommended modes for mode following
366 xtb_normalmodes, xtb_localmodes
368 binary dump for mode following
369 TOUCH
371 xtbmdok
372 generated by successful MD
373 .xtbok
375 generated after each successful xtb(1) run
376 .sccnotconverged
378 generated after failed SCC with printlevel=2
379
381 xtb(1) can generate the two types of warnings, the first warning
382 section is printed immediately after the normal banner at startup,
383 summing up the evaluation of all input sources (commandline, xcontrol,
384 xtbrc). To check this warnings exclusively before running an expensive
385 calculation a input check is implemented via the --define flag. Please,
386 study this warnings carefully!
387 After xtb(1) has evaluated the all input sources it immediately enters
389 the production mode. Severe errors will lead to an abnormal termination
390 which is signalled by the printout to STDERR and a non-zero return
391 value (usually 128). All non-fatal errors are summerized in the end of
392 the calculation in one block, right bevor the timing analysis.
393 To aid the user to fix the problems generating these warnings a brief
395 summary of each warning with its respective string representation in
396 the output will be shown here:
397 ANCopt failed to converge the optimization
399 geometry optimization has failed to converge in the given number
400 optimization cycles. This is not neccessary a problem if only a
401 small number of cycles was given for the optimization on purpose.
402 All further calculations are done on the last geometry of the
403 optimization.
404 Hessian on incompletely optimized geometry!
406 This warning will be issued twice, once before the Hessian,
407 calculations starts (it would otherwise take some time before this
408 this warning could be detected) and in the warning block in the
409 end. The warning will be generated if the gradient norm on the
410 given geometry is higher than a certain threshold.
411
413 0
414 normal termination of xtb(1)
415 128
417 Failure (termination via error stop generates 128 as return value)
418
420 please report all bugs with an example input, --copy dump of internal
421 settings and the used geometry, as well as the --verbose output to
422 xtb@thch.uni-bonn.de
423
425 Main web site: http://grimme.uni-bonn.de/software/xtb
426
428 Copyright (C) 2015-2018 S. Grimme. For non-commerical, academia use
429 only.
430 2022-01-22 XTB(1)