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 --optts [LEVEL] [ROOT]
164 call ancopt(3) to perform a transition state optimization, may need
165 to perform a hessian calculation first
166 --hess
168 perform a numerical hessian calculation on input geometry
169 --ohess [LEVEL]
171 perform a numerical hessian calculation on an ancopt(3) optimized
172 geometry
173 --bhess [LEVEL]
175 perform a biased numerical hessian calculation on an ancopt(3)
176 optimized geometry
177 --md
179 molecular dynamics simulation on start geometry
180 --metadyn [int]
182 meta dynamics simulation on start geometry, saving int snapshots of
183 the trajectory to bias the simulation (6.1 only)
184 --omd
186 molecular dynamics simulation on ancopt(3) optimized geometry, a
187 loose optimization level will be chosen
188 --metaopt [LEVEL]
190 call ancopt(3) to perform a geometry optimization, then try to find
191 other minimas by meta dynamics (6.1 only)
192 --path [FILE]
194 use meta dynamics to calculate a path from the input geometry to
195 the given product structure (6.1 only)
196 --reactor
198 experimental (6.1 only)
199 --siman
201 conformational search by simulated annealing based on molecular
202 dynamics. Conformers are optimized with ancopt(3).
203 --modef INT
205 modefollowing algorithm. INT specifies the mode that should be used
206 for the modefollowing.
207 GENERAL
209 -I, --input FILE
210 use FILE as input source for xcontrol(7) instructions
211 --namespace STRING
213 give this xtb(1) run a namespace. All files, even temporary ones,
214 will be named according to STRING (might not work everywhere).
215 --[no]copy
217 copies the xcontrol file at startup (default = true)
218 --[no]restart
220 restarts calculation from xtbrestart (default = true)
221 -P, --parallel INT
223 number of parallel processes
224 --define
226 performs automatic check of input and terminate
227 --json
229 write xtbout.json file
230 --citation
232 print citation and terminate
233 --license
235 print license and terminate
236 -v, --verbose
238 be more verbose (not supported in every unit)
239 -s, --silent
241 clutter the screen less (not supported in every unit)
242 --ceasefiles
244 reduce the amount of output and files written
245 --strict
247 turns all warnings into hard errors
248 -h, --help
250 show help page
251
253 xtb(1) accesses a path-like variable to determine the location of its
254 parameter files, you have to provide the XTBPATH variable in the same
255 syntax as the system PATH variable. If this variable is not set, xtb(1)
256 will try to generate the XTBPATH from the deprecated XTBHOME variable.
257 In case the XTBHOME variable is not set it will be generated from the
258 HOME variable. So in principle storing the parameter files in the users
259 home directory is suffient but might lead to come cluttering.
260 Since the XTBHOME variable is deprecated with version 6.0 and newer
262 xtb(1) will issue a warning if XTBHOME is not part of the XTBPATH since
263 the XTBHOME variable is not used in production runs.
264
266 xtb(1) accesses a number of local files in the current working
267 directory and also writes some output in specific files. Note that not
268 all input and output files allow the --namespace option.
269 INPUT
271 .CHRG
272 molecular charge as int
273 .UHF
275 Nalpha-Nbeta as int
276 mdrestart
278 contains restart information for MD, --namespace compatible.
279 pcharge
281 point charge input, format is real real real real [int]. The first
282 real is used as partial charge, the next three entries are the
283 cartesian coordinates and the last is an optional atom type. Note
284 that the point charge input is not affected by a CMA
285 transformation. Also parallel Hessian calculations will fail due to
286 I/O errors when using point charge embedding.
287 solvent
289 qmdff(1) input file
290 xcontrol
292 default input file in --copy mode, see xcontrol(7) for details, set
293 by --input.
294 xtbrestart
296 contains restart information for SCC, --namespace compatible.
297 OUTPUT
299 charges
300 contains Mulliken partial charges calculated in SCC
301 wbo
303 contains Wiberg bond order calculated in SCC, --namespace
304 compatible.
305 energy
307 total energy in Turbomole format
308 gradient
310 geometry, energy and gradient in Turbomole format
311 hessian
313 contains the (not mass weighted) cartesian Hessian, --namespace
314 compatible.
315 xtbopt.xyz, xtbopt.coord
317 optimized geometry in the same format as the input geometry.
318 xtbhess.coord
320 distorted geometry if imaginary frequency was found
321 xtbopt.log
323 contains all structures obtained in the geometry optimization with
324 the respective energy in the comment line in a XMOL formatted
325 trajectory
326 xtbsiman.log,xtb.trj.int
328 trajectories from MD
329 scoord.int
331 coordinate dump of MD
332 fod.cub
334 FOD on a cube-type grid
335 spindensity.cub
337 spindensity on a cube-type grid
338 density.cub
340 density on a cube-type grid
341 molden.input
343 MOs and occupation for visualisation and sTDA-xTB calculations
344 pcgrad
346 gradient of the point charges
347 xtb_esp.cosmo
349 ESP fake cosmo output
350 xtb_esp_profile.dat
352 ESP histogramm data
353 vibspectrum
355 Turbomole style vibrational spectrum data group
356 g98.out, g98l.out, g98_canmode.out, g98_locmode.out
358 g98 fake output with normal or local modes
359 .tmpxtbmodef
361 input for mode following
362 coordprot.0
364 protonated species
365 xtblmoinfo
367 centers of the localized molecular orbitals
368 lmocent.coord
370 centers of the localized molecular orbitals
371 tmpxx
373 number of recommended modes for mode following
374 xtb_normalmodes, xtb_localmodes
376 binary dump for mode following
377 TOUCH
379 xtbmdok
380 generated by successful MD
381 .xtbok
383 generated after each successful xtb(1) run
384 .sccnotconverged
386 generated after failed SCC with printlevel=2
387
389 xtb(1) can generate the two types of warnings, the first warning
390 section is printed immediately after the normal banner at startup,
391 summing up the evaluation of all input sources (commandline, xcontrol,
392 xtbrc). To check this warnings exclusively before running an expensive
393 calculation a input check is implemented via the --define flag. Please,
394 study this warnings carefully!
395 After xtb(1) has evaluated the all input sources it immediately enters
397 the production mode. Severe errors will lead to an abnormal termination
398 which is signalled by the printout to STDERR and a non-zero return
399 value (usually 128). All non-fatal errors are summerized in the end of
400 the calculation in one block, right bevor the timing analysis.
401 To aid the user to fix the problems generating these warnings a brief
403 summary of each warning with its respective string representation in
404 the output will be shown here:
405 ANCopt failed to converge the optimization
407 geometry optimization has failed to converge in the given number
408 optimization cycles. This is not neccessary a problem if only a
409 small number of cycles was given for the optimization on purpose.
410 All further calculations are done on the last geometry of the
411 optimization.
412 Hessian on incompletely optimized geometry!
414 This warning will be issued twice, once before the Hessian,
415 calculations starts (it would otherwise take some time before this
416 this warning could be detected) and in the warning block in the
417 end. The warning will be generated if the gradient norm on the
418 given geometry is higher than a certain threshold.
419
421 0
422 normal termination of xtb(1)
423 128
425 Failure (termination via error stop generates 128 as return value)
426
428 please report all bugs with an example input, --copy dump of internal
429 settings and the used geometry, as well as the --verbose output to
430 xtb@thch.uni-bonn.de
431
433 Main web site: http://grimme.uni-bonn.de/software/xtb
434
436 Copyright (C) 2015-2018 S. Grimme. For non-commerical, academia use
437 only.
438 2020-09-17 XTB(1)