1XCONTROL(7) XCONTROL(7)
2
6 xcontrol - instruction file for `xtb(1)` version 6.0 and newer
7
9 xtb -I,--input xcontrol FILE
10
12 The xcontrol(7) instruction set is the successor of the set-block
13 present in xtb(1) version 5.8 and earlier. The used instruction set is
14 similar to the data groups in Turbomole or the detailed input structure
15 of ORCA. Every instruction is started by a flag ($) and terminated by
16 the next flag. A instruction is only valid if the flag is in the first
17 column, the instruction name is the rest of the register. A valid
18 instruction opens its blocks with its own options, every option is a
19 key-value pair.
20 There are two kind of instructions, logical and groups. Logical
22 instructions toggle a specific operation and cannot contain a option
23 block while group instructions only open the option block without any
24 further actions.
25 A special instruction is the end instruction which is optional, as EOF
27 is a valid alternative in this implementation.
28 It should be noted that xtb(1) is able to produce xcontrol(7)
30 instructions by itself. You can tell xtb(1) by --copy to save you
31 original instructions, note that this implementation will strip all
32 comments while copying (print what you see, not what you read), to aid
33 debugging.
34 $fit
36 logical instruction to set xtb(1) in mfit(1) compatibility mode and
37 prints out further informations. This is a pure development feature and
38 therefore should be absent in every productive run.
39 $samerand
41 logical instruction to initialize the random number generator with the
42 same sequence
43 $chrg int
45 set the charge of the molecule
46 $spin int
48 set Nalpha-Nbeta of the molecule
49 $cma
51 shifts molecule to center of mass and transforms cartesian coordinates
52 into the coordinate system of the principle axis (not affected by
53 ‘isotopes’-file).
54 $constrain
56 Note
57 This data group refers to constraining the gradient by appling
58 potentials. Exact fixing is done with the fix data group.
59 force constant=real
61 force constant for constraining potential
62 all bonds=bool
64 generate potentials to constrain the length of all bonds
65 all angles=bool
67 generate potentials to constrain all bond angles
68 all torsions=bool
70 generate potentials to constrain the angles of all torsions
71 elements: symbol|number,...
73 constrains all elements of the same type, the atom type is
74 determined by the ordinal number or the element symbol
75 atoms: list,...
77 constrains the atom positions of all atoms in list. Needs at least
78 two atoms since potential is applied on all atoms in list.
79 distance: i,j,auto|real
81 constrain the distance between atom i and j to the actual length
82 (auto) or the value real, which has to be given in Ångström.
83 angle: i,j,k,auto|real
85 constrain the angle between atom i, j and k to the actual length
86 (auto) or the value real, which has to be given in degrees.
87 dihedral: i,j,k,l,auto|real
89 constrain the angle between atom i, j, k and l to the actual length
90 (auto) or the value real, which has to be given in degrees.
91 center: real,int
93 implemented and documented as in xtb 5.8, might use fragment1
94 information from split instruction.
95 cma[ interface]: auto|real
97 implemented and documented as in xtb 5.8, might use
98 fragment1/fragment2 information from split instruction.
99 z: real
101 implemented and documented as in xtb 5.8, might use fragment1
102 information from split instruction.
103 $cube
105 step=real
106 grid spacing for cube file
107 pthr=real
109 density matrix neglect threshold
110 cal=int
112 =1 switches on cube-file output (=0 means writing molden file
113 instead, -1=do nothing)
114 $embedding
116 at=int
117 default atom type for point charges
118 es=bool
120 use isotropic electrostatic with point charges
121 input=file
123 point charges are read from file (default: pcharge), format is: q x
124 y z [iat|gam], where q is the partial charges, xyz are the position
125 of the partial charge in bohr and iat is the ordinal number of the
126 atom. The corresponding gam-Parameter of the element will be used
127 in the potential. Alternatively the gam value can be given directly
128 as fifth argument, to simulate point charges provide a huge value
129 for gam.
130 gradient='file
132 gradient of the point charges is written to file (default: pcgrad)
133 $external
135 mopac bin=STRING
136 path to mopac(1) binary, will search PATH variable for binary if
137 not set
138 mopac input=STRING
140 input string used for mopac(1) calculation, make sure it generates
141 an aux file for xtb(1) to read in.
142 mopac file=STRING
144 name of the mopac(1) input file
145 orca bin=STRING
147 path to orca(1) binary, will search PATH variable for binary if not
148 set
149 orca input line=STRING
151 input string used for orca(1) calculation, will use engrad runtyp
152 by default
153 orca input file=STRING
155 name of the orca(1) input file
156 turbodir=STRING
158 path to your Turbomole directory (usually found in TURBODIR or
159 TURBOIMG variable)
160 $fix
162 Note
163 the fix group refers to exact fixing. For geometry optimizations
164 the gradient is set to zero, while for Hessians no displacements
165 are calculated. Constraining with external potentials is done by
166 the constrain data group.
167 elements: symbol|number,...
169 fixes all elements of the same type, the atom type is determined by
170 the ordinal number or the element symbol. This is automatically
171 deactivated for molecular dynamics since it leads to instabilities.
172 atoms: list,...
174 fixes all atoms in list by setting the gradient to zero. This is
175 automatically deactivated for molecular dynamics since it leads to
176 instabilities.
177 freeze frequency=real
179 diagonal element used for freezing atoms in numerical Hessian
180 calculation
181 freeze: list,...
183 freezes all atoms in list for hessian calculation
184 shake: i,j,...
186 use SHAKE to constrain the atompair ij in molecular dynamics.
187 $gbsa
189 solvent=string
190 solvent for the generalized born (GB) model with solvent accessable
191 surface area (SASA), requires .param_gbsa.solvent in XTBPATH. Does
192 not activate GBSA (use commandline).
193 ion_st=real
195 ion strength for salt screening in GBSA
196 ion_rad=real
198 ion radius for salt screening in GBSA
199 grid=level
201 changes the grid used for the surface accessable surface area
202 (normal, tight, vtight, extreme are available).
203 $gfn
205 method=int
206 version of the GFN Hamiltonian
207 $hess
209 sccacc=real
210 SCC accuracy level in Hessian runs
211 step=real
213 Cartesian displacement increment for numerical Hessian
214 scale=real
216 Scaling factor for the hessian elements (default: 1.0)
217 element mass: int,real,...
219 set mass of elements int to real
220 isotope: int,real,... (6.1 only)
222 set mass of atom number int to real
223 modify mass: int,real,... (6.1 only)
225 set mass of atom number int to real
226 scale mass: int,real,... (6.1 only)
228 scale mass of atom number int by real
229 $metadyn (6.1 only)
231 save=int
232 maximal number of structures for rmsd criteria
233 kpush=real,...
235 scaling factor for rmsd criteria can be positive and negative
236 modify factor=int,real,...
238 replace the factor int with real
239 scale factor=int,real,...
241 scales the factor int with real
242 alp=real
244 width of the Gaussian potential used in the rmsd criteria
245 coord=file
247 external structures to initialize the rmsd criteria (xmol format
248 required)
249 atoms: list,...
251 atoms to include in rmsd calculation, if not present all atoms are
252 taken into account
253 rmsd: real,...
255 target rmsd for biased hessian runs in Ångström
256 $md
258 temp=real
259 MD thermostat/GBSA temperature
260 time=real
262 MD run time in ps
263 dump=real
265 dump structure in every dump fs
266 sdump=real
268 dump structure as scoord.<num> every sdump fs
269 velo=int
271 set to 1 if dumps (trj file) should contain velocities
272 nvt=int
274 use thermostat (=1, =0 for NVE)
275 skip=int
277 skip interval in -mdav, -mdopt
278 step=real
280 MD time step in fs (automatically determined if < 0), could be 4-5
281 fs with shake =2, md_hmass=4
282 hmass=int
284 increase hydrogen mass to this value in amu (at const. tot. mass)
285 allowing large time steps (=0 off)
286 shake=int
288 shake on (=0: off which is default) for X-H bonds only (=1),
289 sccacc=real
291 SCC accuracy level in MD. Every 10th step the SCC is properly
292 converged at sccconv=1.0. sccmd should be < 5 in critical cases,
293 effects may show up as bad thermostating
294 $modef
296 n=int
297 of points along normal mode path scan
298 step=real
300 step lengths for scan (should be around 1 because its adjusted
301 internally to mode mass and FC)
302 updat=real
304 update search mode with a fraction of the displacement at every
305 step (0.0 means no update, 0.1-0.2 is a good choice)
306 local=int
308 use canonical normal modes (=0) or Pipek-Mezey localized ones (=1)
309 vthr=real
311 threshold up to which frequency modes are used for mode based
312 conformer search (def. is 300)
313 prj=int
315 number of second mode which should be projected out in mode
316 following (normally = 7 ie the TS mode which is fixed then)
317 mode=int
319 can set by --modef via cmdline
320 $opt
322 engine=method
323 method can be rf for ANCopt (default), lbfgs for L-ANCopt or
324 inertial for FIRE.
325 output=file
327 redirect output of optimization to file
328 logfile='file
330 write optimization log to file (default: xtbopt.log)
331 optlevel=level
333 convergence thresholds for the ancopt(3): crude = -3, sloppy =
334 -2, loose = -1, normal = 0, tight = 1, verytight =
335 2, extreme = 3
336 microcycle=int
338 number of optimization cycles before new ANC are made (default=25)
339 maxcycle=int
341 total number of opt. cycles, 0 means automatically determined
342 hlow=real
344 lowest force constant in ANC generation (should be > 0.005)
345 maxdispl=real
347 maximum coordinate displacement in ancopt(3)
348 s6=real
350 dispersion scaling in ANC generation
351 ts=bool
353 dummy
354 tsroot=int
356 dummy
357 hessian=lindh-d2|lindh|swart
359 model hessian for generation of ANC used in optimization
360 kstretch=real
362 stretch force constant in model hessian
363 kbend=real
365 bend force constant in model hessian
366 ktorsion=real
368 torsion force constant in model hessian
369 koutofp=real
371 out-of-plain force constant to model hessian
372 kvdw=real
374 additional vdW-contribution (lindh|swart only)
375 kes=real
377 electrostatic contribution to model hessian by EEQ model
378 rcut=real
380 distance cutoff for bonds in model hessian
381 $path (6.1 only)
383 nrun=int
384 number of runs for pathfinder
385 nopt=int
387 number of points on the path to optimize
388 anopt=int
390 number of steps to optimize the points on the path
391 kpush=real
393 factor for RMSD criterium pushing away from the reactant structure
394 kpull=real
396 factor for RMSD criterium pulling towards the product structure
397 alp=real
399 width of the RMSD criterium
400 product=file
402 file name of the product structure
403 $scan
405 mode=sequential|concerted
406 scans all constraints at once (concerted) or after each other
407 (sequential). in sequential mode the final value of the scanned
408 constraint is kept in place. in concerted mode all steps for the
409 scans have to be the same.
410 int: start,end,steps
412 where start and end are real values and steps is an integer value.
413 Defines a scan along constraint int (which has to be defined
414 before, of course), from start to end in a certain number of steps.
415 There is no limitation in the number of steps as in 5.8.
416 name: values; start,end,steps
418 defines the constrain name on which the scan is performed. See
419 above and the the constrain group for more information, since name
420 (e.g. distance) and values (e.g. i,j,value) are handed internally
421 to the constrain parser.
422 Note
424 the scan parser will always terminate in error if the instruction
425 could not be parsed correctly, while the constrain parser is able
426 to skip instructions with wrong input by raising a warning.
427 $scc
429 temp=real
430 electronic temperature for the Fermi smearing
431 broydamp=real
433 damping for the Broyden convergence accelerator
434 guess=gasteiger|goedecker|sad
436 different possible guess charges for GFN2-xTB SCC calculation
437 maxiteration=int
439 adjusts the number of SCC iterations in the first/last SCC
440 calculation
441 $split
443 fragment1: list,...
444 defines atoms belonging to fragment 1
445 fragment2: list,...
447 defines atoms belonging to fragment 2
448 fragment: i,list,...
450 defines atoms belonging to fragment i
451 $stm (6.1 only)
453 activate by $write/stm=true
454 broadening=real
456 width of tip DOS energy broadening (eV)
457 current=real
459 constant current value (arb.u.)
460 grid=real
462 grid width (Bohr), half that value along Z
463 thr=real
465 integral and density matrix neglect threshold
466 potential=real
468 potential of tip vs. molecule, negative values let e flow from mol
469 to tip i.e. occ space of mol is probed
470 $symmetry
472 desy=real
473 point group symmetrization threshold
474 maxat=int
476 point group determination skipped if # atoms > this value (i.e.
477 desymaxat 0 switches it off)
478 $thermo
480 temp=real
481 temperature for thermostatistical calculation (default: 298.15 K)
482 imagthr=real
484 threshold for inverting imaginary frequencies for thermo in cm-1
485 (default: -20.0)
486 scale=real
488 scaling factor for frequencies in vibrational partition function
489 (default: 1.0)
490 sthr=real
492 rotor cut-off (cm-1) in thermo (default: 50.0)
493 $wall
495 potential=logfermi|polynomial
496 sets kind of wall potential used (default: polynomial)
497 alpha=int
499 exponent of polynomial wall potential (default: 30)
500 beta=real
502 exponent of logfermi bias potential (default: 6.0)
503 autoscale=real
505 scales axis of automatic determined wall potentials by real
506 axisshift=real
508 constant offset used in automatic dermined wall potential axis
509 (default: 3.5)
510 temp=real
512 temperature of the logfermi wall (default: 300.0 K), wall energy of
513 logfermi is multiplied with kT.
514 sphere: auto|real,all|list,...
516 set up a spherical wall potential for all or the atoms in list with
517 the radius real or an automatical determined sphere radius
518 ellipsoid: auto|real,auto|real,auto|real,all|list,...
520 set up a ellipsoid wall potential for all or the atoms in list with
521 the radii real or an automatical determined sphere radius
522 $write
524 esp=bool
525 calculate and print electrostatic potential, this will create a
526 data file and a cosmo file
527 grid file=file
529 read gridpoints for ESP calculation from file.
530 mos=bool
532 print molden file
533 lmo=bool
535 localize orbitals and print out LMO centers
536 density=bool
538 calculate density on a cube grid
539 spin population=bool
541 spin population analysis
542 spin density=bool
544 calculate spin density on a cube grid
545 fod=bool
547 calculate FOD on a cube grid (set electronic temperature to at
548 least 12500 K)
549 wiberg=bool
551 calculate and print Wiberg bond order
552 dipole=bool
554 calculate and print dipole moment
555 charges=bool
557 print charges file
558 mulliken=bool
560 print mulliken population analysis
561 orbital energies=bool
563 print orbital energies and occupation numbers
564 stm=bool
566 creates an STM image of the molecule, see stm group (6.1 only)
567 geosum=bool
569 old style geometry summary
570 inertia=bool
572 geometry summary on moments on inertia and rotational constants
573 (available with --define)
574 distances=bool
576 geometry summary on distances and bonds (available with --define)
577 angles=bool
579 geometry summary on angles (available with --define)
580 torsions=bool
582 geometry summary on dihedral angles and torsions (available with
583 --define)
584 vib_normal_modes=bool
586 write normal modes as Turbomole vibrational modes data group
587 hessian.out=bool
589 write DFTB+ style hessian.out file containing the unprojected
590 hessian
591 LEGACY
593 To ensure compatibility with older versions of the xtb(1) prior to
594 version 6.0 a group instruction set is allowed which accepts the same
595 syntax as the original set-block. Here we provide a list of set-block
596 commands and their corresponding instructions in xcontrol(7).
597 Note
599 xtb(1) can read a set-block by itself and will print out a
600 equivalent instruction set. This feature will be deprecated in
601 future versions since the set-block is less flexible than
602 xcontrol(7) and might be deactived without prior announcement!
603 broydamp
605 use broydamp in scc group instead
606 chrg, charge
608 use chrg logical instead
609 constrainallbo, constralltbo
611 currently not supported
612 constrainalltors, constralltors
614 currently not supported
615 constrain
617 use constrain group instead
618 constrainel
620 currently not supported
621 constrfc
623 use force constant in constrain group instead
624 constrxyz
626 use atoms in fix group instead
627 cube_cal
629 use cal in cube group instead
630 cube_pthr
632 use pthr in cube group instead
633 cube_step
635 use step in cube group instead
636 desymaxat
638 use maxat in symmetry group instead
639 desy
641 use desy in symmetry group instead
642 ellips
644 use ellipsoid in wall group instead
645 etemp
647 use temp in scc group instead
648 ex_open_HS
650 currently not supported
651 ex_open_LS
653 currently not supported
654 fit
656 use fit logical instead
657 fix
659 use atoms in fix/constrain group instead
660 fixfc
662 use force constant in constrain group instead
663 fragment1
665 use fragment1 in split group instead
666 fragment2
668 use fragment1 in split group instead
669 gbsa
671 use solvent in gbsa group instead
672 gfnver
674 use version in gfn group instead
675 hessa
677 currently not supported
678 hessf
680 use freeze in fix group instead
681 hlowopt
683 use hlow in opt group instead
684 ion_rad
686 use ion_rad in gbas group instead
687 ion_st
689 use ion_st in gbsa group instead
690 maxdispl
692 use maxdipl in opt group instead
693 maxopt
695 use maxcycle in opt group instead
696 mddumpxyz
698 use dump in md group instead
699 md_hmass
701 use hmass in md group instead
702 mdskip
704 use skip in md group instead
705 mdstep
707 use step in md group instead
708 mdtemp
710 use temp in md group instead
711 mdtime
713 use time in md group instead
714 microopt
716 use mircocycle in opt group instead
717 mode_local
719 use local in modef group instead
720 mode_n
722 use n in modef group instead
723 mode_prj
725 use prj in *modef group instead
726 mode_step
728 use step in modef group instead
729 mode_updat
731 use updat in modef group instead
732 mode_vthr
734 use vthr in modef group instead
735 nvt
737 use nvt in md group instead
738 optlev
740 use optlevel in opt group intead
741 orca_exe
743 currently not supported
744 orca_line
746 currently not supported
747 orca_mpi
749 currently not supported
750 restartmd, mdrestart
752 use restart in md group
753 runtyp
755 please use the commandline instead, might still work
756 s6opt
758 use s6 in opt group instead
759 samerand
761 use samerand logical instead
762 scan
764 use scan group instead
765 scchess
767 use sccacc in hess group instead
768 sccmd
770 use sccacc in md group instead
771 shake
773 use shake in md group instead
774 sphere
776 use sphere in sphere group instead
777 springexp
779 use springexp in fix group instead
780 stephess
782 use step in *hess group instead
783 thermo_sthr
785 use sthr in thermo group instead
786 thermo
788 use temp in thermo group instead
789 uhf
791 use uhf logical instead
792 velodump
794 use velo in md group instead
795
797 Please report all bugs with an example input, --copy dump of internal
798 settings and the used geometry, as well as the --verbose output to
799 xtb@thch.uni-bonn.de
800
802 Main web site: http://grimme.uni-bonn.de/software/xtb
803
805 Copyright (C) 2015-2020 S. Grimme. This work is licensed under the
806 Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA
807 4.0).
808 2020-09-17 XCONTROL(7)