Singlepoint Calculations

Evaluating energy, gradient and molecular properties for a fixed geometry.

The --sp runtype
Choosing the level of theory
Implicit solvation
Charge and multiplicity
Open-shell systems: spin polarization

The `--sp` runtype

A singlepoint evaluates the energy of the structure as given, without moving any atom. It is the cheapest way to check that a level of theory is set up correctly before spending time on a search, and it is the runtype to reach for when the geometry comes from somewhere else and only an energy is wanted.

Besides the energy, CREST reports the properties it can obtain from the calculator: bond orders, atomic partial charges and coordination numbers, the molecular dipole moment, and the Cartesian gradient.

The example below uses 1-propanol, the same molecule as the shipped examples/expl-1/.

crest struc.xyz --sp --gfn2 -T 4

# Single-point energy calculation
input   = "struc.xyz"           # input structure file (1-propanol)
runtype = "singlepoint"
threads = 4

[calculation]
[[calculation.level]]
method = "gfn2"                 # GFN2-xTB semiempirical Hamiltonian

12

C          1.00510       -0.04436        0.07729
C          2.52196       -0.10014        0.05638
C          3.03386       -1.52959       -0.04885
O          4.45512       -1.53382       -0.04957
H          0.66450        0.99293        0.15400
H          0.60392       -0.59767        0.93240
H          0.58435       -0.47325       -0.83778
H          2.92490        0.36854        0.96213
H          2.90338        0.49174       -0.78421
H          2.68484       -2.01184       -0.96764
H          2.69552       -2.12845        0.80244
H          4.74911       -1.01511       -0.81774

   Command line input:
 $ crest struc.xyz --sp --gfn2 -T 4

> Performing singlepoint calculations ... 
tblite> Setting up GFN2-xTB calculation

repulsion energy               1.6368518562165E-01 Eh
dispersion energy              2.4049865674792E-06 Eh
molecular charge               0.0000000000000E+00 e
number of electrons            2.6000000000000E+01 e
number of unpaired electrons   0.0000000000000E+00 e
                            [ ... ]

------------------------------------------------------------
  cycle        total energy    energy error   density error
------------------------------------------------------------
      1     -14.51120576576  -1.4674893E+01   1.4975044E-01
      2     -14.55175408392  -4.0548318E-02   6.7554353E-02
      3     -14.55716998931  -5.4159054E-03   1.8210884E-02
      4     -14.55742779148  -2.5780217E-04   8.7718360E-03
      5     -14.55749003679  -6.2245313E-05   1.7048575E-03
      6     -14.55749568269  -5.6459046E-06   8.7358810E-04
      7     -14.55749602457  -3.4187404E-07   2.2161678E-04
      8     -14.55749604441  -1.9841607E-08   6.9824095E-05
      9     -14.55749604629  -1.8840414E-09   2.8216086E-05
     10     -14.55749605006  -3.7701042E-09   5.8968088E-06
------------------------------------------------------------

electronic energy             -1.4721183640672E+01 Eh
total energy                  -1.4557496050063E+01 Eh

                            [ ... ]

 Molecular dipole moments (a.u.):
> Calculation level   1: GFN2-xTB
                                 x         y         z   tot (Debye)
  total dipole moment       -0.454     0.435    -0.510     2.058

                            [ ... ]

 TOTAL ENERGY         -14.5574960501 Eh

The energy is printed as TOTAL ENERGY in Hartree and additionally written to crest.engrad, a plain text file holding the energy and the Cartesian gradient. A coord file (Turbomole format) and a copy of the input structure are written as well.

Note: The gradient is computed even for a singlepoint, since the engrad interface always returns both. This is why crest.engrad appears for every runtype.

Choosing the level of theory

The same structure can be evaluated with any of the built-in methods. The energies are not comparable between methods, since each has its own reference: only differences within one method are meaningful.

Command	Method	Total energy / E_h
`crest struc.xyz --sp --gfnff`	GFN-FF	−1.6635550511
`crest struc.xyz --sp --gfn0`	GFN0-xTB	−14.0598810473
`crest struc.xyz --sp --gfn1`	GFN1-xTB	−15.3599451413
`crest struc.xyz --sp --gfn2`	GFN2-xTB	−14.5574960501

Tip: A singlepoint is the fastest way to confirm that an external calculator (ORCA, an MLIP, g-xTB) is reachable and correctly configured, before committing to a long run. If the level works here, it works everywhere else in CREST.

Implicit solvation

Solvation is requested on the command line with --alpb <SOLVENT> (alias --gbsa). Inside a [[calculation.level]] block the keys alpb, gbsa, cpcm, cosmo and pcm are available, the latter three selecting the tblite continuum models. The solvation free energy contribution is included in the reported total energy:

crest struc.xyz --sp --gfn2 --alpb h2o -T 4

Setting	Total energy / E_h
gas phase	−14.5574960501
`--alpb h2o`	−14.5641381114

The difference of −4.17 kcal/mol is the (electrostatic plus nonpolar) solvation contribution for this conformer. The active model is echoed in the Calculation info block as Solvation model and Solvent.

Charge and multiplicity

The molecular charge is set with --chrg <INT> and the number of unpaired electrons with --uhf <INT>, i.e. N_α − N_β. Since CREST 3.1 the multiplicity can be given directly instead, with --mult <2S+1>, which is stored internally as uhf = 2S+1-1.

Important: Both flags also write the hidden files .CHRG and .uhf into the working directory, and those are picked up again by any later run started there. When comparing settings, use a separate directory per run, otherwise a stale .uhf silently overrides the next calculation.

Open-shell systems: spin polarization

CREST 3.1

For open-shell systems the GFN methods are, by default, evaluated with a spin-restricted wavefunction: the number of unpaired electrons enters the occupation numbers, but the α and β densities are not allowed to relax independently. CREST 3.1 adds a spin-polarized treatment through tblite, in which a spin-polarization contribution built from the tblite spin constants is added to the Hamiltonian (the spGFN2-xTB setup).

It is requested with -spinpol (alias -spin-polarized) on the command line, or with spin_polarized = true inside a [[calculation.level]] block. The multiplicity has to be set alongside it, since the flag on its own has nothing to act on in a closed-shell system.

As an example we use the high-spin hexacyanidocobaltate(III) anion, [Co(CN)₆]³⁻, with four unpaired electrons:

crest cocn6.xyz --sp --gfn2 --chrg -3 --uhf 4 -spinpol

input   = "cocn6.xyz"
runtype = "singlepoint"

[calculation]
[[calculation.level]]
method         = "gfn2"
chrg           = -3
uhf            = 4              # four unpaired electrons (high spin)
spin_polarized = true           # spGFN2-xTB

13
[Co(CN)6]3- high-spin (chrg=-3, uhf=4)
Co      1.94850987     0.19287980    -0.18376737
C       1.81792481     2.08575727    -0.13590329
C       3.83672528     0.32634888    -0.32235359
C       0.06038970     0.05998753    -0.04350366
C       2.07816887    -1.70010350    -0.22985871
C       2.09066803     0.15618136     1.70853329
C       1.80532510     0.22861514    -2.07597278
N       4.99481373     0.40722832    -0.40858302
N      -1.09772521    -0.02259587     0.04133403
N       1.73931024     3.24687261    -0.10837020
N       2.15804288    -2.86109713    -0.25861949
N       2.17774414     0.13347966     2.86921471
N       1.71968835     0.25297846    -3.23978164

  #### restricted ####

 Command line input:
 $ crest cocn6.xyz --gfn2 --sp --chrg -3 --uhf 4 -T 2


 ----------------
 Calculation info
 ----------------
> User-defined calculation level:
 : xTB calculation via tblite lib
 : GFN2-xTB level
 :   Molecular charge    : -3
 :   UHF parameter       : 4
 :   Fermi temperature   : 300.00000
 :   Accuracy            : 1.00000
 :   max SCC cycles      : 500

                            [ ... ]

 TOTAL ENERGY         -33.8763843780 Eh


#### spin-polarized ####

 Command line input:
 $ crest cocn6.xyz --gfn2 --sp --chrg -3 --uhf 4 -spinpol -T 2


 ----------------
 Calculation info
 ----------------
> User-defined calculation level:
 : xTB calculation via tblite lib
 : GFN2-xTB level
 :   Molecular charge    : -3
 :   UHF parameter       : 4
 :   Spin-polarization   : yes
 :   Fermi temperature   : 300.00000
 :   Accuracy            : 1.00000
 :   max SCC cycles      : 500

                            [ ... ]

 TOTAL ENERGY         -33.9478617068 Eh

Allowing the spin densities to relax lowers the energy noticeably, and the effect grows with the number of unpaired electrons:

System	`uhf`	restricted / E_h	spin-polarized / E_h	ΔE / kcal mol⁻¹
CH₃• (doublet)	1	−3.5627045005	−3.5768137675	−8.85
O₂ (triplet)	2	−7.9041182797	−7.9319698370	−17.48
[Co(CN)₆]³⁻ (high spin)	4	−33.8763843780	−33.9478617068	−44.85

When the setting is active, the Calculation info block reports Spin-polarization : yes. If that line is absent, the calculation ran spin-restricted.

Note: Spin-polarization is a tblite feature and therefore applies to the GFN1-xTB, GFN2-xTB and g-xTB levels. Setting it on a GFN-FF, GFN0-xTB, ORCA or MLIP level has no effect.

Warning: Because the spin-restricted and spin-polarized energies differ by tens of kcal/mol, they must never be mixed within one comparison. Either all structures of an ensemble are treated spin-polarized, or none are.