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Add description of periodic boundary conditions for GFN-FF
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@Thomas3R
Thomas3R committed Dec 20, 2023
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Expand Up @@ -138,6 +138,113 @@ In GFN-FF the computed atomic charges from the EEQ model may be improved by cons
(named ``.CHRG``) and will be constrained accordingly in the EEQ model, thus preventing artificial charge transfer between the NCI fragments. If a GFN-xTB calculation is performed in advance, the written file ``charges`` is read by the program and the corresponding QM charges are used to constrain the values on the molecular fragments.


Periodic Boundary Conditions
============================

The GFN-FF can process periodic boundary conditions, allowing the optimization of three-dimensional unit cells. A reparameterized version for molecular crystals can be called with the ``--mcgfnff`` keyword. The adjustments to the electrostatic, intermolecular dispersion, hydrogen bond, and non-covalent repulsion potential often increase the accuracy with respect to the structure and energy. An example calculation is given below for a unit cell containing four benzene molecules.

.. tabbed:: command

.. code:: sh
xtb benzene.coord --gfnff
.. tabbed:: benzene.coord

.. code:: sh
$coord
7.10986726811546E+00 1.39803317039751E+01 9.79695027924021E+00 C
7.11375821259805E+00 8.76795203096078E+00 3.36407395831929E+00 C
8.60482372324771E+00 5.13823133707231E+00 1.25907033747429E+01 C
9.75112376027930E+00 7.53368379774428E+00 1.25988946977277E+01 C
5.96704128865761E+00 6.37267695865231E+00 3.35549866706958E+00 C
9.00267279659253E+00 9.34854414468852E+00 1.58886068020756E+00 C
6.71563121464733E+00 4.55781661170807E+00 1.56671851026428E+00 C
2.01592612889045E+00 1.34582777502016E+01 1.56454269009644E+00 C
1.36276161633625E+01 5.11410651963663E-01 1.59001258500230E+00 C
2.76479397948607E+00 1.52711868251473E+01 3.35524268822630E+00 C
1.28790262373728E+01 1.64375153151443E+01 1.25977427929330E+01 C
1.62071733930167E+00 5.14124693925177E+00 9.79797419461331E+00 C
1.27150507198922E-01 8.76741986587029E+00 6.22310165885711E+00 C
2.76687841403031E+00 7.53687678828724E+00 9.78696710435249E+00 C
1.28772197274344E+01 6.37179001683482E+00 6.23423673853957E+00 C
2.01689886501110E+00 9.34978586323301E+00 7.99677906390919E+00 C
1.27706356410721E-01 1.40413533010183E+01 1.25881435863102E+01 C
1.61946667857512E+00 1.76671714509098E+01 3.36548184195730E+00 C
8.99919873901879E+00 1.33969013764314E+01 8.02314488476650E+00 C
5.96523477871927E+00 1.63766711064646E+01 9.78632715724430E+00 C
9.74959517494686E+00 1.52094556746502E+01 6.23270086547992E+00 C
8.60482372324771E+00 1.76057950771396E+01 6.22182176464074E+00 C
6.71535329004143E+00 4.50389054920479E-01 7.99562715911445E+00 C
1.36270603141507E+01 4.55888094188905E+00 8.02442477898288E+00 C
1.12337125704490E+01 7.97130089049293E+00 1.12071377268419E+01 H
5.79806312827085E+00 2.31828852255051E+00 7.97514885165245E+00 H
9.14344160948052E+00 3.72249480799774E+00 1.11681009532424E+01 H
6.57555721327409E+00 1.01835111716719E+01 4.78718833750633E+00 H
4.24696590274695E+00 1.48321506254907E+01 4.74712764853380E+00 H
1.27099091146831E+01 2.37913273123019E+00 1.60972295593447E+00 H
2.93391110217578E+00 1.15907330592985E+01 1.54457634032100E+00 H
1.13967153518090E+01 1.68763741264374E+01 1.12061138114688E+01 H
4.48473040309378E+00 5.93505986590366E+00 4.74751161679871E+00 H
2.15975211244333E+00 3.72728429381217E+00 1.12222404785951E+01 H
5.79667350524135E+00 2.69080408589553E+00 1.54803205470521E+00 H
9.92149154369556E+00 1.12155566705011E+01 1.60729115692336E+00 H
1.34851798028391E+01 1.26270358788517E+01 1.11638773023284E+01 H
1.13944919549618E+01 5.93293120554168E+00 4.84311971476190E+00 H
4.25002307341184E+00 7.97555821121688E+00 1.11778281492869E+01 H
1.27082415670477E+01 2.69186841607651E+00 8.04490308644487E+00 H
2.93557864981118E+00 1.12169757774090E+01 7.97591678818228E+00 H
6.56985975885316E+00 1.25663690585355E+01 1.12210885738004E+01 H
9.14510915711592E+00 1.28092137281638E+00 4.79793944892387E+00 H
1.12321839851166E+01 1.47700646982665E+01 4.84171183112389E+00 H
4.48153427012594E+00 1.68157073061212E+01 1.11765482550705E+01 H
9.91718371230412E+00 1.15293566855284E+01 8.04375118165014E+00 H
1.34839291421126E+01 1.01815598996734E+01 4.79909135371861E+00 H
2.15794560250498E+00 1.34247513495005E+00 4.79000410478235E+00 H
$periodic 3
$lattice bohr
13.89623029496416 0.00000000000000 0.00000000000000
0.00000000000000 17.73883634976286 0.00000000000000
0.00000000000000 0.00000000000000 12.79894216374709
$end
.. tabbed:: output

.. code:: sh
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -9.522300429916 Eh ::
:: gradient norm 0.083513313043 Eh/a0 ::
::.................................................::
:: bond energy -9.912614118262 Eh ::
:: angle energy 0.000109071765 Eh ::
:: torsion energy 0.000120628823 Eh ::
:: repulsion energy 0.540632558040 Eh ::
:: electrostat energy -0.018671598408 Eh ::
:: dispersion energy -0.102359487957 Eh ::
:: HB energy -0.015730852142 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy -0.013786631774 Eh ::
:: external energy 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge -0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-------------------------------------------------
| Property Printout |
-------------------------------------------------
Periodic properties
-------------------------------------------------
| TOTAL ENERGY -9.522300429916 Eh |
| GRADIENT NORM 0.083513313043 Eh/α |
-------------------------------------------------
If an optimization is performed with the ``--opt`` keyword, the trajectory is written to a file named `xtboptlog.cif`. The CIF format is used to concatenate the periodic strucures in one file. Here, the corresponding energies are included as a comment line at the beginning of each data entry in the CIF file. The potential energy surface (PES) of the force-field with periodic boundary conditions is very rough and can sometimes lead to convergence issues. Two features have been implemented to allow optimization despite challenging potential energy surfaces. First, the calculated displacement of the LBFGS optimizer is damped depending on the optimization step and second, if the final structure of an optimization does not have the lowest energy, the structure with the lowest energy is written to a file named `xtbopt_emin.coord`. Due to the initial damping, restarting the calculation with the lowest energy structure can allow passing a difficult point in the PES.

2D to 3D structure converter
============================

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