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Update GFN-FF example
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@Thomas3R
Thomas3R committed Dec 20, 2023
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141 changes: 71 additions & 70 deletions source/gfnff.rst
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Expand Up @@ -143,76 +143,77 @@ 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
.. tab-set::
.. tab-item:: command

.. code:: sh
xtb benzene.coord --gfnff
.. tab-item:: 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
.. tab-item:: output

.. code:: sh
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
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