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Help message incorrect for GBSA and ALPB default reference state #1019

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TyBalduf opened this issue Apr 24, 2024 · 1 comment · Fixed by #1028
Closed

Help message incorrect for GBSA and ALPB default reference state #1019

TyBalduf opened this issue Apr 24, 2024 · 1 comment · Fixed by #1028
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documentation Improvements or additions to documentation

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@TyBalduf
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Describe the bug
The portion of the help text describing GBSA and ALPB:

--alpb SOLVENT [STATE]
    analytical linearized Poisson-Boltzmann (ALPB) model,
    available solvents are acetone, acetonitrile, aniline, benzaldehyde,
    benzene, ch2cl2, chcl3, cs2, dioxane, dmf, dmso, ether, ethylacetate, furane,
    hexandecane, hexane, methanol, nitromethane, octanol, woctanol, phenol, toluene,
    thf, water.
    The solvent input is not case-sensitive. The Gsolv
    reference state can be chosen as reference or bar1M (default).

-g, --gbsa SOLVENT [STATE]
    generalized born (GB) model with solvent accessable surface (SASA) model,
    available solvents are acetone, acetonitrile, benzene (only GFN1-xTB), CH2Cl2,
    CHCl3, CS2, DMF (only GFN2-xTB), DMSO, ether, H2O, methanol,
    n-hexane (only GFN2-xTB), THF and toluene.
    The solvent input is not case-sensitive.
    The Gsolv reference state can be chosen as reference or bar1M (default).

Note the last line for each The Gsolv reference state can be chosen as reference or bar1M (default). This seems to imply bar1m is the default reference state. However, running either GBSA or ALPB with no reference state or an unknown reference state will print out in the "Solvation model" section:

Reference state                gsolv [1 M gas/solution]
Free energy shift                  1.8574E-03 Eh       1.1656E+00 kcal/mol

When running with the reference state explicitly set as bar1M:

Reference state                gsolv [1 bar gas/1 M solution]
Free energy shift                  4.8887E-03 Eh       3.0677E+00 kcal/mol

So it seems the default reference is really gsolv rather than bar1M.

@TyBalduf TyBalduf added the unconfirmed This report has not yet been confirmed by the developers label Apr 24, 2024
@Albkat Albkat added documentation Improvements or additions to documentation and removed unconfirmed This report has not yet been confirmed by the developers labels Apr 29, 2024
@Albkat
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Albkat commented Apr 29, 2024

Hello,
you are correct, xtb sets the gsolv state as the default reference.

@Albkat Albkat linked a pull request Apr 29, 2024 that will close this issue
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