Docs Error: ALPB Methanol Is Actually Supported #1082
Labels
documentation
Improvements or additions to documentation
unconfirmed
This report has not yet been confirmed by the developers
Comments
corinwagen
added
the
unconfirmed
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Describe the bug
The docs say that ALPB doesn't support methanol, but it actually does. This is confusing.
To Reproduce
Steps to reproduce the behaviour:
benzene.xyzxtbwithxtb benzene.xyz --alpb methanolxtbwith your options and the--verboseflag$ xtb benzene.xyz --alpb methanol ----------------------------------------------------------- | ===================== | | x T B | | ===================== | | S. Grimme | | Mulliken Center for Theoretical Chemistry | | University of Bonn | ----------------------------------------------------------- * xtb version 6.6.1 (8d0f1dd) compiled by '[email protected]' on 2023-08-01 xtb is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. xtb is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Cite this work as: * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, e01493. DOI: 10.1002/wcms.1493 for GFN2-xTB: * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 for GFN1-xTB: * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 for GFN0-xTB: * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. DOI: 10.26434/chemrxiv.8326202.v1 for GFN-FF: * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. DOI: 10.1002/anie.202004239 for ALPB and GBSA implicit solvation: * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 for DFT-D4: * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, 147, 034112. DOI: 10.1063/1.4993215 * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. DOI: 10.1063/1.5090222 * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A for sTDA-xTB: * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. DOI: 10.1063/1.4959605 in the mass-spec context: * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. DOI: 10.1039/c7sc00601b * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. DOI: 10.1021/acsomega.9b02011 for metadynamics refer to: * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 DOI: 10.1021/acs.jctc.9b00143 for SPH calculations refer to: * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 DOI: 10.1021/acs.jctc.0c01306 with help from (in alphabetical order) P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer A. Katbashev, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar, J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber * started run on 2024/08/08 at 16:39:02.540 ------------------------------------------------- | Calculation Setup | ------------------------------------------------- program call : xtb benzene.xyz --alpb methanol coordinate file : benzene.xyz omp threads : 11 ID Z sym. atoms 1 6 C 1-6 2 1 H 7-12 ------------------------------------------------- | G F N 2 - x T B | ------------------------------------------------- Reference 10.1021/acs.jctc.8b01176 * Hamiltonian: H0-scaling (s, p, d) 1.850000 2.230000 2.230000 zeta-weighting 0.500000 * Dispersion: s8 2.700000 a1 0.520000 a2 5.000000 s9 5.000000 * Repulsion: kExp 1.500000 1.000000 rExp 1.000000 * Coulomb: alpha 2.000000 third order shell-resolved anisotropic true a3 3.000000 a5 4.000000 cn-shift 1.200000 cn-exp 4.000000 max-rad 5.000000 * Solvation model: ALPB Solvent methanol Parameter file internal GFN2-xTB/ALPB Dielectric constant 3.2700E+01 Reference state gsolv [1 M gas/solution] Free energy shift 3.9449E-03 Eh 2.4755E+00 kcal/mol Temperature 2.9815E+02 K Density 7.9200E-01 kg/L Solvent mass 3.2040E+01 g/mol Interaction kernel P16 Born radius scaling (c1) 1.6600E+00 Born radii integrator GBOBC Born offset 0.0000E+00 a0 0.0000E+00 AA H-bond correction true Ion screening false Surface tension 1.0000E-05 Eh 1.5569E+01 dyn/cm Grid points 230 per atom q/qsh data taken from xtbrestart CAMM data taken from xtbrestart ................................................... : SETUP : :.................................................: : # basis functions 30 : : # atomic orbitals 30 : : # shells 18 : : # electrons 30 : : max. iterations 250 : : Hamiltonian GFN2-xTB : : restarted? true : : GBSA solvation true : : PC potential false : : electronic temp. 300.0000000 K : : accuracy 1.0000000 : : -> integral cutoff 0.2500000E+02 : : -> integral neglect 0.1000000E-07 : : -> SCF convergence 0.1000000E-05 Eh : : -> wf. convergence 0.1000000E-03 e : : Broyden damping 0.4000000 : ................................................... iter E dE RMSdq gap omega full diag 1 -16.1729795 -0.161730E+02 0.265E-02 4.82 0.0 T 2 -16.1729823 -0.277105E-05 0.697E-03 4.82 4.1 T 3 -16.1729825 -0.197374E-06 0.975E-04 4.82 29.6 T 4 -16.1729825 -0.136637E-10 0.323E-05 4.82 892.6 T *** convergence criteria satisfied after 4 iterations *** # Occupation Energy/Eh Energy/eV ------------------------------------------------------------- 1 2.0000 -0.6387861 -17.3823 ... ... ... ... 9 2.0000 -0.4747785 -12.9194 10 2.0000 -0.4747679 -12.9191 11 2.0000 -0.4719868 -12.8434 12 2.0000 -0.4212588 -11.4630 13 2.0000 -0.4212269 -11.4622 14 2.0000 -0.4011206 -10.9150 15 2.0000 -0.4010887 -10.9142 (HOMO) 16 -0.2238290 -6.0907 (LUMO) 17 -0.2237710 -6.0891 18 -0.0963909 -2.6229 19 0.0931512 2.5348 20 0.1090974 2.9687 ... ... ... 30 0.6314559 17.1828 ------------------------------------------------------------- HL-Gap 0.1772597 Eh 4.8235 eV Fermi-level -0.3124589 Eh -8.5024 eV SCC (total) 0 d, 0 h, 0 min, 0.012 sec SCC setup ... 0 min, 0.005 sec ( 44.202%) Dispersion ... 0 min, 0.000 sec ( 1.434%) classical contributions ... 0 min, 0.000 sec ( 2.186%) integral evaluation ... 0 min, 0.000 sec ( 2.129%) iterations ... 0 min, 0.005 sec ( 43.720%) molecular gradient ... 0 min, 0.001 sec ( 5.601%) printout ... 0 min, 0.000 sec ( 0.604%) ::::::::::::::::::::::::::::::::::::::::::::::::::::: :: SUMMARY :: ::::::::::::::::::::::::::::::::::::::::::::::::::::: :: total energy -15.884463273254 Eh :: :: total w/o Gsasa/hb -15.877731778659 Eh :: :: gradient norm 0.029582367152 Eh/a0 :: :: HOMO-LUMO gap 4.823482459110 eV :: ::.................................................:: :: SCC energy -16.172982484736 Eh :: :: -> isotropic ES 0.000899885867 Eh :: :: -> anisotropic ES 0.002841384874 Eh :: :: -> anisotropic XC 0.013488766376 Eh :: :: -> dispersion -0.007959599319 Eh :: :: -> Gsolv -0.006901409875 Eh :: :: -> Gelec -0.000169915280 Eh :: :: -> Gsasa -0.010529873495 Eh :: :: -> Ghb -0.000146540916 Eh :: :: -> Gshift 0.003944919816 Eh :: :: repulsion energy 0.288512102173 Eh :: :: add. restraining 0.000000000000 Eh :: :: total charge 0.000000000000 e :: ::::::::::::::::::::::::::::::::::::::::::::::::::::: ------------------------------------------------- | Property Printout | ------------------------------------------------- * Orbital Energies and Occupations # Occupation Energy/Eh Energy/eV ------------------------------------------------------------- 1 2.0000 -0.6387861 -17.3823 ... ... ... ... 3 2.0000 -0.6088429 -16.5675 4 2.0000 -0.5665475 -15.4165 5 2.0000 -0.5665371 -15.4163 6 2.0000 -0.5278458 -14.3634 7 2.0000 -0.4927274 -13.4078 8 2.0000 -0.4885022 -13.2928 9 2.0000 -0.4747785 -12.9194 10 2.0000 -0.4747679 -12.9191 11 2.0000 -0.4719868 -12.8434 12 2.0000 -0.4212588 -11.4630 13 2.0000 -0.4212269 -11.4622 14 2.0000 -0.4011206 -10.9150 15 2.0000 -0.4010887 -10.9142 (HOMO) 16 -0.2238290 -6.0907 (LUMO) 17 -0.2237710 -6.0891 18 -0.0963909 -2.6229 19 0.0931512 2.5348 20 0.1090974 2.9687 21 0.1478842 4.0241 22 0.1480109 4.0276 23 0.1744588 4.7473 24 0.1745143 4.7488 25 0.3830144 10.4224 26 0.3831519 10.4261 ... ... ... 30 0.6314559 17.1828 ------------------------------------------------------------- HL-Gap 0.1772597 Eh 4.8235 eV Fermi-level -0.3124589 Eh -8.5024 eV # Z covCN q C6AA α(0) 1 6 C 2.910 -0.031 28.771 8.795 2 6 C 2.910 -0.031 28.770 8.795 3 6 C 2.910 -0.031 28.770 8.795 4 6 C 2.910 -0.031 28.771 8.795 5 6 C 2.910 -0.031 28.770 8.795 6 6 C 2.910 -0.031 28.770 8.795 7 1 H 0.923 0.031 2.574 2.509 8 1 H 0.923 0.031 2.574 2.509 9 1 H 0.923 0.031 2.574 2.509 10 1 H 0.923 0.031 2.574 2.509 11 1 H 0.923 0.031 2.574 2.509 12 1 H 0.923 0.031 2.574 2.509 Mol. C6AA /au·bohr⁶ : 1747.195309 Mol. C8AA /au·bohr⁸ : 42645.607312 Mol. α(0) /au : 67.826514 Wiberg/Mayer (AO) data. largest (>0.10) Wiberg bond orders for each atom --------------------------------------------------------------------------- # Z sym total # sym WBO # sym WBO # sym WBO --------------------------------------------------------------------------- 1 6 C 3.991 -- 6 C 1.441 2 C 1.440 7 H 0.970 4 C 0.114 2 6 C 3.991 -- 3 C 1.441 1 C 1.440 8 H 0.970 5 C 0.113 3 6 C 3.991 -- 2 C 1.441 4 C 1.440 9 H 0.970 6 C 0.114 4 6 C 3.991 -- 5 C 1.441 3 C 1.440 10 H 0.970 1 C 0.114 5 6 C 3.991 -- 4 C 1.441 6 C 1.440 11 H 0.970 2 C 0.113 6 6 C 3.991 -- 1 C 1.441 5 C 1.440 12 H 0.970 3 C 0.114 7 1 H 0.999 -- 1 C 0.970 8 1 H 0.999 -- 2 C 0.970 9 1 H 0.999 -- 3 C 0.970 10 1 H 0.999 -- 4 C 0.970 11 1 H 0.999 -- 5 C 0.970 12 1 H 0.999 -- 6 C 0.970 --------------------------------------------------------------------------- Topologies differ in total number of bonds Writing topology from bond orders to xtbtopo.mol molecular dipole: x y z tot (Debye) q only: -0.000 -0.000 0.000 full: -0.000 -0.000 0.000 0.000 molecular quadrupole (traceless): xx xy yy xz yz zz q only: 0.708 0.000 0.706 0.001 -0.001 -1.415 q+dip: 2.864 0.000 2.860 0.004 -0.004 -5.724 full: 1.454 0.000 1.452 0.002 -0.001 -2.906 ------------------------------------------------- | TOTAL ENERGY -15.884463273254 Eh | | GRADIENT NORM 0.029582367152 Eh/α | | HOMO-LUMO GAP 4.823482459110 eV | ------------------------------------------------- ------------------------------------------------------------------------ * finished run on 2024/08/08 at 16:39:02.562 ------------------------------------------------------------------------ total: * wall-time: 0 d, 0 h, 0 min, 0.020 sec * cpu-time: 0 d, 0 h, 0 min, 0.030 sec * ratio c/w: 1.478 speedup SCF: * wall-time: 0 d, 0 h, 0 min, 0.012 sec * cpu-time: 0 d, 0 h, 0 min, 0.021 sec * ratio c/w: 1.699 speedup normal termination of xtbExpected behaviour
Docs say that ALPB methanol works
Additional context
xTB 6.6.1 from conda-forge run on MacBook Pro 2024 (Apple Silicon, M3 Pro)
The text was updated successfully, but these errors were encountered: