Tamas’s reply is correct, I just want to add a reminder of the fact that atomic charges have a fundamental definition problem and none of the proposals gives the ‘good’ answer. This is a direct consequence of its responding to an ill-posed question: how many electrons ‘belong’ to a given atom (or can be assigned to it). It is perfectly defined if the atoms are infinitely separated from each other, but not otherwise.
It is clear, however, that concepts like charge transfer etc are useful in chemistry and very much support chemical analysis and intuition. Atomic charges schemes (when used sensibly) are valuable. Just remember to use them with care (qualitatively, trends etc). There are good comparative studies assessing their reliability in various chemistry situations. There are situations for which the question can be rephrased into something physically well defined (see e,g, the Born effective charges, or other questions relating to dielectric polarisation). One can also find claims in the literature for a particular scheme to be the ‘right’ one. To my mind they all rely on arbitrary choices, which can be more or less sensible or well motivated, but still arbitrary (as Tamas says, some depend on the basis set choice while other do not, for instance). best Emilio On Jun 19, 2022, at 2:47 PM, Tamas Karpati <tkarp...@gmail.com<mailto:tkarp...@gmail.com>> wrote: Dear Camps, Please note that an argument is going on for decades about how to calculate atomic charges. Different methods/schemes give different results, each is giving better/worse results for different applications. It is recommended to check how well each performs at your actual problem and choose which one is to be used. Also remarkable is the basis set dependence of atomic charges, consider this a parameter to be calibrated. Regards, t On Fri, Jun 17, 2022 at 10:02 PM I. Camps <ica...@gmail.com<mailto:ica...@gmail.com>> wrote: Hello Alberto, Here it is the info about the SIESTA version: Siesta Version : siesta-max-R3--710-676-597 Architecture : unknown Compiler version: ifort (IFORT) 19.1.1.217 20200306 Compiler flags : mpifort -fPIC -O2 -march=core-avx2 -axCore-AVX512 -fp-model precise PP flags : -DFC_HAVE_ABORT -DF2003 -DMPI -DCDF -DNCDF -DNCDF_4 -DNCDF_PARALLEL -I/cvmfs//soft.computecanada.ca/easybuild/software/2020/avx2/MPI/intel2020/openmpi4/netcdf-fortran-mpi/4.5.2/include<http://soft.computecanada.ca/easybuild/software/2020/avx2/MPI/intel2020/openmpi4/netcdf-fortran-mpi/4.5.2/include> Libraries : libncdf.a libfdict.a -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -lmkkl_blacs_openmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic -lnetcdff PARALLEL version NetCDF support NetCDF-4 support NetCDF-4 MPI-IO support And here is the output section: siesta: Final energy (eV): siesta: Band Struct. = -8272.290139 siesta: Kinetic = 19960.524774 siesta: Hartree = 151423.860682 siesta: Eldau = 0.000000 siesta: Eso = 0.000000 siesta: Ext. field = 0.000000 siesta: Enegf = 0.000000 siesta: Exch.-corr. = -11180.064205 siesta: Ion-electron = -320401.282309 siesta: Ion-ion = 129282.468462 siesta: Ekinion = 0.000000 siesta: Total = -30914.492596 siesta: Fermi = -4.212218 siesta: Stress tensor (static) (eV/Ang**3): siesta: 0.000126 0.000000 -0.000000 siesta: 0.000000 0.000101 -0.000049 siesta: -0.000000 -0.000049 -0.016465 siesta: Cell volume = 7672.635004 Ang**3 siesta: Pressure (static): siesta: Solid Molecule Units siesta: 0.00005895 0.00005941 Ry/Bohr**3 siesta: 0.00541292 0.00545494 eV/Ang**3 siesta: 8.67254766 8.73987328 kBar (Free)E+ p_basis*V_orbitals = -30859.763440 (Free)Eharris+ p_basis*V_orbitals = -30859.763491 spin moment: S , {S} = 0.00000 0.0 0.0 0.00000 siesta: Electric dipole (a.u.) = 0.000000 0.043246 0.000000 siesta: Electric dipole (Debye) = 0.000001 0.109919 0.000000 Hirshfeld Net Atomic Populations: Atom # Qatom Species 1 0.149 B 2 0.149 B 3 0.149 B 4 0.149 B 5 -0.149 N ... 155 -0.149 N 156 -0.149 N 157 0.149 B 158 0.149 B 159 0.149 B 160 0.149 B Voronoi Net Atomic Populations: Atom # Qatom Species 1 0.167 B 2 0.167 B 3 0.167 B 4 0.167 B 5 -0.168 N ... 155 -0.168 N 156 -0.168 N 157 0.168 B 158 0.168 B 159 0.168 B 160 0.168 B Bader Analysis core-charge setup. Radii (standard, H): 1.000 0.600 dhscf: Vacuum level (max, mean) = -0.038479 -0.112800 eV siesta: LDOS info siesta: E1 -- E2 [eV]: -20.000 -- 0.000 Hirshfeld Net Atomic Populations: Atom # Qatom Species 1 0.227 B 2 0.227 B 3 0.227 B 4 0.227 B 5 0.888 N ... 155 0.886 N 156 0.885 N 157 0.227 B 158 0.227 B 159 0.227 B 160 0.227 B Voronoi Net Atomic Populations: Atom # Qatom Species 1 0.119 B 2 0.120 B 3 0.120 B 4 0.120 B 5 0.996 N ... 155 0.993 N 156 0.993 N 157 0.119 B 158 0.119 B 159 0.119 B 160 0.119 B End of run: 10-NOV-2021 11:48:50 Job completed []'s, Camps On Thu, Jun 16, 2022 at 5:02 PM Alberto Garcia <alber...@icmab.es<mailto:alber...@icmab.es>> wrote: Hi, I cannot reproduce your results. Which version of Siesta are you using? Can you show your output? The expected behavior is something like this (obtained with the 4.1 branch version): [...] siesta: Electric dipole (a.u.) = -0.000000 0.558297 -0.000000 siesta: Electric dipole (Debye) = -0.000000 1.419050 -0.000000 Hirshfeld Net Atomic Populations: Atom # Qatom Species 1 -0.224 O 2 0.113 H 3 0.113 H Voronoi Net Atomic Populations: Atom # Qatom Species 1 -0.164 O 2 0.082 H 3 0.082 H Bader Analysis core-charge setup. Radii (standard, H): 1.000 0.600 dhscf: Vacuum level (max, mean) = 0.636991 -0.068255 eV cite: Please see "h2o.bib" for an exhaustive BiBTeX file. [...] in which one gets two blocks, one for Voronoi and another one for Hirshfeld populations. Alberto ----- El 14 de Junio de 2022, a las 22:18, I. Camps ica...@gmail.com<mailto:ica...@gmail.com> escribió: | Hello, | | I set my input to calculate and export the charges using Voronoi, Bader and | Hirshfeld approaches. | | My output has at the end two sets, one after the energy decomposition/final | energy/etc. section, and then after some info about Bader/Vacuum level/LDOS | info. | | Both sets return different charges. | | My questions are: | - Why two sets of charges? | - Which one is the "good" one? | | []'s, | | Camps | | | -- | SIESTA is supported by the Spanish Research Agency (AEI) and by the European | H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- Emilio Artacho Theory Group, Nanogune, 20018 San Sebastian, Spain, and Theory of Condensed Matter, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
