I completely agree with Tamas and Emilio BUT my question *is not* related
to which charge calculation scheme is "better".
My question is that in my calculations, two different sets of data of the
same type of charges are appearing in the output file, instead only one for
each. I have two outputs for Hirshfeld and two outputs for Voronoi charges.
[]'s,
Camps
On Mon, Jun 20, 2022 at 5:02 PM Emilio Artacho <e.arta...@nanogune.eu>
wrote:
> 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> 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> 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
> 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> 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
> 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/)
>
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
