Dear Camps, Emilio,
True, I overlooked the point in the original question (my apologies!)
but thought that the doubling of charge prints is simply due to a spin
polarized calculation.
I was wrong, as that doubling also appears in case of closed shell
singlets' outputs. What is more, the two lists are quite different.
Conclusion: I don't know the reason (only I can think of the initial
and final data of an iterative charge calculation but it's just an
idea).
Question: Could someone clarify this?
Best regards,
t
On Tue, Jun 21, 2022 at 10:03 PM I. Camps <ica...@gmail.com> wrote:
>
> 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/)
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
