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/)
