[CP2K-user] [CP2K:19981] Does the boundary setting affect the charge distribution under the electric field?

[Evelyn Navarro]

Hi
I work with two-dimensional hexagonal boron nitride. The valency of the N 
（B) element calculated by XTB is -0.45(0.45), and I've seen some papers 
give it as -2.6. I don't know if that's right. I've been told by some 
scholars that changes in charge are important. The value of charge is 
affected by the way it is divided, and the value of charge is also 
different from the way it is divided, so I do not care about the size of 
the value of charge. (I don't know what you mean by physically  sound  )
I have calculated the mechanical properties of hexagonal boron nitride with 
XTB, and the results are in a reasonable range.

regards
EN


On Friday, March 1, 2024 at 4:58:05 PM UTC+8 Jürg Hutter wrote:

> Hi
>
> did you check that the xTB Hamiltonian correctly describes your basic 
> system?
> Are fundamental properties correct (without EField)?
> You also disable the check on atomic charges, did you make sure that the
> final atomic charges (again without Efield) are physically sound?
>
> regards
> JH
>
> ________________________________________
> From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Evelyn 
> Navarro <easa... at gmail.com>
> Sent: Thursday, February 29, 2024 3:33 PM
> To: cp2k
> Subject: Re: [CP2K:19978] Does the boundary setting affect the charge 
> distribution under the electric field?
>
> Hi
> I tried to use the periodic electric field to calculate the 
> two-dimensional piezoelectric material at the periodic boundary, but the 
> charge seemed to accumulate towards the middle of the two-dimensional 
> material, which was unreasonable. The normal ones should gather towards 
> both ends of the material. I want to know what the problem is. (This does 
> not seem to be a problem with aperiodic boundaries.)
> &GLOBAL
> PROJECT 468-zhouqi-0.003d-xyzbianjie-2024-M-EWALD
> PRINT_LEVEL LOW
> RUN_TYPE MD
> &END GLOBAL
>
> &FORCE_EVAL
> METHOD Quickstep
> &SUBSYS
> &CELL
> ABC 38.9946780817 32.5196269485 100.000
> PERIODIC XYZ #Direction of applied PBC (geometry aspect)
> &END CELL
> &TOPOLOGY
> COORD_FILE_FORMAT XYZ
> COORD_FILE_NAME 468.xyz
> &CENTER_COORDINATES #Centering the atoms in the box
> &END
> &END
> # &VELOCITY #You can set initial atomic velocities in this section
> # &END VELOCITY
> &END SUBSYS
>
> &DFT
> # WFN_RESTART_FILE_NAME 400-RESTART.wfn
> CHARGE 0 #Net charge
> MULTIPLICITY 1 #Spin multiplicity
>
> &PERIODIC_EFIELD
> INTENSITY 0.003
> POLARISATION -1.00000 0.00000 0.00000
> &END
>
> &QS
> EPS_DEFAULT 1E-10 #This is default. Set all EPS_xxx to values such that 
> the energy will be correct up to this value
> EXTRAPOLATION ASPC #Extrapolation for wavefunction during e.g. MD. ASPC is 
> default, PS also be used
> EXTRAPOLATION_ORDER 3 #Order for PS or ASPC extrapolation. 3 is default
> METHOD xTB
> &xTB
> DO_EWALD T
> CHECK_ATOMIC_CHARGES F #xTB calculation often crashes without setting this 
> to false
> &PARAMETER
> DISPERSION_PARAMETER_FILE dftd3.dat
> PARAM_FILE_NAME xTB_parameters
> &END PARAMETER
> &END xTB
> &END QS
> &POISSON
> &EWALD
> ALPHA 1.0
> EWALD_TYPE SPME
> GMAX 75
> &END EWALD
>
> PERIODIC XYZ #Direction(s) of PBC for calculating electrostatics
> PSOLVER PERIODIC ##ANALYTIC #The way to solve Poisson equation
> &END POISSON
> &SCF
> MAX_SCF 20 #Maximum number of steps of inner SCF
> EPS_SCF 1.0E-05 #Convergence threshold of density matrix of inner SCF
> # SCF_GUESS RESTART #Use wavefunction from WFN_RESTART_FILE_NAME file as 
> initial guess
> &OT
> PRECONDITIONER FULL_SINGLE_INVERSE
> MINIMIZER DIIS #CG is worth to consider in difficult cases
> LINESEARCH 2PNT #1D line search algorithm for CG. 2PNT is default, 3PNT is 
> better but more costly. GOLD is best but very expensive
> &END OT
> &OUTER_SCF
> MAX_SCF 20 #Maximum number of steps of outer SCF
> EPS_SCF 1.0E-05 #Convergence threshold of outer SCF
> &END OUTER_SCF
> &PRINT
> &RESTART OFF #Do not generate wfn file to suppress meaningless I/O cost
> &END RESTART
> &END PRINT
> &END SCF
> &PRINT
> &MULLIKEN
> FILENAME muliken
> &EACH
> MD 1
> &END
> PRINT_ALL F #If T, then printing full net AO and overlap population matrix
> &END MULLIKEN
> &END PRINT
>
> &END DFT
> &END FORCE_EVAL
>
> &MOTION
> &MD
> ENSEMBLE NVT
> STEPS 250000 #Number of steps to run
> TIMESTEP 1.0 #Step size in fs. Decrease it properly for high temperature 
> simulation
> TEMPERATURE 5 #Initial and maintained temperature (K)
> &THERMOSTAT
> TYPE NOSE
> &END THERMOSTAT
> &END MD
> &CONSTRAINT
> &FIXED_ATOMS #Set atoms to be fixed
> COMPONENTS_TO_FIX XYZ #Which fractional components will be fixed, can be 
> X, Y, Z, XY, XZ, YZ, XYZ
> LIST 357..468
>
> &END FIXED_ATOMS
> &END CONSTRAINT
> &PRINT
> &TRAJECTORY
> &EACH
> MD 1 #Output frequency of coordinate
> &END EACH
> FORMAT xyz
> &END TRAJECTORY
> &RESTART
> BACKUP_COPIES 0 #Maximum number of backing up restart file, 0 means never
> &EACH
> MD 100 #Frequency of updating last restart file. Default is 20
> &END EACH
> &END RESTART
> &RESTART_HISTORY
> &EACH
> MD 1000 #How many steps a history .restart file is generated. Default is 
> 500
> &END EACH
> &END RESTART_HISTORY
> &END PRINT
> &END MOTION
>
> On Monday, February 26, 2024 at 5:07:59 PM UTC+8 Jürg Hutter wrote:
> Hi
>
> you are using a probably not tested combination of features.
> xTB with 2D periodicity and external electrical field (and hoping
> for the correct default Ewald setting) might not result in a
> correct setup. You should also use the PERIODIC_EFIELD option.
> I would suggest to simplify your system: use 3 D periodic cell with a large
> vacuum space (e.g. 80 A). This should correctly choose the Ewald settings
> and together with PERIODIC_EFIELD might work.
>
> regards
> JH
>
> ________________________________________
> From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Evelyn 
> Navarro <easa... at gmail.com>
> Sent: Friday, February 23, 2024 2:03 PM
> To: cp2k
> Subject: [CP2K:19964] Does the boundary setting affect the charge 
> distribution under the electric field?
>
> Dear all
> I was studying the charge changes of two-dimensional piezoelectric 
> materials under electric fields, and found that when the boundary is set as 
> a period, the charge is actually concentrated in the middle of the 
> material, which is not understandable. But if you use aperiodic boundaries, 
> the charge will accumulate towards both ends of the material, which is 
> normal. I tried the electric field and the periodic electric field 
> respectively, and as long as the boundary is periodic, the charge will 
> gather in the middle, which is incomprehensible, and I want to know why. 
> What I want to study is periodic materials, and this periodic boundary is 
> unavoidable.
>
> &GLOBAL
> PROJECT 468-zhouqi-0.004d-xybianjie-2024
> PRINT_LEVEL LOW
> RUN_TYPE MD
> &END GLOBAL
>
> &FORCE_EVAL
> METHOD Quickstep
> &SUBSYS
> &CELL
> ABC 38.9946780817 32.5196269485 20.000
> PERIODIC XY #Direction of applied PBC (geometry aspect)
> &END CELL
> &TOPOLOGY
> COORD_FILE_FORMAT XYZ
> COORD_FILE_NAME 468.xyz<http://468.xyz>
> &CENTER_COORDINATES #Centering the atoms in the box
> &END
> &END
> # &VELOCITY #You can set initial atomic velocities in this section
> # &END VELOCITY
> &END SUBSYS
>
> &DFT
> # WFN_RESTART_FILE_NAME 400-RESTART.wfn
> CHARGE 0 #Net charge
> MULTIPLICITY 1 #Spin multiplicity
>
> &EFIELD
> INTENSITY 0.004
> POLARISATION -1.00000 0.00000 0.00000
> &END
>
> &QS
> EPS_DEFAULT 1E-10 #This is default. Set all EPS_xxx to values such that 
> the energy will be correct up to this value
> EXTRAPOLATION ASPC #Extrapolation for wavefunction during e.g. MD. ASPC is 
> default, PS also be used
> EXTRAPOLATION_ORDER 3 #Order for PS or ASPC extrapolation. 3 is default
> METHOD xTB
> &xTB
> CHECK_ATOMIC_CHARGES F #xTB calculation often crashes without setting this 
> to false
> &PARAMETER
> DISPERSION_PARAMETER_FILE dftd3.dat
> PARAM_FILE_NAME xTB_parameters
> &END PARAMETER
> &END xTB
> &END QS
> &POISSON
> PERIODIC XY #Direction(s) of PBC for calculating electrostatics
> PSOLVER ANALYTIC #The way to solve Poisson equation
> &END POISSON
> &SCF
> MAX_SCF 20 #Maximum number of steps of inner SCF
> EPS_SCF 1.0E-05 #Convergence threshold of density matrix of inner SCF
> # SCF_GUESS RESTART #Use wavefunction from WFN_RESTART_FILE_NAME file as 
> initial guess
> &OT
> PRECONDITIONER FULL_SINGLE_INVERSE
> MINIMIZER DIIS #CG is worth to consider in difficult cases
> LINESEARCH 2PNT #1D line search algorithm for CG. 2PNT is default, 3PNT is 
> better but more costly. GOLD is best but very expensive
> &END OT
> &OUTER_SCF
> MAX_SCF 20 #Maximum number of steps of outer SCF
> EPS_SCF 1.0E-05 #Convergence threshold of outer SCF
> &END OUTER_SCF
> &PRINT
> &RESTART OFF #Do not generate wfn file to suppress meaningless I/O cost
> &END RESTART
> &END PRINT
> &END SCF
> &END DFT
> &END FORCE_EVAL
>
> &MOTION
> &MD
> ENSEMBLE NVT
> STEPS 250000 #Number of steps to run
> TIMESTEP 1.0 #Step size in fs. Decrease it properly for high temperature 
> simulation
> TEMPERATURE 5 #Initial and maintained temperature (K)
> &THERMOSTAT
> TYPE NOSE
> &END THERMOSTAT
> &END MD
> &CONSTRAINT
> &FIXED_ATOMS #Set atoms to be fixed
> COMPONENTS_TO_FIX XYZ #Which fractional components will be fixed, can be 
> X, Y, Z, XY, XZ, YZ, XYZ
> LIST 357..468
>
> &END FIXED_ATOMS
> &END CONSTRAINT
> &PRINT
> &TRAJECTORY
> &EACH
> MD 1 #Output frequency of coordinate
> &END EACH
> FORMAT xyz
> &END TRAJECTORY
> &RESTART
> BACKUP_COPIES 0 #Maximum number of backing up restart file, 0 means never
> &EACH
> MD 100 #Frequency of updating last restart file. Default is 20
> &END EACH
> &END RESTART
> &RESTART_HISTORY
> &EACH
> MD 1000 #How many steps a history .restart file is generated. Default is 
> 500
> &END EACH
> &END RESTART_HISTORY
> &END PRINT
> &END MOTION
>
> Thanks
> Evelyn Navarro
>
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