[CP2K-user] [CP2K:19979] Does the boundary setting affect the charge distribution under the electric field?
Jürg Hutter
hutter at chem.uzh.ch
Fri Mar 1 08:57:55 UTC 2024
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: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Evelyn Navarro <easauasqc 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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