[CP2K-user] [CP2K:16332] PBC problem
kj43 tem
ktem395 at gmail.com
Fri Dec 3 09:39:57 UTC 2021
Greetings, I have recently started using cp2k and I'm a beginner. I'm
writing to you because I need help with a molecular dynamics calculation.
My system consists of a silver surface that interacts with an aqueous
solution. I applied the PBCs only along the X and Y axes, but not along Z
(in that Z direction I have the solution that interacts with the surface).
The silver surface is parallel to the XY plane I set in the & POISSON
section:
POISSON_SOLVER ANALYTIC Unfortunately, however, it happens that the bonds
of some water molecules tend to break when they reach the edge of the
simulation box along Z, as if the atoms interacted with the image of my
surface, which is located along Z. I tried to change the algorithm to
POISSON_SOLVER but got the same results. At this point, with the VMD
software I entered the size of the simulation box that I entered in the
Cp2k input and I visualized the system image along z. I observed (as you
can see in the following image) that the hydrogen atoms tend to collapse
towards the silver atoms of the image along z (this however should not
happen because in PERIODIC I have set only the X and Y axes). These are the
dimensions of the simulation box:
&CELL ABC 16.36 16.36 16.78 PERIODIC XY &END CELL
In the following images, however, we can see how the atoms that are subject
to breaking of the bonds are "attracted" by atoms of the image surface
along z (which should not exist, however).
In the following image there is the initial situation:
[image: 01.png]
The following image shows the breaking of some chemical bonds: (this occurs
after a few thousand of molecular dynamics steps)
[image: 02.png]
Finally, in this image I show the image of the system along Z, and it is
evident that the hydrogen atoms converge towards a silver atom in the image: [image:
03.png]
Here is my input: (I apologize for any mistakes but I am learning and I may
have made many mistakes)
&FORCE_EVAL
METHOD QUICKSTEP
&DFT
&QS
METHOD xTB
&xTB
&PARAMETER
DISPERSION_PARAMETER_FILE dftd3.dat
&END PARAMETER
DO_EWALD T
CHECK_ATOMIC_CHARGES F
STO_NG 6
&END xTB
&END QS
&POISSON
PERIODIC XY
POISSON_SOLVER IMPLICIT
&EWALD
EWALD_TYPE SPME
&END EWALD
&END POISSON
&SCF
SCF_GUESS ATOMIC
MAX_SCF 250
EPS_SCF 1.e-6
&OT
MINIMIZER CG
PRECONDITIONER FULL_ALL
ENERGY_GAP 0.01
&END
&OUTER_SCF
EPS_SCF 1.e-6
MAX_SCF 250
&END
&END SCF
&END DFT
&SUBSYS
&CELL
ABC 16.36 16.36 16.78
PERIODIC XY
&END CELL
&COORD
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&END COORD
&END SUBSYS
&END FORCE_EVAL
&MOTION
&CONSTRAINT
&FIXED_ATOMS
COMPONENTS_TO_FIX XYZ
LIST 1..128
&END FIXED_ATOMS
&END CONSTRAINT
&MD
ENSEMBLE NVE
STEPS 10000
TIMESTEP 0.1
TEMPERATURE 300.0
TEMP_TOL 50.0
&END MD
&END MOTION
&GLOBAL
PROJECT testAg_surf
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
Thank you very much for your help.
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