Setting simulation parameters - Probe-Particle/ppafm GitHub Wiki
Simulation parameters to ppafm can be set in multiple ways:
Using command line arguments of the scripts.
Using the params.ini/params.toml file put in the simulation folder. If no such file is provided, the defaults are used (see PpafmParameters class).
In the table below we list all accepted parameters.
The parameter types stand for
bool: Boolean (True or False)
int: Integer number
real: Real number
string: String of text
list(type): A list of values of the given type.
Force-field grid parameters
Parameter
Default value
Type
Units
Description
PBC
True
bool
-
To use or not the periodic boundary conditions for calculating the grid force field. (note: electrostatic potential from DFT is always considered as PBC)
nPBC
[1, 1, 1]
list(int)
-
The number of cell replicas along each lattice vector if PBC is True.
gridN
[-1, -1, -1]
list(int)
-
The number of sampling points along each lattice vector for grid force field, if not taken from XSF or cube input file. When <0 approximate spacing of 0.1 Ångström is used for calculating gridN automatically
gridO
[0.0, 0.0, 0.0]
list(real)
-
TBC
gridA
[20.0, 0.0, 0.0 ]
list(real)
Ångström
The lattice vector a of the grid force field. Should be in format [ax,ay,0.0].
gridB
[0.0, 20.0, 0.0 ]
list(real)
Ångström
The lattice vector b of the grid force field. Should be in format [bx,by,0.0].
gridC
[0, 0, 20.0 ]
list(real)
Ångström
The lattice vector c of the grid force field. Should be in the format [0.0,0.0,cz].
FFgrid0
[ -1.0, -1.0, -1.0 ]
list(real)
Ångström
Force-field grid origin used in the GUI/OpenCL. Usually does not need to be specified manually.
FFgridA
[ -1.0, -1.0, -1.0 ]
list(real)
Ångström
Force-field grid lattice vector a used in the GUI/OpenCL. Usually does not need to be specified manually.
FFgridB
[ -1.0, -1.0, -1.0 ]
list(real)
Ångström
Force-field grid lattice vector b used in the GUI/OpenCL. Usually does not need to be specified manually.
FFgridC
[ -1.0, -1.0, -1.0 ]
list(real)
Ångström
Force-field grid lattice vector c used in the GUI/OpenCL. Usually does not need to be specified manually.
Force-field model parameters
Parameter
Default value
Type
Units
Description
ffModel
LJ
string
-
London+Pauli potential model Morse or LJ, or vdW for the Full-density based model.
vdWDampKind
2
int
-
Kind of damping function used when ffModel is vdW (together with density-overlap)
Exponent for density-overlap E_pauli = Apauli (rho_tip*rho_sample) ^ Bpauli density-overlap use just 'vdW'
Rcore
0.7
real
Ångström
Radius of core-density subtracted from input density of grid to ensure the neutrality of atoms (simulate charge of nuclei or neutral atom)
Tip Parameters
Parameter
Default value
Type
Units
Description
probeType
O
string
-
Type of atom that is set to the probe particle (oxygen by default).
charge
0.0
real
e
Charge of the probe particle (if tip density is not provided). For CO tip we normally use <-0.1,-0.05>
r0Probe
[0.0, 0.0, 4.0]
list(real)
Ångström
The equilibrium position of the probe particle under the tip relative to the anchor point. In the Cu-CO tip, the oxygen is normally 3 Ångström below the last Cu atom.
tip
s
string
-
tip electrostatics model if no tip-charge density is provided, typical choice s,pz,dz2, for other see here. dz2 is the most common choice for the CO tip, with the quadrupole moment being then Q*sigma**2 .
sigma
0.7
real
Ångström
The radius of Gaussian tip charge density when no tip-charge density is provided.
stiffness
[-1.0, -1.0, -1.0]
list(real)
N/m
The stiffness of the probe particle x,y, and radial, if negative klat,krad is used.
klat
0.5
real
N/m
The lateral stiffness (tilt; used if stiffness vector is <0). Normally <0.2,0.25> for the CO tip.
krad
20.00
real
N/m
The radial stiffness (bond length; used if stiffness vector is <0) ?
Scan Parameters
Parameter
Default value
Type
Units
Description
scanStep
[0.10, 0.10, 0.10]
list(real)
Ångström
Sampling step of 3D volume of resulting AFM Force data grid.
scanMin
[0.0, 0.0, 5.0]
list(real)
Ångström
The start of scanning volume grid relative to sample coordinates. Normally you start max(sample_atom)_z+rProbe_z + 2.8 or even higher.
scanMax
[20.0, 20.0, 8.0 ]
list(real)
Ångström
The end of scanning volume grid relative to sample coordinates.
scanTilt
[0.0, 0.0, -0.1]
list(real)
Ångström
Tip oscillation direction when tiltedScan==True.
tiltedScan
False
bool
-
Optionally, the tip can oscillate in a tilted direction (e.g. in Lateral-mode AFM).
Conversion parameters Fz->df
The Giessibl's Formula is used to perform the conversion.
Parameter
Default value
Type
Units
Description
kCantilever
1800.0
real
N/m
Cantilever stiffness
f0Cantilever
30300.0
real
Hz
Cantilever base frequency
Amplitude
1.0
real
Ångström
Peak-to-peak amplitude
Plotting / Conversions parameters
Parameter
Default value
Type
Units
Description
plotSliceFrom
16
int
-
The first z-slice for plotting from computed df-grid.
plotSliceTo
22
int
-
The last z-slice for plottig from computed df-grid.
plotSliceBy
1
int
-
Plotting density, e.g. if 1 plot every slice, if 2 plot every 2nd slice etc.
imageInterpolation
bicubic
string
-
Interpolation used in matplotlib.imshow() for plotting df-images.
colorscale
gray
string
-
The color scale used in matplotlib.imshow() for ploting df-images.
colorscale_kpfm
seismic
string
-
The colorscale used in matplotlib.imshow() for plotting kpfm-images.
ddisp
0.05
real
Ångström
The displacement used for computing the probe particle vibration modes for IETS.
aMorse
-1.6
real
1/A
Exponent for morse potential E_Morse=E0*(1-exp(aMorse*norm(r-r_0)))^2.
KPFM parameters.
Parameter
Default value
Type
Units
Description
Rtip
30.0
real
Ångström
Radius of the metallic apex of the tip used to calculate the mesoscopic cuadratic term of the CPD in the KPFM mode. This term is calculated acording to: https://doi.org/10.1007/s100510050219
permit
0.00552634959
real
(e^2)/(eV·Ångström)
Vacuum permittivity.
Vrange
0.0
real
Volts
Range of voltages within which the LCPD parabolas are calculated in KPFM. The default 0.0 means implies that no KPFM will be performed.