bafm.cpp File Reference

Simulation of AFM experiments. More...

#include "rwimg.h"
#include "utilities.h"
#include "options.h"
#include "timer.h"

Functions
Bimage *	afm_generate_tip (Vector3< long > size, Vector3< double > sampling, double radius, double angle, double resolution)
	Generates a rounded conical AFM tip. More...
Bplot *	afm_simulate (Bimage *ptip, Bimage *p, double spring, double modulus, double thick)
	Simulates and AFM experiment. More...
Bimage *	afm_force_to_height (Bimage *pf, double force_step)
	Converts an AFM force map into a set of 2D height images at different constant force values. More...
int	main (int argc, char **argv)
int	afm_simulate_at_xy (Bimage *ptip, Bimage *p, long ii, float *force, double spring, double modulus, double thick)

Variables
int	verbose
const char *	use []

Detailed Description

Simulation of AFM experiments.

Author

Bernard Heymann

Date

Created: 19990124

Modified: 20170612

Function Documentation

afm_force_to_height()

Bimage * afm_force_to_height	(	Bimage *	pf,
		double	force_step
	)

Converts an AFM force map into a set of 2D height images at different constant force values.

Parameters

*pf	force map.
force_step	force intervals for height images

Returns

*ph height images.

afm_generate_tip()

Bimage * afm_generate_tip	(	Vector3< long >	size,
		Vector3< double >	sampling,
		double	radius,
		double	angle,
		double	resolution
	)

Generates a rounded conical AFM tip.

Parameters

size	size of the tip density
sampling	sampling/spacing (in angstrom/pixel)
radius	radius of the tip curvature (in angstrom)
angle	angle of the tip side (in radians)
resolution	the resolution affects the tip surface softness

Returns

Bimage* tip 3D map.

A 2D image of a conical tip is generated, with a 45 degree angle and
a rounding tip with the desired radius and softness.
The 2D image is then converted to a 3D surface using the function 
img_to_surface and returned.  The density of beta-silicon nitride
of 1.925 Da/A3 is used.

afm_simulate()

Bplot * afm_simulate	(	Bimage *	ptip,
		Bimage *	p,
		double	spring,
		double	modulus,
		double	thick
	)

Simulates and AFM experiment.

Parameters

*ptip	AFM tip density map - converted to force map.
*p	specimen density map.
spring	AFM cantilever spring constant (N/m).
modulus	bulk modules (N/m2).
thick	sample thickness (angstrom).

Returns

Bplot* force curve.

The elastic force on an AFM tip is calculated as:
    F = kt*dz = kb*dV/d
where   kt is the cantilever spring constant, typically 0.01 - 0.1 N/m.
        dz is the tip displacement due to specimen interaction.
        kb is the bulk modulus of the specimen, typically 1e9 N/m2.
        dV is the volume of the specimen displaced by the tip. This
            volume is here approximated as the density overlap volume.
        d is the specimen thickness in angstrom.
The tip is positioned at each point (x,y,z) in the density map and the
overlap volume calculated (i.e., a type of convolution).  This tip
position corresponds to a zero displacement.  The correct tip position
is found by shifting the tip upwards (in the z-direction) until the 
displacement and elastic forces are approximately equal.  The tip 
displacement is refined by interpolation and the force calculated.  
The force map is returned in place of the original density map.
Forces are calculated in piconewton. 
The origin of the tip density is taken as nx/2, ny/2, 0.

afm_simulate_at_xy()

int afm_simulate_at_xy	(	Bimage *	ptip,
		Bimage *	p,
		long	ii,
		float *	force,
		double	spring,
		double	modulus,
		double	thick
	)

main()

int main	(	int	argc,
		char **	argv
	)

Variable Documentation

use

const char* use[]

verbose

int verbose

extern