afmYoungModulus: afmYoungModulus

In rbensua/afmToolkit: Functions for Atomic Force Microscope Force-Distance Curves Analysis

Description

This function computes the Young's Modulus of the sample from the approach curve using Hertz's contact model for a pyramidal tip.

Usage

afmYoungModulus(afmdata, thickness = NULL, model = "Hertz", geometry =
  c("pyramid","paraboloid"), silent = TRUE, params)

Arguments

afmdata	An afmdata object. It should be a valid afmdata object upon which the Contact Point, the baseline correction and the Zero Force Point and the Indentation must have been calculated first (using functions afmContactPoint(), afmBaselineCorrection(), afmZeroPointSlope(), and afmIndentation())
thickness	Thickness (in m) of the surface. The Force - Indentation fit will be done for values of the Indentation variable smaller than the thickness. If no value is given, it will be done for all values in the curve for which the Indentation is negative.
model	Contact mechanics model to be used. Currently only Hertz's pure elastic model is available.
geometry	Geometry of the tip. Currently only pyramidal (default) and paraboloid geometries are implemented.
showfit	Logical value. If FALSE it prints the fit model summary (via summary.lm()). Default value is FALSE
params	A list containing different parameters of the model: e.g. nu (Poisson's ratio) or alpha (internal angle, in degrees, of the pyramidal tip) or R (tip radius, in the paraboloid geometry)
silent	Logical value. If TRUE supresses the message indicating the name of the curve being processed (useful for batch-processing large number of curves). Defaults to FALSE

Value

An afmdata class variable which will consist on the original input afmdata variable plus a new list named YoungModulus with the following fields:

YoungModulus The Young's modulus value (in Pa).

fitYM The Force vs Indentation^2 fit as an lm object.

fitdata The subset of the data used in the fit.

Examples

data <- afmReadJPK("force-save-JPK-2h.txt.gz", path = path.package("afmToolkit"))
data <- afmContactPoint(data, width = 20, mul1 = 1, mul2 = 20)
data <- afmDetachPoint(data, width = 40, mul1 = 3, mul2 = 40)
data <- afmBaselineCorrection(data)
data <- afmZeroPointSlope(data, segment = "approach")
data <- afmIndentation(data)
data <- afmYoungModulus(data, thickness = 1e-8, params = list(alpha = 22),
                        silent = TRUE)
print(data$YoungModulus$YoungModulus)

rbensua/afmToolkit documentation built on Dec. 1, 2020, 2:14 a.m.