In jrminter/rpemepma: Processing of data from PENEPMA simulations using R

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = NA
)

Our objective is to construct a PENEPMA .geo file.

Note: Rmarkdown interferes with the use of the sink() function which permits us to divert output to a system file. The code below, when run from a R script, writes the file L3-20-250-bulk.geo to the Desktop,

An R script that works

library(rpenepma)
geoPath <- "~/Desktop/L3-20-250-bulk.geo"

# define the cumulative layer thickness values
cum_layer_t_nm <- c(-20.0, -270.0, (-1.0e7 - 270.))

# start sink
sink(file=geoPath)

# write a header line of x's
penepma_geo_hdr_x()
# Wite a blank comment
penepma_geo_hdr_c()
# write a descriptive comment
penepma_geo_hdr_cmt("Cylindrical layers - distances all in cm")
# Start writing the layers
penepma_geo_add_surf_z(1, "Plane Z=0 - surface plane", c(0, 0, 0, 1, 0), NA)
penepma_geo_add_surf_z(2, "Plane Z=-20 nm (1st film, 20 nm thick)",
                       c(0, 0, 0, 1, 0), cum_layer_t_nm[1])
penepma_geo_add_surf_z(3, "Plane Z=-270 nm (2nd film, 250 nm thick)",
                       c(0, 0, 0, 1, 0), cum_layer_t_nm[2])
penepma_geo_add_surf_z(4, "Plane Z=-1 cm (3rd matl, substrate)",
                       c(0, 0, 0, 1, 0),  cum_layer_t_nm[3])
# Add a cylindrical bounding layer 1 cm in radius
penepma_geo_add_surf_cyl(5, "Cylinder, 1 cm radius", 1.0)
# Write out the layer descriptions
penepma_geo_add_body(1, "top layer")
penepma_geo_add_body(2, "middle layer")
penepma_geo_add_body(3, "bottom layer")
# finish up
penepma_geo_fini()
# close the sink file
sink()