phr_surface: Specify a surface
In paleolimbot/tidyphreeqc: Tidy geochemical modeling using PHREEQC

Description Usage Arguments See Also Examples

Surface specification happens in three places: phr_surface_master_species(), which defines the binding site names, phr_surface_species(), which defines the log_k values for the binding of solution species to the site, and this function, which defines the number and density of binding sites (defined in phr_surface_master_species()) that exist in the solution specified by the 'equilibrate' parameter. It is worth noting that "hydrous ferric oxide" (Hfo) are included in the main (and several other) databases, including log_k values for many metals with this surface. These are split into the strong (Hfo_s) and weak (Hfo_w) sites.

phr_surface(.number = 1, .name = NA, ..., equilibrate = 1,
  sites_units = "absolute")

phr_surface_item(sites, specific_area_per_gram = NULL, grams = NULL,
  diffusion_coefficient = NULL)

`.number, .name`	Identifiers for this surface
`...`	One or more phr_surface_item() objects or key/value pairs added to the block. Surface items should be in the form binding_site_name = phr_surface_item(...) (where binding_site_name is defined in `phr_surface_master_species()`).
`equilibrate`	A `phr_solution()` number with which this surface should equilibrate. Defaults to 1.
`sites_units`	Either absolute (sites speciried in moles) or density (sites specified in sites/ng).
`sites`	The number of sites in moles (if sites_units is "absolute"), or the density of sites in sites / square nanometer (if sites_units is "density").
`specific_area_per_gram`	Area of the surface per gram, in square meters / gram
`grams`	The number of grams, for specific area calculation
`diffusion_coefficient`	The diffusion coefficient in square meters / second, which applies in a TRANSPORT calculation to make the surface transport in space (like a colloid rather than an immobile surface).

https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/phreeqc3-html/phreeqc3-45.htm

A phr_input_section()

# specify a hydrous ferric oxide surface and see if there is any sorption by Zn
# similar to example 8 in the documentation
phr_input(
  phr_solution(pH = 8, Zn = 0.1),
  phr_surface(
    Hfo_sOH = phr_surface_item(sites = 5e-6, specific_area_per_gram = 600, grams = 0.09),
    # no need to specify mass of this binding site, because it shares a surface
    # with Hfo
    Hfo_wOH = phr_surface_item(sites = 2e-4),
  ),
  phr_selected_output(molalities = c("Zn+2", "Hfo_sOZn+", "Hfo_wOZn+"))
) %>%
  phr_run()