This function produces, for simple cases, input files for PELMO 4.01 as distributed with FOCUS PELMO 5.5.4

PELMO_psm(chent, comment = "", identifier = if (is.character(chent))
  chent else names(chent$identifier), filename = paste0(identifier,
  ".psm"), path = "E:/FOCUSPELMO.553", overwrite = FALSE, rate = 100,
  timing = 0, timing_ref = 0, period = 1, mw = chent$mw,
  diff_air = 0.05, boundary = 0.1, calc_henry = !is.na(p0),
  henry = c(`20` = 0, `30` = 0), cwsat = NA, p0 = NA, Hv = 98400,
  PUF = 0, topology = NA, degradation = list(parent = list(Inf)),
  deg_temp = NA, Q10 = NA, moist_exp = NA, moist_abs = NA,
  moist_rel = NA, rel_deg_neq = NA, Q10_default = 2.58,
  moist_exp_default = 0.7, deg_temp_default = 20,
  rel_deg_neq_default = 0, moist_abs_default = 0,
  moist_rel_default = 100, degradation_flag = 0, k_photo = 0,
  ref_photo = 500, sorption = data.frame(Kfoc = 0, N = 1),
  Freundlich_limit = 0, calc_Kd = TRUE, horizons = data.frame(Kd =
  numeric(0), N = numeric(0), rel_deg = numeric(0)))

Arguments

chent

Either a string with the name of the active substance, or a chent object

comment

An optional comment

identifier

The name of the active substance

filename

The file name

path

The directory where the file should be placed

overwrite

If FALSE (default), the function stops if the file already exists

rate

Application rates in g/ha used in each growing season reaching the soil

timing

The application times. Either a numeric vector with relative application dates, or a list of vectors with absolute application dates specified as character string with the format MM-DD, named with the first three letters of the respective scenario (e.g. list(Ham = c('04-15', '04-30')) for applications on 15th and 30th of April in the Hamburg scenario.

timing_ref

A vector of reference points used for relative application dates used in the timing argument. 0 is first emergence, 1 is first maturation, 2 is first harvest, 3 is second emergence, 4 is second maturation, 5 is second harvest

period

The period for growing seasons in which applications are made, in years. 1 means annual application, 2 means biennial application, 3 means application every third year.

mw

Molecular weight for parent and metabolites

diff_air

Diffusion coefficient in air at 20°C in cm2/s

boundary

Thickness of the boundary layer for volatilisation in cm

calc_henry

Should the Henry constant of the parent compound be calculated from vapour pressure and water solubility?

henry

A vector with Henry constants of the parent compound in J/mol (equivalent to SI units of Pa m3/mol) with one or two temperatures in degrees as index

cwsat

A vector with one or two water solubilities of the parent compound in mg/L, named with temperatures in degrees centigrade. Temperatures should be as used for henry. If not a named vector, the water solubility measured at 20°C.

p0

A vector with one or two vapour pressures of the parent compound in Pa, named with temperatures in degrees centigrade. Temperatures should be as used for henry. If not a named vector, the vapour pressure measured at 20°C.

Hv

Presumably the enthalpy of volatilisation

PUF

The plant uptake factor for the parent compound

topology

Specifies the topology to be used for the transformation products.

degradation

An optional list of lists with a special syntax for specifying DT50 values and formation fractions. Overrides rate constant arguments specified above (k_*), but not k_photo.

deg_temp

Temperature for degradation rate

Q10

The Q10 factor for temperature dependence of degradation

moist_exp

The exponent for moisture dependence of degradation

moist_abs

Absolute moisture

moist_rel

Relative moisture

rel_deg_neq

Relative degradation in non-equilibrium compartment

Q10_default

Default value for the Q10 (temperature dependence of soil degradation)

moist_exp_default

Default value for the soil moisture exponent (moisture dependence of soil degradation)

deg_temp_default

Default temperature for degradation data

rel_deg_neq_default

Default value for rel_deg_neq

moist_abs_default

Default absolute moisture

moist_rel_default

Default relative moisture

degradation_flag

0 (default) or 3: degradation according to degradation factors, 1 or 4: constant with depth, 2 or 5: individual. If >2, degradation only in the liquid phase

k_photo

First order photolysis rate constant to sink in 1/day

ref_photo

Reference radiation for photolysis rate constant in W/m2

sorption

dataframe holding Kfoc and Freundlich exponent N for OC dependent sorption for the parent and the transformation products. If no rownames are present, it is assumed that the values are in the same order as the list of transformation products in the chent object, or, if no chent object is supplied, the order of metabolites in the mw argument is used.

Freundlich_limit

The lower limit of Freundlich sorption in µg/L

calc_Kd

Should the Kd be calculated from the Kfoc and the organic carbon content of the soil? The alternative is only implemented for the parent compound.

horizons

Data frame containing columns Kd, Freundlich exponents N and relative degradation rel_deg for direct input, overriding what has been specified in the adsorption argument for the parent compound. If degradation_flag is 2, rel_deg is used for parent compound and metabolites (which needs to be done manually in the FOCUS PELMO GUI).

Note

It is not clear how exactly the numbers in the volatilization section (henry, cwsat and p0) and their temperatures are used in the model, so it is recommended to stick to simple use cases like specifying 0 for henry constants at 20 and 30 degrees centigrade (switching off volatilisation).