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pathogen

Purpose

The pathogen module simulates user-listed pathogens across soil, foliage, channel water, benthic sediment, and aquifers. The set of pathogens simulated is declared in constituents.cs, which populates cs_db%num_paths. The files below load the parameter database and the per-object initial conditions.

Activation

The pathogen database pathogens.pth is referenced from file.cio as in_parmdb%pathcom_db (default pathogens.pth). The initial-condition files are referenced via in_init%path_soil (default path_hru.ini) and in_init%path_water (default path_water.ini).

path_parm_read is called from proc_db.f90. path_hru_aqu_read is called from proc_read.f90. path_cha_res_read is called later from main.f90.

Files

pathogens.pth

Pathogen parameter database. One row per pathogen.

# Field Units Description
1 pathnm - pathogen name
2 do_soln 1/day die-off factor in soil solution
3 gr_soln 1/day growth factor in soil solution
4 do_sorb 1/day die-off factor sorbed to soil particles
5 gr_sorb 1/day growth factor sorbed to soil particles
6 kd none partition coefficient between solution and sorbed phase in surface runoff
7 t_adj none temperature adjustment factor for die-off and growth
8 washoff none fraction on foliage washed off by a rainfall event
9 do_plnt 1/day die-off factor on foliage
10 gr_plnt 1/day growth factor on foliage
11 fr_manure none fraction of manure with active colony forming units
12 perco none percolation coefficient, ratio of solution bacteria in the surface layer
13 det_thrshd cfu/m^2 detection threshold below which soil pathogen levels are zeroed
14 do_stream 1/day die-off factor in streams
15 gr_stream 1/day growth factor in streams
16 do_res 1/day die-off factor in reservoirs
17 gr_res 1/day growth factor in reservoirs
18 conc_min - minimum pathogen concentration

path_hru.ini

Initial pathogen concentrations for HRU soils and plants. One block per record.

  • Reader: src/path_hru_aqu_read.f90
  • Type: path_soil_ini (type cs_soil_init_concentrations) in src/constituent_mass_module.f90. Fields: name, soil(num_paths), plt(num_paths) in cfu/m^2.
  • Format: one title line, then per record: a header line, a name line, then one line containing name, soil(:), plt(:) for all pathogens in constituents.cs order.

The same reader allocates cs_path_solsor(num_paths).

path_water.ini

Initial pathogen concentrations for channels and reservoirs (water column and benthic).

  • Reader: src/path_cha_res_read.f90
  • Type: path_water_ini (type cs_water_init_concentrations) in src/constituent_mass_module.f90. Fields: name, water(num_paths), benthic(num_paths). Record names are stored in path_init_name.
  • Format: title line, header line, then per record: name line, then num_paths pairs of lines (water value, benthic value). On the second pass the reader reads a single line name, water(:), benthic(:) per record.