PFAS fate and transport

Surface-water PFAS fate & transport turns on when the SWAT+ working directory (Scenarios/Default/TxtInOut) contains pfas.dat. Without that file the engine skips the PFAS module entirely. This chapter covers the file schemas and the edit workflow.

Where the files go

Scenarios/Default/TxtInOut/          # run directory for swatplus
├── pfas.dat                         # REQUIRED to enable PFAS (compounds + chemistry)
├── pfas_hru.ini                     # REQUIRED for soil IC + sorption (HRU order)
├── pfas_calib.dat                   # optional: soil_scale koc_scale
├── pfas_cha.dat                     # optional: in-stream koc/settle/resus/bury + IC
├── pfas_leach.map                   # research daily MF6 coupling only (with mf6.con)
├── soils.sol                        # layer thickness, bd, OC, texture (generator input)
├── hru-data.hru                     # soil + lu_mgt names (generator input)
└── … standard SWAT+ inputs …

<model_root>/                        # SWAT_MODEL_Web_Application (sibling of TxtInOut tree)
└── pfas_data/                       # OBSERVATIONS only (optional order / add-on snap)
    ├── pfas_stations_assignment.csv
    ├── stations.shp
    ├── <channel>_<site_id>.csv
    └── README.md

Produce the soil inputs

pfas_hru.ini is required whenever pfas.dat is present. You can hand-edit it, start from a research/example package that already includes it, or derive a background PFOS initial condition from the soils and HRU tables already in TxtInOut (soils.sol + hru-data.hru). A typical offline derivation writes PFOS only (num_pconta=1, enr=1.0), maps each layer’s OC/clay/sand to the nearest of six reference soils S1–S6 for (kf, n, d50), and seeds sol_pfas from land-use background µg/kg × bulk density × thickness × 1e4 with surface-weighted depth decay 0.5^k. Field-level detail is under pfas_hru.ini below.

Loadings / sources — what you edit

• Initial soil mass: edit sol_pfas columns in pfas_hru.ini (µg ha⁻¹), or raise land-use / site concentrations and regenerate the background IC from soils.sol + hru-data.hru.
• Chemistry / AWI sorption: edit mw, sol, kl, lm, percop in pfas.dat.
• Solid sorption: edit kf / nf per layer in pfas_hru.ini (or change soils so the S1–S6 match shifts).
• In-stream partition / bed exchange: pfas_cha.dat (or rely on defaults).
• Global scale during cal: pfas_calib.dat.
• Point / channel initial concentrations: trailing water_ppt / benthic_ppt on pfas_cha.dat rows.

Observation package (not engine IC)

• Optional order / dashboard add-on places monitoring under pfas_data/ at the model root. Use those CSVs to compare against channel_pfas_day.txt — they are not read as model IC.
• Public PFAS inventory APIs and MCP tools serve monitoring data; they do not write pfas.dat / pfas_hru.ini into TxtInOut.

Outputs to check after a run

• pfas_hru_aa.txt — per-HRU budget (kg ha⁻¹): init/final, surq, latq, perc (leach toward GW), sed, resid.
• channel_pfas_day.txt — daily reach mass terms + conc_ngL.
• pfas_balance.out / pfas_cha_balance.out — land-phase and channel mass-balance checks.
• Coupled research path (mf6.con + pfas_leach.map): mf6/pfas.ucn, mf6/pfas.lst — see the MODFLOW coupling chapter. Ordinary MODFLOW_250m packages do not include these.

Product vs research scope

• Standard distribution: SWAT+ package download; optional pfas_data observation snap; hand-edited or offline-derived pfas.dat / pfas_hru.ini for engine IC.
• Requires a PFAS-enabled engine binary locally (see Compile the SWAT+ fork), or a research package that already includes the pfas.* inputs. Standard hosted builds do not auto-emit pfas.dat.
• Research scope (not the default order): daily BMI PFAS leach maps, MF6 groundwater transport outputs (pfas.ucn), vadose-zone pathways, multi-analyte setups, and joint SW–GW calibration.

pfas.dat — compound database

PFAS compound database. Its presence in TxtInOut enables the PFAS fate & transport module; absent file is a clean no-op.

Two header lines, then one free-format row per compound; a row with id ≤ 0 terminates the list. The compound order defines the compound index used by every other PFAS file.

pfas.dat: PFAS compound database (PFOS example)
 id  name        mw         sol        kl        lm        percop
  1  PFOS    0.50013    680.0      0.137     2500.0     0.20
  0  END     0.0        0.0        0.0       0.0        0.0

pfas_hru.ini — soil initial condition

Per-HRU soil initial condition and Freundlich sorption parameters for every compound in pfas.dat. Required when pfas.dat is present.

One block per HRU in engine HRU order (record k → HRU k). The block declares its own layer count (nly in the header); the reader stores layers 1…min(file nly, soil layer count from soils.sol) and derives the working layer count from the soil, not the file.

hru <id> nly <nlayers>
<num_pconta>                         # contaminated-site count (0 coerced to 1)
<d50_L1> … <d50_Lnly>                # median grain diameter per layer (mm)
<pid> <sol_pfas_L1> … <sol_pfas_Ln>  # initial soil PFAS mass per layer
<pid> <kf_L1> … <kf_Ln>              # Freundlich kf per layer
<pid> <nf_L1> … <nf_Ln>              # Freundlich n per layer
<pid> <enr>                          # sediment enrichment ratio
# repeat the four <pid>… lines once per compound in pfas.dat (ip = 1..npfas)
# pid ≤ 0 → no PFAS in this HRU (remaining PFAS rows for that HRU skipped)

How a background IC is typically produced

• Inputs already in the package: soils.sol (layer thickness, bulk density, OC, texture) and hru-data.hru (soil + land-use names).
• Background template commonly writes PFOS only: num_pconta=1, enr=1.0.
• Sorption (kf, n, d50) per layer: nearest of six reference soils S1–S6 by OC/clay/sand.
• Initial mass: land-use background µg/kg × bulk density × layer thickness × 1e4, with surface-weighted depth decay 0.5^k.

pfas_cha.dat and pfas_calib.dat

Optional in-stream PFAS parameters and initial reach concentrations (pfas_cha.dat) and global calibration multipliers (pfas_calib.dat).

pfas_cha.dat — in-stream parameters

Optional. Absent file → PFOS-like defaults and PFAS-free initial reaches; HRU loads still route through the channel phase. Two header lines, then one row per compound; id ≤ 0 terminates. Compound ids must align with pfas.dat.

pfas_calib.dat — calibration multipliers

Optional single line: soil_scale koc_scale (e.g. 0.11 1.0). Missing file → both 1.0.

Output files

The four PFAS output surfaces the engine writes when the PFAS module is active: per-HRU budget, daily channel series, and two mass-balance checks. Written by pfas_output.f90 and cha_pfas_output.f90.

pfas_hru_aa.txt — per-HRU budget (once per run)

Written once at the end of the simulation by pfas_output. Only HRU × compound rows with a nonzero initial pool are emitted.

channel_pfas_day.txt — daily reach series

Written per reach per day (on the daily print schedule from print.prt) by cha_pfas_output; a twin CSV is written when csvout = y. Mass terms are daily kg per reach.

Mass-balance checks (once per run)

• pfas_balance.out — area-weighted basin totals per compound: init_kg, final_kg, surq_kg, latq_kg, perc_kg, sed_kg, loss_kg, resid_kg, resid_pct; footer reports the worst per-HRU residual (abs/rel) and its HRU index.
• pfas_cha_balance.out — run-cumulative channel-phase totals (kg): reach-days active, point-source input, cumulative inflow/outflow, cumulative burial, final channel storage.