fix(sipnet): use max timesteps per day to detect out_day, fixing partial first-day edge case

models/sipnet/NEWS.md

@@ -2,6 +2,7 @@
 
 * `split_inputs.SIPNET` now avoids internal time format conversions, giving a
   substantial speedup and reduced memory use when processing multi-year files.
+* `model2netcdf.SIPNET` now detects the number of timesteps per day by taking the maximum count across all days in the first simulation year, rather than reading only from day 1. This prevents a factor-of-N error in flux unit conversions when the first day of output is partial (fewer timesteps than a complete day) (#3624, #3989).
 * Fixed a unit error in model2netcdf.SIPNET's calculation of `GWBI` (kgC/m2/sec)
     from `woodCreation` (actually gC/m2/timestep, was being treated as gC/m2/day).
 * `model2netcdf.SIPNET` now takes NPP directly from sipnet.out rather than repeat

models/sipnet/R/model2netcdf.SIPNET.R

@@ -80,12 +80,14 @@ model2netcdf.SIPNET <- function(outdir, sitelat, sitelon, start_date, end_date,
 
   # get number of model timesteps per day
   # outday is the number of time steps in a day - for example 6 hours would have out_day of 4
-
-  out_day <- sum(
-    sipnet_output$year == simulation_years[1] &
-      sipnet_output$day == unique(sipnet_output$day)[1],
-    na.rm = TRUE
-  ) # switched to day 2 in case first day is partial
+  #
+  # Count rows per day in the first simulation year, then take the max.
+  # This correctly handles edge cases where the first or last day of the
+  # simulation is partial (has fewer timesteps than a complete day).
+  steps_per_day <- table(
+    sipnet_output$day[sipnet_output$year == simulation_years[1]]
+  )
+  out_day <- max(steps_per_day)
 
 
   timestep.s <- 86400 / out_day

models/sipnet/tests/testthat/test-model2netcdf.SIPNET.R

@@ -239,3 +239,55 @@ test_that("fluxes are converted from gC/m2/timestep to kg/m2/sec", {
   )
   expect_equal(pec2$GWBI, sip2$woodCreation / 1000 / ts, tolerance = 1e-6)
 })
+
+test_that("out_day is correct when the first day of output is partial", {
+  # Simulate a run where SIPNET started mid-day on day 1 (only 1 timestep),
+  # while days 2 and 3 are complete (2 timesteps each, i.e. 12-hour intervals).
+  # The correct out_day is 2; the old code would have returned 1 by reading
+  # only the count from day 1, causing a factor-of-2 error in flux conversions.
+
+  base_row <- make_base_sipnet(n = 4L)[1, ]
+  sipnet_partial <- rbind(
+    transform(base_row, day = 1, time = 18),          # day 1: only 1 row
+    transform(base_row, day = 2, time =  6),           # day 2: row 1
+    transform(base_row, day = 2, time = 18),           # day 2: row 2
+    transform(base_row, day = 3, time =  6),           # day 3: row 1
+    transform(base_row, day = 3, time = 18)            # day 3: row 2
+  )
+  sipnet_partial$cumNEE <- cumsum(rep(0.1, 5))
+
+  base    <- withr::local_tempdir()
+  outdir  <- file.path(base, "out", "run1")
+  rundir  <- file.path(base, "run", "run1")
+  dir.create(outdir,  recursive = TRUE)
+  dir.create(rundir,  recursive = TRUE)
+  writeLines("leafCSpWt\t32", file.path(rundir, "sipnet.param"))
+
+  out_path <- file.path(outdir, "sipnet.out")
+  writeLines(
+    c("Notes: units in g/m2 per timestep; water in cm",
+      paste(colnames(sipnet_partial), collapse = " ")),
+    out_path
+  )
+  write.table(sipnet_partial, file = out_path, append = TRUE,
+              row.names = FALSE, col.names = FALSE, quote = FALSE, sep = "\t")
+
+  model2netcdf.SIPNET(
+    outdir     = outdir,
+    sitelat    = 38.0,
+    sitelon    = -121.0,
+    start_date = "2002-01-01",
+    end_date   = "2002-01-03"
+  )
+
+  nc <- ncdf4::nc_open(file.path(outdir, "2002.nc"))
+  on.exit(ncdf4::nc_close(nc), add = TRUE)
+
+  gpp <- as.vector(ncdf4::ncvar_get(nc, "GPP"))
+
+  # out_day = 2 (from the complete days), timestep.s = 43200 s (12 hours)
+  # If the old code had used day 1 (out_day = 1), timestep.s = 86400 and
+  # the values would be half as large.
+  ts_correct <- 86400 / 2
+  expect_equal(gpp, rep(base_row$gpp * 1e-3 / ts_correct, 5), tolerance = 1e-10)
+})