updating code to run w/ new soils data

main/implementation/01_main-simulation-runner.R

@@ -158,25 +158,42 @@ for (j in 1:2){#alljid) { # TO DO: use "while" not "for"
   # the closest longitude 
   soilLon_i <- which((soilGridLons-Long) == min(abs(soilGridLons-Long)))
     #round(soilGridLons,2)==round(Long,2))
-  #clay
+  #clay (as a percentage...convert to a fraction by dividing by 100)
   clay_i <- var.get.nc(soils_gridClay, "claytotal", start = c(soilLon_i, soilLat_i,1), 
-             count = c(1,1,dim.inq.nc(soils_gridClay, "vertical")$length))
-  #sand
+             count = c(1,1,dim.inq.nc(soils_gridClay, "vertical")$length))/100
+  #sand (as a percentage...convert to a fraction by dividing by 100)
   sand_i <- var.get.nc(soils_gridSand, "sandtotal", start = c(soilLon_i, soilLat_i,1), 
-                       count = c(1,1,dim.inq.nc(soils_gridSand, "vertical")$length))
-  #silt
+                       count = c(1,1,dim.inq.nc(soils_gridSand, "vertical")$length))/100
+  #silt (as a percentage...convert to a fraction by dividing by 100)
   silt_i <- var.get.nc(soils_gridSilt, "silttotal", start = c(soilLon_i, soilLat_i,1), 
-                       count = c(1,1,dim.inq.nc(soils_gridSilt, "vertical")$length))
-  #coarse material
+                       count = c(1,1,dim.inq.nc(soils_gridSilt, "vertical")$length))/100
+  #coarse material (as a percentage...convert to a fraction by dividing by 100)
   coarse_i <- var.get.nc(soils_gridCoarse, "fragvol", start = c(soilLon_i, soilLat_i,1), 
-                       count = c(1,1,dim.inq.nc(soils_gridCoarse, "vertical")$length))
+                       count = c(1,1,dim.inq.nc(soils_gridCoarse, "vertical")$length))/100
   #thickness
-  thickness_i <- 100*var.get.nc(soils_gridThickness, "slthick", start = c(soilLon_i, soilLat_i,1), 
-                       count = c(1,1,12))   # also convert thickness to centimeters from meters
-  # bulk density 
-  bulkdensity_i <- var.get.nc(soils_gridDensity, "slbdensity", start = c(soilLon_i, soilLat_i,1), 
-                       count = c(1,1,12))
-
+  thickness_i <- var.get.nc(soils_gridThickness, "hzthk", start = c(soilLon_i, soilLat_i,1), 
+                       count = c(1,1,dim.inq.nc(soils_gridThickness, "vertical")$length))   
+    # units are in cm
+
+  bulkdensity_i <- var.get.nc(soils_gridDensity, "dbovendry", start = c(soilLon_i, soilLat_i,1), 
+                       count = c(1,1,dim.inq.nc(soils_gridDensity, "vertical")$length)) # units = g/cm3
+
+  ## get the depths also (the "vertical_bnds" dimension contains a matrix with 
+  # the upper and lower bounds of each depth band--we want the lower bounds)
+
+  depths_i <- var.get.nc(soils_gridThickness, "vertical_bnds")[2,]
+  ##AES this part below is a test... see what other folks think about this...
+  # trim soils data so that there are not NAs (the data stops at the depth for which we have data)
+  # also get the depths for the layers included
+  depths_i <- depths_i[!is.na(clay_i)]
+  clay_i <- clay_i[!is.na(clay_i)] 
+  sand_i <- sand_i[!is.na(sand_i)]
+  silt_i <- silt_i[!is.na(silt_i)]
+  coarse_i <- coarse_i[!is.na(coarse_i)]
+  thickness_i <- thickness_i[!is.na(thickness_i)]
+  bulkdensity_i <- bulkdensity_i[!is.na(bulkdensity_i)]
+
+  # depths 
   ################### ----------------------------------------------------------
   # Part 2 - Sets SW parameters besides weather
   ################### ----------------------------------------------------------
@@ -202,7 +219,7 @@ for (j in 1:2){#alljid) { # TO DO: use "while" not "for"
   # could be problematic if some soils are shallow--maybe should indicate how much depth is represented in each 
 
   Soils <- data.frame(sw_in@soils@Layers)[,c('depth_cm', 'sand_frac', 'clay_frac')]
-  Soils$width <- diff(c(0, Soils$depth_cm))
+  Soils$width <- thickness_i#diff(c(0, Soils$depth_cm))
   SoilsDF <- merge(Soils, SoilsDF, by = 'depth_cm')
   SoilsDF$variable <- paste0('Lyr_',1:dim(SoilsDF)[1])
 

main/test_code/TestGISSMOutput.R

@@ -19,4 +19,7 @@ gissm_pred_nc <- open.nc("./outputs/20240827/GISSM_yr_gridSTDF_prediction_082024
 # get the data in the netcdf
 test <- var.get.nc(gissm_pred_nc, variable = "probability")#, start = c(194, 435, 1, 1), count = c(10, 1, 30, 2))
 
+LonDat<- RNetCDF::var.get.nc(gissm_pred_nc, variable = "simulation")
+
 RNetCDF::print.nc(gissm_pred_nc)
+