Development for v6.3.0

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "src/SOILWAT2"]
 	path = src/SOILWAT2
 	url = https://github.com/DrylandEcology/SOILWAT2
-	branch = master
+	branch = feature_nc_input

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rSOILWAT2
-Version: 6.2.0
+Version: 6.3.0-9000
 Title: An Ecohydrological Ecosystem-Scale Water Balance Simulation Model
 Description: Access to the C-based SOILWAT2 v8.0.1 and functionality for
   SQLite-database of weather data.

NEWS.md

@@ -1,3 +1,6 @@
+# rSOILWAT2 v6.3.0-9000
+
+
 # rSOILWAT2 v6.2.0
 * Simulation output remains the same as the previous version unless
   relative humidity is calculated from vapor pressure or specific humidity.

inst/extdata/example1/Input/domain.in

@@ -26,8 +26,11 @@ ymin_bbox 39.59
 xmax_bbox -105.58
 ymax_bbox 39.59
 
+# Domain Coordinates
+SpatialTolerance 1e-6            # Tolerance used to identify matching domain space
+
 # Spinup
-SpinupMode      1               # Mode ( 1: repeated random resample; 2: sequence of m years ), default = 1
-SpinupScope     1               # Scope ( N ): use first N years of simulation, default = 1
-SpinupDuration  0               # Duration ( M ): sample M years of the first N years (no spinup: M = 0), default = 0
-SpinupSeed      11              # Seed for randomly generating years for mode 1, default = 11
+SpinupMode       1               # Mode ( 1: repeated random resample; 2: sequence of m years ), default = 1
+SpinupScope      1               # Scope ( N ): use first N years of simulation, default = 1
+SpinupDuration   0               # Duration ( M ): sample M years of the first N years (no spinup: M = 0), default = 0
+SpinupSeed       11              # Seed for randomly generating years for mode 1, default = 11

inst/extdata/example1/Input/siteparam.in

@@ -78,10 +78,18 @@ RCP85
 
 
 # --- Soil characterization ---
+# Is the soil layer depth profile and number of soil layers identical (1) across the entire domain or do they vary among sites/gridcells (0)?
+1
+
 # Are inputs of density representing bulk soil (type 1) or the matric component (type 0)?
 0
 
 
+# --- Organic matter ---
+# Depth [cm] at which characteristics of organic matter have completely switched from fibric to sapric peat
+50
+
+
 #--- Soil water retention curve (SWRC) ------
 #
 # Implemented options (`swrc_name`/`ptf_name`, see `swrc2str[]`/`ptf2str[]`):
@@ -99,7 +107,7 @@ Campbell1974				# Specify soil water retention curve
 Cosby1984AndOthers	# Specify pedotransfer function
 										# (if not implemented, then provide SWRC parameters via "swrc_params.in")
 
-0			# Has SWRC parameters (see `has_swrcp`)?
+0			# Has SWRC parameters for the mineral soil component (see `has_swrcp`)?
 			#    0: Estimate with specified pedotransfer function
 			#    1: Use values from "swrc_params.in"
 

inst/extdata/example1/Input/soils.in

@@ -15,18 +15,19 @@
 #   - imperm = (frac, 0-1) proportion of 'impermeability' to water
 #     percolation(/infiltration/drainage)
 #   - soiltemp = (C) initial temperature
+#   - %om = (frac, 0-1) proportion of organic matter by weight
 
 # USER: the evco and trco columns must sum to 1.0 or they will be normalized.
 
 # The minimum number of soil layers is 1 and the maximum number is `MAX_LAYERS`
 # which is defined in `SW_Defines.h`.
 
-# depth    matricd    gravel_content    evco    trco_grass    trco_shrub    trco_tree    trco_forb    %sand    %clay    imperm    soiltemp
-  5.0      1.430      0.100          0.813        0.0496         0.134       0.0496        0.134    0.510    0.150     0.000      -1.000
- 10.0      1.410      0.100          0.153        0.0495         0.094       0.0495        0.094    0.440    0.260     0.000      -1.000
- 20.0      1.390      0.100          0.034        0.1006         0.176       0.1006        0.176    0.350    0.410     0.000      -1.000
- 30.0      1.390      0.100          0.000        0.1006         0.175       0.1006        0.175    0.320    0.450     0.000      -1.000
- 40.0      1.380      0.200          0.000        0.1006         0.110       0.1006        0.110    0.310    0.470     0.000       0.000
- 60.0      1.150      0.200          0.000        0.1997         0.109       0.1997        0.109    0.320    0.470     0.000       0.000
- 80.0      1.310      0.200          0.000        0.1997         0.101       0.1997        0.101    0.570    0.280     0.000       1.000
-100.0      1.310      0.200          0.000        0.1997         0.101       0.1997        0.101    0.570    0.280     0.000       1.000
+# depth    matricd    gravel_content    evco    trco_grass    trco_shrub    trco_tree    trco_forb    %sand    %clay    imperm    soiltemp   %om
+  5.0      1.430      0.100          0.813        0.0496         0.134       0.0496        0.134    0.510    0.150     0.000      -1.000     0.0
+ 10.0      1.410      0.100          0.153        0.0495         0.094       0.0495        0.094    0.440    0.260     0.000      -1.000     0.0
+ 20.0      1.390      0.100          0.034        0.1006         0.176       0.1006        0.176    0.350    0.410     0.000      -1.000     0.0
+ 30.0      1.390      0.100          0.000        0.1006         0.175       0.1006        0.175    0.320    0.450     0.000      -1.000     0.0
+ 40.0      1.380      0.200          0.000        0.1006         0.110       0.1006        0.110    0.310    0.470     0.000       0.000     0.0
+ 60.0      1.150      0.200          0.000        0.1997         0.109       0.1997        0.109    0.320    0.470     0.000       0.000     0.0
+ 80.0      1.310      0.200          0.000        0.1997         0.101       0.1997        0.101    0.570    0.280     0.000       1.000     0.0
+100.0      1.310      0.200          0.000        0.1997         0.101       0.1997        0.101    0.570    0.280     0.000       1.000     0.0

inst/extdata/example1/Input/swrc_params.in

@@ -1,7 +1,7 @@
-#------ Input for Soil Water Retention Curves (by soil layer) ------
+#------ Input for Soil Water Retention Curves ------
 
-# A table with up to `MAX_LAYERS` rows (soil layers) and 6 columns:
-#   - the soil layers must match `soils.in`
+
+# Tables with 6 columns:
 #   - the interpretation of columns (SWRC parameters) depends on the
 #     selected SWRC (see `siteparam.in`)
 #   - unused columns are ignored (if selected SWRC uses fewer than 6 parameters)
@@ -28,12 +28,23 @@
 #   * param6 = L, tortuosity/connectivity parameter [-]
 
 
+# Table with two sets of six SWRC parameters
+#   * first set (row): characteristics of fibric peat
+#   * second set (row): characteristics of sapric peat
+#   * source: Letts et al. 2000, doi:10.1080/07055900.2000.9649643
+# param1  param2   param3   param4     param5   param6
+    1.03    0.93      2.7   2419.2     0.0000   0.0000
+    1.01    0.83     12.0      0.864   0.0000   0.0000
+
+
+# Table with six SWRC parameters for up to `MAX_LAYERS` rows (soil layers)
+#   * the soil layers must match `soils.in`
 # param1  param2   param3   param4     param5   param6
-18.6080  0.42703   5.3020   24.03047   0.0000   0.0000
-20.4644  0.43290   7.0500   14.94351   0.0000   0.0000
-22.8402  0.44013   9.4320   13.71177   0.0000   0.0000
-24.0381  0.44291  10.0690   13.43171   0.0000   0.0000
-24.2159  0.44359  10.3860   14.14351   0.0000   0.0000
-23.3507  0.44217  10.3830   40.63764   0.0000   0.0000
-12.3880  0.41370   7.3250   37.22899   0.0000   0.0000
-12.3880  0.41370   7.3250   37.22899   0.0000   0.0000
+18.6080  0.42703   5.3020   53.90697   0.0000   0.0000
+20.4644  0.43290   7.0500   37.41493   0.0000   0.0000
+22.8402  0.44013   9.4320   23.10175   0.0000   0.0000
+24.0381  0.44291  10.0690   19.96388   0.0000   0.0000
+24.2159  0.44359  10.3860   18.82977   0.0000   0.0000
+23.3507  0.44217  10.3830   19.38407   0.0000   0.0000
+12.3880  0.41370   7.3250   52.97183   0.0000   0.0000
+12.3880  0.41370   7.3250   52.97183   0.0000   0.0000

inst/extdata/example1/Input/swrc_params_FXW.in

@@ -1,7 +1,6 @@
 #------ Input for Soil Water Retention Curves (by soil layer) ------
 
-# A table with up to `MAX_LAYERS` rows (soil layers) and 6 columns:
-#   - the soil layers must match `soils.in`
+# Tables with 6 columns:
 #   - the interpretation of columns (SWRC parameters) depends on the
 #     selected SWRC (see `siteparam.in`)
 #   - unused columns are ignored (if selected SWRC uses fewer than 6 parameters)
@@ -15,6 +14,19 @@
 #   * param6 = L, tortuosity/connectivity parameter [-]
 
 
+# Table with two sets of six SWRC parameters
+#   * first set (row): characteristics of fibric peat
+#   * second set (row): characteristics of sapric peat
+#   * source: Letts et al. 2000, doi:10.1080/07055900.2000.9649643
+#       * Note: values for the van Genuchten SWRC assumed for
+#         comparable parameters; however, param4 (m) and param6 (L) are missing
+# param1  param2   param3   param4     param5   param6
+    0.93   0.08       1.9   NaN      2419.2     NaN
+    0.83   0.003      1.6   NaN         0.864   NaN
+
+
+# Table with six SWRC parameters for up to `MAX_LAYERS` rows (soil layers)
+#   * the soil layers must match `soils.in`
 # param1 param2   param3   param4   param5     param6
 0.437461 0.050757 1.247689 0.308681  22.985379 2.697338
 0.452401 0.103033 1.146533 0.195394  89.365566 2.843288

inst/extdata/example1/Input/swrc_params_vanGenuchten1980.in

@@ -1,7 +1,6 @@
 #------ Input for Soil Water Retention Curves (by soil layer) ------
 
-# A table with up to `MAX_LAYERS` rows (soil layers) and 6 columns:
-#   - the soil layers must match `soils.in`
+# Tables with 6 columns:
 #   - the interpretation of columns (SWRC parameters) depends on the
 #     selected SWRC (see `siteparam.in`)
 #   - unused columns are ignored (if selected SWRC uses fewer than 6 parameters)
@@ -13,6 +12,18 @@
 #   * param4 = n, measure of the pore-size distribution [-]
 #   * param5 = saturated hydraulic conductivity [cm/day]
 
+
+# Table with two sets of six SWRC parameters
+#   * first set (row): characteristics of fibric peat
+#   * second set (row): characteristics of sapric peat
+#   * source: Letts et al. 2000, doi:10.1080/07055900.2000.9649643
+# param1  param2   param3   param4     param5   param6
+    0.04    0.93    0.08       1.9   2419.2     0.0000
+    0.22    0.83    0.003      1.6      0.864   0.0000
+
+
+# Table with six SWRC parameters for up to `MAX_LAYERS` rows (soil layers)
+#   * the soil layers must match `soils.in`
 # param1   param2    param3      param4   param5    param6
 0.07564425 0.3925437 0.010035788 1.412233 19.871040    0
 0.10061329 0.4011315 0.009425738 1.352274  9.090754    0