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CUG-hydro · Feb 22, 2024 · c2957eb · c2957eb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -51,6 +51,6 @@ Suggests:
 LinkingTo: 
     RcppArmadillo,
     Rcpp
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -13,6 +13,8 @@ export(vic_params)
 export(vic_version)
 import(magrittr)
 importFrom(Rcpp,sourceCpp)
+importFrom(foreach,"%do%")
+importFrom(foreach,foreach)
 importFrom(lubridate,day)
 importFrom(lubridate,month)
 importFrom(lubridate,year)

diff --git a/R/VIC5-package.R b/R/VIC5-package.R
@@ -4,6 +4,7 @@
 #' @docType package
 #' @importFrom Rcpp sourceCpp
 #' @importFrom stats setNames convolve median
+#' @importFrom foreach %do% foreach
 #' @importFrom utils str read.table
 #' @keywords internal
 "_PACKAGE"
@@ -13,3 +14,11 @@
 ## usethis namespace: start
 ## usethis namespace: end
 NULL
+
+.onLoad <- function (libname, pkgname){
+  if(getRversion() >= "2.15.1") {
+    utils::globalVariables(
+      c(".", "i")
+    )
+  }
+}
diff --git a/R/tools.R b/R/tools.R
@@ -29,7 +29,7 @@ set_dimnames <- function(x, value) {
 
 check_matrix <- function(x) {
   if (is.vector(x)) {
-    lake %<>% t()
+    x %<>% t()
   } else if (!is.null(x)) {
     x %<>% as.matrix()
   }

diff --git a/R/vic_forcing.R b/R/vic_forcing.R
@@ -153,14 +153,14 @@ check_forcing <- function(forcing, soil = NULL) {
   ngrid = ncol(forcing[[1]])
   # Estimate forcing data that not supplied.
   if ("PRESS" %in% forc_lack) {
-    forcing$PRESS = foreach(i = 1:ngrid, icount(), .c = cbind) %do% {
-      cal_Pa(frocing$TEMP[, i], elev = soil[, "ELEV"])
+    forcing$PRESS = foreach(i = 1:ngrid, .c = cbind) %do% {
+      cal_Pa(forcing$TEMP[, i], elev = soil[, "ELEV"])
     }
   }
 
   if ("LW" %in% forc_lack) {
     J <- get_J()
-    forcing$LW = foreach(i = 1:ngrid, icount(), .c = cbind) %do% {
+    forcing$LW = foreach(i = 1:ngrid, .c = cbind) %do% {
       lat = soil[i, "LAT"]
       cal_lw(forcing$TEMP[, i], forcing$VP[, i], forcing$SW[, i], lat, J)
     }

diff --git a/man/VIC5.Rd b/man/VIC5.Rd
diff --git a/src/Makevars b/src/Makevars
@@ -19,7 +19,7 @@ PKG_CPPFLAGS = $(HDRS) \
 
 SOURCES_C = vic/vic_run/src/advected_sensible_heat.c vic/vic_run/src/alloc_and_free.c vic/vic_run/src/arno_evap.c vic/vic_run/src/calc_atmos_energy_bal.c vic/vic_run/src/calc_gridcell_avg_albedo.c vic/vic_run/src/calc_Nscale_factors.c vic/vic_run/src/calc_rainonly.c vic/vic_run/src/calc_snow_coverage.c vic/vic_run/src/calc_surf_energy_bal.c vic/vic_run/src/calc_veg_params.c vic/vic_run/src/CalcAerodynamic.c vic/vic_run/src/CalcBlowingSnow.c vic/vic_run/src/canopy_assimilation.c vic/vic_run/src/canopy_evap.c vic/vic_run/src/comparisons.c vic/vic_run/src/compute_coszen.c vic/vic_run/src/compute_derived_lake_dimensions.c vic/vic_run/src/compute_pot_evap.c vic/vic_run/src/compute_soil_resp.c vic/vic_run/src/compute_zwt.c vic/vic_run/src/correct_precip.c vic/vic_run/src/estimate_T1.c vic/vic_run/src/faparl.c vic/vic_run/src/frozen_soil.c vic/vic_run/src/func_atmos_energy_bal.c vic/vic_run/src/func_atmos_moist_bal.c vic/vic_run/src/func_canopy_energy_bal.c vic/vic_run/src/func_surf_energy_bal.c vic/vic_run/src/ice_melt.c vic/vic_run/src/IceEnergyBalance.c vic/vic_run/src/initialize_lake.c vic/vic_run/src/interpoloation.c vic/vic_run/src/lake_utils.c vic/vic_run/src/lakes.eb.c vic/vic_run/src/latent_heat_from_snow.c vic/vic_run/src/massrelease.c vic/vic_run/src/newt_raph_func_fast.c vic/vic_run/src/penman.c vic/vic_run/src/photosynth.c vic/vic_run/src/physics.c vic/vic_run/src/prepare_full_energy.c vic/vic_run/src/root_brent.c vic/vic_run/src/runoff.c vic/vic_run/src/snow_intercept.c vic/vic_run/src/snow_melt.c vic/vic_run/src/snow_utility.c vic/vic_run/src/SnowPackEnergyBalance.c vic/vic_run/src/soil_carbon_balance.c vic/vic_run/src/soil_conduction.c vic/vic_run/src/soil_thermal_eqn.c vic/vic_run/src/solve_snow.c vic/vic_run/src/StabilityCorrection.c vic/vic_run/src/surface_fluxes.c vic/vic_run/src/svp.c vic/vic_run/src/vic_run.c vic/vic_run/src/water_energy_balance.c vic/vic_run/src/water_under_ice.c vic/vic_run/src/write_layer.c vic/vic_run/src/write_vegvar.c vic/drivers/shared_all/src/agg_data.c vic/drivers/shared_all/src/alarms.c vic/drivers/shared_all/src/calc_root_fraction.c vic/drivers/shared_all/src/cmd_proc.c vic/drivers/shared_all/src/compress_files.c vic/drivers/shared_all/src/compute_derived_state_vars.c vic/drivers/shared_all/src/compute_lake_params.c vic/drivers/shared_all/src/compute_treeline.c vic/drivers/shared_all/src/forcing_utils.c vic/drivers/shared_all/src/free_all_vars.c vic/drivers/shared_all/src/free_vegcon.c vic/drivers/shared_all/src/generate_default_lake_state.c vic/drivers/shared_all/src/generate_default_state.c vic/drivers/shared_all/src/get_parameters.c vic/drivers/shared_all/src/history_metadata.c vic/drivers/shared_all/src/initialize_energy.c vic/drivers/shared_all/src/initialize_global.c vic/drivers/shared_all/src/initialize_options.c vic/drivers/shared_all/src/initialize_parameters.c vic/drivers/shared_all/src/initialize_snow.c vic/drivers/shared_all/src/initialize_soil.c vic/drivers/shared_all/src/initialize_veg.c vic/drivers/shared_all/src/input_tools.c vic/drivers/shared_all/src/make_all_vars.c vic/drivers/shared_all/src/make_cell_data.c vic/drivers/shared_all/src/make_dmy.c vic/drivers/shared_all/src/make_energy_bal.c vic/drivers/shared_all/src/make_snow_data.c vic/drivers/shared_all/src/make_veg_var.c vic/drivers/shared_all/src/open_file.c vic/drivers/shared_all/src/print_library_shared.c vic/drivers/shared_all/src/put_data.c vic/drivers/shared_all/src/set_output_defaults.c vic/drivers/shared_all/src/soil_moisture_from_water_table.c vic/drivers/shared_all/src/timing.c vic/drivers/shared_all/src/update_step_vars.c vic/drivers/shared_all/src/vic_history.c vic/drivers/shared_all/src/vic_log.c vic/drivers/shared_all/src/vic_time.c vic/drivers/shared_all/src/zero_output_list.c
 
-SOURCES_CPP = ./conv.cpp ./display_current_settings.cpp ./force.cpp ./get_options.cpp ./globals.cpp ./initiate.cpp ./make_output_info.cpp ./make_params.cpp ./RcppExports.cpp ./vic_run_cell.cpp ./vic_version.cpp vic_run_cells_all.cpp XAJ.cpp
+SOURCES_CPP = ./conv.cpp ./force.cpp ./get_options.cpp ./globals.cpp ./initiate.cpp ./make_output_info.cpp ./make_params.cpp ./RcppExports.cpp ./vic_run_cell.cpp ./vic_version.cpp vic_run_cells_all.cpp XAJ.cpp
 # profile.cpp
 
 OBJECTS = $(SOURCES_C:.c=.o) $(SOURCES_CPP:.cpp=.o)

diff --git a/src/display_current_settings.cpp b/src/display_current_settings.cpp
diff --git a/src/force.cpp b/src/force.cpp
@@ -1,20 +1,19 @@
 #include <vic_R.h>
 
 void make_force(force_data_struct &force, NumericMatrix &forcing_data,
-           soil_con_struct* soil_con, int rec, dmy_struct *dmy) {
-
-  extern option_struct       options;
-  //extern global_param_struct global_param;
-  extern parameters_struct   param;
-  extern size_t              NR, NF;
+                soil_con_struct *soil_con, int rec, dmy_struct *dmy) {
+  extern option_struct options;
+  // extern global_param_struct global_param;
+  extern parameters_struct param;
+  extern size_t NR, NF;
 
-  int                        offset;
-  double                     t_offset;
-  size_t                     i;
-  size_t                     uidx;
-  double                    *Tfactor;
+  int offset;
+  double t_offset;
+  size_t i;
+  size_t uidx;
+  double *Tfactor;
 
-  Tfactor = soil_con -> Tfactor;
+  Tfactor = soil_con->Tfactor;
   t_offset = Tfactor[0];
   for (i = 1; i < options.SNOW_BAND; i++) {
     if (Tfactor[i] < t_offset) {
@@ -45,35 +44,34 @@ void make_force(force_data_struct &force, NumericMatrix &forcing_data,
     }
     // air density in kg/m3
     force.density[i] = air_density(force.air_temp[i],
-                                        force.pressure[i]);
+                                   force.pressure[i]);
     // wind speed in m/s
     force.wind[i] = forcing_data(uidx, 6);
     // snow flag
     force.snowflag[i] = will_it_snow(&(force.air_temp[i]),
-                                          t_offset,
-                                          param.SNOW_MAX_SNOW_TEMP,
-                                          &(force.prec[i]), 1);
+                                     t_offset,
+                                     param.SNOW_MAX_SNOW_TEMP,
+                                     &(force.prec[i]), 1);
 
     // Optional inputs
     if (options.LAKES) {
       // Channel inflow from upstream (into lake)
       // if (param_set.TYPE[CHANNEL_IN].SUPPLIED) {
-      if (false) { // TODO: for channel in.
-        offset ++;
-        force.channel_in[i] = forcing_data(uidx, 6+offset);
-      }
-      else {
+      if (false) {  // TODO: for channel in.
+        offset++;
+        force.channel_in[i] = forcing_data(uidx, 6 + offset);
+      } else {
         force.channel_in[i] = 0;
       }
     }
     if (options.CARBON) {
-      offset ++;
+      offset++;
       // Atmospheric CO2 concentration
-      force.Catm[i] = forcing_data(uidx, 6+offset);
+      force.Catm[i] = forcing_data(uidx, 6 + offset);
       // Fraction of shortwave that is direct
-      force.fdir[i] = forcing_data(uidx, 7+offset);
+      force.fdir[i] = forcing_data(uidx, 7 + offset);
       // photosynthetically active radiation
-      force.par[i] = forcing_data(uidx, 8+offset);
+      force.par[i] = forcing_data(uidx, 8 + offset);
       // Cosine of solar zenith angle
       force.coszen[i] = compute_coszen(soil_con->lat,
                                        soil_con->lng,
@@ -102,7 +100,7 @@ void make_force(force_data_struct &force, NumericMatrix &forcing_data,
     }
     if (options.LAKES) {
       force.channel_in[NR] =
-        average(force.channel_in, NF) * NF;
+          average(force.channel_in, NF) * NF;
     }
     if (options.CARBON) {
       force.Catm[NR] = average(force.Catm, NF);
@@ -119,35 +117,32 @@ void make_force(force_data_struct &force, NumericMatrix &forcing_data,
 }
 
 IntegerVector get_veg_force_types(NumericMatrix &forcing_veg_data) {
-  //extern option_struct       options;
-
-  CharacterVector            veg_par_types;
-  int                        Ntypes;
+  // extern option_struct       options;
 
-  IntegerVector              temp;
+  CharacterVector veg_par_types;
+  int Ntypes;
 
-  if(is<CharacterVector>(forcing_veg_data.attr("types"))) {
+  IntegerVector temp;
 
+  if (is<CharacterVector>(forcing_veg_data.attr("types"))) {
     veg_par_types = as<CharacterVector>(forcing_veg_data.attr("types"));
     Ntypes = veg_par_types.length();
     temp = IntegerVector(Ntypes, -1);
 
-    for(int i = 0; i < Ntypes; i++) {
+    for (int i = 0; i < Ntypes; i++) {
       if (veg_par_types[i] == "albedo") {
         temp[i] = 0;
-      }
-      else if (veg_par_types[i] == "LAI") {
+      } else if (veg_par_types[i] == "LAI") {
         temp[i] = 1;
-      }
-      else if (veg_par_types[i] == "fcanopy") {
+      } else if (veg_par_types[i] == "fcanopy") {
         temp[i] = 2;
-      }
-      else {
-        log_err("Invalid vegetation forcing data type:"
-                  " %s.", ((String)veg_par_types[i]).get_cstring());
+      } else {
+        log_err(
+            "Invalid vegetation forcing data type:"
+            " %s.",
+            ((String)veg_par_types[i]).get_cstring());
       }
     }
-
   }
 
   return temp;
@@ -156,19 +151,18 @@ IntegerVector get_veg_force_types(NumericMatrix &forcing_veg_data) {
 void make_force_veg(NumericMatrix &forcing_veg_data,
                     IntegerVector &veg_force_types,
                     all_vars_struct *all_vars,
-                    veg_con_struct  *veg_con,
+                    veg_con_struct *veg_con,
                     int rec, dmy_struct *dmy) {
-
   extern option_struct options;
 
-  unsigned short       iveg;
-  size_t               Nveg;
-  unsigned short       band;
-  size_t               Nbands;
-  veg_var_struct     **veg_var;
-  CharacterVector      veg_par_types;
-  int                  Ntypes;
-  double               tmp_veg_val;
+  unsigned short iveg;
+  size_t Nveg;
+  unsigned short band;
+  size_t Nbands;
+  veg_var_struct **veg_var;
+  CharacterVector veg_par_types;
+  int Ntypes;
+  double tmp_veg_val;
 
   veg_var = all_vars->veg_var;
 
@@ -179,78 +173,74 @@ void make_force_veg(NumericMatrix &forcing_veg_data,
   for (iveg = 0; iveg <= Nveg; iveg++) {
     for (band = 0; band < Nbands; band++) {
       veg_var[iveg][band].albedo =
-        veg_con[iveg].albedo[dmy[rec].month - 1];
+          veg_con[iveg].albedo[dmy[rec].month - 1];
       veg_var[iveg][band].displacement =
-        veg_con[iveg].displacement[dmy[rec].month - 1];
+          veg_con[iveg].displacement[dmy[rec].month - 1];
       veg_var[iveg][band].fcanopy =
-        veg_con[iveg].fcanopy[dmy[rec].month - 1];
+          veg_con[iveg].fcanopy[dmy[rec].month - 1];
       veg_var[iveg][band].LAI =
-        veg_con[iveg].LAI[dmy[rec].month - 1];
+          veg_con[iveg].LAI[dmy[rec].month - 1];
       veg_var[iveg][band].roughness =
-        veg_con[iveg].roughness[dmy[rec].month - 1];
+          veg_con[iveg].roughness[dmy[rec].month - 1];
     }
   }
 
   Ntypes = veg_force_types.length();
   for (iveg = 0; iveg <= Nveg; iveg++) {
     for (band = 0; band < Nbands; band++) {
-      for(int i = 0; i < Ntypes; i++) {
+      for (int i = 0; i < Ntypes; i++) {
         tmp_veg_val = forcing_veg_data(rec, iveg + i * Nveg);
 
-        if(veg_force_types[i] == 0 && options.ALB_SRC == FROM_VEGHIST) {
+        if (veg_force_types[i] == 0 && options.ALB_SRC == FROM_VEGHIST) {
           veg_var[iveg][band].albedo = tmp_veg_val;
-        }
-        else if(veg_force_types[i] == 1 && options.LAI_SRC == FROM_VEGHIST) {
+        } else if (veg_force_types[i] == 1 && options.LAI_SRC == FROM_VEGHIST) {
           veg_var[iveg][band].LAI = tmp_veg_val;
-        }
-        else if(veg_force_types[i] == 2 && options.FCAN_SRC == FROM_VEGHIST) {
+        } else if (veg_force_types[i] == 2 && options.FCAN_SRC == FROM_VEGHIST) {
           veg_var[iveg][band].fcanopy = tmp_veg_val;
         }
       }
     }
   }
-
 }
 
-void alloc_force(force_data_struct &force)
-{
+void alloc_force(force_data_struct &force) {
   extern option_struct options;
   extern size_t NR;
 
-  force.air_temp = (double*)calloc(NR + 1, sizeof(force.air_temp));
+  force.air_temp = (double *)calloc(NR + 1, sizeof(force.air_temp));
   check_alloc_status(force.air_temp, "Memory allocation error.");
-  force.density = (double*)calloc(NR + 1, sizeof(force.density));
+  force.density = (double *)calloc(NR + 1, sizeof(force.density));
   check_alloc_status(force.density, "Memory allocation error.");
-  force.longwave = (double*)calloc(NR + 1, sizeof(force.longwave));
+  force.longwave = (double *)calloc(NR + 1, sizeof(force.longwave));
   check_alloc_status(force.longwave, "Memory allocation error.");
-  force.prec = (double*)calloc(NR + 1, sizeof(force.prec));
+  force.prec = (double *)calloc(NR + 1, sizeof(force.prec));
   check_alloc_status(force.prec, "Memory allocation error.");
-  force.pressure = (double*)calloc(NR + 1, sizeof(force.pressure));
+  force.pressure = (double *)calloc(NR + 1, sizeof(force.pressure));
   check_alloc_status(force.pressure, "Memory allocation error.");
-  force.shortwave = (double*)calloc(NR + 1, sizeof(force.shortwave));
+  force.shortwave = (double *)calloc(NR + 1, sizeof(force.shortwave));
   check_alloc_status(force.shortwave, "Memory allocation error.");
-  force.snowflag = (bool*)calloc(NR + 1, sizeof(force.snowflag));
+  force.snowflag = (bool *)calloc(NR + 1, sizeof(force.snowflag));
   check_alloc_status(force.snowflag, "Memory allocation error.");
-  force.vp = (double*)calloc(NR + 1, sizeof(force.vp));
+  force.vp = (double *)calloc(NR + 1, sizeof(force.vp));
   check_alloc_status(force.vp, "Memory allocation error.");
-  force.vpd = (double*)calloc(NR + 1, sizeof(force.vpd));
+  force.vpd = (double *)calloc(NR + 1, sizeof(force.vpd));
   check_alloc_status(force.vpd, "Memory allocation error.");
-  force.wind = (double*)calloc(NR + 1, sizeof(force.wind));
+  force.wind = (double *)calloc(NR + 1, sizeof(force.wind));
   check_alloc_status(force.wind, "Memory allocation error.");
   if (options.LAKES) {
     force.channel_in =
-      (double*)calloc(NR + 1, sizeof(force.channel_in));
+        (double *)calloc(NR + 1, sizeof(force.channel_in));
     check_alloc_status(force.channel_in,
                        "Memory allocation error.");
   }
   if (options.CARBON) {
-    force.Catm = (double*)calloc(NR + 1, sizeof(force.Catm));
+    force.Catm = (double *)calloc(NR + 1, sizeof(force.Catm));
     check_alloc_status(force.Catm, "Memory allocation error.");
-    force.coszen = (double*)calloc(NR + 1, sizeof(force.coszen));
+    force.coszen = (double *)calloc(NR + 1, sizeof(force.coszen));
     check_alloc_status(force.coszen, "Memory allocation error.");
-    force.fdir = (double*)calloc(NR + 1, sizeof(force.fdir));
+    force.fdir = (double *)calloc(NR + 1, sizeof(force.fdir));
     check_alloc_status(force.fdir, "Memory allocation error.");
-    force.par = (double*)calloc(NR + 1, sizeof(force.par));
+    force.par = (double *)calloc(NR + 1, sizeof(force.par));
     check_alloc_status(force.par, "Memory allocation error.");
   }
 }
@@ -278,4 +268,3 @@ void free_force(force_data_struct &force) {
     free(force.par);
   }
 }
-