Fix some issues.

Author: yinghaoSunn

models/lpjguess/NAMESPACE

@@ -16,7 +16,6 @@ export(write_binary_LPJGUESS)
 export(write_restart.LPJGUESS)
 importFrom(PEcAn.utils,days_in_year)
 importFrom(Rcpp,sourceCpp)
-importFrom(dplyr,"%>%")
 importFrom(ncdf4,nc_close)
 importFrom(ncdf4,ncatt_get)
 importFrom(ncdf4,ncatt_put)

models/lpjguess/R/read_restart.LPJGUESS.R

@@ -10,13 +10,15 @@
 #' @return X_tmp      vector of forecasts
 #' @export
 #' @examples
-#' # example code
-#' outdir = "/fs/data2/output//PEcAn_1000010473/out"
-#' runid = 1002656839
-#' stop.time = "1960-12-31 23:59:59 UTC"
-#' load("/fs/data2/output/PEcAn_1000010473/SDAsettings_develop.Rdata")
-#' var.names = c("AGB.pft", "TotSoilCarb")
-#' load("/fs/data2/output/PEcAn_1000010473/SDAparams_develop.Rdata")
+#' \dontrun{
+#'   rx <- read_restart.LPJGUESS(
+#'            outdir   = "/projectnb/…/LPJ_output",
+#'            runid    = "123456",
+#'            stop.time = as.POSIXct("2001-12-31 23:59:59", tz = "UTC"),
+#'            settings = settings,
+#'            var.names = c("AGB.pft"),
+#'            params = params)
+#' }
 #' @author Istem Fer, Yinghao Sun
 read_restart.LPJGUESS <- function(outdir, runid, stop.time, settings, var.names, params){
 

models/lpjguess/R/read_state.R

@@ -205,7 +205,7 @@ write.insfile.LPJGUESS <- function(settings, trait.values, rundir, outdir, run.i
   # when using cru input, lpjguess will not use these clim files
   cru.file <- settings$run$inputs$met$path
   misc.file <- sub("\\.bin$", "misc.bin", cru.file)
-  guessins <- gsub("@SOIL_FILE@", cru.file, guessins)
+  guessins <- gsub("@MET_AND_SOIL_FILE@", cru.file, guessins)
   guessins <- gsub("@MISC_FILE@", misc.file, guessins)
 
   # create and write CO2 file
@@ -247,8 +247,7 @@ write.insfile.LPJGUESS <- function(settings, trait.values, rundir, outdir, run.i
   # version check
   if(!is.null(settings$model$revision)){
     if(settings$model$revision == "PalEON"){
-      #rm_inds <- which(grepl("@@@@@ Remove in PalEON version @@@@@", paramsins))
-      rm_inds <- which(grepl("##### Remove in PalEON version #####", paramsins))
+      rm_inds <- which(grepl("@@@@@ Remove in PalEON version @@@@@", paramsins))
       paramsins <- paramsins[-(rm_inds[1]:rm_inds[2])]
     }
   }

models/lpjguess/R/write.config.LPJGUESS.R

@@ -33,7 +33,9 @@ write_restart.LPJGUESS <- function(outdir, runid,
                 file.path(outdir, runid, paste0("lpjguess.", as.Date(start.time), ".out")))
     system(paste("rm", file.path(rundir, runid, "lpjguess.clim")))
   } else {
-    print(paste("Files not renamed -- Need to rerun timestep", start.time, "before next time step"))
+    PEcAn.logger::logger.severe(paste("rename = FALSE: Restart cannot proceed without output file",
+                                      "lpjguess.out being renamed for", start.time))
+    stop("RENAME flag is FALSE. Must rerun this timestep before continuing.")
   }
 
   settings$run$start.date <- start.time
@@ -47,8 +49,6 @@ write_restart.LPJGUESS <- function(outdir, runid,
   pos_list <- new.params$LPJGUESS_state$pos_list
   siz_list <- new.params$LPJGUESS_state$siz_list
 
-
-  
   ## ---- Build PFT parameter table from new.params ----
   # TODO: find accurate parameters; read params from settings
   pft_par_table <- data.frame()
@@ -90,7 +90,7 @@ write_restart.LPJGUESS <- function(outdir, runid,
   ## --- Update state ---
   # choose a minimum diameter
   min.diam = 0.5
-  Gridcell_updated <- update_state_LPJGUESS(Gridcell, pft_par_table, 
+    Gridcell_updated <- update_state_LPJGUESS(Gridcell, pft_par_table, 
                                             dens.init, dens.targ,
                                             agb.init, agb.targ,
                                             AbvGrndWood.epsilon = 0.05,

models/lpjguess/R/write_restart.LPJGUESS.R

@@ -133,7 +133,7 @@ run_pasture 0	      ! whether to simulate pasture (1) or not (0)
 run_natural 1	      ! whether to simulate natural vegetation (1) or not (0)
 run_peatland 1	      ! whether to simulate peatland (1) or not (0)
 
-! Remove in PalEON version 
+@@@@@ Remove in PalEON version @@@@@
 lcfrac_fixed 0        	! use landcover fractions (%) below (1) or read from input file (0)
 lc_fixed_urban 0   	! URBAN
 lc_fixed_cropland 50	! CROPLAND
@@ -142,7 +142,7 @@ lc_fixed_forest 0   	! FOREST
 lc_fixed_natural 25 	! NATURAL
 lc_fixed_peatland 25 	! PEATLAND
 equal_landcover_area 0	! divide gridcell into equal active landcover fractions
-! Remove in PalEON version 
+@@@@@ Remove in PalEON version @@@@@
 !///////////////////////////////////////////////////////////////////////////////////////
 
 

models/lpjguess/inst/pecan.ins

@@ -17,7 +17,7 @@ coordinates_precision 2
 param "file_gridlist" (str "@GRID_FILE@")
 
 param "file_co2"      (str "@CO2_FILE@")
-param "file_cru"      (str "@SOIL_FILE@")
+param "file_cru"      (str "@MET_AND_SOIL_FILE@")
 param "file_cru_misc"  (str "@MISC_FILE@")
 
 ! N deposition (blank string to use constant pre-industrial level of 2 kgN/ha/year)