temp

Author: yinghaoSunn

guess.log

@@ -0,0 +1 @@
+Error: could not open guess.ins for input

modules/assim.sequential/NAMESPACE

@@ -51,7 +51,7 @@ export(rwtmnorm)
 export(sample_met)
 export(sampler_toggle)
 export(sda.enkf)
-export(sda.enkf.multisite)
+export(sda.enkf.multisite_hoptest)
 export(sda.enkf.original)
 export(sda_weights_site)
 export(simple.local)

modules/assim.sequential/R/sda.enkf_MultiSite.R

@@ -37,14 +37,15 @@
 #' @import nimble furrr
 #' @export
 #' 
-sda.enkf.multisite <- function(settings, 
+sda.enkf.multisite_hoptest <- function(settings, 
                                obs.mean, 
                                obs.cov, 
                                Q = NULL, 
                                restart = NULL, 
                                pre_enkf_params = NULL,
                                ensemble.samples = NULL,
-                               control=list(trace = TRUE,
+                               control=list(hop_test = TRUE,
+                                            trace = TRUE,
                                             TimeseriesPlot = FALSE,
                                             debug = FALSE,
                                             pause = FALSE,
@@ -57,6 +58,7 @@ sda.enkf.multisite <- function(settings,
                                             run_parallel = TRUE,
                                             MCMC.args = NULL),
                                ...) {
+  
   #add if/else for when restart points to folder instead if T/F set restart as T
   if(is.list(restart)){
     old.dir <- restart$filepath
@@ -206,6 +208,7 @@ sda.enkf.multisite <- function(settings,
   register.xml <- system.file(paste0("register.", model, ".xml"), package = paste0("PEcAn.", model))
   register <- XML::xmlToList(XML::xmlParse(register.xml))
   no_split <- !as.logical(register$exact.dates)
+  # no_split <- TRUE
 
   if (!exists(my.split_inputs)  &  !no_split) {
     PEcAn.logger::logger.warn(my.split_inputs, "does not exist")
@@ -245,6 +248,7 @@ sda.enkf.multisite <- function(settings,
 
         }
       } else{
+        inputs <- settings$run$inputs$met$path
         inputs.split <- inputs
       }
       settings
@@ -280,7 +284,7 @@ sda.enkf.multisite <- function(settings,
       #assuming that will only use previous unconstrained forecast runs for first run with SDA which means we are at t=1
       #sim.time<-seq_len(nt)
       #create params object using previous forecast ensemble members
-      new.params <- sda_matchparam(settings, ensemble.samples, site.ids, nens)
+      new.params <- PEcAnAssimSequential:::sda_matchparam(settings, ensemble.samples, site.ids, nens)
 
       #create inputs object for met using previous forecast ensemble members
       ####add function here, pause on this feature until we add feature to model runs that saves driver ensemble members
@@ -766,5 +770,39 @@ sda.enkf.multisite <- function(settings,
 #      unlink(list.files(outdir, "*.nc", recursive = TRUE, full.names = TRUE))
 #    }
       ## MCD: I commented the above "if" out because if you are restarting from a previous forecast, this might delete the files in that earlier folder
-  } ### end loop over time
-} # sda.enkf
+      
+      
+      # # Added in the for(t in 1:nt) loop of sda.enkf_MultiSite.R:
+      # if (t == 2) {
+      #   hop_test_dir <- file.path(settings$outdir, "hop_test_snapshot_t2")
+      #   dir.create(hop_test_dir, showWarnings = FALSE)
+      #   
+      #   # Copy all LPJ-GUESS status files to the snapshot directory
+      #   state_files <- list.files(
+      #     path = file.path(settings$modeloutdir, runid),
+      #     pattern = "guess\\..*\\.bin",
+      #     full.names = TRUE
+      #   )
+      #   file.copy(state_files, hop_test_dir)
+      #   
+      #   PEcAn.logger::logger.info("Hop test: the state file was saved to ", hop_test_dir)
+      # }
+      
+      # Suppose that hop test is triggered at t=2
+      if (t == 2 && control$hop_test) {
+        # Save the current state to the specified directory
+        hop_test_dir <- file.path(settings$outdir, "hop_test_snapshot")
+        dir.create(hop_test_dir, showWarnings = FALSE)
+        file.copy(
+          list.files(settings$outdir, full.names = TRUE, recursive = TRUE),
+          hop_test_dir,
+          recursive = TRUE
+        )
+        PEcAn.logger::logger.info("Hop test: Saved state at t=2. Manually restart from this snapshot.")
+        break  # Exit loop to simulate "stop"
+      }
+      
+      
+      } ### end loop over time
+} # sda.enkf
+# 

modules/assim.sequential/R/sda_matchparam.R

@@ -14,10 +14,20 @@ sda_matchparam <- function(settings, ensemble.samples, site.ids, nens){
   new.params <- list()
   all.pft.names <- names(ensemble.samples)
 
+  # Determines whether settings are single-site (list contains "run" directly) 
+  # or multi-site (list contains multiple settings)
+  single_site <- "run" %in% names(settings)
+  
+  # If it is a single site, convert to a list 
+  if (single_site) {
+    settings <- list(settings)  
+    site.ids <- list(site.ids)  
+  }
+  
   #loop over each site.
   for (i in seq_along(site.ids)) {
     #match pft name
-    site.pft.name <- settings[[i]]$run$site$site.pft$pft.name
+    site.pft.name <- unlist(settings[[i]]$run$site$site.pft)
     if(is.null(site.pft.name)){
       site_pft = utils::read.csv(settings[[i]]$run$inputs$pft.site$path)
       site.pft.name = site_pft$pft[site_pft$site == settings[[i]]$run$site$id]
@@ -35,4 +45,4 @@ sda_matchparam <- function(settings, ensemble.samples, site.ids, nens){
   names(new.params) <- site.ids
 
   return(new.params)
-}
+}

…sim.sequential/man/sda.enkf.multisite.Rd …ential/man/sda.enkf.multisite_hoptest.Rdmodules/assim.sequential/man/sda.enkf.multisite.Rd renamed to modules/assim.sequential/man/sda.enkf.multisite_hoptest.Rd modules/assim.sequential/man/sda.enkf.multisite.Rd renamed to modules/assim.sequential/man/sda.enkf.multisite_hoptest.Rd

@@ -212,7 +212,6 @@ get.ensemble.samples <- function(ensemble.size, pft.samples, env.samples,
 ##' @author David LeBauer, Carl Davidson, Hamze Dokoohaki
 write.ensemble.configs <- function(defaults, ensemble.samples, settings, model, 
                                    clean = FALSE, write.to.db = TRUE, restart = NULL, rename = FALSE) {
-  
   con <- NULL
   my.write.config <- paste("write.config.", model, sep = "")
   my.write_restart <- paste0("write_restart.", model)