Merge pull request #155 from NOAA-EDAB/dev_branch

NEUS V2.0.1
NEFSC · Apr 26, 2022 · 2537259 · 2537259
2 parents af835e3 + 24773ff
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diff --git a/Geometry/NEUSlookup.csv b/Geometry/NEUSlookup.csv
@@ -1,3 +1,4 @@
+box,face,level,x
 0,113,1,1
 0,113,2,1
 0,147,1,1

diff --git a/R/GLORYS/call_make_GLORYS_files_extraction.R b/R/GLORYS/call_make_GLORYS_files_extraction.R
@@ -0,0 +1,165 @@
+# Wrapper script to fully process GLORYS data
+# A) make GLORYS Atlantis Format (make_GLORYS_files) 1993-2017
+# B) make transport files w/ hydroconstruct (make_force_annual) 1993-2017
+# C) make tempsalt files using alternative method (make_force_statevar) 1993-2017
+# D) create spinup forcing w/ alternative tempsalt and hydroconstruct transport (make_force_spinup) 1964-1992
+
+glorys.dir = 'C:/Users/joseph.caracappa/Documents/GLORYS/'
+glorys.atl.dir = paste0(glorys.dir,'Atlantis_Format/')
+obs.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/'
+final.force.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Forcing_Files/Annual_Output/'
+git.force.dir = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/currentVersion/tsfiles/Annual_Files/'
+
+# A) Make GLORYS Atlantis Format (make_GLORYS_files) 1993-2017 ------------
+
+source(here::here('R','GLORYS','make_GLORYS_files_extract.R'))
+dir.names = 1993:2018
+
+for(yr in 1:length(dir.names)){
+
+  # Set from and to directories
+  in.dir = paste0(glorys.dir,'Data/',dir.names[yr],'/')
+  out.dir = paste0(glorys.dir,'Atlantis_Format/',dir.names[yr],'/')
+  in.files = list.files(in.dir,paste0('GLORYS_REANALYSIS_*'),full.names = F)
+
+  make_GLORYS_files(
+    glorys.dir = in.dir,
+    glorys.prefix = paste0('GLORYS_REANALYSIS_*'),
+    glorys.files = in.files,
+    out.dir = 'C:/Users/joseph.caracappa/Documents/GLORYS/Summary/NEUS_level_alt/',
+    dz.file = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/Geometry/dz.csv',
+    bgm.file = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/Geometry/neus_tmerc_RM2.bgm',
+    bgm.ll.file = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/Geometry/neus_ll_WGS84.bgm',
+    shp.file = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/Geometry/gis/Neus_ll_0p01.shp',
+    name.out = 'GLORYS_Atlantis_',
+    make.hflux = F,
+    make.physvars = T
+  )
+  print(paste0('##################  ',yr,'   #################'))
+}
+
+for(yr in 1:length(dir.names)){
+
+  # Set from and to directories
+  in.dir = paste0(glorys.dir,'Data/',dir.names[yr],'/')
+  in.files = list.files(in.dir,paste0('GLORYS_REANALYSIS_*'),full.names = F)
+
+  make_GLORYS_files(
+    glorys.dir = in.dir,
+    glorys.prefix = paste0('GLORYS_REANALYSIS_*'),
+    glorys.files = in.files,
+    out.dir = 'C:/Users/joseph.caracappa/Documents/GLORYS/Summary/NEUS_level_hflux/',
+    dz.file = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/Geometry/dz.csv',
+    bgm.file = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/Geometry/neus_tmerc_RM2.bgm',
+    bgm.ll.file = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/Geometry/neus_ll_WGS84.bgm',
+    shp.file = 'C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/Geometry/gis/Neus_ll_0p01.shp',
+    name.out = 'GLORYS_Atlantis_',
+    make.hflux = T,
+    make.physvars = F
+  )
+  print(paste0('##################  ',yr,'   #################'))
+}
+
+# 
+# # B) run append_vflux from ECCO -------------------------------------------
+# #moves statevar files from glorys.atl.dir to Obs_Hindcast/statevars/
+# source(here::here('R','ECCO','append_vflux.R'))
+# 
+# #STOP run 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/append_vflux_ECCO.sh
+# 
+# # C) Make transport files w/ hydroconstruct (make_force_annual) 19 --------
+# source(here::here('R','synch_force_time.R'))
+# source(here::here('R','make_force_annual.R'))
+# 
+# # D) make tempsalt files  using alternative method (make_force_statevar)--------
+# source(here::here('R','make_force_statevar.R'))
+# 
+# .packages = c("devtools","tidyverse","stringi","RNetCDF", "data.table")
+# lapply(.packages, require, character.only=TRUE)
+# 
+# force.vars = final.vars = c('temperature','salinity')
+# var.units = c('degrees Celcius','PSU')
+# long.names = c('Temperature','Salinity')
+# fill.val = c(15,0)
+# miss.val = c(15,0)
+# valid.min = c(-2,0)
+# valid.max = c(999,999)
+# 
+# years = 1993:2017
+# 
+# for(yr in 1:length(years)){
+#   in.dir = paste0(obs.dir,'statevars/')
+#   in.file = paste0(in.dir,'Obs_Hindcast_statevars_',years[yr],'.nc')
+#   
+#   make_force_statevar(roms.dir = in.dir,
+#                       roms.file = in.file,
+#                       out.dir = paste0(final.force.dir,'phys_statevars_alternate/'),
+#                       force.vars = force.vars,
+#                       var.units = var.units,
+#                       final.vars = final.vars,
+#                       fill.val = fill.val,
+#                       long.names = long.names,
+#                       miss.val = miss.val,
+#                       valid.min = valid.min,
+#                       valid.max = valid.max,
+#                       out.prefix = 'GLORYS_tempsalt_force_',
+#                       dupe.bottom = T)
+#   
+# }
+# 
+# # E) create spinup forcing 1964-1992 --------
+# 
+# start.year = 1964
+# years = 1964:1992
+# 
+# source('C:/Users/joseph.caracappa/Documents/GitHub/neus-atlantis/R/make_force_spinup.R')
+# # obs.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Forcing_Files/Annual_Output/'
+# obs.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/'
+# for(i in 1:length(years)){
+#   
+#   make_force_spinup(
+#     do.hydroconstruct =F,
+#     out.dir = obs.dir,
+#     trans.prefix = 'GLORYS_Atlantis_Transport_',
+#     statevar.prefix = 'Obs_Hindcast_statevars_',
+#     anyvar.prefix = NA,
+#     transport.file = paste0(obs.dir,'Forcing_Files/Annual_Output/combined_years/transport_DOY_climatology.nc'),
+#     statevar.file = paste0(obs.dir,'Forcing_Files/Annual_Output/combined_years/Physics_DOY_climatology.nc'),
+#     anyvar.file = NA,
+#     anyvar.out = NA,
+#     force.dir =paste0(obs.dir,'Forcing_Files/'),
+#     start.year = 1964,
+#     new.year = years[i],
+#     param.temp = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Forcing_Files/obs_hindcast_hydroconstruct_template.prm',
+#     bat.temp = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Forcing_Files/hydroconstruct_run_template.bat'
+#   )
+#   
+#   # make_force_spinup(
+#   #   do.hydroconstruct = F,
+#   #   out.dir = pasteo(obs.dir,'phys_statevars_alternate_DOY_spinup/'),
+#   #   trans.prefix = NA,
+#   #   statevar.prefix = NA,
+#   #   anyvar.prefix = 'GLORYS_tempsalt_force_',
+#   #   transport.file = NA,
+#   #   statevar.file = NA,
+#   #   anyvar.file = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Forcing_Files/Annual_Output/combined_years/Physics_DOY_Climatology.nc',
+#   #   # anyvar.out = paste0(final.force.dir,'phys_statevars_alternate/'),
+#   #   anyvar.out = paste0(obs.dir,'phys_statevars_alternate_DOY_spinup/'),
+#   #   # force.dir = paste0(obs.dir,'Forcing_Files/'),
+#   #   force.dir = paste0(obs.dir,'phys_statevars_alternate_DOY_spinup/'),
+#   #   start.year = 1964,
+#   #   new.year = years[i],
+#   #   param.temp = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Forcing_Files/obs_hindcast_hydroconstruct_template.prm',
+#   #   bat.temp = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Forcing_Files/hydroconstruct_run_template.bat'
+#   # )
+#   print(i)
+#   
+# }
+# 
+# 
+# # F) Copy files to Git Directory ------------------------------------------
+# final.transport = list.files(paste0(final.force.dir,'transport/'),'^flow.*\\.nc$',full.names = T)
+# final.tempsalt = list.files(paste0(final.force.dir,'phys_statevars_alternate/'),'GLORYS_tempsalt_force_*',full.names = T)
+# 
+# file.copy(final.transport,git.force.dir,overwrite = T)
+# file.copy(final.tempsalt,git.force.dir,overwrite = T)
diff --git a/R/GLORYS/make_GLORYS_NEUS_statevar_summary.R b/R/GLORYS/make_GLORYS_NEUS_statevar_summary.R
@@ -0,0 +1,53 @@
+#Script to combine Altantis-formatted GLORYS data into one data file
+library(dplyr)
+library(ggplot2)
+
+data.dir = 'C:/Users/joseph.caracappa/Documents/GLORYS/Atlantis_Format/'
+out.dir = 'C:/Users/joseph.caracappa/Documents/GLORYS/Summary/'
+years = 1993:2017
+var.names = c('temperature','salinity')
+
+out.data.ls = list()
+yr =1
+for(yr in 1:length(years)){
+
+  dat.file = paste0(data.dir,years[yr],'/GLORYS_Atlantis_statevars_',years[yr],'.R')
+  load(dat.file)
+
+  #format temperature
+  yr.temp = temperature %>%
+    reshape2::melt()%>%
+    mutate(value = ifelse(value < 0, NA,value))%>%
+    rename(level = 'Var1',
+           box = 'Var2',
+           time = 'Var3',
+           temperature = 'value')%>%
+    mutate(date = as.Date(as.POSIXct((time-1)*86400,origin = paste0(years[yr],'-01-01 00:00:00',tz = 'UTC'))),
+           box = box-1)%>%
+    filter(!is.na(temperature))
+
+  yr.salt = salinity %>%
+    reshape2::melt()%>%
+    mutate(value = ifelse(value < 0, NA,value))%>%
+    rename(level = 'Var1',
+           box = 'Var2',
+           time = 'Var3',
+           salinity = 'value')%>%
+    mutate(date = as.Date(as.POSIXct((time-1)*86400,origin = paste0(years[yr],'-01-01 00:00:00',tz = 'UTC'))),
+           box= box-1)%>%
+    filter(!is.na(salinity))
+
+  out.data.ls[[yr]] = yr.temp %>%
+    left_join(yr.salt)%>%
+    select(date,level,box,time,temperature,salinity)
+
+  print(years[yr])
+
+}
+
+out.data = bind_rows(out.data.ls)
+
+write.csv(out.data,file = paste0(out.dir,'GLORYS_Atlantis_Level_Statevars_all.csv'),row.names = F)
+# ggplot(out.data,aes(x=date,y=temperature,color = factor(level)))+
+#   geom_line()+
+#   facet_wrap(~box)