From ba974e351ff65fea69a4e78475bebbdce4b7fce4 Mon Sep 17 00:00:00 2001
From: Yisreal <huyucong34@gmail.com>
Date: Fri, 6 Sep 2024 19:26:22 +0800
Subject: [PATCH 1/4] Only Generate job.sh

---
 models/fates/R/write.configs.FATES.R | 773 ++++++---------------------
 1 file changed, 164 insertions(+), 609 deletions(-)

diff --git a/models/fates/R/write.configs.FATES.R b/models/fates/R/write.configs.FATES.R
index 5b8fabb6a6..67d82a4496 100644
--- a/models/fates/R/write.configs.FATES.R
+++ b/models/fates/R/write.configs.FATES.R
@@ -9,23 +9,40 @@
 ##' @return none
 ##' @export
 ##' @author Mike Dietze, Shawn Serbin
+##-------------------------------------------------------------------------------------------------# # nolint
+
+# example trait.values list
+trait.values <- list()
+trait.values$temperate.coniferous <- list()
+trait.values$env <- list()
+
+tc_traits <- as.data.frame(matrix(c(9999, 8888), nrow=1, ncol=2))
+colnames(tc_traits) <- c("leaf_turnover_rate", "veg_respiration_Q10")
+# Fates names for these params are "fates_leaf_long", "q10_mr"
+
+trait.values$temperate.coniferous <- tc_traits
+settings <- './test.fates.xml'
+run.id <- 'test_oneyear'
+
+# example trait.values list
+
 write.config.FATES <- function(defaults, trait.values, settings, run.id){
 
    ## site information
    site <- settings$run$site
-   site.id <- as.numeric(site$id)
+   site.id <- site$id # change1: 772 -> SOD1
   
    # find out where things are
-   local.rundir <- file.path(settings$rundir, run.id) ## this is on local machine for staging
-   rundir       <- file.path(settings$host$rundir, run.id)  ## this is on remote machine for execution
-   casedir      <- file.path(rundir,"case") 
-   outdir       <- file.path(settings$host$outdir, run.id)
-   refcase      <- settings$model$binary
-   bld          <- file.path(refcase,"bld")
-   binary       <- file.path(bld,"cesm.exe")
-   indir        <- file.path(rundir,"input") ## input directory
-   default      <- settings$run$inputs$default$path ## reference inputs file structure
-   site_name    <- paste0(site.id %/% 1000000000, "-", site.id %% 1000000000)
+   #local.rundir <- file.path(settings$rundir, run.id) ## this is on local machine for staging
+   #rundir       <- file.path(settings$host$rundir, run.id)  ## this is on remote machine for execution
+   #casedir      <- rundir # file.path(rundir,run.id) ## /ctsm-api/resources/cases/case_SOD1, change2: 'case' -> site.id
+   #outdir       <- file.path(settings$host$outdir, run.id)
+   #refcase      <- settings['model']['binary'] # question1: refcase==casedir?
+   #bld          <- file.path(refcase,"bld")
+   #binary       <- file.path(bld,"cesm.exe")
+   #indir        <- file.path(rundir,"data/shared") ## input directory
+   #default      <- settings$run$inputs$default$path ## reference inputs file structure
+   #site_name    <- paste0(site.id, "_c", run.id) ## change3 
    
    ## DATES
    ## CLM is a bit odd and takes a start date and length, so we need to precompute
@@ -42,49 +59,50 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
 
    ## SITE INFO --> DOMAIN FILE (lat/lon)
    #  - should also store this in the refcase directory for PEcAn so we can grab from there, and not the PEcAn package
-   gridres <- 0.125  ## ultimately this should be a variable
-   lat <- as.numeric(site$lat)
-   lon <- (as.numeric(site$lon) + 360) %% 360 ## make sure coords in 0-360 range, not negative
-   domain.default <- system.file("domain.lnd.1x1pt-brazil_navy.090715.nc",package="PEcAn.FATES")
-   domain.file <- file.path(local.rundir,paste0("domain.lnd.",site_name,".nc"))
-   file.copy(domain.default,domain.file)
-   domain.nc <- ncdf4::nc_open(domain.file,write=TRUE)
-   ncdf4::ncvar_put(nc=domain.nc, varid='xc', vals=lon)
-   ncdf4::ncvar_put(nc=domain.nc, varid='yc', vals=lat)
-   ncdf4::ncvar_put(nc=domain.nc, varid='xv', vals=lon+c(-1,1,1,-1)*gridres)
-   ncdf4::ncvar_put(nc=domain.nc, varid='yv', vals=lat+c(-1,-1,1,1)*gridres)
-   ncdf4::ncvar_put(nc=domain.nc, varid='area', vals=(2*gridres*pi/180)^2)   
-   ncdf4::nc_close(domain.nc)
+   #gridres <- 0.125  ## ultimately this should be a variable
+   #lat <- as.numeric(site$lat)
+   #lon <- (as.numeric(site$lon) + 360) %% 360 ## make sure coords in 0-360 range, not negative
+   #domain.default <- system.file("domain.lnd.360x720_gswp3.0v1.c170606.nc",package="PEcAn.FATES")
+   #domain.file <- file.path(local.rundir,paste0("domain.lnd.fv0.9x1.25_gx1v7_",site_name,".nc"))
+   #file.copy(domain.default,domain.file)
+   #domain.nc <- ncdf4::nc_open(domain.file,write=TRUE)
+   #ncdf4::ncvar_put(nc=domain.nc, varid='xc', vals=lon)
+   #ncdf4::ncvar_put(nc=domain.nc, varid='yc', vals=lat)
+   #ncdf4::ncvar_put(nc=domain.nc, varid='xv', vals=lon+c(-1,1,1,-1)*gridres)
+   #ncdf4::ncvar_put(nc=domain.nc, varid='yv', vals=lat+c(-1,-1,1,1)*gridres)
+   #ncdf4::ncvar_put(nc=domain.nc, varid='area', vals=(2*gridres*pi/180)^2)   
+   #ncdf4::nc_close(domain.nc)
    
    ## SURF - should also store this in the refcase directory for PEcAn so we can grab from there, and not the PEcAn package
-   surf.default <- system.file("surfdata_1x1_brazil_16pfts_Irrig_CMIP6_simyr2000_c171214.nc",package = "PEcAn.FATES")
-   surf.file    <- file.path(local.rundir,paste0("surfdata_",site_name,"_simyr2000.nc"))
-   file.copy(surf.default,surf.file)
-   Sys.chmod(surf.file)
-   surf.nc <- ncdf4::nc_open(surf.file,write=TRUE)
-   ncdf4::ncvar_put(nc=surf.nc, varid='LONGXY', vals=lon)
-   ncdf4::ncvar_put(nc=surf.nc, varid='LATIXY', vals=lat)
-   ncdf4::nc_close(surf.nc)   
+   #surf.default <- system.file("surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc",package = "PEcAn.FATES")
+   #surf.file    <- file.path(local.rundir,paste0("surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_",site_name, ".nc"))
+   #file.copy(surf.default,surf.file)
+   #Sys.chmod(surf.file)
+   #surf.nc <- ncdf4::nc_open(surf.file,write=TRUE)
+   #ncdf4::ncvar_put(nc=surf.nc, varid='LONGXY', vals=lon)
+   #ncdf4::ncvar_put(nc=surf.nc, varid='LATIXY', vals=lat)
+   #ncdf4::nc_close(surf.nc)   
    
+   ## DATM & DATM Stream??
    ## MET HEADERS
-   if(!is.null(settings$run$inputs$met)){
+   #if(!is.null(settings$run$inputs$met)){
 
      ## DATM HEADER: datm_atm_in
-     datm <- readLines(con=system.file("datm_atm_in.template",package = "PEcAn.FATES"),n=-1)
-     datm <- gsub('@DOMAIN@', file.path(indir,"share/domains/domain.clm",basename(domain.file)), datm)
-     datm <- gsub('@START_YEAR@',lubridate::year(start_date), datm)
-     datm <- gsub('@END_YEAR@',lubridate::year(end_date), datm)
-     writeLines(datm, con=file.path(local.rundir, "datm_atm_in"))
+     #datm <- readLines(con=system.file("datm_atm_in.template",package = "PEcAn.FATES"),n=-1)
+     #datm <- gsub('@DOMAIN@', file.path(indir,"share/domains/domain.clm",basename(domain.file)), datm)
+     #datm <- gsub('@START_YEAR@',lubridate::year(start_date), datm)
+     #datm <- gsub('@END_YEAR@',lubridate::year(end_date), datm)
+     #writeLines(datm, con=file.path(local.rundir, "datm_atm_in"))
      
-     ## DATM STREAM MET
-     met <- readLines(con=system.file("datm.streams.txt.PEcAn_met.template",package = "PEcAn.FATES"),n=-1)
-     met <- gsub('@INDIR@',indir, met)
+     ### DATM STREAM MET
+     #met <- readLines(con=system.file("datm.streams.txt.PEcAn_met.template",package = "PEcAn.FATES"),n=-1)
+     #met <- gsub('@INDIR@',indir, met)
      #domain.file.name <- paste0("domain.lnd.",site_name,".nc")
      #met <- gsub('@DOMAIN@',domain.file.name, met)  # attempting to provide correct domain file name
-     met <- gsub('@MET_PATH@',settings$run$inputs$met$path, met)
-     met.files <- dir(settings$run$inputs$met$path,"*.nc")
-     met <- gsub('@MET_FILES@',paste(met.files,collapse = "\n            "), met)
-     writeLines(met, con=file.path(local.rundir, "datm.streams.txt.PEcAn_met"))
+     #met <- gsub('@MET_PATH@',settings$run$inputs$met$path, met)
+     #met.files <- dir(settings$run$inputs$met$path,"*.nc")
+     #met <- gsub('@MET_FILES@',paste(met.files,collapse = "\n"), met)
+     #writeLines(met, con=file.path(local.rundir, "datm.streams.txt.PEcAn_met"))
      
    }
 #   ... need to set this up so that if MET is blank it can run with default CLM met
@@ -105,70 +123,64 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
      jobsh <- readLines(con=system.file("template.job", package = "PEcAn.FATES"), n=-1)
    }
    
- # create host specific setttings
-   hostsetup <- ""
-   if (!is.null(settings$model$prerun)) {
-     hostsetup <- paste(hostsetup, sep="\n", paste(settings$model$prerun, collapse="\n"))
-   }
-   if (!is.null(settings$host$prerun)) {
-     hostsetup <- paste(hostsetup, sep="\n", paste(settings$host$prerun, collapse="\n"))
-   }
+ # create host specific settings
+  # hostsetup <- ""
+  # if (!is.null(settings$model$prerun)) {
+  #   hostsetup <- paste(hostsetup, sep="\n", paste(settings$model$prerun, collapse="\n"))
+  # }
+  # if (!is.null(settings$host$prerun)) {
+  #   hostsetup <- paste(hostsetup, sep="\n", paste(settings$host$prerun, collapse="\n"))
+  # }
 
-   hostteardown <- ""
-   if (!is.null(settings$model$postrun)) {
-     hostteardown <- paste(hostteardown, sep="\n", paste(settings$model$postrun, collapse="\n"))
-   }
-   if (!is.null(settings$host$postrun)) {
-     hostteardown <- paste(hostteardown, sep="\n", paste(settings$host$postrun, collapse="\n"))
-   }
+  # hostteardown <- ""
+  # if (!is.null(settings$model$postrun)) {
+  #   hostteardown <- paste(hostteardown, sep="\n", paste(settings$model$postrun, collapse="\n"))
+  # }
+  # if (!is.null(settings$host$postrun)) {
+  #   hostteardown <- paste(hostteardown, sep="\n", paste(settings$host$postrun, collapse="\n"))
+  # }
 
 # create job.sh
-   jobsh <- gsub('@HOST_SETUP@', hostsetup, jobsh)
-   jobsh <- gsub('@HOST_TEARDOWN@', hostteardown, jobsh)
+   #jobsh <- gsub('@HOST_SETUP@', hostsetup, jobsh)
+   #jobsh <- gsub('@HOST_TEARDOWN@', hostteardown, jobsh)
    
    ## Machine configs
-   #   ./create_newcase -case @CASEDIR@ -res 1x1_brazil -compset ICLM45ED -mach @MACHINE@ -compiler @COMPILER@ -project @PROJECT@
+   #   ./create_newcase –case A –res @RES@ –compset @COMPSET@ –driver @DRIVER@ –machine @MACHINE@ –run-unsupported
    if (!is.null(settings$model$machine)) {
      machine <- paste(settings$model$machine, collapse="\n") 
    } else {
-     machine <- "eddi"
+     machine <- "container-nlp"
    }
    jobsh <- gsub('@MACHINE@', machine, jobsh)
-   if (!is.null(settings$model$compiler)) {
-     compiler <- paste(settings$model$compiler, collapse="\n")
+   if (!is.null(settings$model$driver)) {
+     driver <- paste(settings$model$driver, collapse="\n")
    } else {
-     compiler <- "gnu"
+     driver <- "nuopc"
    }
-   jobsh <- gsub('@COMPILER@', compiler, jobsh)
-   if (!is.null(settings$model$resolution)) {
-     resolution <- paste(settings$model$resolution, collapse="\n")
-   } else {
-     resolution <- "1x1_brazil"
-   }
-   jobsh <- gsub('@RES@', resolution, jobsh)
+   jobsh <- gsub('@DRIVER@', driver, jobsh)
    if (!is.null(settings$model$compset)) {
      compset <- paste(settings$model$compset, collapse="\n")
    } else {
-     compset <- "I2000Clm50FatesGs"
+     compset <- "2000_DATM%GSWP3v1_CLM51%FATES_SICE_SOCN_MOSART_SGLC_SWAV"
    }
    jobsh <- gsub('@COMPSET@', compset, jobsh)
-   if (!is.null(settings$model$project)) {
-     project <- paste(settings$model$project, collapse="\n")
+   if (!is.null(settings$model$res)) {
+     res <- paste(settings$model$res, collapse="\n")
    } else {
-     project <- "pecan"
+     res <- "CLM_USRDAT"
    }
-   jobsh <- gsub('@PROJECT@', project, jobsh)
+   jobsh <- gsub('@RES@', res, jobsh)
    
    ## PATHS
-   jobsh <- gsub('@RUNDIR@', rundir, jobsh)
-   jobsh <- gsub('@CASEDIR@', casedir, jobsh)
-   jobsh <- gsub('@OUTDIR@', outdir, jobsh)
-   jobsh <- gsub('@REFCASE@', refcase, jobsh)
-   jobsh <- gsub('@BLD@', bld, jobsh)
-   jobsh <- gsub('@BINARY@', binary, jobsh)
-   jobsh <- gsub('@INDIR@', indir, jobsh)
-   jobsh <- gsub('@DEFAULT@', default, jobsh)
-   jobsh <- gsub('@SITE_NAME@', site_name, jobsh) 
+   #jobsh <- gsub('@RUNDIR@', rundir, jobsh)
+   #jobsh <- gsub('@CASEDIR@', casedir, jobsh)
+   #jobsh <- gsub('@OUTDIR@', outdir, jobsh)
+   #jobsh <- gsub('@REFCASE@', refcase, jobsh)
+   #jobsh <- gsub('@BLD@', bld, jobsh)
+   #jobsh <- gsub('@BINARY@', binary, jobsh)
+   #jobsh <- gsub('@INDIR@', indir, jobsh)
+   #jobsh <- gsub('@DEFAULT@', default, jobsh)
+   #jobsh <- gsub('@SITE_NAME@', site_name, jobsh) 
   
    ## DATES -> ENV_RUN
    jobsh <- gsub('@START_DATE@', start_date, jobsh)
@@ -181,7 +193,8 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
    
    writeLines(jobsh, con=file.path(settings$rundir, run.id, "job.sh"))
    Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
-#   
+
+write.config.FATES(default, trait.values, test.fates.xml, run.id)
 #   ## Write PARAMETER file
    
    ## COPY AND OPEN DEFAULT PARAMETER FILES
@@ -191,103 +204,76 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
    # CLM
    #clm.param.default <- system.file("clm5_params.c171117.nc",package="PEcAn.FATES")
    #clm.param.file <- file.path(local.rundir,paste0("clm_params.",run.id,".nc"))
-   clm.param.default <- file.path(refcase,"clm5_params.c171117.nc") # probably need to allow custom param file names here (pecan.xml?)
-   clm.param.file <- file.path(local.rundir,paste0("clm_params.",run.id,".nc"))
-   file.copy(clm.param.default,clm.param.file)
-   clm.param.nc <- ncdf4::nc_open(clm.param.file,write=TRUE)
+   ## Position of parameters file?
+   #clm.param.default <- file.path(refcase,"clm5_params.c171117.nc") # probably need to allow custom param file names here (pecan.xml?)
+   #clm.param.file <- file.path(local.rundir,paste0("clm_params.",run.id,".nc"))
+   #file.copy(clm.param.default,clm.param.file)
+   #clm.param.nc <- ncdf4::nc_open(clm.param.file,write=TRUE)
    
    # FATES
    #fates.param.default <- system.file("fates_params_2troppftclones.c171018_sps.nc",package="PEcAn.FATES")
    # above is a temporary param file corrected for the tropics by lowering freezing tolerace parameters
-   fates.param.default <- file.path(refcase,"fates_params_2troppftclones.c171018_sps.nc") # probably need to allow custom param file names here (pecan.xml?)
-   fates.param.file <- file.path(local.rundir,paste0("fates_params.",run.id,".nc"))
-   file.copy(fates.param.default,fates.param.file)
-   fates.param.nc <- ncdf4::nc_open(fates.param.file,write=TRUE)
+   #fates.param.default <- file.path(refcase,"fates_params_2troppftclones.c171018_sps.nc") # probably need to allow custom param file names here (pecan.xml?)
+   #fates.param.file <- file.path(local.rundir,paste0("fates_params.",run.id,".nc"))
+   #file.copy(fates.param.default,fates.param.file)
+   #fates.param.nc <- ncdf4::nc_open(fates.param.file,write=TRUE)
    
    ## Loop over PFTS
-   npft <- length(trait.values)
-   PEcAn.logger::logger.debug(npft)
-   PEcAn.logger::logger.debug(dim(trait.values))
-   PEcAn.logger::logger.debug(names(trait.values))
+   #npft <- length(trait.values)
+   #PEcAn.logger::logger.debug(npft)
+   #PEcAn.logger::logger.debug(dim(trait.values))
+   #PEcAn.logger::logger.debug(names(trait.values))
    #pftnames <- stringr::str_trim(tolower(ncvar_get(param.nc,"pftname"))) 
-   pftnames <- stringr::str_trim(tolower(ncdf4::ncvar_get(clm.param.nc,"pftname")))
-   PEcAn.logger::logger.debug(paste0("CLM PFT names: "),pftnames)
-   for (i in seq_len(npft)) {
-     pft <- trait.values[[i]]
-     print(c("PFT",i))
-     PEcAn.logger::logger.info(pft)
-     pft.name <- names(trait.values)[i]
-     if(is.null(pft.name) | is.na(pft.name)){
-       PEcAn.logger::logger.error("pft.name missing")
-     } else {
-       PEcAn.logger::logger.info(paste("PFT =",pft.name))
-       PEcAn.logger::logger.debug(paste0("fates-clm PFT number: ",which(pftnames==pft.name)))
-     }
-     if(pft.name == 'env') next   ## HACK, need to remove env from default
+   #pftnames <- stringr::str_trim(tolower(ncdf4::ncvar_get(clm.param.nc,"pftname")))
+   #PEcAn.logger::logger.debug(paste0("CLM PFT names: "),pftnames)
+   #for (i in seq_len(npft)) {
+     #pft <- trait.values[[i]]
+     #print(c("PFT",i))
+     #PEcAn.logger::logger.info(pft)
+     #pft.name <- names(trait.values)[i]
+     #if(is.null(pft.name) | is.na(pft.name)){
+       #PEcAn.logger::logger.error("pft.name missing")
+     #} else {
+       #PEcAn.logger::logger.info(paste("PFT =",pft.name))
+       #PEcAn.logger::logger.debug(paste0("fates-clm PFT number: ",which(pftnames==pft.name)))
+     #}
+     #if(pft.name == 'env') next   ## HACK, need to remove env from default
      
      ## Match PFT name to COLUMN
-     ipft <- match(tolower(pft.name),pftnames)
-     PEcAn.logger::logger.debug(paste0("ipft: ",ipft))
+     #ipft <- match(tolower(pft.name),pftnames)
+     #PEcAn.logger::logger.debug(paste0("ipft: ",ipft))
                                       
-     if(is.na(ipft)){
-       PEcAn.logger::logger.severe(paste("Unmatched PFT",pft.name,
-                          "in FATES. PEcAn does not yet support non-default PFTs for this model"))
-     }
+     #if(is.na(ipft)){
+       #PEcAn.logger::logger.severe(paste("Unmatched PFT",pft.name,
+                          #"in FATES. PEcAn does not yet support non-default PFTs for this model"))
+     #}
      
      # hard code hack until we can use more than 2 pfts in FATES 
-     ipft <- 2
-     PEcAn.logger::logger.debug(paste0("*** PFT number hard-coded to ", ipft," in fates. This will be updated when FATES allows more PFTs"))
+     #ipft <- 2
+     #PEcAn.logger::logger.debug(paste0("*** PFT number hard-coded to ", ipft," in fates. This will be updated when FATES allows more PFTs"))
      
      ## Special variables used in conversions
 #     leafC <- pft['leafC']/100  ## percent to proportion
-     leafC <- NA
-     if(is.na(leafC)) leafC <- 0.48
+     #leafC <- NA
+     #if(is.na(leafC)) leafC <- 0.48
      
      # determine photo pathway
-     photo_flag <- ncdf4::ncvar_get(fates.param.nc,varid="fates_c3psn", start = ipft, count = 1)
-     PEcAn.logger::logger.debug(paste0("Photosynthesis pathway flag value: ", photo_flag))
+     #photo_flag <- ncdf4::ncvar_get(fates.param.nc,varid="fates_c3psn", start = ipft, count = 1)
+     #PEcAn.logger::logger.debug(paste0("Photosynthesis pathway flag value: ", photo_flag))
      
      ## Loop over VARIABLES
-     for (v in seq_along(pft)) {
-       var <- names(pft)[v]
+     #for (v in seq_along(pft)) {
+       #var <- names(pft)[v]
 
        ## THESE NEED SOME FOLLOW UP
        
        ### ----- Leaf physiological parameters
        # Vcmax
-       if(var == "Vcmax"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_vcmax25top', start = ipft, count = 1,
-                   vals=pft[v])  ## (umol CO2 m-2 s-1)
-       }
        # Ball-Berry slope
-       if(var == "stomatal_slope.BB"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_BB_slope', start = ipft, count = 1,
-                          vals=pft[v])
-       }
-       
+
        # Ball-Berry intercept - c3.  We need to figure out how to set either C3 or C4 values? Based on the PFT?
        # TODO: allow setting this for C3 and/or C4 PFTs
        # right now, each are just one dimension, will need to revist this if this changes.
-       if(var == "cuticular_cond"){
-         if (photo_flag==0) {
-           PEcAn.logger::logger.debug("** Setting C4 cuticular conductance value")
-           ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_bbopt_c4', start = 1, count = 1,
-                            vals=pft[v])
-         } else if (photo_flag==1) {
-           PEcAn.logger::logger.debug("** Setting C3 cuticular conductance value")
-           ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_bbopt_c3', start = 1, count = 1,
-                            vals=pft[v])
-         } else {
-           PEcAn.logger::logger.warn(" ** FATES photosynthesis pathway flag not set. cuticular conductance not set **")
-         }
-       }
-       
-       ## missing from params.nc 
-       #       if(var == "cuticular_cond"){
-       #         gH2O_per_mol <- 18.01528
-       #         ncvar_put(nc=param.nc, varid='gsmin', start = ipft, count = 1,
-       #                   vals=pft[v]*gH2O_per_mol*1e-12)   ### umol H2O m-2 s-1 ->  [m s-1]
-       #       }
        
        # T response params - modified Arrhenius params for Vcmax, Jmax, and TPU
        # -- NOT YET IMPLEMENTED IN BETYdb. FATES params:
@@ -295,39 +281,17 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
        # fates_vcmaxse, fates_jmaxse, fates_tpuse
       
        # Ha activation energy for vcmax - FATES units: J/mol
-       if(var == "Ha_Modified_Arrhenius_Vcmax"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_vcmaxha', start = ipft, count = 1,
-                          vals=pft[v]*1000)  ## convert from kj/mol to J/mol (FATES units)
-       }
-       
+
        # Hd deactivation energy for vcmax - FATES units: J/mol
-       if(var == "Hd_Modified_Arrhenius_Vcmax"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_vcmaxhd', start = ipft, count = 1,
-                          vals=pft[v]*1000)  ## convert from kj/mol to J/mol (FATES units)
-       }
-       
+
        # Ha activation energy for Jmax - FATES units: J/mol
-       if(var == "Ha_Modified_Arrhenius_Jmax"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_jmaxha', start = ipft, count = 1,
-                          vals=pft[v]*1000)  ## convert from kj/mol to J/mol (FATES units)
-       }
        
        # Hd deactivation energy for Jmax - FATES units: J/mol
-       if(var == "Hd_Modified_Arrhenius_Jmax"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_jmaxhd', start = ipft, count = 1,
-                          vals=pft[v]*1000)  ## convert from kj/mol to J/mol (FATES units)
-       }
-       
+
        # deltaS Vcmax - BETY units:J/mol/K;  FATES units: J/mol/K
-       if(var == "deltaS_Vcmax"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_vcmaxse', start = ipft, count = 1,
-                          vals=pft[v])  ## convert from kj/mol to J/mol (FATES units)
-       }
+       
        # deltaS Jmax - BETY units:J/mol/K;  FATES units: J/mol/K
-       if(var == "deltaS_Jmax"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_jmaxse', start = ipft, count = 1,
-                          vals=pft[v])  ## convert from kj/mol to J/mol (FATES units)
-       }
+
        ### ----- Leaf physiological parameters
        
        
@@ -337,56 +301,15 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
 #         ncvar_put(nc=param.nc, varid='background_mort_rate', start = ipft, count = 1,
 #                   vals=pft[v])  
 #       }
-       if(var == "r_fract"){                    ## Fraction of carbon balance remaining after maintenance costs have been met that is dedicated to seed production.	[0-1]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_seed_alloc', start = ipft, count = 1,
-                   vals=pft[v])  
-       }
-       ## This one is currently allpft level but should be pft level  - no longer in FATES params, what was this changed to?
-        if(var == "agf_bs"){                    ## The fraction of sapwood and structural biomass that is above ground [0-1]
-          ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_allom_agb_frac', start = ipft, count = 1,
-                    vals=pft[v])  
-       }
-       
        ## PFT-level variables
-       if(var == "seed_rain_kgC"){                    ## External seed rain from outside site (non-mass conserving) ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_seed_rain', start = ipft, count = 1,
-                   vals=pft[v])  
-       }
+
 ## missing from params.nc 
 #       if(var == "cuticular_cond"){
 #         gH2O_per_mol <- 18.01528
 #         ncvar_put(nc=param.nc, varid='gsmin', start = ipft, count = 1,
 #                   vals=pft[v]*gH2O_per_mol*1e-12)   ### umol H2O m-2 s-1 ->  [m s-1]
 #       }
-       if(var == "DBH_at_HTMAX"){                    ## note in FATES parameter list about switching to HTMAX
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_allom_dbh_maxheight', start = ipft, count = 1,
-                   vals=pft[v])  ## [cm]
-       }
-       if(var == "growth_resp_factor"){                    ## r_growth = grperc * (gpp+r_maint)  fates_grperc:long_name = "Growth respiration factor" ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_grperc', start = ipft, count = 1,
-                   vals=pft[v])  
-       }
-       if(var == "SLA"){                                  ## default 0.012
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_slatop', start = ipft, count = 1,  
-                   vals=PEcAn.utils::ud_convert(pft[v],"m2 kg-1","m2 g-1")/leafC)
-       }
-       if(var == "leaf_turnover_rate"){                   ## fates_leaf_long:long_name = "Leaf longevity (ie turnover timescale)" ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_leaf_long', start = ipft, count = 1,
-                   vals=1/pft[v]) ## leaf_long = 1/leaf_turnover_rate, 1/years -> years
-       }
-       if(var == "root_turnover_rate"){                   ## fates_root_long:long_name = "root longevity (alternatively, turnover time)" ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_root_long', start = ipft, count = 1,
-                   vals=1/pft[v]) ## root_long = 1/root_turnover_rate, 1/years -> years
-       }
-       if(var == "c2n_leaf"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_leafcn', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "fineroot2leaf"){ #"Allocation parameter: new fine root C per new leaf C" units = "gC/gC"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_froot_leaf', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       
+
        # if(var == "sapwood_ratio"){         # leaf to sapwood area ratio. IS THIS NOW fates_sapwood_ratio(fates_pft)??
        #   ncvar_put(nc=fates.param.nc, varid='latosa', start = ipft, count = 1,
        #             vals=PEcAn.utils::ud_convert(pft[v],"m2 m-2","m2 cm-2"))
@@ -402,224 +325,16 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
        # fates_allom_latosa_slp:units = "unitless" ;
        # fates_allom_latosa_int = 0.001, 0.001 ;
        # fates_allom_latosa_slp = 0, 0 ;
-       if(var == "sapwood_ratio"){         
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_allom_latosa_int', start = ipft, count = 1,
-                   vals=PEcAn.utils::ud_convert(pft[v],"m2 m-2","m2 cm-2"))
-       }
-       if(var == "leaf_width"){            # Characteristic leaf dimension use for aerodynamic resistance
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_dleaf', start = ipft, count = 1,
-                   vals=PEcAn.utils::ud_convert(pft[v],"mm","m"))
-         #PEcAn.logger::logger.debug(paste0("fates_dleaf: ",PEcAn.utils::ud_convert(pft[v],"mm","m"))) # temp debugging
-       }
-       ## Currently not in param.nc file despite being on NGEE-T parameter list       
-       #       if(var == "nonlocal_dispersal"){    # Place-holder parameter for important seed dispersal parameters
-       #         ncvar_put(nc=param.nc, varid='seed_dispersal_x', start = ipft, count = 1,
-       #                   vals=pft[v])
-       #       }
-       if(var == "hgt_min"){               # the minimum height (ie starting height) of a newly recruited plant" ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_hgt_min', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "leaf_reflect_nir"){      # Leaf reflectance: near-IR	[0-1]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_rholnir', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "leaf_reflect_vis"){      # Leaf reflectance: visible	[0-1]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_rholvis', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "wood_reflect_nir"){      # Stem reflectance: near-IR	[0-1]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_rhosnir', start = ipft, count = 1,
-                   vals=pft[v])
-       }
 
-       if(var == "wood_reflect_vis"){      # Stem reflectance: visible	[0-1]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_rhosvis', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "leaf_trans_nir"){        # Leaf transmittance: near-IR
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_taulnir', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "leaf_trans_vis"){        # Leaf transmittance: visible	pft
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_taulvis', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "wood_trans_nir"){        # Stem transmittance: near-IR
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_tausnir', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "wood_trans_vis"){        # Stem transmittance: visible
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_tausvis', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "orient_factor"){         # Leaf/stem orientation index	[-0/4 <xl< 0.6], fates_xl:valid_range = -1., 1. ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_xl', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "wood_density"){         # Wood Specific Gravity (ie density of wood relative to density of water),
-                                          #fates_wood_density:long_name = "mean density of woody tissue in plant" ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_wood_density', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "roota_par"){            # CLM rooting distribution parameter [1/m]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='roota_par', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rootb_par"){            # CLM rooting distribution parameter [1/m] 
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rootb_par', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       #if(var == "gsmax"){         # Maximum stomatal conductance [m s-1]  -- removed??
-       #  ncdf4::ncvar_put(nc=fates.param.nc, varid='gsmax', start = ipft, count = 1,
-       #            vals=pft[v])
-       #}
-       if(var == "psi_stomata_closure"){         # Soil water potential at full stomatal closure	[mm]
-                                                 # fates_smpsc:long_name = "Soil water potential at full stomatal closure" ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_smpsc', start = ipft, count = 1,
-                   vals=PEcAn.utils::ud_convert(pft[v],"m","mm"))
-       }
-       if(var == "psi_stomata_open"){            # Soil water potential at full stomatal opening	pft	[mm]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_smpso', start = ipft, count = 1,
-                   vals=PEcAn.utils::ud_convert(pft[v],"m","mm"))
-       }
-       
+
        ## --- update these to match new FATES hydro code when that code-base is added to FATES master -- ##
-       if(var == "root_bulk_modulus"){         # coarse root bulk elastic modulus (εroot)	[MPa] - NOT IN FATES ANYMORE??
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='epsil_root', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "sapwood_bulk_modulus"){         # sapwood bulk elastic modulus (εstem)	[MPa] - NOT IN FATES ANYMORE??
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='epsil_stem', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "leaf_bulk_modulus"){         # leaf bulk elastic modulus (εleaf) [MPa] - NOT IN FATES ANYMORE??
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='epsil_leaf', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "root_osmotic_potential"){         # coarse root osmotic potential at full turgor (πoroot)	[MPa] - NOT IN FATES ANYMORE??
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='pinot_root', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "sapwood_osmotic_potential"){         # sapwood osmotic potential at full turgor (πostem) [MPa]  - NOT IN FATES ANYMORE??
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='pinot_stem', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "leaf_osmotic_potential"){         # leaf osmotic potential at full turgor (πoleaf) [MPa]  - NOT IN FATES ANYMORE??
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='pinot_leaf', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "kmax_leaf"){         # Maximum leaf hydraulic conductivity per unit leaf area [mmol m-2 s-1 Mpa-1]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='kmax_leaf', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "kmax_root"){         # Maximum root hydraulic conductivity per unit xs sapwood [kg m-1 s-1 Mpa-1]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='kmax_root', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "kmax_stem"){         # Maximum stem hydraulic conductivity per unit xs sapwood area	[kg m-1 s-1 Mpa-1]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='kmax_stem', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "p50_gs"){         # leaf water potential at 50% loss of stomatal conductance (Pgs50)	[MPa]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='p50_gs', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "p50_leaf"){         # leaf water potential at 50% loss of leaf hydraulic conductivity (P50leaf)	pft	[MPa]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='p50_leaf', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "p50_root"){         # root water potential at 50% loss of root hydraulic conductivity	[MPa]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='p50_root', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "p50_stem"){         # stem water potential at 50% loss of stem hydraulic conductivity [MPa]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='p50_stem', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "water_content_TLP_root"){         # coarse root relative water content at turgor loss (RWCtlproot)
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rwctlp_root', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "water_content_TLP_sapwood"){         # sapwood relative water content at turgor loss
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rwctlp_stem', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "water_content_TLP_leaf"){         # leaf relative water content at turgor loss
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rwctlp_leaf', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "leafp_min"){         # Minimum leaf water potential [MPa]
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='leafp_min', start = ipft, count = 1,
-                   vals=pft[v])
-       }
        ## --- update these to match new FATES hydro code when that code-base is added to FATES master -- ##
        
-       if(var == "clone_alloc"){         # A carbon allocation that is added on to seed_alloc for trees larger than dbh_max.	[0-1]
-                                         # fates_clone_alloc:long_name = "fraction of available carbon balance allocated to clonal reproduction"
-         ncvar_put(nc=fates.param.nc, varid='fates_clone_alloc', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "storage_target_ratio"){         # The target fraction of storage carbon over leaf carbon	[0-1]
-                                                  # fates_cushion:long_name = "maximum size of storage C pool, relative to maximum size of leaf C pool" ;
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_cushion', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "crown_depth_fraction"){         # Crown depth fraction of a cohort relative to its total height [0-1]
-                                                  # fates_crown_depth_frac:long_name = "the depth of a cohorts crown as a fraction of its height"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_crown_depth_frac', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "hydraulic_stress_mortality"){         # The mortality rate imposed on plants meeting hydraulic stress failure condition [1/yr]
-                                                        # fates_stress_mort:long_name = "mortality rate associated with hydraulic stress exceedence"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_stress_mort', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "PPA_comp_exclusion"){         # Competetive exclusion parameter for weighting demotions from the upper canopy classification in PPA
-                                                #fates_comp_excln:long_name = "weighting factor (exponent on dbh) for canopy layer exclusion and promotion"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_comp_excln', start = ipft, count = 1,
-                   vals=pft[v])
-       }
        #if(var == "grass_spread"){         # Controls the area footprint of a grass pft, as a function of number density and dbh
        #  ncdf4::ncvar_put(nc=fates.param.nc, varid='grass_spread', start = ipft, count = 1,
        #            vals=pft[v])
        #}
-       if(var == "leaf_stor_priority"){         # Leaf turnover vs labile carbon use prioritisation. This is the fraction of maintenance demand that 
-                                                # will be replenished at all costs and before storage is filled.	pft	[0-1]
-                                                # fates_leaf_stor_priority:long_name = "factor governing priority of replacing storage with NPP"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_leaf_stor_priority', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "understory_treefall_mortality"){         # The fraction of trees in understory that die from impacts of large treefalls. 
-                                                           # In the model this is not a rate 1/year, so we need to convert it
-                                                           # fates_understorey_death:long_name = "fraction of plants in understorey cohort impacted by overstorey tree-fall"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_understorey_death', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "displar"){                              # fates_displar:long_name = "Ratio of displacement height to canopy top height"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_displar', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "z0mr"){                                 # Ratio of momentum roughness length to canopy top height
-                                                          # fates_z0mr:long_name = "Ratio of momentum roughness length to canopy top height"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_z0mr', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "inital_stem_density"){         # Stem density of different PFTs during a bare ground initialization.	[/m2]
-                                                 # fates_initd:long_name = "initial seedling density for a cold-start near-bare-ground simulation"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_initd', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "bark_scaler"){         # Fraction of tree diameter that is bark. Used in fire.	[0-1]
-                                         # fates_bark_scaler:long_name = "the thickness of a cohorts bark as a fraction of its dbh"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_bark_scaler', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "crown_kill"){                    ## SPITFIRE: Mortality from fire scorching susceptibility parameter
-                                                   # fates_crown_kill:long_name = "fire parameter, see equation 22 in Thonicke et al 2010"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_crown_kill', start = ipft, count = 1,
-                   vals=pft[v])  
-       }
+       
        
 
        ## BINARY FLAGS: These should be set-able by PEcAn but not sampled
@@ -627,161 +342,17 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
        #  ncdf4::ncvar_put(nc=fates.param.nc, varid='c3psn', start = ipft, count = 1,
        #            vals=as.numeric(pft[v] == 3))
        #}
-       if(var == "crop"){         # Binary crop flag: 0. = not crop, 1. = crop
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "irrigated"){         # Binary Irrigated PFT flag
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='irrigated', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "cold_deciduous"){         # Binary flag for seasonal-deciduous leaf habit (0-not,1-it is)
-                                            # fates_season_decid:flag_meanings = "NOT seasonal-deciduous"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_season_decid', start = ipft, count = 1,
-                   vals=pft[v])
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_evergreen', start = ipft, count = 1,
-                   vals=0)
-       }
-       if(var == "stress_deciduous"){         # Binary flag for stress-deciduous leaf habit (0-not,1-it is)
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_stress_decid', start = ipft, count = 1,
-                   vals=pft[v])
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_evergreen', start = ipft, count = 1,
-                   vals=0)
-       }
-       if(var == "woody"){         # Binary woody lifeform flag (0-is not woody, 1-it is woody)
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_woody', start = ipft, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "evergreen"){         # Binary flag for evergreen leaf habit
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_evergreen', start = ipft, count = 1,
-                   vals=pft[v])
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_stress_decid', start = ipft, count = 1,
-                   vals=0)
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_season_decid', start = ipft, count = 1,
-                   vals=0)
-       }
+       
        
        ## ALLPFT indexed (size = 1) 
-       if(var == "veg_respiration_Q10"){            ## Q10 for maintenance respiration. CLM param. q10_mr(allpfts)
-         ncdf4::ncvar_put(nc=clm.param.nc, varid='q10_mr', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "CelluloseS"){            ## Cellulose fraction for CWD
-         ncvar_put(nc=fates.param.nc, varid='fates_cwd_fcel', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "s_lignin"){            ## Lignin fraction for CWD
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_cwd_flig', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "c2n_som1"){            ## C:N for SOM pool 1. CLM param
-         ncdf4::ncvar_put(nc=clm.param.nc, varid='cn_s1_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "c2n_som2"){            ## C:N for SOM pool 2. CLM param
-         ncdf4::ncvar_put(nc=clm.param.nc, varid='cn_s2_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "c2n_som3"){            ## C:N for SOM pool 3. CLM param
-         ncdf4::ncvar_put(nc=clm.param.nc, varid='cn_s3_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "cnscalefactor"){            ## Scale factor on CN decomposition for assigning methane flux . CLM param
-         ncdf4::ncvar_put(nc=clm.param.nc, varid='cnscalefactor', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "decomp_depth_efolding"){            ## e-folding depth for reduction in decomposition. 
-                                                      ## Set to large number for depth-independance. CLM param
-         ncdf4::ncvar_put(nc=clm.param.nc, varid='decomp_depth_efolding', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "CWD_fragmentation_rate"){            ## Fragmentation rate for CWD. units = "1/day", CLM param
-         ncvar_put(nc=clm.param.nc, varid='k_frag', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rf_cwdl2_bgc"){            ## respiration fraction from CWD to litter 2 - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rf_cwdl2_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rf_cwdl3_bgc"){            ## respiration fraction from CWD to litter 3 - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rf_cwdl3_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rf_l1s1_bgc"){            ## Respiration fraction for litter 1 -> SOM 1 - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rf_l1s1_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rf_l2s1_bgc"){            ## respiration fraction litter 2 to SOM 1 - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rf_l2s1_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rf_l3s2_bgc"){            ## respiration fraction from litter 3 to SOM 2 - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rf_l3s2_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rf_s2s1_bgc"){            ## respiration fraction SOM 2 to SOM 1 - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rf_s2s1_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rf_s2s3_bgc"){            ## Respiration fraction for SOM 2 -> SOM 3 - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rf_s2s3_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "rf_s3s1_bgc"){            ## respiration fraction SOM 3 to SOM 1 - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='rf_s3s1_bgc', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "Q10_frozen_soil"){            ## Separate q10 for frozen soil respiration rates - REMOVED FROM FATES PARAMS?
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='froz_q10', start = 1, count = 1,
-                   vals=pft[v])
-       }
+       #if(var == "veg_respiration_Q10"){            ## Q10 for maintenance respiration. CLM param. q10_mr(allpfts)
+         #ncdf4::ncvar_put(nc=clm.param.nc, varid='q10_mr', start = 1, count = 1,
+                   #vals=pft[v])
+       #}
        
        ## NONE indexed
        ##   -- FIRE
-       if(var == "max_fire_duration"){            ## maximum duration of fire	none	hours
-                                                  # fates_max_durat:long_name = "spitfire parameter, fire maximum duration, Equation 14 Thonicke et al 2010"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_max_durat',vals=pft[v])
-       }
-       if(var == "nfires"){            ## The number of fires initiated per m2 per year, from lightning and humans
-                                       # fates_nignitions:long_name = "number of daily ignitions (nfires = nignitions*FDI*area_scaling)"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_nignitions',vals=pft[v])
-       }
-       if(var == "fuel_energy"){            ## energy content of fuel [kj kg-1]
-                                            # fates_fuel_energy:long_name = "pitfire parameter, heat content of fuel"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_fuel_energy',vals=pft[v])
-       }
-       if(var == "fuel_particle_density"){            ## particle density of fuel [kg m-3]
-                                                      # fates_part_dens:long_name = "spitfire parameter, oven dry particle density, Table A1 Thonicke et al 2010"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_part_dens',vals=pft[v])
-       }
-       if(var == "durat_slope"){            ## SPITFIRE: change in fire duration with fire danger index. from Canadian Forest Service	
-                                            # fates_durat_slope:long_name = "spitfire parameter, fire max duration slope, Equation 14 Thonicke et al 2010"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_durat_slope',vals=pft[v])
-       }
-       if(var == "miner_damp"){            ## SPITFIRE mineral dampening coefficient
-                                           # fates_miner_damp:long_name = "spitfire parameter, mineral-dampening coefficient EQ A1 Thonicke et al 2010 "
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_miner_damp',vals=pft[v])
-       }
-       if(var == "fuel_minerals"){            ## mineral content of fuel
-                                              # fates_miner_total:long_name = "spitfire parameter, total mineral content, Table A1 Thonicke et al 2010"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_miner_total',vals=pft[v])
-       }
-       if(var == "alpha_scorch_height"){            ## SPITFIRE scorch height parameter
-                                                    # fates_alpha_SH:long_name = "spitfire parameter, alpha scorch height, Equation 16 Thonicke et al 2010"
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_alpha_SH',vals=pft[v])
-       }
-       if(var == "fdi_a"){            ## SPITFIRE Constant in calculation of dewpoint for Fire Danger Index (FDI)
-                                      # fates_fdi_a:long_name = "spitfire parameter (unknown) "
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_fdi_a',vals=pft[v])
-       }
-       if(var == "fdi_alpha"){            ## SPITFIRE Constant in calculation of dewpoint for Fire Danger Index (FDI)
-                                          # fates_fdi_alpha:long_name = "spitfire parameter, EQ 7 Venevsky et al. GCB 2002,(modified EQ 8 Thonicke et al. 2010) "
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_fdi_alpha',vals=pft[v])
-       }
-       if(var == "fdi_b"){            ## SPITFIRE Constant in calculation of dewpoint for Fire Danger Index (FDI)
-                                      # fates_fdi_b:long_name = "spitfire parameter (unknown) "
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_fdi_b',vals=pft[v])
-       }
+
        ##   -- CANOPY
        #if(var == "canopy_max_spread"){            ## Maximum allowable "dynamic ratio of dbh to canopy area" for cohorts in closed canopies.	-	[cm/m2]
        #  ncdf4::ncvar_put(nc=fates.param.nc, varid='maxspread',vals=pft[v])
@@ -804,32 +375,16 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
        # SAV	Surface Area to Volume Ratio of fuel class 	litterclass	cm-1
        
        ## NCWD dimensioned       Size:4
-       if(var == "CWD_frac1"){            ##Fraction of coarse woody debris (CWD) that is moved into each of the four woody fuel classes
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_CWD_frac', start = 1, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "CWD_frac2"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_CWD_frac', start = 2, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "CWD_frac3"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_CWD_frac', start = 3, count = 1,
-                   vals=pft[v])
-       }
-       if(var == "CWD_frac4"){
-         ncdf4::ncvar_put(nc=fates.param.nc, varid='fates_CWD_frac', start = 4, count = 1,
-                   vals=pft[v])
-       }
        
        
-     } ## end loop over VARIABLES
-   } ## end loop over PFTs
+     #} ## end loop over VARIABLES
+   #} ## end loop over PFTs
    #ncdf4::nc_close(param.nc)
-   ncdf4::nc_close(clm.param.nc)
-   ncdf4::nc_close(fates.param.nc)
+   #ncdf4::nc_close(clm.param.nc)
+   #ncdf4::nc_close(fates.param.nc)
    
 #   ## Write SETTINGS file
 #     
-}
+#}
 #---------------------------------------------------------------------------------------------------------------------#
 ### EOF

From 69af60e4fb8cf795e9eba064d2d5646ec36dcbc9 Mon Sep 17 00:00:00 2001
From: Yisreal <huyucong34@gmail.com>
Date: Tue, 10 Sep 2024 05:11:43 +0800
Subject: [PATCH 2/4] remove extra lines

---
 models/fates/R/write.configs.FATES.R | 27 ++++++---------------------
 1 file changed, 6 insertions(+), 21 deletions(-)

diff --git a/models/fates/R/write.configs.FATES.R b/models/fates/R/write.configs.FATES.R
index 67d82a4496..e04bbfb073 100644
--- a/models/fates/R/write.configs.FATES.R
+++ b/models/fates/R/write.configs.FATES.R
@@ -10,20 +10,6 @@
 ##' @export
 ##' @author Mike Dietze, Shawn Serbin
 ##-------------------------------------------------------------------------------------------------# # nolint
-
-# example trait.values list
-trait.values <- list()
-trait.values$temperate.coniferous <- list()
-trait.values$env <- list()
-
-tc_traits <- as.data.frame(matrix(c(9999, 8888), nrow=1, ncol=2))
-colnames(tc_traits) <- c("leaf_turnover_rate", "veg_respiration_Q10")
-# Fates names for these params are "fates_leaf_long", "q10_mr"
-
-trait.values$temperate.coniferous <- tc_traits
-settings <- './test.fates.xml'
-run.id <- 'test_oneyear'
-
 # example trait.values list
 
 write.config.FATES <- function(defaults, trait.values, settings, run.id){
@@ -49,7 +35,7 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
    ## this needs to be generalized to fractional years, but accounting for 365 day year
    start_date <- as.Date(settings$run$start.date)
    end_date   <- as.Date(settings$run$end.date)
-   stop_n     <- as.numeric(end_date - start_date, units="days") - PEcAn.utils::n_leap_day(start_date,end_date) + 1  
+   stop_n     <- as.numeric(end_date - start_date, units="days") #- PEcAn.utils::n_leap_day(start_date,end_date) + 1  
    
    ##-----------------------------------------------------------------------##
    ##                                                                       ##
@@ -104,7 +90,7 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
      #met <- gsub('@MET_FILES@',paste(met.files,collapse = "\n"), met)
      #writeLines(met, con=file.path(local.rundir, "datm.streams.txt.PEcAn_met"))
      
-   }
+   #}
 #   ... need to set this up so that if MET is blank it can run with default CLM met
 #   ... fill in this template, the met template, and then have jobs.sh put them in the right place. 
 #   ... Test, then adjust DB to have met required
@@ -120,7 +106,8 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
    if (!is.null(settings$model$jobtemplate) && file.exists(settings$model$jobtemplate)) {
      jobsh <- readLines(con=settings$model$jobtemplate, n=-1)
    } else {
-     jobsh <- readLines(con=system.file("template.job", package = "PEcAn.FATES"), n=-1)
+     jobsh <- readLines("/Users/mac/Documents/pecan/models/fates/R/template.job")
+     #jobsh <- readLines(con=system.file("template.job", package = "PEcAn.FATES"), n=-1)
    }
    
  # create host specific settings
@@ -190,11 +177,9 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
    ## MET --> DATM
 #   jobsh <- gsub('@SITE_MET@', settings$run$inputs$met$path, jobsh)
    ## FOR FIRST STEP, CAN USE DEFAULT
-   
-   writeLines(jobsh, con=file.path(settings$rundir, run.id, "job.sh"))
+   writeLines(jobsh, file.path(settings$rundir, run.id, "job.sh"))
    Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
 
-write.config.FATES(default, trait.values, test.fates.xml, run.id)
 #   ## Write PARAMETER file
    
    ## COPY AND OPEN DEFAULT PARAMETER FILES
@@ -385,6 +370,6 @@ write.config.FATES(default, trait.values, test.fates.xml, run.id)
    
 #   ## Write SETTINGS file
 #     
-#}
+}
 #---------------------------------------------------------------------------------------------------------------------#
 ### EOF

From b169a7a6d6883514e14a312d316f18e02990bde0 Mon Sep 17 00:00:00 2001
From: Yisreal <huyucong34@gmail.com>
Date: Tue, 24 Sep 2024 21:50:03 +0800
Subject: [PATCH 3/4] update model_info.json for fates

---
 models/fates/model_info.json | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 models/fates/model_info.json

diff --git a/models/fates/model_info.json b/models/fates/model_info.json
new file mode 100644
index 0000000000..50c853d8f1
--- /dev/null
+++ b/models/fates/model_info.json
@@ -0,0 +1,16 @@
+{
+  "name": "FATES",
+  "type": "FATES",
+  "version": "@VERSION@",
+  "binary": "@BINARY@",
+  "description": "FATES is a numerical terrestrial ecosystem model, which is an external module running in the given “Host Land Model”, such as CLM-CTSM, E3SM and ELM.",
+  "creator": "Rob Kooper <kooper@illinois.edu>",
+  "contributors": [],
+  "links": {
+    "source": "https://github.com/NGEET/fates",
+    "issues": "https://github.com/NGEET/fates/issues",
+    "documentation": "https://fates-users-guide.readthedocs.io/en/latest/"
+  },
+  "inputs": {},
+  "bibtex": []
+}

From dd2feced40b2b11b17617e626e7a3559d4e0c5f9 Mon Sep 17 00:00:00 2001
From: Yisreal <huyucong34@gmail.com>
Date: Tue, 24 Sep 2024 21:51:10 +0800
Subject: [PATCH 4/4] Initially update Dockerfile of fates from sipnet

---
 models/fates/Dockerfile | 42 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 models/fates/Dockerfile

diff --git a/models/fates/Dockerfile b/models/fates/Dockerfile
new file mode 100644
index 0000000000..36ce339541
--- /dev/null
+++ b/models/fates/Dockerfile
@@ -0,0 +1,42 @@
+# this needs to be at the top, what version are we building
+ARG IMAGE_VERSION="latest"
+
+# ----------------------------------------------------------------------
+# BUILD SIPNET BINARY
+# ----------------------------------------------------------------------
+FROM pecan/models:${IMAGE_VERSION} as model-binary 
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# download, unzip and build sipnet
+WORKDIR /src
+RUN git clone https://github.com/PecanProject/fates.git \
+    && cd sipnet \
+    && if [ "${MODEL_VERSION}" != "git" ]; then git checkout ${MODEL_VERSION}; fi \
+    && make
+
+########################################################################
+
+# ----------------------------------------------------------------------
+# BUILD PECAN FOR FATES
+# ----------------------------------------------------------------------
+FROM pecan/models:${IMAGE_VERSION} 
+
+
+# ----------------------------------------------------------------------
+# SETUP FOR SPECIFIC SIPNET VERSION
+# ----------------------------------------------------------------------
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# Setup model_info file
+COPY model_info.json /work/model.json
+RUN sed -i -e "s/@VERSION@/${MODEL_VERSION}/g" \
+           -e "s#@BINARY@#/usr/local/bin/fates.${MODEL_VERSION}#g" /work/model.json
+
+# COPY sipnet binary
+COPY --from=model-binary /src/CESM/fates /usr/local/bin/fates.${MODEL_VERSION} 
+
+# /src/CESM/fates?