Update write.configs.FATES.R

CITATION.cff

@@ -120,9 +120,7 @@ authors:
   - given-names: Eric R. Scott
     affiliation: University of Arizona
     orcid: 'https://orcid.org/0000-0002-7430-7879'
-  - given-names: Harunobu Ishii
-    affiliation: Boston University Software & Application Innovation Lab(SAIL)
-
+
 preferred-citation:
   type: article
   title: Facilitating feedbacks between field measurements and ecosystem models

docker-compose.dev.yml

@@ -2,6 +2,8 @@
 # 
 # docker-compose -f docker-compose.yml -f docker-compose.dev.yml
 
+version: '3.2'
+
 services:
 
   # web application. This expects the config.php to be copied from docker/web

docker-compose.https.yml

@@ -1,4 +1,5 @@
 # Use this file to enable https
+version: "3.2"
 
 services:
   traefik:

docker-compose.yml

@@ -1,3 +1,5 @@
+version: "3.2"
+
 services:
 
   # webserver to handle all traffic. This can use let's encrypt to generate a SSL cert.

docker/docker-compose.example.yml

@@ -1,3 +1,7 @@
+# you need a version entry, and this should be the same version as the
+# docker-compose.yml file.
+version: "3"
+
 # if you change any of the services you will need the services header.
 services:
 

models/fates/R/model2netcdf.FATES.R

@@ -32,7 +32,7 @@
 model2netcdf.FATES <- function(outdir, sitelat, sitelon, start_date, end_date, vars_names, pfts){
   ## Tips: matched_var could be expanded for more selected variables
   matched_var <- tibble::tribble(
-    ~fatesname, ~pecanname, ~pecanunits, ~longname,
+    ~fatesname,~pecanname,~pecanunits,~longname,
     "FATES_GPP_PF","GPP","kgC m-2 s-1","Gross Primary Productivity", 
     "FATES_NPP_PF","NPP","kg m-2 yr-1", "Total PFT-level NPP in kg carbon per m2 land area per second",
     "NEE","NEE","kgC m-2 s-1", "Net Ecosystem Exchange of carbon, includes fire and hrv_xsmrpool",

models/fates/R/test.fates.xml

@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<pecan>
+  <outdir>pecan</outdir>
+  <rundir>/pecan/models/fates/data</rundir>
+  <host>
+    <rundir>/pecan/models/fates</rundir>
+    <ourdir>/pecan/models/fates/out</outdir>
+  </host>
+  <database>
+    <bety>
+      <driver>PostgreSQL</driver>
+      <user>bety</user>
+      <password>bety</password>
+      <host>localhost</host>
+      <dbname>bety</dbname>
+      <write>FALSE</write>
+    </bety>
+  </database>
+  <pfts>
+    <pft>
+      <name>temperate.coniferous</name> ## 
+    </pft>
+  </pfts>
+
+  <model>
+    <binary>/pecan/models/fates/test_oneyear</binary> #
+    <type>FATES</type>
+    <prerun>?</prerun>
+    <postrun>?</postrun>
+  </model>
+
+  <run>
+    <site>
+      <id>SOD1</id> #772
+      <lat>26.6385</lat>
+      <lon>67.3623</lon>
+    </site>
+    <inputs>
+      <met>/data/sites/niwot/niwot.clim</met> #
+    </inputs>
+    <start.date>2002-01-01 00:00:00</start.date>
+    <end.date>2005-12-31 00:00:00</end.date>
+    <host>
+      <name>localhost</name>
+    </host>
+    <dbfiles>pecan/dbfiles</dbfiles>
+  </run>
+</pecan>