Added CMEM as a model package

.gitignore

@@ -119,3 +119,4 @@ dbfiles/
 **/temperate.coniferous/
 *.sensitivity.analysis.*.pdf
 *.variance.decomposition.*.pdf
+models/rcmem/R/water_level_functions/data/Kopp_2014_projections_long.csv

CHANGELOG.md

@@ -9,6 +9,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 ## Unreleased
 
 ### Added
+- Added PEcAn.RCMEM model, no demo run yet, just an initial pull request
 - Added PEcAn.PEPRMT model, including a demo run with example data
 - Add `format_try_for_ma()` and `try_trait_mapping()` to `PEcAn.data.remote` to convert trait data from the external TRY database into the tabular format required by the PEcAn meta-analysis module (#3717).
 - Add function `qsub_sda()` for submitting SDA batch jobs by splitting a large number of sites into multiple small groups of sites (#3634).

CITATION.cff

@@ -129,6 +129,9 @@ authors:
     affiliation: National Institute of Technology, Tiruchirappalli
   - given-names: Om Kapale
     affiliation: Chatrapati Shahu Maharaj CSCOE, Maharashtra
+  - given-names: James R Holmquist
+    affiliation: Smithsonian Environmental Research Center
+    orcid: 'https://orcid.org/0000-0003-2546-6766'
 
 
 preferred-citation:

models/peprmt/demo_run/input_demo_mcmc_out/run/ENS-00001-US_DMG/README.txt

@@ -0,0 +1,16 @@
+runtype     : ensemble
+ workflow id :  2026-05-04-12-23-39 
+ ensemble id :  6fe7391ab410e3cf22e79721d1461505 
+ run         :  1 / 10 
+ run id      :  ENS-00001-US_DMG 
+ pft names   :  default default_mcmc 
+ model       :  PEPRMT 
+ model id    :  peprmt_0_1_0 
+ site        :  US_DMG 
+ site  id    :  US_DMG 
+ met         : data/met/ERA5_38N_121.5W/ERA5.8.2021-12-15.2024-12-19.dat
+ start date  :  2021-12-15 
+ end date    :  2024-12-19 
+ hostname    :  localhost 
+ rundir      :  /Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/run/ENS-00001-US_DMG 
+ outdir      :  /Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_DMG 

models/peprmt/demo_run/input_demo_mcmc_out/run/ENS-00001-US_DMG/job.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+
+
+mkdir -p /Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_DMG
+
+# Redirect output
+exec 3>&1
+exec &> "$(realpath /Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_DMG)/logfile.txt"
+
+# host specific setup
+
+
+# cdo setup
+# @CDO_SETUP@
+
+# Run PEPRMT
+Rscript \
+  -e 'dat <- read.csv(file.path("/Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/run/ENS-00001-US_DMG", "run_data.csv"))' \
+  -e 'res <- do.call(PEPRMT::run_PEPRMT, c(list(a0 = 0.744082512141497, a1 = 1.15544289485085, Ha = 119.589297901609, Hd = 93.6537118831357, Ea_SOM = 17.6939861598126, kM_SOM = 9907.39505784586, Ea_labile = 10.4679888669531, kM_labile = 94.4321891176514, Ea_SOM_CH4 = 83.3468674710418, kM_SOM_CH4 = 20.6126951904004, Ea_labile_CH4 = 87.3040938196751, kM_labile_CH4 = 21.0943910116999, Ea_oxi_CH4 = 91.3871460132901, kM_oxi_CH4 = 23.2262669730873, kI_SO4 = 100.248951010205, kI_NO3 = 2.46019191158601, wetland_type = 2),
+    list(data = dat)
+  ))' \
+  -e 'write.csv(res, file.path("/Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_DMG", "out.csv"), row.names = FALSE)'
+
+# convert output to PEcAn format
+Rscript -e 'PEcAn.PEPRMT::model2netcdf.PEPRMT(
+  outdir = "/Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_DMG",
+  sitelat = 38.0015,
+  sitelon = -121.6691,
+  start_date = "2021-12-15",
+  end_date = "2024-12-19",
+  delete_raw = FALSE
+)'

models/peprmt/demo_run/input_demo_mcmc_out/run/ENS-00001-US_EDN/README.txt

@@ -0,0 +1,16 @@
+runtype     : ensemble
+ workflow id :  2026-05-04-12-23-39 
+ ensemble id :  41e0ce8fdf11e1ba6e84415388012ec8 
+ run         :  1 / 10 
+ run id      :  ENS-00001-US_EDN 
+ pft names   :  default default_mcmc 
+ model       :  PEPRMT 
+ model id    :  peprmt_0_1_0 
+ site        :  US_EDN 
+ site  id    :  US_EDN 
+ met         : data/met/ERA5_37.5N_122W/ERA5.8.2018-04-03.2021-06-16.dat
+ start date  :  2018-04-03 
+ end date    :  2021-06-16 
+ hostname    :  localhost 
+ rundir      :  /Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/run/ENS-00001-US_EDN 
+ outdir      :  /Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_EDN 

models/peprmt/demo_run/input_demo_mcmc_out/run/ENS-00001-US_EDN/job.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+
+
+mkdir -p /Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_EDN
+
+# Redirect output
+exec 3>&1
+exec &> "$(realpath /Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_EDN)/logfile.txt"
+
+# host specific setup
+
+
+# cdo setup
+# @CDO_SETUP@
+
+# Run PEPRMT
+Rscript \
+  -e 'dat <- read.csv(file.path("/Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/run/ENS-00001-US_EDN", "run_data.csv"))' \
+  -e 'res <- do.call(PEPRMT::run_PEPRMT, c(list(a0 = 0.744082512141497, a1 = 1.15544289485085, Ha = 119.589297901609, Hd = 93.6537118831357, Ea_SOM = 17.6939861598126, kM_SOM = 9907.39505784586, Ea_labile = 10.4679888669531, kM_labile = 94.4321891176514, Ea_SOM_CH4 = 83.3468674710418, kM_SOM_CH4 = 20.6126951904004, Ea_labile_CH4 = 87.3040938196751, kM_labile_CH4 = 21.0943910116999, Ea_oxi_CH4 = 91.3871460132901, kM_oxi_CH4 = 23.2262669730873, kI_SO4 = 100.248951010205, kI_NO3 = 2.46019191158601, wetland_type = 2),
+    list(data = dat)
+  ))' \
+  -e 'write.csv(res, file.path("/Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_EDN", "out.csv"), row.names = FALSE)'
+
+# convert output to PEcAn format
+Rscript -e 'PEcAn.PEPRMT::model2netcdf.PEPRMT(
+  outdir = "/Users/jamesholmquist/GitHub/pecan/models/peprmt/demo_run/input_demo_mcmc_out/out/ENS-00001-US_EDN",
+  sitelat = 37.615,
+  sitelon = -122.114,
+  start_date = "2018-04-03",
+  end_date = "2021-06-16",
+  delete_raw = FALSE
+)'