Merge branch 'PecanProject:develop' into SDA_observation

Makefile

@@ -44,6 +44,8 @@ MODELS_D := $(MODELS:%=.doc/%)
 MODULES_D := $(MODULES:%=.doc/%)
 ALL_PKGS_D := $(BASE_D) $(MODULES_D) $(MODELS_D)
 
+SRCS_TO_CLEAN := $(strip $(foreach d,$(ALL_PKGS),$(wildcard ${d}/src)))
+
 SETROPTIONS := "options(Ncpus = ${NCPUS})"
 
 EXPECTED_ROXYGEN_VERSION := 7.3.2
@@ -101,7 +103,7 @@ depends = .doc/$(1) .install/$(1) .check/$(1) .test/$(1)
 
 ### Rules
 
-.PHONY: all install check test document shiny \
+.PHONY: all install check test document clean shiny \
             check_base check_models check_modules document help
 
 all: install document
@@ -125,13 +127,19 @@ book:
 .doc .install .check .test .shiny_depends $(call depends,base) $(call depends,models) $(call depends,modules):
 	mkdir -p $@
 
+clean:
+	rm -rf .install .check .test .doc
+	for p in $(SRCS_TO_CLEAN); do \
+		find "$$p" \( -name \*.mod -o -name \*.o -o -name \*.so \) -delete; \
+	done
+
 help:
 	@echo "Usage: make [target]"
 	@echo ""
 	@echo "Examples:"
 	@echo "  make all"
 	@echo "  make document"
-	@echo "  make document modules/assim.sequential  # Generate documentation for a specific package"
+	@echo "  make .doc/modules/assim.sequential  # Generate documentation for a specific package"
 	@echo ""
 	@echo "Notes:"
 	@echo "  - Components not included: cable (models), data.mining and DART (modules)."
@@ -163,11 +171,6 @@ $(subst .doc/models/template,,$(MODELS_D)): .install/models/template
 # target need not be rebuilt when a prerequisite changes)
 include Makefile.depends
 
-clean: 
-	rm -rf .install .check .test .doc
-	find modules/rtm/src \( -name \*.mod -o -name \*.o -o -name \*.so \) -delete
-	find models/basgra/src \( -name \*.mod -o -name \*.o -o -name \*.so \) -delete
-
 .install/devtools: | .install
 	+ ./scripts/time.sh "devtools ${1}" Rscript -e ${SETROPTIONS} -e "if(!requireNamespace('devtools', quietly = TRUE)) install.packages('devtools')"
 	echo `date` > $@

docker-compose.prod.yml

@@ -73,6 +73,7 @@ services:
   # ----------------------------------------------------------------------
   bety:
     image: pecan/bety:${BETY_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -97,6 +98,7 @@ services:
   # PEcAn documentation as well as PEcAn home page
   docs:
     image: pecan/docs:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -152,6 +154,7 @@ services:
   executor:
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/executor:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -174,6 +177,7 @@ services:
   basgra:
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-basgra-basgra_n_v1.0:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -188,6 +192,7 @@ services:
   sipnet:
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-sipnet-git:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -203,6 +208,7 @@ services:
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-ed2-2.2.0:${PECAN_VERSION:-latest}
     restart: unless-stopped
+    platform: linux/amd64
     networks:
       - pecan
     environment:
@@ -216,6 +222,7 @@ services:
   maespa:
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-maespa-git:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan

docker-compose.yml

@@ -113,6 +113,7 @@ services:
   # ----------------------------------------------------------------------
   rstudio:
     hostname: rstudio
+    platform: linux/amd64
     image: pecan/base:${PECAN_VERSION:-latest}
     command: /work/rstudio.sh
     restart: unless-stopped
@@ -158,6 +159,7 @@ services:
   docs:
     hostname: docs
     image: pecan/docs:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -207,6 +209,7 @@ services:
     hostname: monitor
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/monitor:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -236,6 +239,7 @@ services:
     hostname: executor
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/executor:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -276,6 +280,7 @@ services:
     hostname: basgra
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-basgra-basgra_n_v1.0:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -292,6 +297,7 @@ services:
     hostname: sipnet-git
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-sipnet-git:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -322,6 +328,7 @@ services:
   # PEcAn MAESPA model runner
   maespa:
     hostname: maespa-git
+    platform: linux/amd64
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-maespa-git:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -340,6 +347,7 @@ services:
     hostname: biocro-0_95
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/model-biocro-0.95:${PECAN_VERSION:-latest}
+    platform: linux/amd64
     restart: unless-stopped
     networks:
       - pecan
@@ -357,6 +365,7 @@ services:
   # PEcAn DB Sync visualization
   dbsync:
     hostname: dbsync
+    platform: linux/amd64
     image: pecan/shiny-dbsync:${PECAN_VERSION:-latest}
     restart: unless-stopped
     networks:
@@ -380,6 +389,7 @@ services:
   # ----------------------------------------------------------------------
   api:
     hostname: api
+    platform: linux/amd64
     user: "${UID:-1001}:${GID:-1001}"
     image: pecan/api:${PECAN_VERSION:-latest}
     restart: unless-stopped
@@ -428,3 +438,4 @@ volumes:
   pecan:
   rstudio:
 
+

docker/depends/pecan_package_dependencies.csv

@@ -125,7 +125,6 @@
 "keras3",">= 1.0.0","modules/assim.sequential","Suggests",FALSE
 "knitr","*","base/visualization","Suggests",FALSE
 "knitr","*","models/biocro","Suggests",FALSE
-"knitr","*","models/ed","Suggests",FALSE
 "knitr","*","models/maat","Suggests",FALSE
 "knitr","*","modules/data.atmosphere","Suggests",FALSE
 "knitr","*","modules/priors","Suggests",FALSE
@@ -495,7 +494,6 @@
 "rlist","*","modules/assim.sequential","Suggests",FALSE
 "rmarkdown","*","base/visualization","Suggests",FALSE
 "rmarkdown","*","models/biocro","Suggests",FALSE
-"rmarkdown","*","models/ed","Suggests",FALSE
 "rmarkdown","*","models/maat","Suggests",FALSE
 "rmarkdown","*","modules/data.atmosphere","Suggests",FALSE
 "rmarkdown","*","modules/priors","Suggests",FALSE

models/ed/DESCRIPTION

@@ -57,13 +57,10 @@ Imports:
 Suggests:
     testthat (>= 1.0.2),
     devtools,
-    knitr,
-    rmarkdown,
     withr
 Additional_repositories: https://pecanproject.r-universe.dev/
 License: BSD_3_clause + file LICENSE
 Copyright: Authors
-VignetteBuilder: knitr, rmarkdown
 LazyData: true
 Encoding: UTF-8
 RoxygenNote: 7.3.2

models/lpjguess/R/adjust.biomass.LPJGUESS.R

@@ -6,13 +6,13 @@
 ##' adjustments to the litter pools.
 ##' 
 ##' @param individual A nested list which encapsulates an LPJ-GUESS 'Individual' as read from a binary state file
-##' @param rel.change A numeric by which to scale the density and C and N pools
+##' @param biomass.inc A numeric value specifying the biomass increment to be applied.
 ##' @param sla The SLA (specific leaf area) (per PFT parameter)
-##' @param k_latosa The leaf area to sapwood area ratio (per PFT parameter)
-##' @param k_allom2,k_allom3, Allometry coefficients (per PFT parameters)
 ##' @param wooddens Wood density (kgC/m^2) (per PFT parameter)
-##' @param crownarea_max Maximum allowed crown area (m^2)  (per PFT parameter)
 ##' @param lifeform An integer code for the lifeform of this individual (cohort): 1 = Tree, 2 = Grass
+##' @param k_latosa The leaf area to sapwood area ratio (per PFT parameter)
+##' @param k_allom2,k_allom3, Allometry coefficients (per PFT parameters)
+##' @param trace Logical; if TRUE, prints details of biomass adjustment process.
 ##' 
 ##' The changes in C pools are determined by the allocation.  The changes in the N pools are designed to 
 ##' maintain the pre-exisiing C:N ratios, so N is just scaled using the updated C with the initial C:N ratio.
@@ -21,13 +21,13 @@
 ##' 
 ##' Note that after this function is called the function \code{allometry} should be used to update the individual
 ##' and to check that the newly updated individual has a 'valid' allometry. The litter pools should also be updated.
-##' This is implemented in the \code{updateState} function following the call to this \code{adjustBiomass} function. 
+##' This is implemented in the \code{update.state.LPJGUESS} function following the call to this \code{adjust.biomass.LPJGUESS} function. 
 ##' 
 ##' 
 ##' @keywords internal
 ##' @return the scaled 'individual' (the initial nested list with update values)
 ##' @author Matthew Forrest
-adjust.biomass.LPJGUESS <- function(individual, rel.change,  sla, wooddens, lifeform, k_latosa, k_allom2, k_allom3){
+adjust.biomass.LPJGUESS <- function(individual, biomass.inc, sla, wooddens, lifeform, k_latosa, k_allom2, k_allom3, trace = TRUE){
 
   # dummy input values to the allocation function below
   # note that they are not actually updated by the function, the updated values are in the returned list
@@ -41,9 +41,12 @@ adjust.biomass.LPJGUESS <- function(individual, rel.change,  sla, wooddens, life
   exceeds_cmass <- 0
 
   # calculate the total biomass and the absolute change based on this
-  biomass.total <- individual$cmass_leaf+individual$cmass_root+individual$cmass_heart+individual$cmass_sap-individual$cmass_debt
-  biomass.inc <- (biomass.total * rel.change) - biomass.total
-
+  biomass.total <- TotalCarbon(individual)
+  rel.change <- (biomass.total + biomass.inc) / biomass.total
+  if(trace) {
+    print(paste(" ------- DURING BIOMASS ADJUSTMENT -------"))
+    print(paste(" ***** Total Biomass Increment =", biomass.inc))
+  }
 
   updated.pools <- allocation(
     # vegetation state

models/lpjguess/R/calculateGridcellVariablePerPFT.LPJGUESS.R

@@ -9,10 +9,12 @@
 ##' @param variable A character string specifying what variable to extract.  This can be chosen based on the LPJ-GUESS variable name
 ##' as recorded in the big list of list (that represents describes the model state in R).  Once special case is "biomass" which
 ##' returns the sum of "cmass_leaf", "cmass_root", "cmass_sap" and "cmass_heart"  
+##' @param pft.params A data frame containing PFT parameters such as allometric coefficients.
+##' @param min.diam Minimum tree diameter (in cm) required for inclusion in calculations.
 ##' @return  A numeric vector, with one entry per PFT
 ##' @export
 ##' @author Matthew Forrest
-calculateGridcellVariablePerPFT <- function(model.state, variable) {
+calculateGridcellVariablePerPFT <- function(model.state, variable, pft.params, min.diam = 5 ) {
 
   # nstands - should always be 1 but lets make sure
   nstands <- unlist(model.state$nstands)
@@ -34,19 +36,12 @@ calculateGridcellVariablePerPFT <- function(model.state, variable) {
 
     # arrays to store the aggregated gridcell level properties
     gc.sum <- numeric(length(model.state$Stand[[stand.counter]]$Standpft$active))
-
+    
     # loop through each patch
-    print(length(model.state$Stand[[stand.counter]]$Patch))
     for(patch.counter in 1:npatches) {
-
-
-      print("-------------------------------------------------------------------------------------")
-      print(paste("--------------------------------  PATCH ", patch.counter, " -------------------------------------"))
-      print("-------------------------------------------------------------------------------------")
-
 
       this.patch <- model.state$Stand[[stand.counter]]$Patch[[patch.counter]]
-
+      
       # pull out the number of individuals and a list of them   
       nindividuals <- length(this.patch$Vegetation)
       all.individuals <- this.patch$Vegetation$Individuals
@@ -55,54 +50,36 @@ calculateGridcellVariablePerPFT <- function(model.state, variable) {
       for(individual.counter in 1:length(all.individuals)) {
         this.individual <- all.individuals[[individual.counter]]
 
-        # print(paste("id = ", this.individual$indiv.pft.id))
-        # print(paste("leaf =" , this.individual$cmass_leaf))
-        # print(paste("root =" , this.individual$cmass_root))
-        # print(paste("sap =" , this.individual$cmass_sap))
-        # print(paste("heart =" , this.individual$cmass_heart)) 
-        # print(paste("debt =" , this.individual$cmass_debt)) 
-        print(paste("alive =" , this.individual$alive)) 
-        print(individual.counter)
-
-        if(this.individual$alive) {
+        # get PFT index and covert the PFT from '0-indexed' C++ style to '1-indexed' R style
+        this.pft.id <- this.individual$indiv.pft.id
+        pft.index <- this.pft.id + 1
+
+        # calculate diameter to exclude small trees (converted to cm)
+        diam = ((this.individual$height / pft.params[pft.index, "k_allom2"]) ^ (1.0 / pft.params[pft.index, "k_allom3"])) * 100
+        print(diam)
+        if(this.individual$alive && diam > min.diam) {
 
           # get the PFT ID
-          this.pft.id <- this.individual$indiv.pft.id
+
+
           if(!this.pft.id %in% active.PFTs) stop(paste0("Found individual of PFT id = ",this.pft.id, 
                                                         " but this doesn't seem to be active in the LPJ-GUESS run"))
 
-          # covert the PFT from '0-indexed' C++ style to '1-indexed' R style
-          pft.index <- this.pft.id+1
 
           # calculate the total cmass and density of individuals per PFT
           if(variable == "cmass") {
             gc.sum[pft.index] <- gc.sum[pft.index] + (this.individual$cmass_leaf+this.individual$cmass_root+this.individual$cmass_heart+this.individual$cmass_sap-this.individual$cmass_debt)/npatches
-
-
-            print(paste("id = ", this.individual$indiv.pft.id))
-            print(paste("leaf =" , this.individual$cmass_leaf))
-            print(paste("root =" , this.individual$cmass_root))
-            print(paste("sap =" , this.individual$cmass_sap))
-            print(paste("heart =" , this.individual$cmass_heart)) 
-            print(paste("debt =" , this.individual$cmass_debt)) 
-
-            print(gc.sum) 
-
-
-         }
+          }
+
           else if(variable == "nmass") {
             gc.sum[pft.index] <- gc.sum[pft.index] + ((this.individual$nmass_leaf+this.individual$nmass_root+this.individual$nmass_heart+
-                                                                 this.individual$nmass_sap+this.individual$nstore_labile+this.individual$nstore_longterm)/npatches)
-            #gc.sum[pft.index] <- gc.sum[pft.index] + ((this.individual$nmass_leaf+this.individual$nmass_root+this.individual$nmass_heart+
-            #                                                     this.individual$nmass_sap)/npatches)
-
-
-            #print(paste("leaf =" , this.individual$nmass_leaf))
-            #print(paste("root =" , this.individual$nmass_root))
-            #print(paste("sap =" , this.individual$nmass_sap))
-            #print(paste("heart =" , this.individual$nmass_heart))
-
+                                                         this.individual$nmass_sap+this.individual$nstore_labile+this.individual$nstore_longterm)/npatches)
           }
+
+          else if(variable == "AbvGrndWood") {
+            gc.sum[pft.index] <- gc.sum[pft.index] + (AbvGrndWood(this.individual)/npatches)
+          }
+
           else  gc.sum[pft.index] <- gc.sum[pft.index] + (this.individual[[variable]]/npatches)
 
         }
@@ -114,7 +91,7 @@ calculateGridcellVariablePerPFT <- function(model.state, variable) {
     }
 
 
-
+    
 
   }