newhall-1.6.4: (BASICSimulationModel) proposed changes to cryic/frigi…

…d logic - Use `fcd` not `1-fcd` for conversion MSAT->MSST for now, check `cs` expression - check `fcd` and `cs` usage -- make sure that the numerator and denominator of this ratios are correctly converted for different temperatures they may be used with and _documented_ as how they should be calculated - More adjustments - don't correct summer temperature threshold twice - JAR 1.6.4-3: clean and working without O/wet toggle
ncss-tech · Jul 23, 2023 · bc50806 · bc50806
1 parent 92388eb
commit bc50806
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Showing 6 changed files with 23 additions and 11 deletions.
diff --git a/R/AAAA.R b/R/AAAA.R
@@ -28,7 +28,7 @@ newhall_version <- function() {
   # rJava::.jpackage(pkgname, lib.loc = libname)
 
   # allow an option to add additional characters to jar file name (custom jar file)
-  jas <- getOption("jNSMR.JAR_SUFFIX", default = "-1.6.4")
+  jas <- getOption("jNSMR.JAR_SUFFIX", default = .get_default_suffix())
 
   # jnf0 <- .jnsm_jar_file()
   jnf <- .jnsm_jar_file(suffix = jas)
@@ -42,7 +42,7 @@ newhall_version <- function() {
 #' @importFrom rJava .jfield .jnew
 #' @importFrom utils packageVersion
 .onAttach <- function(libname, pkgname) {
-  jas <- getOption("jNSMR.JAR_SUFFIX", default = "-1.6.4")
+  jas <- getOption("jNSMR.JAR_SUFFIX", default = .get_default_suffix())
   jnf <- .jnsm_jar_file(suffix = jas)
   packageStartupMessage(paste0("jNSMR (", packageVersion("jNSMR"), ") -- R interface to the classic Newhall Simulation Model\nAdded JAR file (", basename(jnf), ") to Java class path."))
 
@@ -52,3 +52,5 @@ newhall_version <- function() {
     name = "NSM_VERSION"
   ))
 }
+
+.get_default_suffix <- function() "-1.6.4-3"
diff --git a/inst/java/newhall-1.6.4-1.jar b/inst/java/newhall-1.6.4-1.jar
diff --git a/inst/java/newhall-1.6.4-2.jar b/inst/java/newhall-1.6.4-2.jar
diff --git a/inst/java/newhall-1.6.4-3.jar b/inst/java/newhall-1.6.4-3.jar
diff --git a/java/org/psu/newhall/sim/BASICSimulationModel.java b/java/org/psu/newhall/sim/BASICSimulationModel.java
@@ -221,9 +221,11 @@ public static NewhallResults runSimulation(double[] temperature,
      }
 
      double dif = Math.abs(at1 - at2);
-     double cs = dif * (1.0D - fcd) / 2.0D;
-/**
-     * The cr[] arrays hold critera to determine temperature regime.  Then
+     // double cs = dif * (1.0D - fcd) / 2.0D; 
+     // TODO: check (1.0D - fcd) v.s. fcd v.s. cr[7] expression
+
+    /**
+     * The cr[] arrays hold criteria to determine temperature regime.  Then
      * the reg[] array holds the flags for each regime.  The last-most flag
      * that is true indicates the temp regime.
      */
@@ -232,14 +234,18 @@ public static NewhallResults runSimulation(double[] temperature,
     boolean[] reg = new boolean[13];
     cr[1] = tma < 0;                      // Mean annual air temp (MAAT) < 0C.
     cr[2] = 0 <= tma && tma < 8;          // 0C <= MAAT <= 8C.
-    cr[3] = (st - cs) < 15;               // Summer temp ave minus (summer/winter difference * (1 - SOIL_AIR_REL) * 0.5) < 15C.
-    cr[7] = (dif * fcd) > 5;              // Summer/winter difference * SOIL_AIR_REL > 5.  Change to 6?
+    // cr[3] = (st - cs) < 15;            // Summer temp ave minus (summer/winter difference * (1 - SOIL_AIR_REL) * 0.5) < 15C.
+                                          // TODO: where did latter part ^^ (... - SWD...) of this come from? Misread cryic crit 1?
+    cr[3] = st >= 0 && st < 15;           // "non-saturated, organic surface, mean _summer_ soil temperature between 0 and 8C/15C
+                                          // TODO: st upper limit depends on saturation, O horizon
+    cr[7] = (dif * fcd) >= 6;             // Summer/winter difference * SOIL_AIR_REL >= 6 
+                                          // NOTE: Taxonomy clearly states difference greater/equal than 6, not 5
     cr[8] = (tma >= 8) && (tma < 15);     // 8C <= MAAT < 15C.
     cr[9] = (tma >= 15) && (tma < 22);    // 15C <= MAAT < 22C.
     cr[10] = tma >= 22;                   // 22C <= MAAT.
     cr[11] = tma < 8;                     // MAAT < 8C.
     reg[1] = cr[1];                       // PERGELIC
-    reg[2] = cr[2] && cr[3];              // CRYIC
+    reg[2] = cr[2] && cr[3];              // CRYIC 
     reg[3] = cr[11] && !cr[3] && cr[7];   // FRIGID
     reg[4] = cr[8] && cr[7];              // MESIC
     reg[5] = cr[9] && cr[7];              // THERMIC
@@ -249,8 +255,8 @@ public static NewhallResults runSimulation(double[] temperature,
     reg[9] = cr[9] && !cr[7];             // ISOTHERMIC
     reg[10] = cr[10] && !cr[7];           // ISOHYPERTHERMIC
 
-     st -= cs;
-     wt += cs;
+     //st -= cs;
+     //wt += cs;
      dif = st - wt;
 
      String trr = "";
@@ -3349,7 +3355,7 @@ public static NewhallResults runSimulation(NewhallDataset dataset, double waterH
      boolean[] reg = new boolean[13];
      cr[1] = (tma < 0.0D);
      cr[2] = (0.0D <= tma && tma < 8.0D);
-     cr[3] = (st - cs < 15.0D);
+     cr[3] = (st * (1 - fcd) < 15.0D);
 /*  230 */     cr[7] = (dif * fcd > 5.0D);
      cr[8] = (tma >= 8.0D && tma < 15.0D);
      cr[9] = (tma >= 15.0D && tma < 22.0D);

diff --git a/misc/classes/META-INF/MANIFEST.MF b/misc/classes/META-INF/MANIFEST.MF
@@ -0,0 +1,4 @@
+Manifest-Version: 1.0
+Main-Class: org.psu.newhall.Newhall
+Created-By: 14.0.2 (Private Build)
+