Merge branch 'master' into ORG81-Add-formatting-auto-checks

Author: Alomir

.gitignore

@@ -1,7 +1,8 @@
 # build artifacts and executables
+# /sipnet instead of just sipnet to NOT ignore test dirs
 *.o
 estimate
-sipnet
+/sipnet
 subsetData
 transpose
 .doxygen.stamp
@@ -10,10 +11,6 @@ transpose
 docs/html
 docs/latex
 
-.DS_Store
-.Rproj.user
-.Rhistory
-
 # System-specific files
 .DS_Store
 .Rproj.user

Makefile

@@ -26,7 +26,7 @@ DOXYFILE = docs/Doxyfile
 DOXYGEN_HTML_DIR = docs/html
 DOXYGEN_LATEX_DIR = docs/latex
 
-all: estimate sipnet transpose subsetData document
+all: estimate sipnet transpose subsetData
 
 # Only update docs if source files or Doxyfile have changed
 document: .doxygen.stamp
@@ -64,21 +64,12 @@ SIPNET_LIB=libsipnet.a
 $(SIPNET_LIB): $(SIPNET_LIB)($(SIPNET_OFILES))
 	ranlib $(SIPNET_LIB)
 
-test: pretest $(SIPNET_TEST_DIRS) posttest $(SIPNET_LIB)
-
-pretest:
-	cp modelStructures.h modelStructures.orig.h
+test: $(SIPNET_TEST_DIRS) $(SIPNET_LIB)
 
 # The dash in the build command tells make to continue if there are errors, allowing cleanup
-$(SIPNET_TEST_DIRS): pretest $(SIPNET_LIB)
-	cp $@/modelStructures.h modelStructures.h
+$(SIPNET_TEST_DIRS): $(SIPNET_LIB)
 	-$(MAKE) -C $@
 
-# This is far from infallible, as model_structures.h will be in a bad place if a test
-# build step fails in a non-catchable way
-posttest: $(SIPNET_TEST_DIRS)
-	mv modelStructures.orig.h modelStructures.h
-
 testrun: $(SIPNET_TEST_DIRS_RUN)
 
 $(SIPNET_TEST_DIRS_RUN):
@@ -91,7 +82,7 @@ $(SIPNET_TEST_DIRS_CLEAN):
 	$(MAKE) -C $(basename $@) clean
 
 .PHONY: all clean document estimate sipnet transpose subsetData doxygen \
-		test $(SIPNET_TEST_DIRS) pretest posttest $(SIPNET_LIB) testrun \
+		test $(SIPNET_TEST_DIRS) $(SIPNET_LIB) testrun \
 		$(SIPNET_TEST_DIRS_RUN) testclean $(SIPNET_TEST_DIRS_CLEAN) help
 
 help:

events.c

@@ -20,7 +20,7 @@
  * - "till": Parameters = [SOM decomposition modifier, litter decomposition modifier]
  * - "plant": Parameters = [emergence lag (days), C (g/m²), N (g/m²)]]
  * - "harv": Parameters = [fraction aboveground removed, fraction belowground removed, ...]
- * See test examples in `tests/sipnet/test_events/`.
+ * See test examples in `tests/sipnet/test_events_infrastructure/`.
  */
 //
 
@@ -57,11 +57,11 @@ EventNode* createEventNode(
     case IRRIGATION:
       {
         double amountAdded;
-        int location;
+        int method;
         IrrigationParams *params = (IrrigationParams*)malloc(sizeof(IrrigationParams));
-        sscanf(eventParamsStr, "%lf %d", &amountAdded, &location);
+        sscanf(eventParamsStr, "%lf %d", &amountAdded, &method);
         params->amountAdded = amountAdded;
-        params->location = location;
+        params->method = method;
         event->eventParams = params;
       }
       break;
@@ -114,7 +114,7 @@ EventNode* createEventNode(
   return event;
 }
 
-enum EventType getEventType(char *eventTypeStr) {
+event_type_t getEventType(char *eventTypeStr) {
   if (strcmp(eventTypeStr, "irrig") == 0) {
     return IRRIGATION;
   } else if (strcmp(eventTypeStr, "fert") == 0) {

events.h

@@ -1,55 +1,63 @@
-//
-// Created by Michael J Longfritz on 11/8/24.
-//
-
 #ifndef EVENTS_H
 #define EVENTS_H
 
-#include "modelStructures.h"
-
-enum EventType {
+typedef enum EventType
+{
   FERTILIZATION,
   HARVEST,
   IRRIGATION,
   PLANTING,
   TILLAGE,
   UNKNOWN_EVENT
-};
+} event_type_t;
 
-typedef struct HarvestParams {
+typedef enum IrrigationMethod
+{
+  CANOPY = 0,
+  SOIL = 1,
+  FLOOD = 2 // placeholder, not supported yet
+} irrigation_method_t;
+
+typedef struct HarvestParams
+{
   double fractionRemovedAbove;
   double fractionRemovedBelow;
   double fractionTransferredAbove; // to surface litter pool
   double fractionTransferredBelow; // to soil litter pool
 } HarvestParams;
 
-typedef struct IrrigationParams {
+typedef struct IrrigationParams
+{
   double amountAdded;
-  int location; // 0=canopy, 1=soil
+  irrigation_method_t method;
 } IrrigationParams;
 
-typedef struct FertilizationParams {
+typedef struct FertilizationParams
+{
   double orgN;
   double orgC;
   double minN;
-  //double nh4_no3_frac; for two-pool version
+  // double nh4_no3_frac; for two-pool version
 } FertilizationParams;
 
-typedef struct PlantingParams {
+typedef struct PlantingParams
+{
   int emergenceLag;
   double addedC;
   double addedN;
 } PlantingParams;
 
-typedef struct TillageParams {
+typedef struct TillageParams
+{
   double fractionLitterTransferred;
   double somDecompModifier;
   double litterDecompModifier;
 } TillageParams;
 
 typedef struct EventNode EventNode;
-struct EventNode {
-  enum EventType type;
+struct EventNode
+{
+  event_type_t type;
   int loc, year, day;
   void *eventParams;
   EventNode *nextEvent;
@@ -62,7 +70,6 @@ struct EventNode {
  * if there are no events). It is assumed that the events are ordered first by location
  * and then by year and day.
  */
-EventNode** readEventData(char *eventFile, int numLocs);
-
+EventNode **readEventData(char *eventFile, int numLocs);
 
-#endif //EVENTS_H
+#endif // EVENTS_H

exitCodes.h

@@ -15,7 +15,7 @@ typedef enum {
   EXIT_CODE_SUCCESS = 0,
   EXIT_CODE_FAILURE = 1, // generic failure
   // code 2 typically has a special meaning, see above
-  EXIT_CODE_UNKNOWN_EVENT = 3
+  EXIT_CODE_UNKNOWN_EVENT_TYPE_OR_PARAM = 3
 } exit_code_t;
 
 #endif

sipnet.c

@@ -78,6 +78,12 @@
 // do we have a separate litter water layer, used for evaporation?
 // if complex water is off, then litter water is off: litter water layer wouldn't do anything
 
+#if LITTER_WATER & EVENT_HANDLER
+#error EVENT_HANDLER and LITTER_WATER may not both be activated
+#endif
+// We do not handle having both LITTER_WATER and EVENT_HANDLING on; this may
+// be implemented in a later phase
+
 #define LITTER_WATER_DRAINAGE 1 && (LITTER_WATER)
 // does water from the top layer drain down into bottom layer even if top layer not overflowing?
 // if litter water is off, then litter water drainage is off: litter water drainage wouldn't do anything
@@ -2271,7 +2277,7 @@ void updateTrackers(double oldSoilWater) {
     trackers.LAI = envi.plantLeafC/params.leafCSpWt;
     trackers.yearlyLitter += fluxes.leafLitter;
     trackers.plantWoodC = envi.plantWoodC;
-    	//note this variable is added for Howland forest multi-model comparison includes ONLY leaf litter
+    //note this variable is added for Howland forest multi-model comparison includes ONLY leaf litter
 
 
   // mean of soil wetness at start of time step at soil wetness at end of time step - assume linear
@@ -2298,9 +2304,28 @@ void processEvents() {
     switch (locEvent->type) {
       // Implementation TBD, as we enable the various event types
       case IRRIGATION:
-        // TBD
-          printf("Irrigation events not yet implemented\n");
-          break;
+        {
+          const IrrigationParams* irrParams = locEvent->eventParams;
+          const double amount = irrParams->amountAdded;
+          if (irrParams->method == CANOPY) {
+            // Part of the irrigation evaporates, and the rest makes it to the soil
+            // Evaporated fraction
+            const double evapAmount = params.immedEvapFrac * amount;
+            fluxes.immedEvap += evapAmount;
+            // Remainder goes to the soil
+            const double soilAmount = amount - evapAmount;
+            envi.soilWater += soilAmount;
+          }
+          else if (irrParams->method == SOIL) {
+            // All goes to the soil
+            envi.soilWater += amount;
+          }
+          else {
+            printf("Unknown irrigation method type: %d\n", irrParams->method);
+            exit(EXIT_CODE_UNKNOWN_EVENT_TYPE_OR_PARAM);
+          }
+        }
+        break;
       case PLANTING:
         // TBD
           printf("Planting events not yet implemented\n");
@@ -2319,7 +2344,7 @@ void processEvents() {
           break;
       default:
         printf("Unknown event type (%d) in processEvents()\n", locEvent->type);
-        exit(EXIT_CODE_UNKNOWN_EVENT);
+        exit(EXIT_CODE_UNKNOWN_EVENT_TYPE_OR_PARAM);
     }
 
     locEvent = locEvent->nextEvent;
@@ -2348,13 +2373,11 @@ void updateState() {
   soilDegradation();    // This updates all the soil functions
 
   #if MODEL_WATER // water pool updating happens here:
-
     #if LITTER_WATER // (2 soil water layers; litter water will only be on if complex water is also on)
         envi.litterWater += (fluxes.rain + fluxes.snowMelt - fluxes.immedEvap - fluxes.fastFlow
              - fluxes.evaporation - fluxes.topDrainage) * climate->length;
         envi.soilWater += (fluxes.topDrainage - fluxes.transpiration - fluxes.bottomDrainage)
         * climate->length;
-
     #else // LITTER_WATER = 0 (only one soil water layer)
       // note: some of these fluxes will always be 0 if complex water is off
         envi.soilWater += (fluxes.rain + fluxes.snowMelt - fluxes.immedEvap - fluxes.fastFlow