Further changes for 0.5 deg LPJ data

debug_config.properties

 BASE_DIR=/Users/peteralexander/Documents/R_Workspace/UNPLUM
-YIELD_DIR=/Users/peteralexander/Documents/LURG/LPJ/yield_anpp_rcps-2016-01-29/rcp8p5_past_fert/output-2016-01-29
+#YIELD_DIR=/Users/peteralexander/Documents/LURG/LPJ/yield_anpp_rcps-2016-01-29/rcp8p5_past_fert/output-2016-01-29
 
-#YIELD_DIR=/Users/peteralexander/Documents/LURG/LPJ/output-2016-10-26.processed
-#SPATIAL_DIR_NAME=halfdeg
-#CELL_SIZE_X=0.5
-#ANPP_FILENAME=anpp.out.2011-2015
-#YIELD_FILENAME=yield.out.2011-2015
-#MIN_FERT_AMOUNT=0
-#MID_FERT_AMOUNT=200
-#MAX_FERT_AMOUNT=1000
-#FERT_AMOUNT_PADDING=4
+YIELD_DIR=/Users/peteralexander/Documents/LURG/LPJ/sam-03Nov2016
+SPATIAL_DIR_NAME=halfdeg
+CELL_SIZE_X=0.5
+ANPP_FILENAME=anpp.out.2011-2015
+YIELD_FILENAME=yield.out.2011-2015
+IRRIG_MAX_WATER_FILENAME=gsirrigation.out.2011-2015
+MIN_FERT_AMOUNT=0
+MID_FERT_AMOUNT=200
+MAX_FERT_AMOUNT=1000
+FERT_AMOUNT_PADDING=4
+PASTURE_FERT_RESPONSE_FROM_LPJ=false
 
 CLEANUP_GAMS_DIR=false
 
 # Properties for testing
 CHANGE_YIELD_DATA_YEAR=false
 CHANGE_DEMAND_YEAR=true
-#MAX_IMPORT_CHANGE=0.2
-#DEBUG_LIMIT_COUNTRIES=false
+DEBUG_LIMIT_COUNTRIES=false
 SSP_SCENARIO=SSP2_v9_130325
 
 END_TIMESTEP=18
@@ -26,6 +27,6 @@ TIMESTEP_SIZE=5
 NUM_CEREAL_CATEGORIES=5
 NUM_PASTURE_CATEGORIES=3
 
-LAND_CHANGE_COST=.6
+LAND_CHANGE_COST=.8
 
-#INTERPOLATE_OUTPUT_YEARS = true
+INTERPOLATE_OUTPUT_YEARS = false

src/ac/ed/lurg/ModelConfig.java

@@ -103,6 +103,7 @@ public class ModelConfig {
 	public static final int LPJG_MONITOR_TIMEOUT_SEC = getIntProperty("LPJG_MONITOR_TIMEOUT", 60*60*2);
 	public static final String ANPP_FILENAME = getProperty("ANPP_FILENAME", "anpp_plum.out");
 	public static final String YIELD_FILENAME = getProperty("YIELD_FILENAME", "yield_plum.out");
+	public static final boolean PASTURE_FERT_RESPONSE_FROM_LPJ = getBooleanProperty("PASTURE_FERT_RESPONSE_FROM_LPJ", true);;
 
 	public static final double CALIB_FACTOR_WHEAT = getDoubleProperty("CALIB_FACTOR_WHEAT", 0.966);
 	public static final double CALIB_FACTOR_MAIZE = getDoubleProperty("CALIB_FACTOR_MAIZE", 0.631);
@@ -158,14 +159,14 @@ public class ModelConfig {
 	
 	public static final double UNHANDLED_CROP_AREA = getDoubleProperty("UNHANDLED_CROP_AREA", 0.4);  // includes fruit veg forage crops set aside and failed crop
 	
-	public static final double OTHER_INTENSITY_COST = getDoubleProperty("OTHER_INTENSITY_COST", 0.3);
+	public static final double OTHER_INTENSITY_COST = getDoubleProperty("OTHER_INTENSITY_COST", 0.4);
 	public static final double OTHER_INTENSITY_PARAM = getDoubleProperty("OTHER_INTENSITY_PARAM", 5.0);
 
 	public static final double IRRIG_COST_SCALE_FACTOR = getDoubleProperty("IRRIG_COST_SCALE_FACTOR", 0.01);
 	public static final double FERTILISER_COST_PER_T = getDoubleProperty("FERTILISER_COST_PER_T", 0.87 * 1.4 * 2); // £900/t N *  1.4$/£ * 2NPK/N
 	public static final double FERTILISER_MAX_COST = FERTILISER_COST_PER_T * MAX_FERT_AMOUNT/1000;
 	
-	public static final double DOMESTIC_PRICE_MARKUP = getDoubleProperty("DOMESTIC_PRICE_MARKUP", 1.5);
+	public static final double DOMESTIC_PRICE_MARKUP = getDoubleProperty("DOMESTIC_PRICE_MARKUP", 1.0);
 	public static final double TRANSPORT_LOSSES = getDoubleProperty("TRANSPORT_LOSSES", 0.1);  // in international trade
 	public static final double TRADE_BARRIER_FACTOR = getDoubleProperty("TRADE_BARRIER_FACTOR", 1.5);  // price factor in international trade, transport cost and real trade barriers
 

src/ac/ed/lurg/country/gams/GamsRasterOptimiser.java

@@ -283,7 +283,7 @@ public class GamsRasterOptimiser {
 			CropType crop = CropType.WHEAT;
 
 			if (yresp != null && (yresp.getYieldMax(crop) < yresp.getYieldFertOnly(crop) || yresp.getYieldMax(crop) < yresp.getYieldIrrigOnly(crop))) {
-				logErrorWithCoord("Inconsistency F only:" + yresp.getYieldFertOnly(crop) + ", I only" + yresp.getYieldIrrigOnly(crop) + ", max " + yresp.getYieldMax(crop) + " at ", key, yieldRaster);
+				logErrorWithCoord(String.format("Inconsistency: F only: %.4f, I only %.4f, max %.4f at ", yresp.getYieldFertOnly(crop), yresp.getYieldIrrigOnly(crop), yresp.getYieldMax(crop)), key, yieldRaster);
 			}
 		}
 

src/ac/ed/lurg/landuse/IrrigationMaxAmountReader.java

@@ -19,7 +19,7 @@ public class IrrigationMaxAmountReader extends AbstractTabularRasterReader<Irrig
 	private YieldRaster yieldSurfaces;
 
 	public IrrigationMaxAmountReader(RasterSet<IrrigationItem> irigCosts, YieldRaster yieldSurfaces) {
-		super(" +", MIN_COLS, irigCosts);
+		super("\\s+", MIN_COLS, irigCosts);
 		this.yieldSurfaces = yieldSurfaces;
 	}
 		

src/ac/ed/lurg/types/FertiliserRate.java

@@ -3,7 +3,7 @@ package ac.ed.lurg.types;
 import ac.ed.lurg.ModelConfig;
 
 public enum FertiliserRate {
-	NO_FERT(String.format( "%0" + ModelConfig.FERT_AMOUNT_PADDING + ".0f", ModelConfig.MIN_FERT_AMOUNT)),
+	NO_FERT(ModelConfig.MIN_FERT_AMOUNT == 0 ? "0" : String.format( "%0" + ModelConfig.FERT_AMOUNT_PADDING + ".0f", ModelConfig.MIN_FERT_AMOUNT)),
 	MID_FERT(String.format("%0" + ModelConfig.FERT_AMOUNT_PADDING + ".0f", ModelConfig.MID_FERT_AMOUNT)),
 	MAX_FERT(String.format("%0" + ModelConfig.FERT_AMOUNT_PADDING + ".0f", ModelConfig.MAX_FERT_AMOUNT));
 

src/ac/ed/lurg/yield/LPJCropTypes.java

@@ -7,8 +7,8 @@ public enum LPJCropTypes {
 	SPRING_WHEAT("TeSW"),
 	RICE("TrRi"),
 	MAIZE("TeCo"),
-	PASTURE_C3("PC3GN"),
-	PASTURE_C4("PC4GN");
+	PASTURE_C3("PC3G"),
+	PASTURE_C4("PC4G");
 	
 	private String lpjName;
 	

src/ac/ed/lurg/yield/LPJYieldResponseMapReader.java

@@ -45,15 +45,17 @@ public class LPJYieldResponseMapReader {
 	
 	private void readNppFile(YieldRaster yieldRaster, String fileToRead) {  // Passed in YieldRaster is updated
 		
-		AbstractTabularRasterReader<YieldResponsesItem> nppReader = new AbstractTabularRasterReader<YieldResponsesItem>("[ |\t]+", 10, yieldRaster) {
+		AbstractTabularRasterReader<YieldResponsesItem> nppReader = new AbstractTabularRasterReader<YieldResponsesItem>("\\s+", 10, yieldRaster) {
 			protected void setData(RasterKey key, YieldResponsesItem item, Map<String, Double> rowValues) {
 				double adjFactor = 2 * 10 * ModelConfig.PASTURE_HARVEST_FRACTION;  // 2 for carbon units,  10 for kg/m2 to t/ha, and 0.5 for half grazed
-				
-				String lowFertString = YieldType.getYieldType(FertiliserRate.NO_FERT, IrrigationRate.NO_IRRIG).getFertIrrigString();
-				boolean isC3 = (getValueForCol(rowValues, LPJCropTypes.PASTURE_C3 + lowFertString) > getValueForCol(rowValues, LPJCropTypes.PASTURE_C4 + lowFertString));
-				
+								
 				for (FertiliserRate fert : FertiliserRate.values()) {
-					double pastureYield = (isC3 ? getValueForCol(rowValues, LPJCropTypes.PASTURE_C3 + fert.getId()) : getValueForCol(rowValues, LPJCropTypes.PASTURE_C4 + fert.getId())) * adjFactor;
+					double pastureYield;
+					if (ModelConfig.PASTURE_FERT_RESPONSE_FROM_LPJ)
+						pastureYield = Math.max(getValueForCol(rowValues, LPJCropTypes.PASTURE_C3 + "N" + fert.getId()), getValueForCol(rowValues, LPJCropTypes.PASTURE_C4 + "N" + fert.getId())) * adjFactor;
+					else
+						pastureYield = Math.max(getValueForCol(rowValues, LPJCropTypes.PASTURE_C3.toString()), getValueForCol(rowValues, LPJCropTypes.PASTURE_C4.toString())) * adjFactor;
+
 					item.setYield(YieldType.getYieldType(fert, IrrigationRate.NO_IRRIG), CropType.PASTURE, pastureYield);
 					item.setYield(YieldType.getYieldType(fert, IrrigationRate.MAX_IRRIG), CropType.PASTURE, pastureYield);
 				}
@@ -65,7 +67,7 @@ public class LPJYieldResponseMapReader {
 
 	private void readYieldFile(YieldRaster yieldRaster, String fileToRead) {  	// Passed in YieldRaster is updated
 		
-		AbstractTabularRasterReader<YieldResponsesItem> yieldReader = new AbstractTabularRasterReader<YieldResponsesItem>(" +", 10, yieldRaster) {
+		AbstractTabularRasterReader<YieldResponsesItem> yieldReader = new AbstractTabularRasterReader<YieldResponsesItem>("\\s+", 10, yieldRaster) {
 			protected void setData(RasterKey key, YieldResponsesItem item, Map<String, Double> rowValues) {
 				double adjFactor = 10;  // 10 for kg/m2 to t/ha
 	
@@ -102,6 +104,6 @@ public class LPJYieldResponseMapReader {
 	}
 	
 	private void setCalibratedYield(YieldResponsesItem item, YieldType yieldType, CropType crop, double yield) {
-		item.setYield(yieldType, crop, yield * crop.getCalibrationFactor());  // this can't go on YieldResponsesItem.setYield as this is called from else where
+		item.setYield(yieldType, crop, yield * crop.getCalibrationFactor());  // applying the calibration factor can't go in YieldResponsesItem.setYield as this is also called from elsewhere
 	}
 }
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