From 418c01f73514b6df9f8c5a39a9c16a1d25d9bdb1 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Mon, 25 Jan 2016 14:40:30 -0700
Subject: [PATCH 01/13] updates to Results class and related changes

---
 src/org/opensha2/calc/CalcConfig.java      |  17 +-
 src/org/opensha2/calc/CalcFactory.java     |   3 +-
 src/org/opensha2/calc/HazardCurveSet.java  |  20 +-
 src/org/opensha2/calc/Results.java         | 269 +++++++++++++++++++--
 src/org/opensha2/eq/model/HazardModel.java |   8 +
 src/org/opensha2/programs/HazardCalc.java  |  25 +-
 src/org/opensha2/util/Parsing.java         |   5 +-
 test/etc/SequenceBenchmark.java            |  11 +-
 8 files changed, 302 insertions(+), 56 deletions(-)

diff --git a/src/org/opensha2/calc/CalcConfig.java b/src/org/opensha2/calc/CalcConfig.java
index f686df122..8f070c487 100644
--- a/src/org/opensha2/calc/CalcConfig.java
+++ b/src/org/opensha2/calc/CalcConfig.java
@@ -6,7 +6,6 @@ import static com.google.common.base.Preconditions.checkNotNull;
 import static com.google.common.base.Preconditions.checkState;
 import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.opensha2.util.TextUtils.format;
-
 import static org.opensha2.data.XySequence.*;
 
 import java.io.IOException;
@@ -19,6 +18,7 @@ import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
 
+import org.opensha2.calc.Results.HazardFormat;
 import org.opensha2.data.Data;
 import org.opensha2.data.XySequence;
 import org.opensha2.gmm.Imt;
@@ -47,6 +47,8 @@ public final class CalcConfig {
 	private final Map<Imt, double[]> customImls;
 	private final boolean optimizeGrids;
 	private final boolean gmmUncertainty;
+	
+	private final HazardFormat hazardFormat;
 
 	private final DeaggData deagg;
 
@@ -69,6 +71,7 @@ public final class CalcConfig {
 			Map<Imt, double[]> customImls,
 			boolean optimizeGrids,
 			boolean gmmUncertainty,
+			HazardFormat hazardFormat,
 			DeaggData deagg,
 			SiteSet sites,
 			Map<Imt, XySequence> modelCurves,
@@ -82,6 +85,7 @@ public final class CalcConfig {
 		this.customImls = customImls;
 		this.optimizeGrids = optimizeGrids;
 		this.gmmUncertainty = gmmUncertainty;
+		this.hazardFormat = hazardFormat;
 		this.deagg = deagg;
 		this.sites = sites;
 		this.modelCurves = modelCurves;
@@ -96,6 +100,7 @@ public final class CalcConfig {
 		DEFAULT_IMLS,
 		CUSTOM_IMLS,
 		GMM_UNCERTAINTY,
+		HAZARD_FORMAT,
 		OPTIMIZE_GRIDS,
 		DEAGG,
 		SITES;
@@ -131,6 +136,7 @@ public final class CalcConfig {
 			.append(customImlStr)
 			.append(format(Key.OPTIMIZE_GRIDS)).append(optimizeGrids)
 			.append(format(Key.GMM_UNCERTAINTY)).append(gmmUncertainty)
+			.append(format(Key.HAZARD_FORMAT)).append(hazardFormat)
 			.append(format("Deaggregation R"))
 			.append("min=").append(deagg.rMin).append(", ")
 			.append("max=").append(deagg.rMax).append(", ")
@@ -184,6 +190,9 @@ public final class CalcConfig {
 		return gmmUncertainty;
 	}
 
+	public HazardFormat hazardFormat() {
+		return hazardFormat;
+	}
 	/**
 	 * Deaggregation configuration data.
 	 */
@@ -294,6 +303,7 @@ public final class CalcConfig {
 		private Map<Imt, double[]> customImls;
 		private Boolean optimizeGrids;
 		private Boolean gmmUncertainty;
+		private HazardFormat hazardFormat;
 		private DeaggData deagg;
 		private SiteSet sites;
 
@@ -310,6 +320,7 @@ public final class CalcConfig {
 			this.customImls = config.customImls;
 			this.optimizeGrids = config.optimizeGrids;
 			this.gmmUncertainty = config.gmmUncertainty;
+			this.hazardFormat = config.hazardFormat;
 			this.deagg = config.deagg;
 			this.sites = config.sites;
 			return this;
@@ -329,6 +340,7 @@ public final class CalcConfig {
 			this.customImls = Maps.newHashMap();
 			this.optimizeGrids = true;
 			this.gmmUncertainty = false;
+			this.hazardFormat = HazardFormat.TOTAL;
 			this.deagg = new DeaggData();
 			this.sites = new SiteSet(Lists.newArrayList(Site.builder().build()));
 			return this;
@@ -348,6 +360,7 @@ public final class CalcConfig {
 			if (that.customImls != null) this.customImls = that.customImls;
 			if (that.optimizeGrids != null) this.optimizeGrids = that.optimizeGrids;
 			if (that.gmmUncertainty != null) this.gmmUncertainty = that.gmmUncertainty;
+			if (that.hazardFormat != null) this.hazardFormat = that.hazardFormat;
 			if (that.deagg != null) this.deagg = that.deagg;
 			if (that.sites != null) this.sites = that.sites;
 			return this;
@@ -397,6 +410,7 @@ public final class CalcConfig {
 			checkNotNull(customImls, MSSG, buildId, Key.CUSTOM_IMLS);
 			checkNotNull(optimizeGrids, MSSG, buildId, Key.OPTIMIZE_GRIDS);
 			checkNotNull(gmmUncertainty, MSSG, buildId, Key.GMM_UNCERTAINTY);
+			checkNotNull(hazardFormat, MSSG, buildId, Key.HAZARD_FORMAT);
 			checkNotNull(deagg, MSSG, buildId, Key.DEAGG);
 			checkNotNull(sites, MSSG, buildId, Key.SITES);
 			built = true;
@@ -419,6 +433,7 @@ public final class CalcConfig {
 				customImls,
 				optimizeGrids,
 				gmmUncertainty,
+				hazardFormat,
 				deagg,
 				sites,
 				curves, logCurves);
diff --git a/src/org/opensha2/calc/CalcFactory.java b/src/org/opensha2/calc/CalcFactory.java
index 9e666e3aa..d52808ab9 100644
--- a/src/org/opensha2/calc/CalcFactory.java
+++ b/src/org/opensha2/calc/CalcFactory.java
@@ -162,8 +162,7 @@ final class CalcFactory {
 
 		return transform(
 			allAsList(curveSets),
-			new CurveSetConsolidator(model, config, site),
-			ex).get();
+			new CurveSetConsolidator(model, config, site), ex).get();
 	}
 
 }
diff --git a/src/org/opensha2/calc/HazardCurveSet.java b/src/org/opensha2/calc/HazardCurveSet.java
index 77036e6e7..d3bfbed22 100644
--- a/src/org/opensha2/calc/HazardCurveSet.java
+++ b/src/org/opensha2/calc/HazardCurveSet.java
@@ -22,8 +22,8 @@ import org.opensha2.gmm.Imt;
 
 /**
  * Container class for hazard curves derived from a {@code SourceSet}. Class
- * stores the {@code HazardGroundMotions}s associated with each {@code Source}
- * used in a hazard calculation and the combined curves for each
+ * stores the {@code GroundMotions}s associated with each {@code Source} used in
+ * a hazard calculation and the individual curves for each
  * {@code GroundMotionModel} used.
  * 
  * <p>The {@code Builder} for this class is used to aggregate the HazardCurves
@@ -37,8 +37,8 @@ import org.opensha2.gmm.Imt;
  * including {@code ClusterSourceSet}s, which are handled differently in hazard
  * calculations. This container marks a point in the calculation pipeline where
  * results from cluster and other sources may be recombined into a single
- * {@code HazardResult}, regardless of {@code SourceSet.type()} for all relevant
- * {@code SourceSet}s.</p>
+ * {@code Hazard} result, regardless of {@code SourceSet.type()} for all
+ * relevant {@code SourceSet}s.</p>
  * 
  * @author Peter Powers
  */
@@ -134,8 +134,10 @@ final class HazardCurveSet {
 				Map<Gmm, XySequence> curveMapBuild = curveMap.get(imt);
 				// loop Gmms based on what's supported at this distance
 				for (Gmm gmm : gmmWeightMap.keySet()) {
-					double weight = gmmWeightMap.get(gmm);
-					curveMapBuild.get(gmm).add(copyOf(curveMapIn.get(gmm)).multiply(weight));
+					double gmmWeight = gmmWeightMap.get(gmm);
+					curveMapBuild.get(gmm).add(copyOf(curveMapIn.get(gmm))
+						.multiply(gmmWeight)
+						.multiply(sourceSet.weight()));
 				}
 			}
 			return this;
@@ -154,7 +156,9 @@ final class HazardCurveSet {
 				// loop Gmms based on what's supported at this distance
 				for (Gmm gmm : gmmWeightMap.keySet()) {
 					double weight = gmmWeightMap.get(gmm) * clusterWeight;
-					curveMapBuild.get(gmm).add(copyOf(curveMapIn.get(gmm)).multiply(weight));
+					curveMapBuild.get(gmm).add(copyOf(curveMapIn.get(gmm))
+						.multiply(weight)
+						.multiply(sourceSet.weight()));
 				}
 			}
 			return this;
@@ -177,14 +181,12 @@ final class HazardCurveSet {
 		 * scaled by their weights while building (above).
 		 */
 		private void computeFinal() {
-			double sourceSetWeight = sourceSet.weight();
 			for (Entry<Imt, Map<Gmm, XySequence>> entry : curveMap.entrySet()) {
 				Imt imt = entry.getKey();
 				XySequence totalCurve = emptyCopyOf(modelCurves.get(imt));
 				for (XySequence curve : entry.getValue().values()) {
 					totalCurve.add(curve);
 				}
-				totalCurve.multiply(sourceSetWeight);
 				totalCurves.put(imt, immutableCopyOf(totalCurve));
 			}
 		}
diff --git a/src/org/opensha2/calc/Results.java b/src/org/opensha2/calc/Results.java
index cb40d4e4f..703657ddf 100644
--- a/src/org/opensha2/calc/Results.java
+++ b/src/org/opensha2/calc/Results.java
@@ -11,6 +11,7 @@ import java.nio.file.Files;
 import java.nio.file.OpenOption;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.EnumMap;
 import java.util.List;
 import java.util.Map;
@@ -18,18 +19,26 @@ import java.util.Map.Entry;
 import java.util.Set;
 
 import org.opensha2.data.XySequence;
+import org.opensha2.eq.model.HazardModel;
+import org.opensha2.eq.model.Source;
+import org.opensha2.eq.model.SourceSet;
 import org.opensha2.eq.model.SourceType;
 import org.opensha2.geo.Location;
+import org.opensha2.gmm.Gmm;
 import org.opensha2.gmm.Imt;
 import org.opensha2.util.Parsing;
 import org.opensha2.util.Parsing.Delimiter;
 
 import com.google.common.base.Function;
+import com.google.common.base.Joiner;
+import com.google.common.collect.FluentIterable;
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
 import com.google.common.collect.Multimap;
+import com.google.common.collect.Sets;
+import com.google.common.primitives.Doubles;
 
 /**
  * Factory class for reducing and exporting various result types.
@@ -38,9 +47,21 @@ import com.google.common.collect.Multimap;
  */
 public class Results {
 
-	private static final String CURVE_FILE_SUFFIX = "-curves.csv";
+	private static final String CURVE_FILE_SUFFIX = ".csv";
 	private static final String RATE_FMT = "%.8e";
 
+	/**
+	 * Output style.
+	 */
+	public enum HazardFormat {
+
+		/** Total mean hazard only. */
+		TOTAL,
+
+		/** Additional curves by {@link Gmm} and {@link SourceType}. */
+		DETAILED;
+	}
+
 	/**
 	 * Write a {@code batch} of {@code HazardResult}s to files in the specified
 	 * directory, one for each {@link Imt} in the {@code batch}. See
@@ -57,7 +78,8 @@ public class Results {
 	 * @throws IOException if a problem is encountered
 	 * @see Files#write(Path, Iterable, java.nio.charset.Charset, OpenOption...)
 	 */
-	public static void writeResults(Path dir, List<Hazard> batch, OpenOption... options)
+	@Deprecated
+	public static void writeResultsOLD(Path dir, List<Hazard> batch, OpenOption... options)
 			throws IOException {
 
 		Function<Double, String> locFmtFunc = Parsing.formatDoubleFunction(Location.FORMAT);
@@ -76,7 +98,7 @@ public class Results {
 				if (namedSites) headings.add("name");
 				headings.add("lon");
 				headings.add("lat");
-				Iterable<? extends Object> header = Iterables.concat(
+				Iterable<?> header = Iterables.concat(
 					headings,
 					demo.config.modelCurves().get(imt).xValues());
 				lineList.add(Parsing.join(header, Delimiter.COMMA));
@@ -91,13 +113,13 @@ public class Results {
 					result.site.location.lat()),
 				locFmtFunc);
 			String name = result.site.name;
-			for (Entry<Imt, ? extends XySequence> entry : result.totalCurves.entrySet()) {
+			for (Entry<Imt, XySequence> entry : result.totalCurves.entrySet()) {
 
 				// enable to output poisson probability - used when running
 				// PEER test cases - TODO should be configurable
-//				Function<Double, String> valueFunction = Functions.compose(
-//					rateFmtFunc,
-//					Mfds.rateToProbConverter());
+				// Function<Double, String> valueFunction = Functions.compose(
+				// rateFmtFunc,
+				// Mfds.rateToProbConverter());
 
 				// enable to output annual rate
 				Function<Double, String> valueFunction = rateFmtFunc;
@@ -121,31 +143,232 @@ public class Results {
 		}
 	}
 
-	public static Map<Imt, Map<SourceType, XySequence>> totalsByType(Hazard hazard) {
+	/*
+	 * Individual Hazard results only contain data relevant to the site of
+	 * interest (e.g. for the NSHM WUS models, hazard in San Fancisco is
+	 * influenced by slab sources whereas hazard in Los Angeles is not because
+	 * it is too far away). For consistency when outputting batches of results,
+	 * files are written for all source types and ground motion models supported
+	 * by the HazardModel being used. This yields curve sets that are consistent
+	 * across all locations in a batch, however, some of the curves may be
+	 * empty. Depending on the extents of a map or list of sites, some curve
+	 * sets may consist exclusively of zero-valued curves.
+	 */
+
+	public static void writeResults(
+			Path dir,
+			List<Hazard> batch,
+			OpenOption... options) throws IOException {
+
+		Function<Double, String> formatter = Parsing.formatDoubleFunction(RATE_FMT);
 
-		ImmutableMap.Builder<Imt, Map<SourceType, XySequence>> imtMapBuilder =
-			ImmutableMap.builder();
+		Hazard demo = batch.get(0);
+		boolean newFile = options.length == 0;
+		boolean namedSites = demo.site.name != Site.NO_NAME;
+		boolean detailed = demo.config.hazardFormat().equals(HazardFormat.DETAILED);
 
-		Map<Imt, XySequence> curves = hazard.curves();
-		Set<Imt> imts = curves.keySet();
+		Map<Imt, List<String>> totalLineMap = Maps.newEnumMap(Imt.class);
+		Map<Imt, Map<SourceType, List<String>>> typeLineMap = Maps.newEnumMap(Imt.class);
+		Map<Imt, Map<Gmm, List<String>>> gmmLineMap = Maps.newEnumMap(Imt.class);
 
-		for (Imt imt : imts) {
+		/* Initialize line maps for all types and gmms referenced by a model */
+		for (Imt imt : demo.totalCurves.keySet()) {
+			List<String> lines = new ArrayList<>();
+			if (newFile) {
+				Iterable<?> header = Iterables.concat(
+					Lists.newArrayList(namedSites ? "name" : null, "lon", "lat"),
+					demo.config.modelCurves().get(imt).xValues());
+				lines.add(Parsing.join(header, Delimiter.COMMA));
+			}
+			totalLineMap.put(imt, lines);
 
-			XySequence modelCurve = emptyCopyOf(curves.get(imt));
-			Map<SourceType, XySequence> typeCurves = new EnumMap<>(SourceType.class);
+			if (detailed) {
+
+				Map<SourceType, List<String>> typeLines = Maps.newEnumMap(SourceType.class);
+				for (SourceType type : demo.model.types()) {
+					typeLines.put(type, Lists.newArrayList(lines));
+				}
+				typeLineMap.put(imt, typeLines);
 
-			Multimap<SourceType, HazardCurveSet> curveSets = hazard.sourceSetCurves;
-			for (SourceType type : curveSets.keySet()) {
-				XySequence typeCurve = copyOf(modelCurve);
-				for (HazardCurveSet curveSet : curveSets.get(type)) {
-					typeCurve.add(curveSet.totalCurves.get(imt));
+				Map<Gmm, List<String>> gmmLines = Maps.newEnumMap(Gmm.class);
+				for (Gmm gmm : gmmSet(demo.model)) {
+					gmmLines.put(gmm, Lists.newArrayList(lines));
 				}
-				typeCurves.put(type, immutableCopyOf(typeCurve));
+				gmmLineMap.put(imt, gmmLines);
 			}
-			imtMapBuilder.put(imt, Maps.immutableEnumMap(typeCurves));
 		}
 
-		return imtMapBuilder.build();
+		/* Process batch */
+		for (Hazard hazard : batch) {
+
+			String name = namedSites ? hazard.site.name : null;
+			List<String> locData = Lists.newArrayList(
+				name,
+				String.format(Location.FORMAT, hazard.site.location.lon()),
+				String.format(Location.FORMAT, hazard.site.location.lat()));
+
+			Map<Imt, Map<SourceType, XySequence>> curvesByType = detailed ?
+				curvesByType(hazard) : null;
+			Map<Imt, Map<Gmm, XySequence>> curvesByGmm = detailed ?
+				curvesByGmm(hazard) : null;
+
+			for (Entry<Imt, XySequence> imtEntry : hazard.totalCurves.entrySet()) {
+				Imt imt = imtEntry.getKey();
+
+				XySequence totalCurve = imtEntry.getValue();
+				Iterable<Double> emptyValues = Doubles.asList(new double[totalCurve.size()]);
+				String emptyLine = toLine(locData, emptyValues, formatter);
+
+				totalLineMap.get(imt).add(toLine(
+					locData,
+					imtEntry.getValue().yValues(),
+					formatter));
+
+				if (detailed) {
+
+					Map<SourceType, XySequence> typeCurves = curvesByType.get(imt);
+					for (Entry<SourceType, List<String>> typeEntry : typeLineMap.get(imt)
+						.entrySet()) {
+						SourceType type = typeEntry.getKey();
+						String typeLine = typeCurves.containsKey(type) ?
+							toLine(locData, typeCurves.get(type).yValues(), formatter) :
+							emptyLine;
+						typeEntry.getValue().add(typeLine);
+					}
+
+					Map<Gmm, XySequence> gmmCurves = curvesByGmm.get(imt);
+					for (Entry<Gmm, List<String>> gmmEntry : gmmLineMap.get(imt).entrySet()) {
+						Gmm gmm = gmmEntry.getKey();
+						String gmmLine = gmmCurves.containsKey(gmm) ?
+							toLine(locData, gmmCurves.get(gmm).yValues(), formatter) :
+							emptyLine;
+						gmmEntry.getValue().add(gmmLine);
+					}
+				}
+			}
+		}
+
+		/* write/append */
+		for (Entry<Imt, List<String>> totalEntry : totalLineMap.entrySet()) {
+			Imt imt = totalEntry.getKey();
+
+			Path imtDir = dir.resolve(imt.name());
+			Files.createDirectories(imtDir);
+			Path totalFile = imtDir.resolve("total" + CURVE_FILE_SUFFIX);
+			Files.write(totalFile, totalEntry.getValue(), US_ASCII, options);
+
+			if (detailed) {
+
+				Path typeDir = imtDir.resolve("type");
+				Files.createDirectories(typeDir);
+				for (Entry<SourceType, List<String>> typeEntry : typeLineMap.get(imt).entrySet()) {
+					Path typeFile = typeDir.resolve(
+						typeEntry.getKey().toString() + CURVE_FILE_SUFFIX);
+					Files.write(typeFile, typeEntry.getValue(), US_ASCII, options);
+				}
+
+				Path gmmDir = imtDir.resolve("gmm");
+				Files.createDirectories(gmmDir);
+				for (Entry<Gmm, List<String>> gmmEntry : gmmLineMap.get(imt).entrySet()) {
+					Path gmmFile = gmmDir.resolve(gmmEntry.getKey().name() + CURVE_FILE_SUFFIX);
+					Files.write(gmmFile, gmmEntry.getValue(), US_ASCII, options);
+				}
+			}
+		}
+	}
+
+	private static String toLine(
+			Iterable<String> location,
+			Iterable<Double> values,
+			Function<Double, String> formatter) {
+
+		return Parsing.join(
+			FluentIterable.from(location).append(Iterables.transform(values, formatter)),
+			Delimiter.COMMA);
+	}
+
+	/**
+	 * Derive maps of curves by source type for each Imt in a {@code Hazard}
+	 * result.
+	 */
+	public static Map<Imt, Map<SourceType, XySequence>> curvesByType(Hazard hazard) {
+
+		EnumMap<Imt, Map<SourceType, XySequence>> imtMap = Maps.newEnumMap(Imt.class);
+
+		// initialize receiver
+		Set<SourceType> types = hazard.sourceSetCurves.keySet();
+		for (Entry<Imt, XySequence> entry : hazard.curves().entrySet()) {
+			imtMap.put(entry.getKey(), initCurves(types, entry.getValue()));
+		}
+
+		for (Entry<SourceType, HazardCurveSet> curveSet : hazard.sourceSetCurves.entries()) {
+			for (Entry<Imt, XySequence> typeTotals : curveSet.getValue().totalCurves.entrySet()) {
+				imtMap.get(typeTotals.getKey())
+					.get(curveSet.getKey())
+					.add(typeTotals.getValue());
+			}
+		}
+		return Maps.immutableEnumMap(imtMap);
 	}
 
+	/**
+	 * Derive maps of curves by groudn motion model for each Imt in a
+	 * {@code Hazard} result.
+	 */
+	public static Map<Imt, Map<Gmm, XySequence>> curvesByGmm(Hazard hazard) {
+
+		EnumMap<Imt, Map<Gmm, XySequence>> imtMap = Maps.newEnumMap(Imt.class);
+
+		// initialize receiver
+		Iterable<SourceSet<? extends Source>> sources = Iterables.transform(
+			hazard.sourceSetCurves.values(),
+			CURVE_SET_TO_SOURCE_SET);
+		Set<Gmm> gmms = gmmSet(sources);
+		for (Entry<Imt, XySequence> entry : hazard.curves().entrySet()) {
+			imtMap.put(entry.getKey(), initCurves(gmms, entry.getValue()));
+		}
+
+		for (HazardCurveSet curveSet : hazard.sourceSetCurves.values()) {
+			for (Entry<Imt, Map<Gmm, XySequence>> imtEntry : curveSet.curveMap.entrySet()) {
+				for (Entry<Gmm, XySequence> gmmEntry : imtEntry.getValue().entrySet()) {
+					imtMap.get(imtEntry.getKey()).get(gmmEntry.getKey()).add(gmmEntry.getValue());
+				}
+			}
+		}
+		return Maps.immutableEnumMap(imtMap);
+	}
+
+	/* Scan the supplied source sets for the set of all GMMs used. */
+	private static Set<Gmm> gmmSet(final Iterable<SourceSet<? extends Source>> sourceSets) {
+		return Sets.immutableEnumSet(
+			FluentIterable.from(sourceSets).transformAndConcat(
+				new Function<SourceSet<? extends Source>, Set<Gmm>>() {
+					@Override public Set<Gmm> apply(SourceSet<? extends Source> sourceSet) {
+						return sourceSet.groundMotionModels().gmms();
+					}
+				})
+			);
+	}
+
+	/* Initalize a map of curves, one entry for each of the supplied enum keys. */
+	private static <K extends Enum<K>> Map<K, XySequence> initCurves(
+			final Set<K> keys,
+			final XySequence model) {
+		return Maps.immutableEnumMap(
+			FluentIterable.from(keys).toMap(
+				new Function<K, XySequence>() {
+					@Override public XySequence apply(K key) {
+						return emptyCopyOf(model);
+					}
+				})
+			);
+	}
+
+	private static final Function<HazardCurveSet, SourceSet<? extends Source>> CURVE_SET_TO_SOURCE_SET =
+		new Function<HazardCurveSet, SourceSet<? extends Source>>() {
+			@Override public SourceSet<? extends Source> apply(HazardCurveSet curves) {
+				return curves.sourceSet;
+			}
+		};
+
 }
diff --git a/src/org/opensha2/eq/model/HazardModel.java b/src/org/opensha2/eq/model/HazardModel.java
index 52e6f1342..0a2e3ca59 100644
--- a/src/org/opensha2/eq/model/HazardModel.java
+++ b/src/org/opensha2/eq/model/HazardModel.java
@@ -7,6 +7,7 @@ import static org.opensha2.util.TextUtils.validateName;
 
 import java.nio.file.Path;
 import java.util.Iterator;
+import java.util.Set;
 
 import org.opensha2.calc.CalcConfig;
 import org.opensha2.gmm.GroundMotionModel;
@@ -99,6 +100,13 @@ public final class HazardModel implements Iterable<SourceSet<? extends Source>>,
 	@Override public String name() {
 		return name;
 	}
+	
+	/**
+	 * The set of {@code SourceType}s included in this model.
+	 */
+	public Set<SourceType> types() {
+		return sourceSetMap.keySet();
+	}
 
 	/**
 	 * Return the default calculation configuration. This may be overridden.
diff --git a/src/org/opensha2/programs/HazardCalc.java b/src/org/opensha2/programs/HazardCalc.java
index 03a792207..223b3824f 100644
--- a/src/org/opensha2/programs/HazardCalc.java
+++ b/src/org/opensha2/programs/HazardCalc.java
@@ -7,7 +7,6 @@ import static org.opensha2.util.TextUtils.NEWLINE;
 import static org.opensha2.util.TextUtils.format;
 
 import java.io.IOException;
-import java.nio.file.Files;
 import java.nio.file.OpenOption;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -100,7 +99,7 @@ public class HazardCalc {
 
 		try {
 
-			log.info("Hazard curve: init...");
+			log.info(PROGRAM + ": init...");
 			Path modelPath = Paths.get(args[0]);
 			HazardModel model = HazardModel.load(modelPath);
 
@@ -132,8 +131,8 @@ public class HazardCalc {
 		} catch (Exception e) {
 			return new StringBuilder()
 				.append(NEWLINE)
-				.append("Hazard Curve: error").append(NEWLINE)
-				.append("   Arguments: ").append(Arrays.toString(args)).append(NEWLINE)
+				.append(PROGRAM + ": error").append(NEWLINE)
+				.append("  Arguments: ").append(Arrays.toString(args)).append(NEWLINE)
 				.append(NEWLINE)
 				.append(Throwables.getStackTraceAsString(e)).append(NEWLINE)
 				.append(NEWLINE)
@@ -157,15 +156,14 @@ public class HazardCalc {
 		ExecutorService execSvc = createExecutor();
 		Optional<Executor> executor = Optional.<Executor> of(execSvc);
 
-		log.info("Hazard Curve: calculating ...");
+		log.info(PROGRAM + ": calculating ...");
 		Stopwatch batchWatch = Stopwatch.createStarted();
 		Stopwatch totalWatch = Stopwatch.createStarted();
 		int count = 0;
 
 		List<Hazard> results = new ArrayList<>();
 		boolean firstBatch = true;
-		Path dir = Paths.get(StandardSystemProperty.USER_DIR.value(), "results");
-		Files.createDirectories(dir);
+		Path dir = Paths.get(StandardSystemProperty.USER_DIR.value());
 
 		for (Site site : sites) {
 			Hazard result = calc(model, config, site, executor);
@@ -175,7 +173,7 @@ public class HazardCalc {
 				OpenOption[] opts = firstBatch ? WRITE_OPTIONS : APPEND_OPTIONS;
 				firstBatch = false;
 				Results.writeResults(dir, results, opts);
-				log.info("       batch: " + (count + 1) + "  " + batchWatch + "  total: " +
+				log.info("      batch: " + (count + 1) + "  " + batchWatch + "  total: " +
 					totalWatch);
 				results.clear();
 				batchWatch.reset();
@@ -188,7 +186,7 @@ public class HazardCalc {
 			OpenOption[] opts = firstBatch ? WRITE_OPTIONS : APPEND_OPTIONS;
 			Results.writeResults(dir, results, opts);
 		}
-		log.info("Hazard Curve: " + count + " complete " + totalWatch);
+		log.info(PROGRAM + ": " + count + " complete " + totalWatch);
 
 		execSvc.shutdown();
 	}
@@ -229,12 +227,13 @@ public class HazardCalc {
 		return newFixedThreadPool(getRuntime().availableProcessors());
 	}
 
-	private static final String USAGE_COMMAND = "java -cp nshmp-haz.jar org.opensha.programs.HazardCurve model [config [sites]]";
-	private static final String USAGE_URL1 = "https://github.com/usgs/nshmp-haz/wiki/Earthquake-Source-Models";
-	private static final String USAGE_URL2 = "https://github.com/usgs/nshmp-haz/wiki/Hazard-Calculations";
+	private static final String PROGRAM = HazardCalc.class.getSimpleName();
+	private static final String USAGE_COMMAND = "java -cp nshmp-haz.jar org.opensha.programs.HazardCalc model [config [sites]]";
+	private static final String USAGE_URL1 = "https://github.com/usgs/nshmp-haz/wiki";
+	private static final String USAGE_URL2 = "https://github.com/usgs/nshmp-haz/tree/master/etc";
 
 	static final String USAGE = new StringBuilder()
-		.append("HazardCurve usage:").append(NEWLINE)
+		.append(PROGRAM).append(" usage:").append(NEWLINE)
 		.append("  ").append(USAGE_COMMAND).append(NEWLINE)
 		.append(NEWLINE)
 		.append("Where:").append(NEWLINE)
diff --git a/src/org/opensha2/util/Parsing.java b/src/org/opensha2/util/Parsing.java
index 01ca380e7..be5df9f26 100644
--- a/src/org/opensha2/util/Parsing.java
+++ b/src/org/opensha2/util/Parsing.java
@@ -829,7 +829,8 @@ public final class Parsing {
 
 	/**
 	 * Returns a {@link Function} for converting {@code double}s to formatted
-	 * strings.
+	 * strings. If a value to format is 0.0, the format string is ignored in 
+	 * favor of always printing the often more compact string: "0.0".
 	 * 
 	 * @param format a format string
 	 * @see String#format(String, Object...)
@@ -846,7 +847,7 @@ public final class Parsing {
 		}
 
 		@Override public String apply(Double value) {
-			return String.format(format, value);
+			return (value == 0.0) ? "0.0" : String.format(format, value);
 		}
 	}
 
diff --git a/test/etc/SequenceBenchmark.java b/test/etc/SequenceBenchmark.java
index 558fcff63..7254ba081 100644
--- a/test/etc/SequenceBenchmark.java
+++ b/test/etc/SequenceBenchmark.java
@@ -46,8 +46,8 @@ class SequenceBenchmark {
 			}
 
 			for (int k = 0; k < numPoints; k++) {
-				double y = adfReceiver.get(k).getY();
-				adfReceiver.set(k, copy.get(k).getY() + y);
+				double y = adfReceiver.getY(k);
+				adfReceiver.set(k, copy.getY(k) + y);
 			}
 		}
 		System.out.println("Time: " + sw.stop());
@@ -76,8 +76,8 @@ class SequenceBenchmark {
 			}
 
 			for (int k = 0; k < numPoints; k++) {
-				double y = edfReceiver.get(k).getY();
-				edfReceiver.set(k, copy.get(k).getY() + y);
+				double y = edfReceiver.getY(k);
+				edfReceiver.set(k, copy.getY(k) + y);
 			}
 		}
 		System.out.println("Time: " + sw.stop());
@@ -91,8 +91,7 @@ class SequenceBenchmark {
 		sw.reset().start();
 		for (int i = 0; i < its; i++) {
 			XySequence copy = XySequence.copyOf(xy);
-			copy.multiply(xy);
-			xyReceiver.add(copy);
+			xyReceiver.add(copy.multiply(xy));
 		}
 		System.out.println("Time: " + sw.stop());
 		System.out.println(xyReceiver);
-- 
GitLab


From 8796402a96c30806678a69fad8d2db4f07e30419 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 26 Jan 2016 09:50:47 -0700
Subject: [PATCH 02/13] reults cleanup; added curve format identifier

---
 src/org/opensha2/calc/Results.java | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/org/opensha2/calc/Results.java b/src/org/opensha2/calc/Results.java
index 703657ddf..58dddd3e9 100644
--- a/src/org/opensha2/calc/Results.java
+++ b/src/org/opensha2/calc/Results.java
@@ -1,9 +1,7 @@
 package org.opensha2.calc;
 
 import static java.nio.charset.StandardCharsets.US_ASCII;
-import static org.opensha2.data.XySequence.copyOf;
 import static org.opensha2.data.XySequence.emptyCopyOf;
-import static org.opensha2.data.XySequence.immutableCopyOf;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
@@ -11,7 +9,6 @@ import java.nio.file.Files;
 import java.nio.file.OpenOption;
 import java.nio.file.Path;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.EnumMap;
 import java.util.List;
 import java.util.Map;
@@ -19,7 +16,6 @@ import java.util.Map.Entry;
 import java.util.Set;
 
 import org.opensha2.data.XySequence;
-import org.opensha2.eq.model.HazardModel;
 import org.opensha2.eq.model.Source;
 import org.opensha2.eq.model.SourceSet;
 import org.opensha2.eq.model.SourceType;
@@ -30,13 +26,10 @@ import org.opensha2.util.Parsing;
 import org.opensha2.util.Parsing.Delimiter;
 
 import com.google.common.base.Function;
-import com.google.common.base.Joiner;
 import com.google.common.collect.FluentIterable;
-import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
-import com.google.common.collect.Multimap;
 import com.google.common.collect.Sets;
 import com.google.common.primitives.Doubles;
 
@@ -49,9 +42,10 @@ public class Results {
 
 	private static final String CURVE_FILE_SUFFIX = ".csv";
 	private static final String RATE_FMT = "%.8e";
+	private static final String CURVE_DIR = "curves";
 
 	/**
-	 * Output style.
+	 * Hazard output format.
 	 */
 	public enum HazardFormat {
 
@@ -61,6 +55,18 @@ public class Results {
 		/** Additional curves by {@link Gmm} and {@link SourceType}. */
 		DETAILED;
 	}
+	
+	/**
+	 * Curve format.
+	 */
+	public enum CurveFormat {
+		
+		/** Write curves as annual-rate. */
+		ANNUAL_RATE,
+		
+		/** Write curves as Poisson probabilities. */
+		POISSON;
+	}
 
 	/**
 	 * Write a {@code batch} of {@code HazardResult}s to files in the specified
@@ -252,7 +258,7 @@ public class Results {
 		for (Entry<Imt, List<String>> totalEntry : totalLineMap.entrySet()) {
 			Imt imt = totalEntry.getKey();
 
-			Path imtDir = dir.resolve(imt.name());
+			Path imtDir = dir.resolve(CURVE_DIR).resolve(imt.name());
 			Files.createDirectories(imtDir);
 			Path totalFile = imtDir.resolve("total" + CURVE_FILE_SUFFIX);
 			Files.write(totalFile, totalEntry.getValue(), US_ASCII, options);
-- 
GitLab


From b7fd1f5a1bd49c706da8fd7cdecd5e434635b972 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 26 Jan 2016 09:52:36 -0700
Subject: [PATCH 03/13] example readme update

---
 etc/examples/README.md | 34 ++++++++++++----------------------
 1 file changed, 12 insertions(+), 22 deletions(-)

diff --git a/etc/examples/README.md b/etc/examples/README.md
index 1d77ec7ba..913681728 100644
--- a/etc/examples/README.md
+++ b/etc/examples/README.md
@@ -1,27 +1,17 @@
-##### Hazard Curves
-The simplest way to run the HazardCalc program via the command-line is to supply it with a source model; all model initialization and calculation configuration data will be read from the model itself. Navigate to the `/etc` in the repository and run:
-```
-java -cp ../dist/nshmp-haz.jar org.opensha2.programs.HazardCalc peer/models/Set1-Case1
-```
-The result of this calculation should be available as a single file containing several hazard curves for PGA in a newly created 'results' directory. Note that not all calculation [configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration) parameters need be supplied; see the [configuration file](../peer/models/Set1-Case1/config.json) for this example model.  
-One can override calculation configuration parameters by supplying an alternate configuration file. For example:
-```
-java -cp ../dist/nshmp-haz.jar org.opensha2.programs.HazardCalc peer/models/Set1-Case1 examples/config-sites.json
-```
-In this case:
-* a truncation will be applied at 3 standard deviations.
-* the list of `imts` (intensity measure types, or periods) for which curves will be calculated has been expanded to 3.
-* the `imls` (the intensity measure levels or x-values) of the resultant curves, have been explicitely defined for each `imt`.
-* two sites have been specified
-The 'results' directory should now include 3 files, one for each `imt`.
+Examples
+--------
+
+1. **Note:** All examples avoid a lengthy call to Java and the HazardCalc program by using the following system alias:
+   
+        ```Shell
+        alias hazard='java -cp /path/to/repo/nshmp-haz/dist/nshmp-haz.jar org.opensha2.programs.HazardCalc'
+        ```
+   
+2. **Note:** All HazardCalc output is written to the current directory from which the program was called.
+
 
-One can also supply a comma-delimited site data file, which may be easier to work with in some applications.
-```
-java -cp ../dist/nshmp-haz.jar org.opensha2.programs.HazardCalc peer/models/Set1-Case1 examples/config-sites.json examples/sites-sf.csv
-```
-See the site file itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any result files.
 
-##### Hazard Maps
+#### Calculating hazard maps
 Hazard maps are generated from numerous uniformely spaced hazard curves. To compute such a curve set, the same program is used, but sites are instead specified as a region.
 ```
 java -cp ../dist/nshmp-haz.jar org.opensha2.programs.HazardCalc peer/models/Set1-Case1 examples/config-region-sf.json
-- 
GitLab


From c3190f5c52a6469c0f4ed529e5f91b76d7508c4b Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 26 Jan 2016 09:53:35 -0700
Subject: [PATCH 04/13] updated individual examples

---
 etc/examples/1-simple-hazard/README.md   | 16 ++++++++++++++++
 etc/examples/2-custom-config/README.md   | 19 +++++++++++++++++++
 etc/examples/2-custom-config/config.json | 24 ++++++++++++++++++++++++
 etc/examples/3-sites-file/README.md      | 12 ++++++++++++
 etc/examples/3-sites-file/config.json    | 24 ++++++++++++++++++++++++
 etc/examples/3-sites-file/sites.csv      | 24 ++++++++++++++++++++++++
 6 files changed, 119 insertions(+)
 create mode 100644 etc/examples/1-simple-hazard/README.md
 create mode 100644 etc/examples/2-custom-config/README.md
 create mode 100644 etc/examples/2-custom-config/config.json
 create mode 100644 etc/examples/3-sites-file/README.md
 create mode 100644 etc/examples/3-sites-file/config.json
 create mode 100644 etc/examples/3-sites-file/sites.csv

diff --git a/etc/examples/1-simple-hazard/README.md b/etc/examples/1-simple-hazard/README.md
new file mode 100644
index 000000000..cb222afe3
--- /dev/null
+++ b/etc/examples/1-simple-hazard/README.md
@@ -0,0 +1,16 @@
+Example 1: A simple hazard calculation
+--------------------------------------
+
+On the command line, navigate to this directory and execute the following:
+
+```Shell
+hazard ../../peer/models/Set1-Case1
+```
+
+The PEER models, such as that designated above, consist of simple cases for different source types commonly encountered in a PSHA and are included in the nshmp-haz repository to support testing. See the [PEER directory](../../peer/) for more information.
+
+The result of this calculation should be available as a single comma-delimited file containing several hazard curves for PGA in a newly created 'curves' directory. In this example, the calculation configuration was derived from the model directory. Note that not all calculation [configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration) parameters need be supplied; see the [configuration file](../peer/models/Set1-Case1/config.json) for this example model.
+
+Also note that when only a model is supplied to the HazardCalc program, all output is written to the current working directory. In the next example, we'll override the model supplied configuration with a custom file.
+
+#### Next: [Example 2](../2-custom-config)
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
new file mode 100644
index 000000000..ab6ef91ce
--- /dev/null
+++ b/etc/examples/2-custom-config/README.md
@@ -0,0 +1,19 @@
+Example 2: Custom configuration
+-------------------------------
+
+Navigate up to the `examples/` directory and execute the following:
+
+```Shell
+hazard ../peer/models/Set1-Case1 2-custom-config/config.json
+```
+
+In this example we've overridden the configuration supplied by the model. Specifically:
+
+* The upper end of each hazard curve has been truncated at 3 standard deviations.
+* Hazard curves have been calculated for 3 `imts` (intensity measure types, or spectral periods) and written to the [2-custom-config]() directory.
+* The `imls` (the intensity measure levels or x-values) of the resultant curves have been explicitely defined for each `imt`.
+* And two different sites have been specified.
+
+**A note on output:** Because we supplied a specific configuration file, all program output will be written to the directory where the config resides, thus keeping a record of calculation settings along with any results.
+
+#### Next: [Example 3](../3-sites-file)
diff --git a/etc/examples/2-custom-config/config.json b/etc/examples/2-custom-config/config.json
new file mode 100644
index 000000000..a96569992
--- /dev/null
+++ b/etc/examples/2-custom-config/config.json
@@ -0,0 +1,24 @@
+{
+  "exceedanceModel": "TRUNCATION_UPPER_ONLY",
+  "truncationLevel": 3.0,
+  "imts": ["PGA", "SA0P2", "SA1P0"],
+  "customImls": {
+    "PGA":   [0.0050, 0.0070, 0.0098, 0.0137, 0.0192, 0.0269, 0.0376, 0.0527, 0.0738, 0.103, 0.145, 0.203, 0.284, 0.397, 0.556, 0.778, 1.09, 1.52, 2.2, 3.3],
+    "SA0P2": [0.0050, 0.0075, 0.0113, 0.0169, 0.0253, 0.0380, 0.0570, 0.0854, 0.128, 0.192, 0.288, 0.432, 0.649, 0.973, 1.46, 2.19, 3.28, 4.92, 7.38],
+    "SA1P0": [0.0025, 0.00375, 0.00563, 0.00844, 0.0127, 0.0190, 0.0285, 0.0427, 0.0641, 0.0961, 0.144, 0.216, 0.324, 0.487, 0.730, 1.09, 1.64, 2.46, 3.69, 5.54]
+  },
+  "sites": [
+    {
+    "name": "San Francisco",
+    "location": [-122.40, 37.75],
+    "vs30": 760,
+    "vsInf": true
+    },
+    {
+    "name": "Oakland",
+    "location": [-122.25, 37.80],
+    "vs30": 760,
+    "vsInf": true
+    }
+  ]
+}
\ No newline at end of file
diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
new file mode 100644
index 000000000..4595da34c
--- /dev/null
+++ b/etc/examples/3-sites-file/README.md
@@ -0,0 +1,12 @@
+Example 3: Using a custom sites file
+------------------------------------
+
+One can also supply a comma-delimited site data file, which may be easier to work with in some applications.
+
+```Shell
+hazard ../peer/models/Set1-Case1 3-sites-file/config.json 3-sites-file/sites.csv
+```
+
+See the [site file](3-sites-file/sites.csv) itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any result files.
+
+#### Next: [Example 4](../4-complex-model)
diff --git a/etc/examples/3-sites-file/config.json b/etc/examples/3-sites-file/config.json
new file mode 100644
index 000000000..a96569992
--- /dev/null
+++ b/etc/examples/3-sites-file/config.json
@@ -0,0 +1,24 @@
+{
+  "exceedanceModel": "TRUNCATION_UPPER_ONLY",
+  "truncationLevel": 3.0,
+  "imts": ["PGA", "SA0P2", "SA1P0"],
+  "customImls": {
+    "PGA":   [0.0050, 0.0070, 0.0098, 0.0137, 0.0192, 0.0269, 0.0376, 0.0527, 0.0738, 0.103, 0.145, 0.203, 0.284, 0.397, 0.556, 0.778, 1.09, 1.52, 2.2, 3.3],
+    "SA0P2": [0.0050, 0.0075, 0.0113, 0.0169, 0.0253, 0.0380, 0.0570, 0.0854, 0.128, 0.192, 0.288, 0.432, 0.649, 0.973, 1.46, 2.19, 3.28, 4.92, 7.38],
+    "SA1P0": [0.0025, 0.00375, 0.00563, 0.00844, 0.0127, 0.0190, 0.0285, 0.0427, 0.0641, 0.0961, 0.144, 0.216, 0.324, 0.487, 0.730, 1.09, 1.64, 2.46, 3.69, 5.54]
+  },
+  "sites": [
+    {
+    "name": "San Francisco",
+    "location": [-122.40, 37.75],
+    "vs30": 760,
+    "vsInf": true
+    },
+    {
+    "name": "Oakland",
+    "location": [-122.25, 37.80],
+    "vs30": 760,
+    "vsInf": true
+    }
+  ]
+}
\ No newline at end of file
diff --git a/etc/examples/3-sites-file/sites.csv b/etc/examples/3-sites-file/sites.csv
new file mode 100644
index 000000000..9bf046cab
--- /dev/null
+++ b/etc/examples/3-sites-file/sites.csv
@@ -0,0 +1,24 @@
+#
+# Comma-delimited site file example.
+#
+# Header row must identify columns. At a minimum, lon and lat
+# must be defined. Columns can be in any order and any missing
+# fields will be populated with default values. 
+#
+# [name,] lon, lat [, vs30] [, vsInf] [, z1p0] [, z2p5]
+#
+# Defaults:
+#     name: Unnamed Site
+#     vs30: 760.0
+#    vsInf: true
+#     z1p0: NaN (GMM will use default basin depth model)
+#     z2p5: NaN (GMM will use default basin depth model)
+#
+name, lon, lat
+Concord, -122.00, 37.95
+Oakland, -122.25, 37.80
+San Francisco, -122.40, 37.75 
+San Jose, -121.90, 37.35
+San Mateo, -122.30, 37.55
+Santa Rosa, -122.70, 38.45
+Vallejo, -122.25, 38.10
-- 
GitLab


From 0ae6602c3c653689b477790bf7cc6258f584b1c6 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 26 Jan 2016 11:23:58 -0700
Subject: [PATCH 05/13] readme updates

---
 etc/examples/1-simple-hazard/README.md | 2 +-
 etc/examples/2-custom-config/README.md | 4 ++--
 etc/examples/README.md                 | 4 +---
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/etc/examples/1-simple-hazard/README.md b/etc/examples/1-simple-hazard/README.md
index cb222afe3..31c47bee1 100644
--- a/etc/examples/1-simple-hazard/README.md
+++ b/etc/examples/1-simple-hazard/README.md
@@ -9,7 +9,7 @@ hazard ../../peer/models/Set1-Case1
 
 The PEER models, such as that designated above, consist of simple cases for different source types commonly encountered in a PSHA and are included in the nshmp-haz repository to support testing. See the [PEER directory](../../peer/) for more information.
 
-The result of this calculation should be available as a single comma-delimited file containing several hazard curves for PGA in a newly created 'curves' directory. In this example, the calculation configuration was derived from the model directory. Note that not all calculation [configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration) parameters need be supplied; see the [configuration file](../peer/models/Set1-Case1/config.json) for this example model.
+The result of this calculation should be available as a single comma-delimited file containing several hazard curves for PGA in a newly created 'curves' directory. In this example, the calculation configuration was derived from the model directory. Note that not all calculation [configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration) parameters need be supplied; see the [configuration file](../../peer/models/Set1-Case1/config.json) for this example model.
 
 Also note that when only a model is supplied to the HazardCalc program, all output is written to the current working directory. In the next example, we'll override the model supplied configuration with a custom file.
 
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
index ab6ef91ce..f62999615 100644
--- a/etc/examples/2-custom-config/README.md
+++ b/etc/examples/2-custom-config/README.md
@@ -10,8 +10,8 @@ hazard ../peer/models/Set1-Case1 2-custom-config/config.json
 In this example we've overridden the configuration supplied by the model. Specifically:
 
 * The upper end of each hazard curve has been truncated at 3 standard deviations.
-* Hazard curves have been calculated for 3 `imts` (intensity measure types, or spectral periods) and written to the [2-custom-config]() directory.
-* The `imls` (the intensity measure levels or x-values) of the resultant curves have been explicitely defined for each `imt`.
+* Hazard curves have been calculated for 3 `imts` (intensity measure types, or spectral periods) and written to the directory containing the config file.
+* The `imls` (intensity measure levels or x-values) of the resultant curves have been explicitely defined for each `imt`.
 * And two different sites have been specified.
 
 **A note on output:** Because we supplied a specific configuration file, all program output will be written to the directory where the config resides, thus keeping a record of calculation settings along with any results.
diff --git a/etc/examples/README.md b/etc/examples/README.md
index 913681728..098bc3fb0 100644
--- a/etc/examples/README.md
+++ b/etc/examples/README.md
@@ -7,9 +7,7 @@ Examples
         alias hazard='java -cp /path/to/repo/nshmp-haz/dist/nshmp-haz.jar org.opensha2.programs.HazardCalc'
         ```
    
-2. **Note:** All HazardCalc output is written to the current directory from which the program was called.
-
-
+Because each example builds on prior concepts, it is best step through all the examples, however quickly.
 
 #### Calculating hazard maps
 Hazard maps are generated from numerous uniformely spaced hazard curves. To compute such a curve set, the same program is used, but sites are instead specified as a region.
-- 
GitLab


From bd2aea3bcbbde8b826151b3e8fbfd5d2f76fc287 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Wed, 27 Jan 2016 15:10:53 -0700
Subject: [PATCH 06/13] readme updates

---
 .../README.md                                 |  2 ++
 etc/examples/2-custom-config/README.md        |  4 +++-
 etc/examples/3-sites-file/README.md           |  4 +++-
 etc/examples/4-hazard-map/README.md           | 14 ++++++++++++
 .../4-hazard-map/config-region-sf.json        | 22 +++++++++++++++++++
 etc/examples/4-hazard-map/config.json         | 22 +++++++++++++++++++
 etc/examples/5-complex-model/README.md        | 20 +++++++++++++++++
 etc/examples/6-enhanced-output/README.md      | 12 ++++++++++
 etc/examples/README.md                        | 18 ++++++---------
 9 files changed, 105 insertions(+), 13 deletions(-)
 rename etc/examples/{1-simple-hazard => 1-hazard-curve}/README.md (94%)
 create mode 100644 etc/examples/4-hazard-map/README.md
 create mode 100644 etc/examples/4-hazard-map/config-region-sf.json
 create mode 100644 etc/examples/4-hazard-map/config.json
 create mode 100644 etc/examples/5-complex-model/README.md
 create mode 100644 etc/examples/6-enhanced-output/README.md

diff --git a/etc/examples/1-simple-hazard/README.md b/etc/examples/1-hazard-curve/README.md
similarity index 94%
rename from etc/examples/1-simple-hazard/README.md
rename to etc/examples/1-hazard-curve/README.md
index 31c47bee1..2abd50407 100644
--- a/etc/examples/1-simple-hazard/README.md
+++ b/etc/examples/1-hazard-curve/README.md
@@ -1,6 +1,8 @@
 Example 1: A simple hazard calculation
 --------------------------------------
 
+Working directory: `/path/to/repo/nshmp-haz/etc/examples/1-hazard-curve`
+
 On the command line, navigate to this directory and execute the following:
 
 ```Shell
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
index f62999615..6197f23bb 100644
--- a/etc/examples/2-custom-config/README.md
+++ b/etc/examples/2-custom-config/README.md
@@ -1,7 +1,9 @@
 Example 2: Custom configuration
 -------------------------------
 
-Navigate up to the `examples/` directory and execute the following:
+Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+
+Navigate up one level to the `examples/` directory and execute the following:
 
 ```Shell
 hazard ../peer/models/Set1-Case1 2-custom-config/config.json
diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
index 4595da34c..43a600394 100644
--- a/etc/examples/3-sites-file/README.md
+++ b/etc/examples/3-sites-file/README.md
@@ -1,6 +1,8 @@
 Example 3: Using a custom sites file
 ------------------------------------
 
+Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+
 One can also supply a comma-delimited site data file, which may be easier to work with in some applications.
 
 ```Shell
@@ -9,4 +11,4 @@ hazard ../peer/models/Set1-Case1 3-sites-file/config.json 3-sites-file/sites.csv
 
 See the [site file](3-sites-file/sites.csv) itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any result files.
 
-#### Next: [Example 4](../4-complex-model)
+#### Next: [Example 4](../4-hazard-map)
diff --git a/etc/examples/4-hazard-map/README.md b/etc/examples/4-hazard-map/README.md
new file mode 100644
index 000000000..1056344d9
--- /dev/null
+++ b/etc/examples/4-hazard-map/README.md
@@ -0,0 +1,14 @@
+Example 4: A simple hazard map
+------------------------------
+
+Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+
+A hazard map is just a lot of hazard curves. To compute curves at reqularly spaced intervals in latitude and longitude, the sites configuration can instead be specified as a polygon.
+
+```Shell
+hazard ../peer/models/Set1-Case1 3-sites-file/config.json
+```
+
+See the [site file](3-sites-file/sites.csv) itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any result files.
+
+#### Next: [Example 5](../5-complex-model)
diff --git a/etc/examples/4-hazard-map/config-region-sf.json b/etc/examples/4-hazard-map/config-region-sf.json
new file mode 100644
index 000000000..8b06f574d
--- /dev/null
+++ b/etc/examples/4-hazard-map/config-region-sf.json
@@ -0,0 +1,22 @@
+{
+  "exceedanceModel": "TRUNCATION_UPPER_ONLY",
+  "truncationLevel": 3.0,
+  "imts": ["PGA", "SA0P2", "SA1P0"],
+  "customImls": {
+    "PGA":   [0.0050, 0.0070, 0.0098, 0.0137, 0.0192, 0.0269, 0.0376, 0.0527, 0.0738, 0.103, 0.145, 0.203, 0.284, 0.397, 0.556, 0.778, 1.09, 1.52, 2.2, 3.3],
+    "SA0P2": [0.0050, 0.0075, 0.0113, 0.0169, 0.0253, 0.0380, 0.0570, 0.0854, 0.128, 0.192, 0.288, 0.432, 0.649, 0.973, 1.46, 2.19, 3.28, 4.92, 7.38],
+    "SA1P0": [0.0025, 0.00375, 0.00563, 0.00844, 0.0127, 0.0190, 0.0285, 0.0427, 0.0641, 0.0961, 0.144, 0.216, 0.324, 0.487, 0.730, 1.09, 1.64, 2.46, 3.69, 5.54]
+  },
+  "sites": {  
+    "region": {
+      "name": "Downtown San Francisco",
+      "spacing": 0.1,
+      "border": [  
+        [-122.7, 37.5],
+        [-122.2, 38.0]
+      ],
+      "vs30": 760,
+      "vsInf": true
+    }
+  }
+}
\ No newline at end of file
diff --git a/etc/examples/4-hazard-map/config.json b/etc/examples/4-hazard-map/config.json
new file mode 100644
index 000000000..8b06f574d
--- /dev/null
+++ b/etc/examples/4-hazard-map/config.json
@@ -0,0 +1,22 @@
+{
+  "exceedanceModel": "TRUNCATION_UPPER_ONLY",
+  "truncationLevel": 3.0,
+  "imts": ["PGA", "SA0P2", "SA1P0"],
+  "customImls": {
+    "PGA":   [0.0050, 0.0070, 0.0098, 0.0137, 0.0192, 0.0269, 0.0376, 0.0527, 0.0738, 0.103, 0.145, 0.203, 0.284, 0.397, 0.556, 0.778, 1.09, 1.52, 2.2, 3.3],
+    "SA0P2": [0.0050, 0.0075, 0.0113, 0.0169, 0.0253, 0.0380, 0.0570, 0.0854, 0.128, 0.192, 0.288, 0.432, 0.649, 0.973, 1.46, 2.19, 3.28, 4.92, 7.38],
+    "SA1P0": [0.0025, 0.00375, 0.00563, 0.00844, 0.0127, 0.0190, 0.0285, 0.0427, 0.0641, 0.0961, 0.144, 0.216, 0.324, 0.487, 0.730, 1.09, 1.64, 2.46, 3.69, 5.54]
+  },
+  "sites": {  
+    "region": {
+      "name": "Downtown San Francisco",
+      "spacing": 0.1,
+      "border": [  
+        [-122.7, 37.5],
+        [-122.2, 38.0]
+      ],
+      "vs30": 760,
+      "vsInf": true
+    }
+  }
+}
\ No newline at end of file
diff --git a/etc/examples/5-complex-model/README.md b/etc/examples/5-complex-model/README.md
new file mode 100644
index 000000000..d5b436155
--- /dev/null
+++ b/etc/examples/5-complex-model/README.md
@@ -0,0 +1,20 @@
+Example 5: A more complex model
+-------------------------------
+
+Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+
+Most PSHAs involve the use of more complex source models, the components of which might use different ground motion models. For this and ensuing examples, we'll use the 2008 USGS National Seismic Hazard Model (NSHM) for the western U.S.
+
+First, clone the 2008 USGS NSHM. Assuming `examples/` is the currnet working directory, the following will create a copy of the model adjacent to nshmp-haz:
+
+```Shell
+git clone https://github.com/usgs/nshmp-model-cous-2008.git ../../..
+```
+
+THe 2008 NSHM repository contains two source models one for the western U.S. and a one for the central and eastern U.S. More complex models make for longer, per-site calculations. The default configurations for the NSHM are set to output very large maps, which are time-consuming and inappropriate as examples. To compute hazard for a few sites in the Western U.S., execute:
+
+```Shell
+hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config.json
+```
+
+#### Next: [Example 6](../4-enhanced-output)
diff --git a/etc/examples/6-enhanced-output/README.md b/etc/examples/6-enhanced-output/README.md
new file mode 100644
index 000000000..08b1d909a
--- /dev/null
+++ b/etc/examples/6-enhanced-output/README.md
@@ -0,0 +1,12 @@
+Example 6: Enhanced output
+--------------------------
+
+Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+
+By default, `HazardCalc` outputs only total mean hazard curves, however, curves by ground motion model and source type can also be written. Execute
+
+```Shell
+hazard ../../../nshmp-model-cous-2008/Western\ US 6-enhanced-output/config.json
+```
+
+#### Next: [Example ????](../)
diff --git a/etc/examples/README.md b/etc/examples/README.md
index 098bc3fb0..5254a1888 100644
--- a/etc/examples/README.md
+++ b/etc/examples/README.md
@@ -1,17 +1,13 @@
 Examples
 --------
 
-1. **Note:** All examples avoid a lengthy call to Java and the HazardCalc program by using the following system alias:
-   
-        ```Shell
-        alias hazard='java -cp /path/to/repo/nshmp-haz/dist/nshmp-haz.jar org.opensha2.programs.HazardCalc'
-        ```
-   
-Because each example builds on prior concepts, it is best step through all the examples, however quickly.
+These examples are designed to be executed locally while following the READMEs on GitHub. All examples avoid a lengthy call to Java and the `HazardCalc` program by using the following system alias:
 
-#### Calculating hazard maps
-Hazard maps are generated from numerous uniformely spaced hazard curves. To compute such a curve set, the same program is used, but sites are instead specified as a region.
-```
-java -cp ../dist/nshmp-haz.jar org.opensha2.programs.HazardCalc peer/models/Set1-Case1 examples/config-region-sf.json
+```Shell
+alias hazard='java -cp /path/to/repo/nshmp-haz/dist/nshmp-haz.jar org.opensha2.programs.HazardCalc'
 ```
 
+Because each example builds on prior concepts, it is best step through all the examples, however quickly.
+
+#### Start: [Example 1](1-hazard-curve)
+
-- 
GitLab


From d48bd64aab9e40a418d3aabaec9711ea6356d855 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Wed, 27 Jan 2016 16:34:21 -0700
Subject: [PATCH 07/13] gitignore cleanup; readme edits; out path keyed to
 config

---
 .gitignore                                |  4 +---
 etc/examples/1-hazard-curve/README.md     |  4 ++--
 etc/examples/2-custom-config/README.md    |  2 +-
 src/org/opensha2/programs/HazardCalc.java | 15 +++++++++------
 4 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/.gitignore b/.gitignore
index d8a429dbb..d1038274c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,8 +4,6 @@
 /dist
 /docs
 /tmp
-/results
-/etc/results
+curves/
 Scratch*.java
 /src/META-INF
-/etc/examples/results
diff --git a/etc/examples/1-hazard-curve/README.md b/etc/examples/1-hazard-curve/README.md
index 2abd50407..ea6cf011d 100644
--- a/etc/examples/1-hazard-curve/README.md
+++ b/etc/examples/1-hazard-curve/README.md
@@ -1,7 +1,7 @@
 Example 1: A simple hazard calculation
 --------------------------------------
 
-Working directory: `/path/to/repo/nshmp-haz/etc/examples/1-hazard-curve`
+Working directory: `/path/to/nshmp-haz/etc/examples/1-hazard-curve`
 
 On the command line, navigate to this directory and execute the following:
 
@@ -13,6 +13,6 @@ The PEER models, such as that designated above, consist of simple cases for diff
 
 The result of this calculation should be available as a single comma-delimited file containing several hazard curves for PGA in a newly created 'curves' directory. In this example, the calculation configuration was derived from the model directory. Note that not all calculation [configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration) parameters need be supplied; see the [configuration file](../../peer/models/Set1-Case1/config.json) for this example model.
 
-Also note that when only a model is supplied to the HazardCalc program, all output is written to the current working directory. In the next example, we'll override the model supplied configuration with a custom file.
+Also note that when only a model is supplied to `HazardCalc`, all output is written to the current working directory. In the next example, we'll override the model supplied configuration with a custom file.
 
 #### Next: [Example 2](../2-custom-config)
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
index 6197f23bb..f4195d59a 100644
--- a/etc/examples/2-custom-config/README.md
+++ b/etc/examples/2-custom-config/README.md
@@ -1,7 +1,7 @@
 Example 2: Custom configuration
 -------------------------------
 
-Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+Working directory: `/path/to/nshmp-haz/etc/examples`
 
 Navigate up one level to the `examples/` directory and execute the following:
 
diff --git a/src/org/opensha2/programs/HazardCalc.java b/src/org/opensha2/programs/HazardCalc.java
index 223b3824f..3a458c124 100644
--- a/src/org/opensha2/programs/HazardCalc.java
+++ b/src/org/opensha2/programs/HazardCalc.java
@@ -104,11 +104,14 @@ public class HazardCalc {
 			HazardModel model = HazardModel.load(modelPath);
 
 			CalcConfig config = model.config();
+			Path out = Paths.get(StandardSystemProperty.USER_DIR.value());
 			if (argCount > 1) {
+				Path userConfigPath = Paths.get(args[1]);
 				config = CalcConfig.builder()
 					.copy(model.config())
-					.extend(CalcConfig.builder(Paths.get(args[1])))
+					.extend(CalcConfig.builder(userConfigPath))
 					.build();
+				out = userConfigPath.getParent();
 			}
 			log.info(config.toString());
 
@@ -125,7 +128,7 @@ public class HazardCalc {
 				log.info(sb.toString());
 			}
 
-			calc(model, config, sites, log);
+			calc(model, config, sites, out, log);
 			return null;
 
 		} catch (Exception e) {
@@ -151,6 +154,7 @@ public class HazardCalc {
 			HazardModel model,
 			CalcConfig config,
 			Iterable<Site> sites,
+			Path out,
 			Logger log) throws IOException {
 
 		ExecutorService execSvc = createExecutor();
@@ -163,7 +167,6 @@ public class HazardCalc {
 
 		List<Hazard> results = new ArrayList<>();
 		boolean firstBatch = true;
-		Path dir = Paths.get(StandardSystemProperty.USER_DIR.value());
 
 		for (Site site : sites) {
 			Hazard result = calc(model, config, site, executor);
@@ -172,8 +175,8 @@ public class HazardCalc {
 			if (results.size() == FLUSH_LIMIT) {
 				OpenOption[] opts = firstBatch ? WRITE_OPTIONS : APPEND_OPTIONS;
 				firstBatch = false;
-				Results.writeResults(dir, results, opts);
-				log.info("      batch: " + (count + 1) + "  " + batchWatch + "  total: " +
+				Results.writeResults(out, results, opts);
+				log.info("     batch: " + (count + 1) + "  " + batchWatch + "  total: " +
 					totalWatch);
 				results.clear();
 				batchWatch.reset();
@@ -184,7 +187,7 @@ public class HazardCalc {
 		// write final batch
 		if (!results.isEmpty()) {
 			OpenOption[] opts = firstBatch ? WRITE_OPTIONS : APPEND_OPTIONS;
-			Results.writeResults(dir, results, opts);
+			Results.writeResults(out, results, opts);
 		}
 		log.info(PROGRAM + ": " + count + " complete " + totalWatch);
 
-- 
GitLab


From 3aab4d1e3fd96b02194be466140ba6c408161635 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Wed, 27 Jan 2016 17:02:45 -0700
Subject: [PATCH 08/13] readme updates; HazardCalc error formatting

---
 etc/examples/3-sites-file/README.md       | 4 ++--
 etc/examples/4-hazard-map/README.md       | 2 +-
 src/org/opensha2/programs/HazardCalc.java | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
index 43a600394..add3f5488 100644
--- a/etc/examples/3-sites-file/README.md
+++ b/etc/examples/3-sites-file/README.md
@@ -1,7 +1,7 @@
 Example 3: Using a custom sites file
 ------------------------------------
 
-Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+Working directory: `/path/to/nshmp-haz/etc/examples`
 
 One can also supply a comma-delimited site data file, which may be easier to work with in some applications.
 
@@ -9,6 +9,6 @@ One can also supply a comma-delimited site data file, which may be easier to wor
 hazard ../peer/models/Set1-Case1 3-sites-file/config.json 3-sites-file/sites.csv
 ```
 
-See the [site file](3-sites-file/sites.csv) itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any result files.
+See the [site file](sites.csv) itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any result files.
 
 #### Next: [Example 4](../4-hazard-map)
diff --git a/etc/examples/4-hazard-map/README.md b/etc/examples/4-hazard-map/README.md
index 1056344d9..3858891de 100644
--- a/etc/examples/4-hazard-map/README.md
+++ b/etc/examples/4-hazard-map/README.md
@@ -1,7 +1,7 @@
 Example 4: A simple hazard map
 ------------------------------
 
-Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+Working directory: `/path/to/nshmp-haz/etc/examples`
 
 A hazard map is just a lot of hazard curves. To compute curves at reqularly spaced intervals in latitude and longitude, the sites configuration can instead be specified as a polygon.
 
diff --git a/src/org/opensha2/programs/HazardCalc.java b/src/org/opensha2/programs/HazardCalc.java
index 3a458c124..9b344e739 100644
--- a/src/org/opensha2/programs/HazardCalc.java
+++ b/src/org/opensha2/programs/HazardCalc.java
@@ -135,7 +135,7 @@ public class HazardCalc {
 			return new StringBuilder()
 				.append(NEWLINE)
 				.append(PROGRAM + ": error").append(NEWLINE)
-				.append("  Arguments: ").append(Arrays.toString(args)).append(NEWLINE)
+				.append(" Arguments: ").append(Arrays.toString(args)).append(NEWLINE)
 				.append(NEWLINE)
 				.append(Throwables.getStackTraceAsString(e)).append(NEWLINE)
 				.append(NEWLINE)
-- 
GitLab


From 26086726eb7fe94bee6d4f4dcd1761199df362d6 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Thu, 28 Jan 2016 11:59:13 -0700
Subject: [PATCH 09/13] readme updates

---
 etc/README.md                                 |  5 +----
 etc/examples/1-hazard-curve/README.md         |  2 +-
 etc/examples/2-custom-config/README.md        |  6 +++--
 etc/examples/3-sites-file/README.md           |  6 ++---
 etc/examples/4-hazard-map/README.md           |  8 +++----
 .../4-hazard-map/config-region-sf.json        | 22 -------------------
 etc/examples/5-complex-model/README.md        |  6 ++---
 etc/examples/6-enhanced-output/README.md      |  2 +-
 etc/examples/README.md                        |  2 +-
 9 files changed, 17 insertions(+), 42 deletions(-)
 delete mode 100644 etc/examples/4-hazard-map/config-region-sf.json

diff --git a/etc/README.md b/etc/README.md
index 58641b18a..9a161d8e9 100644
--- a/etc/README.md
+++ b/etc/README.md
@@ -2,7 +2,4 @@ See the [examples](examples) directory as a starting point for command-line use
 
 [Matlab](matlab) shows how to take advantage of the ground motion model implementations in nshmp-haz.
 
-[Peer](peer) is a collection of simple source models that are also a good starting point.
-
-
-
+[Peer](peer) is a collection of simple source models that are used for testing.
diff --git a/etc/examples/1-hazard-curve/README.md b/etc/examples/1-hazard-curve/README.md
index ea6cf011d..74aefb8eb 100644
--- a/etc/examples/1-hazard-curve/README.md
+++ b/etc/examples/1-hazard-curve/README.md
@@ -15,4 +15,4 @@ The result of this calculation should be available as a single comma-delimited f
 
 Also note that when only a model is supplied to `HazardCalc`, all output is written to the current working directory. In the next example, we'll override the model supplied configuration with a custom file.
 
-#### Next: [Example 2](../2-custom-config)
+#### Next: [Example 2 – A custom configuration](../2-custom-config)
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
index f4195d59a..31a3f4b75 100644
--- a/etc/examples/2-custom-config/README.md
+++ b/etc/examples/2-custom-config/README.md
@@ -1,4 +1,4 @@
-Example 2: Custom configuration
+Example 2: A custom configuration
 -------------------------------
 
 Working directory: `/path/to/nshmp-haz/etc/examples`
@@ -16,6 +16,8 @@ In this example we've overridden the configuration supplied by the model. Specif
 * The `imls` (intensity measure levels or x-values) of the resultant curves have been explicitely defined for each `imt`.
 * And two different sites have been specified.
 
+See the [configuration specification](https://github.com/usgs/nshmp-haz/wiki/Configuration) for details on default values and supported options and formats.
+
 **A note on output:** Because we supplied a specific configuration file, all program output will be written to the directory where the config resides, thus keeping a record of calculation settings along with any results.
 
-#### Next: [Example 3](../3-sites-file)
+#### Next: [Example 3 – Using a custom sites file](../3-sites-file)
diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
index add3f5488..3001cb9ce 100644
--- a/etc/examples/3-sites-file/README.md
+++ b/etc/examples/3-sites-file/README.md
@@ -3,12 +3,12 @@ Example 3: Using a custom sites file
 
 Working directory: `/path/to/nshmp-haz/etc/examples`
 
-One can also supply a comma-delimited site data file, which may be easier to work with in some applications.
+One may also supply a comma-delimited site data file, which may be easier to work with in some applications.
 
 ```Shell
 hazard ../peer/models/Set1-Case1 3-sites-file/config.json 3-sites-file/sites.csv
 ```
 
-See the [site file](sites.csv) itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any result files.
+See the [site file](sites.csv) itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any curve files.
 
-#### Next: [Example 4](../4-hazard-map)
+#### Next: [Example 4 – A simple hazard map](../4-hazard-map)
diff --git a/etc/examples/4-hazard-map/README.md b/etc/examples/4-hazard-map/README.md
index 3858891de..45c766cfc 100644
--- a/etc/examples/4-hazard-map/README.md
+++ b/etc/examples/4-hazard-map/README.md
@@ -3,12 +3,10 @@ Example 4: A simple hazard map
 
 Working directory: `/path/to/nshmp-haz/etc/examples`
 
-A hazard map is just a lot of hazard curves. To compute curves at reqularly spaced intervals in latitude and longitude, the sites configuration can instead be specified as a polygon.
+A hazard map is just a lot of hazard curves. To compute curves at reqularly spaced intervals in latitude and longitude, the [sites configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration#four-sites) can instead be specified as a polygon.
 
 ```Shell
-hazard ../peer/models/Set1-Case1 3-sites-file/config.json
+hazard ../peer/models/Set1-Case1 4-hazard-map/config.json
 ```
 
-See the [site file](3-sites-file/sites.csv) itself for details on the expected file structure. Under all use cases, if the name of a site is supplied, it will be included in the first column of any result files.
-
-#### Next: [Example 5](../5-complex-model)
+#### Next: [Example 5 – A more complex model](../5-complex-model)
diff --git a/etc/examples/4-hazard-map/config-region-sf.json b/etc/examples/4-hazard-map/config-region-sf.json
deleted file mode 100644
index 8b06f574d..000000000
--- a/etc/examples/4-hazard-map/config-region-sf.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-  "exceedanceModel": "TRUNCATION_UPPER_ONLY",
-  "truncationLevel": 3.0,
-  "imts": ["PGA", "SA0P2", "SA1P0"],
-  "customImls": {
-    "PGA":   [0.0050, 0.0070, 0.0098, 0.0137, 0.0192, 0.0269, 0.0376, 0.0527, 0.0738, 0.103, 0.145, 0.203, 0.284, 0.397, 0.556, 0.778, 1.09, 1.52, 2.2, 3.3],
-    "SA0P2": [0.0050, 0.0075, 0.0113, 0.0169, 0.0253, 0.0380, 0.0570, 0.0854, 0.128, 0.192, 0.288, 0.432, 0.649, 0.973, 1.46, 2.19, 3.28, 4.92, 7.38],
-    "SA1P0": [0.0025, 0.00375, 0.00563, 0.00844, 0.0127, 0.0190, 0.0285, 0.0427, 0.0641, 0.0961, 0.144, 0.216, 0.324, 0.487, 0.730, 1.09, 1.64, 2.46, 3.69, 5.54]
-  },
-  "sites": {  
-    "region": {
-      "name": "Downtown San Francisco",
-      "spacing": 0.1,
-      "border": [  
-        [-122.7, 37.5],
-        [-122.2, 38.0]
-      ],
-      "vs30": 760,
-      "vsInf": true
-    }
-  }
-}
\ No newline at end of file
diff --git a/etc/examples/5-complex-model/README.md b/etc/examples/5-complex-model/README.md
index d5b436155..567a07e34 100644
--- a/etc/examples/5-complex-model/README.md
+++ b/etc/examples/5-complex-model/README.md
@@ -1,17 +1,17 @@
 Example 5: A more complex model
 -------------------------------
 
-Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+Working directory: `/path/to/nshmp-haz/etc/examples`
 
 Most PSHAs involve the use of more complex source models, the components of which might use different ground motion models. For this and ensuing examples, we'll use the 2008 USGS National Seismic Hazard Model (NSHM) for the western U.S.
 
-First, clone the 2008 USGS NSHM. Assuming `examples/` is the currnet working directory, the following will create a copy of the model adjacent to nshmp-haz:
+First, clone the 2008 USGS NSHM. Assuming `examples/` is the current working directory, the following will create a copy of the model adjacent to nshmp-haz:
 
 ```Shell
 git clone https://github.com/usgs/nshmp-model-cous-2008.git ../../..
 ```
 
-THe 2008 NSHM repository contains two source models one for the western U.S. and a one for the central and eastern U.S. More complex models make for longer, per-site calculations. The default configurations for the NSHM are set to output very large maps, which are time-consuming and inappropriate as examples. To compute hazard for a few sites in the Western U.S., execute:
+The 2008 NSHM repository contains two source models: one for the western U.S. and a one for the central and eastern U.S. More complex models make for longer, per-site calculations. To compute hazard for a few sites in the Western U.S., execute:
 
 ```Shell
 hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config.json
diff --git a/etc/examples/6-enhanced-output/README.md b/etc/examples/6-enhanced-output/README.md
index 08b1d909a..71ba7e543 100644
--- a/etc/examples/6-enhanced-output/README.md
+++ b/etc/examples/6-enhanced-output/README.md
@@ -1,7 +1,7 @@
 Example 6: Enhanced output
 --------------------------
 
-Working directory: `/path/to/repo/nshmp-haz/etc/examples`
+Working directory: `/path/to/nshmp-haz/etc/examples`
 
 By default, `HazardCalc` outputs only total mean hazard curves, however, curves by ground motion model and source type can also be written. Execute
 
diff --git a/etc/examples/README.md b/etc/examples/README.md
index 5254a1888..cdb605686 100644
--- a/etc/examples/README.md
+++ b/etc/examples/README.md
@@ -9,5 +9,5 @@ alias hazard='java -cp /path/to/repo/nshmp-haz/dist/nshmp-haz.jar org.opensha2.p
 
 Because each example builds on prior concepts, it is best step through all the examples, however quickly.
 
-#### Start: [Example 1](1-hazard-curve)
+#### Start: [Example 1 – A simple hazard calculation](1-hazard-curve)
 
-- 
GitLab


From a975266d509d8d5abfc7f23e9b3f262e39c1f4f4 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Thu, 28 Jan 2016 14:15:07 -0700
Subject: [PATCH 10/13] readme and example edits

---
 README.md                                     |  2 +-
 etc/examples/4-hazard-map/config.json         | 11 +++-------
 etc/examples/5-complex-model/README.md        | 14 ++++++++++---
 etc/examples/5-complex-model/config-map.json  | 12 +++++++++++
 .../5-complex-model/config-sites.json         | 20 +++++++++++++++++++
 src/org/opensha2/programs/HazardCalc.java     |  7 ++++---
 6 files changed, 51 insertions(+), 15 deletions(-)
 create mode 100644 etc/examples/5-complex-model/config-map.json
 create mode 100644 etc/examples/5-complex-model/config-sites.json

diff --git a/README.md b/README.md
index db3033806..9e8f8132a 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 nshmp-haz
 =========
 
-USGS National Seismic Hazard Model Program Codes
+U.S. Geological Survey (USGS) National Seismic Hazard Model Project (NSHMP) codes.
 
 Information relevant to obtaining, building, and running the code may be found in the [wiki](https://github.com/usgs/nshmp-haz/wiki/).
diff --git a/etc/examples/4-hazard-map/config.json b/etc/examples/4-hazard-map/config.json
index 8b06f574d..c81727a86 100644
--- a/etc/examples/4-hazard-map/config.json
+++ b/etc/examples/4-hazard-map/config.json
@@ -2,18 +2,13 @@
   "exceedanceModel": "TRUNCATION_UPPER_ONLY",
   "truncationLevel": 3.0,
   "imts": ["PGA", "SA0P2", "SA1P0"],
-  "customImls": {
-    "PGA":   [0.0050, 0.0070, 0.0098, 0.0137, 0.0192, 0.0269, 0.0376, 0.0527, 0.0738, 0.103, 0.145, 0.203, 0.284, 0.397, 0.556, 0.778, 1.09, 1.52, 2.2, 3.3],
-    "SA0P2": [0.0050, 0.0075, 0.0113, 0.0169, 0.0253, 0.0380, 0.0570, 0.0854, 0.128, 0.192, 0.288, 0.432, 0.649, 0.973, 1.46, 2.19, 3.28, 4.92, 7.38],
-    "SA1P0": [0.0025, 0.00375, 0.00563, 0.00844, 0.0127, 0.0190, 0.0285, 0.0427, 0.0641, 0.0961, 0.144, 0.216, 0.324, 0.487, 0.730, 1.09, 1.64, 2.46, 3.69, 5.54]
-  },
   "sites": {  
     "region": {
-      "name": "Downtown San Francisco",
+      "name": "Bay Area",
       "spacing": 0.1,
       "border": [  
-        [-122.7, 37.5],
-        [-122.2, 38.0]
+        [-123.0, 37.0],
+        [-121.0, 39.0]
       ],
       "vs30": 760,
       "vsInf": true
diff --git a/etc/examples/5-complex-model/README.md b/etc/examples/5-complex-model/README.md
index 567a07e34..68590eb6b 100644
--- a/etc/examples/5-complex-model/README.md
+++ b/etc/examples/5-complex-model/README.md
@@ -8,13 +8,21 @@ Most PSHAs involve the use of more complex source models, the components of whic
 First, clone the 2008 USGS NSHM. Assuming `examples/` is the current working directory, the following will create a copy of the model adjacent to nshmp-haz:
 
 ```Shell
-git clone https://github.com/usgs/nshmp-model-cous-2008.git ../../..
+git clone https://github.com/usgs/nshmp-model-cous-2008.git ../../../nshmp-model-cous-2008
 ```
 
 The 2008 NSHM repository contains two source models: one for the western U.S. and a one for the central and eastern U.S. More complex models make for longer, per-site calculations. To compute hazard for a few sites in the Western U.S., execute:
 
 ```Shell
-hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config.json
+hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config-sites.json
 ```
 
-#### Next: [Example 6](../4-enhanced-output)
+More complex models make for longer, per-site calculations. `HazardCalc` will automatically use all cores available and therefore performs better on multi-core systems. To compute a small, low-resolution map for the central San Francisco Bay Area, execute:
+
+```Shell
+hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config-map.json
+```
+
+This computes 121 curves over a 2° by 2° area and will give you a sense of how long a larger map might take.
+
+#### Next: [Example 6 – Enhanced output](../4-enhanced-output)
diff --git a/etc/examples/5-complex-model/config-map.json b/etc/examples/5-complex-model/config-map.json
new file mode 100644
index 000000000..178352754
--- /dev/null
+++ b/etc/examples/5-complex-model/config-map.json
@@ -0,0 +1,12 @@
+{
+  "sites": {  
+    "region": {
+      "name": "Bay Area",
+      "spacing": 0.2,
+      "border": [  
+        [-123.0, 37.0],
+        [-121.0, 39.0]
+      ]
+    }
+  }
+}
\ No newline at end of file
diff --git a/etc/examples/5-complex-model/config-sites.json b/etc/examples/5-complex-model/config-sites.json
new file mode 100644
index 000000000..c913fccbb
--- /dev/null
+++ b/etc/examples/5-complex-model/config-sites.json
@@ -0,0 +1,20 @@
+{
+  "sites": [
+    {
+    "name": "Los Angeles",
+    "location": [-118.25, 34.05]
+    },
+    {
+    "name": "San Francisco",
+    "location": [-122.40, 37.75]
+    },
+    {
+    "name": "Seattle",
+    "location": [-122.30, 47.60]
+    },
+    {
+    "name": "Salt Lake City",
+    "location": [-111.90, 40.75]
+    }
+  ]
+}
\ No newline at end of file
diff --git a/src/org/opensha2/programs/HazardCalc.java b/src/org/opensha2/programs/HazardCalc.java
index 9b344e739..b59781e02 100644
--- a/src/org/opensha2/programs/HazardCalc.java
+++ b/src/org/opensha2/programs/HazardCalc.java
@@ -176,10 +176,11 @@ public class HazardCalc {
 				OpenOption[] opts = firstBatch ? WRITE_OPTIONS : APPEND_OPTIONS;
 				firstBatch = false;
 				Results.writeResults(out, results, opts);
-				log.info("     batch: " + (count + 1) + "  " + batchWatch + "  total: " +
-					totalWatch);
+				log.info(
+					"     batch: " + (count + 1) + "  " + batchWatch +
+					"  total: " + totalWatch);
 				results.clear();
-				batchWatch.reset();
+				batchWatch.reset().start();
 			}
 
 			count++;
-- 
GitLab


From 8eede1597065be78051fafaf9915c97e5f39d1ba Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Thu, 28 Jan 2016 14:45:40 -0700
Subject: [PATCH 11/13] readme and example edits

---
 etc/README.md                            | 4 ++--
 etc/examples/1-hazard-curve/README.md    | 2 +-
 etc/examples/2-custom-config/README.md   | 6 +++---
 etc/examples/3-sites-file/README.md      | 2 +-
 etc/examples/4-hazard-map/README.md      | 2 +-
 etc/examples/5-complex-model/README.md   | 8 ++++----
 etc/examples/6-enhanced-output/README.md | 2 +-
 etc/peer/README.md                       | 2 +-
 8 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/etc/README.md b/etc/README.md
index 9a161d8e9..6f852a99e 100644
--- a/etc/README.md
+++ b/etc/README.md
@@ -1,5 +1,5 @@
-See the [examples](examples) directory as a starting point for command-line use of nshmp-haz.
+See the [examples](examples) directory as a starting point for command-line use of `nshmp-haz`.
 
-[Matlab](matlab) shows how to take advantage of the ground motion model implementations in nshmp-haz.
+[Matlab](matlab) shows how to take advantage of the ground motion model implementations in `nshmp-haz`.
 
 [Peer](peer) is a collection of simple source models that are used for testing.
diff --git a/etc/examples/1-hazard-curve/README.md b/etc/examples/1-hazard-curve/README.md
index 74aefb8eb..b9997bf75 100644
--- a/etc/examples/1-hazard-curve/README.md
+++ b/etc/examples/1-hazard-curve/README.md
@@ -1,7 +1,7 @@
 Example 1: A simple hazard calculation
 --------------------------------------
 
-Working directory: `/path/to/nshmp-haz/etc/examples/1-hazard-curve`
+__Working directory:__ `/path/to/nshmp-haz/etc/examples/1-hazard-curve`
 
 On the command line, navigate to this directory and execute the following:
 
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
index 31a3f4b75..e4d3ad739 100644
--- a/etc/examples/2-custom-config/README.md
+++ b/etc/examples/2-custom-config/README.md
@@ -1,7 +1,7 @@
 Example 2: A custom configuration
 -------------------------------
 
-Working directory: `/path/to/nshmp-haz/etc/examples`
+__Working directory:__ `/path/to/nshmp-haz/etc/examples`
 
 Navigate up one level to the `examples/` directory and execute the following:
 
@@ -12,12 +12,12 @@ hazard ../peer/models/Set1-Case1 2-custom-config/config.json
 In this example we've overridden the configuration supplied by the model. Specifically:
 
 * The upper end of each hazard curve has been truncated at 3 standard deviations.
-* Hazard curves have been calculated for 3 `imts` (intensity measure types, or spectral periods) and written to the directory containing the config file.
+* Hazard curves have been calculated for 3 `imts` ([intensity measure types](http://usgs.github.io/nshmp-haz/javadoc/index.html?org/opensha2/gmm/Imt.html), or spectral periods) and written to the directory containing the config file.
 * The `imls` (intensity measure levels or x-values) of the resultant curves have been explicitely defined for each `imt`.
 * And two different sites have been specified.
 
 See the [configuration specification](https://github.com/usgs/nshmp-haz/wiki/Configuration) for details on default values and supported options and formats.
 
-**A note on output:** Because we supplied a specific configuration file, all program output will be written to the directory where the config resides, thus keeping a record of calculation settings along with any results.
+**A note on output:** Because we supplied a specific configuration file, all program output is written to the directory where the config resides, thus keeping a record of calculation settings along with any results.
 
 #### Next: [Example 3 – Using a custom sites file](../3-sites-file)
diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
index 3001cb9ce..8e0f05af7 100644
--- a/etc/examples/3-sites-file/README.md
+++ b/etc/examples/3-sites-file/README.md
@@ -1,7 +1,7 @@
 Example 3: Using a custom sites file
 ------------------------------------
 
-Working directory: `/path/to/nshmp-haz/etc/examples`
+__Working directory:__ `/path/to/nshmp-haz/etc/examples`
 
 One may also supply a comma-delimited site data file, which may be easier to work with in some applications.
 
diff --git a/etc/examples/4-hazard-map/README.md b/etc/examples/4-hazard-map/README.md
index 45c766cfc..81278f0f8 100644
--- a/etc/examples/4-hazard-map/README.md
+++ b/etc/examples/4-hazard-map/README.md
@@ -1,7 +1,7 @@
 Example 4: A simple hazard map
 ------------------------------
 
-Working directory: `/path/to/nshmp-haz/etc/examples`
+__Working directory:__ `/path/to/nshmp-haz/etc/examples`
 
 A hazard map is just a lot of hazard curves. To compute curves at reqularly spaced intervals in latitude and longitude, the [sites configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration#four-sites) can instead be specified as a polygon.
 
diff --git a/etc/examples/5-complex-model/README.md b/etc/examples/5-complex-model/README.md
index 68590eb6b..bf5e087ed 100644
--- a/etc/examples/5-complex-model/README.md
+++ b/etc/examples/5-complex-model/README.md
@@ -1,7 +1,7 @@
 Example 5: A more complex model
 -------------------------------
 
-Working directory: `/path/to/nshmp-haz/etc/examples`
+__Working directory:__ `/path/to/nshmp-haz/etc/examples`
 
 Most PSHAs involve the use of more complex source models, the components of which might use different ground motion models. For this and ensuing examples, we'll use the 2008 USGS National Seismic Hazard Model (NSHM) for the western U.S.
 
@@ -11,13 +11,13 @@ First, clone the 2008 USGS NSHM. Assuming `examples/` is the current working dir
 git clone https://github.com/usgs/nshmp-model-cous-2008.git ../../../nshmp-model-cous-2008
 ```
 
-The 2008 NSHM repository contains two source models: one for the western U.S. and a one for the central and eastern U.S. More complex models make for longer, per-site calculations. To compute hazard for a few sites in the Western U.S., execute:
+The 2008 NSHM repository contains two source models: one for the western U.S. and a one for the central and eastern U.S. To compute hazard for a few sites in the Western U.S., execute:
 
 ```Shell
 hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config-sites.json
 ```
 
-More complex models make for longer, per-site calculations. `HazardCalc` will automatically use all cores available and therefore performs better on multi-core systems. To compute a small, low-resolution map for the central San Francisco Bay Area, execute:
+Note that more complex models take longer to initialize, although this only occurs once per calculation, and make for longer, per-site calculations. However, `HazardCalc` will automatically use all cores available and therefore performs better on multi-core systems. To compute a small, low-resolution map for the central San Francisco bay area, execute:
 
 ```Shell
 hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config-map.json
@@ -25,4 +25,4 @@ hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config-map.jso
 
 This computes 121 curves over a 2° by 2° area and will give you a sense of how long a larger map might take.
 
-#### Next: [Example 6 – Enhanced output](../4-enhanced-output)
+#### Next: [Example 6 – Enhanced output](../6-enhanced-output)
diff --git a/etc/examples/6-enhanced-output/README.md b/etc/examples/6-enhanced-output/README.md
index 71ba7e543..a639f8132 100644
--- a/etc/examples/6-enhanced-output/README.md
+++ b/etc/examples/6-enhanced-output/README.md
@@ -1,7 +1,7 @@
 Example 6: Enhanced output
 --------------------------
 
-Working directory: `/path/to/nshmp-haz/etc/examples`
+__Working directory:__ `/path/to/nshmp-haz/etc/examples`
 
 By default, `HazardCalc` outputs only total mean hazard curves, however, curves by ground motion model and source type can also be written. Execute
 
diff --git a/etc/peer/README.md b/etc/peer/README.md
index 5f359e688..ec9359cf4 100644
--- a/etc/peer/README.md
+++ b/etc/peer/README.md
@@ -1,5 +1,5 @@
 #### PEER Test Cases
 
-The PEER PSHA validation project developed a number of source models for the purpose of examining the sensitivity of seismic hazard to different PSHA implementations (codes). These test cases are used as end-to-end unit tests in nshmp-haz. 
+The PEER PSHA validation project developed a number of source models for the purpose of examining the sensitivity of seismic hazard to different PSHA implementations (codes). These test cases are used as end-to-end unit tests in `nshmp-haz`. 
 
 For more information, including source model specifications, result tables, and summary reports, please see the [PEER](http://peer.berkeley.edu) PSHA validation project (TODO: link; no site as yet).
-- 
GitLab


From d38790efaf65b35931bde426236f5848b7ef58d2 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Fri, 5 Feb 2016 11:13:03 -0700
Subject: [PATCH 12/13] readme and config updates

---
 README.md                                  |  2 +-
 etc/examples/1-hazard-curve/README.md      |  2 +-
 etc/examples/5-complex-model/README.md     |  2 +-
 etc/examples/6-enhanced-output/README.md   |  6 ++++--
 etc/examples/6-enhanced-output/config.json | 21 +++++++++++++++++++++
 5 files changed, 28 insertions(+), 5 deletions(-)
 create mode 100644 etc/examples/6-enhanced-output/config.json

diff --git a/README.md b/README.md
index 9e8f8132a..e1d67a222 100644
--- a/README.md
+++ b/README.md
@@ -3,4 +3,4 @@ nshmp-haz
 
 U.S. Geological Survey (USGS) National Seismic Hazard Model Project (NSHMP) codes.
 
-Information relevant to obtaining, building, and running the code may be found in the [wiki](https://github.com/usgs/nshmp-haz/wiki/).
+Information relevant to obtaining, building, and running the code may be found in the [Wiki](https://github.com/usgs/nshmp-haz/wiki/).
diff --git a/etc/examples/1-hazard-curve/README.md b/etc/examples/1-hazard-curve/README.md
index b9997bf75..84b901d3e 100644
--- a/etc/examples/1-hazard-curve/README.md
+++ b/etc/examples/1-hazard-curve/README.md
@@ -11,7 +11,7 @@ hazard ../../peer/models/Set1-Case1
 
 The PEER models, such as that designated above, consist of simple cases for different source types commonly encountered in a PSHA and are included in the nshmp-haz repository to support testing. See the [PEER directory](../../peer/) for more information.
 
-The result of this calculation should be available as a single comma-delimited file containing several hazard curves for PGA in a newly created 'curves' directory. In this example, the calculation configuration was derived from the model directory. Note that not all calculation [configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration) parameters need be supplied; see the [configuration file](../../peer/models/Set1-Case1/config.json) for this example model.
+The result of this calculation should be available as a single comma-delimited file containing several total mean hazard curves for PGA in a newly created 'curves' directory. In this example, the calculation configuration was derived from the model directory. Note that not all calculation [configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration) parameters need be supplied; see the [configuration file](../../peer/models/Set1-Case1/config.json) for this example model.
 
 Also note that when only a model is supplied to `HazardCalc`, all output is written to the current working directory. In the next example, we'll override the model supplied configuration with a custom file.
 
diff --git a/etc/examples/5-complex-model/README.md b/etc/examples/5-complex-model/README.md
index bf5e087ed..3f8e321e4 100644
--- a/etc/examples/5-complex-model/README.md
+++ b/etc/examples/5-complex-model/README.md
@@ -23,6 +23,6 @@ Note that more complex models take longer to initialize, although this only occu
 hazard ../../../nshmp-model-cous-2008/Western\ US 5-complex-model/config-map.json
 ```
 
-This computes 121 curves over a 2° by 2° area and will give you a sense of how long a larger map might take.
+This computes 121 curves over a 2° by 2° area and will give you a sense of how long a larger map might take. These results overwrite those of the prior site-specific calculation.
 
 #### Next: [Example 6 – Enhanced output](../6-enhanced-output)
diff --git a/etc/examples/6-enhanced-output/README.md b/etc/examples/6-enhanced-output/README.md
index a639f8132..eafa33ccf 100644
--- a/etc/examples/6-enhanced-output/README.md
+++ b/etc/examples/6-enhanced-output/README.md
@@ -3,10 +3,12 @@ Example 6: Enhanced output
 
 __Working directory:__ `/path/to/nshmp-haz/etc/examples`
 
-By default, `HazardCalc` outputs only total mean hazard curves, however, curves by ground motion model and source type can also be written. Execute
+While mean hazard is of broad interest, it can be useful to preserve individual components of a total curve, particularly with more complex models. Execute the following to write curves for each source type and ground motion model (GMM) used in the 2008 NSHM:
 
 ```Shell
 hazard ../../../nshmp-model-cous-2008/Western\ US 6-enhanced-output/config.json
 ```
 
-#### Next: [Example ????](../)
+Note that the output curves directory now contains additional derectories of curves by source type and GMM.
+
+See the `nshmp-haz` wiki and JavDocs for more information on source types ([Wiki](https://github.com/usgs/nshmp-haz/wiki/Source-Types), [JavaDoc](http://usgs.github.io/nshmp-haz/javadoc/index.html?org/opensha2/eq/model/SourceType.html)) and GMMs ([Wiki](https://github.com/usgs/nshmp-haz/wiki/Ground-Motion-Models), [JavaDoc](http://usgs.github.io/nshmp-haz/javadoc/index.html?org/opensha2/gmm/Gmm.html)).
diff --git a/etc/examples/6-enhanced-output/config.json b/etc/examples/6-enhanced-output/config.json
new file mode 100644
index 000000000..c1fc16cab
--- /dev/null
+++ b/etc/examples/6-enhanced-output/config.json
@@ -0,0 +1,21 @@
+{
+  "hazardFormat": "DETAILED",
+  "sites": [
+    {
+    "name": "Los Angeles",
+    "location": [-118.25, 34.05]
+    },
+    {
+    "name": "San Francisco",
+    "location": [-122.40, 37.75]
+    },
+    {
+    "name": "Seattle",
+    "location": [-122.30, 47.60]
+    },
+    {
+    "name": "Salt Lake City",
+    "location": [-111.90, 40.75]
+    }
+  ]
+}
\ No newline at end of file
-- 
GitLab


From 0879cc77e4a3e018d4559e9b1722176879133011 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Mon, 8 Feb 2016 11:57:14 -0700
Subject: [PATCH 13/13] imrpoved calc console output; readme updates

---
 etc/examples/3-sites-file/sites.csv   | 14 +++++++-------
 etc/examples/README.md                |  2 +-
 src/org/opensha2/calc/CalcConfig.java |  5 +++--
 src/org/opensha2/calc/Site.java       | 14 +++++++++-----
 src/org/opensha2/calc/SiteSet.java    |  8 +++++---
 src/org/opensha2/util/TextUtils.java  | 25 +++++++++++++++++++++----
 6 files changed, 46 insertions(+), 22 deletions(-)

diff --git a/etc/examples/3-sites-file/sites.csv b/etc/examples/3-sites-file/sites.csv
index 9bf046cab..f63172287 100644
--- a/etc/examples/3-sites-file/sites.csv
+++ b/etc/examples/3-sites-file/sites.csv
@@ -15,10 +15,10 @@
 #     z2p5: NaN (GMM will use default basin depth model)
 #
 name, lon, lat
-Concord, -122.00, 37.95
-Oakland, -122.25, 37.80
-San Francisco, -122.40, 37.75 
-San Jose, -121.90, 37.35
-San Mateo, -122.30, 37.55
-Santa Rosa, -122.70, 38.45
-Vallejo, -122.25, 38.10
+Concord,       -122.00, 37.95
+Oakland,       -122.25, 37.80
+San Francisco, -122.40, 37.75
+San Jose,      -121.90, 37.35
+San Mateo,     -122.30, 37.55
+Santa Rosa,    -122.70, 38.45
+Vallejo,       -122.25, 38.10
diff --git a/etc/examples/README.md b/etc/examples/README.md
index cdb605686..5f0873f32 100644
--- a/etc/examples/README.md
+++ b/etc/examples/README.md
@@ -4,7 +4,7 @@ Examples
 These examples are designed to be executed locally while following the READMEs on GitHub. All examples avoid a lengthy call to Java and the `HazardCalc` program by using the following system alias:
 
 ```Shell
-alias hazard='java -cp /path/to/repo/nshmp-haz/dist/nshmp-haz.jar org.opensha2.programs.HazardCalc'
+alias hazard='java -cp /path/to/nshmp-haz/dist/nshmp-haz.jar org.opensha2.programs.HazardCalc'
 ```
 
 Because each example builds on prior concepts, it is best step through all the examples, however quickly.
diff --git a/src/org/opensha2/calc/CalcConfig.java b/src/org/opensha2/calc/CalcConfig.java
index 8f070c487..972c1289a 100644
--- a/src/org/opensha2/calc/CalcConfig.java
+++ b/src/org/opensha2/calc/CalcConfig.java
@@ -6,6 +6,7 @@ import static com.google.common.base.Preconditions.checkNotNull;
 import static com.google.common.base.Preconditions.checkState;
 import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.opensha2.util.TextUtils.format;
+import static org.opensha2.util.TextUtils.wrap;
 import static org.opensha2.data.XySequence.*;
 
 import java.io.IOException;
@@ -122,7 +123,7 @@ public final class CalcConfig {
 			StringBuilder sb = new StringBuilder();
 			for (Entry<Imt, double[]> entry : customImls.entrySet()) {
 				String imtStr = "(override) " + entry.getKey().name();
-				sb.append(format(imtStr)).append(Arrays.toString(entry.getValue()));
+				sb.append(format(imtStr)).append(wrap(Arrays.toString(entry.getValue())));
 			}
 			customImlStr = sb.toString();
 		}
@@ -132,7 +133,7 @@ public final class CalcConfig {
 			.append(format(Key.EXCEEDANCE_MODEL)).append(exceedanceModel)
 			.append(format(Key.TRUNCATION_LEVEL)).append(truncationLevel)
 			.append(format(Key.IMTS)).append(Parsing.enumsToString(imts, Imt.class))
-			.append(format(Key.DEFAULT_IMLS)).append(Arrays.toString(defaultImls))
+			.append(format(Key.DEFAULT_IMLS)).append(wrap(Arrays.toString(defaultImls)))
 			.append(customImlStr)
 			.append(format(Key.OPTIMIZE_GRIDS)).append(optimizeGrids)
 			.append(format(Key.GMM_UNCERTAINTY)).append(gmmUncertainty)
diff --git a/src/org/opensha2/calc/Site.java b/src/org/opensha2/calc/Site.java
index 06c0b679f..76ae1ba99 100644
--- a/src/org/opensha2/calc/Site.java
+++ b/src/org/opensha2/calc/Site.java
@@ -14,6 +14,7 @@ import org.opensha2.geo.Location;
 import org.opensha2.gmm.GroundMotionModel;
 import org.opensha2.util.Named;
 
+import com.google.common.base.Strings;
 import com.google.common.collect.Range;
 import com.google.gson.JsonArray;
 import com.google.gson.JsonDeserializationContext;
@@ -51,14 +52,14 @@ public class Site implements Named {
 	public static final double MAX_Z1P0 = 2.0;
 
 	/** The name used for {@code Site}s with no supplied name. */
-	public static final String NO_NAME = "Unnamed Site";
+	public static final String NO_NAME = "Unnamed";
 
 	/** {@link #MIN_VS_30} and {@link #MAX_VS_30} as a closed {@code Range}. */
 	public static final Range<Double> VS30_RANGE = Range.closed(MIN_VS_30, MAX_VS_30);
-	
+
 	/** {@link #MIN_Z2P5} and {@link #MAX_Z2P5} as a closed {@code Range}. */
 	public static final Range<Double> Z2P5_RANGE = Range.closed(MIN_Z2P5, MAX_Z2P5);
-	
+
 	/** {@link #MIN_Z1P0} and {@link #MAX_Z1P0} as a closed {@code Range}. */
 	public static final Range<Double> Z1P0_RANGE = Range.closed(MIN_Z1P0, MAX_Z1P0);
 
@@ -133,8 +134,11 @@ public class Site implements Named {
 	}
 
 	@Override public String toString() {
-		return String.format("Site: {name=%s, loc=%s, vs30=%s, vsInf=%s, z1p0=%s, z2p5=%s}", name,
-			location, vs30, vsInferred, z1p0, z2p5);
+		return new StringBuilder(Strings.padEnd(name, 16, ' '))
+			.append(String.format("%.3f %.3f Vs30=%s ", location.lon(), location.lat(), vs30))
+			.append(vsInferred ? "inferred " : "measured ")
+			.append(String.format("Z1.0=%s Z2.5=%s", z1p0, z2p5))
+			.toString();
 	}
 
 	@Override public String name() {
diff --git a/src/org/opensha2/calc/SiteSet.java b/src/org/opensha2/calc/SiteSet.java
index f697395e9..490fe074f 100644
--- a/src/org/opensha2/calc/SiteSet.java
+++ b/src/org/opensha2/calc/SiteSet.java
@@ -12,6 +12,7 @@ import static org.opensha2.calc.Site.Key.Z1P0;
 import static org.opensha2.calc.Site.Key.Z2P5;
 import static org.opensha2.geo.BorderType.MERCATOR_LINEAR;
 import static org.opensha2.util.TextUtils.ALIGN_COL;
+import static org.opensha2.util.TextUtils.format;
 
 import java.io.IOException;
 import java.lang.reflect.Type;
@@ -117,9 +118,10 @@ final class SiteSet implements Iterable<Site> {
 			.append(" [size=").append(size()).append("]");
 		if (region == null) {
 			for (Site site : Iterables.limit(sites, TO_STRING_LIMIT)) {
-				sb.append(TextUtils.NEWLINE)
-					.append(repeat(" ", ALIGN_COL - 4))
-					.append(site);
+				sb.append(format("Site")).append(site);
+//				sb.append(TextUtils.NEWLINE)
+//					.append(repeat(" ", ALIGN_COL - 4))
+//					.append(site);
 			}
 			if (sites.size() > TO_STRING_LIMIT) {
 				int delta = sites.size() - TO_STRING_LIMIT;
diff --git a/src/org/opensha2/util/TextUtils.java b/src/org/opensha2/util/TextUtils.java
index 9dfad5696..a7cc5f146 100644
--- a/src/org/opensha2/util/TextUtils.java
+++ b/src/org/opensha2/util/TextUtils.java
@@ -2,8 +2,7 @@ package org.opensha2.util;
 
 import static com.google.common.base.Preconditions.checkArgument;
 import static com.google.common.base.Strings.padStart;
-import static org.opensha2.util.TextUtils.ALIGN_COL;
-import static org.opensha2.util.TextUtils.NEWLINE;
+import static com.google.common.base.Strings.repeat;
 
 import java.util.Map;
 
@@ -20,6 +19,9 @@ public class TextUtils {
 
 	public static final String NEWLINE = StandardSystemProperty.LINE_SEPARATOR.value();
 	public static final int ALIGN_COL = 24;
+	private static final int MAX_COL = 100;
+	private static final int DELTA_COL = MAX_COL - ALIGN_COL - 2;
+	private static final String INDENT = NEWLINE + repeat(" ", ALIGN_COL + 2);
 	
 	
 	private static final Joiner.MapJoiner MAP_JOIN = Joiner.on(", ").withKeyValueSeparator(": ");
@@ -35,8 +37,23 @@ public class TextUtils {
 	public static String format(String s) {
 		return NEWLINE + padStart(s, ALIGN_COL, ' ') + ": ";
 	}
-
-
+	
+	public static String wrap(String s) {
+		return wrap(s, false);
+	}
+	
+	/*
+	 * Used internally; pad flag indents lines consistent with format(s)
+	 */
+	private static String wrap(String s, boolean pad) {
+		if (s.length() <= DELTA_COL) return pad ? INDENT + s : s;
+		StringBuilder sb = new StringBuilder();
+		int lastCommaIndex = s.substring(0, DELTA_COL).lastIndexOf(',') + 1;
+		if (pad) sb.append(INDENT);
+		sb.append(s.substring(0, lastCommaIndex));
+		sb.append(wrap(s.substring(lastCommaIndex).trim(), true));
+		return sb.toString();
+	}
 
 	/**
 	 * Verifies that the supplied {@code String} is neither {@code null} or
-- 
GitLab