examples directory cleanup and testing

.gitignore

@@ -5,6 +5,7 @@
 /docs
 /tmp
 /results
+/etc/results
 Scratch*.java
 /src/META-INF
 /etc/examples/results

etc/examples/README.md

-#### Tutorial
-
 ##### Hazard Curves
-The simplest way to run the HazardCurve 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 examples directory and run:
+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.HazardCurve model
+java -cp ../dist/nshmp-haz.jar org.opensha2.programs.HazardCalc peer/models/Set1-Case1
 ```
-By way of example, the [configuration file](https://github.com/usgs/nshmp-haz/blob/master/etc/examples/model/config.json) in the model above omits any site data and a default Los Angeles site is used. Remember that [calculation configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration) parameters need not be supplied. The result of this calculation should be available as a single file containing one hazard curve for PGA in a newly created 'results' directory.
-
+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](/usgs/nshmp-haz/blob/master/etc/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.HazardCurve model config-sites.json
+java -cp ../dist/nshmp-haz.jar org.opensha2.programs.HazardCalc peer/models/Set1-Case1 examples/config-sites.json
 ```
 In this case:
-* the `truncationLevel` has been increased to `3.0`.
+* 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.
+* 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 intensity measure type.
+The 'results' directory should now include 3 files, one for each `imt`.
 
 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.HazardCurve model config-sites.json sites-wus.csv
+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
 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.HazardCurve model config-region.json
+java -cp ../dist/nshmp-haz.jar org.opensha2.programs.HazardCalc peer/models/Set1-Case1 examples/config-region-sf.json
 ```
 

etc/examples/config-region.json → etc/examples/config-region-la.json

 {
+  "exceedanceModel": "TRUNCATION_UPPER_ONLY",
   "truncationLevel": 3.0,
   "imts": ["PGA", "SA0P2", "SA1P0"],
   "customImls": {
@@ -14,10 +15,8 @@
         [-118.5, 33.8],
         [-118.0, 34.3]
       ],
-      "vs30": 459,
-      "vsInf": true,
-      "z1p0": 0.48,
-      "z2p5": 1.62
+      "vs30": ,
+      "vsInf": true
     }
   }
 }
\ No newline at end of file

etc/examples/config-region-sf.json

+{
+  "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

etc/examples/config-sites.json

 {
+  "exceedanceModel": "TRUNCATION_UPPER_ONLY",
   "truncationLevel": 3.0,
   "imts": ["PGA", "SA0P2", "SA1P0"],
   "customImls": {
@@ -8,14 +9,14 @@
   },
   "sites": [
     {
-    "name": "Los Angeles",
-    "location": [-118.25, 34.05],
+    "name": "San Francisco",
+    "location": [-122.40, 37.75],
     "vs30": 760,
     "vsInf": true
     },
     {
-    "name": "San Francisco",
-    "location": [-122.40, 37.75],
+    "name": "Oakland",
+    "location": [-122.25, 37.80],
     "vs30": 760,
     "vsInf": true
     }

etc/examples/sites-sf.csv

+#
+# 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

etc/matlab/README.md

@@ -5,9 +5,9 @@ All recent versions of Matlab include a Java runtime environment and it is there
 
 #### Requirements
 
-1. Matlab R2013B or higher (nshmp-haz targets Java 7; prior versions of Matlab use Java 6).
-2. A [build](/usgs/nshmp-haz/wiki/Building-&-Running) of nshmp-haz.
-3. nshmp-haz.jar on Matlab's classpath. Save a file with the name `javaclasspath.txt` to the Matlab preferences directory, as specified by the `prefdir` command, and with contents:
+1.  Matlab R2013B or higher (nshmp-haz targets Java 7; prior versions of Matlab use Java 6).
+2.  A [build](/usgs/nshmp-haz/wiki/Building-&-Running) of nshmp-haz.
+3.  nshmp-haz.jar on Matlab's classpath. Save a file with the name `javaclasspath.txt` to the Matlab preferences directory, as specified by the `prefdir` command, and with contents:
 
   ```
   <before>

src/org/opensha2/programs/HazardCalc.java

@@ -44,7 +44,7 @@ import com.google.common.base.Throwables;
  */
 public class HazardCalc {
 
-	private static final int FLUSH_LIMIT = 2;
+	private static final int FLUSH_LIMIT = 5;
 
 	/**
 	 * Entry point for a hazard calculation.