update exmaples, fix site file extension check

etc/examples/1-hazard-curve/README.md

@@ -14,11 +14,9 @@ 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 total mean hazard curves for PGA in a newly created `hazout` directory. In this example,
- the calculation configuration was derived from the model directory and the site was specified
-  as a comma-delimited string. The string must have the form:
-   `name,lon,lat[,vs30,vsInf[,z1p0,z2p5]]`, where `vs30`, `vsInf`, `z1p0`, and `z2p5`
-   are optional. See the [site specification](https://github.com/usgs/nshmp-haz/wiki/sites)
-   page for more details.
+the calculation configuration was derived from the model directory and the site is defined in
+file `site.csv`. See the [site specification](https://github.com/usgs/nshmp-haz/wiki/sites)
+page for more details.
 
 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)

etc/examples/1-hazard-curve/site.csv

+name,lon,lat
+Test Site, -122.0, 38.0

etc/examples/2-custom-config/README.md

@@ -5,7 +5,7 @@ __Working directory:__ `/path/to/nshmp-haz/etc/examples/2-custom-config`
 Navigate to the directory above and execute the following:
 
 ```Shell
-hazard ../../peer/models/Set1-Case1 "San Francisco, -122.40, 37.75" config.json
+hazard ../../peer/models/Set1-Case1 site.csv config.json
 ```
 
 In this example we've overridden the configuration supplied by the model. Specifically:

etc/examples/2-custom-config/site.csv

+name,lon,lat
+San Francisco, -122.40, 37.75

etc/examples/3-sites-file/README.md

@@ -19,9 +19,6 @@ The [site specification](https://github.com/usgs/nshmp-haz/wiki/sites)
 wiki page provides details on the two file formats. Note that with either format,
 if the name of a site is supplied, it will be included in the first column of any output curve files.
 
-Note that both formats ([CSV](sites.csv) and [GeoJSON](sites.geojson)) are elegantly
-rendered by GitHub.
-
 __Results directory structure:__
 
 ```text

etc/examples/4-hazard-map/README.md

@@ -4,8 +4,8 @@ __Working directory:__ `/path/to/nshmp-haz/etc/examples/4-hazard-map`
 
 A hazard map is just a collection of values plucked from a lot of hazard curves.
 To compute curves at reqularly spaced intervals in latitude and longitude over a region,
- a [GeoJSON site file](https://github.com/usgs/nshmp-haz/wiki/sites#geojson-format-geojson)
- may instead specify a polygon and a site spacing.
+a [GeoJSON site file](https://github.com/usgs/nshmp-haz/wiki/sites#geojson-format-geojson)
+may instead specify a polygon and a site spacing.
 
 ```Shell
 hazard ../../peer/models/Set1-Case1 map.geojson config.json

etc/examples/5-complex-model/README.md

@@ -4,30 +4,33 @@ __Working directory:__ `/path/to/nshmp-haz/etc/examples/5-complex-model`
 
 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. `nshmp-haz` uses an
+2018 USGS National Seismic Hazard Model (NSHM) for the western U.S. `nshmp-haz` uses an
 in-memory source model. The USGS NSHMs are quite large, so it's helpful to increase the amount
 memory available to Java when calling `HazardCalc`. For example, set your alias to:
 
 ```Shell
-alias hazard='java -Xms1g -Xmx4g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.HazardCalc'
+alias hazard='java -Xms4g -Xmx8g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.HazardCalc'
 ```
 
-This will increase the minimum amount of memory Java requires to 1GB and will allow it to claim
-up to 4GB, assuming that much is available.
+This will increase the minimum amount of memory Java requires to 4GB and will allow it to claim
+up to 8GB, assuming that much is available.
 
-First, clone the 2008 USGS NSHM. Assuming you are in the current working directory (above), the
-following will create a copy of the model adjacent to nshmp-haz:
+First, clone the USGS CONUS NSHM repository and checkout the 2018 CONUS NSHM tag. Assuming you
+are in the current working directory (above), the following will create a copy of the model
+adjacent to nshmp-haz:
 
 ```Shell
-git clone https://github.com/usgs/nshm-cous-2008.git ../../../../nshm-cous-2008
+git clone https://code.usgs.gov/ghsc/nshmp/nshms/nshm-conus.git ../../../../nshm-conus
+# git checkout tags/5.1.0 -b 2018_CONUS_NSHM
 ```
 
-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. at 1.0s and 2.0s
+TODO: checkout tag for nshm-conus-2018 release (current 5.1.0 tag does not load)
+
+To compute hazard for a few sites in the Western U.S. at 1.0s and 2.0s
 spectral periods, execute:
 
 ```Shell
-hazard ../../../../nshm-cous-2008/Western\ US sites.geojson config-sites.json
+hazard ../../../../nshm-conus sites.geojson config-sites.json
 ```
 
 Note that more complex models take longer to initialize, although this only occurs once per
@@ -37,12 +40,12 @@ use all cores available by default and therefore performs better on multi-core s
 To compute a small, low-resolution map for the central San Francisco bay area, execute:
 
 ```Shell
-hazard ../../../../nshm-cous-2008/Western\ US map.geojson config-map.json
+hazard ../../../../nshm-conus map.geojson 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. Note that in the above two examples we specified different output directories in the
-config files for each calculation.
+might take. This small coarse map may take 10 minutes to complete. Note that in the above two
+examples we specified different output directories in the config files for each calculation.
 
 __Results directory structure:__
 

etc/examples/5-complex-model/config-sites.json

@@ -3,7 +3,6 @@
     "imts": ["SA1P0", "SA2P0"]
   },
   "output": {
-    "directory": "hazout-sites",
-    "flushLimit": 1
+    "directory": "hazout-sites"
   }
 }

etc/examples/6-enhanced-output/README.md

@@ -4,25 +4,26 @@ __Working directory:__ `/path/to/nshmp-haz/etc/examples/6-enhanced-output`
 
 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:
+each source type and ground motion model (GMM) used in the 2018 NSHM (cloned in the previous
+example):
 
 ```Shell
-hazard ../../../../nshm-cous-2008/Western\ US sites.geojson config.json
+hazard ../../../../nshm-conus sites.geojson config.json
 ```
 
-The [config](https://github.com/usgs/nshmp-haz/blob/master/etc/examples/6-enhanced-output/config.json)
-file for this example specified `GMM` and `SOURCE` as
-[output data types](https://github.com/usgs/nshmp-haz/wiki/configuration#calculation-configuration-parameters).
- Note that the output curves directory now contains additional directories of curves by source
- type and GMM. We also specified an
- [output flush limit](https://github.com/usgs/nshmp-haz/wiki/configuration#calculation-configuration-parameters)
-  of `1`. Doing so gives feedback on how long it takes each site calculation to run on a particular system.
+The config file for this example, `config.json`, specified `GMM` and `SOURCE` as
+[output data types][output_types]. Note that the output curves directory now contains additional
+directories of curves by source type and GMM.
 
-See the `nshmp-haz` wiki and Javacocs 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?gov/usgs/earthquake/nshmp/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?gov/usgs/earthquake/nshmp/gmm/Gmm.html)).
+[output_types]: ../../../docs/pages/Calculation-Configuration.md#calculation-configuration
+
+See the `nshmp-haz` wiki and javadocs for more information on source types ([Wiki][source_wiki],
+[JavaDoc][source_javadoc]) and GMMs ([Wiki][gmm_wiki], [JavaDoc][gmm_javadoc]).
+
+[source_wiki]: ../../../docs/pages/Source-Types.md
+[source_javadoc]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/model/SourceType.html
+[gmm_wiki]: ./../../docs/pages/Ground-Motion-Models.md
+[gmm_javadoc]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/package-summary.html
 
 __Results directory structure:__
 
@@ -32,19 +33,25 @@ __Results directory structure:__
       ├─ config.json
       ├─ HazardCalc.log
       ├─ PGA/
+      │   ├─ curves-truncated.csv
       │   ├─ curves.csv
+      │   ├─ map.csv
       │   ├─ gmm/
-      │   │   ├─ AB_03_CASCADIA_SLAB/
-      │   │   │   └─ curves.csv
+      │   │   ├─ AM_09_INTERFACE_BASIN/
+      │   │   │   ├─ curves.csv
+      │   │   │   └─ map.csv
       │   │   ├─ ...
-      │   │   └─ ZHAO_06_INTERFACE/
-      │   │       └─ curves.csv
+      │   │   └─ ZHAO_06_SLAB_BASIN/
+      │   │       ├─ curves.csv
+      │   │       └─ map.csv
       │   └─ source/
       │       ├─ FAULT/
-      │       │   └─ curves.csv
+      │       │   ├─ curves.csv
+      │       │   └─ map.csv
       │       ├─ ...
       │       └─ SLAB/
-      │           └─ curves.csv
+      │           ├─ curves.csv
+      │           └─ map.csv
       ├─ SA0P2/
       │   └─ ...
       └─ SA1P0/

etc/examples/6-enhanced-output/config.json

 {
+  "hazard": {
+    "imts": ["PGA", "SA0P1", "SA0P5", "SA1P0", "SA2P0"]
+  },
   "output": {
-    "dataTypes": ["TOTAL", "GMM", "SOURCE"],
-    "flushLimit": 1
+    "dataTypes": ["TOTAL", "GMM", "SOURCE"]
   }
 }

etc/examples/7-deaggregation/README.md

@@ -8,25 +8,21 @@ file of distance, magnitude, and epsilon bins, and a text file of summary statis
 contributing sources. For this, it can be helpful to create a second system alias:
 
 ```Shell
-alias deagg='java -Xms1g -Xmx4g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.DeaggCalc'
+alias deagg='java -Xms4g -Xmx8g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.DeaggCalc'
 ```
 
 `DeaggCalc` is similar to `HazardCalc` in every way except that the return-period of interest
 must be specified. For example, execute:
 
 ```Shell
-deagg ../../../../nshm-cous-2008/Western\ US sites.geojson 2475 config.json
+deagg ../../../../nshm-conus sites.geojson 2475 config.json
 ```
 
 The results of the deaggregation are saved along with hazard curves in `deagg` directories.
- As with `HazardCalc`, if the `GMM` ddata type has been specified (as it has in the
- [config](https://github.com/usgs/nshmp-haz/blob/master/etc/examples/7-deaggregation/config.json)
- file for this example) additional deaggregation results for each GMM are generated as well.
- Deaggregations by individual `SOURCE` type are also possible.
-
-See the following pages for more information on
-[deaggregation](https://github.com/usgs/nshmp-haz/wiki/about-deaggregation)
-and the meaning of [epsilon](https://github.com/usgs/nshmp-haz/wiki/what-is-epsilon%3F).
+As with `HazardCalc`, if the `GMM` ddata type has been specified (as it has in the
+[config](../../../docs/pages/Calculation-Configuration.md#calculation-configuration)
+file for this example) additional deaggregation results for each GMM are generated as well.
+Deaggregations by individual `SOURCE` type are also possible.
 
 __Results directory structure:__
 
@@ -36,8 +32,9 @@ __Results directory structure:__
       ├─ config.json
       ├─ DeaggCalc.log
       ├─ PGA/
+      │   ├─ curves-truncated.csv
       │   ├─ curves.csv
-      │   ├─ deagg/
+      │   ├─ disagg/
       │   │   ├─ Los Angeles CA/
       │   │   │   ├─ data.csv
       │   │   │   └─ summary.txt
@@ -51,9 +48,9 @@ __Results directory structure:__
       │   │       ├─ data.csv
       │   │       └─ summary.txt
       │   └─ gmm/
-      │       ├─ AB_03_CASCADIA_SLAB/
+      │       ├─ AM_09_INTERFACE_BASIN/
       │       │   ├─ curves.csv
-      │       │   └─ deagg/
+      │       │   └─ disagg/
       │       │       ├─ San Francisco CA/
       │       │       │   ├─ data.csv
       │       │       │   └─ summary.txt
@@ -61,7 +58,7 @@ __Results directory structure:__
       │       │           ├─ data.csv
       │       │           └─ summary.txt
       │       ├─ ...
-      │       ├─ CB_08/
+      │       ├─ CB_14_BASIN/
       │       │   ├─ curves.csv
       │       │   └─ deagg/
       │       │       ├─ Los Angeles CA/
@@ -77,14 +74,13 @@ __Results directory structure:__
       │       │           ├─ data.csv
       │       │           └─ summary.txt
       │       └─ ...
-      ├─ SA0P2/
+      ├─ SA0P1/
       │   └─ ...
-      └─ SA1P0/
-          └─ ...
+      └─ ...
 ```
 
 Note that in the output above, there are only deaggregation results for
-subduction GMMs (e.g. `AB_03_CASCADIA_SLAB`) for sites closer to the Cascadia subduction zone;
+subduction GMMs (e.g. `AM_09_INTERFACE_BASIN`) for sites closer to the Cascadia subduction zone;
 empty results will not be saved.
 
 <!-- markdownlint-disable MD001 -->

etc/examples/7-deaggregation/config.json

 {
+  "hazard": {
+    "imts": ["PGA", "SA0P1", "SA0P5", "SA1P0", "SA2P0"]
+  },
   "output": {
-    "dataTypes": ["TOTAL", "GMM"],
-    "flushLimit": 1
+    "dataTypes": ["TOTAL", "GMM"]
   }
 }

etc/examples/8-probabilities/README.md

@@ -13,19 +13,19 @@ all sources should be included, and a `timespan` used for conversion to Poisson
 For this example, the following system alias is helpful:
 
 ```Shell
-alias rate='java -Xms1g -Xmx4g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.RateCalc'
+alias rate='java -Xms4g -Xmx8g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.RateCalc'
 ```
 
-Assuming a copy of the 2008 USGS NSHM is available (see [Example 5](../5-complex-model)), execute:
+Assuming a copy of the 2018 USGS NSHM is available (see [Example 5](../5-complex-model)), execute:
 
 ```Shell
-rate ../../../../nshm-cous-2008/Western\ US sites.csv config-sites.json
+rate ../../../../nshm-conus sites.csv config-sites.json
 ```
 
 to generate incremental, annual-rate output for a list of sites, or
 
 ```Shell
-rate ../../../../nshm-cous-2008/Western\ US map.geojson config-map.json
+rate ../../../../nshm-conus map.geojson config-map.json
 ```
 
 to generate a map of cumulative Poisson probabilities (i.e. P ≥ M).

src/main/java/gov/usgs/earthquake/nshmp/HazardCalc.java

@@ -143,7 +143,7 @@ public class HazardCalc {
     Path path = Paths.get(arg);
     log.info("Sites file: " + path.toAbsolutePath().normalize());
     String fname = arg.toLowerCase();
-    checkArgument(fname.endsWith(".csv") || fname.endsWith(".json"),
+    checkArgument(fname.endsWith(".csv") || fname.endsWith(".geojson"),
         "Sites file [%s] must be a path to a *.csv or *.geojson file", arg);
 
     try {