ex readme/config updates with dir struct

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

@@ -11,11 +11,21 @@ hazard ../../peer/models/Set1-Case1 "Test Site, -122.0, 38.0"
 
 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 total mean hazard curves for PGA in a newly created 'curves' 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 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.
 
 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 all output is written to a `curves` directory by default, but the output destination can be specified via the [`output.directory`](https://github.com/usgs/nshmp-haz/wiki/configuration#config-output) parameter. In addition to hazard curves, the calculation configuration and a log of the calculation are also saved.
+Also note that all output is written to a `hazout` directory by default, but the output destination can be specified via the [`output.directory`](https://github.com/usgs/nshmp-haz/wiki/configuration#config-output) parameter. In addition to hazard curves, the calculation configuration and a log of the calculation are also saved.
+
+__Results directory structure:__
+```
+1-hazard-curve/
+  └─ hazout/
+      ├─ config.json
+      ├─ HazardCalc.log
+      └─ PGA/
+          └─ curves.csv
+```
 
 In the next example, we'll override the model supplied configuration with a custom file.
 

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

@@ -18,4 +18,18 @@ In this example we've overridden the configuration supplied by the model. Specif
 
 See the [configuration specification](https://github.com/usgs/nshmp-haz/wiki/configuration) for details on default values and supported options and formats.
 
+__Results directory structure:__
+```
+2-custom-config/
+  └─ hazout/
+      ├─ config.json
+      ├─ HazardCalc.log
+      ├─ PGA/
+      │   └─ curves.csv
+      ├─ SA0P2/
+      │   └─ curves.csv
+      └─ SA1P0/
+          └─ curves.csv
+```
+
 #### Next: [Example 3 – Using a custom sites file](../3-sites-file)

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

@@ -19,4 +19,18 @@ The [site specification](https://github.com/usgs/nshmp-haz/wiki/sites) wiki page
 
 Note that both formats ([CSV](sites.csv) and [GeoJSON](sites.geojson)) are elegantly rendered by GitHub.
 
+__Results directory structure:__
+```
+3-sites-file/
+  └─ hazout/
+      ├─ config.json
+      ├─ HazardCalc.log
+      ├─ PGA/
+      │   └─ curves.csv
+      ├─ SA0P2/
+      │   └─ curves.csv
+      └─ SA1P0/
+          └─ curves.csv
+```
+
 #### Next: [Example 4 – A simple hazard map](../4-hazard-map)

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

@@ -9,4 +9,18 @@ A hazard map is just a collection of values plucked from a lot of hazard curves.
 hazard ../../peer/models/Set1-Case1 map.geojson config.json
 ```
 
+__Results directory structure:__
+```
+4-hazard-map/
+  └─ hazout/
+      ├─ config.json
+      ├─ HazardCalc.log
+      ├─ PGA/
+      │   └─ curves.csv
+      ├─ SA0P2/
+      │   └─ curves.csv
+      └─ SA1P0/
+          └─ curves.csv
+```
+
 #### Next: [Example 5 – A more complex model](../5-complex-model)

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

@@ -33,4 +33,24 @@ hazard ../../../../nshm-cous-2008/Western\ US 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.
 
+__Results directory structure:__
+```
+5-complex-model/
+  ├─ hazout-sites/
+  │   ├─ config.json
+  │   ├─ HazardCalc.log
+  │   ├─ SA1P0/
+  │   │   └─ curves.csv
+  │   └─ SA2P0/
+  │       └─ curves.csv
+  │
+  └─ hazout-map/
+      ├─ config.json
+      ├─ HazardCalc.log
+      ├─ SA1P0/
+      │   └─ curves.csv
+      └─ SA2P0/
+          └─ curves.csv
+```
+
 #### Next: [Example 6 – Enhanced output](../6-enhanced-output)

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

@@ -3,6 +3,6 @@
     "imts": ["SA1P0", "SA2P0"]
   },
   "output": {
-    "directory": "curves-map"
+    "directory": "hazout-map"
   }
 }

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

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

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

@@ -11,7 +11,33 @@ hazard ../../../../nshm-cous-2008/Western\ US 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 curve 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.
 
-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?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)).
+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)).
+
+__Results directory structure:__
+```
+6-enhanced-output/
+  └─ hazout/
+      ├─ config.json
+      ├─ HazardCalc.log
+      ├─ PGA/
+      │   ├─ curves.csv
+      │   ├─ gmm/
+      │   │   ├─ AB_03_CASCADIA_SLAB/
+      │   │   │   └─ curves.csv
+      │   │   ├─ ...
+      │   │   └─ ZHAO_06_INTERFACE/
+      │   │       └─ curves.csv
+      │   └─ source/
+      │       ├─ FAULT/
+      │       │   └─ curves.csv
+      │       ├─ ...
+      │       └─ SLAB/
+      │           └─ curves.csv
+      ├─ SA0P2/
+      │   └─ ...
+      └─ SA1P0/
+          └─ ...
+```
 
 #### Next: [Example 7 – Deaggregation](../7-deaggregation)
 

etc/examples/7-deaggregation/README.md

@@ -15,9 +15,64 @@ alias deagg='java -Xms1g -Xmx4g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar
 deagg ../../../../nshm-cous-2008/Western\ US sites.geojson 2475 config.json
 ```
 
-The results of the deaggregation are saved to a `deagg` directory along with hazard curves. As with `HazardCalc`, if `GMM` 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.
+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).
 
+__Results directory structure:__
+```
+7-deaggregation/
+  └─ hazout/
+      ├─ config.json
+      ├─ DeaggCalc.log
+      ├─ PGA/
+      │   ├─ curves.csv
+      │   ├─ deagg/
+      │   │   ├─ Los Angeles CA/
+      │   │   │   ├─ data.csv
+      │   │   │   └─ summary.txt
+      │   │   ├─ Salt Lake City UT/
+      │   │   │   ├─ data.csv
+      │   │   │   └─ summary.txt
+      │   │   ├─ San Francisco CA/
+      │   │   │   ├─ data.csv
+      │   │   │   └─ summary.txt
+      │   │   └─ Seattle WA/
+      │   │       ├─ data.csv
+      │   │       └─ summary.txt
+      │   └─ gmm/
+      │       ├─ AB_03_CASCADIA_SLAB/
+      │       │   ├─ curves.csv
+      │       │   └─ deagg/
+      │       │       ├─ San Francisco CA/
+      │       │       │   ├─ data.csv
+      │       │       │   └─ summary.txt
+      │       │       └─ Seattle WA/
+      │       │           ├─ data.csv
+      │       │           └─ summary.txt
+      │       ├─ ...
+      │       ├─ CB_08/
+      │       │   ├─ curves.csv
+      │       │   └─ deagg/
+      │       │       ├─ Los Angeles CA/
+      │       │       │   ├─ data.csv
+      │       │       │   └─ dsummary.txt
+      │       │       ├─ Salt Lake City UT/
+      │       │       │   ├─ data.csv
+      │       │       │   └─ summary.txt
+      │       │       ├─ San Francisco CA/
+      │       │       │   ├─ data.csv
+      │       │       │   └─ summary.txt
+      │       │       └─ Seattle WA/
+      │       │           ├─ data.csv
+      │       │           └─ summary.txt
+      │       └─ ...
+      ├─ SA0P2/
+      │   └─ ...
+      └─ 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; empty results will not be saved.
+
 #### Next: [Example 8 – Earthquake probabilities and rates](../8-probabilities)
 

etc/examples/8-probabilities/README.md

@@ -25,4 +25,18 @@ rate ../../../../nshm-cous-2008/Western\ US map.geojson config-map.json
 
 to generate a map of cumulative Poisson probabilities (i.e. P ≥ M).
 
-Unless an output directory is specified in a supplied config, output will be placed in either an `eq-rate` or `eq-prob` directory. Like `HazardCalc`, `RateCalc` observes the `config.output.curveTypes` `SOURCE` option and will include a `source` directory with rates or probabilities for all contributing source types.
+Like `HazardCalc`, `RateCalc` observes the `config.output.dataTypes` `SOURCE` option and will include a `source` directory with rates or probabilities for all contributing source types.
+
+__Results directory structure:__
+```
+8-probabilities/
+  ├─ hazout-rate-sites/
+  │   ├─ config.json
+  │   ├─ RateCalc.log
+  │   └─ rates.csv
+  └─ hazout-prob-map/
+      ├─ config.json
+      ├─ RateCalc.log
+      └─ probs.csv
+```
+

etc/examples/8-probabilities/config-map.json

 {
   "output": {
-    "dataTypes": ["SOURCE"]
+    "dataTypes": ["SOURCE"],
+    "directory": "hazout-prob-map"
   },
   "rate": {
     "distance": 10.0,

etc/examples/8-probabilities/config-sites.json

 {
   "output": {
-    "dataTypes": ["SOURCE"]
+    "dataTypes": ["SOURCE"],
+    "directory": "hazout-rate-sites"
   }
 }