From 9703f2ed94c26d110cf3806ae56db63aa973b756 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Thu, 30 Nov 2017 12:58:06 -0700
Subject: [PATCH] ex readme/config updates with dir struct
---
etc/examples/1-hazard-curve/README.md | 14 ++++-
etc/examples/2-custom-config/README.md | 14 +++++
etc/examples/3-sites-file/README.md | 14 +++++
etc/examples/4-hazard-map/README.md | 14 +++++
etc/examples/5-complex-model/README.md | 20 +++++++
etc/examples/5-complex-model/config-map.json | 2 +-
.../5-complex-model/config-sites.json | 2 +-
etc/examples/6-enhanced-output/README.md | 28 ++++++++-
etc/examples/7-deaggregation/README.md | 57 ++++++++++++++++++-
etc/examples/8-probabilities/README.md | 16 +++++-
etc/examples/8-probabilities/config-map.json | 3 +-
.../8-probabilities/config-sites.json | 3 +-
12 files changed, 178 insertions(+), 9 deletions(-)
diff --git a/etc/examples/1-hazard-curve/README.md b/etc/examples/1-hazard-curve/README.md
index 9226bf0b3..ae19cae4e 100644
--- a/etc/examples/1-hazard-curve/README.md
+++ b/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.
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
index e508d0b33..42528d0f5 100644
--- a/etc/examples/2-custom-config/README.md
+++ b/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)
diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
index 3b99f5fce..a69c53d0f 100644
--- a/etc/examples/3-sites-file/README.md
+++ b/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)
diff --git a/etc/examples/4-hazard-map/README.md b/etc/examples/4-hazard-map/README.md
index c2ce5fb67..f4dd6e5e9 100644
--- a/etc/examples/4-hazard-map/README.md
+++ b/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)
diff --git a/etc/examples/5-complex-model/README.md b/etc/examples/5-complex-model/README.md
index 850a208ec..2cfd63b05 100644
--- a/etc/examples/5-complex-model/README.md
+++ b/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)
diff --git a/etc/examples/5-complex-model/config-map.json b/etc/examples/5-complex-model/config-map.json
index eb5b93211..52b01318b 100644
--- a/etc/examples/5-complex-model/config-map.json
+++ b/etc/examples/5-complex-model/config-map.json
@@ -3,6 +3,6 @@
"imts": ["SA1P0", "SA2P0"]
},
"output": {
- "directory": "curves-map"
+ "directory": "hazout-map"
}
}
diff --git a/etc/examples/5-complex-model/config-sites.json b/etc/examples/5-complex-model/config-sites.json
index 5db53ac58..31a32a602 100644
--- a/etc/examples/5-complex-model/config-sites.json
+++ b/etc/examples/5-complex-model/config-sites.json
@@ -3,7 +3,7 @@
"imts": ["SA1P0", "SA2P0"]
},
"output": {
- "directory": "curves-sites",
+ "directory": "hazout-sites",
"flushLimit": 1
}
}
diff --git a/etc/examples/6-enhanced-output/README.md b/etc/examples/6-enhanced-output/README.md
index 040ccb1c2..5f6bfd7d7 100644
--- a/etc/examples/6-enhanced-output/README.md
+++ b/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)
diff --git a/etc/examples/7-deaggregation/README.md b/etc/examples/7-deaggregation/README.md
index c2139daf4..d65e35c68 100644
--- a/etc/examples/7-deaggregation/README.md
+++ b/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)
diff --git a/etc/examples/8-probabilities/README.md b/etc/examples/8-probabilities/README.md
index 5ba695c87..acaca18e4 100644
--- a/etc/examples/8-probabilities/README.md
+++ b/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
+```
+
diff --git a/etc/examples/8-probabilities/config-map.json b/etc/examples/8-probabilities/config-map.json
index 44e663c7e..8fe147938 100644
--- a/etc/examples/8-probabilities/config-map.json
+++ b/etc/examples/8-probabilities/config-map.json
@@ -1,6 +1,7 @@
{
"output": {
- "dataTypes": ["SOURCE"]
+ "dataTypes": ["SOURCE"],
+ "directory": "hazout-prob-map"
},
"rate": {
"distance": 10.0,
diff --git a/etc/examples/8-probabilities/config-sites.json b/etc/examples/8-probabilities/config-sites.json
index 2c5b56ccf..fa865014f 100644
--- a/etc/examples/8-probabilities/config-sites.json
+++ b/etc/examples/8-probabilities/config-sites.json
@@ -1,5 +1,6 @@
{
"output": {
- "dataTypes": ["SOURCE"]
+ "dataTypes": ["SOURCE"],
+ "directory": "hazout-rate-sites"
}
}
--
GitLab