From 724f5dc584717ac5145904d54b053dd9958a49d1 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Mon, 18 Jan 2016 21:43:58 -0700
Subject: [PATCH] examples directory cleanup and testing
---
.gitignore | 1 +
etc/examples/README.md | 21 +++++++---------
...nfig-region.json => config-region-la.json} | 7 +++---
etc/examples/config-region-sf.json | 22 +++++++++++++++++
etc/examples/config-sites.json | 9 +++----
etc/examples/sites-sf.csv | 24 +++++++++++++++++++
etc/matlab/README.md | 6 ++---
src/org/opensha2/programs/HazardCalc.java | 2 +-
8 files changed, 68 insertions(+), 24 deletions(-)
rename etc/examples/{config-region.json => config-region-la.json} (89%)
create mode 100644 etc/examples/config-region-sf.json
create mode 100644 etc/examples/sites-sf.csv
diff --git a/.gitignore b/.gitignore
index 6895b20f5..d8a429dbb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
/docs
/tmp
/results
+/etc/results
Scratch*.java
/src/META-INF
/etc/examples/results
diff --git a/etc/examples/README.md b/etc/examples/README.md
index 230a68e05..1ffb23593 100644
--- a/etc/examples/README.md
+++ b/etc/examples/README.md
@@ -1,32 +1,29 @@
-#### 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
```
diff --git a/etc/examples/config-region.json b/etc/examples/config-region-la.json
similarity index 89%
rename from etc/examples/config-region.json
rename to etc/examples/config-region-la.json
index 5a17e7155..3e700ff36 100644
--- a/etc/examples/config-region.json
+++ b/etc/examples/config-region-la.json
@@ -1,4 +1,5 @@
{
+ "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
diff --git a/etc/examples/config-region-sf.json b/etc/examples/config-region-sf.json
new file mode 100644
index 000000000..8b06f574d
--- /dev/null
+++ b/etc/examples/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/config-sites.json b/etc/examples/config-sites.json
index 6a7c5178d..a96569992 100644
--- a/etc/examples/config-sites.json
+++ b/etc/examples/config-sites.json
@@ -1,4 +1,5 @@
{
+ "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
}
diff --git a/etc/examples/sites-sf.csv b/etc/examples/sites-sf.csv
new file mode 100644
index 000000000..9bf046cab
--- /dev/null
+++ b/etc/examples/sites-sf.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
diff --git a/etc/matlab/README.md b/etc/matlab/README.md
index 814afc6aa..05c8c7786 100644
--- a/etc/matlab/README.md
+++ b/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>
diff --git a/src/org/opensha2/programs/HazardCalc.java b/src/org/opensha2/programs/HazardCalc.java
index b867082c5..03a792207 100644
--- a/src/org/opensha2/programs/HazardCalc.java
+++ b/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.
--
GitLab