diff --git a/docs/pages/Building-&-Running.md b/docs/pages/Building-&-Running.md
index 121fa83b869057e136eb739edd925a41fc109755..77c51d06c48d763c44d673577b9be4a3108b4d4f 100644
--- a/docs/pages/Building-&-Running.md
+++ b/docs/pages/Building-&-Running.md
@@ -1,13 +1,6 @@
# Building & Running
-## Related Pages
-
-* [Building & Running](./Building-&-Running.md#building-&-running)
- * [Developer Basics](./Developer-Basics.md#developer-basics)
- * [Calculation Configuration](./Calculation-Configuration.md#calculation-configuration)
- * [Site Specification](./Site-Specification.md#site-specification)
- * [Using Docker](./Using-Docker.md#using-docker)
- * See also the [examples](../../etc/examples) directory
+[TOC]
## Build and Run Locally
@@ -16,7 +9,7 @@ Building and running *nshmp-haz* requires prior installation of Git and Java. Pl
### Building
-_nshmp-haz_ uses the [Gradle](https://gradle.org/) build tool. Navigate to a location on your
+*nshmp-haz* uses the [Gradle](https://gradle.org/) build tool. Navigate to a location on your
system where you want *nshmp-haz* code to reside, clone the repository, and compile:
```bash
@@ -33,7 +26,7 @@ downloading all required dependencies, including Gradle itself.
### Running
-_nshmp-haz_ applications may be run from the command line or as a local web service. Command line
+*nshmp-haz* applications may be run from the command line or as a local web service. Command line
applications are recommended for long running hazard and disaggregation calculations, but most
users will find the web service endpoints to be more flexible. Web services return
[JSON](https://www.json.org/json-en.html) responses that can be parsed by most programming
@@ -41,7 +34,7 @@ languages and data analaysis and visualization programs (e.g. Matlab).
### Web Servies
-To run _nshmp-haz_ web services:
+To run *nshmp-haz* web services:
```bash
./gradlew run
@@ -57,7 +50,9 @@ java -jar build/libs/nshmp-haz.jar --model=path/to/model
After startup, web services and documentation are now available at
[http://localhost:8080/](http://localhost:8080/).
-See the [Matlab](../../etc/matlab) directory for examples of how to call the web services.
+See the [Matlab](../../etc/matlab) directory for examples of how to call the web services. To
+run the ground motion model (GMM) web services, please use the
+[*nshmp-haz-ws*](https://code.usgs.gov/ghsc/nshmp/nshmp-ws) repository.
### Command Line Hazard Calculation
@@ -68,11 +63,11 @@ measures. For example:
java -cp path/to/nshmp-haz.jar gov.usgs.earthquake.nshmp.HazardCalc model sites [config]
```
-At a minimum, the hazard source [model](./Hazard-Model.md) and the
+At a minimum, the hazard source [model](./Hazard-Model.md) and the
[site](./Site-Specification.md)(s) at which to perform calculations must be specified. The source
model should specified a path to a directory. A single site may be specified with a string;
multiple sites must be specified using either a comma-delimited (CSV) or
-[GeoJSON](http://geojson.org) file. The path to a custom
+[GeoJSON](http://geojson.org) file. The path to a custom
[configuration](./Calculation-Configuration.md) file containing user-specific settings may
optionally be supplied as a third argument. It can be used to override any calculation settings;
if absent [default](./Calculation-Configuration.md) values are used.
@@ -96,6 +91,14 @@ files. Disaggregations also have some independent
---
+## Related Pages
+
+* [Building & Running](./Building-&-Running.md#building-&-running)
+ * [Developer Basics](./Developer-Basics.md#developer-basics)
+ * [Calculation Configuration](./Calculation-Configuration.md#calculation-configuration)
+ * [Site Specification](./Site-Specification.md#site-specification)
+ * [Using Docker](./Using-Docker.md#using-docker)
+ * See also the [examples](../../etc/examples) directory
* [**Documentation Index**](../README.md)
---
diff --git a/docs/pages/Calculation-Configuration.md b/docs/pages/Calculation-Configuration.md
index cb84d1b3cae8423b296ccdf90b1254106fbc1e79..0ba6e1faa5fb9725015765502fef5ed5133c6869 100644
--- a/docs/pages/Calculation-Configuration.md
+++ b/docs/pages/Calculation-Configuration.md
@@ -13,7 +13,7 @@ may be overridden. See [building and running](./Building-&-Running.md) and the
Parameter | Type | Default | Notes |
--------- | ---- | ------- | ----- |
-__`hazard`__
+**`hazard`**
`.exceedanceModel` |`String` | `"TRUNCATION_3SIGMA_UPPER"`| [`ExceedanceModel`][url-exceedance]
`.truncationLevel` |`Double` | `3.0` | [1](#notes)
`.imts` |`String[]` | `["PGV","PGA","SA0P01","SA0P02",`<br>`"SA0P03","SA0P05","SA0P075",`<br>`"SA0P1","SA0P15","SA0P2","SA0P25",`<br>`"SA0P3","SA0P4","SA0P5","SA0P75",`<br>`"SA1P0","SA1P5","SA2P0","SA3P0",`<br>`"SA4P0","SA5P0","SA7P5","SA10P0"]` | [`Imt`][url-imt]
@@ -23,25 +23,25 @@ __`hazard`__
`.useSiteData` |`Boolean` | `true` | Enable site data (e.g. basin depths)
`.customImls` |`Map<String, Double[]>` | `{}` (empty object) | [2](#notes)
`.valueFormat` |`String` | `"ANNUAL_RATE"` | [`ValueFormat`][url-valueformat]
-__`gmm`__
+**`gmm`**
`.dampingRatio` |`Double` | `0.05` (5%) | Limited to range [0.005..0.3] 0.5% to 30%
`.sigmaScale` |`Double` | `1.0` (100%, no scaling) | Limited to range [0.5..1.0] 50% to 100%
`.vertical` |`Boolean` | `false` | Compute vertical ground motions
-__`disagg`__
+**`disagg`**
`.returnPeriod` |`Double` | `2475` |
`.bins` |`Object` | | [4](#notes)
`.contributorLimit` |`Double` | `0.1` | [5](#notes)
-__`rate`__
+**`rate`**
`.bins` |`Object` | | [6](#notes)
`.distance` |`Double` | `20` km
`.distributionFormat` |`String` | `"INCREMENTAL"` | [`DistributionFormat`][url-distribution]
`.timespan` |`Double` | `30` years
`.valueFormat` |`String` | `"ANNUAL_RATE"` | [`ValueFormat`][url-valueformat]
-__`output`__ |
+**`output`** |
`.directory` |`String` | `hazout`
`.dataTypes` |`String[]` | `["TOTAL","MAP"]` | [`DataType`][url-datatype]
`.returnPeriods` |`Double[]` | `[475,975,2475,10000]` | [`ReturnPeriods`][url-returnperiods]
-__`performance`__
+**`performance`**
`.optimizeGrids` |`Boolean` | `true` | [7](#notes)
`.smoothGrids` |`Boolean` | `true` | [8](#notes)
`.systemPartition` |`Integer` | `1000` | [9](#notes)
@@ -111,7 +111,7 @@ T ≤ 10 s | 0.000333, 0.000499, 0.000749, 0.00112, 0.00169, 0.00253, <br>0.00
* [Site Specification](./Site-Specification.md#site-specification)
* [Using Docker](./Using-Docker.md#using-docker)
* See also the [examples](../../etc/examples) directory
-* [__Documentation Index__](../README.md)
+* [**Documentation Index**](../README.md)
---
 [U.S. Geological Survey](https://www.usgs.gov)
diff --git a/docs/pages/Code-Versions.md b/docs/pages/Code-Versions.md
index 801a9b66faf3a8eef92d1605d50b02a7a16b6d39..973190a4bbfd150422780efe85fe0f415ad19db4 100644
--- a/docs/pages/Code-Versions.md
+++ b/docs/pages/Code-Versions.md
@@ -1,35 +1,35 @@
# Code Versions
The static datasets of USGS NSHMs prior to 2014 were computed using Fortran (see
-[_nshmp-haz-fortran_](https://github.com/usgs/nshmp-haz-fortran])). The static datasets for the
+[*nshmp-haz-fortran*](https://github.com/usgs/nshmp-haz-fortran])). The static datasets for the
2014 Conterminous U.S. NSHM were computed using the Fortran codes and
[OpenSHA](https://opensha.org/) (for the California portion of the model). The dynamic versions
of the 2008 and 2014 Conterminous U.S. models were then implemented in the 1st version of
-[_nshmp-haz_](https://github.com/usgs/nshmp-haz) (on GitHub). This updated Java codebase uses XML
+[*nshmp-haz*](https://github.com/usgs/nshmp-haz) (on GitHub). This updated Java codebase uses XML
source models and supports the web services behind the dynamic calculations of the [Unified Hazard
Hazard Tool](https://earthquake.usgs.gov/hazards/interactive/) (UHT).
-The 2nd version of _nshmp-haz_ (this repository) supercedes prior codebases. The development of this
+The 2nd version of *nshmp-haz* (this repository) supercedes prior codebases. The development of this
version involved a significant refactoring of both the computational code and source model format.
The source models are now defined using JSON, GeoJSON, and CSV files to better reflect the
underlying logic trees and support uncertainty analysis.
-## Transitioning from _nshmp-haz_ v1 to v2
+## Transitioning from *nshmp-haz* v1 to v2
NSHMs are very detailed and migrating from one format to another is not trivial and prone to error.
Moreover, approximations (e.g. using 3.1415 for Pi rather than the the value built into most
languages) can yield different results. When multiple such small changes exist, deciphering what
is giving rise to differences in results can be challenging.
-To document the transition from _nshmp-haz_ v1 to v2, we here attach comparison maps at four return
+To document the transition from *nshmp-haz* v1 to v2, we here attach comparison maps at four return
periods (475, 975, 2475, and 10,000 year) for the 2018 Conterminous U.S. model. Maps are included
for PGA and 3 spectral periods ( 0.2 s, 1 s, and 5 s). There are no differences in the Central &
Eastern U.S. and differences in the WUS are <<1%. The difference in hazard in the vicinity of
-Salt Lake City arises from the cluster models in _nshmp-haz_ v1 not being able to consider the
+Salt Lake City arises from the cluster models in *nshmp-haz* v1 not being able to consider the
additional epistemic uncertainty added to the the NGA-West2 ground motion models.
We continue to investigate the cause of other differences but they are small enough that we are
-comfortable moving forward deploying _nshmp-haz_ v2 codes and models to our public web services and
+comfortable moving forward deploying *nshmp-haz* v2 codes and models to our public web services and
applications. This repository includes end-to-end tests for supported NSHMs that may be run
on demand.
diff --git a/docs/pages/Developer-Basics.md b/docs/pages/Developer-Basics.md
index 03640b54a3d5668d67b295bae81b6474608ea401..346ace6479fb6f141107d9f25728f5cbe9df3691 100644
--- a/docs/pages/Developer-Basics.md
+++ b/docs/pages/Developer-Basics.md
@@ -60,7 +60,7 @@ git clone https://code.usgs.gov/ghsc/nshmp/nshmp-haz.git
* [Site Specification](./Site-Specification.md#site-specification)
* [Using Docker](./Using-Docker.md#using-docker)
* See also the [examples](../../etc/examples) directory
-* [__Documentation Index__](../README.md)
+* [**Documentation Index**](../README.md)
---
 [U.S. Geological Survey](https://www.usgs.gov)
diff --git a/docs/pages/Functional-PSHA.md b/docs/pages/Functional-PSHA.md
index 0b936d6c172bf47d1b0d0bce55f18878a22204d5..b797d8f6a26d0db7a363a56f5d0b4c4726de4557 100644
--- a/docs/pages/Functional-PSHA.md
+++ b/docs/pages/Functional-PSHA.md
@@ -29,17 +29,17 @@ in magnitude, *M*, and distance, *R*). This formulation relies on models of grou
give the probability that an intensity measure level of interest will be exceeded conditioned on
the occurrence of a particular earthquake. Such models are commonly referred to as:
-* __Intensity measure relationships__
-* __Attenuation relationships__
-* __Ground motion prediction equations (GMPEs)__
-* __Ground motion models (GMMs)__
+* **Intensity measure relationships**
+* **Attenuation relationships**
+* **Ground motion prediction equations (GMPEs)**
+* **Ground motion models (GMMs)**
The parameterization of modern models (e.g. NGA-West2; Bozorgnia et al., 2014) extends to much
more than magnitude and distance, including, but not limited to:
-* __Multiple distance metrics__ (e.g. rJB, rRup, rX, rY)
-* __Fault geometry__ (e.g. dip, width, rupture depth, hypocentral depth)
-* __Site characteristics__ (e.g. basin depth terms, site type or Vs30 value)
+* **Multiple distance metrics** (e.g. rJB, rRup, rX, rY)
+* **Fault geometry** (e.g. dip, width, rupture depth, hypocentral depth)
+* **Site characteristics** (e.g. basin depth terms, site type or Vs30 value)
## Simple, yes, but used for so much more…
@@ -119,10 +119,10 @@ foreach IMT {
Break the traditional PSHA formulation down into discrete steps and preserve the data associated
with each step:
-* __[1]__ Source & Site parameterization
-* __[2]__ Ground motion calculation (mean and standard deviation only)
-* __[3]__ Exceedance curve calculation (per source)
-* __[4]__ Recombine
+* **[1]** Source & Site parameterization
+* **[2]** Ground motion calculation (mean and standard deviation only)
+* **[3]** Exceedance curve calculation (per source)
+* **[4]** Recombine
Whereas the traditional pipeline looks something like this:
@@ -132,9 +132,9 @@ The functional pipeline can be processed stepwise:
-__Need a disaggregation?__ Revisit and parse the results of steps 1 and 2
+**Need a disaggregation?** Revisit and parse the results of steps 1 and 2
-__Need a response spectra?__ Spawn more calculations, one for each IMT, at step 2.
+**Need a response spectra?** Spawn more calculations, one for each IMT, at step 2.
## Benefits
@@ -161,7 +161,7 @@ __Need a response spectra?__ Spawn more calculations, one for each IMT, at step
---
-[__Documentation Index__](../README.md)
+[**Documentation Index**](../README.md)
---
 [U.S. Geological Survey](https://www.usgs.gov)
diff --git a/docs/pages/Ground-Motion-Models.md b/docs/pages/Ground-Motion-Models.md
index 4419608b253ecbb12e63dbf91aee99498d324aec..cb69268a8757f50219ed9686a8918dc5b8fb33e7 100644
--- a/docs/pages/Ground-Motion-Models.md
+++ b/docs/pages/Ground-Motion-Models.md
@@ -5,7 +5,7 @@ the occurrence of various earthquakes. The following tables list the GMMs suppor
is not uncommon for a GMM to have multiple concrete implementations. For instance, most subduction
GMMs, as published, support both interface and intraslab events.
-[[_TOC_]]
+[TOC]
## GMM Configuration
@@ -44,7 +44,7 @@ The following sample `gmm-config.json` file applies the NGA-West 2 epistemic unc
## GMM Uncertainty Models
-_nshmp-haz_ supports additional epistemic uncertainty models derived from the PEER NGA-West 1
+*nshmp-haz* supports additional epistemic uncertainty models derived from the PEER NGA-West 1
and PEER NGA-West 2 projects. These models both have factors for distance (`Rrup`) bins
Rrup < 10 km, 10 km <= Rrup, < 30 km, and 30 km <= Rrup, and for magnitude bins M < 6.0, 6.0 <=
M < 7.0, and 7.0 <= M. These models can be applied within the `gmm-config.json` file as shown in
@@ -52,14 +52,14 @@ the [GMM Uncertainty](#gmm-uncertainty) section above.
## GMMs By Tectonic Setting
-GMMs available in _nshmp-haz_ are tabulated by tectonic setting below. See the javadocs for the
+GMMs available in *nshmp-haz* are tabulated by tectonic setting below. See the javadocs for the
[GMM Package](https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/package-summary.html)
for implementation details of each GMM and comprehensive lists of GMM IDs.
### Active Crust GMMs
Reference | ID | Component | Notes
-:---------|:--:|:---------:|:------:
+:---------|:---|:----------|:------:
**NGA-West 2**
[Abrahamson et al., 2014](http://dx.doi.org/10.1193/070913EQS198M) | ASK_14<br>ASK_14_BASIN | RotD50 |
[Boore et al., 2014](http://dx.doi.org/10.1193/070113EQS184M) | BSSA_14<br>BSSA_14_BASIN | RotD50 |
@@ -93,7 +93,7 @@ NGA-East<br>[Goulet et al., 2017](https://peer.berkeley.edu/sites/default/files/
[Shahjouei and Pezeshk, 2016](http://dx.doi.org/10.1785/0120140367) | NGA_EAST_SEED_SP16 | RotD50 | 3
**Other**
[Atkinson, 2008](http://dx.doi.org/10.1785/0120070199)<br>[Atkinson & Boore, 2011](http://dx.doi.org/10.1785/0120100270) | ATKINSON_08_PRIME | horizontal | 4
-[Atkinson & Boore, 2006](http://dx.doi.org/10.1785/0120050245) | _AB\_06\_\*<br>140BAR\|200BAR<br>none\|\_AB\|\_J_ | horizontal | 4
+[Atkinson & Boore, 2006](http://dx.doi.org/10.1785/0120050245) | AB_06_*<br>140BAR \| 200BAR<br>none \| \_AB \| \_J | horizontal | 4
[Atkinson & Boore, 2006](http://dx.doi.org/10.1785/0120050245)<br>[Atkinson & Boore, 2011](http://dx.doi.org/10.1785/0120100270) | AB_06_PRIME | horizontal | 4
[Campbell, 2003](http://dx.doi.org/10.1785/0120020002) | CAMPBELL_03<br>CAMPBELL_03_AB<br>CAMPBELL_03_J | Geometric mean | 4
[Frankel et al., 1996](https://pubs.usgs.gov/of/1996/532/) | FRANKEL_96<br>FRANKEL_96_AB<br>FRANKEL_96_J | not specified | 4
@@ -112,30 +112,28 @@ for individual NGA-East component model IDs
### Subduction GMMs
-_Note: See the [GMM javadocs](https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/Gmm.html)
-for a comprehensive list of GMM IDs._
+*Note: See the [GMM javadocs](https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/Gmm.html)
+for a comprehensive list of GMM IDs.*
Reference | ID | Component | Notes
:---------|:---|:----------|:------:
**NGA-Subduction**
-[Abrahamson & Gülerce, 2020](https://peer.berkeley.edu/sites/default/files/2020_25.pdf) | _AG\_20\_\*<br>GLOBAL\|CASCADIA\|ALASKA<br>INTERFACE\|SLAB<br>no basin\|\_BASIN_ | RotD50
-[Kuehn et al., 2020](https://peer.berkeley.edu/sites/default/files/2020_04_kuehn_final.pdf) | _KBCG\_20\_\*<br>GLOBAL\|CASCADIA\|ALASKA<br>INTERFACE\|SLAB<br>no basin\|\_BASIN_ | RotD50
-[Parker et al., 2020](https://peer.berkeley.edu/sites/default/files/2020_03_parker_final.pdf) | _PSHAB\_20\_\*<br>GLOBAL\|CASCADIA\|ALASKA<br>INTERFACE\|SLAB<br>no basin\|\_BASIN_ | RotD50
+[Abrahamson & Gülerce, 2020](https://peer.berkeley.edu/sites/default/files/2020_25.pdf) | AG_20_*<br>GLOBAL \| CASCADIA \| ALASKA<br>INTERFACE \| SLAB<br> (none) \| \_BASIN | RotD50
+[Kuehn et al., 2020](https://peer.berkeley.edu/sites/default/files/2020_04_kuehn_final.pdf) | KBCG_20_*<br>GLOBAL \| CASCADIA \| ALASKA<br>INTERFACE \| SLAB<br>(none) \| \_BASIN | RotD50
+[Parker et al., 2020](https://peer.berkeley.edu/sites/default/files/2020_03_parker_final.pdf) | PSHAB_20_*<br>GLOBAL \| CASCADIA \| ALASKA<br>INTERFACE \| SLAB<br>(none) \|\_BASIN | RotD50
**Other**
-[Atkinson & Boore, 2003](http://dx.doi.org/10.1785/0120020156) | _AB\_03\*<br>GLOBAL\|CASCADIA<br>INTERFACE\|SLAB<br>none\|\_LOW_SAT_| horizontal |
+[Atkinson & Boore, 2003](http://dx.doi.org/10.1785/0120020156) | AB_03_*<br>GLOBAL \| CASCADIA<br>INTERFACE \| SLAB<br> (none) \| \_LOW_SAT| horizontal |
[Atkinson & Macias, 2009](http://dx.doi.org/10.1785/0120080147) | AM_09_INTERFACE<br>AM_09_INTERFACE_BASIN | Geometric mean | 1
-BC Hydro<br>[Abrahamson et al., 2016](http://dx.doi.org/10.1193/051712EQS188MR) | _BCHYDRO\_12\_\*<br>INTERFACE\|SLAB<br>none\|\_BASIN<br>none\|\_BACKARC_ | Geometric mean |
-BC Hydro NGA<br>[Abrahamson et al., 2018](https://peer.berkeley.edu/sites/default/files/2018_02_abrahamson_9.10.18.pdf)² | _BCHYDRO\_18\_NGA\_\*<br>INTERFACE\|SLAB<br>none\|\_NO_EPI_ | Geometric mean | 3
+BC Hydro<br>[Abrahamson et al., 2016](http://dx.doi.org/10.1193/051712EQS188MR) | BCHYDRO_12_*<br>INTERFACE \| SLAB<br> (none) \| \_BASIN<br>(none) \| \_BACKARC | Geometric mean |
+BC Hydro NGA<br>[Abrahamson et al., 2018](https://peer.berkeley.edu/sites/default/files/2018_02_abrahamson_9.10.18.pdf)² | BCHYDRO_18_NGA_*<br>INTERFACE \| SLAB<br> (none) \| \_NO_EPI | Geometric mean | 3
[McVerry et al., 2000](http://doi.org/10.5459/BNZSEE.39.1.1-58) | MCVERRY_00_INTERFACE<br>MCVERRY_00_SLAB<br>MCVERRY_00_VOLCANIC | Max-horizontal,<br>also supports geometric mean | 4
[Youngs et al., 1997](http://dx.doi.org/10.1785/gssrl.68.1.58) | YOUNGS_97_INTERFACE<br>YOUNGS_97_SLAB | Geometric mean |
-[Zhao et al., 2006](http://dx.doi.org/10.1785/0120050122) | _ZHAO\_06\_\*<br>INTERFACE\|SLAB<br>none\|\_BASIN_ | Geometric mean |
-[Zhao et al., 2016](http://dx.doi.org/10.1785/0120150034)<br>[Zhao et al., 2016](http://dx.doi.org/10.1785/0120150056) | ZHAO_16_INTERFACE<br>ZHAO_16_SLAB<br>_ZHAO_16_UPPER_MANTLE_ | Geometric mean<br>(random orientation) | 5
+[Zhao et al., 2006](http://dx.doi.org/10.1785/0120050122) | ZHAO_06_*<br>INTERFACE \| SLAB<br> (none) \| \_BASIN | Geometric mean |
¹ Interface only
² Likely to be superseded by the final EQ Spectra paper
³ Calibrated for Cascadia use only
â´ New Zealand model, does not correspond directly with US site class model
-âµ Subduction Slab and Interface
### Regional and Specialized GMMs
diff --git a/docs/pages/Logic-Trees-&-Uncertainty.md b/docs/pages/Logic-Trees-&-Uncertainty.md
index 8a7201f36a672816d65116523d3001500ef6c783..e1c4f102267fdbca1a8b024050724bf0ce729123 100644
--- a/docs/pages/Logic-Trees-&-Uncertainty.md
+++ b/docs/pages/Logic-Trees-&-Uncertainty.md
@@ -3,7 +3,7 @@
The following page details the logic trees of epistemic uncertainty considered in NSHMs supported
by *nshmp-haz*. Logic trees are represented in a NSHM using files ending in `-tree.json`.
-[[_TOC_]]
+[[*TOC*]]
## Terminology
diff --git a/docs/pages/Magnitude-Frequency-Distributions.md b/docs/pages/Magnitude-Frequency-Distributions.md
index 365758f1398e11c08e0bfa9ae578605ad9a183e1..743e0535184195b379bf55912a2feee022de1dcc 100644
--- a/docs/pages/Magnitude-Frequency-Distributions.md
+++ b/docs/pages/Magnitude-Frequency-Distributions.md
@@ -5,7 +5,7 @@ capable of generating, otherwise known as a magnitude-frequency distribution (MF
types of MFDs supported in a hazard model are described below. Unless otherwise noted, all the
members listed in the JSON examples below are required.
-[[_TOC_]]
+[TOC]
## Single
diff --git a/docs/pages/Model-Editions.md b/docs/pages/Model-Editions.md
index 206a5de5641af0303b0bcd23770a1b739535462f..fb9923317a5466cdfa0d84c0369072e0694a2472 100644
--- a/docs/pages/Model-Editions.md
+++ b/docs/pages/Model-Editions.md
@@ -46,7 +46,7 @@ Hawaii | 1998 | 1.1.0 | | TBD | |
Hawaii | 1998 | 1.0.0 |:small_blue_diamond:| | ASCE7-10 |
Puerto Rico & <br/> U.S. Virgin Islands | 2003 | v1.0.0 | | | |
-<sup>†</sup> __Note on the 2014 conterminous U.S. NSHM:__ Initial publication of the
+<sup>†</sup> **Note on the 2014 conterminous U.S. NSHM:** Initial publication of the
[2014 model](https://www.usgs.gov/natural-hazards/earthquake-hazards/science/2014-united-states-lower-48-seismic-hazard-long-term)
included data to support updates to the U.S. Building Code, specifically hazard curves for peak
ground acceleration (PGA), and 0.2 and 1.0 second spectral accelerations, all at a BC boundary site
@@ -99,7 +99,7 @@ one of the dynamic editions is likely better.
* [Model Editions](./Model-Editions.md#model-editions)
* [Logic Trees & Uncertainty](./Logic-Trees-&-Uncertainty.md#logic-trees-&-uncertainty)
* [Code Versions](./Code-Versions.md#code-versions)
-* [__Documentation Index__](../README.md)
+* [**Documentation Index**](../README.md)
---
 [U.S. Geological Survey](https://www.usgs.gov)
diff --git a/docs/pages/Model-Files.md b/docs/pages/Model-Files.md
index 347935dd0c9ff96f8cd04cf9bde1a7bd746b3b48..36cc69f821e21e64d1b2979522a6cdd0f2f5ae34 100644
--- a/docs/pages/Model-Files.md
+++ b/docs/pages/Model-Files.md
@@ -4,7 +4,7 @@ A variety of logic tree, configuration, and data files that are common to all mo
types are described below and on related pages for specific model components, for example, ground
motion models (GMMs) or magnitude-frequency distributions (MFDs).
-[[_TOC_]]
+[TOC]
## Model and Calculation Configuration
@@ -81,7 +81,7 @@ or its children will be processed; any standalone sources will be ignored. For e
**source-group.json:** A specialized form of logic tree that describes model branches that are
additive and therefore does not include weights. Examples from the NSHM for the conterminous U.S.
NSHM include the Cascadia segmented and partial-rupture models, and the New Madrid 1500-yr cluster
-branches. The branch objects in a source group _may_ include an optional `scale` member that can
+branches. The branch objects in a source group *may* include an optional `scale` member that can
be used to impose a probability of occurrence or other scaling requred by a NSHM. If absent, the
`scale` value is one.
@@ -99,7 +99,7 @@ be used to impose a probability of occurrence or other scaling requred by a NSHM
```
**tree-info.json:** Top level source trees and groups must be accompanied by a file that contains
-a unique integer ID for the logic tree. This file _may_ also include a `name` field that, if
+a unique integer ID for the logic tree. This file *may* also include a `name` field that, if
present, will be used instead of the enclosing directory name, but it is not required.
```json
@@ -124,7 +124,7 @@ For example:
```
See the [ground motion models](./Ground-Motion-Models.md) page for details on GMMs supported in
-_nshmp-haz_ and the related `gmm-config.json` files that governs GMM behavior.
+*nshmp-haz* and the related `gmm-config.json` files that governs GMM behavior.
### MFD Logic Trees
@@ -151,7 +151,7 @@ source-tree branches.
How MFDs are intialized (or realized) depends on the presence and contents of `mfd-config.json` and
`rate-tree.json` files. See the
[magnitude frequency distributions](./Magnitude-Frequency-Distributions.md) page for details on
-these files and the types of MFDs supported in _nshmp-haz_.
+these files and the types of MFDs supported in *nshmp-haz*.
## Rupture Sets
diff --git a/docs/pages/Model-Structure.md b/docs/pages/Model-Structure.md
index 7af9614f651144e7cac763a1821d63663a66ae4a..20e324791be3bc9133392630b0102386b4aec5a2 100644
--- a/docs/pages/Model-Structure.md
+++ b/docs/pages/Model-Structure.md
@@ -6,7 +6,7 @@ self describing and represent logic trees and other relationships between source
(JSON), source geometry (GeoJSON features), and earthquake rate data (CSV). JSON is well-suited
for representing model data and relationships and is supported in most programming languages.
-[[_TOC_]]
+[TOC]
## Directory Structure
diff --git a/docs/pages/Site-Specification.md b/docs/pages/Site-Specification.md
index 2f1af5014d7a4817c5f7f4fcd1e968a227851d6f..3b7990ed0d80c67de5d8add86722439e27f6c8d9 100644
--- a/docs/pages/Site-Specification.md
+++ b/docs/pages/Site-Specification.md
@@ -4,7 +4,7 @@ The sites at which to perform hazard and related calculations may be defined in
ways. Examples of the file formats described below are available in the resource directory:
[`etc/nshm`](../../etc/nshm/README.md).
-__Note on Coordinates:__ *nshmp-haz* supports longitude and latitude values in the closed
+**Note on Coordinates:** *nshmp-haz* supports longitude and latitude values in the closed
ranges `[-360° ‥ 360°]` and `[-90° ‥ 90°]`. However, mixing site and/or source
coordinates across the antimeridian (the -180° to 180° transition) will yield unexpected results.
For Pacific models and calculations, always use positive or negative longitudes exclusively.
@@ -106,7 +106,7 @@ outside the 'calculation' polygon are set to zero. For an example, see the
* [Site Specification](./Site-Specification.md#site-specification)
* [Using Docker](./Using-Docker.md#using-docker)
* See also the [examples](../../etc/examples) directory
-* [__Documentation Index__](../README.md)
+* [**Documentation Index**](../README.md)
---
 [U.S. Geological Survey](https://www.usgs.gov)
diff --git a/docs/pages/Source-Types.md b/docs/pages/Source-Types.md
index 76d90b847cbb4d1ab2e1444c3106429b7e12a4a6..ddaa27b71989f2129eece8ddff5eaab11ab3f108 100644
--- a/docs/pages/Source-Types.md
+++ b/docs/pages/Source-Types.md
@@ -10,17 +10,17 @@ represent models of smoothed seismicity in both crustal and subduction intraslab
may also be used for fault zones where there is a history of large earthquakes but the fault
geometry itself is unknown or very poorly defined.
-[[_TOC_]]
+[TOC]
-Source models for use with _nshmp-haz_ are defined using [JSON](https://www.json.org) and
-[GeoJSON](https://geojson.org). _nshmp-haz_ makes determinations about how to represent a source
+Source models for use with *nshmp-haz* are defined using [JSON](https://www.json.org) and
+[GeoJSON](https://geojson.org). *nshmp-haz* makes determinations about how to represent a source
based on a GeoJSON geometry type in conjunction with supporting JSON configuration files. Example
source configuration files, `*-config.json`, are provided with each source type description.
Configuration files must be fully specified with `null` JSON member values used to specify 'do
nothing' where appropriate. Any configuration member value in ALL_CAPS indicates the value is one
of a fixed number of options commonly referred to as an enum.
-__Note on Coordinates:__ _nshmp-haz_ supports longitude and latitude values in the closed ranges
+**Note on Coordinates:** *nshmp-haz* supports longitude and latitude values in the closed ranges
`[-360°‥360°]` and `[-90°‥90°]`. Note, however, that mixing site and/or source coordinates across
the antimeridian (the -180° to 180° transition) will yield unexpected results. For Pacific models
and calculations, always use positive or negative longitudes exclusively.
@@ -43,7 +43,7 @@ Grid sources are represented in a model using a logic tree with a `rupture-sets.
ruptures on each branch. Because gridded seismicity models may be governed by regionally
varying MFD properties (e.g. `mMax`), rupture sets for grids are defined in a JSON array.
-__rupture-sets.json__: Defines an array of one or more rupture sets. Multiple rupture sets are
+**rupture-sets.json**: Defines an array of one or more rupture sets. Multiple rupture sets are
used to model regional differences in MFD properties such as maximum magnitude. The `feature`
member points to the ID of a geojson feature (in the `grid-sources/features` directory) that
defines the bounds of the gridded seismicity source. A grid rupture set `mfd-tree` is never
@@ -62,7 +62,7 @@ defined inline and always points to a tree in a
]
```
-__grid-config.json__: A `grid-depth-map` defines a mapping of magnitude ranges to logic trees of
+**grid-config.json**: A `grid-depth-map` defines a mapping of magnitude ranges to logic trees of
depth distributions. The map can use arbitrary names as keys, but the magnitude ranges defined by
each member must be non-overlapping. The magnitude ranges are interpreted as closed (inclusive) –
open (exclusive), e.g. [mMin..mMax). `maxDepth` constrains the maximum depth of any pseudo fault
@@ -107,7 +107,7 @@ to upper-right). While most gridded rate files contain columns of longitude, lat
some may contain depth values (intraslab sources), maximum magnitude caps, or other values. Scaled
spatial PDFs are the preferred approach to modeling regional rate variations, however it is also
possible to define explicit MFDs at each grid node. To do so, the `spatial-pdf` member
-of a __rupture-sets.json__ is replaced with `grid-mfds`. See
+of a **rupture-sets.json** is replaced with `grid-mfds`. See
`2018 CONUS NSHM > active-crust > grid-sources` for examples of both approaches.
## Zone Sources
@@ -149,7 +149,7 @@ directly.
}
```
-__zone-config.json:__ Zone source model configuration is identical to a grid source configuration.
+**zone-config.json:** Zone source model configuration is identical to a grid source configuration.
```json
{
@@ -188,7 +188,7 @@ they occur in multiple locations on the fault surface with appropriately scaled
associated with finite fault models may be explicitly defined or derived from slip rates.
Fault rupture rates may be modeled using explicitly defined MFDs or logic trees of slip rate.
-__fault-source.geojson__: Defines the geometry and properties of a single source. In the example
+**fault-source.geojson**: Defines the geometry and properties of a single source. In the example
below the presence of a `rate-map` property indicates MFDs should be constructed from the supplied
slip rates and using the weights defined in a `rate-tree.json`.
@@ -235,7 +235,7 @@ slip rates and using the weights defined in a `rate-tree.json`.
}
```
-__fault-config.json__: Controls the point spacing on a gridded surface used to realize the fault
+**fault-config.json**: Controls the point spacing on a gridded surface used to realize the fault
geometry as well as define the models to use for magnitude scaling and rupture floating. Dip
variations and an associated slip-rate scaling model are also supported for normal faults.
@@ -249,9 +249,9 @@ variations and an associated slip-rate scaling model are also supported for norm
}
```
-__rupture-set.json__: When a fault source is represented with a logic tree a
-`rupture-set.json` defines the ruptures for each branch. A rupture set _may_ also define custom
-properties and _may_ also contain a `sections` member that defines the fault sections for the
+**rupture-set.json**: When a fault source is represented with a logic tree a
+`rupture-set.json` defines the ruptures for each branch. A rupture set *may* also define custom
+properties and *may* also contain a `sections` member that defines the fault sections for the
rupture set (see note on fault section stitching, [below](#fault-section-stitching)).
```json
@@ -272,10 +272,10 @@ rupture set (see note on fault section stitching, [below](#fault-section-stitchi
When multiple sections are defined for a rupture, the ruptures must be defined in an order that
preserves the U.S. structural geology right-hand-rule. When stitched together, repeated locations
at the enpoints of adjacent sections, if present, are removed. The properties of the first section
-govern the properties of the stitched fault, however, a rupture-set _may_ include a properties
+govern the properties of the stitched fault, however, a rupture-set *may* include a properties
member, the contents of which will override the properties of the first stitched section. Although
it would be better to have geometric properties of stitched sections be calculated dynamically,
-the current approach preserves support for past models. A rupture-set _may_ also include a
+the current approach preserves support for past models. A rupture-set *may* also include a
`coordinates` member that can be used to represent a smoothed trace geometry where stitched
sections do not share common endpoints.
@@ -287,9 +287,9 @@ as the joint probability of exceeding ground motions from each independent event
a cluster may only have an mfd-tree composed of `Mfd.Type.SINGLE` MFDs and the mfd-trees must
match across all sources in a cluster (i.e. each mfd-tree has the same IDs and weights).
-__cluster-set.json__ A specialized type of rupture set, this file defines the array of fault
+**cluster-set.json** A specialized type of rupture set, this file defines the array of fault
rupture sets that make up a 'cluster'. As with fault sources, the nested rupture sets in a cluster
-set _may_ define `properties` and `sections` members.
+set *may* define `properties` and `sections` members.
```json
{
@@ -320,13 +320,13 @@ This specialized fault source type supports inversion based rupture rate estimat
on a fault network such as that used for UCERF3 in the 2014 and 2018 NSHMs for the conterminous
U.S. Fault system source sets require three files: `rupture_set.json`, `sections.geojson`, and
`ruptures.csv` that are placed together within folders defining branches of a fault system
-logic tree. Note that system sources _may_ have complementary gridded seismicity source models
+logic tree. Note that system sources *may* have complementary gridded seismicity source models
with matching logic trees.
-__rupture-set.json__: Provides identifying information for the ruptures defined in the adjacant
+**rupture-set.json**: Provides identifying information for the ruptures defined in the adjacant
sections and ruptures files.
-__sections.geojson__: defines a feature collection of the fault sections in a fault network.
+**sections.geojson**: defines a feature collection of the fault sections in a fault network.
Because fault sections are derived by dividing larger faults into subsections, section features
contain several properties that differ from standalone fault section source models (e.g.
`dip-direction`).
@@ -362,7 +362,7 @@ contain several properties that differ from standalone fault section source mode
}
```
-__ruptures.csv__: Defines the properties of every rupture. The last column in a rupture file
+**ruptures.csv**: Defines the properties of every rupture. The last column in a rupture file
defines the ordered array of participating fault section IDs using the shorthand
`1127:1131-2411:2412`. Colons denote continous ranges of sections and hyphens denote breaks.
@@ -389,7 +389,7 @@ using an `slab-config.json` file.
* [Magnitude Frequency Distributions (MFDs)](./Magnitude-Frequency-Distributions.md#magnitude-frequency-distributions)
* [Rupture Scaling Relations](./Rupture-Scaling-Relations.md#rupture-scaling-relations)
* [Ground Motion Models (GMMs)](./Ground-Motion-Models.md#ground-motion-models)
-* [__Documentation Index__](../README.md)
+* [**Documentation Index**](../README.md)
---
 [U.S. Geological Survey](https://www.usgs.gov)
diff --git a/docs/pages/Using-Docker.md b/docs/pages/Using-Docker.md
index d943d7e05dbebf51ce7a4d6c966dd4e4beab5709..501d12566a66914f746aea275f4fb7b739fab7d8 100644
--- a/docs/pages/Using-Docker.md
+++ b/docs/pages/Using-Docker.md
@@ -260,7 +260,7 @@ respectively.
* [Site Specification](./Site-Specification.md#site-specification)
* [Using Docker](./Using-Docker.md#using-docker)
* See also the [examples](../../etc/examples) directory
-* [__Documentation Index__](../README.md)
+* [**Documentation Index**](../README.md)
---
 [U.S. Geological Survey](https://www.usgs.gov)
diff --git a/etc/examples/README.md b/etc/examples/README.md
index 96cb1e00667995109ec2cf83242fd62001309c07..21de19b155e0a32322d1b0487aa237e4651f8d11 100644
--- a/etc/examples/README.md
+++ b/etc/examples/README.md
@@ -12,8 +12,6 @@ system alias:
alias hazard='java -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.HazardCalc'
```
-
-
<!-- markdownlint-disable MD001 -->
#### Start: [Example 1 – A simple hazard calculation](1-hazard-curve/README.md)