cleaning

Author: peer-open-source

source/manual/files.md

@@ -6,19 +6,21 @@ Two types of metadata are provided in the dowloaded archive.
 The first type is metadata for the  rupture realizations and the second type is metadata for the ground motion histories. 
 The metadata for the realizations is provided in a file titled ``Simulations_Flatfile.xlsx``, and includes three sets of information:
 - A general description of the simulated earthquake including the region name, corresponding region code, and the realization number.
+
 - Fault rupture parameters, including fault geometry characterized by the fault name; rupture geometry defined by fault length and width, depth to top of rupture, dip, strike, and rake; earthquake magnitude and hypocenter location; the rupture model utilized in the regional simulations (e.g., the *Graves-Pitarka* kinematic rupture model) and slip characteristics. 
-A  graphic that displays the slip, slip-rate and rise time across the fault rupture is also provided to assist in interpretation.
+  A  graphic that displays the slip, slip-rate and rise time across the fault rupture is also provided to assist in interpretation.
 
-- Simulation model parameters, which include maximum frequency resolved, minimum shear wave velocity included in the model (Vsmin), surface grid spacing that defines the distance between computational nodes in the simulation model, output spacing that provides distance between the down-sampled grid points where ground motion data is available, and the geologic velocity model utilized in the simulation (e.g., the USGS velocity model for SFBA).
+- Simulation model parameters, which include maximum frequency resolved, minimum shear wave velocity included in the model (Vsmin), surface grid spacing that defines the distance between computational nodes in the simulation model, output spacing that provides distance between the down-sampled grid points where ground motion data is available, and the geologic velocity model utilized in the simulation (e.g., the USGS velocity model for the {ref}`sfba` region).
 
 For each region, the metadata for the ground motions of all realizations are provided in a separate file. 
-The metadata includes two sets of information; the first set includes the *name*, *latitude* and *longitude* coordinates of the grid point, the vertical elevation of the grid point from sea level, the 2D cartesian coordinates of the grid point in the computational model domain (with X and Y axes in the fault normal and parallel directions respectively), the $V_{s30}$, and the depth at which the shear-wave velocity reaches $1.0 \mathrm{~km} / \mathrm{s}$ and $2.5 \mathrm{~km} / \mathrm{s}(\mathrm{Z} 1.0$ and Z $2.5$ at the location of the grid point. 
+This metadata includes two sets of information; the first set includes the *name*, *latitude* and *longitude* coordinates of the grid point, the vertical elevation of the grid point from sea level, the 2D cartesian coordinates of the grid point in the computational model domain (with X and Y axes in the fault normal and parallel directions respectively), the $V_{s30}$, and the depth at which the shear-wave velocity reaches $1.0 \mathrm{~km} / \mathrm{s}$ and $2.5 \mathrm{~km} / \mathrm{s}(\mathrm{Z} 1.0$ and Z $2.5$ at the location of the grid point. 
 The second set consists of the distance parameters ( $R_{jb}$ , $R_{\mathrm{rup}}$ and $R_x$ ) and peak ground motion values (*RotD50*, *PGA*, *PGV*, and *PGD*). 
-The file for the SFBA region is titled ``Hayward_M7_GMs_Flatfile.xlsx``.
+The file for the {ref}`SFBA <sfba>` region is titled ``Hayward_M7_GMs_Flatfile.xlsx``.
 
 ## Data
 
-The naming convention of the downloaded files consists of five parts:
+Ground motion data is stored accross several text files.
+The naming convention of the these files consists of five parts:
 the *region*, *realization*, *location*, *direction* and *quantity*.
 
 ```{eval-rst}
@@ -35,7 +37,7 @@ See {ref}`region`.
 
 ### Location
 
-The location is identified by three integers, separated by two underscores (``_``). These
+The location is identified by three integers, separated by underscores (``_``). These
 integers identify the index of the point in the grid. In order these correspond to:
 
 1. The coordinate parallel to the fault,

source/manual/realizations.md

@@ -8,15 +8,15 @@ After selecting the region, the next window allows the user to search for ground
    :width: 50%
 
 ```
+- All search parameters are initially deactivated. Users can activate the parameters of interest using the Switch buttons (Figures 3-6). 
+  At least one parameter must be activated for the search, and users can utilize as many parameters as needed.
 
 - Users can select any number of realizations of interest; at least one realization must be selected. 
   Each *realization* represents a unique earthquake, and it is recommended that users make themselves familiar with all the 50 realizations, details of which are provided in the file [`Simulations_Flatfile.xlsx`](Simulations_Flatfile.xlsx).
 
-- All search parameters are initially deactivated. Users can activate the parameters of interest using the Switch buttons (Figures 3-6). 
-  At least one parameter must be activated for the search, and users can utilize as many parameters as needed.
-
 - If a user wants to search for a specific location, such as the site of a building or a bridge, they should set the maximum latitude equal to the minimum latitude and the maximum longitude equal to the minimum longitude. 
   This search finds ground motions at the locations closest to the specified coordinates. 
   The distances between the specified location and the locations of the identified motions are provided in a summary file titled *"Distance Results."*
+
 - Search parameters are described in {ref}`parameters`.
 

source/manual/search.md

@@ -8,6 +8,9 @@ Search Parameters
 
 - Latitude and longitude: Geographical coordinates.
 - $\mathrm{V}_{\mathrm{s} 30}$ : The time averaged shear wave velocity to 30 m depth.
-- $\mathrm{R}_{\mathrm{jb}}$ : Joyner-Boore distance, shortest horizontal distance from the site to the vertical projection of the rupture, $\mathrm{R}_{\text {rup }}$ : Closest distance from the site to the fault rupture, $\mathrm{R}_{\mathrm{x}}$ : Horizontal distance from the surface projection of the top edge of the fault rupture to the site.
-- PGA, PGV, PGD: RotD50 Peak ground acceleration, velocity and displacement. The RotD50 metric represents the median from the two horizontal components rotated across 180 orientations, ranging from $0^{\circ}$ to $179^{\circ}$.
+- $\mathrm{R}_{\mathrm{jb}}$ : *Joyner-Boore distance*, shortest horizontal distance from the site to the vertical projection of the rupture, 
+- $\mathrm{R}_{\text {rup }}$ : Closest distance from the site to the fault rupture, 
+- $\mathrm{R}_{\mathrm{x}}$ : Horizontal distance from the surface projection of the top edge of the fault rupture to the site.
+- PGA, PGV, PGD: *RotD50* Peak ground acceleration, velocity and displacement. 
+  The *RotD50* metric represents the median from the two horizontal components rotated across 180 orientations, ranging from $0^{\circ}$ to $179^{\circ}$.
 

source/regions/sfba.md

@@ -0,0 +1,7 @@
+```{eval-rst}
+.. _sfba:
+```
+
+# San Francisco Bay
+
+