subsurface user manual update

References to literature on gradient factors changed (see dive profile
section, also preferences section)

Section on preference settings added.

Signed-off-by: Willem Ferguson <willemferguson@zoology.up.ac.za>
Signed-off-by: Dirk Hohndel <dirk@hohndel.org>

Documentation/user-manual.txt

@@ -552,6 +552,7 @@ The Dive Info tab gives some summary information about a particular dive that ha
 
 The Stats tab gives summary statistics for more than one dive, assuming that more than one dive have been selected in the *Dive List*. Select more than one dive by the standard Ctrl-click or Shift-click of the mouse. If only one dive has been selected, figures pertaining to only that dive are given. This tab shows the number of dives selected, the total amount of dive time in these dives, as well as the minimum, maximum and mean for the dive duration, dive depth, water temperature and surface air consumption (SAC).
 
+[[S_DiveProfile]]
 === The *Dive Profile*
 
 image::images/Profile2.png["Typical dive profile",align="left"]
@@ -584,9 +585,10 @@ The graph can also include the dive computer reported *ceiling* (or more precise
 
 For a more detailed explanation of _gradient factors_, use the following links:
 
-- link:References/GradientFactors1.html[Watts K. 2006. Gradient factors for dummies. Rebreatherworld.].
+- link:http://www.tek-dive.com/portal/upload/M-Values.pdf[Understanding M-values, by Erik Baker, _Immersed_ Vol. 3, No. 3.]
+
+- link:http://www.rebreatherworld.com/general-and-new-to-rebreather-articles/5037-gradient-factors-for-dummies.html[Gradient factors for dummies, by Kevin Watts]
 
-- link:References/UnderstandingM-values.pdf[Baker EC. 1998. Understanding M-values. _Immersed_ Vol. 3, No. 3.]
 
 
 == Organising the logbook
@@ -669,6 +671,57 @@ In order to save the WHOLE dive log (i.e. all trips and dives), select *File* fr
 
 In order to save only one or more dives or one or two trips, select the appropriate dives or trips in the *Dive List* panel. Then right-click the selected dives to bring up the context menu. To save in _subsurface_ XML format, select _Save as_ from the context menu. To save in UDDF format, select _Export as UDDF_ from the context menu.
 
+
+== Setting your *Preferences* for _subsurface_
+
+There are several settings within _subsurface_ that the user can specify. These are found when selecting _File->Preferences_. The settings are performed in three groups: *Defaults*, *Units* and *Graph*. All three sections operate on the same principles: specify the settings you wish to change, then save these using the *Apply* button. After applying the new settings one can leave the settings panel by selecting *OK*.
+
+=== Defaults
+
+There are four settings in the *Defaults* panel:
+
+  ** *Lists and tables*: Here one can specify the font type and font size of the Dive Table panel. By decreasing the font size of the Dive table,
+one can see more dives on a screen.
+
+  ** *Dives*: Here one needs to specify the directory and file name of your electronic dive log book. This is a file with filename extension .xml. _subsurface_ will then automatically load the dive log book specified.
+
+  ** *Display invalid*:  [red]#??????????????????????????#
+
+  ** *Use Default cylinder*: Here one can specify the default cylinder listed in the *Equipment* tab of the *Dive Notes* panel.
+
+=== Units
+Here one can choose between metric and imperial measures of depth, pressure, volume, temperature and mass. By selecting the Metric or Imperial radio button at the top, one can specify that all units are in the chosen measurement system. Alternatively, if one selects the *Personalise* radio button, one can select a mixture with some measurements being metric while others are in imperial measures.
+
+=== Graph
+This panel allows two type of selections:
+
+* *Show*: Here one specifies the amount of information that is shown as part of the dive profile:
+** Gas pressure graphs: _subsurface_ can display the pressures of the gases with which you dive. If you dive breathing air, then the only important gas is nitrogen. You can instruct _subsurface_ to plot the nitrogen pressure during your dive. If you dive breathing nitrox, then you acn selct a graph of both the nitrogen and oxygen pressures during your dive. If you dive with trimix or heliox, you can select the display of the helium pressure as well. For each of these graphs you can specify a threshold value on the right-hand side of the panel. If any of the graphs go above this threshold level, the graph is highlighted in red, indicationg that the threshold value has been exceeded (see figure below).
+
+** Ceiling: Ascent ceilings arise when a direct ascent to the surface exposes the diver to decompression sickness (DCS) and it is necessary to either ascend slower or to perform decompression stop(s) before ascending to the surface. _subsurface_ can indicate these ceilings above which the diver should not ascend at a particular point in time (see the green-shaded areas in the figure in the section on <<S_DiveProfile,Dive Profiles>>) and in the figure below:
+
+*** If one checks *Calculted ceiling*, then a ceiling is shown if it exists for a particular dive (*A* in figure below)
+
+*** If one checks *show all tissues*, the ceiling is shown for the tissue compartments following the Bühlmann model (*B* in figure below).
+
+*** If one checks *3m increments*, then the ceiling is indicated in 3m-increments (*C* in figure below).
+
+*** If the dive computer itself calculates a ceiling and makes it available to _subsurface_ during upload of dives, this can be
+shown by checking *Dive computer reported ceiling* and it can be drawn in red by checking *Draw ceiling red*.
+
+** If a _Maximum operating depth (MOD)_ or an _Effective air depth (EAD)_ applies to a dive profile, these can be shown by checking the appropriate boxes.
+
+** If a _Maximum parial pressure of oxygen (maxPPO2)_ applies to dives, then this can be specifies in the appropriate text box. In addition, if a _no-decompression limit(NDL)_ is to be shown in the *info* box, then check the appropriate box.
+
+
+image::images/Ceilings.png["Figure: Ceiling with 3m resolution",align="center"]
+
+
+* *Misc*: Here one can set the _gradient factors_ used while diving. GF_Low is the gradient factor at deep depths and GF_High is used just below the surface. At intermediate depths gradient factor between GF_Low and GF_High are used. Gradient factors add conservatism to the nitrogen exposure during a dive, in a similar way that many dive computers have a conservatism setting. The lower the value of a gradient factor, the more conservative the calculations are with respect to nitrogen loading and the lower the ascent ceilings are. Gradient factors of 25/60 are considered conservative and values of 60/90 are considered harsh. Checking *GFLow at max depth* box causes GF_Low to be used at the deepest depth of a dive. For more information see:
+
+  ** http://www.tek-dive.com/portal/upload/M-Values.pdf[Understanding M-values by Erik Baker, , _Immersed_ Vol. 3, No. 3.]
+
+
 == APPENDIX A: Operating system pecific information for importing dive information from dive computer.
 
 === Make sure that your OS has the required drivers installed
@@ -891,8 +944,6 @@ this, but it is reported to be solved sometimes by one of these steps:
 
 Please add any topics you think are important:
 
-* Setting the preferences
-
 * The Main Menu items need to be covered systematically, providing in-document links where appropriate:
 
 * Importing GPS positions from subsurface mobile API
@@ -900,5 +951,3 @@ Please add any topics you think are important:
 * Importing data from other electronic resources - Present information comes from subsurface 3.1.1 manual. How much of it is still valid? Needs to be verified.
 
 * Importing data from dive computers - Appendices A and B come mainly from subsurface 3.1.1 manual. How much of it is still valid? Needs to be verified. Difficult work, but **critical** for the success of subsurface.
-
-* A short technical section on Gradient Factors and GFMin for the uninitiated. This should probably follow the section on dive profiles with in-document link(s) to the Preferences section where GFs are specified.