Working on the User's Manual. See #46.

ChangeLog

@@ -26,7 +26,7 @@ Changes since 0.4 (around June 1, 2011) (in no particular order, need to be orga
 	* Implemented -tauc_to_phi
 	* Updated and improved modeling examples
 	* Removed pgrn
-	* Removed EISMINT-Ross
+	* Removed EISMINT-Ross (and the pross executable)	
 	* Inverse modeling tools (not part of the release)
 
 

doc/browser/std_names.txt

@@ -2,8 +2,8 @@
 
 \section existing Existing standard names
 
-We start by listing standard names from the CF 1.4 Standard Name Table. The subset here
-is a small subset of the <a href="http://cf-pcmdi.llnl.gov/documents/cf-standard-names/">CF 1.4 standard name table</a>.  We list only
+We start by listing standard names from the CF 1.6 Standard Name Table. The subset here
+is a small subset of the <a href="http://cf-pcmdi.llnl.gov/documents/cf-standard-names/">CF 1.6 standard name table</a>.  We list only
 \li those with "land_ice" in the name and/or
 \li those currently used by the <a href="http://www.pism-docs.org/">Parallel Ice Sheet Model (PISM)</a>.
 
@@ -58,7 +58,7 @@ These are merely proposed by Bueler and Aschwanden, for now.
   <tr><td>land_ice_basal_material_yield_stress</td><td>Pa</td><td>tauc</td><td>vtauc [IceModelVec2S]</td><td></td></tr>
   <tr><td>land_ice_basal_material_friction_angle</td><td>degree</td><td>tillphi</td><td>vtillphi [IceModelVec2S]</td><td>majority of standard names with "angle" use canonical units "degree"</td></tr>
   <tr><td>land_ice_surface_temperature_below_firn</td><td>K</td><td>artm</td><td>artm [IceModelVec2S]</td><td></td></tr>
-  <tr><td>land_ice_upward_velocity</td><td>m s-1</td><td>wvel</td><td>w3 [IceModelVec3]</td><td>compare CF 1.4 names "upward_air_velocity" and "upward_sea_water_velocity"</td></tr>
+  <tr><td>land_ice_upward_velocity</td><td>m s-1</td><td>wvel</td><td>w3 [IceModelVec3]</td><td>compare CF 1.6 names "upward_air_velocity" and "upward_sea_water_velocity"</td></tr>
   <tr><td>lithosphere_temperature</td><td>K</td><td>litho_temp</td><td>Tb3 [IceModelVec3Bedrock]</td><td>here top of lithosphere is at "bedrock_altitude"; is that standard?</td></tr>
   <tr><td>upward_geothermal_flux_in_lithosphere</td><td>W m-2</td><td>bheatflx</td><td>vGhf [IceModelVec2S]</td><td>typically applied at depth in lithosphere; compare "upward_geothermal_heat_flux_at_sea_floor"</td></tr>
   <tr><td>land_ice_specific_enthalpy</td><td>J kg-1</td><td>enthalpy</td><td>Enth3 [IceModelVec3]</td><td>enthalpy is defined in PISM to be sensible plus latent heat, plus potential energy of pressure; there is a nontrivial issue of the scaling; the enthalpy value for 273.15 K (cold) ice at atmospheric pressure is a possible standard</td></tr>

doc/userman/hard-choices.tex

@@ -44,6 +44,7 @@ \subsection{Controlling basal strength}  \label{subsect:basestrength}
     \textbf{Option} & \textbf{Description}
     \\\midrule
     \txtopt{topg_to_phi}{\emph{list of 4 numbers}} & Compute $\phi$ using \eqref{eq:1} and \eqref{eq:2}.\\
+    \intextoption{pseudo_plastic} & enables the pseudo-plastic till model \\
     \txtopt{plastic_pwfrac}{\emph{pure number}} & Set what fraction of overburden pressure is assumed as the till pore water pressure.  Only relevant at basal points where there is a positive amount of basal water.\\
     \intextoption{plastic_c0} & Set the value of the till cohesion ($c_{0}$) in the plastic till model.  The value is a pressure, given in kPa.\\
     \txtopt{plastic_reg}{(m/a)} & Set the value of $\eps$ regularization of plastic till; this is the second ``$\eps$'' in formula (4.1) in \cite{SchoofStream}. The default is $0.01$.\\
@@ -57,7 +58,7 @@ \subsection{Controlling basal strength}  \label{subsect:basestrength}
 \label{tab:basal-strength}
 \end{table}
 
-Option \texttt{-plastic_pwfrac} determines $\alpha$, the quantity controlling how $p_w$ is determined from the effective thickness of basal water, the quantity $w=$\texttt{bwat}; see the next subsection.  The formula is $p_w = \alpha\, w \rho g H$.  See \cite{BKAJS}.
+Option \texttt{-plastic_pwfrac} determines $\alpha$, the quantity controlling how $p_w$ is determined from the effective thickness of basal water, the quantity $w=\mathtt{bwat}$; see the next subsection.  The formula is $p_w = \alpha\, w \rho g H$.  See \cite{BKAJS}.
 
 We find that an effective, though heuristic, way to determine \texttt{tillphi} is to make it a function of bed elevation \cite{BKAJS}.  This heuristic is motivated by hypothesis that basal material with a marine history should be weak \cite{HuybrechtsdeWolde}.
 
@@ -78,6 +79,11 @@ \subsection{Controlling basal strength}  \label{subsect:basestrength}
    $$\tau_b = \tau_c \frac{|\mathbf{u}|^{q-1}}{u_{\text{threshold}}^q}\, \mathbf{u}.$$
 Here $\tau_c$ corresponds to the variable \texttt{tauc} in PISM input and output files, $q$ is the power controlled by \texttt{-pseudo_plastic_q}, and the threshold velocity $u_{\text{threshold}}$ is controlled by \texttt{-pseudo_plastic_uthreshold}.  The purely plastic case is $q=0$---see \cite{SchoofStream} for precise interpretation---and the linear case is $q=1$, in which case the coefficient of velocity, $\tau_c/u_{\text{threshold}}$, is more commonly called $\beta$ or $\beta^2$ \cite{MacAyeal}.
 
+\begin{quote}
+  \textbf{WARNING!} Options \texttt{-pseudo_plastic_q} and \texttt{-pseudo_plastic_uthreshold} have no effect if \texttt{-preudo_plastic} is not set.
+\end{quote}
+
+
 See \emph{PISM Source Code browser}, source files in \texttt{src/base/basal_resistance}, and \cite{BBssasliding,BKAJS} for more details.
 
 The major example of \texttt{-ssa_sliding} usage is in the first section of this manual.  A made-up example, in which sliding happens in the ``trough'', is

doc/userman/manual.tex

@@ -405,15 +405,15 @@ \subsection{Initialization from a saved model state}  ``Initialization''\index{i
 ignore these velocities use \texttt{-dontreadSSAvels}.
 
 \subsubsection*{\texttt{-i} file format}
-PISM produces\footnote{Or, more accurately, attempts to produce; please let us know about violations you come across.} CF-1.4 compliant NetCDF\index{PISM!NetCDF file format}\index{NetCDF} files.  The easiest way to learn the output format \emph{and} the \texttt{-i} format is to do a simple run and then look at the metadata in the resulting file, like this:
+PISM produces\footnote{Or, more accurately, attempts to produce; please let us know about violations you come across.} CF-1.5 compliant NetCDF\index{PISM!NetCDF file format}\index{NetCDF} files.  The easiest way to learn the output format \emph{and} the \texttt{-i} format is to do a simple run and then look at the metadata in the resulting file, like this:
 \begin{verbatim}
 $ pisms -eisII A -y 10 -o foo.nc
 $ ncdump -h foo.nc | less
 \end{verbatim}
 
 Note that variables have a \texttt{pism_intent}\index{PISM!\texttt{pism_intent} attribute} attribute.  When that attribute is \texttt{diagnostic}, the variable can be deleted from the file without affecting whether PISM can use it as a \texttt{-i} input file.  Variables with \texttt{pism_intent} = \texttt{model_state}, by contrast, must be present for use with \texttt{-i}.
 
-Regarding the automatically produced time variable, which has a \texttt{units} attribute like \texttt{"years since 1-1-1"}, note that CF metadata conventions require using a reference date in the units string of a time (\texttt{t}) variable.  PISM completely ignores this reference date.
+Regarding the automatically produced time variable, which has a \texttt{units} attribute like \texttt{"seconds since 1-1-1"}, note that CF metadata conventions require using a reference date in the units string of a time (\texttt{time}) variable. By default PISM ignores this reference date.
 
 
 \subsection{Bootstrapping}
@@ -437,6 +437,8 @@ \subsection{Bootstrapping}
 
 When using \fileopt{boot_file} you will need to specify both grid dimensions (using \texttt{-Mx}, \texttt{-My} and \texttt{-Mz}) and the height of the computational box for the ice with \texttt{-Lz}.  The data read from the file can determine the horizontal extent of the model, if options \texttt{-Lx}, \texttt{-Ly} are not set.  The additional specification of vertical extent by \texttt{-Lz} is reasonably natural because realistic data used in ``bootstrapping'' are two-dimensional.  Not specifying all four options \texttt{-Mx}, \texttt{-My}, \texttt{-Mz}, \texttt{-Lz} \emph{when bootstrapping with} \texttt{-boot_file} is an error.
 
+If \texttt{-Lx} and \texttt{-Ly} specify horizontal grid dimensions smaller than in the bootstrapping file, PISM will cut out the \emph{center} portion of the domain. Options \intextoption{x_range} and \intextoption{y_range} each take a list of two numbers, a list of minimum and maximum $x$ and $y$ coordinates, respectively (in meters). This makes it possible to select a subset that is not in the center of a bootstrapping file grid.
+
 \subsubsection*{\texttt{-boot_file} file format}
 \label{sec:bootstrapping-format}  Allowed formats for a bootstrapping file are relatively simple to describe. 
 \begin{enumerate}