update namoptions document and changelog for 4.4.1

CHANGELOG.md

@@ -1,6 +1,38 @@
 Changes in DALES
 ================
 
+Version 4.4.1 - 2023-06-07
+--------------------------
+
+A minor release with fixes, improved error reporting and statistics output.
+
+### Bugs fixed
+
+* Fix unsafe boundary exchange of ustar, commits f2d07e82, 45e38ace1
+* Fix output units and long_name attribute, commits 3358143c, 0744378c0, c8fdb21
+* fix #79: dtmax < 0.1 leads to crash, commit 4df5e0e1f1
+
+### Improvements
+
+* 2D radiation statistics, commit 7e58773660e
+* Add variance budget module, commit 4646ff8e
+* modgenstat: add per-level cloud fraction, cfrac, to profiles.nnn.nc, commit 8aee2cb63c47
+* Make lCnstAlbedo true by default for less surprising behavior,  commit 989e13a33675
+* Allow multiple planes for crossxz, crossyz and in any MPI tile, commit a4640bd20b
+* Add namelist option RUN/loutdirs to save model output in separate directories for each row, commit 3576a917ef
+
+### Improved error checking
+
+* Stop with error message if any dzh or dzf is zero or negative, commit 5f9f67046c
+* Add error checking when opening *.inp.nnn files, commit f1a38f24d
+* Print MPI error string on error, catch and explain nprocx * nprocy != nprocs, commit b6c5887ad8
+* Add MPI error checking in initialization, commit 6060f13a2ad
+* Check FFTW plan creation result for errors, commit a2666269b6
+
+### Optimization
+
+* bulkmicrophysics: give more of the temporary 3D fields configurable precision (field_r), commit fe5f0ea9
+
 
 Version 4.4 - 2022-06-20
 ------------------------

README.md

@@ -9,6 +9,7 @@ The following documents are included in the DALES repository (but are not fully
 * Documentation of the configuration options [Namoptions.pdf](https://github.com/dalesteam/dales/blob/master/utils/doc/input/Namoptions.pdf)
 * [readme.pdf](https://github.com/dalesteam/dales/blob/master/utils/doc/input/readme.pdf)
 * [INSTALL.md](https://github.com/dalesteam/dales/blob/master/INSTALL.md) contains installation instructions
+* [CHANGELOG.md](https://github.com/dalesteam/dales/blob/master/CHANGELOG.md) documents the changes between versions
 * The [DALES Wiki](https://github.com/dalesteam/dales/wiki/) contains [Installation instructions](https://github.com/dalesteam/dales/wiki/Installation-notes) for various systems and notes for [visualizing and processing](https://github.com/dalesteam/dales/wiki/Visualizing-and-processing-output) the model output
 
 ## License

utils/doc/input/Namoptions.tex

@@ -18,7 +18,13 @@
 \usepackage{mdwlist}		% Kan dingen met lijsten. Geeft ook de optie itemize* (geen witregels tussen items)
 \usepackage{multirow}		% Combine multiple rows within a tabular
 %\usepackage{array}
-
+\usepackage{xcolor}             %
+\hypersetup{                    % color text of links instead of surrounding them with red or green boxes
+    colorlinks,
+    linkcolor={red!50!black},
+    citecolor={blue!50!black},
+    urlcolor={blue!80!black}
+}
 
 \topmargin= -5 mm
 \textwidth 15.5cm
@@ -163,7 +169,7 @@ \subsection{Namelist DYNAMICS}\label{par:dynamics}
 \end{tabular}} & \multirow{11}{*}{\begin{tabular}{@{\hspace{0cm}}p{4cm}}$x \in \{1,$ $2,$ $5,$ $52,$ $55,$ $6,$ $62,$ $7\}$\end{tabular}}	& Advection scheme for momentum, TKE, $\theta_l$, $q_t$ and scalars: & \multirow{11}{*}{-}\\
   	&		&				& 1 = 1$^{\text{st}}$ order upwind					&\\
   	&		&				& 2 = 2$^{\text{nd}}$ order central difference			&\\
-  	&		&				& 5 = Option 6 + 5$^{\text{th}}$ order upwind	&\\
+  	&		&				& 5 = 6$^{\text{th}}$ order central + 5$^{\text{th}}$ order upwind	&\\
   	&		&				& 52 = Horizontal 5$^{\text{th}}$ \& vertical 2$^{\text{nd}}$	&\\
   	&		&				& 55 = Hybrid scheme	&\\
   	&		&				& 555 = Alternative hybrid scheme	&\\
@@ -330,7 +336,7 @@ \subsection{Namelist RUN}\label{par:run}
   \hypertarget{nprocy}{nprocy}	& 0	& $x = N_{\text{processors}} / \text{nprocx}$	& Number of processors in $y$ direction; if set to 0, MPI will determine suitable value	& - \\
   loutdirs	& .false.	& $x\in\{\text{.false.},\text{.true.}\}$		& If .true., per-task output files are stored in subdirectory myidy/ & -\\
 \end{supertabular}
-$^*$If $\hyperlink{iadvmom}{\text{iadv\_mom}} \in \lbrace6, 62\rbrace$ or any value of\hyperlink{iadvtke}{\text{iadv\_tke}}, \hyperlink{iadvthl}{\text{iadv\_thl}}, \hyperlink{iadvqt}{\text{iadv\_qt}} or \hyperlink{iadvsv}{\text{iadv\_sv}} $\in \lbrace6, 62, 7\rbrace$, courant = 0.7 as standard. Otherwise default value is 1.
+$^*$If $\hyperlink{iadvmom}{\text{iadv\_mom}} \in \lbrace6, 62\rbrace$ or any value of \hyperlink{iadvtke}{\text{iadv\_tke}}, \hyperlink{iadvthl}{\text{iadv\_thl}}, \hyperlink{iadvqt}{\text{iadv\_qt}} or \hyperlink{iadvsv}{\text{iadv\_sv}} $\in \lbrace6, 62, 7\rbrace$, courant = 0.7 as standard. Otherwise default value is 1.
 \end{center}
 
 %\newpage
@@ -719,11 +725,14 @@ \subsection{Namelist NAMCROSSSECTION}\label{par:crosssection}
   }
 \begin{supertabular}{|l|p{1.6cm}|p{4cm}|p{6cm}|l|}
   lcross	& .false.	& $x\in\{\text{.false.},\text{.true.}\}$	& Switch for dumping of crosssections of the field	& -\\
-  lbinary	& .false.	& $x\in\{\text{.false.},\text{.true.}\}$	& Switch to dump crosssections in binary files	& -\\
+  lbinary	& .false.	& $x\in\{\text{.false.},\text{.true.}\}$	& Switch to dump crosssections in binary files	        & -\\
+  lxy           & .true.        & $x\in\{\text{.false.},\text{.true.}\}$	& Enable horizontal xy crosssection                     & -\\
+  lxz           & .true.        & $x\in\{\text{.false.},\text{.true.}\}$	& Enable vertical xz crosssection	                & -\\
+  lyz           & .true.        & $x\in\{\text{.false.},\text{.true.}\}$	& Enable vertical yz crosssection         	        & -\\
   dtav		& dtav\_glob	& $x = n \cdot \text{dtmax}, \quad n \in \mathbb{N}^*$	& Time interval for sampling of statistics	& s\\
-  crossheight(1:100)& 1: $x=2$ & $x \in \mathbb{N}, \quad 1 \leq x \leq \text{kmax}$	& Heights of the horizontal crosssection		& -\\
-  crossplane	& 2		& $x \in \mathbb{N}, \quad 1 \leq x \leq {\text{jtot}}/{N_\text{processors}}$	& Location of the vertical (xz) plane on every processor& -\\
-  crossortho	& 2	& $x \in \mathbb{N}, \quad 1 \leq x \leq \text{itot}$	& Location of the vertical (yz) plane & - \\
+  crossheight(1:100)& 1: $x=2$ & $x \in \mathbb{N}, \quad 1 \leq x \leq \text{kmax}$	& Heights of the horizontal crosssection	& -\\
+  crossplane	& 2		& $x \in \mathbb{N}, \quad 1 \leq x \leq {\text{jtot}}/{N_\text{processors}}$	& List of locations of vertical (xz) planes& -\\
+  crossortho	& 2	& $x \in \mathbb{N}, \quad 1 \leq x \leq \text{itot}$	& List of locations of vertical (yz) planes & - \\
 \end{supertabular}
 \end{center}
 
@@ -789,8 +798,16 @@ \subsection{Namelist NAMFIELDDUMP}\label{par:fielddump}
   klow		& 1		& $x \in \mathbb{N}, \quad 1 \le x \le \text{khigh}$	& Lowest level of the 3d-field output		& -\\
   khigh		& $kmax$	& $x \in \mathbb{N}, \quad \text{klow} \le x \le \text{kmax}$	& Highest level of the 3d-field output		& -\\
   ncoarse		& 1	& $x \in \mathbb{N}, \quad x \geq 1 $	& Factor by which to reduce (sample) the 3d-field to be written (in each horizontal direction)	& -\\
-  tmin		& 0.0		& $x \in \mathbb{R}, \quad x \geq 0$	& Start time of field dump; not active yet	& s \\
-  tmax		& $10^8$	& $x \in \mathbb{R}, \quad x \geq 0$	& End time of field dump; not active yet	& s \\
+  tmin		& 0.0		& $x \in \mathbb{R}, \quad x \geq 0$	& Start time of field dump	& s \\
+  tmax		& $10^8$	& $x \in \mathbb{R}, \quad x \geq 0$	& End time of field dump	& s \\
+  lu	       & .true.	        & $x\in\{\text{.false.},\text{.true.}\}$	& Save $u$ 	& -\\
+  lv	       & .true.	        & $x\in\{\text{.false.},\text{.true.}\}$	& Save $v$ 	& -\\
+  lw	       & .true.	        & $x\in\{\text{.false.},\text{.true.}\}$	& Save $w$ 	& -\\
+  lqt	       & .true.	        & $x\in\{\text{.false.},\text{.true.}\}$	& Save $q_t$ 	& -\\
+  lql	       & .true.	        & $x\in\{\text{.false.},\text{.true.}\}$	& Save $q_l$ 	& -\\
+  lthl	       & .true.	        & $x\in\{\text{.false.},\text{.true.}\}$	& Save $\theta_l$ & -\\
+  lbuoy	       & .true.	        & $x\in\{\text{.false.},\text{.true.}\}$	& Save buoyancy field & -\\
+  lsv	       & .true.         & $x\in\{\text{.false.},\text{.true.}\}$	& List of booleans for saving sv001, sv002, ... & -\\
 \end{supertabular}
 \end{center}
 
@@ -1184,6 +1201,34 @@ \subsection{Namelist NAMRADFIELD}\label{par:radfield}
 \end{supertabular}
 \end{center}
 
+\subsection{Namelist NAMVARBUDGET}\label{par:varbudget}
+
+\begin{center}
+	  \tablefirsthead{
+        \multicolumn{1}{c}{Option} & \multicolumn{1}{c}{Default} & \multicolumn{1}{c}{Possible values} & \multicolumn{1}{c}{Description} & \multicolumn{1}{c}{Unit}\\
+        \hline &&&&\\
+  }
+  \tablehead{
+        \multicolumn{5}{l}{\small \it Continued from previous page}\\
+        \multicolumn{5}{c}{}\\
+        \multicolumn{1}{c}{Option} & \multicolumn{1}{c}{Default} & \multicolumn{1}{c}{Possible values} & \multicolumn{1}{c}{Description} & \multicolumn{1}{c}{Unit}\\
+        \hline &&&&\\
+  }
+  \tabletail{
+        &&&&\\\hline
+        \multicolumn{5}{c}{}\\
+        \multicolumn{5}{r}{\small \it Continued on next page}\\
+  }
+  \tablelasttail{
+        &&&&\\\hline
+  }
+\begin{supertabular}{|l|p{2cm}|p{4cm}|p{6cm}|l|}
+  lvarbudget	& .false.	& $x\in\{\text{.false.},\text{.true.}\}$	        & Switch to turn on variance budget output      & -\\
+  dtav		& dtav\_glob	& $x = n \cdot \text{dtmax}, \quad n \in \mathbb{N}^*$	& Time interval for sampling of variance budget	& s\\
+  timeav	& timeav\_glob	& $x = n \cdot \text{dtav},  \quad n \in \mathbb{N}^*$	& Time interval for writing statistics		& s\\
+\end{supertabular}
+\end{center}
+
 \newpage
 \subsection{Namelist NAMSAMPLING}\label{par:sampling}
 \begin{center}