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diff --git a/doc/solps/ELM_cycles.pdf b/doc/solps/ELM_cycles.pdf
new file mode 100644
index 000000000..cbad72cfa
Binary files /dev/null and b/doc/solps/ELM_cycles.pdf differ
diff --git a/doc/solps/b2.transport.inputfile.ELMs b/doc/solps/b2.transport.inputfile.ELMs
new file mode 100644
index 000000000..7a60616d3
--- /dev/null
+++ b/doc/solps/b2.transport.inputfile.ELMs
@@ -0,0 +1,28 @@
+ &TRANSPORT
+ ndata(1, 1 , 1 )= 6 ,
+ tdata(1, 1 , 1 , 1 )= -4.00E-02 , tdata(2, 1 , 1 , 1 )= 1.30 , tdata(3, 1 , 1 , 1 )= 10.00 ,
+ tdata(1, 2 , 1 , 1 )= -1.50E-02 , tdata(2, 2 , 1 , 1 )= 1.30 , tdata(3, 2 , 1 , 1 )= 10.00 ,
+ tdata(1, 3 , 1 , 1 )= -1.40E-02 , tdata(2, 3 , 1 , 1 )= 0.05 , tdata(3, 3 , 1 , 1 )= 10.00 ,
+ tdata(1, 4 , 1 , 1 )=  5.00E-03 , tdata(2, 4 , 1 , 1 )= 0.05 , tdata(3, 4 , 1 , 1 )= 10.00 ,
+ tdata(1, 5 , 1 , 1 )=  5.50E-03 , tdata(2, 5 , 1 , 1 )= 1.30 , tdata(3, 5 , 1 , 1 )= 10.00 ,
+ tdata(1, 6 , 1 , 1 )=  2.50E-02 , tdata(2, 6 , 1 , 1 )= 1.30 , tdata(3, 6 , 1 , 1 )= 10.00 ,
+ ndata(1, 3 , 1 )= 6 ,
+ tdata(1, 1 , 3 , 1 )= -4.00E-02 , tdata(2, 1 , 3 , 1 )= 2.00 , tdata(3, 1 , 3 , 1 )= 10.00 ,
+ tdata(1, 2 , 3 , 1 )= -1.50E-02 , tdata(2, 2 , 3 , 1 )= 2.00 , tdata(3, 2 , 3 , 1 )= 10.00 ,
+ tdata(1, 3 , 3 , 1 )= -1.40E-02 , tdata(2, 3 , 3 , 1 )= 0.07 , tdata(3, 3 , 3 , 1 )= 10.00 ,
+ tdata(1, 4 , 3 , 1 )=  5.00E-03 , tdata(2, 4 , 3 , 1 )= 0.07 , tdata(3, 4 , 3 , 1 )= 10.00 ,
+ tdata(1, 5 , 3 , 1 )=  5.50E-03 , tdata(2, 5 , 3 , 1 )= 2.00 , tdata(3, 5 , 3 , 1 )= 10.00 ,
+ tdata(1, 6 , 3 , 1 )=  2.50E-02 , tdata(2, 6 , 3 , 1 )= 2.00 , tdata(3, 6 , 3 , 1 )= 10.00 ,
+ ndata(1, 4 , 1 )= 6 ,
+ tdata(1, 1 , 4 , 1 )= -4.00E-02 , tdata(2, 1 , 4 , 1 )= 2.00 , tdata(3, 1 , 4 , 1 )= 10.00 ,
+ tdata(1, 2 , 4 , 1 )= -1.50E-02 , tdata(2, 2 , 4 , 1 )= 2.00 , tdata(3, 2 , 4 , 1 )= 10.00 ,
+ tdata(1, 3 , 4 , 1 )= -1.40E-02 , tdata(2, 3 , 4 , 1 )= 0.07 , tdata(3, 3 , 4 , 1 )= 10.00 ,
+ tdata(1, 4 , 4 , 1 )=  5.00E-03 , tdata(2, 4 , 4 , 1 )= 0.07 , tdata(3, 4 , 4 , 1 )= 10.00 ,
+ tdata(1, 5 , 4 , 1 )=  5.50E-03 , tdata(2, 5 , 4 , 1 )= 2.00 , tdata(3, 5 , 4 , 1 )= 10.00 ,
+ tdata(1, 6 , 4 , 1 )=  2.50E-02 , tdata(2, 6 , 4 , 1 )= 2.00 , tdata(3, 6 , 4 , 1 )= 10.00 ,
+ ELM_TIME_PERIOD=0.001,
+ ELM_TIME_BEGIN=0.0002,
+ ELM_TIME_PLATEAU=0.0002,
+ ELM_TIME_RECOVERY=0.0006,
+ ELM_TIME_END=0.0006,
+ /
diff --git a/doc/solps/solps.tex b/doc/solps/solps.tex
index badee1f2b..594902b65 100644
--- a/doc/solps/solps.tex
+++ b/doc/solps/solps.tex
@@ -1370,7 +1370,7 @@ \section{runs}
   \item[res\_D+O]\index{res\_D+O} non-species dependent residuals for a $D+O$ case
   \item[res\_D+C+He]\index{res\_D+C+He} non-species dependent residuals for a $D+C+He$ case
   \item[res\_D+C+Ar+Ne+He]\index{res\_D+C+Ar+Ne+He} non-species dependent residuals for a $D+C+Ar+Ne+He$ case
-  \item[resco]\index{resco} continuity residuals
+  \item[resco]\index{resco} continuity residuals per species
   \item[resco\_reg]\index{resco\_reg} continuity residuals per region
   \item[resco\_reg\_region \#1]\index{resco\_reg\_region} continuity residuals per region for species \#1 (default 0)
   \item[resco\_D+C]\index{resco\_D+C} continuity residuals for a $D+C$ case
@@ -1383,7 +1383,9 @@ \section{runs}
   \item[resmo\_D+O]\index{resmo\_D+O} parallel momentum residuals for a $D+O$ case
   \item[resmo\_D+C+He]\index{resmo\_D+C+He} parallel momentum residuals for a $D+C+He$ case
   \item[resmt\_reg]\index{resmt\_reg} residuals of the total parallel momentum equation
+  \item[reshe]\index{reshe} residuals of the electron heat equation
   \item[reshe\_reg]\index{reshe\_reg} residuals of the electron heat equation per region
+  \item[reshi]\index{reshe} residuals of the ion heat equation
   \item[reshi\_reg]\index{reshi\_reg} residuals of the ion heat equation per region
   \item[respo] \index{respo} residuals of the potential equation, including the internal iterations
   \item[respo\_num] \index{respo\_num} the number of internal potential equation iterations
@@ -1464,7 +1466,7 @@ \section{runs}
     \begin{verbatim}
 setenv GNUPLOT_BATCH yes
 setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid'
-setenv PRINT_PLOT b2time2d.ps
+setenv PRINT_PLOT b2time2d_time_traces.ps
 rm -f GNUPLOT_COUNT gnuplot.cmd
 echo 0 > GNUPLOT_COUNT
 
@@ -1543,16 +1545,45 @@ \section{runs}
  \end{description}
 \item Detailed run diagnostics (Many of these invoke the {\tt plot} command described above and can be toggled to use a logarithmic $y$ scale by use of an additional {\tt l} argument while {\tt L} also plots the absolute values of negative quantities on the same scale and {\tt M} the absolute values of negative quantities in a separate plot)
  \begin{description}
-  \item[2d]\index{2d} plots time-dependent quantities from {\tt b2time.nc} (Appendix \ref{cha:b2time}), 2$^{nd}$, 3$^{rd}$ {\it etc.\ versus} the 1$^{st}$ argument.
-  \item[2da]\index{2da} prints time-dependent quantities from {\tt b2time.nc} (Appendix \ref{cha:b2time}), 2$^{nd}$, 3$^{rd}$ {\it etc.\ versus} the 1$^{st}$ argument.
-  \item[2dt]\index{2dt} plots time-dependent quantities from {\tt b2time.nc} (Appendix \ref{cha:b2time}) versus time. A python version of this script also exists (Python 2.7 and 3.5 compatible).
+  \item[2d]\index{2d} plots time-dependent quantities from {\tt b2time.nc} (Appendix \ref{cha:b2time}), 2$^{nd}$, 3$^{rd}$ {\it etc.\ versus} the 1$^{st}$ argument. Multi-species quantities should be called as {\tt \$\{name\}\allowbreak\$\{is\}}, where {\tt \$\{is\}} is the {\tt B2.5} species index (the species names can be retrieved using the {\bf species} command). E.g.:
+  \begin{verbatim}
+  > 2d timesa nesepm
+  > 2d timesa tesepm tisepm
+  > 2d timesa nasepm1 nasepm9
+  \end{verbatim}
+  \item[2da]\index{2da} prints time-dependent quantities from {\tt b2time.nc} (Appendix \ref{cha:b2time}), 2$^{nd}$, 3$^{rd}$ {\it etc.\ versus} the 1$^{st}$ argument. Multi-species quantities should be called as {\tt \$\{name\}\allowbreak\$\{is\}}, where {\tt \$\{is\}} is the {\tt B2.5} species index (the species names can be retrieved using the {\bf species} command). E.g.:
+  \begin{verbatim}
+  > 2da timesa nesepm
+  > 2da timesa tesepm tisepm
+  > 2da timesa nasepm1 nasepm9
+  \end{verbatim}
+  \item[2dds]\index{2dds} prints profiles from {\tt b2time.nc} (Appendix \ref{cha:b2time}) versus the corresponding space coordinate. Multi-species quantities should be called as {\tt \$\{name\}\allowbreak\$\{is\}}, where {\tt \$\{is\}} is the {\tt B2.5} species index (the species names can be retrieved using the {\bf species} command). E.g.:
+  \begin{verbatim}
+  > 2dds ne3da
+  > 2dds te3da ti3da
+  > 2dds na3da1 na3da9
+  \end{verbatim}
+  By default, the plotted profiles will be averaged over the last 10 snapshots. If the number of available snapshots is less than 10, the default will be to average over all the snapshots available. The averaging limits can be adjusted with the two further arguments which should be added at end of the command (default values are 10 and 0 respectively).
+  \item[2dt]\index{2dt} plots time-dependent quantities from {\tt b2time.nc} (Appendix \ref{cha:b2time}) versus time. Multi-species quantities should be called as {\tt \$\{name\}\allowbreak\$\{is\}}, where {\tt \$\{is\}} is the {\tt B2.5} species index (the species names can be retrieved using the {\bf species} command). E.g.:
+  \begin{verbatim}
+  > 2dt nesepm
+  > 2dt tesepm tisepm
+  > 2dt nasepm1 nasepm9
+  \end{verbatim}
+  A python version of this script also exists (Python 2.7 and 3.5 compatible).
   \item[2dt\_tallies.py]\index{2dt\_tallies.py} plots time-dependent quantities from {\tt b2tallies.nc} (Appendix \ref{cha:b2tallies}) versus time (Python 3.5 compatible).
-  \item[2dt\_av]\index{2dt\_av} plots averaged time-dependent quantities from {\tt b2time.nc} (Appendix \ref{cha:b2time}) versus time.
+  \item[2dt\_tracing]\index{2dt\_tracing} plots time-dependent quantities from the run tracing files {\tt tracing/*.trc}.
+  \item[2dt\_av]\index{2dt\_av} plots averaged time-dependent quantities from {\tt b2time.nc} (Appendix \ref{cha:b2time}) versus time. Multi-species quantities should be called as {\tt \$\{name\}\allowbreak\$\{is\}}, where {\tt \$\{is\}} is the {\tt B2.5} species index (the species names can be retrieved using the {\bf species} command). E.g.:
+  \begin{verbatim}
+  > 2dt_av nesepm
+  > 2dt_av tesepm tisepm
+  > 2dt_av nasepm1 nasepm9
+  \end{verbatim}
   \item[2dvi]\index{2dvi} prepares a \btwoplot command file {\tt TDV/contr.b2p} for production of input files to start a {\tt DIVIMP} run.
-  \item[2d\_plots]\label{script:2dplots}\index{2d\_plots} prepares {\tt b2time2d.ps} from {\tt b2time.nc} (Appendix \ref{cha:b2time}). This uses the batch feature of the {\tt plot} command.
-  \item[2d\_plots\_av]\index{2d\_plots\_av} prepares {\tt b2time2d\_av.ps} from averaged values in {\tt b2time.nc} (Appendix \ref{cha:b2time}). This uses the batch feature of the {\tt plot} command.
-  \item[2d\_profiles]\index{2d\_profiles} creates {\tt *.last10} files for plotting. When processing fluxes, divides them by the area of contact to the neighbouring cell. By default, the profiles will be averaged over the last 10 snapshots. If the number of available snapshots is less than 10, the default will be to average over all the snapshots available. The averaging limits can be adjusted with the \#1 and \#2 arguments (default values are 10 and 0 respectively).
-  \item[2d\_profiles\_extended]\index{2d\_profiles\_extended} creates {\tt *.last10} files for plotting. When processing fluxes, divides them by the area of contact to the neighbouring cell. The flux files ending in {\tt P.last10} are divided by the perpendicular area of the cell face. By default, the profiles will be averaged over the last 10 snapshots. If the number of available snapshots is less than 10, the default will be to average over all the snapshots available. The averaging number can be adjusted with the \#1 argument (default value is 10).
+  \item[2d\_plots]\label{script:2dplots}\index{2d\_plots} prepares {\tt b2time2d\_time\_traces.ps} from {\tt b2time.nc} (Appendix \ref{cha:b2time}) containing several relevant time traces.
+  \item[2d\_plots\_av]\index{2d\_plots\_av} prepares {\tt b2time2d\_time\_traces\_av.ps} from averaged values in {\tt b2time.nc} (Appendix \ref{cha:b2time}) containing several relevant time traces. This uses the batch feature of the {\tt plot} command.
+  \item[2d\_profiles]\index{2d\_profiles} creates {\tt *.last10} files containing several relevant plasma profiles at relevant locations (inner/outer midplane and divertor targets), and plots the important ones on {\tt b2time2d\_profiles.ps}. When processing fluxes, divides them by the area of contact to the neighbouring cell. By default, the printed profiles will be averaged over the last 10 snapshots. If the number of available snapshots is less than 10, the default will be to average over all the snapshots available. The averaging limits can be adjusted with the \#1 and \#2 arguments (default values are 10 and 0 respectively).
+  \item[2d\_profiles\_extended]\index{2d\_profiles\_extended} creates {\tt *.last10} files containing several relevant plasma profiles at relevant locations (inner/outer midplane and divertor targets). When processing fluxes, divides them by the area of contact to the neighbouring cell. The flux files ending in {\tt P.last10} are divided by the perpendicular area of the cell face. By default, the printed profiles will be averaged over the last 10 snapshots. If the number of available snapshots is less than 10, the default will be to average over all the snapshots available. The averaging number can be adjusted with the \#1 argument (default value is 10).
   \item[2d.summarize]\index{2d.summarize} Outputs the time-dependent quantities from the last time point in {\tt b2time.nc}.
   \item[b2favere\_OK]\index{b2favere\_OK} Checks that the {\tt b2favere} file is of correct size and content.
   \item[b2fstate\_OK]\index{b2fstate\_OK} Checks that the {\tt b2fstate} file is of correct size and content.
@@ -1582,6 +1613,7 @@ \section{runs}
   \item[energy\_balance\_core\_extended]\index{energy\_balance\_core\_extended} Plots an extended version including volumetric sources of the energy balance for the core plasma.
   \item[energy\_balance\_coupled]\index{energy\_balance\_coupled} Plots the energy balance, including sources from {\tt Eirene}.
   \item[energy\_balance\_extended]\index{energy\_balance\_extended} Plots an extended version including volumetric sources of the energy balance.
+  \item[energy\_balance\_tracing]\index{energy\_balance\_tracing} prepares the {\tt energy\_balance.ps} file from {\tt tracing/blne.trc} containing the full energy balance of the run (in order: total energy balance, decomposition of radiation terms, decomposition of the energy load onto the inner target, decomposition of the energy load onto the outer target, decomposition of the energy load onto the main wall).
   \item[fchxreg]\index{fchxreg} Plots the electric current flow across important $x$-directed surfaces in {\tt B2.5}.
   \item[fchyreg]\index{fchyreg} Plots the electric current flow across important $y$-directed surfaces in {\tt B2.5}.
   \item[fhexreg]\index{fhexreg} Plots the electron energy flow across important $x$-directed surfaces in {\tt B2.5}.
@@ -1599,6 +1631,7 @@ \section{runs}
   \item[fluid\_fluxes \#1 \#2]\index{fluid\_fluxes} Plots the sum of fluid fluxes for species numbers varying from \#1 to \#2 (respective defaults are 0 and 1). Also exists as a Python script. Fluxes into the domain are shown as negative values, fluxes out of the domain as positive values.
   \item[fluxt \#1]\index{fluxt}\index{b2mod\_dimensions.F} Gives the flux strength for the first \#1 {\tt Eirene} strata. The default value is all the strata, as read from the {\tt b2.neutrals.parameters} file, or if not present, the {\tt \$\{SOLPSTOP\}/modules/B2.5/src\allowbreak/modules.local/b2mod\_dimensions.F} file, or if not present, the {\tt \$\{SOLPSTOP\}/modules/B2.5\allowbreak /src/modules/b2mod\_dimensions.F} file.
   \item[get\_solps\_fluids]\index{get\_solps\_fluids} A utility script to obtain the list of fluid species labels from the {\tt run.log} file.
+  \item[groups\_species]\index{groups\_species} Obtains the ordered numbers of species contained in each isonuclear sequence.
   \item[internal\_energy\_balance]\index{internal\_energy\_balance} Outputs the energy balance tallies.
   \item[internal\_energy\_balance\_coupled]\index{internal\_energy\_balance\_coupled} Outputs the energy balance tallies for a coupled run.
   \item[joule\_heating]\index{joule\_heating} Plots the amount of Joule heating per region.
@@ -1614,7 +1647,9 @@ \section{runs}
   \item[nesepm\_feedback\_by\_pfr]\index{nesepm\_feedback\_by\_pfr} Plots in {\tt feedback.ps} the parameters of the {\em nesepm\_pfr} feedback scheme.
   \item[nesepm\_feedback\_fluid]\index{nesepm\_feedback\_fluid} Plots in {\tt feedback.ps} the parameters of the {\em nesepm\_sol} feedback scheme for fluid runs.
   \item[nireg]\index{nireg} Shows averaged total ion density per region.
+  \item[particle\_balance\_tracing]\index{particle\_balance\_tracing} prepares the {\tt particle\_balance.ps} file from {\tt tracing/blnn\_SPb.trc} containing the full particle balance of the run (in order: total particle balance and ion balance, both for all fluid species).
   \item[particle\_conservation\_coupled]\index{particle\_conservation\_coupled} Plots the particle balance for multi-species coupled runs
+  \item[plot\_residuals]\index{plot\_residuals} prepares the {\tt residuals.ps} containing the time traces of all the run residuals.
   \item[print\_species]\index{print\_species} Prints the list of species included in the run.
   \item[reflection]\index{reflection} Shows reflected particle fluxes (for {\tt B2.5} standalone runs).
   \item[reflection\_energy]\index{reflection\_energy} Shows reflected energy fluxes (for {\tt B2.5} standalone runs).
@@ -1674,6 +1709,7 @@ \section{runs}
   \item[plot\_trc]\index{plot\_trc} Produces {\tt trc.pdf} file (or {\tt trc.ps} if {\tt PLOT\_TRC\_FMT} environment variable is set to {\tt ps}) containing desired figures based on the data from {\tt tracing/*.trc} and {\tt b2time.nc} (potentially other similarly formatted files as well) according to {\tt plot\_trc.cmd} file (default example of this file can be found in {\tt \$SOLPSTOP/scripts/commands}). Read the script header for further details.
   \item[plot\_trg]\index{plot\_trg} Produces {\tt trg.pdf} file (or {\tt trg.pdf} if {\tt PLOT\_TRC\_FMT} environment variable is set to {\tt ps}) containing desired figures based on the data from {\tt ld\_tg\_*.dat} and {\tt fp\_tg\_*.dat} (potentially other similarly formatted files as well) according to {\tt plot\_trg.cmd} file (default example of this file can be found in {\tt \$SOLPSTOP/scripts/commands}). Also produces {\tt trg\_sum.dat} file containing some integral, peak and average quantities at the targets. Read the script header for further details.
   \item[quote\_pwd]\index{quote\_pwd} Returns the current working directory as a string with quotes (c.f.\ {\tt noquote\_pwd}).
+  \item[replace\_links]\index{replace\_links} This script recursively replaces all symbolic links in a directory and subdirectories (in the current directory if called without arguments, or in a directory specified as argument) with the real file or folder to which they are linked, keeping the same name of the original link (if the real linked file/folder currently exists).
   \item[rlndr]\index{rlndr} Replaces a link address by another.
   \item[saveb2]\index{saveb2} Workflow script used to backup and save current run data. Intended usage would be running {\tt saveb2 -l} whenever the run is stopped for the diagnostic purpose. This will create {\tt backup.date} directory, copy all the important files there and move tracing files there as well (this allows to keep the whole run history and simultaneously limit the size of current tracing files for faster plotting and better space management). After that {\tt b2mndr\_stime} switch should be set to the current timestamp (can be done by running {\tt STIME -l} script) and run can be continued. After the run is converged {\tt saveb2 -s run\_name} can be used to copy all the necessary files to {\tt run\_name.save} directory and the current {\tt run\_name} directory can be safely deleted to clean-up the space. The script can also be used to setup a workspace on scratch, copy results back and clean-up the workspace.
   \item[STIME]\index{STIME} Auxiliary script to handle {\tt b2mndr\_stime} with {\tt saveb2} workflow, run {\tt STIME -h} for details.
@@ -3357,6 +3393,67 @@ \subsection{b2.transport.inputfile}
 
 \VerbatimInput[fontsize=\footnotesize]{b2.transport.inputfile}
 
+\subsubsection{ELM model}
+\index{ELM\_model}\index{ELMs}\label{lab:elm:model}
+
+A simplified model is available to emulate ELM events through a periodic increase
+of the anomalous transport coefficients declared in {\tt b2.transport.inputfile}.
+This is done by declaring further variables {\tt tdata(3,m,i,j)} corresponding to
+the values of the coefficients at the plateau of the ELM events. The values declared
+by {\tt tdata(2,m,i,j)} will correspond, in this case, to the inter-ELM coefficients.\\
+The characteristics of the ELM dynamics are controlled through the following variables
+(see also Appendix \ref{lis:b2cdcn}): 
+
+\begin{description}
+  \item[elm\_period]\index{elm\_period} is a real number indicating the period (in seconds) of the simulated ELMs.
+  \item[elm\_time\_begin]\index{elm\_time\_begin} is an array of 9 reals determining the times (in seconds), within
+    an ELM cycle, at which the overall ELM phase begins (i.e.\ the transport coefficients
+    start to ramp up from the {\tt tdata(2,m,i,j)} values to the {\tt tdata(3,m,i,j)} values).
+  \item[elm\_time\_plateau]\index{elm\_time\_plateau} is an array of 9 reals determining the times (in seconds), within
+    an ELM cycle, at which the ELM phase reaches its plateau (i.e.\ the transport coefficients
+    start keeping constant values equal to the {\tt tdata(3,m,i,j)}).
+  \item[elm\_time\_recovery]\index{elm\_time\_recovery} is an array of 9 reals determining the times (in seconds), within
+    an ELM cycle, at which the ELM plateau phase ends (i.e.\ the transport coefficients
+    start to ramp down from the {\tt tdata(3,m,i,j)} values to the {\tt tdata(2,m,i,j)} values).
+  \item[elm\_time\_end]\index{elm\_time\_end} is an array of 9 reals determining the times (in seconds), within
+    an ELM cycle, at which the overall ELM phase ends (i.e.\ the transport coefficients
+    start again keeping costant values equal to the {\tt tdata(2,m,i,j)}).
+  \item[elm\_crash\_factor]\index{elm\_crash\_factor} is an array of 9 reals determining the factors describing
+    a logarithmic-type increase of the transport coefficients from the {\tt tdata(2,m,i,j)} values
+    to the {\tt tdata(3,m,i,j)} values during the ELM crash phase. By default (very low values) the increase is linear in time.
+    For higher values, the increase is faster at the beginning and slower towards the end of the crash phase.
+  \item[elm\_recovery\_factor]\index{elm\_recovery\_factor} is an array of 9 reals determining the factors describing
+    an exponential-type decrease of the transport coefficients from the {\tt tdata(3,m,i,j)} values
+    to the {\tt tdata(2,m,i,j)} values during the ELM recovery phase. By default (very low values) the decrease is linear in time.
+    For higher values, the decrease is faster at the beginning and slower towards the end of the recovery phase.
+  \item[elm\_ballooning\_exp]\index{elm\_ballooning\_exp} is an array of 9 reals determining the exponents of a ballooning-type
+    cosine distribution describing a poloidal dependence of the ELM profiles, with default peaking at the outer midplane.
+    See Appendix \ref{lis:b2cdcn} for further details.
+  \item[elm\_dynamics\_multiple]\index{elm\_dynamics\_multiple} is a logical determining whether all the 9 types
+    of transport coefficients have the same dynamics for the ELM phases. If true, then the 9 different values of the
+    above-mentioned variables are applied to the 9 types of transport coefficients. If false, then the first value
+    of the above-mentioned variables is applied to all the 9 types of transport coefficients.
+\end{description}
+
+The following contains an example where the ELM model is used, simulating
+ELM events at a repetition rate of 1000 $Hz$, through a step increase of the transport
+coefficients for a duration of 0.4 $ms$.
+
+\VerbatimInput[fontsize=\footnotesize]{b2.transport.inputfile.ELMs}
+
+Examples of the resulting shapes of the transport coefficients at a given radial location,
+simulating repetitive ELM events, are shown in Fig.~\ref{fig:elm-cycles}.
+
+\begin{figure}[hbtp]
+\ifpdf
+    \centerline{\includegraphics[height=12cm]{ELM_cycles.pdf}}
+\else
+    \centerline{\includegraphics[height=12cm]{ELM_cycles.eps}}
+\fi
+    \caption{Examples of different dynamics for the transport coefficients during ELM cycles.}
+    \label{fig:elm-cycles}
+\end{figure}
+
 \subsection{b2.sources.profile}
 \index{b2.sources.profile}\index{b2sral}\index{b2sral\_inputfile}\index{sources}\label{lab:b2:sources:profile}
 
@@ -14947,32 +15044,66 @@ \chapter{Quantities stored in b2time.nc}
 feixap \index{feixap}\index{b2time.nc, feixap} & integrated poloidal ion energy flux, Eastern edge & $W$ \\
 fetxap \index{fetxap}\index{b2time.nc, fetxap} & integrated poloidal total internal energy flux, Eastern edge & $W$ \\
 fchxap \index{fchxap}\index{b2time.nc, fchxap} & integrated poloidal current, Eastern edge & $A$ \\
+nasepi \index{nasepi}\index{b2time.nc, nasepi} & separatrix fluid species density & \\
+                                               & \hspace{1cm} (for each fluid species), Western edge & $m^{-3}$ \\
 nesepi \index{nesepi}\index{b2time.nc, nesepi} & separatrix electron density, Western edge & $m^{-3}$ \\
 tesepi \index{tesepi}\index{b2time.nc, tesepi} & separatrix electron temperature, Western edge & $eV$ \\
 tisepi \index{tisepi}\index{b2time.nc, tisepi} & separatrix ion temperature, Western edge & $eV$ \\
+dabsepi \index{dabsepi}\index{b2time.nc, dabsepi} & separatrix {\tt Eirene} atom density & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Western edge & $m^{-3}$ \\
+dmbsepi \index{dmbsepi}\index{b2time.nc, dmbsepi} & separatrix {\tt Eirene} molecule density & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Western edge & $m^{-3}$ \\
+tabsepi \index{tabsepi}\index{b2time.nc, tabsepi} & separatrix {\tt Eirene} atom temperature & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Western edge & $eV$ \\
+tmbsepi \index{tmbsepi}\index{b2time.nc, tmbsepi} & separatrix {\tt Eirene} molecule temperature & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Western edge & $eV$ \\
 tpsepi \index{tpsepi}\index{b2time.nc, tpsepi} & separatrix target temperature, Western edge & $K$ \\
 posepi \index{posepi}\index{b2time.nc, posepi} & separatrix potential, Western edge & $V $ \\
+nasepm \index{nasepm}\index{b2time.nc, nasepm} & separatrix fluid species density & \\
+                                               & \hspace{1cm} (for each fluid species), outer midplane & $m^{-3}$ \\
 nesepm \index{nesepm}\index{b2time.nc, nesepm} & separatrix electron density, outer midplane & $m^{-3}$ \\
 tesepm \index{tesepm}\index{b2time.nc, tesepm} & separatrix electron temperature, outer midplane & $eV$ \\
 tisepm \index{tisepm}\index{b2time.nc, tisepm} & separatrix ion temperature, outer midplane & $eV$ \\
+dabsepm \index{dabsepm}\index{b2time.nc, dabsepm} & separatrix {\tt Eirene} atom density & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outer midplane & $m^{-3}$ \\
+dmbsepm \index{dmbsepm}\index{b2time.nc, dmbsepm} & separatrix {\tt Eirene} molecule density & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outer midplane & $m^{-3}$ \\
+tabsepm \index{tabsepm}\index{b2time.nc, tabsepm} & separatrix {\tt Eirene} atom temperature & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outer midplane & $eV$ \\
+tmbsepm \index{tmbsepm}\index{b2time.nc, tmbsepm} & separatrix {\tt Eirene} molecule temperature & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outer midplane & $eV$ \\
 posepm \index{posepm}\index{b2time.nc, posepm} & separatrix potential, outer midplane & $V$ \\
-dnsepm \index{dnsepm}\index{b2time.nc, dnsepm} & main ion density diffusion coefficient, outer midplane & $m^2.s^{-1}$ \\
-dpsepm \index{dpsepm}\index{b2time.nc, dpsepm} & main neutral pressure diffusion coefficient, outer midplane & $m^2.s^{-1}$ \\
-kesepm \index{kesepm}\index{b2time.nc, kesepm} & electron thermal diffusivity, outer midplane & $m^2.s^{-1}$ \\
-kisepm \index{kisepm}\index{b2time.nc, kisepm} & ion thermal diffusivity, outer midplane & $m^2.s^{-1}$ \\
-vxsepm \index{vxsepm}\index{b2time.nc, vxsepm} & main ion poloidal pinch velocity, outer midplane & $m.s^{-1}$ \\
-vysepm \index{vysepm}\index{b2time.nc, vysepm} & main ion radial pinch velocity, outer midplane & $m.s^{-1}$ \\
-vssepm \index{vssepm}\index{b2time.nc, vssepm} & main ion particle viscosity, outer midplane & $m^2.s^{-1}$ \\
+dnsepm \index{dnsepm}\index{b2time.nc, dnsepm} & separatrix main ion density diffusion coefficient, outer midplane & $m^2.s^{-1}$ \\
+dpsepm \index{dpsepm}\index{b2time.nc, dpsepm} & separatrix main neutral pressure diffusion coefficient, outer midplane & $m^2.s^{-1}$ \\
+kesepm \index{kesepm}\index{b2time.nc, kesepm} & separatrix electron thermal diffusivity, outer midplane & $m^2.s^{-1}$ \\
+kisepm \index{kisepm}\index{b2time.nc, kisepm} & separatrix ion thermal diffusivity, outer midplane & $m^2.s^{-1}$ \\
+vxsepm \index{vxsepm}\index{b2time.nc, vxsepm} & separatrix main ion poloidal pinch velocity, outer midplane & $m.s^{-1}$ \\
+vysepm \index{vysepm}\index{b2time.nc, vysepm} & separatrix main ion radial pinch velocity, outer midplane & $m.s^{-1}$ \\
+vssepm \index{vssepm}\index{b2time.nc, vssepm} & separatrix main ion particle viscosity, outer midplane & $m^2.s^{-1}$ \\
+nasepa \index{nasepa}\index{b2time.nc, nasepa} & separatrix fluid species density & \\
+                                               & \hspace{1cm} (for each fluid species), Eastern edge & $m^{-3}$ \\
 nesepa \index{nesepa}\index{b2time.nc, nesepa} & separatrix electron density, Eastern edge & $m^{-3}$ \\
 tesepa \index{tesepa}\index{b2time.nc, tesepa} & separatrix electron temperature, Eastern edge & $eV$ \\
 tisepa \index{tisepa}\index{b2time.nc, tisepa} & separatrix ion temperature, Eastern edge & $eV$ \\
+dabsepa \index{dabsepa}\index{b2time.nc, dabsepa} & separatrix {\tt Eirene} atom density & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Eastern edge & $m^{-3}$ \\
+dmbsepa \index{dmbsepa}\index{b2time.nc, dmbsepa} & separatrix {\tt Eirene} molecule density & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Eastern edge & $m^{-3}$ \\
+tabsepa \index{tabsepa}\index{b2time.nc, tabsepa} & separatrix {\tt Eirene} atom temperature & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Eastern edge & $eV$ \\
+tmbsepa \index{tmbsepa}\index{b2time.nc, tmbsepa} & separatrix {\tt Eirene} molecule temperature & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Eastern edge & $eV$ \\
 tpsepa \index{tpsepa}\index{b2time.nc, tpsepa} & separatrix target temperature, Eastern edge & $K$ \\
 posepa \index{posepa}\index{b2time.nc, posepa} & separatrix potential, Eastern edge & $V $ \\
+namxip \index{namxip}\index{b2time.nc, namxip} & maximum fluid species density & \\
+                                               & \hspace{1cm} (for each fluid species), Western edge & $m^{-3}$ \\
 nemxip \index{nemxip}\index{b2time.nc, nemxip} & maximum electron density, Western edge & $m^{-3}$ \\
 temxip \index{temxip}\index{b2time.nc, temxip} & maximum electron temperature, Western edge & $eV$ \\
 timxip \index{timxip}\index{b2time.nc, timxip} & maximum ion temperature, Western edge & $eV$ \\
 tpmxip \index{tpmxip}\index{b2time.nc, tpmxip} & maximum target temperature, Western edge & $K$ \\
 pomxip \index{pomxip}\index{b2time.nc, pomxip} & maximum potential, Western edge & $V$ \\
+namxap \index{namxap}\index{b2time.nc, namxap} & maximum fluid species density & \\
+                                               & \hspace{1cm} (for each fluid species), Eastern edge & $m^{-3}$ \\
 nemxap \index{nemxap}\index{b2time.nc, nemxap} & maximum electron density, Eastern edge & $m^{-3}$ \\
 temxap \index{temxap}\index{b2time.nc, temxap} & maximum electron temperature, Eastern edge & $eV$ \\
 timxap \index{timxap}\index{b2time.nc, timxap} & maximum ion temperature, Eastern edge  & $eV$ \\
@@ -15052,13 +15183,16 @@ \chapter{Quantities stored in b2time.nc}
     \multicolumn{3}{|l|}{\small\it continued on next page} \\
     \hline \endfoot
     \endlastfoot
-fn3dl \index{fn3dl}\index{b2time.nc, fn3dl} & poloidal particle flux of main ion, Western edge & $s^{-1}.m^{-2}$ \\
+fn3dl \index{fn3dl}\index{b2time.nc, fn3dl} & poloidal particle flux & \\
+                                            & \hspace{1cm} (for each fluid species), Western edge & $s^{-1}.m^{-2}$ \\
 fl3dl \index{fl3dl}\index{b2time.nc, fl3dl} & poloidal electron flux, Western edge & $s^{-1}.m^{-2}$ \\
 fo3dl \index{fo3dl}\index{b2time.nc, fo3dl} & poloidal total ion flux, Western edge & $s^{-1}.m^{-2}$ \\
 fe3dl \index{fe3dl}\index{b2time.nc, fe3dl} & poloidal electron energy flux, Western edge & $W.m^{-2}$ \\
 fi3dl \index{fi3dl}\index{b2time.nc, fi3dl} & poloidal ion energy flux, Western edge & $W.m^{-2}$ \\
 ft3dl \index{ft3dl}\index{b2time.nc, ft3dl} & poloidal total internal energy flux, Western edge & $W.m^{-2}$ \\
 fc3dl \index{fc3dl}\index{b2time.nc, fc3dl} & poloidal current, Western edge & $A.m^{-2}$ \\
+na3dl \index{ne3dl}\index{b2time.nc, ne3dl} & fluid species density & \\
+                                            & \hspace{1cm} (for each fluid species), Western edge & $m^{-3}$ \\
 ne3dl \index{ne3dl}\index{b2time.nc, ne3dl} & electron density, Western edge & $m^{-3}$ \\
 te3dl \index{te3dl}\index{b2time.nc, te3dl} & electron temperature, Western edge & $eV$ \\
 ti3dl \index{ti3dl}\index{b2time.nc, ti3dl} & ion temperature, Western edge & $eV$ \\
@@ -15066,32 +15200,72 @@ \chapter{Quantities stored in b2time.nc}
 po3dl \index{po3dl}\index{b2time.nc, po3dl} & potential, Western edge & $V$ \\
 an3dl \index{an3dl}\index{b2time.nc, an3dl} & atom density of main neutral, Western edge & $m^{-3}$ \\
 mn3dl \index{mn3dl}\index{b2time.nc, mn3dl} & molecule density of $1^{st}$ molecule, Western edge & $m^{-3}$ \\
+dab3dl \index{dab3dl}\index{b2time.nc, dab3dl} & {\tt Eirene} atom density & \\
+                                               & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Western edge & $m^{-3}$ \\
+dmb3dl \index{dmb3dl}\index{b2time.nc, dmb3dl} & {\tt Eirene} molecule density & \\
+                                               & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Western edge & $m^{-3}$ \\
+tab3dl \index{tab3dl}\index{b2time.nc, tab3dl} & {\tt Eirene} atom temperature & \\
+                                               & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Western edge & $eV$ \\
+tmb3dl \index{tmb3dl}\index{b2time.nc, tmb3dl} & {\tt Eirene} molecule temperature & \\
+                                               & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Western edge & $eV$ \\
+na3di \index{na3di}\index{b2time.nc, na3di} & fluid species density & \\
+                                            & \hspace{1cm} (for each fluid species), inboard midplane & $m^{-3}$ \\
 ne3di \index{ne3di}\index{b2time.nc, ne3di} & electron density, inboard midplane & $m^{-3}$ \\
 te3di \index{te3di}\index{b2time.nc, te3di} & electron temperature, inboard midplane & $eV$ \\
 ti3di \index{ti3di}\index{b2time.nc, ti3di} & ion temperature, inboard midplane & $eV$ \\
 po3di \index{po3di}\index{b2time.nc, po3di} & potential, inboard midplane & $V$ \\
 an3di \index{an3di}\index{b2time.nc, an3di} & atom density of main neutral, inboard midplane & $m^{-3}$ \\
 mn3di \index{mn3di}\index{b2time.nc, mn3di} & molecule density of $1^{st}$ molecule, inboard midplane & $m^{-3}$ \\
-dn3di \index{dn3di}\index{b2time.nc, dn3di} & particle density diffusivity, inboard midplane & $m^2.s^{-1}$ \\
-dp3di \index{dp3di}\index{b2time.nc, dp3di} & particle pressure diffusivity, inboard midplane & $m^2.s^{-1}$ \\
+dab3di \index{dab3di}\index{b2time.nc, dab3di} & {\tt Eirene} atom density & \\
+                                               & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), inboard midplane & $m^{-3}$ \\
+dmb3di \index{dmb3di}\index{b2time.nc, dmb3di} & {\tt Eirene} molecule density & \\
+                                               & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), inboard midplane & $m^{-3}$ \\
+tab3di \index{tab3di}\index{b2time.nc, tab3di} & {\tt Eirene} atom temperature & \\
+                                               & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), inboard midplane & $eV$ \\
+tmb3di \index{tmb3di}\index{b2time.nc, tmb3di} & {\tt Eirene} molecule temperature & \\
+                                               & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), inboard midplane & $eV$ \\
+dn3di \index{dn3di}\index{b2time.nc, dn3di} & particle density diffusivities & \\
+                                            & \hspace{1cm} (for each fluid species), inboard midplane & $m^2.s^{-1}$ \\
+dp3di \index{dp3di}\index{b2time.nc, dp3di} & particle pressure diffusivities & \\
+                                            & \hspace{1cm} (for each fluid species), inboard midplane & $m^2.s^{-1}$ \\
 ke3di \index{ke3di}\index{b2time.nc, ke3di} & electron heat diffusivity, inboard midplane & $m^2.s^{-1}$ \\
 ki3di \index{ki3di}\index{b2time.nc, ki3di} & ion heat diffusivity, inboard midplane & $m^2.s^{-1}$ \\
-vs3di \index{vs3di}\index{b2time.nc, vs3di} & main ion viscosity, inboard midplane & $m^2.s^{-1}$ \\
-vx3di \index{vx3di}\index{b2time.nc, vx3di} & main ion poloidal pinch velocity, inboard midplane & $m.s^{-1}$ \\
-vy3di \index{vy3di}\index{b2time.nc, vy3di} & main ion radial pinch velocity, inboard midplane & $m.s^{-1}$ \\
+vs3di \index{vs3di}\index{b2time.nc, vs3di} & viscosities & \\
+                                            & \hspace{1cm} (for each fluid species), inboard midplane & $m^2.s^{-1}$ \\
+vx3di \index{vx3di}\index{b2time.nc, vx3di} & poloidal pinch velocities & \\
+                                            & \hspace{1cm} (for each fluid species), inboard midplane & $m.s^{-1}$ \\
+vy3di \index{vy3di}\index{b2time.nc, vy3di} & radial pinch velocities & \\
+                                            & \hspace{1cm} (for each fluid species), inboard midplane & $m.s^{-1}$ \\
+na3da \index{na3da}\index{b2time.nc, na3da} & fluid species density & \\
+                                            & \hspace{1cm} (for each fluid species), outboard midplane & $m^{-3}$ \\
 ne3da \index{ne3da}\index{b2time.nc, ne3da} & electron density, outboard midplane & $m^{-3}$ \\
 te3da \index{te3da}\index{b2time.nc, te3da} & electron temperature, outboard midplane & $eV$ \\
 ti3da \index{ti3da}\index{b2time.nc, ti3da} & ion temperature, outboard midplane & $eV$ \\
 po3da \index{po3da}\index{b2time.nc, po3da} & potential, outboard midplane & $V$ \\
 an3da \index{an3da}\index{b2time.nc, an3da} & atom density of main neutral, outboard midplane & $m^{-3}$ \\
 mn3da \index{mn3da}\index{b2time.nc, mn3da} & molecule density of $1^{st}$ molecule, outboard midplane & $m^{-3}$ \\
-dn3da \index{dn3da}\index{b2time.nc, dn3da} & particle density diffusivity, outboard midplane & $m^2.s^{-1}$ \\
-dp3da \index{dp3da}\index{b2time.nc, dp3da} & particle pressure diffusivity, outboard midplane & $m^2.s^{-1}$ \\
+dab3da \index{dab3da}\index{b2time.nc, dab3da} & {\tt Eirene} atom density & \\
+                                               & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outboard midplane & $m^{-3}$ \\
+dmb3da \index{dmb3da}\index{b2time.nc, dmb3da} & {\tt Eirene} molecule density & \\
+                                               & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outboard midplane & $m^{-3}$ \\
+tab3da \index{tab3da}\index{b2time.nc, tab3da} & {\tt Eirene} atom temperature & \\
+                                               & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outboard midplane & $eV$ \\
+tmb3da \index{tmb3da}\index{b2time.nc, tmb3da} & {\tt Eirene} molecule temperature & \\
+                                               & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outboard midplane & $eV$ \\
+dn3da \index{dn3da}\index{b2time.nc, dn3da} & particle density diffusivities & \\
+                                            & \hspace{1cm} (for each fluid species), outboard midplane & $m^2.s^{-1}$ \\
+dp3da \index{dp3da}\index{b2time.nc, dp3da} & particle pressure diffusivities & \\
+                                            & \hspace{1cm} (for each fluid species), outboard midplane & $m^2.s^{-1}$ \\
 ke3da \index{ke3da}\index{b2time.nc, ke3da} & electron heat diffusivity, outboard midplane & $m^2.s^{-1}$ \\
 ki3da \index{ki3da}\index{b2time.nc, ki3da} & ion heat diffusivity, outboard midplane & $m^2.s^{-1}$ \\
-vs3da \index{vs3da}\index{b2time.nc, vs3da} & main ion viscosity, outboard midplane & $m^2.s^{-1}$ \\
-vx3da \index{vx3da}\index{b2time.nc, vx3da} & main ion poloidal pinch velocity, outboard midplane & $m.s^{-1}$ \\
-vy3da \index{vy3da}\index{b2time.nc, vy3da} & main ion radial pinch velocity, outboard midplane & $m.s^{-1}$ \\
+vs3da \index{vs3da}\index{b2time.nc, vs3da} & viscosities & \\
+                                            & \hspace{1cm} (for each fluid species), outboard midplane & $m^2.s^{-1}$ \\
+vx3da \index{vx3da}\index{b2time.nc, vx3da} & poloidal pinch velocities & \\
+                                            & \hspace{1cm} (for each fluid species), outboard midplane & $m.s^{-1}$ \\
+vy3da \index{vy3da}\index{b2time.nc, vy3da} & radial pinch velocities & \\
+                                            & \hspace{1cm} (for each fluid species), outboard midplane & $m.s^{-1}$ \\
+na3dr \index{na3dr}\index{b2time.nc, na3dr} & fluid species density & \\
+                                            & \hspace{1cm} (for each fluid species), Eastern edge & $m^{-3}$ \\
 ne3dr \index{ne3dr}\index{b2time.nc, ne3dr} & electron density, Eastern edge & $m^{-3}$ \\
 te3dr \index{te3dr}\index{b2time.nc, te3dr} & electron temperature, Eastern edge & $eV$ \\
 ti3dr \index{ti3dr}\index{b2time.nc, ti3dr} & ion temperature, Eastern edge & $eV$ \\
@@ -15099,7 +15273,16 @@ \chapter{Quantities stored in b2time.nc}
 po3dr \index{po3dr}\index{b2time.nc, po3dr} & potential, Eastern edge & $V$ \\
 an3dr \index{an3dr}\index{b2time.nc, an3dr} & atom density of main neutral, Eastern edge & $m^{-3}$ \\
 mn3dr \index{mn3dr}\index{b2time.nc, mn3dr} & molecule density of $1^{st}$ molecule, Eastern edge & $m^{-3}$ \\
-fn3dr \index{fn3dr}\index{b2time.nc, fn3dr} & poloidal particle flux of main ion, Eastern edge & $s^{-1}.m^{-2}$ \\
+dab3dr \index{dab3dr}\index{b2time.nc, dab3dr} & {\tt Eirene} atom density & \\
+                                               & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Eastern edge & $m^{-3}$ \\
+dmb3dr \index{dmb3dr}\index{b2time.nc, dmb3dr} & {\tt Eirene} molecule density & \\
+                                               & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Eastern edge & $m^{-3}$ \\
+tab3dr \index{tab3dr}\index{b2time.nc, tab3dr} & {\tt Eirene} atom temperature & \\
+                                               & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Eastern edge & $eV$ \\
+tmb3dr \index{tmb3dr}\index{b2time.nc, tmb3dr} & {\tt Eirene} molecule temperature & \\
+                                               & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Eastern edge & $eV$ \\
+fn3dr \index{fn3dr}\index{b2time.nc, fn3dr} & poloidal particle flux & \\
+                                            & \hspace{1cm} (for each fluid species), Eastern edge & $s^{-1}.m^{-2}$ \\
 fe3dr \index{fe3dr}\index{b2time.nc, fe3dr} & poloidal electron energy flux, Eastern edge & $W.m^{-2}$ \\
 fi3dr \index{fi3dr}\index{b2time.nc, fi3dr} & poloidal ion energy flux, Eastern edge & $W.m^{-2}$ \\
 ft3dr \index{ft3dr}\index{b2time.nc, ft3dr} & poloidal total internal energy flux, Eastern edge & $W.m^{-2}$ \\
@@ -15133,6 +15316,8 @@ \chapter{Quantities stored in b2time.nc}
     \multicolumn{3}{|l|}{\small\it continued on next page} \\
     \hline \endfoot
     \endlastfoot
+na3dtl \index{na3dtl}\index{b2time.nc, na3dtl} & fluid species density & \\
+                                               & \hspace{1cm} (for each fluid species), inboard top divertor & $m^{-3}$ \\
 ne3dtl \index{ne3dtl}\index{b2time.nc, ne3dtl} & electron density, inboard top divertor & $m^{-3}$ \\
 te3dtl \index{te3dtl}\index{b2time.nc, te3dtl} & electron temperature, inboard top divertor & $eV$ \\
 ti3dtl \index{ti3dtl}\index{b2time.nc, ti3dtl} & ion temperature, inboard top divertor & $eV$ \\
@@ -15140,13 +15325,24 @@ \chapter{Quantities stored in b2time.nc}
 po3dtl \index{po3dtl}\index{b2time.nc, po3dtl} & potential, inboard top divertor & $V $ \\
 an3dtl \index{an3dtl}\index{b2time.nc, an3dtl} & atom density of main neutral, inboard top divertor & $m^{-3}$ \\
 mn3dtl \index{mn3dtl}\index{b2time.nc, mn3dtl} & molecule density of $1^{st}$ molecule, inboard top divertor & $m^{-3}$ \\
-fn3dtl \index{fn3dtl}\index{b2time.nc, fn3dtl} & poloidal particle flux of main ion, inboard top divertor & $s^{-1}$ \\
+dab3dtl \index{dab3dtl}\index{b2time.nc, dab3dtl} & {\tt Eirene} atom density & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), inboard top divertor & $m^{-3}$ \\
+dmb3dtl \index{dmb3dtl}\index{b2time.nc, dmb3dtl} & {\tt Eirene} molecule density & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), inboard top divertor & $m^{-3}$ \\
+tab3dtl \index{tab3dtl}\index{b2time.nc, tab3dtl} & {\tt Eirene} atom temperature & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), inboard top divertor & $eV$ \\
+tmb3dtl \index{tmb3dtl}\index{b2time.nc, tmb3dtl} & {\tt Eirene} molecule temperature & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), inboard top divertor & $eV$ \\
+fn3dtl \index{fn3dtl}\index{b2time.nc, fn3dtl} & poloidal particle flux & \\
+                                               & \hspace{1cm} (for each fluid species), inboard top divertor & $s^{-1}$ \\
 fe3dtl \index{fe3dtl}\index{b2time.nc, fe3dtl} & poloidal electron energy flux, inboard top divertor & $W$ \\
 fi3dtl \index{fi3dtl}\index{b2time.nc, fi3dtl} & poloidal ion energy flux, inboard top divertor & $W$ \\
 ft3dtl \index{ft3dtl}\index{b2time.nc, ft3dtl} & poloidal total internal energy flux, inboard top divertor & $W$ \\
 fc3dtl \index{fc3dtl}\index{b2time.nc, fc3dtl} & poloidal current, inboard top divertor  & $A$ \\
 fl3dtl \index{fl3dtl}\index{b2time.nc, fl3dtl} & poloidal electron flux, inboard top divertor & $s^{-1}$ \\
 fo3dtl \index{fo3dtl}\index{b2time.nc, fo3dtl} & poloidal total ion flux, inboard top divertor & $s^{-1}$ \\
+na3dtr \index{na3dtr}\index{b2time.nc, na3dtr} & fluid species density & \\
+                                               & \hspace{1cm} (for each fluid species), outboard top divertor & $m^{-3}$ \\
 ne3dtr \index{ne3dtr}\index{b2time.nc, ne3dtr} & electron density, outboard top divertor & $m^{-3}$ \\
 te3dtr \index{te3dtr}\index{b2time.nc, te3dtr} & electron temperature, outboard top divertor & $eV$ \\
 ti3dtr \index{ti3dtr}\index{b2time.nc, ti3dtr} & ion temperature, outboard top divertor & $eV$ \\
@@ -15154,7 +15350,16 @@ \chapter{Quantities stored in b2time.nc}
 po3dtr \index{po3dtr}\index{b2time.nc, po3dtr} & potential, outboard top divertor & $V $ \\
 an3dtr \index{an3dtr}\index{b2time.nc, an3dtr} & atom density of main neutral, outboard top divertor & $m^{-3}$ \\
 mn3dtr \index{mn3dtr}\index{b2time.nc, mn3dtr} & molecule density of $1^{st}$ molecule, outboard top divertor & $m^{-3}$ \\
-fn3dtr \index{fn3dtr}\index{b2time.nc, fn3dtr} & poloidal particle flux of main ion, outboard top divertor & $s^{-1}$ \\
+dab3dtr \index{dab3dtr}\index{b2time.nc, dab3dtr} & {\tt Eirene} atom density & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outboard top divertor & $m^{-3}$ \\
+dmb3dtr \index{dmb3dtr}\index{b2time.nc, dmb3dtr} & {\tt Eirene} molecule density & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outboard top divertor & $m^{-3}$ \\
+tab3dtr \index{tab3dtr}\index{b2time.nc, tab3dtr} & {\tt Eirene} atom temperature & \\
+                                                  & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outboard top divertor & $eV$ \\
+tmb3dtr \index{tmb3dtr}\index{b2time.nc, tmb3dtr} & {\tt Eirene} molecule temperature & \\
+                                                  & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outboard top divertor & $eV$ \\
+fn3dtr \index{fn3dtr}\index{b2time.nc, fn3dtr} & poloidal particle flux & \\
+                                               & \hspace{1cm} (for each fluid species), outboard top divertor & $s^{-1}$ \\
 fe3dtr \index{fe3dtr}\index{b2time.nc, fe3dtr} & poloidal electron energy flux, outboard top divertor & $W$ \\
 fi3dtr \index{fi3dtr}\index{b2time.nc, fi3dtr} & poloidal ion energy flux, outboard top divertor & $W$ \\
 ft3dtr \index{ft3dtr}\index{b2time.nc, ft3dtr} & poloidal total internal energy flux, outboard top divertor & $W$ \\
@@ -15186,6 +15391,7 @@ \chapter{Quantities stored in b2time.nc}
     \endlastfoot
     \multicolumn{3}{|c|}{If {\tt b2mwti\_2dwrite} $\ge$ 1} \\
     \hline
+    na2d \index{na2d}\index{b2time.nc, na2d} & fluid species density (for each fluid species) & $m^{-3}$ \\
     ne2d \index{ne2d}\index{b2time.nc, ne2d} & electron density & $m^{-3}$ \\
     te2d \index{te2d}\index{b2time.nc, te2d} & electron temperature & $eV$ \\
     ti2d \index{ti2d}\index{b2time.nc, ti2d} & ion temperature & $eV$ \\
@@ -15235,42 +15441,110 @@ \chapter{Quantities stored in b2time.nc}
     \endlastfoot
 nastep \index{nastep}\index{b2time.nc, nastep} & timestep index & $ $ \\
 batchsa \index{batchsa}\index{b2time.nc, batchsa} & time stamp for averaged batch & $s$ \\
+nasepi\_av \index{nasepi\_av}\index{b2time.nc, nasepi\_av} & averaged separatrix fluid species density & \\
+                                                           & \hspace{1cm} (for each fluid species), Western edge & $m^{-3}$ \\
 nesepi\_av \index{nesepi\_av}\index{b2time.nc, nesepi\_av} & averaged separatrix electron density, Western edge & $m^{-3}$ \\
 tesepi\_av \index{tesepi\_av}\index{b2time.nc, tesepi\_av} & averaged separatrix electron temperature, Western edge & $eV$ \\
 tisepi\_av \index{tisepi\_av}\index{b2time.nc, tisepi\_av} & averaged separatrix ion temperature, Western edge & $eV$ \\
+dabsepi\_av \index{dabsepi\_av}\index{b2time.nc, dabsepi\_av} & averaged separatrix {\tt Eirene} atom density & \\
+                                                              & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Western edge & $m^{-3}$ \\
+dmbsepi\_av \index{dmbsepi\_av}\index{b2time.nc, dmbsepi\_av} & averaged separatrix {\tt Eirene} molecule density & \\
+                                                              & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Western edge & $m^{-3}$ \\
+tabsepi\_av \index{tabsepi\_av}\index{b2time.nc, tabsepi\_av} & averaged separatrix {\tt Eirene} atom temperature & \\
+                                                              & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Western edge & $eV$ \\
+tmbsepi\_av \index{tmbsepi\_av}\index{b2time.nc, tmbsepi\_av} & averaged separatrix {\tt Eirene} molecule temperature & \\
+                                                              & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Western edge & $eV$ \\
 posepi\_av \index{posepi\_av}\index{b2time.nc, posepi\_av} & averaged separatrix potential, Western edge & $V$ \\
+nasepm\_av \index{nasepm\_av}\index{b2time.nc, nasepm\_av} & averaged separatrix fluid species density & \\
+                                                           & \hspace{1cm} (for each fluid species), outer midplane & $m^{-3}$ \\
 nesepm\_av \index{nesepm\_av}\index{b2time.nc, nesepm\_av} & averaged separatrix electron density, outer midplane & $m^{-3}$ \\
 tesepm\_av \index{tesepm\_av}\index{b2time.nc, tesepm\_av} & averaged separatrix electron temperature, outer midplane & $eV$ \\
 tisepm\_av \index{tisepm\_av}\index{b2time.nc, tisepm\_av} & averaged separatrix ion temperature, outer midplane & $eV$ \\
+dabsepm\_av \index{dabsepm\_av}\index{b2time.nc, dabsepm\_av} & averaged separatrix {\tt Eirene} atom density & \\
+                                                              & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outer midplane & $m^{-3}$ \\
+dmbsepm\_av \index{dmbsepm\_av}\index{b2time.nc, dmbsepm\_av} & averaged separatrix {\tt Eirene} molecule density & \\
+                                                              & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outer midplane & $m^{-3}$ \\
+tabsepm\_av \index{tabsepm\_av}\index{b2time.nc, tabsepm\_av} & averaged separatrix {\tt Eirene} atom temperature & \\
+                                                              & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outer midplane & $eV$ \\
+tmbsepm\_av \index{tmbsepm\_av}\index{b2time.nc, tmbsepm\_av} & averaged separatrix {\tt Eirene} molecule temperature & \\
+                                                              & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outer midplane & $eV$ \\
 posepm\_av \index{posepm\_av}\index{b2time.nc, posepm\_av} & averaged separatrix potential, outer midplane & $V$ \\
+nasepa\_av \index{nasepa\_av}\index{b2time.nc, nasepa\_av} & averaged separatrix fluid species density & \\
+                                                           & \hspace{1cm} (for each fluid species), Eastern edge & $m^{-3}$ \\
 nesepa\_av \index{nesepa\_av}\index{b2time.nc, nesepa\_av} & averaged separatrix electron density, Eastern edge & $m^{-3}$ \\
 tesepa\_av \index{tesepa\_av}\index{b2time.nc, tesepa\_av} & averaged separatrix electron temperature, Eastern edge & $eV$ \\
 tisepa\_av \index{tisepa\_av}\index{b2time.nc, tisepa\_av} & averaged separatrix ion temperature, Eastern edge & $eV$ \\
+dabsepa\_av \index{dabsepa\_av}\index{b2time.nc, dabsepa\_av} & averaged separatrix {\tt Eirene} atom density & \\
+                                                              & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Eastern edge & $m^{-3}$ \\
+dmbsepa\_av \index{dmbsepa\_av}\index{b2time.nc, dmbsepa\_av} & averaged separatrix {\tt Eirene} molecule density & \\
+                                                              & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Eastern edge & $m^{-3}$ \\
+tabsepa\_av \index{tabsepa\_av}\index{b2time.nc, tabsepa\_av} & averaged separatrix {\tt Eirene} atom temperature & \\
+                                                              & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Eastern edge & $eV$ \\
+tmbsepa\_av \index{tmbsepa\_av}\index{b2time.nc, tmbsepa\_av} & averaged separatrix {\tt Eirene} molecule temperature & \\
+                                                              & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Eastern edge & $eV$ \\
 posepa\_av \index{posepa\_av}\index{b2time.nc, posepa\_av} & averaged separatrix potential, Eastern edge & $V$ \\
+namxip\_av \index{namxip\_av}\index{b2time.nc, namxip\_av} & averaged maximum fluid species density & \\
+                                                           & \hspace{1cm} (for each fluid species), Western edge & $m^{-3}$ \\
 nemxip\_av \index{nemxip\_av}\index{b2time.nc, nemxip\_av} & averaged maximum electron density, Western edge & $m^{-3}$ \\
 temxip\_av \index{temxip\_av}\index{b2time.nc, temxip\_av} & averaged maximum electron temperature, Western edge & $eV$ \\
 timxip\_av \index{timxip\_av}\index{b2time.nc, timxip\_av} & averaged maximum ion temperature, Western edge & $eV$ \\
 pomxip\_av \index{pomxip\_av}\index{b2time.nc, pomxip\_av} & averaged maximum potential, Western edge & $V$ \\
+namxap\_av \index{namxap\_av}\index{b2time.nc, namxap\_av} & averaged maximum fluid species density & \\
+                                                           & \hspace{1cm} (for each fluid species), Eastern edge & $m^{-3}$ \\
 nemxap\_av \index{nemxap\_av}\index{b2time.nc, nemxap\_av} & averaged maximum electron density, Eastern edge & $m^{-3}$ \\
 temxap\_av \index{temxap\_av}\index{b2time.nc, temxap\_av} & averaged maximum electron temperature, Eastern edge & $eV$ \\
 timxap\_av \index{timxap\_av}\index{b2time.nc, timxap\_av} & averaged maximum ion temperature, Eastern edge & $eV$ \\
 pomxap\_av \index{pomxap\_av}\index{b2time.nc, pomxap\_av} & averaged maximum potential, Eastern edge & $ $ \\
-nesepi\_std \index{nesepi\_std}\index{b2time.nc, nesepi\_std} & averaged separatrix electron density, Western edge & $m^{-3}$ \\
-tesepi\_std \index{tesepi\_std}\index{b2time.nc, tesepi\_std} & averaged separatrix electron temperature, Western edge & $eV$ \\
-tisepi\_std \index{tisepi\_std}\index{b2time.nc, tisepi\_std} & averaged separatrix ion temperature, Western edge & $eV$ \\
-posepi\_std \index{posepi\_std}\index{b2time.nc, posepi\_std} & averaged separatrix potential, Western edge & $V$ \\
+nasepi\_std \index{nasepi\_std}\index{b2time.nc, nasepi\_std} & variance for separatrix fluid species density & \\
+                                                              & \hspace{1cm} (for each fluid species), Western edge & $m^{-3}$ \\
+nesepi\_std \index{nesepi\_std}\index{b2time.nc, nesepi\_std} & variance for separatrix electron density, Western edge & $m^{-3}$ \\
+tesepi\_std \index{tesepi\_std}\index{b2time.nc, tesepi\_std} & variance for separatrix electron temperature, Western edge & $eV$ \\
+tisepi\_std \index{tisepi\_std}\index{b2time.nc, tisepi\_std} & variance for separatrix ion temperature, Western edge & $eV$ \\
+dabsepi\_std \index{dabsepi\_std}\index{b2time.nc, dabsepi\_std} & variance for separatrix {\tt Eirene} atom density & \\
+                                                                 & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Western edge & $m^{-3}$ \\
+dmbsepi\_std \index{dmbsepi\_std}\index{b2time.nc, dmbsepi\_std} & variance for separatrix {\tt Eirene} molecule density & \\
+                                                                 & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Western edge & $m^{-3}$ \\
+tabsepi\_std \index{tabsepi\_std}\index{b2time.nc, tabsepi\_std} & variance for separatrix {\tt Eirene} atom temperature & \\
+                                                                 & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Western edge & $eV$ \\
+tmbsepi\_std \index{tmbsepi\_std}\index{b2time.nc, tmbsepi\_std} & variance for separatrix {\tt Eirene} molecule temperature & \\
+                                                                 & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Western edge & $eV$ \\
+posepi\_std \index{posepi\_std}\index{b2time.nc, posepi\_std} & variance for separatrix potential, Western edge & $V$ \\
+nasepm\_std \index{nasepm\_std}\index{b2time.nc, nasepm\_std} & variance for separatrix fluid species density & \\
+                                                              & \hspace{1cm} (for each fluid species), outer midplane & $m^{-3}$ \\
 nesepm\_std \index{nesepm\_std}\index{b2time.nc, nesepm\_std} & variance for separatrix electron density, outer midplane & $m^{-3}$ \\
 tesepm\_std \index{tesepm\_std}\index{b2time.nc, tesepm\_std} & variance for separatrix electron temperature, outer midplane & $eV$ \\
 tisepm\_std \index{tisepm\_std}\index{b2time.nc, tisepm\_std} & variance for separatrix ion temperature, outer midplane & $eV$ \\
+dabsepm\_std \index{dabsepm\_std}\index{b2time.nc, dabsepm\_std} & variance for separatrix {\tt Eirene} atom density & \\
+                                                                 & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outer midplane & $m^{-3}$ \\
+dmbsepm\_std \index{dmbsepm\_std}\index{b2time.nc, dmbsepm\_std} & variance for separatrix {\tt Eirene} molecule density & \\
+                                                                 & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outer midplane & $m^{-3}$ \\
+tabsepm\_std \index{tabsepm\_std}\index{b2time.nc, tabsepm\_std} & variance for separatrix {\tt Eirene} atom temperature & \\
+                                                                 & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), outer midplane & $eV$ \\
+tmbsepm\_std \index{tmbsepm\_std}\index{b2time.nc, tmbsepm\_std} & variance for separatrix {\tt Eirene} molecule temperature & \\
+                                                                 & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), outer midplane & $eV$ \\
 posepm\_std \index{posepm\_std}\index{b2time.nc, posepm\_std} & variance for separatrix potential, outer midplane & $V $ \\
+nasepa\_std \index{nasepa\_std}\index{b2time.nc, nasepa\_std} & variance for separatrix fluid species density & \\
+                                                              & \hspace{1cm} (for each fluid species), Eastern edge & $m^{-3}$ \\
 nesepa\_std \index{nesepa\_std}\index{b2time.nc, nesepa\_std} & variance for separatrix electron density, Eastern edge & $m^{-3}$ \\
 tesepa\_std \index{tesepa\_std}\index{b2time.nc, tesepa\_std} & variance for separatrix electron temperature, Eastern edge & $eV$ \\
 tisepa\_std \index{tisepa\_std}\index{b2time.nc, tisepa\_std} & variance for separatrix ion temperature, Eastern edge & $eV$ \\
+dabsepa\_std \index{dabsepa\_std}\index{b2time.nc, dabsepa\_std} & variance for separatrix {\tt Eirene} atom density & \\
+                                                                 & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Eastern edge & $m^{-3}$ \\
+dmbsepa\_std \index{dmbsepa\_std}\index{b2time.nc, dmbsepa\_std} & variance for separatrix {\tt Eirene} molecule density & \\
+                                                                 & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Eastern edge & $m^{-3}$ \\
+tabsepa\_std \index{tabsepa\_std}\index{b2time.nc, tabsepa\_std} & variance for separatrix {\tt Eirene} atom temperature & \\
+                                                                 & \hspace{1cm} (for each atom species, if {\tt Eirene} is used), Eastern edge & $eV$ \\
+tmbsepa\_std \index{tmbsepa\_std}\index{b2time.nc, tmbsepa\_std} & variance for separatrix {\tt Eirene} molecule temperature & \\
+                                                                 & \hspace{1cm} (for each molecule species, if {\tt Eirene} is used), Eastern edge & $eV$ \\
 posepa\_std \index{posepa\_std}\index{b2time.nc, posepa\_std} & variance for separatrix potential, Eastern edge & $V$ \\
+namxip\_std \index{namxip\_std}\index{b2time.nc, namxip\_std} & variance for maximum fluid species density & \\
+                                                              & \hspace{1cm} (for each fluid species), Western edge & $m^{-3}$ \\
 nemxip\_std \index{nemxip\_std}\index{b2time.nc, nemxip\_std} & variance for maximum electron density, Western edge & $m^{-3}$ \\
 temxip\_std \index{temxip\_std}\index{b2time.nc, temxip\_std} & variance for maximum electron temperature, Western edge & $eV$ \\
 timxip\_std \index{timxip\_std}\index{b2time.nc, timxip\_std} & variance for maximum ion temperature, Western edge & $eV$ \\
 pomxip\_std \index{pomxip\_std}\index{b2time.nc, pomxip\_std} & variance for maximum potential, Western edge & $V$ \\
+namxap\_std \index{namxap\_std}\index{b2time.nc, namxap\_std} & variance for maximum fluid species density & \\
+                                                              & \hspace{1cm} (for each fluid species), Eastern edge & $m^{-3}$ \\
 nemxap\_std \index{nemxap\_std}\index{b2time.nc, nemxap\_std} & variance for maximum electron density, Eastern edge & $m^{-3}$ \\
 temxap\_std \index{temxap\_std}\index{b2time.nc, temxap\_std} & variance for maximum electron temperature, Eastern edge & $eV$ \\
 timxap\_std \index{timxap\_std}\index{b2time.nc, timxap\_std} & variance for maximum ion temperature, Eastern edge & $eV$ \\
@@ -15311,6 +15585,7 @@ \chapter{Quantities stored in b2movies.nc and eirenemovies.nc}
     \hline
     na \index{na}\index{b2movies.nc, na} & Density of fluid species (for each species) & $m^{-3}$ \\
     ne \index{ne}\index{b2movies.nc, ne} & Electron density & $m^{-3}$ \\
+    ua \index{ua}\index{b2movies.nc, ua} & Parallel velocity of fluid species (for each species) & $m s^{-1}$ \\
     te \index{te}\index{b2movies.nc, te} & Electron temperature & $eV$ \\
     ti \index{ti}\index{b2movies.nc, ti} & Ion temperature & $eV$ \\
     po \index{po}\index{b2movies.nc, po} & Electric potential & $V$ \\
@@ -15342,6 +15617,16 @@ \chapter{Quantities stored in b2movies.nc and eirenemovies.nc}
     rqrad \index{rqrad}\index{b2movies.nc, rqrad} & Volumetric line radiation rate (for each fluid species) & $W m^{-3}$ \\
     rqahesum \index{rqahesum}\index{b2movies.nc, rqahesum} & Total volumetric line radiation rate & $W m^{-3}$ \\
     \hline
+    \multicolumn{3}{|c|}{If {\tt cdfmovie\_b25\_transport} $\ge$ 1} \\
+    \hline
+    dna \index{dna}\index{b2movies.nc, dna} & Particle density-driven diffusivity (for each fluid species) & $m^{-2} s^{-1}$ \\
+    dpa \index{dna}\index{b2movies.nc, dpa} & Particle pressure-driven diffusivity (for each fluid species) & $m^{-2} s^{-1}$ \\
+    hci \index{hci}\index{b2movies.nc, hci} & Ion thermal anomalous diffusivity & $m^{-2} s^{-1}$ \\
+    hce \index{hce}\index{b2movies.nc, hce} & Electron thermal anomalous diffusivity & $m^{-2} s^{-1}$ \\
+    vlax \index{vlax}\index{b2movies.nc, vlax} & Poloidal anomalous pinch velocity (for each fluid species) & $m s^{-1}$ \\
+    vlay \index{vlay}\index{b2movies.nc, vlay} & Radial anomalous pinch velocity (for each fluid species) & $m s^{-1}$ \\
+    vsa \index{vsa}\index{b2movies.nc, vsa} & Anomalous viscosity (for each fluid species) & $m kg^{-1} s^{-1}$ \\
+    \hline
     \multicolumn{3}{|c|}{If {\tt cdfmovie\_eirene\_state\_variables} $\ge$ 1 (if {\tt Eirene} is used)} \\
     \hline
     dab2 \index{dab2}\index{b2movies.nc, dab2} & Atom density (for each atom species) & $m^{-3}$ \\
@@ -15391,6 +15676,7 @@ \chapter{Quantities stored in b2movies.nc and eirenemovies.nc}
 \item If {\tt cdfmovie\_b25\_state\_variables} $\ge$ 1: 40 kB per {\tt B2.5} fluid species per outputted timestep.
 \item If {\tt cdfmovie\_b25\_fluxes} $\ge$ 1: 75 kB per {\tt B2.5} fluid species per outputted timestep.
 \item If {\tt cdfmovie\_b25\_sources} $\ge$ 1: 250 kB per {\tt B2.5} fluid species per outputted timestep.
+\item If {\tt cdfmovie\_b25\_transport} $\ge$ 1: 160 kB per {\tt B2.5} fluid species per outputted timestep.
 \item If {\tt cdfmovie\_eirene\_state\_variables} $\ge$ 1: 60 kB per {\tt Eirene} atom/molecule species per outputted timestep.
 \item If {\tt cdfmovie\_eirene\_fluxes} $\ge$ 1: 120 kB per {\tt Eirene} atom/molecule species per outputted timestep.
 \item If {\tt cdfmovie\_eirene\_sources} $\ge$ 1: 100 kB per {\tt B2.5} fluid species + 45 kB per {\tt Eirene} atom/molecule species per outputted timestep.
@@ -15400,11 +15686,12 @@ \chapter{Quantities stored in b2movies.nc and eirenemovies.nc}
 \item Setting the switch {\tt cdfmovie\_b25\_state\_variables} $\ge$ 1 will cause additional 480 MB of filesize.
 \item Setting the switch {\tt cdfmovie\_b25\_fluxes} $\ge$ 1 will cause additional 900 MB of filesize.
 \item Setting the switch {\tt cdfmovie\_b25\_sources} $\ge$ 1 will cause additional 3.0 GB of filesize.
+\item Setting the switch {\tt cdfmovie\_b25\_transport} $\ge$ 1 will cause additional 1.9 GB of filesize.
 \item Setting the switch {\tt cdfmovie\_eirene\_state\_variables} $\ge$ 1 will cause additional 240 MB of filesize.
 \item Setting the switch {\tt cdfmovie\_eirene\_fluxes} $\ge$ 1 will cause additional 480 MB of filesize.
 \item Setting the switch {\tt cdfmovie\_eirene\_sources} $\ge$ 1 will cause additional 1.4 GB of filesize.
 \end{itemize}
-If all the aforementioned switches are $\ge$ 1, then a filesize of roughly 6.5 GB can be expected after 1000 outputted timesteps.
+If all the aforementioned switches are $\ge$ 1, then a filesize of roughly 8.4 GB can be expected after 1000 outputted timesteps.
 
 The arrays outputted to {\tt eirenemovies.nc} are, instead, described in the below Table
 \ref{tab:eirenemoviesarrays}. The file is created, in case of couples runs, only if the switch {\tt cdfmovie\_triangles} $\ge$ 1.
diff --git a/modules/B2.5 b/modules/B2.5
index 8e142a8f9..b7e55e10d 160000
--- a/modules/B2.5
+++ b/modules/B2.5
@@ -1 +1 @@
-Subproject commit 8e142a8f946a7f597f05158bf853c847cf68d291
+Subproject commit b7e55e10d63af95a6facbb1383a36cf22d33caf6
diff --git a/runs/Makefile b/runs/Makefile
index a5e492288..152765048 100644
--- a/runs/Makefile
+++ b/runs/Makefile
@@ -278,6 +278,7 @@ endif
 	-[ -s b2mn.exe.dir/b2time.nc ] && mv b2mn.exe.dir/b2time.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2batch.nc ] && mv b2mn.exe.dir/b2batch.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2wall.nc ] && mv b2mn.exe.dir/b2wall.nc . || echo > /dev/null
+	-[ -s b2mn.exe.dir/b2neo.nc ] && mv b2mn.exe.dir/b2neo.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2movies.nc ] && mv b2mn.exe.dir/b2movies.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/eirenemovies.nc ] && mv b2mn.exe.dir/eirenemovies.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2tallies.nc ] && mv b2mn.exe.dir/b2tallies.nc . || echo > /dev/null
@@ -378,6 +379,7 @@ endif
 	-[ -s b2mn.exe.dir/b2time.nc ] && mv b2mn.exe.dir/b2time.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2batch.nc ] && mv b2mn.exe.dir/b2batch.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2wall.nc ] && mv b2mn.exe.dir/b2wall.nc . || echo > /dev/null
+	-[ -s b2mn.exe.dir/b2neo.nc ] && mv b2mn.exe.dir/b2neo.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2movies.nc ] && mv b2mn.exe.dir/b2movies.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/eirenemovies.nc ] && mv b2mn.exe.dir/eirenemovies.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2tallies.nc ] && mv b2mn.exe.dir/b2tallies.nc . || echo > /dev/null
diff --git a/scripts/2d b/scripts/2d
index 1418218e7..f293987d6 100755
--- a/scripts/2d
+++ b/scripts/2d
@@ -1,16 +1,24 @@
 #! /bin/csh -f
+
 if ("X$1" == "X-lx") then
   set lx="l"
   shift
 else
   set lx=""
 endif
+
 if ("X$1" == "X-ly") then
   set ly="l"
   shift
 else
   set ly=""
 endif
+
+if ( $#argv < 2 ) then
+    echo "Error: You must provide at least two arguments (2nd, 3rd, etc. arguments will be plotted vs. the 1st one)."
+    exit 1
+endif
+
 set x=$1
 shift
 set source=b2mn.exe.dir/b2time.nc
@@ -36,23 +44,92 @@ endif
 
 cp /dev/null ${tmpdir}gnuplot.data.tmp
 if ($no_nc2text == 1) then
-  ncdump $source -f f -v $x | \
-  awk 'BEGIN {ORS="";} /data:/{found1=1;next;} /$x/{if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}} END {print "\n";}' | \
-  sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+  if ("$x" =~ *[0-9]) then
+      # Multi-species quantities, called as $x = $name$is (e.g. $x = 'nasepm1')
+      echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+      exit 1
+  else
+      # Time, called as $x = 'timesa', or single species quantities, called as $x = $name (e.g. $x = 'nesepm')
+      ncdump $source -f f -v $x | \
+      awk 'BEGIN {ORS="";} /data:/{found1=1;next;} /$x/{if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}} END {print "\n";}' | \
+      sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+  endif
+else
+  if ("$x" =~ *[0-9]) then 
+      # Multi-species quantities, called as $x = $name$is (e.g. $x = 'nasepm1')
+      set is = `echo "$x" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+      set name = `echo "$x" | sed -E 's/([0-9]+)$//'`
+      @ is_plus_1 = $is + 1
+      echo `nc2text -n 9999999 $source "$name(:,$is_plus_1)"` >> ${tmpdir}gnuplot.data.tmp
+  else
+      # Time, called as $x = 'timesa', or single species quantities, called as $x = $name (e.g. $x = 'nesepm')
+      echo `nc2text -n 9999999 $source $x` >> ${tmpdir}gnuplot.data.tmp
+  endif
+endif
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
 else
-  echo `nc2text -n 9999999 $source $x` >> ${tmpdir}gnuplot.data.tmp
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
 endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+
 start:
   if ($no_nc2text == 1) then
-    ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
-    sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+    if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+        exit 1
+    else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
+        sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+    endif
   else
-    echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+    if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+        set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+        @ is_plus_1 = $is + 1
+        echo `nc2text -n 9999999 $source "$name(:,$is_plus_1)"` >> ${tmpdir}gnuplot.data.tmp
+    else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+    endif
   endif
   shift
   if ("X$1X" != "XX") goto start
 
-awk.transpose < ${tmpdir}gnuplot.data.tmp | awk 'NR==1{saveNF=NF}NF==saveNF{print $0}' | plot ${lx}x${ly}yplot$nargs $args $x '' $PWD
+# Find species names, in case of multi-species array
+set args_plot=""
+set field_names = ( $args )
+foreach i ($field_names)
+  if ("$i" =~ *[0-9]) then
+      # Multi-species quantities, called as $i = $name$is (e.g. $i = 'nasepm1')
+      set is = `echo "$i" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+      set name = `echo "$i" | sed -E 's/([0-9]+)$//'`
+      @ is_plus_1 = $is + 1
+      if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+        setenv species_name $neutral_species_names[$is_plus_1]
+      else
+        setenv species_name $species_names[$is_plus_1]
+      endif
+      set args_plot="$args_plot $name($species_name)"
+  else
+      set args_plot="$args_plot $i"
+  endif
+end
+
+awk.transpose < ${tmpdir}gnuplot.data.tmp | awk 'NR==1{saveNF=NF}NF==saveNF{print $0}' | plot ${lx}x${ly}yplot$nargs $args_plot $x '' $PWD
 rm ${tmpdir}gnuplot.data.tmp
 
 if ($netcdf4 == 1) then
diff --git a/scripts/2d_plots b/scripts/2d_plots
index 0345d5c32..16913eb47 100755
--- a/scripts/2d_plots
+++ b/scripts/2d_plots
@@ -7,18 +7,31 @@ else
 endif
 setenv GNUPLOT_BATCH yes
 setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid noenhanced'
-setenv PRINT_PLOT b2time2d.ps
+setenv PRINT_PLOT b2time2d_time_traces.ps
 rm -f ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.cmd
 echo 0 > ${tmpdir}GNUPLOT_COUNT
 
+set source=b2mn.exe.dir/b2time.nc
+if (! -s $source) set source=b2time.nc
+set ns = `ncdump -h $source | grep -w "ns =" | sed -E 's/.*= *([0-9]+) *;.*/\1/'`
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_index = -1
+
 set nreg=`climb_and_look_for NREG`
 set nnreg=`pipe_run.log | grep -a ^nnreg | head -1`
 if (-s $nreg) then
   setenv NREG `cat $nreg`
-  echo Set NREG to $NREG "(based on $nreg)"
+  #echo Set NREG to $NREG "(based on $nreg)"
 else
   set NREG=$nnreg[2]
-  echo Set NREG to $NREG "(based on log file)"
+  #echo Set NREG to $NREG "(based on log file)"
 endif
 if (! $?NREG) set NREG = 4
 if ("X$nnreg" != "X") then
@@ -29,8 +42,110 @@ if ("X$nnreg" != "X") then
 endif
 
 2dt nesepm
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepm if run with Eirene, nasepm if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepm fields exist --> coupled run --> call dabsepm
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepm$neutral_species_index "
+      else
+        # dabsepm fields do not exist --> standalone run --> call nasepm
+        set na_dens="$na_dens nasepm$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepm
+      set na_dens="$na_dens nasepm$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt $group
+    @ offset = $end + 1
+end
 2dt tesepm tisepm
 2dt nesepi nemxip nesepa nemxap
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepi if run with Eirene, nasepi if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepi fields exist --> coupled run --> call dabsepi
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepi$neutral_species_index "
+      else
+        # dabsepi fields do not exist --> standalone run --> call nasepi
+        set na_dens="$na_dens nasepi$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepi
+      set na_dens="$na_dens nasepi$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt $group
+    @ offset = $end + 1
+end
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepa if run with Eirene, nasepa if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepa fields exist --> coupled run --> call dabsepa
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepa$neutral_species_index "
+      else
+        # dabsepa fields do not exist --> standalone run --> call nasepa
+        set na_dens="$na_dens nasepa$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepa
+      set na_dens="$na_dens nasepa$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt $group
+    @ offset = $end + 1
+end
 2dt tesepi temxip tesepa temxap
 2dt tisepi timxip tisepa timxap
 2dt fnixip fnixap
diff --git a/scripts/2d_plots_av b/scripts/2d_plots_av
index 1d32ec790..6919bc54d 100755
--- a/scripts/2d_plots_av
+++ b/scripts/2d_plots_av
@@ -1,4 +1,3 @@
-### eval '(exit $?0)' && eval 'exec tcsh $0 ${1+"$@"}' && eval 'exec tcsh $0 $argv:q'
 #! /bin/tcsh -f
 
 if($?GNUPLOT_TMP) then
@@ -8,12 +7,25 @@ else
 endif
 setenv GNUPLOT_BATCH yes
 setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid noenhanced'
-setenv PRINT_PLOT b2time2d_av.ps
+setenv PRINT_PLOT b2time2d_time_traces_av.ps
 rm -f ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.cmd
 echo 0 > ${tmpdir}GNUPLOT_COUNT
 
+set source=b2mn.exe.dir/b2time.nc
+if (! -s $source) set source=b2time.nc
+set ns = `ncdump -h $source | grep -w "ns =" | sed -E 's/.*= *([0-9]+) *;.*/\1/'`
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_index = -1
+
 set nreg=`climb_and_look_for NREG`
-set nnreg=`pipe_run.log | grep ^nnreg | head -1`
+set nnreg=`pipe_run.log | grep -a ^nnreg | head -1`
 if (-s $nreg) then
   setenv NREG `cat $nreg`
   echo Set NREG to $NREG "(based on $nreg)"
@@ -30,8 +42,110 @@ if ("X$nnreg" != "X") then
 endif
 
 2dt_av nesepm
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepm if run with Eirene, nasepm if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepm fields exist --> coupled run --> call dabsepm
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepm$neutral_species_index "
+      else
+        # dabsepm fields do not exist --> standalone run --> call nasepm
+        set na_dens="$na_dens nasepm$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepm
+      set na_dens="$na_dens nasepm$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt_av $group
+    @ offset = $end + 1
+end
 2dt_av tesepm tisepm
 2dt_av nesepi nemxip nesepa nemxap
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepi if run with Eirene, nasepi if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepi fields exist --> coupled run --> call dabsepi
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepi$neutral_species_index "
+      else
+        # dabsepi fields do not exist --> standalone run --> call nasepi
+        set na_dens="$na_dens nasepi$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepi
+      set na_dens="$na_dens nasepi$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt_av $group
+    @ offset = $end + 1
+end
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepa if run with Eirene, nasepa if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepa fields exist --> coupled run --> call dabsepa
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepa$neutral_species_index "
+      else
+        # dabsepa fields do not exist --> standalone run --> call nasepa
+        set na_dens="$na_dens nasepa$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepa
+      set na_dens="$na_dens nasepa$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt_av $group
+    @ offset = $end + 1
+end
 2dt_av tesepi temxip tesepa temxap
 2dt_av tisepi timxip tisepa timxap
 2dt_av fnixip fnixap
diff --git a/scripts/2d_profiles b/scripts/2d_profiles
index 09539a39e..56a9418e7 100755
--- a/scripts/2d_profiles
+++ b/scripts/2d_profiles
@@ -4,31 +4,38 @@ if ("X$1X" != "XX") set NUM=$1
 set END=-0
 if ("X$2X" != "XX") set END=$2
 @ NUM = 1 + $END - $NUM
-echo $NUM $END
+#echo $NUM $END
 set nreg=`climb_and_look_for NREG`
 if (-s $nreg) then
   setenv NREG `cat $nreg`
-  echo Set NREG to $NREG "(based on $nreg)"
+  #echo Set NREG to $NREG "(based on $nreg)"
 else
   set nnreg=`pipe_run.log | grep -a ^nnreg | head -1`
   set NREG=$nnreg[2]
-  echo Set NREG to $NREG "(based on log file)"
+  #echo Set NREG to $NREG "(based on log file)"
 endif
-set usual="fn3dl fe3dl fi3dl fc3dl fl3dl fo3dl ft3dl ne3dl te3dl ti3dl po3dl an3dl mn3dl ne3di te3di ti3di po3di an3di mn3di ne3da te3da ti3da po3da an3da mn3da ne3dr te3dr ti3dr po3dr an3dr mn3dr fn3dr fe3dr fi3dr fc3dr fl3dr fo3dr ft3dr dn3di dn3da dp3di dp3da ke3di ke3da ki3di ki3da vx3di vx3da vy3di vy3da vs3di vs3da tp3dl tp3dr"
+set usual="fe3dl fi3dl fc3dl fl3dl fo3dl ft3dl ne3dl te3dl ti3dl po3dl an3dl mn3dl ne3di te3di ti3di po3di an3di mn3di ne3da te3da ti3da po3da an3da mn3da ne3dr te3dr ti3dr po3dr an3dr mn3dr fe3dr fi3dr fc3dr fl3dr fo3dr ft3dr ke3di ke3da ki3di ki3da tp3dl tp3dr"
+set usual_multi="fn3dl na3dl na3di na3da fn3dr na3dr dn3di dn3da dp3di dp3da vx3di vx3da vy3di vy3da vs3di vs3da"
 set extra=""
+set extra_multi=""
 if ($?NREG) then
   if ($NREG == 8) then
-    set extra="fn3dtl fe3dtl fi3dtl fc3dtl fl3dtl fo3dtl ft3dtl ne3dtl te3dtl ti3dtl po3dtl an3dtl mn3dtl ne3dtr te3dtr ti3dtr po3dtr an3dtr mn3dtr fn3dtr fe3dtr fi3dtr fc3dtr fl3dtr fo3dtr ft3dtr tp3dtl tp3dtr"
+    set extra="fe3dtl fi3dtl fc3dtl fl3dtl fo3dtl ft3dtl ne3dtl te3dtl ti3dtl po3dtl an3dtl mn3dtl ne3dtr te3dtr ti3dtr po3dtr an3dtr mn3dtr fe3dtr fi3dtr fc3dtr fl3dtr fo3dtr ft3dtr tp3dtl tp3dtr"
+    set extra_multi="fn3dtl na3dtl fn3dtr na3dtr"
   endif
   if ($NREG == 7) then
-    set extra="fn3dtl fe3dtl fi3dtl fc3dtl fl3dtl fo3dtl ft3dtl ne3dtl te3dtl ti3dtl po3dtl an3dtl mn3dtl ne3dtr te3dtr ti3dtr po3dtr an3dtr mn3dtr fn3dtr fe3dtr fi3dtr fc3dtr fl3dtr fo3dtr ft3dtr tp3dtl tp3dtr"
+    set extra="fe3dtl fi3dtl fc3dtl fl3dtl fo3dtl ft3dtl ne3dtl te3dtl ti3dtl po3dtl an3dtl mn3dtl ne3dtr te3dtr ti3dtr po3dtr an3dtr mn3dtr fe3dtr fi3dtr fc3dtr fl3dtr fo3dtr ft3dtr tp3dtl tp3dtr"
+    set extra_multi="fn3dtl na3dtl fn3dtr na3dtr"
   endif
 endif
 
 if($?GNUPLOT_TMP) then
   set tmpdir="$GNUPLOT_TMP/"
 else
-  set tmpdir=""
+  set tmpdir="2d_profiles/"
+  if (! -d 2d_profiles) then
+    mkdir 2d_profiles
+  endif
 endif
 set source=b2mn.exe.dir/b2time.nc
 if (! -s $source) set source=b2time.nc
@@ -60,6 +67,8 @@ if ($no_nc2text == 1) then
 #  echo $jstart $jend
 else
   set nt = `nc2text $source "ntstep" | awk '{printf "%d", $1}'`
+  set ns = `ncdump -h $source | grep -w "ns =" | sed -E 's/.*= *([0-9]+) *;.*/\1/'`
+  @ ns_minus_1 = $ns - 1
 #  echo "nt $nt"
   @ jstart = $nt + $NUM
   if ($jstart < 0) then
@@ -114,21 +123,253 @@ foreach i ($usual $extra)
       ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste $dsfile - $dsFILEP | awk '{print $1,$2/$3}' >! ${tmpdir}$i'P'.last10
     endif
   else
+    nc2text -n 9999999 $source "ds${suffix}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsfile
+    if ("$suffix" != "a" && "$suffix" != "i") then
+      nc2text -n 9999999 $source "ds${SUFFIX}T" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILET
+      nc2text -n 9999999 $source "ds${SUFFIXP}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILEP
+    endif
     if ($prefix == "f" && -s $dsFILE) then
-      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste $dsfile - $dsFILE | awk '{print $1,$2/$3}' >! ${tmpdir}$i.last10
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILET | awk '{print $1,$2/$3}' >! ${tmpdir}$i.last10
     else if ($prefix == "t" && $pr2fix != "p") then
-      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1/1.602176634e-19}' | paste $dsfile - >! ${tmpdir}$i.last10
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1/1.602176634e-19}' | paste ${tmpdir}dsfile - >! ${tmpdir}$i.last10
     else if ($prefix == "t" && $pr2fix == "p") then
-      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste $dsfile - >! ${tmpdir}$i.last10
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - >! ${tmpdir}$i.last10
     else
-      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste $dsfile - >! ${tmpdir}$i.last10
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - >! ${tmpdir}$i.last10
     endif
     if ($prefix == "f" && -s $dsFILEP) then
-      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste $dsfile - $dsFILEP | awk '{print $1,$2/$3}' >! ${tmpdir}$i'P'.last10
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILEP | awk '{print $1,$2/$3}' >! ${tmpdir}$i'P'.last10
     endif
   endif
 end
 
+foreach i ($usual_multi $extra_multi)
+  set prefix=`echo $i | cut -c1`
+  set pr2fix=`echo $i | cut -c2`
+  set suffix=`echo $i | cut -c5-`
+  set SUFFIX=`echo $suffix | tr 'a-z' 'A-Z'`
+  set SUFFIXP=`echo $suffix | tr 'a-z' 'A-Z'`P
+  set dsfile=b2mn.exe.dir/ds$suffix
+  if (! -s $dsfile) set dsfile=ds$suffix
+  set dsFILE=b2mn.exe.dir/ds$SUFFIX
+  if (! -s $dsFILE) set dsFILE=ds$SUFFIX
+  set dsFILEP=b2mn.exe.dir/ds$SUFFIXP
+  if (! -s $dsFILEP) set dsFILEP=ds$SUFFIXP
+#  echo $i $prefix $pr2fix $suffix $SUFFIX $SUFFIXP $dsfile $dsFILE $dsFILEP
+  if ($no_nc2text == 1) then
+    # TODO
+  else
+    nc2text -n 9999999 $source "ds${suffix}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsfile
+    if ("$suffix" != "a" && "$suffix" != "i") then
+      nc2text -n 9999999 $source "ds${SUFFIX}T" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILET
+      nc2text -n 9999999 $source "ds${SUFFIXP}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILEP
+    endif
+    if ($prefix == "f" && -s $dsFILE) then
+      foreach is (`seq 1 $ns`)
+        @ is_minus_1 = $is - 1
+        nc2text -n 9999999 $source "$i(:,$is,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILET | awk '{print $1,$2/$3}' >! ${tmpdir}$i$is_minus_1.last10
+      end
+    else
+      foreach is (`seq 1 $ns`)
+        @ is_minus_1 = $is - 1
+        nc2text -n 9999999 $source "$i(:,$is,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - >! ${tmpdir}$i$is_minus_1.last10
+      end
+    endif
+    if ($prefix == "f" && -s $dsFILEP) then
+      foreach is (`seq 1 $ns`)
+        @ is_minus_1 = $is - 1
+        nc2text -n 9999999 $source "$i(:,$is,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILEP | awk '{print $1,$2/$3}' >! ${tmpdir}$i'P'$is_minus_1.last10
+      end
+    endif
+  endif
+end
+
+[ -f "${tmpdir}dsfile" ] && rm "${tmpdir}dsfile"
+[ -f "${tmpdir}dsFILET" ] && rm "${tmpdir}dsFILET"
+[ -f "${tmpdir}dsFILEP" ] && rm "${tmpdir}dsFILEP"
+
+if($?GNUPLOT_TMP) then
+    set tmpdir="$GNUPLOT_TMP/"
+else
+    set tmpdir=""
+endif
+setenv GNUPLOT_BATCH yes
+setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid noenhanced'
+setenv PRINT_PLOT b2time2d_profiles.ps
+rm -f ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.cmd
+echo 0 > ${tmpdir}GNUPLOT_COUNT
+
+set nreg=`climb_and_look_for NREG`
+set nnreg=`pipe_run.log | grep -a ^nnreg | head -1`
+if (-s $nreg) then
+  setenv NREG `cat $nreg`
+  #echo Set NREG to $NREG "(based on $nreg)"
+else
+  set NREG=$nnreg[2]
+  #echo Set NREG to $NREG "(based on log file)"
+endif
+if (! $?NREG) set NREG = 4
+if ("X$nnreg" != "X") then
+  if ($NREG != $nnreg[2]) then
+    echo "NREG in file ($nnreg[2]) does not match $NREG"
+    exit
+  endif
+endif
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+
+if ( $NUM < 0 ) then
+    @ abs_num = -1 * $NUM
+else
+    @ abs_num = $NUM
+endif
+@ NUM = $abs_num + 1
+if ( $END < 0 ) then
+    @ abs_end = -1 * $END
+else
+    @ abs_end = $END
+endif
+@ END = $abs_end
+
+2dds ne3da $NUM $END
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dab3da* if run with Eirene, na3da* if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dab3da* fields exist --> coupled run --> call dab3da*
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dab3da$neutral_species_index "
+      else
+        # dab3da* fields do not exist --> standalone run --> call na3da*
+        set na_dens="$na_dens na3da$is_minus_1 "
+      endif
+    else
+      # ion species: always call na3da*
+      set na_dens="$na_dens na3da$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dds $group $NUM $END
+    @ offset = $end + 1
+end
+2dds te3da ti3da $NUM $END
+2dds ne3dl $NUM $END
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dab3dl* if run with Eirene, na3dl* if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dab3dl* fields exist --> coupled run --> call dab3dl*
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dab3dl$neutral_species_index "
+      else
+        # dab3dl* fields do not exist --> standalone run --> call na3dl*
+        set na_dens="$na_dens na3dl$is_minus_1 "
+      endif
+    else
+      # ion species: always call na3dl*
+      set na_dens="$na_dens na3dl$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dds $group $NUM $END
+    @ offset = $end + 1
+end
+2dds te3dl ti3dl $NUM $END
+2dds ne3dr $NUM $END
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dab3dr* if run with Eirene, na3dr* if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dab3dr* fields exist --> coupled run --> call dab3dr*
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dab3dr$neutral_species_index "
+      else
+        # dab3dr* fields do not exist --> standalone run --> call na3dr*
+        set na_dens="$na_dens na3dr$is_minus_1 "
+      endif
+    else
+      # ion species: always call na3dl*
+      set na_dens="$na_dens na3dr$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dds $group $NUM $END
+    @ offset = $end + 1
+end
+2dds te3dr ti3dr $NUM $END
+2dds fo3dl $NUM $END
+2dds ft3dl $NUM $END
+2dds fo3dr $NUM $END
+2dds ft3dr $NUM $END
+switch ($NREG)
+  case "8":
+    2dds fo3dtl $NUM $END
+    2dds ft3dtl $NUM $END
+    2dds fo3dtr $NUM $END
+    2dds ft3dtr $NUM $END
+  breaksw
+  case "7":
+    2dds fo3dtl $NUM $END
+    2dds ft3dtl $NUM $END
+    2dds fo3dtr $NUM $END
+    2dds ft3dtr $NUM $END
+  breaksw
+endsw
+
+gnuplot ${tmpdir}gnuplot.cmd
+rm ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.*data ${tmpdir}gnuplot.cmd
+[ -f "${tmpdir}dsfile" ] && rm "${tmpdir}dsfile"
+[ -f "${tmpdir}dsFILET" ] && rm "${tmpdir}dsFILET"
+[ -f "${tmpdir}dsFILEP" ] && rm "${tmpdir}dsFILEP"
+
 if ($netcdf4 == 1) then
   rm $source
 endif
diff --git a/scripts/2da b/scripts/2da
index f67264e76..4d41192d5 100755
--- a/scripts/2da
+++ b/scripts/2da
@@ -1,4 +1,5 @@
 #! /bin/csh -f
+
 set source=b2mn.exe.dir/b2time.nc
 if (! -s $source) set source=b2time.nc
 if ("X$1" == "X-s") then
@@ -26,41 +27,125 @@ else
   set netcdf4=0
 endif
 
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+
 /bin/cp /dev/null ${tmpdir}gnuplot.data.tmp
 start:
   set count=`echo "$1" | sed -e 's:[^()]::g' | wc -c`
   if ($count == "1") then
     if ($no_nc2text == 1) then
-      set check=`ncdump $source -v $1 | sed -n 'x;$p' | sed 's/;//g'`
+      if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        echo "Error: Printing multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+        exit 1
+      else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        set check=`ncdump $source -v $1 | sed -n 'x;$p' | sed 's/;//g'`
+      endif
     else
-      set check=`nc2text -n 999999 $source "$1(1)"`
+      if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+        set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+        @ is_plus_1 = $is + 1
+        set check=`nc2text -n 999999 $source "$name(1,$is_plus_1)"`
+        # There is currently a bug when calling nc2text -n 999999 $source "$name(1,$is_plus_1)"
+        # for multi-species quantities: all time values are printed instead of only the first one
+        # Probably a mistake while adding additional dimensions to nc2text
+        # Temporary fix:
+        set check = ( $check[1] )
+      else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        set check=`nc2text -n 999999 $source "$1(1)"`
+      endif
     endif
   else
     set check="1"
   endif
   if ($#check == 1) then
     if ($no_nc2text == 1) then
-      ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
-      sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        echo "Error: Printing multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+        exit 1
+      else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
+        sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+        set args="$args $1"
+      endif
     else
-      echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+        set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+        @ is_plus_1 = $is + 1
+        echo `nc2text -n 9999999 $source "$name(:,$is_plus_1)"` >> ${tmpdir}gnuplot.data.tmp
+        if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+          setenv species_name $neutral_species_names[$is_plus_1]
+        else
+          setenv species_name $species_names[$is_plus_1]
+        endif
+        set args="$args $name($species_name)"
+      else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+        set args="$args $1"
+      endif
     endif
-    set args="$args $1"
   else
     if ($no_nc2text == 1) then
-      ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}' | \
-      awk 'BEGIN {FS=","} {for (i=1;i<=NF;i++) if (i%2==1) {ORS=" ";print $i;}}' | sed 's/;//g' | \
-      awk.transpose >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        echo "Error: Printing multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+        exit 1
+      else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}' | \
+        awk 'BEGIN {FS=","} {for (i=1;i<=NF;i++) if (i%2==1) {ORS=" ";print $i;}}' | sed 's/;//g' | \
+        awk.transpose >> ${tmpdir}gnuplot.data.tmp
+        set args="$args `count -p $1. 1 $#check`"
+      endif
     else
-      nc2text -n 9999999 $source $1 | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+        set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+        @ is_plus_1 = $is + 1
+        nc2text -n 9999999 $source "$name(:,$is_plus_1)" | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+        if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+          setenv species_name $neutral_species_names[$is_plus_1]
+        else
+          setenv species_name $species_names[$is_plus_1]
+        endif
+        set args="$args `count -p $name($species_name). 1 $#check`"
+      else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        nc2text -n 9999999 $source $1 | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+        set args="$args `count -p $1. 1 $#check`"
+      endif
     endif
-    set args="$args `count -p $1. 1 $#check`"
   endif
   shift
   if ("X$1X" != "XX") goto start
 
 echo "# $args"
 awk.transpose < ${tmpdir}gnuplot.data.tmp
+rm ${tmpdir}gnuplot.data.tmp
 
 if ($netcdf4 == 1) then
   rm $source
diff --git a/scripts/2dds b/scripts/2dds
new file mode 100755
index 000000000..d18054464
--- /dev/null
+++ b/scripts/2dds
@@ -0,0 +1,286 @@
+#! /bin/csh -f
+
+nc2text -n 9999999 b2time.nc "dsl" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! dsfile
+
+set x=$1
+if ("X$1" == "X-lx") then
+  set lx="l"
+  shift
+else
+  set lx=""
+endif
+
+if ("X$1" == "X-ly") then
+  set ly="l"
+  shift
+else
+  set ly=""
+endif
+
+if ( $#argv < 1 ) then
+    echo "Error: You must provide at least one argument (1st, 2nd, etc. arguments will be plotted vs. ds*)."
+    exit 1
+endif
+
+set source=b2mn.exe.dir/b2time.nc
+if (! -s $source) set source=b2time.nc
+
+set args = ( $argv )
+set nargs=$#argv
+
+set last = $argv[$nargs]
+@ second_last_index = $nargs - 1
+set second_last = $argv[$second_last_index]
+
+set test_last = `echo $last | grep '^[0-9]*$'`
+set test_second_last = `echo $second_last | grep '^[0-9]*$'`
+
+set NUM=10
+if ((($test_last) || ($test_last == 0)) && !(($test_second_last) || ($test_second_last == 0)) ) then
+    set NUM=$last
+    @ n = $#args - 1
+    set args = ( $args[1-$n] )
+    set nargs=$#args
+endif
+set END=-0
+if ((($test_last) || ($test_last == 0)) && (($test_second_last) || ($test_second_last == 0)) ) then
+    set NUM=$second_last
+    set END=$last
+    @ n = $#args - 2
+    set args = ( $args[1-$n] )
+    set nargs=$#args
+endif
+@ NUM = 1 + $END - $NUM
+
+if($?GNUPLOT_TMP) then
+    set tmpdir="$GNUPLOT_TMP/"
+else
+    set tmpdir=""
+endif
+
+which nc2text > /dev/null && set no_nc2text=0 || set no_nc2text=1
+if (-e b2mn.exe.dir/.netcdf4) then
+  ln -sf $source ${tmpdir}b2time.nc.tmp
+  set source=${tmpdir}b2time.nc.tmp
+  gtfl $source
+  set netcdf4=1
+else
+  set netcdf4=0
+endif
+
+set nt = `nc2text $source "ntstep" | awk '{printf "%d", $1}'`
+set ns = `ncdump -h $source | grep -w "ns =" | sed -E 's/.*= *([0-9]+) *;.*/\1/'`
+@ jstart = $nt + $NUM
+if ($jstart < 0) then
+  @ NUM = -$nt + 1
+endif
+@ jend = $nt + $END
+if ($jend > $nt) then
+ set END = -0
+endif
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+
+set is_first = 1
+
+set labels=""
+
+set neutral_species_index = -1
+
+foreach i ($args)
+
+if ($is_first) then
+
+  if ("$i" !~ *[0-9]) then
+
+    set prefix=`echo $i | cut -c1`
+    set pr2fix=`echo $i | cut -c2`
+    set suffix=`echo $i | cut -c5-`
+    set SUFFIX=`echo $suffix | tr 'a-z' 'A-Z'`
+    set SUFFIXP=`echo $suffix | tr 'a-z' 'A-Z'`P
+    set dsfile=b2mn.exe.dir/ds$suffix
+    if (! -s $dsfile) set dsfile=ds$suffix
+    set dsFILE=b2mn.exe.dir/ds$SUFFIX
+    if (! -s $dsFILE) set dsFILE=ds$SUFFIX
+    set dsFILEP=b2mn.exe.dir/ds$SUFFIXP
+    if (! -s $dsFILEP) set dsFILEP=ds$SUFFIXP
+    nc2text -n 9999999 $source "ds${suffix}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsfile
+    if ("$suffix" != "a" && "$suffix" != "i") then
+      nc2text -n 9999999 $source "ds${SUFFIX}T" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILET
+      nc2text -n 9999999 $source "ds${SUFFIXP}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILEP
+    endif
+
+    set labels="$labels $i"
+
+    if ($prefix == "f" && -s $dsFILE) then
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILET | awk '{print $1,$2/$3}' >! ${tmpdir}gnuplot.data.tmp
+    else if ($prefix == "t" && $pr2fix != "p") then
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1/1.602176634e-19}' | paste ${tmpdir}dsfile - >! ${tmpdir}gnuplot.data.tmp
+    else if ($prefix == "t" && $pr2fix == "p") then
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - >! ${tmpdir}gnuplot.data.tmp
+    else
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - >! ${tmpdir}gnuplot.data.tmp
+    endif
+    if ($prefix == "f" && -s $dsFILEP) then
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILEP | awk '{print $1,$2/$3}' >! ${tmpdir}gnuplot.data.tmp
+    endif
+
+  else
+
+    set is = `echo "$i" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+    set name = `echo "$i" | sed -E 's/([0-9]+)$//'`
+    @ is_plus_1 = $is + 1
+
+    if ("$i" =~ dab* || "$i" =~ dmb* || "$i" =~ tab* || "$i" =~ tmb*) then
+      set prefix=`echo $name | cut -c2`
+      set pr2fix=`echo $name | cut -c3`
+      set suffix=`echo $name | cut -c6-`
+    else
+      set prefix=`echo $name | cut -c1`
+      set pr2fix=`echo $name | cut -c2`
+      set suffix=`echo $name | cut -c5-`
+    endif
+    set SUFFIX=`echo $suffix | tr 'a-z' 'A-Z'`
+    set SUFFIXP=`echo $suffix | tr 'a-z' 'A-Z'`P
+    set dsfile=b2mn.exe.dir/ds$suffix
+    if (! -s $dsfile) set dsfile=ds$suffix
+    set dsFILE=b2mn.exe.dir/ds$SUFFIX
+    if (! -s $dsFILE) set dsFILE=ds$SUFFIX
+    set dsFILEP=b2mn.exe.dir/ds$SUFFIXP
+    if (! -s $dsFILEP) set dsFILEP=ds$SUFFIXP
+    nc2text -n 9999999 $source "ds${suffix}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsfile
+    if ("$suffix" != "a" && "$suffix" != "i") then
+      nc2text -n 9999999 $source "ds${SUFFIX}T" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILET
+      nc2text -n 9999999 $source "ds${SUFFIXP}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILEP
+    endif
+
+    if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+      setenv species_name $neutral_species_names[$is_plus_1]
+    else
+      setenv species_name $species_names[$is_plus_1]
+    endif
+    set labels="$labels $name($species_name)"
+
+    if ($prefix == "f" && -s $dsFILE) then
+        nc2text -n 9999999 $source "$name(:,$is_plus_1,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILET | awk '{print $1,$2/$3}' >! ${tmpdir}gnuplot.data.tmp
+    else
+        nc2text -n 9999999 $source "$name(:,$is_plus_1,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - >! ${tmpdir}gnuplot.data.tmp
+    endif
+    if ($prefix == "f" && -s $dsFILEP) then
+        nc2text -n 9999999 $source "$name(:,$is_plus_1,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILEP | awk '{print $1,$2/$3}' >! ${tmpdir}gnuplot.data.tmp
+    endif
+
+  endif
+
+set is_first = 0
+
+else
+
+  if ("$i" !~ *[0-9]) then
+
+    set prefix=`echo $i | cut -c1`
+    set pr2fix=`echo $i | cut -c2`
+    set suffix=`echo $i | cut -c5-`
+    set SUFFIX=`echo $suffix | tr 'a-z' 'A-Z'`
+    set SUFFIXP=`echo $suffix | tr 'a-z' 'A-Z'`P
+    set dsfile=b2mn.exe.dir/ds$suffix
+    if (! -s $dsfile) set dsfile=ds$suffix
+    set dsFILE=b2mn.exe.dir/ds$SUFFIX
+    if (! -s $dsFILE) set dsFILE=ds$SUFFIX
+    set dsFILEP=b2mn.exe.dir/ds$SUFFIXP
+    if (! -s $dsFILEP) set dsFILEP=ds$SUFFIXP
+    nc2text -n 9999999 $source "ds${suffix}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsfile
+    if ("$suffix" != "a" && "$suffix" != "i") then
+      nc2text -n 9999999 $source "ds${SUFFIX}T" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILET
+      nc2text -n 9999999 $source "ds${SUFFIXP}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILEP
+    endif
+
+    set labels="$labels $i"
+
+    if ($prefix == "f" && -s $dsFILE) then
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILET | awk '{print $2/$3}' >! ${tmpdir}gnuplot.data.tmp.tmp
+    else if ($prefix == "t" && $pr2fix != "p") then
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1/1.602176634e-19}' | paste ${tmpdir}dsfile - | awk '{print $2}' >! ${tmpdir}gnuplot.data.tmp.tmp
+    else if ($prefix == "t" && $pr2fix == "p") then
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - | awk '{print $2}' >! ${tmpdir}gnuplot.data.tmp.tmp
+    else
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - | awk '{print $2}' >! ${tmpdir}gnuplot.data.tmp.tmp
+    endif
+    if ($prefix == "f" && -s $dsFILEP) then
+      nc2text -n 9999999 $source "$i(:,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILEP | awk '{print $2/$3}' >! ${tmpdir}gnuplot.data.tmp.tmp
+    endif
+
+  else
+
+    set is = `echo "$i" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+    set name = `echo "$i" | sed -E 's/([0-9]+)$//'`
+    @ is_plus_1 = $is + 1
+
+    if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+      set prefix=`echo $name | cut -c2`
+      set pr2fix=`echo $name | cut -c3`
+      set suffix=`echo $name | cut -c6-`
+    else
+      set prefix=`echo $name | cut -c1`
+      set pr2fix=`echo $name | cut -c2`
+      set suffix=`echo $name | cut -c5-`
+    endif
+    set SUFFIX=`echo $suffix | tr 'a-z' 'A-Z'`
+    set SUFFIXP=`echo $suffix | tr 'a-z' 'A-Z'`P
+    set dsfile=b2mn.exe.dir/ds$suffix
+    if (! -s $dsfile) set dsfile=ds$suffix
+    set dsFILE=b2mn.exe.dir/ds$SUFFIX
+    if (! -s $dsFILE) set dsFILE=ds$SUFFIX
+    set dsFILEP=b2mn.exe.dir/ds$SUFFIXP
+    if (! -s $dsFILEP) set dsFILEP=ds$SUFFIXP
+    nc2text -n 9999999 $source "ds${suffix}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsfile
+    if ("$suffix" != "a" && "$suffix" != "i") then
+      nc2text -n 9999999 $source "ds${SUFFIX}T" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILET
+      nc2text -n 9999999 $source "ds${SUFFIXP}" | ave.awk | tr ' ' '\n' | awk 'NF>0 { printf("  % .16E\n", $1) }' >! ${tmpdir}dsFILEP
+    endif
+
+    if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+      setenv species_name $neutral_species_names[$is_plus_1]
+    else
+      setenv species_name $species_names[$is_plus_1]
+    endif
+    set labels="$labels $name($species_name)"
+
+    if ($prefix == "f" && -s $dsFILE) then
+        nc2text -n 9999999 $source "$name(:,$is_plus_1,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILET | awk '{print $2/$3}' >! ${tmpdir}gnuplot.data.tmp.tmp
+    else
+        nc2text -n 9999999 $source "$name(:,$is_plus_1,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - | awk '{print $2}' >! ${tmpdir}gnuplot.data.tmp.tmp
+    endif
+    if ($prefix == "f" && -s $dsFILEP) then
+        nc2text -n 9999999 $source "$name(:,$is_plus_1,${NUM}:${END})" | ave.awk | tr ' ' '\n' | awk 'NF>0{print $1}' | paste ${tmpdir}dsfile - ${tmpdir}dsFILEP | awk '{print $2/$3}' >! ${tmpdir}gnuplot.data.tmp.tmp
+    endif
+
+  endif
+
+  paste ${tmpdir}gnuplot.data.tmp ${tmpdir}gnuplot.data.tmp.tmp >! ${tmpdir}gnuplot.data.tmp.tmp.tmp
+  mv ${tmpdir}gnuplot.data.tmp.tmp.tmp ${tmpdir}gnuplot.data.tmp
+  rm ${tmpdir}gnuplot.data.tmp.tmp
+
+endif
+
+end
+
+awk 'NR==1{saveNF=NF} NF==saveNF{print $0}' ${tmpdir}gnuplot.data.tmp | plot ${lx}x${ly}yplot$nargs $labels $dsfile '' `chop_pwd 60`
+rm ${tmpdir}gnuplot.data.tmp
+[ -f "${tmpdir}dsfile" ] && rm "${tmpdir}dsfile"
+[ -f "${tmpdir}dsFILET" ] && rm "${tmpdir}dsFILET"
+[ -f "${tmpdir}dsFILEP" ] && rm "${tmpdir}dsFILEP"
diff --git a/scripts/2dt b/scripts/2dt
index 0cf89b395..34340b415 100755
--- a/scripts/2dt
+++ b/scripts/2dt
@@ -1,4 +1,5 @@
 #! /bin/csh -f
+
 set x=$1
 if ("X$1" == "X-lx") then
   set lx="l"
@@ -6,12 +7,19 @@ if ("X$1" == "X-lx") then
 else
   set lx=""
 endif
+
 if ("X$1" == "X-ly") then
   set ly="l"
   shift
 else
   set ly=""
 endif
+
+if ( $#argv < 1 ) then
+    echo "Error: You must provide at least one argument (1st, 2nd, etc. arguments will be plotted vs. time)."
+    exit 1
+endif
+
 set source=b2mn.exe.dir/b2time.nc
 if (! -s $source) set source=b2time.nc
 
@@ -46,42 +54,125 @@ else
   nc2text -n 9999999 $source timesa >> ${tmpdir}gnuplot.data.tmp
 endif
 
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+
 start:
   if ($no_nc2text == 1) then
   # Here just dump variable and check how many entries are on the second to last line.
   # Works for two, did not have any cases to confirm this works for more.
   # Could break if there are enough columns that it extends across multiple lines.
-    set check=`ncdump $source -v $1 | sed -n 'x;$p' | sed 's/;//g'`
+    if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+        exit 1
+    else
+        # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        set check=`ncdump $source -v $1 | sed -n 'x;$p' | sed 's/;//g'`
+    endif
   else
-    set check=`nc2text -n 999999 $source "$1(1)"`
+    if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+        set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+        @ is_plus_1 = $is + 1
+        set check=`nc2text -n 999999 $source "$name(1,$is_plus_1)"`
+        # There is currently a bug when calling nc2text -n 999999 $source "$name(1,$is_plus_1)"
+        # for multi-species quantities: all time values are printed instead of only the first one
+        # Probably a mistake while adding additional dimensions to nc2text
+        # Temporary fix:
+        set check = ( $check[1] )
+    else
+        # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        set check=`nc2text -n 999999 $source "$1(1)"`
+    endif
   endif
   @ nargs += $#check
   if ($#check == 1) then
     if ($no_nc2text == 1) then
     # Same as timesa except we pass the variable name as string
-      ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
-      sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+          # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+          echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+          exit 1
+      else
+          # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+          ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
+          sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+          set args="$args $1"
+      endif
     else
-      echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+          # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+          set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+          set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+          @ is_plus_1 = $is + 1
+          echo `nc2text -n 9999999 $source "$name(:,$is_plus_1)"` >> ${tmpdir}gnuplot.data.tmp
+          if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+            setenv species_name $neutral_species_names[$is_plus_1]
+          else
+            setenv species_name $species_names[$is_plus_1]
+          endif
+          set args="$args $name($species_name)"
+      else
+          # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+          echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+          set args="$args $1"
+      endif
     endif
-    set args="$args $1"
   else
     if ($no_nc2text == 1) then
     # If the data has more than one column we dump as before,
     # then assemble data into columns to be processed by awk.transpose
-      ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}' | \
-      awk 'BEGIN {FS=","} {for (i=1;i<=NF;i++) if (i%2==1) {ORS=" ";print $i;}}' | sed 's/;//g' | \
-      awk.transpose >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+          # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+          echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+          exit 1
+      else
+          # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+          ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}' | \
+          awk 'BEGIN {FS=","} {for (i=1;i<=NF;i++) if (i%2==1) {ORS=" ";print $i;}}' | sed 's/;//g' | \
+          awk.transpose >> ${tmpdir}gnuplot.data.tmp
+          set args="$args `count -p $1 1 $#check`"
+      endif
     else
-      nc2text -n 9999999 $source $1 | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+          # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+          set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+          set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+          @ is_plus_1 = $is + 1
+          nc2text -n 9999999 $source "$name(:,$is_plus_1)" | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+          if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+            setenv species_name $neutral_species_names[$is_plus_1]
+          else
+            setenv species_name $species_names[$is_plus_1]
+          endif
+          set args="$args `count -p $name($species_name) 1 $#check`"
+      else
+          # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+          nc2text -n 9999999 $source $1 | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+          set args="$args `count -p $1 1 $#check`"
+      endif
     endif
-    set args="$args `count -p $1 1 $#check`"
   endif
   shift
   if ("X$1X" != "XX") goto start
 
 awk.transpose < ${tmpdir}gnuplot.data.tmp | awk 'NR==1{saveNF=NF}NF==saveNF{print $0}' | plot ${lx}x${ly}yplot$nargs $args time '' `chop_pwd 60`
-/bin/rm ${tmpdir}gnuplot.data.tmp
+rm ${tmpdir}gnuplot.data.tmp
 
 if ($netcdf4 == 1) then
   rm $source
diff --git a/scripts/2dt_av b/scripts/2dt_av
index c5a90b07c..717d8effb 100755
--- a/scripts/2dt_av
+++ b/scripts/2dt_av
@@ -1,4 +1,5 @@
 #! /bin/csh -f
+
 set x=$1
 if ("X$1" == "X-lx") then
   set lx="l"
@@ -6,12 +7,19 @@ if ("X$1" == "X-lx") then
 else
   set lx=""
 endif
+
 if ("X$1" == "X-ly") then
   set ly="l"
   shift
 else
   set ly=""
 endif
+
+if ( $#argv < 1 ) then
+    echo "Error: You must provide at least one argument (1st, 2nd, etc. arguments will be plotted vs. time)."
+    exit 1
+endif
+
 set source=b2mn.exe.dir/b2batch.nc
 if (! -s $source) then
   set source=b2batch.nc
@@ -52,36 +60,119 @@ else
   nc2text -n 9999999 $source batchsa >> ${tmpdir}gnuplot.data.tmp
 endif
 
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+
 start:
   if ($no_nc2text == 1) then
   # Here just dump variable and check how many entries are on the second to last line.
   # Works for two, did not have any cases to confirm this works for more.
   # Could break if there are enough columns that it extends across multiple lines.
-    set check=`ncdump $source -v $1 | sed -n 'x;$p' | sed 's/;//g'`
+    if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+        exit 1
+    else
+        # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        set check=`ncdump $source -v $1 | sed -n 'x;$p' | sed 's/;//g'`
+    endif
   else
-    set check=`nc2text -n 999999 $source "$1(1)"`
+    if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+        set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+        @ is_plus_1 = $is + 1
+        set check=`nc2text -n 999999 $source "$name(1,$is_plus_1)"`
+        # There is currently a bug when calling nc2text -n 999999 $source "$name(1,$is_plus_1)"
+        # for multi-species quantities: all time values are printed instead of only the first one
+        # Probably a mistake while adding additional dimensions to nc2text
+        # Temporary fix:
+        set check = ( $check[1] )
+    else
+        # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        set check=`nc2text -n 999999 $source "$1(1)"`
+    endif
   endif
   @ nargs += $#check
   if ($#check == 1) then
     if ($no_nc2text == 1) then
     # Same as batchsa except we pass the variable name as string
-      ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
-      sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+          # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+          echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+          exit 1
+      else
+          # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+          ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
+          sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+          set args="$args $1"
+      endif
     else
-      echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+          # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+          set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+          set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+          @ is_plus_1 = $is + 1
+          echo `nc2text -n 9999999 $source "$name(:,$is_plus_1)"` >> ${tmpdir}gnuplot.data.tmp
+          if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+            setenv species_name $neutral_species_names[$is_plus_1]
+          else
+            setenv species_name $species_names[$is_plus_1]
+          endif
+          set args="$args $name($species_name)"
+      else
+          # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+          echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+          set args="$args $1"
+      endif
     endif
-    set args="$args $1"
   else
     if ($no_nc2text == 1) then
     # If the data has more than one column we dump as before, 
     # then assemble data into columns to be processed by awk.transpose
-      ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}' | \
-      awk 'BEGIN {FS=","} {for (i=1;i<=NF;i++) if (i%2==1) {ORS=" ";print $i;}}' | sed 's/;//g' | \
-      awk.transpose >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+          # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+          echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+          exit 1
+      else
+          # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+          ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}' | \
+          awk 'BEGIN {FS=","} {for (i=1;i<=NF;i++) if (i%2==1) {ORS=" ";print $i;}}' | sed 's/;//g' | \
+          awk.transpose >> ${tmpdir}gnuplot.data.tmp
+          set args="$args `count -p $1 1 $#check`"
+      endif
     else
-      nc2text -n 9999999 $source $1 | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+      if ("$1" =~ *[0-9]) then
+          # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+          set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+          set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+          @ is_plus_1 = $is + 1
+          nc2text -n 9999999 $source "$name(:,$is_plus_1)" | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+          if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+            setenv species_name $neutral_species_names[$is_plus_1]
+          else
+            setenv species_name $species_names[$is_plus_1]
+          endif
+          set args="$args `count -p $name($species_name) 1 $#check`"
+      else
+          # Single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+          nc2text -n 9999999 $source $1 | awk.transpose >> ${tmpdir}gnuplot.data.tmp
+          set args="$args `count -p $1 1 $#check`"
+      endif
     endif
-    set args="$args `count -p $1 1 $#check`"
   endif
   shift
   if ("X$1X" != "XX") goto start
diff --git a/scripts/2dt_tracing b/scripts/2dt_tracing
new file mode 100755
index 000000000..9b1d63dd8
--- /dev/null
+++ b/scripts/2dt_tracing
@@ -0,0 +1,99 @@
+#! /bin/csh -f
+
+set x=$1
+if ("X$1" == "X-lx") then
+  set lx="l"
+  shift
+else
+  set lx=""
+endif
+
+if ("X$1" == "X-ly") then
+  set ly="l"
+  shift
+else
+  set ly=""
+endif
+
+if ( $#argv < 1 ) then
+    echo "Error: You must provide at least one argument (1st, 2nd, etc. arguments will be plotted vs. time)."
+    exit 1
+endif
+
+set args=""
+set nargs=0
+
+if($?GNUPLOT_TMP) then
+    set tmpdir="$GNUPLOT_TMP/"
+else
+    set tmpdir=""
+endif
+
+/bin/cp /dev/null ${tmpdir}gnuplot.data.tmp
+
+set source=b2mn.exe.dir/tracing/blnn_SPb.trc
+if (! -s $source) set source=tracing/blnn_SPb.trc
+
+echo `awk 'NR==3 {sub(/^# */, ""); for(i=1;i<=NF;i++) if($i=="time") col=i; next} NR>3 && col {print $col}' $source` >> ${tmpdir}gnuplot.data.tmp
+
+set groups_blnn_SPb="ion_core ntr_targ_tot ntr_targ_rec ntr_targ_spt ntr_targ_pmp ion_wall ntr_wall_tot ntr_wall_rec ntr_wall_spt ntr_wall_pmp src_ioniz ntr_puff flux_tot src_ext ion_dn/dt"
+
+set groups_blne="pwr_totl pwr_tscl tot_core tot_targ tot_wall tot_rad heat_cor ptnt_cor ntrl_cor plsm_trg ntrl_trg plsm_wll ntrl_wll brms_rad ntrl_rad imp_rad tot_enrg tot_enre tot_enri imp_rad pwr_totl_il pwr_plsm_il pwr_neut_il pwr_ionz_il pwr_diss_il pwr_totl_ol pwr_plsm_ol pwr_neut_ol pwr_ionz_ol pwr_diss_ol pwr_totl_wl pwr_plsm_wl pwr_neut_wl pwr_ionz_wl pwr_diss_wl"
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+set isonuclear_species_names = ()
+foreach name ($neutral_species_names)
+    set name = `echo $name | sed 's/0$//'`
+    set isonuclear_species_names = ($isonuclear_species_names $name)
+end
+
+start:
+  foreach species ($isonuclear_species_names)
+    if ("$1" =~ "*_$species") then
+      set var = `echo "$1" | sed "s/_"$species"//g"`
+      break
+    else
+      set var = "$1"
+    endif
+  end
+  foreach item ($groups_blnn_SPb)
+    if ("$var" == "$item") then
+      set source=b2mn.exe.dir/tracing/blnn_SPb.trc
+      if (! -s $source) set source=tracing/blnn_SPb.trc
+      break
+    endif
+  end
+  foreach item ($groups_blne)
+    if ("$var" == "$item") then
+      set source=b2mn.exe.dir/tracing/blne.trc
+      if (! -s $source) set source=tracing/blne.trc
+      break
+    endif
+  end
+  set check=`awk -v field="$1" 'NR==3 {sub(/^# */, ""); for(i=1;i<=NF;i++) if($i==field) col=i; next} NR>3 && col && seen != 1 {print $col; seen=1}' $source`
+  @ nargs += $#check
+  if ($#check == 1) then
+    echo `awk -v field="$1" 'NR==3 {sub(/^# */, ""); for(i=1;i<=NF;i++) if($i==field) col=i; next} NR>3 && col {print $col}' $source` >> ${tmpdir}gnuplot.data.tmp
+    set args="$args $1"
+  else
+    set args="$args `count -p $1 1 $#check`"
+  endif
+  shift
+  if ("X$1X" != "XX") goto start
+
+awk.transpose < ${tmpdir}gnuplot.data.tmp | awk 'NR==1{saveNF=NF}NF==saveNF{print $0}' | plot ${lx}x${ly}yplot$nargs $args time '' `chop_pwd 60`
+rm ${tmpdir}gnuplot.data.tmp
diff --git a/scripts/darwinsubmit b/scripts/darwinsubmit
index e2c94b36f..800b6dc7c 100755
--- a/scripts/darwinsubmit
+++ b/scripts/darwinsubmit
@@ -2,6 +2,7 @@
 
 set standalone='no'
 set compress='no'
+set PAR_STRING = ""
 
 echo Started SOLPS-ITER run
 
@@ -47,7 +48,7 @@ EOF
     set PROCS="$1"
     echo Asking for MPI run with a total of $PROCS processors
     shift
-    set PAR_STRING = '-m "mpiexec -np '$PROCS'"'
+    set PAR_STRING = `echo $PAR_STRING -m \"mpiexec -np $PROCS\"`
     goto argloop
   endif
   if ("X${1}X" == "X-tX") then
@@ -59,7 +60,7 @@ EOF
     set THREADS="$1"
     echo Asking for OpenMP run with $THREADS threads
     shift
-    set PAR_STRING = '-t '$THREADS''
+    set PAR_STRING = "$PAR_STRING -t $THREADS"
     goto argloop
   endif
 
@@ -73,13 +74,13 @@ if (-s fort.1 && ${standalone} == "no") then
   if (${compress} == "-gz") then
     (b2run $PAR_STRING b2mn < fort.1 | gzip -9 >& run.log.gz) &
   else
-    (b2run $PAR_STRING b2mn < fort.1 >& run.log) &
+    (b2run $PAR_STRING b2mn < fort.1 >& run.log && [ -e run.log ] && gzip -9 -f run.log) &
   endif
 else
   if ($standalone == "no") echo No fort.1 file found: reverting to a standalone run
   if (${compress} == "-gz") then
     (b2run $PAR_STRING -s b2mn | gzip -9 >& run.log.gz) &
   else
-    (b2run $PAR_STRING -s b2mn >& run.log) &
+    (b2run $PAR_STRING -s b2mn >& run.log && [ -e run.log ] && gzip -9 -f run.log) &
   endif
 endif
diff --git a/scripts/energy_balance_tracing b/scripts/energy_balance_tracing
new file mode 100755
index 000000000..284d74a14
--- /dev/null
+++ b/scripts/energy_balance_tracing
@@ -0,0 +1,48 @@
+#! /bin/tcsh -f
+
+if($?GNUPLOT_TMP) then
+    set tmpdir="$GNUPLOT_TMP/"
+else
+    set tmpdir=""
+endif
+setenv GNUPLOT_BATCH yes
+setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid noenhanced'
+setenv PRINT_PLOT energy_balance.ps
+rm -f ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.cmd
+echo 0 > ${tmpdir}GNUPLOT_COUNT
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+set isonuclear_species_names = ()
+foreach name ($neutral_species_names)
+    set name = `echo $name | sed 's/0$//'`
+    set isonuclear_species_names = ($isonuclear_species_names $name)
+end
+
+set impurity_names = ($isonuclear_species_names[2-])
+
+2dt_tracing tot_core pwr_totl_il pwr_totl_ol pwr_totl_wl tot_rad pwr_totl
+set imp_rad = ""
+foreach species ($impurity_names)
+  set imp_rad="$imp_rad imp_rad_$species "
+end
+2dt_tracing brms_rad ntrl_rad $imp_rad
+2dt_tracing pwr_plsm_il pwr_neut_il pwr_ionz_il pwr_diss_il
+2dt_tracing pwr_plsm_ol pwr_neut_ol pwr_ionz_ol pwr_diss_ol
+2dt_tracing pwr_plsm_wl pwr_neut_wl pwr_ionz_wl pwr_diss_wl
+
+gnuplot ${tmpdir}gnuplot.cmd
+rm ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.*data ${tmpdir}gnuplot.cmd
diff --git a/scripts/get_solps_fluids b/scripts/get_solps_fluids
index a960e12d0..5424cba0c 100755
--- a/scripts/get_solps_fluids
+++ b/scripts/get_solps_fluids
@@ -3,5 +3,5 @@ set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
 if (-s $solps_fluids) then
   echo `cat $solps_fluids`
 else
-  pipe_run.log | egrep -a -m 1 '^species' | awk '{for (j=3;j<=NF;j++) {printf $j; print "\t"}}' | awk.transpose
+  pipe_run.log |& grep -a -m 1 '^species' | awk '{for (j=3;j<=NF;j++) {printf $j; print "\t"}}' | awk.transpose
 endif
diff --git a/scripts/groups_species b/scripts/groups_species
new file mode 100755
index 000000000..260f5f6d5
--- /dev/null
+++ b/scripts/groups_species
@@ -0,0 +1,32 @@
+#! /bin/tcsh -f
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_index = -1
+
+set na_dens = "$1"
+
+set bases = ()
+foreach s ($species_names)
+  set base = `echo $s | sed 's/[+0-9].*//'`
+  set bases = ($bases $base)
+end
+set counts = ()
+set prev = ""
+set count = 0
+foreach b ($bases)
+  if ("$b" == "$prev") then
+    @ count++
+  else
+    if ("$prev" != "") set counts = ($counts $count)
+    set count = 1
+    set prev = $b
+  endif
+end
+set counts = ($counts $count)
+echo $counts
\ No newline at end of file
diff --git a/scripts/move_save_files b/scripts/move_save_files
index 28be8f4e6..9b5e8c90e 100755
--- a/scripts/move_save_files
+++ b/scripts/move_save_files
@@ -10,6 +10,9 @@ if ($?B2FSTATE_ONLY) then
   foreach i (`echo $PLASMASTATE:t | sed -e 's:plasmastate:b2wall.nc:'`)
     [ -e $i ] && rm $i || echo > /dev/null
   end
+  foreach i (`echo $PLASMASTATE:t | sed -e 's:plasmastate:b2neo.nc:'`)
+    [ -e $i ] && rm $i || echo > /dev/null
+  end
   foreach i (`echo $PLASMASTATE:t | sed -e 's:plasmastate:b2movies.nc:'`)
     [ -e $i ] && rm $i || echo > /dev/null
   end
@@ -104,6 +107,9 @@ end
 foreach i (`echo $PLASMASTATE:t | sed -e 's:plasmastate:b2wall.nc:'`)
   [ -s $i ] && mv -v $i ../b2wall.nc || echo > /dev/null
 end
+foreach i (`echo $PLASMASTATE:t | sed -e 's:plasmastate:b2neo.nc:'`)
+  [ -s $i ] && mv -v $i ../b2neo.nc || echo > /dev/null
+end
 foreach i (`echo $PLASMASTATE:t | sed -e 's:plasmastate:b2movies.nc:'`)
   [ -s $i ] && mv -v $i ../b2movies.nc || echo > /dev/null
 end
diff --git a/scripts/nc2text_simple/nc2text_simple.F90 b/scripts/nc2text_simple/nc2text_simple.F90
index 272599cdd..5dff9d0c5 100644
--- a/scripts/nc2text_simple/nc2text_simple.F90
+++ b/scripts/nc2text_simple/nc2text_simple.F90
@@ -14,10 +14,10 @@ Program nc2text_simple
   Integer, Parameter :: I8 = Selected_int_kind(8)
 
   Integer :: ncid, iret, varid, nvdims, vartyp, dimids(MAXVDIMS), numcmdarg
-  Integer(I8) :: i, j, i1=1, i2=0, j1=1, j2=0, itmp
+  Integer(I8) :: i, j, k, i1=1, i2=0, j1=1, j2=0, k1=1, k2=0, itmp
   Logical :: use_index = .false.
   Integer, Allocatable  :: dimlen(:)
-  Real(R8), Allocatable :: rdata(:,:)
+  Real(R8), Allocatable :: rdata(:,:,:)
   Character(LEN = 20) :: hlp_frm
   Character(Len = 256) :: filename, varname
   Character(Len = MAXNCNAM) :: dimnam
@@ -59,23 +59,31 @@ Program nc2text_simple
   Case (NCDOUBLE)
      Select Case (nvdims)
      Case (0)
-        Allocate(rdata(1,1))
+        Allocate(rdata(1,1,1))
         i1 = 1
         i2 = 1
         j1 = 1
         j2 = 1
+        k1 = 1
+        k2 = 1
      Case (1)
-        Allocate(rdata(dimlen(1),1))
+        Allocate(rdata(dimlen(1),1,1))
         itmp = i1
         i1 = j1
         j1 = itmp
         itmp = i2
         i2 = j2
         j2 = itmp
+        k1 = 1
+        k2 = 1
      Case (2)
-        Allocate(rdata(dimlen(1),dimlen(2)))
+        Allocate(rdata(dimlen(1),dimlen(2),1))
+        k1 = 1
+        k2 = 1
+     Case (3)
+        Allocate(rdata(dimlen(1),dimlen(2),dimlen(3)))
      Case Default
-        Write(0,*) "Error: Only scalars, 1-, or 2-dimensional arrays supported"
+        Write(0,*) "Error: Only scalars, 1-, 2-, or 3-dimensional arrays supported"
         Stop
      End Select
      iret = NF_GET_VAR_DOUBLE(ncid,varid,rdata)
@@ -93,28 +101,35 @@ Program nc2text_simple
   If (i2 .le. 0) i2 = Size(rdata,1) + i2
   If (j1 .le. 0) j1 = Size(rdata,2) + j1
   If (j2 .le. 0) j2 = Size(rdata,2) + j2
+  If (k1 .le. 0) k1 = Size(rdata,3) + k1
+  If (k2 .le. 0) k2 = Size(rdata,3) + k2
   itmp = i1
   i1 = Min(i1,i2)
   i2 = Max(itmp,i2)
   itmp = j1
   j1 = Min(j1,j2)
   j2 = Max(itmp,j2)
-  If (debug) Write(0,'(a,i0,a,i0,a,i0,a,i0,a)') ' Subscripts processed to (',i1,':',i2,',',j1,':',j2,')'
+  itmp = k1
+  k1 = Min(k1,k2)
+  k2 = Max(itmp,k2)
+  If (debug) Write(0,'(a,i0,a,i0,a,i0,a,i0,a,i0,a,i0,a)') ' Subscripts processed to (',i1,':',i2,',',j1,':',j2,',',k1,':',k2,')'
 
   ! Check dimensions
-  If( (i2 .gt. Size(rdata,1)) .OR. (j2 .gt. Size(rdata,2)) .OR. &
-       (i1 .le. 0) .OR. (j1 .le. 0) ) Then
+  If( (i2 .gt. Size(rdata,1)) .OR. (j2 .gt. Size(rdata,2)) .OR. (k2 .gt. Size(rdata,3)) .OR. &
+       (i1 .le. 0) .OR. (j1 .le. 0) .OR. (k1 .le. 0) ) Then
      Write(0,*) "Error: index out of bounds"
      Write(0,*) "Size is ",dimlen
-     Write(0,'(a,i0,a,i0,a,i0,a,i0,a)') ' Subscripts processed to (',i1,':',i2,',',j1,':',j2,')'
+     Write(0,'(a,i0,a,i0,a,i0,a,i0,a)') ' Subscripts processed to (',i1,':',i2,',',j1,':',j2,',',k1,':',k2,')'
      Stop
   Endif
 
   ! Output
   Write(hlp_frm,'(a,i8,a)') '(1p,',i2-i1+1,'e18.10)'
-  Do j = j1,j2
-     Write(*,hlp_frm) (rdata(i,j),i=i1,i2)
-  Enddo
+  Do k = k1, k2
+     Do j = j1, j2
+        Write(*,hlp_frm) (rdata(i,j,k), i=i1, i2)
+     End Do
+  End Do
 
   Deallocate(rdata)
   Deallocate(dimlen)
@@ -197,10 +212,11 @@ Function handle_cmd_arg() Result(ierr)
           Endif
           i1 = 1
           i2 = 0
-       Else
+       
+       ElseIf (CountOccurrences(varname, ',') == 1) Then
 
-          ! There is a comma, look for two dimensions
-          If (debug) Write(0,*) "--Found a ',', attempting to get two dimensions"
+          ! There is one comma, look for two dimensions
+          If (debug) Write(0,*) "--Found one ',', attempting to get two dimensions"
 
           ! Check for semicolon in first dimension
           temp = varname(Index(varname,'(')+1:Index(varname,',')-1)
@@ -234,6 +250,59 @@ Function handle_cmd_arg() Result(ierr)
              If (debug) Write(0,*) "--Range found:",j1,j2
           Endif
 
+       ElseIf (CountOccurrences(varname, ',') == 2) Then
+
+         ! There are two commas, look for three dimensions
+         If (debug) Write(0,*) "--Found two ',', attempting to get three dimensions"
+
+         ! Check for semicolon in first dimension
+         temp = varname(Index(varname,'(')+1:Index(varname,',')-1)
+         If (Index(temp,':') .eq. 0) Then
+            If (debug) Write(0,*) "--Single value identified in dim1"
+            If (Len(Trim(temp)) .ne. 0) Read(temp,'(I10)') i1
+            If (debug) Write(0,*) "--Single subscript found:",i1
+            i2 = i1
+         Else
+            If (debug) Write(0,*) "--Range identified in dim1"
+            temp2 = temp(1:Index(temp,':')-1)
+            If (Len(Trim(temp2)) .ne. 0) Read(temp2,'(I10)') i1
+            temp2 = temp(Index(temp,':')+1:)
+            If (Len(Trim(temp2)) .ne. 0) Read(temp2,'(I10)') i2
+            If (debug) Write(0,*) "--Range found:",i1,i2
+         Endif
+
+         ! Check for semicolon in second dimension
+         temp = varname(Index(varname,',')+1:Index(varname,',')+Index(varname(Index(varname,',')+1:),',')-1)
+         If (Index(temp,':') .eq. 0) Then
+            If (debug) Write(0,*) "--Single value identified in dim2"
+            If (Len(Trim(temp)) .ne. 0) Read(temp,'(I10)') j1
+            If (debug) Write(0,*) "--Single subscript found:",j1
+            j2 = j1
+         Else
+            If (debug) Write(0,*) "--Range identified in dim2"
+            temp2 = temp(1:Index(temp,':')-1)
+            If (Len(Trim(temp2)) .ne. 0) Read(temp2,'(I10)') j1
+            temp2 = temp(Index(temp,':')+1:)
+            If (Len(Trim(temp2)) .ne. 0) Read(temp2,'(I10)') j2
+            If (debug) Write(0,*) "--Range found:",j1,j2
+         Endif
+
+         ! Check for semicolon in third dimension
+         temp = varname(Index(varname,',')+Index(varname(Index(varname,',')+1:),',')+1:Index(varname,')')-1)
+         If (Index(temp,':') .eq. 0) Then
+            If (debug) Write(0,*) "--Single value identified in dim3"
+            If (Len(Trim(temp)) .ne. 0) Read(temp,'(I10)') k1
+            If (debug) Write(0,*) "--Single subscript found:",k1
+            k2 = k1
+         Else
+            If (debug) Write(0,*) "--Range identified in dim3"
+            temp2 = temp(1:Index(temp,':')-1)
+            If (Len(Trim(temp2)) .ne. 0) Read(temp2,'(I10)') k1
+            temp2 = temp(Index(temp,':')+1:)
+            If (Len(Trim(temp2)) .ne. 0) Read(temp2,'(I10)') k2
+            If (debug) Write(0,*) "--Range found:",k1,k2
+         Endif
+
        Endif
        varname = varname(1:Index(varname,'(')-1)
     Endif
@@ -242,27 +311,42 @@ Function handle_cmd_arg() Result(ierr)
   End Function handle_cmd_arg
   !-----------------------------------------------------------------------------
 
+  function CountOccurrences(string, char) result(count)
+    character(len=*) :: string
+    character(len=1) :: char
+    integer :: count, i
+
+    count = 0
+    do i = 1, len(string)
+        if (string(i:i) == char) then
+            count = count + 1
+        end if
+    end do
+   end function CountOccurrences
+  !-----------------------------------------------------------------------------
+
   Subroutine Print_help()
     Write(0,'(a)') ' '
-    Write(0,'(a)') 'usage: nc2text_simple [OPTIONS] filename variable(i1:i2,j1:j2)'
+    Write(0,'(a)') 'usage: nc2text_simple [OPTIONS] filename variable(i1:i2,j1:j2,k1:k2)'
     Write(0,'(a)') ' '
     Write(0,'(a)') 'Outputs variable from netcdf file'
     Write(0,'(a)') ' '
     Write(0,'(a)') '   OPTION -n #, number of columns to display data in. This arg accepted but ignored for compatibility'
     Write(0,'(a)') ' '
-    Write(0,'(a)') "   Optional syntax 'variable(i1:i2,j1:j2)' can return a range"
+    Write(0,'(a)') "   Optional syntax 'variable(i1:i2,j1:j2,k1:k2)' can return a range"
     Write(0,'(a)') ' '
     Write(0,'(a)') '   Missing i1..j2 will evaluate as array bounds'
     Write(0,'(a)') '   Ranges start from 1'
     Write(0,'(a)') '   Zero or regative subscripts count from end of array'
     Write(0,'(a)') ' '
-    Write(0,'(a)') 'Current restrictions: only scalars, 1D and 2D arrays of type double supported'
+    Write(0,'(a)') 'Current restrictions: only scalars, 1D, 2D and 3D arrays of type double supported'
     Write(0,'(a)') ' '
     Write(0,'(a)') 'Examples:'
     Write(0,'(a)') '   nc2text_simple b2time.nc tesepa'
     Write(0,'(a)') '   nc2text_simple -n 999999 b2time.nc tesepa'
     Write(0,'(a)') "   nc2text_simple b2time.nc 'tesepa(1)'"
-    Write(0,'(a)') "   nc2text_simple b2time.nc 'fn3dl(-9:-0,:)'"
+    Write(0,'(a)') "   nc2text_simple b2time.nc 'ne3da(:,-9:-0)'"
+    Write(0,'(a)') "   nc2text_simple b2time.nc 'fn3dl(:,2,-9:-0)'"
 
     Return
   End Subroutine Print_help
diff --git a/scripts/obtain_tracing_files b/scripts/obtain_tracing_files
index 3af188645..1b8a2bf06 100755
--- a/scripts/obtain_tracing_files
+++ b/scripts/obtain_tracing_files
@@ -49,9 +49,9 @@ typeset -i nfiles
 }
 rm $NAME
 
-( ls -l b2mn.exe.dir/b2time.nc b2mn.exe.dir/b2batch.nc b2mn.exe.dir/b2wall.nc b2mn.exe.dir/b2tallies.nc b2mn.exe.dir/b2movies.nc b2mn.exe.dir/eirenemovies.nc | grep -v 'total ' | grep -v ' 0 ' | wc -l > $NAME ) 2> /dev/null
+( ls -l b2mn.exe.dir/b2time.nc b2mn.exe.dir/b2batch.nc b2mn.exe.dir/b2wall.nc b2mn.exe.dir/b2tallies.nc b2mn.exe.dir/b2neo.nc b2mn.exe.dir/b2movies.nc b2mn.exe.dir/eirenemovies.nc | grep -v 'total ' | grep -v ' 0 ' | wc -l > $NAME ) 2> /dev/null
 nfiles=`cat $NAME`
-ncfiles=`ls -l b2mn.exe.dir/b2time.nc b2mn.exe.dir/b2batch.nc b2mn.exe.dir/b2wall.nc b2mn.exe.dir/b2tallies.nc b2mn.exe.dir/b2movies.nc b2mn.exe.dir/eirenemovies.nc | grep -v 'total ' | grep -v ' 0 ' | awk '{printf "%s ",$NF,"\n"}'`
+ncfiles=`ls -l b2mn.exe.dir/b2time.nc b2mn.exe.dir/b2batch.nc b2mn.exe.dir/b2wall.nc b2mn.exe.dir/b2tallies.nc b2mn.exe.dir/b2neo.nc b2mn.exe.dir/b2movies.nc b2mn.exe.dir/eirenemovies.nc | grep -v 'total ' | grep -v ' 0 ' | awk '{printf "%s ",$NF,"\n"}'`
 [ $nfiles -ne 1 ] && {
   echo "Found" $nfiles "non-empty NetCDF tracing files in b2mn.exe.dir"
 } || {
@@ -59,7 +59,7 @@ ncfiles=`ls -l b2mn.exe.dir/b2time.nc b2mn.exe.dir/b2batch.nc b2mn.exe.dir/b2wal
 }
 
 [ $nfiles -gt 0 ] && {
-  filelist=`ls -1s b2mn.exe.dir/b2time.nc b2mn.exe.dir/b2batch.nc b2mn.exe.dir/b2wall.nc b2mn.exe.dir/b2tallies.nc b2mn.exe.dir/b2movies.nc b2mn.exe.dir/eirenemovies.nc | grep -v ' 0 ' | grep -v '^0 ' | awk '{printf "%s ",$NF,"\n"}'`
+  filelist=`ls -1s b2mn.exe.dir/b2time.nc b2mn.exe.dir/b2batch.nc b2mn.exe.dir/b2wall.nc b2mn.exe.dir/b2tallies.nc b2mn.exe.dir/b2neo.nc b2mn.exe.dir/b2movies.nc b2mn.exe.dir/eirenemovies.nc | grep -v ' 0 ' | grep -v '^0 ' | awk '{printf "%s ",$NF,"\n"}'`
   set -A f -- $filelist
   i=0
   for z in $filelist; do {
@@ -67,16 +67,16 @@ ncfiles=`ls -l b2mn.exe.dir/b2time.nc b2mn.exe.dir/b2batch.nc b2mn.exe.dir/b2wal
     ((i+=1))
   }; done
 } || {
-  ( ls -l b2time.nc b2batch.nc b2wall.nc b2tallies.nc b2movies.nc eirenemovies.nc | grep -v 'total ' | grep -v ' 0 ' | wc -l > $NAME ) 2> /dev/null
+  ( ls -l b2time.nc b2batch.nc b2wall.nc b2tallies.nc b2neo.nc b2movies.nc eirenemovies.nc | grep -v 'total ' | grep -v ' 0 ' | wc -l > $NAME ) 2> /dev/null
   n2files=`cat $NAME`
-  ncfiles=`ls -l b2time.nc b2batch.nc b2wall.nc b2tallies.nc b2movies.nc eirenemovies.nc | grep -v 'total ' | grep -v ' 0 ' | awk '{printf "%s ",$NF,"\n"}'`
+  ncfiles=`ls -l b2time.nc b2batch.nc b2wall.nc b2tallies.nc b2neo.nc b2movies.nc eirenemovies.nc | grep -v 'total ' | grep -v ' 0 ' | awk '{printf "%s ",$NF,"\n"}'`
   [ $n2files -ne 1 ] && {
     echo "Found" $n2files "non-empty NetCDF tracing files in run directory"
   } || {
     echo "Found" $n2files "non-empty NetCDF tracing file in run directory"
   }
   [ $n2files -gt 0 ] && {
-    filelist=`ls -1s b2time.nc b2batch.nc b2wall.nc b2tallies.nc b2movies.nc eirenemovies.nc | grep -v ' 0 ' | grep -v '^0 ' | awk '{printf "%s ",$NF,"\n"}'`
+    filelist=`ls -1s b2time.nc b2batch.nc b2wall.nc b2tallies.nc b2neo.nc b2movies.nc eirenemovies.nc | grep -v ' 0 ' | grep -v '^0 ' | awk '{printf "%s ",$NF,"\n"}'`
     set -A f -- $filelist
     i=0
     for z in $filelist; do {
diff --git a/scripts/particle_balance_tracing b/scripts/particle_balance_tracing
new file mode 100755
index 000000000..1dd28c15d
--- /dev/null
+++ b/scripts/particle_balance_tracing
@@ -0,0 +1,41 @@
+#! /bin/tcsh -f
+
+if($?GNUPLOT_TMP) then
+    set tmpdir="$GNUPLOT_TMP/"
+else
+    set tmpdir=""
+endif
+setenv GNUPLOT_BATCH yes
+setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid noenhanced'
+setenv PRINT_PLOT particle_balance.ps
+rm -f ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.cmd
+echo 0 > ${tmpdir}GNUPLOT_COUNT
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+set isonuclear_species_names = ()
+foreach name ($neutral_species_names)
+    set name = `echo $name | sed 's/0$//'`
+    set isonuclear_species_names = ($isonuclear_species_names $name)
+end
+
+foreach is ($isonuclear_species_names)
+  2dt_tracing ntr_puff_$is ntr_core_$is ion_core_$is ntr_targ_pmp_$is ntr_wall_pmp_$is ntr_targ_spt_$is ntr_wall_spt_$is
+  2dt_tracing ion_core_$is ion_targ_$is ion_wall_$is src_ioniz_$is ion_dn/dt_$is
+end
+
+gnuplot ${tmpdir}gnuplot.cmd
+rm ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.*data ${tmpdir}gnuplot.cmd
diff --git a/scripts/plot_residuals b/scripts/plot_residuals
new file mode 100755
index 000000000..1b444cbf7
--- /dev/null
+++ b/scripts/plot_residuals
@@ -0,0 +1,20 @@
+#! /bin/tcsh -f
+
+if($?GNUPLOT_TMP) then
+    set tmpdir="$GNUPLOT_TMP/"
+else
+    set tmpdir=""
+endif
+setenv GNUPLOT_BATCH yes
+setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid noenhanced'
+setenv PRINT_PLOT residuals.ps
+rm -f ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.cmd
+echo 0 > ${tmpdir}GNUPLOT_COUNT
+
+resco
+resmo
+reshe
+reshi
+
+gnuplot ${tmpdir}gnuplot.cmd
+rm ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.*data ${tmpdir}gnuplot.cmd
diff --git a/scripts/replace_links b/scripts/replace_links
new file mode 100755
index 000000000..7ea72ed99
--- /dev/null
+++ b/scripts/replace_links
@@ -0,0 +1,63 @@
+#!/bin/tcsh
+
+# Recursively replace all symbolic links in the specified directory and subdirectories
+# with the real file or folder to which they are linked, keeping the same name of the original link.
+# Only works if the real linked file/folder currently exists.
+
+if ( $#argv >= 1 ) then
+    set dir = "$argv[1]"
+else
+    set dir = "$cwd"
+endif
+
+echo "Do you want to recursively replace ALL the symbolic links in the directory"
+echo "$dir"
+echo -n "and subdirectories with the original files/folder? (y/n) [n]"
+set REPLACE_LINKS = $<
+
+if ( "$REPLACE_LINKS" == "" ) then
+    set REPLACE_LINKS = "n"
+endif
+
+if ( "$REPLACE_LINKS" == "y" ) then
+
+    set links = (`find $dir -type l`)
+
+    if ( $#links == 0 ) then
+
+        echo "No symbolic links recursively found in the directory."
+        echo "$dir"
+        echo
+
+    else
+
+        foreach link ($links)
+            if ( -d "$link" ) then
+                set target = `realpath $link`
+                if ( -e "$target" ) then
+                    rm "$link"
+                    cp -a "$target" "$link"
+                    echo "Replaced link $link with folder $target"
+                endif
+            endif
+        end
+
+        foreach link ($links)
+            if ( ! -d "$link" ) then
+                set target = `realpath $link`
+                if ( -e "$target" ) then
+                    rm "$link"
+                    cp -p "$target" "$link"
+                    echo "Replaced link $link with file $target"
+                endif
+            endif
+        end
+
+    endif
+
+    echo "All symbolic links recursively found in the directory"
+    echo "$dir"
+    echo "were replaced, if the original linked file/folder existed."
+    echo
+
+endif
diff --git a/scripts/resco b/scripts/resco
index 585e78fba..fe27233f6 100755
--- a/scripts/resco
+++ b/scripts/resco
@@ -7,13 +7,13 @@ endif
 set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
 if (-s $solps_fluids) then
   setenv SOLPS_FLUIDS "`cat $solps_fluids`"
-  echo Set SOLPS_FLUIDS to $SOLPS_FLUIDS "(based on $solps_fluids)"
+  #echo Set SOLPS_FLUIDS to $SOLPS_FLUIDS "(based on $solps_fluids)"
 else
   setenv SOLPS_FLUIDS "`get_solps_fluids`"
-  echo Set SOLPS_FLUIDS to $SOLPS_FLUIDS "(based on log file)"
+  #echo Set SOLPS_FLUIDS to $SOLPS_FLUIDS "(based on log file)"
 endif
 set n=`echo $SOLPS_FLUIDS | wc -w`
-echo $n
+#echo $n
 if (-X zcat) then
   set ZCAT="zcat --force"
 else
@@ -29,4 +29,4 @@ $ZCAT $FILE | \
   awk 'BEGIN{ig=0}/data/&&ig==0{ig=1}/data/&&ig==2{printf "\n"}/^[^*]/&&ig>0{ig=2;printf "%s",$0}' | \
   resopt $argv | \
   awk '{printf "%s",$2; for (i=1;i<='$n';i++) printf " %s",$(i+2);printf "\n"}' >! ${tmpdir}PLOT_FROM_FILE
-  plot xlyplot$n $SOLPS_FLUIDS iteration 'norm of residual of continuity equation' `noquote_pwd 3`
+  plot xlyplot$n $SOLPS_FLUIDS iteration 'norm of residuals of continuity equation' $PWD
diff --git a/scripts/reshe b/scripts/reshe
new file mode 100755
index 000000000..e3d5f9fc1
--- /dev/null
+++ b/scripts/reshe
@@ -0,0 +1,23 @@
+#! /bin/tcsh -f
+if (-s b2mn.exe.dir/b2ftrace) then
+  set FILE=b2mn.exe.dir/b2ftrace
+else
+  set FILE=b2ftrace
+endif
+if (-X zcat) then
+  set ZCAT="zcat --force"
+else
+  set ZCAT="gzip --decompress --force --stdout"
+endif
+if($?GNUPLOT_TMP) then
+  set tmpdir="$GNUPLOT_TMP/"
+else
+  set tmpdir=""
+endif
+
+setenv PLOT_FROM_FILE "gnuplot.temp"
+$ZCAT $FILE | \
+  awk 'BEGIN{ig=0}/data/&&ig==0{ig=1}/data/&&ig==2{printf "\n"}/^[^*]/&&ig>0{ig=2;printf "%s",$0}' | \
+  resopt $argv | \
+  awk '{print $2,$8}' >! ${tmpdir}PLOT_FROM_FILE
+plot xlyplot '' iteration 'norm of residual of electron energy equation' $PWD
diff --git a/scripts/reshi b/scripts/reshi
new file mode 100755
index 000000000..964d65f24
--- /dev/null
+++ b/scripts/reshi
@@ -0,0 +1,23 @@
+#! /bin/tcsh -f
+if (-s b2mn.exe.dir/b2ftrace) then
+  set FILE=b2mn.exe.dir/b2ftrace
+else
+  set FILE=b2ftrace
+endif
+if (-X zcat) then
+  set ZCAT="zcat --force"
+else
+  set ZCAT="gzip --decompress --force --stdout"
+endif
+if($?GNUPLOT_TMP) then
+  set tmpdir="$GNUPLOT_TMP/"
+else
+  set tmpdir=""
+endif
+
+setenv PLOT_FROM_FILE "gnuplot.temp"
+$ZCAT $FILE | \
+  awk 'BEGIN{ig=0}/data/&&ig==0{ig=1}/data/&&ig==2{printf "\n"}/^[^*]/&&ig>0{ig=2;printf "%s",$0}' | \
+  resopt $argv | \
+  awk '{print $2,$9}' >! ${tmpdir}PLOT_FROM_FILE
+plot xlyplot '' iteration 'norm of residual of ion energy equation' $PWD
diff --git a/scripts/resmo b/scripts/resmo
index dfd1a35c6..018793021 100755
--- a/scripts/resmo
+++ b/scripts/resmo
@@ -1,4 +1,4 @@
-#! /bin/csh -f
+#! /bin/tcsh -f
 if (-s b2mn.exe.dir/b2ftrace) then
   set FILE=b2mn.exe.dir/b2ftrace
 else
@@ -7,13 +7,13 @@ endif
 set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
 if (-s $solps_fluids) then
   setenv SOLPS_FLUIDS "`cat $solps_fluids`"
-  echo Set SOLPS_FLUIDS to $SOLPS_FLUIDS "(based on $solps_fluids)"
+  #echo Set SOLPS_FLUIDS to $SOLPS_FLUIDS "(based on $solps_fluids)"
 else
   setenv SOLPS_FLUIDS "`get_solps_fluids`"
-  echo Set SOLPS_FLUIDS to $SOLPS_FLUIDS "(based on log file)"
+  #echo Set SOLPS_FLUIDS to $SOLPS_FLUIDS "(based on log file)"
 endif
 set n=`echo $SOLPS_FLUIDS | wc -w`
-echo $n
+#echo $n
 if (-X zcat) then
   set ZCAT="zcat --force"
 else
@@ -26,7 +26,7 @@ else
 endif
 setenv PLOT_FROM_FILE "gnuplot.temp"
 $ZCAT $FILE | \
-    awk 'BEGIN{ig=0}/data/&&ig==0{ig=1}/data/&&ig==2{printf "\n"}/^[^*]/&&ig>0{ig=2;printf "%s",$0}' | \
-    resopt $argv | \
-    awk '{printf "%s",$2; for (i=1;i<='$n';i++) printf " %s",$(i+'$n'+2);printf "\n"}' >! ${tmpdir}PLOT_FROM_FILE
-plot xlyplot$n $SOLPS_FLUIDS iteration 'norm of residual of momentum equation' $PWD
+  awk 'BEGIN{ig=0}/data/&&ig==0{ig=1}/data/&&ig==2{printf "\n"}/^[^*]/&&ig>0{ig=2;printf "%s",$0}' | \
+  resopt $argv | \
+  awk '{printf "%s",$2; for (i=1;i<='$n';i++) printf " %s",$(i+'$n'+2);printf "\n"}' >! ${tmpdir}PLOT_FROM_FILE
+  plot xlyplot$n $SOLPS_FLUIDS iteration 'norm of residuals of momentum equation' $PWD
diff --git a/scripts/save_initial_files b/scripts/save_initial_files
index 24d29282c..f944e261f 100755
--- a/scripts/save_initial_files
+++ b/scripts/save_initial_files
@@ -8,6 +8,7 @@
 [ -s b2time.nc ] && cp b2time.nc b2time.nc.i || echo > /dev/null
 [ -s b2batch.nc ] && cp b2batch.nc b2batch.nc.i || echo > /dev/null
 [ -s b2wall.nc ] && cp b2wall.nc b2wall.nc.i || echo > /dev/null
+[ -s b2neo.nc ] && cp b2neo.nc b2neo.nc.i || echo > /dev/null
 [ -s b2movies.nc ] && cp b2movies.nc b2movies.nc.i || echo > /dev/null
 [ -s eirenemovies.nc ] && cp eirenemovies.nc eirenemovies.nc.i || echo > /dev/null
 [ -s b2tallies.nc ] && cp b2tallies.nc b2tallies.nc.i || echo > /dev/null
diff --git a/scripts/summarize_run b/scripts/summarize_run
index 0c0553b96..3e17af615 100755
--- a/scripts/summarize_run
+++ b/scripts/summarize_run
@@ -1,12 +1,6 @@
 #! /bin/tcsh -f
 
-setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid noenhanced'
-setenv PRINT_PLOT resrest.ps ; resrest && rm -f gnuplot.data gnuplot.cmd
-setenv PRINT_PLOT resco.ps ; resco && rm -f gnuplot.data gnuplot.cmd PLOT_FROM_FILE
-setenv PRINT_PLOT resmo.ps ; resmo && rm -f gnuplot.data gnuplot.cmd PLOT_FROM_FILE
-setenv PRINT_PLOT rqahereg.ps ; rqahereg && rm -f gnuplot.data gnuplot.cmd PLOT_FROM_FILE
-setenv PRINT_PLOT energy_analysis_total.ps ; energy_analysis_total && rm -f gnuplot.data gnuplot.cmd PLOT_FROM_FILE
-setenv PRINT_PLOT density.ps ; density l && rm -f gnuplot.data gnuplot.cmd PLOT_FROM_FILE
 2d_profiles
 2d_plots
+plot_residuals
 last10