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cGENIE.Parameter_reference_guide.tex
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cGENIE.Parameter_reference_guide.tex
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% cGENIE namelist table
% Babette Hoogakker, November 2010
%
% ---------------------------------------------------------------------------------------------------------------------------------
% 10/12/05: tidying-up and minor fixes
% 11/03/24: tidying-up and minor fixes
% 18/12/01: JS updated ocean and sediment tracers
% ---------------------------------------------------------------------------------------------------------------------------------
\documentclass[english,10pt,twoside]{article}
\usepackage[paper=a4paper,portrait=true,margin=2.5cm,voffset=0pt,ignorehead,footnotesep=1cm]{geometry}
\usepackage{babel}
\usepackage{graphicx}
\usepackage{hyperref}
\usepackage{paralist}
\usepackage{caption}
\usepackage{float}
\linespread{1.1}
\setlength{\pltopsep}{2.5pt}
\setlength{\plparsep}{2.5pt}
\setlength{\partopsep}{2.5pt}
\setlength{\parskip}{2.5pt}
\usepackage{multirow}
\usepackage{wasysym}
\title{A brief guide to cGENIE parameters ('namelists')}
\author{Babette Hoogakker, Jun Shao}
\date{\today}
\begin{document}
%=================================================================================================================================
%=== BEGIN DOCUMENT ==============================================================================================================
%=================================================================================================================================
\maketitle
%---------------------------------------------------------------------------------------------------------------------------------
Parameters in the model are controlled via `namelists'. The default parameter values are listed in the following Tables. To effect a change in parameter value, the parameter name is simply assigned the new value, typically in the user config file.
Namelist settings can simply be edited in the user config file if they are already present, or a namelist assignment can be added (either under a relevant heading, or at the bottom of the file - it does not matter). The assignment takes the form:
namelist = value\\
Note that where the value is a string, the syntax is:\\
\texttt{namelist = `string'}
The syntax for logical (true/false) assignments is:\\
\texttt{namelist = .true.}
\texttt{(or namelist = .false.)}
For selecting (or de-selecting) atmospheric tracers, the syntax is: gm\_atm\_select\_n = .true.
where n is the index of the tracer as detailed in the Tables. For ocean and sediment (particulate) tracers, the namlist names take the same form except with `ocn' or `sed' in the namlist parameter name.\\
NOTE: If the number of selected tracers in the ocean is changed, so to must the value of GOLDSTEINNTRACSOPTS, which sets the array dimensions in the ocean and the number of tracers that must be advected, convected, and diffused in the
ocean. For example, for 16 selected ocean tracers (including temperature and salinity), add the line:
GOLDSTEINNTRACSOPTS = `\$(DEFINE)GOLDSTEINNTRACS=16'\\
For setting initial values of atmospheric tracers, the syntax is:
gm\_atm\_init\_n = 278.0E-6\\
where again, n is the index of the tracer (detailed below). Ocean tracers are initialized similarly.\\
NOTE: There is no user-configurable initialization of deep-sea sediment composition (in SEDGEM).\\
\begin{tabular}{ | l | l | l | l | l | l | l |}
\hline
& &\multicolumn{2}{|l|}{SELECTION} &\multicolumn{2}{|l|}{INITILIZATION} & \\
& &\multicolumn{2}{|l|}{gm\_atm\_select\_n} &\multicolumn{2}{|l|}{ac\_atm\_init\_n} & \\ \hline
TRACER & INDEX & DEFAULT & UNITS & DEFAULT & UNITS & TRACER \\
MNEMONIC & n & VALUE & & VALUE & & DESCRIPTION \\ \hline
\multicolumn{7}{|l|}{ATMOSPHERIC (GASEOUS) TRACERS} \\ \hline
ia\_temp & 1 & .true. & logical & n/a (0.0) & K & surface air temperature \\ \hline
ia\_humidity & 2 & .true. & logical & n/a (0.0) & & specific humidity \\ \hline
ia\_pCO2 & 3 & .false. & logical & 0.0 & atm & carbon dioxide (CO$_{2}$) \\ \hline
ia\_pCO2\_13C & 4 & .false. & logical & 0.0 & \permil & d$^{13}$C of CO$_{2}$ \\ \hline
ia\_pCO2\_14C & 5 & .false. & logical& 0.0 & \permil & d$^{14}$C of CO$_{2}$ \\ \hline
ia\_pO2 & 6 & .false. & logical & 0.0 & atm & oxygen (O$_{2}$) \\ \hline
ia\_pO2\_18O & 7 & .false. & logical & 0.0 & \permil & $^{18}$O of O$_{2}$ \\ \hline
ia\_pN2 & 8 & .false. & logical & 0.0 & atm & nitrogen (N$_{2}$) \\ \hline
ia\_pN2\_15N & 9 & .false. & logical & 0.0 & \permil & $^{15}$N of N$_{2}$ \\ \hline
ia\_pCH4 & 10 & .false. & logical & 0.0 & atm & methane (CH$_{4}$) \\ \hline
ia\_pCH4\_13C & 11 & .false. & logical & 0.0 & \permil & $^{13}$C of CH$_{4}$ \\ \hline
ia\_pCH4\_14C & 12 & .false. & logical & 0.0 & \permil & $^{14}$C of CH$_{4}$ \\ \hline
ia\_pSF6 & 13 & .false. & logical & 0.0 & atm & sulphur hexafloride (SF6) \\ \hline
ia\_pN2O & 14 & .false. & logical & 0.0 & atm & nitrous oxide (N$_{2}$O) \\ \hline
ia\_pN2O\_15N & 15 & .false. & logical & 0.0 & \permil & $^{15}$N of N$_{2}$O \\ \hline
ia\_pH2S & 16 & .false. & logical & 0.0 & atm & hydrogen sulphide (H$_{2}$S) \\ \hline
ia-pH2S\_34S & 17 & .false. & logical & 0.0 & \permil & $^{34}$S of H$_{2}$S \\ \hline
ia\_pCFC11 & 18 & .false. & logical & 0.0 & atm & CFC-11 \\ \hline
ia\_pCFC12 & 19 & .false. & logical & 0.0 & atm & CFC-12 \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l | l | l | l |}
\hline
& &\multicolumn{2}{|l|}{SELECTION} &\multicolumn{2}{|l|}{INITILIZATION} & \\
& &\multicolumn{2}{|l|}{gm\_ocn\_select\_n} &\multicolumn{2}{|l|}{bg\_ocn\_init\_n} & \\ \hline
TRACER & INDEX & DEFAULT & UNITS & DEFAULT & UNITS & TRACER \\
MNEMONIC & n & VALUE & & VALUE & & DESCRIPTION \\ \hline
\multicolumn{7}{|l|}{OCEAN (DISSOLVED) TRACERS} \\ \hline
io\_temp & 1 & .true. & logical & n/a (0.0) & K & temperature \\ \hline
io\_sal & 2 & .true. & logical & n/a (0.0) & PSU & salinity \\ \hline
io\_DIC & 3 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved inorganic carbon (DIC) \\ \hline
io\_DIC\_13C & 4 & .false. & logical & 0.0 & \permil & d$^{13}$C of DIC \\ \hline
io\_DIC\_14C & 5 & .false. & logical & 0.0 & \permil & d$^{14}$C of DIC \\ \hline
io\_NO3 & 6 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved nitrate (NO$_{3}$) \\ \hline
io\_NO3\_15N & 7 & .false. & logical & 0.0 & \permil & d$^{15}$N of NO$_{3}$ \\ \hline
io\_PO4 &8 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved phosphate (PO$_{4}$) \\ \hline
io\_O2 & 10 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved oxygen (O$_{2}$) \\ \hline
io\_O2\_18O & 11 & .false. & logical & 0.0 & \permil & d$^{18}$O of O$_{2}$ \\ \hline
io\_ALK & 12 & .false. & logical & 0.0 & mol kg$^{-1}$ & alkalinity (ALK) \\ \hline
io\_SiO2 & 13 & .false. & logical & 0.0 & mol kg$^{-1}$ & aqueous silicic acid (H$_{4}$SiO$_{4}$) \\ \hline
io\_SiO2\_30Si & 14 & .false. & logical & 0.0 & \permil & d$^{30}$Si of H$_{4}$SiO$_{4}$ \\ \hline
io\_DOM\_C & 15 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved organic matter (DOM); C \\ \hline
io\_DOM\_C\_13C & 16 & .false. & logical & 0.0 & \permil & d$^{13}$C of DOM-C \\ \hline
io\_DOM\_C\_14C & 17 & .false. & logical & 0.0 & \permil & d$^{14}$C of DOM-C \\ \hline
io\_DOM\_N & 18 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved organic matter; nitrogen \\ \hline
io\_DOM\_N\_15N & 19 & .false. & logical & 0.0 & \permil & d$^{15}$N of DOM-N \\ \hline
io\_DOM\_P & 20 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved organic matter; P \\ \hline
io\_DOM\_Cd & 21 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved organic matter; cadmium \\ \hline
io\_DOM\_Cd\_114Cd & 52 & .false. & logical & 0.0 & \permil & d$^{114}$Cd of DOM-Cd \\ \hline
io\_DOM\_Fe & 22 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved organic matter; iron \\ \hline
io\_DOM\_Fe\_56Fe & 81 & .false. & logical & 0.0 & \permil & d$^{56}$Fe of DOM-Fe \\ \hline
io\_DOM\_I & 94 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved organic matter; iodine \\ \hline
io\_RDOM\_C & 67 & .false. & logical & 0.0 & mol kg$^{-1}$ & R dissolved organic matter (RDOM); C \\ \hline
io\_RDOM\_C\_13C & 68 & .false. & logical & 0.0 & \permil & d$^{13}$C of RDOM-C \\ \hline
io\_RDOM\_C\_14C & 69 & .false. & logical & 0.0 & \permil & d$^{14}$C of RDOM-C \\ \hline
io\_RDOM\_N & 70 & .false. & logical & 0.0 & mol kg$^{-1}$ & R dissolved organic matter; nitrogen \\ \hline
io\_RDOM\_N\_15N & 71 & .false. & logical & 0.0 & \permil & d$^{15}$N of RDOM-N \\ \hline
io\_RDOM\_P & 72 & .false. & logical & 0.0 & mol kg$^{-1}$ & R dissolved organic matter; P \\ \hline
io\_RDOM\_Cd & 73 & .false. & logical & 0.0 & mol kg$^{-1}$ & R dissolved organic matter; cadmium \\ \hline
io\_RDOM\_Cd\_114Cd & 74 & .false. & logical & 0.0 & \permil & d$^{114}$Cd of RDOM-Cd \\ \hline
io\_RDOM\_Fe & 75 & .false. & logical & 0.0 & mol kg$^{-1}$ & R dissolved organic matter; iron \\ \hline
io\_RDOM\_Fe\_56Fe & 82 & .false. & logical & 0.0 & \permil & d$^{56}$Fe of RDOM-Fe \\ \hline
io\_RDOM\_I & 95 & .false. & logical & 0.0 & mol kg$^{-1}$ & R dissolved organic matter; iodine \\ \hline
io\_CH4 & 25 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved methane (CH$_{4}$) \\ \hline
io\_CH4\_13C & 26 & .false. & logical & 0.0 & \permil & d$^{13}$C of CH$_{4}$ \\ \hline
io\_CH4\_14C & 27 & .false. & logical & 0.0 & \permil & d$^{14}$C of CH$_{4}$ \\ \hline
io\_NH4 & 28 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved ammonium (NH$_{4}$) \\ \hline
io\_NH4\_15N & 29 & .false. & logical & 0.0 & \permil & d$^{15}$N of NH$_{4}$ \\ \hline
io\_N2 & 30 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved nitrogen (N$_{2}$) \\ \hline
io\_N2\_15N & 31 & .false. & logical & 0.0 & \permil & d$^{15}$N of N$_{2}$ \\ \hline
io\_N2O & 32 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved nitrous oxide (N$_{2}$O) \\ \hline
io\_N2O\_15N & 33 & .false. & logical & 0.0 & \permil & d$^{15}$N of N$_{2}$O \\ \hline
io\_Cd & 34 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved cadmium (Cd) \\ \hline
io\_Cd\_114 & 51 & .false. & logical & 0.0 & \permil & d$^{114}$Cd of dissolved cadmium (Cd) \\ \hline
io\_Ca & 35 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved calcium (Ca) \\ \hline
io\_Ca\_44 & 76 & .false. & logical & 0.0 & \permil & d$^{44}$Ca of dissolved calcium (Ca) \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l | l | l | l |}
\hline
& &\multicolumn{2}{|l|}{SELECTION} &\multicolumn{2}{|l|}{INITILIZATION} & \\
& &\multicolumn{2}{|l|}{gm\_ocn\_select\_n} &\multicolumn{2}{|l|}{bg\_ocn\_init\_n} & \\ \hline
TRACER & INDEX & DEFAULT & UNITS & DEFAULT & UNITS & TRACER \\
MNEMONIC & n & VALUE & & VALUE & & DESCRIPTION \\ \hline
\multicolumn{7}{|l|}{OCEAN (DISSOLVED) TRACERS continued} \\ \hline
io\_B & 36 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved boron (B) \\ \hline
io\_F & 37 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved florine (F) \\ \hline
io\_SO4 & 38 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved sulphate (SO$_{4}$) \\ \hline
io\_SO4\_34S & 39 & .false. & logical & 0.0 & \permil & d$^{34}$S of SO$_{4}$ \\ \hline
io\_H2S & 40 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved hydrogen sulphide (H$_{2}$) \\ \hline
io\_H2S\_34S & 41 & .false. & logical & 0.0 & \permil & d$^{34}$S of H$_{2}$S \\ \hline
io\_Ge & 42 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved germanium (Ge) \\ \hline
io\_Mo & 77 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved molybdenum (Mo) \\ \hline
io\_Mo\_98Mo & 78 & .false. & logical & 0.0 & \permil & d$^{98}$Mo of Mo\\ \hline
io\_231Pa & 43 & .false. & logical & 0.0 & mol kg$^{-1}$ & $^{231}$Pa \\ \hline
io\_230Th & 44 & .false. & logical & 0.0 & mol kg$^{-1}$ & $^{230}$Th \\ \hline
io\_CFC11 & 45 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved CFC-11 \\ \hline
io\_CFC12 & 46 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved CFC-12 \\ \hline
io\_Mg & 50 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved magnesium (Mg) \\ \hline
io\_Li & 53 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved lithium (Li) \\ \hline
io\_Li\_7 & 54 & .false. & logical & 0.0 & \permil & $^{7}$Li of Li \\ \hline
io\_Nd & 55 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved neodymium (Nd) \\ \hline
io\_Nd\_144 & 56 & .false. & logical & 0.0 & \permil & $^{144}$Nd of Nd \\ \hline
io\_SF6 & 47 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved sulphur hexafloride (SF6) \\ \hline
io\_colr & 48 & .false. & logical & 0.0 & n/a & RED numerical (color) tracer \\ \hline
io\_colb & 49 & .false. & logical & 0.0 & n/a & BLUE numerical (color) tracer \\ \hline
io\_col0 & 57 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col1 & 58 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col2 & 59 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col3 & 60 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col4 & 61 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col5 & 62 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col6 & 63 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col7 & 64 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col8 & 65 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_col9 & 66 & .false. & logical & 0.0 & n/a & numerical (color) tracer \\ \hline
io\_Fe & 9 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved iron III (Fe) \\ \hline
io\_Fe2 & 83 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved iron II (Fe) \\ \hline
io\_L & 24 & .false. & logical & 0.0 & mol kg$^{-1}$ & free ligand (iron binding) \\ \hline
io\_L2 & 84 & .false. & logical & 0.0 & mol kg$^{-1}$ & free ligand 2 (iron binding) \\ \hline
io\_FeL & 23 & .false. & logical & 0.0 & mol kg$^{-1}$ & ligand-bound Fe \\ \hline
io\_FeL2 & 85 & .false. & logical & 0.0 & mol kg$^{-1}$ & ligand2-bound Fe \\ \hline
io\_Fe\_56Fe & 86 & .false. & logical & 0.0 & \permil & $^{56}$Fe of dissolved iron III (Fe) \\ \hline
io\_Fe2\_56 & 87 & .false. & logical & 0.0 & \permil & $^{56}$Fe of dissolved iron II (Fe) \\ \hline
io\_L\_56 & 88 & .false. & logical & 0.0 & \permil & $^{56}$Fe of free ligand (iron binding) \\ \hline
io\_L2\_56 & 89 & .false. & logical & 0.0 & \permil & $^{56}$Fe of free ligand 2 (iron binding) \\ \hline
io\_TDFe\_56Fe & 90 & .false. & logical & 0.0 & mol kg$^{-1}$ & total dissolved Fe \\ \hline
io\_TDFe2\_56 & 91 & .false. & logical & 0.0 & \permil & $^{56}$Fe of total dissolved Fe \\ \hline
io\_TL & 42 & .false. & logical & 0.0 & mol kg$^{-1}$ & total dissolved ligand \\ \hline
io\_I & 92 & .false. & logical & 0.0 & mol kg$^{-1}$ & iodide \\ \hline
io\_IO3 & 93 & .false. & logical & 0.0 & mol kg$^{-1}$ & iodate \\ \hline
io\_Ba & 96 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved barium (Ba) \\ \hline
io\_Ba\_138Ba & 97 & .false. & logical & 0.0 & \permil & $^{138}$Ba of Ba \\ \hline
io\_Sr & 98 & .false. & logical & 0.0 & mol kg$^{-1}$ & dissolved strontium (Sr) \\ \hline
io\_Sr\_87Sr & 99 & .false. & logical & 0.0 & \permil & $^{87}$Sr of Sr \\ \hline
io\_Sr\_88Sr & 100 & .false. & logical & 0.0 & \permil & $^{88}$Sr of Sr \\ \hline
io\_H2O & 101 & .false. & logical & 0.0 & mol kg$^{-1}$ & water! \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l | l | l | l |}
\hline
& &\multicolumn{2}{|l|}{SELECTION} &\multicolumn{2}{|l|}{INITILIZATION} & \\
& &\multicolumn{2}{|l|}{gm\_sed\_select\_n} &\multicolumn{2}{|l|}{} & \\ \hline
TRACER & INDEX & DEFAULT & UNITS & DEFAULT & UNITS & TRACER \\
MNEMONIC & n & VALUE & & VALUE & & DESCRIPTION \\ \hline
\multicolumn{7}{|l|}{SEDIMENT (SOLID, PARTICULATE) TRACERS} \\ \hline
is\_NULL1 & 1 & .false. & logical & n/a & n/a & dummy index \\ \hline
is\_NULL2 & 2 & .false. & logical & n/a & n/a & dummy index \\ \hline
is\_POC & 3 & .false. & logical & 0.0 & wt\% & particulate organic carbon (POC) \\ \hline
is\_POC\_13C & 4 & .false. & logical & 0.0 & \permil & d$^{13}$C of POC \\ \hline
is\_POC\_14C & 5 & .false. & logical & 0.0 & \permil & d$^{14}$C of POC \\ \hline
is\_PON & 6 & .false. & logical & 0.0 & wt\% & particulate organic nitrogen (PON) \\ \hline
is\_PON\_15N & 7 & .false. & logical & 0.0 & \permil & d$^{15}$N of PON \\ \hline
is\_POP & 8 & .false. & logical & 0.0 & wt\% & particulate organic phosphate \\
& & & & & & (POP) \\ \hline
is\_POCd & 9 & .false. & logical & 0.0 & wt\% & particulate organic cadmium \\
& & & & & & (POCd) \\ \hline
is\_POCd\_114Cd & 43 & .false. & logical & 0.0 & \permil & d$^{114}$Cd of POC inorporated \\
& & & & & & cadmium \\ \hline
is\_POFe & 10 & .false. & logical & 0.0 & wt\% & particulate organic iron (POFe) \\ \hline
is\_POI & 79 & .false. & logical & 0.0 & wt\% & particulate organic iodine (POI) \\ \hline
is\_POBa & 80 & .false. & logical & 0.0 & wt\% & particulate organic barium (POBa) \\ \hline
is\_POBa\_138Ba & 81 & .false. & logical & 0.0 & wt\% &d$^{138}$Ba pf particulate organic Ba (POBa) \\ \hline
is\_POM\_231Pa & 11 & .false. & logical & 0.0 & wt\% & POM scavenged $^{231}$Pa \\ \hline
is\_POM\_230Th & 12 & .false. & logical & 0.0 & wt\% & POM scavenged $^{230}$Th \\ \hline
is\_POM\_Fe & 13 & .false. & logical & 0.0 & wt\% & POM scavenged Fe \\ \hline
is\_POM\_Fe\_56Fe & 75 & .false. & logical & 0.0 & \permil & d$^{56}$Fe of POM scavenged Fe\\ \hline
is\_POM\_Nd & 47 & .false. & logical & 0.0 & wt\% & POM scavenged Nd \\ \hline
is\_POM\_Nd\_144Nd & 48 & .false. & logical & 0.0 & \permil & POM scavenged $^{144}$Nd \\ \hline
is\_POM\_MoS2 & 58 & .false. & logical & 0.0 & wt\% & POM scavenged MoS2 \\ \hline
is\_POM\_MoS2\_98Mo & 59 & .false. & logical & 0.0 & \permil & POM scavenged $^{98}$Mo \\ \hline
is\_POM\_MoS2\_34S & 60 & .false. & logical & 0.0 & \permil & POM scavenged $^{34}$S \\ \hline
is\_POM\_S & 73 & .false. & logical & 0.0 & wt\% & POM scavenged S \\ \hline
is\_POM\_S\_34S & 74 & .false. & logical & 0.0 & \permil & d$^{34}$S of POM scavenged S\\ \hline
is\_POM\_BaSO4 & 82 & .false. & logical & 0.0 & wt\% & POM scavenged BaSO4 \\ \hline
is\_POM\_BaSO4\_138Ba & 83 & .false. & logical & 0.0 & \permil & d$^{138}$Ba of POM scavenged BaSO4\\ \hline
is\_CaCO3 & 14 & .false. & logical & 0.0 & wt\% & calcium carbonate (CaCO$_{3}$) \\ \hline
is\_CaCO3\_13C & 15 & .false. & logical & 0.0 & \permil & d$^{13}$C of CaCO$_{3}$ \\ \hline
is\_CaCO3\_14C & 16 & .false. & logical & 0.0 & \permil & d$^{14}$C of CaCO$_{3}$ \\ \hline
is\_CaCO3\_18O & 17 & .false. & logical & 0.0 & \permil & d$^{18}$O of CaCO$_{3}$ \\ \hline
is\_CaCO3\_44Ca & 17 & .false. & logical & 0.0 & \permil & d$^{44}$Ca of CaCO$_{3}$ \\ \hline
is\_CdCO3 & 18 & .false. & logical & 0.0 & wt\% & CaCO$_{3}$ incorporated cadmium \\ \hline
is\_CdCO3\_114Cd & 44 & .false. & logical & 0.0 & \permil & d$^{114}$Cd of CaCO$_{3}$ incorporated \\
& & & & & & cadium \\ \hline
is\_LiCO3 & 45 & .false. & logical & 0.0 & wt\% & CaCO$_{3}$ incorporated lithium \\ \hline
is\_LiCO3\_7Li & 46 & .false. & logical & 0.0 & \permil & d$^{7}$Li of CaCO$_{3}$ incorporated \\
& & & & & & lithium \\ \hline
is\_CaCO3\_231Pa & 19 & .false. & logical & 0.0 & wt\% & CaCO$_{3}$ scavenged $^{231}$Pa \\ \hline
is\_CaCO3\_230Th & 20 & .false. & logical & 0.0 & wt\% & CaCO$_{3}$ scavenged $^{230}$Th \\ \hline
is\_CaCO3\_Fe & 21 & .false. & logical & 0.0 & wt\% & CaCO$_{3}$ scavenged Fe \\ \hline
is\_CaCO3\_Fe\_56Fe & 76 & .false. & logical & 0.0 & wt\% & d$^{56}$Fe of CaCO3 scavenged Fe \\ \hline
is\_CaCO3\_Nd & 49 & .false. & logical & 0.0 & wt\% & CaCO$_{3}$ scavenged Nd \\ \hline
is\_CaCO3\_Nd\_144Nd & 50 & .false. & logical & 0.0 & \permil & CaCO$_{3}$ scavenged $^{144}$Nd \\ \hline
is\_CaCO3\_MoS2 & 61 & .false. & logical & 0.0 & wt\% & CaCO3 scavenged MoS2 \\ \hline
is\_CaCO3\_MoS2\_98Mo & 62 & .false. & logical & 0.0 & \permil & CaCO3 scavenged $^{98}$Mo \\ \hline
is\_CaCO3\_MoS2\_34S & 63 & .false. & logical & 0.0 & \permil & CaCO3 scavenged $^{34}$S \\ \hline
is\_SrCO3 & 84 & .false. & logical & 0.0 & wt\% & CaCO3 incorporated strontium \\ \hline
is\_SrCO3\_87Sr & 85 & .false. & logical & 0.0 & \permil & d$^{87}$Sr of SrCO$_{3}$ \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l | l | l | l |}
\hline
& &\multicolumn{2}{|l|}{SELECTION} &\multicolumn{2}{|l|}{INITILIZATION} & \\
& &\multicolumn{2}{|l|}{gm\_sed\_select\_n} &\multicolumn{2}{|l|}{} & \\ \hline
TRACER & INDEX & DEFAULT & UNITS & DEFAULT & UNITS & TRACER \\
MNEMONIC & n & VALUE & & VALUE & & DESCRIPTION \\ \hline
\multicolumn{7}{|l|}{SEDIMENT (SOLID, PARTICULATE) TRACERS continued} \\ \hline
is\_SrCO3\_88Sr & 86 & .false. & logical & 0.0 & \permil & d$^{88}$Sr of SrCO$_{3}$ \\ \hline
is\_det & 22 & .false. & logical & 0.0 & wt\% & detrital (refractory) material \\ \hline
is\_det\_Li & 55 & .false. & logical & 0.0 & wt\% & detrital scavanged lithium \\ \hline
is\_det\_Li\_7Li & 56 & .false. & logical & 0.0. & \permil & detrital scavenged $^{7}$Li \\ \hline
is\_det\_231Pa & 23 & .false. & logical & 0.0 & wt\% & detrital scavenged $^{231}$Pa \\ \hline
is\_det\_230Th & 24 & .false. & logical & 0.0 & wt\% & detrital scavenged $^{230}$Th \\ \hline
is\_det\_Fe & 25 & .false. & logical & 0.0 & wt\% & detrital scavenged Fe \\ \hline
is\_det\_Fe\_56Fe & 77 & .false. & logical & 0.0 & wt\% & d$^{56}$Fe of detrital scavenged Fe \\ \hline
is\_det\_Nd & 51 & .false. & logical & 0.0 & wt\% & detrital scavenged Nd \\ \hline
is\_det\_Nd\_144Nd & 52 & .false. & logical & 0.0 & \permil & detrital scavenged $^{144}$Nd \\ \hline
is\_det\_MoS2 & 64 & .false. & logical & 0.0 & wt\% & det scavenged MoS2 \\ \hline
is\_det\_MoS2\_98Mo & 65 & .false. & logical & 0.0 & \permil & det scavenged $^{98}$Mo \\ \hline
is\_det\_MoS2\_34S & 66 & .false. & logical & 0.0 & \permil & det scavenged $^{34}$S \\ \hline
is\_opal & 26 & .false. & logical & 0.0 & wt\% & opal \\ \hline
is\_opal\_30Si & 27 & .false. & logical & 0.0 & \permil & d$^{30}$Si of opal \\ \hline
is\_opal\_Ge & 28 & .false. & logical & 0.0 & wt\% & opal incorporated germanium \\ \hline
is\_opal\_231Pa & 29 & .false. & logical & 0.0 & wt\% & opal scavenged $^{231}$Pa \\ \hline
is\_opal\_230Th & 30 & .false. & logical & 0.0 & wt\% & opal scavenged $^{230}$Th \\ \hline
is\_opal\_Fe & 31 & .false. & logical & 0.0 & wt\% & opal scavenged Fe \\ \hline
is\_opal\_Fe\_56Fe & 78 & .false. & logical & 0.0 & wt\% & d$^{56}$Fe of opal scavenged Fe \\ \hline
is\_opal\_Nd & 53 & .false. & logical & 0.0 & wt\% & opal scavenged Nd \\ \hline
is\_opal\_Nd\_144Nd & 54 & .false. & logical & 0.0 & \permil & opal scavenged $^{144}$Nd \\ \hline
is\_opal\_MoS2 & 67 & .false. & logical & 0.0 & wt\% & opal scavenged MoS2 \\ \hline
is\_opal\_MoS2\_98Mo & 68 & .false. & logical & 0.0 & \permil & opal scavenged $^{98}$Mo \\ \hline
is\_opal\_MoS2\_34S & 69 & .false. & logical & 0.0 & \permil & opal scavenged $^{34}$S \\ \hline
is\_ash & 32 & .false. & logical & 0.0 & wt\% & ash \\ \hline
is\_POC\_frac2 & 33 & .false. & logical & 0.0 & (ratio) & n/a \\ \hline
is\_CaCO3\_frac2 & 34 & .false. & logical & 0.0 & (ratio) & n/a \\ \hline
is\_opal\_frac2 & 35 & .false. & logical & 0.0 & (ratio) & n/a\\ \hline
% \multicolumn{7}{|l|}{1- The ocean is initialized with no particulates in the ocean. Sediment composition is initialized with 100 wt percent ash in the surface sediment layer} & \\
%& &\multicolumn{7}{|l|}{and 100 wt percent detrital material in the underlying stack layers, so as to enable the construction of a constant sedimentation rate chronology (based)} & \\
%& &\multicolumn{7}{|l|}{on locating the consequential ash `peak'). These values are hard-coded} & \\
%& &\multicolumn{7}{|l|}{(in:~/genie/genie-sedgem/src/fortran/sedgem\_data.f90).} \\ \hline
% \multicolumn{7}{|l|}{1- The ocean is initialized with no particulates in the ocean. Sediment composition is initialized with 100 wt percent ash in the surface sediment layer
%and 100 wt percent detrital material in the underlying stack layers, so as to enable the construction of a constant sedimentation rate chronology (based
%on locating the consequential ash `peak'). These values are hard-coded
%(in:~/genie/genie-sedgem/src/fortran/sedgem\_data.f90).\\
%2- The units are given for sediment composition. Particulate tracers in the ocean are in units of mol kg$^{-1}$ and per mil (\permil), corresponding to
%sediment units of wt percent and \permil, respectively.} \\ \hline
is\_CaCO3\_age & 36 & .false. & logical & 0.0 & years & CaCO$_{3}$ numerical age tracer \\ \hline
is\_ash\_age & 70 & .false. & logical & 0.0 & years & det numerical age tracer \\ \hline
is\_POC\_size & 87 & .false. & logical & 0.0 & n/a & n/a \\ \hline
is\_CaCO3\_red & 71 & .false. & logical & 0.0 & n/a &red numerical (color) tracer \\ \hline
is\_CaCO3\_blue & 72 & .false. & logical & 0.0 & n/a &blue numerical (color) tracer \\ \hline
is\_foram\_p\_13C & 37 & .false. & logical & 0.0 & \permil & planktic foraminiferal CaCO$_{3}$ d$^{13}$C \\ \hline
is\_foram\_p\_14C & 38 & .false. & logical & 0.0 & \permil & planktic foraminiferal CaCO$_{3}$ d$^{14}$C \\ \hline
is\_foram\_p\_18O & 39 & .false. & logical & 0.0 & \permil & planktic foraminiferal CaCO$_{3}$ d$^{18}$O \\ \hline
is\_foram\_b\_13C & 40 & .false. & logical & 0.0 & \permil & benthic foraminiferal CaCO$_{3}$ d$^{13}$C \\ \hline
is\_foram\_b\_14C & 41 & .false. & logical & 0.0 & \permil & benthic foraminiferal CaCO$_{3}$ d$^{14}$C \\ \hline
is\_foram\_b\_18O & 42 & .false. & logical & 0.0 & \permil & benthic foraminiferal CaCO$_{3}$ d$^{18}$O \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{TIME STEPPING} \\ \hline
ma\_koverall\_total & & (INTEGER) & overall model number of time-steps$^{1}$\\ \hline
ma\_genie\_timestep & & s & length of each time-step \\ \hline
bg\_par\_misc\_t\_start & 0.0 & years & simulation start year \\ \hline
bg\_par\_misc\_t\_runtime & 1001.0 & years & simulation run length$^{2}$\\ \hline
bg\_ctrl\_misc\_t\_BP & .false. & (LOGICAL) & simulation time scale as years Before Present \\ \hline
sg\_par\_misc\_t\_runtime & 1001.0 & yr & simulation run length1 \\ \hline
ma\_katm\_loop & 1 $^{3}$ & (INTEGER?) & \\ \hline
ma\_ksic\_loop & 5 & (INTEGER) & relative frequency of updating of sea-ice \\ \hline
ma\_kocn\_loop & 5 & (INTEGER) & relative frequency of updating of ocean \\ \hline
ma\_conv\_kocn\_katchem & 5 & (INTEGER) & time-stepping ratio between ATCHEM and ocean \\ \hline
ma\_conv\_kocn\_ksedgem & 50 & (INTEGER) & time-stepping ratio between SEDGEM and ocean \\ \hline
ma\_conv\_kocn\_kbiogem & 5 & (INTEGER) & time-stepping ratio between BIOGEM and ocean \\ \hline
ma\_conv\_kocn\_krokgem & 5 & (INTEGER) & time-stepping ratio between ROKGEM and ocean \\ \hline
ma\_dt\_write & 720 & (INTEGER) & default interval of output $^{4}$ \\ \hline
rg\_par\_screen\_output & 200 & (INTEGER) & ROKGEM reporting frequency \\
& & & (in ROKGEM time-steps) \\ \hline
ea\_3 & 1000 & (INTEGER) & frequency of 'health check' diagnostics reporting$^{5}$\\ \hline
go\_3 & 1000 & (INTEGER) & frequency of 'health check' diagnostics reporting5 \\ \hline
gs\_3 & 1000 & (INTEGER) & frequency of 'health check' diagnostics reporting5 \\ \hline
ea\_5 & 100 & (INTEGER) & 'time series' frequency5 \\ \hline
go\_5 & 100 & (INTEGER) & 'time series' frequency5 \\ \hline
gs\_5 & 100 & (INTEGER) & 'time series' frequency5 \\ \hline
ea\_6 & 50000 & (INTEGER) & 'average' frequency5 \\ \hline
go\_6 & 50000 & (INTEGER) & 'average' frequency5 \\ \hline
gs\_6 & 50000 & (INTEGER) & 'average' frequency5 \\ \hline
\end{tabular}
$^{1}$ This parameter sets the 'aging' of pre-existing (i.g., restart) sedimentary material consistent with the duration of a run. It must be equal to the run length of everything else. Obviously ;)\\
$^{2}$ The length of each time-step is determined by the value of ma\_genie\_timestep (seconds), and is defined in genie\_eb\_go\_gs\_ac\_bg\_sg.config by: ma\_genie\_timestep = 365.25*24.0/500 * 3600.0, i.e., ma\_genie\_timestep=63115.2, giving 500 time-steps per year.\\
$^{3}$ This means that the atmosphere (the EMBM in this case) is updated every GENIE time-step.\\
$^{4}$ In multiples of the GENIE time-step.
$^{5}$ When set equal to ma\_genie\_timestep+1, this effectively disables this feature.\\
\begin{tabular}{ | l | l | l |}
\hline
\multicolumn{3}{|l|}{ARRAY SPECIFICATION: GRID} \\ \hline
NAME & DEFAULT VALUE & DESCRIPTION \\ \hline
GENIENXOPTS & `\$(DEFINE)GENIENX=36' & x (i) direction resolution in atmosphere \\ \hline
GENIENYOPTS & `\$(DEFINE)GENIENY=36' & y (j) direction resolution in atmosphere \\ \hline
GENIENLOPTS & `\$(DEFINE)GENIENL=1' & number of levels in atmosphere \\ \hline
GOLDSTEINNLONSOPTS & `\$(DEFINE)GOLDSTEINNLONS=36' & x (i) direction resolution in ocean \\ \hline
GOLDSTEINNLATSOPTS & `\$(DEFINE)GOLDSTEINNLATS=36' & y (j) direction resolution in oxcean \\ \hline
GOLDSTEINNLEVSOPTS & `\$(DEFINE)GOLDSTEINNLEVS=8' & number of (depth) levels in ocean \\ \hline
SEDGEMNLONSOPTS & `\$(DEFINE)SEDGEMNLONS=36' & x (i) direction resolution in sediments \\ \hline
SEDGEMNLATSOPTS & `\$(DEFINE)SEDGEMNLATS=36' & y (j) direction resolution in sediments \\ \hline
ROKGEMNLONSOPTS & `\$(DEFINE)ROKGEMNLONS=36' & x (i) direction resolution on land surface \\ \hline
ROKGEMNLATSOPTS & `\$(DEFINE)ROKGEMNLATS=36' & y (j) direction resolution on land surface \\ \hline
gm\_par\_grid\_lon\_offset & -260.0 & assumed longitudinal offset of the grid for \\
& & ATCHEM, BIOGEM, SEDGEM 2- and \\
& & 3-D field data saving \\
& & (units of degrees East) \\ \hline
\multicolumn{3}{|l|}{ARRAY SPECIFICATION: NUMBER OF TRACERS} \\ \hline
GOLDSTEINNTRACSOPTS & `\$(DEFINE)GOLDSTEINNTRACS=10' & number of dissolved tracers in ocean \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l |}
\hline
NAME & DEFAULT VALUE & DESCRIPTION \\ \hline
\multicolumn{3}{|l|}{RUN RE-START SPECIFICATION} \\ \hline
ea\_7 & `n' & new/continuing run? (i.e., use restart?) \\ \hline
ea\_rstdir\_name & `\$RUNTIME\_ROOT & \\
& /genie-embm/data/input' & restart (input) directory \\ \hline
ea\_35 & `tmp.1' & input ASCII restart file name \\ \hline
ea\_29 & `spn' & output file number (restart file string) \\ \hline
go\_7 & `n' & new/continuing run? (i.e., use restart?) \\ \hline
go\_rstdir\_name & `\$RUNTIME\_ROOT & \\
& /genie-goldsteindata/input' & restart (input) directory \\ \hline
go\_23 & `tmp.1' & input ASCII restart file name \\ \hline
go\_17 & `spn' & output file number (restart file string) \\ \hline
gs\_7 & `n' & new/continuing run? (i.e., use restart?) \\ \hline
gs\_rstdir\_name & `\$RUNTIME\_ROOT & \\
& /genie-seaice/data/input' & restart (input) directory \\ \hline
gs\_18 & `tmp.1' & input ASCII restart file name \\ \hline
gs\_12 & `spn' & output file number (restart file string) \\ \hline
ac\_ctrl\_continuing & .false. & continuing ATCHEM run? (i.e., use restart?) \\ \hline
ac\_par\_rstdir\_name & `\$RUNTIME\_ROOT& \\
& /genie-atchem/data/input' & ATCHEM restart (input) directory \\ \hline
ac\_par\_infile\_name & `atchem' & input restart filename \\ \hline
ac\_par\_outfile\_name & `atchem' & output restart filename \\ \hline
bg\_ctrl\_continuing & .false. & continuing BIOGEM run? (i.e., use restart?) \\ \hline
bg\_par\_rstdir\_name & '\$RUNTIME\_ROOT & \\
& /genie-biogem/data/input' & BIOGEM restart (input) directory \\ \hline
bg\_par\_infile\_name & `biogem' & input restart filename \\ \hline
bg\_par\_outfile\_name & `biogem' & output restart filename \\ \hline
sg\_ctrl\_continuing & .false. & continuing SEDGEM run? (i.e., use restart?) \\ \hline
sg\_par\_rstdir\_name & `\$RUNTIME\_ROOT & \\
& /genie-sedgem/data/input' & SEDGEM restart (input) directory \\ \hline
sg\_par\_infile\_name & `sedgem' & input restart filename \\ \hline
sg\_par\_outfile\_name & `sedgem' & output restart filename \\ \hline
rg\_ctrl\_continuing & .false. & continuing ROKGEM run? (i.e., use restart?) \\ \hline
- & - & - \\ \hline
rg\_par\_infile\_name & `rokgem' & input restart filename \\ \hline
rg\_par\_outfile\_name & `rokgem' & output restart filename \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l |}
\hline
NAME & DEFAULT VALUE & DESCRIPTION \\ \hline
\multicolumn{3}{|l|}{INPUT/OUTPUT DIRECTORY SPECIFICATION} \\ \hline
gm\_par\_gem\_indir\_name & `\$RUNTIME\_ROOT/ & \\
& genie-main/data/input' & GEM data input directory \\ \hline
ea\_1 & `\$RUNTIME\_ROOT & \\
& /genie-embm/data/input' & data input directory \\ \hline
ea\_2 & `\$RUNTIME\_OUTDIR & \\
& /embm' & results output directory \\ \hline
go\_1 & `\$RUNTIME\_ROOT & \\
& /genie-goldstein/data/input' & data input directory \\ \hline
go\_2 & `\$RUNTIME\_OUTDIR & \\
& /goldstein' & results output directory \\ \hline
gs\_1 & `\$RUNTIME\_ROOT & \\
& /genie-seaice/data/input' & data input directory \\ \hline
gs\_2 & `\$RUNTIME\_OUTDIR & \\
& /seaice' & results output directory \\ \hline
ac\_par\_indir\_name & `\$RUNTIME\_ROOT & \\
& /genie-atchem/data/input'1 & ATCHEM data input directory \\ \hline
ac\_par\_outdir\_name & `\$RUNTIME\_OUTDIR & \\
& /atchem' & ATCHEM results output directory \\ \hline
bg\_par\_indir\_name & `\$RUNTIME\_ROOT & \\
& /genie-biogem/data/input' & BIOGEM data input directory \\ \hline
bg\_par\_outdir\_name & `\$RUNTIME\_OUTDIR & \\
& /biogem' & BIOGEM results output directory \\ \hline
bg\_par\_fordir\_name & `\$RUNTIME\_ROOT & \\
& /genie-biogem/data/input' & BIOGEM forcings (input) directory \\ \hline
sg\_par\_indir\_name & `\$RUNTIME\_ROOT & \\
& /genie-sedgem/data/input' & SEDGEM data input directory \\ \hline
sg\_par\_outdir\_name & `\$RUNTIME\_OUTDIR & \\
& /sedgem' & SEDGEM results output directory \\ \hline
rg\_par\_indir\_name & `\$RUNTIME\_ROOT & \\
& /genie-rokgem/data/input' & ROKEM data input directory \\ \hline
rg\_par\_outdir\_name & `\$RUNTIME\_OUTDIR & \\
& /rokgem' & ROKGEM results output directory \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{USEFUL(!) CLIMATE VARIABLES} \\ \hline
ma\_genie\_solar\_constant & 1368.0 & W m-2 & solar constant \\ \hline
ea\_topo & `worbe2' & (STRING) & topography name1 \\ \hline
ea\_dosc & .true. & (LOGICAL) & seasonal insolation forcing?2 \\ \hline
ea\_diffa\_scl & 1.0 & (REAL) & atmospheric diffusivity scaling factor \\ \hline
ea\_diffa\_len & 0 & (INTEGER) & grid point distance over which scalar is \\
& & & applied (j direction) \\ \hline
ea\_36 & `n' & ('y'/'n') & use ATCHEM CO2 to calculate radioative \\
& & & forcing (else climate is invarient)? \\ \hline
ea\_delf2x & 5.77 & W m-2 & climate sensitivity; radiative forcing \\
& & & in W m-2 for a doubling of CO2 is \\
& & & calculated as: delf2x x ln(2.0) \\ \hline
go\_topo `worbe2' & (STRING) & & topography filename1 \\ \hline
go\_dosc & .true. & (LOGICAL) & seasonal insolation forcing?2 \\ \hline
go\_ocnconv & 0 & (INTEGER) & ocean convection scheme3 \\ \hline
gs\_dosc & .true. & (LOGICAL) & seasonal insolation forcing?2 \\ \hline
\end{tabular}
1 Note that an extension of ``.k1'' is added automatically.
2 The three climate components modules must all include seasonal insolation forcing together or not (i.e., the 3 namelist prameter values must
have the same value).
1 Current options are: 0 = original; 1 = Mueller.
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{GENERAL BIOGEOCHEMISTRY} \\ \hline
gm\_par\_carbconstset\_name & ``Mehrbach'' & (STRING) & carbonate dissociation constants set \\ \hline
& & & \\ \hline
& & & \\ \hline
& & & \\ \hline
& & & \\ \hline
\multicolumn{4}{|l|}{ATMOSPHERE BIOGEOCHEMISTRY} \\ \hline
ac\_par\_atm\_wetlands\_FCH4 & 0.0 & mol yr$^{-1}$ & Wetlands CH$_{4}$ flux \\ \hline
ac\_par\_atm\_wetlands\_FCH4\_d13C & 0.0 & \permil & Wetlands CH$_{4}$ d$^{13}$C \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: MISC CONTROL} \\ \hline
bg\_ctrl\_misc\_Snorm & .true. & (LOGICAL) & tracer update with salinity \\
& & & normalization \\ \hline
bg\_ctrl\_misc\_noSnorm & .false. & (LOGICAL) & tracer update without salinity \\
& & & normalization \\ \hline
bg\_ctrl\_misc\_nobioupdate & .false. & (LOGICAL) & tracer update with no \\
& & & biological overprint \\ \hline
bg\_ctrl\_misc\_brinerejection\_bgc & .false. & (LOGICAL) & Include biogeochem in Sea-ice brine \\
& & & rejection? \\ \hline
bg\_par\_misc\_brinerejection\_frac & 0.0 & (LOGICAL) & Sea-ice brine rejection fraction \\ \hline
bg\_par\_misc\_brinerejection\_jmax & 36 & (LOGICAL & Max j for sea-ice brine rejection \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: BOUNDARY CONDITIONS} \\ \hline
bg\_ctrl\_force\_sed\_closedsystem & .true. & (LOGICAL) & Dissolution flux = rain flux to \\
& & & close system? \\ \hline
bg\_ctrl\_force\_GOLDSTEInTS & .false. & (LOGICAL) & Allow temperature / salinity \\
& & & forcing of climate? \\ \hline
bg\_ctrl\_force\_seaice & .false. & (LOGICAL) & Replace internal fractional \\
& & & sea-ice cover field? \\ \hline
bg\_ctrl\_force\_windspeed & .true. & (LOGICAL) & Replace internal wind-speed field? \\ \hline
bg\_ctrl\_force\_CaCO3toPOCrainratio & .false. & (LOGICAL) & Replace internal CaCO$_{3}$:POC \\
& & & export rain ratio? \\ \hline
bg\_ctrl\_force\_POCdtoPOCrainratio & .false. & (LOGICAL) & Replace internal POCd:POC \\
& & & export rain ratio? \\ \hline
bg\_ctrl\_force\_Cd\_alpha & .false. & (LOGICAL) & Replace internal [Cd/P]POM/\\
& & & [Cd/P]SW alpha? \\ \hline
bg\_ctrl\_force\_scav\_fpart\_POC & .false. & (LOGICAL) & Replace internal POC flux for $^{230}$Th\\
& & & and 231Pa isotope scavenging? \\ \hline
bg\_ctrl\_force\_scav\_fpart\_CaCO3 & .false. & (LOGICAL) & Replace internal CaCO$_{3}$ flux for $^{230}$Th\\
& & & and $^{231}$Pa isotope scavenging? \\ \hline
bg\_ctrl\_force\_scav\_fpart\_opal & .false. & (LOGICAL) & Replace internal opal flux for $^{230}$Th and \\
& & & $^{231}$Pa isotope scavenging? \\ \hline
bg\_ctrl\_force\_scav\_fpart\_det & .false. & (LOGICAL) & Replace internal det flux for $^{230}$Th \\
& & & and $^{231}$Pa isotope scavenging? \\ \hline
bg\_ctrl\_force\_solconst & .false. & (LOGICAL) & Replace solar constant \\
& & & (with time-varying IP)? \\ \hline
bg\_ctrl\_force\_oldformat & .false. & (LOGICAL) & Use old tracer forcing \\
& & & file format? \\ \hline
bg\_par\_seaice\_file & 'seaice.dat' & (STRING) & Filename for prescribed BIOGEM \\
& & & seaice boundary condition \\ \hline
bg\_par\_windspeed\_file & 'windspeed.dat' &(STRING) & Filename for prescribed \\
& & & BIOGEM windspeed (air-sea gas\\
& & & exchange) boundary condition \\ \hline
bg\_par\_CaCO3toPOCrainratio\_file & 'CaCO3toPOC' & (STRING) & Filename for prescribed \\
& & & BIOGEM CaCO$_{3}$:POC rain \\
& rainratio.dat' & & ratio boundary condition \\ \hline
bg\_par\_POCdtoPOCrainratio\_file & 'POCdtoPOC' & (STRING) & Filename for prescribed \\
& & & BIOGEM POCd:POC rain \\
& rainratio.dat' & & ratio boundary condition \\ \hline
bg\_par\_Cd\_alpha\_file 'Cd\_alpha.dat' & & (STRING) & Filename for prescribed Cd partition \\
& & & coefficient alpha field \\ \hline
bg\_par\_gastransfer\_a & 0.310 & ??? & Value of Wanninkhof [1992] gas \\
& & & transfer coeff, a \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: MISC CONTROL continued ..} \\ \hline
bg\_par\_scav\_fpart\_POC\_file & scav\_fpart\_POC.dat & (STRING) & \\ \hline
bg\_par\_scav\_fpart\_CaCO3\_file & scav\_fpart\_CaCO3.dat & (STRING) & \\ \hline
bg\_par\_scav\_fpart\_opal\_file & scav\_fpart\_opal.dat & (STRING) & \\ \hline
bg\_par\_scav\_fpart\_det\_file & scav\_fpart\_det.dat & (STRING) & \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: BIOLOGICAL NEW PRODUCTION} \\ \hline
bg\_par\_bio\_prodopt & '1N1T\_PO4MM' & (STRING) & biological scheme ID \\ \hline
bg\_par\_bio\_k0\_PO4 & 2.0E-06 & mol kg$^{-1}$ yr$^{-1}$ & maximum PO$_{4}$ consumption rate \\ \hline
bg\_par\_bio\_k0\_NO3 & 32.0E-06 & mol kg$^{-1}$ yr$^{-1}$ & maximum NO3 consumption rate \\ \hline
bg\_par\_bio\_c0\_PO4 & 0.050E-06 & mol kg$^{-1}$ & [PO$_{4}$] M-M half-sat value \\ \hline
bg\_par\_bio\_c0\_NO3 & 3.200E-06 & mol kg$^{-1}$ & [NO3] M-M half-sat value \\ \hline
bg\_par\_bio\_c0\_N & 1.600E-06 & mol kg$^{-1}$ & [NO3]+[NH$_{4}$] M-M half-sat value \\ \hline
bg\_par\_bio\_c0\_Fe & 0.030E-09 & mol kg$^{-1}$ & [Fe] M-M half-sat value \\ \hline
bg\_par\_bio\_c0\_Fe\_sp & 0.125E-09 & mol kg$^{-1}$ & [Fe] M-M half-sat value for siliceous \\
& & & phytoplankton \\ \hline
bg\_par\_bio\_c0\_Fe\_nsp & 0.067E-09 & mol kg$^{-1}$ & [Fe] M-M half-sat value for non-siliceous \\
& & & phytoplankton \\ \hline
bg\_par\_bio\_c0\_SiO2 & 10.0E-06 & mol kg$^{-1}$ & [H$_{4}$SiO$_{4}$] M-M half-sat value \\ \hline
bg\_par\_bio\_zc & 75.0 & m & Biological production zone depth \\
& & & (OCMIP-2) \\ \hline
bg\_par\_bio\_tau & 15 & days & Biological production time-scale \\
& & & (OCMIP-2) \\ \hline
bg\_par\_bio\_relprod\_sp & 0.952381 & ratio & Fractional production of siliceous \\
& & & phytoplankton in Si/Fe-replete conditions. \\
& & & (20:1 for siliceous to non-siliceous \\
& & & phytoplanktion production \\
& & & (Ridgwell, 2001, PhD. Thesis) \\ \hline
bg\_par\_bio\_I\_eL & 20.0 & m & Light e-folding depth (OCMIP-2) \\ \hline
bg\_par\_bio\_kT0 & 0.59 & & coefficient for temperature-dependent \\
& & & uptake rate modifier \\ \hline
bg\_par\_bio\_kT\_eT & 15.8 & K & e-folding temperature for T-dep. \\
& & & uptake rate modifier \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT & UNITS & DESCRIPTION \\
& VALUE & & \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: ORGANIC MATTER UPTAKE (EXPORT) RATIOS} \\ \hline
bg\_par\_bio\_red\_POP\_PON & 16.0 & n/a & N/P organic matter Redfield ratio \\ \hline
bg\_par\_bio\_red\_POP\_POC & 106.0 & n/a & C/P organic matter Redfield ratio \\ \hline
bg\_par\_bio\_red\_POP\_PO2 & -138.0 & n/a & O2/P organic matter pseudo-Redfield ratio \\ \hline
bg\_par\_bio\_red\_PON\_ALK & -1.00 & n/a & ALK/N alkalinty correction factor \\ \hline
bg\_par\_bio\_red\_DOMfrac & 0.66 & n/a & production fraction of dissolved organic matter \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: INORGANIC MATTER UPTAKE (EXPORT) RATIOS} \\ \hline
bg\_par\_bio\_red\_POC\_CaCO3 & 0.2 & (LOGICAL) & base CaCO$_{3}$:POC export ratio \\ \hline
bg\_par\_bio\_red\_POC\_CaCO3\_pP & 0.0 & (LOGICAL) & exponent for modifier of \\
& & & CaCO$_{3}$:POC export ratio \\ \hline
bg\_par\_bio\_red\_POC\_opal & 1.0 & (LOGICAL) & base opal:POC export ratio \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT & UNITS & DESCRIPTION \\
& VALUE & & \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: REMINERALIZATION} \\ \hline
bg\_par\_bio\_remin\_DOMlifetime & 0.5 & yrs & DOC lifetime \\ \hline
bg\_par\_bio\_remin\_CH4rate & 1.0e-4 & d$^{-1}$ & Specific CH$_{4}$ oxidation rate \\ \hline
bg\_ctrl\_bio\_remin\_POC\_fixed & .true. & (LOGICAL) & fixed-profile POM remineralization? \\ \hline
bg\_ctrl\_bio\_remin\_POC\_ballast & .false. & (LOGICAL) & Ballasting parameterization? \\ \hline
bg\_par\_bio\_remin\_POC\_frac2 & 0.05 & n/a & initial fractional abundance of fraction \#2 \\ \hline
bg\_par\_bio\_remin\_POC\_eL1 & 500.0 & m & remineralization length: fraction \#1 \\ \hline
bg\_par\_bio\_remin\_POC\_eL2 & 1000000.0 & m & remineralization length: fraction \#2 \\ \hline
bg\_ctrl\_bio\_remin\_CaCO3\_fixed & .true. & (LOGICAL) & fixed-profile CaCO$_{3}$ remineralization? \\ \hline
bg\_par\_bio\_remin\_CaCO3\_frac2 & 0.5 & n/a & initial fractional abundance of fraction \#2 \\ \hline
bg\_par\_bio\_remin\_CaCO3\_eL1 & 1000.0 & m & remineralization length: fraction \#1 \\ \hline
bg\_par\_bio\_remin\_CaCO3\_eL2 & 1000000.0 & m & remineralization length: fraction \#2 \\ \hline
bg\_ctrl\_bio\_remin\_opal\_fixed & .false. & (LOGICAL) & fixed-profile opal remineralization? \\ \hline
bg\_par\_bio\_remin\_opal\_frac2 & 0.5 & n/a & initial fractional abundance of fraction \#2 \\ \hline
bg\_par\_bio\_remin\_opal\_eL1 & 1000.0 & m & remineralization length: fraction \#1 \\ \hline
bg\_par\_bio\_remin\_opal\_eL2 & 1000000.0 & m & remineralization length: fraction \#2 \\ \hline
bg\_par\_bio\_remin\_sinkingrate & 125.0 & m d$^{-1}$ & prescribed particle sinking rate \\ \hline
bg\_par\_bio\_remin\_ballast\_kc & 0.130 & & Organic matter carrying capacity of CaCO$_{3}$ \\ \hline
bg\_par\_bio\_remin\_ballast\_ko & 0.0 & & Organic matter carrying capacity of opal \\ \hline
bg\_par\_bio\_remin\_ballast\_kl & 0.0 & & Organic matter carrying capacity of lithogenics \\ \hline
bg\_ctrl\_bio\_remin\_ONtoNH4 & .false. & (LOGICAL) & aerobic remineralization of ON; \\
& & & NH$_{4}$ (not NO3) \\ \hline
bg\_par\_bio\_remin\_denitrO2thresh & 0.0 & mol kg$^{-1}$ & Denitrification [O2] threshold \\ \hline
bg\_ctrl\_bio\_remin\_reminfix & .false. & (LOGICAL) & Stop rapidly-oxidizing species going $<$ 0.0? \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: ISOTOPIC FRACTIONATION} \\ \hline
bg\_par\_d13C\_DIC\_Corg\_ef & 25 & & Fractionation for intercellular C fixation \\
& & & (Ridgwell, 2001, PhD. Thesis) \\ \hline
bg\_par\_d13C\_DIC\_Corg\_ef\_sp & 25 & & Fractionation for intercellular C fixation of \\
& & & siliceous phytoplanktion (Ridgwell, 2001, \\
& & & PhD. Thesis) \\ \hline
bg\_par\_d13C\_DIC\_Corg\_ef\_nsp & 20 & & Fractionation for intercellular C fixation of \\
& & & non-siliceous phytoplanktion \\
& & & (Ridgwell, 2001, PhD. Thesis) \\ \hline
bg\_ar\_d30Si\_opal\_epsilon & -1.1 & \permil & Fractionation of $^{30}$ during opal formation by \\
& & & diatoms. Default value: -1.1 \\
& & & (De La Rocha et al., 1997) \\ \hline
bg\_par\_d114Cd\_POCd\_epsilon & -1.0 & & \*\*\* d$^{114}$Cd = 1.0006 \*\*\* \\ \hline
bg\_par\_d7Li\_LiCO3\_epsilon & 3.0 & & 7/6Li fractionation between Li and LiCO \\ \hline
bg\_opt\_bio\_foram\_p\_13C\_delta & NONE & (STRING) & Planktic foram $^{13}$C fractionation \\
& & & scheme ID string \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT & UNITS & DESCRIPTION \\
& VALUE & & \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: IRON} \\ \hline
bg\_par\_det\_Fe\_sol & 1.0 & n/a & fractional aeolian Fe solubility \\ \hline
bg\_par\_det\_Fe\_sol\_exp & 1.0 & n/a & exponent for aeolian Fe solubility1 \\ \hline
bg\_ctrl\_bio\_red\_fixedFetoC & .false. & (LOGICAL) & fixed cellular Fe:C ratio? \\ \hline
bg\_par\_bio\_red\_POFe\_POC & 250000.0 & n/a & C/Fe organic matter ratio \\ \hline
bg\_ctrl\_bio\_Fe\_fixedKscav & .false. & fixed scavening & \\
& & rate & (if not: Parekh scheme)? \\ \hline
bg\_par\_scav\_Fe\_Ks & 0.1E-3 & d$^{-1}$ & fixed Fe scavenging rate \\ \hline
bg\_par\_scav\_Fe\_sf\_POC & 0.300 & n/a & Parekh Fe scavenging rate scale \\
& & & factor: POC \\ \hline
bg\_par\_scav\_Fe\_sf\_CaCO3 & 0.0 & n/a & Parekh Fe scavenging rate scale \\
& & & factor: CaCO$_{3}$ \\ \hline
bg\_par\_scav\_Fe\_sf\_opal & 0.0 & n/a & Parekh Fe scavenging rate scale \\
& & & factor: opal \\ \hline
bg\_par\_scav\_Fe\_sf\_det & 0.0 & n/a & Parekh Fe scavenging rate scale \\
& & & factor: det \\ \hline
bg\_par\_scav\_fremin & 1.0 & n/a & Fraction of scavenged Fe remineralizable \\ \hline
bg\_ctrl\_bio\_NO\_fsedFe & .true. & (LOGICAL) & Prevent return of Fe \\
& & & from the sediments? \\ \hline
bg\_par\_K\_FeL\_pP & 11.0 & & log10 of Fe ligand stability constant K'(FeL) \\ \hline
bg\_par\_bio\_FetoC\_pP & -0.4225 & & [FeT] dependent Fe:C ratio \\
& & & [Ridgwell, 2001] -- power \\ \hline
bg\_par\_bio\_FetoC\_K & 94500.0 & & [FeT] dependent Fe:C ratio \\
& & & [Ridgwell, 2001] -- scaling \\ \hline
bg\_par\_bio\_FetoC\_C & 0.0 & & [FeT] dependent Fe:C ratio \\
& & & [Ridgwell, 2001] -- constant \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: SILICA} \\ \hline
& & & \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: NITROGEN} \\ \hline
bg\_par\_bio\_mu1 & 1.0 & yr$^{-1}$ mu$^{-1}$ & maximum rate of export production \\ \hline
bg\_par\_bio\_mu2 & 0.2 & yr$^{-1}$ mu-2 & maximum rate of export production \\
& & & from N$_{2}$-fixation \\ \hline
bg\_par\_bio\_N2fixthresh & 100.0E-06 & mol yr$^{-1}$ & Threshold NO3 + NH$_{4}$ to \\
& & & encourage N$_{2}$ fixation \\ \hline
bg\_par\_bio\_Nstar\_offset & 2.90E-06 & mol yr$^{-1}$ & N-star calculation offset \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: TRACE METALS} \\ \hline
bg\_par\_bio\_red\_POC\_POCd & 0.0E-6 & n/a & Default cellular C:Cd (Cd/C) ratio \\ \hline
bg\_par\_bio\_red\_POC\_POCd\_alpha & 10.0 & n/a & [Cd/P]POM/[Cd/P]SW partition \\
& & & coefficient (alpha) \\ \hline
bg\_ctrl\_bio\_red\_CdtoC\_Felim & .true. & (LOGICAL) & Fe-limitation dependent \\
& & & Cd:C 'Redfield' uptake ratio? \\ \hline
bg\_par\_bio\_red\_CdtoC\_Felim\_min & 3.000E-6 & n/a & Minimum (Fe replete) \\
& & & Cd:C uptake ratio \\ \hline
bg\_par\_bio\_red\_CdtoC\_Felim\_max & 6.000E-6 & n/a & Maximum (Fe limited) \\
& & & Cd:C uptake ratio \\ \hline
bg\_par\_bio\_red\_CaCO3\_LiCO3 & 0.0E-6 & & Default CaCO$_{3}$ Ca:Li ratio \\ \hline
bg\_par\_bio\_red\_CaCO3\_LiCO3\_alpha & 1.0 & & partition coefficient (alpha) \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT & UNITS & DESCRIPTION \\
& VALUE & & \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: $^{230}$Th AND $^{231}$Pa} \\ \hline
bg\_par\_scav\_230Th\_scavopt & & (STRING) & Scavenging scheme ID string for $^{230}$Th \\ \hline
bg\_par\_scav\_231Pa\_scavopt & & (STRING) & Scavenging scheme ID string for $^{231}$Pa \\ \hline
bg\_par\_scav\_230Th\_KPOC & 1.e7 & & Equilibrium partition coefficient for POC associated \\
& & & $^{230}$Th. Default value of 1e7 used by Siddall et al.\\
& & & (2005) in their control simulation. \\ \hline
bg\_par\_scav\_230Th\_KCaCO3 & 1.e7 & & Equilibrium partition coefficient for CaCO$_{3}$ \\
& & & associated $^{230}$Th. Default value of 1e7 \\
& & & used by Siddall et al. (2005) in their \\
& & & control simulation. \\ \hline
bg\_par\_scav\_230Th\_Kopal & 0.05e7 & & Equilibrium partition coefficient for opal associated \\
& & & $^{230}$Th. Default value of 0.05e7 used by Siddall et al.\\
& & & (2005)in their control simulation. \\ \hline
bg\_par\_scav\_230Th\_Kdet & 0 & & Equilibrium partition coefficient for detrital \\
& & & associated $^{230}$Th. Default value of 0 used by Siddall \\
& & & et al. (2005) in their control simulation. \\ \hline
bg\_par\_scav\_231Pa\_KPOC & 1.e7 & & quilibrium partition coefficient for POC associated \\
& & & $^{231}$Pa. Default value of 1e7 used by Siddall \\
& & & et al. (2005) in their control simulation. \\ \hline
bg\_par\_scav\_231Pa\_KCaCO3 & 0.025e7 & & Equilibrium partition coefficient for CaCO$_{3}$ \\
& & & associated $^{231}$Pa. Default value of 0.025e7 \\
& & & used by Siddall et al. (2005) in their control \\
& & & simulation. \\ \hline
bg\_par\_scav\_231Pa\_Kopal & 0.1667e7 & & Equilibrium partition coefficient for opal \\
& & & associated $^{231}$Pa. Default value of 0.1667e7 \\
& & & used by Siddall et al. (2005)in their \\
& & & control simulation. \\ \hline
bg\_par\_scav\_231Pa\_Kdet & 0 & & Equilibrium partition coefficient for detrital \\
& & & associated $^{231}$Pa. Default value of 1e7 used by \\
& & & Siddall et al. (2005) in their control simulation. \\ \hline
bg\_par\_scav\_230Th\_indepsinkingvel & 1000.0 & m yr$^{-1}$ & Independent scheme for sinking of particle \\
& & & associated $^{230}$Th: non-zero velocity enables \\
& & & independent scheme and disables settling in \\
& & & accord with the settling of the scavenging \\
& & & particulate type. Default value of 1000.0 \\
& & & used by Siddall et al. (2005)in their control \\
& & & simulation. \\ \hline
bg\_par\_scav\_231Pa\_indepsinkingvel & 1000.0 & m yr$^{-1}$ & Independent scheme for sinking of particle\\
& & & associated $^{231}$Pa: non-zero velocity enables \\
& & & independent scheme and disbles settling in \\
& & & accord with the settling of the scavenging \\
& & & particulate type. Default value of 1000.0 \\
& & & used by Siddall et al. (2005)in their control \\
& & & simulation. \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: ABIOTIC PRECIPITATION} \\ \hline
bg\_par\_bio\_CaCO3precip\_sf & 0.0 & & Scale factor for CaCO$_{3}$ precipitation \\ \hline
bg\_par\_bio\_CaCO3precip\_exp & 0.0 & & Rate law power for CaCO$_{3}$ precipitation \\ \hline
bg\_ctrl\_bio\_CaCO3precip & .false. & (LOGICAL) & Allow abiotic CaCO$_{3}$ precipitation? \\ \hline
bg\_ctrl\_bio\_CaCO3precip\_sur & .true. & (LOGICAL) & Restrict precipitation to surface layer? \\ \hline
\end{tabular}
1 Use a value of 1.0 for uniform solubility.
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: DATA SAVING: TIME-SLICES} \\ \hline
bg\_ctrl\_data\_save\_slice\_ocnatm & .false. & (LOGICAL) & atmospheric (interface) composition (2D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_ocn & .true. & (LOGICAL) & ocean composition (3D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_ocnsed & .false. & (LOGICAL) & sediment (interface) composition (2D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_fairsea & .true. & (LOGICAL) & Air-sea gas exchange (2D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_focnatm & .false. & (LOGICAL) & ocean-atmosphere flux (2D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_focnsed & .false. & (LOGICAL) & ocean-sediment flux (2D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_fsedocn & .false. & (LOGICAL) & sediment-ocean flux (2D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_bio & .true. & (LOGICAL) & biological fluxes (3D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_carb & .true. & (LOGICAL) & aqueous carbonate system properties (3D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_carbconst & .false. & (LOGICAL) & aqueous carbonate system constants (3D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_phys\_atm & .false. & (LOGICAL) & atmospheric physical properties (2D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_phys\_ocn & .false. & (LOGICAL) & ocean physical properties (3D)? \\ \hline
bg\_ctrl\_data\_save\_slice\_misc & .true. & (LOGICAL) & miscellaneous properties (-)? \\ \hline
bg\_ctrl\_data\_save\_slice\_diag & .false. & (LOGICAL) & biogeochemical diagnostics? \\ \hline
bg\_par\_data\_save\_slice\_dt & 1.0 & yr & integration interval \\ \hline
bg\_par\_infile\_slice\_name & `biogem\_save & (STRING) & time-slice mid-point specification filename \\
& \_timeslice.dat' & & \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: DATA SAVING: TIME-SERIES} \\ \hline
bg\_ctrl\_data\_save\_sig\_ocnatm & .true. & (LOGICAL) & atmospheric (interface) composition? \\ \hline
bg\_ctrl\_data\_save\_sig\_ocn & .true. & (LOGICAL) & oceanic composition? \\ \hline
bg\_ctrl\_data\_save\_sig\_fexport & .true. & (LOGICAL) & export flux? \\ \hline
bg\_ctrl\_data\_save\_sig\_fairsea & .true. & (LOGICAL) & Air-sea gas exchange? \\ \hline
bg\_ctrl\_data\_save\_sig\_ocnsed & .true. & (LOGICAL) & sediment (interface) composition? \\ \hline
bg\_ctrl\_data\_save\_sig\_focnatm & .false. & (LOGICAL) & ocean->atmosphere flux? \\ \hline
bg\_ctrl\_data\_save\_sig\_focnsed & .true. & (LOGICAL) & ocean->sediment flux? \\ \hline
bg\_ctrl\_data\_save\_sig\_fsedocn & .true. & (LOGICAL) & sediment->ocean flux? \\ \hline
bg\_ctrl\_data\_save\_sig\_ocnSS & .true. & (LOGICAL) & ocean surface tracers? \\ \hline
bg\_ctrl\_data\_save\_sig\_carbSS & .true. & (LOGICAL) & ocean surface carbonate chemistry? \\ \hline
bg\_ctrl\_data\_save\_sig\_misc & .true. & (LOGICAL) & miscellaneous properties? \\ \hline
bg\_ctrl\_data\_save\_sig\_diag & .true. & (LOGICAL) & biogeochemical diagnostics? \\ \hline
bg\_par\_data\_save\_sig\_dt & 1.0 & yr & integration interval \\ \hline
bg\_par\_infile\_sig\_name & `biogem\_save\_sig.dat' & (STRING) & time-slice mid-point specification filename \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: DATA SAVING: TIME-MISC} \\ \hline
bg\_ctrl\_data\_save\_derived & .false. & (LOGICAL) & save `derived'1 data? \\ \hline
bg\_ctrl\_data\_save\_GLOBAL & .true. & (LOGICAL) & save global diagnostics2? \\ \hline
bg\_ctrl\_data\_save\_slice\_ascii & .false. & (LOGICAL) & save time-slices in ASCII format? \\ \hline
bg\_ctrl\_data\_save\_sig\_ascii & .true. & (LOGICAL) & save time-series in ASCII format? \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{OCEAN BIOGEOCHEMISTRY: TRACER AUDITING AND DEBUGGING OPTIONS} \\ \hline
bg\_ctrl\_audit & .true. & (LOGICAL) & audit tracer inventory? \\ \hline
bg\_ctrl\_audit\_fatal & .false. & (LOGICAL) & halt on audit fail? \\ \hline
bg\_par\_misc\_audit\_relerr & 1.0E-08 & n/a & threshold of relative inventory change to\\
& & & trigger audit error \\ \hline
bg\_ctrl\_debug\_reportwarnings & .false. & (LOGICAL) & report all run-time warnings? \\ \hline
bg\_ctrl\_debug\_lvl1 & .false. & (LOGICAL) & report level \#1 debug? \\ \hline
bg\_ctrl\_debug\_lvl2 & .false. & (LOGICAL) & report level \#2 debug? \\ \hline
\end{tabular}
1 e.g., salinity-normalized ocean tracers, tracer inventories of each cell.
2 Saved at time-slice intervals.
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT VALUE & UNITS & DESCRIPTION \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: RUN CONTROL} \\ \hline
sg\_ctrl\_continuing & .false. & (LOGICAL) & continuing sedgem? \\ \hline
sg\_start\_year & 0.0 & & Simulation start year [REAL] \\ \hline
sg\_par\_misc\_t\_runtime & 1000.0 & yr & Simulation run length \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: PHYSICAL CONFIGURATION} \\ \hline
sg\_par\_sed\_top\_th & 1.0 & cm & top ('well-mixed') sediment layer \\
& & & thickness \\ \hline
sg\_par\_sed\_poros\_det & 0.880 & cm3 cm-3 & detrital porosity \\ \hline
sg\_par\_sed\_poros\_CaCO3 & 0.610 & cm3 cm-3 & carbonate porosity in top layer \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: DIAGENESIS SCHEME: SELECTION} \\ \hline \\ \hline
sg\_par\_sed\_diagen\_CaCO3opt & `archer1991explicit' & (STRING) & CaCO$_{3}$ diagenesis scheme \\ \hline
sg\_par\_sed\_diagen\_opalopt & `none' & (STRING) & opal diagenesis scheme \\ \hline
sg\_par\_sed\_diagen\_Corgopt 7 & `none' & (STRING) & organic matter diagenesis scheme \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: DIAGENESIS SCHEME: CONTROl} \\ \hline
sg\_ctrl\_sed\_bioturb & .true. & (LOGICAL) & bioturbate sediment stack? \\ \hline
sg\_ctrl\_sed\_bioturb\_Archer & .true. & (LOGICAL) & use Archer et al. [2002] bioturbation \\
& & & scheme? \\ \hline
sg\_par\_n\_sed\_mix & 20 & n/a &maximum layer depth for bioturbation \\ \hline
sg\_par\_sed\_mix\_k\_sur\_max & 0.15 & cm2 yr$^{-1}$ & maximum surface bioturbation mixing \\
& & & rate \\ \hline
sg\_par\_sed\_mix\_k\_sur\_min & 0.15 & cm2 yr$^{-1}$ & minimum surface bioturbation mixing \\
& & & rate \\ \hline
sg\_par\_sed\_fdet & 0.150 & g cm-2 kyr$^{-1}$ & prescribed (additional) flux of detrital\\
& & & material to the seds \\ \hline
sg\_par\_sed\_diagen\_fPOCfrac & 1.0 & n/a & fraction of POC rain available for driving \\
& & & CaCO$_{3}$ dissolution \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: DIAGENEIS SCHEME: ARCHER 1991} \\ \hline
sg\_par\_sed\_archer1991\_dissc & 1.1574e-5 & -s & dissolution rate constant \\ \hline
sg\_par\_sed\_archer1991\_dissn & 4.5 & n/a & dissolution rate order \\ \hline
sg\_par\_sed\_archer1991\_rc & 2.E-9 & -s & organic degradation rate constant \\ \hline
sg\_par\_sed\_archer1991\_iterationmax & 20 & & loop limit in 'o2org' subroutine \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: MISC CONTROLS} \\ \hline
sg\_par\_sed\_CaCO3precip\_sf & 0.0 & & CaCO$_{3}$ precipitation scale factor (abiotic) \\ \hline
sg\_par\_sed\_CaCO3precip\_exp & 2.0 & & CaCO$_{3}$ precipitation rate law lower \\
& & & (abiotic) \\ \hline
sg\_par\_sed\_reef\_CaCO3precip\_sf & 0.0 & & CaCO$_{3}$ precipitation scale factor (corals) \\ \hline
sg\_par\_sed\_reef\_CaCO3precip\_exp & 1.0 & & CaCO$_{3}$ precipitation rate law power\\
& & & (corals) \\ \hline
sg\_par\_sed\_reef\_calcite & .true. & (LOGICAL) & CaCO$_{3}$ precipitation as calcite (otherwise \\
& & & aragonite)? \\ \hline
sg\_par\_sed\_CaCO3\_abioticohm\_min & 10.0 & & Min threshold for abiotic CaCO$_{3}$ \\
& & & precipitation \\ \hline
sg\_par\_sed\_CaCO3\_coralohm\_max & 10.0 & & Max threshold for coral CaCO$_{3}$ \\
& & & precipitation \\ \hline
sg\_par\_sed\_poros\_CaCO3\_reef & 0.5 & cm3 cm-3 & Reef CaCO$_{3}$ porosity \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: DEEP-SEA SEDIMENTS: ISOTOPIC FRACTIONATION} \\ \hline
sg\_opt\_sed\_foram\_b\_13C\_delta & NONE & (STRING) & Benthic foram $^{13}$C fractionation \\
& & & scheme ID string \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT & UNITS & DESCRIPTION \\
& VALUE & & \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: DEEP-SEA SEDIMENTS: HYDROTHERMAL AND OCEAN CRUSTAL WEATHERING} \\ \hline
sg\_par\_sed\_hydroip\_fLi & 0.0 & mol -yr & hydrothermal Li flux \\ \hline
sg\_par\_sed\_hydroip\_fLi\_d7Li & 4.0 & \permil & hydrothermal Li flux d$^{7}$Li \\ \hline
sg\_par\_sed\_lowTalt\_fLi\_alpha & 0.0 & mol -yr & Li low temperature alteration sink (Li/Ca normalized) \\ \hline
sg\_par\_sed\_lowTalt\_7Li\_epsilon & -15.0 & \permil & Li low temperature alteration sink $^{7}$Li epsilon \\ \hline
sg\_par\_sed\_clay\_fLi\_alpha & 0.0 & mol -yr & Li clay formation sink (Li/Ca normalized) \\ \hline
sg\_par\_sed\_clay\_7Li\_epsilon & -15.0 & \permil & Li clay formation sink $^{7}$Li epsilon \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: DEEP-SEA SEDIMENTS: MISC CONTROLS} \\ \hline
sg\_ctrl\_sed\_forcedohmega\_ca & .true. & (LOGICAL) & Ca-only adjustment for forced ocean saturation? \\ \hline
sg\_par\_sed\_ohmegamin & 0.00 & n/a & forced minimum saturation (calcite omega) anywhere \\ \hline
sg\_par\_sed\_ohmegamin\_flux & 0.00 & mol Ca cm-2 & per time-step imposed sed->ocn flux for saturation \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: DEEP-SEA SEDIMENTS: DATA FILENAMES} \\ \hline
sg\_par\_sed\_topo\_D & `sedgem\_topo & (STRING) & sediment water depth grid name \\
& \_D.36x36' & & \\ \hline
sg\_par\_sedcore\_save\_mask\_name & `sedgem\_save & (STRING) & sediment core save mask name \\
& \_mask.36x36' & & \\ \hline
sg\_par\_sed\_mix\_k\_name & `'sedgem\_sed & (STRING) & biodiffusion profile name \\
& \_mix\_k.dat' & & \\ \hline
\multicolumn{4}{|l|}{DEEP-SEA SEDIMENTS: DEEP-SEA SEDIMENTS: I/O: MISC} \\ \hline
sg\_ctrl\_data\_save\_ascii & .false. & (LOGICAL) & save 2-D data fields in ASCII format? \\ \hline
sg\_ctrl\_data\_save\_wtfrac & .true. & (LOGICAL) & report sediment data as a mass fraction? \\ \hline
sg\_ctrl\_misc\_debug1 & .false. & (LOGICAL) & debug level \#1? \\ \hline
sg\_ctrl\_misc\_debug2 & .false. & (LOGICAL) & debug level \#2? \\ \hline
sg\_ctrl\_misc\_debug3 & .false. & (LOGICAL) & debug level \#3? \\ \hline
sg\_ctrl\_misc\_debug4 & .false. & (LOGICAL) & debug level \#4? \\ \hline
sg\_ctrl\_misc\_report\_err & .false. & (LOGICAL) & report errors? \\ \hline
sg\_par\_misc\_debug\_i & 1 & n/a & i sediment coordinate for debug reporting \\ \hline
sg\_par\_misc\_debug\_j & 1 & n/a & j sediment coordinate for debug reporting \\ \hline
\end{tabular}
\begin{tabular}{ | l | l | l | l |}
\hline
NAME & DEFAULT & UNITS & DESCRIPTION \\
& VALUE & & \\ \hline
\multicolumn{4}{|l|}{TERRESTRIAL WEATHERING: RIVER ROUTING PARAMETERS} \\ \hline
rg\_topo & 'worbe2.k1' & n/a & continental config and river routing \\
& & & filename \\ \hline
\multicolumn{4}{|l|}{TERRESTRIAL WEATHERING: WEATHERING SCHEME PARAMETER} \\ \hline
rg\_par\_weathopt & `Global\_avg' & (STRING) & weathering option \\ \hline
rg\_opt\_weather\_T\_Ca & .false. & (LOGICAL) & CaCO$_{3}$ weathering - temperature \\
& & & feedback \\ \hline
rg\_opt\_weather\_T\_Si & .false. & (LOGICAL) & CaSiO3 weathering - temperature \\
& & & feedback \\ \hline
rg\_opt\_weather\_R\_explicit & .true. & (LOGICAL) & if true then R/R\_0 is used rather than \\
& & & the 1 + 0.045(T-T\_0) \\
& & & parameterisation from GEOCARB \\ \hline
rg\_opt\_weather\_R\_Ca & .false. & (LOGICAL) & CaCO$_{3}$ weathering - runoff feedback \\ \hline
rg\_opt\_weather\_R\_Si & .false. & (LOGICAL) & CaSiO3 weathering - runoff feedback \\ \hline
rg\_opt\_weather\_P\_explicit & .false. & (LOGICAL) & if true then P/P\_0 is used rather than \\
& & & the [2RCO2/(1+RCO2)]\^0.4 \\
& & & parameterisation from GEOCARB \\ \hline
rg\_opt\_weather\_P\_Ca & .false. & (LOGICAL) & CaCO$_{3}$ weathering - productivity \\
& & & feedback \\ \hline
rg\_opt\_weather\_P\_Si & .false. & (LOGICAL) & CaSiO3 weathering - productivity \\
& & & feedback \\ \hline
rg\_par\_prodopt & `GPP' & (STRING) & prodictivity to use (`GPP' or `NPP') \\ \hline
rg\_par\_weather\_T0 & 8.4777 & deg C & eathering reference mean global land \\
& & & surface temperature \\ \hline
rg\_par\_weather\_R0 & 5.619E-06 & mm -s & weathering reference mean global \\
& & & runoff \\ \hline
rg\_par\_weather\_P0 & 1.2585 & kg C m-2 yr$^{-1}$ & weathering reference mean global \\
& & & land productivity \\ \hline
rg\_par\_weather\_CO20 & 278 & ppm & weathering reference mean atmospheric \\
& & & CO2 level \\ \hline
rg\_par\_outgas\_CO2 & 0.0 & mol C yr$^{-1}$ & outgassing rate [5.00E12] \\ \hline
rg\_par\_outgas\_CO2\_13C & -5.000 & \permil & mean volcanic/metamorphic d$^{13}$C \\ \hline
\multicolumn{4}{|l|}{TERRESTRIAL WEATHERING: GLOBAL AVERAGE WEATHERING PARAMETERS} \\ \hline
rg\_opt\_weather\_CaCO3 & .FALSE. & (LOGICAL) & CaCO$_{3}$\_weathering-temperature \\
& & & feedback? \\ \hline
rg\_opt\_weather\_CaSiO3 & .FALSE. & (LOGICAL) & CaSiO3\_weathering-temperature \\
& & & feedback? \\ \hline
rg\_opt\_weather\_P & .FALSE. & (LOGICAL) & productivity-weathering feedback \\ \hline
rg\_par\_weather\_T0 & 8.451890 & C & weathering reference mean global land \\