Index: /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.bib
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.bib	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.bib	(revision 9394)
@@ -100,4 +100,8 @@
 @STRING{Tellus = {Tellus}}
 
+%% No dash for repeated names
+@IEEEtranBSTCTL{IEEEexample:BSTcontrol,
+  CTLdash_repeated_names = "no"
+}
 
 @ARTICLE{Adcroft_Campin_OM04,
@@ -109,5 +113,4 @@
   pages = {269--284},
   doi = {10.1016/j.ocemod.2003.09.003},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2003.09.003}
 }
 
@@ -192,5 +195,4 @@
   pages = {1942--1954},
   doi = {10.1016/j.dsr.2009.06.004},
-  url = {http://dx.doi.org/10.1016/j.dsr.2009.06.004}
 }
 
@@ -221,5 +223,4 @@
   volume = {107},
   doi = {10.1029/2001JC000922},
-  url = {http://dx.doi.org/10.1029/2001JC000922}
 }
 
@@ -232,5 +233,4 @@
   volume = {1}, pages = {71--106},
   doi = {10.1029/2001JC000922},
-  url = {http://dx.doi.org/10.1029/2001JC000922}
 }
 
@@ -257,5 +257,4 @@
   pages = {543--567},
   doi = {10.1007/s10236-006-0082-1},
-  url = {http://dx.doi.org/10.1007/s10236-006-0082-1}
 }
 
@@ -350,5 +349,4 @@
   pages = {909--925},
   doi = {10.1007/s00382-008-0429-z},
-  url = {http://dx.doi.org/10.1007/s00382-008-0429-z}
 }
 
@@ -371,5 +369,4 @@
   pages = {L03609},
   doi = {10.1029/2007GL032644},
-  url = {http://dx.doi.org/10.1029/2007GL032644}
 }
 
@@ -383,5 +380,4 @@
   pages = {6599-6615},
   doi = {10.1175/2008JCLI2404.1},
-  url = {http://dx.doi.org/10.1175/2008JCLI2404.1}
 }
 
@@ -486,5 +482,4 @@
 	volume = {61-62},
 	issn = {03770265},
-	url = {http://dx.doi.org/10.1016/j.dynatmoce.2013.02.002},
 	doi = {10.1016/j.dynatmoce.2013.02.002},
 	journal = DAO,
@@ -511,5 +506,4 @@
   pages = {174--184},
   doi = {10.1016/j.ocemod.2009.01.004},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2009.01.004}
 }
 
@@ -533,5 +527,4 @@
 issn = "1463-5003",
 doi = "http://dx.doi.org/10.1016/j.ocemod.2013.02.004",
-url = "http://www.sciencedirect.com/science/article/pii/S1463500313000309",
 }
 
@@ -544,5 +537,4 @@
 NUMBER = {5},
 PAGES = {1285--1297},
-URL = {http://www.geosci-model-dev.net/8/1285/2015/},
 DOI = {10.5194/gmd-8-1285-2015}
 }
@@ -577,5 +569,4 @@
   pages = {C12003},
   doi = {10.1029/2004JC002378},
-  url = {http://dx.doi.org/10.1029/2004JC002378}
 }
 
@@ -635,5 +626,4 @@
   pages = {347--361},
   doi = {10.1016/S1463-5003(02)00009-4},
-  url = {http://dx.doi.org/10.1016/S1463-5003(02)00009-4}
 }
 
@@ -655,5 +645,4 @@
   pages = {1--14},
   doi = {10.1016/j.ocemod.2008.05.005},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2008.05.005}
 }
 
@@ -675,5 +664,4 @@
   volume = {30},  number = {6},
   doi = {10.1029/2002GL016473},
-  url = {http://dx.doi.org/10.1029/2002GL016473}
 }
 
@@ -790,5 +778,4 @@
 	journal = {J. Climate},
 	pages = {1192--1208},
-        url = {http://dx.doi.org/10.1175/2007JCLI1508.1}
 }
 @ARTICLE{Dandonneau_al_S04,
@@ -824,6 +811,5 @@
 	title = {On Antarctic Bottom Water consumption in the abyssal ocean},
 	issn = {0022-3670},
-	url = {http://dx.doi.org/10.1175/JPO-D-14-0201.1},
-	doi = {10.1175/JPO-D-14-0201.1},
+	doi= {10.1175/JPO-D-14-0201.1},
 	abstract = {In studies of ocean mixing, it is generally assumed that small-scale turbulent overturns lose 15-20 \% of their energy in eroding the background stratification. Accumulating evidence that this energy fraction, or mixing efficiency Rf, significantly varies depending on flow properties challenges this assumption, however. Here, we examine the implications of a varying mixing efficiency for ocean energetics and deep water mass transformation. Combining current parameterizations of internal wave-driven mixing with a recent model expressing Rf as a function of a turbulence intensity parameter Reb = εν/νN2, we show that accounting for reduced mixing efficiencies in regions of weak stratification or energetic turbulence (high Reb) strongly limits the ability of breaking internal waves to supply oceanic potential energy and drive abyssal upwelling. Moving from a fixed Rf = 1/6 to a variable efficiency Rf(Reb) causes Antarctic Bottom Water upwelling induced by locally-dissipating internal tides and lee waves to fall from 9 to 4 Sv, and the corresponding potential energy source to plunge from 97 to 44 GW. When adding the contribution of remotely-dissipating internal tides under idealized distributions of energy dissipation, the total rate of Antarctic Bottom Water upwelling is reduced by about a factor of 2, reaching 5-15 Sv compared to 10-33 Sv for a fixed efficiency. Our results suggest that distributed mixing, overflow-related boundary processes and geothermal heating are more effective in consuming abyssal waters than topographically-enhanced mixing by breaking internal waves. Our calculations also point to the importance of accurately constraining Rf(Reb) and including the effect in ocean models.},
 	journal = {Journal of Physical Oceanography},
@@ -836,5 +822,4 @@
 	title = {The impact of a variable mixing efficiency on the abyssal overturning},
 	issn = {0022-3670},
-	url = {http://dx.doi.org//10.1175/JPO-D-14-0259.1},
 	doi = {10.1175/JPO-D-14-0259.1},
 	abstract = {In studies of ocean mixing, it is generally assumed that small-scale turbulent overturns lose 15-20 \% of their energy in eroding the background stratification. Accumulating evidence that this energy fraction, or mixing efficiency Rf, significantly varies depending on flow properties challenges this assumption, however. Here, we examine the implications of a varying mixing efficiency for ocean energetics and deep water mass transformation. Combining current parameterizations of internal wave-driven mixing with a recent model expressing Rf as a function of a turbulence intensity parameter Reb = εν/νN2, we show that accounting for reduced mixing efficiencies in regions of weak stratification or energetic turbulence (high Reb) strongly limits the ability of breaking internal waves to supply oceanic potential energy and drive abyssal upwelling. Moving from a fixed Rf = 1/6 to a variable efficiency Rf(Reb) causes Antarctic Bottom Water upwelling induced by locally-dissipating internal tides and lee waves to fall from 9 to 4 Sv, and the corresponding potential energy source to plunge from 97 to 44 GW. When adding the contribution of remotely-dissipating internal tides under idealized distributions of energy dissipation, the total rate of Antarctic Bottom Water upwelling is reduced by about a factor of 2, reaching 5-15 Sv compared to 10-33 Sv for a fixed efficiency. Our results suggest that distributed mixing, overflow-related boundary processes and geothermal heating are more effective in consuming abyssal waters than topographically-enhanced mixing by breaking internal waves. Our calculations also point to the importance of accurately constraining Rf(Reb) and including the effect in ocean models.},
@@ -889,5 +874,4 @@
   pages = {GB3017},
   doi = {10.1029/2003GB002150},
-  url = {http://dx.doi.org/10.1029/2003GB002150}
 }
 
@@ -941,5 +925,4 @@
   pages = {L01305},
   doi = {10.1029/2003GL018906},
-  url = {http://dx.doi.org/10.1029/2003GL018906}
 }
 
@@ -978,5 +961,5 @@
   volume = {10},  number = {1-2},
   pages = {257--273},
-  url = {http://dx.doi.org/10.1007/s10652-009-9159-y}
+  doi = {10.1007/s10652-009-9159-y}
 }
 
@@ -1001,5 +984,4 @@
   pages = {L12605},
   doi = {10.1029/2005GL022463},
-  url = {http://dx.doi.org/10.1029/2005GL022463}
 }
 
@@ -1190,4 +1172,5 @@
   pages = {14703--14726}
 }
+
 @ARTICLE{Gerdes1991,
 	Author = {Gerdes, R{\"u}diger and K{\"o}berle, Cornelia and Willebrand, J{\"u}rgen},
@@ -1197,5 +1180,4 @@
 	Pages = {211--226},
 	Title = {The influence of numerical advection schemes on the results of ocean general circulation models},
-	Url = {http://dx.doi.org/10.1007/BF00210006},
 	Volume = {5},
 	Year = {1991},
@@ -1219,5 +1201,4 @@
 	title = {Global prediction of abyssal hill root-mean-square heights from small-scale altimetric gravity variability},
 	issn = {2156-2202},
-	url = {http://dx.doi.org/10.1029/2010JB007867},
 	doi = {10.1029/2010JB007867},
 	abstract = {Abyssal hills, which are pervasive landforms on the seafloor of the Earth's oceans, represent a potential tectonic record of the history of mid-ocean ridge spreading. However, the most detailed global maps of the seafloor, derived from the satellite altimetry-based gravity field, cannot be used to deterministically characterize such small-scale ({\textless}10 km) morphology. Nevertheless, the small-scale variability of the gravity field can be related to the statistical properties of abyssal hill morphology using the upward continuation formulation. In this paper, I construct a global prediction of abyssal hill root-mean-square (rms) heights from the small-scale variability of the altimetric gravity field. The abyssal hill-related component of the gravity field is derived by first masking distinct features, such as seamounts, mid-ocean ridges, and continental margins, and then applying a newly designed adaptive directional filter algorithm to remove fracture zone/discontinuity fabric. A noise field is derived empirically by correlating the rms variability of the small-scale gravity field to the altimetric noise field in regions of very low relief, and the noise variance is subtracted from the small-scale gravity variance. Suites of synthetically derived, abyssal hill formed gravity fields are generated as a function of water depth, basement rms heights, and sediment thickness and used to predict abyssal hill seafloor rms heights from corrected small-scale gravity rms height. The resulting global prediction of abyssal hill rms heights is validated qualitatively by comparing against expected variations in abyssal hill morphology and quantitatively by comparing against actual measurements of rms heights. Although there is scatter, the prediction appears unbiased.},
@@ -1246,5 +1227,4 @@
   pages = {L05609},
   doi = {10.1029/2006GL028210},
-  url = {http://dx.doi.org/10.1029/2006GL028210}
 }
 
@@ -1256,5 +1236,5 @@
   volume = {43},
   pages = {838--862},
-  url ={http://dx.doi.org/10.1175/JPO-D-11-0188.1}
+  doi = {10.1175/JPO-D-11-0188.1}
 }
 
@@ -1298,5 +1278,4 @@
   pages = {1--46},
   doi = {10.1016/j.ocemod.2008.08.007},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2008.08.007}
 }
 
@@ -1339,5 +1318,5 @@
   volume = {128},  
   pages = {2935–-2946},
- url = {http://dx.doi.org/10.1175/1520-0493(2000)128}
+  doi = {10.1175/1520-0493(2000)128}
 }
 
@@ -1488,5 +1467,4 @@
   pages = {70--86},
   doi = {10.1016/j.ocemod.2009.12.003},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2009.12.003},
   issn = {1463-5003},
 }
@@ -1553,5 +1531,4 @@
   pages = {891--908},
   doi = {10.1007/s00382-008-0416-4},
-  url = {http://dx.doi.org/10.1007/s00382-008-0416-4}
 }
 
@@ -1645,5 +1622,5 @@
   volume = {35},  number = {4},
   pages = {669--683},
-  url = {http://dx.doi.org/10.1007/s00382-009-0655-z}
+  doi = {10.1007/s00382-009-0655-z}
 }
 
@@ -1663,5 +1640,4 @@
 	volume = {44},
 	issn = {0022-3670},
-	url = {http://dx.doi.org/10.1175/JPO-D-14-0027.1},
 	doi = {10.1175/JPO-D-14-0027.1},
 	number = {10},
@@ -1801,5 +1777,4 @@
   pages = {891--904},
   doi = {10.1007/s00382-009-0642-4},
-  url = {http://dx.doi.org/10.1007/s00382-009-0642-4}
 }
 
@@ -1812,5 +1787,4 @@
   pages = {289--309},
   doi = {10.1007/s10236-008-0155-4},
-  url = {http://dx.doi.org/10.1007/s10236-008-0155-4}
 }
 
@@ -1823,5 +1797,4 @@
   pages = {L04604},
   doi = {10.1029/2006GL028405},
-  url = {http://dx.doi.org/10.1029/2006GL028405}
 }
 
@@ -1834,5 +1807,4 @@
   pages = {275--288},
   doi = {10.1007/s10236-008-0154-5},
-  url = {http://dx.doi.org/10.1007/s10236-008-0154-5}
 }
 
@@ -1862,5 +1834,4 @@
 issn = "1463-5003",
 doi = "http://dx.doi.org/10.1016/j.ocemod.2012.04.007",
-url = "http://www.sciencedirect.com/science/article/pii/S1463500312000674",
 }
 
@@ -1875,5 +1846,4 @@
   pages = {124--148},
   doi = {10.1016/j.ocemod.2015.06.006},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2015.06.006}
 }
 
@@ -1911,5 +1881,4 @@
   volume = {34},  number = {1-2},
   doi = {10.1016/j.ocemod.2010.04.001},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2010.04.001}
 }
 
@@ -1959,5 +1928,4 @@
   pages = {363--404},
   doi = {10.1029/94RG01872},
-  url = {http://dx.doi.org/10.1029/94RG01872}
 }
 
@@ -2001,5 +1969,4 @@
   pages = {1--14},
   doi = {10.1016/j.ocemod.2008.11.007},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2008.11.007}
 }
 
@@ -2020,5 +1987,4 @@
   pages = {88-94},
   doi = {10.1016/j.ocemod.2009.06.006},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2009.06.006}
 }
 
@@ -2030,5 +1996,4 @@
   volume = {37},  pages = {139--152}, 
   doi = {10.1016/j.ocemod.2011.02.001},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2011.02.001}
 }
 
@@ -2058,5 +2023,4 @@
   year = {2002},
   doi = {10.1029/2001JC000841},
-  url = {http://dx.doi.org/10.1029/2001JC000841}
 }
 
@@ -2070,5 +2034,4 @@
   pages = {3345},
   doi = {10.1029/2002JC001704},
-  url = {http://dx.doi.org/10.1029/2002JC001704}
 }
 
@@ -2081,5 +2044,4 @@
   pages = {L21602},
   doi = {10.1029/2009GL040145},
-  url = {http://dx.doi.org/10.1029/2009GL040145}
 }
 
@@ -2244,5 +2206,5 @@
   year = {1991},
   author = {G. Madec and M. Cr\'{e}pon}
-  }
+}
 
 @ARTICLE{Madec1997,
@@ -2349,5 +2311,4 @@
   pages = {61--89},
   doi = {10.1016/j.ocemod.2007.07.005},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2007.07.005}
 }
 
@@ -2360,5 +2321,4 @@
 NUMBER = {5},
 PAGES = {1547--1562},
-url = {HTTP://www.geosci-model-dev.net/8/1547/2015/},
 DOI = {10.5194/gmd-8-1547-2015}
 }
@@ -2373,5 +2333,4 @@
 issn = {1463-5003},
 doi = {10.1016/j.ocemod.2010.05.001},
-url = {http://dx.doi.org/10.1016/j.ocemod.2010.05.001}
 }
 
@@ -2409,5 +2368,4 @@
   pages = {1--26},
   doi = {10.1007/s00382-009-0640-6},
-  url = {http://dx.doi.org/10.1007/s00382-009-0640-6}
 }
 
@@ -2433,5 +2391,4 @@
   and H. Sasaki and K. Takahashi and F. Svensson},
   doi = {10.1007/978-3-540-74384-2},
-  url = {http://dx.doi.org/10.1007/978-3-540-74384-2}
 }
 
@@ -2447,5 +2404,4 @@
   pages = {L07703},
   doi = {10.1029/2004GL021980},
-  url = {http://dx.doi.org/10.1029/2004GL021980}
 }
 
@@ -2476,5 +2432,4 @@
 year = {2004},
 doi = {10.1175/2517.1},
-URL = {http://journals.ametsoc.org/doi/abs/10.1175/2517.1}
 }
 
@@ -2613,5 +2568,4 @@
   pages = {71--92},
   doi = {10.1175/2008JCLI2261.1},
-  url = {http://dx.doi.org/10.1175/2008JCLI2261.1}
 }
 
@@ -2670,5 +2624,4 @@
   pages = {193--254},
   doi = {10.2307/1993202},
-  url = {http://dx.doi.org/10.2307/1993202}
 }
 
@@ -2742,5 +2695,4 @@
   pages = {L14314},
   doi = {10.1029/2004GL019764},
-  url = {http://dx.doi.org/10.1029/2004GL019764}
 }
 
@@ -2752,5 +2704,4 @@
   volume = {30},  number = {2},
   doi = {10.1029/2002GL016003},
-  url = {http://dx.doi.org/10.1029/2002GL016003}
 }
 
@@ -2763,5 +2714,4 @@
 NUMBER = {15},
 PAGES = {4077--4098},
-URL = {HTTP://www.biogeosciences.net/11/4077/2014/},
 DOI = {10.5194/bg-11-4077-2014}
 }
@@ -2794,5 +2744,4 @@
 issn = "1463-5003",
 doi = "10.1016/j.ocemod.2015.04.002",
-url = "http://dx.doi.org/10.1016/j.ocemod.2015.04.002"
 }
 
@@ -2805,5 +2754,4 @@
 year = "2015",
 doi = "10.1175/JPO-D-15-0080.1",
-url = "http://dx.doi.org/10.1175/JPO-D-15-0080.1"
 }
 
@@ -2826,5 +2774,4 @@
   volume = {8}, pages={2991--3005},
   doi = {10.5194/gmd-8-2991-2015},
-  url = {http://dx.doi.org/10.5194/gmd-8-2991-2015}
 }
 
@@ -2884,5 +2831,4 @@
   pages = {3090},
   doi = {10.1029/2001JC001047},
-  url = {http://dx.doi.org/10.1029/2001JC001047}
 }
 
@@ -2903,4 +2849,5 @@
   pages = {submitted},
 }
+
 @ARTICLE{Simmons_al_OM04,
   author = {H. L. Simmons and S. R. Jayne and L. C. {St. Laurent} and A. J. Weaver},
@@ -2998,5 +2945,4 @@
   pages = {3029--3042},
   doi = {10.1016/j.dsr2.2004.09.008},
-  url = {http://dx.doi.org/10.1016/j.dsr2.2004.09.008}
 }
 
@@ -3009,5 +2955,4 @@
   pages = {2106},
   doi = {10.1029/2002GL015633},
-  url = {http://dx.doi.org/10.1029/2002GL015633}
 }
 
@@ -3142,5 +3087,4 @@
   pages = {568--580},
   doi = {10.1007/s10236-006-0069-y},
-  url = {http://dx.doi.org/10.1007/s10236-006-0069-y}
 }
 
@@ -3234,5 +3178,4 @@
   pages = {33--53},
   doi = {10.1016/j.ocemod.2008.10.005},
-  url = {http://dx.doi.org/10.1016/j.ocemod.2008.10.005}
 }
 
@@ -3256,5 +3199,4 @@
   pages = {81--113},
   doi = {10.1016/j.ocemod.2003.12.003},
-  url = {http://dx.doi.org/j.ocemod.2003.12.003}
 }
 
@@ -3323,5 +3265,4 @@
   pages = {108--123},
   doi = {10.1016/j.dynatmoce.2009.02.001},
-  url = {http://dx.doi.org/10.1016/j.dynatmoce.2009.02.001}
 }
 
@@ -3334,5 +3275,4 @@
   pages = {L08706},
   doi = {10.1029/2007GL029275},
-  url = {http://dx.doi.org/10.1029/2007GL029275}
 }
 
Index: /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.sty
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.sty	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.sty	(revision 9394)
@@ -7,16 +7,17 @@
 %% ==============================================================================
 
-\usepackage{natbib}		% bib
-\usepackage{caption}		% caption
-\usepackage{xcolor}		% color
-\usepackage{silence}		% compilation
-\usepackage{times}		% font
-\usepackage{hyperref}	% hyper
-\usepackage{enumitem}	% list
-\usepackage{minted}		% listing
-\usepackage{amsmath}		% maths
-\usepackage{fancyhdr}	% page
-\usepackage{minitoc}		% toc
-\usepackage{subfiles}	% subdocs
+\usepackage{natbib}		%% bib
+\usepackage{caption}		%% caption
+\usepackage{xcolor}		%% color
+\usepackage{silence}		%% compilation
+\usepackage{times}		%% font
+\usepackage{hyperref}	%% hyper
+\usepackage{idxlayout}	%% index
+\usepackage{enumitem}	%% list
+\usepackage{minted}		%% listing
+\usepackage{amsmath}		%% maths
+\usepackage{fancyhdr}	%% page
+\usepackage{minitoc}		%% toc
+\usepackage{subfiles}	%% subdocs
 
 
@@ -34,4 +35,7 @@
 	colorlinks
 }
+\idxlayout{font=footnotesize, columns=3}
+\renewcommand{\bibfont}{\footnotesize}
+\renewcommand{\bibsep}{3pt}
 
 
@@ -41,4 +45,5 @@
 \pagestyle{fancy}
 \bibliographystyle{../tex_sub/ametsoc}
+
 
 %% Additionnal fonts
@@ -121,6 +126,6 @@
 %% New commands
 
-\newcommand{ \gmcomment}[1]{}
-\newcommand{ \sfcomment}[1]{}
+\newcommand{\gmcomment}[1]{}
+\newcommand{\sfcomment}[1]{}
 \newcommand{\sgacomment}[1]{}
 
@@ -161,2 +166,4 @@
 \newcommand{\mygstrut}[2]{\rule[#1 em]{0pt}{#2 em}}
 \newcommand{\mystrut}{\rule[-.9 em]{0pt}{1.79 em}}
+
+\newcommand{\doi}[1]{\href{http://dx.doi.org/#1}{full-text}}
Index: /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.tex	(revision 9394)
@@ -140,15 +140,19 @@
 
 
+%% Bibliography
+
+\cleardoublepage
+\phantomsection
+\addcontentsline{toc}{chapter}{Bibliography}
+\bibliography{../tex_main/NEMO_manual}
+
+
 %% Index
 
+\cleardoublepage
+\phantomsection
 \addcontentsline{toc}{chapter}{Index}
 \printindex
 
 
-%% Bibliography
-
-\addcontentsline{toc}{chapter}{Bibliography}
-\bibliography{../tex_main/NEMO_manual}
-
-
 \end{document}
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_CONFIG.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_CONFIG.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_CONFIG.tex	(revision 9394)
@@ -290,7 +290,7 @@
 $z$-coordinates and is forced with tidal lateral boundary conditions
 using a flather boundary condition from the BDY module.
-The AMM configuration  uses the GLS (key\_zdfgls) turbulence scheme, the
-VVL non-linear free surface(key\_vvl) and time-splitting
-(key\_dynspg\_ts).
+The AMM configuration  uses the GLS (\key{zdfgls}) turbulence scheme, the
+VVL non-linear free surface(\key{vvl}) and time-splitting
+(\key{dynspg\_ts}).
 
 In addition to the tidal boundary condition the model may also take
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex	(revision 9394)
@@ -229,5 +229,5 @@
 with the size of the array passed to iomput. 
 The grid\_ref attribute refers to definitions set in iodef.xml which, in turn, reference grids 
-and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in iom.F90) 
+and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) 
 or defined in the domain\_def.xml file. $e.g.$:
 \begin{xmllines}
@@ -236,5 +236,5 @@
 Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step, 
 add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$ 
-which has been defined with the correct frequency of operations (iom\_set\_field\_attr in iom.F90)
+which has been defined with the correct frequency of operations (iom\_set\_field\_attr in \mdl{iom})
 
 \item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules)
@@ -566,5 +566,5 @@
 \subsubsection{Other controls of the XML attributes from NEMO}
 
-The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in iom.F90). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary). 
+The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in \mdl{iom}). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary). 
 
 Here is the list of these attributes:\\
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIU.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIU.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIU.tex	(revision 9394)
@@ -25,6 +25,6 @@
 \end{itemize}
 
-Models are provided for both the warm layer, diurnal\_bulk.F90, and the cool skin,
-cool\_skin.F90.  Foundation SST is not considered as it can be obtained
+Models are provided for both the warm layer, \mdfl{diurnal_bulk}, and the cool skin,
+\mdl{cool_skin}.  Foundation SST is not considered as it can be obtained
 either from the main NEMO model ($i.e.$ from the temperature of the top few model levels)
 or from some other source.  
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DYN.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DYN.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_DYN.tex	(revision 9394)
@@ -45,5 +45,5 @@
 For term \textit{ttt} in the momentum equations, the logical namelist variables are \textit{ln\_dynttt\_xxx}, 
 where \textit{xxx} is a 3 or 4 letter acronym corresponding to each optional scheme. 
-If a CPP key is used for this term its name is \textbf{key\_ttt}. The corresponding 
+If a CPP key is used for this term its name is \key{ttt}. The corresponding 
 code can be found in the \textit{dynttt\_xxx} module in the DYN directory, and it is 
 usually computed in the \textit{dyn\_ttt\_xxx} subroutine.
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_LDF.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_LDF.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_LDF.tex	(revision 9394)
@@ -337,5 +337,5 @@
 The specification of the space variation of the coefficient is made in 
 \mdl{ldftra} and \mdl{ldfdyn}, or more precisely in include files 
-\textit{traldf\_cNd.h90} and \textit{dynldf\_cNd.h90}, with N=1, 2 or 3. 
+\hf{traldf\_cNd} and \hf{dynldf\_cNd}, with N=1, 2 or 3. 
 The user can modify these include files as he/she wishes. The way the 
 mixing coefficient are set in the reference version can be briefly described 
@@ -343,5 +343,5 @@
 
 \subsubsection{Constant mixing coefficients (default option)}
-When none of the \textbf{key\_dynldf\_...} and \textbf{key\_traldf\_...} keys are 
+When none of the \key{dynldf\_...} and \key{traldf\_...} keys are 
 defined, a constant value is used over the whole ocean for momentum and 
 tracers, which is specified through the \np{rn\_ahm0} and \np{rn\_aht0} namelist 
@@ -430,5 +430,5 @@
 the eddy induced coefficient has to be defined. Its space variations are controlled 
 by the same CPP variable as for the eddy diffusivity coefficient ($i.e.$ 
-\textbf{key\_traldf\_cNd}). 
+\key{traldf\_cNd}). 
 
 (5) the eddy coefficient associated with a biharmonic operator must be set to a \emph{negative} value.
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_OBS.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_OBS.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_OBS.tex	(revision 9394)
@@ -882,6 +882,6 @@
 
 In addition to \emph{OPA\_SRC} the offline obs oper requires the inclusion
-of the \emph{OOO\_SRC} directory. \emph{OOO\_SRC} contains a replacement \textbf{nemo.f90} and
-\textbf{nemogcm.F90} which overwrites the resultant \textbf{nemo.exe}. This is the approach taken
+of the \emph{OOO\_SRC} directory. \emph{OOO\_SRC} contains a replacement \mdl{nemo} and
+\mdl{nemogcm} which overwrites the resultant \textbf{nemo.exe}. This is the approach taken
 by \emph{SAS\_SRC} and \emph{OFF\_SRC}.
 
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex	(revision 9394)
@@ -161,5 +161,5 @@
 
 A generic interface has been introduced to manage the way input data (2D or 3D fields, 
-like surface forcing or ocean T and S) are specify in \NEMO. This task is archieved by fldread.F90. 
+like surface forcing or ocean T and S) are specify in \NEMO. This task is archieved by \mdl{fldread}. 
 The module was design with four main objectives in mind: 
 \begin{enumerate}  
@@ -449,5 +449,5 @@
 
 \begin{itemize}
-\item \mdl{nemogcm} : This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (step.F90)
+\item \mdl{nemogcm} : This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (\mdl{step})
        Since the ocean state is not calculated all associated initialisations have been removed.
 \item  \mdl{step} : The main time stepping routine now only needs to call the sbc routine (and a few utility functions).
@@ -1272,6 +1272,6 @@
 and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used (seek advice from UKMO 
 if necessary).  Currently the code is only designed to work when using the CORE forcing option for NEMO (with
-\textit{calc\_strair~=~true} and \textit{calc\_Tsfc~=~true} in the CICE name-list), or alternatively when NEMO 
-is coupled to the HadGAM3 atmosphere model (with \textit{calc\_strair~=~false} and \textit{calc\_Tsfc~=~false}).
+\textit{calc\_strair}\forcode{ = .true.} and \textit{calc\_Tsfc}\forcode{ = .true.} in the CICE name-list), or alternatively when NEMO 
+is coupled to the HadGAM3 atmosphere model (with \textit{calc\_strair}\forcode{ = .false.} and \textit{calc\_Tsfc}\forcode{ = false}).
 The code is intended to be used with \np{nn\_fsbc} set to 1 (although coupling ocean and ice less frequently 
 should work, it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly - the
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_TRA.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_TRA.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_TRA.tex	(revision 9394)
@@ -53,5 +53,5 @@
 For each equation term  \textit{TTT}, the namelist logicals are \textit{ln\_traTTT\_xxx}, 
 where \textit{xxx} is a 3 or 4 letter acronym corresponding to each optional scheme. 
-The CPP key (when it exists) is \textbf{key\_traTTT}. The equivalent code can be 
+The CPP key (when it exists) is \key{traTTT}. The equivalent code can be 
 found in the \textit{traTTT} or \textit{traTTT\_xxx} module, in the NEMO/OPA/TRA directory.
 
@@ -146,5 +146,5 @@
 The choice is made in the \textit{\ngn{namtra\_adv}} namelist, by 
 setting to \forcode{.true.} one of the logicals \textit{ln\_traadv\_xxx}. 
-The corresponding code can be found in the \textit{traadv\_xxx.F90} module, 
+The corresponding code can be found in the \mdl{traadv\_xxx} module, 
 where \textit{xxx} is a 3 or 4 letter acronym corresponding to each scheme. 
 By default ($i.e.$ in the reference namelist, \ngn{namelist\_ref}), all the logicals 
@@ -1138,5 +1138,5 @@
 \np{ln\_zero\_top\_layer} specifies that the restoration coefficient should be zero in the surface layer. 
 Finally \np{ln\_custom} specifies that the custom module will be called. 
-This module is contained in the file custom.F90 and can be edited by users. For example damping could be applied in a specific region.
+This module is contained in the file \mdl{custom} and can be edited by users. For example damping could be applied in a specific region.
 
 The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}. 
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_misc.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_misc.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_misc.tex	(revision 9394)
@@ -203,5 +203,5 @@
 duplicated rows and columns due to cyclic or north fold boundary condition as well as 
 overlap MPP areas). The self-compensated summation method should be used in all summation
-in i- and/or j-direction. See closea.F90 module for an example.
+in i- and/or j-direction. See \mdl{closea} module for an example.
 Note also that this implementation may be sensitive to the optimization level. 
 
Index: /branches/2017/dev_merge_2017/DOC/tex_sub/chap_time_domain.tex
===================================================================
--- /branches/2017/dev_merge_2017/DOC/tex_sub/chap_time_domain.tex	(revision 9393)
+++ /branches/2017/dev_merge_2017/DOC/tex_sub/chap_time_domain.tex	(revision 9394)
@@ -92,5 +92,5 @@
 where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin 
 coefficient. $\gamma$ is initialized as \np{rn\_atfp} (namelist parameter). 
-Its default value is \np{rn_atfp}\forcode{ = 10.e-3} (see \S~\ref{STP_mLF}), 
+Its default value is \np{rn\_atfp}\forcode{ = 10.e-3} (see \S~\ref{STP_mLF}), 
 causing only a weak dissipation of high frequency motions (\citep{Farge1987}). 
 The addition of a time filter degrades the accuracy of the 
