Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_archfile.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_archfile.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_archfile.sh	(revision 1972)
@@ -0,0 +1,71 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ==================
+# Fcheck_archfile.sh
+# ==================
+#
+# --------------------------
+# Check the compilation file
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fcheck_archfile.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Check the choice of the compiler.
+# Three cases :  
+
+# - There was a previous choice
+# - A new one has be specified
+# - No information, exit 
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fcheck_archfile.sh COMPILER
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+if [ ${#1} -eq 0 ]; then
+   if [ ! -f ${TOOLS_DIR}/arch.fcm ]; then
+   echo "Warning !!!"
+   echo "NO compiler chosen"
+   echo "Try makenemo_fcm -h for help"
+   echo "EXITING..."
+   exit 1 
+   fi
+else
+   ln -sf ${MAIN_DIR}/ARCH/arch-${1}.fcm ${TOOLS_DIR}/arch.fcm
+fi
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_config.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_config.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_config.sh	(revision 1972)
@@ -0,0 +1,84 @@
+#!/bin/bash
+######################################################
+# Author : Rachid Benshila for NEMO
+# Contact : rblod@locean-ipsl.upmc.fr
+#
+# Some functions called from makenemo_fcm
+# Fcheck_config   : config checking 
+######################################################
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ================
+# Fcheck_config.sh
+# ================
+#
+# --------------------------
+# Check the configuration
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fcheck_config.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Check the choice of the configuration:
+
+# - Two cases
+# - One is explicitely set
+# - Nothing set, use the previous in use (default ORA2_LIM)
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fcheck_config.sh
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+declare -a ZTAB
+if [ ${#1} -eq 0 ]; then
+   tail -1  ${TOOLS_DIR}/cfg.txt	> ${TOOLS_DIR}/cfg.tmp
+   read -a ZTAB < ${TOOLS_DIR}/cfg.tmp
+   NEW_CONF=${ZTAB[0]} ; TAB=( ${ZTAB[@]:1} )
+   \rm ${TOOLS_DIR}/cfg.tmp
+   echo "Warning !!!"
+   echo "No configuration specified"
+   echo "Use makenemo_fcm -n MYCONFIG"
+   echo "or  makenemo_fcm -h for help"
+   echo "Using defaut configuration : ${NEW_CONF}"
+fi
+cat ${TOOLS_DIR}/cfg.txt | grep "${NEW_CONF} " > ${TOOLS_DIR}/cfg.tmp
+read -a ZTAB < ${TOOLS_DIR}/cfg.tmp
+NEW_CONF=${ZTAB[0]} ; TAB=( ${ZTAB[@]:1} )
+\rm ${TOOLS_DIR}/cfg.tmp
+
+unset -v ZTAB
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_script.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_script.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcheck_script.sh	(revision 1972)
@@ -0,0 +1,64 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ================
+# Fcheck_script.sh
+# ================
+#
+# --------------------------
+# Check
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fcheck_script.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Check if utilities are in the path
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fcheck_script.sh scriptname
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+myscript=`which $1`
+if [ ${#myscript} -eq 0 ]; then
+echo "WARNING !!!"
+echo "$1 has to be installed first"
+echo "Exiting......................"
+exit 1
+fi
+
+unset -v myscript
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fclean_var.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fclean_var.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fclean_var.sh	(revision 1972)
@@ -0,0 +1,67 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# =============
+# Fclean_var.sh
+# =============
+#
+# ----------------------------
+# Clean environement variables
+# ----------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fclean_var.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Clean environement variables
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fclean_var.sh
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+#- Unset variables
+
+unset -v NSTOP
+unset -v TAB
+unset -v NEW_CONF
+unset -v REF_CONF
+unset -v CMP_NAM
+unset -v NBR_PRC
+unset -v NEM_SUBDIR
+unset -v MAIN_DIR
+unset -v CONFIG_DIR
+unset -v TOOLS_DIR
+unset -v NEMO_DIR
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcopy_dir.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcopy_dir.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fcopy_dir.sh	(revision 1972)
@@ -0,0 +1,63 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ============
+# Fcopy_dir.sh
+# ============
+#
+# --------------------------
+# Copy a reference directory
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fcopy_dir.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# When a refenrence configuration is set, 
+# Copy NEMO sub-directories needed
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fcopy_dir.sh REF_DIR
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+declare -a ZTAB
+grep "$1 " ${TOOLS_DIR}/cfg.txt > ${TOOLS_DIR}/cfg.tmp
+read -a ZTAB < ${TOOLS_DIR}/cfg.tmp
+TAB=( ${ZTAB[@]:1} )
+\rm ${TOOLS_DIR}/cfg.tmp
+
+unset -v ZTAB
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fgo_to_TOOLS.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fgo_to_TOOLS.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fgo_to_TOOLS.sh	(revision 1972)
@@ -0,0 +1,57 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ===============
+# Fgo_to_tools.sh
+# ===============
+#
+# --------------------------
+# Go to the TOOLS directory
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fgo_to_tools.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Go to the TOOLS directory
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fgo_to_tools.sh
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+local MAIN_DIR=${PWD%/NEMOGCM/*}/NEMOGCM
+cd ${MAIN_DIR}/TOOLS
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_WORK.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_WORK.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_WORK.sh	(revision 1972)
@@ -0,0 +1,104 @@
+#!/bin/bash
+######################################################
+# Author : Rachid Benshila for NEMO
+# Contact : rblod@locean-ipsl.upmc.fr
+#
+# Some functions called from makenemo_fcm
+# Fmake_WORK      : create links in the WORK
+######################################################
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# =============
+# Fmake_WORK.sh
+# =============
+#
+# --------------------------
+# Make the WORK directory
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fmake_WORK.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Make the WORK directory:
+#
+# - Create lin in NEW_CONF/WORK
+# - Use specified sub-directories previously
+# - OPA has to be done first !!!
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fmake_WORK.sh
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+declare ZCONF=$1 ; shift 
+ZTAB=( $@ )
+declare i=0 ; declare NDIR=${#ZTAB[@]}
+
+echo "Creating ${ZCONF}/WORK = ${ZTAB[*]} for ${ZCONF}"
+echo ""
+
+[ ! -d ${ZCONF}/MY_SRC ] && \mkdir ${ZCONF}/MY_SRC
+[   -d ${ZCONF}/WORK   ] || \mkdir ${ZCONF}/WORK
+
+\rm -f ../${1}/WORK/*
+
+while [ $i -lt $NDIR ]
+do
+   [ "${ZTAB[i]}" = "OPA_SRC" ] && ln -sf ${NEMO_DIR}/OPA_SRC/*.[Ffh]90 ${ZCONF}/WORK
+   [ "${ZTAB[i]}" = "OPA_SRC" ] && ln -sf ${NEMO_DIR}/OPA_SRC/*/*.[Ffh]90 ${ZCONF}/WORK && break
+   let i=$i+1
+done
+
+i=0
+while [ $i -lt $NDIR ]
+do
+   if [ "${ZTAB[i]}" != "OPA_SRC" ]; then
+      ln -sf ${NEMO_DIR}/${ZTAB[i]}/*.[Ffh]90 ${ZCONF}/WORK
+      ln -sf ${NEMO_DIR}/${ZTAB[i]}/*/*.[Ffh]90 ${ZCONF}/WORK 2>/dev/null
+   fi
+   let i=$i+1
+done
+
+for i in `(cd ${ZCONF}/MY_SRC ; ls *.[Ffh]90 2>/dev/null ) `
+   do
+      [ -f ${ZCONF}/MY_SRC/$i ] &&  ln -sf $PWD/${ZCONF}/MY_SRC/${i} ${ZCONF}/WORK/.
+   done
+
+unset -v  ZCONF
+unset -v ZTAB
+unset -v  i
+unset -v NDIR
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_bld.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_bld.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_bld.sh	(revision 1972)
@@ -0,0 +1,62 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ============
+# Fmake_bld.sh
+# ============
+#
+# --------------------------
+# Make build directory
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fmake_bld.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# - Make the build directory 
+# - Create repositories needed :
+#  
+#  - BLD for compilation 
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fmake_bld.sh CONFIG_NAME  TMP_DIR
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+[ ! -d ${2}/${1} ] && \mkdir   ${2}/${1}
+[ ! -d ${2}/${1}/BLD ] && \mkdir  ${2}/${1}/BLD
+ln -sf ${2}/${1}/BLD ${CONFIG_DIR}/${1}/BLD
+#ln -sf ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ${TOOLS_DIR}/cpp.fcm
+rm -f  ${CONFIG_DIR}/${NEW_CONF}/BLD/fcm.bld.lock
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_config.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_config.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fmake_config.sh	(revision 1972)
@@ -0,0 +1,65 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ===============
+# Fmake_config.sh
+# ===============
+#
+# --------------------------
+# Make the config 
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fmake_config.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# - Make the config directory 
+# - Create repositories needed :
+#  
+#  - EXP00 for namelist
+#  - MY_SRC for user sources
+#  - BLD for compilation 
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fmake_config.sh CONFIG_NAME REF_CONFIG_NAME 
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+\mkdir  ${1}
+\mkdir  ${1}/EXP00
+\mkdir  ${1}/MY_SRC
+\cp -R  ${2}/cpp_${2}.fcm ${1}/cpp_${1}.fcm
+\cp -R  ${2}/EXP00/*namelist* ${1}/EXP00/.
+[ -d    ${2}/MY_SRC ] && \cp  ${2}/MY_SRC/* ${1}/MY_SRC/. 2> /dev/null
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fprep_agrif.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fprep_agrif.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fprep_agrif.sh	(revision 1972)
@@ -0,0 +1,71 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ==============
+# Fprep_agrif.sh
+# ==============
+#
+# --------------------------
+# Preparation for AGRIF
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fprep_agrif.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Prepare directories for AGRIF
+#
+# Compile the conv
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fprep_agrif.sh CONFIG_NAME
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+#- AGRIF conv
+if [ "$AGRIFUSE" == 1 ]; then
+
+#- CONV
+[ ! -d $2/$1/AGRIFLIB ] && mkdir -p $2/$1/AGRIFLIB
+fcm build ${TOOLS_DIR}/conv.cfg || exit 1
+
+#- AGRIF sources
+[ ! -d $2/$1/OPAFILES ] && mkdir  $2/$1/OPAFILES
+[ ! -d $2/$1/OPAFILES/AGRIF_INC ] && mkdir  $2/$1/OPAFILES/AGRIF_INC
+[ ! -d $2/$1/OPAFILES/AGRIF_MODELFILES ] && mkdir  $2/$1/OPAFILES/AGRIF_MODELFILES
+cp -f -r ${MAIN_DIR}/EXTERNAL/AGRIF/agrif_opa.in  $2/$1/OPAFILES/
+
+fi
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fread_dir.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fread_dir.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/Fread_dir.sh	(revision 1972)
@@ -0,0 +1,84 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ============
+# Fread_dir.sh
+# ============
+#
+# --------------------------
+# Read user directories
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ Fread_dir.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Read directoires needed from standard input
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./Fread_dir.sh Directory_NAME YES/NO
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+if [ "$2" == "YES" ]; then
+   echo -n " $1 [Y/n] "
+   read answer
+   answer=`echo $answer | sed 's/^[yY].*$/y/'`
+   if [  -z "$answer" -o "x$answer" = "xy" ]; then
+      TAB[$ind]="$1"
+      let ind=ind+1
+      echo " $1 selected "
+      echo "  "
+   else
+      echo " $1 Not selected "
+      echo "  "
+   fi
+   unset -v answer
+else
+   echo -n " $1 [y/N] "
+   read answer
+   answer=`echo $answer | sed 's/^[nN].*$/N/'`
+   if [ "x$answer" = "xy" ]; then
+      TAB[$ind]="$1"
+      let ind =ind+1
+      echo " $1 selected "
+      echo "  "
+   else
+      echo " $1 Not selected "
+      echo "  "
+   fi
+   unset -v answer
+fi
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/README
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/README	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/README	(revision 1972)
@@ -0,0 +1,7 @@
+CSHRC :
+setenv PATH ~/NEMOGCM/TOOLS:$PATH
+setenv NEMO_TDIR /users/rblod/tmp
+
+BASH :
+export PATH=$PATH:~/NEMOGCM/TOOLS'
+export NEMO_TDIR=/users/rblod/tmp
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/*.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/*.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/*.sh.rst	(revision 1972)
@@ -0,0 +1,52 @@
+
+==================
+Fcheck_archfile.sh
+==================
+
+--------------------------
+Check the compilation file
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcheck_archfile.sh
+
+
+DESCRIPTION
+===========
+
+
+Check the choice of the compiler.
+Three cases :  
+
+- There was a previous choice
+- A new one has be specified
+- No information, exit 
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcheck_archfile.sh COMPILER
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_archfile.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_archfile.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_archfile.sh.rst	(revision 1972)
@@ -0,0 +1,52 @@
+
+==================
+Fcheck_archfile.sh
+==================
+
+--------------------------
+Check the compilation file
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcheck_archfile.sh
+
+
+DESCRIPTION
+===========
+
+
+Check the choice of the compiler.
+Three cases :  
+
+- There was a previous choice
+- A new one has be specified
+- No information, exit 
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcheck_archfile.sh COMPILER
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_config.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_config.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_config.sh.rst	(revision 1972)
@@ -0,0 +1,51 @@
+
+================
+Fcheck_config.sh
+================
+
+--------------------------
+Check the configuration
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcheck_config.sh
+
+
+DESCRIPTION
+===========
+
+
+Check the choice of the configuration:
+
+- Two cases
+- One is explicitely set
+- Nothing set, use the previous in use (default ORA2_LIM)
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcheck_config.sh
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_script.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_script.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcheck_script.sh.rst	(revision 1972)
@@ -0,0 +1,47 @@
+
+================
+Fcheck_script.sh
+================
+
+--------------------------
+Check
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcheck_script.sh
+
+
+DESCRIPTION
+===========
+
+
+Check if utilities are in the path
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcheck_script.sh scriptname
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fclean_var.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fclean_var.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fclean_var.sh.rst	(revision 1972)
@@ -0,0 +1,47 @@
+
+=============
+Fclean_var.sh
+=============
+
+----------------------------
+Clean environement variables
+----------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fclean_var.sh
+
+
+DESCRIPTION
+===========
+
+
+Clean environement variables
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fclean_var.sh
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcopy_dir.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcopy_dir.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fcopy_dir.sh.rst	(revision 1972)
@@ -0,0 +1,48 @@
+
+============
+Fcopy_dir.sh
+============
+
+--------------------------
+Copy a reference directory
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcopy_dir.sh
+
+
+DESCRIPTION
+===========
+
+
+When a refenrence configuration is set, 
+Copy NEMO sub-directories needed
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcopy_dir.sh REF_DIR
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fgo_to_TOOLS.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fgo_to_TOOLS.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fgo_to_TOOLS.sh.rst	(revision 1972)
@@ -0,0 +1,47 @@
+
+===============
+Fgo_to_tools.sh
+===============
+
+--------------------------
+Go to the UTIL directory
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fgo_to_tools.sh
+
+
+DESCRIPTION
+===========
+
+
+Go to the UTIL directory
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fgo_to_tools.sh
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_WORK.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_WORK.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_WORK.sh.rst	(revision 1972)
@@ -0,0 +1,51 @@
+
+=============
+Fmake_WORK.sh
+=============
+
+--------------------------
+Make the WORK directory
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fmake_WORK.sh
+
+
+DESCRIPTION
+===========
+
+
+Make the WORK directory:
+
+- Create lin in NEW_CONF/WORK
+- Use specified sub-directories previously
+- OPA has to be done first !!!
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fmake_WORK.sh
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_bld.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_bld.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_bld.sh.rst	(revision 1972)
@@ -0,0 +1,50 @@
+
+============
+Fmake_bld.sh
+============
+
+--------------------------
+Make build directory
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fmake_bld.sh
+
+
+DESCRIPTION
+===========
+
+
+- Make the build directory 
+- Create repositories needed :
+ 
+ - BLD for compilation 
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fmake_bld.sh CONFIG_NAME  TMP_DIR
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_config.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_config.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fmake_config.sh.rst	(revision 1972)
@@ -0,0 +1,52 @@
+
+===============
+Fmake_config.sh
+===============
+
+--------------------------
+Make the config 
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fmake_config.sh
+
+
+DESCRIPTION
+===========
+
+
+- Make the config directory 
+- Create repositories needed :
+ 
+ - EXP00 for namelist
+ - MY_SRC for user sources
+ - BLD for compilation 
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fmake_config.sh CONFIG_NAME REF_CONFIG_NAME 
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fprep_agrif.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fprep_agrif.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fprep_agrif.sh.rst	(revision 1972)
@@ -0,0 +1,49 @@
+
+==============
+Fprep_agrif.sh
+==============
+
+--------------------------
+Preparation for AGRIF
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fprep_agrif.sh
+
+
+DESCRIPTION
+===========
+
+
+Prepare directories for AGRIF
+
+Compile the conv
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fprep_agrif.sh CONFIG_NAME
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fread_dir.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fread_dir.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/Fread_dir.sh.rst	(revision 1972)
@@ -0,0 +1,47 @@
+
+============
+Fread_dir.sh
+============
+
+--------------------------
+Read user directories
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fread_dir.sh
+
+
+DESCRIPTION
+===========
+
+
+Read directoires needed from standard input
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fread_dir.sh Directory_NAME YES/NO
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/agrifpp.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/agrifpp.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/agrifpp.sh.rst	(revision 1972)
@@ -0,0 +1,50 @@
+
+==========
+agrifpp.sh
+==========
+
+----------------------------
+Preform AGrif pre-processing
+----------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ agrifpp.sh
+
+
+DESCRIPTION
+===========
+
+
+Look after key agrif
+
+EXAMPLES
+========
+
+::
+
+ $ ./agrifpp.sh 1 -Dkey
+
+ or
+
+ $ ./agrifpp.sh -Dkey
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/extract_rst.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/extract_rst.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/extract_rst.sh	(revision 1972)
@@ -0,0 +1,311 @@
+#! /bin/sh
+#+
+#
+# ==========
+# extract.sh
+# ==========
+#
+# -----------------------------------------
+# extract ReStructuredText from source file
+# -----------------------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ``extract_rst.sh -i filein -l language -o fileout``
+#
+# DESCRIPTION
+# ===========
+#
+# ``extract_rst.sh`` extracts ReST comments from the file given in argument
+#
+# -i  input file
+# -o  output file (ReST)
+# -l  language
+#
+# Comment block (start, end) identification depends on language :
+#
+#  *F90*
+#   FORTRAN source free form
+#  *fortran*
+#   FORTRAN source fixed form
+#  *sh*
+#   shell scripts
+#  *IDL*
+#   IDL source
+#  *xml*
+#   XML and XSL
+#  *dot*
+#   graphviz files
+#  *php*
+#   PHP files
+#  *matlab*
+#   matlab or octave files
+#
+# EXAMPLES
+# ========
+#
+# To extract ReST comments of this shell script::
+#
+#  $ extract_rst.sh -i extract_rst.sh -l sh -o extract_rst.sh.rst
+#  iii : rst lines of extract_rst.sh are in extract_rst.sh.rst
+#
+# You can produce HTML file from this new file::
+#
+#  $ rst2html.py --input-encoding=ISO-8859-15 extract_rst.sh.rst \
+#    /usr/temp/${LOGNAME}/extract_rst.sh.html
+#
+# You can produce PDF file from this new file::
+#
+#  $ rst2newlatex.py --input-encoding=ISO-8859-15 extract_rst.sh.rst \
+#    /usr/temp/${LOGNAME}/extract_rst.sh.tex
+#  $ pdflatex extract_rst.sh.tex
+#
+# Of course beware of consistency of path on links.
+#
+# CAUTIONS
+# ========
+#
+# Becaue of poor implementation of Standard FORTRAN in cpp (prepocessing)
+# within gfortran and g95, ReST comments might induce trouble in
+# FORTRAN sources.
+#
+# For example following line is pointed out be gfortran with
+# ``error: unterminated comment``.
+# This is because ``/*`` is the beginning of a C style comment !!
+# ::
+#
+#      !    **MEAN** = sum( *X*\ (:) )/*ntime*
+#
+#
+#
+# One can modify this ReST line with
+# ::
+#
+#      !    **MEAN** = sum( *X*\ (:) ) / *ntime*
+#
+# TODO
+# ====
+#
+# check parameters
+#
+# log
+#
+# add perl
+#
+# SEE ALSO
+# ========
+#
+# ReStructuredText_
+#
+# .. _ReStructuredText: http://docutils.sourceforge.net/rst.html
+#
+# Docutils_
+#
+# .. _Docutils: http://docutils.sourceforge.net/
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+# - fplod 2009-04-20T08:13:37Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add CAUTIONS paragraph to warn about possible FORTRAN compiling problem
+#
+# - fplod 2009-04-03T14:53:18Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * usage of tr instead of sed to remove ``\r``
+#     due to difference between ``/sw/bin/sed`` and ``/usr/bin/sed`` (the last
+#     one do not work coorectly on ``\r`` interpertation ie: remove the first occurence of
+#     ``r``)
+#
+# - fplod 2009-02-10T10:46:23Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add language fortran for FORTRAN source in fixed form
+#
+# - fplod 2009-01-05T11:41:33Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * remove \\r (CRLF) from file before awk and sed (otherwise ReST block
+#     was not found in "ISO-8859 text, with CRLF line terminators" files
+#
+# - fplod 2008-12-22T10:37:37Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add matlab (octave)
+#
+# - fplod 2008-09-17T13:40:37Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add php language
+#
+# - fplod 2008-09-08T09:34:04Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add F90 language
+#
+# - fplod 2008-08-08T08:28:30Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add KML files (with other XML files)
+#   * add parameters ``-i`` ``-l`` ``-o``
+#
+# - fplod 200807
+#
+#   * creation
+#
+#-
+#
+system=$(uname)
+case "${system}" in
+   AIX|IRIX64)
+      echo " www : no specific posix checking"
+   ;;
+   *)
+      set -o posix
+   ;;
+esac
+unset system
+#
+command=$(basename ${0})
+log_date=$(date -u +"%Y%m%dT%H%M%SZ")
+log=/tmp/$(basename ${command} .sh).log.${log_date}
+#
+usage=" Usage : ${command} -i filein -l language -o fileout"
+#
+minargcount=6
+#echo " narg ${#}"
+if [ ${#} -lt ${minargcount} ]
+then
+   echo "eee : not enought arguments"
+   echo "${usage}"
+   exit 1
+fi
+#
+# default
+# n.a.
+#
+while [ ! -z "${1}" ]
+do
+   case ${1} in
+      -i)
+         filein=${2}
+         shift
+      ;;
+      -o)
+         fileout=${2}
+         shift
+      ;;
+      -l)
+         language=${2}
+         shift
+      ;;
+      -h)
+         echo "${usage}"
+         exit 0
+      ;;
+      *)
+         echo "eee : unknown option ${1}"
+         echo "${usage}"
+         exit 1
+      ;;
+   esac
+   # next flag
+   shift
+done
+#
+set -u
+#
+# ++ check param
+#
+case "${language}" in
+   fortran)
+      awkblockstart="^C\+$"
+      awkblockend="^C-$"
+      sedblockstart="^C+$"
+      sedblockend="^C-$"
+      comment="^C"
+   ;;
+   F90)
+      awkblockstart="^!\+$"
+      awkblockend="^!-$"
+      sedblockstart="^!+$"
+      sedblockend="^!-$"
+      comment="^!"
+   ;;
+   IDL)
+      awkblockstart="^;\+$"
+      awkblockend="^;-$"
+      sedblockstart="^;+$"
+      sedblockend="^;-$"
+      comment="^;"
+   ;;
+   xml)
+      awkblockstart="^<!--rst$"
+      awkblockend="-->$"
+      sedblockstart="^<!--rst$"
+      sedblockend="-->$"
+      comment=""
+   ;;
+   sh)
+      # iii : awk '/^\#\+/,/^\#\-/' $file
+      awkblockstart="^\#\+$"
+      awkblockend="^\#\-$"
+      sedblockstart="^#+"
+      sedblockend="^#-"
+      comment="^#"
+   ;;
+   dot|php)
+      awkblockstart="^\/\*rst$"
+      awkblockend="*\/"
+      sedblockstart="^\/\*rst$"
+      sedblockend="^\*\/"
+      comment=""
+   ;;
+   matlab)
+      awkblockstart="^%\+$"
+      awkblockend="^%-$"
+      sedblockstart="^%+$"
+      sedblockend="^%-$"
+      comment="^%"
+   ;;
+   *)
+      echo "eee : ${language} not implemented"
+      exit 1
+   ;;
+esac
+#
+# just in case suppress \r at the end of lines
+tr -d '\r' < ${filein} > /tmp/${$}_0
+#
+# put rst blocks in one temporary file
+#awk '/^;+/,/^;-/' a.pro | sed -e "/^;+$/d" -e "/^;-$/d" -e "s/^;//"
+cmdawk="awk '/${awkblockstart}/,/${awkblockend}/' /tmp/${$}_0 > /tmp/${$}_1" #++
+eval ${cmdawk}
+if [ ! -s /tmp/${$}_1 ]
+then
+   rm /tmp/${$}_0 /tmp/${$}_1
+   echo "iii : no rst comments in ${filein}"
+   exit 1
+fi
+#
+# suppress begin and end of each block
+sedcmd="sed -e \"/${sedblockstart}/d\" -e \"/${sedblockend}/d\" /tmp/${$}_1 > /tmp/${$}_2"
+eval ${sedcmd}
+#
+# suppress comment at the beginning of each line
+if [ "${comment}" != "" ]
+then
+   sedcmd="sed -e \"s/${comment}//\" /tmp/${$}_2 > /tmp/${$}_3"
+   eval ${sedcmd}
+   # suppress first blank
+   cp /tmp/${$}_3 /tmp/${$}_2
+   sed -e "s/^ //" /tmp/${$}_2 > /tmp/${$}_3
+   cp /tmp/${$}_3 ${fileout}
+else
+   cp /tmp/${$}_2 ${fileout}
+fi
+#
+echo "iii : rst lines of ${filein} are in ${fileout}"
+#
+# clean
+rm /tmp/${$}_0 /tmp/${$}_1 /tmp/${$}_2 /tmp/${$}_3 2> /dev/null
+#
+# exit
+exit 0
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/index_many.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/index_many.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/index_many.rst	(revision 1972)
@@ -0,0 +1,62 @@
+=================
+NEMO_UTIL manuals
+=================
+ 
+Shell scripts
+=============
+ 
+Fcheck_archfile.sh_
+ 
+.. _Fcheck_archfile.sh : Fcheck_archfile.sh.html
+ 
+Fcheck_config.sh_
+ 
+.. _Fcheck_config.sh : Fcheck_config.sh.html
+ 
+Fcheck_script.sh_
+ 
+.. _Fcheck_script.sh : Fcheck_script.sh.html
+ 
+Fclean_var.sh_
+ 
+.. _Fclean_var.sh : Fclean_var.sh.html
+ 
+Fcopy_dir.sh_
+ 
+.. _Fcopy_dir.sh : Fcopy_dir.sh.html
+ 
+Fgo_to_TOOLS.sh_
+ 
+.. _Fgo_to_TOOLS.sh : Fgo_to_TOOLS.sh.html
+ 
+Fmake_WORK.sh_
+ 
+.. _Fmake_WORK.sh : Fmake_WORK.sh.html
+ 
+Fmake_bld.sh_
+ 
+.. _Fmake_bld.sh : Fmake_bld.sh.html
+ 
+Fmake_config.sh_
+ 
+.. _Fmake_config.sh : Fmake_config.sh.html
+ 
+Fprep_agrif.sh_
+ 
+.. _Fprep_agrif.sh : Fprep_agrif.sh.html
+ 
+Fread_dir.sh_
+ 
+.. _Fread_dir.sh : Fread_dir.sh.html
+ 
+agrifpp.sh_
+ 
+.. _agrifpp.sh : agrifpp.sh.html
+ 
+chk_iomput.sh_
+ 
+.. _chk_iomput.sh : chk_iomput.sh.html
+ 
+makenemo_fcm.sh_
+ 
+.. _makenemo_fcm.sh : makenemo_fcm.sh.html
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/install.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/install.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/install.sh	(revision 1972)
@@ -0,0 +1,193 @@
+#!/bin/sh -x
+#+
+#
+# ==========
+# install.sh
+# ==========
+#
+# ----------------------------------------------
+# publication of HTML files and associated files
+# ----------------------------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ install.sh -w dirwww -p dirpublish -u urlpublish -l login
+#
+# DESCRIPTION
+# ===========
+#
+# publication (rsync) of dirwww content on dirpublish given in argument
+#
+# If the host of publication is cerbere.locean-ipsl.upmc.fr, a specific update
+# is launched.
+#
+# -w  input directort
+# -p  output directory
+# -u  output url
+# -l  login used to access on output url
+#
+# If needed, existing directories might be removed before (to erase obsolete
+# files), using ncftp tool :
+#
+# For example, to clean directory on LOCEAN web server ::
+#
+#  $ ncftp -u fplod www.locean-ipsl.upmc.fr
+#  ncftp> cd fplod
+#  ncftp> rm -f pageperso/.DS_Store
+#  ncftp> rm -rf pageperso
+#  ncftp> exit
+#
+# EXAMPLES
+# ========
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id: install.sh 101 2010-04-26 12:12:15Z pinsard $
+#
+# - fplod 2008-09-16T15:24:26Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * comments in ReStructured Text
+#
+# - fplod 2008-06-17T09:10:19Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add -l parameter only used in specific case at LOCEAN when user
+#     parameter of persoweb must be different tthan login (ex: acmo vs fplod)
+#   * replace http://www.lodyc.jussieu.fr/info_reseau/persoweb/?fastupdate=1&user=${user}" by
+#     http://intranet.locean-ipsl.upmc.fr/persoweb/?fastupdate=1&user=${user}
+#
+# - fplod 2008-03-28T10:26:58Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * new personnal webpages policy at LOCEAN so new command and new parameter (-u)
+#
+# - fplod 2007-09-28T09:30:43Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * parametrisation and translation
+#
+# - smasson 2007-06-07T16:43:42Z arete.locean-ipsl.upmc.fr (Darwin)
+#
+#   * can give the answer with input parameters
+#
+# - fplod 2007-04-26T11:51:42Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#-
+system=$(uname)
+case "${system}" in
+   AIX|IRIX64)
+      echo " www : no specific posix checking"
+   ;;
+   *)
+      set -o posix
+   ;;
+esac
+unset system
+#
+command=$(basename ${0})
+log_date=$(date -u +"%Y%m%dT%H%M%SZ")
+log=/tmp/$(basename ${command} .sh).log.${log_date}
+#
+usage=" Usage : ${command} -w dirwww -p dirpublish -u urlpublish -l login"
+#
+minargcount=4
+#echo " narg ${#}"
+if [ ${#} -lt ${minargcount} ]
+then
+   echo "eee : not enought arguments"
+   echo "${usage}"
+   exit 1
+fi
+unset minargcount
+#
+# default
+dirpublish="none"
+urlpublish="none"
+login="none"
+#
+while [ ! -z "${1}" ]
+do
+   case ${1} in
+      -w)
+         dirwww=${2}
+         shift
+      ;;
+      -p)
+         dirpublish=${2}
+         shift
+      ;;
+      -u)
+         urlpublish=${2}
+         shift
+      ;;
+      -l)
+         login=${2}
+         shift
+      ;;
+   esac
+   # next flag
+   shift
+done
+#
+set -u
+#
+# ++ check directories
+#
+answer=${1:-" "}
+case ${answer} in
+   y|Y|n|N)
+   ;;
+   *)
+      if [ "${dirpublish}" != "none" ]
+      then
+         echo "Do you want to install on ${dirpublish} (y|[n]) ?"
+         read answer
+      fi
+      if [ "${urlpublish}" != "none" ]
+      then
+         echo "Do you want to install on ${urlpublish} (y|[n]) ?"
+         read answer
+      fi
+   ;;
+esac
+#
+case  ${answer} in
+   y|Y)
+      if [ "${dirpublish}" != "none" ]
+      then
+         # copy of ${dirwww} on $dirpublish
+         echo "iii : update of ${dirpublish}"
+         rsync -av --exclude=".DS_Store" -e ssh ${dirwww}/ ${dirpublish}
+         # detect if in dirpublish following this pattern [USER@]HOST:SRC, HOST
+         # is cerbere.locean-ipsl.upmc.fr. If so, a specific update is launched
+         userhost=${dirpublish%%:*}
+         host=${userhost##*@}
+         if [ ${login} = "none" ]
+         then
+            user=${userhost%%@*}
+         else
+            user=${login}
+         fi
+         if [ "${host}" = "cerbere.locean-ipsl.upmc.fr" ]
+         then
+            wget -q "http://intranet.locean-ipsl.upmc.fr/persoweb/?fastupdate=1&user=${user}" -O /dev/null
+         fi
+      else
+         # urlpublish=http://www.locean-ipsl.upmc.fr/~ginette/produit
+         dirpublish=${urlpublish##*~}
+         cd ${dirwww}
+         #lftp -e "mirror -R . ${dirpublish};quit" -u ${LOGNAME} skyros.locean-ipsl.upmc.fr
+         lftp -e "mirror -R . ${dirpublish};quit" -u ${LOGNAME} localhost
+         # pour acmo a la main ++
+         #++lftp -e 'mirror -R . acmo/nouveaux/;quit' -u fplod www.locean-ipsl.upmc.fr
+         # ++ log
+      fi
+   ;;
+   *)
+      echo "no update of ${dirpublish} or ${urlpublish}"
+   ;;
+esac
+#
+# normal exit
+exit 0
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/makefile
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/makefile	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/makefile	(revision 1972)
@@ -0,0 +1,349 @@
+#+
+#
+# ========
+# makefile
+# ========
+#
+# ---------------------------------------
+# generation of documentation of superbib
+# ---------------------------------------
+#
+# TODO
+# ====
+#
+# add -W to sphinx command when encoding problems are solved
+#
+# usage of sphinx/source/Makefile
+#
+# revision of manual section of php and xsl
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id: makefile 101 2010-04-26 12:12:15Z pinsard $
+#
+# - fplod 20100419T145702Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * remove rest2web (sphinx is prefered)
+#
+# - fplod 20100323T135104Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * remove one pdf and html
+#
+# - fplod 20100311T143131Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add rest2web (alternative to sphinx)
+#
+# - fplod 20100310T190253Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add php and xsl files to man_troff
+#
+# - fplod 20100310T182201Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * usage of sphinx (for the first time !) not yet ok ...
+#
+# - fplod 20100310T091541Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add man_troff with shell scripts possible now with docutils 0.6
+#     can be test with
+#      $ man -M ../doc//manuals/man bibopa.sh
+#
+# - fplod 2009-05-13T14:08:49Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * implicit rules
+#
+#     nb : may be will only work wih GNU make
+#     but easier to update : only one line to add in thi makefile when
+#     a new file is added in $(DIRSRC) directory
+#
+#   * rst2latex usage of manuals_many.sty and manual_one.sty (for TOC and parindent)
+#   * bug fix for PDF manual (missing one pdf2latex)
+#
+# - fplod 2008-10-28T10:59:44Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * add newpage directive
+#     (thanks to http://docutils.sourceforge.net/docs/user/latex.html)
+#
+# - fplod 2008-09-17T09:16:08Z aedon.locean-ipsl.upmc.fr (Darwin)
+#   * add xsl files
+#
+# - fplod 2008-09-16T14:59:02Z aedon.locean-ipsl.upmc.fr (Darwin)
+#   * creation
+#
+# SEE ALSO
+# ========
+#
+# extract_rst.sh_
+#
+# .. _extract_rst.sh: ../extract_rst.sh.html
+#
+#-
+#
+PRODUCT = \
+NEMO_UTIL
+
+PRODUCTNAME = \
+$$(echo $(PRODUCT) | tr [:lower:] [:upper:])
+
+DIRSRC = \
+../
+
+DIRADM = \
+./
+
+DIRTMP = \
+./
+
+DIRDESIGN = \
+./design/
+
+DIRWWW = \
+../doc/
+
+URLPUBLISH = \
+http://192.168.0.12/~rblod/$(PRODUCT)
+
+LIST_SRCSH = $(wildcard $(DIRSRC)/*.sh)
+#$(DIRSRC)/Fcheck_archfile.sh \
+#$(DIRSRC)/Fcheck_config.sh \
+#$(DIRSRC)/Fclean_var.sh \
+#$(DIRSRC)/Fgo_to_TOOLS.sh \
+#$(DIRSRC)/Fmake_config.sh \
+#$(DIRSRC)/Fcopy_dir.sh  \
+#$(DIRSRC)/Fmake_WORK.sh  \
+#$(DIRSRC)/Fread_dir.sh \
+#$(DIRSRC)/makenemo_fcm.sh
+
+LIST_SRCSH_RST = \
+$(shell echo "$(LIST_SRCSH)" | \
+	sed -e "s+$(DIRSRC)+$(DIRTMP)/+g" \
+	    -e "s+\.sh+.sh.rst+g")
+
+LIST_SRCSH_R2W = \
+$(shell echo "$(LIST_SRCSH)" | \
+	sed -e "s+$(DIRSRC)+$(DIRTMP)/rest2web_tmpdir+g" \
+	    -e "s+\.s+.s.txt+g")
+
+
+LIST_SRCSH_TROFF = \
+$(shell echo "$(LIST_SRCSH)" | \
+	sed -e "s+$(DIRSRC)+$(DIRWWW)/manuals/man/man1/+g" \
+	    -e "s+\.sh+.sh.1+g")
+
+LIST_SRCSH_HTML = \
+$(shell echo "$(LIST_SRCSH)" | \
+	sed -e "s+$(DIRSRC)+$(DIRWWW)/manuals/html/many/+g" \
+	    -e "s+\.sh+.sh.html+g")
+
+LIST_SRCSH_PDF = \
+$(shell echo "$(LIST_SRCSH)" | \
+	sed -e "s+$(DIRSRC)+$(DIRWWW)/manuals/pdf/many/+g" \
+	    -e "s+\.sh+.sh.pdf+g")
+
+RST2MAN = \
+rst2man.py
+
+RST2HTML = \
+rst2html.py
+
+RST2LATEX = \
+rst2latex.py
+
+RST2LATEX_OPTIONS_MANY = \
+--documentclass=article \
+--stylesheet=manuals_many.sty \
+--traceback \
+--use-verbatim-when-possible
+
+.PHONY : \
+help \
+before \
+clean \
+cleantmp \
+design \
+htmllinkcheckb \
+htmllinkchecka \
+spellcheck \
+all \
+man \
+man_troff \
+man_html \
+man_html_many \
+man_html_sphinx \
+man_pdf \
+man_pdf_many \
+man_pdf_sphinx
+
+help :
+	@echo "Prepare output directories :"
+	@echo "\$$ make before"
+	@echo ""
+	@echo "Following commands are available to build outputs :"
+	@echo "\$$ make all"
+	@echo " "
+	@echo "Check links before installation : "
+	@echo "\$$ make htmllinkcheckb"
+	@echo " "
+	@echo "Last step = installation"
+	@echo "\$$ make install"
+	@echo " "
+	@echo "Check links after installation : "
+	@echo "\$$ make htmllinkchecka"
+	@echo " "
+
+before :
+	@mkdir -p $(DIRWWW)/manuals/man/man1/
+	@mkdir -p $(DIRWWW)/manuals/html/many/
+	@mkdir -p $(DIRWWW)/manuals/html/rest2web/
+	@mkdir -p $(DIRWWW)/manuals/html/rest2web/css/
+	@mkdir -p $(DIRWWW)/manuals/html/sphinx/
+	@mkdir -p $(DIRWWW)/manuals/pdf/many/
+	@mkdir -p $(DIRWWW)/manuals/pdf/sphinx/
+	@mkdir -p $(DIRTMP)/sphinx_tmpdir/doctrees/
+	@mkdir -p $(DIRTMP)/rest2web_tmpdir/
+
+install :
+	@install.sh -w $(DIRWWW) -u $(URLPUBLISH)
+
+clean : \
+cleantmp
+	-@rm -fr $(DIRWWW)/
+	-@rm -fr $(DIRWWW)/manuals/man/
+	-@rm -fr $(DIRWWW)/manuals/html/
+	-@rm -fr $(DIRWWW)/manuals/pdf/
+
+cleantmp :
+	-@rm -f $(DIRTMP)/all.xml
+	-@rm -f $(DIRTMP)/*.rst
+	-@rm -f $(DIRTMP)/*.tex
+	-@rm -rf $(DIRTMP)/rest2web_tmpdir/
+	-@rm -f $(DIRTMP)/rest2web.log
+	-@rm -f $(DIRWWW)/manuals/pdf/many/*.aux
+	-@rm -f $(DIRWWW)/manuals/pdf/many/*.log
+	-@rm -f $(DIRWWW)/manuals/pdf/many/*.out
+	-@rm -rf $(DIRTMP)/sphinx_tmpdir/
+	-@rm -f $(DIRTMP)/sphinx_*.log
+
+design : \
+$(DIRDESIGN)/images/$(PRODUCT)_fulldependencies.png \
+$(DIRDESIGN)/images/$(PRODUCT)_fulldependencies.svg
+
+htmllinkcheckb :
+	@linkchecker.sh -d $(DIRWWW)/manuals/html/
+
+htmllinkchecka :
+	@linkchecker.sh -u $(URLPUBLISH)
+
+spellcheck :
+	@++aspell --mode=sgml --master=francais -c \
+	$(DIRSRC)/$(PRODUCT).xml
+
+all : \
+man_troff \
+man_html \
+man_pdf
+
+man_troff : \
+$(LIST_SRCSH_TROFF) 
+
+man_html : \
+man_html_many \
+man_html_sphinx
+
+man_html_many : \
+$(DIRWWW)/manuals/html/many/index.html \
+$(LIST_SRCSH_HTML) 
+
+man_html_sphinx : \
+$(DIRADM)/sphinx/conf.py \
+$(DIRTMP)/sphinx_tmpdir/index.rst \
+$(LIST_SRCSH_RST) 
+	@cp $(LIST_SRCSH_RST) $(DIRTMP)/sphinx_tmpdir/
+	sphinx-build -b html -c $(DIRADM)/sphinx \
+	    -d $(DIRTMP)/sphinx_tmpdir/doctrees \
+	    -w $(DIRTMP)/sphinx_html.log \
+	    $(DIRTMP)/sphinx_tmpdir/ \
+	    $(DIRWWW)/manuals/html/sphinx/
+
+man_pdf : \
+man_pdf_many \
+man_pdf_sphinx
+
+man_pdf_many : \
+$(LIST_SRCSH_PHP) 
+
+man_pdf_sphinx : \
+$(DIRADM)/sphinx/conf.py \
+$(DIRTMP)/sphinx_tmpdir/index.rst \
+$(LIST_SRCSH_RST) 
+	@cp $(LIST_SRCSH_RST) $(DIRTMP)/sphinx_tmpdir/
+	@sphinx-build -b latex -c $(DIRADM)/sphinx \
+	    -d $(DIRTMP)/sphinx_tmpdir/doctrees \
+	    -w $(DIRTMP)/sphinx_pdf.log \
+	    $(DIRTMP)/sphinx_tmpdir/ \
+	    $(DIRTMP)/sphinx_tmpdir/latex_output
+	cd $(DIRTMP)/sphinx_tmpdir/latex_output/; make all-pdf
+	cp $(DIRTMP)/sphinx_tmpdir/latex_output/*.pdf \
+	   $(DIRWWW)/manuals/pdf/sphinx/
+
+$(DIRWWW)/manuals/html/many/index.html : \
+$(DIRTMP)/index_many.rst
+	@$(RST2HTML) --input-encoding=ISO-8859-15 --strict \
+	$< $@
+
+$(DIRTMP)/index_many.rst :
+	@echo "$(PRODUCTNAME) manuals" | tr [:print:] = > $@
+	@echo "$(PRODUCTNAME) manuals" >> $@
+	@echo "$(PRODUCTNAME) manuals" | tr [:print:] = >> $@
+	@echo " " >> $@
+	@echo "Shell scripts" >> $@
+	@echo "Shell scripts" | tr [:print:] = >> $@
+	@for file in $(LIST_SRCSH); do echo " ";echo "$$(basename $${file})_"; echo " "; echo ".. _$$(basename $${file}) : $$(basename $${file}).html"; done >> $@
+
+$(DIRTMP)/sphinx_tmpdir/index.rst :
+	@echo ".. _index:" >> $@
+	@echo " " >> $@
+	@echo "$(PRODUCTNAME) manuals" | tr [:print:] = >> $@
+	@echo "$(PRODUCTNAME) manuals" >> $@
+	@echo "$(PRODUCTNAME) manuals" | tr [:print:] = >> $@
+	@echo " " >> $@
+	@echo "Shell scripts" >> $@
+	@echo "Shell scripts" | tr [:print:] = >> $@
+	@echo ".. toctree::" >> $@
+	@echo "   :maxdepth: 1" 1>> $@
+	@echo "   :glob:" 1>> $@
+	@echo " " >> $@
+	@for file in $(LIST_SRCSH); \
+	do \
+	   echo "   $$(basename $${file})"; \
+	done >> $@
+	@echo " " >> $@
+
+$(DIRWWW)/manuals/man/man1/%.1:$(DIRTMP)/%.rst
+	@$(RST2MAN) --input-encoding=ISO-8859-15 --strict \
+	$< $@
+
+$(DIRWWW)/manuals/html/many/%.html:$(DIRTMP)/%.rst
+	@$(RST2HTML) --input-encoding=ISO-8859-15 --strict \
+	$< $@
+
+$(DIRWWW)/manuals/pdf/many/%.pdf : $(DIRTMP)/%.tex
+	@-pdflatex -output-directory $(DIRWWW)/manuals/pdf/many/ $<
+	@-pdflatex -output-directory $(DIRWWW)/manuals/pdf/many/ $<
+
+$(DIRTMP)/%.tex : $(DIRTMP)/%.rst
+	@$(RST2LATEX) $(RST2LATEX_OPTIONS_MANY) --input-encoding=ISO-8859-15 --strict \
+	$< $@
+
+$(DIRTMP)/%.sh.rst : $(DIRSRC)/%.sh
+	@$(DIRADM)/extract_rst.sh -i $< -l sh -o $@
+
+$(DIRDESIGN)/images/%.png : $(DIRDESIGN)/images/%.svg
+	@convert $< $@
+
+$(DIRDESIGN)/images/%.svg : $(DIRDESIGN)/%.dot
+	@dot -Tsvg -o $@ $<
+
+$(DIRDESIGN)/$(PRODUCT)_fulldependencies.dot : \
+./makefile
+	@makeppgraph --graphviz --output=$@
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/makenemo_fcm.sh.rst
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/makenemo_fcm.sh.rst	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/adm/makenemo_fcm.sh.rst	(revision 1972)
@@ -0,0 +1,71 @@
+
+===============
+makenemo_fcm.sh
+===============
+
+--------------------------
+Compile NEMO
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ makenemo_fcm.sh
+
+
+DESCRIPTION
+===========
+
+
+This script aims :
+
+- to choose MYCONFIG
+- to choose compiler options  
+- to create the CONFIG/MYCONFIG/WORK directory
+- to compile this configuration
+
+ Variables used :
+
+ From user input
+
+- NEW_CONF    : configuration to be created
+- REF_CONF    : reference configuration to build the new one 
+- CMP_NAM     : compiler name 
+- NBR_PRC     : number of processes used to compile  
+- NEM_SUBDIR  : NEMO subdirectory used (specified)
+
+ Locally defined :
+
+- TAB         : NEMO subdirectory used (read)  
+- MAIN_DIR : self explaining
+- CONFIG_DIR  :   "    "    "   
+- MODELES_DIR :   "    "    " 
+- TOOLS_DIR   :   "    "    " 
+- NEMO_DIR    :   "    "    "
+
+EXAMPLES
+========
+
+::
+
+ $ ./makenemo_fcm -t ifort_osx - j3 -n ORCA2_LIM
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/agrifpp.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/agrifpp.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/agrifpp.sh	(revision 1972)
@@ -0,0 +1,91 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u
+#set -e
+#+
+#
+# ==========
+# agrifpp.sh
+# ==========
+#
+# ----------------------------
+# Preform AGrif pre-processing
+# ----------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ agrifpp.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# Look after key agrif
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./agrifpp.sh 1 -Dkey
+# 
+#  or
+#
+#  $ ./agrifpp.sh -Dkey
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+if [ "$1" == "1" ]; then
+   shift
+   MYFILE=`echo $* |awk -F" " '{print $NF}' `  
+   FPP_OPT=` echo $* |awk '{  for (i=1 ; i<NF ; i++ )  { printf " %s",  $i } }'`
+
+
+   MYFILE=`echo $* |awk -F" " '{print $NF}' `
+   if [ "${MYFILE}" != "par_oce.F90" -a  ! -f ${NEMO_TDIR}/${NEW_CONF}}/OPAFILES/param_done ]; then
+      cpp -P -C -traditional  ${FPP_OPT} ${CONFIG_DIR}/${NEW_CONF}/WORK/par_oce.F90 > ${NEMO_TDIR}/${NEW_CONF}/OPAFILES/par_oce.F90
+      (cd ${NEMO_TDIR}/${NEW_CONF}/OPAFILES ; ${NEMO_TDIR}/${NEW_CONF}/AGRIFLIB/bin/conv agrif_opa.in -rm -comdirin ./ -comdirout AGRIF_MODELFILES/ -convfile par_oce.F90 > /dev/null )
+      cpp -P -C -traditional  -I${NEMO_TDIR}/${NEW_CONF}/OPAFILES/AGRIF_INC  ${NEMO_TDIR}/${NEW_CONF}/OPAFILES/AGRIF_MODELFILES/par_oce.F90 > ${NEMO_TDIR}/${NEW_CONF}/OPAFILES/par_oce.F90
+      touch ${NEMO_TDIR}/${NEW_CONF}/OPAFILES/param_done
+   elif  [ "${MYFILE}" == "par_oce.F90" -a -f ${NEMO_TDIR}/${NEW_CONF}/OPAFILES/param_done ] ; then
+      cd  ${NEMO_TDIR}/${NEW_CONF}/OPAFILES
+      cpp -P -C -traditional -I${NEMO_TDIR}/${NEW_CONF}/OPAFILES/AGRIF_INC ${MYFILE}
+      exit
+   fi
+
+   if [ "${MYFILE}" == agrif2model.F90 ]; then
+      cpp  -P -C -traditional -I${NEMO_TDIR}/${NEW_CONF}/OPAFILES/AGRIF_INC $@
+      exit
+   fi 
+
+   cpp   -P -traditional -I${NEMO_TDIR}/${NEW_CONF}/OPAFILES/AGRIF_INC $@ > ${NEMO_TDIR}/${NEW_CONF}/OPAFILES/${MYFILE}
+   ( cd ${NEMO_TDIR}/${NEW_CONF}/OPAFILES ; ${NEMO_TDIR}/${NEW_CONF}/AGRIFLIB/bin/conv agrif_opa.in -rm -comdirin ./ -comdirout AGRIF_MODELFILES/ -convfile ${MYFILE} > /dev/null )
+   cd  ${NEMO_TDIR}/${NEW_CONF}
+   mv -f OPAFILES/AGRIF_MODELFILES/${MYFILE} OPAFILES/${MYFILE}
+   cpp  -P -C -traditional -IOPAFILES/AGRIF_INC OPAFILES/${MYFILE} 
+else
+   shift
+   cpp -P -C -traditional $@
+fi
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/bld.cfg
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/bld.cfg	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/bld.cfg	(revision 1972)
@@ -0,0 +1,71 @@
+# ----------------------- FCM extract configuration file -----------------------
+cfg::type                           bld
+cfg::version                        1.0
+
+
+# ------------------------------------------------------------------------------
+# Build information
+# ------------------------------------------------------------------------------
+
+inc $MAIN_DIR/TOOLS/arch.fcm
+inc $MAIN_DIR/TOOLS/cpp.fcm
+
+%FFLAGS                   %FFLAGS %NCDF_INC  
+%LD_FLAGS                 %BASE_LD %NCDF_LIB
+src::agrif                $MAIN_DIR/EXTERNAL/AGRIF/AGRIF_FILES
+src::ioipsl               $MAIN_DIR/EXTERNAL/IOIPSL/src
+src::xmlf90               $MAIN_DIR/EXTERNAL/XMLF90/src
+src::xmlio_server         $MAIN_DIR/EXTERNAL/XMLIO_SERVER/src
+src::nemo                 $CONFIG_DIR/$NEW_CONF/WORK
+
+
+#bld::target              model.exe
+
+bld::exe_dep 
+
+
+dir::root            $NEMO_TDIR/$NEW_CONF/BLD
+
+#search_src           1
+
+bld::tool::fc        %FC 
+bld::tool::ld        %LD
+bld::tool::ar        %AR
+bld::tool::arflags   %ARFLAGS
+bld::tool::make      %M_K
+bld::tool::fflags    %FFLAGS 
+bld::tool::ldflags   %LD_FLAGS 
+
+bld::tool::cppflags  %FPP_FLAGS 
+bld::tool::fppflags  %FPP_FLAGS
+
+
+# Pre-process code before analysing dependencies
+bld::pp::nemo 1
+bld::tool::fpp       $TOOLS_DIR/agrifpp.sh
+bld::tool::fppflags  %FPP_FLAGS
+bld::tool::fppflags::nemo $AGRIFUSE
+
+# Ignore the following dependencies
+bld::excl_dep        inc::netcdf.inc
+bld::excl_dep        use::netcdf
+bld::excl_dep        h::netcdf.inc
+bld::excl_dep        h::mpif.h
+bld::excl_dep        inc::mpif.h
+bld::excl_dep        use::mod_prism_proto
+bld::excl_dep        use::mod_prism_def_partition_proto
+bld::excl_dep        use::mod_prism_get_proto
+bld::excl_dep        use::mod_prism_put_proto
+bld::excl_dep        use::mkl_dfti
+# Don't generate interface files
+bld::tool::geninterface none
+
+# Allow ".h90" as an extension for CPP include files
+bld::infile_ext::h90  CPP::INCLUDE
+
+# extension for module output
+bld::outfile_ext::mod .mod
+
+# rename executable to nemo.exe
+bld::exe_name::model  nemo.exe
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/cfg.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/cfg.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/cfg.txt	(revision 1972)
@@ -0,0 +1,7 @@
+ORCA2_OFF_PISCES OFF_SRC TOP_SRC
+GYRE OPA_SRC LIM_SRC_2 C1D_SRC
+ORCA2_LIM_PISCES OPA_SRC LIM_SRC_2 NST_SRC C1D_SRC TOP_SRC
+toto OPA_SRC LIM_SRC_2 C1D_SRC NST_SRC
+GYRE_LOBSTER OPA_SRC LIM_SRC_2 NST_SRC C1D_SRC TOP_SRC
+ORCA2_LIM_OFF OPA_SRC LIM_SRC_2 C1D_SRC NST_SRC OFF_SRC
+ORCA2_LIM OPA_SRC LIM_SRC_2 NST_SRC C1D_SRC
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/conv.cfg
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/conv.cfg	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/conv.cfg	(revision 1972)
@@ -0,0 +1,27 @@
+# ----------------------- FCM extract configuration file -----------------------
+cfg::type                           bld
+cfg::version                        1.0
+
+
+# ------------------------------------------------------------------------------
+# Build information
+# ------------------------------------------------------------------------------
+
+src::convsrc   $MAIN_DIR/EXTERNAL/AGRIF/LIB
+
+ #----------------------------------------------------------------------------
+# Build options (code-specific, machine-independent)
+# ----------------------------------------------------------------------------
+dir::root            $NEMO_TDIR/$NEW_CONF/AGRIFLIB
+
+bld::tool::cflags::convsrc  -O
+bld::tool::ld::convsrc   cc
+bld::tool::ldflags::convsrc -O  
+bld::pp
+
+bld::exe_name::main conv
+bld::target                              libconvsrc.a  fortran.o main.o  conv
+bld::exe_dep::conv      
+
+
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_archfile.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_archfile.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_archfile.sh.html	(revision 1972)
@@ -0,0 +1,349 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
+<title>Fcheck_archfile.sh</title>
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
+:Copyright: This stylesheet has been placed in the public domain.
+
+Default cascading style sheet for the HTML output of Docutils.
+
+See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
+customize this style sheet.
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+  margin-top: 0.4em }
+
+h1.title {
+  text-align: center }
+
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+  text-align: center }
+
+hr.docutils {
+  width: 75% }
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+  clear: left ;
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+  float: right ;
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+  list-style-type: none }
+
+</style>
+</head>
+<body>
+<div class="document" id="fcheck-archfile-sh">
+<h1 class="title">Fcheck_archfile.sh</h1>
+<h2 class="subtitle" id="check-the-compilation-file">Check the compilation file</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fcheck_archfile.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Check the choice of the compiler.
+Three cases :</p>
+<ul class="simple">
+<li>There was a previous choice</li>
+<li>A new one has be specified</li>
+<li>No information, exit</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fcheck_archfile.sh COMPILER
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_config.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_config.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_config.sh.html	(revision 1972)
@@ -0,0 +1,348 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
+<title>Fcheck_config.sh</title>
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
+:Copyright: This stylesheet has been placed in the public domain.
+
+Default cascading style sheet for the HTML output of Docutils.
+
+See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
+customize this style sheet.
+*/
+
+/* used to remove borders from tables and images */
+.borderless, table.borderless td, table.borderless th {
+  border: 0 }
+
+table.borderless td, table.borderless th {
+  /* Override padding for "table.docutils td" with "! important".
+     The right padding separates the table cells. */
+  padding: 0 0.5em 0 0 ! important }
+
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+  /* Override more specific margin styles with "! important". */
+  margin-top: 0 ! important }
+
+.last, .with-subtitle {
+  margin-bottom: 0 ! important }
+
+.hidden {
+  display: none }
+
+a.toc-backref {
+  text-decoration: none ;
+  color: black }
+
+blockquote.epigraph {
+  margin: 2em 5em ; }
+
+dl.docutils dd {
+  margin-bottom: 0.5em }
+
+/* Uncomment (and remove this text!) to get bold-faced definition list terms
+dl.docutils dt {
+  font-weight: bold }
+*/
+
+div.abstract {
+  margin: 2em 5em }
+
+div.abstract p.topic-title {
+  font-weight: bold ;
+  text-align: center }
+
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+div.hint, div.important, div.note, div.tip, div.warning {
+  margin: 2em ;
+  border: medium outset ;
+  padding: 1em }
+
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+  font-weight: bold ;
+  font-family: sans-serif }
+
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+div.danger p.admonition-title, div.error p.admonition-title,
+div.warning p.admonition-title {
+  color: red ;
+  font-weight: bold ;
+  font-family: sans-serif }
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+<h1 class="title">Fcheck_config.sh</h1>
+<h2 class="subtitle" id="check-the-configuration">Check the configuration</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fcheck_config.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Check the choice of the configuration:</p>
+<ul class="simple">
+<li>Two cases</li>
+<li>One is explicitely set</li>
+<li>Nothing set, use the previous in use (default ORA2_LIM)</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fcheck_config.sh
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_script.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_script.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcheck_script.sh.html	(revision 1972)
@@ -0,0 +1,343 @@
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+<div class="document" id="fcheck-script-sh">
+<h1 class="title">Fcheck_script.sh</h1>
+<h2 class="subtitle" id="check">Check</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fcheck_script.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Check if utilities are in the path</p>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fcheck_script.sh scriptname
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fclean_var.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fclean_var.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fclean_var.sh.html	(revision 1972)
@@ -0,0 +1,343 @@
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+<h2 class="subtitle" id="clean-environement-variables">Clean environement variables</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fclean_var.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Clean environement variables</p>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fclean_var.sh
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcopy_dir.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcopy_dir.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fcopy_dir.sh.html	(revision 1972)
@@ -0,0 +1,344 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
+<title>Fcopy_dir.sh</title>
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
+:Copyright: This stylesheet has been placed in the public domain.
+
+Default cascading style sheet for the HTML output of Docutils.
+
+See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
+customize this style sheet.
+*/
+
+/* used to remove borders from tables and images */
+.borderless, table.borderless td, table.borderless th {
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+     The right padding separates the table cells. */
+  padding: 0 0.5em 0 0 ! important }
+
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+  margin-top: 0 ! important }
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+  margin-bottom: 0 ! important }
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+  display: none }
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+  text-decoration: none ;
+  color: black }
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+blockquote.epigraph {
+  margin: 2em 5em ; }
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+  margin-bottom: 0.5em }
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+  font-weight: bold }
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+  font-family: sans-serif }
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+  margin-left: 50% }
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+  font-size: larger ;
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+  margin-bottom: 0 ;
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+  font: inherit }
+
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+  margin-left: 2em ;
+  margin-right: 2em }
+
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+  font-family: sans-serif ;
+  font-style: oblique }
+
+span.classifier-delimiter {
+  font-family: sans-serif ;
+  font-weight: bold }
+
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+  font-family: sans-serif }
+
+span.option {
+  white-space: nowrap }
+
+span.pre {
+  white-space: pre }
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+  color: red }
+
+span.section-subtitle {
+  /* font-size relative to parent (h1..h6 element) */
+  font-size: 80% }
+
+table.citation {
+  border-left: solid 1px gray;
+  margin-left: 1px }
+
+table.docinfo {
+  margin: 2em 4em }
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+  margin-top: 0.5em ;
+  margin-bottom: 0.5em }
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+  border-left: solid 1px black;
+  margin-left: 1px }
+
+table.docutils td, table.docutils th,
+table.docinfo td, table.docinfo th {
+  padding-left: 0.5em ;
+  padding-right: 0.5em ;
+  vertical-align: top }
+
+table.docutils th.field-name, table.docinfo th.docinfo-name {
+  font-weight: bold ;
+  text-align: left ;
+  white-space: nowrap ;
+  padding-left: 0 }
+
+h1 tt.docutils, h2 tt.docutils, h3 tt.docutils,
+h4 tt.docutils, h5 tt.docutils, h6 tt.docutils {
+  font-size: 100% }
+
+ul.auto-toc {
+  list-style-type: none }
+
+</style>
+</head>
+<body>
+<div class="document" id="fcopy-dir-sh">
+<h1 class="title">Fcopy_dir.sh</h1>
+<h2 class="subtitle" id="copy-a-reference-directory">Copy a reference directory</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fcopy_dir.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>When a refenrence configuration is set,
+Copy NEMO sub-directories needed</p>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fcopy_dir.sh REF_DIR
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fgo_to_TOOLS.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fgo_to_TOOLS.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fgo_to_TOOLS.sh.html	(revision 1972)
@@ -0,0 +1,343 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
+<title>Fgo_to_tools.sh</title>
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
+:Copyright: This stylesheet has been placed in the public domain.
+
+Default cascading style sheet for the HTML output of Docutils.
+
+See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
+customize this style sheet.
+*/
+
+/* used to remove borders from tables and images */
+.borderless, table.borderless td, table.borderless th {
+  border: 0 }
+
+table.borderless td, table.borderless th {
+  /* Override padding for "table.docutils td" with "! important".
+     The right padding separates the table cells. */
+  padding: 0 0.5em 0 0 ! important }
+
+.first {
+  /* Override more specific margin styles with "! important". */
+  margin-top: 0 ! important }
+
+.last, .with-subtitle {
+  margin-bottom: 0 ! important }
+
+.hidden {
+  display: none }
+
+a.toc-backref {
+  text-decoration: none ;
+  color: black }
+
+blockquote.epigraph {
+  margin: 2em 5em ; }
+
+dl.docutils dd {
+  margin-bottom: 0.5em }
+
+/* Uncomment (and remove this text!) to get bold-faced definition list terms
+dl.docutils dt {
+  font-weight: bold }
+*/
+
+div.abstract {
+  margin: 2em 5em }
+
+div.abstract p.topic-title {
+  font-weight: bold ;
+  text-align: center }
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+  margin: 2em ;
+  border: medium outset ;
+  padding: 1em }
+
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+div.tip p.admonition-title {
+  font-weight: bold ;
+  font-family: sans-serif }
+
+div.attention p.admonition-title, div.caution p.admonition-title,
+div.danger p.admonition-title, div.error p.admonition-title,
+div.warning p.admonition-title {
+  color: red ;
+  font-weight: bold ;
+  font-family: sans-serif }
+
+/* Uncomment (and remove this text!) to get reduced vertical space in
+   compound paragraphs.
+div.compound .compound-first, div.compound .compound-middle {
+  margin-bottom: 0.5em }
+
+div.compound .compound-last, div.compound .compound-middle {
+  margin-top: 0.5em }
+*/
+
+div.dedication {
+  margin: 2em 5em ;
+  text-align: center ;
+  font-style: italic }
+
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+  font-weight: bold ;
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+
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+
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+  text-align: center }
+
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+  text-align: center }
+
+hr.docutils {
+  width: 75% }
+
+img.align-left, .figure.align-left{
+  clear: left ;
+  float: left ;
+  margin-right: 1em }
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+  text-align: left }
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+  list-style: upper-roman }
+
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+  margin-left: 50% }
+
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+  font-style: italic }
+
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+  font-style: italic ;
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+
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+  white-space: nowrap }
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+  font-size: larger ;
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+  white-space: pre }
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+  color: red }
+
+span.section-subtitle {
+  /* font-size relative to parent (h1..h6 element) */
+  font-size: 80% }
+
+table.citation {
+  border-left: solid 1px gray;
+  margin-left: 1px }
+
+table.docinfo {
+  margin: 2em 4em }
+
+table.docutils {
+  margin-top: 0.5em ;
+  margin-bottom: 0.5em }
+
+table.footnote {
+  border-left: solid 1px black;
+  margin-left: 1px }
+
+table.docutils td, table.docutils th,
+table.docinfo td, table.docinfo th {
+  padding-left: 0.5em ;
+  padding-right: 0.5em ;
+  vertical-align: top }
+
+table.docutils th.field-name, table.docinfo th.docinfo-name {
+  font-weight: bold ;
+  text-align: left ;
+  white-space: nowrap ;
+  padding-left: 0 }
+
+h1 tt.docutils, h2 tt.docutils, h3 tt.docutils,
+h4 tt.docutils, h5 tt.docutils, h6 tt.docutils {
+  font-size: 100% }
+
+ul.auto-toc {
+  list-style-type: none }
+
+</style>
+</head>
+<body>
+<div class="document" id="fgo-to-tools-sh">
+<h1 class="title">Fgo_to_tools.sh</h1>
+<h2 class="subtitle" id="go-to-the-util-directory">Go to the UTIL directory</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fgo_to_tools.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Go to the UTIL directory</p>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fgo_to_tools.sh
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_WORK.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_WORK.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_WORK.sh.html	(revision 1972)
@@ -0,0 +1,348 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
+<title>Fmake_WORK.sh</title>
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
+:Copyright: This stylesheet has been placed in the public domain.
+
+Default cascading style sheet for the HTML output of Docutils.
+
+See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
+customize this style sheet.
+*/
+
+/* used to remove borders from tables and images */
+.borderless, table.borderless td, table.borderless th {
+  border: 0 }
+
+table.borderless td, table.borderless th {
+  /* Override padding for "table.docutils td" with "! important".
+     The right padding separates the table cells. */
+  padding: 0 0.5em 0 0 ! important }
+
+.first {
+  /* Override more specific margin styles with "! important". */
+  margin-top: 0 ! important }
+
+.last, .with-subtitle {
+  margin-bottom: 0 ! important }
+
+.hidden {
+  display: none }
+
+a.toc-backref {
+  text-decoration: none ;
+  color: black }
+
+blockquote.epigraph {
+  margin: 2em 5em ; }
+
+dl.docutils dd {
+  margin-bottom: 0.5em }
+
+/* Uncomment (and remove this text!) to get bold-faced definition list terms
+dl.docutils dt {
+  font-weight: bold }
+*/
+
+div.abstract {
+  margin: 2em 5em }
+
+div.abstract p.topic-title {
+  font-weight: bold ;
+  text-align: center }
+
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+  margin-left: 1px }
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+  margin: 2em 4em }
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+  margin-top: 0.5em ;
+  margin-bottom: 0.5em }
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+  font-size: 100% }
+
+ul.auto-toc {
+  list-style-type: none }
+
+</style>
+</head>
+<body>
+<div class="document" id="fmake-work-sh">
+<h1 class="title">Fmake_WORK.sh</h1>
+<h2 class="subtitle" id="make-the-work-directory">Make the WORK directory</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fmake_WORK.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Make the WORK directory:</p>
+<ul class="simple">
+<li>Create lin in NEW_CONF/WORK</li>
+<li>Use specified sub-directories previously</li>
+<li>OPA has to be done first !!!</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fmake_WORK.sh
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_bld.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_bld.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_bld.sh.html	(revision 1972)
@@ -0,0 +1,351 @@
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+<body>
+<div class="document" id="fmake-bld-sh">
+<h1 class="title">Fmake_bld.sh</h1>
+<h2 class="subtitle" id="make-build-directory">Make build directory</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fmake_bld.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<ul class="simple">
+<li>Make the build directory</li>
+<li>Create repositories needed :</li>
+</ul>
+<blockquote>
+<ul class="simple">
+<li>BLD for compilation</li>
+</ul>
+</blockquote>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fmake_bld.sh CONFIG_NAME  TMP_DIR
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_config.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_config.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fmake_config.sh.html	(revision 1972)
@@ -0,0 +1,353 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
+<title>Fmake_config.sh</title>
+<style type="text/css">
+
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+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
+:Copyright: This stylesheet has been placed in the public domain.
+
+Default cascading style sheet for the HTML output of Docutils.
+
+See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
+customize this style sheet.
+*/
+
+/* used to remove borders from tables and images */
+.borderless, table.borderless td, table.borderless th {
+  border: 0 }
+
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+  padding: 0 0.5em 0 0 ! important }
+
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+  /* Override more specific margin styles with "! important". */
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+  margin-bottom: 0 ! important }
+
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+  display: none }
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+  text-decoration: none ;
+  color: black }
+
+blockquote.epigraph {
+  margin: 2em 5em ; }
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+  margin-bottom: 0.5em }
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+<body>
+<div class="document" id="fmake-config-sh">
+<h1 class="title">Fmake_config.sh</h1>
+<h2 class="subtitle" id="make-the-config">Make the config</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fmake_config.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<ul class="simple">
+<li>Make the config directory</li>
+<li>Create repositories needed :</li>
+</ul>
+<blockquote>
+<ul class="simple">
+<li>EXP00 for namelist</li>
+<li>MY_SRC for user sources</li>
+<li>BLD for compilation</li>
+</ul>
+</blockquote>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fmake_config.sh CONFIG_NAME REF_CONFIG_NAME
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fprep_agrif.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fprep_agrif.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fprep_agrif.sh.html	(revision 1972)
@@ -0,0 +1,344 @@
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+<h1 class="title">Fprep_agrif.sh</h1>
+<h2 class="subtitle" id="preparation-for-agrif">Preparation for AGRIF</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fprep_agrif.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Prepare directories for AGRIF</p>
+<p>Compile the conv</p>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fprep_agrif.sh CONFIG_NAME
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fread_dir.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fread_dir.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/Fread_dir.sh.html	(revision 1972)
@@ -0,0 +1,343 @@
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+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
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+
+ul.auto-toc {
+  list-style-type: none }
+
+</style>
+</head>
+<body>
+<div class="document" id="fread-dir-sh">
+<h1 class="title">Fread_dir.sh</h1>
+<h2 class="subtitle" id="read-user-directories">Read user directories</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ Fread_dir.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Read directoires needed from standard input</p>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./Fread_dir.sh Directory_NAME YES/NO
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/agrifpp.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/agrifpp.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/agrifpp.sh.html	(revision 1972)
@@ -0,0 +1,347 @@
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+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
+<title>agrifpp.sh</title>
+<style type="text/css">
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+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
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+<div class="document" id="agrifpp-sh">
+<h1 class="title">agrifpp.sh</h1>
+<h2 class="subtitle" id="preform-agrif-pre-processing">Preform AGrif pre-processing</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ agrifpp.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>Look after key agrif</p>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./agrifpp.sh 1 -Dkey
+
+or
+
+$ ./agrifpp.sh -Dkey
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/index.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/index.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/index.html	(revision 1972)
@@ -0,0 +1,327 @@
+<?xml version="1.0" encoding="utf-8" ?>
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+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
+<title>NEMO_UTIL manuals</title>
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
+:Copyright: This stylesheet has been placed in the public domain.
+
+Default cascading style sheet for the HTML output of Docutils.
+
+See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
+customize this style sheet.
+*/
+
+/* used to remove borders from tables and images */
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+  padding: 0 0.5em 0 0 ! important }
+
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+  /* Override more specific margin styles with "! important". */
+  margin-top: 0 ! important }
+
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+  margin-bottom: 0 ! important }
+
+.hidden {
+  display: none }
+
+a.toc-backref {
+  text-decoration: none ;
+  color: black }
+
+blockquote.epigraph {
+  margin: 2em 5em ; }
+
+dl.docutils dd {
+  margin-bottom: 0.5em }
+
+/* Uncomment (and remove this text!) to get bold-faced definition list terms
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+*/
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+div.abstract {
+  margin: 2em 5em }
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+div.abstract p.topic-title {
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+  margin-left: 1px }
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+  margin: 2em 4em }
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+  margin-bottom: 0.5em }
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+  white-space: nowrap ;
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+h1 tt.docutils, h2 tt.docutils, h3 tt.docutils,
+h4 tt.docutils, h5 tt.docutils, h6 tt.docutils {
+  font-size: 100% }
+
+ul.auto-toc {
+  list-style-type: none }
+
+</style>
+</head>
+<body>
+<div class="document" id="nemo-util-manuals">
+<h1 class="title">NEMO_UTIL manuals</h1>
+<h2 class="subtitle" id="shell-scripts">Shell scripts</h2>
+
+<p><a class="reference external" href="Fcheck_archfile.sh.html">Fcheck_archfile.sh</a></p>
+<p><a class="reference external" href="Fcheck_config.sh.html">Fcheck_config.sh</a></p>
+<p><a class="reference external" href="Fcheck_script.sh.html">Fcheck_script.sh</a></p>
+<p><a class="reference external" href="Fclean_var.sh.html">Fclean_var.sh</a></p>
+<p><a class="reference external" href="Fcopy_dir.sh.html">Fcopy_dir.sh</a></p>
+<p><a class="reference external" href="Fgo_to_TOOLS.sh.html">Fgo_to_TOOLS.sh</a></p>
+<p><a class="reference external" href="Fmake_WORK.sh.html">Fmake_WORK.sh</a></p>
+<p><a class="reference external" href="Fmake_bld.sh.html">Fmake_bld.sh</a></p>
+<p><a class="reference external" href="Fmake_config.sh.html">Fmake_config.sh</a></p>
+<p><a class="reference external" href="Fprep_agrif.sh.html">Fprep_agrif.sh</a></p>
+<p><a class="reference external" href="Fread_dir.sh.html">Fread_dir.sh</a></p>
+<p><a class="reference external" href="agrifpp.sh.html">agrifpp.sh</a></p>
+<p><a class="reference external" href="chk_iomput.sh.html">chk_iomput.sh</a></p>
+<p><a class="reference external" href="makenemo_fcm.sh.html">makenemo_fcm.sh</a></p>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/makenemo_fcm.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/makenemo_fcm.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/many/makenemo_fcm.sh.html	(revision 1972)
@@ -0,0 +1,370 @@
+<?xml version="1.0" encoding="utf-8" ?>
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+</head>
+<body>
+<div class="document" id="makenemo-fcm-sh">
+<h1 class="title">makenemo_fcm.sh</h1>
+<h2 class="subtitle" id="compile-nemo">Compile NEMO</h2>
+
+<div class="section" id="synopsis">
+<h1>SYNOPSIS</h1>
+<pre class="literal-block">
+$ makenemo_fcm.sh
+</pre>
+</div>
+<div class="section" id="description">
+<h1>DESCRIPTION</h1>
+<p>This script aims :</p>
+<ul class="simple">
+<li>to choose MYCONFIG</li>
+<li>to choose compiler options</li>
+<li>to create the CONFIG/MYCONFIG/WORK directory</li>
+<li>to compile this configuration</li>
+</ul>
+<blockquote>
+<p>Variables used :</p>
+<p>From user input</p>
+</blockquote>
+<ul class="simple">
+<li>NEW_CONF    : configuration to be created</li>
+<li>REF_CONF    : reference configuration to build the new one</li>
+<li>CMP_NAM     : compiler name</li>
+<li>NBR_PRC     : number of processes used to compile</li>
+<li>NEM_SUBDIR  : NEMO subdirectory used (specified)</li>
+</ul>
+<blockquote>
+Locally defined :</blockquote>
+<ul class="simple">
+<li>TAB         : NEMO subdirectory used (read)</li>
+<li>MAIN_DIR : self explaining</li>
+<li>CONFIG_DIR  :   &quot;    &quot;    &quot;</li>
+<li>MODELES_DIR :   &quot;    &quot;    &quot;</li>
+<li>TOOLS_DIR   :   &quot;    &quot;    &quot;</li>
+<li>NEMO_DIR    :   &quot;    &quot;    &quot;</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h1>EXAMPLES</h1>
+<pre class="literal-block">
+$ ./makenemo_fcm -t ifort_osx - j3 -n ORCA2_LIM
+</pre>
+</div>
+<div class="section" id="todo">
+<h1>TODO</h1>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h1>EVOLUTIONS</h1>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/*.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/*.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/*.sh.html	(revision 1972)
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fcheck_archfile.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fcheck-archfile-sh">
+<h1>Fcheck_archfile.sh<a class="headerlink" href="#fcheck-archfile-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="check-the-compilation-file">
+<h2>Check the compilation file<a class="headerlink" href="#check-the-compilation-file" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fcheck_archfile.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Check the choice of the compiler.
+Three cases :</p>
+<ul class="simple">
+<li>There was a previous choice</li>
+<li>A new one has be specified</li>
+<li>No information, exit</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fcheck_archfile.sh COMPILER</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fcheck_archfile.sh</a><ul>
+<li><a class="reference external" href="#check-the-compilation-file">Check the compilation file</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/.buildinfo
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/.buildinfo	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/.buildinfo	(revision 1972)
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 386ef30eaadeaaa97a741592535ebb1b
+tags: fbb0d17656682115ca4d033fb2f83ba1
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_archfile.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_archfile.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_archfile.sh.html	(revision 1972)
@@ -0,0 +1,153 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fcheck_archfile.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" />
+    <link rel="next" title="Fcheck_config.sh" href="Fcheck_config.sh.html" />
+    <link rel="prev" title="NEMO_UTIL manuals" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fcheck_config.sh.html" title="Fcheck_config.sh"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
+          <a href="index.html" title="NEMO_UTIL manuals"
+             accesskey="P">previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fcheck-archfile-sh">
+<h1>Fcheck_archfile.sh<a class="headerlink" href="#fcheck-archfile-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="check-the-compilation-file">
+<h2>Check the compilation file<a class="headerlink" href="#check-the-compilation-file" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fcheck_archfile.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Check the choice of the compiler.
+Three cases :</p>
+<ul class="simple">
+<li>There was a previous choice</li>
+<li>A new one has be specified</li>
+<li>No information, exit</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fcheck_archfile.sh COMPILER</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fcheck_archfile.sh</a><ul>
+<li><a class="reference external" href="#check-the-compilation-file">Check the compilation file</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="index.html"
+                                  title="previous chapter">NEMO_UTIL manuals</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="Fcheck_config.sh.html"
+                                  title="next chapter">Fcheck_config.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="Fcheck_config.sh.html" title="Fcheck_config.sh"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="index.html" title="NEMO_UTIL manuals"
+             >previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_config.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_config.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_config.sh.html	(revision 1972)
@@ -0,0 +1,152 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fcheck_config.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" />
+    <link rel="next" title="Fclean_var.sh" href="Fclean_var.sh.html" />
+    <link rel="prev" title="Fcheck_archfile.sh" href="Fcheck_archfile.sh.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fclean_var.sh.html" title="Fclean_var.sh"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
+          <a href="Fcheck_archfile.sh.html" title="Fcheck_archfile.sh"
+             accesskey="P">previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fcheck-config-sh">
+<h1>Fcheck_config.sh<a class="headerlink" href="#fcheck-config-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="check-the-configuration">
+<h2>Check the configuration<a class="headerlink" href="#check-the-configuration" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fcheck_config.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Check the choice of the configuration:</p>
+<ul class="simple">
+<li>Two cases</li>
+<li>One is explicitely set</li>
+<li>Nothing set, use the previous in use (default ORA2_LIM)</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fcheck_config.sh</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fcheck_config.sh</a><ul>
+<li><a class="reference external" href="#check-the-configuration">Check the configuration</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="Fcheck_archfile.sh.html"
+                                  title="previous chapter">Fcheck_archfile.sh</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="Fclean_var.sh.html"
+                                  title="next chapter">Fclean_var.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
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+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
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+          <a href="Fclean_var.sh.html" title="Fclean_var.sh"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="Fcheck_archfile.sh.html" title="Fcheck_archfile.sh"
+             >previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_script.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_script.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcheck_script.sh.html	(revision 1972)
@@ -0,0 +1,127 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fcheck_script.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fcheck-script-sh">
+<h1>Fcheck_script.sh<a class="headerlink" href="#fcheck-script-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="check">
+<h2>Check<a class="headerlink" href="#check" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fcheck_script.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Check if utilities are in the path</p>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fcheck_script.sh scriptname</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fcheck_script.sh</a><ul>
+<li><a class="reference external" href="#check">Check</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fclean_var.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fclean_var.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fclean_var.sh.html	(revision 1972)
@@ -0,0 +1,147 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fclean_var.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" />
+    <link rel="next" title="Fgo_to_tools.sh" href="Fgo_to_TOOLS.sh.html" />
+    <link rel="prev" title="Fcheck_config.sh" href="Fcheck_config.sh.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fgo_to_TOOLS.sh.html" title="Fgo_to_tools.sh"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
+          <a href="Fcheck_config.sh.html" title="Fcheck_config.sh"
+             accesskey="P">previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fclean-var-sh">
+<h1>Fclean_var.sh<a class="headerlink" href="#fclean-var-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="clean-environement-variables">
+<h2>Clean environement variables<a class="headerlink" href="#clean-environement-variables" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fclean_var.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Clean environement variables</p>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fclean_var.sh</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fclean_var.sh</a><ul>
+<li><a class="reference external" href="#clean-environement-variables">Clean environement variables</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="Fcheck_config.sh.html"
+                                  title="previous chapter">Fcheck_config.sh</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="Fgo_to_TOOLS.sh.html"
+                                  title="next chapter">Fgo_to_tools.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
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+          <a href="Fgo_to_TOOLS.sh.html" title="Fgo_to_tools.sh"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="Fcheck_config.sh.html" title="Fcheck_config.sh"
+             >previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcopy_dir.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcopy_dir.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fcopy_dir.sh.html	(revision 1972)
@@ -0,0 +1,148 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fcopy_dir.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" />
+    <link rel="next" title="Fmake_WORK.sh" href="Fmake_WORK.sh.html" />
+    <link rel="prev" title="Fmake_config.sh" href="Fmake_config.sh.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fmake_WORK.sh.html" title="Fmake_WORK.sh"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
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+             accesskey="P">previous</a> |</li>
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+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fcopy-dir-sh">
+<h1>Fcopy_dir.sh<a class="headerlink" href="#fcopy-dir-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="copy-a-reference-directory">
+<h2>Copy a reference directory<a class="headerlink" href="#copy-a-reference-directory" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fcopy_dir.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>When a refenrence configuration is set,
+Copy NEMO sub-directories needed</p>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fcopy_dir.sh REF_DIR</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fcopy_dir.sh</a><ul>
+<li><a class="reference external" href="#copy-a-reference-directory">Copy a reference directory</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="Fmake_config.sh.html"
+                                  title="previous chapter">Fmake_config.sh</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="Fmake_WORK.sh.html"
+                                  title="next chapter">Fmake_WORK.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="Fmake_WORK.sh.html" title="Fmake_WORK.sh"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="Fmake_config.sh.html" title="Fmake_config.sh"
+             >previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fgo_to_TOOLS.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fgo_to_TOOLS.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fgo_to_TOOLS.sh.html	(revision 1972)
@@ -0,0 +1,147 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fgo_to_tools.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" />
+    <link rel="next" title="Fmake_config.sh" href="Fmake_config.sh.html" />
+    <link rel="prev" title="Fclean_var.sh" href="Fclean_var.sh.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fmake_config.sh.html" title="Fmake_config.sh"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
+          <a href="Fclean_var.sh.html" title="Fclean_var.sh"
+             accesskey="P">previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fgo-to-tools-sh">
+<h1>Fgo_to_tools.sh<a class="headerlink" href="#fgo-to-tools-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="go-to-the-util-directory">
+<h2>Go to the UTIL directory<a class="headerlink" href="#go-to-the-util-directory" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fgo_to_tools.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Go to the UTIL directory</p>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fgo_to_tools.sh</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fgo_to_tools.sh</a><ul>
+<li><a class="reference external" href="#go-to-the-util-directory">Go to the UTIL directory</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="Fclean_var.sh.html"
+                                  title="previous chapter">Fclean_var.sh</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="Fmake_config.sh.html"
+                                  title="next chapter">Fmake_config.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="Fmake_config.sh.html" title="Fmake_config.sh"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="Fclean_var.sh.html" title="Fclean_var.sh"
+             >previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_WORK.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_WORK.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_WORK.sh.html	(revision 1972)
@@ -0,0 +1,152 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fmake_WORK.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" />
+    <link rel="next" title="Fread_dir.sh" href="Fread_dir.sh.html" />
+    <link rel="prev" title="Fcopy_dir.sh" href="Fcopy_dir.sh.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fread_dir.sh.html" title="Fread_dir.sh"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
+          <a href="Fcopy_dir.sh.html" title="Fcopy_dir.sh"
+             accesskey="P">previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fmake-work-sh">
+<h1>Fmake_WORK.sh<a class="headerlink" href="#fmake-work-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="make-the-work-directory">
+<h2>Make the WORK directory<a class="headerlink" href="#make-the-work-directory" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fmake_WORK.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Make the WORK directory:</p>
+<ul class="simple">
+<li>Create lin in NEW_CONF/WORK</li>
+<li>Use specified sub-directories previously</li>
+<li>OPA has to be done first !!!</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fmake_WORK.sh</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fmake_WORK.sh</a><ul>
+<li><a class="reference external" href="#make-the-work-directory">Make the WORK directory</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="Fcopy_dir.sh.html"
+                                  title="previous chapter">Fcopy_dir.sh</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="Fread_dir.sh.html"
+                                  title="next chapter">Fread_dir.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="Fread_dir.sh.html" title="Fread_dir.sh"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="Fcopy_dir.sh.html" title="Fcopy_dir.sh"
+             >previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_bld.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_bld.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_bld.sh.html	(revision 1972)
@@ -0,0 +1,135 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fmake_bld.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fmake-bld-sh">
+<h1>Fmake_bld.sh<a class="headerlink" href="#fmake-bld-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="make-build-directory">
+<h2>Make build directory<a class="headerlink" href="#make-build-directory" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fmake_bld.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<ul class="simple">
+<li>Make the build directory</li>
+<li>Create repositories needed :</li>
+</ul>
+<blockquote>
+<ul class="simple">
+<li>BLD for compilation</li>
+</ul>
+</blockquote>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fmake_bld.sh CONFIG_NAME  TMP_DIR</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fmake_bld.sh</a><ul>
+<li><a class="reference external" href="#make-build-directory">Make build directory</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_config.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_config.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fmake_config.sh.html	(revision 1972)
@@ -0,0 +1,157 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fmake_config.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" />
+    <link rel="next" title="Fcopy_dir.sh" href="Fcopy_dir.sh.html" />
+    <link rel="prev" title="Fgo_to_tools.sh" href="Fgo_to_TOOLS.sh.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fcopy_dir.sh.html" title="Fcopy_dir.sh"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
+          <a href="Fgo_to_TOOLS.sh.html" title="Fgo_to_tools.sh"
+             accesskey="P">previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fmake-config-sh">
+<h1>Fmake_config.sh<a class="headerlink" href="#fmake-config-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="make-the-config">
+<h2>Make the config<a class="headerlink" href="#make-the-config" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fmake_config.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<ul class="simple">
+<li>Make the config directory</li>
+<li>Create repositories needed :</li>
+</ul>
+<blockquote>
+<ul class="simple">
+<li>EXP00 for namelist</li>
+<li>MY_SRC for user sources</li>
+<li>BLD for compilation</li>
+</ul>
+</blockquote>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fmake_config.sh CONFIG_NAME REF_CONFIG_NAME</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fmake_config.sh</a><ul>
+<li><a class="reference external" href="#make-the-config">Make the config</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="Fgo_to_TOOLS.sh.html"
+                                  title="previous chapter">Fgo_to_tools.sh</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="Fcopy_dir.sh.html"
+                                  title="next chapter">Fcopy_dir.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="Fcopy_dir.sh.html" title="Fcopy_dir.sh"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="Fgo_to_TOOLS.sh.html" title="Fgo_to_tools.sh"
+             >previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fprep_agrif.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fprep_agrif.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fprep_agrif.sh.html	(revision 1972)
@@ -0,0 +1,128 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fprep_agrif.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fprep-agrif-sh">
+<h1>Fprep_agrif.sh<a class="headerlink" href="#fprep-agrif-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="preparation-for-agrif">
+<h2>Preparation for AGRIF<a class="headerlink" href="#preparation-for-agrif" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fprep_agrif.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Prepare directories for AGRIF</p>
+<p>Compile the conv</p>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fprep_agrif.sh CONFIG_NAME</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fprep_agrif.sh</a><ul>
+<li><a class="reference external" href="#preparation-for-agrif">Preparation for AGRIF</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fread_dir.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fread_dir.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/Fread_dir.sh.html	(revision 1972)
@@ -0,0 +1,137 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Fread_dir.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" />
+    <link rel="prev" title="Fmake_WORK.sh" href="Fmake_WORK.sh.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fmake_WORK.sh.html" title="Fmake_WORK.sh"
+             accesskey="P">previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="fread-dir-sh">
+<h1>Fread_dir.sh<a class="headerlink" href="#fread-dir-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="read-user-directories">
+<h2>Read user directories<a class="headerlink" href="#read-user-directories" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ Fread_dir.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Read directoires needed from standard input</p>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./Fread_dir.sh Directory_NAME YES/NO</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">Fread_dir.sh</a><ul>
+<li><a class="reference external" href="#read-user-directories">Read user directories</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="Fmake_WORK.sh.html"
+                                  title="previous chapter">Fmake_WORK.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="Fmake_WORK.sh.html" title="Fmake_WORK.sh"
+             >previous</a> |</li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/*.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/*.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/*.sh.txt	(revision 1972)
@@ -0,0 +1,52 @@
+
+==================
+Fcheck_archfile.sh
+==================
+
+--------------------------
+Check the compilation file
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcheck_archfile.sh
+
+
+DESCRIPTION
+===========
+
+
+Check the choice of the compiler.
+Three cases :  
+
+- There was a previous choice
+- A new one has be specified
+- No information, exit 
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcheck_archfile.sh COMPILER
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_archfile.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_archfile.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_archfile.sh.txt	(revision 1972)
@@ -0,0 +1,52 @@
+
+==================
+Fcheck_archfile.sh
+==================
+
+--------------------------
+Check the compilation file
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcheck_archfile.sh
+
+
+DESCRIPTION
+===========
+
+
+Check the choice of the compiler.
+Three cases :  
+
+- There was a previous choice
+- A new one has be specified
+- No information, exit 
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcheck_archfile.sh COMPILER
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_config.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_config.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_config.sh.txt	(revision 1972)
@@ -0,0 +1,51 @@
+
+================
+Fcheck_config.sh
+================
+
+--------------------------
+Check the configuration
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcheck_config.sh
+
+
+DESCRIPTION
+===========
+
+
+Check the choice of the configuration:
+
+- Two cases
+- One is explicitely set
+- Nothing set, use the previous in use (default ORA2_LIM)
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcheck_config.sh
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_script.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_script.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcheck_script.sh.txt	(revision 1972)
@@ -0,0 +1,47 @@
+
+================
+Fcheck_script.sh
+================
+
+--------------------------
+Check
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcheck_script.sh
+
+
+DESCRIPTION
+===========
+
+
+Check if utilities are in the path
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcheck_script.sh scriptname
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fclean_var.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fclean_var.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fclean_var.sh.txt	(revision 1972)
@@ -0,0 +1,47 @@
+
+=============
+Fclean_var.sh
+=============
+
+----------------------------
+Clean environement variables
+----------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fclean_var.sh
+
+
+DESCRIPTION
+===========
+
+
+Clean environement variables
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fclean_var.sh
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcopy_dir.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcopy_dir.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fcopy_dir.sh.txt	(revision 1972)
@@ -0,0 +1,48 @@
+
+============
+Fcopy_dir.sh
+============
+
+--------------------------
+Copy a reference directory
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fcopy_dir.sh
+
+
+DESCRIPTION
+===========
+
+
+When a refenrence configuration is set, 
+Copy NEMO sub-directories needed
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fcopy_dir.sh REF_DIR
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fgo_to_TOOLS.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fgo_to_TOOLS.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fgo_to_TOOLS.sh.txt	(revision 1972)
@@ -0,0 +1,47 @@
+
+===============
+Fgo_to_tools.sh
+===============
+
+--------------------------
+Go to the UTIL directory
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fgo_to_tools.sh
+
+
+DESCRIPTION
+===========
+
+
+Go to the UTIL directory
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fgo_to_tools.sh
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_WORK.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_WORK.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_WORK.sh.txt	(revision 1972)
@@ -0,0 +1,51 @@
+
+=============
+Fmake_WORK.sh
+=============
+
+--------------------------
+Make the WORK directory
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fmake_WORK.sh
+
+
+DESCRIPTION
+===========
+
+
+Make the WORK directory:
+
+- Create lin in NEW_CONF/WORK
+- Use specified sub-directories previously
+- OPA has to be done first !!!
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fmake_WORK.sh
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_bld.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_bld.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_bld.sh.txt	(revision 1972)
@@ -0,0 +1,50 @@
+
+============
+Fmake_bld.sh
+============
+
+--------------------------
+Make build directory
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fmake_bld.sh
+
+
+DESCRIPTION
+===========
+
+
+- Make the build directory 
+- Create repositories needed :
+ 
+ - BLD for compilation 
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fmake_bld.sh CONFIG_NAME  TMP_DIR
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_config.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_config.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fmake_config.sh.txt	(revision 1972)
@@ -0,0 +1,52 @@
+
+===============
+Fmake_config.sh
+===============
+
+--------------------------
+Make the config 
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fmake_config.sh
+
+
+DESCRIPTION
+===========
+
+
+- Make the config directory 
+- Create repositories needed :
+ 
+ - EXP00 for namelist
+ - MY_SRC for user sources
+ - BLD for compilation 
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fmake_config.sh CONFIG_NAME REF_CONFIG_NAME 
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fprep_agrif.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fprep_agrif.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fprep_agrif.sh.txt	(revision 1972)
@@ -0,0 +1,49 @@
+
+==============
+Fprep_agrif.sh
+==============
+
+--------------------------
+Preparation for AGRIF
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fprep_agrif.sh
+
+
+DESCRIPTION
+===========
+
+
+Prepare directories for AGRIF
+
+Compile the conv
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fprep_agrif.sh CONFIG_NAME
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fread_dir.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fread_dir.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/Fread_dir.sh.txt	(revision 1972)
@@ -0,0 +1,47 @@
+
+============
+Fread_dir.sh
+============
+
+--------------------------
+Read user directories
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ Fread_dir.sh
+
+
+DESCRIPTION
+===========
+
+
+Read directoires needed from standard input
+
+EXAMPLES
+========
+
+::
+
+ $ ./Fread_dir.sh Directory_NAME YES/NO
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/agrifpp.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/agrifpp.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/agrifpp.sh.txt	(revision 1972)
@@ -0,0 +1,50 @@
+
+==========
+agrifpp.sh
+==========
+
+----------------------------
+Preform AGrif pre-processing
+----------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ agrifpp.sh
+
+
+DESCRIPTION
+===========
+
+
+Look after key agrif
+
+EXAMPLES
+========
+
+::
+
+ $ ./agrifpp.sh 1 -Dkey
+
+ or
+
+ $ ./agrifpp.sh -Dkey
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/index.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/index.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/index.txt	(revision 1972)
@@ -0,0 +1,21 @@
+.. _index:
+ 
+=================
+NEMO_UTIL manuals
+=================
+ 
+Shell scripts
+=============
+.. toctree::
+   :maxdepth: 1
+   :glob:
+ 
+   Fcheck_archfile.sh
+   Fcheck_config.sh
+   Fclean_var.sh
+   Fgo_to_TOOLS.sh
+   Fmake_config.sh
+   Fcopy_dir.sh
+   Fmake_WORK.sh
+   Fread_dir.sh
+ 
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/makenemo_fcm.sh.txt
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/makenemo_fcm.sh.txt	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_sources/makenemo_fcm.sh.txt	(revision 1972)
@@ -0,0 +1,71 @@
+
+===============
+makenemo_fcm.sh
+===============
+
+--------------------------
+Compile NEMO
+--------------------------
+
+SYNOPSIS
+========
+
+::
+
+ $ makenemo_fcm.sh
+
+
+DESCRIPTION
+===========
+
+
+This script aims :
+
+- to choose MYCONFIG
+- to choose compiler options  
+- to create the CONFIG/MYCONFIG/WORK directory
+- to compile this configuration
+
+ Variables used :
+
+ From user input
+
+- NEW_CONF    : configuration to be created
+- REF_CONF    : reference configuration to build the new one 
+- CMP_NAM     : compiler name 
+- NBR_PRC     : number of processes used to compile  
+- NEM_SUBDIR  : NEMO subdirectory used (specified)
+
+ Locally defined :
+
+- TAB         : NEMO subdirectory used (read)  
+- MAIN_DIR : self explaining
+- CONFIG_DIR  :   "    "    "   
+- MODELES_DIR :   "    "    " 
+- TOOLS_DIR   :   "    "    " 
+- NEMO_DIR    :   "    "    "
+
+EXAMPLES
+========
+
+::
+
+ $ ./makenemo_fcm -t ifort_osx - j3 -n ORCA2_LIM
+
+
+TODO
+====
+
+option debug
+
+
+EVOLUTIONS
+==========
+
+$Id$
+
+
+- rblod 2010-06-20T16:11:47Z
+
+  * creation
+
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/basic.css
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/basic.css	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/basic.css	(revision 1972)
@@ -0,0 +1,417 @@
+/**
+ * Sphinx stylesheet -- basic theme
+ * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ */
+
+/* -- main layout ----------------------------------------------------------- */
+
+div.clearer {
+    clear: both;
+}
+
+/* -- relbar ---------------------------------------------------------------- */
+
+div.related {
+    width: 100%;
+    font-size: 90%;
+}
+
+div.related h3 {
+    display: none;
+}
+
+div.related ul {
+    margin: 0;
+    padding: 0 0 0 10px;
+    list-style: none;
+}
+
+div.related li {
+    display: inline;
+}
+
+div.related li.right {
+    float: right;
+    margin-right: 5px;
+}
+
+/* -- sidebar --------------------------------------------------------------- */
+
+div.sphinxsidebarwrapper {
+    padding: 10px 5px 0 10px;
+}
+
+div.sphinxsidebar {
+    float: left;
+    width: 230px;
+    margin-left: -100%;
+    font-size: 90%;
+}
+
+div.sphinxsidebar ul {
+    list-style: none;
+}
+
+div.sphinxsidebar ul ul,
+div.sphinxsidebar ul.want-points {
+    margin-left: 20px;
+    list-style: square;
+}
+
+div.sphinxsidebar ul ul {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+div.sphinxsidebar form {
+    margin-top: 10px;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #98dbcc;
+    font-family: sans-serif;
+    font-size: 1em;
+}
+
+img {
+    border: 0;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+    margin: 10px 0 0 20px;
+    padding: 0;
+}
+
+ul.search li {
+    padding: 5px 0 5px 20px;
+    background-image: url(file.png);
+    background-repeat: no-repeat;
+    background-position: 0 7px;
+}
+
+ul.search li a {
+    font-weight: bold;
+}
+
+ul.search li div.context {
+    color: #888;
+    margin: 2px 0 0 30px;
+    text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+    font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+    width: 90%;
+}
+
+table.contentstable p.biglink {
+    line-height: 150%;
+}
+
+a.biglink {
+    font-size: 1.3em;
+}
+
+span.linkdescr {
+    font-style: italic;
+    padding-top: 5px;
+    font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable td {
+    text-align: left;
+    vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+    height: 10px;
+}
+
+table.indextable tr.cap {
+    margin-top: 10px;
+    background-color: #f2f2f2;
+}
+
+img.toggler {
+    margin-right: 3px;
+    margin-top: 3px;
+    cursor: pointer;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+a.headerlink {
+    visibility: hidden;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink {
+    visibility: visible;
+}
+
+div.body p.caption {
+    text-align: inherit;
+}
+
+div.body td {
+    text-align: left;
+}
+
+.field-list ul {
+    padding-left: 1em;
+}
+
+.first {
+    margin-top: 0 !important;
+}
+
+p.rubric {
+    margin-top: 30px;
+    font-weight: bold;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar {
+    margin: 0 0 0.5em 1em;
+    border: 1px solid #ddb;
+    padding: 7px 7px 0 7px;
+    background-color: #ffe;
+    width: 40%;
+    float: right;
+}
+
+p.sidebar-title {
+    font-weight: bold;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+div.topic {
+    border: 1px solid #ccc;
+    padding: 7px 7px 0 7px;
+    margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+    font-size: 1.1em;
+    font-weight: bold;
+    margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    padding: 7px;
+}
+
+div.admonition dt {
+    font-weight: bold;
+}
+
+div.admonition dl {
+    margin-bottom: 0;
+}
+
+p.admonition-title {
+    margin: 0px 10px 5px 0px;
+    font-weight: bold;
+}
+
+div.body p.centered {
+    text-align: center;
+    margin-top: 25px;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+    border: 0;
+    border-collapse: collapse;
+}
+
+table.docutils td, table.docutils th {
+    padding: 1px 8px 1px 0;
+    border-top: 0;
+    border-left: 0;
+    border-right: 0;
+    border-bottom: 1px solid #aaa;
+}
+
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
+table.footnote td, table.footnote th {
+    border: 0 !important;
+}
+
+th {
+    text-align: left;
+    padding-right: 5px;
+}
+
+/* -- other body styles ----------------------------------------------------- */
+
+dl {
+    margin-bottom: 15px;
+}
+
+dd p {
+    margin-top: 0px;
+}
+
+dd ul, dd table {
+    margin-bottom: 10px;
+}
+
+dd {
+    margin-top: 3px;
+    margin-bottom: 10px;
+    margin-left: 30px;
+}
+
+dt:target, .highlight {
+    background-color: #fbe54e;
+}
+
+dl.glossary dt {
+    font-weight: bold;
+    font-size: 1.1em;
+}
+
+.field-list ul {
+    margin: 0;
+    padding-left: 1em;
+}
+
+.field-list p {
+    margin: 0;
+}
+
+.refcount {
+    color: #060;
+}
+
+.optional {
+    font-size: 1.3em;
+}
+
+.versionmodified {
+    font-style: italic;
+}
+
+.system-message {
+    background-color: #fda;
+    padding: 5px;
+    border: 3px solid red;
+}
+
+.footnote:target  {
+    background-color: #ffa
+}
+
+.line-block {
+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+.line-block .line-block {
+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+    overflow: auto;
+}
+
+td.linenos pre {
+    padding: 5px 0px;
+    border: 0;
+    background-color: transparent;
+    color: #aaa;
+}
+
+table.highlighttable {
+    margin-left: 0.5em;
+}
+
+table.highlighttable td {
+    padding: 0 0.5em 0 0.5em;
+}
+
+tt.descname {
+    background-color: transparent;
+    font-weight: bold;
+    font-size: 1.2em;
+}
+
+tt.descclassname {
+    background-color: transparent;
+}
+
+tt.xref, a tt {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
+    background-color: transparent;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+    vertical-align: middle;
+}
+
+div.body div.math p {
+    text-align: center;
+}
+
+span.eqno {
+    float: right;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+    div.document,
+    div.documentwrapper,
+    div.bodywrapper {
+        margin: 0 !important;
+        width: 100%;
+    }
+
+    div.sphinxsidebar,
+    div.related,
+    div.footer,
+    #top-link {
+        display: none;
+    }
+}
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/default.css
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/default.css	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/default.css	(revision 1972)
@@ -0,0 +1,230 @@
+/**
+ * Sphinx stylesheet -- default theme
+ * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ */
+
+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+    font-family: sans-serif;
+    font-size: 100%;
+    background-color: #11303d;
+    color: #000;
+    margin: 0;
+    padding: 0;
+}
+
+div.document {
+    background-color: #1c4e63;
+}
+
+div.documentwrapper {
+    float: left;
+    width: 100%;
+}
+
+div.bodywrapper {
+    margin: 0 0 0 230px;
+}
+
+div.body {
+    background-color: #ffffff;
+    color: #000000;
+    padding: 0 20px 30px 20px;
+}
+
+div.footer {
+    color: #ffffff;
+    width: 100%;
+    padding: 9px 0 9px 0;
+    text-align: center;
+    font-size: 75%;
+}
+
+div.footer a {
+    color: #ffffff;
+    text-decoration: underline;
+}
+
+div.related {
+    background-color: #133f52;
+    line-height: 30px;
+    color: #ffffff;
+}
+
+div.related a {
+    color: #ffffff;
+}
+
+div.sphinxsidebar {
+}
+
+div.sphinxsidebar h3 {
+    font-family: 'Trebuchet MS', sans-serif;
+    color: #ffffff;
+    font-size: 1.4em;
+    font-weight: normal;
+    margin: 0;
+    padding: 0;
+}
+
+div.sphinxsidebar h3 a {
+    color: #ffffff;
+}
+
+div.sphinxsidebar h4 {
+    font-family: 'Trebuchet MS', sans-serif;
+    color: #ffffff;
+    font-size: 1.3em;
+    font-weight: normal;
+    margin: 5px 0 0 0;
+    padding: 0;
+}
+
+div.sphinxsidebar p {
+    color: #ffffff;
+}
+
+div.sphinxsidebar p.topless {
+    margin: 5px 10px 10px 10px;
+}
+
+div.sphinxsidebar ul {
+    margin: 10px;
+    padding: 0;
+    color: #ffffff;
+}
+
+div.sphinxsidebar a {
+    color: #98dbcc;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #98dbcc;
+    font-family: sans-serif;
+    font-size: 1em;
+}
+
+/* -- body styles ----------------------------------------------------------- */
+
+a {
+    color: #355f7c;
+    text-decoration: none;
+}
+
+a:hover {
+    text-decoration: underline;
+}
+
+div.body p, div.body dd, div.body li {
+    text-align: justify;
+    line-height: 130%;
+}
+
+div.body h1,
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+    font-family: 'Trebuchet MS', sans-serif;
+    background-color: #f2f2f2;
+    font-weight: normal;
+    color: #20435c;
+    border-bottom: 1px solid #ccc;
+    margin: 20px -20px 10px -20px;
+    padding: 3px 0 3px 10px;
+}
+
+div.body h1 { margin-top: 0; font-size: 200%; }
+div.body h2 { font-size: 160%; }
+div.body h3 { font-size: 140%; }
+div.body h4 { font-size: 120%; }
+div.body h5 { font-size: 110%; }
+div.body h6 { font-size: 100%; }
+
+a.headerlink {
+    color: #c60f0f;
+    font-size: 0.8em;
+    padding: 0 4px 0 4px;
+    text-decoration: none;
+}
+
+a.headerlink:hover {
+    background-color: #c60f0f;
+    color: white;
+}
+
+div.body p, div.body dd, div.body li {
+    text-align: justify;
+    line-height: 130%;
+}
+
+div.admonition p.admonition-title + p {
+    display: inline;
+}
+
+div.admonition p {
+    margin-bottom: 5px;
+}
+
+div.admonition pre {
+    margin-bottom: 5px;
+}
+
+div.admonition ul, div.admonition ol {
+    margin-bottom: 5px;
+}
+
+div.note {
+    background-color: #eee;
+    border: 1px solid #ccc;
+}
+
+div.seealso {
+    background-color: #ffc;
+    border: 1px solid #ff6;
+}
+
+div.topic {
+    background-color: #eee;
+}
+
+div.warning {
+    background-color: #ffe4e4;
+    border: 1px solid #f66;
+}
+
+p.admonition-title {
+    display: inline;
+}
+
+p.admonition-title:after {
+    content: ":";
+}
+
+pre {
+    padding: 5px;
+    background-color: #eeffcc;
+    color: #333333;
+    line-height: 120%;
+    border: 1px solid #ac9;
+    border-left: none;
+    border-right: none;
+}
+
+tt {
+    background-color: #ecf0f3;
+    padding: 0 1px 0 1px;
+    font-size: 0.95em;
+}
+
+.warning tt {
+    background: #efc2c2;
+}
+
+.note tt {
+    background: #d6d6d6;
+}
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/doctools.js
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/doctools.js	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/doctools.js	(revision 1972)
@@ -0,0 +1,232 @@
+/// XXX: make it cross browser
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+ */
+if (!window.console || !console.firebug) {
+  var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml",
+      "group", "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd"];
+  window.console = {};
+  for (var i = 0; i < names.length; ++i)
+    window.console[names[i]] = function() {}
+}
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+  return decodeURIComponent(x).replace(/\+/g, ' ');
+}
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+  if (typeof s == 'undefined')
+    s = document.location.search;
+  var parts = s.substr(s.indexOf('?') + 1).split('&');
+  var result = {};
+  for (var i = 0; i < parts.length; i++) {
+    var tmp = parts[i].split('=', 2);
+    var key = jQuery.urldecode(tmp[0]);
+    var value = jQuery.urldecode(tmp[1]);
+    if (key in result)
+      result[key].push(value);
+    else
+      result[key] = [value];
+  }
+  return result;
+}
+
+/**
+ * small function to check if an array contains
+ * a given item.
+ */
+jQuery.contains = function(arr, item) {
+  for (var i = 0; i < arr.length; i++) {
+    if (arr[i] == item)
+      return true;
+  }
+  return false;
+}
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+  function highlight(node) {
+    if (node.nodeType == 3) {
+      var val = node.nodeValue;
+      var pos = val.toLowerCase().indexOf(text);
+      if (pos >= 0 && !jQuery.className.has(node.parentNode, className)) {
+        var span = document.createElement("span");
+        span.className = className;
+        span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+        node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+          document.createTextNode(val.substr(pos + text.length)),
+          node.nextSibling));
+        node.nodeValue = val.substr(0, pos);
+      }
+    }
+    else if (!jQuery(node).is("button, select, textarea")) {
+      jQuery.each(node.childNodes, function() {
+        highlight(this)
+      });
+    }
+  }
+  return this.each(function() {
+    highlight(this);
+  });
+}
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+  init : function() {
+    this.fixFirefoxAnchorBug();
+    this.highlightSearchWords();
+    this.initModIndex();
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS : {},
+  PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
+  LOCALE : 'unknown',
+
+  // gettext and ngettext don't access this so that the functions
+  // can savely bound to a different name (_ = Documentation.gettext)
+  gettext : function(string) {
+    var translated = Documentation.TRANSLATIONS[string];
+    if (typeof translated == 'undefined')
+      return string;
+    return (typeof translated == 'string') ? translated : translated[0];
+  },
+
+  ngettext : function(singular, plural, n) {
+    var translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated == 'undefined')
+      return (n == 1) ? singular : plural;
+    return translated[Documentation.PLURALEXPR(n)];
+  },
+
+  addTranslations : function(catalog) {
+    for (var key in catalog.messages)
+      this.TRANSLATIONS[key] = catalog.messages[key];
+    this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+    this.LOCALE = catalog.locale;
+  },
+
+  /**
+   * add context elements like header anchor links
+   */
+  addContextElements : function() {
+    $('div[id] > :header:first').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this headline')).
+      appendTo(this);
+    });
+    $('dt[id]').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this definition')).
+      appendTo(this);
+    });
+  },
+
+  /**
+   * workaround a firefox stupidity
+   */
+  fixFirefoxAnchorBug : function() {
+    if (document.location.hash && $.browser.mozilla)
+      window.setTimeout(function() {
+        document.location.href += '';
+      }, 10);
+  },
+
+  /**
+   * highlight the search words provided in the url in the text
+   */
+  highlightSearchWords : function() {
+    var params = $.getQueryParameters();
+    var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+    if (terms.length) {
+      var body = $('div.body');
+      window.setTimeout(function() {
+        $.each(terms, function() {
+          body.highlightText(this.toLowerCase(), 'highlight');
+        });
+      }, 10);
+      $('<li class="highlight-link"><a href="javascript:Documentation.' +
+        'hideSearchWords()">' + _('Hide Search Matches') + '</a></li>')
+          .appendTo($('.sidebar .this-page-menu'));
+    }
+  },
+
+  /**
+   * init the modindex toggle buttons
+   */
+  initModIndex : function() {
+    var togglers = $('img.toggler').click(function() {
+      var src = $(this).attr('src');
+      var idnum = $(this).attr('id').substr(7);
+      console.log($('tr.cg-' + idnum).toggle());
+      if (src.substr(-9) == 'minus.png')
+        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+      else
+        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+    }).css('display', '');
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_MODINDEX) {
+        togglers.click();
+    }
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords : function() {
+    $('.sidebar .this-page-menu li.highlight-link').fadeOut(300);
+    $('span.highlight').removeClass('highlight');
+  },
+
+  /**
+   * make the url absolute
+   */
+  makeURL : function(relativeURL) {
+    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+  },
+
+  /**
+   * get the current relative url
+   */
+  getCurrentURL : function() {
+    var path = document.location.pathname;
+    var parts = path.split(/\//);
+    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+      if (this == '..')
+        parts.pop();
+    });
+    var url = parts.join('/');
+    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+  }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+  Documentation.init();
+});
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/jquery.js
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/jquery.js	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/jquery.js	(revision 1972)
@@ -0,0 +1,32 @@
+/*
+ * jQuery 1.2.6 - New Wave Javascript
+ *
+ * Copyright (c) 2008 John Resig (jquery.com)
+ * Dual licensed under the MIT (MIT-LICENSE.txt)
+ * and GPL (GPL-LICENSE.txt) licenses.
+ *
+ * $Date: 2008-05-24 14:22:17 -0400 (Sat, 24 May 2008) $
+ * $Rev: 5685 $
+ */
+(function(){var _jQuery=window.jQuery,_$=window.$;var jQuery=window.jQuery=window.$=function(selector,context){return new jQuery.fn.init(selector,context);};var quickExpr=/^[^<]*(<(.|\s)+>)[^>]*$|^#(\w+)$/,isSimple=/^.[^:#\[\.]*$/,undefined;jQuery.fn=jQuery.prototype={init:function(selector,context){selector=selector||document;if(selector.nodeType){this[0]=selector;this.length=1;return this;}if(typeof selector=="string"){var match=quickExpr.exec(selector);if(match&&(match[1]||!context)){if(match[1])selector=jQuery.clean([match[1]],context);else{var elem=document.getElementById(match[3]);if(elem){if(elem.id!=match[3])return jQuery().find(selector);return jQuery(elem);}selector=[];}}else
+return jQuery(context).find(selector);}else if(jQuery.isFunction(selector))return jQuery(document)[jQuery.fn.ready?"ready":"load"](selector);return this.setArray(jQuery.makeArray(selector));},jquery:"1.2.6",size:function(){return this.length;},length:0,get:function(num){return num==undefined?jQuery.makeArray(this):this[num];},pushStack:function(elems){var ret=jQuery(elems);ret.prevObject=this;return ret;},setArray:function(elems){this.length=0;Array.prototype.push.apply(this,elems);return this;},each:function(callback,args){return jQuery.each(this,callback,args);},index:function(elem){var ret=-1;return jQuery.inArray(elem&&elem.jquery?elem[0]:elem,this);},attr:function(name,value,type){var options=name;if(name.constructor==String)if(value===undefined)return this[0]&&jQuery[type||"attr"](this[0],name);else{options={};options[name]=value;}return this.each(function(i){for(name in options)jQuery.attr(type?this.style:this,name,jQuery.prop(this,options[name],type,i,name));});},css:function(key,value){if((key=='width'||key=='height')&&parseFloat(value)<0)value=undefined;return this.attr(key,value,"curCSS");},text:function(text){if(typeof text!="object"&&text!=null)return this.empty().append((this[0]&&this[0].ownerDocument||document).createTextNode(text));var ret="";jQuery.each(text||this,function(){jQuery.each(this.childNodes,function(){if(this.nodeType!=8)ret+=this.nodeType!=1?this.nodeValue:jQuery.fn.text([this]);});});return ret;},wrapAll:function(html){if(this[0])jQuery(html,this[0].ownerDocument).clone().insertBefore(this[0]).map(function(){var elem=this;while(elem.firstChild)elem=elem.firstChild;return elem;}).append(this);return this;},wrapInner:function(html){return this.each(function(){jQuery(this).contents().wrapAll(html);});},wrap:function(html){return this.each(function(){jQuery(this).wrapAll(html);});},append:function(){return this.domManip(arguments,true,false,function(elem){if(this.nodeType==1)this.appendChild(elem);});},prepend:function(){return this.domManip(arguments,true,true,function(elem){if(this.nodeType==1)this.insertBefore(elem,this.firstChild);});},before:function(){return this.domManip(arguments,false,false,function(elem){this.parentNode.insertBefore(elem,this);});},after:function(){return this.domManip(arguments,false,true,function(elem){this.parentNode.insertBefore(elem,this.nextSibling);});},end:function(){return this.prevObject||jQuery([]);},find:function(selector){var elems=jQuery.map(this,function(elem){return jQuery.find(selector,elem);});return this.pushStack(/[^+>] [^+>]/.test(selector)||selector.indexOf("..")>-1?jQuery.unique(elems):elems);},clone:function(events){var ret=this.map(function(){if(jQuery.browser.msie&&!jQuery.isXMLDoc(this)){var clone=this.cloneNode(true),container=document.createElement("div");container.appendChild(clone);return jQuery.clean([container.innerHTML])[0];}else
+return this.cloneNode(true);});var clone=ret.find("*").andSelf().each(function(){if(this[expando]!=undefined)this[expando]=null;});if(events===true)this.find("*").andSelf().each(function(i){if(this.nodeType==3)return;var events=jQuery.data(this,"events");for(var type in events)for(var handler in events[type])jQuery.event.add(clone[i],type,events[type][handler],events[type][handler].data);});return ret;},filter:function(selector){return this.pushStack(jQuery.isFunction(selector)&&jQuery.grep(this,function(elem,i){return selector.call(elem,i);})||jQuery.multiFilter(selector,this));},not:function(selector){if(selector.constructor==String)if(isSimple.test(selector))return this.pushStack(jQuery.multiFilter(selector,this,true));else
+selector=jQuery.multiFilter(selector,this);var isArrayLike=selector.length&&selector[selector.length-1]!==undefined&&!selector.nodeType;return this.filter(function(){return isArrayLike?jQuery.inArray(this,selector)<0:this!=selector;});},add:function(selector){return this.pushStack(jQuery.unique(jQuery.merge(this.get(),typeof selector=='string'?jQuery(selector):jQuery.makeArray(selector))));},is:function(selector){return!!selector&&jQuery.multiFilter(selector,this).length>0;},hasClass:function(selector){return this.is("."+selector);},val:function(value){if(value==undefined){if(this.length){var elem=this[0];if(jQuery.nodeName(elem,"select")){var index=elem.selectedIndex,values=[],options=elem.options,one=elem.type=="select-one";if(index<0)return null;for(var i=one?index:0,max=one?index+1:options.length;i<max;i++){var option=options[i];if(option.selected){value=jQuery.browser.msie&&!option.attributes.value.specified?option.text:option.value;if(one)return value;values.push(value);}}return values;}else
+return(this[0].value||"").replace(/\r/g,"");}return undefined;}if(value.constructor==Number)value+='';return this.each(function(){if(this.nodeType!=1)return;if(value.constructor==Array&&/radio|checkbox/.test(this.type))this.checked=(jQuery.inArray(this.value,value)>=0||jQuery.inArray(this.name,value)>=0);else if(jQuery.nodeName(this,"select")){var values=jQuery.makeArray(value);jQuery("option",this).each(function(){this.selected=(jQuery.inArray(this.value,values)>=0||jQuery.inArray(this.text,values)>=0);});if(!values.length)this.selectedIndex=-1;}else
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+for(var j in a)if(a[j]&&a[j].constructor==Array)jQuery.each(a[j],function(){s.push(encodeURIComponent(j)+"="+encodeURIComponent(this));});else
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+e.custom(start,val,"");}});return true;});},queue:function(type,fn){if(jQuery.isFunction(type)||(type&&type.constructor==Array)){fn=type;type="fx";}if(!type||(typeof type=="string"&&!fn))return queue(this[0],type);return this.each(function(){if(fn.constructor==Array)queue(this,type,fn);else{queue(this,type).push(fn);if(queue(this,type).length==1)fn.call(this);}});},stop:function(clearQueue,gotoEnd){var timers=jQuery.timers;if(clearQueue)this.queue([]);this.each(function(){for(var i=timers.length-1;i>=0;i--)if(timers[i].elem==this){if(gotoEnd)timers[i](true);timers.splice(i,1);}});if(!gotoEnd)this.dequeue();return this;}});var queue=function(elem,type,array){if(elem){type=type||"fx";var q=jQuery.data(elem,type+"queue");if(!q||array)q=jQuery.data(elem,type+"queue",jQuery.makeArray(array));}return q;};jQuery.fn.dequeue=function(type){type=type||"fx";return this.each(function(){var q=queue(this,type);q.shift();if(q.length)q[0].call(this);});};jQuery.extend({speed:function(speed,easing,fn){var opt=speed&&speed.constructor==Object?speed:{complete:fn||!fn&&easing||jQuery.isFunction(speed)&&speed,duration:speed,easing:fn&&easing||easing&&easing.constructor!=Function&&easing};opt.duration=(opt.duration&&opt.duration.constructor==Number?opt.duration:jQuery.fx.speeds[opt.duration])||jQuery.fx.speeds.def;opt.old=opt.complete;opt.complete=function(){if(opt.queue!==false)jQuery(this).dequeue();if(jQuery.isFunction(opt.old))opt.old.call(this);};return opt;},easing:{linear:function(p,n,firstNum,diff){return firstNum+diff*p;},swing:function(p,n,firstNum,diff){return((-Math.cos(p*Math.PI)/2)+0.5)*diff+firstNum;}},timers:[],timerId:null,fx:function(elem,options,prop){this.options=options;this.elem=elem;this.prop=prop;if(!options.orig)options.orig={};}});jQuery.fx.prototype={update:function(){if(this.options.step)this.options.step.call(this.elem,this.now,this);(jQuery.fx.step[this.prop]||jQuery.fx.step._default)(this);if(this.prop=="height"||this.prop=="width")this.elem.style.display="block";},cur:function(force){if(this.elem[this.prop]!=null&&this.elem.style[this.prop]==null)return this.elem[this.prop];var r=parseFloat(jQuery.css(this.elem,this.prop,force));return r&&r>-10000?r:parseFloat(jQuery.curCSS(this.elem,this.prop))||0;},custom:function(from,to,unit){this.startTime=now();this.start=from;this.end=to;this.unit=unit||this.unit||"px";this.now=this.start;this.pos=this.state=0;this.update();var self=this;function t(gotoEnd){return self.step(gotoEnd);}t.elem=this.elem;jQuery.timers.push(t);if(jQuery.timerId==null){jQuery.timerId=setInterval(function(){var timers=jQuery.timers;for(var i=0;i<timers.length;i++)if(!timers[i]())timers.splice(i--,1);if(!timers.length){clearInterval(jQuery.timerId);jQuery.timerId=null;}},13);}},show:function(){this.options.orig[this.prop]=jQuery.attr(this.elem.style,this.prop);this.options.show=true;this.custom(0,this.cur());if(this.prop=="width"||this.prop=="height")this.elem.style[this.prop]="1px";jQuery(this.elem).show();},hide:function(){this.options.orig[this.prop]=jQuery.attr(this.elem.style,this.prop);this.options.hide=true;this.custom(this.cur(),0);},step:function(gotoEnd){var t=now();if(gotoEnd||t>this.options.duration+this.startTime){this.now=this.end;this.pos=this.state=1;this.update();this.options.curAnim[this.prop]=true;var done=true;for(var i in this.options.curAnim)if(this.options.curAnim[i]!==true)done=false;if(done){if(this.options.display!=null){this.elem.style.overflow=this.options.overflow;this.elem.style.display=this.options.display;if(jQuery.css(this.elem,"display")=="none")this.elem.style.display="block";}if(this.options.hide)this.elem.style.display="none";if(this.options.hide||this.options.show)for(var p in this.options.curAnim)jQuery.attr(this.elem.style,p,this.options.orig[p]);}if(done)this.options.complete.call(this.elem);return false;}else{var n=t-this.startTime;this.state=n/this.options.duration;this.pos=jQuery.easing[this.options.easing||(jQuery.easing.swing?"swing":"linear")](this.state,n,0,1,this.options.duration);this.now=this.start+((this.end-this.start)*this.pos);this.update();}return true;}};jQuery.extend(jQuery.fx,{speeds:{slow:600,fast:200,def:400},step:{scrollLeft:function(fx){fx.elem.scrollLeft=fx.now;},scrollTop:function(fx){fx.elem.scrollTop=fx.now;},opacity:function(fx){jQuery.attr(fx.elem.style,"opacity",fx.now);},_default:function(fx){fx.elem.style[fx.prop]=fx.now+fx.unit;}}});jQuery.fn.offset=function(){var left=0,top=0,elem=this[0],results;if(elem)with(jQuery.browser){var parent=elem.parentNode,offsetChild=elem,offsetParent=elem.offsetParent,doc=elem.ownerDocument,safari2=safari&&parseInt(version)<522&&!/adobeair/i.test(userAgent),css=jQuery.curCSS,fixed=css(elem,"position")=="fixed";if(elem.getBoundingClientRect){var box=elem.getBoundingClientRect();add(box.left+Math.max(doc.documentElement.scrollLeft,doc.body.scrollLeft),box.top+Math.max(doc.documentElement.scrollTop,doc.body.scrollTop));add(-doc.documentElement.clientLeft,-doc.documentElement.clientTop);}else{add(elem.offsetLeft,elem.offsetTop);while(offsetParent){add(offsetParent.offsetLeft,offsetParent.offsetTop);if(mozilla&&!/^t(able|d|h)$/i.test(offsetParent.tagName)||safari&&!safari2)border(offsetParent);if(!fixed&&css(offsetParent,"position")=="fixed")fixed=true;offsetChild=/^body$/i.test(offsetParent.tagName)?offsetChild:offsetParent;offsetParent=offsetParent.offsetParent;}while(parent&&parent.tagName&&!/^body|html$/i.test(parent.tagName)){if(!/^inline|table.*$/i.test(css(parent,"display")))add(-parent.scrollLeft,-parent.scrollTop);if(mozilla&&css(parent,"overflow")!="visible")border(parent);parent=parent.parentNode;}if((safari2&&(fixed||css(offsetChild,"position")=="absolute"))||(mozilla&&css(offsetChild,"position")!="absolute"))add(-doc.body.offsetLeft,-doc.body.offsetTop);if(fixed)add(Math.max(doc.documentElement.scrollLeft,doc.body.scrollLeft),Math.max(doc.documentElement.scrollTop,doc.body.scrollTop));}results={top:top,left:left};}function border(elem){add(jQuery.curCSS(elem,"borderLeftWidth",true),jQuery.curCSS(elem,"borderTopWidth",true));}function add(l,t){left+=parseInt(l,10)||0;top+=parseInt(t,10)||0;}return results;};jQuery.fn.extend({position:function(){var left=0,top=0,results;if(this[0]){var offsetParent=this.offsetParent(),offset=this.offset(),parentOffset=/^body|html$/i.test(offsetParent[0].tagName)?{top:0,left:0}:offsetParent.offset();offset.top-=num(this,'marginTop');offset.left-=num(this,'marginLeft');parentOffset.top+=num(offsetParent,'borderTopWidth');parentOffset.left+=num(offsetParent,'borderLeftWidth');results={top:offset.top-parentOffset.top,left:offset.left-parentOffset.left};}return results;},offsetParent:function(){var offsetParent=this[0].offsetParent;while(offsetParent&&(!/^body|html$/i.test(offsetParent.tagName)&&jQuery.css(offsetParent,'position')=='static'))offsetParent=offsetParent.offsetParent;return jQuery(offsetParent);}});jQuery.each(['Left','Top'],function(i,name){var method='scroll'+name;jQuery.fn[method]=function(val){if(!this[0])return;return val!=undefined?this.each(function(){this==window||this==document?window.scrollTo(!i?val:jQuery(window).scrollLeft(),i?val:jQuery(window).scrollTop()):this[method]=val;}):this[0]==window||this[0]==document?self[i?'pageYOffset':'pageXOffset']||jQuery.boxModel&&document.documentElement[method]||document.body[method]:this[0][method];};});jQuery.each(["Height","Width"],function(i,name){var tl=i?"Left":"Top",br=i?"Right":"Bottom";jQuery.fn["inner"+name]=function(){return this[name.toLowerCase()]()+num(this,"padding"+tl)+num(this,"padding"+br);};jQuery.fn["outer"+name]=function(margin){return this["inner"+name]()+num(this,"border"+tl+"Width")+num(this,"border"+br+"Width")+(margin?num(this,"margin"+tl)+num(this,"margin"+br):0);};});})();
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/pygments.css
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/pygments.css	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/pygments.css	(revision 1972)
@@ -0,0 +1,61 @@
+.hll { background-color: #ffffcc }
+.c { color: #408090; font-style: italic } /* Comment */
+.err { border: 1px solid #FF0000 } /* Error */
+.k { color: #007020; font-weight: bold } /* Keyword */
+.o { color: #666666 } /* Operator */
+.cm { color: #408090; font-style: italic } /* Comment.Multiline */
+.cp { color: #007020 } /* Comment.Preproc */
+.c1 { color: #408090; font-style: italic } /* Comment.Single */
+.cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
+.gd { color: #A00000 } /* Generic.Deleted */
+.ge { font-style: italic } /* Generic.Emph */
+.gr { color: #FF0000 } /* Generic.Error */
+.gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.gi { color: #00A000 } /* Generic.Inserted */
+.go { color: #303030 } /* Generic.Output */
+.gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
+.gs { font-weight: bold } /* Generic.Strong */
+.gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.gt { color: #0040D0 } /* Generic.Traceback */
+.kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.kp { color: #007020 } /* Keyword.Pseudo */
+.kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
+.kt { color: #902000 } /* Keyword.Type */
+.m { color: #208050 } /* Literal.Number */
+.s { color: #4070a0 } /* Literal.String */
+.na { color: #4070a0 } /* Name.Attribute */
+.nb { color: #007020 } /* Name.Builtin */
+.nc { color: #0e84b5; font-weight: bold } /* Name.Class */
+.no { color: #60add5 } /* Name.Constant */
+.nd { color: #555555; font-weight: bold } /* Name.Decorator */
+.ni { color: #d55537; font-weight: bold } /* Name.Entity */
+.ne { color: #007020 } /* Name.Exception */
+.nf { color: #06287e } /* Name.Function */
+.nl { color: #002070; font-weight: bold } /* Name.Label */
+.nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
+.nt { color: #062873; font-weight: bold } /* Name.Tag */
+.nv { color: #bb60d5 } /* Name.Variable */
+.ow { color: #007020; font-weight: bold } /* Operator.Word */
+.w { color: #bbbbbb } /* Text.Whitespace */
+.mf { color: #208050 } /* Literal.Number.Float */
+.mh { color: #208050 } /* Literal.Number.Hex */
+.mi { color: #208050 } /* Literal.Number.Integer */
+.mo { color: #208050 } /* Literal.Number.Oct */
+.sb { color: #4070a0 } /* Literal.String.Backtick */
+.sc { color: #4070a0 } /* Literal.String.Char */
+.sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
+.s2 { color: #4070a0 } /* Literal.String.Double */
+.se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
+.sh { color: #4070a0 } /* Literal.String.Heredoc */
+.si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
+.sx { color: #c65d09 } /* Literal.String.Other */
+.sr { color: #235388 } /* Literal.String.Regex */
+.s1 { color: #4070a0 } /* Literal.String.Single */
+.ss { color: #517918 } /* Literal.String.Symbol */
+.bp { color: #007020 } /* Name.Builtin.Pseudo */
+.vc { color: #bb60d5 } /* Name.Variable.Class */
+.vg { color: #bb60d5 } /* Name.Variable.Global */
+.vi { color: #bb60d5 } /* Name.Variable.Instance */
+.il { color: #208050 } /* Literal.Number.Integer.Long */
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/searchtools.js
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/searchtools.js	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/_static/searchtools.js	(revision 1972)
@@ -0,0 +1,467 @@
+/**
+ * helper function to return a node containing the
+ * search summary for a given text. keywords is a list
+ * of stemmed words, hlwords is the list of normal, unstemmed
+ * words. the first one is used to find the occurance, the
+ * latter for highlighting it.
+ */
+
+jQuery.makeSearchSummary = function(text, keywords, hlwords) {
+  var textLower = text.toLowerCase();
+  var start = 0;
+  $.each(keywords, function() {
+    var i = textLower.indexOf(this.toLowerCase());
+    if (i > -1)
+      start = i;
+  });
+  start = Math.max(start - 120, 0);
+  var excerpt = ((start > 0) ? '...' : '') +
+  $.trim(text.substr(start, 240)) +
+  ((start + 240 - text.length) ? '...' : '');
+  var rv = $('<div class="context"></div>').text(excerpt);
+  $.each(hlwords, function() {
+    rv = rv.highlightText(this, 'highlight');
+  });
+  return rv;
+}
+
+/**
+ * Porter Stemmer
+ */
+var PorterStemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+  _index : null,
+  _queued_query : null,
+  _pulse_status : -1,
+
+  init : function() {
+      var params = $.getQueryParameters();
+      if (params.q) {
+          var query = params.q[0];
+          $('input[name="q"]')[0].value = query;
+          this.performSearch(query);
+      }
+  },
+
+  /**
+   * Sets the index
+   */
+  setIndex : function(index) {
+    var q;
+    this._index = index;
+    if ((q = this._queued_query) !== null) {
+      this._queued_query = null;
+      Search.query(q);
+    }
+  },
+
+  hasIndex : function() {
+      return this._index !== null;
+  },
+
+  deferQuery : function(query) {
+      this._queued_query = query;
+  },
+
+  stopPulse : function() {
+      this._pulse_status = 0;
+  },
+
+  startPulse : function() {
+    if (this._pulse_status >= 0)
+        return;
+    function pulse() {
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      var dotString = '';
+      for (var i = 0; i < Search._pulse_status; i++)
+        dotString += '.';
+      Search.dots.text(dotString);
+      if (Search._pulse_status > -1)
+        window.setTimeout(pulse, 500);
+    };
+    pulse();
+  },
+
+  /**
+   * perform a search for something
+   */
+  performSearch : function(query) {
+    // create the required interface elements
+    this.out = $('#search-results');
+    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+    this.dots = $('<span></span>').appendTo(this.title);
+    this.status = $('<p style="display: none"></p>').appendTo(this.out);
+    this.output = $('<ul class="search"/>').appendTo(this.out);
+
+    $('#search-progress').text(_('Preparing search...'));
+    this.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (this.hasIndex())
+      this.query(query);
+    else
+      this.deferQuery(query);
+  },
+
+  query : function(query) {
+    // stem the searchterms and add them to the
+    // correct list
+    var stemmer = new PorterStemmer();
+    var searchterms = [];
+    var excluded = [];
+    var hlterms = [];
+    var tmp = query.split(/\s+/);
+    var object = (tmp.length == 1) ? tmp[0].toLowerCase() : null;
+    for (var i = 0; i < tmp.length; i++) {
+      // stem the word
+      var word = stemmer.stemWord(tmp[i]).toLowerCase();
+      // select the correct list
+      if (word[0] == '-') {
+        var toAppend = excluded;
+        word = word.substr(1);
+      }
+      else {
+        var toAppend = searchterms;
+        hlterms.push(tmp[i].toLowerCase());
+      }
+      // only add if not already in the list
+      if (!$.contains(toAppend, word))
+        toAppend.push(word);
+    };
+    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+    console.debug('SEARCH: searching for:');
+    console.info('required: ', searchterms);
+    console.info('excluded: ', excluded);
+
+    // prepare search
+    var filenames = this._index.filenames;
+    var titles = this._index.titles;
+    var terms = this._index.terms;
+    var descrefs = this._index.descrefs;
+    var modules = this._index.modules;
+    var desctypes = this._index.desctypes;
+    var fileMap = {};
+    var files = null;
+    var objectResults = [];
+    var regularResults = [];
+    $('#search-progress').empty();
+
+    // lookup as object
+    if (object != null) {
+      for (var module in modules) {
+        if (module.indexOf(object) > -1) {
+          fn = modules[module];
+          descr = _('module, in ') + titles[fn];
+          objectResults.push([filenames[fn], module, '#module-'+module, descr]);
+        }
+      }
+      for (var prefix in descrefs) {
+        for (var name in descrefs[prefix]) {
+          var fullname = (prefix ? prefix + '.' : '') + name;
+          if (fullname.toLowerCase().indexOf(object) > -1) {
+            match = descrefs[prefix][name];
+            descr = desctypes[match[1]] + _(', in ') + titles[match[0]];
+            objectResults.push([filenames[match[0]], fullname, '#'+fullname, descr]);
+          }
+        }
+      }
+    }
+
+    // sort results descending
+    objectResults.sort(function(a, b) {
+      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+    });
+
+
+    // perform the search on the required terms
+    for (var i = 0; i < searchterms.length; i++) {
+      var word = searchterms[i];
+      // no match but word was a required one
+      if ((files = terms[word]) == null)
+        break;
+      if (files.length == undefined) {
+        files = [files];
+      }
+      // create the mapping
+      for (var j = 0; j < files.length; j++) {
+        var file = files[j];
+        if (file in fileMap)
+          fileMap[file].push(word);
+        else
+          fileMap[file] = [word];
+      }
+    }
+
+    // now check if the files don't contain excluded terms
+    for (var file in fileMap) {
+      var valid = true;
+
+      // check if all requirements are matched
+      if (fileMap[file].length != searchterms.length)
+        continue;
+
+      // ensure that none of the excluded terms is in the
+      // search result.
+      for (var i = 0; i < excluded.length; i++) {
+        if (terms[excluded[i]] == file ||
+            $.contains(terms[excluded[i]] || [], file)) {
+          valid = false;
+          break;
+        }
+      }
+
+      // if we have still a valid result we can add it
+      // to the result list
+      if (valid)
+        regularResults.push([filenames[file], titles[file], '', null]);
+    }
+
+    // delete unused variables in order to not waste
+    // memory until list is retrieved completely
+    delete filenames, titles, terms;
+
+    // now sort the regular results descending by title
+    regularResults.sort(function(a, b) {
+      var left = a[1].toLowerCase();
+      var right = b[1].toLowerCase();
+      return (left > right) ? -1 : ((left < right) ? 1 : 0);
+    });
+
+    // combine both
+    var results = regularResults.concat(objectResults);
+
+    // print the results
+    var resultCount = results.length;
+    function displayNextItem() {
+      // results left, load the summary and display it
+      if (results.length) {
+        var item = results.pop();
+        var listItem = $('<li style="display:none"></li>');
+        listItem.append($('<a/>').attr(
+          'href',
+          item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+          highlightstring + item[2]).html(item[1]));
+        if (item[3]) {
+          listItem.append($('<span> (' + item[3] + ')</span>'));
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+          $.get('_sources/' + item[0] + '.txt', function(data) {
+            listItem.append($.makeSearchSummary(data, searchterms, hlterms));
+            Search.output.append(listItem);
+            listItem.slideDown(5, function() {
+              displayNextItem();
+            });
+          });
+        } else {
+          // no source available, just display title
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        }
+      }
+      // search finished, update title and status message
+      else {
+        Search.stopPulse();
+        Search.title.text(_('Search Results'));
+        if (!resultCount)
+          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+        else
+            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+        Search.status.fadeIn(500);
+      }
+    }
+    displayNextItem();
+  }
+}
+
+$(document).ready(function() {
+  Search.init();
+});
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/agrifpp.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/agrifpp.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/agrifpp.sh.html	(revision 1972)
@@ -0,0 +1,131 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>agrifpp.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="agrifpp-sh">
+<h1>agrifpp.sh<a class="headerlink" href="#agrifpp-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="preform-agrif-pre-processing">
+<h2>Preform AGrif pre-processing<a class="headerlink" href="#preform-agrif-pre-processing" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ agrifpp.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>Look after key agrif</p>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./agrifpp.sh 1 -Dkey
+
+or
+
+$ ./agrifpp.sh -Dkey</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">agrifpp.sh</a><ul>
+<li><a class="reference external" href="#preform-agrif-pre-processing">Preform AGrif pre-processing</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/genindex.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/genindex.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/genindex.html	(revision 1972)
@@ -0,0 +1,89 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Index &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="#" title="General Index"
+             accesskey="I">index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+
+   <h1 id="index">Index</h1>
+
+   
+
+   <hr />
+
+   
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+
+   
+
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="#" title="General Index"
+             >index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/index.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/index.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/index.html	(revision 1972)
@@ -0,0 +1,114 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>NEMO_UTIL manuals &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="#" />
+    <link rel="next" title="Fcheck_archfile.sh" href="Fcheck_archfile.sh.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="Fcheck_archfile.sh.html" title="Fcheck_archfile.sh"
+             accesskey="N">next</a> |</li>
+        <li><a href="#">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="nemo-util-manuals">
+<span id="index"></span><h1>NEMO_UTIL manuals<a class="headerlink" href="#nemo-util-manuals" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="shell-scripts">
+<h2>Shell scripts<a class="headerlink" href="#shell-scripts" title="Permalink to this headline">¶</a></h2>
+<ul>
+<li class="toctree-l1"><a class="reference external" href="Fcheck_archfile.sh.html">Fcheck_archfile.sh</a></li>
+<li class="toctree-l1"><a class="reference external" href="Fcheck_config.sh.html">Fcheck_config.sh</a></li>
+<li class="toctree-l1"><a class="reference external" href="Fclean_var.sh.html">Fclean_var.sh</a></li>
+<li class="toctree-l1"><a class="reference external" href="Fgo_to_TOOLS.sh.html">Fgo_to_tools.sh</a></li>
+<li class="toctree-l1"><a class="reference external" href="Fmake_config.sh.html">Fmake_config.sh</a></li>
+<li class="toctree-l1"><a class="reference external" href="Fcopy_dir.sh.html">Fcopy_dir.sh</a></li>
+<li class="toctree-l1"><a class="reference external" href="Fmake_WORK.sh.html">Fmake_WORK.sh</a></li>
+<li class="toctree-l1"><a class="reference external" href="Fread_dir.sh.html">Fread_dir.sh</a></li>
+</ul>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="#">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">NEMO_UTIL manuals</a><ul>
+<li><a class="reference external" href="#shell-scripts">Shell scripts</a><ul>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+            <h4>Next topic</h4>
+            <p class="topless"><a href="Fcheck_archfile.sh.html"
+                                  title="next chapter">Fcheck_archfile.sh</a></p>
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="Fcheck_archfile.sh.html" title="Fcheck_archfile.sh"
+             >next</a> |</li>
+        <li><a href="#">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/makenemo_fcm.sh.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/makenemo_fcm.sh.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/makenemo_fcm.sh.html	(revision 1972)
@@ -0,0 +1,154 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>makenemo_fcm.sh &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="makenemo-fcm-sh">
+<h1>makenemo_fcm.sh<a class="headerlink" href="#makenemo-fcm-sh" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="compile-nemo">
+<h2>Compile NEMO<a class="headerlink" href="#compile-nemo" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="synopsis">
+<h3>SYNOPSIS<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ makenemo_fcm.sh</pre>
+</div>
+</div>
+<div class="section" id="description">
+<h3>DESCRIPTION<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h3>
+<p>This script aims :</p>
+<ul class="simple">
+<li>to choose MYCONFIG</li>
+<li>to choose compiler options</li>
+<li>to create the CONFIG/MYCONFIG/WORK directory</li>
+<li>to compile this configuration</li>
+</ul>
+<blockquote>
+<p>Variables used :</p>
+<p>From user input</p>
+</blockquote>
+<ul class="simple">
+<li>NEW_CONF    : configuration to be created</li>
+<li>REF_CONF    : reference configuration to build the new one</li>
+<li>CMP_NAM     : compiler name</li>
+<li>NBR_PRC     : number of processes used to compile</li>
+<li>NEM_SUBDIR  : NEMO subdirectory used (specified)</li>
+</ul>
+<blockquote>
+Locally defined :</blockquote>
+<ul class="simple">
+<li>TAB         : NEMO subdirectory used (read)</li>
+<li>MAIN_DIR : self explaining</li>
+<li>CONFIG_DIR  :   &#8221;    &#8221;    &#8220;</li>
+<li>MODELES_DIR :   &#8221;    &#8221;    &#8220;</li>
+<li>TOOLS_DIR   :   &#8221;    &#8221;    &#8220;</li>
+<li>NEMO_DIR    :   &#8221;    &#8221;    &#8220;</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h3>EXAMPLES<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-python"><pre>$ ./makenemo_fcm -t ifort_osx - j3 -n ORCA2_LIM</pre>
+</div>
+</div>
+<div class="section" id="todo">
+<h3>TODO<a class="headerlink" href="#todo" title="Permalink to this headline">¶</a></h3>
+<p>option debug</p>
+</div>
+<div class="section" id="evolutions">
+<h3>EVOLUTIONS<a class="headerlink" href="#evolutions" title="Permalink to this headline">¶</a></h3>
+<p>$Id$</p>
+<ul class="simple">
+<li>rblod 2010-06-20T16:11:47Z<ul>
+<li>creation</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+            <h3><a href="index.html">Table Of Contents</a></h3>
+            <ul>
+<li><a class="reference external" href="#">makenemo_fcm.sh</a><ul>
+<li><a class="reference external" href="#compile-nemo">Compile NEMO</a><ul>
+<li><a class="reference external" href="#synopsis">SYNOPSIS</a></li>
+<li><a class="reference external" href="#description">DESCRIPTION</a></li>
+<li><a class="reference external" href="#examples">EXAMPLES</a></li>
+<li><a class="reference external" href="#todo">TODO</a></li>
+<li><a class="reference external" href="#evolutions">EVOLUTIONS</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+          <div id="searchbox" style="display: none">
+            <h3>Quick search</h3>
+              <form class="search" action="search.html" method="get">
+                <input type="text" name="q" size="18" />
+                <input type="submit" value="Go" />
+                <input type="hidden" name="check_keywords" value="yes" />
+                <input type="hidden" name="area" value="default" />
+              </form>
+              <p class="searchtip" style="font-size: 90%">
+              Enter search terms or a module, class or function name.
+              </p>
+          </div>
+          <script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/objects.inv
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/objects.inv	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/objects.inv	(revision 1972)
@@ -0,0 +1,3 @@
+# Sphinx inventory version 1
+# Project: NEMO FCM
+# Version: 1.0.0
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/search.html
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/search.html	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/search.html	(revision 1972)
@@ -0,0 +1,91 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Search &mdash; NEMO FCM v1.0.0 documentation</title>
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '#',
+        VERSION:     '1.0.0',
+        COLLAPSE_MODINDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <script type="text/javascript" src="_static/searchtools.js"></script>
+    <link rel="top" title="NEMO FCM v1.0.0 documentation" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <h1 id="search-documentation">Search</h1>
+  <div id="fallback" class="admonition warning">
+  <script type="text/javascript">$('#fallback').hide();</script>
+  <p>
+    Please activate JavaScript to enable the search
+    functionality.
+  </p>
+  </div>
+  <p>
+    From here you can search these documents. Enter your search
+    words into the box below and click "search". Note that the search
+    function will automatically search for all of the words. Pages
+    containing fewer words won't appear in the result list.
+  </p>
+  <form action="" method="get">
+    <input type="text" name="q" value="" />
+    <input type="submit" value="search" />
+    <span id="search-progress" style="padding-left: 10px"></span>
+  </form>
+  
+  <div id="search-results">
+  
+  </div>
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li><a href="index.html">NEMO FCM v1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+  
+    <div class="footer">
+      &copy; Copyright 2010, CNRS.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 0.6.5.
+    </div>
+  <script type="text/javascript" src="searchindex.js"></script>
+
+  </body>
+</html>
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/searchindex.js
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/searchindex.js	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/html/sphinx/searchindex.js	(revision 1972)
@@ -0,0 +1,1 @@
+Search.setIndex({desctypes:{},terms:{rblod:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],previous:6,explain:1,configur:[1,5,13],myconfig:1,fprep_agrif:10,input:[1,12],local:1,sourc:14,synopsi:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],read:[1,12],util:[2,8],opa:6,"new":[1,9,3],directory_nam:12,name:1,choic:[9,3,13],config_nam:[4,10,14],manual:0,agrifpp:11,directoir:12,debug:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],fcheck_script:2,compil:[1,3,4,10,9,14],fgo_to_tool:[0,8],set:[5,13],creation:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],orca2_lim:1,self:1,new_conf:[1,6],config_dir:1,ora2_lim:13,variabl:[1,7],fmake_config:[0,14],sub:[5,6],defin:1,exit:[9,3],bld:[4,14],makenemo_fcm:1,dkei:11,refer:[1,5],namelist:14,previou:[9,3,13],tmp_dir:4,kei:11,standard:12,fcopy_dir:[0,5],repositori:[4,14],my_src:14,tools_dir:1,path:2,cmp_nam:1,first:6,refenr:5,number:1,two:13,done:6,"20t16":[1,2,3,4,5,6,7,8,9,10,11,12,13,14],from:[1,12],conv:10,script:[0,1],evolut:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],shell:0,option:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],fcheck_config:[0,13],ref_config_nam:14,specifi:[1,9,3,6],"case":[9,3,13],look:11,"default":13,prepar:10,work:[1,6],aim:1,fclean_var:[0,7],three:[9,3],main_dir:1,exp00:14,pre:11,file:[9,3],creat:[1,4,6,14],nemo_dir:1,process:[1,11],descript:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],nemo:[1,5],modeles_dir:1,tab:1,need:[4,5,12,14],agrif:[11,10],check:[2,9,3,13],nemo_util:0,fcheck_archfil:[0,9,3],ifort_osx:1,todo:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],make:[4,6,14],when:5,fread_dir:[0,12],build:[1,4],scriptnam:2,subdirectori:1,"47z":[1,2,3,4,5,6,7,8,9,10,11,12,13,14],config:[1,14],noth:13,copi:5,ref_conf:1,clean:7,fmake_bld:4,fmake_work:[0,6],after:11,user:[1,12,14],preform:11,nem_subdir:1,nbr_prc:1,directori:[1,4,5,10,8,6,12,14],explicit:13,inform:[9,3],exampl:[1,2,3,4,5,6,7,8,9,10,11,12,13,14],environ:7,thi:1,choos:1,ref_dir:5,lin:6},titles:["NEMO_UTIL manuals","makenemo_fcm.sh","Fcheck_script.sh","Fcheck_archfile.sh","Fmake_bld.sh","Fcopy_dir.sh","Fmake_WORK.sh","Fclean_var.sh","Fgo_to_tools.sh","Fcheck_archfile.sh","Fprep_agrif.sh","agrifpp.sh","Fread_dir.sh","Fcheck_config.sh","Fmake_config.sh"],modules:{},descrefs:{},filenames:["index","makenemo_fcm.sh","Fcheck_script.sh","*.sh","Fmake_bld.sh","Fcopy_dir.sh","Fmake_WORK.sh","Fclean_var.sh","Fgo_to_TOOLS.sh","Fcheck_archfile.sh","Fprep_agrif.sh","agrifpp.sh","Fread_dir.sh","Fcheck_config.sh","Fmake_config.sh"]})
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_archfile.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_archfile.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_archfile.sh.1	(revision 1972)
@@ -0,0 +1,53 @@
+.TH FCHECK_ARCHFILE.SH  "" "" ""
+.SH NAME
+Fcheck_archfile.sh \- Check the compilation file
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fcheck_archfile.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Check the choice of the compiler.
+Three cases :
+.INDENT 0.0
+.IP \(bu 2
+.
+There was a previous choice
+.IP \(bu 2
+.
+A new one has be specified
+.IP \(bu 2
+.
+No information, exit
+.UNINDENT
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fcheck_archfile.sh COMPILER
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_config.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_config.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_config.sh.1	(revision 1972)
@@ -0,0 +1,52 @@
+.TH FCHECK_CONFIG.SH  "" "" ""
+.SH NAME
+Fcheck_config.sh \- Check the configuration
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fcheck_config.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Check the choice of the configuration:
+.INDENT 0.0
+.IP \(bu 2
+.
+Two cases
+.IP \(bu 2
+.
+One is explicitely set
+.IP \(bu 2
+.
+Nothing set, use the previous in use (default ORA2_LIM)
+.UNINDENT
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fcheck_config.sh
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_script.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_script.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcheck_script.sh.1	(revision 1972)
@@ -0,0 +1,41 @@
+.TH FCHECK_SCRIPT.SH  "" "" ""
+.SH NAME
+Fcheck_script.sh \- Check
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fcheck_script.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Check if utilities are in the path
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fcheck_script.sh scriptname
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fclean_var.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fclean_var.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fclean_var.sh.1	(revision 1972)
@@ -0,0 +1,41 @@
+.TH FCLEAN_VAR.SH  "" "" ""
+.SH NAME
+Fclean_var.sh \- Clean environement variables
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fclean_var.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Clean environement variables
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fclean_var.sh
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcopy_dir.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcopy_dir.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fcopy_dir.sh.1	(revision 1972)
@@ -0,0 +1,42 @@
+.TH FCOPY_DIR.SH  "" "" ""
+.SH NAME
+Fcopy_dir.sh \- Copy a reference directory
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fcopy_dir.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+When a refenrence configuration is set,
+Copy NEMO sub\-directories needed
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fcopy_dir.sh REF_DIR
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fgo_to_TOOLS.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fgo_to_TOOLS.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fgo_to_TOOLS.sh.1	(revision 1972)
@@ -0,0 +1,41 @@
+.TH FGO_TO_TOOLS.SH  "" "" ""
+.SH NAME
+Fgo_to_tools.sh \- Go to the UTIL directory
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fgo_to_tools.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Go to the UTIL directory
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fgo_to_tools.sh
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_WORK.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_WORK.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_WORK.sh.1	(revision 1972)
@@ -0,0 +1,52 @@
+.TH FMAKE_WORK.SH  "" "" ""
+.SH NAME
+Fmake_WORK.sh \- Make the WORK directory
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fmake_WORK.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Make the WORK directory:
+.INDENT 0.0
+.IP \(bu 2
+.
+Create lin in NEW_CONF/WORK
+.IP \(bu 2
+.
+Use specified sub\-directories previously
+.IP \(bu 2
+.
+OPA has to be done first !!!
+.UNINDENT
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fmake_WORK.sh
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_bld.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_bld.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_bld.sh.1	(revision 1972)
@@ -0,0 +1,56 @@
+.TH FMAKE_BLD.SH  "" "" ""
+.SH NAME
+Fmake_bld.sh \- Make build directory
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fmake_bld.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.INDENT 0.0
+.IP \(bu 2
+.
+Make the build directory
+.IP \(bu 2
+.
+Create repositories needed :
+.UNINDENT
+.INDENT 0.0
+.INDENT 3.5
+.INDENT 0.0
+.IP \(bu 2
+.
+BLD for compilation
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fmake_bld.sh CONFIG_NAME  TMP_DIR
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_config.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_config.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fmake_config.sh.1	(revision 1972)
@@ -0,0 +1,62 @@
+.TH FMAKE_CONFIG.SH  "" "" ""
+.SH NAME
+Fmake_config.sh \- Make the config
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fmake_config.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.INDENT 0.0
+.IP \(bu 2
+.
+Make the config directory
+.IP \(bu 2
+.
+Create repositories needed :
+.UNINDENT
+.INDENT 0.0
+.INDENT 3.5
+.INDENT 0.0
+.IP \(bu 2
+.
+EXP00 for namelist
+.IP \(bu 2
+.
+MY_SRC for user sources
+.IP \(bu 2
+.
+BLD for compilation
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fmake_config.sh CONFIG_NAME REF_CONFIG_NAME
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fprep_agrif.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fprep_agrif.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fprep_agrif.sh.1	(revision 1972)
@@ -0,0 +1,43 @@
+.TH FPREP_AGRIF.SH  "" "" ""
+.SH NAME
+Fprep_agrif.sh \- Preparation for AGRIF
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fprep_agrif.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Prepare directories for AGRIF
+.sp
+Compile the conv
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fprep_agrif.sh CONFIG_NAME
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fread_dir.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fread_dir.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/Fread_dir.sh.1	(revision 1972)
@@ -0,0 +1,41 @@
+.TH FREAD_DIR.SH  "" "" ""
+.SH NAME
+Fread_dir.sh \- Read user directories
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ Fread_dir.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Read directoires needed from standard input
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./Fread_dir.sh Directory_NAME YES/NO
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/agrifpp.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/agrifpp.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/agrifpp.sh.1	(revision 1972)
@@ -0,0 +1,45 @@
+.TH AGRIFPP.SH  "" "" ""
+.SH NAME
+agrifpp.sh \- Preform AGrif pre-processing
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ agrifpp.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+Look after key agrif
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./agrifpp.sh 1 \-Dkey
+
+or
+
+$ ./agrifpp.sh \-Dkey
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/makenemo_fcm.sh.1
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/makenemo_fcm.sh.1	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/doc/manuals/man/man1/makenemo_fcm.sh.1	(revision 1972)
@@ -0,0 +1,106 @@
+.TH MAKENEMO_FCM.SH  "" "" ""
+.SH NAME
+makenemo_fcm.sh \- Compile NEMO
+.\" Man page generated from reStructeredText.
+.
+.SH SYNOPSIS
+.sp
+.nf
+.ft C
+$ makenemo_fcm.sh
+.ft P
+.fi
+.SH DESCRIPTION
+.sp
+This script aims :
+.INDENT 0.0
+.IP \(bu 2
+.
+to choose MYCONFIG
+.IP \(bu 2
+.
+to choose compiler options
+.IP \(bu 2
+.
+to create the CONFIG/MYCONFIG/WORK directory
+.IP \(bu 2
+.
+to compile this configuration
+.UNINDENT
+.INDENT 0.0
+.INDENT 3.5
+.sp
+Variables used :
+.sp
+From user input
+.UNINDENT
+.UNINDENT
+.INDENT 0.0
+.IP \(bu 2
+.
+NEW_CONF    : configuration to be created
+.IP \(bu 2
+.
+REF_CONF    : reference configuration to build the new one
+.IP \(bu 2
+.
+CMP_NAM     : compiler name
+.IP \(bu 2
+.
+NBR_PRC     : number of processes used to compile
+.IP \(bu 2
+.
+NEM_SUBDIR  : NEMO subdirectory used (specified)
+.UNINDENT
+.INDENT 0.0
+.INDENT 3.5
+.sp
+Locally defined :
+.UNINDENT
+.UNINDENT
+.INDENT 0.0
+.IP \(bu 2
+.
+TAB         : NEMO subdirectory used (read)
+.IP \(bu 2
+.
+MAIN_DIR : self explaining
+.IP \(bu 2
+.
+CONFIG_DIR  :   "    "    "
+.IP \(bu 2
+.
+MODELES_DIR :   "    "    "
+.IP \(bu 2
+.
+TOOLS_DIR   :   "    "    "
+.IP \(bu 2
+.
+NEMO_DIR    :   "    "    "
+.UNINDENT
+.SH EXAMPLES
+.sp
+.nf
+.ft C
+$ ./makenemo_fcm \-t ifort_osx \- j3 \-n ORCA2_LIM
+.ft P
+.fi
+.SH TODO
+.sp
+option debug
+.SH EVOLUTIONS
+.sp
+$Id$
+.INDENT 0.0
+.IP \(bu 2
+.
+rblod 2010\-06\-20T16:11:47Z
+.INDENT 2.0
+.IP \(bu 2
+.
+creation
+.UNINDENT
+.UNINDENT
+.\" Generated by docutils manpage writer.
+.\" 
+.
Index: /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/makenemo_fcm.sh
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/makenemo_fcm.sh	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/TOOLS/makenemo_fcm.sh	(revision 1972)
@@ -0,0 +1,236 @@
+#!/bin/bash
+#set -x
+set -o posix
+#set -u 
+#set -e
+#+
+#
+# ===============
+# makenemo_fcm.sh
+# ===============
+#
+# --------------------------
+# Compile NEMO
+# --------------------------
+#
+# SYNOPSIS
+# ========
+#
+# ::
+#
+#  $ makenemo_fcm.sh
+#
+#
+# DESCRIPTION
+# ===========
+#
+#
+# This script aims :
+#
+# - to choose MYCONFIG
+# - to choose compiler options  
+# - to create the CONFIG/MYCONFIG/WORK directory
+# - to compile this configuration
+#
+#  Variables used :
+#
+#  From user input
+#
+# - NEW_CONF    : configuration to be created
+# - REF_CONF    : reference configuration to build the new one 
+# - CMP_NAM     : compiler name 
+# - NBR_PRC     : number of processes used to compile  
+# - NEM_SUBDIR  : NEMO subdirectory used (specified)
+#
+#  Locally defined :
+#
+# - TAB         : NEMO subdirectory used (read)  
+# - MAIN_DIR : self explaining
+# - CONFIG_DIR  :   "    "    "   
+# - MODELES_DIR :   "    "    " 
+# - TOOLS_DIR   :   "    "    " 
+# - NEMO_DIR    :   "    "    "
+#
+# EXAMPLES
+# ========
+#
+# ::
+#
+#  $ ./makenemo_fcm -t ifort_osx - j3 -n ORCA2_LIM
+#
+#
+# TODO
+# ====
+#
+# option debug
+#
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+#
+# - rblod 2010-06-20T16:11:47Z
+#
+#   * creation
+#
+#-
+
+#- Local variables ---
+b_n=$(basename ${0})
+export MAIN_DIR=${PWD%/NEMOGCM*}/NEMOGCM
+export CONFIG_DIR=${MAIN_DIR}/CONFIG
+export TOOLS_DIR=${MAIN_DIR}/TOOLS
+export NEMO_DIR=${MAIN_DIR}/NEMO
+export AGRIFUSE=0
+declare -a TAB
+#-
+#- FCM and functions location ---
+#RB Should we add fcm as a vendor ???
+#export PATH=${MAIN_DIR}/modeles/fcm/bin:$PATH
+
+#-
+#- Choice of the options ---
+x_d="";
+x_n="";
+x_r="";
+x_m="";
+x_t="";
+x_j=1;
+while getopts :hld:n:r:m:j:t: V
+  do
+	 case $V in
+		(h)  echo "Usage	 : "${b_n} \
+					 " [-h] [-l] [-n name] [-m arch] [-d "dir1 dir2"] [-r conf] [-j No]";
+			  echo " -h		: help";
+			  echo " -l		: list existing configurations";
+			  echo " -n name : config name";
+			  echo " -m arch : choose machine";
+			  echo " -d dir  : choose NEMO sub-directories";
+			  echo " -r conf : choose reference configuration";
+			  echo " -j No	 : number of processes used to compile (0=nocompilation)";
+			  echo " -t dir  : remporary directory for compilation"
+			  echo "";
+			  echo "Example to install a new configuration MY_CONFIG";
+			  echo "with OPA_SRC and LIM_SRC_2 ";
+			  echo "makenemo_fcm -n MY_CONFIG -d \"OPA_SRC LIM_SRC_2\"";
+			  echo "";
+			  echo "Defaults	  : ";
+			  echo "";
+			  exit 0;;
+		(d)  x_d=${OPTARG};;
+		(n)  x_n=${OPTARG};;
+		(r)  x_r=${OPTARG};;
+		(m)  x_m=${OPTARG};;
+		(j)  x_j=${OPTARG};;
+		(t)  x_t=${OPTARG};;
+		(l)  echo "Available configurations :"; cat ${TOOLS_DIR}/cfg.txt; exit;;
+		(:)  echo ${b_n}" : -"${OPTARG}" option : missing value" 1>&2;
+			  exit 2;;
+		(\?) echo ${b_n}" : -"${OPTARG}" option : not supported" 1>&2;
+			  exit 2;;
+	 esac
+  done
+shift $(($OPTIND-1));
+
+#-
+#- Go to NEMOGCM/config directory ---
+cd ${CONFIG_DIR}
+
+#-
+#- Initialisation from input ---
+export NEW_CONF=${x_n}
+NBR_PRC=${x_j}
+CMP_NAM=${x_m}
+NEM_SUBDIR=${x_d}
+REF_CONF=${x_r}
+NEMO_TDIR=${x_t:-$NEMO_TDIR}
+export NEMO_TDIR=${NEMO_TDIR:-$CONFIG_DIR}
+
+#-
+#- Find fcm ---
+. Fcheck_script.sh fcm || exit
+
+#-
+#- When used for the first time, choose a compiler ---
+. Fcheck_archfile.sh ${CMP_NAM} || exit
+
+#-
+#- Choose a default configuration if needed ---
+#- ORCA2_LIM or last one used ---
+. Fcheck_config.sh ${NEW_CONF} || exit 
+
+if [ ${#NEW_CONF} -eq 0 ] ; then
+	if [ ${#NEM_SUBDIR} -eq 0 -a ${#REF_CONF} -eq 0 ]; then
+		echo "You are  installing a new configuration"
+		ind=0
+		. Fread_dir.sh OPA_SRC	YES 
+		. Fread_dir.sh LIM_SRC_2 YES 
+		. Fread_dir.sh LIM_SRC_3 NO  
+		. Fread_dir.sh TOP_SRC	NO  
+		. Fread_dir.sh C1D_SRC	YES 
+		. Fread_dir.sh NST_SRC	YES 
+		. Fread_dir.sh OFF_SRC	NO  
+		REF_CONF=ORCA2_LIM
+	elif [ ${#NEM_SUBDIR} -gt 0 ] && [ ${#REF_CONF} -eq 0 ]; then
+		echo "You are  installing a new configuration"
+		TAB=( ${NEM_SUBDIR} )
+		REF_CONF=ORCA2_LIM
+	elif [ ${#NEM_SUBDIR} -eq 0 ] && [ ${#REF_CONF} -gt 0 ]; then
+		echo "You are  installing a new configuration based on ${REF_CONF}"
+		Fcopy_dir.sh ${REF_CONF}  
+	fi
+	NEW_CONF=${x_n}
+    . Fmake_config.sh ${NEW_CONF} ${REF_CONF}
+else
+	sed -e "/${NEW_CONF} /d"  ${TOOLS_DIR}/cfg.txt >  ${TOOLS_DIR}/cfg.tmp
+	\mv  ${TOOLS_DIR}/cfg.tmp  ${TOOLS_DIR}/cfg.txt
+fi
+
+#-
+#- Save new configuration and directories names ---
+echo ${NEW_CONF} ${TAB[*]} >> ${TOOLS_DIR}/cfg.txt
+
+#-
+#- Create the WORK ---
+#- Clean links and librairies ---
+#- Creating the good links, at first on OPA_SRC ---
+. Fmake_WORK.sh ${NEW_CONF} ${TAB[*]} || exit
+
+##SF   exit
+
+. Fmake_bld.sh ${NEW_CONF}  ${NEMO_TDIR} || exit
+
+#- At this stage the configuration has beeen chosen
+#- We look after agrif
+grep key_agrif ${TOOLS_DIR}/cpp.fcm && export AGRIFUSE=1
+. Fprep_agrif.sh ${NEW_CONF} ${NEMO_TDIR} || exit
+
+#-
+#_ END OF CONFIGURATION PHASE
+#_
+
+#-
+#- Compile ---
+
+if [ "${NBR_PRC}" -gt 0 ]; then
+cd ${NEMO_TDIR}/${NEW_CONF} || cd -
+
+#if AGRIF we do a first preprocessing
+[ "$AGRIFUSE" == 1 ] && fcm build --ignore-lock -s 2 ${TOOLS_DIR}/bld.cfg 
+[ "$AGRIFUSE" == 1 ] && rm -rf  ${NEMO_TDIR}/${NEW_CONF}/BLD/*
+fcm build --ignore-lock -v 1 -j ${NBR_PRC} ${TOOLS_DIR}/bld.cfg || cd -
+[ -f ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe ] && ln -sf ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe  ${CONFIG_DIR}/${NEW_CONF}/EXP00/opa
+fi
+
+#-
+#- Come back to original directory ---
+cd -
+
+#-
+#- Unset variables
+Fclean_var.sh
+
+
+exit 0;
Index: /branches/DEV_r1879_FCM/NEMOGCM/arch.fcm
===================================================================
--- /branches/DEV_r1879_FCM/NEMOGCM/arch.fcm	(revision 1972)
+++ /branches/DEV_r1879_FCM/NEMOGCM/arch.fcm	(revision 1972)
@@ -0,0 +1,1 @@
+link ../ARCH/arch-SX8_BRODIE.fcm
