--- MITgcm/pkg/seaice/seaice_jacvec.F	2013/04/04 07:02:51	1.5
+++ MITgcm/pkg/seaice/seaice_jacvec.F	2017/05/23 16:24:46	1.8
@@ -1,4 +1,4 @@
-C $Header: /home/ubuntu/mnt/e9_copy/MITgcm/pkg/seaice/seaice_jacvec.F,v 1.5 2013/04/04 07:02:51 mlosch Exp $
+C $Header: /home/ubuntu/mnt/e9_copy/MITgcm/pkg/seaice/seaice_jacvec.F,v 1.8 2017/05/23 16:24:46 mlosch Exp $
 C $Name:  $
 
 #include "SEAICE_OPTIONS.h"
@@ -69,11 +69,23 @@
       _RL epsilon, reps
 CEOP
 C     Instructions for using TAF or TAMC to generate exact Jacobian times
-C     vector operations:
+C     vector operations (if SEAICE_ALLOW_MOM_ADVECTION is defined, the
+C     file list also needs to include seaice_mom_advection.f, 
+C     mom_calc_hfacz.f, mom_calc_ke.f, mom_calc_relvort3.f, 
+C     mom_vi_u_coriolis.f, mom_vi_u_coriolis_c4.f, mom_vi_u_grad_ke.f,
+C     mom_vi_v_coriolis.f, mom_vi_v_coriolis_c4.f, mom_vi_v_grad_ke.f
+C     plus flow information for diagnostics_fill.f:
+CCCCCCCADJ SUBROUTINE DIAGNOSTICS_FILL INPUT  = 1,2,3,4,5,6,7,8
+CCCCCCCADJ SUBROUTINE DIAGNOSTICS_FILL OUTPUT =
+C     )
 C
 C     1. make small_f
-C     2. cat seaice_calc_residual.f seaice_oceandrag_coeffs.f seaice_calc_strainrates.f seaice_calc_viscosities.f seaice_calc_rhs.f seaice_calc_lhs.f > taf_input.f
-C     3. staf -v1 -forward -toplevel seaice_calc_residual -input uIceLoc,viceLoc -output uIceRes,vIceRes taf_input.f
+C     2. cat seaice_calc_residual.f seaice_oceandrag_coeffs.f \
+C        seaice_bottomdrag_coeffs.f seaice_calc_stressdiv.f \
+C        seaice_calc_strainrates.f seaice_calc_viscosities.f \
+C        seaice_calc_rhs.f seaice_calc_lhs.f > taf_input.f
+C     3. staf -v1 -forward -toplevel seaice_calc_residual \
+C             -input uIceLoc,viceLoc -output uIceRes,vIceRes taf_input.f
 C     4. insert content of taf_input_ftl.f at the end of this file
 C     5. add the following code and comment out the finite difference code
 C
@@ -81,14 +93,21 @@
 C     starting with version 2.0):
 C
 C     1. make small_f
-C     2. staf -forward -toplevel seaice_calc_residual -input uIceLoc,viceLoc -output uIceRes,vIceRes seaice_calc_residual.f seaice_oceandrag_coeffs.f seaice_calc_strainrates.f seaice_calc_viscosities.f seaice_calc_rhs.f seaice_calc_lhs.f
-C     3. copy files seaice_*_tl.f to the corresponding seaice_*.f files, 
+C     2. files="seaice_calc_residual.f seaice_oceandrag_coeffs.f \
+C               seaice_bottomdrag_coeffs.f seaice_calc_stressdiv.f \
+C               seaice_calc_strainrates.f seaice_calc_viscosities.f \
+C               seaice_calc_rhs.f seaice_calc_lhs.f"
+C     3. staf -forward -toplevel seaice_calc_residual \
+C             -input uIceLoc,viceLoc -output uIceRes,vIceRes $files
+C     4. copy files seaice_*_tl.f to the corresponding seaice_*.f files, 
 C        e.g. with this bash script:
-C     for file in `ls seaice_*_tl.f`; do 
-C       nfile=`echo $file | awk -F_ '{printf "%s_%s_%s.f", $1,$2,$3}'`; 
-C       \cp -f $file $nfile
+C     for file in $files; do 
+C       nfile=`echo $file | awk -F. '{printf "%s_tl.f", $1}'`; 
+C       \cp -f $nfile $file
 C     done
-C     4. add the following code, change "call g_seaice_calc_residual" to "call seaice_calc_residual_tl", and comment out the finite difference code
+C     5. add the following code, change "call g_seaice_calc_residual" 
+C        to "call seaice_calc_residual_tl", and comment out the finite 
+C        difference code
 CML      _RL g_duIce(1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
 CML      _RL g_dvIce(1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
 CML      _RL g_uIceRes(1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)