#### We are using the nubblelized oax output file that had the 
####  inversions removed
####

../SRC/break_into_levs ../new_postNUB_BOB/Jan_hb_cleaned_notime_nub_zlevs_smoothed.out
 
 rm sab_summ_clim2.lst         
 
 ../SRC/run_BIO2LST	    
 
 rm sab_clim2.bound.data       

 ../SRC/pick_lst < ../input_files/pick_lst.in        

 rm sab_summ_clim2.elev        

 ../SRC/sss1_xy_lst2 < ../input_files/sss1_xy_lst2.in
 
 mkdir hydrography
 
 cp ../new_postNUB_BOB/Jan_hb_cleaned_notime_nub_sg.out hydrography/jan_clim_fem_bat.out

 ../SRC/run_f6bc
 
mv zetageo_summ.s2r Jan/zetageo_Jan_nub.s2r
mv uvsurfgeo_summ.v2r Jan/uvsurfgeo_Jan_nub.v2r
mv uvbargeo_summ.v2r Jan/uvbargeo_Jan_nub.v2r
mv uvbottgeo_summ.v2r Jan/uvbottgeo_Jan_nub.v2r
mv F6.HOT.icq4 Jan/F6.HOT.Jan_nub.icq4



../SRC/break_into_levs ../new_postNUB_BOB/Feb_hb_cleaned_notime_nub_zlevs_smoothed.out
 
 rm sab_summ_clim2.lst         
 
 ../SRC/run_BIO2LST	    
 
 rm sab_clim2.bound.data       

 ../SRC/pick_lst < ../input_files/pick_lst.in        

 rm sab_summ_clim2.elev        

 ../SRC/sss1_xy_lst2 < ../input_files/sss1_xy_lst2.in
 
 cp ../new_postNUB_BOB/Feb_hb_cleaned_notime_nub_sg.out hydrography/jan_clim_fem_bat.out

 ../SRC/run_f6bc
 
mv zetageo_summ.s2r Feb/zetageo_Feb_nub.s2r
mv uvsurfgeo_summ.v2r Feb/uvsurfgeo_Feb_nub.v2r
mv uvbargeo_summ.v2r Feb/uvbargeo_Feb_nub.v2r
mv uvbottgeo_summ.v2r Feb/uvbottgeo_Feb_nub.v2r
mv F6.HOT.icq4 Feb/F6.HOT.Feb_nub.icq4




../SRC/break_into_levs ../new_postNUB_BOB/Mar_hb_cleaned_notime_nub_zlevs_smoothed.out
 
 rm sab_summ_clim2.lst         
 
 ../SRC/run_BIO2LST	    
 
 rm sab_clim2.bound.data       

 ../SRC/pick_lst < ../input_files/pick_lst.in        

 rm sab_summ_clim2.elev        

 ../SRC/sss1_xy_lst2 < ../input_files/sss1_xy_lst2.in
 
 cp ../new_postNUB_BOB/Mar_hb_cleaned_notime_nub_sg.out hydrography/jan_clim_fem_bat.out

 ../SRC/run_f6bc
 
mv zetageo_summ.s2r Mar/zetageo_Mar_nub.s2r
mv uvsurfgeo_summ.v2r Mar/uvsurfgeo_Mar_nub.v2r
mv uvbargeo_summ.v2r Mar/uvbargeo_Mar_nub.v2r
mv uvbottgeo_summ.v2r Mar/uvbottgeo_Mar_nub.v2r
mv F6.HOT.icq4 Mar/F6.HOT.Mar_nub.icq4




../SRC/break_into_levs ../new_postNUB_BOB/Apr_hb_cleaned_notime_nub_zlevs_smoothed.out
 
 rm sab_summ_clim2.lst         
 
 ../SRC/run_BIO2LST	    
 
 rm sab_clim2.bound.data       

 ../SRC/pick_lst < ../input_files/pick_lst.in        

 rm sab_summ_clim2.elev        

 ../SRC/sss1_xy_lst2 < ../input_files/sss1_xy_lst2.in
 
 cp ../new_postNUB_BOB/Apr/Apr_hb_cleaned_notime_nub_sg.out hydrography/jan_clim_fem_bat.out

 ../SRC/run_f6bc
 
mv zetageo_summ.s2r Apr/zetageo_Apr_nub.s2r
mv uvsurfgeo_summ.v2r Apr/uvsurfgeo_Apr_nub.v2r
mv uvbargeo_summ.v2r Apr/uvbargeo_Apr_nub.v2r
mv uvbottgeo_summ.v2r Apr/uvbottgeo_Apr_nub.v2r
mv F6.HOT.icq4 Apr/F6.HOT.Apr_nub.icq4