Index: /issm/trunk-jpl/test/NightlyRun/test4005.m
===================================================================
--- /issm/trunk-jpl/test/NightlyRun/test4005.m	(revision 27598)
+++ /issm/trunk-jpl/test/NightlyRun/test4005.m	(revision 27599)
@@ -3,5 +3,5 @@
 %
 %Script control parameters
-steps=1:11;
+steps=[1:5 7:11];
 final_time=1;
 
@@ -648,11 +648,11 @@
     results=md.results;
 
-    for t=0:time_step:final_time
+    for t=0:time_step:4*time_step
 		 disp(['Year: ' num2str(t)])
 
 		 %Initialize time steps
-		 md.timestepping.final_time=(t+1)*time_step;
+		 md.timestepping.final_time=t+time_step;
 		 md.timestepping.time_step=time_step;
-		 md.timestepping.start_time=t*time_step;;
+		 md.timestepping.start_time=t;
 
 		 %Calculate dynamic thinning and write 
@@ -669,21 +669,29 @@
 		 % {{{ system call to run MITgcm
 		 cd run
+
+                 newline = [' niter0 = ' num2str(t*y2s/MITgcmDeltaT)];
+		 command=['!sed "s/.*niter0.*/' newline '/" data > data.temp; mv data.temp data'];
+		 eval(command)
+
+
        ds=round(endtime/MITgcmDeltaT);
        ts=round((t+time_step)*y2s/MITgcmDeltaT);
+                 
 		 eval(['!mpirun -np ' int2str(nPx*nPy) ' ./mitgcmuv']);
-		 eval(['!\mv STDERR.0000 STDERR_' myint2str(t) '.data'])
-		 eval(['!\mv STDOUT.0000 STDOUT_' myint2str(t) '.data'])
-		 eval(['!\cp hFacC.data hFacC_' myint2str(t) '.data'])
-		 eval(['!\cp icetopo.bin icetopo_' myint2str(t) '.data'])
-		 for fld={'S','T','U','V','Eta', ...
-				 'SHICE_heatFluxtave','SHICE_fwFluxtave'}
-			 eval(['!\mv ' fld{1} '.' myint2str(ds,10) '.data ' ...
-				 fld{1} '_' myint2str(t,10) '.data'])
-		 end
+		 eval(['!\mv STDERR.0000 STDERR_' myint2str(t/time_step) '.data'])
+		 eval(['!\mv STDOUT.0000 STDOUT_' myint2str(t/time_step) '.data'])
+		 eval(['!\cp hFacC.data hFacC_' myint2str(t/time_step) '.data'])
+		 eval(['!\cp icetopo.bin icetopo_' myint2str(t/time_step) '.data'])
+%		 for fld={'S','T','U','V','Eta', ...
+%				 'SHICE_heatFluxtave','SHICE_fwFluxtave'}
+%			 eval(['!\mv ' fld{1} '.' myint2str(ds,10) '.data ' ...
+%				 fld{1} '_' myint2str(t,10) '.data'])
+%		 end
 		 cd ..
 		 % }}}
 
-		 system(['cp run/SHICE_fwFluxtave.' myint2str((t+1)*2160,10) '.data run/melt.data'])
-		 system(['mv run/SHICE_fwFluxtave.' myint2str((t+1)*2160,10) '.data run/melt' int2str(t) '.data'])
+		 system(['cp run/SHICE_fwFluxtave.' myint2str((t+time_step)*y2s/MITgcmDeltaT,10) '.data run/melt.data'])
+%		 system(['cp run/SHICE_fwFluxtave.' myint2str((t+1)*2160,10) '.data run/melt.data'])
+%		 system(['mv run/SHICE_fwFluxtave.' myint2str((t+1)*2160,10) '.data run/melt' int2str(t) '.data'])
 
        melt=readbin('./run/melt.data',[Nx,Ny]);
@@ -713,11 +721,11 @@
 
 %Fields and tolerances to track changes
-fnm=['run/SHICE_fwFluxtave_0000004380.data'];
+fnm=['run/SHICE_fwFluxtave.0000004380.data'];
 melting_rate_1=readbin(fnm,[Nx Ny]);
-fnm=['run/SHICE_fwFluxtave_0000008760.data'];
+fnm=['run/SHICE_fwFluxtave.0000008760.data'];
 melting_rate_2=readbin(fnm,[Nx Ny]);
-fnm=['run/SHICE_fwFluxtave_0000013140.data'];
+fnm=['run/SHICE_fwFluxtave.0000013140.data'];
 melting_rate_3=readbin(fnm,[Nx Ny]);
-fnm=['run/SHICE_fwFluxtave_0000017520.data'];
+fnm=['run/SHICE_fwFluxtave.0000017520.data'];
 melting_rate_4=readbin(fnm,[Nx Ny]);
 field_names     ={'Base1','Melting1','Vx2','Vy2','Thickness2','Base2','MaskOceanLevelset2','FloatingiceMeltingRate2',...