<p><b>dwj07@fsu.edu</b> 2012-03-19 15:35:20 -0600 (Mon, 19 Mar 2012)</p><p><br>
        -- BRANCH COMMIT --<br>
<br>
        Cleaning up directories for two test cases some more.<br>
</p><hr noshade><pre><font color="gray">Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/getErrors.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/getErrors.sh        2012-03-19 20:38:14 UTC (rev 1673)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/getErrors.sh        2012-03-19 21:35:20 UTC (rev 1674)
@@ -25,5 +25,5 @@
 for ERROR_FILE in ${ERROR_FILES}
 do
         sort -n ${ERROR_FILE} &gt; temp
-        mv temp ${ERROR_FILE}
+        mv temp advective_transport_${ERROR_FILE}
 done

Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/makeMeshes.sh        2012-03-19 20:38:14 UTC (rev 1673)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/makeMeshes.sh        2012-03-19 21:35:20 UTC (rev 1674)
@@ -181,6 +181,10 @@
                 NX=`echo &quot;(${X_EXTENT} / ${SPACING})&quot; | bc`
                 DC=`echo &quot;${SPACING}.0&quot;`
 
+                ## Compute scaled spacing, time_step, and viscosities
+                D_SPACING=`echo &quot;scale=4; ${SPACING}/${REF_SPACING}&quot; | bc`
+                SCALED_TIME_STEP=`echo &quot;scale=4; $D_SPACING * $REF_TIME_STEP&quot; | bc`
+
                 echo &quot;     Converting ${NAME} mesh to have ${VERTLEV} levels&quot;
 
                 ln -s ${TCNAME}_${NAME}.grid.nc grid.nc
@@ -191,8 +195,6 @@
 
                 mkdir -p ${NAME}_${VERTLEV}levs
 
-                mv ocean.nc ${TCNAME}_${NAME}_${VERTLEV}levs.grid.nc
-                mv graph.info ${TCNAME}_${NAME}_${VERTLEV}levs.graph.info
 
                 for TIME_STEPPER in ${TIME_STEPPERS}
                 do
@@ -228,16 +230,14 @@
                                                 D_SPACING=`echo &quot;scale=4; ${SPACING}/${REF_SPACING}&quot; | bc`
                                                 STATS=`echo &quot; $TOTAL_TIME / $TIME_STEP / 10 &quot; | bc`
 
-                                                RUN_NAME=${NAME}_${VERTLEV}levs/${TIME_STEPPER}_${TIME_STEP}_${ADVECTION_ROUTINE}/${PROC}procs
+                                                RUN_NAME=${NAME}_${VERTLEV}levs/.batch_runs/${TIME_STEPPER}_${TIME_STEP}_${ADVECTION_ROUTINE}/${PROC}procs
 
                                                 mkdir -p ${RUN_NAME}
 
-                                                pmetis ${TCNAME}_${NAME}_${VERTLEV}levs.graph.info $PROC &gt; /dev/null
+                                                ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/graph.info ${RUN_NAME}/graph.info
+                                                ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/graph.info.part.${PROC} ${RUN_NAME}/graph.info.part.${PROC}
+                                                ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/grid.nc ${RUN_NAME}/grid.nc
 
-                                                ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.graph.info ${RUN_NAME}/graph.info
-                                                ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.graph.info.part.${PROC} ${RUN_NAME}/graph.info.part.${PROC}
-                                                ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.grid.nc ${RUN_NAME}/grid.nc
-
                                                 ## Copy executable to run directory
                                                 if [ $# -ge 1  ]; then
                                                         if [ -e ${RUN_NAME}/ocean_model.exe ]; then
@@ -255,6 +255,7 @@
                                                 echo &quot;${CUR_DIR}/${RUN_NAME}&quot; &gt;&gt; run_paths
 
                                                 ## Generate new namelist.input file for test case
+                                                STATS=`echo &quot; $TOTAL_TIME / $TIME_STEP / 10 &quot; | bc`
                                                 cat MPAS-namelist.input.template  \
                                                         | sed &quot;s/config_time_integration .*/config_time_integration = ${TIME_INTEGRATOR}/g&quot; \
                                                         | sed &quot;s/config_n_btr_subcycles .*/config_n_btr_subcycles = ${SUB_CYCLES}/g&quot; \
@@ -268,7 +269,36 @@
                         done
                 done
 
-                mv ${TCNAME}_${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
+                mv ocean.nc ${NAME}_${VERTLEV}levs/grid.nc
+                mv graph.info ${NAME}_${VERTLEV}levs/graph.info
+
+                cd ${NAME}_${VERTLEV}levs
+
+                for PROC in $PROCS
+                do
+                        pmetis graph.info $PROC &gt; /dev/null
+                done
+                ## Copy executable to run directory
+                if [ $# -ge 1  ]; then
+                        if [ -e ocean_model.exe ]; then
+                                unlink ocean_model.exe
+                        fi
+
+                        ln -s $1 ocean_model.exe
+                fi
+                cd ${CUR_DIR}
+
+                ## Generate new namelist.input file for test case
+                STATS=`echo &quot; $TOTAL_TIME / $SCALED_TIME_STEP / 10 &quot; | bc`
+                cat MPAS-namelist.input.template  \
+                        | sed &quot;s/config_time_integration .*/config_time_integration = ${DEFAULT_TIME_INTEGRATOR}/g&quot; \
+                        | sed &quot;s/config_n_btr_subcycles .*/config_n_btr_subcycles = ${DEFAULT_SUBCYCLES}/g&quot; \
+                        | sed &quot;s/config_dt .*/config_dt = ${SCALED_TIME_STEP}/g&quot; \
+                        | sed &quot;s/config_stats_interval .*/config_stats_interval = ${STATS}/g&quot; \
+                        | sed &quot;s/config_monotonic .*/config_monotonic = ${FCT_ON}/g&quot; \
+                        | sed &quot;s/config_horiz_tracer_adv_order .*/config_horiz_tracer_adv_order = ${ADV_ORDER}/g&quot; \
+                        &gt; ${NAME}_${VERTLEV}levs/namelist.input
+
         done
 
         rm map

Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh        2012-03-19 20:38:14 UTC (rev 1673)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh        2012-03-19 21:35:20 UTC (rev 1674)
@@ -184,9 +184,6 @@
                 unlink grid.nc
 
                 mkdir -p ${NAME}_${VERTLEV}levs
-
-                mv ocean.nc ${TCNAME}_${NAME}_${VERTLEV}levs.grid.nc
-                mv graph.info ${TCNAME}_${NAME}_${VERTLEV}levs.graph.info
                 
                 for TIME_STEPPER in ${TIME_STEPPERS}
                 do
@@ -211,11 +208,9 @@
 
                                         mkdir -p ${RUN_NAME}
 
-                                        pmetis ${TCNAME}_${NAME}_${VERTLEV}levs.graph.info $PROC &gt; /dev/null
-
-                                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.graph.info ${RUN_NAME}/graph.info
-                                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.graph.info.part.${PROC} ${RUN_NAME}/graph.info.part.${PROC}
-                                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.grid.nc ${RUN_NAME}/grid.nc
+                                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/graph.info ${RUN_NAME}/graph.info
+                                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/graph.info.part.${PROC} ${RUN_NAME}/graph.info.part.${PROC}
+                                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/grid.nc ${RUN_NAME}/grid.nc
                                         ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/dx ${RUN_NAME}/dx
 
                                         ## Copy executable to run directory
@@ -250,18 +245,14 @@
                         done
                 done
 
-                mv ${TCNAME}_${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
+                mv ocean.nc ${NAME}_${VERTLEV}levs/grid.nc
+                mv graph.info ${NAME}_${VERTLEV}levs/graph.info
                 mv dx ${NAME}_${VERTLEV}levs/.
 
-
                 cd ${NAME}_${VERTLEV}levs
-                ln -s ${TCNAME}_${NAME}_${VERTLEV}levs.grid.nc grid.nc
-                ln -s ${TCNAME}_${NAME}_${VERTLEV}levs.graph.info graph.info
-
                 for PROC in $PROCS
                 do
-                        ln -s ${TCNAME}_${NAME}_${VERTLEV}levs.graph.info.part.${PROC} graph.info.part.${PROC}
-
+                        pmetis graph.info $PROC &gt; /dev/null
                 done
                 cd ${CUR_DIR}
 

</font>
</pre>