<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} > 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 "(${X_EXTENT} / ${SPACING})" | bc`
                DC=`echo "${SPACING}.0"`
+                ## Compute scaled spacing, time_step, and viscosities
+                D_SPACING=`echo "scale=4; ${SPACING}/${REF_SPACING}" | bc`
+                SCALED_TIME_STEP=`echo "scale=4; $D_SPACING * $REF_TIME_STEP" | bc`
+
                echo " Converting ${NAME} mesh to have ${VERTLEV} levels"
                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 "scale=4; ${SPACING}/${REF_SPACING}" | bc`
                                                STATS=`echo " $TOTAL_TIME / $TIME_STEP / 10 " | bc`
-                                                RUN_NAME=${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 > /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 ${RUN_NAME}/ocean_model.exe ]; then
@@ -255,6 +255,7 @@
                                                echo "${CUR_DIR}/${RUN_NAME}" >> run_paths
                                                ## Generate new namelist.input file for test case
+                                                STATS=`echo " $TOTAL_TIME / $TIME_STEP / 10 " | bc`
                                                cat MPAS-namelist.input.template \
                                                        | sed "s/config_time_integration .*/config_time_integration = ${TIME_INTEGRATOR}/g" \
                                                        | sed "s/config_n_btr_subcycles .*/config_n_btr_subcycles = ${SUB_CYCLES}/g" \
@@ -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 > /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 " $TOTAL_TIME / $SCALED_TIME_STEP / 10 " | bc`
+                cat MPAS-namelist.input.template \
+                        | sed "s/config_time_integration .*/config_time_integration = ${DEFAULT_TIME_INTEGRATOR}/g" \
+                        | sed "s/config_n_btr_subcycles .*/config_n_btr_subcycles = ${DEFAULT_SUBCYCLES}/g" \
+                        | sed "s/config_dt .*/config_dt = ${SCALED_TIME_STEP}/g" \
+                        | sed "s/config_stats_interval .*/config_stats_interval = ${STATS}/g" \
+                        | sed "s/config_monotonic .*/config_monotonic = ${FCT_ON}/g" \
+                        | sed "s/config_horiz_tracer_adv_order .*/config_horiz_tracer_adv_order = ${ADV_ORDER}/g" \
+                        > ${NAME}_${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 > /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 > /dev/null
                done
                cd ${CUR_DIR}
</font>
</pre>