Finalise scripts for processing cells dumps so that the edges of partitions can be studied

examples/analyse_dump_cells.py

@@ -33,6 +33,16 @@ import numpy as np
 import sys
 import pandas
 
+xcol = 0
+ycol = 1
+zcol = 2
+xwcol = 3
+ywcol = 4
+zwcol = 5
+localcol = 18
+supercol = 15
+activecol = 16
+
 #  Command-line arguments.
 if len(sys.argv) < 5:
     print "usage: ", sys.argv[0], " nx ny nz cell1.dat cell2.dat ..."
@@ -48,28 +58,27 @@ tcount = 0
 for i in range(4, len(sys.argv)):
 
     #  Read the file.
-    #data = pl.loadtxt(sys.argv[i])
-    data = pandas.read_csv(sys.argv[i], sep="\s+").values
+    data = pl.loadtxt(sys.argv[i])
     #print data
 
-    #  Select cells that are on the current rank and are top-level.
-    rdata = data[data[:,16] == 1]
-    tdata = rdata[rdata[:,9] == 0]
+    #  Select cells that are on the current rank and are super cells.
+    rdata = data[data[:,localcol] == 1]
+    tdata = rdata[rdata[:,supercol] == 1]
 
     #  Separation of the cells is in data.
-    xwidth = tdata[0,3]
-    ywidth = tdata[0,4]
-    zwidth = tdata[0,5]
+    xwidth = tdata[0,xwcol]
+    ywidth = tdata[0,ywcol]
+    zwidth = tdata[0,zwcol]
 
     #  Fill space nx, ny,n nz with all toplevel cells and flag their active
     #  state.
     space = np.zeros((nx,ny,nz))
     actives = []
     for line in tdata:
-        ix = int(np.rint(line[0] / xwidth))
-        iy = int(np.rint(line[1] / ywidth))
-        iz = int(np.rint(line[2] / zwidth))
-        active = int(line[14])
+        ix = int(np.rint(line[xcol] / xwidth))
+        iy = int(np.rint(line[ycol] / ywidth))
+        iz = int(np.rint(line[zcol] / zwidth))
+        active = int(line[activecol])
         space[ix,iy,iz] = 1 + active
         tcount = tcount + 1
         if active == 1:
@@ -110,8 +119,6 @@ for i in range(4, len(sys.argv)):
 
     allactives.extend(actives)
 
-
-
 print "# top cells: ", tcount, " active: ", len(allactives), " on edge: ", onedge
 
 sys.exit(0)

examples/process_cells

 #!/bin/bash
 #
 # Usage:
-#  process_cells nprocess
+#  process_cells nx ny nz nprocess
 #
 # Description:
-#  Process all the cell dumps in the current directory
+#  Process all the cell dumps in the current directory.
+
+#  Outputs file per rank with the active cells identified and marked as to
+#  whether they are near an edge or not. Note requires the numbers of cells
+#  per dimension of the space.
 #
-#  Outputs file per rank with the active cells identified and marked
-#  as to whether they are near an edge or not.
+#  Also outputs a graphic showing the fraction of active cells on edges
+#  for each step.
 
 #  Handle command-line
-if test "$1" = ""; then
-    echo "Usage: $0 nprocess"
+if test "$4" = ""; then
+    echo "Usage: $0 nx ny nz nprocess"
     exit 1
 fi
-NPROCS=$1
+NX=$1
+NY=$2
+NZ=$3
+NPROCS=$4
 
 #  Locate script.
 SCRIPTHOME=$(dirname "$0")
@@ -33,19 +40,25 @@ echo "Number of ranks = $ranks"
 #  Now construct a list of files ordered by rank, not step.
 files=$(ls cells_*.dat | sort -t "_" -k 3,3 -n | xargs -n 4)
 
+#  Need number of steps.
+nfiles=$(echo $files| wc -w)
+echo "Number of files = $nfiles"
+steps=$(( $nfiles / $ranks + 1 ))
+echo "Number of steps = $steps"
+
 #  And process them,
 echo "Processing cell dumps files..."
-echo $files | xargs -P $NPROCS -n 4 /bin/bash -c "${SCRIPTHOME}/process_cells_helper 20 20 20 \$0 \$1 \$2 \$3"
+#echo $files | xargs -P $NPROCS -n 4 /bin/bash -c "${SCRIPTHOME}/process_cells_helper $NX $NY $NZ \$0 \$1 \$2 \$3"
 
 #  Create summary.
 grep "top cells" step*-active-cells.dat | sort -h > active_cells.log
 
 #  And plot of active cells to edge cells.
-stilts plot2plane ifmt=ascii in=active_cells.log xmin=-0.1 xmax=1.1 ymin=-100 ymax=2200 grid=1 \
+stilts plot2plane ifmt=ascii in=active_cells.log xmin=-0.1 xmax=1.1 ymin=0 ymax=$steps grid=1 \
        legend=false xpix=600 ypix=500 xlabel="Edge cells/Active cells" ylabel="Step" \
-       layer1=mark x1="col9/1.0/col6" y1="index*7" size1=3 shading1=aux auxmap=rainbow \
+       layer1=mark x1="col9/1.0/col6" y1="index" size1=3 shading1=aux auxmap=rainbow \
        aux=col6 auxfunc=log auxlabel="Active cells" layer2=histogram x2="col9/1.0/col6" \
-       color2=grey binsize2=0.01 phase2=0.5 barform2=semi_steps weight2=30 thick2=1 \
+       color2=grey binsize2=0.01 phase2=0.5 barform2=semi_steps thick2=1 \
        out=active_cells.png
 
 exit

examples/process_cells_helper

@@ -6,6 +6,7 @@
 SCRIPTHOME=$(dirname "$0")
 
 step=$(echo $4|sed 's,cells_\(.*\)_\(.*\).dat,\2,')
+echo "${SCRIPTHOME}/analyse_dump_cells.py $* > step${step}-active-cells.dat"
 ${SCRIPTHOME}/analyse_dump_cells.py $* > step${step}-active-cells.dat
 
 exit