Changes between Version 4 and Version 5 of 2019WP/KERNEL-02_Storkey_Coward_IMMERSE_first_steps

Timestamp:

2019-02-08T16:35:51+01:00 (5 years ago)

Author:

acc

Comment:

--

2019WP/KERNEL-02_Storkey_Coward_IMMERSE_first_steps

@@ -82 +82 @@
 [=#preview]
 
-Part of the reorganisation for RK3 requires the refactoring of arrays such as un, ub into a single, 4 dimensional array with a time-level dimension. It is expected that much of the work required here can be automated to the extent that it is feasible to re-apply these changes after the annual merge. Below is a working example of how this might be achieved. Perl is used to carry out the pattern matching and substitution because of its ability to match patterns extending over several lines. A random subset of source files are used in this example and several to illustrate the successes and caveats for the method. 
+Part of the reorganisation for RK3 requires the refactoring of arrays such as un, ub into a single, 4 dimensional array with a time-level dimension. It is expected that much of the work required here can be automated to the extent that it is feasible to re-apply these changes after the annual merge. Below is a working example of how this might be achieved. Perl is used to carry out the pattern matching and substitution because of its ability to match patterns extending over several lines. A random subset of source files are used in this example and serve to illustrate the successes and caveats for the method. 
 
 '''Step 1'''
@@ -109 +109 @@
  echo "Index: "$f >> patch.list
  echo "==============================" >> patch.list
- n=0
  for n in `seq 0 1 $(( ${#INVARS[*]} - 1 ))`
  do
@@ -117 +116 @@
  echo "}}}" >> patch.list
 done
+}}}
+
+'''The refactoring script explained'''
+
+{{{
+# Some bash arrays to list the old names, new names and associated time-level index. 
+# The choice of names here is not meant to reflect a desired choice. Note all three arrays 
+# must have the same number of entries
+
+   INVARS=( ub  vb  wb  un  vn  wn )
+  OUTVARS=( uu  vv  ww  uu  vv  ww )
+    TLEVS=( jtb jtb jtb jtn jtn jtn )
+#
+# Lines referring to patch.list are just generating some output for this Wiki page. 
+# They can be ignored for the purposes of explaining the script
+
+# Loop over all files in test directory
+
+  for f in TEST_FILES/*.F90
+  do
+
+# Loop over each input variable name
+
+   for n in `seq 0 1 $(( ${#INVARS[*]} - 1 ))`
+   do
+
+# The perl command:
+
+# -0777 -pi  are the options that force replace in place operation. 
+# Could elect to redirect to new files
+
+# The substitute command matches the INVAR string preceded by any of: +.(,whitespace-/*%
+# Any match here goes into the first pattern space (\1)
+
+# The INVAR string can have any amount of whitespace (including none) between it and an 
+# opening bracket. This whitespace is not preserved (but it could be, TBD)
+
+# Everything following the opening bracket to (but not including) the next closing bracket 
+# is stored in pattern space 2
+
+# The RHS of the substitute command rebuilds the line replacing INVAR with OUTVAR and
+# adding a ,TLEV before the closing bracket
+
+    perl -0777 -pi -e 's:([+.(,\s\-\/\*\%])'${INVARS[$n]}'\s*\(([^)]*)\):\1'${OUTVARS[$n]}'\(\2,'${TLEVS[$n]}'\):g'  $f
+
+# End of variable loop
+
+   done
+ 
+# End of file loop
+
+  done
 }}}
 
@@ -193 +244 @@
 }}}
 
-So all changes were made correctly (apart from the last which was expected). Also those entries which were potential pitfalls (pun and abc_fwb) were correctly ignored. Time to try a real set:
+So all changes were made correctly (apart from the last which was expected). Also those entries which were potential pitfalls (pun and sbc_fwb) were correctly ignored. Time to try a real set:
 
 '''The results on the sample set of files (patch.list):'''