--- MITgcm_contrib/jmc_script/README	2006/01/07 16:23:29	1.3
+++ MITgcm_contrib/jmc_script/README	2018/03/08 18:55:29	1.18
@@ -1,27 +1,62 @@
-Some basic scripts are gather here. 
-They are not specially design to be general and obviously 
-need to be modified/customized for each application.
-
-a) the restart test : "1+1=2"
-script: tst1+1
- call 2 short scripts: rnp & add0upto10c
-
-* no input argument but few comments within the file tst1+1
-  (needs to be edited and modify).
-* an example of data.tst file is provided 
-Note: the script is sensitive to space and upper-case / lower
-  case characters regarding nIter0 line and nTimeSteps line.
+Some basic scripts are gather here.
+
+a) the restart test: "2+2=4"
+
+script: tst_2+2
+- to use in a run dir. after a successful "testreport"
+- input argument: '0','1','2','3','4' or 'All':
+  proceed step by step or all steps at once
+- tst_2+2 (no argument) -> print "usage"
+- know problems: specific restart procedure (with fizhi pkg or offline pkg)
+  not yet implemented
+
+script: do_test_2+2
+- call restart test "tst_2+2" multiple times, in every test experiment.
+- needs to be in MITgcm/verification (with a copy of tst_2+2i script)
+  and can only be used after a successful "testreport"
+- do_test_2+2 -help -> print "usage"
+
+NOTE: scripts "tst_2+2" & "do_test_2+2" have been moved (Dec 25, 2007)
+ to: MITgcm/tools/
+
+script: tst_2+2_cpl
+ = version of tst_2+2 adapted for coupled set-up (verification/cpl_aim+ocn)
 
 b) PBS-batch script that re-submit itself (loop).
 script: runScript
- call 2 short scripts: add0upto3c & add0upto10c
 
-* used (and tested) on myrinet-3 cluster.
-* suffer from a lack of meaningful comments.
-  
+- used (and tested) on myrinet-3 cluster.
+- suffer from a lack of meaningful comments.
+- not specially design to be general and obviously
+  need to be modified/customized for each set-up.
+
 c) A short script to split the ASCII Diagnostics-Stats output file
-   into separated files (one per field) that are easy to read/load 
+   into separated files (one per field) that are easy to read/load
    (e.g., in matlab, just use "load" command)
 script: extract_StD
  no known dependency
++  A matlab script to load in 1 array all the separated files:
+matlab-script: read_StD.m
+ no known dependency
++  2 example scripts to make simple plots from Stat-Diags output:
+matlab-script: grph_StD.m (uses read_StD.m)
+matlab-script: plot_StD.m (uses read_StD.m, c_levs.m)
+
+d) script: rn_pickup
+- Rename 'pickup*.ckpt[A,B].*' files to 'pickup*.[10-digits-iter].*'
+  with several selection options.
+- rn_pickup (no argument) -> print "usage"
+
+e) script: mk_mkfile
+- run genmake2 with the same options as when "Makefile" was generated
+ (needs an existing previous "Makefile") ; this replaces "make makefile".
+ in addition, link *_mpi files from the MODS directory when -mpi was
+ used to generate the previous Makefile.
+
+f) script: derive_other_types
+  from 1 src file, derive other type (R4,RS,RL,RS) version. For now, can
+  only be applied to the 4 src files: "mdsio_pass_r{4,8}tor{l,s}.F"
+
+g) script: mk_options_list
+  generate list of CPP Options used in Fortran source files