Initial import (fingers crossed)

git-svn-id: https://cvmix.googlecode.com/svn/trunk@2 ec264166-b127-864d-6cb2-e100125a5c76

Author: mnlevy1981

README

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+Right now, the stand-alone driver isn't very powerful. It is set up to run
+Bryan-Lewis mixing on a single column, and output the diffusivity coefficients
+at each level. Obviously this program will grow as we develop CVMix, but it
+seems like a good starting point.
+
+Directory structure:
+
+bld/ -- Contains the Makefile, is also where the build process will store .o
+        and .mod files.
+
+doc/ -- Contains documentation. At this point, it only has a PDF of the latest
+        protex in-code notes.
+
+exe/ -- Where the Makefile will put the vmix executable, also contains two
+        namelists that can be used to recreate Fig. 3.1 in Steve's notes.
+
+src/ -- Contains the source code. Right now it just contains the driver and
+        the subdirectory shared/, which is all the modules that are needed
+        to use CVMix with an outside model. (At some point, src/shared/ will
+        be picked up as an svn:external for POP and, I assume, MPAS and MOM.
+
+ncl/ -- Will eventually contain NCL scripts for making various plots depending
+        on the namelist settings. At this point, it contains one script for
+        generating the comparison of two Bryan-Lewis parameter sets. To use
+        right now, you need to run 
+
+        exe/] $ vmix < low_lat.ncl > diff1.txt
+        exe/] $ vmix < high_lat.ncl > diff2.txt
+        ncl/] $ ncl make_diff_plot-BryanLewis.ncl
+
+reg_tests/ -- This is a place-holder, but at some point we will want to create
+              a suite of regression tests to ensure everything in CVMix is
+              functioning correctly.
+
+INSTALLATION NOTES:
+
+The bld directory contains a Makefile and a 'setup' utility. bld/setup is a
+python script that asks for compiler / netcdf information (it only needs to
+be run once, info is saved in bld/.CVMix_env). If you just run 'make' without
+.CVMix_env, then setup will run automatically.
+
+To build with netcdf, run 'make netcdf' instead of just 'make'.

bld/Makefile

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+.SUFFIXES: .F90 .o
+
+extension = .F90
+
+# Name of executable
+EXE = ../exe/cvmix
+# File containing information about compiler and netCDF (generated by ./setup)
+ENV_FILE = .CVMix_env
+# File containing information about whether or not the last build linked to
+# netCDF (see below for more details)
+INFO_FILE = .netcdf_info
+
+COMPILE_FLAGS = -cpp -O2
+LINKING_FLAGS =
+
+# The variables FC, NETCDF_INC, NETCDF_LIB, and NETCDF_LINK are read in from
+# CVMix_env. If the file doesn't exist, then the python script "setup" is run
+# to generate the file.
+ifeq ($(wildcard $(ENV_FILE)),)
+  tmp := $(shell ./setup >&2)
+endif
+include $(ENV_FILE)
+
+# If you build without netCDF and then decide you want to build with netCDF (or
+# vice versa), you need to clean the old object files. The way this is handled
+# is by storing whether the last compilation used netCDF or not in the hidden
+# file .netcdf_info; whether the current built is using netCDF or not is stored
+# in the variable NEW_NETCDF while the contents of .netcdf_info is stored in the
+# variable OLD_NETCDF. The target "check" compares these two variables and runs
+# make clean if they differ. If the file doesn't exist, the two variables are
+# equal.
+ifdef USE_NETCDF
+  COMPILE_FLAGS += -D_NETCDF -I$(NETCDF_INC)
+  LINKING_FLAGS += -L$(NETCDF_LIB) -lnetcdf
+  # Check for netcdf4 library
+  ifneq ($(wildcard $(NETCDF_LIB)/libnetcdff.a),)
+    LINKING_FLAGS += -lnetcdff
+  endif
+  NEW_NETCDF = YES
+else
+  NEW_NETCDF = NO
+endif
+
+ifneq ($(wildcard $(INFO_FILE)),)
+  OLD_NETCDF = $(shell cat $(INFO_FILE))
+else
+  OLD_NETCDF = $(NEW_NETCDF)
+endif
+
+ifneq ($(OLD_NETCDF), $(NEW_NETCDF))
+  REBUILD = TRUE
+endif
+
+
+# ORDER MATTERS UNTIL I SET UP DEPENDENCIES
+# Also, directories will change once we get a new repository
+F_FILES = ../src/shared/vmix_kinds_and_types.F90 \
+          ../src/shared/vmix_background.F90      \
+          ../src/shared/vmix_convection.F90      \
+          ../src/shared/vmix_put_get.F90         \
+          ../src/vmix_output.F90                 \
+          ../src/vmix_driver.F90
+
+O_FILES = $(subst shared/,,$(subst ../src/,,$(F_FILES:$(extension)=.o)))
+
+### TARGETS ###
+
+.PHONY: check
+
+all: vmix
+
+# Possible executables: with and without netCDF
+netcdf:
+	$(MAKE) USE_NETCDF=TRUE
+
+vmix: check $(O_FILES)
+	$(FC) -o $(EXE) $(O_FILES) $(LINKING_FLAGS)
+	$(shell echo $(NEW_NETCDF) > $(INFO_FILE))
+
+# .o files -- until I can handle dependencies automatically, have to be specific
+vmix_kinds_and_types.o: ../src/shared/vmix_kinds_and_types.F90
+	$(FC) $(COMPILE_FLAGS) -c $< -o $@
+
+vmix_background.o: ../src/shared/vmix_background.F90  \
+                   ../src/shared/vmix_kinds_and_types.F90
+	$(FC) $(COMPILE_FLAGS) -c $< -o $@
+
+vmix_convection.o: ../src/shared/vmix_convection.F90  \
+                   ../src/shared/vmix_kinds_and_types.F90
+	$(FC) $(COMPILE_FLAGS) -c $< -o $@
+
+vmix_put_get.o: ../src/shared/vmix_put_get.F90        \
+                ../src/shared/vmix_kinds_and_types.F90
+	$(FC) $(COMPILE_FLAGS) -c $< -o $@
+
+vmix_output.o: ../src/vmix_output.F90                 \
+               ../src/shared/vmix_kinds_and_types.F90
+	$(FC) $(COMPILE_FLAGS) -c $< -o $@
+
+vmix_driver.o: ../src/vmix_driver.F90                 \
+               ../src/shared/vmix_kinds_and_types.F90 \
+               ../src/shared/vmix_background.F90      \
+               ../src/shared/vmix_convection.F90      \
+               ../src/shared/vmix_put_get.F90         \
+               ../src/vmix_output.F90
+	$(FC) $(COMPILE_FLAGS) -c $< -o $@
+
+# Utilities: check sees if we need to rebuild stand-alone components using
+#            -D_NETCDF, clean is standard, distclean removes $ENV_FILE so you
+#            will need to re-run setup
+check:
+	$(if $(REBUILD), rm -f vmix_output.o vmix_driver.o)
+
+clean:
+	/bin/rm -rf $(EXE) $(INFO_FILE) *.mod *.o
+
+distclean: clean
+	/bin/rm -rf $(ENV_FILE)

bld/README

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+To build, run
+
+$ make
+
+If this is your first time building, you will be prompted for some basic setup (compiler, location of netcdf). These values are saved in the file CVMix_env if they need to be editted later, or you can run
+
+$ ./setup
+
+To run with netCDF support, use
+
+$ make netcdf
+
+or
+
+$ make USE_NETCDF=[any non-empty string]

bld/setup

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+#!/usr/bin/env python
+
+# Allow tab completion
+try:
+  import readline,glob
+except ImportError:
+  print "Can not find readline or glob package, so tab-complete will not work"
+else:
+  def complete(text, state):
+    return(glob.glob(text+'*')+[None])[state]
+  readline.set_completer_delims(' \t\n;')
+  readline.parse_and_bind("tab: complete")
+  readline.set_completer(complete)
+
+# Print standard information about this tool
+print "This utility needs to be run before the included Makefile will"
+print "successfully compile CVMix. It collects information about your compiler"
+print "and associated libraries, and saves it in the .CVMix_env file. Note that"
+print "it only needs to be run once, though you should run it again if anything"
+print "changes.\n"
+
+# For now, just need fortran compiler and netCDF location / flags
+compiler = raw_input('Fortran compiler (mpi not necessary): ')
+netcdf_dir = raw_input('Directory containing netcdf (enter "need_both" to enter netcdf include directory and netcdf lib directory separately): ')
+if netcdf_dir == "need_both":
+  netcdf_inc = raw_input('netCDF/include location: ')
+  netcdf_lib = raw_input('netCDF/include location: ')
+else:
+  netcdf_inc = netcdf_dir+"/include"
+  netcdf_lib = netcdf_dir+"/lib"
+
+fid = open(".CVMix_env", 'w')
+fid.write("FC = " + compiler+"\n")
+fid.write("NETCDF_INC = " + netcdf_inc+"\n")
+fid.write("NETCDF_LIB = " + netcdf_lib+"\n")

doc/protex_documentation.pdf

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+&cvmix_nml
+mixing    ='BryanLewis'
+nlev      = 30
+ocn_depth = 5250
+/
+&BryanLewis_nml
+! Low  latitude: 6.50e-5, 1.15e-4, 4.5e-3, 2500
+! High latitude: 7.50e-5, 0.95e-4, 4.5e-3, 2500
+! Orig BL paper: 8.00e-5, 1.05e-4, 4.5e-3, 2500
+!
+vdc1 = 7.50d-5
+vdc2 = 0.95d-4
+linv = 4.5d-3
+dpth = 2500.0d0
+/

exe/high_lat.nl

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+&cvmix_nml
+mixing    ='BryanLewis'
+nlev      = 30
+ocn_depth = 5250
+/
+&BryanLewis_nml
+! Low  latitude: 6.50e-5, 1.15e-4, 4.5e-3, 2500
+! High latitude: 7.50e-5, 0.95e-4, 4.5e-3, 2500
+! Orig BL paper: 8.00e-5, 1.05e-4, 4.5e-3, 2500
+!
+vdc1 = 6.50d-5
+vdc2 = 1.15d-4
+linv = 4.5d-3
+dpth = 2500.0d0
+/

exe/low_lat.nl

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+load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
+load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
+
+begin
+
+; Create Color Table
+  my_color_map = (/"White", "Black"/)
+
+  nml   = asciiread("../exe/low_lat.nl", -1, "integer")
+  nlev  = nml(0)
+  datal = asciiread("../exe/diff1.txt", (/nlev+1,2/), "double")
+  datah = asciiread("../exe/diff2.txt", (/nlev+1,2/), "double")
+
+  x = new((/2, nlev+1/), "double")
+  x(0,:) = datal(:,1)
+  x(1,:) = datah(:,1)
+
+  y = new(nlev+1, "double")
+  y = datal(:,0)
+
+  ; out_type = "ps"
+  out_type = "X11"
+  wks = gsn_open_wks(out_type, "Bryan-Lewis_CVMix")
+  gsn_define_colormap(wks, my_color_map)
+
+  ; Basic Graphics set up (don't draw / advance frame to add legend!)
+  res          = True
+  res@gsnDraw  = False
+  res@gsnFrame = False
+
+  ; line & marker styles / axes ranges (y decreases to bottom)
+  res@xyMonoMarkLineMode = True
+  res@xyMarkLineMode     = "MarkLines"
+  res@xyMarkers          = (/0,4/)
+  res@xyDashPatterns     = (/0,0/)
+  res@trXMinF            = 0
+  res@trXMaxF            = 1.4
+  res@trYMinF            = 0
+  res@trYMaxF            = 5500
+  res@trYReverse         = True
+
+  ; Plot / font size, tick marks
+  res@vpHeightF               = 0.55
+  res@vpWidthF                = 0.77
+  res@tiMainFontHeightF       = 0.02
+  res@tiXAxisFontHeightF      = 0.015
+  res@tiYAxisFontHeightF      = 0.015
+  res@tmXBLabelFontHeightF    = 0.015
+  res@tmYLLabelFontHeightF    = 0.015
+  res@tmXBMinorOn             = False
+  res@tmYLMinorOn             = False
+  res@tmXBMajorOutwardLengthF = 0
+  res@tmYLMajorOutwardLengthF = 0
+
+  ; Title / axes labels
+  res@tiMainString  = "Background vertical tracer diffusivity"
+  res@tiXAxisString = "Diffusivity (1e-4 m:S:2:N:/sec)"
+  res@tiYAxisString = "Depth (m)"
+
+  plot = gsn_csm_xy(wks, 1e4*x, y, res)
+
+  ; Legend
+  lres = True
+  lres@vpWidthF         = 0.30
+  lres@vpHeightF        = 0.14
+  lres@lgMonoItemType   = True
+  lres@lgItemType         = "Markers"
+  lres@lgAutoManage     = False
+  lres@lgLabelFontHeightF = 0.035
+  lres@lgMonoMarkerIndex = False
+  lres@lgMarkerIndexes  = (/0, 4/)
+  lres@lgLineLabelsOn   = False
+
+  leg_text = (/"Low", "High"/)+" latitudes"
+  legend = gsn_create_legend(wks, 2, leg_text, lres)
+
+  ares = True
+  ares@amParallelPosF = 0.27
+  ares@amOrthogonalPosF = -0.33
+  annotate = gsn_add_annotation(plot, legend, ares)
+  draw(plot)
+  frame(wks)
+
+end

ncl/make_diff_plot-BryanLewis.ncl

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+Initial import (fingers crossed)
+
+--This line, and those below, will be ignored--
+
+A    .

old.tmp

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+I think all the regression testing can be done via various namelist settings. I
+still need to figure out what, exactly, to test, and the best way to automate
+the process. This file will grow as more decisions are made.