Merge pull request #32 from andreasschmittner/master

updated READMEs

README.md

@@ -1,5 +1,5 @@
 # UVic2.9 with updated Marine Iron Biogeochemistry
-This version contains the new marine iron biogeochemistry modifications from Somes et al., (2021; https://doi.org/10.1029/2021GB006948), which has now been implemented into MOBI2.1 updates level 09. Please note some marine biogeochemical parameter changes in run/control.in. 
+This version contains the new marine iron biogeochemistry modifications from Somes et al., (2021; https://doi.org/10.1029/2021GB006948), which has now been implemented into MOBI2.2 updates level 09. Please note some marine biogeochemical parameter changes in run/control.in. 
 
 # UVic2.9
 This is the base code of the University of Victoria (UVic) climate model version 2.9 used at OSU. The source directory should not be changed. It is the original code without updates. 

run/mk.ver

@@ -0,0 +1,160 @@
+Updates_Level = latest
+Auto_Update = true
+
+Source_Comment_Character = !
+Code_Extension = f
+Object_Extension = o
+Include_Extension = h inc
+Source_Extension = F f F90 f90
+Notify_User = aschmitt@coas.oregonstate.edu
+Run_Copy = restatm.nc restocn.nc rest.nc restart.nc data
+End_String = UVIC_ESCM integration is complete
+Nice = -19
+Run_File_Local = run/run
+
+Step_Start_File = Step_Start
+Step_End_File = Step_End
+
+Remote_Machine = kikou
+Remote_Directory = /net/kikou
+
+# uncomment this section for code that uses compiler preprocessing
+#Preprocessor_Compile = true
+#Preprocessor_aix = xlf90
+#Option_Prefix_aix = -WF,-D
+#Preprocessor_linux = ifort
+#Preprocessor_linux-gnu = ifort
+#Option_Prefix_linux = -cpp -D
+#Option_Prefix_linux-gnu = -cpp -D
+
+#set defaults for any UNSET variables that may be OSTYPE or HOST dependent
+Option_Prefix_Default = -D
+#Preprocessor_Default = /lib/cpp -traditional -P -C
+Preprocessor_Default = /lib/cpp -P
+Module_Extension_Default = mod
+Run_File_Default = run/run
+Libraries_Default = -lnetcdf
+Libraries_Directory_Default = lib_linux
+Libraries_Directory_Prefix_Default = -L
+Compiler_Default_F = ifort -r8 -O3 -warn nouncalled -c
+Compiler_Default_f = ifort -r8 -O3 -warn nouncalled -c
+Compiler_Default_F90 = ifort -r8 -O3 -warn nouncalled -FR -c
+Compiler_Default_f90 = ifort -r8 -O3 -warn nouncalled -FR -c
+Linker_Default = ifort -r8 -O3 -warn nouncalled -o
+
+# linux
+Preprocessor_linux = /lib/cpp -traditional -P -C
+Module_Extension_linux = mod
+Run_File_linux = run/run_pbs
+Libraries_Directory_linux = lib_linux
+# intel linux compiler
+Compiler_F_linux = ifort -r8 -O3 -warn nouncalled -c
+Compiler_f_linux = ifort -r8 -O3 -warn nouncalled -c
+Compiler_F90_linux = ifort -r8 -O3 -warn nouncalled -FR -c
+Compiler_f90_linux = ifort -r8 -O3 -warn nouncalled -FR -c
+Linker_linux = ifort -r8 -O3 -warn nouncalled -o
+
+# use this for de-bugging
+#Compiler_F_linux = ifort -r8 -align -check -warn interfaces -fpe0 -traceback -c
+#Compiler_f_linux = ifort -r8 -align -check -warn interfaces -fpe0 -traceback -c
+#Compiler_F90_linux = ifort -r8 -align -check -warn interfaces -fpe0 -traceback -FR -c
+#Compiler_f90_linux = ifort -r8 -align -check -warn interfaces -fpe0 -traceback -FR -c
+#Linker_linux = ifort -r8 -align -check -warn interfaces -fpe0 -traceback -o
+
+# lahey 64 8.0 PRO fortran compiler
+#Compiler_F_linux = lfc --o3 --dbl -c
+#Compiler_f_linux = lfc --o3 --dbl -c
+#Compiler_F90_linux = lfc --o3 --dbl -c
+#Compiler_f90_linux = lfc --o3 --dbl -c
+#Linker_linux = lfc --o3 --dbl -o 
+
+# gnu compiler on Aspen cluster
+#Compiler_F_linux = gfortran -O3 -c
+#Compiler_f_linux = gfortran -O3 -c
+#Compiler_F90_linux = gfortran -O3 -c
+#Compiler_f90_linux = gfortran -O3 -c
+#Linker_linux = gfortran -O3 -o
+
+# mare (64 bit linux netcdf library)
+Libraries_Directory_mare = lib_mare
+
+# sx (nec cross compiler on linux)
+Preprocessor_sx = /lib/cpp -traditional -P -C
+Libraries_Directory_sx = lib_super-ux
+Module_Extension_sx = mod
+Run_File_sx = run/run_nqsII
+Libraries_Directory_sx = lib_super-ux
+Compiler_F_sx = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f0 -pi line=1000 nest=2 -c
+Compiler_f_sx = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f0 -pi line=1000 nest=2 -c
+Compiler_F90_sx = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f4 -pi line=1000 nest=2 -c
+Compiler_f90_sx = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f4 -pi line=1000 nest=2 -c
+Linker_sx = /SX/usr/bin/sxf90 -o
+
+# kikou (nec cross compiler on linux)
+Preprocessor_kikou = /lib/cpp -traditional -P -C
+Libraries_Directory_kikou = lib_super-ux
+Module_Extension_kikou = mod
+Run_File_kikou = run/run_nqsII
+Libraries_Directory_kikou = lib_super-ux
+Compiler_F_kikou = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f0 -pi line=1000 nest=2 -c
+Compiler_f_kikou = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f0 -pi line=1000 nest=2 -c
+Compiler_F90_kikou = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f4 -pi line=1000 nest=2 -c
+Compiler_f90_kikou = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f4 -pi line=1000 nest=2 -c
+Linker_kikou = /SX/usr/bin/sxf90 -o
+
+# super-ux (NEC)
+Preprocessor_super-ux = /lib/cpp -P -C
+Libraries_Directory_super-ux = lib_super-ux
+Module_Extension_super-ux = mod
+Run_File_super-ux = run/run_nqsII
+Libraries_super-ux = -lnetcdf
+Compiler_F_super-ux = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f0 -pi line=1000 nest=2 -c
+Compiler_f_super-ux = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f0 -pi line=1000 nest=2 -c
+Compiler_F90_super-ux = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f4 -pi line=1000 nest=2 -c
+Compiler_f90_super-ux = /SX/usr/bin/sxf90 -C hopt -Wf,"-A idbl4,-pvctl noassume loopcnt=1000000" -f4-pi line=1000 nest=2  -c
+Linker_super-ux = /SX/usr/bin/sxf90 -o
+
+# darwin (Apple)
+Preprocessor_darwin = /usr/bin/cpp -P -C -traditional-cpp
+Libraries_Directory_darwin = lib_darwin
+Module_Extension_darwin = mod
+Run_File_darwin = run/run
+Libraries_darwin = -lnetcdf
+Compiler_F_darwin = ifort -r8 -O3 -warn nouncalled -c
+Compiler_f_darwin = ifort -r8 -O3 -warn nouncalled -c
+Compiler_F90_darwin = ifort -r8 -O3 -warn nouncalled -c
+Compiler_f90_darwin = ifort -r8 -O3 -warn nouncalled -c
+Linker_darwin = ifort -r8 -O3 -warn nouncalled -o
+
+# aix (IBM)
+Preprocessor_aix = /lib/cpp -P -C
+Libraries_Directory_aix = lib_aix
+Module_Extension_aix = mod
+Run_File_aix = run/run_loadleveler
+Libraries_aix = -lnetcdf -lmass -lesslp2.m
+Compiler_F_aix = xlf90 -O3 -qstrict -qfixed=132 -qarch=pwr3 -qrealsize=8 -c
+Compiler_f_aix = xlf90 -O3 -qstrict -qfixed=132 -qarch=pwr3 -qrealsize=8 -c
+Compiler_F90_aix = xlf90 -O3 -qstrict -qarch=pwr3 -qrealsize=8 -c
+Compiler_f90_aix = xlf90 -O3 -qstrict -qarch=pwr3 -qrealsize=8 -c
+Linker_aix = xlf90 -bmaxdata:0x80000000 -o 
+# parallel
+Run_File_Parallel_aix = run/run_parallel_loadleveler
+Libraries_Parallel_aix = -lnetcdf -lmass -lessl_r -lxlsmp
+Compiler_Parallel_F_aix = xlf90_r -qsmp=noauto -O3 -qstrict -qfixed=132 -qarch=pwr3 -qrealsize=8 -c
+Compiler_Parallel_f_aix = xlf90_r -qsmp=noauto -O3 -qstrict -qfixed=132 -qarch=pwr3 -qrealsize=8 -c
+Compiler_Parallel_F90_aix = xlf90_r -qsmp=noauto -O3 -qstrict -qarch=pwr3 -qrealsize=8 -c
+Compiler_Parallel_f90_aix = xlf90_r -qsmp=noauto -O3 -qstrict -qarch=pwr3 -qrealsize=8 -c
+Linker_Parallel_aix = xlf90_r -qsmp -bmaxdata:0x80000000 -o
+
+#irix (SGI)
+#Preprocessor_irix = /usr/freeware/bin/cpp -traditional -P -C
+Preprocessor_irix = /lib/cpp -P -C
+Libraries_Directory_irix = lib_irix
+Module_Extension_irix = kmo
+Run_File_irix = run/run
+Libraries_irix = -lnetcdf
+Compiler_F_irix = f90 -O2 -OPT:Olimit=0 -r8 -fixedform -c
+Compiler_f_irix = f90 -O2 -OPT:Olimit=0 -r8 -fixedform -c
+Compiler_F90_irix = f90 -r8 -O2 -OPT:Olimit=0 -freeform -c
+Compiler_f90_irix = f90 -r8 -O2 -OPT:Olimit=0 -freeform -c
+Linker_irix = f90 -o

updates/README.md

@@ -1,3 +1,5 @@
+Jul 22, 2022: 09 updates (MOBI2.2) include Nate's variable P:N and Si:N stoichiometry and Chris' updates to the iron model
+
 Mar 18, 2021: 08 updates corresponds to MOBI2 with silicon cycling.
 1) Si cycling simplified from Karin Kvale's model in that it does not include external sources and sinks. 
 Opal has been included as an additional prognostic tracer.