Fixed bugs + some other improvements (#49)

* Addition of .gitignore

* Changed integer constants to real constants to satisfy API in loop.f90

* Addition of CPP directives for enabling MPI

* Set restartwritefreq to 1 to avoid trigggering a IEEE FP issue (division by 0)

* Improved README.md in the directory expt

* Update formatting, wording, etc.

* Make source files non-executable

* Clean up arch files and Makefile; remove unused stuff

---------

Co-authored-by: Vandenplas, Jeremie <jeremie.vandenplas@wur.nl>
Co-authored-by: milancurcic <caomaco@gmail.com>

Author: 3 people

.gitignore

@@ -0,0 +1,2 @@
+*.o
+*.mod

cms-master/arch/gfortran_compiler

@@ -1,22 +1,21 @@
-# Makefile
+# GNU arch file
+# Include and link paths are default for Ubuntu.
+# Edit if they're installed somewhere else on your system.
 
 #the Fortran compiler to create object files
 FC            = gfortran
 #the Fortran flags to create object files
-FCFLAGS      = -I/usr/local/Cellar/netcdf/4.6.1_4/include -I/usr/local/opt/netcdf/include -I/usr/local/include
+FCFLAGS      = -I/usr/include -cpp
 #the C-compiler to create object files
 CC            = gcc
 #the C flags to create object files
 CCFLAGS       = -O 
-
 #the Fortran compiler to create executable
 LD            = $(FC)
 #the Fortran flags to create executable
-LDFLAGS       = -L/usr/local/Cellar/netcdf/4.6.1_4/lib -L/usr/local/opt/netcdf/lib -L/usr/local/lib -lnetcdf -lnetcdff -lcurl -lm
-EXTRALIBS     = -L/usr/local/Cellar/netcdf/4.6.1_4/lib -lnetcdf -lhdf5_hl -lhdf5 -lsz -lz -ldl -lm -lcurl
+LDFLAGS       = -L/usr/lib/x86_64-linux-gnu -lnetcdf -lnetcdff -lcurl -lm
 
 # Rules
-
 .c.o:
 	$(CC) -c $*.c $(CCFLAGS) 
 
@@ -25,5 +24,3 @@ EXTRALIBS     = -L/usr/local/Cellar/netcdf/4.6.1_4/lib -lnetcdf -lhdf5_hl -lhdf5
 
 .f.o:
 	$(FC) -c $*.f $(FCFLAGS) 
-
-

cms-master/arch/mpi_compiler

@@ -1,22 +1,21 @@
-# Makefile
+# MPI arch file
+# Include and link paths are default for GNU compiled NetCDF on Ubuntu.
+# Edit if they are different on your system.
 
 #the Fortran compiler to create object files
 FC            = mpif90
 #the Fortran flags to create object files
-FCFLAGS      = -I/usr/local/netcdf/include -I/usr/local/include
+FCFLAGS      = -I/usr/include -cpp -D_MPI
 #the C-compiler to create object files
 CC            = gcc
 #the C flags to create object files
 CCFLAGS       = -O 
-
 #the Fortran compiler to create executable
 LD            = $(FC)
 #the Fortran flags to create executable
-LDFLAGS       = -L/usr/local/netcdf/lib -L/usr/local/lib -lnetcdf -lnetcdff -lcurl -lm
-EXTRALIBS     = 
+LDFLAGS       = -L/usr/lib/x86_64-linux-gnu -lnetcdf -lnetcdff -lcurl -lm
 
 # Rules
-
 .c.o:
 	$(CC) -c $*.c $(CCFLAGS) 
 
@@ -25,5 +24,3 @@ EXTRALIBS     =
 
 .f.o:
 	$(FC) -c $*.f $(FCFLAGS) 
-
-

cms-master/expt/README.md

@@ -39,7 +39,7 @@ loopfilesendday      = 0
 !Options for saving restart files and restarting
 writerestart         = .false.
 restartfromfile      = .false.
-restartwritefreq     = 0            !in seconds
+restartwritefreq     = 1            !in seconds
 !====================================================================!
 !Options for mixed layer physics
 mixedlayerphysics    = .false.

cms-master/expt/input_example/runconf.list

@@ -1,6 +1,7 @@
-#
+# CMS Makefile
+# Please edit the include line to point to the correct arch file
 
-include ../arch/mpi_compiler
+include ../arch/gfortran_compiler
 
 .SUFFIXES: 
 .SUFFIXES: .cpp .c .F .f .o .f90
@@ -31,10 +32,10 @@ MODS_larva = $(MODS) mod_buoyancy_larva.o mod_mort_larva.o
 OBJS_larva = $(OBJS)
 
 cms	:	$(MODS_larva) $(OBJS_larva)
-	        $(LD) $(MODS_larva) $(OBJS_larva) $(LDFLAGS) -o cms $(EXTRALIBS)	        	       
+	        $(LD) $(MODS_larva) $(OBJS_larva) $(LDFLAGS) -o cms
 
 getdata :	$(MODS_getdata) $(OBJS_getdata)
-		$(LD) $(MODS_getdata) $(OBJS_getdata)  $(LDFLAGS) -o getdata $(EXTRALIBS)	        
+		$(LD) $(MODS_getdata) $(OBJS_getdata)  $(LDFLAGS) -o getdata
 
 cms.o: cms.f90
 getdata.o: getdata.f90

cms-master/expt/readme

@@ -24,7 +24,9 @@
 
 PROGRAM CMS
 
+#ifdef _MPI
  USE MPI !remove if not using mpi
+#endif
  USE globalvariables
  USE mod_random
 
@@ -39,12 +41,14 @@ PROGRAM CMS
  my_id = 0 !used if not using mpi
  npes = 1 !used if not using mpi
 
+#ifdef _MPI
 !initialise MPI
  CALL MPI_INIT(ierr) !remove if not using mpi
 !what processor am I (what is my rank)?
  CALL MPI_COMM_RANK(MPI_COMM_WORLD, my_id, ierr) !remove if not using mpi
 !how many processors are there?
  CALL MPI_COMM_SIZE(MPI_COMM_WORLD, npes, ierr) !remove if not using mpi
+#endif
 
 !check which experiment to run
  IF (command_argument_count() .eq. 0) THEN
@@ -90,7 +94,9 @@ PROGRAM CMS
 !finish up
  CALL dealloc_all 
 
+#ifdef _MPI
 !quit MPI
  CALL MPI_FINALIZE(ierr) !remove if not using mpi
+#endif
 
-END PROGRAM CMS
+END PROGRAM CMS