Organized Makefile.incs and cleaned up

src/Makefile.inc.geodyncomp

-# Define our compilers.................................
-#
-# on geodyncomp, the defaults are OpenMPI (1.4.3), 
-# built with the GNU compilers
-# F90 = mpif90
-# F77 = mpif90
-# cc  = mpicc
-# on geodyncomp, we also have an intel compiler
-F90 = ifort
-F77 = ifort
-cc = icc
-
-# we take the standard ar
-# AR=ar
-AR=xiar
-
-# There are no BITS
-BITS=-ifort-dbg-openmpi
-
-# no MKL
-# IMKL = /scinet/gpc/intel/Compiler/11.1/056/mkl/include
-# IMKL = /scinet/gpc/intel/Compiler/11.1/072/mkl/include
-# INCLUDE=-I$(IMKL)
-
-# Define MPI include files for ifort.
-# these should match the build of wsmp; see below.
-# for openmpi, these work
-MPI_INC=-I /opt/openmpi/include
-MPI_LIB=-L/opt/openmpi/lib -lmpi -lmpi_f77 -lmpi_f90
-# for mpich2
-# MPI_INC=-I /opt/mpich2/gnu/include
-# MPI_LIB=-L/opt/mpich2/gnu/lib -lmpichf90 -lfmpich -lmpich
-
-INCLUDE = $(MPI_INC)
-
-# Define FORTRAN compiler flags.......................
-#
-GFORTRAN_FLAGS = -ffree-line-length-0
-# This gives us, at run time,
-# error while loading shared libraries: libimf.so: cannot open shared object file
-# No such file or directory
-# IFORT_FLAGS = -O2 -fp-model strict -mcmodel=large -shared-intel
-# IFORT_FLAGS = -fast
-IFORT_FLAGS = -O2
-IFORT_DEBUG = -g -warn all -check all -debug all
-# IFORT_DEBUG =
-F90FLAGS = ${IFORT_FLAGS} ${IFORT_DEBUG}
-F77FLAGS = ${IFORT_FLAGS} ${IFORT_DEBUG}
-FFLAGS=${F90FLAGS}
-# Define C compiler flags.............................
-#
-ICC_FLAGS = 
-CFLAGS = -O2 ${ICC_FLAGS}
-
-# no Intel MKL library
-#
-# LMKL = /scinet/gpc/intel/Compiler/11.1/056/mkl/lib
-# LMKL = /scinet/gpc/intel/Compiler/11.1/072/mkl/lib
-
-# MPI libraries
-# (use the default)
-
-# WSMP Library
-#
-# wsmp, with gnu and openMPI
-WSMP = -L/opt/wsmp/wsmp-Linux64/lib/GNU/openmpi -lpwsmp64
-# wsmp, with intel and mpich2
-# WSMP = -L/opt/wsmp/wsmp-Linux64/lib/Intel/mpich2 -lpwsmp64
-
-# Not using Google's TCMalloc
-# TCML   = /home/dwhipp/software/tcml
-
-LIBS = \
- -LOCTREE -lOctree$(BITS) \
- -LNN -lnn_f$(BITS) \
- -LNN -lnn_c$(BITS) \
- -LCASCADE -lcascade$(BITS) \
- -LRESAMPLE -lresample$(BITS) \
- $(WSMP) -lblas \
- $(MPI_LIB) \
- -lpthread
-
-# The Makefiles look at compile output with this
-PAGER=more
-
-# compile rules.......................................
-#
-COMPILE_OUT=$(NAME)$(BITS).compile
-.SUFFIXES:
-.SUFFIXES: .o .c .f .f90
-.f90.o:
-	@echo "--"                                   >>$(COMPILE_OUT) 2>&1
-	@echo "$(F90) $(F90FLAGS) $(INCLUDE) -c $<" >>$(COMPILE_OUT) 2>&1
-	$(F90) $(F90FLAGS) $(INCLUDE) -c $<         >>$(COMPILE_OUT) 2>&1
-
-.f.o:
-	@echo "--"                                   >>$(COMPILE_OUT) 2>&1
-	@echo "$(F77) $(F77FLAGS) $(INCLUDE) -c $<" >>$(COMPILE_OUT) 2>&1
-	$(F77) $(F77FLAGS) $(INCLUDE) -c $<         >>$(COMPILE_OUT) 2>&1
-
-.c.o:
-	@echo "--"                                 >>$(COMPILE_OUT) 2>&1
-	@echo "$(CC) $(CFLAGS) -c $<"              >>$(COMPILE_OUT) 2>&1
-	$(CC) $(CFLAGS) -c $<                      >>$(COMPILE_OUT) 2>&1

src/README

-one can run the code as follows:
-
-mpirun -np <nb_of_processors> ./douar
-
-In this case, the program reads the 'input.txt' file and uses the user-defined boundary conditions in define_bc.f90.
-
-On the other hand, on can also run the code as follows:
-
-mpirun -np <nb_of_processors> ./douar input.txt_3Dp
-mpirun -np <nb_of_processors> ./douar input.txt_2Dp
-mpirun -np <nb_of_processors> ./douar input.txt_fold
-
-these three input files are in the main directory, and if used, their corresponding boundary conditions are defined in 
-define_bc.f90 and are automatically chosen by the code.
-
-input.txt_3Dp  : square punch    (plasticity, one surface, linear viscosity)
-input.txt_2Dp  : pseudo2D punch  (plasticity, one surface, linear viscosity)
-input.txt_fold : folding problem (no plasticity, three surfaces, nonlinear viscosity)