add makefile for Alambix

MDLIB/Makefiles/makefile_Alambix

@@ -0,0 +1,63 @@
+# MDOODZ 7.0 makefile
+SHELL := /bin/bash
+
+LINK_HDF5_LIB = /usr/lib/x86_64-linux-gnu/
+LINK_HDF5_INC = /usr/include/hdf5/serial/
+LINK_SUSP_LIB = /opt/suitesparse/latest/lib/
+LINK_SUSP_INC = /opt/suitesparse/latest/include/
+
+# Compiler
+CC = gcc
+
+# Path to setup file folder
+SET_PATH = ../SETS
+
+#---------------------------------------------------#
+# C flags
+CFLAGS = -I ${LINK_HDF5_INC} -I ${LINK_SUSP_INC} -std=c99 -D _UMFPACK_ -I ./include/ -I ./ -Doff64_t=__off64_t -std=gnu99
+
+ifeq ($(OPT),yes)	
+	CFLAGS += -O3 -ftree-vectorize -funroll-loops -finline -fomit-frame-pointer -march=native
+else
+	CFLAGS += -g -Wall  -O0 -fno-inline -fno-omit-frame-pointer
+endif
+
+ifeq ($(OMP),yes)
+	CFLAGS += -fopenmp -D _OMP_
+else
+	CFLAGS += -Wno-unknown-pragmas 
+endif
+
+ifeq ($(VG),yes)
+	CFLAGS += -D _VG_ -Wno-format-zero-length
+endif
+
+ifeq ($(NEW_INPUT),yes)
+	CFLAGS += -D _NEW_INPUT_
+endif
+
+CFLAGS += -Wno-unused-variable  -Wno-comment
+#---------------------------------------------------#
+# Libraries
+LIBS = -lm -lz -L ${LINK_HDF5_LIB} -lhdf5_serial
+
+# Related to SuiteSparse
+LIBS += -L ${LINK_SUSP_LIB}  -llapack -lcxsparse -lumfpack -lcblas -lamd -lcholmod -lcolamd -lbtf -lsuitesparseconfig -lblas
+
+# Link to openmp
+ifeq ($(OMP),yes)
+    LIBS += -lgomp
+endif
+
+#---------------------------------------------------#
+# Rules
+FILES = MeltingRoutines.o AnisotropyRoutines.o Main_DOODZ.o FD_Jacobian.o  RheologyParticles.o ChemicalRoutines.o ParticleReseeding.o Solvers.o StokesRoutines.o StokesAssemblyDecoupled.o AdvectionRoutines.o RheologyDensity.o HDF5Output.o SparseTools.o ThermalRoutines.o ThermalSolver.o ParticleRoutines.o FreeSurface.o FlowLaws.o MemoryAllocFree.o InputOutput.o MiscFunctions.o GridRoutines.o Setup.o $(SET_PATH)/$(SET).o 
+
+
+all: Doodzi_$(SET) 
+Doodzi_$(SET): ${FILES}
+	$(CC) ${FILES} -o $(SET) ${LIBS}
+
+clean:
+	cp $(SET_PATH)/$(SET).txt . 
+	rm -rf *o ./$(SET_PATH)/*.o $(SET) 

MDLIB/Makefiles/makefile_Physix

@@ -1,23 +1,63 @@
-run-tests:
-	cd cmake-build && ctest --extra-verbose --output-on-failure
+# MDOODZ 7.0 makefile
+SHELL := /bin/bash
 
-run:
-	cd cmake-exec/$(SET) && ./$(SET) $(TXT)
+LINK_HDF5_LIB = /usr/lib/x86_64-linux-gnu/
+LINK_HDF5_INC = /usr/include/hdf5/serial/
+LINK_SUSP_LIB = /opt/suitesparse/latest/lib/
+LINK_SUSP_INC = /opt/suitesparse/latest/include/
 
-run-vis:
-	cd visualtests-out && ./visualtests
+# Compiler
+CC = gcc
 
-build-dev:
-	cmake -B ./cmake-build -DOPT=$(OPT) -DOMP=$(OMP) -DVIS=$(VIS) -DSET=$(SET) -DTXT=$(TXT) -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ && cmake --build ./cmake-build
+# Path to setup file folder
+SET_PATH = ../SETS
 
-build:
-	cmake -DOPT=ON -DOMP=ON -B ./cmake-build -DSET=$(SET) -DTXT=$(TXT) && cmake --build ./cmake-build
+#---------------------------------------------------#
+# C flags
+CFLAGS = -I ${LINK_HDF5_INC} -I ${LINK_SUSP_INC} -std=c99 -D _UMFPACK_ -I ./include/ -I ./ -Doff64_t=__off64_t -std=gnu99
 
-clean:
-	rm -rf *build*/ && rm -rf *exec*/
+ifeq ($(OPT),yes)	
+	CFLAGS += -O3 -ftree-vectorize -funroll-loops -finline -fomit-frame-pointer -march=native
+else
+	CFLAGS += -g -Wall  -O0 -fno-inline -fno-omit-frame-pointer
+endif
+
+ifeq ($(OMP),yes)
+	CFLAGS += -fopenmp -D _OMP_
+else
+	CFLAGS += -Wno-unknown-pragmas 
+endif
+
+ifeq ($(VG),yes)
+	CFLAGS += -D _VG_ -Wno-format-zero-length
+endif
+
+ifeq ($(NEW_INPUT),yes)
+	CFLAGS += -D _NEW_INPUT_
+endif
+
+CFLAGS += -Wno-unused-variable  -Wno-comment
+#---------------------------------------------------#
+# Libraries
+LIBS = -lm -lz -L ${LINK_HDF5_LIB} -lhdf5_serial
 
-deps:
-	rm -rf deps && git clone https://github.com/kulakovri/MDOODZ-dependencies deps && cd deps && make install-hdf5 && make install-suitesparse
+# Related to SuiteSparse
+LIBS += -L ${LINK_SUSP_LIB}  -llapack -lcxsparse -lumfpack -lcblas -lamd -lcholmod -lcolamd -lbtf -lsuitesparseconfig -lblas
 
-install-suitesparse:
-	rm -rf deps && git clone https://github.com/kulakovri/MDOODZ-dependencies deps && cd deps && make install-suitesparse
+# Link to openmp
+ifeq ($(OMP),yes)
+    LIBS += -lgomp
+endif
+
+#---------------------------------------------------#
+# Rules
+FILES = MeltingRoutines.o AnisotropyRoutines.o Main_DOODZ.o FD_Jacobian.o  RheologyParticles.o ChemicalRoutines.o ParticleReseeding.o Solvers.o StokesRoutines.o StokesAssemblyDecoupled.o AdvectionRoutines.o RheologyDensity.o HDF5Output.o SparseTools.o ThermalRoutines.o ThermalSolver.o ParticleRoutines.o FreeSurface.o FlowLaws.o MemoryAllocFree.o InputOutput.o MiscFunctions.o GridRoutines.o Setup.o $(SET_PATH)/$(SET).o 
+
+
+all: Doodzi_$(SET) 
+Doodzi_$(SET): ${FILES}
+	$(CC) ${FILES} -o $(SET) ${LIBS}
+
+clean:
+	cp $(SET_PATH)/$(SET).txt . 
+	rm -rf *o ./$(SET_PATH)/*.o $(SET)