reverted Makefile to manual dependency specification for better compa…

…tibility; minor revisions on alcon.F90

Makefile

@@ -26,7 +26,7 @@
 MPIF90 := mpif90
 
 # compiling options
-FFLAGS := -O2
+FFLAGS := -O3
 
 # MPI executor
 MPIEXEC := mpiexec
@@ -35,42 +35,39 @@ MPIEXEC := mpiexec
 NPE := 2
 
 
-# module object files
-MODOBJ := alcon_input.o alcon_eqdata.o alcon_solver.o alcon_output.o \
- cspline_petsc.o
-
 .PHONY : build run clean cleanoutput
 
 build : alcon
 
 # SLEPc variables
 -include $(SLEPC_DIR)/conf/slepc_variables
 
-# first layer dependency files .d1
--include $(MODOBJ:.o=.d1)
-
-# use GNU tools to build module dependency files .d1
-# each .d1 file gives rules to generate corresponding .d2 file
-# .d2 files are generated by Fortran compiler with -MM option
-# corresponding .mod files are generated when compiler generates .d2 files
-$(MODOBJ:.o=.d1) : %.d1 : %.F90
-	@echo 'making $@...'
-	@echo '-include $(@:.d1=.d2)' > $@
-	@exec echo -n '$(@:.d1=.d2) : $< ' >> $@
-	@exec sed -n 's/^[ \t]*use \([^ \t,]*\).*$$/\1.mod/p' $< | sort | uniq | paste -s --delimiters=" " >> $@
-	@exec echo -e '\t$$(MPIF90) $(FFLAGS) -MM $$< $$(FCPPFLAGS) > $$@' >> $@
-	@echo 'finished making $@'
-
-# compile main program and link all modules
-alcon : alcon.F90 $(MODOBJ)
-	$(MPIF90) $(FFLAGS) -o $@ $^ $(FCPPFLAGS) $(SLEPC_LIB)
-
-# compile testcsp
-testcsp : testcsp.F90 cspline_petsc.o
-	$(MPIF90) $(FFLAGS) -o $@ $^ $(FCPPFLAGS) $(SLEPC_LIB)
-
-# compile modules
-$(MODOBJ) : %.o : %.F90 %.d2
+alcon : alcon.o alcon_input.o alcon_eqdata.o alcon_solver.o alcon_output.o \
+ cspline_petsc.o
+	$(MPIF90) $(FFLAGS) -o $@ $^ $(SLEPC_LIB)
+
+testcsp : testcsp.o cspline_petsc.o
+	$(MPIF90) $(FFLAGS) -o $@ $^ $(SLEPC_LIB)
+
+testcsp.o : testcsp.F90 cspline_petsc.o
+	$(MPIF90) $(FFLAGS) -c -o $@ $< $(FCPPFLAGS)
+
+alcon.o : alcon.F90 alcon_input.o alcon_eqdata.o alcon_solver.o
+	$(MPIF90) $(FFLAGS) -c -o $@ $< $(FCPPFLAGS)
+
+cspline_petsc.o : cspline_petsc.F90
+	$(MPIF90) $(FFLAGS) -c -o $@ $< $(FCPPFLAGS)
+
+alcon_input.o : alcon_input.F90
+	$(MPIF90) $(FFLAGS) -c -o $@ $< $(FCPPFLAGS)
+
+alcon_eqdata.o : alcon_eqdata.F90 alcon_input.o cspline_petsc.o
+	$(MPIF90) $(FFLAGS) -c -o $@ $< $(FCPPFLAGS)
+
+alcon_solver.o : alcon_solver.F90 alcon_input.o alcon_output.o
+	$(MPIF90) $(FFLAGS) -c -o $@ $< $(FCPPFLAGS)
+
+alcon_output.o : alcon_output.F90 alcon_input.o
 	$(MPIF90) $(FFLAGS) -c -o $@ $< $(FCPPFLAGS)
 
 run : alcon cleanoutput
@@ -81,7 +78,7 @@ runtestcsp : testcsp
 	$(MPIEXEC) -n $(NPE) ./$< 2>&1 | tee $<.log
 
 clean :
-	rm -f alcon testcsp *.o *.mod *.d1 *.d2 *.log
+	rm -f alcon testcsp *.o *.mod *.log
 
 cleanoutput :
 	rm -f output/*

README.md

@@ -1,6 +1,6 @@
 ALCON
 =====
-version 2012-08-24 23:04:13-04:00
+version 2012-09-26 21:32:19-04:00
 ---------------------------------
 
 ALCON is a code for solving ideal MHD Alfven continua in tokamaks,

alcon.F90

@@ -25,7 +25,7 @@ program alcon
 #include "finclude/petsc.h90"
 #include "finclude/slepc.h"
 
-character(25), parameter :: version = '2012-08-24 23:04:13-04:00'
+character(25), parameter :: version = '2012-09-26 21:32:19-04:00'
 
 ! indexing variables
 PetscInt :: i
@@ -59,14 +59,16 @@ program alcon
 call MPI_Comm_rank(MPI_COMM_WORLD, mype, ierr)
 CHKERRQ(ierr)
 if (mype == 0) then
-  write (*, "(a)") "Error: ALCON requires complex version of PETSc. Please re-compiled it with complex version of PETSc."
+  write (*, "(a)") "Error: ALCON requires complex version of PETSc. Please use complex version of PETSc."
 end if
 call MPI_Finalize(ierr)
 CHKERRQ(ierr)
 stop 1
 #endif
 
-! initialization
+!!!!!!!!!!!!!!!!!!
+! initialization !
+!!!!!!!!!!!!!!!!!!
 call SlepcInitialize(PETSC_NULL_CHARACTER, ierr)
 CHKERRQ(ierr)
 wt1 = MPI_Wtime() ! record start time
@@ -154,7 +156,9 @@ program alcon
   CHKERRQ(ierr)
 end if
 
-! radial domain and solver decomposition
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+! radial domain and solver decomposition !
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 call MPI_Comm_size(MPI_COMM_WORLD, npe, ierr)
 CHKERRQ(ierr)
 ndom_rad = ceiling(real(npe) / npe_solver)
@@ -197,7 +201,7 @@ program alcon
   write (*, "(a)") trim(adjustl(msg))
 end if
 
-! solver initialization, create PETSc and SLEPc objects
+! solver initialization, create PETSc and SLEPc objects !
 call alcon_solver_init(comm_solver)
 
 if (verbosity >= 1) then
@@ -217,7 +221,9 @@ program alcon
   iprogress = 1
 end if
 
-! main loop over radial grids
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+! main loop over radial grids !
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 do irad = irad_low, irad_high
 !do irad = 1, nrad
 !do irad = iraddiag - 1, iraddiag
@@ -238,22 +244,6 @@ program alcon
   !   [Nuclear Fusion 52, 043006 (2012)](http://wdeng.info/?p=117)
   call alcon_solver_prepare(irad)
 
-  ! this doesn't work anymore after radial domain decomposition
-  ! so here set condition to "verbosity >= 10" to disable it
-  if (verbosity >= 10 .and. mydom_rad == 0) then
-    ! print out matA, matB on irad == 1 and irad == iraddiag
-    if (irad == 1 .or. irad == iraddiag) then
-      call PetscPrintf(MPI_COMM_WORLD, "Info: matA:\n", ierr)
-      CHKERRQ(ierr)
-      call MatView(acs_matA, PETSC_VIEWER_STDOUT_WORLD, ierr)
-      CHKERRQ(ierr)
-      call PetscPrintf(MPI_COMM_WORLD, "Info: matB:\n", ierr)
-      CHKERRQ(ierr)
-      call MatView(acs_matB, PETSC_VIEWER_STDOUT_WORLD, ierr)
-      CHKERRQ(ierr)
-    end if
-  end if
-
   ! solve for eigenvalues (continua frequencies) and output
   call alcon_solver_solve(acdprofile(1, irad), acdprofile(5, irad))
 end do
@@ -262,7 +252,9 @@ program alcon
   CHKERRQ(ierr)
 end if
 
-
+!!!!!!!!!!
+! output !
+!!!!!!!!!!
 if (verbosity >= 1) then
   call PetscPrintf(MPI_COMM_WORLD, "Info: writing data output files...\n", ierr)
   CHKERRQ(ierr)
@@ -284,10 +276,12 @@ program alcon
   CHKERRQ(ierr)
 end if
 
+!!!!!!!!!!!!!!!!
+! finalization !
+!!!!!!!!!!!!!!!!
 ! solver finalization, destroy PETSc and SLEPc objects
 call alcon_solver_final
 
-
 if (verbosity >= 1) then
   wt2 = MPI_Wtime()
   call PetscPrintf(MPI_COMM_WORLD, "Info: time spent by ALCON: " // sec2text(wt2 - wt1) // "\n", ierr)