Two major changes to makefiles:

- Debug level can be now one of three levels:
  1) default one (formerly release) - no debug symbols, no warnings, maximum optimization.
  2) DEBUG - turns on producing debug symbols (-g) and warnings and brings optimization down to O2 (to produce all possible warnings by the compiler).
  3) DEBUGFULL turns off optimization completely (for more accurate debugging symbols) and turns on additional diagnostic messages in the source code (formerly DEBUG).
Debugging seems to be working in a bundle Eclipse-MinGW-gdb. Fixes issue 65.

- Compilation options are now saved to .lastopts. If new options are different from the last ones (as unordered sets of words), then complete recompilation is performed. This allows safe and efficient passing compilation options to makefiles through the command line.

Other changes in the source files: 
- DEBUG changed to DEBUGFULL
- several minor edits to remove 'uninitialized' and 'unused' warnings

src/CalculateE.c

@@ -222,6 +222,7 @@ void MuellerMatrix(void)
 
 	// redundant initialization to remove warnings
 	mueller=ampl=NULL;
+	co=si=0;
 
 	// Everything is done on ROOT only
 	if (!IFROOT) return;

src/Makefile

@@ -41,6 +41,11 @@ PROGSEQ  = adda
 PROGMPI  = adda_mpi
 # Targets implying compilation (empty one is always included)
 NONTRIVIAL = all seq mpi
+# targets implying sequential or mpi compilation. This duplicates the functionality of the target
+# designation, but is required for timely update of .lastopts
+SEQGOALS = seq all
+MPIGOALS = mpi all
+LASTOPTSFILE = .lastopts
 
 #===================================================================================================
 # !!! Start of control section. Flags and options here can be modified by user. However, the default
@@ -67,11 +72,16 @@ ifneq ($(if $(MAKECMDGOALS),$(if $(filter $(NONTRIVIAL),$(MAKECMDGOALS)),1,),1),
 # separated by spaces, e.g. 'make OPTIONS="DEBUG FFT_TEMPERTON" ...'. OPTIONS that are uncommented
 # below are appended to the list specified elsewhere.
 # Full list of possible options is the following:
-VALID_OPTS=DEBUG FFT_TEMPERTON PRECISE_TIMING NOT_USE_LOCK ONLY_LOCKFILE NO_FORTRAN \
+VALID_OPTS=DEBUG DEBUGFULL FFT_TEMPERTON PRECISE_TIMING NOT_USE_LOCK ONLY_LOCKFILE NO_FORTRAN \
            OVERRIDE_STDC_TEST
 
-# Debug mode (debug.h).
+# Debug mode. By default, release configuration is used (no debug, no warnings, maximum
+# optimization). DEBUG turns on producing debugging symbols (-g) and warnings and brings
+# optimization down to O2 (this is required to produce all possible warnings by the compiler).
+# DEBUGFULL turns off optimization completely (for more accurate debugging symbols) and turns on
+# additional diagnostic messages in the source code (debug.c/h).
 #override OPTIONS += DEBUG
+#override OPTIONS += DEBUGFULL
 
 # Temperton FFT (fft.h).
 #override OPTIONS += FFT_TEMPERTON
@@ -111,9 +121,6 @@ COMPILER = gnu
 # command line of make (see explanation above for OPTIONS).
 override EXTRA_CFLAGS +=
 
-# --Warnings-- If uncommented, all warning are suppressed
-RELEASE = on
-
 # --FFTW3 paths--
 # Specify path to headers and libraries of FFTW3. Some systems do not need them at all, some specify
 # special global variables (first or second 2 lines), on some - FFTW3 is installed under user
@@ -177,9 +184,20 @@ $(foreach var,$(filter-out $(VALID_OPTS),$(OPTIONS)),\
               $(warning The option '$(var)' is not recognized. Please check the spelling.))
 
 $(info --- Compilation options: ---)
-ifneq ($(filter DEBUG,$(OPTIONS)),)
+ifneq ($(filter DEBUGFULL,$(OPTIONS)),)
+  $(info Full debug mode)
+  DBGLVL = 2
+  CDEFS += -DDEBUGFULL
+  ifneq ($(filter DEBUG,$(OPTIONS)),)
+    $(warning DEBUG has no effect when DEBUGFULL is enabled)
+  endif
+else ifneq ($(filter DEBUG,$(OPTIONS)),)
   $(info Debug mode)
+  DBGLVL = 1
   CDEFS += -DDEBUG
+else
+  $(info Release mode)
+  DBGLVL = 0
 endif
 ifneq ($(filter FFT_TEMPERTON,$(OPTIONS)),)
   $(info Temperton FFT)
@@ -241,22 +259,26 @@ ifeq ($(COMPILER),gnu)
   # You can add '-march=...' or 'mcpu=...' to COPT and FOPT in this section
   CC    = gcc
   CF    = g77
-  COPT  = -std=c99 -O3 -ffast-math -funroll-loops
+  CSTD  = -std=c99
+  CDBG  = -g
+  COPT1 = -O2
+  COPT2 = -O3 -ffast-math -funroll-loops
+  CWARN = -Wall -Wextra -pedantic -Wcast-qual -Wpointer-arith -Wwrite-strings -Wstrict-prototypes \
+          -Wstrict-aliasing=1 -Wshadow -Wcast-align -Wnested-externs -Wcomment -Wno-unknown-pragmas
   FOPT  = -O
   FLIBS += -lg2c
-  CWARN = -Wall -Wextra -pedantic -Wcast-qual -Wpointer-arith \
-          -Wwrite-strings -Wstrict-prototypes -Wstrict-aliasing=1 -Wshadow \
-          -Wcast-align -Wnested-externs -Wcomment \
-          -Wno-unknown-pragmas
 
 else ifeq ($(COMPILER),intel)
   CC    = icc
   CF    = ifort
-  COPT  = -std=c99 -O3
+  CSTD  = -std=c99
+  CDBG  = -g
+  COPT1 = -O2
+  COPT2 = -O3
+  CWARN = -Wall -Wcheck -diag-disable 981,1418,1419,1572,2259 -vec-report0
   FOPT  = -O3
   FWARN += -vec-report0
   FLIBS += -lifcore
-  CWARN = -Wall -Wcheck -diag-disable 981,1418,1419,1572,2259 -vec-report0
   # if IPO is used, corresponding flags should be added to linker options: LDFLAGS += ...
 else ifeq ($(COMPILER),compaq)
   # This compiler was not tested since 2007. In particular, warning options may not fit exactly the
@@ -266,7 +288,10 @@ else ifeq ($(COMPILER),compaq)
   # You can add option '-arch host' to COPT and FOPT in this section
   CC    = cc
   CF    = f77
-  COPT  = -fast
+  #CSTD  = -std=c99
+  CDBG  = -g
+  COPT1 = -O2
+  COPT2 = -fast
   CWARN = -w0 -msg_disable nestedcomment,unknownpragma,unreachcode
 else ifeq ($(COMPILER),ibm)
   # This compiler was not tested since 2008. In particular, it is not clear, whether and what FLIBS
@@ -277,15 +302,20 @@ else ifeq ($(COMPILER),ibm)
   # Then use '-O3 -qarch=... -qtune=...' instead
   CC      = xlc
   CF      = xlf
-  COPT    = -O3 -qcache=auto -qlanglvl=extc99
+  CSTD  = -qlanglvl=extc99
+  CDBG  = -g
+  COPT1 = -O2
+  COPT2 = -O3 -qcache=auto
   # DFREDIRECT = 2>nul -qipa=level=2 -qhot
   DEPFLAG = -qmakedep=gcc -qsyntaxonly
   CWARN   = -qsuppress=1506-224:1506-342:1500-036
 else ifeq ($(COMPILER),hpux)
   CC    = cc
   CF    = f90
-  FOPT  = +O3  +DD64
-  COPT  =  -AC99 +O3  +DD64
+  CSTD  = -AC99
+  CDBG  = -g
+  COPT1 = +O2 +DD64
+  COPT2 = +O3 +DD64
   CWARN =
   CFLAGS += -DNOT_USE_LOCK
 else ifeq ($(COMPILER),other)
@@ -300,17 +330,35 @@ ifneq ($(strip $(FSOURCE)),)
   LDLIBS += $(FLIBS)
 endif
 # if 'release' turn off warningns
-ifdef RELEASE
-  $(info All warnings are suppressed)
+ifeq ($(DBGLVL),0)
   CWARN = -w
   LDFLAGS += -w
+  COPT = $(COPT2)
+  CDBG =
+else ifeq ($(DBGLVL),1)
+  COPT = $(COPT1)
+else ifeq ($(DBGLVL),2)
+  COPT =
 endif
 # Finalize option flags (almost)
-CFLAGS += $(COPT) $(CWARN)
+CFLAGS += $(CSTD) $(CDBG) $(COPT) $(CWARN)
 FFLAGS += $(FOPT) $(FWARN)
 
 FOBJECTS = $(FSOURCE:.f=.o)
 
+ifneq ($(if $(MAKECMDGOALS),$(if $(filter $(SEQGOALS),$(MAKECMDGOALS)),1,),1),)
+  -include $(SEQ)/$(LASTOPTSFILE)
+  ifneq ($(strip $(filter-out $(LASTOPTS),$(OPTIONS)) $(filter-out $(OPTIONS),$(LASTOPTS))),)
+    $(shell rm -f $(SEQ)/$(LASTOPTSFILE))
+  endif
+endif
+ifneq ($(if $(MAKECMDGOALS),$(if $(filter $(MPIGOALS),$(MAKECMDGOALS)),1,),1),)
+  -include $(MPI)/$(LASTOPTSFILE)
+  ifneq ($(strip $(filter-out $(LASTOPTS),$(OPTIONS)) $(filter-out $(OPTIONS),$(LASTOPTS))),)
+    $(shell rm -f $(MPI)/$(LASTOPTSFILE))
+  endif
+endif
+
 $(info ----------------------------)
 
 #===================================================================================================
@@ -337,8 +385,8 @@ clean: cleanseq cleanmpi
 # Moving 'clean' commands to child makefiles is problematic due to included dependency files
 cleanseq:
 	@echo "Removing sequential compiled files"
-	cd $(SEQ) && rm -f *.o *.d $(PROGSEQ) $(PROGSEQ).exe
+	cd $(SEQ) && rm -f *.o *.d $(LASTOPTSFILE) $(PROGSEQ) $(PROGSEQ).exe
 
 cleanmpi:
 	@echo "Removing MPI compiled files"
-	cd $(MPI) && rm -f *.o *.d $(PROGMPI) $(PROGMPI).exe
+	cd $(MPI) && rm -f *.o *.d $(LASTOPTSFILE) $(PROGMPI) $(PROGMPI).exe

src/Romberg.c

@@ -308,7 +308,7 @@ static double InnerRomberg(const int fixed,double * restrict res,const bool onep
 	double err;
 
 	// redundant initialization to remove warnings
-	abs_err=err=0;
+	abs_err=err=int_err=0;
 
 	if (input[PHI].Grid_size==1 ||  onepoint) { // if only one point (really or assumed)
 		int_err=(*func)(fixed,0,res);
@@ -416,7 +416,7 @@ static double OuterRomberg(double * restrict res)
 	double err;
 
 	// redundant initialization to remove warnings
-	err=0;
+	err=int_err=0;
 
 	if (input[THETA].Grid_size==1) { // if only one point
 		N_eval=0;

src/debug.c

@@ -1,7 +1,7 @@
 /* File: debug.c
  * $Author$
  * $Date::                            $
- * Descr: functions for printing debugging information when compiling with option -DDEBUG
+ * Descr: functions for printing debugging information when compiling with option -DDEBUGFULL
  *
  *        Previous versions by "vesseur"
  *
@@ -30,7 +30,7 @@
 #include "io.h"
 #include "vars.h"
 
-#ifdef DEBUG
+#ifdef DEBUGFULL
 //============================================================
 
 void DebugPrintf(ERR_LOC_DECL,const char * restrict fmt, ... )
@@ -66,4 +66,4 @@ void FieldPrint (doublecomplex * restrict x)
 	fprintf(logfile,"E = "CFORM3V,x[i][RE],x[i][IM],x[i+1][RE],x[i+1][IM],x[i+2][RE],x[i+2][IM]);
 }
 
-#endif // DEBUG
+#endif // DEBUGFULL

src/debug.h

@@ -27,9 +27,9 @@
  * and convenient tool to generate such messages is used.
  */
 
-//#define DEBUG // uncomment to degug
+//#define DEBUGFULL // uncomment to degug
 
-#ifdef DEBUG
+#ifdef DEBUGFULL
 
 #	include "function.h" // for function attributes
 #	include "const.h"    // for POS

src/fft.c

@@ -43,14 +43,17 @@
  */
 #	define PLAN_FFTW FFTW_MEASURE
 #	define PLAN_FFTW_DM FFTW_ESTIMATE
+#	define ONLY_FOR_FFTW3
+#else
+#	define ONLY_FOR_FFTW3 ATT_UNUSED
 #endif
 // for transpose YZ
 #define TR_BLOCK 64
 
 #ifdef FFT_TEMPERTON
-#define ONLY_FOR_TEMPERTON
+#	define ONLY_FOR_TEMPERTON
 #else
-#define ONLY_FOR_TEMPERTON ATT_UNUSED
+#	define ONLY_FOR_TEMPERTON ATT_UNUSED
 #endif
 
 // SEMI-GLOBAL VARIABLES
@@ -422,7 +425,7 @@ int fftFit(int x,int divis)
 
 //=============================================================
 
-static void fftInitBeforeD(const int lengthZ)
+static void fftInitBeforeD(const int lengthZ ONLY_FOR_FFTW3)
 // initialize fft before initialization of Dmatrix
 {
 #ifdef FFTW3

src/make_particle.c

@@ -746,7 +746,7 @@ static double PlaceGranules(void)
 	 * small and large granules is largely independent (although there are some common parts, which
 	 * motivates against complete separation of them into two functions).
 	 */
-	zerofit=gX2=gY2=gZ2=locgZ2=id0=id1=jd0=jd1=kd0=kd1=indZ=locgZ=gr_locgN=0;
+	zerofit=gX2=gY2=gZ2=locgZ2=id0=id1=jd0=jd1=kd0=kd1=indZ=locgZ=gr_locgN=sx=sy=sz=0;
 	gdXh=gdYh=gdZh=0;
 	ginX=ginY=ginZ=NULL;
 	dom=NULL;

src/mpi/Makefile

@@ -77,19 +77,22 @@ $(PROGMPI): $(COBJECTS) $(FOBJECTS)
 	@echo "Building $@"
 	$(MPICC) -o $@ $(LDFLAGS) $(COBJECTS) $(FOBJECTS) $(LDLIBS)
 
-# Everything is recompiled when any of makefiles is changed)
-$(COBJECTS): %.o: %.c %.d $(MFILES)
+$(COBJECTS): %.o: %.c %.d
 	$(MPICC) -c $(CFLAGS) $(CDEFS) $<
 
 $(FOBJECTS): %.o: %.f $(MFILES)
 	$(CF) -c $(FFLAGS) $<
 
-# Dependencies are only generated for C sources; we assume that each Fortran file is completely
-# independent or all of them are compiled at once
+# Dependencies are only generated for C sources; we assume that each Fortran file is completely 
+# independent or all of them are compiled at once. 
+# Everything is recompiled when any of makefiles or .lastopts is changed
 
-$(CDEPEND): %.d: %.c $(MFILES)
-	$(MPICC) $(DEPFLAG) $(CFLAGS) $(CDEFS) $< $(DFFLAG) $@.$$$$; \
+$(CDEPEND): %.d: %.c $(MFILES) $(LASTOPTSFILE)
+	$(CC) $(DEPFLAG) $(CFLAGS) $(CDEFS) $< $(DFFLAG) $@.$$$$; \
 	sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@; \
 	rm -f $@.$$$$
 
+$(LASTOPTSFILE):
+	echo LASTOPTS = $(OPTIONS) > $@
+
 -include $(CDEPEND)

src/param.c

@@ -54,8 +54,10 @@
 #	endif
 #	define LOCK_WAIT 1 // in seconds
 #	define MAX_LOCK_WAIT_CYCLES 60
+#	define ONLY_FOR_LOCK
 #else
 #	define FILEHANDLE int
+#	define ONLY_FOR_LOCK ATT_UNUSED
 #endif
 
 // GLOBAL VARIABLES
@@ -350,8 +352,8 @@ static struct opt_struct options[]={
 	{PAR(asym),"","Calculate the asymmetry vector. Implies '-Csca' and '-vec'",0,NULL},
 	{PAR(beam),"<type> [<args>]","Sets a type of the incident beam. Four other float arguments are "
 		"relevant for all beam types except 'plane'. These are the width and x, y, z coordinates of "
-		"the center of the beam respectively (all in um). The latter three can be omitted (then "
-		"beam center is located in the origin).\n"
+		"the center of the beam respectively in the laboratory reference fram (all in um). The "
+		"latter three can be omitted (then beam center is located in the origin).\n"
 		"Default: plane",UNDEF,beam_opt},
 	{PAR(chp_dir),"<dirname>","Sets directory for the checkpoint (both for saving and loading).\n"
 		"Default: "FD_CHP_DIR,1,NULL},
@@ -1348,7 +1350,9 @@ PARSE_FUNC(V)
 		printf(" (%d-bit)\n",bits);
 		// extra build flags
 		strncpy(build_opts,
-#ifdef DEBUG
+#ifdef DEBUGFULL
+		"DEBUGFULL, "
+#elif defined(DEBUG)
 		"DEBUG, "
 #endif
 #ifdef FFT_TEMPERTON
@@ -1417,7 +1421,7 @@ PARSE_FUNC(yz)
 // end of parsing functions
 //=============================================================
 
-static FILEHANDLE CreateLockFile(const char * restrict fname)
+static FILEHANDLE CreateLockFile(const char * restrict fname ONLY_FOR_LOCK)
 // create lock file; works only if USE_LOCK is enabled
 {
 #ifdef USE_LOCK
@@ -1475,7 +1479,7 @@ static FILEHANDLE CreateLockFile(const char * restrict fname)
 
 //============================================================
 
-static void RemoveLockFile(FILEHANDLE fd,const char * restrict fname)
+static void RemoveLockFile(FILEHANDLE fd ONLY_FOR_LOCK,const char * restrict fname ONLY_FOR_LOCK)
 // closes and remove lock file; works only if USE_LOCK is enabled
 {
 #ifdef USE_LOCK

src/seq/Makefile

@@ -34,19 +34,22 @@ $(PROGSEQ): $(COBJECTS) $(FOBJECTS)
 	@echo "Building $@"
 	$(CC) -o $@ $(LDFLAGS) $(COBJECTS) $(FOBJECTS) $(LDLIBS)
 
-# Everything is recompiled when any of makefiles is changed
-$(COBJECTS): %.o: %.c %.d $(MFILES)
+$(COBJECTS): %.o: %.c %.d
 	$(CC) -c $(CFLAGS) $(CDEFS) $<
 
 $(FOBJECTS): %.o: %.f $(MFILES)
 	$(CF) -c $(FFLAGS) $<
 
 # Dependencies are only generated for C sources; we assume that each Fortran file is completely 
-# independent or all of them are compiled at once
+# independent or all of them are compiled at once. 
+# Everything is recompiled when any of makefiles or .lastopts is changed
 
-$(CDEPEND): %.d: %.c $(MFILES)
+$(CDEPEND): %.d: %.c $(MFILES) $(LASTOPTSFILE)
 	$(CC) $(DEPFLAG) $(CFLAGS) $(CDEFS) $< $(DFFLAG) $@.$$$$; \
 	sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@; \
 	rm -f $@.$$$$
 
+$(LASTOPTSFILE):
+	echo LASTOPTS = $(OPTIONS) > $@
+
 -include $(CDEPEND)