-DHAVE_CONFIG_H

Makefile.in

@@ -51,7 +51,7 @@ $(distdir): $(qmckl_h) $(qmckl_f) $(static_lib) $(shared_lib) $(srcdir)/src/Make
 	cp $(srcdir)/munit/munit.h munit/munit.c $(distdir)/munit/
 	cp $(srcdir)/src/*.c src/*.h src/*.f90 $(distdir)/src/
 	cp $(srcdir)/src/Makefile.generated.in $(distdir)/src/Makefile.in
-	cp $(srcdir)/config.h.in $(distdir)/config.h.in
+	cp $(srcdir)/include/config.h.in $(distdir)/include/config.h.in
 	cp $(qmckl_h) $(distdir)/include
 	cp $(srcdir)/Makefile.in $(distdir)/
 	cp $(srcdir)/share/doc/qmckl/html/*.html $(distdir)/share/doc/qmckl/html/

autogen.sh

@@ -1,5 +1,6 @@
 #!/bin/bash
 
 autoreconf --install
-automake --add-missing --copy > /dev/null 2>&1
+automake --add-missing --copy &> /dev/null
+exit 0
 

configure.ac

@@ -10,7 +10,7 @@ AC_INIT([QMCkl],[0.1.1],
         [https://trex-coe.github.io/qmckl/index.html])
 
 AC_CONFIG_SRCDIR([src/README.org])
-AC_CONFIG_HEADERS([config.h])
+AC_CONFIG_HEADERS([include/config.h])
 AC_CONFIG_MACRO_DIR([m4])
 #AM_MAINTAINER_MODE
 
@@ -40,6 +40,7 @@ AC_PROG_INSTALL
 AC_PROG_LN_S
 AC_PROG_CC_C99
 AC_CHECK_PROGS([EMACS],[emacs26 emacs],[no])
+AC_CHECK_PROGS([HAS_CPPCHECK],[cppcheck],[no])
 PKG_PROG_PKG_CONFIG()
 PKG_LIBS=""
 PKG_CFLAGS=""
@@ -52,6 +53,13 @@ if test x${EMACS} == xno ; then
   ])
 fi
 
+if test x${HAS_CPPCHECK} == xno ; then
+        HAS_CPPCHECK=0
+else
+        HAS_CPPCHECK=1
+fi
+AC_SUBST([HAS_CPPCHECK])
+
 # fPIC option
 AC_MSG_CHECKING(whether fPIC compiler option is accepted in C)
 SAVED_CFLAGS="${CFLAGS}"
@@ -120,22 +128,26 @@ if test "$ok" = "yes"; then
 -traceback -check all -debug all -fpe-all=0  -implicitnone"
         fi
 	AC_DEFINE(DEBUG,1,[Define to turn on debugging checks])
+        ARGS="${ARGS} debug"
 fi
 
-AC_ARG_ENABLE(debug-malloc, [AC_HELP_STRING([--enable-debug-malloc],[use debug malloc/free])], ok=$enableval, ok=no)
+AC_ARG_ENABLE(malloc-trace, [AC_HELP_STRING([--enable-malloc-trace],[use debug malloc/free])], ok=$enableval, ok=no)
 if test "$ok" = "yes"; then
-	AC_DEFINE(DEBUG_MALLOC,1,[Define to use debugging malloc/free])
+	AC_DEFINE(MALLOC_TRACE,"malloc_trace.dat",[Define to use debugging malloc/free])
+        ARGS="${ARGS} malloc-trace"
 fi
 
 AC_ARG_ENABLE(prof, [AC_HELP_STRING([--enable-prof],[compile for profiling])], ok=$enableval, ok=no)
 if test "$ok" = "yes"; then
 	CFLAGS="${CFLAGS} -pg"
 	AC_DEFINE(ENABLE_PROF,1,[Define when using the profiler tool])
+        ARGS="${ARGS} prof"
 fi
 
 AC_ARG_WITH(efence, [AC_HELP_STRING([--with-efence],[use ElectricFence library])], ok=$withval, ok=no)
 if test "$ok" = "yes"; then
 	AC_CHECK_LIB(efence, malloc)
+        ARGS="${ARGS} efence"
 fi
 
 AC_ARG_WITH(munit, [AC_HELP_STRING([--without-munit],[use munit for testing])], ok=yes, ok=no)
@@ -147,9 +159,9 @@ AC_CHECK_FILE([munit/munit.h], [],
   $ git submodule update --init
   -------------------------------------------------
 ]) )
-
+else
-  AC_DEFINE(ENABLE_MUNIT,1,[Define when using munit])
+  ARGS="${ARGS} munit"
-  HAVE_MUNIT=1
+  AC_DEFINE(HAVE_MUNIT,1,[Define when using munit])
 fi
 
 
@@ -223,7 +235,7 @@ LDFLAGS:      ${LDFLAGS}
 LIBS:         ${LIBS}
 
 Package features:
-  Compilation with HDF5: ${hdf5}
+  ${ARGS}
 
 Now type 'make @<:@<target>@:>@'
 where the optional <target> is:

include/config.h.in

@@ -1,14 +1,8 @@
-/* config.h.in.  Generated from configure.ac by autoheader.  */
+/* include/config.h.in.  Generated from configure.ac by autoheader.  */
 
 /* Define to turn on debugging checks */
 #undef DEBUG
 
-/* Define to use debugging malloc/free */
-#undef DEBUG_MALLOC
-
-/* Define when using munit */
-#undef ENABLE_MUNIT
-
 /* Define when using the profiler tool */
 #undef ENABLE_PROF
 
@@ -80,6 +74,9 @@
 /* Define to 1 if you have the `memset' function. */
 #undef HAVE_MEMSET
 
+/* Define when using munit */
+#undef HAVE_MUNIT
+
 /* Define to 1 if you have the `nl_langinfo' function. */
 #undef HAVE_NL_LANGINFO
 
@@ -150,6 +147,9 @@
 /* Define to 1 if the system has the type `_Bool'. */
 #undef HAVE__BOOL
 
+/* Define to use debugging malloc/free */
+#undef MALLOC_TRACE
+
 /* Define to 1 if your C compiler doesn't accept -c and -o together. */
 #undef NO_MINUS_C_MINUS_O
 

src/Makefile.generated.in

@@ -6,8 +6,11 @@ version = @PACKAGE_VERSION@
 
 prefix   = @prefix@
 
-CC    = @CC@
+CC       = @CC@
-CFLAGS= @CFLAGS@ -I../munit/ -I../include
+DEFS     = @DEFS@
+CFLAGS   = @CFLAGS@ -I../munit/ -I../include -I. -I$(srcdir)
+CPPFLAGS = @CPPFLAGS@
+LIBS     = @LIBS@
 
 FC     = @FC@
 FCFLAGS= @FCFLAGS@ 
@@ -20,7 +23,7 @@ TESTS_F =  test_qmckl_ao_f.o test_qmckl_distance_f.o
 LIBS   = @LIBS@
 FCLIBS = @FCLIBS@
 
-QMCKL_ROOT=$(shell dirname $(CURDIR))
+QMCKL_ROOT=..
 shared_lib=$(QMCKL_ROOT)/lib/libqmckl.so
 static_lib=$(QMCKL_ROOT)/lib/libqmckl.a
 qmckl_h=$(QMCKL_ROOT)/include/qmckl.h
@@ -55,12 +58,13 @@ qmckl_f.o: $(qmckl_f)
 	$(FC) $(FCFLAGS) -c $(qmckl_f) -o $@
 
 test_qmckl: test_qmckl.c $(qmckl_h) $(static_lib) $(TESTS) $(TESTS_F)
-	$(CC) $(CFLAGS) $(munit) $(TESTS) $(TESTS_F) $(static_lib) $(LIBS) \
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) $(munit) $(TESTS) $(TESTS_F) \
-	$(FCLIBS) test_qmckl.c -o $@
+	$(static_lib) $(LIBS) $(FCLIBS) test_qmckl.c -o $@
 
 test_qmckl_shared: test_qmckl.c $(qmckl_h) $(shared_lib) $(TESTS) $(TESTS_F)
-	$(CC) $(CFLAGS) -Wl,-rpath,$(QMCKL_ROOT)/lib -L$(QMCKL_ROOT)/lib  \
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) \
-		$(munit) $(TESTS) $(TESTS_F) -lqmckl $(LIBS) $(FCLIBS) test_qmckl.c -o $@
+	-Wl,-rpath,$(QMCKL_ROOT)/lib -L$(QMCKL_ROOT)/lib $(munit) $(TESTS) \
+	$(TESTS_F) -lqmckl $(LIBS) $(FCLIBS) test_qmckl.c -o $@
 
 check: test_qmckl test_qmckl_shared
 	./test_qmckl
@@ -95,7 +99,7 @@ uninstall:
 .SUFFIXES: .c .f90 .o
 
 .c.o:
-	$(CC) $(CFLAGS) -c $*.c -o $*.o
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $*.c -o $*.o
 
 .f90.o: qmckl_f.o
 	$(FC) $(FCFLAGS) -c $*.f90 -o $*.o

src/Makefile.in

@@ -18,20 +18,24 @@ FC      = @FC@
 CFLAGS  = @CFLAGS@
 FCFLAGS = @FCFLAGS@
 LDFLAGS = @LDFLAGS@
+DEFS    = @DEFS@
 
 # Variables
 
 
 HAS_CPPCHECK = @HAS_CPPCHECK@
 
-QMCKL_ROOT=$(shell dirname $(CURDIR))
+# VPATH-related substitution variables
+srcdir = @srcdir@
+VPATH  = @srcdir@
 
+QMCKL_ROOT=$(srcdir)/..
 shared_lib=$(QMCKL_ROOT)/lib/libqmckl.so
 static_lib=$(QMCKL_ROOT)/lib/libqmckl.a
 qmckl_h=$(QMCKL_ROOT)/include/qmckl.h
 qmckl_f=$(QMCKL_ROOT)/share/qmckl/fortran/qmckl_f.f90
 
-export CC CFLAGS FC FCFLAGS LIBS QMCKL_ROOT
+export CC CFLAGS DEFS FC FCFLAGS LIBS QMCKL_ROOT
 
 ORG_SOURCE_FILES=$(wildcard $(QMCKL_ROOT)/*.org)
 C_SOURCE_FILES=$(patsubst %.org,%.c,$(ORG_SOURCE_FILES))

src/qmckl_ao.org

@@ -36,24 +36,33 @@ gradients and Laplacian of the atomic basis functions.
 * Headers                                                          :noexport:
   #+begin_src elisp :noexport :results none
 (org-babel-lob-ingest "../tools/lib.org")
-#+end_src
+  #+end_src
 
 
   #+begin_src c :tangle (eval h_private_type)
 #ifndef QMCKL_AO_HPT
 #define QMCKL_AO_HPT
+
 #include <stdbool.h>
   #+end_src
 
   #+begin_src c :tangle (eval c_test) :noweb yes
 #include "qmckl.h"
 #include "munit.h"
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 MunitResult test_<<filename()>>() {
   qmckl_context context;
   context = qmckl_context_create();
   #+end_src
 
   #+begin_src c :tangle (eval c)
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>
@@ -911,7 +920,7 @@ munit_assert(qmckl_ao_basis_provided(context));
           const double* X,
           const int32_t* LMAX,
           double* const P,
-          const int64_t ldp );
+          const int64_t ldp ); 
     #+end_src
 
 *** Source

src/qmckl_context.org

@@ -7,6 +7,9 @@
   #+begin_src c :tangle (eval c_test) :noweb yes
 #include "qmckl.h"
 #include "munit.h"
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 MunitResult test_<<filename()>>() {
   #+end_src
 
@@ -25,6 +28,9 @@ MunitResult test_<<filename()>>() {
   #+end_src
 
   #+begin_src c :tangle (eval c)
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 #include <stdint.h>
 #include <assert.h>
 #include <math.h>

src/qmckl_distance.org

@@ -12,6 +12,9 @@ Functions for the computation of distances between particles.
   #+begin_src c :comments link :tangle (eval c_test) :noweb yes
 #include "qmckl.h"
 #include "munit.h"
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 MunitResult test_<<filename()>>() {
   qmckl_context context;
   context = qmckl_context_create();

src/qmckl_electron.org

@@ -21,12 +21,18 @@ up-spin and down-spin electrons, and the electron coordinates.
   #+begin_src c :tangle (eval c_test) :noweb yes
 #include "qmckl.h"
 #include "munit.h"
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 MunitResult test_<<filename()>>() {
   qmckl_context context;
   context = qmckl_context_create();
   #+end_src
 
   #+begin_src c :tangle (eval c)
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>

src/qmckl_error.org

@@ -10,6 +10,9 @@
    #+end_src
 
    #+begin_src c :tangle (eval c)
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 #include <stdint.h>
 #include <string.h>
 #include <assert.h>
@@ -27,6 +30,9 @@
    #+begin_src c :tangle (eval c_test) :noweb yes
 #include "qmckl.h"
 #include "munit.h"
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 MunitResult test_<<filename()>>() {
    #+end_src
 

src/qmckl_memory.org

@@ -9,6 +9,9 @@ optimized libraries to fine-tune the memory allocation.
 * Headers                                                          :noexport:
 
   #+begin_src c :tangle (eval c)
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>
@@ -28,6 +31,9 @@ optimized libraries to fine-tune the memory allocation.
   #+begin_src c :tangle (eval c_test) :noweb yes
 #include "qmckl.h"
 #include "munit.h"
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 #include "qmckl_context_private_type.h"
 #include "qmckl_memory_private_func.h"
 MunitResult test_<<filename()>>() {

src/qmckl_numprec.org

@@ -7,6 +7,9 @@
   #+begin_src c :tangle (eval c_test) :noweb yes
 #include "qmckl.h"
 #include "munit.h"
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 MunitResult test_<<filename()>>() {
   #+end_src
 
@@ -18,6 +21,9 @@ MunitResult test_<<filename()>>() {
   #+end_src
 
   #+begin_src c :tangle (eval c)
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 #include <stdint.h>
 #include <assert.h>
 #include <math.h>

src/test_qmckl.org

@@ -82,6 +82,9 @@ echo "#+end_src"
 #include "qmckl.h"
 #include "munit.h"
 #include "mcheck.h"
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
 <<headers>>
 
 int main(int argc, char* argv[MUNIT_ARRAY_PARAM(argc + 1)]) {

tools/Building.org

@@ -91,6 +91,7 @@ FC      = @FC@
 CFLAGS  = @CFLAGS@
 FCFLAGS = @FCFLAGS@
 LDFLAGS = @LDFLAGS@
+DEFS    = @DEFS@
 
 #+end_src
 
@@ -109,7 +110,7 @@ static_lib=$(QMCKL_ROOT)/lib/libqmckl.a
 qmckl_h=$(QMCKL_ROOT)/include/qmckl.h
 qmckl_f=$(QMCKL_ROOT)/share/qmckl/fortran/qmckl_f.f90
 
-export CC CFLAGS FC FCFLAGS LIBS QMCKL_ROOT
+export CC CFLAGS DEFS FC FCFLAGS LIBS QMCKL_ROOT
 
 ORG_SOURCE_FILES=$(wildcard $(QMCKL_ROOT)/*.org)
 C_SOURCE_FILES=$(patsubst %.org,%.c,$(ORG_SOURCE_FILES))
@@ -243,8 +244,11 @@ version = @PACKAGE_VERSION@
 
 prefix   = @prefix@
 
-CC    = @CC@
+CC       = @CC@
-CFLAGS= @CFLAGS@ -I../munit/ -I../include
+DEFS     = @DEFS@
+CFLAGS   = @CFLAGS@ -I../munit/ -I../include -I. -I\$(srcdir)
+CPPFLAGS = @CPPFLAGS@
+LIBS     = @LIBS@
 
 FC     = @FC@
 FCFLAGS= @FCFLAGS@ 
@@ -268,7 +272,7 @@ and the rules:
 
 #+NAME: rules
   #+begin_src makefile :tangle no
-QMCKL_ROOT=$(shell dirname $(CURDIR))
+QMCKL_ROOT=..
 shared_lib=$(QMCKL_ROOT)/lib/libqmckl.so
 static_lib=$(QMCKL_ROOT)/lib/libqmckl.a
 qmckl_h=$(QMCKL_ROOT)/include/qmckl.h
@@ -303,12 +307,13 @@ qmckl_f.o: $(qmckl_f)
 	$(FC) $(FCFLAGS) -c $(qmckl_f) -o $@
 
 test_qmckl: test_qmckl.c $(qmckl_h) $(static_lib) $(TESTS) $(TESTS_F)
-	$(CC) $(CFLAGS) $(munit) $(TESTS) $(TESTS_F) $(static_lib) $(LIBS) \
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) $(munit) $(TESTS) $(TESTS_F) \
-	$(FCLIBS) test_qmckl.c -o $@
+	$(static_lib) $(LIBS) $(FCLIBS) test_qmckl.c -o $@
 
 test_qmckl_shared: test_qmckl.c $(qmckl_h) $(shared_lib) $(TESTS) $(TESTS_F)
-	$(CC) $(CFLAGS) -Wl,-rpath,$(QMCKL_ROOT)/lib -L$(QMCKL_ROOT)/lib  \
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) \
-		$(munit) $(TESTS) $(TESTS_F) -lqmckl $(LIBS) $(FCLIBS) test_qmckl.c -o $@
+	-Wl,-rpath,$(QMCKL_ROOT)/lib -L$(QMCKL_ROOT)/lib $(munit) $(TESTS) \
+	$(TESTS_F) -lqmckl $(LIBS) $(FCLIBS) test_qmckl.c -o $@
 
 check: test_qmckl test_qmckl_shared
 	./test_qmckl
@@ -343,7 +348,7 @@ uninstall:
 .SUFFIXES: .c .f90 .o
 
 .c.o:
-	$(CC) $(CFLAGS) -c $*.c -o $*.o
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $*.c -o $*.o
 
 .f90.o: qmckl_f.o
 	$(FC) $(FCFLAGS) -c $*.f90 -o $*.o

tools/create_makefile.sh

@@ -71,8 +71,11 @@ version = @PACKAGE_VERSION@
 
 prefix   = @prefix@
 
-CC    = @CC@
+CC       = @CC@
-CFLAGS= @CFLAGS@ -I../munit/ -I../include
+DEFS     = @DEFS@
+CFLAGS   = @CFLAGS@ -I../munit/ -I../include -I. -I\$(srcdir)
+CPPFLAGS = @CPPFLAGS@
+LIBS     = @LIBS@
 
 FC     = @FC@
 FCFLAGS= @FCFLAGS@ 
@@ -87,7 +90,7 @@ FCLIBS = @FCLIBS@
 EOF
 
 echo '
-QMCKL_ROOT=$(shell dirname $(CURDIR))
+QMCKL_ROOT=..
 shared_lib=$(QMCKL_ROOT)/lib/libqmckl.so
 static_lib=$(QMCKL_ROOT)/lib/libqmckl.a
 qmckl_h=$(QMCKL_ROOT)/include/qmckl.h
@@ -122,12 +125,13 @@ qmckl_f.o: $(qmckl_f)
 	$(FC) $(FCFLAGS) -c $(qmckl_f) -o $@
 
 test_qmckl: test_qmckl.c $(qmckl_h) $(static_lib) $(TESTS) $(TESTS_F)
-	$(CC) $(CFLAGS) $(munit) $(TESTS) $(TESTS_F) $(static_lib) $(LIBS) \
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) $(munit) $(TESTS) $(TESTS_F) \
-	$(FCLIBS) test_qmckl.c -o $@
+	$(static_lib) $(LIBS) $(FCLIBS) test_qmckl.c -o $@
 
 test_qmckl_shared: test_qmckl.c $(qmckl_h) $(shared_lib) $(TESTS) $(TESTS_F)
-	$(CC) $(CFLAGS) -Wl,-rpath,$(QMCKL_ROOT)/lib -L$(QMCKL_ROOT)/lib  \
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) \
-		$(munit) $(TESTS) $(TESTS_F) -lqmckl $(LIBS) $(FCLIBS) test_qmckl.c -o $@
+	-Wl,-rpath,$(QMCKL_ROOT)/lib -L$(QMCKL_ROOT)/lib $(munit) $(TESTS) \
+	$(TESTS_F) -lqmckl $(LIBS) $(FCLIBS) test_qmckl.c -o $@
 
 check: test_qmckl test_qmckl_shared
 	./test_qmckl
@@ -162,7 +166,7 @@ uninstall:
 .SUFFIXES: .c .f90 .o
 
 .c.o:
-	$(CC) $(CFLAGS) -c $*.c -o $*.o
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $*.c -o $*.o
 
 .f90.o: qmckl_f.o
 	$(FC) $(FCFLAGS) -c $*.f90 -o $*.o