Merge branch 'master' into rescaled_deriv_vj

.gitignore

@@ -1,17 +1,10 @@
+*.la
+*.lo
 .deps/
-compile
+.dirstamp
-depcomp
+.libs
-generated.mk
-stamp-h1
-libtool
-ltmain.sh
-missing
-m4/libtool.m4
-m4/ltoptions.m4
-m4/ltsugar.m4
-m4/ltversion.m4
-m4/lt~obsolete.m4
 Makefile
+Makefile.in
 aclocal.m4
 autom4te.cache/
 config.guess
@@ -19,13 +12,20 @@ config.log
 config.status
 config.sub
 configure
-install-sh
+generated.mk
-qmckl.pc
+m4/libtool.m4
-Makefile.in
+m4/ltoptions.m4
-test-driver
+m4/ltsugar.m4
-.libs
+m4/ltversion.m4
-.dirstamp
+m4/lt~obsolete.m4
-*.la
-*.lo
 qmckl-*.tar.gz
 qmckl.mod
+qmckl.pc
+stamp-h1
+tools/compile
+tools/depcomp
+tools/install-sh
+tools/libtool
+tools/ltmain.sh
+tools/missing
+tools/test-driver

Makefile.am

@@ -159,14 +159,16 @@ tests/chbrclf.h: $(qmckl_h)
 	
 
 generated.mk: $(ORG_FILES)
-	python $(srcdir)/tools/build_makefile.py
+	$(PYTHON) $(srcdir)/tools/build_makefile.py
 
 cppcheck: cppcheck.out
 	
 cppcheck.out: $(qmckl_h)
 	cd src/ && \
 	cppcheck --addon=cert -q --error-exitcode=0  \
-          --enable=all \
+          --enable=all --suppress="unusedStructMember"\
+	  --suppress="unusedFunction" \
+	  --suppress="missingIncludeSystem" \
           --language=c --std=c99 -rp --platform=unix64  \
           -I../include *.c *.h 2>../$@
 

README.md

@@ -1,6 +1,6 @@
 # QMCkl: Quantum Monte Carlo Kernel Library
 
-![Build Status](https://github.com/TREX-CoE/qmckl/workflows/test-build/badge.svg?branch=main)
+![Build Status](https://github.com/TREX-CoE/qmckl/workflows/test-build/badge.svg?branch=master)
 
 The domain of quantum chemistry needs a library in which the main
 kernels of Quantum Monte Carlo (QMC) methods are implemented. In the
@@ -9,7 +9,7 @@ simple language and provide a standard API and tests to enable the
 development of high-performance QMCkl implementations taking
 advantage of modern hardware.
 
-See the [source code](https://github.com/TREX-CoE/qmckl/tree/main/src)
+See the [source code](https://github.com/TREX-CoE/qmckl/blob/master/org/qmckl.org)
 to read the documentation.
 
 

configure.ac

@@ -38,13 +38,13 @@ AC_PREREQ([2.69])
 AC_INIT([qmckl],[0.1.1],
         [https://github.com/TREX-CoE/qmckl/issues], [],
         [https://trex-coe.github.io/qmckl/index.html])
+AC_CONFIG_AUX_DIR(tools)
 AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
 AM_MAINTAINER_MODE()
 LT_INIT
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])
 AC_CONFIG_MACRO_DIR([m4])
-#AM_MAINTAINER_MODE
 
 VERSION_MAJOR=`echo ${PACKAGE_VERSION} | cut -d. -f1`
 VERSION_MINOR=`echo ${PACKAGE_VERSION} | cut -d. -f2`
@@ -64,6 +64,9 @@ AC_LANG(C)
 
 # Checks for programs.
 AC_PROG_CC
+# Make sure the c compiler supports C99
+m4_version_prereq([2.70],[], [AC_PROG_CC_C99])
+AS_IF([test "$ac_cv_prog_cc_c99" = "no"], [AC_MSG_ERROR([The compiler does not support C99])])
 AC_PROG_CC_C_O
 AC_PROG_FC
 AC_PROG_FC_C_O
@@ -72,13 +75,10 @@ AC_FC_FREEFORM
 AC_PROG_LIBTOOL
 AC_PROG_INSTALL
 AC_PROG_LN_S
-AC_PROG_CC_C99
 PKG_PROG_PKG_CONFIG([])
 PKG_LIBS=""
 PKG_CFLAGS=""
 
-AC_SUBST([HAS_CPPCHECK])
-
 # Checks for libraries.
 
 AC_FC_LIBRARY_LDFLAGS
@@ -178,15 +178,8 @@ if test "x${QMCKL_DEVEL}" != "x"; then
 
   QMCKL_DEVEL=" -- Developer mode"
   AC_PROG_AWK
-  AC_CHECK_PROGS([PYTHON],[python python3 python2],[no])
+  AM_PATH_PYTHON
-  if test x${PYTHON} == xno ; then
+  ${PYTHON} ${srcdir}/tools/build_makefile.py
-    AC_MSG_ERROR([
-    --------------------------------------------
-    Error: Python is required to build makefiles
-    --------------------------------------------
-    ])
-  fi
-  python ${srcdir}/tools/build_makefile.py
 
   AC_CHECK_PROGS([EMACS],[emacs26 emacs],[no])
   if test x${EMACS} == xno ; then
@@ -211,6 +204,8 @@ LIBS="${LAPACK_LIBS} ${BLAS_LIBS} ${LIBS}"
 PKG_LIBS="${PKG_LIBS} ${LIBS}"
 AC_SUBST([PKG_LIBS])
 AC_SUBST([PKG_CFLAGS])
+AC_SUBST([HAS_CPPCHECK])
+
 
 AC_CONFIG_FILES([Makefile
                  pkgconfig/qmckl.pc

org/.gitignore

@@ -1,2 +1,3 @@
+ltximg/
 *.tangled
 *.exported

org/qmckl_context.org

@@ -31,6 +31,9 @@ int main() {
 #include "qmckl_nucleus_private_type.h"
 #include "qmckl_electron_private_type.h"
 #include "qmckl_ao_private_type.h"
+#include "qmckl_nucleus_private_func.h"
+#include "qmckl_electron_private_func.h"
+#include "qmckl_ao_private_func.h"
   #+end_src
 
   #+begin_src c :tangle (eval c)
@@ -213,17 +216,26 @@ qmckl_context qmckl_context_create() {
   }
 
  /* Initialize data */
-  ctx->tag = VALID_TAG;
+  {
+    ctx->tag = VALID_TAG;
+    
+    const qmckl_context context = (const qmckl_context) ctx;
+    assert ( qmckl_context_check(context) != QMCKL_NULL_CONTEXT );
+    
+    qmckl_exit_code rc;
+    
+    ctx->numprec.precision = QMCKL_DEFAULT_PRECISION;
+    ctx->numprec.range = QMCKL_DEFAULT_RANGE;
 
-  const qmckl_context context = (const qmckl_context) ctx;
+    rc = qmckl_init_electron(context);
-  assert ( qmckl_context_check(context) != QMCKL_NULL_CONTEXT );
+    assert (rc == QMCKL_SUCCESS);
-
+    
-  ctx->numprec.precision = QMCKL_DEFAULT_PRECISION;
+    rc = qmckl_init_nucleus(context);
-  ctx->numprec.range = QMCKL_DEFAULT_RANGE;
+    assert (rc == QMCKL_SUCCESS);
-
+    
-  ctx->ao_basis.uninitialized = (1 << 10) - 1;
+    rc = qmckl_init_ao_basis(context);
-  ctx->nucleus.uninitialized  = (1 << 4) - 1;
+    assert (rc == QMCKL_SUCCESS);
-  ctx->electron.uninitialized = (1 << 3) - 1;
+  }
 
  /* Allocate qmckl_memory_struct */
   {

org/qmckl_electron.org

@@ -87,6 +87,7 @@ int main() {
    | ~en_distance_rescaled_deriv_e~      | ~double[walk_num][4][num][num]~   | Electron-electron rescaled distances derivatives                     |
    | ~en_distance_rescaled_deriv_e_date~ | ~uint64_t~                        | Last modification date of the electron-electron distance derivatives |
 
+
 ** Data structure
 
    #+begin_src c :comments org :tangle (eval h_private_type)
@@ -115,16 +116,41 @@ typedef struct qmckl_electron_struct {
   int32_t   uninitialized;
   bool      provided;
 } qmckl_electron_struct;
+
    #+end_src
 
    The ~uninitialized~ integer contains one bit set to one for each
-   initialization function which has not bee called. It becomes equal
+   initialization function which has not been called. It becomes equal
    to zero after all initialization functions have been called. The
    struct is then initialized and ~provided == true~.
+   Some values are initialized by default, and are not concerned by
+   this mechanism.
 
-   When all the data relative to electrons have been set, the
+   #+begin_src c :comments org :tangle (eval h_private_func) 
-   following function returns ~true~.
+qmckl_exit_code qmckl_init_electron(qmckl_context context);
+   #+end_src
+   
+   #+begin_src c :comments org :tangle (eval c)
+qmckl_exit_code qmckl_init_electron(qmckl_context context) {
 
+  if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
+    return false;
+  }
+
+  qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
+  assert (ctx != NULL);
+
+  ctx->electron.uninitialized = (1 << 2) - 1;
+
+ /* Default values */
+  ctx->electron.rescale_factor_kappa_ee = 1.0;
+  ctx->electron.rescale_factor_kappa_en = 1.0;
+
+  return QMCKL_SUCCESS;
+}
+   #+end_src
+   
+   
       #+begin_src c :comments org :tangle (eval h_func)
 bool qmckl_electron_provided (const qmckl_context context);
       #+end_src
@@ -295,13 +321,13 @@ qmckl_get_electron_walk_num (const qmckl_context context, int64_t* const walk_nu
 *** Scaling factors Kappa
 
       #+begin_src c :comments org :tangle (eval h_func) :exports none
-qmckl_exit_code qmckl_get_kappa_ee   (const qmckl_context context, double* const rescale_factor_kappa_ee);
+qmckl_exit_code qmckl_get_electron_rescale_factor_ee (const qmckl_context context, double* const rescale_factor_kappa_ee);
-qmckl_exit_code qmckl_get_kappa_en   (const qmckl_context context, double* const rescale_factor_kappa_en);
+qmckl_exit_code qmckl_get_electron_rescale_factor_en (const qmckl_context context, double* const rescale_factor_kappa_en);
       #+end_src
 
       #+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
 qmckl_exit_code
-qmckl_get_kappa_ee (const qmckl_context context, double* const rescale_factor_kappa_ee) {
+qmckl_get_electron_rescale_factor_ee (const qmckl_context context, double* const rescale_factor_kappa_ee) {
 
   if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
     return QMCKL_INVALID_CONTEXT;
@@ -310,27 +336,22 @@ qmckl_get_kappa_ee (const qmckl_context context, double* const rescale_factor_ka
   if (rescale_factor_kappa_ee == NULL) {
     return qmckl_failwith( context,
                            QMCKL_INVALID_ARG_2,
-                           "qmckl_get_kappa_ee",
+                           "qmckl_get_electron_rescale_factor_ee",
                            "rescale_factor_kappa_ee is a null pointer");
   }
 
   qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
   assert (ctx != NULL);
 
-  int32_t mask = 1 << 2;
+  assert (ctx->electron.rescale_factor_kappa_ee > 0.0);
 
-  if ( (ctx->electron.uninitialized & mask) != 0) {
+  *rescale_factor_kappa_ee = ctx->electron.rescale_factor_kappa_ee;
-    return QMCKL_NOT_PROVIDED;
-  }
-
-  // TODO: assert (ctx->electron.rescale_factor_kappa_ee > (double) 0);
-  ,*rescale_factor_kappa_ee = ctx->electron.rescale_factor_kappa_ee;
   return QMCKL_SUCCESS;
 }
 
 
 qmckl_exit_code
-qmckl_get_kappa_en (const qmckl_context context, double* const rescale_factor_kappa_en) {
+qmckl_get_electron_rescale_factor_en (const qmckl_context context, double* const rescale_factor_kappa_en) {
   if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
     return QMCKL_INVALID_CONTEXT;
   }
@@ -338,21 +359,15 @@ qmckl_get_kappa_en (const qmckl_context context, double* const rescale_factor_ka
   if (rescale_factor_kappa_en == NULL) {
     return qmckl_failwith( context,
                            QMCKL_INVALID_ARG_2,
-                           "qmckl_get_kappa_en",
+                           "qmckl_get_electron_rescale_factor_en",
                            "rescale_factor_kappa_en is a null pointer");
   }
 
   qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
   assert (ctx != NULL);
 
-  int32_t mask = 1 << 2;
+  assert (ctx->electron.rescale_factor_kappa_en > 0.0);
-
+  *rescale_factor_kappa_en = ctx->electron.rescale_factor_kappa_en;
-  if ( (ctx->electron.uninitialized & mask) != 0) {
-    return QMCKL_NOT_PROVIDED;
-  }
-
-  // TODO: assert (ctx->electron.rescale_factor_kappa_en > (double) 0);
-  ,*rescale_factor_kappa_en = ctx->electron.rescale_factor_kappa_en;
   return QMCKL_SUCCESS;
 }
       #+end_src
@@ -443,10 +458,12 @@ qmckl_get_electron_coord (const qmckl_context context, const char transp, double
    both allocated.
 
    #+begin_src c :comments org :tangle (eval h_func)
-qmckl_exit_code  qmckl_set_electron_num        (qmckl_context context, const int64_t up_num, const int64_t down_num);
+qmckl_exit_code qmckl_set_electron_num      (qmckl_context context, const int64_t up_num, const int64_t down_num);
-qmckl_exit_code  qmckl_set_kappa               (qmckl_context context, const double rescale_factor_kappa_ee, const double rescale_factor_kappa_en);
+qmckl_exit_code qmckl_set_electron_walk_num (qmckl_context context, const int64_t walk_num);
-qmckl_exit_code  qmckl_set_electron_walk_num   (qmckl_context context, const int64_t walk_num);
+qmckl_exit_code qmckl_set_electron_coord    (qmckl_context context, const char transp, const double* coord);
-qmckl_exit_code  qmckl_set_electron_coord      (qmckl_context context, const char transp, const double* coord);
+
+qmckl_exit_code qmckl_set_electron_rescale_factor_ee (qmckl_context context, const double kappa_ee);
+qmckl_exit_code qmckl_set_electron_rescale_factor_en (qmckl_context context, const double kappa_en);
    #+end_src
 
    #+NAME:pre2
@@ -559,32 +576,37 @@ qmckl_set_electron_walk_num(qmckl_context context, const int64_t walk_num) {
 
    #+begin_src c :comments org :tangle (eval c) :noweb yes  :exports none
 qmckl_exit_code
-qmckl_set_kappa(qmckl_context context,
+qmckl_set_electron_rescale_factor_ee(qmckl_context context,
-                const double rescale_factor_kappa_ee,
+                const double rescale_factor_kappa_ee) {
+  <<pre2>>
+
+  if (rescale_factor_kappa_ee <= 0.0) {
+    return qmckl_failwith( context,
+                           QMCKL_INVALID_ARG_2,
+                           "qmckl_set_electron_rescale_factor_ee",
+                           "rescale_factor_kappa_ee <= 0.0");
+  }
+
+  ctx->electron.rescale_factor_kappa_ee = rescale_factor_kappa_ee;
+
+  return QMCKL_SUCCESS;
+}
+
+qmckl_exit_code
+qmckl_set_electron_rescale_factor_en(qmckl_context context,
                 const double rescale_factor_kappa_en) {
   <<pre2>>
 
-  // TODO: Check for 0 values
+  if (rescale_factor_kappa_en <= 0.0) {
-  //if (rescale_factor_kappa_ee != 0) {
+    return qmckl_failwith( context,
-  //  return qmckl_failwith( context,
+                           QMCKL_INVALID_ARG_2,
-  //                         QMCKL_INVALID_ARG_2,
+                           "qmckl_set_electron_rescale_factor_en",
-  //                         "qmckl_set_kappa",
+                           "rescale_factor_kappa_en <= 0.0");
-  //                         "rescale_factor_kappa_ee == 0");
+  }
-  //}
 
-  //if (rescale_factor_kappa_en <= 0) {
-  //  return qmckl_failwith( context,
-  //                         QMCKL_INVALID_ARG_3,
-  //                         "qmckl_set_kappa",
-  //                         "rescale_factor_kappa_en == 0");
-  //}
-
-  int32_t mask = 1 << 2;
-
-  ctx->electron.rescale_factor_kappa_ee = rescale_factor_kappa_ee;
   ctx->electron.rescale_factor_kappa_en = rescale_factor_kappa_en;
 
-  <<post2>>
+  return QMCKL_SUCCESS;
 }
    #+end_src
 
@@ -688,14 +710,13 @@ int64_t walk_num      = chbrclf_walk_num;
 int64_t elec_num      = chbrclf_elec_num;
 int64_t elec_up_num   = chbrclf_elec_up_num;
 int64_t elec_dn_num   = chbrclf_elec_dn_num;
-double  rescale_factor_kappa_ee      = 1.0; // TODO Get rescale_factor_kappa_ee from chbrclf
+double  rescale_factor_kappa_ee = 2.0;
-double  rescale_factor_kappa_en      = 1.0; // TODO Get rescale_factor_kappa_en from chbrclf
+double  rescale_factor_kappa_en = 3.0;
 double* elec_coord    = &(chbrclf_elec_coord[0][0][0]);
 
 int64_t  nucl_num      = chbrclf_nucl_num;
 double*  charge        = chbrclf_charge;
 double*  nucl_coord    = &(chbrclf_nucl_coord[0][0]);
-double   nucl_rescale_factor_kappa    = 1.0; // TODO Change get rescale_factor_kappa from chbrclf example
 
 /* --- */
 
@@ -730,23 +751,27 @@ rc = qmckl_get_electron_num (context, &n);
 assert(rc == QMCKL_SUCCESS);
 assert(n == elec_num);
 
-double k_ee;
+double k_ee = 0.;
-double k_en;
+double k_en = 0.;
-rc = qmckl_get_kappa_ee (context, &k_ee);
+rc = qmckl_get_electron_rescale_factor_ee (context, &k_ee);
-assert(rc == QMCKL_NOT_PROVIDED);
-
-rc = qmckl_get_kappa_en (context, &k_en);
-assert(rc == QMCKL_NOT_PROVIDED);
-
-rc = qmckl_set_kappa (context, rescale_factor_kappa_ee, rescale_factor_kappa_en);
 assert(rc == QMCKL_SUCCESS);
-assert(!qmckl_electron_provided(context));
+assert(k_ee == 1.0);
 
-rc = qmckl_get_kappa_ee (context, &k_ee);
+rc = qmckl_get_electron_rescale_factor_en (context, &k_en);
+assert(rc == QMCKL_SUCCESS);
+assert(k_en == 1.0);
+
+rc = qmckl_set_electron_rescale_factor_en(context, rescale_factor_kappa_en);
+assert(rc == QMCKL_SUCCESS);
+
+rc = qmckl_set_electron_rescale_factor_ee(context, rescale_factor_kappa_ee);
+assert(rc == QMCKL_SUCCESS);
+
+rc = qmckl_get_electron_rescale_factor_ee (context, &k_ee);
 assert(rc == QMCKL_SUCCESS);
 assert(k_ee == rescale_factor_kappa_ee);
 
-rc = qmckl_get_kappa_en (context, &k_en);
+rc = qmckl_get_electron_rescale_factor_en (context, &k_en);
 assert(rc == QMCKL_SUCCESS);
 assert(k_en == rescale_factor_kappa_en);
 
@@ -1538,7 +1563,10 @@ qmckl_exit_code qmckl_provide_en_distance(qmckl_context context)
   assert (ctx != NULL);
 
   if (!(ctx->nucleus.provided)) {
-    return QMCKL_NOT_PROVIDED;
+    return qmckl_failwith( context,
+                           QMCKL_NOT_PROVIDED,
+                           "qmckl_provide_en_distance",
+                           NULL);
   }
 
  /* Compute if necessary */
@@ -1719,9 +1747,6 @@ assert(qmckl_electron_provided(context));
 rc = qmckl_set_nucleus_num (context, nucl_num);
 assert(rc == QMCKL_SUCCESS);
 
-rc = qmckl_set_nucleus_kappa (context, nucl_rescale_factor_kappa);
-assert(rc == QMCKL_SUCCESS);
-
 rc = qmckl_set_nucleus_charge (context, charge);
 assert (rc == QMCKL_SUCCESS);
 
@@ -2009,9 +2034,6 @@ assert(qmckl_electron_provided(context));
 rc = qmckl_set_nucleus_num (context, nucl_num);
 assert(rc == QMCKL_SUCCESS);
 
-rc = qmckl_set_nucleus_kappa (context, nucl_rescale_factor_kappa);
-assert(rc == QMCKL_SUCCESS);
-
 rc = qmckl_set_nucleus_charge (context, charge);
 assert (rc == QMCKL_SUCCESS);
 
@@ -2023,6 +2045,7 @@ assert(qmckl_nucleus_provided(context));
 double en_distance_rescaled[walk_num][nucl_num][elec_num];
 
 rc = qmckl_get_electron_en_distance_rescaled(context, &(en_distance_rescaled[0][0][0]));
+
 assert (rc == QMCKL_SUCCESS);
 
 // (e,n,w) in Fortran notation
@@ -2290,27 +2313,28 @@ assert(qmckl_nucleus_provided(context));
 double en_distance_rescaled_deriv_e[walk_num][4][nucl_num][elec_num];
 
 rc = qmckl_get_electron_en_distance_rescaled_deriv_e(context, &(en_distance_rescaled_deriv_e[0][0][0][0]));
+
 assert (rc == QMCKL_SUCCESS);
 
 // TODO: check exact values
 //// (e,n,w) in Fortran notation
 //// (1,1,1)
-//assert(fabs(en_distance[0][0][0] - 7.546738741619978) < 1.e-12);
+//assert(fabs(en_distance_rescaled[0][0][0] - 7.546738741619978) < 1.e-12);
 //
 //// (1,2,1)
-//assert(fabs(en_distance[0][1][0] - 8.77102435246984) < 1.e-12);
+//assert(fabs(en_distance_rescaled[0][1][0] - 8.77102435246984) < 1.e-12);
 //
 //// (2,1,1)
-//assert(fabs(en_distance[0][0][1] - 3.698922010513608) < 1.e-12);
+//assert(fabs(en_distance_rescaled[0][0][1] - 3.698922010513608) < 1.e-12);
 //
 //// (1,1,2)
-//assert(fabs(en_distance[1][0][0] - 5.824059436060509) < 1.e-12);
+//assert(fabs(en_distance_rescaled[1][0][0] - 5.824059436060509) < 1.e-12);
 //
 //// (1,2,2)
-//assert(fabs(en_distance[1][1][0] - 7.080482110317645) < 1.e-12);
+//assert(fabs(en_distance_rescaled[1][1][0] - 7.080482110317645) < 1.e-12);
 //
 //// (2,1,2)
-//assert(fabs(en_distance[1][0][1] - 3.1804527583077356) < 1.e-12);
+//assert(fabs(en_distance_rescaled[1][0][1] - 3.1804527583077356) < 1.e-12);
 
      #+end_src
 

org/qmckl_error.org

@@ -104,7 +104,8 @@ typedef int32_t qmckl_exit_code;
    | ~QMCKL_ALLOCATION_FAILED~   |  104 | 'Allocation failed'    |
    | ~QMCKL_DEALLOCATION_FAILED~ |  105 | 'De-allocation failed' |
    | ~QMCKL_NOT_PROVIDED~        |  106 | 'Not provided'         |
-   | ~QMCKL_INVALID_EXIT_CODE~   |  107 | 'Invalid exit code'    |
+   | ~QMCKL_OUT_OF_BOUNDS~       |  107 | 'Index out of bounds'  |
+   | ~QMCKL_INVALID_EXIT_CODE~   |  108 | 'Invalid exit code'    |
 
    # We need to force Emacs not to indent the Python code:
    # -*- org-src-preserve-indentation: t
@@ -162,7 +163,8 @@ return '\n'.join(result)
    #define  QMCKL_ALLOCATION_FAILED        ((qmckl_exit_code) 104)
    #define  QMCKL_DEALLOCATION_FAILED      ((qmckl_exit_code) 105)
    #define  QMCKL_NOT_PROVIDED             ((qmckl_exit_code) 106)
-   #define  QMCKL_INVALID_EXIT_CODE        ((qmckl_exit_code) 107)
+   #define  QMCKL_OUT_OF_BOUNDS            ((qmckl_exit_code) 107)
+   #define  QMCKL_INVALID_EXIT_CODE        ((qmckl_exit_code) 108)
    #+end_src
 
    #+begin_src f90 :comments org :tangle (eval fh_type) :exports none
@@ -193,7 +195,8 @@ return '\n'.join(result)
       integer(qmckl_exit_code), parameter :: QMCKL_ALLOCATION_FAILED        = 104
       integer(qmckl_exit_code), parameter :: QMCKL_DEALLOCATION_FAILED      = 105
       integer(qmckl_exit_code), parameter :: QMCKL_NOT_PROVIDED             = 106
-      integer(qmckl_exit_code), parameter :: QMCKL_INVALID_EXIT_CODE        = 107
+      integer(qmckl_exit_code), parameter :: QMCKL_OUT_OF_BOUNDS            = 107
+      integer(qmckl_exit_code), parameter :: QMCKL_INVALID_EXIT_CODE        = 108
    #+end_src
    :end:
 

org/qmckl_nucleus.org

@@ -92,20 +92,49 @@ typedef struct qmckl_nucleus_struct {
   int32_t   uninitialized;
   bool      provided;
 } qmckl_nucleus_struct;
+
    #+end_src
 
    The ~uninitialized~ integer contains one bit set to one for each
    initialization function which has not been called. It becomes equal
    to zero after all initialization functions have been called. The
    struct is then initialized and ~provided == true~.
+   Some values are initialized by default, and are not concerned by
+   this mechanism.
 
+   #+begin_src c :comments org :tangle (eval h_private_func) 
+qmckl_exit_code qmckl_init_nucleus(qmckl_context context);
+   #+end_src
+   
+   #+begin_src c :comments org :tangle (eval c)
+qmckl_exit_code qmckl_init_nucleus(qmckl_context context) {
+
+  if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
+    return false;
+  }
+
+  qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
+  assert (ctx != NULL);
+
+  ctx->nucleus.uninitialized = (1 << 3) - 1;
+
+ /* Default values */
+  ctx->nucleus.rescale_factor_kappa = 1.0;
+
+  return QMCKL_SUCCESS;
+}
+   #+end_src
+   
+
+   
 ** Access functions
    
    #+begin_src c :comments org :tangle (eval h_func) :exports none
-qmckl_exit_code qmckl_get_nucleus_num         (const qmckl_context context, int64_t* const num);
+qmckl_exit_code qmckl_get_nucleus_num    (const qmckl_context context, int64_t* const num);
-qmckl_exit_code qmckl_get_nucleus_charge      (const qmckl_context context, double* const charge);
+qmckl_exit_code qmckl_get_nucleus_charge (const qmckl_context context, double* const charge);
-qmckl_exit_code qmckl_get_nucleus_kappa       (const qmckl_context context, double* const rescale_factor_kappa);
+qmckl_exit_code qmckl_get_nucleus_coord  (const qmckl_context context, const char transp, double* const coord);
-qmckl_exit_code qmckl_get_nucleus_coord       (const qmckl_context context, const char transp, double* const coord);
+
+qmckl_exit_code qmckl_get_nucleus_rescale_factor (const qmckl_context context, double* const rescale_factor_kappa);
    #+end_src
 
    #+NAME:post
@@ -136,7 +165,7 @@ qmckl_get_nucleus_num (const qmckl_context context, int64_t* const num) {
   int32_t mask = 1 << 0;
 
   if ( (ctx->nucleus.uninitialized & mask) != 0) {
-    *num = (int64_t) 0;
+    ,*num = (int64_t) 0;
     return qmckl_failwith( context,
                            QMCKL_NOT_PROVIDED,
                            "qmckl_get_nucleus_num",
@@ -187,23 +216,25 @@ qmckl_get_nucleus_charge (const qmckl_context context, double* const charge) {
 
 
 qmckl_exit_code
-qmckl_get_nucleus_kappa (const qmckl_context context, double* const rescale_factor_kappa) {
+qmckl_get_nucleus_rescale_factor (const qmckl_context context,
+                                  double* const rescale_factor_kappa)
+{
 
   if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
     return QMCKL_INVALID_CONTEXT;
   }
 
+  if (rescale_factor_kappa == NULL) {
+    return qmckl_failwith( context,
+                           QMCKL_INVALID_ARG_2,
+                           "qmckl_get_nucleus_rescale_factor",
+                           "rescale_factor_kappa is a null pointer");
+  }
+
   qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
   assert (ctx != NULL);
 
-  int32_t mask = 1 << 2;
+  assert (ctx->nucleus.rescale_factor_kappa > 0.0);
-
-  if ( (ctx->nucleus.uninitialized & mask) != 0) {
-    return qmckl_failwith( context,
-                           QMCKL_NOT_PROVIDED,
-                           "qmckl_get_nucleus_kappa",
-                           "nucleus data is not provided");
-  }
 
   (*rescale_factor_kappa) = ctx->nucleus.rescale_factor_kappa;
 
@@ -235,7 +266,7 @@ qmckl_get_nucleus_coord (const qmckl_context context, const char transp, double*
   qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
   assert (ctx != NULL);
 
-  int32_t mask = 1 << 3;
+  int32_t mask = 1 << 2;
 
   if ( (ctx->nucleus.uninitialized & mask) != 0) {
     return qmckl_failwith( context,
@@ -295,8 +326,9 @@ bool qmckl_nucleus_provided(const qmckl_context context) {
    #+begin_src c :comments org :tangle (eval h_func)
 qmckl_exit_code  qmckl_set_nucleus_num    (qmckl_context context, const int64_t num);
 qmckl_exit_code  qmckl_set_nucleus_charge (qmckl_context context, const double* charge);
-qmckl_exit_code  qmckl_set_nucleus_kappa  (qmckl_context context, const double rescale_factor_kappa);
 qmckl_exit_code  qmckl_set_nucleus_coord  (qmckl_context context, const char transp, const double* coord);
+
+qmckl_exit_code  qmckl_set_nucleus_rescale_factor (qmckl_context context, const double rescale_factor_kappa);
    #+end_src
 
    #+NAME:pre2
@@ -331,7 +363,7 @@ qmckl_set_nucleus_num(qmckl_context context, const int64_t num) {
                            "num <= 0");
   }
 
-  int32_t mask = 1;
+  int32_t mask = 1 << 0;
 
   ctx->nucleus.num = num;
 
@@ -388,25 +420,19 @@ qmckl_set_nucleus_charge(qmckl_context context, const double* charge) {
 
    #+begin_src c :comments org :tangle (eval c) :noweb yes  :exports none
 qmckl_exit_code
-qmckl_set_nucleus_kappa(qmckl_context context, const double rescale_factor_kappa) {
+qmckl_set_nucleus_rescale_factor(qmckl_context context, const double rescale_factor_kappa) {
   <<pre2>>
 
-  //TODO: Check for small values of kappa
+  if (rescale_factor_kappa <= 0.0) {
-  //if (rescale_factor_kappa == 0) {
+    return qmckl_failwith( context,
-  //  return qmckl_failwith( context,
+                           QMCKL_INVALID_ARG_2,
-  //                         QMCKL_INVALID_ARG_2,
+                           "qmckl_set_nucleus_kappa",
-  //                         "qmckl_set_nucleus_kappa",
+                           "rescale_factor_kappa cannot be <= 0.");
-  //                         "rescale_factor_kappa cannot be 0");
+  }
-  //}
-
-  int32_t mask = 1 << 2;
-
-  int64_t num;
-  qmckl_exit_code rc;
 
   ctx->nucleus.rescale_factor_kappa = rescale_factor_kappa;
 
-  <<post2>>
+  return QMCKL_SUCCESS;
 }
     #+end_src
 
@@ -421,7 +447,7 @@ qmckl_set_nucleus_coord(qmckl_context context, const char transp, const double*
   int64_t nucl_num = (int64_t) 0;
   qmckl_exit_code rc;
 
-  int32_t mask = 1 << 3;
+  int32_t mask = 1 << 2;
 
   rc = qmckl_get_nucleus_num(context, &nucl_num);
   if (rc != QMCKL_SUCCESS) return rc;
@@ -462,7 +488,7 @@ qmckl_set_nucleus_coord(qmckl_context context, const char transp, const double*
 const int64_t   nucl_num      = chbrclf_nucl_num;
 const double*   nucl_charge   = chbrclf_charge;
 const double*   nucl_coord    = &(chbrclf_nucl_coord[0][0]);
-const double    nucl_rescale_factor_kappa    = 1.0; // TODO Change get rescale_factor_kappa from chbrclf example
+const double    nucl_rescale_factor_kappa = 2.0; 
 
 /* --- */
 
@@ -484,15 +510,15 @@ assert(rc == QMCKL_SUCCESS);
 assert(n == nucl_num);
 
 double k;
-rc = qmckl_get_nucleus_kappa (context, &k);
+rc = qmckl_get_nucleus_rescale_factor (context, &k);
-assert(rc == QMCKL_NOT_PROVIDED);
-
-
-rc = qmckl_set_nucleus_kappa (context, nucl_rescale_factor_kappa);
 assert(rc == QMCKL_SUCCESS);
-assert(!qmckl_nucleus_provided(context));
+assert(k == 1.0);
 
-rc = qmckl_get_nucleus_kappa (context, &k);
+
+rc = qmckl_set_nucleus_rescale_factor (context, nucl_rescale_factor_kappa);
+assert(rc == QMCKL_SUCCESS);
+
+rc = qmckl_get_nucleus_rescale_factor (context, &k);
 assert(rc == QMCKL_SUCCESS);
 assert(k == nucl_rescale_factor_kappa);
 
@@ -535,7 +561,7 @@ for (size_t i=0 ; i<nucl_num ; ++i) {
  }
 assert(qmckl_nucleus_provided(context));
     #+end_src
-
+    
 * Computation
 
   The computed data is stored in the context so that it can be reused
@@ -836,7 +862,7 @@ end function qmckl_compute_nn_distance_rescaled_f
 
     #+begin_src c :tangle (eval h_private_func) :comments org :exports none
 qmckl_exit_code qmckl_compute_nn_distance_rescaled (
-          const qmckl_context context,
+                                                    const qmckl_context context,
           const int64_t nucl_num,
           const double  rescale_factor_kappa,
           const double* coord,

org/qmckl_tests.org

@@ -523,6 +523,344 @@ F   1
 
     #+END_example
 
+#+begin_src c :tangle ../tests/chbrclf.h
+#define chbrclf_shell_num 72
+#define chbrclf_prim_num 297
+
+int64_t chbrclf_basis_nucleus_index[chbrclf_nucl_num] = {0, 14, 23, 27, 53};
+
+int64_t chbrclf_basis_nucleus_shell_num[chbrclf_nucl_num] = {14, 9, 14, 16, 19};
+
+int32_t chbrclf_basis_shell_ang_mom[chbrclf_shell_num] =
+  {0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 3, 3, 0, 0, 0, 0, 1, 1, 1, 2, 2, 0, 
+   0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 3, 3, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
+   2, 2, 2, 3, 3, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3}; 
+
+int64_t chbrclf_basis_shell_prim_num[chbrclf_shell_num] =
+  {10, 10, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10,
+   10, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 1, 1, 1, 9, 9, 1, 1, 1,
+   1, 1, 1, 1, 1, 20, 20, 20, 20, 1, 1, 1, 13, 13, 13, 1, 1, 1, 8, 1, 1, 1, 1,
+   1};
+
+int64_t chbrclf_basis_shell_prim_index[chbrclf_shell_num] =
+  {0, 10, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44,
+   45, 46, 47, 48, 49, 59, 69, 70, 71, 72, 77, 78, 79, 80, 81, 82, 83, 84, 85,
+   100, 115, 130, 131, 132, 133, 142, 151, 152, 153, 154, 155, 156, 157, 158,
+   159, 179, 199, 219, 239, 240, 241, 242, 255, 268, 281, 282, 283, 284, 292,
+   293, 294, 295, 296};
+
+double chbrclf_basis_shell_factor[chbrclf_shell_num] =
+  {1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
+   1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
+   1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
+   1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.}; 
+
+double chbrclf_basis_exponent[chbrclf_prim_num] =
+  {8.2360000000000000e+03, 1.2350000000000000e+03, 2.8080000000000001e+02,
+   7.9269999999999996e+01, 2.5590000000000000e+01, 8.9969999999999999e+00,
+   3.3190000000000000e+00, 9.0590000000000004e-01, 3.6430000000000001e-01,
+   1.2850000000000000e-01, 8.2360000000000000e+03, 1.2350000000000000e+03,
+   2.8080000000000001e+02, 7.9269999999999996e+01, 2.5590000000000000e+01,
+   8.9969999999999999e+00, 3.3190000000000000e+00, 9.0590000000000004e-01,
+   3.6430000000000001e-01, 1.2850000000000000e-01, 9.0590000000000004e-01,
+   1.2850000000000000e-01, 4.4019999999999997e-02, 1.8710000000000001e+01,
+   4.1330000000000000e+00, 1.2000000000000000e+00, 3.8269999999999998e-01,
+   1.2089999999999999e-01, 3.8269999999999998e-01, 1.2089999999999999e-01,
+   3.5690000000000000e-02, 1.0970000000000000e+00, 3.1800000000000000e-01,
+   1.0000000000000001e-01, 7.6100000000000001e-01, 2.6800000000000002e-01,
+   3.3869999999999997e+01, 5.0949999999999998e+00, 1.1590000000000000e+00,
+   3.2579999999999998e-01, 1.0270000000000000e-01, 3.2579999999999998e-01,
+   1.0270000000000000e-01, 2.5260000000000001e-02, 1.4070000000000000e+00,
+   3.8800000000000001e-01, 1.0199999999999999e-01, 1.0569999999999999e+00,
+   2.4700000000000000e-01, 1.9500000000000000e+04, 2.9230000000000000e+03,
+   6.6450000000000000e+02, 1.8750000000000000e+02, 6.0619999999999997e+01,
+   2.1420000000000002e+01, 7.9500000000000002e+00, 2.2570000000000001e+00,
+   8.8149999999999995e-01, 3.0409999999999998e-01, 1.9500000000000000e+04,
+   2.9230000000000000e+03, 6.6450000000000000e+02, 1.8750000000000000e+02,
+   6.0619999999999997e+01, 2.1420000000000002e+01, 7.9500000000000002e+00,
+   2.2570000000000001e+00, 8.8149999999999995e-01, 3.0409999999999998e-01,
+   2.2570000000000001e+00, 3.0409999999999998e-01, 9.1579999999999995e-02,
+   4.3880000000000003e+01, 9.9260000000000002e+00, 2.9300000000000002e+00,
+   9.1320000000000001e-01, 2.6719999999999999e-01, 9.1320000000000001e-01,
+   2.6719999999999999e-01, 7.3609999999999995e-02, 3.1070000000000002e+00,
+   8.5499999999999998e-01, 2.9199999999999998e-01, 1.9170000000000000e+00,
+   7.2399999999999998e-01, 4.5610000000000000e+05, 6.8330000000000000e+04,
+   1.5550000000000000e+04, 4.4050000000000000e+03, 1.4390000000000000e+03,
+   5.2039999999999998e+02, 2.0309999999999999e+02, 8.3959999999999994e+01,
+   3.6200000000000003e+01, 1.5830000000000000e+01, 6.3339999999999996e+00,
+   2.6940000000000000e+00, 9.7680000000000000e-01, 4.3130000000000002e-01,
+   1.6250000000000001e-01, 4.5610000000000000e+05, 6.8330000000000000e+04,
+   1.5550000000000000e+04, 4.4050000000000000e+03, 1.4390000000000000e+03,
+   5.2039999999999998e+02, 2.0309999999999999e+02, 8.3959999999999994e+01,
+   3.6200000000000003e+01, 1.5830000000000000e+01, 6.3339999999999996e+00,
+   2.6940000000000000e+00, 9.7680000000000000e-01, 4.3130000000000002e-01,
+   1.6250000000000001e-01, 4.5610000000000000e+05, 6.8330000000000000e+04,
+   1.5550000000000000e+04, 4.4050000000000000e+03, 1.4390000000000000e+03,
+   5.2039999999999998e+02, 2.0309999999999999e+02, 8.3959999999999994e+01,
+   3.6200000000000003e+01, 1.5830000000000000e+01, 6.3339999999999996e+00,
+   2.6940000000000000e+00, 9.7680000000000000e-01, 4.3130000000000002e-01,
+   1.6250000000000001e-01, 9.7680000000000000e-01, 1.6250000000000001e-01,
+   5.9100000000000000e-02, 6.6329999999999995e+02, 1.5680000000000001e+02,
+   4.9979999999999997e+01, 1.8420000000000002e+01, 7.2400000000000002e+00,
+   2.9220000000000002e+00, 1.0220000000000000e+00, 3.8179999999999997e-01,
+   1.3009999999999999e-01, 6.6329999999999995e+02, 1.5680000000000001e+02,
+   4.9979999999999997e+01, 1.8420000000000002e+01, 7.2400000000000002e+00,
+   2.9220000000000002e+00, 1.0220000000000000e+00, 3.8179999999999997e-01,
+   1.3009999999999999e-01, 1.0220000000000000e+00, 1.3009999999999999e-01,
+   4.1900000000000000e-02, 1.0460000000000000e+00, 3.4399999999999997e-01,
+   1.3500000000000001e-01, 7.0599999999999996e-01, 3.1200000000000000e-01,
+   1.0639000000000000e+07, 1.5934000000000000e+06, 3.6261000000000000e+05,
+   1.0270000000000000e+05, 3.3501000000000000e+04, 1.2093000000000000e+04,
+   4.7158999999999996e+03, 1.9555999999999999e+03, 8.5261000000000001e+02,
+   3.8767000000000002e+02, 1.8268000000000001e+02, 8.8245000000000005e+01,
+   3.9262999999999998e+01, 1.9234000000000002e+01, 9.4056999999999995e+00,
+   4.1600999999999999e+00, 1.8995000000000000e+00, 6.0472000000000004e-01,
+   3.0114000000000002e-01, 1.2515000000000001e-01, 1.0639000000000000e+07,
+   1.5934000000000000e+06, 3.6261000000000000e+05, 1.0270000000000000e+05,
+   3.3501000000000000e+04, 1.2093000000000000e+04, 4.7158999999999996e+03,
+   1.9555999999999999e+03, 8.5261000000000001e+02, 3.8767000000000002e+02,
+   1.8268000000000001e+02, 8.8245000000000005e+01, 3.9262999999999998e+01,
+   1.9234000000000002e+01, 9.4056999999999995e+00, 4.1600999999999999e+00,
+   1.8995000000000000e+00, 6.0472000000000004e-01, 3.0114000000000002e-01,
+   1.2515000000000001e-01, 1.0639000000000000e+07, 1.5934000000000000e+06,
+   3.6261000000000000e+05, 1.0270000000000000e+05, 3.3501000000000000e+04,
+   1.2093000000000000e+04, 4.7158999999999996e+03, 1.9555999999999999e+03,
+   8.5261000000000001e+02, 3.8767000000000002e+02, 1.8268000000000001e+02,
+   8.8245000000000005e+01, 3.9262999999999998e+01, 1.9234000000000002e+01,
+   9.4056999999999995e+00, 4.1600999999999999e+00, 1.8995000000000000e+00,
+   6.0472000000000004e-01, 3.0114000000000002e-01, 1.2515000000000001e-01,
+   1.0639000000000000e+07, 1.5934000000000000e+06, 3.6261000000000000e+05,
+   1.0270000000000000e+05, 3.3501000000000000e+04, 1.2093000000000000e+04,
+   4.7158999999999996e+03, 1.9555999999999999e+03, 8.5261000000000001e+02,
+   3.8767000000000002e+02, 1.8268000000000001e+02, 8.8245000000000005e+01,
+   3.9262999999999998e+01, 1.9234000000000002e+01, 9.4056999999999995e+00,
+   4.1600999999999999e+00, 1.8995000000000000e+00, 6.0472000000000004e-01,
+   3.0114000000000002e-01, 1.2515000000000001e-01, 6.0472000000000004e-01,
+   1.2515000000000001e-01, 4.5593000000000002e-02, 8.6765000000000000e+03,
+   2.0559000000000001e+03, 6.6623000000000002e+02, 2.5309999999999999e+02,
+   1.0612000000000000e+02, 4.7241999999999997e+01, 2.1824999999999999e+01,
+   9.9684000000000008e+00, 4.5171000000000001e+00, 1.9982000000000000e+00,
+   7.0987999999999996e-01, 2.8144999999999998e-01, 1.0204000000000001e-01,
+   8.6765000000000000e+03, 2.0559000000000001e+03, 6.6623000000000002e+02,
+   2.5309999999999999e+02, 1.0612000000000000e+02, 4.7241999999999997e+01,
+   2.1824999999999999e+01, 9.9684000000000008e+00, 4.5171000000000001e+00,
+   1.9982000000000000e+00, 7.0987999999999996e-01, 2.8144999999999998e-01,
+   1.0204000000000001e-01, 8.6765000000000000e+03, 2.0559000000000001e+03,
+   6.6623000000000002e+02, 2.5309999999999999e+02, 1.0612000000000000e+02,
+   4.7241999999999997e+01, 2.1824999999999999e+01, 9.9684000000000008e+00,
+   4.5171000000000001e+00, 1.9982000000000000e+00, 7.0987999999999996e-01,
+   2.8144999999999998e-01, 1.0204000000000001e-01, 7.0987999999999996e-01,
+   1.0204000000000001e-01, 3.5142000000000000e-02, 4.0382999999999998e+02,
+   1.2117000000000000e+02, 4.6344999999999999e+01, 1.9721000000000000e+01,
+   8.8623999999999992e+00, 3.9962000000000000e+00, 1.7636000000000001e+00,
+   7.0618999999999998e-01, 7.0618999999999998e-01, 2.6390000000000002e-01,
+   1.0470000000000000e-01, 5.5149999999999999e-01, 2.5800000000000001e-01};
+
+double chbrclf_basis_coefficient[chbrclf_prim_num] =
+  {5.3100000000000000e-04, 4.1079999999999997e-03, 2.1087000000000002e-02,
+  8.1852999999999995e-02, 2.3481700000000000e-01, 4.3440099999999998e-01,
+  3.4612900000000002e-01, 3.9378000000000003e-02, -8.9829999999999997e-03,
+  2.3850000000000000e-03, -1.1300000000000000e-04, -8.7799999999999998e-04,
+  -4.5399999999999998e-03, -1.8133000000000000e-02, -5.5759999999999997e-02,
+  -1.2689500000000001e-01, -1.7035200000000000e-01, 1.4038200000000001e-01,
+  5.9868399999999999e-01, 3.9538899999999999e-01, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.4031000000000000e-02,
+  8.6865999999999999e-02, 2.9021599999999997e-01, 5.0100800000000001e-01,
+  3.4340599999999999e-01, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  6.0679999999999996e-03, 4.5308000000000001e-02, 2.0282200000000000e-01,
+  5.0390299999999999e-01, 3.8342100000000001e-01, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 5.0699999999999996e-04, 3.9230000000000003e-03,
+  2.0199999999999999e-02, 7.9009999999999997e-02, 2.3043900000000000e-01,
+  4.3287199999999998e-01, 3.4996400000000000e-01, 4.3233000000000001e-02,
+  -7.8919999999999997e-03, 2.3839999999999998e-03, -1.1700000000000000e-04,
+  -9.1200000000000005e-04, -4.7169999999999998e-03, -1.9085999999999999e-02,
+  -5.9655000000000000e-02, -1.4001000000000000e-01, -1.7678199999999999e-01,
+  1.7162500000000000e-01, 6.0504300000000000e-01, 3.6951200000000001e-01,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.6664999999999999e-02, 1.0447200000000000e-01, 3.1725999999999999e-01,
+  4.8734300000000003e-01, 3.3460400000000001e-01, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 4.9296999999999999e-05, 3.8302900000000001e-04,
+  2.0085400000000001e-03, 8.3855800000000001e-03, 2.9470300000000001e-02,
+  8.7832499999999994e-02, 2.1147299999999999e-01, 3.6536400000000002e-01,
+  3.4088400000000002e-01, 1.0213300000000000e-01, 3.1167500000000002e-03,
+  1.0575100000000000e-03, -3.7800000000000003e-04, 1.5613600000000000e-04,
+  -5.1412600000000003e-05, -1.3830400000000001e-05, -1.0727900000000000e-04,
+  -5.6508299999999997e-04, -2.3613499999999999e-03, -8.4588600000000003e-03,
+  -2.5963799999999999e-02, -6.8636199999999994e-02, -1.4187400000000000e-01,
+  -1.9931900000000000e-01, -1.9566199999999999e-02, 4.9974099999999999e-01,
+  5.6373600000000001e-01, 7.9032500000000006e-02, -8.3509099999999996e-03,
+  2.3245599999999998e-03, 4.1854599999999997e-06, 3.2439500000000000e-05,
+  1.7110500000000001e-04, 7.1417599999999996e-04, 2.5670500000000000e-03,
+  7.8855200000000000e-03, 2.1086700000000000e-02, 4.4226399999999999e-02,
+  6.5167000000000003e-02, 6.0301199999999999e-03, -2.0649500000000001e-01,
+  -4.0587099999999998e-01, 7.5955800000000004e-02, 7.2566100000000000e-01,
+  3.9442300000000002e-01, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 2.4044800000000001e-03, 1.9214800000000001e-02,
+  8.8509699999999997e-02, 2.5602000000000003e-01, 4.3692700000000001e-01,
+  3.5033399999999998e-01, 5.8549499999999997e-02, -4.5842299999999999e-03,
+  2.2696999999999999e-03, -6.5214500000000003e-04, -5.1944499999999998e-03,
+  -2.4693799999999998e-02, -7.2816699999999998e-02, -1.3403000000000001e-01,
+  -9.4774200000000003e-02, 2.6228899999999999e-01, 5.6466700000000003e-01,
+  3.4125000000000000e-01, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  5.9000000000000003e-06, 4.6100000000000002e-05, 2.4220000000000001e-04,
+  1.0226000000000000e-03, 3.7112999999999998e-03, 1.1978500000000000e-02,
+  3.4692700000000000e-02, 8.9123900000000006e-02, 1.9345570000000001e-01,
+  3.2090190000000002e-01, 3.2992329999999997e-01, 1.4941209999999999e-01,
+  1.4993800000000000e-02, -9.1650000000000000e-04, 4.3800000000000002e-04,
+  -2.3980000000000000e-04, 7.3600000000000000e-05, -3.6699999999999998e-05,
+  2.3900000000000002e-05, -5.5999999999999997e-06, -1.9000000000000000e-06,
+  -1.4500000000000000e-05, -7.6100000000000007e-05, -3.2100000000000000e-04,
+  -1.1708999999999999e-03, -3.7967999999999999e-03, -1.1230700000000000e-02,
+  -2.9927700000000002e-02, -7.1270600000000003e-02, -1.4031360000000001e-01,
+  -2.0307629999999999e-01, -9.6098500000000003e-02, 3.5580859999999997e-01,
+  5.9217920000000002e-01, 2.2159770000000001e-01, 1.3764800000000001e-02,
+  8.3949999999999997e-04, -4.5099999999999998e-05, -8.4999999999999999e-06,
+  -1.2400000000000000e-05, 6.9999999999999997e-07, 5.6999999999999996e-06,
+  3.0300000000000001e-05, 1.2750000000000001e-04, 4.6589999999999999e-04,
+  1.5096000000000000e-03, 4.4852000000000000e-03, 1.1983499999999999e-02,
+  2.8957100000000000e-02, 5.8156600000000003e-02, 8.8813299999999998e-02,
+  4.4524399999999999e-02, -2.0603869999999999e-01, -5.1270170000000004e-01,
+  -1.5093490000000001e-01, 6.7892030000000003e-01, 5.8176969999999995e-01,
+  4.6755499999999998e-02, -1.1182500000000000e-02, 2.4402000000000000e-03,
+  -1.9999999999999999e-07, -1.7999999999999999e-06, -9.3000000000000007e-06,
+  -3.9100000000000002e-05, -1.4280000000000000e-04, -4.6279999999999997e-04,
+  -1.3749999999999999e-03, -3.6784000000000001e-03, -8.8981000000000008e-03,
+  -1.7952900000000001e-02, -2.7573199999999999e-02, -1.4095300000000000e-02,
+  6.7256099999999999e-02, 1.7669280000000001e-01, 5.2886099999999998e-02,
+  -3.0759550000000002e-01, -4.7006579999999998e-01, 2.5587610000000000e-01,
+  6.9803409999999999e-01, 2.9672559999999998e-01, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 4.3570000000000002e-04,
+  3.7815000000000001e-03, 2.0478199999999998e-02, 7.9283400000000004e-02,
+  2.1784729999999999e-01, 3.8785849999999999e-01, 3.5943500000000000e-01,
+  1.1219949999999999e-01, 4.3873999999999996e-03, 1.7809000000000000e-03,
+  -4.5760000000000001e-04, 2.1220000000000001e-04, -7.3399999999999995e-05,
+  -1.7479999999999999e-04, -1.5263000000000000e-03, -8.3399000000000008e-03,
+  -3.3220300000000001e-02, -9.5418000000000003e-02, -1.8240260000000000e-01,
+  -1.5583079999999999e-01, 1.8678990000000001e-01, 5.4277330000000001e-01,
+  3.8733089999999998e-01, 4.5306899999999997e-02, -4.3784000000000002e-03,
+  1.8110999999999999e-03, 4.5099999999999998e-05, 3.9639999999999999e-04,
+  2.1554999999999999e-03, 8.6719999999999992e-03, 2.4868000000000001e-02,
+  4.8547199999999999e-02, 3.9615600000000001e-02, -6.0574900000000001e-02,
+  -1.8716990000000000e-01, -1.3777570000000000e-01, 2.9280210000000001e-01,
+  5.7608959999999998e-01, 3.0786170000000002e-01, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.4732000000000000e-03,
+  1.2672500000000000e-02, 5.8045100000000002e-02, 1.7051030000000000e-01,
+  3.1859579999999998e-01, 3.8450230000000002e-01, 2.7377370000000001e-01,
+  7.4396699999999996e-02, 1.0000000000000000e+00, 1.0000000000000000e+00,
+  1.0000000000000000e+00, 1.0000000000000000e+00, 1.0000000000000000e+00};
+
+double chbrclf_basis_prim_factor[chbrclf_prim_num] =
+  {6.1616545431994848e+02, 1.4847738511079908e+02, 4.8888635917437597e+01,
+  1.8933972232608955e+01, 8.1089160941724145e+00, 3.7024003863155635e+00,
+  1.7525302846177560e+00, 6.6179013183966806e-01, 3.3419848027174592e-01,
+  1.5296336817449557e-01, 6.1616545431994848e+02, 1.4847738511079908e+02,
+  4.8888635917437597e+01, 1.8933972232608955e+01, 8.1089160941724145e+00,
+  3.7024003863155635e+00, 1.7525302846177560e+00, 6.6179013183966806e-01,
+  3.3419848027174592e-01, 1.5296336817449557e-01, 6.6179013183966806e-01,
+  1.5296336817449557e-01, 6.8493225861981921e-02, 5.5466699238441954e+01,
+  8.3998560685400019e+00, 1.7902622143452276e+00, 4.2905519588435126e-01,
+  1.0161854305479753e-01, 4.2905519588435126e-01, 1.0161854305479753e-01,
+  2.2111758010684022e-02, 1.9354014159719681e+00, 2.2164447815916102e-01,
+  2.9269105913429974e-02, 7.9628755341813429e-01, 7.6077763383300537e-02,
+  1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01,
+  3.0734305383061117e-01, 1.2929684417481876e-01, 3.0734305383061117e-01,
+  1.2929684417481876e-01, 4.5158041868216925e-02, 2.1842769845268308e+00,
+  4.3649547399719840e-01, 8.2165651391863506e-02, 1.8135965626177861e+00,
+  1.4243906834168285e-01, 1.1760777961352585e+03, 2.8332291650568584e+02,
+  9.3278452222064189e+01, 3.6112790320330610e+01, 1.5483603491420400e+01,
+  7.0961811262237955e+00, 3.3743135718917610e+00, 1.3123774561862465e+00,
+  6.4837584903810197e-01, 2.9185854115641796e-01, 1.1760777961352585e+03,
+  2.8332291650568584e+02, 9.3278452222064189e+01, 3.6112790320330610e+01,
+  1.5483603491420400e+01, 7.0961811262237955e+00, 3.3743135718917610e+00,
+  1.3123774561862465e+00, 6.4837584903810197e-01, 2.9185854115641796e-01,
+  1.3123774561862465e+00, 2.9185854115641796e-01, 1.1864804090515012e-01,
+  1.6098053319659394e+02, 2.5113539500925100e+01, 5.4641751683240054e+00,
+  1.2724697488890255e+00, 2.7383291850797253e-01, 1.2724697488890255e+00,
+  2.7383291850797253e-01, 5.4652635549581594e-02, 1.1967588544907814e+01,
+  1.2512674783228661e+00, 1.9091033786232964e-01, 6.3658177914201666e+00,
+  7.1181350527019893e-01, 1.2508497509090121e+04, 3.0120949486045815e+03,
+  9.9244828879919498e+02, 3.8536256746518035e+02, 1.6651589181438584e+02,
+  7.7653861740552273e+01, 3.8343569039456206e+01, 1.9768076572700657e+01,
+  1.0518202315565855e+01, 5.6561481770276556e+00, 2.8455658258813377e+00,
+  1.4986778401686554e+00, 7.0026807980299932e-01, 3.7931034358525295e-01,
+  1.8241061862759339e-01, 1.2508497509090121e+04, 3.0120949486045815e+03,
+  9.9244828879919498e+02, 3.8536256746518035e+02, 1.6651589181438584e+02,
+  7.7653861740552273e+01, 3.8343569039456206e+01, 1.9768076572700657e+01,
+  1.0518202315565855e+01, 5.6561481770276556e+00, 2.8455658258813377e+00,
+  1.4986778401686554e+00, 7.0026807980299932e-01, 3.7931034358525295e-01,
+  1.8241061862759339e-01, 1.2508497509090121e+04, 3.0120949486045815e+03,
+  9.9244828879919498e+02, 3.8536256746518035e+02, 1.6651589181438584e+02,
+  7.7653861740552273e+01, 3.8343569039456206e+01, 1.9768076572700657e+01,
+  1.0518202315565855e+01, 5.6561481770276556e+00, 2.8455658258813377e+00,
+  1.4986778401686554e+00, 7.0026807980299932e-01, 3.7931034358525295e-01,
+  1.8241061862759339e-01, 7.0026807980299932e-01, 1.8241061862759339e-01,
+  8.5428091252337218e-02, 4.7981915824835833e+03, 7.9090197643220097e+02,
+  1.8942417420993877e+02, 5.4394140688380837e+01, 1.6928298001679121e+01,
+  5.4455324755334713e+00, 1.4647169510384077e+00, 4.2779429930932966e-01,
+  1.1137474138247395e-01, 4.7981915824835833e+03, 7.9090197643220097e+02,
+  1.8942417420993877e+02, 5.4394140688380837e+01, 1.6928298001679121e+01,
+  5.4455324755334713e+00, 1.4647169510384077e+00, 4.2779429930932966e-01,
+  1.1137474138247395e-01, 1.4647169510384077e+00, 1.1137474138247395e-01,
+  2.7021385701525968e-02, 1.7806964960637739e+00, 2.5432363995130330e-01,
+  4.9487276238674341e-02, 6.7261264398159915e-01, 1.0710316041250582e-01,
+  1.3276564169936487e+05, 3.1963453883259335e+04, 1.0531492549479324e+04,
+  4.0887252186430137e+03, 1.7648322054568350e+03, 8.2188420053589937e+02,
+  4.0558653897685440e+02, 2.0958978573126603e+02, 1.1245348234327012e+02,
+  6.2266827352587455e+01, 3.5414274108483511e+01, 2.0520014948183928e+01,
+  1.1178864762092555e+01, 6.5457935075374944e+00, 3.8278369835025656e+00,
+  2.0760505305870112e+00, 1.1531599898261422e+00, 4.8873770086696849e-01,
+  2.8972530369835303e-01, 1.4996269365355971e-01, 1.3276564169936487e+05,
+  3.1963453883259335e+04, 1.0531492549479324e+04, 4.0887252186430137e+03,
+  1.7648322054568350e+03, 8.2188420053589937e+02, 4.0558653897685440e+02,
+  2.0958978573126603e+02, 1.1245348234327012e+02, 6.2266827352587455e+01,
+  3.5414274108483511e+01, 2.0520014948183928e+01, 1.1178864762092555e+01,
+  6.5457935075374944e+00, 3.8278369835025656e+00, 2.0760505305870112e+00,
+  1.1531599898261422e+00, 4.8873770086696849e-01, 2.8972530369835303e-01,
+  1.4996269365355971e-01, 1.3276564169936487e+05, 3.1963453883259335e+04,
+  1.0531492549479324e+04, 4.0887252186430137e+03, 1.7648322054568350e+03,
+  8.2188420053589937e+02, 4.0558653897685440e+02, 2.0958978573126603e+02,
+  1.1245348234327012e+02, 6.2266827352587455e+01, 3.5414274108483511e+01,
+  2.0520014948183928e+01, 1.1178864762092555e+01, 6.5457935075374944e+00,
+  3.8278369835025656e+00, 2.0760505305870112e+00, 1.1531599898261422e+00,
+  4.8873770086696849e-01, 2.8972530369835303e-01, 1.4996269365355971e-01,
+  1.3276564169936487e+05, 3.1963453883259335e+04, 1.0531492549479324e+04,
+  4.0887252186430137e+03, 1.7648322054568350e+03, 8.2188420053589937e+02,
+  4.0558653897685440e+02, 2.0958978573126603e+02, 1.1245348234327012e+02,
+  6.2266827352587455e+01, 3.5414274108483511e+01, 2.0520014948183928e+01,
+  1.1178864762092555e+01, 6.5457935075374944e+00, 3.8278369835025656e+00,
+  2.0760505305870112e+00, 1.1531599898261422e+00, 4.8873770086696849e-01,
+  2.8972530369835303e-01, 1.4996269365355971e-01, 4.8873770086696849e-01,
+  1.4996269365355971e-01, 7.0320786489653203e-02, 1.1936329579215313e+05,
+  1.9732975244933248e+04, 4.8247000542937221e+03, 1.4389816948051262e+03,
+  4.8549709936386239e+02, 1.7654297142185436e+02, 6.7240804881705529e+01,
+  2.5247705079657806e+01, 9.3867385006594475e+00, 3.3864040992879496e+00,
+  9.2879798315626561e-01, 2.9220769881703862e-01, 8.2205930646140513e-02,
+  1.1936329579215313e+05, 1.9732975244933248e+04, 4.8247000542937221e+03,
+  1.4389816948051262e+03, 4.8549709936386239e+02, 1.7654297142185436e+02,
+  6.7240804881705529e+01, 2.5247705079657806e+01, 9.3867385006594475e+00,
+  3.3864040992879496e+00, 9.2879798315626561e-01, 2.9220769881703862e-01,
+  8.2205930646140513e-02, 1.1936329579215313e+05, 1.9732975244933248e+04,
+  4.8247000542937221e+03, 1.4389816948051262e+03, 4.8549709936386239e+02,
+  1.7654297142185436e+02, 6.7240804881705529e+01, 2.5247705079657806e+01,
+  9.3867385006594475e+00, 3.3864040992879496e+00, 9.2879798315626561e-01,
+  2.9220769881703862e-01, 8.2205930646140513e-02, 9.2879798315626561e-01,
+  8.2205930646140513e-02, 2.1688183591227813e-02, 5.9876577632594533e+04,
+  7.2836806319891484e+03, 1.3549226646722386e+03, 3.0376315094739988e+02,
+  7.4924579607137730e+01, 1.8590543353806009e+01, 4.4423176930919421e+00,
+  8.9541051939952665e-01, 8.9541051939952665e-01, 1.5992942988584680e-01,
+  3.1718756222897104e-02, 3.8586186799894789e-01, 6.9839124768946298e-02};
+
+#+end_src
+
+** TODO Molecular orbitals
 ** Electron coordinates
 
    Electron coordinates are stored in atomic units in normal format.

pkgconfig/qmckl.pc.in

@@ -7,7 +7,7 @@ Name: @PACKAGE_NAME@
 Description: Quantum Monte Carlo kernel library
 URL: https://github.com/trex-coe/qmckl
 Version: @PACKAGE_VERSION@
-Cflags:  -I${includedir} @PKG_CFLAGS@
+Cflags:  -I${includedir}
-Libs: -L${libdir} -lqmckl @PKG_LIBS@
+Libs: -L${libdir} -lqmckl
-Requires: @PKG_BLAS@
+Libs.private: @PKG_LIBS@
 

tools/build_doc.sh

@@ -19,7 +19,7 @@ function extract_doc()
   html=${DOCS}/html/$(basename ${org%.org}.html)
   text=${DOCS}/text/$(basename ${org%.org}.txt)
 
-  ./missing emacs --batch  \
+  ./tools/missing emacs --batch  \
         --load ${HTMLIZE}          \
         --load ${CONFIG_DOC}       \
         ${org}                     \
@@ -34,8 +34,9 @@ function extract_doc()
 for i in $@
 do
     exported=${i%.org}.exported
+    exported=$(dirname $exported)/.$(basename $exported)
     NOW=$(date +"%m%d%H%M.%S")
-    extract_doc ${i} &> $exported
+    extract_doc ${i} > $exported
 
     # Make log file older than the exported files
     touch -t ${NOW} $exported

tools/build_makefile.py

@@ -33,8 +33,8 @@ def main():
 
     for org in glob("org/*.org"):
         i         =  org.split('/')[-1].rsplit(".",1)[0]
-        tangled   =  "org/"+i+".tangled"
+        tangled   =  "org/."+i+".tangled"
-        exported  =  "org/"+i+".exported"
+        exported  =  "org/."+i+".exported"
         c_test_x  =  "tests/test_"+i
         c_test_o  =  "tests/test_"+i+".$(OBJEXT)"
         f_test_o  =  "tests/test_"+i+"_f.$(OBJEXT)"

tools/install_htmlize.sh

@@ -2,7 +2,7 @@
 #
 # Installs the htmlize Emacs plugin
 
-./missing git clone "https://github.com/hniksic/emacs-htmlize"
+./tools/missing git clone "https://github.com/hniksic/emacs-htmlize"
 mv emacs-htmlize/htmlize.el $1
 rm -rf emacs-htmlize
 

tools/tangle.sh

@@ -24,7 +24,7 @@ function tangle()
     elif [[ ${org_file} -ot ${f_file} ]] ; then
         return
     fi
-    ./missing \
+    ./tools/missing \
         emacs --batch ${org_file} \
          --load=${PWD}/tools/config_tangle.el \
         -f org-babel-tangle
@@ -33,8 +33,9 @@ function tangle()
 for i in $@
 do
     tangled=${i%.org}.tangled
+    tangled=$(dirname $tangled)/.$(basename $tangled)
     NOW=$(date +"%m%d%H%M.%S")
-    tangle ${i} &> $tangled
+    tangle ${i} > $tangled
 
     # Make log file older than the tangled files
     touch -t ${NOW} $tangled

tools/theme.setup

@@ -6,7 +6,7 @@
 #+INFOJS_OPT: toc:t mouse:underline path:org-info.js
 #+HTML_HEAD: <link rel="stylesheet" title="Standard" href="qmckl.css" type="text/css" />
 
-#+STARTUP:    align fold nodlcheck hidestars oddeven lognotestate
+#+STARTUP:    align fold nodlcheck hidestars oddeven lognotestate latexpreview
 #+AUTHOR:     TREX CoE
 #+LANGUAGE:   en