Merge branch 'master' into csf

.github/workflows/actions.yml

@@ -52,10 +52,10 @@ jobs:
           ./configure --enable-silent-rules
 
       - name: compile TREXIO
-        run: make -j 2
+        run: make -j2
 
       - name: check TREXIO
-        run: make check
+        run: make -j2 check
 
       - name: create virtual environment
         run: |
@@ -82,8 +82,22 @@ jobs:
           name: pytrexio-source
           path: ./trexio-*.tar.gz
 
-      - name: clean
+      - name: maintainer clean
-        run: make clean
+        run: make maintainer-clean
+
+      - name: reconfigure with clang and AddressSanitizer
+        run: |
+          ./autogen.sh
+          ./configure CC=clang-11 CFLAGS="-O2 -fsanitize=address -fno-omit-frame-pointer" LDFLAGS="-fsanitize=address" --enable-silent-rules
+
+      - name: recompile TREXIO
+        run: make -j2
+
+      - name: recheck TREXIO for memory leaks
+        run: make -j2 check
+
+      - name: maintainer clean
+        run: make maintainer-clean
 
   trexio_macos:
 

ChangeLog

@@ -4,6 +4,7 @@ CHANGES
 2.3
 ---
 
+- Added trexio_to_bitfield_list functionality
 - Added `trexio_has_group` functionality
 - Added OCaml binding
 - Added spin and energy in MOs

Makefile.am

@@ -34,7 +34,11 @@
 
 ACLOCAL_AMFLAGS = -I m4
 CLEANFILES = trexio.mod
+if HAVE_FORTRAN
 BUILT_SOURCES = trexio.mod
+else
+BUILT_SOURCES = 
+endif
 EXTRA_DIST = .git_hash
 
 PACKAGE_VERSION = @PACKAGE_VERSION@
@@ -48,7 +52,10 @@ pkgconfig_DATA = pkgconfig/trexio.pc
 trexio_h = $(srcdir)/include/trexio.h
 trexio_f = $(srcdir)/include/trexio_f.f90
 
-include_HEADERS = $(trexio_h) $(trexio_f)
+include_HEADERS = $(trexio_h) 
+if HAVE_FORTRAN
+include_HEADERS += $(trexio_f)
+endif
 
 AM_CPPFLAGS = -I$(srcdir)/src -I$(srcdir)/include
 
@@ -136,15 +143,19 @@ TESTS_C += \
   tests/overwrite_all_hdf5
 endif
 
+TESTS = $(TESTS_C) 
+if HAVE_FORTRAN
 TESTS_F = \
   tests/test_f
+TESTS += $(TESTS_F)
+endif
 
-TESTS = $(TESTS_C) $(TESTS_F)
 check_PROGRAMS = $(TESTS)
 
 # specify common LDADD options for all tests
 LDADD = src/libtrexio.la
 
+if HAVE_FORTRAN
 test_trexio_f = $(srcdir)/tests/trexio_f.f90
 
 $(test_trexio_f): $(trexio_f)
@@ -153,10 +164,16 @@ $(test_trexio_f): $(trexio_f)
 trexio.mod: tests/trexio_f.o
 
 tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
+endif
 
 clean-local:
 	-rm -rf -- *.dir/ *.h5 __pycache__/
 
+# =============== GUIX MANIFEST =============== #
+
+trexio_scm = $(srcdir)/tools/trexio.scm
+EXTRA_DIST += $(trexio_scm)
+
 # =============== DOCUMENTATION =============== #
 
 HTML_TANGLED = docs/index.html            \

README.md

@@ -77,6 +77,33 @@ conda install trexio -c conda-forge
 More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
 Note that both parallel (see `mpi_openmpi` prefix) and serial (`nompi`) variants are provided.
 
+## Installation procedure for Guix users
+
+The official releases of TREXIO `>=2.0.0` can be installed using the
+[GNU Guix](https://guix.gnu.org) functional package manager.
+The [trexio.scm](https://github.com/TREX-CoE/trexio/blob/master/tools/trexio.scm)
+Schema file contains the manifest specification for the `trexio` package.
+It can be installed within the selected `$GUIX_PROFILE` as follows:
+
+```
+guix package \
+	--profile=$GUIX_PROFILE \
+	--cores=<n_cores> \
+	--install-from-file=trexio.scm
+```
+
+## Installation procedure for Spack users
+
+The official releases `>=2.0.0` and the development version of TREXIO can be installed using the
+[Spack](https://spack.io/) package manager.
+The [trexio/package.py](https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/trexio/package.py)
+file contains the Spack specifications required to build different variants of `trexio` library.
+It can be installed as follows
+
+```
+spack install --jobs <n_cores> trexio
+```
+
 ## Compilation without the HDF5 library
 
 By default, the configuration step proceeds to search for the [HDF5 library](https://portal.hdfgroup.org/display/HDF5/HDF5).

configure.ac

@@ -19,8 +19,8 @@ LT_INIT
 # Activate developer mode when the source is the git repository.
 # Otherwise, it is the source distribution and the developer mode should not be activated.
 TEST_IFEXISTS=".git"
-AC_CHECK_FILE([$TEST_IFEXISTS],
+AS_IF([test -d $TEST_IFEXISTS],
-        [enable_maintainer_mode="yes"],
+        [enable_maintainer_mode="yes"]
 )
 
 VERSION_MAJOR=`echo ${PACKAGE_VERSION} | cut -d. -f1`
@@ -50,12 +50,18 @@ AS_IF([test "$ac_cv_prog_cc_c99" = "no"],
       [AC_MSG_ERROR([The compiler does not support C99])])
 AC_PROG_CC_C_O
 
-# Fortran
+
-AC_PROG_FC
+# Fortran API [default: --with-fortran], do not disable in the dev mode
-AC_FC_FREEFORM
+AC_ARG_WITH(fortran, [AS_HELP_STRING([--without-fortran],[do not test and install the Fortran API])], ok=$withval, ok=yes)
-AC_FC_SRCEXT([f90])
+if test "$ok" = "yes"; then
-AC_PROG_FC_C_O
+        AC_PROG_FC
-AC_FC_LIBRARY_LDFLAGS
+        AC_FC_FREEFORM
+        AC_FC_SRCEXT([f90])
+        AC_PROG_FC_C_O
+        AC_FC_LIBRARY_LDFLAGS
+fi
+
+AM_CONDITIONAL([HAVE_FORTRAN],[test "$ok" = "yes"])
 
 # pkg-config
 PKG_PROG_PKG_CONFIG()
@@ -66,6 +72,31 @@ AC_PROG_INSTALL
 AC_PROG_LN_S
 AC_PROG_GREP
 
+# Specific options required with some compilers
+case $FC in
+ *gfortran*)
+      FCFLAGS="$FCFLAGS -fPIC"
+      ;;
+ *flang*)
+      FCFLAGS="$FCFLAGS -fPIC"
+      ;;
+ *ifort*)
+      FCFLAGS="$FCFLAGS -fPIC"
+      ;;
+esac
+
+case $CC in
+  *gcc*)
+        CFLAGS="$CFLAGS -fPIC"
+        ;;
+  *clang*)
+        CFLAGS="$CFLAGS -fPIC"
+        ;;
+  *icc*)
+        CFLAGS="$CFLAGS -fPIC"
+        ;;
+esac
+
 
 ## ---------
 ## Libraries
@@ -138,7 +169,7 @@ AC_TYPE_UINT32_T
 AC_TYPE_UINT64_T
 
 # Checks for library functions.
-AC_FUNC_MALLOC
+# AC_FUNC_MALLOC
 AC_CHECK_FUNCS([memset mkdir strerror])
 
 if test "x$enable_maintainer_mode" == "xyes"; then

m4/ax_lib_hdf5.m4

@@ -257,7 +257,7 @@ HDF5 support is being disabled (equivalent to --with-hdf5=no).
           AC_MSG_WARN([Unable to compile HDF5 test program])
         fi
         dnl Look for HDF5's high level library
-        AC_HAVE_LIBRARY([hdf5_hl], [HDF5_LIBS="-lhdf5_hl $HDF5_LIBS"], [], [])
+        AC_CHECK_LIB([hdf5_hl], [main],[HDF5_LIBS="-lhdf5_hl $HDF5_LIBS"], [], [])
 
         CC=$ax_lib_hdf5_save_CC
         CPPFLAGS=$ax_lib_hdf5_save_CPPFLAGS

python/setup.py

@@ -94,6 +94,7 @@ pytrexio_module = Extension('pytrexio._pytrexio',
                             include_dirs = [h5_cflags, srcpath, numpy_includedir],
                             libraries = ['hdf5', 'hdf5_hl'],
                             extra_compile_args = [
+                                '-std=c99',
                                 '-Wno-discarded-qualifiers',
                                 '-Wno-unused-variable',
                                 '-Wno-unused-but-set-variable'

python/test/benzene_data.py

@@ -43,4 +43,7 @@ dets      = [i for i in range(det_num * int64_num * 2)]
 coeffs    = [float(i/det_num)   for i in range(det_num)]
 coeffs_s2 = [float(i*2/det_num) for i in range(det_num)]
 
-det_test  = [1, 2, 3, 2, 1, 3]
+det_test  = [1, 2, 3, 2, 1, 3]
+
+orb_up_test = [0, 65, 128, 129]
+orb_dn_test = [1, 64, 128, 129]

python/test/test_api.py

@@ -39,6 +39,17 @@ def test_orbital_list():
     assert orb_list_dn[0] == 1
 
 
+def test_bitfield_list():
+    """Convert lists of occupied up- and down-spin orbitals into determinants."""
+    # convert det_test list into a numpy array for .all() assertion to work
+    det_test_np = np.array(det_test, dtype=np.int64)
+
+    det_list_up = trexio.to_bitfield_list(int64_num, orb_up_test)
+    assert (det_list_up == det_test_np[:int64_num]).all()
+    det_list_dn = trexio.to_bitfield_list(int64_num, orb_dn_test)
+    assert (det_list_dn == det_test_np[int64_num:]).all()
+
+
 class TestIO:
     """Unit tests for writing/reading different blocks of the TREXIO file."""
 

src/pytrexio.i

@@ -104,6 +104,9 @@ import_array();
 %apply (int64_t* ARGOUT_ARRAY1, int64_t DIM1) {(int64_t* const dset_up_out, const int64_t dim_up_out)};
 %apply (int64_t* ARGOUT_ARRAY1, int64_t DIM1) {(int64_t* const dset_dn_out, const int64_t dim_dn_out)};
 %apply (bitfield_t* IN_ARRAY1, int64_t DIM1) {(const bitfield_t* dset_in, const int64_t dim_in)};
+%apply (int32_t* IN_ARRAY1, int32_t DIM1) {(const int32_t* orb_list, const int32_t occupied_num)};
+/* For some reasons SWIG does not apply the proper bitfield_t typemap, so one has to manually specify int64_t* ARGOUT_ARRAY1 below */
+%apply (int64_t* ARGOUT_ARRAY1, int32_t DIM1) {(bitfield_t* const bit_list, const int32_t N_int)};
 
 /* This tells SWIG to treat char ** dset_in pattern as a special case
    Enables access to trexio_[...]_write_dset_str set of functions directly, i.e.

src/templates_front/templator_front.org

@@ -5281,6 +5281,9 @@ def has_determinant_coefficient(trexio_file) -> bool:
  ~trexio_to_orbital_list_up_dn~ function does the same but for both up- and down-spin components
   of the determinant and returns two list of orbitals each corresponding to a different component.
 
+ ~trexio_to_bitfield_list~ function converts the list of occupied orbitals (up- or down-spin)
+  into the corresponding ~int64_t~ bitfield representation of the determinant.
+
 ** C
 
      #+begin_src c :tangle prefix_front.h
@@ -5289,16 +5292,50 @@ trexio_exit_code trexio_mark_safety(trexio_t* const file, const int32_t safety_f
 
 typedef int64_t  bitfield_t;
 
-#define TREXIO_ORBITAL_SHIFT  1
+#define TREXIO_ORBITAL_SHIFT      1
-#define TREXIO_INT_SIZE       64
+#define TREXIO_INT_SIZE           64
-#define TREXIO_NORB_PER_INT   ( 8*sizeof(bitfield_t) )
+#define TREXIO_NORB_PER_INT       ( 8*sizeof(bitfield_t) )
-#
+#define TREXIO_NORB_PER_INT_SHIFT ( trailz( TREXIO_NORB_PER_INT ) )
+
 trexio_exit_code trexio_to_orbital_list (const int32_t N_int, const bitfield_t* d1, int32_t* const list, int32_t* const occupied_num);
 trexio_exit_code trexio_to_orbital_list_up_dn (const int32_t N_int, const bitfield_t* d1, int32_t* const list_up, int32_t* const list_dn, int32_t* const occ_num_up, int32_t* const occ_num_dn);
 trexio_exit_code trexio_safe_to_orbital_list (const int32_t N_int, const bitfield_t* dset_in, const int64_t dim_in, int32_t* const dset_out, const int64_t dim_out, int32_t* const num);
 trexio_exit_code trexio_safe_to_orbital_list_up_dn (const int32_t N_int, const bitfield_t* dset_in, const int64_t dim_in, int32_t* const dset_up_out, const int64_t dim_up_out, int32_t* const dset_dn_out, const int64_t dim_dn_out, int32_t* const num_up, int32_t* const num_dn);
+trexio_exit_code trexio_to_bitfield_list (const int32_t* orb_list, const int32_t occupied_num, bitfield_t* const bit_list, const int32_t N_int);
      #+end_src
 
+
+    #+begin_src c :tangle prefix_front.c
+trexio_exit_code trexio_to_bitfield_list (const int32_t* orb_list,
+                                          const int32_t occupied_num,
+                                          bitfield_t* const bit_list,
+                                          const int32_t N_int)
+{
+  if (orb_list == NULL)  return TREXIO_INVALID_ARG_1;
+  if (occupied_num <= 0) return TREXIO_INVALID_ARG_2;
+  if (bit_list == NULL)  return TREXIO_INVALID_ARG_3;
+  if (N_int <= 0)        return TREXIO_INVALID_ARG_4;
+
+  uint32_t i;
+  uint32_t k;
+  uint32_t iorb;
+
+  for (int32_t j = 0 ; j < N_int ; j++) {
+      bit_list[j] = (bitfield_t) 0;
+  }
+
+  for (int32_t pos = 0 ; pos < occupied_num ; pos++) {
+    iorb = ((uint32_t) (orb_list[pos] + 1)) - TREXIO_ORBITAL_SHIFT;
+    i = (uint32_t) (iorb >> TREXIO_NORB_PER_INT_SHIFT);
+    k = (uint32_t) (iorb & (TREXIO_NORB_PER_INT - 1) );
+    bit_list[i] |= ((bitfield_t) 1) << k;
+  }
+
+  return TREXIO_SUCCESS;
+}
+    #+end_src
+
+
      #+begin_src c :tangle prefix_front.c
 trexio_exit_code trexio_to_orbital_list(const int32_t N_int,
                                         const bitfield_t* d1,
@@ -5478,10 +5515,24 @@ interface
 end interface
    #+end_src
 
+   #+begin_src f90 :tangle prefix_fortran.f90
+interface
+   integer(trexio_exit_code) function trexio_to_bitfield_list_c(list, occupied_num, det_list, N_int) &
+   bind(C, name="trexio_to_bitfield_list")
+     use, intrinsic :: iso_c_binding
+     import
+     integer(c_int32_t), intent(in)        :: list(*)
+     integer(c_int32_t), intent(in), value :: occupied_num
+     integer(c_int64_t), intent(inout)     :: det_list(*)
+     integer(c_int32_t), intent(in), value :: N_int
+   end function trexio_to_bitfield_list_c
+end interface
+   #+end_src
 
    #+begin_src f90 :tangle prefix_fortran.f90
 interface
-   integer(trexio_exit_code) function trexio_to_orbital_list_c(N_int, d1, list, occupied_num) bind(C, name="trexio_to_orbital_list")
+   integer(trexio_exit_code) function trexio_to_orbital_list_c(N_int, d1, list, occupied_num) &
+   bind(C, name="trexio_to_orbital_list")
      use, intrinsic :: iso_c_binding
      import
      integer(c_int32_t), intent(in), value :: N_int
@@ -5520,6 +5571,33 @@ def info():
    #+end_src
 
 
+   #+begin_src python :tangle basic_python.py
+def to_bitfield_list(n_int: int, orbitals: list) -> list:
+    """Convert a list of occupied orbitals into a bitfield determinant.
+
+    Input:
+ ~orbitals~ - list of occupied orbital indices fields (integers)
+ ~n_int~ - number of bitfields per determinant of a given spin
+
+    Returns:
+ ~bitfield_list~: list
+
+    Raises:
+        - Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
+        - Exception from some other error (e.g. RuntimeError).
+    """
+
+
+    rc, bitfield_list = pytr.trexio_to_bitfield_list(orbitals, n_int)
+    if rc != TREXIO_SUCCESS:
+        raise Error(rc)
+    if len(bitfield_list) != n_int:
+        raise Exception("Inconsistent size of the bitfield_list.")
+
+    return bitfield_list
+   #+end_src
+
+
    #+begin_src python :tangle basic_python.py
 def to_orbital_list(n_int: int, determinant: list) -> list:
     """Convert a given determinant into a list of occupied orbitals.
@@ -5546,8 +5624,10 @@ def to_orbital_list(n_int: int, determinant: list) -> list:
         raise Exception("Inconsistent size of the orbital_list.")
 
     return orbital_list[0:occ_num]
+   #+end_src
 
 
+   #+begin_src python :tangle basic_python.py
 def to_orbital_list_up_dn(n_int: int, determinant: list) -> tuple:
     """Convert a given determinant into two lists of occupied orbitals.
 
@@ -5631,6 +5711,29 @@ contains
   by 1 since in Fortran arrays are 1-based and C/Python they are 0-based.
 
   #+begin_src f90 :tangle helper_fortran.f90
+   integer(trexio_exit_code) function trexio_to_bitfield_list(list, occupied_num, det_list, N_int)
+     use, intrinsic :: iso_c_binding
+     implicit none
+
+     integer(c_int32_t), intent(in)        :: list(*)
+     integer(c_int32_t), intent(in), value :: occupied_num
+     integer(c_int64_t), intent(out)       :: det_list(*)
+     integer(c_int32_t), intent(in), value :: N_int
+     integer(c_int32_t)                    :: list_0based(occupied_num)
+
+     integer :: i
+     do i = 1,occupied_num
+       list_0based(i) = list(i) - 1
+     enddo
+
+     trexio_to_bitfield_list = trexio_to_bitfield_list_c(list_0based, occupied_num, det_list, N_int)
+     if (trexio_to_bitfield_list /= TREXIO_SUCCESS) then
+       return
+     endif
+
+   end function trexio_to_bitfield_list
+
+
    integer(trexio_exit_code) function trexio_to_orbital_list(N_int, d1, list, occupied_num)
      use, intrinsic :: iso_c_binding
      implicit none

src/templates_text/templator_text.org

@@ -143,7 +143,15 @@ trexio_text_inquire (const char* file_name)
 
   if (file_exists) {
 
-    bool is_a_directory = st.st_mode & S_IFDIR;
+    bool is_a_directory = false;
+#ifdef S_IFDIR
+    is_a_directory = st.st_mode & S_IFDIR;
+#elif S_ISDIR
+    is_a_directory = S_ISDIR(s.st_mode);
+#else
+    printf("Some important macros are missing for directory handling.\n");
+    return TREXIO_FAILURE;
+#endif
     if (!is_a_directory) return TREXIO_FILE_ERROR;
 
     return TREXIO_SUCCESS;
@@ -420,13 +428,14 @@ trexio_text_read_$group$ (trexio_text_t* const file)
             /* conventional fcanf with "%s" only return the string before the first space character
              * to read string with spaces use "%[^\n]" possible with space before or after, i.e. " %[^\n]"
              */
-            rc = fscanf(f, " %1023[^\n]", tmp_$group_dset$);
+            rc = fscanf(f, " %1023[^\n]", buffer);
             if (rc != 1) {
               trexio_text_free_read_$group$(buffer, f, file, $group$);
               return NULL;
             }
 
-            size_t tmp_$group_dset$_len = strlen($group$->$group_dset$[i]);
+            size_t tmp_$group_dset$_len = strlen(buffer);
+            strncpy(tmp_$group_dset$, buffer, 32);
             tmp_$group_dset$ += tmp_$group_dset$_len + 1;
           }
         }
@@ -484,14 +493,15 @@ trexio_text_read_$group$ (trexio_text_t* const file)
             return NULL;
           }
 
-          rc = fscanf(f, " %1023[^\n]", $group$->$group_str$);
+          rc = fscanf(f, " %1023[^\n]", buffer);
           if (rc != 1) {
             trexio_text_free_read_$group$(buffer, f, file, $group$);
             return NULL;
           }
+ /* Safer string conversion to avoid buffer overflow in fscanf */
+          strncpy($group$->$group_str$, buffer, $group$->len_$group_str$);
 
         }
-
       // END REPEAT GROUP_ATTR_STR
       } else {
         continue;

tests/io_determinant_hdf5.c

@@ -307,6 +307,14 @@ static int test_read_determinant (const char* file_name, const back_end_t backen
   printf("\n");
   */
 
+  // check conversion of one orbital list into the bitfield determinant representation
+  int64_t* det_list_check = (int64_t*) calloc(int_num, sizeof(int64_t));
+
+  rc = trexio_to_bitfield_list (orb_list_up, occ_num_up, det_list_check, int_num);
+  assert (rc == TREXIO_SUCCESS);
+  for (int i=0; i<int_num; i++) {
+    assert (det_list_check[i] == det_list_read[2*int_num*5+i]);
+  }
 
   // close current session
   rc = trexio_close(file);
@@ -316,6 +324,7 @@ static int test_read_determinant (const char* file_name, const back_end_t backen
   free(det_list_read);
   free(det_coef_read);
   free(det_coef_s2_read);
+  free(det_list_check);
   free(orb_list_up);
   free(orb_list_dn);
 

tests/io_determinant_text.c

@@ -307,6 +307,14 @@ static int test_read_determinant (const char* file_name, const back_end_t backen
   printf("\n");
   */
 
+  // check conversion of one orbital list into the bitfield determinant representation
+  int64_t* det_list_check = (int64_t*) calloc(int_num, sizeof(int64_t));
+
+  rc = trexio_to_bitfield_list (orb_list_up, occ_num_up, det_list_check, int_num);
+  assert (rc == TREXIO_SUCCESS);
+  for (int i=0; i<int_num; i++) {
+    assert (det_list_check[i] == det_list_read[2*int_num*5+i]);
+  }
 
   // close current session
   rc = trexio_close(file);
@@ -316,6 +324,7 @@ static int test_read_determinant (const char* file_name, const back_end_t backen
   free(det_list_read);
   free(det_coef_read);
   free(det_coef_s2_read);
+  free(det_list_check);
   free(orb_list_up);
   free(orb_list_dn);
 

tests/test_f.f90

@@ -6,11 +6,11 @@ program test_trexio
   integer :: rc
   logical :: have_hdf5
 
-  print *      , "============================================"
+  print'(a)'   , "============================================"
   print'(a,a)' , "         TREXIO VERSION STRING : ", TREXIO_PACKAGE_VERSION
   print'(a,i3)', "         TREXIO MAJOR VERSION  : ", TREXIO_VERSION_MAJOR
   print'(a,i3)', "         TREXIO MINOR VERSION  : ", TREXIO_VERSION_MINOR
-  print *      , "============================================"
+  print'(a)'   , "============================================"
 
   rc = trexio_info()
 
@@ -288,6 +288,7 @@ subroutine test_read(file_name, back_end)
 
   ! determinant data
   integer*8 :: det_list(6,50)
+  integer*8 :: det_list_check(3)
   integer*8 :: read_buf_det_size = 20
   integer*8 :: offset_det_read = 10
   integer*8 :: offset_det_data_read = 5
@@ -349,9 +350,11 @@ subroutine test_read(file_name, back_end)
   endif
 
 
-  rc = trexio_read_nucleus_label(trex_file, label, 2)
+  rc = trexio_read_nucleus_label(trex_file, label, 4)
   call trexio_assert(rc, TREXIO_SUCCESS)
-  if (trim(label(2)) == 'Na') then
+  if (trim(label(2)) == 'Na'   .and. &
+      trim(label(4)) == 'C 66' .and. &
+      trim(label(5)) == 'C')   then
     write(*,*) 'SUCCESS READ LABEL'
   else
     print *, 'FAILURE LABEL CHECK'
@@ -477,6 +480,26 @@ subroutine test_read(file_name, back_end)
     call exit(-1)
   endif
 
+  ! convert one orbital list into a bitfield determinant representation
+  rc = trexio_to_bitfield_list(orb_list_up, occ_num_up, det_list_check, 3)
+  !write(*,*) occ_num_up, occ_num_dn
+  ! Print occupied orbitals for an up-spin component of a given determinant
+  !write(*,*) orb_list_up(1:occ_num_up)
+  ! Print integers representanting a given determinant fully (up- and down-spin components)
+  !write(*,*) det_list(1:3, offset_det_data_read+1)
+  !write(*,*) det_list_check(1:3)
+  ! Print binary representation of the first integer bit field of a given determinant
+  !write(*,'(B64.64)') det_list(1, offset_det_data_read+1)
+  call trexio_assert(rc, TREXIO_SUCCESS)
+  if (det_list_check(1) == det_list(1, offset_det_data_read+1) .and. &
+      det_list_check(2) == det_list(2, offset_det_data_read+1) .and. &
+      det_list_check(3) == det_list(3, offset_det_data_read+1)) then
+    write(*,*) 'SUCCESS CONVERT ORB LIST'
+  else
+    print *, 'FAILURE ORB CONVERT CHECK'
+    call exit(-1)
+  endif
+
   rc = trexio_read_mo_num(trex_file, mo_num)
   call trexio_assert(rc, TREXIO_SUCCESS)
 

tools/trexio.scm

@@ -1,15 +1,15 @@
-(define-module (gnu packages trexio)
+(define-module (trexio)
   #:use-module (guix packages)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages autotools)
-  #:use-module (gnu packages maths)
+  #:use-module (gnu packages maths)  ;; contains hdf5
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
   #:use-module (guix licenses))
 
-(define-public trexio
+(define-public trexio-2.0
   (package
     (name "trexio")
     (version "2.0")
@@ -20,15 +20,48 @@
                                   ".tar.gz"))
               (sha256
                (base32
+		;; the hash below is produced by guix download <url>
 		"1d2cn4w2r9gfid5b9wrq9q290kqdnbjdmvli76s1i5r58kdg5vkf"
                 ))))
     (build-system gnu-build-system)
     (arguments '(#:configure-flags '("--enable-silent-rules")))
-    (inputs `(("hdf5" ,hdf5-1.12) ("gfortran", gfortran)))
+    (inputs `(("hdf5" ,hdf5) ("gfortran", gfortran)))
-    (synopsis "TREX I/O lbrary: trexio package")
+    (synopsis "TREX I/O library")
-    (description "APIs in C and Fortran to exchange wavefunction data.
+    (description "The TREXIO library defines a standard format for storing wave functions, together with
-		  Supports HDF5 and TEXT back ends.")
+		 an C-compatible API such that it can be easily used in any programming language.")
     (home-page "https://trex-coe.github.io/trexio")
     (license bsd-3)))
 
+(define-public trexio-2.1
+  (package/inherit trexio-2.0
+    (version "2.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/TREX-CoE/trexio/releases/download/v" version
+				  "/trexio-" version
+                                  ".tar.gz"))
+              (sha256
+               (base32
+		;; the hash below is produced by guix download <url>
+		"10syfw4mq3wpp9anahmxnm7660bm1ya5xd9l5njai3xr8g4nca13"
+                ))))))
+
+(define-public trexio-2.2
+  (package/inherit trexio-2.0
+    (version "2.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/TREX-CoE/trexio/releases/download/v" version
+				  "/trexio-" version
+                                  ".tar.gz"))
+              (sha256
+               (base32
+		;; the hash below is produced by guix download <url>
+		"1n9n1gbk5hgvg73am991xrv7ap002rz719a3nvh8m8ff9x10qd76"
+                ))))))
+
+(define-public trexio
+  ;; Default version of TREXIO.
+  trexio-2.2)
+
 trexio