Merge branch 'master' into debug_flags

.github/workflows/actions.yml

@@ -71,7 +71,7 @@ jobs:
         run: make -j2
 
       - name: check TREXIO
-        run: make -j1 check  # Non-parallel run 
+        run: make -j2 check
 
       - name: Archive test log file
         if: failure()

python/test/test_api.py

@@ -6,6 +6,62 @@ import trexio
 from benzene_data import *
 
 
+# this function is copied from the trexio-tools github repository (BSD-3 license):
+# https://github.com/TREX-CoE/trexio_tools/blob/master/src/trexio_tools/group_tools/determinant.py
+def to_determinant_list(orbital_list: list, int64_num: int) -> list:
+    """
+    Convert a list of occupied orbitals from the `orbital_list`
+    into a list of Slater determinants (in their bit string representation).
+
+    Orbitals in the `orbital_list` should be 0-based, namely the lowest orbital has index 0, not 1.
+
+    int64_num is the number of 64-bit integers needed to represent a Slater determinant bit string.
+    It depends on the number of molecular orbitals as follows: int64_num = int((mo_num-1)/64) + 1
+    """
+
+    if not isinstance(orbital_list, list):
+        raise TypeError(f"orbital_list should be a list, not {type(orbital_list)}")
+
+    det_list = []
+    bitfield = 0
+    shift    = 0
+
+    # since orbital indices are 0-based but the code below works for 1-based --> increment the input indices by +1
+    orb_list_upshifted = [ orb+1 for orb in orbital_list]
+
+    # orbital list has to be sorted in increasing order for the bitfields to be set correctly
+    orb_list_sorted = sorted(orb_list_upshifted)
+
+    for orb in orb_list_sorted:
+
+        if orb-shift > 64:
+            # this removes the 0 bit from the beginning of the bitfield
+            bitfield = bitfield >> 1
+            # append a bitfield to the list
+            det_list.append(bitfield)
+            bitfield = 0
+
+        modulo = int((orb-1)/64)
+        shift  = modulo*64
+        bitfield |= (1 << (orb-shift))
+
+    # this removes the 0 bit from the beginning of the bitfield
+    bitfield = bitfield >> 1
+    det_list.append(bitfield)
+    #print('Popcounts: ', [bin(d).count('1') for d in det_list)
+    #print('Bitfields: ', [bin(d) for d in det_list])
+
+    bitfield_num = len(det_list)
+    if bitfield_num > int64_num:
+        raise Exception(f'Number of bitfields {bitfield_num} cannot be more than the int64_num {int64_num}.')
+    if bitfield_num < int64_num:
+        for _ in range(int64_num - bitfield_num):
+            print("Appending an empty bitfield.")
+            det_list.append(0)
+
+    return det_list
+
+
 def clean(back_end, filename):
     """Remove test files."""
     if back_end == trexio.TREXIO_HDF5:
@@ -206,16 +262,36 @@ class TestIO:
         """Write CI determinants and coefficients."""
         self.open()
         # write mo_num (needed later to write determinants)
-        trexio.write_mo_num(self.test_file, mo_num)
+        MO_NUM_TEST = 100
+        trexio.write_mo_num(self.test_file, MO_NUM_TEST)
         # get the number of bit-strings per spin component
+        INT64_NUM_TEST = int((MO_NUM_TEST-1)/64) + 1
         int_num = trexio.get_int64_num(self.test_file)
-        assert int_num == int64_num
+        assert int_num == INT64_NUM_TEST
+        # write the number of up and down electrons
+        trexio.write_electron_up_num(self.test_file, 4)
+        trexio.write_electron_dn_num(self.test_file, 3)
+        # orbital lists
+        orb_list_up = [0,1,2,3]
+        orb_list_dn = [0,1,2]
+
+        # data to write
+        DET_NUM_TEST = 100
+        det_up = to_determinant_list(orb_list_up, INT64_NUM_TEST)
+        det_dn = to_determinant_list(orb_list_dn, INT64_NUM_TEST)
+
+        det_list = []
+        coeff_list = []
+        for i in range(DET_NUM_TEST):
+            det_list.append(det_up + det_dn)
+            coeff_list.append(3.14 + float(i))
+
         # write the data for the ground state
         offset = 0
         trexio.write_state_id(self.test_file, 0)
-        trexio.write_determinant_list(self.test_file, offset, det_num, dets)
+        trexio.write_determinant_list(self.test_file, offset, DET_NUM_TEST, det_list)
         assert trexio.has_determinant_list(self.test_file)
-        trexio.write_determinant_coefficient(self.test_file, offset, det_num, coeffs)
+        trexio.write_determinant_coefficient(self.test_file, offset, DET_NUM_TEST, coeff_list)
         assert trexio.has_determinant_coefficient(self.test_file)
         # manually check the consistency between coefficient_size and number of determinants
         assert trexio.read_determinant_coefficient_size(self.test_file) == trexio.read_determinant_num(self.test_file)
@@ -350,26 +426,6 @@ class TestIO:
         if self.test_file.isOpen:
             self.test_file.close()
 
-    def test_determinant_read(self):
-        """Read the CI determinants."""
-        self.open(mode='r')
-        # read determinants (list of ints and float coefficients)
-        buf_size    = 100
-        offset_file = 0
-        # read full buf_size (i.e. the one that does not reach EOF)
-        dets_np, read_buf_size, eof = trexio.read_determinant_list(self.test_file, offset_file, buf_size)
-        #print(f'First complete read of determinant list: {read_buf_size}')
-        assert not eof
-        assert read_buf_size == buf_size
-        assert dets_np[0][0] == 0
-        assert dets_np[read_buf_size-1][int64_num*2-1] == read_buf_size * int64_num * 2- 1
-
-        coefficients_np, read_buf_size, eof = trexio.read_determinant_coefficient(self.test_file, offset_file, buf_size)
-        #print(f'First complete read of determinant coefficients: {read_buf_size}')
-        assert not eof
-        assert read_buf_size == buf_size
-        if self.test_file.isOpen:
-            self.test_file.close()
 
     def test_array_str_read(self):
         """Read an array of strings."""

src/templates_front/templator_front.org

@@ -6379,6 +6379,7 @@ trexio_exit_code trexio_evaluate_nao_radial_all_py (const int32_t shell_num,
       trexio_evaluate_nao_radial_py(shell_index, r, grid_start, n_grid_st, grid_size,
                                     n_grid_si, grid_r, n_grid_r, interpolator, n_interp,
                                     normalization, n_norm, &amplitudes[shell_index]);
+
     if (rc != TREXIO_SUCCESS)
       return rc;
   }

src/templates_text/templator_text.org

@@ -1705,6 +1705,7 @@ trexio_exit_code trexio_text_read_determinant_list(trexio_t* const file,
 
   /* Specify the line length in order to offset properly.
      Each 64-bit integer takes 20 slots and requires one space,
+
      we have int_num integers per up-spin determinant,
      then this number is doubled because we have the same number for down-spin electrons,
      and then one newline char.

tests/io_determinant.c

@@ -108,7 +108,6 @@ static int test_write_determinant (const char* file_name, const back_end_t backe
   // free the allocated memeory
   free(det_list);
   free(det_coef);
-  printf("write determinants OK\n");
 
 /*================= END OF TEST ==================*/
 
@@ -145,7 +144,6 @@ static int test_has_determinant(const char* file_name, const back_end_t backend)
   assert (rc == TREXIO_SUCCESS);
 
 /*================= END OF TEST ==================*/
-  printf("has_determinant OK\n");
 
   return 0;
 }
@@ -340,7 +338,6 @@ int main(){
     assert (rc == 0);
 
   // check the first write attempt (SIZE elements written in N_CHUNKS chunks)
-    printf("mo_num = %d\n", mo_nums[i]);
     test_write_determinant (TREXIO_FILE, TEST_BACKEND, 0L, mo_nums[i]);
     test_has_determinant   (TREXIO_FILE, TEST_BACKEND);
     test_read_determinant  (TREXIO_FILE, TEST_BACKEND, 0L);