diff --git a/python/test/test_api.py b/python/test/test_api.py index 543eb3d..b1ea2df 100644 --- a/python/test/test_api.py +++ b/python/test/test_api.py @@ -67,7 +67,7 @@ charges = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.] #charges_np = np.array(charges, dtype=np.float32) charges_np = np.array(charges, dtype=np.int32) -# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived +# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived # from the size of the list/array by SWIG using typemaps from numpy.i trexio.write_nucleus_charge(test_file, charges_np) @@ -80,7 +80,7 @@ indices_np = np.array(indices, dtype=np.int64) # first write basis_shell_num because it is needed to check dimensions of basis_nucleus_index in TREXIO >= 2.0.0 trexio.write_basis_shell_num(test_file, basis_shell_num) -# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived +# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived # from the size of the list/array by SWIG using typemacs from numpy.i trexio.write_basis_nucleus_index(test_file, indices_np) @@ -103,11 +103,25 @@ coords = [ # write coordinates in the file trexio.write_nucleus_coord(test_file, coords) -point_group = 'B3U' + +# write mo_num (needed later to write sparse mo_2e_int_eri integrals) +trexio.write_mo_num(test_file, 600) + +# write sparse data in the file +num_integrals = 100 +indices = [i for i in range(num_integrals*4)] +values = [(3.14 + float(i)) for i in range(num_integrals)] + +trexio.write_mo_2e_int_eri(test_file, 0, num_integrals, indices, values) + # write nucleus_point_group in the file +point_group = 'B3U' + trexio.write_nucleus_point_group(test_file, point_group) + +# write nucleus_label in the file labels = [ 'C', 'C', @@ -122,14 +136,13 @@ labels = [ 'H', 'H'] -# write nucleus_label in the file trexio.write_nucleus_label(test_file,labels) -# close TREXIO file +# close TREXIO file # this call is no longer needed as we introduced TREXIO_File class which has a desctructor that closes the file #trexio.close(test_file) -# without calling destructor on test_file the TREXIO_FILE is not getting created and the data is not written when using TEXT back end. -# This, the user still has to explicitly call destructor on test_file object instead of the trexio.close function. +# without calling destructor on test_file the TREXIO_FILE is not getting created and the data is not written when using TEXT back end. +# This, the user still has to explicitly call destructor on test_file object instead of the trexio.close function. # This is only an issue when the data is getting written and read in the same session (e.g. in Jupyter notebook) del test_file @@ -147,6 +160,7 @@ assert trexio.has_nucleus_charge assert trexio.has_nucleus_coord assert trexio.has_nucleus_label assert trexio.has_nucleus_point_group +assert trexio.has_mo_2e_int_eri # read nucleus_num from file rnum = trexio.read_nucleus_num(test_file2) @@ -189,6 +203,33 @@ np.testing.assert_array_almost_equal(rcoords_np, np.array(coords).reshape(nucleu # set doReshape to False to get a flat 1D array (e.g. when reading matrices like nuclear coordinates) #rcoords_reshaped_2 = trexio.read_nucleus_coord(test_file2, doReshape=False) +# read number of integrals already present in the file +assert trexio.has_mo_2e_int_eri(test_file2) +assert trexio.read_mo_2e_int_eri_size(test_file2)==num_integrals + +# read sparse arrays on mo_2e_int_eri integrals +buf_size = 60 +offset_file = 0 +# read full buf_size (i.e. the one that does not reach EOF) +indices_sparse_np, value_sparse_np, read_buf_size, eof = trexio.read_mo_2e_int_eri(test_file2, offset_file, buf_size) +print(f'First complete sparse read size: {read_buf_size}') +#print(indices_sparse_np) +assert not eof +assert read_buf_size==buf_size +assert indices_sparse_np[0][0]==0 +assert indices_sparse_np[read_buf_size-1][3]==read_buf_size*4-1 +offset_file += buf_size + +# read incomplete buf_size (i.e. the one that does reach EOF) +indices_sparse_np, value_sparse_np, read_buf_size, eof2 = trexio.read_mo_2e_int_eri(test_file2, offset_file, buf_size) +print(f'Second incomplete sparse read size: {read_buf_size}') +#print(indices_sparse_np) +assert eof2 +assert read_buf_size==(num_integrals - buf_size) +assert indices_sparse_np[0][0]==offset_file*4 +assert indices_sparse_np[read_buf_size-1][3]==(offset_file+read_buf_size)*4-1 + + # read array of nuclear labels rlabels_2d = trexio.read_nucleus_label(test_file2, dim=nucleus_num) print(rlabels_2d) @@ -197,13 +238,13 @@ for i in range(nucleus_num): # read a string corresponding to nuclear point group rpoint_group = trexio.read_nucleus_point_group(test_file2) -assert rpoint_group==point_group +assert rpoint_group==point_group # another way to read only if the variable exists -if trexio.has_mo_num(test_file2): - rmo_num = trexio.read_mo_num(test_file2) +if trexio.has_ao_num(test_file2): + rmo_num = trexio.read_ao_num(test_file2) else: - print("Pass on reading the non-existing variable mo_num: checked") + print("Pass on reading the non-existing variable ao_num: checked") # close TREXIO file #trexio.close(test_file2)