symfc 1.3.2__tar.gz → 1.3.3__tar.gz

{symfc-1.3.2/src/symfc.egg-info → symfc-1.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: symfc
-Version: 1.3.2
+Version: 1.3.3
 Summary: This is the symfc module.
 Author-email: Atsuto Seko <seko@cms.mtl.kyoto-u.ac.jp>
 Maintainer-email: Atsushi Togo <atztogo@gmail.com>

{symfc-1.3.2 → symfc-1.3.3}/src/symfc/utils/matrix_tools_O2.py

@@ -103,7 +103,7 @@ def optimize_batch_size_sum_rules_O2(natom: int, n_batch: Optional[int] = None):
     return batch_size
 
 
-def compressed_projector_sum_rules_O2_index_atoms(
+def compressed_projector_sum_rules_O2(
     trans_perms: np.ndarray,
     n_a_compress_mat: csr_array,
     atomic_decompr_idx: Optional[np.ndarray] = None,
@@ -135,14 +135,15 @@ def compressed_projector_sum_rules_O2_index_atoms(
         atomic_decompr_idx = _get_atomic_lat_trans_decompr_indices(trans_perms)
 
     decompr_idx = atomic_decompr_idx.reshape((natom, natom)).T.reshape(-1) * 9
-    if fc_cutoff is None:
-        indep_atoms = get_indep_atoms_by_lat_trans(trans_perms)
-        nonzero = np.zeros((natom, natom), dtype=bool)
-        nonzero[indep_atoms, :] = True
-        nonzero = nonzero.reshape(-1)
-    else:
-        nonzero = fc_cutoff.nonzero_atomic_indices_fc2()
-        nonzero = nonzero.reshape((natom, natom)).T.reshape(-1)
+
+    indep_atoms = get_indep_atoms_by_lat_trans(trans_perms)
+    nonzero = np.zeros((natom, natom), dtype=bool)
+    nonzero[indep_atoms, :] = True
+    nonzero = nonzero.reshape(-1)
+    if fc_cutoff is not None:
+        nonzero_c = fc_cutoff.nonzero_atomic_indices_fc2()
+        nonzero_c = nonzero_c.reshape((natom, natom)).T.reshape(-1)
+        nonzero = nonzero & nonzero_c
 
     batch_size = optimize_batch_size_sum_rules_O2(natom, n_batch=n_batch)
     ab = np.arange(9)
@@ -171,11 +172,11 @@ def compressed_projector_sum_rules_O2_index_atoms(
         c_sum_cplmt = dot_product_sparse(c_sum_cplmt, n_a_compress_mat, use_mkl=use_mkl)
         proj_cplmt += dot_product_sparse(c_sum_cplmt.T, c_sum_cplmt, use_mkl=use_mkl)
 
-    proj_cplmt /= n_lp * natom
+    proj_cplmt /= natom
     return scipy.sparse.identity(proj_cplmt.shape[0]) - proj_cplmt
 
 
-def compressed_projector_sum_rules_O2(
+def compressed_projector_sum_rules_O2_stable(
     trans_perms: np.ndarray,
     n_a_compress_mat: csr_array,
     atomic_decompr_idx: Optional[np.ndarray] = None,

{symfc-1.3.2 → symfc-1.3.3}/src/symfc/utils/matrix_tools_O3.py

@@ -308,7 +308,7 @@ def optimize_batch_size_sum_rules_O3(natom: int, n_batch: Optional[int] = None):
     return batch_size
 
 
-def compressed_projector_sum_rules_O3_indep_atoms(
+def compressed_projector_sum_rules_O3(
     trans_perms: np.ndarray,
     n_a_compress_mat: csr_array,
     atomic_decompr_idx: Optional[np.ndarray] = None,
@@ -343,14 +343,14 @@ def compressed_projector_sum_rules_O3_indep_atoms(
 
     decompr_idx = atomic_decompr_idx.reshape((natom, NN)).T.reshape(-1) * 27
 
-    if fc_cutoff is None:
-        indep_atoms = get_indep_atoms_by_lat_trans(trans_perms)
-        nonzero = np.zeros((natom, natom, natom), dtype=bool)
-        nonzero[indep_atoms, :, :] = True
-        nonzero = nonzero.reshape(-1)
-    else:
-        nonzero = fc_cutoff.nonzero_atomic_indices_fc3()
-        nonzero = nonzero.reshape((natom, NN)).T.reshape(-1)
+    indep_atoms = get_indep_atoms_by_lat_trans(trans_perms)
+    nonzero = np.zeros((natom, natom, natom), dtype=bool)
+    nonzero[indep_atoms, :, :] = True
+    nonzero = nonzero.reshape(-1)
+    if fc_cutoff is not None:
+        nonzero_c = fc_cutoff.nonzero_atomic_indices_fc3()
+        nonzero_c = nonzero_c.reshape((natom, NN)).T.reshape(-1)
+        nonzero = nonzero & nonzero_c
 
     batch_size = optimize_batch_size_sum_rules_O3(natom, n_batch=n_batch)
     abc = np.arange(27)
@@ -381,11 +381,11 @@ def compressed_projector_sum_rules_O3_indep_atoms(
         c_sum_cplmt = dot_product_sparse(c_sum_cplmt, n_a_compress_mat, use_mkl=use_mkl)
         proj_cplmt += dot_product_sparse(c_sum_cplmt.T, c_sum_cplmt, use_mkl=use_mkl)
 
-    proj_cplmt /= n_lp * natom
+    proj_cplmt /= natom
     return scipy.sparse.identity(proj_cplmt.shape[0]) - proj_cplmt
 
 
-def compressed_projector_sum_rules_O3(
+def compressed_projector_sum_rules_O3_stable(
     trans_perms: np.ndarray,
     n_a_compress_mat: csr_array,
     atomic_decompr_idx: Optional[np.ndarray] = None,

{symfc-1.3.2 → symfc-1.3.3}/src/symfc/utils/matrix_tools_O4.py

@@ -255,7 +255,7 @@ def optimize_batch_size_sum_rules_O4(natom: int, n_batch: Optional[int] = None):
     return batch_size
 
 
-def compressed_projector_sum_rules_O4_indep_atoms(
+def compressed_projector_sum_rules_O4(
     trans_perms: np.ndarray,
     n_a_compress_mat: csr_array,
     atomic_decompr_idx: Optional[np.ndarray] = None,
@@ -269,7 +269,7 @@ def compressed_projector_sum_rules_O4_indep_atoms(
     Calculate a complementary projector for sum rules.
     This is compressed by C_trans and n_a_compress_mat without
     allocating C_trans.
-    Memory efficient version using get_atomic_lat_trans_decompr_indices_O3.
+    Memory efficient version using get_atomic_lat_trans_decompr_indices_O4.
 
     Return
     ------
@@ -289,42 +289,47 @@ def compressed_projector_sum_rules_O4_indep_atoms(
         atomic_decompr_idx = get_atomic_lat_trans_decompr_indices_O4(trans_perms)
 
     decompr_idx = atomic_decompr_idx.reshape((natom, NNN)).T.reshape(-1) * 81
-
-    if fc_cutoff is None:
-        indep_atoms = get_indep_atoms_by_lat_trans(trans_perms)
-        nonzero = np.zeros((natom, natom, natom, natom), dtype=bool)
-        nonzero[indep_atoms, :, :, :] = True
-        nonzero = nonzero.reshape(-1)
-    else:
+    if fc_cutoff is not None:
         nonzero = fc_cutoff.nonzero_atomic_indices_fc4()
         nonzero = nonzero.reshape((natom, NNN)).T.reshape(-1)
 
     batch_size = optimize_batch_size_sum_rules_O4(natom, n_batch=n_batch)
     abcd = np.arange(81)
     for begin, end in zip(*get_batch_slice(NNNN, batch_size)):
+        if verbose:
+            print("Complementary P (Sum rule):", str(end) + "/" + str(NNNN), flush=True)
         size = end - begin
         size_vector = size * 81
         size_row = size_vector // natom
 
-        nonzero_b = nonzero[begin:end]
-        size_data = np.count_nonzero(nonzero_b) * 81
-        if size_data == 0:
-            continue
-
-        if verbose:
-            print("Complementary P (Sum rule):", str(end) + "/" + str(NNN), flush=True)
-        decompr_idx_b = decompr_idx[begin:end][nonzero_b]
-        c_sum_cplmt = csr_array(
-            (
-                np.ones(size_data, dtype="double"),
+        if fc_cutoff is None:
+            c_sum_cplmt = csr_array(
                 (
-                    np.repeat(np.arange(size_row), natom)[np.tile(nonzero_b, 81)],
-                    (abcd[:, None] + decompr_idx_b[None, :]).reshape(-1),
+                    np.ones(size_vector, dtype="double"),
+                    (
+                        np.repeat(np.arange(size_row), natom),
+                        (abcd[:, None] + decompr_idx[begin:end][None, :]).reshape(-1),
+                    ),
                 ),
-            ),
-            shape=(size_row, NNNN81 // n_lp),
-            dtype="double",
-        )
+                shape=(size_row, NNNN81 // n_lp),
+                dtype="double",
+            )
+        else:
+            nonzero_b = nonzero[begin:end]
+            decompr_idx_b = decompr_idx[begin:end][nonzero_b]
+            size_data = np.count_nonzero(nonzero_b) * 81
+            c_sum_cplmt = csr_array(
+                (
+                    np.ones(size_data, dtype="double"),
+                    (
+                        np.repeat(np.arange(size_row), natom)[np.tile(nonzero_b, 81)],
+                        (abcd[:, None] + decompr_idx_b[None, :]).reshape(-1),
+                    ),
+                ),
+                shape=(size_row, NNNN81 // n_lp),
+                dtype="double",
+            )
+
         c_sum_cplmt = dot_product_sparse(c_sum_cplmt, n_a_compress_mat, use_mkl=use_mkl)
         proj_cplmt += dot_product_sparse(c_sum_cplmt.T, c_sum_cplmt, use_mkl=use_mkl)
 
@@ -332,7 +337,7 @@ def compressed_projector_sum_rules_O4_indep_atoms(
     return scipy.sparse.identity(proj_cplmt.shape[0]) - proj_cplmt
 
 
-def compressed_projector_sum_rules_O4(
+def compressed_projector_sum_rules_O4_indep_atoms(
     trans_perms: np.ndarray,
     n_a_compress_mat: csr_array,
     atomic_decompr_idx: Optional[np.ndarray] = None,
@@ -346,7 +351,7 @@ def compressed_projector_sum_rules_O4(
     Calculate a complementary projector for sum rules.
     This is compressed by C_trans and n_a_compress_mat without
     allocating C_trans.
-    Memory efficient version using get_atomic_lat_trans_decompr_indices_O4.
+    Memory efficient version using get_atomic_lat_trans_decompr_indices_O3.
 
     Return
     ------
@@ -366,47 +371,42 @@ def compressed_projector_sum_rules_O4(
         atomic_decompr_idx = get_atomic_lat_trans_decompr_indices_O4(trans_perms)
 
     decompr_idx = atomic_decompr_idx.reshape((natom, NNN)).T.reshape(-1) * 81
+
+    indep_atoms = get_indep_atoms_by_lat_trans(trans_perms)
+    nonzero = np.zeros((natom, natom, natom, natom), dtype=bool)
+    nonzero[indep_atoms, :, :, :] = True
+    nonzero = nonzero.reshape(-1)
     if fc_cutoff is not None:
-        nonzero = fc_cutoff.nonzero_atomic_indices_fc4()
-        nonzero = nonzero.reshape((natom, NNN)).T.reshape(-1)
+        nonzero_c = fc_cutoff.nonzero_atomic_indices_fc4()
+        nonzero_c = nonzero_c.reshape((natom, NNN)).T.reshape(-1)
+        nonzero = nonzero & nonzero_c
 
     batch_size = optimize_batch_size_sum_rules_O4(natom, n_batch=n_batch)
     abcd = np.arange(81)
     for begin, end in zip(*get_batch_slice(NNNN, batch_size)):
-        if verbose:
-            print("Complementary P (Sum rule):", str(end) + "/" + str(NNNN), flush=True)
         size = end - begin
         size_vector = size * 81
         size_row = size_vector // natom
 
-        if fc_cutoff is None:
-            c_sum_cplmt = csr_array(
-                (
-                    np.ones(size_vector, dtype="double"),
-                    (
-                        np.repeat(np.arange(size_row), natom),
-                        (abcd[:, None] + decompr_idx[begin:end][None, :]).reshape(-1),
-                    ),
-                ),
-                shape=(size_row, NNNN81 // n_lp),
-                dtype="double",
-            )
-        else:
-            nonzero_b = nonzero[begin:end]
-            decompr_idx_b = decompr_idx[begin:end][nonzero_b]
-            size_data = np.count_nonzero(nonzero_b) * 81
-            c_sum_cplmt = csr_array(
+        nonzero_b = nonzero[begin:end]
+        size_data = np.count_nonzero(nonzero_b) * 81
+        if size_data == 0:
+            continue
+
+        if verbose:
+            print("Complementary P (Sum rule):", str(end) + "/" + str(NNN), flush=True)
+        decompr_idx_b = decompr_idx[begin:end][nonzero_b]
+        c_sum_cplmt = csr_array(
+            (
+                np.ones(size_data, dtype="double"),
                 (
-                    np.ones(size_data, dtype="double"),
-                    (
-                        np.repeat(np.arange(size_row), natom)[np.tile(nonzero_b, 81)],
-                        (abcd[:, None] + decompr_idx_b[None, :]).reshape(-1),
-                    ),
+                    np.repeat(np.arange(size_row), natom)[np.tile(nonzero_b, 81)],
+                    (abcd[:, None] + decompr_idx_b[None, :]).reshape(-1),
                 ),
-                shape=(size_row, NNNN81 // n_lp),
-                dtype="double",
-            )
-
+            ),
+            shape=(size_row, NNNN81 // n_lp),
+            dtype="double",
+        )
         c_sum_cplmt = dot_product_sparse(c_sum_cplmt, n_a_compress_mat, use_mkl=use_mkl)
         proj_cplmt += dot_product_sparse(c_sum_cplmt.T, c_sum_cplmt, use_mkl=use_mkl)
 

{symfc-1.3.2 → symfc-1.3.3}/src/symfc/version.py

@@ -1,3 +1,3 @@
 """Version number of the package."""
 
-__version__ = "1.3.2"
+__version__ = "1.3.3"

{symfc-1.3.2 → symfc-1.3.3/src/symfc.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: symfc
-Version: 1.3.2
+Version: 1.3.3
 Summary: This is the symfc module.
 Author-email: Atsuto Seko <seko@cms.mtl.kyoto-u.ac.jp>
 Maintainer-email: Atsushi Togo <atztogo@gmail.com>