[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

dpdata/lammps/dump.py

@@ -133,7 +133,7 @@ def safe_get_posi(lines, cell, orig=np.zeros(3), unwrap=False):
 
 
 def get_spintype(keys):
-    key_sp  = ["sp", "spx", "spy", "spz"]
+    key_sp = ["sp", "spx", "spy", "spz"]
     key_csp = ["c_spin[1]", "c_spin[2]", "c_spin[3]", "c_spin[4]"]
     lmp_sp_type = [key_sp, key_csp]
     for k in range(2):
@@ -147,7 +147,7 @@ def safe_get_spin_force(lines):
     sp_type = get_spintype(keys)
     assert sp_type is not None, "Dump file does not contain spin!"
     id_idx = keys.index("id") - 2
-    sp  = keys.index(sp_type[0]) - 2
+    sp = keys.index(sp_type[0]) - 2
     spx = keys.index(sp_type[1]) - 2
     spy = keys.index(sp_type[2]) - 2
     spz = keys.index(sp_type[3]) - 2
@@ -254,10 +254,10 @@ def system_data(lines, type_map=None, type_idx_zero=True, unwrap=False):
     system["coords"] = [safe_get_posi(lines, cell, np.array(orig), unwrap)]
     contain_spin = False
     blk, head = _get_block(lines, "ATOMS")
-    if 'sp' in head:
+    if "sp" in head:
         contain_spin = True
         spin_force = safe_get_spin_force(lines)
-        system['spins'] = [spin_force[:, :1] * spin_force[:, 1:4]]
+        system["spins"] = [spin_force[:, :1] * spin_force[:, 1:4]]
     for ii in range(1, len(array_lines)):
         bounds, tilt = get_dumpbox(array_lines[ii])
         orig, cell = dumpbox2box(bounds, tilt)
@@ -271,7 +271,10 @@ def system_data(lines, type_map=None, type_idx_zero=True, unwrap=False):
             safe_get_posi(array_lines[ii], cell, np.array(orig), unwrap)[idx]
         )
         if contain_spin:
-            system['spins'].append(safe_get_spin_force(array_lines[ii])[:, :1] * safe_get_spin_force(array_lines[ii])[:, 1:4])
+            system["spins"].append(
+                safe_get_spin_force(array_lines[ii])[:, :1]
+                * safe_get_spin_force(array_lines[ii])[:, 1:4]
+            )
     if contain_spin:
         system["spins"] = np.array(system["spins"])
     system["cells"] = np.array(system["cells"])

dpdata/lammps/lmp.py

@@ -126,6 +126,7 @@ def get_posi(lines):
         posis.append([float(jj) for jj in ii.split()[2:5]])
     return np.array(posis)
 
+
 def get_spins(lines):
     atom_lines = get_atoms(lines)
     if len(atom_lines[0].split()) < 8:
@@ -138,6 +139,7 @@ def get_spins(lines):
     spins = np.array(spins_ori) * np.array(spins_norm)
     return spins
 
+
 def get_lmpbox(lines):
     box_info = []
     tilt = np.zeros(3)
@@ -163,8 +165,8 @@ def system_data(lines, type_map=None, type_idx_zero=True):
     system = {}
     system["atom_numbs"] = get_natoms_vec(lines)
     spins = get_spins(lines)
-    if spins is not None: 
-        system['spins'] = np.array([spins])
+    if spins is not None:
+        system["spins"] = np.array([spins])
     system["atom_names"] = []
     if type_map is None:
         for ii in range(len(system["atom_numbs"])):
@@ -230,9 +232,9 @@ def from_system_data(system, f_idx=0):
         + ptr_float_fmt
         + "\n"
     )
-    if 'spins' in system.keys():
+    if "spins" in system.keys():
         coord_fmt = (
-            coord_fmt.strip('\n') 
+            coord_fmt.strip("\n")
             + " "
             + ptr_float_fmt
             + " "
@@ -243,19 +245,19 @@ def from_system_data(system, f_idx=0):
             + ptr_float_fmt
             + "\n"
         )
-        spins_norm = np.linalg.norm(system['spins'][f_idx], axis=1)
+        spins_norm = np.linalg.norm(system["spins"][f_idx], axis=1)
     for ii in range(natoms):
-        if 'spins' in system.keys():
+        if "spins" in system.keys():
             if spins_norm[ii] != 0:
                 ret += coord_fmt % (
                     ii + 1,
                     system["atom_types"][ii] + 1,
                     system["coords"][f_idx][ii][0] - system["orig"][0],
                     system["coords"][f_idx][ii][1] - system["orig"][1],
                     system["coords"][f_idx][ii][2] - system["orig"][2],
-                    system['spins'][f_idx][ii][0]/spins_norm[ii],
-                    system['spins'][f_idx][ii][1]/spins_norm[ii],
-                    system['spins'][f_idx][ii][2]/spins_norm[ii],
+                    system["spins"][f_idx][ii][0] / spins_norm[ii],
+                    system["spins"][f_idx][ii][1] / spins_norm[ii],
+                    system["spins"][f_idx][ii][2] / spins_norm[ii],
                     spins_norm[ii],
                 )
             else:
@@ -265,9 +267,9 @@ def from_system_data(system, f_idx=0):
                     system["coords"][f_idx][ii][0] - system["orig"][0],
                     system["coords"][f_idx][ii][1] - system["orig"][1],
                     system["coords"][f_idx][ii][2] - system["orig"][2],
-                    system['spins'][f_idx][ii][0],
-                    system['spins'][f_idx][ii][1],
-                    system['spins'][f_idx][ii][2]+1,
+                    system["spins"][f_idx][ii][0],
+                    system["spins"][f_idx][ii][1],
+                    system["spins"][f_idx][ii][2] + 1,
                     spins_norm[ii],
                 )
         else:

dpdata/plugins/vasp_deltaspin.py

@@ -1,6 +1,9 @@
-import numpy as np
+from __future__ import annotations
+
 import re
 
+import numpy as np
+
 import dpdata.vasp_deltaspin.outcar
 import dpdata.vasp_deltaspin.poscar
 from dpdata.format import Format
@@ -14,7 +17,7 @@ class VASPPoscarFormat(Format):
     def from_system(self, file_name, **kwargs):
         with open(file_name) as fp:
             lines = [line.rstrip("\n") for line in fp]
-        with open(file_name[:-6] + 'INCAR') as fp:
+        with open(file_name[:-6] + "INCAR") as fp:
             lines_incar = [line.rstrip("\n") for line in fp]
         data = dpdata.vasp_deltaspin.poscar.to_system_data(lines, lines_incar)
         data = uniq_atom_names(data)
@@ -38,10 +41,12 @@ def to_system(self, data, file_name, frame_idx=0, **kwargs):
         with open(file_name, "w") as fp:
             fp.write(w_str)
 
-        with open(file_name[:-6] + 'INCAR') as fp:
+        with open(file_name[:-6] + "INCAR") as fp:
             tmp_incar = fp.read()
-        res_incar = re.sub(r'MAGMOM[\s\S]*?\n\nM_CONST[\s\S]*?\n\n', m_str, tmp_incar, re.S)
-        with open(file_name[:-6] + 'INCAR', 'w') as fp:
+        res_incar = re.sub(
+            r"MAGMOM[\s\S]*?\n\nM_CONST[\s\S]*?\n\n", m_str, tmp_incar, re.S
+        )
+        with open(file_name[:-6] + "INCAR", "w") as fp:
             fp.write(res_incar)
 
 
@@ -78,10 +83,10 @@ def from_labeled_system(
             data["atom_types"],
             data["cells"],
             data["coords"],
-            data['spins'],
+            data["spins"],
             data["energies"],
             data["forces"],
-            data['mag_forces'],
+            data["mag_forces"],
             tmp_virial,
         ) = dpdata.vasp_deltaspin.outcar.get_frames(
             file_name,
@@ -100,5 +105,3 @@ def from_labeled_system(
                 data["virials"][ii] *= v_pref * vol
         data = uniq_atom_names(data)
         return data
-
-

dpdata/system.py

@@ -1215,7 +1215,9 @@ class LabeledSystem(System):
         DataType(
             "forces", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), deepmd_name="force"
         ),
-        DataType("mag_forces", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), required=False),
+        DataType(
+            "mag_forces", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), required=False
+        ),
         DataType(
             "virials",
             np.ndarray,

dpdata/vasp_deltaspin/outcar.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import re
 import warnings
 
@@ -93,11 +95,13 @@ def get_frames(fname, begin=0, step=1, ml=False, convergence_check=True):
         blk = get_outcar_block(fp, ml)
         cc += 1
 
-    with open(fname[:-6] + 'OSZICAR') as f:
+    with open(fname[:-6] + "OSZICAR") as f:
         oszicar_blk = f.read()
-    mag_blk = re.findall(r'Magnetic Force(.*?)\n  \n', oszicar_blk, re.S)[-1].split('\n')
+    mag_blk = re.findall(r"Magnetic Force(.*?)\n  \n", oszicar_blk, re.S)[-1].split(
+        "\n"
+    )
     mag_force = [list(map(float, ss.split()[-3:])) for ss in mag_blk[1:]]
-    spin_blk = re.findall(r'MW_current(.*?)\n ion', oszicar_blk, re.S)[-1].split('\n')
+    spin_blk = re.findall(r"MW_current(.*?)\n ion", oszicar_blk, re.S)[-1].split("\n")
     spin = [list(map(float, ss.split()[1:4])) for ss in spin_blk[1:]]
     all_mag_forces.append(mag_force)
     all_spins.append(spin)

dpdata/vasp_deltaspin/poscar.py

@@ -1,4 +1,5 @@
 #!/usr/bin/python3
+from __future__ import annotations
 
 import numpy as np
 
@@ -35,16 +36,16 @@ def _to_system_data_lower(lines, lines_incar, cartesian=True):
     system["coords"] = np.array(system["coords"])
 
     for idx, incar_param in enumerate(lines_incar):
-        if 'MAGMOM' in incar_param:
+        if "MAGMOM" in incar_param:
             start_index = idx
-        elif 'M_CONSTR' in incar_param:
+        elif "M_CONSTR" in incar_param:
             end_index = idx
-    system['spins'] = [lines_incar[start_index].replace('=', '').strip().split()[1:4]]
-    for idx in range(start_index+1, end_index-1):
-        system['spins'].append(lines_incar[idx].strip().split()[:3])
-    system['spins'] = np.array([system['spins']]).astype('float64')
-    count = np.sum(np.linalg.norm(system['spins'][0], axis=1) > 0)
-    spins_idx = np.where(np.cumsum(system['atom_numbs']) <= count)
+    system["spins"] = [lines_incar[start_index].replace("=", "").strip().split()[1:4]]
+    for idx in range(start_index + 1, end_index - 1):
+        system["spins"].append(lines_incar[idx].strip().split()[:3])
+    system["spins"] = np.array([system["spins"]]).astype("float64")
+    count = np.sum(np.linalg.norm(system["spins"][0], axis=1) > 0)
+    spins_idx = np.where(np.cumsum(system["atom_numbs"]) <= count)
     return system
 
 
@@ -100,16 +101,20 @@ def from_system_data(system, f_idx=0, skip_zeros=True):
 
     magmom_incar = "MAGMOM = "
     mconstr_incar = "M_CONSTR = "
-    for idx, tmp_spin in enumerate(system['spins'][f_idx]):
+    for idx, tmp_spin in enumerate(system["spins"][f_idx]):
         if idx == 0:
-            magmom_incar  += f"{tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \ \n"
-            mconstr_incar += f"{tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \ \n"
-        elif idx == len(system['spins'][f_idx]) - 1:
-            magmom_incar  += f"       {tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \n"
+            magmom_incar += (
+                f"{tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \ \n"
+            )
+            mconstr_incar += (
+                f"{tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \ \n"
+            )
+        elif idx == len(system["spins"][f_idx]) - 1:
+            magmom_incar += f"       {tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \n"
             mconstr_incar += f"       {tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \n"
         else:
-            magmom_incar  += f"       {tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \ \n"
+            magmom_incar += f"       {tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \ \n"
             mconstr_incar += f"       {tmp_spin[0]:10.5f}  {tmp_spin[1]:10.5f}  {tmp_spin[2]:10.5f} \ \n"
-    magmom_incar += '\n' + mconstr_incar + '\n'
+    magmom_incar += "\n" + mconstr_incar + "\n"
 
     return ret, magmom_incar