Merge e8cd20d into 5bba75a

cp2kdata/block_parser/atomic_kind.py

@@ -15,13 +15,15 @@
     re.VERBOSE
 )
 
+
 def parse_num_atomic_kinds(output_file):
     num_atomic_kinds_list = []
 
     for match in NUM_ATOMIC_KINDS_RE.finditer(output_file):
         num_atomic_kinds_list.append(int(match["num_atomic_kind"]))
     return num_atomic_kinds_list
 
+
 def parse_atomic_kinds(output_file):
     num_atomic_kinds_list = parse_num_atomic_kinds(output_file)
     atomic_kinds = []
@@ -31,4 +33,4 @@ def parse_atomic_kinds(output_file):
         # only return the last atomic kinds
         return np.array(atomic_kinds[-num_atomic_kinds_list[-1]:], dtype=str)
     else:
-        return None
+        return None

cp2kdata/block_parser/cells.py

@@ -30,10 +30,11 @@
     re.VERBOSE
 )
 
+
 def parse_all_cells(output_file):
     all_cells = []
     for match in ALL_CELL_RE.finditer(output_file):
-        #print(match)
+        # print(match)
         cell = [
             [match["xx"], match["xy"], match["xz"]],
             [match["yx"], match["yy"], match["yz"]],
@@ -46,6 +47,7 @@ def parse_all_cells(output_file):
     else:
         return None
 
+
 ALL_MD_CELL_RE_V7 = re.compile(
     r"""
     \sCELL\sLNTHS\[bohr\]\s{13}=\s
@@ -83,6 +85,7 @@ def parse_all_cells(output_file):
     re.VERBOSE
 )
 
+
 def parse_all_md_cells(output_file: List[str],
                        cp2k_info: Cp2kInfo,
                        init_cell_info=None):
@@ -105,9 +108,9 @@ def parse_all_md_cells(output_file: List[str],
     if init_cell_info is None:
         # for NPT_F parser, cell info is complete in MD| block
         for match in ALL_MD_CELL_RE.finditer(output_file):
-            #print(match)
+            # print(match)
             cell = [match["a"], match["b"], match["c"],
-                match["alpha"], match["beta"], match["gamma"]]
+                    match["alpha"], match["beta"], match["gamma"]]
             cell = np.array(cell, dtype=float)
             # convert bohr to angstrom
             cell[:3] = cell[:3] * au2A
@@ -119,16 +122,15 @@ def parse_all_md_cells(output_file: List[str],
         init_cell_param = cell_to_cellpar(init_cell_info)
         init_cell_angles = init_cell_param[3:]
         for match in ALL_MD_CELL_RE.finditer(output_file):
-            #print(match)
+            # print(match)
             cell = [match["a"], match["b"], match["c"],
-                match["alpha"], match["beta"], match["gamma"]]
+                    match["alpha"], match["beta"], match["gamma"]]
             cell = np.array(cell, dtype=float)
             cell[3:] = init_cell_angles
             cell = cellpar_to_cell(cell)
             all_md_cells.append(cell)
 
-
     if all_md_cells:
         return np.array(all_md_cells, dtype=float)
     else:
-        return None
+        return None

cp2kdata/block_parser/converge.py

@@ -7,35 +7,38 @@
 class ConvergeInfo:
     converge: bool = False
 
+
 CONVERGE_PATTERN = \
     r"""(?xm)
     ^\s{1,2}\*\*\*\sSCF\srun\sconverged\sin
     """
 
+
 def parse_e_f_converge(filename) -> ConvergeInfo:
 
     info_dict = regrep(
         filename=filename,
         reverse=True,
         patterns={"converge": CONVERGE_PATTERN},
         terminate_on_match=True
-        )
+    )
 
     if info_dict['converge']:
         converge_info = ConvergeInfo(converge=True)
     else:
         converge_info = ConvergeInfo(converge=False)
     return converge_info
 
+
 def parse_md_converge(filename):
 
     info_dict = regrep(
         filename=filename,
         reverse=True,
         patterns={"converge": CONVERGE_PATTERN},
         terminate_on_match=False
-        )
-    #print(info_dict['converge'])
+    )
+    # print(info_dict['converge'])
 
 # if __name__ == "__main__":
 #     file_name = "e_f"

cp2kdata/block_parser/coordinates.py

@@ -27,7 +27,7 @@
 def parse_init_atomic_coordinates(output_file):
 
     match = INIT_ATOMIC_COORDINATES_RE.search(output_file)
-        # only get the first match
+    # only get the first match
     init_atomic_coordinates = []
     chemical_symbols = []
     for x, y, z in zip(*match.captures("x", "y", "z")):
@@ -38,4 +38,4 @@ def parse_init_atomic_coordinates(output_file):
     if init_atomic_coordinates:
         return np.array(init_atomic_coordinates, dtype=float), np.array(atom_kind_list, dtype=int), chemical_symbols
     else:
-        return None
+        return None

cp2kdata/block_parser/dft_plus_u.py

@@ -25,6 +25,8 @@
 #        \s+(?P<spin_moment>[\s-]\d+\.\d+)
 #        \n
 #    )+
+
+
 def parse_dft_plus_u_occ(output_file):
     dft_plus_u_occ = []
     for match in PLUS_U_RE.finditer(output_file):
@@ -40,7 +42,7 @@ def parse_dft_plus_u_occ(output_file):
 #                    "spin_moment": float(spin_moment)
 #                }
 #            )
-    if  dft_plus_u_occ:
+    if dft_plus_u_occ:
         return dft_plus_u_occ
     else:
-        return None
+        return None

cp2kdata/block_parser/dipole.py

@@ -13,7 +13,8 @@
     re.VERBOSE
 )
 
-#TODO write a pytest for this
+# TODO write a pytest for this
+
 
 def parse_dipole_list(output_file):
     dipole_list = []
@@ -26,6 +27,7 @@ def parse_dipole_list(output_file):
     else:
         return None
 
+
 """
    Reference Point [Bohr]              0.00000000      0.00000000      0.00000000
    Charges
@@ -37,4 +39,4 @@ def parse_dipole_list(output_file):
    [Z] [    0.00000000     0.00000000    54.47313965 ] [k]
    Dipole moment [Debye]
      X=   -0.07183634 Y=   -0.07690441 Z=    1.13302571     Total=     1.13790246
-"""
+"""

cp2kdata/block_parser/energies.py

@@ -8,6 +8,7 @@
     re.VERBOSE
 )
 
+
 def parse_energies_list(output_file):
 
     energies_list = []
@@ -17,5 +18,3 @@ def parse_energies_list(output_file):
         return np.array(energies_list, dtype=float)
     else:
         return None
-
-

cp2kdata/block_parser/errors_handle.py

@@ -7,12 +7,11 @@
 )
 
 
-
 def parse_errors(output_file):
     errors_info = {}
 
     for match in EXCEED_WALL_TIME_RE.finditer(output_file):
-        #print(match)
+        # print(match)
         if match:
             errors_info = {
                 "exceed_wall_time": True

cp2kdata/block_parser/fep.py

@@ -1,4 +1,6 @@
 import numpy as np
+
+
 def parse_vertical_gap(mix_ener_file, r_col=3, p_col=4):
     r_ener = np.loadtxt(mix_ener_file, usecols=r_col)
     p_ener = np.loadtxt(mix_ener_file, usecols=p_col)

cp2kdata/block_parser/forces.py

@@ -19,6 +19,7 @@
     re.VERBOSE
 )
 
+
 def parse_atomic_forces_list(output_file):
     atomic_forces_list = []
     for match in ATOMIC_FORCES_RE.finditer(output_file):
@@ -29,4 +30,4 @@ def parse_atomic_forces_list(output_file):
     if atomic_forces_list:
         return np.array(atomic_forces_list, dtype=float)
     else:
-        return None
+        return None

cp2kdata/block_parser/header_info.py

@@ -8,19 +8,21 @@
 class Cp2kInfo:
     version: str = None
 
+
 CP2K_INFO_VERSION_PATTERN = \
     r"""(?xm)
     ^\sCP2K\|\sversion\sstring:\s{10,42}
     CP2K\sversion\s(?P<version>\d{1,4}\.\d)(?:\s\(Development\sVersion\))?$
     """
 
+
 def parse_cp2k_info(filename) -> Cp2kInfo:
 
     cp2k_info = regrep(
         filename=filename,
         patterns={"version": CP2K_INFO_VERSION_PATTERN},
         terminate_on_match=True
-        )
+    )
 
     return Cp2kInfo(version=cp2k_info["version"][0][0][0])
 
@@ -30,6 +32,7 @@ class GlobalInfo:
     run_type: str = None
     print_level: str = None
 
+
 # PATTERNS
 GLOBAL_INFO_RUN_TYPE_PATTERN = \
     r"""(?xm)
@@ -40,6 +43,7 @@ class GlobalInfo:
     ^\sGLOBAL\|\sGlobal\sprint\slevel\s{42,}(?P<print_level>\w+)\n
     """
 
+
 def parse_global_info(filename) -> GlobalInfo:
     global_info = {}
 
@@ -49,7 +53,7 @@ def parse_global_info(filename) -> GlobalInfo:
                   "print_level": GLOBAL_INFO_PRINT_LEVEL_PATTERN
                   },
         terminate_on_match=True
-        )
+    )
 
     return GlobalInfo(run_type=global_info["run_type"][0][0][0],
                       print_level=global_info["print_level"][0][0][0]
@@ -76,6 +80,7 @@ class DFTInfo:
     ^\sDFT\|\sMultiplicity\s{57,}(\d{1,4})$
     """
 
+
 def parse_dft_info(filename) -> DFTInfo:
     dft_info = {}
 
@@ -86,26 +91,26 @@ def parse_dft_info(filename) -> DFTInfo:
             "multiplicity": DFT_INFO_MULTIPLICITY_PATTERN
         },
         terminate_on_match=True
-        )
+    )
 
     if dft_info:
         return DFTInfo(ks_type=dft_info["ks_type"][0][0][0], multiplicity=dft_info["multiplicity"][0][0][0])
     else:
         return None
 
 
-
-
 @dataclass
 class MDInfo:
     ensemble_type: str = None
 
+
 # PATTERNS
 MD_INFO_ENSEMBLE_TYPE_PATTERN = \
     r"""(?xm)
     ^\s(?:MD_PAR|MD)\|\sEnsemble\s(?:t|T)ype\s{39,60}(?P<ensemble_type>\w{3,16})
     """
 
+
 def parse_md_info(filename):
     md_info = {}
 
@@ -115,6 +120,6 @@ def parse_md_info(filename):
             "ensemble_type": MD_INFO_ENSEMBLE_TYPE_PATTERN
         },
         terminate_on_match=True
-        )
+    )
 
-    return MDInfo(ensemble_type=md_info["ensemble_type"][0][0][0])
+    return MDInfo(ensemble_type=md_info["ensemble_type"][0][0][0])

cp2kdata/block_parser/hirshfeld.py

@@ -21,6 +21,7 @@
     re.VERBOSE
 )
 
+
 def parse_hirshfeld_pop_list(output_file):
     hirshfeld_pop_list = []
     for match in HIRSHFELD_RE.finditer(output_file):
@@ -36,7 +37,7 @@ def parse_hirshfeld_pop_list(output_file):
                 }
             )
         hirshfeld_pop_list.append(hirshfeld_pop)
-    if  hirshfeld_pop_list:
-        return  hirshfeld_pop_list[:-1]
+    if hirshfeld_pop_list:
+        return hirshfeld_pop_list[:-1]
     else:
         return None