cleaning up the code (classify4me_prototypes.py)

normalizer/normalizer-prototypes/classify4me_prototypes.py

@@ -13,7 +13,7 @@ __author__ = "Daria M. Tomecka and Fawzi Mohamed"
 __copyright__ = "Copyright 2017, The NOMAD Project"
 __maintainer__ = "Daria M. Tomecka"
 __email__ = "tomeckadm@gmail.com;"
-__date__ = "18/05/17"
+__date__ = "12/07/17"
 
 import sys
 import ase.io
@@ -28,13 +28,8 @@ import functools
 import fractions
 
 import setup_paths
-#from nomad_sim.wrappers import get_json_list
-#from nomad_sim.wrappers import plot, logger
-#from nomad_sim.utils_crystals import get_spacegroup
-#from nomad_sim.utils_crystals import create_supercell
-#from nomad_sim.wrappers import get_json_list
-#from nomad_sim.nomad_structures import NOMADStructure
-###
+
+### new updated location for the prototypes
 from nomadcore.structure_types import \
     structure_types_by_spacegroup as str_types_by_spg
 from nomadcore.parse_streamed_dicts import ParseStreamedDicts
@@ -43,24 +38,20 @@ from nomadcore.parser_backend import JsonParseEventsWriterBackend
 
 
 #prototypes_file = os.path.normpath("/nomad-lab-base/analysis-tools/structural-similarity/python-modules/nomad_sim/structure_types.py")
-#Classification of json calculartion using encyclopedia preprocessor
 
 import sys
 #print(sys.path)
 sys.path.append('/home/beaker/py3k/lib/python3.5/')
 import spglib
-#import Nomad
+
 import logging
-#from Nomad.Preprocessing.System import structure, preprocessormaterial3d
-#from Nomad import ProcessingEngine
 
 #LOGGER = logging.getLogger(__name__)
 #logging.basicConfig(level=logging.ERROR)
 
-#json_list = beaker.json_list
 
 atomSpecies = None
-#atomSpecies = atom_species
+
 cell = None
 
 def get_normalized_wyckoff(atomic_number, wyckoff):
@@ -145,17 +136,9 @@ def get_structure_type(space_group, norm_wyckoff):
     """Returns the information on the prototype.
     """
     structure_type_info = {}
-    #wyckoff_letters_compact = "".join(sorted(set(wyckoff_letters)))
-
-    #print("Wyckoff1", norm_wyckoff)#_compact)
-    #print("Space Gr", space_group)
 
     for type_description in str_types_by_spg.get((space_group), []):
-        #current_bravais_lattice = type_description['Pearsons Symbol'][0:2]
-        #current_wyckoffs = type_description['Wyckoff Positions']
-
-        #if current_bravais_lattice == bravais_lattice \
-         #       and current_wyckoffs == wyckoff_letters_compact:        current_norm_wyckoffs = type_description.get('normalized_wyckoff')
+        
         current_norm_wyckoffs = type_description.get("normalized_wyckoff_spg")
         if current_norm_wyckoffs and current_norm_wyckoffs == norm_wyckoff:
             structure_type_info = type_description
@@ -167,14 +150,13 @@ def get_structure_type(space_group, norm_wyckoff):
 
 
 
-#from preprocessor
-
 def _structure_type_info(self):
     """Known structure types"""
     return get_structure_type(
         self.space_group,
         self.normalized_wyckoff)
 
+
 def toAtomNr(string):
     "returns the atom number of the given symbol"
     baseStr = string[:3].title()
@@ -188,6 +170,7 @@ def toAtomNr(string):
         return 0
 
 def dictToNarray(dictValue):
+    """function that gets the dictionary with flat data ans shape and give the array"""
     v=dictValue['flatData']
     return np.reshape(np.asarray(v), dictValue['shape'])
 
@@ -217,21 +200,11 @@ def systemToSpg(cell, atomSpecies, atomPos):
     symm = spglib.get_symmetry_dataset((acell, np.dot(atomPos,cellInv), atomSpecies),
                                                  0.002, -1) # use m instead of Angstrom?
 
-    #symm = spglib.get_symmetry_dataset(filename)
-    #                                  sym = spglib.get_symmetry_dataset((number,wyckoff, pearsons_symbol)
     return symm
 
 def classify_by_norm_wyckoff(sectionSystem):
     try:
-        #try:
-        #    simulation_cell = json_file_name.get('lattice_vectors')
-        #    labels = json_file_name.get('atom_labels')
-        #    atom_pos = json_file_name.get('atom_positions')
-        #    if not simulation_cell or not labels or not atom_pos:
-        #        raise Exception("Parsed invalid geometry for space group %d, %s" % (spaceGroupNr, protoDict))
-
-        #    proc = ProcessingEngine(mode="debug")
-        #results = proc.process(json_file_name)
+        
         ###
         #atomic_number = atom_species
         #as in the normalized version
@@ -252,17 +225,8 @@ def classify_by_norm_wyckoff(sectionSystem):
         symm = systemToSpg(cell, atomSpecies, atomPos)
         wyckoffs = symm.get("wyckoffs")
         spg_nr = symm.get("number")
-        #norm_wyckoff = get_normalized_wyckoff
-
-        # preprocessor = list(results.values())
-        # if len(preprocessor) == 1:
-        #     preprocessor = preprocessor[0]
-        #     spg_nr = preprocessor["space_group"]
-        #     norm_wyckoff = preprocessor["normalized_wyckoff"]
-
-        ###
-        #                pearson - symm.get("xxx")
-        #space_group = symmetry_dataset["number"]
+        
+        ### adds recalculated wyckoff positions
         updatePrototypesWyckoff(str_types_by_spg)
 
         ###