wien2kparser/parser_wien2k.py

 from builtins import object
 # import setup_paths
 import numpy as np
+import ase.io
 import os
 import sys
 
@@ -13,7 +14,7 @@ import wien2kparser.wien2k_parser_in1c as wien2k_parser_in1c
 import wien2kparser.wien2k_parser_in2c as wien2k_parser_in2c
 import wien2kparser.wien2k_parser_in1 as wien2k_parser_in1
 import wien2kparser.wien2k_parser_in2 as wien2k_parser_in2
-import logging as _logging
+import logging
 
 from nomad.parsing.legacy import CoESimpleMatcherParser
 
@@ -173,7 +174,6 @@ class Wien2kContext(object):
         if atom_labels is not None:
            backend.addArrayValues('atom_labels', np.asarray(atom_labels))
 
-
         # atom force
         atom_force = []
         for i in ['x', 'y', 'z']:
@@ -184,20 +184,34 @@ class Wien2kContext(object):
             # need to transpose array since its shape is [number_of_atoms,3] in\the metadata
            backend.addArrayValues('atom_forces', np.transpose(np.asarray(atom_force)))
 
+        # Parse the structure file
         mainFile = self.parser.fIn.fIn.name
         fName = mainFile[:-4] + ".struct"
         if os.path.exists(fName):
-            structSuperContext = wien2k_parser_struct.Wien2kStructContext()
-            structParser = AncillaryParser(
-                fileDescription = wien2k_parser_struct.buildStructureMatchers(),
-                parser = self.parser,
-                cachingLevelForMetaName = wien2k_parser_struct.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
-                superContext = structSuperContext)
-
-            with open(fName) as fIn:
-                structParser.parseFile(fIn)
-
 
+            # ASE does not support reading file object for WIEN2k structure files.
+            try:
+                atoms = ase.io.read(fName, format="struct")
+            except Exception:
+                logging.error("Could not read/parse the WIEN2k structure file.")
+            else:
+                pos = atoms.get_positions() * 1E-10
+                symbols = atoms.get_chemical_symbols()
+                cell = atoms.get_cell() * 1E-10
+                pbc = atoms.get_pbc()
+                backend.addArrayValues('lattice_vectors', cell)
+                backend.addArrayValues("configuration_periodic_dimensions", pbc)
+                backend.addValue("atom_labels", symbols)
+                backend.addArrayValues('atom_positions', pos)
+
+            with open(fName, "r") as fin:
+                structSuperContext = wien2k_parser_struct.Wien2kStructContext()
+                structParser = AncillaryParser(
+                    fileDescription = wien2k_parser_struct.buildStructureMatchers(),
+                    parser = self.parser,
+                    cachingLevelForMetaName = wien2k_parser_struct.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
+                    superContext = structSuperContext)
+                structParser.parseFile(fin)
 
     def onClose_section_scf_iteration(self, backend, gIndex, section):
         #Trigger called when section_scf_iteration is closed.

wien2kparser/wien2k_parser_struct.py

@@ -30,7 +30,8 @@ __maintainer__ = "Daria M. Tomecka"
 __email__ = "tomeckadm@gmail.com;"
 __date__ = "15/05/2017"
 
-class Wien2kStructContext(object):
+
+class Wien2kStructContext():
     """context for wien2k struct parser"""
 
     def __init__(self):
@@ -46,46 +47,6 @@ class Wien2kStructContext(object):
         # allows to reset values if the same superContext is used to parse different files
         self.initialize_values()
 
-    def onClose_section_system(self, backend, gIndex, section):
-        #   unit_cell
-        unit_cell_params = []
-        for i in ['a', 'b', 'c']:
-            uci = section['x_wien2k_unit_cell_param_' + i]
-            #if uci is not None:
-            unit_cell_params.append(uci[0])
-        for i in ['alfa', 'beta', 'gamma']:
-            uci = section['x_wien2k_angle_between_unit_axis_' + i]
-            # if uci is not None:
-            unit_cell_params.append(uci[0])
-
-        unit_cell = ase.geometry.cellpar_to_cell(unit_cell_params)
-        backend.addArrayValues('simulation_cell', unit_cell)
-        backend.addArrayValues("configuration_periodic_dimensions", np.ones(3, dtype=bool))
-
-        equiv_atoms = section["x_wien2k_section_equiv_atoms"]
-        #logging.error("section: %s", section)
-        labels = []
-        pos = []
-
-        for eqAtoms in equiv_atoms:
-            label = eqAtoms["x_wien2k_atom_name"][0]
-            x = eqAtoms["x_wien2k_atom_pos_x"]
-            y = eqAtoms["x_wien2k_atom_pos_y"]
-            z = eqAtoms["x_wien2k_atom_pos_z"]
-            #logging.error("equiv_atoms: %s x %s y %s z %s",eqAtoms, x, y, z)
-            if len(x) != len(y) or len(x) != len(z):
-                raise Exception("incorrect parsing, different number of x,y,z components")
-            groupPos = [[x[i],y[i],z[i]] for i in range(len(x))]
-            nAt = len(groupPos)
-            labels += [label for i in range(nAt)]
-            pos += groupPos
-        backend.addValue("atom_labels", labels)
-
-        #backend.addArrayValues("atom_positions", np.dot(pos,unit_cell))
-        #backend.addArrayValues('atom_positions', np.transpose(np.asarray(pos)))
-        backend.addArrayValues('atom_positions', np.asarray(pos))
-
-
 
 # description of the input
 def buildStructureMatchers():