code for properly parsing arrays

parser/parser-siesta/parser.py

@@ -3,10 +3,13 @@ import os
 import sys
 import setup_paths
 
+import numpy as np
+from ase.data import chemical_symbols
+
 from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 from nomadcore.unit_conversion.unit_conversion \
-    import register_userdefined_quantity
+    import register_userdefined_quantity, convert_unit
 
 from util import floating
 
@@ -23,6 +26,77 @@ def siesta_energy(title, meta):
     return SM(r'siesta:\s*%s\s*=\s*(?P<%s__eV>\S*)' % (title, meta),
               name=meta)
 
+def array_matcher():
+
+    def getarray():
+        pass
+
+    sm = SM()
+    return sm
+
+#class ArrayParser(SM):
+#    def __init__(self, *args, **kwargs):
+#        SM.__init__(self, *args, adHoc=get_ar**kwargs)
+
+#def array_line_matcher(*args, **kwargs):
+#    def 
+#    sm = SimpleMatcher(*args, repeats=True, **kwargs)
+#    return sm
+
+def get_positions_and_labels(parser):
+    rows = []
+    atomic_numbers = []
+    line = parser.fIn.readline()
+    while line.startswith('siesta:'):
+        tokens = line.split()
+        rows.append([float(x) for x in tokens[1:4]])
+        atomic_numbers.append(int(tokens[4]))
+        line = parser.fIn.readline()
+    rows = np.array(rows, float)
+    labels = np.array([chemical_symbols[Z] for Z in atomic_numbers])
+
+    b = parser.backend.superBackend
+    b.addArrayValues('atom_positions', convert_unit(rows, 'bohr'))
+    b.addArrayValues('atom_labels', labels)
+
+#def get_cell(parser):
+#    
+
+
+def ArraySM(header, row, end, build):
+    lines = []
+
+    def addrow(parser):
+        line = parser.fIn.readline()
+        lines.append(line)
+
+    def _build_array(parser):
+        build(parser.backend.superBackend, lines)
+
+    sm = SM(header,
+            name='startarray',
+            required=True,
+            subFlags=SM.SubFlags.Sequenced,
+            subMatchers=[
+                SM(row, name='array', repeats=True,
+                   forwardMatch=True,
+                   adHoc=addrow, required=True),
+                SM(end, name='endarray', required=True),
+                SM(r'', adHoc=_build_array, name='dummy', forwardMatch=True)
+            ])
+    return sm
+
+def build_cell(backend, lines):
+    cell = np.array([[float(x) for x in line.split()] for line in lines])
+    backend.addArrayValues('simulation_cell', convert_unit(cell, 'angstrom'))
+
+def add_positions_and_labels(backend, lines):
+    matrix = np.array([line.split() for line in lines], object)
+    positions = matrix[:, 1:4].astype(float)
+    labels = np.array([chemical_symbols[i] for i in matrix[:, 5].astype(int)])
+    backend.addArrayValues('atom_positions', convert_unit(positions, 'bohr'))
+    backend.addArrayValues('atom_labels', labels)
+
 infoFileDescription = SM(
     name='root',
     weak=True,
@@ -33,11 +107,15 @@ infoFileDescription = SM(
     subMatchers=[
         SM(r'Siesta Version: (?P<program_name>siesta)-(?P<program_version>\S*)',
            name='name&version'),
-        SM(r'outcell: Unit cell vectors \(Ang\):', name='cell_header'),
+        ArraySM(r'siesta: Atomic coordinates \(Bohr\) and species',
+                r'siesta:', r'', add_positions_and_labels),
         SM(r'\s*Single-point calculation',
            name='singleconfig',
            sections=['section_single_configuration_calculation'],
            subMatchers=[
+               ArraySM(r'outcell: Unit cell vectors \(Ang\):',
+                       r'\s*\S+\s*\S+\s*\S+',
+                       r'\s*', build_cell),
                SM(r'siesta: Final energy \(eV\):',
                   name='energy_header',
                   subMatchers=[