added lattice vectors

parser/parser-elk/parser_elk.py

@@ -22,6 +22,24 @@ class ElkContext(object):
         # allows to reset values if the same superContext is used to parse different files
         self.initialize_values()
 
+    def onClose_x_elk_section_lattice_vectors(self, backend, gIndex, section):
+      latticeX = section["x_elk_geometry_lattice_vector_x"]
+      latticeY = section["x_elk_geometry_lattice_vector_y"]
+      latticeZ = section["x_elk_geometry_lattice_vector_z"]
+      cell = [[latticeX[0],latticeY[0],latticeZ[0]],
+              [latticeX[1],latticeY[1],latticeZ[1]],
+              [latticeX[2],latticeY[2],latticeZ[2]]]
+      backend.addValue("simulation_cell", cell)
+
+    def onClose_x_elk_section_reciprocal_lattice_vectors(self, backend, gIndex, section):
+      recLatticeX = section["x_elk_geometry_reciprocal_lattice_vector_x"]
+      recLatticeY = section["x_elk_geometry_reciprocal_lattice_vector_y"]
+      recLatticeZ = section["x_elk_geometry_reciprocal_lattice_vector_z"]
+      recCell = [[recLatticeX[0],recLatticeY[0],recLatticeZ[0]],
+              [recLatticeX[1],recLatticeY[1],recLatticeZ[1]],
+              [recLatticeX[2],recLatticeY[2],recLatticeZ[2]]]
+      backend.addValue("x_elk_simulation_reciprocal_cell", recCell)
+
 # description of the input
 mainFileDescription = \
     SM(name = "root matcher",
@@ -34,11 +52,22 @@ mainFileDescription = \
             sections = ["section_run", "section_method"],
          subMatchers = [
            SM(name = 'input',
-               startReStr = r"All units  are atomic \(Hartree, Bohr, etc.\)\s",
-#              startReStr = r"\|\sGround-state run starting from atomic densities\s\|\s",
-#              endReStr = r"\|\sDensity and potential initialised from atomic data\s",
+              startReStr = r"\|\sGround-state run starting from atomic densities\s\|\s",
+              endReStr = r"\|\sDensity and potential initialised from atomic data\s",
               sections = ['section_system'],
               subMatchers = [
+                SM(startReStr = r"\s*Lattice vectors :",
+                sections = ["x_elk_section_lattice_vectors"],
+                subMatchers = [
+
+    SM(startReStr = r"\s*(?P<x_elk_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<x_elk_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<x_elk_geometry_lattice_vector_z__bohr>[-+0-9.]+)", repeats = True)
+                ]),
+                SM(startReStr = r"Reciprocal lattice vectors :",
+                sections = ["x_elk_section_reciprocal_lattice_vectors"],
+                subMatchers = [
+
+    SM(startReStr = r"\s*(?P<x_elk_geometry_reciprocal_lattice_vector_x__bohr_1>[-+0-9.]+)\s+(?P<x_elk_geometry_reciprocal_lattice_vector_y__bohr_1>[-+0-9.]+)\s+(?P<x_elk_geometry_reciprocal_lattice_vector_z__bohr_1>[-+0-9.]+)", repeats = True)
+                ]),
     SM(r"\s*Unit cell volume\s*:\s*(?P<x_elk_unit_cell_volume__bohr3>[-0-9.]+)"),
     SM(r"\s*Brillouin zone volume\s*:\s*(?P<x_elk_brillouin_zone_volume__bohr_3>[-0-9.]+)")
            ] )
@@ -52,6 +81,17 @@ parserInfo = {
 metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/elk.nomadmetainfo.json"))
 metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
 
+cachingLevelForMetaName = {
+                            "x_elk_geometry_lattice_vector_x":CachingLevel.Cache,
+                            "x_elk_geometry_lattice_vector_y":CachingLevel.Cache,
+                            "x_elk_geometry_lattice_vector_z":CachingLevel.Cache,
+                            "x_elk_section_lattice_vectors": CachingLevel.Ignore,
+                            "x_elk_geometry_reciprocal_lattice_vector_x":CachingLevel.Cache,
+                            "x_elk_geometry_reciprocal_lattice_vector_y":CachingLevel.Cache,
+                            "x_elk_geometry_reciprocal_lattice_vector_z":CachingLevel.Cache,
+                            "x_elk_section_reciprocal_lattice_vectors": CachingLevel.Ignore
+                          }
+
 if __name__ == "__main__":
     superContext = ElkContext()
     mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext)