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Commit 9ebe08f4 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
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fixed problem with atom labels

parent 929df8d2
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parser/parser-exciting/parser_exciting.py
View file @ 9ebe08f4
......@@ -5,7 +5,6 @@ from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.caching_backend import CachingLevel
from nomadcore.unit_conversion import unit_conversion
from nomadcore.local_backend import LocalBackend
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_input
class ExcitingParserContext(object):
......@@ -19,19 +18,19 @@ class ExcitingParserContext(object):
latticeX = section["x_exciting_geometry_lattice_vector_x"]
latticeY = section["x_exciting_geometry_lattice_vector_y"]
latticeZ = section["x_exciting_geometry_lattice_vector_z"]
cell = np.array([[latticeX[0],latticeY[0],latticeZ[0]],
cell = [[latticeX[0],latticeY[0],latticeZ[0]],
[latticeX[1],latticeY[1],latticeZ[1]],
[latticeX[2],latticeY[2],latticeZ[2]]])
backend.addArrayValues("simulation_cell", cell)
[latticeX[2],latticeY[2],latticeZ[2]]]
backend.addValue("simulation_cell", cell)
def onClose_x_exciting_section_reciprocal_lattice_vectors(self, backend, gIndex, section):
recLatticeX = section["x_exciting_geometry_reciprocal_lattice_vector_x"]
recLatticeY = section["x_exciting_geometry_reciprocal_lattice_vector_y"]
recLatticeZ = section["x_exciting_geometry_reciprocal_lattice_vector_z"]
recCell = np.array([[recLatticeX[0],recLatticeY[0],recLatticeZ[0]],
recCell = [[recLatticeX[0],recLatticeY[0],recLatticeZ[0]],
[recLatticeX[1],recLatticeY[1],recLatticeZ[1]],
[recLatticeX[2],recLatticeY[2],recLatticeZ[2]]])
backend.addArrayValues("x_exciting_simulation_reciprocal_cell", recCell)
[recLatticeX[2],recLatticeY[2],recLatticeZ[2]]]
backend.addValue("x_exciting_simulation_reciprocal_cell", recCell)
def onClose_x_exciting_section_xc(self, backend, gIndex, section):
xcNr = section["x_exciting_xc_functional"][0]
......@@ -108,7 +107,7 @@ class ExcitingParserContext(object):
backend.addArrayValues("eigenvalues_kpoints", np.asarray(eigvalKpoint))
backend.addArrayValues("eigenvalues_values", np.asarray([eigvalVal]))
backend.addArrayValues("eigenvalues_occupation", np.asarray([eigvalOcc]))
backend.closeSection("section_eigenvalues", eigvalGIndex)
backend.closeSection("section_eigenvalues",eigvalGIndex)
# print ("values= ", eigvalVal)
# print ("kpoints= ", eigvalKpoint)
......@@ -155,7 +154,7 @@ class ExcitingParserContext(object):
else:
values[-1].append(float(st[0]))
elif len(s) < 5 and len(st) == 1:
number_of_bands = st[0]
number_of_bands = st[0]
mesh_size = grid[0]*grid[1]*grid[2]
origin.append(all_vectors[0])
vectors.append(all_vectors[1:])
......@@ -170,18 +169,18 @@ class ExcitingParserContext(object):
#######################TOTAL FORCES####################
f_st = []
if f_st:
f_st = section['x_exciting_store_total_forces']
atom_forces = [[],[]]
coord = []
for i in range (0, len(f_st)):
f_st[i] = f_st[i].split()
atom_forces[0].append(int(f_st[i][0]))
atom_forces[1].append([])
for j in range (3,6):
atom_forces[1][-1].append(float(f_st[i][j]))
backend.addArrayValues("x_exciting_atom_forces",np.asarray(f_st))
##### f_st = []
##### if f_st:
##### f_st = section['x_exciting_store_total_forces']
##### atom_forces = [[],[]]
##### coord = []
##### for i in range (0, len(f_st)):
##### f_st[i] = f_st[i].split()
##### atom_forces[0].append(int(f_st[i][0]))
##### atom_forces[1].append([])
##### for j in range (3,6):
##### atom_forces[1][-1].append(float(f_st[i][j]))
# backend.addArrayValues("x_exciting_atom_forces",np.asarray(f_st))
def onClose_section_system(self, backend, gIndex, section):
# dirPath = os.path.dirname(self.parser.fIn.name)
......@@ -197,9 +196,9 @@ class ExcitingParserContext(object):
backend.addArrayValues('atom_positions', np.asarray(self.atom_pos))
self.atom_pos = []
if self.atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(self.atom_labels, dtype=np.str))
backend.addArrayValues('atom_labels', np.asarray(self.atom_labels))
self.atom_labels = []
def onClose_x_exciting_section_atoms_group(self, backend, gIndex, section):
pos = [section['x_exciting_geometry_atom_positions_' + i] for i in ['x', 'y', 'z']]
......@@ -243,8 +242,8 @@ mainFileDescription = \
SM(r"\s*Species\s*:\s*[0-9]\s*\((?P<x_exciting_geometry_atom_labels>[-a-zA-Z0-9]+)\)", repeats = True,
sections = ["x_exciting_section_atoms_group"],
subMatchers = [
SM(r"\s*muffin-tin radius\s*:\s*(?P<x_exciting_muffin_tin_radius__bohr>[-0-9.]+)", repeats = True),
SM(r"\s*# of radial points in muffin-tin\s*:\s*(?P<x_exciting_muffin_tin_points>[-0-9.]+)", repeats = True),
# SM(r"\s*muffin-tin radius\s*:\s*(?P<x_exciting_muffin_tin_radius__bohr>[-0-9.]+)", repeats = True),
# SM(r"\s*# of radial points in muffin-tin\s*:\s*(?P<x_exciting_muffin_tin_points>[-0-9.]+)", repeats = True),
SM(startReStr = r"\s*atomic positions\s*\(lattice\)\s*:\s*",
subMatchers = [
SM(r"\s*(?P<x_exciting_geometry_atom_number>[+0-9]+)\s*:\s*(?P<x_exciting_geometry_atom_positions_x__bohr>[-+0-9.]+)\s*(?P<x_exciting_geometry_atom_positions_y__bohr>[-+0-9.]+)\s*(?P<x_exciting_geometry_atom_positions_z__bohr>[-+0-9.]+)", repeats = True)
......@@ -349,10 +348,11 @@ mainFileDescription = \
SM(name="total_forces",
startReStr = r"\s*Total atomic forces including IBS \(cartesian\)\s*:",
## SM(r"\s*atom\s*(?P<x_exciting_store_total_forces>[0-9]+\s*[A-Za-z]+\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+\s*[A-Za-z]+\s*[A-Za-z]+)",
subMatchers = [
SM(r"\s*atom\s*(?P<x_exciting_store_total_forces>[0-9]+\s*[A-Za-z]+\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+)",
repeats = True)
] )
##### subMatchers = [
##### SM(r"\s*atom\s*(?P<x_exciting_store_total_forces>[0-9]+\s*[A-Za-z]+\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+)",
##### repeats = True)
##### ] )
)
# print ("number atoms=", x_exciting_number_of_atoms)
# SM(name="force_components",
# startReStr = r"\s*Atomic force components including IBS \(cartesian\)\s*:",
......@@ -362,7 +362,7 @@ mainFileDescription = \
# SM(r"\s*(?P<x_exciting_store_total_forces>\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+\s*[A-Za-z]+\s*[A-Za-z]+)"),
# SM(r"\s*(?P<x_exciting_store_total_forces>\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+\s*[A-Za-z]+\s*[A-Za-z]+)")
# SM(r"\s*(?P<x_exciting_store_total_forces>\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+\s*[A-Za-z]+\s*[A-Za-z]+)"),
# ]
# ]
# )
])
]
......@@ -395,15 +395,4 @@ cachingLevelForMetaName = {
if __name__ == "__main__":
# for name in metaInfoEnv.infoKinds:
# print 'nameo', name
# Production
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext())
# Debug
# local_backend = LocalBackend(metaInfoEnv)
# mainFunction(mainFileDescription, metaInfoEnv, parserInfo, outF=local_backend.fileOut, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext(), superBackend=local_backend)
# results = local_backend.results
# program_name = results["program_name"]
# atom_labels = results["atom_labels"]
# print(program_name)
# print(atom_labels)
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