From d05af29c3567d2e8f2fe64f502d0692f47cab995 Mon Sep 17 00:00:00 2001
From: lopa <pardini@physik.hu-berlin.de>
Date: Wed, 16 Nov 2016 14:39:00 +0100
Subject: [PATCH] fixed bug with atom positions
---
parser/parser-elk/parser_elk.py | 41 +++++++++++++++++++++++++--------
1 file changed, 31 insertions(+), 10 deletions(-)
diff --git a/parser/parser-elk/parser_elk.py b/parser/parser-elk/parser_elk.py
index 600daa3..b167319 100644
--- a/parser/parser-elk/parser_elk.py
+++ b/parser/parser-elk/parser_elk.py
@@ -22,7 +22,10 @@ class ElkContext(object):
self.parser = parser
# allows to reset values if the same superContext is used to parse different files
self.initialize_values()
+
self.enTot = []
+ self.atom_pos = []
+ self.atom_labels = []
def onClose_x_elk_section_lattice_vectors(self, backend, gIndex, section):
latticeX = section["x_elk_geometry_lattice_vector_x"]
@@ -118,16 +121,33 @@ class ElkContext(object):
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
self.secSystemDescriptionIndex = gIndex
- atom_pos = []
- for i in ['x', 'y', 'z']:
- api = section['x_elk_geometry_atom_positions_' + i]
- if api is not None:
- atom_pos.append(api)
- if atom_pos:
- backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos)))
- atom_labels = section['x_elk_geometry_atom_labels']
- if atom_labels is not None:
- backend.addArrayValues('atom_labels', np.asarray(atom_labels))
+# atom_pos = []
+# for i in ['x', 'y', 'z']:
+# api = section['x_elk_geometry_atom_positions_' + i]
+# if api is not None:
+# atom_pos.append(api)
+# if atom_pos:
+# backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos)))
+# atom_labels = section['x_elk_geometry_atom_labels']
+# if atom_labels is not None:
+# backend.addArrayValues('atom_labels', np.asarray(atom_labels))
+
+ if self.atom_pos:
+ 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))
+ self.atom_labels = []
+
+ def onClose_x_elk_section_atoms_group(self, backend, gIndex, section):
+ pos = [section['x_elk_geometry_atom_positions_' + i] for i in ['x', 'y', 'z']]
+ pl = [len(comp) for comp in pos]
+ natom = pl[0]
+ if pl[1] != natom or pl[2] != natom:
+ raise Exception("invalid number of atoms in various components %s" % pl)
+ for i in range(natom):
+ self.atom_pos.append([pos[0][i], pos[1][i], pos[2][i]])
+ self.atom_labels = self.atom_labels + (section['x_elk_geometry_atom_labels'] * natom)
def onClose_section_scf_iteration(self, backend, gIndex, section):
Etot = section["energy_total_scf_iteration"]
@@ -164,6 +184,7 @@ mainFileDescription = \
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.]+)"),
SM(r"\s*Species\s*:\s*[0-9]\s*\((?P<x_elk_geometry_atom_labels>[-a-zA-Z0-9]+)\)", repeats = True,
+ sections = ["x_elk_section_atoms_group"],
subMatchers = [
SM(r"\s*muffin-tin radius\s*:\s*(?P<x_elk_muffin_tin_radius__bohr>[-0-9.]+)"),
SM(r"\s*number of radial points in muffin-tin\s*:\s*(?P<x_elk_muffin_tin_points>[-0-9.]+)"),
--
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