From cde754b33a5afd8c1eb9c7ba7c108fec2effdcd7 Mon Sep 17 00:00:00 2001
From: Daria Tomecka <zarvok79@yahoo.com>
Date: Mon, 3 Oct 2016 15:33:34 +0200
Subject: [PATCH] wien2k: update of units and atom positions
---
parser/parser-wien2k/wien2k_parser.py | 39 ++++++----------
parser/parser-wien2k/wien2k_parser_struct.py | 48 +++++++++++---------
2 files changed, 42 insertions(+), 45 deletions(-)
diff --git a/parser/parser-wien2k/wien2k_parser.py b/parser/parser-wien2k/wien2k_parser.py
index c0fe715..3011f50 100644
--- a/parser/parser-wien2k/wien2k_parser.py
+++ b/parser/parser-wien2k/wien2k_parser.py
@@ -3,7 +3,7 @@ import setup_paths
from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
+import os, sys, json, logging
import wien2k_parser_struct, wien2k_parser_in0, wien2k_parser_in1c, wien2k_parser_in2c, wien2k_parser_in1, wien2k_parser_in2
@@ -39,18 +39,6 @@ class Wien2kContext(object):
def onOpen_section_system(self, backend, gIndex, section):
self.secSystemIndex = gIndex
- 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)
def onOpen_section_method(self, backend, gIndex, section):
@@ -141,10 +129,10 @@ class Wien2kContext(object):
backend.addValue('x_wien2k_smearing_kind', value)
- smearing_width = section['x_wien2k_smearing_width__rydberg']
+ smearing_width = section['x_wien2k_smearing_width']
if smearing_width is not None:
# value = ''
- backend.addValue('x_wien2k_smearing_width__rydberg', value)
+ backend.addValue('x_wien2k_smearing_width', value)
# atom labels
atom_labels = section['x_wien2k_atom_name']
@@ -162,15 +150,18 @@ 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)))
- # unit_cell
- unit_cell = []
- for i in ['a', 'b', 'c']:
- uci = section['x_wien2k_unit_cell_param_' + i]
- if uci is not None:
- unit_cell.append(uci)
- if unit_cell:
- backend.addArrayValues('simulation_cell', np.asarray(unit_cell))
- backend.addArrayValues("configuration_periodic_dimensions", np.ones(3, dtype=bool))
+ 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)
diff --git a/parser/parser-wien2k/wien2k_parser_struct.py b/parser/parser-wien2k/wien2k_parser_struct.py
index 08a3660..35d8cd6 100644
--- a/parser/parser-wien2k/wien2k_parser_struct.py
+++ b/parser/parser-wien2k/wien2k_parser_struct.py
@@ -5,6 +5,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
import os, sys, json, logging
import numpy as np
+import ase.geometry
################################################################
@@ -29,15 +30,32 @@ class Wien2kStructContext(object):
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"]
+ #OB 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))]
@@ -45,24 +63,12 @@ class Wien2kStructContext(object):
labels += [label for i in range(nAt)]
pos += groupPos
backend.addValue("atom_labels", labels)
- backend.addValue("atom_positions", pos)
-##OR
-"""
- # atom_positions
- atom_pos = []
- for i in ['x', 'y', 'z']:
- api = section['x_wien2k_atom_pos_' + i]
- if api is not None:
- atom_pos.append(api)
- if atom_pos:
- # need to transpose array since its shape is [number_of_atoms,3] in the metadata
- backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos)))
-
- # atom labels
- atom_labels = section['x_wien2k_atom_name']
- if atom_labels is not None:
- backend.addArrayValues('atom_labels', np.asarray(atom_labels))
-"""
+ #backend.addValue("atom_positions", np.dot(pos,unit_cell))
+ #ok#backend.addArrayValues('atom_positions', np.transpose(np.asarray(pos)))
+ backend.addArrayValues('atom_positions', np.asarray(pos))
+
+
+
# description of the input
def buildStructureMatchers():
return SM(
@@ -76,12 +82,12 @@ def buildStructureMatchers():
SM(r"\w+\s*LATTICE,NONEQUIV\.ATOMS.\s*(?P<x_wien2k_nonequiv_atoms>[0-9]+)"),
SM(r"(?P<x_wien2k_calc_mode>.*)"),
# SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9.eEdD]+)\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9.eEdD]+)\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9.eEdD]+)\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+0-9.eEdD]{9})\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+0-9.eEdD]{9})\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+0-9.eEdD]+)"),
- SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
- SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
+ SM(r"\s*(?P<x_wien2k_unit_cell_param_a__angstrom>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b__angstrom>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c__angstrom>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
+ SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x__angstrom>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y__angstrom>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z__angstrom>[-+0-9.eEdD]+)",
repeats=True,
sections=["x_wien2k_section_equiv_atoms"],
subMatchers=[
- SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
+ SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x__angstrom>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y__angstrom>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z__angstrom>[-+0-9.eEdD]+)",
repeats=True
),
# SM(r"\s*(?P<atom>.{10})\s*NPT=\s*(?P<NPT>[0-9]+)\s*R0=(?P<r0>[0-9.]+)\s*RMT=\s*(?P<rmt>[0-9.]+)\s*Z:\s*(?P<z>[0-9.]+)",)
--
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