diff --git a/parser/parser-castep/CastepParser.py b/parser/parser-castep/CastepParser.py
index b1d35c3878ddd027e41eac8e2ba908d11f8573b1..5657090ecbc9a38ee9dacfe14695b3d41b7310c2 100644
--- a/parser/parser-castep/CastepParser.py
+++ b/parser/parser-castep/CastepParser.py
@@ -27,12 +27,16 @@ import logging, os, re, sys
logger = logging.getLogger("nomad.CastepParser")
+def dftPlusU(parser):
+ parser.superContext.method="DFT+U"
+
class CastepParserContext(object):
def __init__(self):
""" Initialise variables used within the current superContext """
- self.secMethodIndex =[]
- self.secSystemDescriptionIndex =[]
+ self.rootSecMethodIndex = None
+ self.secMethodIndex = None
+ self.secSystemDescriptionIndex = None
self.functionals = []
self.func_total = []
self.relativistic = []
@@ -166,11 +170,11 @@ class CastepParserContext(object):
#converting mass in Kg from AMU
mass[i] = float(mass[i]) * 1.66053904e-27
- backend.openSection('section_atom_type')
+ atomGIndex = backend.openSection('section_atom_type')
backend.addValue('atom_type_mass', float(mass[i]))
backend.addValue('atom_type_name', name[i])
- backend.closeSection('section_atom_type', gIndex+i)
+ backend.closeSection('section_atom_type', atomGIndex)
def onClose_x_castep_section_functionals(self, backend, gIndex, section):
"""When all the functional definitions have been gathered, matches them
@@ -268,8 +272,15 @@ class CastepParserContext(object):
def onClose_x_castep_section_geom_optimisation_method(self, backend, gIndex, section):
self.optim_method = section["x_castep_geometry_optim_method"]
- def onClose_section_method(self, backend, gIndex, section):
+ def onOpen_section_method(self, backend, gIndex, section):
+ if self.rootSecMethodIndex is None:
+ self.rootSecMethodIndex = gIndex
self.secMethodIndex = gIndex
+
+ def onClose_section_method(self, backend, gIndex, section):
+ if not self.method:
+ self.method = 'DFT'
+ backend.addValue('electronic_structure_method',self.method)
self.van_der_waals_name = section["van_der_Waals_method"]
if self.van_der_waals_name is not None:
@@ -294,10 +305,10 @@ class CastepParserContext(object):
self.func_and_weight = []
for i in range(len(self.functional_types)):
self.func_total.append(self.functionals[i]+'_'+self.functional_weight[i])
- backend.openSection('section_XC_functionals')
+ xcIndex = backend.openSection('section_XC_functionals')
backend.addValue('XC_functional_name', self.functionals[i])
backend.addValue('XC_functional_weight', self.functional_weight[i])
- backend.closeSection('section_XC_functionals',gIndex+i)
+ backend.closeSection('section_XC_functionals', xcIndex)
# Push the functional string into the backend
# Push the relativistic treatment string into the backend
backend.addValue('XC_functional', "_".join(sorted(self.functionals)))
@@ -363,10 +374,8 @@ class CastepParserContext(object):
if section['x_castep_smearing_kind'] and section['x_castep_smearing_width']:
sm_kind = section['x_castep_smearing_kind']
sm_width = section['x_castep_smearing_width']
- gindexsis = backend.openSection('section_method')
backend.addValue('smearing_kind', sm_kind[0])
backend.addValue('smearing_width', sm_width[0])
- backend.closeSection('section_method',gindexsis)
# Here we add basis set name and kind for the plane wave code
def onClose_section_basis_set_cell_dependent(self, backend, gIndex, section):
ecut_str = section['x_castep_basis_set_planewave_cutoff']
@@ -452,7 +461,6 @@ class CastepParserContext(object):
* math.cos(np.deg2rad(self.gamma[0])) ) * self.a[0]*self.b[0]*self.c[0]
# Storing the total energy of each SCF iteration in an array
-
# Processing forces acting on atoms (final converged forces)
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
@@ -679,9 +687,11 @@ class CastepParserContext(object):
################ Triggers on closure section_system ######################
######################################################################################
+ def onOpen_section_system(self, backend, gIndex, section):
+ self.secSystemDescriptionIndex = gIndex
+
def onClose_section_system(self, backend, gIndex, section):
"""trigger called when _section_system is closed"""
- self.secSystemDescriptionIndex = gIndex
# Processing the atom positions in fractionary coordinates (as given in the CASTEP output)
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
pos = section['x_castep_store_atom_positions']
@@ -986,10 +996,8 @@ class CastepParserContext(object):
self.k_start_end = cellSuperContext.k_sgt_start_end # recover k path segments coordinartes from *.cell file
self.k_path_nr = len(self.k_start_end)
# backend.openSection('section_single_configuration_to_calculation_ref')
- if self.n_spin_channels_bands:
- backend.openSection('section_method')
- backend.addValue('number_of_spin_channels',self.n_spin_channels_bands)
- backend.closeSection('section_method',gIndex+1)
+ # if self.n_spin_channels_bands:
+ # backend.addValue('number_of_spin_channels',self.n_spin_channels_bands)
########################################################################################
def get_last_index(el, check): # function that returns end index for each k path segment
@@ -1046,13 +1054,6 @@ class CastepParserContext(object):
def onClose_section_run(self, backend, gIndex, section):
# self.basis_set_type = 'plane_waves'
- if section['x_castep_elec_methd']:
- self.method = 'DFT+U'
- else:
- self.method = 'DFT'
- meth_ind=backend.openSection('section_method')
- backend.addValue('electronic_structure_method',self.method)
- backend.closeSection('section_method',meth_ind)
backend.addValue('program_basis_set_type', self.basis_set_kind)
f_st_band = section['x_castep_store_atom_forces_band']
evAtoN = float(1.6021766e-9)
@@ -1118,13 +1119,13 @@ class CastepParserContext(object):
gIndexGroupscf = backend.openSection('section_scf_iteration')
for i in range(len(self.frame_atom_forces)):
- backend.openSection('section_system')
+ backend.openNonOverlappingSection('section_system')
backend.addArrayValues('atom_velocities', np.asarray(self.frame_atom_veloc[i]))
backend.addArrayValues('atom_labels', np.asarray(self.atom_labels))
backend.addArrayValues('atom_positions', np.asarray(self.frame_position[i]))
backend.addArrayValues('simulation_cell', np.asarray(self.frame_cell[i]))
backend.addArrayValues('x_castep_velocities_cell_vector',np.asarray(self.frame_vet_velocities[i]))
- backend.closeSection('section_system',i+2)
+ backend.closeNonOverlappingSection('section_system')
backend.openSection('section_single_configuration_calculation')
backend.addArrayValues('atom_forces', np.asarray(self.frame_atom_forces[i]))
@@ -1259,7 +1260,7 @@ def build_CastepMainFileSimpleMatcher():
calculationMethodSubMatcher = SM(name = 'calculationMethods',
startReStr = r"\s\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* Exchange-Correlation Parameters \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*",
forwardMatch = True,
- sections = ["section_method"],
+ sections = [],
subMatchers = [
SM(name = "castepXC",
@@ -2201,7 +2202,7 @@ def build_CastepMainFileSimpleMatcher():
startReStr = r"\s\|\s*CCC\s*AA\s*SSS\s*TTTTT\s*EEEEE\s*PPPP\s*\|\s*",
required = True,
forwardMatch = True,
- sections = ['section_run'],
+ sections = ['section_run', "section_method"],
subMatchers = [
@@ -2271,7 +2272,7 @@ def build_CastepMainFileSimpleMatcher():
#endReStr = "\n",),
]), # CLOSING section_atom_topology
- SM(r"\s*Units for (?P<x_castep_elec_methd>[a-zA-Z]+)\sU\svalues\sare+"),
+ SM(r"\s*Units for (?P<x_castep_elec_methd>[a-zA-Z]+)\sU\svalues\sare+", adHoc = dftPlusU ), # x_castep_elec_methd should be in the section method...
SM(r"\s*Point group of crystal\s\=\s*[0-9.]+\:\s(?P<x_castep_crystal_point_group>[a-zA-Z0-9.]+)"),
SM(r"\s*Space group of crystal\s\=\s*[0-9.]+\:\s(?P<x_castep_space_group>[a-zA-Z0-9.]+)"),