diff --git a/parser/parser-qbox/QboxInputParser.py b/parser/parser-qbox/QboxInputParser.py
new file mode 100644
index 0000000000000000000000000000000000000000..0fb28bc34f963f6de9b28f148f2fdee175dba241
--- /dev/null
+++ b/parser/parser-qbox/QboxInputParser.py
@@ -0,0 +1,303 @@
+from builtins import object
+import setup_paths
+import numpy as np
+import nomadcore.ActivateLogging
+from nomadcore.caching_backend import CachingLevel
+from nomadcore.simple_parser import AncillaryParser, mainFunction
+from nomadcore.simple_parser import SimpleMatcher as SM
+from QboxCommon import get_metaInfo
+import logging, os, re, sys
+
+############################################################
+# This is the parser for the input file of qbox.
+############################################################
+
+
+############################################################
+###############[1] transfer PARSER CONTEXT #################
+############################################################
+logger = logging.getLogger("nomad.qboxInputParser")
+
+class QboxInputParserContext(object):
+
+ def __init__(self):
+ self.functionals = []
+
+
+ def initialize_values(self):
+ """Initializes the values of certain variables.
+
+ This allows a consistent setting and resetting of the variables,
+ when the parsing starts and when a section_run closes.
+ """
+ self.secMethodIndex = None
+ self.secSystemDescriptionIndex = None
+
+ self.singleConfCalcs = []
+
+
+ def startedParsing(self, fInName, parser):
+ """Function is called when the parsing starts.
+
+ Get compiled parser, filename and metadata.
+
+ Args:
+ fInName: The file name on which the current parser is running.
+ parser: The compiled parser. Is an object of the class SimpleParser in nomadcore.simple_parser.py.
+ """
+ self.parser = parser
+ self.fName = fInName
+ # save metadata
+ self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
+ # allows to reset values if the same superContext is used to parse different files
+ self.initialize_values()
+
+
+ def onClose_section_run(self, backend, gIndex, section):
+ """Trigger called when section_run is closed.
+ """
+ # reset all variables
+ self.initialize_values()
+ # frame sequence
+ sampling_method = "geometry_optimization"
+
+ samplingGIndex = backend.openSection("section_sampling_method")
+ backend.addValue("sampling_method", sampling_method)
+ backend.closeSection("section_sampling_method", samplingGIndex)
+ frameSequenceGIndex = backend.openSection("section_frame_sequence")
+ backend.addValue("frame_sequence_to_sampling_ref", samplingGIndex)
+ backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs))
+ backend.closeSection("section_frame_sequence", frameSequenceGIndex)
+
+
+
+ def onClose_x_qbox_section_functionals(self, backend, gIndex, section):
+ functional_list = section["x_qbox_functional_name"]
+
+ if not functional_list: # default is LDA in qbox
+ functional = "LDA"
+ else :
+ functional = functional_list[-1] # use the xc appeared the last time
+
+
+ if functional:
+ functionalMap = {
+ "LDA": ["LDA_X", "LDA_C_PZ"],
+ "VMN": ["LDA_X", "LDA_C_VWN"],
+ "PBE": ["GGA_X_PBE","GGA_C_PBE"],
+ "PBE0": ["GGA_X_PBE","GGA_C_PBE"],
+ "B3LYP": ["HYB_GGA_XC_B3LYP5"]
+ #need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
+ }
+ # Push the functional string into the backend
+ nomadNames = functionalMap.get(functional)
+ if not nomadNames:
+ raise Exception("Unhandled xc functional %s found" % functional)
+ for name in nomadNames:
+ s = backend.openSection("section_XC_functionals")
+ backend.addValue('XC_functional_name', name)
+ backend.closeSection("section_XC_functionals", s)
+
+
+
+
+ ###################################################################
+ # (3.4) onClose for geometry and force (section_system)
+ # todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
+ ###################################################################
+ def onOpen_section_method(self, backend, gIndex, section):
+ # keep track of the latest method section
+ self.secMethodIndex = gIndex
+
+
+ def onOpen_section_system(self, backend, gIndex, section):
+ # keep track of the latest system description section
+ self.secSystemDescriptionIndex = gIndex
+
+
+ def onClose_section_system(self, backend, gIndex, section):
+ """Trigger called when section_system is closed.
+ Writes atomic positions, atom labels and lattice vectors.
+ """
+ # keep track of the latest system description section
+ self.secSystemDescriptionIndex = gIndex
+
+ #------1.atom_positions
+ atom_pos = []
+ for i in ['x', 'y', 'z']:
+ api = section['x_qbox_geometry_atom_positions_' + 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)))
+
+ #------2.atom labels
+ atom_labels = section['x_qbox_geometry_atom_labels']
+ if atom_labels is not None:
+ backend.addArrayValues('atom_labels', np.asarray(atom_labels))
+
+
+
+ #----3. unit_cell
+ unit_cell = []
+ for i in ['x', 'y', 'z']:
+ uci = section['x_qbox_geometry_lattice_vector_' + 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))
+
+
+
+
+ def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
+ self.singleConfCalcs.append(gIndex)
+
+ def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
+# write the references to section_method and section_system
+ backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
+ backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemDescriptionIndex)
+
+
+
+
+
+
+#############################################################
+#################[2] MAIN PARSER STARTS HERE ###############
+#############################################################
+
+def build_QboxInputFileSimpleMatcher():
+ """Builds the SimpleMatcher to parse the input file of qbox (*.i) .
+
+ First, several subMatchers are defined, which are then used to piece together
+ the final SimpleMatcher.
+ SimpleMatchers are called with 'SM (' as this string has length 4,
+ which allows nice formating of nested SimpleMatchers in python.
+
+ Returns:
+ SimpleMatcher that parses input file of qbox.
+ """
+
+
+
+
+ ####################################################################
+ # (2) submatcher for control method that echo INPUT file (section_method)
+ ####################################################################
+ calculationMethodSubMatcher = SM(name = 'calculationMethods',
+ startReStr = "",
+ #endReStr = r"\s*",
+ repeats = True,
+ sections = ["section_method"],
+ subMatchers = [
+
+
+ #--------k_point-------------
+ SM(r"\s*kpoint add\s+(?P<x_qbox_k_point_x>[-+0-9.eEdD]+)\s+(?P<x_qbox_k_point_y>[-+0-9.eEdD]+)\s+(?P<x_qbox_k_point_z>[-+0-9.eEdD]+)\s+(?P<x_qbox_k_point_weight>[-+0-9.eEdD]+)\s*",repeats = True),
+
+ #--------set method---------
+ SM(r"\s*set\s+ecut\s+(?P<x_qbox_ecut__rydberg>[0-9.]+)\s*"),
+ SM(r"\s*set\s+wf_dyn\s+(?P<x_qbox_wf_dyn>[A-Za-z0-9]+)\s*"),
+ SM(r"\s*set\s+atoms_dyn\s+(?P<x_qbox_atoms_dyn>[A-Za-z0-9]+)\s*"),
+ SM(r"\s*set\s+cell_dyn\s+(?P<x_qbox_cell_dyn>[A-Za-z0-9]+)\s*"),
+
+ #--------set xc---------
+ SM(name = "qboxXC",
+ startReStr = r"\s*set\s+xc\s+(?P<x_qbox_functional_name>[A-Za-z0-9]+)\s*",
+ sections = ["x_qbox_section_functionals"]
+ ),
+
+ #-------set efield---------
+ SM (r"\s*set\s+e_field\s*(?P<x_qbox_efield_x>[-+0-9.]+)\s+(?P<x_qbox_efield_y>[-+0-9.]+)\s+(?P<x_qbox_efield_z>[-+0-9.]+)\s*",repeats = True)
+ #???both this version adn qbox_section_efield version could not give mather for efield, need to check.
+ ])
+
+
+
+
+
+
+ ########################################
+ # return main Parser
+ ########################################
+ return SM (name = 'Root',
+
+ startReStr = "",
+ forwardMatch = True,
+ weak = True,
+ subMatchers = [
+
+ #=============================================================================
+ # read OUPUT file *.r, the method part comes from INPUT file *.i, so we
+ # do not need to parser INPUT file, the OUTPUT file contains all information
+ #=============================================================================
+ SM (name = 'NewRun',
+ startReStr = r"",
+ #endReStr = r"\s*<end_time",
+ repeats = False,
+ required = True,
+ forwardMatch = True,
+ fixedStartValues={'program_name': 'qbox', 'program_basis_set_type': 'plane waves'},
+ sections = ['section_run'],
+ subMatchers = [
+
+ #-----------input method---------------------
+ calculationMethodSubMatcher
+
+ ]) # CLOSING SM NewRun
+
+
+ ]) # END Root
+
+def get_cachingLevelForMetaName(metaInfoEnv):
+ """Sets the caching level for the metadata.
+
+ Args:
+ metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
+
+ Returns:
+ Dictionary with metaname as key and caching level as value.
+ """
+ # manually adjust caching of metadata
+ cachingLevelForMetaName = {
+ 'eigenvalues_values': CachingLevel.Cache,
+ 'eigenvalues_kpoints':CachingLevel.Cache
+ }
+
+ # Set caching for temparary storage variables
+ for name in metaInfoEnv.infoKinds:
+ if ( name.startswith('x_qbox_store_')
+ or name.startswith('x_qbox_cell_')):
+ cachingLevelForMetaName[name] = CachingLevel.Cache
+ return cachingLevelForMetaName
+
+
+
+
+def main():
+ """Main function.
+
+ Set up everything for the parsing of the qbox main file and run the parsing.
+ """
+ # get main file description
+ QboxInputFileSimpleMatcher = build_QboxInputFileSimpleMatcher()
+ # loading metadata from nomad-meta-info/meta_info/nomad_meta_info/qbox.nomadmetainfo.json
+ metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../nomad-meta-info/meta_info/nomad_meta_info/qbox.nomadmetainfo.json"))
+ metaInfoEnv = get_metaInfo(metaInfoPath)
+ # set parser info
+ parserInfo = {'name':'qbox-input-parser', 'version': '1.0'}
+ # get caching level for metadata
+ cachingLevelForMetaName = get_cachingLevelForMetaName(metaInfoEnv)
+ # start parsing
+ mainFunction(mainFileDescription = QboxInputFileSimpleMatcher,
+ metaInfoEnv = metaInfoEnv,
+ parserInfo = parserInfo,
+ cachingLevelForMetaName = cachingLevelForMetaName,
+ superContext = QboxInputParserContext())
+
+if __name__ == "__main__":
+ main()
+
diff --git a/parser/parser-qbox/QboxParser.py b/parser/parser-qbox/QboxParser.py
index fecf929a3c95436d2f81d7738f213b5d710446bf..be995ead97bbaa5ae5c23d14407c28a79cbf9364 100644
--- a/parser/parser-qbox/QboxParser.py
+++ b/parser/parser-qbox/QboxParser.py
@@ -10,7 +10,7 @@ import QboxXMLParser
import logging, os, re, sys
############################################################
-# This is the parser for the main file of qbox.
+# This is the parser for the main file of qbox (for the output file *.r) .
############################################################
@@ -74,11 +74,11 @@ class QboxParserContext(object):
#################################################################
# (2) onClose for INPUT control (section_method)
#################################################################
- def onClose_qbox_section_xml_file(self, backend, gIndex, section):
+ def onClose_x_qbox_section_xml_file(self, backend, gIndex, section):
- qbox_loading_xml_file_list = section['qbox_loading_xml_file']
+ x_qbox_loading_xml_file_list = section['x_qbox_loading_xml_file']
- xml_file = qbox_loading_xml_file_list[-1]
+ xml_file = x_qbox_loading_xml_file_list[-1]
if xml_file is not None:
logger.warning("This output showed this calculation need to load xml file, so we need this xml file ('%s') to read geometry information" % os.path.normpath(xml_file) )
@@ -99,8 +99,8 @@ class QboxParserContext(object):
logger.warning("Could not find xml file in directory '%s'. " % os.path.dirname(os.path.abspath(self.fName)))
- def onClose_qbox_section_functionals(self, backend, gIndex, section):
- functional_list = section["qbox_functional_name"]
+ def onClose_x_qbox_section_functionals(self, backend, gIndex, section):
+ functional_list = section["x_qbox_functional_name"]
if not functional_list: # default is LDA in qbox
functional = "LDA"
@@ -195,7 +195,7 @@ class QboxParserContext(object):
#------1.atom_positions
atom_pos = []
for i in ['x', 'y', 'z']:
- api = section['qbox_geometry_atom_positions_' + i]
+ api = section['x_qbox_geometry_atom_positions_' + i]
if api is not None:
atom_pos.append(api)
if atom_pos:
@@ -203,14 +203,14 @@ class QboxParserContext(object):
backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos)))
#------2.atom labels
- atom_labels = section['qbox_geometry_atom_labels']
+ atom_labels = section['x_qbox_geometry_atom_labels']
if atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
#------3.atom force
atom_force = []
for i in ['x', 'y', 'z']:
- api = section['qbox_atom_force_' + i]
+ api = section['x_qbox_atom_force_' + i]
if api is not None:
atom_force.append(api)
if atom_force:
@@ -221,7 +221,7 @@ class QboxParserContext(object):
#----4. unit_cell
unit_cell = []
for i in ['x', 'y', 'z']:
- uci = section['qbox_geometry_lattice_vector_' + i]
+ uci = section['x_qbox_geometry_lattice_vector_' + i]
if uci is not None:
unit_cell.append(uci)
if unit_cell:
@@ -240,15 +240,15 @@ class QboxParserContext(object):
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemDescriptionIndex)
- def onClose_qbox_section_stress_tensor(self, backend, gIndex, section):
- qbox_stress_tensor = []
+ def onClose_x_qbox_section_stress_tensor(self, backend, gIndex, section):
+ x_qbox_stress_tensor = []
for i in ['xx', 'yy', 'zz', 'xy', 'yz', 'xz']:
- api = section['qbox_stress_tensor_' + i]
+ api = section['x_qbox_stress_tensor_' + i]
if api is not None:
- qbox_stress_tensor.append(api)
- if qbox_stress_tensor:
+ x_qbox_stress_tensor.append(api)
+ if x_qbox_stress_tensor:
# need to transpose array since its shape is [number_of_atoms,3] in the metadata
- backend.addArrayValues('stress_tensor', np.transpose(np.asarray(qbox_stress_tensor)))
+ backend.addArrayValues('stress_tensor', np.transpose(np.asarray(x_qbox_stress_tensor)))
@@ -276,14 +276,14 @@ def build_QboxMainFileSimpleMatcher():
#####################################################################
# (1) submatcher for header
- #note: we add qbox_section_functionals here because we want to add
+ #note: we add x_qbox_section_functionals here because we want to add
# a default LDA here even 'set xc' is not shown in *.i file.
#####################################################################
headerSubMatcher = SM(name = 'ProgramHeader',
startReStr = r"\s*I qbox\s+(?P<program_version>[0-9.]+)",
- sections = ["qbox_section_functionals"],
+ sections = ["x_qbox_section_functionals"],
subMatchers = [
- SM(r"\s*<nodename>\s+(?P<qbox_nodename>[a-zA-Z0-9.-]+)\s+</nodename>")
+ SM(r"\s*<nodename>\s+(?P<x_qbox_nodename>[a-zA-Z0-9.-]+)\s+</nodename>")
])
####################################################################
@@ -313,28 +313,28 @@ def build_QboxMainFileSimpleMatcher():
SM(name = "qboxXMLfile",
startReStr = r"\s*LoadCmd",
forwardMatch = True, #use this or not like qboxXC
- sections = ["qbox_section_xml_file"],
+ sections = ["x_qbox_section_xml_file"],
subMatchers = [
- SM(r"\s*LoadCmd:\s*loading from\s+(?P<qbox_loading_xml_file>[A-Za-z0-9./-_]+)"),
+ SM(r"\s*LoadCmd:\s*loading from\s+(?P<x_qbox_loading_xml_file>[A-Za-z0-9./-_]+)"),
]), # CLOSING qbox_section_xml_file
#--------k_point-------------
- SM(r"\s*\[qbox\]\s+<cmd>\s*kpoint add\s+(?P<qbox_k_point_x>[-+0-9.eEdD]+)\s+(?P<qbox_k_point_y>[-+0-9.eEdD]+)\s+(?P<qbox_k_point_z>[-+0-9.eEdD]+)\s+(?P<qbox_k_point_weight>[-+0-9.eEdD]+)\s*</cmd>",repeats = True),
+ SM(r"\s*\[qbox\]\s+<cmd>\s*kpoint add\s+(?P<x_qbox_k_point_x>[-+0-9.eEdD]+)\s+(?P<x_qbox_k_point_y>[-+0-9.eEdD]+)\s+(?P<x_qbox_k_point_z>[-+0-9.eEdD]+)\s+(?P<x_qbox_k_point_weight>[-+0-9.eEdD]+)\s*</cmd>",repeats = True),
#--------set method---------
- SM(r"\s*\[qbox\]\s*\[qbox\]\s*<cmd>\s*set\s+ecut\s+(?P<qbox_ecut__rydberg>[0-9.]+)\s*</cmd>"),
- SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+wf_dyn\s+(?P<qbox_wf_dyn>[A-Za-z0-9]+)\s*</cmd>"),
- SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+atoms_dyn\s+(?P<qbox_atoms_dyn>[A-Za-z0-9]+)\s*</cmd>"),
- SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+cell_dyn\s+(?P<qbox_cell_dyn>[A-Za-z0-9]+)\s*</cmd>"),
+ SM(r"\s*\[qbox\]\s*\[qbox\]\s*<cmd>\s*set\s+ecut\s+(?P<x_qbox_ecut__rydberg>[0-9.]+)\s*</cmd>"),
+ SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+wf_dyn\s+(?P<x_qbox_wf_dyn>[A-Za-z0-9]+)\s*</cmd>"),
+ SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+atoms_dyn\s+(?P<x_qbox_atoms_dyn>[A-Za-z0-9]+)\s*</cmd>"),
+ SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+cell_dyn\s+(?P<x_qbox_cell_dyn>[A-Za-z0-9]+)\s*</cmd>"),
#--------set xc---------
SM(name = "qboxXC",
- startReStr = r"\s*\[qbox\]\s+<cmd>\s*set\s+xc\s+(?P<qbox_functional_name>[A-Za-z0-9]+)\s*</cmd>",
- sections = ["qbox_section_functionals"]
+ startReStr = r"\s*\[qbox\]\s+<cmd>\s*set\s+xc\s+(?P<x_qbox_functional_name>[A-Za-z0-9]+)\s*</cmd>",
+ sections = ["x_qbox_section_functionals"]
),
#-------set efield---------
- SM (r"\s*\[qbox\]\s*\[qbox\]\s*<cmd>\s*set\s+e_field\s*(?P<qbox_efield_x>[-+0-9.]+)\s+(?P<qbox_efield_y>[-+0-9.]+)\s+(?P<qbox_efield_z>[-+0-9.]+)\s*</cmd>",repeats = True)
+ SM (r"\s*\[qbox\]\s*\[qbox\]\s*<cmd>\s*set\s+e_field\s*(?P<x_qbox_efield_x>[-+0-9.]+)\s+(?P<x_qbox_efield_y>[-+0-9.]+)\s+(?P<x_qbox_efield_z>[-+0-9.]+)\s*</cmd>",repeats = True)
#???both this version adn qbox_section_efield version could not give mather for efield, need to check.
])
@@ -381,51 +381,51 @@ def build_QboxMainFileSimpleMatcher():
subMatchers = [
SM (startReStr = r"\s*<unit_cell\s*",
subMatchers = [
- SM (r"\s*[a-z]=\"\s*(?P<qbox_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_lattice_vector_z__bohr>[-+0-9.]+)\s*\"", repeats = True)
+ SM (r"\s*[a-z]=\"\s*(?P<x_qbox_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_lattice_vector_z__bohr>[-+0-9.]+)\s*\"", repeats = True)
]),
- SM (startReStr = r"\s*<atom\s+name=\"(?P<qbox_geometry_atom_labels>[a-zA-Z0-9]+)\"",
+ SM (startReStr = r"\s*<atom\s+name=\"(?P<x_qbox_geometry_atom_labels>[a-zA-Z0-9]+)\"",
subMatchers = [
- SM (r"\s*<position>\s+(?P<qbox_geometry_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_atom_positions_z__bohr>[-+0-9.]+)\s*</position>", repeats = True),
- SM (r"\s*<force>\s+(?P<qbox_atom_force_x__hartree_bohr_1>[-+0-9.]+)\s+(?P<qbox_atom_force_y__hartree_bohr_1>[-+0-9.]+)\s+(?P<qbox_atom_force_z__hartree_bohr_1>[-+0-9.]+)\s*</force>", repeats = True)
+ SM (r"\s*<position>\s+(?P<x_qbox_geometry_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_atom_positions_z__bohr>[-+0-9.]+)\s*</position>", repeats = True),
+ SM (r"\s*<force>\s+(?P<x_qbox_atom_force_x__hartree_bohr_1>[-+0-9.]+)\s+(?P<x_qbox_atom_force_y__hartree_bohr_1>[-+0-9.]+)\s+(?P<x_qbox_atom_force_z__hartree_bohr_1>[-+0-9.]+)\s*</force>", repeats = True)
], repeats = True)
])
#####################################################################
- # (3.5) submatcher for OUTPUT stress_tensor(qbox_section_stress_tensor)
+ # (3.5) submatcher for OUTPUT stress_tensor(x_qbox_section_stress_tensor)
#####################################################################
stresstensorSubMatcher = SM(name = 'StressTensor',
startReStr = r"\s*<stress_tensor\s*unit=\"GPa\">",
- sections = ['qbox_section_stress_tensor'],
+ sections = ['x_qbox_section_stress_tensor'],
subMatchers = [
- SM (r"\s*<sigma_xx>\s+(?P<qbox_stress_tensor_xx__GPa>[-+0-9.]+)\s*</sigma_xx>"),
- SM (r"\s*<sigma_yy>\s+(?P<qbox_stress_tensor_yy__GPa>[-+0-9.]+)\s*</sigma_yy>"),
- SM (r"\s*<sigma_zz>\s+(?P<qbox_stress_tensor_zz__GPa>[-+0-9.]+)\s*</sigma_zz>"),
- SM (r"\s*<sigma_xy>\s+(?P<qbox_stress_tensor_xy__GPa>[-+0-9.]+)\s*</sigma_xy>"),
- SM (r"\s*<sigma_yz>\s+(?P<qbox_stress_tensor_yz__GPa>[-+0-9.]+)\s*</sigma_yz>"),
- SM (r"\s*<sigma_xz>\s+(?P<qbox_stress_tensor_xz__GPa>[-+0-9.]+)\s*</sigma_xz>")
+ SM (r"\s*<sigma_xx>\s+(?P<x_qbox_stress_tensor_xx__GPa>[-+0-9.]+)\s*</sigma_xx>"),
+ SM (r"\s*<sigma_yy>\s+(?P<x_qbox_stress_tensor_yy__GPa>[-+0-9.]+)\s*</sigma_yy>"),
+ SM (r"\s*<sigma_zz>\s+(?P<x_qbox_stress_tensor_zz__GPa>[-+0-9.]+)\s*</sigma_zz>"),
+ SM (r"\s*<sigma_xy>\s+(?P<x_qbox_stress_tensor_xy__GPa>[-+0-9.]+)\s*</sigma_xy>"),
+ SM (r"\s*<sigma_yz>\s+(?P<x_qbox_stress_tensor_yz__GPa>[-+0-9.]+)\s*</sigma_yz>"),
+ SM (r"\s*<sigma_xz>\s+(?P<x_qbox_stress_tensor_xz__GPa>[-+0-9.]+)\s*</sigma_xz>")
])
####################################################################
- # (4.1) submatcher for properties : MLWF (qbox_section_MLWF)
+ # (4.1) submatcher for properties : MLWF (x_qbox_section_MLWF)
####################################################################
MLWFSubMatcher = SM(name = 'MLWF',
startReStr = r"\s*<mlwfs>",
- sections = ["qbox_section_MLWF"],
+ sections = ["x_qbox_section_MLWF"],
subMatchers = [
- SM (r"\s*<mlwf center=\"\s*(?P<qbox_geometry_MLWF_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_MLWF_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_MLWF_atom_positions_z__bohr>[-+0-9.]+)\s*\"\s+spread=\"\s*(?P<qbox_geometry_MLWF_atom_spread__bohr>[-+0-9.]+)\s*\"", repeats = True)
+ SM (r"\s*<mlwf center=\"\s*(?P<x_qbox_geometry_MLWF_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_MLWF_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_MLWF_atom_positions_z__bohr>[-+0-9.]+)\s*\"\s+spread=\"\s*(?P<x_qbox_geometry_MLWF_atom_spread__bohr>[-+0-9.]+)\s*\"", repeats = True)
])
####################################################################
- # (4.2) submatcher for properties : dipole (qbox_section_dipole)
+ # (4.2) submatcher for properties : dipole (x_qbox_section_dipole)
####################################################################
dipoleSubMatcher = SM(name = 'Dipole',
startReStr = r"\s*<dipole>",
- sections = ["qbox_section_dipole"],
+ sections = ["x_qbox_section_dipole"],
subMatchers = [
- SM (r"\s*<dipole_total>\s+(?P<qbox_dipole_x>[-+0-9.]+)\s+(?P<qbox_dipole_y>[-+0-9.]+)\s+(?P<qbox_dipole_z>[-+0-9.]+)\s*</dipole_total>", repeats = True)
+ SM (r"\s*<dipole_total>\s+(?P<x_qbox_dipole_x>[-+0-9.]+)\s+(?P<x_qbox_dipole_y>[-+0-9.]+)\s+(?P<x_qbox_dipole_z>[-+0-9.]+)\s*</dipole_total>", repeats = True)
])
########################################
@@ -507,8 +507,8 @@ def get_cachingLevelForMetaName(metaInfoEnv):
# Set caching for temparary storage variables
for name in metaInfoEnv.infoKinds:
- if ( name.startswith('qbox_store_')
- or name.startswith('qbox_cell_')):
+ if ( name.startswith('x_qbox_store_')
+ or name.startswith('x_qbox_cell_')):
cachingLevelForMetaName[name] = CachingLevel.Cache
return cachingLevelForMetaName
diff --git a/parser/parser-qbox/QboxXMLParser.py b/parser/parser-qbox/QboxXMLParser.py
index 34ba223993289cb16ea95d9138757b906169fc5c..570f4051f8f1c940c8f7690fdb9a195db6bf4dbb 100644
--- a/parser/parser-qbox/QboxXMLParser.py
+++ b/parser/parser-qbox/QboxXMLParser.py
@@ -46,7 +46,7 @@ class QboxXMLParserContext(object):
#------1.atom_positions
atom_pos = []
for i in ['x', 'y', 'z']:
- api = section['qbox_geometry_atom_positions_' + i]
+ api = section['x_qbox_geometry_atom_positions_' + i]
if api is not None:
atom_pos.append(api)
if atom_pos:
@@ -54,7 +54,7 @@ class QboxXMLParserContext(object):
backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos)))
#------2.atom labels
- atom_labels = section['qbox_geometry_atom_labels']
+ atom_labels = section['x_qbox_geometry_atom_labels']
if atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
@@ -82,11 +82,11 @@ def build_QboxXMLFileSimpleMatcher():
subMatchers = [
SM (startReStr = r"\s*<unit_cell\s*",
subMatchers = [
- SM (r"\s*[a-z]=\"\s*(?P<qbox_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_lattice_vector_z__bohr>[-+0-9.]+)\s*\"", repeats = True)
+ SM (r"\s*[a-z]=\"\s*(?P<x_qbox_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_lattice_vector_z__bohr>[-+0-9.]+)\s*\"", repeats = True)
]),
- SM (startReStr = r"\s*<atom\s+name=\"(?P<qbox_geometry_atom_labels>[a-zA-Z0-9]+)\"",
+ SM (startReStr = r"\s*<atom\s+name=\"(?P<x_qbox_geometry_atom_labels>[a-zA-Z0-9]+)\"",
subMatchers = [
- SM (r"\s*<position>\s+(?P<qbox_geometry_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_atom_positions_z__bohr>[-+0-9.]+)\s*</position>", repeats = True),
+ SM (r"\s*<position>\s+(?P<x_qbox_geometry_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_atom_positions_z__bohr>[-+0-9.]+)\s*</position>", repeats = True),
], repeats = True)
])
@@ -130,7 +130,7 @@ def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
}
# Set all band metadata to Cache as they need post-processsing.
for name in metaInfoEnv.infoKinds:
- if name.startswith('qbox_'):
+ if name.startswith('x_qbox_'):
cachingLevelForMetaName[name] = CachingLevel.Cache
return cachingLevelForMetaName