diff --git a/parser/parser-exciting/parser_exciting.py b/parser/parser-exciting/parser_exciting.py
index ec49f0d50aa83d8ecee3d013d65fa79b215c890c..f130b23eecce13d41565a23463e90d80570c25d0 100644
--- a/parser/parser-exciting/parser_exciting.py
+++ b/parser/parser-exciting/parser_exciting.py
@@ -33,12 +33,14 @@ class ExcitingParserContext(object):
def initialize_values(self):
self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
+ self.atom_pos = []
+ self.atom_labels = []
def startedParsing(self, path, parser):
self.parser=parser
self.initialize_values()
- self.atom_pos = []
- self.atom_labels = []
+# self.atom_pos = []
+# self.atom_labels = []
self.secMethodIndex = None
self.secSystemIndex = None
self.secSingleConfIndex = None
@@ -50,21 +52,75 @@ class ExcitingParserContext(object):
self.xcName = None
self.gmaxvr = 0
self.energy_thresh = []
-
+ self.samplingMethod = None
+ self.secSamplingMethodIndex = None
+ self.geometryForceThreshold = 0
+ self.frameSequence = []
+ self.samplingGIndex = 0
+ self.dummy = 0
+
+ def onOpen_section_sampling_method(self, backend, gIndex, section):
+ self.secSamplingMethodIndex = gIndex
+ backend.addValue("sampling_method", "geometry_optimization")
+# print("self.secSamplingMethodIndex=",self.secSamplingMethodIndex)
+ self.samplingMethod = "geometry_optimization"
+# print("self.samplingMethod=",self.samplingMethod)
+
def onOpen_section_system(self, backend, gIndex, section):
self.secSystemIndex = gIndex
def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
if self.secSingleConfIndex is None:
self.secSingleConfIndex = gIndex
+ self.frameSequence.append(gIndex)
def onOpen_section_method(self, backend, gIndex, section):
if self.secMethodIndex is None:
self.secMethodIndex = gIndex
+ def onOpen_x_exciting_section_geometry_optimization(self, backend, gIndex, section):
+# """Trigger called when x_abinit_section_dataset is opened.
+# """
+ self.samplingGIndex = backend.openSection("section_sampling_method")
+
def onClose_section_run(self, backend, gIndex, section):
self.secRunIndex = gIndex
+ def onClose_x_exciting_section_geometry_optimization(self, backend, gIndex, section):
+ """Trigger called when x_abinit_section_dataset is closed.
+ """
+# print("len(self.frameSequence)=",len(self.frameSequence))
+ if len(self.frameSequence) > 1:
+ frameGIndex = backend.openSection("section_frame_sequence")
+# if section["x_abinit_geometry_optimization_converged"] is not None:
+# if section["x_abinit_geometry_optimization_converged"][-1] == "are converged":
+ backend.addValue("geometry_optimization_converged", True)
+# else:
+# backend.addValue("geometry_optimization_converged", False)
+ backend.closeSection("section_frame_sequence", frameGIndex)
+# self.frameSequence = []
+ backend.closeSection("section_sampling_method", self.samplingGIndex)
+
+ def onClose_section_frame_sequence(self, backend, gIndex, section):
+ """Trigger called when section_framce_sequence is closed.
+ """
+ backend.addValue("number_of_frames_in_sequence", len(self.frameSequence))
+ backend.addArrayValues("frame_sequence_local_frames_ref", np.array(self.frameSequence))
+ backend.addValue("frame_sequence_to_sampling_ref", self.samplingGIndex)
+
+# print("self.samplingMethod=",self.samplingMethod)
+ if self.samplingMethod == "geometry_optimization":
+# gix = backend.openSection("section_sampling_method")
+# backend.addValue("XC_functional_name", xcName)
+# backend.closeSection("section_sampling_method", gix)
+# geometryForceThreshold = section["x_exciting_geometry_optimization_threshold_force"]
+# print("geometryForceThreshold=",self.geometryForceThreshold)
+ gi = backend.openSection("section_sampling_method")
+ backend.addValue("geometry_optimization_threshold_force", self.geometryForceThreshold)
+ backend.closeSection("section_sampling_method", gi)
+ else:
+ pass
+
mainFile = self.parser.fIn.fIn.name
dirPath = os.path.dirname(self.parser.fIn.name)
gw_File = os.path.join(dirPath, "GW_INFO.OUT")
@@ -138,6 +194,13 @@ class ExcitingParserContext(object):
# logging.error("BASE onClose_section_single_configuration_calculation")
backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemIndex)
+# print("self.samplingMethod=",self.samplingMethod)
+ if self.samplingMethod == "geometry_optimization":
+ self.geometryForceThreshold = section["x_exciting_geometry_optimization_threshold_force"][0]
+# print("geometryForceThreshold=",geometryForceThreshold)
+# backend.addValue("geometry_optimization_threshold_force", geometryForceThreshold)
+# else:
+# pass
#
##############TO DO. FIX FORCES#####################
# forceX = section["x_exciting_atom_forces_x"]
@@ -330,6 +393,8 @@ class ExcitingParserContext(object):
if self.atom_pos and self.cell_format[0] == 'cartesian':
backend.addArrayValues('atom_positions', np.asarray(self.atom_pos))
elif self.atom_pos and self.cell_format[0] == 'lattice':
+# print("aaaself.atom_pos=",self.atom_pos)
+# print("aaaself.atom_labels=",self.atom_labels)
atoms = Atoms(self.atom_labels, self.atom_pos, cell=[(1, 0, 0),(0, 1, 0),(0, 0, 1)])
atoms.set_cell(self.sim_cell, scale_atoms=True)
self.atom_pos = atoms.get_positions()
@@ -347,25 +412,47 @@ class ExcitingParserContext(object):
"Extended": ['tetrahedra']
}
- for smName in smearing_internal_map[excSmearingKind[0]]:
- backend.addValue("smearing_kind", smName)
+ if self.samplingMethod is not "geometry_optimization":
+ for smName in smearing_internal_map[excSmearingKind[0]]:
+ backend.addValue("smearing_kind", smName)
+ else:
+ pass
def onClose_x_exciting_section_atoms_group(self, backend, gIndex, section):
fromB = unit_conversion.convert_unit_function("bohr", "m")
formt = section['x_exciting_atom_position_format']
+ if self.atom_pos is not None: self.atom_pos = []
+ if self.atom_labels is not None: self.atom_labels = []
self.cell_format = formt
pos = [section['x_exciting_geometry_atom_positions_' + i] for i in ['x', 'y', 'z']]
+# print("pos=",pos)
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):
+# print("i=",i)
+# print("natom=",natom)
+# print("[pos[0][i]=",pos[0][i])
+# print("[pos[1][i]=",pos[1][i])
+# print("[pos[2][i]=",pos[2][i])
+# print("self.atom_pos=",self.atom_pos)
if formt[0] == 'cartesian':
self.atom_pos.append([fromB(pos[0][i]), fromB(pos[1][i]), fromB(pos[2][i])])
else:
+# print("self.atom_labels_prima=",self.atom_labels)
+# print("self.atom_pos_prima=",self.atom_pos)
self.atom_pos.append([pos[0][i], pos[1][i], pos[2][i]])
- self.atom_labels = self.atom_labels + (section['x_exciting_geometry_atom_labels'] * natom)
-
+# print("self.atom_pos_dopo=",self.atom_pos)
+# print("self.atom_labels_dopo=",self.atom_labels)
+# print("natom=",natom)
+# print("section['x_exciting_geometry_atom_labels']=",section['x_exciting_geometry_atom_labels'])
+# print("self.samplingMethod[0]=",self.samplingMethod)
+ if self.samplingMethod is not "geometry_optimization":
+ self.atom_labels = self.atom_labels + (section['x_exciting_geometry_atom_labels'] * natom)
+ else:
+ self.atom_labels = self.atom_labels + section['x_exciting_geometry_atom_labels']
+# print("self.atom_labels_dopodopo=",self.atom_labels)
def onClose_section_method(self, backend, gIndex, section):
if gIndex == self.secMethodIndex:
@@ -519,54 +606,78 @@ mainFileDescription = \
SM(r"\s*interstitial\s*:\s*(?P<x_exciting_interstitial_charge>[-0-9.]+)"),
SM(r"\s*total charge in muffin-tins\s*:\s*(?P<x_exciting_total_MT_charge>[-0-9.]+)"),
SM(r"\s*Estimated fundamental gap\s*:\s*(?P<x_exciting_gap__hartree>[-0-9.]+)")
- ]),
- SM(name="final_forces",
-# startReStr = r"\| Writing atomic positions and forces\s*\-",
- startReStr = r"\s*Total atomic forces including IBS \(cartesian\) \s*:",
- endReStr = r"\|\s*Groundstate module stopped\s*\*",
-# endReStr = r"\s* Atomic force components including IBS \(cartesian\)\s*:",
- floating = True,
- subMatchers = [
-# SM(name="total_forces",
-# startReStr = r"\s*Total atomic forces including IBS \(cartesian\)\s*:",
- SM(r"\s*atom\s*[0-9]+\s*[A-Za-z]+\s*\:\s*(?P<x_exciting_atom_forces_x>[-0-9.]+)\s*(?P<x_exciting_atom_forces_y>[-0-9.]+)\s*(?P<x_exciting_atom_forces_z>[-0-9.]+)",
- 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*:",
-# forwardMatch = 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\.]+\s*[A-Za-z]+\s*[A-Za-z]+)", weak = True),
-# 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]+)"),
-# ]
-# )
- ]),
- SM(name="force_components",
- startReStr = r"\s* Atomic force components including IBS \(cartesian\)\s*:",
- endReStr = r"\|\s* Groundstate module stopped\s* \*",
- subMatchers = [
+ ]) #,
+# SM(name="final_forces",
+## startReStr = r"\| Writing atomic positions and forces\s*\-",
+# startReStr = r"\s*Total atomic forces including IBS \(cartesian\) \s*:",
+# endReStr = r"\|\s*Groundstate module stopped\s*\*",
+## endReStr = r"\s* Atomic force components including IBS \(cartesian\)\s*:",
+# floating = True,
+# subMatchers = [
+## SM(name="total_forces",
+## startReStr = r"\s*Total atomic forces including IBS \(cartesian\)\s*:",
+# SM(r"\s*atom\s*[0-9]+\s*[A-Za-z]+\s*\:\s*(?P<x_exciting_atom_forces_x>[-0-9.]+)\s*(?P<x_exciting_atom_forces_y>[-0-9.]+)\s*(?P<x_exciting_atom_forces_z>[-0-9.]+)",
+# 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*:",
+## forwardMatch = 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\.]+\s*[A-Za-z]+\s*[A-Za-z]+)", weak = True),
+## 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]+)"),
+## ]
+## )
+# ]),
+# SM(name="force_components",
# startReStr = r"\s* Atomic force components including IBS \(cartesian\)\s*:",
- SM(r"\s*atom\s*[0-9]+\s*[A-Za-z]+\s*\:\s*(?P<x_exciting_atom_HF_forces_x>[-0-9.]+)\s*(?P<x_exciting_atom_HF_forces_y>[-0-9.]+)\s*(?P<x_exciting_atom_HF_forces_z>[-0-9.]+)\s*HF force",
- repeats = True,
- floating = True),
- SM(r"\s*\:\s*(?P<x_exciting_atom_core_forces_x>[-0-9.]+)\s*(?P<x_exciting_atom_core_forces_y>[-0-9.]+)\s*(?P<x_exciting_atom_core_forces_z>[-0-9.]+)\s*core correction",
- repeats = True,
- floating = True),
- SM(r"\s*\:\s*(?P<x_exciting_atom_IBS_forces_x>[-0-9.]+)\s*(?P<x_exciting_atom_IBS_forces_y>[-0-9.]+)\s*(?P<x_exciting_atom_IBS_forces_z>[-0-9.]+)\s*IBS correction",
- repeats = True,
- floating = True),
-# SM(r"(?P<x_exciting_store_total_forces>.*)",
-# repeats = True,
- ] )
+# endReStr = r"\|\s* Groundstate module stopped\s* \*",
+# subMatchers = [
+## startReStr = r"\s* Atomic force components including IBS \(cartesian\)\s*:",
+# SM(r"\s*atom\s*[0-9]+\s*[A-Za-z]+\s*\:\s*(?P<x_exciting_atom_HF_forces_x>[-0-9.]+)\s*(?P<x_exciting_atom_HF_forces_y>[-0-9.]+)\s*(?P<x_exciting_atom_HF_forces_z>[-0-9.]+)\s*HF force",
+# repeats = True,
+# floating = True),
+# SM(r"\s*\:\s*(?P<x_exciting_atom_core_forces_x>[-0-9.]+)\s*(?P<x_exciting_atom_core_forces_y>[-0-9.]+)\s*(?P<x_exciting_atom_core_forces_z>[-0-9.]+)\s*core correction",
+# repeats = True,
+# floating = True),
+# SM(r"\s*\:\s*(?P<x_exciting_atom_IBS_forces_x>[-0-9.]+)\s*(?P<x_exciting_atom_IBS_forces_y>[-0-9.]+)\s*(?P<x_exciting_atom_IBS_forces_z>[-0-9.]+)\s*IBS correction",
+# repeats = True,
+# floating = True),
+## SM(r"(?P<x_exciting_store_total_forces>.*)",
+## repeats = True,
+# ] )
]
- )
+ ),
+ SM(name = "geometry optimization",
+ startReStr = r"\|\s*Structure-optimization module started*\s*\*",
+ sections = ["section_sampling_method","x_exciting_section_geometry_optimization"],
+# fixedStartValues={'sampling_method': 'geometry_optimization'},
+# repeats = True,
+ subMatchers = [
+ SM(name = "optimization steps",
+ startReStr = r"\|\s*Optimization step\s*(?P<x_exciting_geometry_optimization_step>[-0-9]+)\s*\(method = (?P<x_exciting_geometry_optimization_method>[A-Za-z]+)\)\s*\-",
+ sections = ["section_single_configuration_calculation"],
+# SM(r"\s*Output level for this task is set to normal\s*"),
+# SM(r"\|\s*Optimization step (?P<x_exciting_geometry_optimization_step>[-0-9]+)\: Initialize optimization\s*\-"),
+ repeats = True,
+ subMatchers = [
+ SM(r"\s*Maximum force magnitude\s*\(target\)\s*:\s*(?P<x_exciting_maximum_force_magnitude__hartree_bohr_1>[0-9]+\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_geometry_optimization_threshold_force__hartree_bohr_1>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)"),
+ SM(r"\s*Total energy at this optimization step\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"),
+ SM(startReStr = r"\s*Atomic positions at this step \s*\((?P<x_exciting_atom_position_format>[-a-zA-Z]+)\)\s*:\s*",
+ endReStr = r"\s*Total atomic forces including IBS \(cartesian\) \:",
+ sections = ["section_system","x_exciting_section_atoms_group"],
+# endReStr = r"\s*magnetic fields\s*",
+ subMatchers = [
+ SM(r"\s*atom\s*(?P<x_exciting_atom_number>[+0-9]+)\s*(?P<x_exciting_geometry_atom_labels>[A-Za-z]+)\s*\:\s*(?P<x_exciting_geometry_atom_positions_x>[-+0-9.]+)\s*(?P<x_exciting_geometry_atom_positions_y>[-+0-9.]+)\s*(?P<x_exciting_geometry_atom_positions_z>[-+0-9.]+)", repeats = True)
+ ])])
+ ]
+ )
])
])