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Commit 56c1aefd authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
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added forces, conv. thresh etc

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parser/parser-exciting/parser_exciting.py
+ 86
− 12
View file @ 56c1aefd
...@@ -6,6 +6,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction ...@@ -6,6 +6,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.caching_backend import CachingLevel from nomadcore.caching_backend import CachingLevel
from nomadcore.unit_conversion import unit_conversion from nomadcore.unit_conversion import unit_conversion
from nomadcore.unit_conversion.unit_conversion import convert_unit_function
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_gw #, exciting_parser_input import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_gw #, exciting_parser_input
from ase import Atoms from ase import Atoms
import logging import logging
...@@ -118,6 +119,35 @@ class ExcitingParserContext(object): ...@@ -118,6 +119,35 @@ class ExcitingParserContext(object):
# logging.error("BASE onClose_section_single_configuration_calculation") # logging.error("BASE onClose_section_single_configuration_calculation")
backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex) backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemIndex) backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemIndex)
forceX = section["x_exciting_atom_forces_x"]
if forceX:
forceY = section["x_exciting_atom_forces_y"]
forceZ = section["x_exciting_atom_forces_z"]
forceCoreX = section["x_exciting_atom_core_forces_x"]
forceCoreY = section["x_exciting_atom_core_forces_y"]
forceCoreZ = section["x_exciting_atom_core_forces_z"]
forceIBSX = section["x_exciting_atom_IBS_forces_x"]
forceIBSY = section["x_exciting_atom_IBS_forces_y"]
forceIBSZ = section["x_exciting_atom_IBS_forces_z"]
forceHFX = section["x_exciting_atom_HF_forces_x"]
forceHFY = section["x_exciting_atom_HF_forces_y"]
forceHFZ = section["x_exciting_atom_HF_forces_z"]
fConv = convert_unit_function("hartree/bohr", "N")
atoms = len(forceX)
atom_forces = []
atom_core_forces = []
atom_IBS_forces = []
atom_HF_forces = []
for i in range(0,atoms):
atom_forces.append([fConv(forceX[i]),fConv(forceY[i]),fConv(forceZ[i])])
atom_core_forces.append([fConv(forceCoreX[i]),fConv(forceCoreY[i]),fConv(forceCoreZ[i])])
atom_IBS_forces.append([fConv(forceIBSX[i]),fConv(forceIBSY[i]),fConv(forceIBSZ[i])])
atom_HF_forces.append([fConv(forceHFX[i]),fConv(forceHFY[i]),fConv(forceHFZ[i])])
backend.addValue("atom_forces",atom_forces)
backend.addValue("x_exciting_atom_core_forces",atom_core_forces)
backend.addValue("x_exciting_atom_IBS_forces",atom_IBS_forces)
backend.addValue("x_exciting_atom_HF_forces",atom_HF_forces)
# print("atom_forces=",atom_forces)
dirPath = os.path.dirname(self.parser.fIn.name) dirPath = os.path.dirname(self.parser.fIn.name)
dosFile = os.path.join(dirPath, "dos.xml") dosFile = os.path.join(dirPath, "dos.xml")
bandFile = os.path.join(dirPath, "bandstructure.xml") bandFile = os.path.join(dirPath, "bandstructure.xml")
...@@ -301,7 +331,15 @@ class ExcitingParserContext(object): ...@@ -301,7 +331,15 @@ class ExcitingParserContext(object):
if gIndex == self.secMethodIndex: if gIndex == self.secMethodIndex:
backend.addValue('electronic_structure_method', "DFT") backend.addValue('electronic_structure_method', "DFT")
energy_thresh = section["x_exciting_scf_threshold_energy_change"][0] energy_thresh = section["x_exciting_scf_threshold_energy_change"][0]
potential_thresh = section["x_exciting_scf_threshold_potential_change_list"][0]
charge_thresh = section["x_exciting_scf_threshold_charge_change_list"][0]
if section["x_exciting_scf_threshold_force_change_list"]:
force_thresh = section["x_exciting_scf_threshold_force_change_list"][0]
backend.addValue('x_exciting_scf_threshold_force_change', force_thresh)
backend.addValue('scf_threshold_energy_change', energy_thresh) backend.addValue('scf_threshold_energy_change', energy_thresh)
backend.addValue('x_exciting_scf_threshold_potential_change', potential_thresh)
backend.addValue('x_exciting_scf_threshold_charge_change', charge_thresh)
# backend.addValue('x_exciting_scf_threshold_force_change', force_thresh)
mainFileDescription = \ mainFileDescription = \
SM(name = "root matcher", SM(name = "root matcher",
...@@ -365,8 +403,8 @@ mainFileDescription = \ ...@@ -365,8 +403,8 @@ mainFileDescription = \
]), ]),
SM(r"\s*Total nuclear charge\s*:\s*(?P<x_exciting_nuclear_charge>[-0-9.]+)"), SM(r"\s*Total nuclear charge\s*:\s*(?P<x_exciting_nuclear_charge>[-0-9.]+)"),
SM(r"\s*Total electronic charge\s*:\s*(?P<x_exciting_electronic_charge>[-0-9.]+)"), SM(r"\s*Total electronic charge\s*:\s*(?P<x_exciting_electronic_charge>[-0-9.]+)"),
SM(r"\s*Total core charge\s*:\s*(?P<x_exciting_core_charge>[-0-9.]+)"), SM(r"\s*Total core charge\s*:\s*(?P<x_exciting_core_charge_initial>[-0-9.]+)"),
SM(r"\s*Total valence charge\s*:\s*(?P<x_exciting_valence_charge>[-0-9.]+)"), SM(r"\s*Total valence charge\s*:\s*(?P<x_exciting_valence_charge_initial>[-0-9.]+)"),
SM(r"\s*Effective Wigner radius, r_s\s*:\s*(?P<x_exciting_wigner_radius>[-0-9.]+)"), SM(r"\s*Effective Wigner radius, r_s\s*:\s*(?P<x_exciting_wigner_radius>[-0-9.]+)"),
SM(r"\s*Number of empty states\s*:\s*(?P<x_exciting_empty_states>[-0-9.]+)"), SM(r"\s*Number of empty states\s*:\s*(?P<x_exciting_empty_states>[-0-9.]+)"),
SM(r"\s*Total number of valence states\s*:\s*(?P<x_exciting_valence_states>[-0-9.]+)"), SM(r"\s*Total number of valence states\s*:\s*(?P<x_exciting_valence_states>[-0-9.]+)"),
...@@ -408,14 +446,17 @@ mainFileDescription = \ ...@@ -408,14 +446,17 @@ mainFileDescription = \
SM(r"\s*Core-electron kinetic energy\s*:\s*(?P<x_exciting_core_electron_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"), SM(r"\s*Core-electron kinetic energy\s*:\s*(?P<x_exciting_core_electron_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Absolute change in total energy (target)\s*:\s*(?P<energy_change_scf_iteration__hartree>[-0-9.]+)\s*(\s*(?P<scf_threshold_energy_change__hartree>[-0-9.]+))"), SM(r"\s*Absolute change in total energy (target)\s*:\s*(?P<energy_change_scf_iteration__hartree>[-0-9.]+)\s*(\s*(?P<scf_threshold_energy_change__hartree>[-0-9.]+))"),
SM(r"\s*DOS at Fermi energy \(states\/Ha\/cell\)\s*:\s*(?P<x_exciting_dos_fermi_scf_iteration__hartree_1>[-0-9.]+)"), SM(r"\s*DOS at Fermi energy \(states\/Ha\/cell\)\s*:\s*(?P<x_exciting_dos_fermi_scf_iteration__hartree_1>[-0-9.]+)"),
SM(r"\s*core\s*:\s*(?P<x_exciting_core_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*core leakage\s*:\s*(?P<x_exciting_core_leakage_scf_iteration>[-0-9.]+)"), SM(r"\s*core leakage\s*:\s*(?P<x_exciting_core_leakage_scf_iteration>[-0-9.]+)"),
SM(r"\s*valence\s*:\s*(?P<x_exciting_valence_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*interstitial\s*:\s*(?P<x_exciting_interstitial_charge_scf_iteration>[-0-9.]+)"), SM(r"\s*interstitial\s*:\s*(?P<x_exciting_interstitial_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*total charge in muffin-tins\s*:\s*(?P<x_exciting_total_MT_charge_scf_iteration>[-0-9.]+)"), SM(r"\s*total charge in muffin-tins\s*:\s*(?P<x_exciting_total_MT_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*Estimated fundamental gap\s*:\s*(?P<x_exciting_gap_scf_iteration__hartree>[-0-9.]+)"), SM(r"\s*Estimated fundamental gap\s*:\s*(?P<x_exciting_gap_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Wall time \(seconds\)\s*:\s*(?P<x_exciting_time_scf_iteration>[-0-9.]+)"), SM(r"\s*Wall time \(seconds\)\s*:\s*(?P<x_exciting_time_scf_iteration>[-0-9.]+)"),
SM(r"\s*RMS change in effective potential \(target\)\s*:\s*(?P<x_exciting_effective_potential_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))"), SM(r"\s*RMS change in effective potential \(target\)\s*:\s*(?P<x_exciting_effective_potential_convergence_scf_iteration__hartree>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_potential_change_list__hartree>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)"),
SM(r"\s*Absolute change in total energy\s*\(target\)\s*:\s*(?P<x_exciting_energy_convergence_scf_iteration>[0-9]+\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_energy_change__hartree>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)"), SM(r"\s*Absolute change in total energy\s*\(target\)\s*:\s*(?P<x_exciting_energy_convergence_scf_iteration>[0-9]+\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_energy_change__hartree>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)"),
SM(r"\s*Charge distance\s*\(target\)\s*:\s*(?P<x_exciting_charge_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))") SM(r"\s*Charge distance\s*\(target\)\s*:\s*(?P<x_exciting_charge_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_charge_change_list>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)"),
SM(r"\s*Abs. change in max-nonIBS-force\s*\(target\)\s*:\s*(?P<x_exciting_force_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_force_change_list>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)")
]), ]),
SM(name="final_quantities", SM(name="final_quantities",
startReStr = r"\| Convergence targets achieved. Performing final SCF iteration\s*\+", startReStr = r"\| Convergence targets achieved. Performing final SCF iteration\s*\+",
...@@ -443,17 +484,21 @@ mainFileDescription = \ ...@@ -443,17 +484,21 @@ mainFileDescription = \
SM(r"\s*Estimated fundamental gap\s*:\s*(?P<x_exciting_gap__hartree>[-0-9.]+)") SM(r"\s*Estimated fundamental gap\s*:\s*(?P<x_exciting_gap__hartree>[-0-9.]+)")
]), ]),
SM(name="final_forces", SM(name="final_forces",
startReStr = r"\| Writing atomic positions and forces\s*\-", # startReStr = r"\| Writing atomic positions and forces\s*\-",
endReStr = r"\s* Atomic force components including IBS \(cartesian\)\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 = [ subMatchers = [
SM(name="total_forces", # SM(name="total_forces",
startReStr = r"\s*Total atomic forces including IBS \(cartesian\)\s*:", # startReStr = r"\s*Total atomic forces including IBS \(cartesian\)\s*:",
## 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]+)", 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 = [ ##### 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\.]+)", ##### 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) ##### repeats = True)
##### ] ) ##### ] )
) #)
# print ("number atoms=", x_exciting_number_of_atoms) # print ("number atoms=", x_exciting_number_of_atoms)
# SM(name="force_components", # SM(name="force_components",
# startReStr = r"\s*Atomic force components including IBS \(cartesian\)\s*:", # startReStr = r"\s*Atomic force components including IBS \(cartesian\)\s*:",
...@@ -465,7 +510,24 @@ mainFileDescription = \ ...@@ -465,7 +510,24 @@ mainFileDescription = \
# 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 = [
# 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,
] )
] ]
) )
]) ])
...@@ -490,7 +552,19 @@ cachingLevelForMetaName = { ...@@ -490,7 +552,19 @@ cachingLevelForMetaName = {
"x_exciting_geometry_reciprocal_lattice_vector_x":CachingLevel.Cache, "x_exciting_geometry_reciprocal_lattice_vector_x":CachingLevel.Cache,
"x_exciting_geometry_reciprocal_lattice_vector_y":CachingLevel.Cache, "x_exciting_geometry_reciprocal_lattice_vector_y":CachingLevel.Cache,
"x_exciting_geometry_reciprocal_lattice_vector_z":CachingLevel.Cache, "x_exciting_geometry_reciprocal_lattice_vector_z":CachingLevel.Cache,
"x_exciting_section_reciprocal_lattice_vectors": CachingLevel.Ignore "x_exciting_section_reciprocal_lattice_vectors": CachingLevel.Ignore,
"x_exciting_atom_forces_x":CachingLevel.Cache,
"x_exciting_atom_forces_y":CachingLevel.Cache,
"x_exciting_atom_forces_z":CachingLevel.Cache,
"x_exciting_atom_HF_forces_x":CachingLevel.Cache,
"x_exciting_atom_HF_forces_y":CachingLevel.Cache,
"x_exciting_atom_HF_forces_z":CachingLevel.Cache,
"x_exciting_atom_core_forces_x":CachingLevel.Cache,
"x_exciting_atom_core_forces_y":CachingLevel.Cache,
"x_exciting_atom_core_forces_z":CachingLevel.Cache,
"x_exciting_atom_IBS_forces_x":CachingLevel.Cache,
"x_exciting_atom_IBS_forces_y":CachingLevel.Cache,
"x_exciting_atom_IBS_forces_z":CachingLevel.Cache
} }
if __name__ == "__main__": if __name__ == "__main__":
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext()) mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext())
parser/parser-exciting/parser_exciting_helium.py
+ 2
− 2
View file @ 56c1aefd
...@@ -283,8 +283,8 @@ mainFileDescription = \ ...@@ -283,8 +283,8 @@ mainFileDescription = \
]), ]),
SM(r"\s*Total nuclear charge\s*:\s*(?P<x_exciting_nuclear_charge>[-0-9.]+)"), SM(r"\s*Total nuclear charge\s*:\s*(?P<x_exciting_nuclear_charge>[-0-9.]+)"),
SM(r"\s*Total electronic charge\s*:\s*(?P<x_exciting_electronic_charge>[-0-9.]+)"), SM(r"\s*Total electronic charge\s*:\s*(?P<x_exciting_electronic_charge>[-0-9.]+)"),
SM(r"\s*Total core charge\s*:\s*(?P<x_exciting_core_charge>[-0-9.]+)"), SM(r"\s*Total core charge\s*:\s*(?P<x_exciting_core_charge_initial>[-0-9.]+)"),
SM(r"\s*Total valence charge\s*:\s*(?P<x_exciting_valence_charge>[-0-9.]+)"), SM(r"\s*Total valence charge\s*:\s*(?P<x_exciting_valence_charge_initial>[-0-9.]+)"),
SM(r"\s*Effective Wigner radius, r_s\s*:\s*(?P<x_exciting_wigner_radius>[-0-9.]+)"), SM(r"\s*Effective Wigner radius, r_s\s*:\s*(?P<x_exciting_wigner_radius>[-0-9.]+)"),
SM(r"\s*Number of empty states\s*:\s*(?P<x_exciting_empty_states>[-0-9.]+)"), SM(r"\s*Number of empty states\s*:\s*(?P<x_exciting_empty_states>[-0-9.]+)"),
SM(r"\s*Total number of valence states\s*:\s*(?P<x_exciting_valence_states>[-0-9.]+)"), SM(r"\s*Total number of valence states\s*:\s*(?P<x_exciting_valence_states>[-0-9.]+)"),
......
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