Skip to content
Snippets Groups Projects
Commit 56c1aefd authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
Browse files

added forces, conv. thresh etc

parent ef195ccb
Branches
No related tags found
No related merge requests found
Show whitespace changes
Inline Side-by-side
parser/parser-exciting/parser_exciting.py
+ 86
− 12
View file @ 56c1aefd
......@@ -6,6 +6,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.caching_backend import CachingLevel
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
from ase import Atoms
import logging
......@@ -118,6 +119,35 @@ 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)
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)
dosFile = os.path.join(dirPath, "dos.xml")
bandFile = os.path.join(dirPath, "bandstructure.xml")
......@@ -301,7 +331,15 @@ class ExcitingParserContext(object):
if gIndex == self.secMethodIndex:
backend.addValue('electronic_structure_method', "DFT")
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('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 = \
SM(name = "root matcher",
......@@ -365,8 +403,8 @@ mainFileDescription = \
]),
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 core charge\s*:\s*(?P<x_exciting_core_charge>[-0-9.]+)"),
SM(r"\s*Total valence charge\s*:\s*(?P<x_exciting_valence_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_initial>[-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*Total number of valence states\s*:\s*(?P<x_exciting_valence_states>[-0-9.]+)"),
......@@ -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*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*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*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*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*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*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",
startReStr = r"\| Convergence targets achieved. Performing final SCF iteration\s*\+",
......@@ -443,17 +484,21 @@ mainFileDescription = \
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*\-",
endReStr = r"\s* Atomic force components including IBS \(cartesian\)\s*:",
subMatchers = [
SM(name="total_forces",
# startReStr = r"\| Writing atomic positions and forces\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]+)",
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*:",
......@@ -465,6 +510,23 @@ 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(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 = {
"x_exciting_geometry_reciprocal_lattice_vector_x":CachingLevel.Cache,
"x_exciting_geometry_reciprocal_lattice_vector_y":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__":
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 = \
]),
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 core charge\s*:\s*(?P<x_exciting_core_charge>[-0-9.]+)"),
SM(r"\s*Total valence charge\s*:\s*(?P<x_exciting_valence_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_initial>[-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*Total number of valence states\s*:\s*(?P<x_exciting_valence_states>[-0-9.]+)"),
......
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please to comment