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Merged
timurbazhirov merged 2 commits into from
Mar 25, 2026
Merged

update: remove munch #153

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ec5d240
update: remove munch
VsevolodX Mar 25, 2026
7f2b19e
update: remove munch 2
VsevolodX Mar 25, 2026
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4 changes: 2 additions & 2 deletions express/parsers/apps/espresso/formats/xml/xml_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,10 @@ class EspressoXMLParserBase(BaseXMLParser):

TAG_VALUE_CAST_MAP = {
"character": lambda v, s, c: v,
"integer": lambda v, s, c: np.array([int(_) for _ in re.findall(GENERAL_REGEX.int_number, v)]).reshape(
"integer": lambda v, s, c: np.array([int(_) for _ in re.findall(GENERAL_REGEX["int_number"], v)]).reshape(
[s // c, c]
),
"real": lambda v, s, c: np.array([float(_) for _ in re.findall(GENERAL_REGEX.double_number, v)]).reshape(
"real": lambda v, s, c: np.array([float(_) for _ in re.findall(GENERAL_REGEX["double_number"], v)]).reshape(
[s // c, c]
),
"logical": lambda v, s, c: False if v in ["F", "false"] else True,
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2 changes: 1 addition & 1 deletion express/parsers/apps/espresso/settings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
WAVEFUNCTION_FILE = "wf_r.dat"

COMMON_REGEX = r"{0}\s+[=:<>]\s*([-+]?\d*\.?\d*([Ee][+-]?\d+)?)"
DOUBLE_REGEX = GENERAL_REGEX.double_number
DOUBLE_REGEX = GENERAL_REGEX["double_number"]

STERNHEIMER_GW0_DIR_PATTERN = "/_gw0/"
STERNHEIMER_GW_TITLE = "SternheimerGW"
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2 changes: 1 addition & 1 deletion express/parsers/apps/nwchem/settings.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
from express.parsers.settings import GENERAL_REGEX

COMMON_REGEX = r"{}\s+[=:<>]\s*([-+]?\d*\.?\d*([Ee][+-]?\d+)?)"
DOUBLE_REGEX = GENERAL_REGEX.double_number
DOUBLE_REGEX = GENERAL_REGEX["double_number"]
NWCHEM_OUTPUT_FILE_REGEX = "Northwest Computational Chemistry Package"

REGEX = {
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22 changes: 11 additions & 11 deletions express/parsers/apps/vasp/settings.py
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Expand Up @@ -8,16 +8,16 @@

REGEX = {
"total_energy": {
"regex": r"F=\s+({0})".format(GENERAL_REGEX.double_number),
"regex": r"F=\s+({0})".format(GENERAL_REGEX["double_number"]),
"start_flag": "entering main loop",
"occurrences": -1,
"output_type": "float",
},
"ibz_kpoints": {
"regex": r"({double})\s+({double})\s+({double})\s+{double}".format(double=GENERAL_REGEX.double_number)
"regex": r"({double})\s+({double})\s+({double})\s+{double}".format(double=GENERAL_REGEX["double_number"])
},
"convergence_electronic": {
"regex": r".+:\s+(\d+)\s+{0}\s+({0})".format(GENERAL_REGEX.double_number),
"regex": r".+:\s+(\d+)\s+{0}\s+({0})".format(GENERAL_REGEX["double_number"]),
"output_type": "float",
"match_groups": [1, 2],
},
Expand All @@ -26,46 +26,46 @@
"regex": r"direct lattice vectors.+\n"
r"\s+({double})\s+({double})\s+({double}).+\n"
r"\s+({double})\s+({double})\s+({double}).+\n"
r"\s+({double})\s+({double})\s+({double})".format(double=GENERAL_REGEX.double_number)
r"\s+({double})\s+({double})\s+({double})".format(double=GENERAL_REGEX["double_number"])
},
"basis_vectors": {
"regex": r"\s+({double})\s+({double})\s+({double})\s+{double}\s+{double}\s+{double}".format(
double=GENERAL_REGEX.double_number
double=GENERAL_REGEX["double_number"]
)
},
"pressure": {
"regex": r"external pressure\s+=\s+({0})\s+kB".format(GENERAL_REGEX.double_number),
"regex": r"external pressure\s+=\s+({0})\s+kB".format(GENERAL_REGEX["double_number"]),
"occurrences": -1,
"output_type": "float",
},
"total_force": {
"regex": r"total drift:\s+({0})\s+({0})\s+({0})".format(GENERAL_REGEX.double_number),
"regex": r"total drift:\s+({0})\s+({0})\s+({0})".format(GENERAL_REGEX["double_number"]),
"occurrences": -1,
"output_type": "float",
"match_groups": [1, 2, 3],
},
"zero_point_energy": {
"regex": r"f\s\s=.*2PiTHz\s+\d+\.\d+\s+cm\-1\s+({0})\s+meV".format(GENERAL_REGEX.double_number),
"regex": r"f\s\s=.*2PiTHz\s+\d+\.\d+\s+cm\-1\s+({0})\s+meV".format(GENERAL_REGEX["double_number"]),
"start_flag": "Eigenvectors and eigenvalues of the dynamical matrix",
"output_type": "float",
},
}

TOTAL_ENERGY_CONTRIBUTIONS = {
"hartree": {
"regex": _COMMON_REGEX.format("Hartree", GENERAL_REGEX.double_number),
"regex": _COMMON_REGEX.format("Hartree", GENERAL_REGEX["double_number"]),
"occurrences": -1,
"output_type": "float",
"match_groups": [1, 2, 3, 4, 5, 6],
},
"ewald": {
"regex": _COMMON_REGEX.format("Ewald", GENERAL_REGEX.double_number),
"regex": _COMMON_REGEX.format("Ewald", GENERAL_REGEX["double_number"]),
"occurrences": -1,
"output_type": "float",
"match_groups": [1, 2, 3, 4, 5, 6],
},
"exchange_correlation": {
"regex": _COMMON_REGEX.format("E\(xc\)", GENERAL_REGEX.double_number),
"regex": _COMMON_REGEX.format("E\(xc\)", GENERAL_REGEX["double_number"]),
"occurrences": -1,
"output_type": "float",
"match_groups": [1, 2, 3, 4, 5, 6],
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22 changes: 8 additions & 14 deletions express/parsers/settings.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
from math import pi
from munch import Munch


class Constant(object):
Expand All @@ -9,7 +8,7 @@ class Constant(object):

_c = 299792458.0 # speed of light, m/s
_mu0 = 4.0e-7 * pi # permeability of vacuum
_eps0 = 1 / _mu0 / _c**2 # permittivity of vacuum
_eps0 = 1 / _mu0 / _c ** 2 # permittivity of vacuum
_Grav = 6.67259e-11 # gravitational constant
_hplanck = 6.6260755e-34 # Planck constant, J s
_hbar = _hplanck / (2 * pi) # Planck constant / 2pi, J s
Expand All @@ -19,9 +18,9 @@ class Constant(object):
_Nav = 6.0221367e23 # Avogadro number
_k = 1.380658e-23 # Boltzmann constant, J/K
_amu = 1.6605402e-27 # atomic mass unit, kg
BOHR = 4e10 * pi * _eps0 * _hbar**2 / _me / _e**2 # Bohr radius in angstrom
BOHR = 4e10 * pi * _eps0 * _hbar ** 2 / _me / _e ** 2 # Bohr radius in angstrom
eV = 1.0
HARTREE = _me * _e**3 / 16 / pi**2 / _eps0**2 / _hbar**2 # in eV
HARTREE = _me * _e ** 3 / 16 / pi ** 2 / _eps0 ** 2 / _hbar ** 2 # in eV
RYDBERG = 0.5 * HARTREE # in eV
Ry = RYDBERG
Ha = HARTREE
Expand All @@ -31,17 +30,12 @@ class Constant(object):
ry_bohr_to_eV_A = 25.71104309541616 # or RYDBERG / BOHR


GENERAL_REGEX = Munch()
GENERAL_REGEX.update({"double_number": r"[-+]?\d*\.\d+(?:[eE][-+]?\d+)?", "int_number": r"[+-]?\d+"})

GENERAL_REGEX = {"double_number": r"[-+]?\d*\.\d+(?:[eE][-+]?\d+)?", "int_number": r"[+-]?\d+"}

# Maps the format keywords used in this code to their corresponding ase keywords.
ASE_FORMATS = {"poscar": "vasp", "cif": "cif", "espresso-in": "espresso-in"}

ATOMIC_REGEX = Munch()
ATOMIC_REGEX.update(
{
"orbitalName": r"[1-9][sSpPdDfF]",
"atomicSpecies": r"[a-zA-Z]{1,2}[\d+]?",
}
)
ATOMIC_REGEX = {
"orbitalName": r"[1-9][sSpPdDfF]",
"atomicSpecies": r"[a-zA-Z]{1,2}[\d+]?",
}
1 change: 0 additions & 1 deletion pyproject.toml
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Expand Up @@ -15,7 +15,6 @@ classifiers = [
"Topic :: Software Development",
]
dependencies = [
"munch==2.5.0",
"pymatgen>=2023.8.10",
"ase>=3.17.0",
"mat3ra-esse>=2026.3.25.post0",
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