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Add unit conversion and nopbc occasion for quip/gap/xyz #606

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Add unit conversion and nopbc occasion for quip/gap/xyz #606

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6744c3f
Add unit conversion and nopbc occasion for quip/gap/xyz
SchrodingersCattt Feb 6, 2024
9af138c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 6, 2024
7c2e4be
Merge branch 'devel' into quip_gap_xyz_mod
SchrodingersCattt Feb 6, 2024
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113 changes: 112 additions & 1 deletion dpdata/xyz/quip_gap_xyz.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,19 @@

import numpy as np

from ..unit import EnergyConversion, ForceConversion

e_conv_kcalpermol2eV = EnergyConversion("kcal_mol", "eV").value()
e_conv_au2eV = EnergyConversion("hartree", "eV").value()
f_conv_kcalpermolperang2eVperang = ForceConversion(
"kcal_mol/angstrom", "eV/angstrom"
).value()
f_conv_auperang2eVperang = ForceConversion("hartree/angstrom", "eV/angstrom").value()
f_conv_kcalpermolperbohr2eVperang = ForceConversion(
"kcal_mol/bohr", "eV/angstrom"
).value()
f_conv_au2eVperang = ForceConversion("hartree/bohr", "eV/angstrom").value()


class QuipGapxyzSystems:
"""deal with QuipGapxyzFile."""
Expand Down Expand Up @@ -164,22 +177,120 @@ def handle_single_xyz_frame(lines):
).astype("float32")
else:
virials = None

"""
info_dict = {}
info_dict["atom_names"] = list(type_num_array[:, 0])
info_dict["atom_numbs"] = list(type_num_array[:, 1].astype(int))
#info_dict["nopbc"] = False
info_dict["atom_types"] = np.array(atom_type_list).astype(int)

info_dict["cells"] = np.array(
[
np.array(list(filter(bool, field_dict["Lattice"].split(" ")))).reshape(
3, 3
)
]
).astype("float32")

if "Lattice" in field_dict:
info_dict["cells"] = np.array(
[
np.array(list(filter(bool, field_dict["Lattice"].split(" ")))).reshape(
3, 3
)
]
).astype("float32")
else:
#info_dict["nopbc"] = True
info_dict["cell"] = [[100.0, 0.0, 0.0], [0.0, 100.0, 0.0], [0.0, 0.0, 100.0]]
#info_dict["cells"] = None

info_dict["coords"] = np.array([coords_array]).astype("float32")
info_dict["energies"] = np.array([field_dict["energy"]]).astype("float32")
info_dict["forces"] = np.array([force_array]).astype("float32")
if virials is not None:
info_dict["virials"] = virials
info_dict["orig"] = np.zeros(3)
return info_dict
"""
e_units = np.array([field_dict["energy-unit"]])
f_units = np.array([field_dict["force-unit"]])
# print(e_units, f_units)

info_dict = {}
info_dict["nopbc"] = False
info_dict["atom_names"] = list(type_num_array[:, 0])
info_dict["atom_numbs"] = list(type_num_array[:, 1].astype(int))
info_dict["atom_types"] = np.array(atom_type_list).astype(int)

info_dict["coords"] = np.array([coords_array]).astype("float32")
"""
info_dict["energies"] = np.array([field_dict["energy"]]).astype("float32")
info_dict["forces"] = np.array([force_array]).astype("float32")
"""
if e_units == "kcal/mol":
info_dict["energies"] = (
np.array([field_dict["energy"]]).astype("float32")
* e_conv_kcalpermol2eV
)
elif e_units == "hartree" or e_units == "au" or e_units == "a.u.":
info_dict["energies"] = (
np.array([field_dict["energy"]]).astype("float32") * e_conv_au2eV
)
elif e_units == "ev":
info_dict["energies"] = np.array([field_dict["energy"]]).astype("float32")
else:
info_dict["energies"] = np.array([field_dict["energy"]]).astype("float32")
print(
f"Warning: The units is {e_units} , but is read as default (eV). Please check carefully!"
)

if f_units == "kcal/mol/angstrom":
info_dict["forces"] = (
np.array([force_array]).astype("float32")
* f_conv_kcalpermolperang2eVperang
)
elif (
f_units == "hartree/angstrom"
or f_units == "hartree/ang"
or f_units == "hartree/ang."
):
info_dict["forces"] = (
np.array([force_array]).astype("float32") * f_conv_auperang2eVperang
)
elif f_units == "kcal/mol/bohr":
info_dict["forces"] = (
np.array([force_array]).astype("float32")
* f_conv_kcalpermolperbohr2eVperang
)
elif f_units == "kcal/mol/bohr":
info_dict["forces"] = (
np.array([force_array]).astype("float32") * f_conv_au2eVperang
)
elif f_units == "ev/angstrom" or f_units == "ev/ang" or f_units == "ev/ang.":
info_dict["forces"] = np.array([force_array]).astype("float32")
else:
info_dict["forces"] = np.array([force_array]).astype("float32")
print(
f"Warning: The units is {f_units}, but is read as default (eV/angstrom). Please check carefully!"
)

if virials is not None:
info_dict["virials"] = virials
info_dict["orig"] = np.zeros(3)
if "Lattice" in field_dict and field_dict["Lattice"].strip():
lattice_values = list(filter(bool, field_dict["Lattice"].split(" ")))
info_dict["cells"] = np.array(
[np.array(lattice_values).reshape(3, 3)]
).astype("float32")
else:
lattice_values = np.array(
[[100.0, 0.0, 0.0], [0.0, 100.0, 0.0], [0.0, 0.0, 100.0]]
)

info_dict["nopbc"] = True
info_dict["cells"] = np.array(
[np.array(lattice_values).reshape(3, 3)]
).astype("float32")

return info_dict
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