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Fix ORCA backend when using Sire interface.
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@lohedges
lohedges committed Jun 5, 2024
1 parent 845ca7b commit c9fc19b
Showing 1 changed file with 74 additions and 22 deletions.
96 changes: 74 additions & 22 deletions emle/calculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -503,7 +503,24 @@ def __init__(
orca_template: str
The path to a template ORCA input file. This is required when using
the ORCA backend when using emle-engine with Sire.
the ORCA backend when using emle-engine with Sire. This should be a
full template, including the charge and multiplicity of the QM region,
along with a placeholder name for the xyz file that will be replaced
with the file generated at runtime, e.g.:
%pal nprocs 4 end
!BLYP 6-31G* verytightscf
%method
grid 4
finalgrid 6
end
%scf
maxiter 100
end
%MaxCore 1024
! ENGRAD
! Angs NoUseSym
*xyzfile 0 1 inpfile.xyz
energy_frequency: int
The frequency of logging energies to file. If 0, then no energies are
Expand Down Expand Up @@ -1095,7 +1112,7 @@ def __init__(
self._save_settings = save_settings

if orca_template is not None:
if not isinstance(template, str):
if not isinstance(orca_template, str):
msg = "'orca_template' must be of type 'str'"
_logger.error(msg)
raise TypeError(msg)
Expand Down Expand Up @@ -1739,7 +1756,7 @@ def _sire_callback(self, atomic_numbers, charges_mm, xyz_qm, xyz_mm):
# ORCA.
elif self._backend == "orca":
try:
E_vac, grad_vac = self._run_orca(orca_input, xyz_file_qm)
E_vac, grad_vac = self._run_orca(elements=elements, xyz_qm=xyz_qm)
except Exception as e:
msg = (
f"Failed to calculate in vacuo energies using ORCA backend: {e}"
Expand Down Expand Up @@ -2826,9 +2843,7 @@ def _run_deepmd(self, xyz, elements):
grad_mean[0] * _EV_TO_HARTREE * _BOHR_TO_ANGSTROM,
)

def _run_orca(
self, orca_input=None, xyz_file_qm=None, atomic_numbers=None, xyz_qm=None
):
def _run_orca(self, orca_input=None, xyz_file_qm=None, elements=None, xyz_qm=None):
"""
Internal function to compute in vacuo energies and gradients using
ORCA.
Expand All @@ -2837,10 +2852,18 @@ def _run_orca(
----------
orca_input: str
The path to the ORCA input file.
The path to the ORCA input file. (Used with the sander interface.)
xyz_file_qm: str
The path to the xyz coordinate file for the QM region.
The path to the xyz coordinate file for the QM region. (Used with the
sander interface.)
elements: [str]
The list of elements. (Used with the Sire interface.)
xyz_qm: numpy.array
The coordinates of the QM region in Angstrom. (Used with the Sire
interface.)
Returns
-------
Expand All @@ -2862,10 +2885,12 @@ def _run_orca(
if xyz_file_qm is not None and not _os.path.isfile(xyz_file_qm):
raise IOError(f"Unable to locate the ORCA QM xyz file: {xyz_file_qm}")

if atomic_numbers is not None and not isinstance(atomic_numbers, _np.ndarray):
raise TypeError("'atomic_numbers' must be of type 'numpy.ndarray'")
if atomic_numbers is not None and atomic_numbers.dtype != _np.int64:
raise TypeError("'atomic_numbers' must have dtype 'int'.")
if elements is not None and not isinstance(elements, (list, tuple)):
raise TypeError("'elements' must be of type 'list' or 'tuple'.")
if elements is not None and not all(
isinstance(element, str) for element in elements
):
raise TypeError("'elements' must be a 'list' of 'str' types.")

if xyz_qm is not None and not isinstance(xyz_qm, _np.ndarray):
raise TypeError("'xyz_qm' must be of type 'numpy.ndarray'")
Expand All @@ -2875,15 +2900,17 @@ def _run_orca(
# ORCA input files take precedence.
is_orca_input = True
if orca_input is None or xyz_file_qm is None:
if atomic_numbers is None:
raise ValueError("No atomic numbers specified!")
if elements is None:
raise ValueError("No elements specified!")
if xyz_qm is None:
raise ValueError("No QM coordinates specified!")

is_orca_input = False

if self._orca_template is None:
raise ValueError("No ORCA template file specified!")
raise ValueError(
"No ORCA template file specified. Use the 'orca_template' keyword."
)

fd_orca_input, orca_input = _tempfile.mkstemp(
prefix="orc_job_", suffix=".inp", text=True
Expand All @@ -2892,19 +2919,44 @@ def _run_orca(
prefix="inpfile_", suffix=".xyz", text=True
)

# Copy the template file.
_shutil.copyfile(self._orca_template, orca_input)
# Parse the ORCA template file. Here we exclude the *xyzfile line,
# which will be replaced later using the correct path to the QM
# coordinate file that is written.
is_xyzfile = False
lines = []
with open(self._orca_template, "r") as f:
for line in f:
if "*xyzfile" in line:
is_xyzfile = True
else:
lines.append(line)

# Add the QM coordinate file path.
if not is_xyzfile:
raise ValueError("ORCA template file doesn't contain *xyzfile line!")

# Try to extract the charge and spin multiplicity from the line.
try:
_, charge, mult, _ = line.split()
except:
raise ValueError(
"Unable to parse charge and spin multiplicity from ORCA template file!"
)

# Write the ORCA input file.
with open(orca_input, "w") as f:
f.write(f'*xyzfile "{_os.path.basename(xyz_file_qm)}"\n')
for line in lines:
f.write(line)

# Add the QM coordinate file path.
with open(orca_input, "a") as f:
f.write(f"*xyzfile {charge} {mult} {_os.path.basename(xyz_file_qm)}\n")

# Write the xyz input file.
with open(xyz_file_qm, "w") as f:
f.write(f"{len(atomic_numbers):5d}\n\n")
for num, xyz in zip(atomic_numbers, xyz_qm):
f.write(f"{len(elements):5d}\n\n")
for elem, xyz in zip(elements, xyz_qm):
f.write(
f"{num:3d} {xyz[0]:21.17f} {xyz[1]:21.17f} {xyz[2]:21.17f}\n"
f"{elem:<3s} {xyz[0]:20.16f} {xyz[1]:20.16f} {xyz[2]:20.16f}\n"
)

# Create a temporary working directory.
Expand Down

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