"""
import numpy as np
hessian = []
hessian_found = False
for line in fchkfile.split("\n"):
if line.startswith("Cartesian Force Constants"):
hessian_found = True
elif hessian_found:
if line.startswith("Nonadiabatic coupling") or line.startswith(
"Dipole Moment"):
hessian_found = False
else:
hessian.extend([float(hess) for hess in line.split()])
# now we can calculate the size of the hessian
# (2 * triangle length) + 0.25 = (x+0.5)^2
hess_size = int(np.sqrt(2 * len(hessian) + 0.25) - 0.5)
full_hessian = np.zeros((hess_size, hess_size))
m = 0
for i in range(hess_size):
for j in range(i + 1):
full_hessian[i, j] = hessian[m]
full_hessian[j, i] = hessian[m]
m += 1
return full_hessian.flatten().tolist()
# register the gaussian harness this must be done so gaussian can be used!
register_program(GaussianHarness())
def failure_engine():
unique_name = "testing_random_name"
class FailEngine(qcng.programs.ProgramHarness):
iter_modes: List[str] = []
ncalls: int = 0
start_distance: float = 5
equilibrium_distance: float = 4
_defaults = {
"name": unique_name,
"scratch": False,
"thread_safe": True,
"thread_parallel": False,
"node_parallel": False,
"managed_memory": False,
}
class Config(qcng.programs.ProgramHarness.Config):
allow_mutation: True
@staticmethod
def found(raise_error: bool = False) -> bool:
return True
def compute(self, input_data: 'ResultInput',
config: 'JobConfig') -> 'Result':
self.ncalls += 1
mode = self.iter_modes.pop(0)
geom = input_data.molecule.geometry
if geom.shape[0] != 2:
raise ValueError(
"Failure Test must have an input size of two.")
grad_value = np.abs(
np.linalg.norm(geom[0] - geom[1]) - self.equilibrium_distance)
grad = [0, 0, -grad_value, 0, 0, grad_value]
if mode == "pass":
return qcel.models.Result(
**{
**input_data.dict(),
**{
"properties": {
"return_energy": grad_value
},
"return_result": grad,
"success": True,
"extras": {
"ncalls": self.ncalls
},
"provenance": {
"creator": "failure_engine",
"ncores": config.ncores
}
}
})
elif mode == "random_error":
raise qcng.exceptions.RandomError("Whoops!")
elif mode == "input_error":
raise qcng.exceptions.InputError("Whoops!")
else:
raise KeyError("Testing error, should not arrive here.")
def get_job(self):
json_data = {
"molecule": {
"symbols": ["He", "He"],
"geometry": [0, 0, 0, 0, 0, self.start_distance]
},
"driver": "gradient",
"model": {
"method": "something"
}
}
return json_data
engine = FailEngine()
qcng.register_program(engine)
yield engine
qcng.unregister_program(engine.name)