'\n')
f.close()
# Calc minimized energies
e = geometry.get_potential_energy()
print('Total energy', e, 'eV')
# Get the forces again
print('Forces:')
print(geometry.get_forces())
# Run the vibrational analysis
vib = Vibrations(geometry, nfree=2)
vib.run()
print(vib.summary())
print(vib.get_zero_point_energy())
# Get freqs
f = vib.get_frequencies()
# Print modes + freq
for i in range(0, len(f)):
print('Mode(' + str(i) + ') Freq: ' + "{:.7e}".format(f[i]))
print(vib.get_mode(i))
'''
# We will alse need to use these functions to get thermo-chem data
thermo = IdealGasThermo(vib_energies=vib_energies,
potentialenergy=potentialenergy,
atoms=atoms,
geometry='linear',
symmetrynumber=2, spin=0)
def vibrate(self, atoms: Atoms, indices: list, read_only=False):
'''
This method uses ase.vibrations module, see more for info.
User provides the FHI-aims parameters, the Atoms object and list
of indices of atoms to be vibrated. Variables related to FHI-aims are governed by the React object.
Calculation folders are generated automatically and a sockets calculator is used for efficiency.
Work in progress
Args:
atoms: Atoms object
indices: list
List of indices of atoms that require vibrations
read_only: bool
Flag for postprocessing - if True, the method only extracts information from existing files,
no calculations are performed
Returns:
Zero-Point Energy: float
'''
'''Retrieve common properties'''
basis_set = self.basis_set
hpc = self.hpc
params = self.params
parent_dir = os.getcwd()
dimensions = sum(atoms.pbc)
if not self.filename:
'''develop a naming scheme based on chemical formula'''
self.filename = atoms.get_chemical_formula()
vib_dir = parent_dir + "/VibData_" + self.filename + "/Vibs"
print(vib_dir)
vib = Vibrations(atoms, indices=indices, name=vib_dir)
'''If a calculation was terminated prematurely (e.g. time limit) empty .json files remain and the calculation
of the corresponding stretch modes would be skipped on restart. The line below prevents this'''
vib.clean(empty_files=True)
'''Extract vibration data from existing files'''
if read_only:
vib.read()
else:
'''Calculate required vibration modes'''
required_cache = [
os.path.join(vib_dir, "cache." + str(x) + y + ".json")
for x in indices
for y in ["x+", "x-", "y+", "y-", "y-", "z+", "z-"]
]
check_required_modes_files = np.array(
[os.path.exists(file) for file in required_cache])
if np.all(check_required_modes_files == True):
vib.read()
else:
'''Set the environment variables for geometry optimisation'''
set_aims_command(hpc=hpc,
basis_set=basis_set,
defaults=2020,
nodes_per_instance=self.nodes_per_instance)
'''Generate a unique folder for aims calculation'''
counter, subdirectory_name = self._restart_setup(
"Vib",
filename=self.filename,
restart=False,
verbose=False)
os.makedirs(subdirectory_name, exist_ok=True)
os.chdir(subdirectory_name)
'''Name the aims output file'''
out = str(counter) + "_" + str(self.filename) + ".out"
'''Calculate vibrations and write the in a separate directory'''
with _calc_generator(params, out_fn=out,
dimensions=dimensions)[0] as calculator:
if not self.dry_run:
atoms.calc = calculator
else:
atoms.calc = EMT()
vib = Vibrations(atoms, indices=indices, name=vib_dir)
vib.run()
vib.summary()
'''Generate a unique folder for aims calculation'''
if not read_only:
os.chdir(vib_dir)
vib.write_mode()
os.chdir(parent_dir)
return vib.get_zero_point_energy()
