def get_coords_CO2(xyzfilename):
_, _, atoms, coords = read_xyz(xyzfilename)
# CO2 is always the last 3 atoms in each file.
coords_CO2 = np.array(coords[-3:])
return coords_CO2
'find /home/eric/Chemistry/calc.sgr/paper_02_CD_SC/NewXYZFiles/ -name "*.xyz" | sort', shell=True
).decode()
xyzfilenames = sorted(find_output.splitlines())
dim = 1001
assert len(xyzfilenames) == dim
possible_n_qm = list(range(1, 64 + 1))
dropnums = {n_qm: [] for n_qm in possible_n_qm}
n_qm_to_distance_from_COM_COM_combined = {n_qm: [] for n_qm in possible_n_qm}
n_qm_to_distance_from_COM_COM_cation = {n_qm: [] for n_qm in possible_n_qm}
n_qm_to_distance_from_COM_COM_anion = {n_qm: [] for n_qm in possible_n_qm}
for xyzfilename in xyzfilenames:
dropnum = os.path.splitext(xyzfilename.split("_")[-1])[0]
print(dropnum)
_, _, elements, coords = read_xyz(xyzfilename)
assert elements[-3:] == ["C", "O", "O"]
grouping_anions, grouping_cations, grouping_CO2 = determine_fragment_grouping(elements)
fragments_anions = make_fragments_from_grouping(elements, coords, grouping_anions)
fragments_cations = make_fragments_from_grouping(elements, coords, grouping_cations)
fragment_CO2 = make_fragments_from_grouping(elements, coords, grouping_CO2)
fragments = fragments_anions + fragments_cations + fragment_CO2
assert len(fragment_CO2) == 1
fragment_CO2 = fragment_CO2[0]
for n_qm in possible_n_qm:
# Wouldn't it be nice if we didn't calculate the distance twice?
closest_cations = get_n_closest_fragments(n_qm, fragment_CO2, fragments_cations, method="centerofmass")
closest_anions = get_n_closest_fragments(n_qm, fragment_CO2, fragments_anions, method="centerofmass")
max_distance_from_COM_COM_combined = -1.0e30
max_distance_from_COM_COM_cation = -1.0e30
max_distance_from_COM_COM_anion = -1.0e30
parser.add_argument('--alpha-slope', type=float, default=-3415.3)
parser.add_argument('--alpha-intercept', type=float, default=9523.8)
parser.add_argument('--beta-slope', type=float, default=1.12)
parser.add_argument('--beta-intercept', type=float, default=-515.7)
args = parser.parse_args()
alpha_slope = args.alpha_slope
alpha_intercept = args.alpha_intercept
beta_slope = args.beta_slope
beta_intercept = args.beta_intercept
l_lower = []
l_upper = []
for xyzfilename in args.xyzfilename:
_, _, atoms, coords = read_xyz(xyzfilename)
coords_CO2 = np.array(coords[-3:])
# Carbon is the first atom!
l12 = distance(coords_CO2[0], coords_CO2[1]) + distance(coords_CO2[0], coords_CO2[2])
angle = bond_angle(coords_CO2[1], coords_CO2[0], coords_CO2[2])
theta = 180.0 - angle
alpha = (alpha_slope * l12) + alpha_intercept
beta = (beta_slope * theta) + beta_intercept
hamiltonian = np.array(
[[alpha, beta],
[beta, alpha]]
)