def absolute_rmsd(fit, energies, angles): # expect energies and angles as dicts
deviations = []
for x in angles:
theta = angles[x]
deviations.append((energies[x] - energy_at_x(fit, theta))**2)
rmsd = np.sqrt(np.mean(deviations))
return rmsd
def determine_fitness(root, molecules, basis_sets, loaded_data):
reference_basis = '631Gd'
for m in molecules:
if m not in loaded_data:
continue
formatting = dict(root=root, mol=m, ref=reference_basis)
with open('{root}/{ref}/{mol}/phased_fitted_curve.txt'.format(**formatting), 'r') as fh:
reference_data = yaml.load(fh)
# absolute is the data as referenced between fit and actual QM results
data_absolute = []
# relative is the data referenced between fit and the reference_basis fit
data_relative = []
for d in basis_sets:
if d not in loaded_data[m]:
continue
formatting['basis'] = d
energies, angles = loaded_data[m][d]
with open('{root}/{basis}/{mol}/phased_fitted_curve.txt'.format(**formatting), 'r') as fh:
fit = yaml.load(fh)
data_absolute.append(dict(rmsd = absolute_rmsd(fit, energies, angles),
basis = d))
data_relative.append(dict(rmsd = relative_rmsd(fit, reference_data),
basis = d))
data = [{'x':angles,
'y':energies,
'marker':'r.-'},]
fit_energies = {}
for z in angles:
fit_energies[z] = energy_at_x(fit, angles[z])
data.append({'x':angles,'y':fit_energies,'marker':'b.-'})
save_path = '{root}/Figures/{mol}/{basis}_with_fit.png'.format(**formatting)
plot_scatters(data,save_path, show_legend=False, xlim=(0,360))
with open('{root}/Figures/{mol}/rmsd_data.txt'.format(**formatting), 'w') as fh:
fh.write('Absolute RMSDs from QM calculations\n')
for d in data_absolute:
fh.write('{basis:>12} : {rmsd:.2f}\n'.format(**d))
fh.write('\n')
fh.write('RMSDs relative to 6-31G(d) basis set fit\n')
for d in data_relative:
fh.write('{basis:>12} : {rmsd:.2f}\n'.format(**d))
fh.write('___________________________________\n')
def relative_rmsd(fit1, fit2):
deviations = []
for theta in range(0,360):
deviations.append((energy_at_x(fit1, theta) - energy_at_x(fit2, theta))**2)
rmsd = np.sqrt(np.mean(deviations))
return rmsd
