def dipolar_spectrum_vs_temp(self, fdd, weights_xi, spinA, spinB,
calc_settings):
Nf = self.Nf
Ntemp = self.temp_bins.size
spc_vs_temp = np.zeros((Ntemp, Nf))
g = self.set_gaxis(spinB['g'])
Ng = g.size
depth_vs_temp = np.zeros((Ntemp, Ng))
for i in range(Ntemp):
sys.stdout.write('\r')
status = int(float(i + 1) / float(Ntemp) * 100)
sys.stdout.write(
"Calculating the dipolar spectrum vs temperature... %d%% " %
(status))
sys.stdout.flush()
temp = self.temp_bins[i]
weights_temp = flip_probabilities(self.gB, spinB['g'],
calc_settings['magnetic_field'],
temp)
weights = self.total_weights(weights_temp, weights_xi)
spc = self.dipolar_spectrum(fdd, weights)
spc_vs_temp[i] = spc
weights_temp2 = flip_probabilities(g, spinB['g'],
calc_settings['magnetic_field'],
temp)
depth_vs_temp[i] = weights_temp2
return [spc_vs_temp, g, depth_vs_temp]
def score_function(parameters, fit_settings, simulator, exp_data, spinA, spinB, calc_settings):
# Set parameters
indices = fit_settings['parameters']['indices']
fixed = fit_settings['parameters']['fixed']
all_parameters = set_parameters(parameters, indices, fixed)
# Calculate the temperature-based weights
weights_temp = []
if (not (indices['temp'] == -1) and calc_settings['g_selectivity'] and (spinB['type'] == "anisotropic")):
weights_temp = flip_probabilities(simulator.gB, spinB['g'], calc_settings['magnetic_field'], all_parameters['temp'])
# Calculate dipolar frequencies
fdd, theta, weights_xi = simulator.dipolar_frequencies(all_parameters, spinA, spinB)
# Calulate the total weights
weights = simulator.total_weights(weights_temp, weights_xi)
if fit_settings['settings']['fitted_data'] == 'spectrum':
# Calculate the dipolar spectrum
fit = simulator.dipolar_spectrum(fdd, weights)
# Calculate the score
score = chi2(fit, exp_data['spc'], exp_data['f'], calc_settings['f_min'], calc_settings['f_max'], calc_settings['noise_std'])
elif fit_settings['settings']['fitted_data'] == 'timetrace':
# Calculate the dipolar timetrace
#fit = simulator.dipolar_timetrace(fdd, weights)
fit = simulator.dipolar_timetrace_fast(fdd, weights)
# Calculate the score
score = chi2(fit, exp_data['sig'], exp_data['t'], calc_settings['t_min'], calc_settings['t_max'], calc_settings['noise_std'])
return score
def score_function(parameters, fit_settings, simulator, exp_data, spinA, spinB,
calc_settings):
# Set parameters
indices = fit_settings['parameters']['indices']
fixed = fit_settings['parameters']['fixed']
all_parameters = set_parameters(parameters, indices, fixed)
# Calculate dipolar frequencies
fdd, theta = simulator.dipolar_frequencies(all_parameters, spinA, spinB)
# Calculate weights for different g-values of spin B
pB = []
if (not (indices['temp'] == -1) and calc_settings['g_selectivity']
and (spinB['type'] == "anisotropic")):
pB = flip_probabilities(simulator.gB, spinB['g'],
calc_settings['magnetic_field'],
all_parameters['temp'])
# Simulate the spectrum or the time trace and score them
if fit_settings['settings']['fitted_data'] == 'spectrum':
# Calculate the dipolar spectrum
fit = simulator.dipolar_spectrum(fdd, pB)
# Calculate the score
score = rmsd(fit, exp_data['spc'], exp_data['f'],
calc_settings['f_min'], calc_settings['f_max'])
elif fit_settings['settings']['fitted_data'] == 'timetrace':
# Calculate the dipolar timetrace
#fit = simulator.dipolar_timetrace(fdd, pB)
fit = simulator.dipolar_timetrace_fast(fdd, pB)
# Calculate the score
score = rmsd(fit, exp_data['sig'], exp_data['t'],
calc_settings['t_min'], calc_settings['t_max'])
return score
def init_fitting(self, fit_settings, exp_data, spinA, spinB,
calc_settings):
# Set the frequency axis
if fit_settings['settings']['fitted_data'] == 'spectrum':
self.f = self.set_faxis(exp_data['f'])
self.Nf = self.f.size
# Set the time axis
elif fit_settings['settings']['fitted_data'] == 'timetrace':
self.t = self.set_taxis(exp_data['t'])
self.Nt = self.t.size
# Set the modulation depth
self.mod_depth = self.set_modulation_depth(exp_data['sig'])
# Generate the ensemble of spin pairs
self.field, self.gA, self.gB, self.qA, self.qB = self.spin_ensemble(
spinA, spinB)
# Calculate the temperature-based weights
if (fit_settings['parameters']['indices']['temp'] == -1
and calc_settings['g_selectivity']
and spinB['type'] == "anisotropic"):
self.weights_temp = flip_probabilities(
self.gB, spinB['g'], calc_settings['magnetic_field'],
fit_settings['parameters']['fixed']['temp'])
def run_simulation(self, sim_settings, exp_data, spinA, spinB,
calc_settings):
sys.stdout.write('Starting the simulation...\n')
sys.stdout.write('Running pre-calculations... ')
# Set the frequency axis
if (sim_settings['modes']['spc']
or sim_settings['modes']['spc_vs_theta']
or sim_settings['modes']['spc_vs_xi']
or sim_settings['modes']['spc_vs_phi']
or sim_settings['modes']['spc_vs_temp']):
self.f = self.set_faxis(exp_data['f'], spinA['g'], spinB['g'],
sim_settings['parameters'])
self.Nf = self.f.size
# Normalize the frequency axis
if sim_settings['settings']['faxis_normalized']:
self.fn = self.normalize_faxis(sim_settings['parameters'])
# Set the time axis
if sim_settings['modes']['timetrace']:
self.t = self.set_taxis(exp_data['t'], spinA['g'], spinB['g'],
sim_settings['parameters'])
self.Nt = self.t.size
# Set the modulation depth parameter
if sim_settings['modes']['timetrace']:
self.mod_depth = self.set_modulation_depth(
exp_data['sig'], sim_settings['settings']['mod_depth'])
# Generate an ensemble of spin pairs
self.field, self.gA, self.gB, self.qA, self.qB = self.spin_ensemble(
spinA, spinB)
# Calculate the temperature-based weights
if (calc_settings['g_selectivity'] and spinB['type'] == "anisotropic"):
self.weights_temp = flip_probabilities(
self.gB, spinB['g'], calc_settings['magnetic_field'],
sim_settings['parameters']['temp'])
# Calculate the dipolar frequencies
weights_xi = []
if (sim_settings['modes']['spc'] or sim_settings['modes']['timetrace']
or sim_settings['modes']['spc_vs_theta']
or sim_settings['modes']['spc_vs_temp']):
fdd, theta, weights_xi = self.dipolar_frequencies(
sim_settings['parameters'], spinA, spinB, self.gA, self.gB,
self.qA, self.qB, sim_settings['modes']['spc_vs_theta'])
# Calulate the total weights
weights = self.total_weights(self.weights_temp, weights_xi)
sys.stdout.write('[DONE]\n')
# Calculate the dipolar spectrum
if sim_settings['modes']['spc']:
sys.stdout.write('Calculating the dipolar spectrum... ')
self.spc = self.dipolar_spectrum(fdd, weights)
sys.stdout.write('[DONE]\n')
if not (exp_data['f'] == []):
score = rmsd(self.spc, exp_data['spc'], exp_data['f'],
calc_settings['f_min'], calc_settings['f_max'])
sys.stdout.write("RMSD = %f \n" % score)
# Calculate the PDS time trace
if sim_settings['modes']['timetrace']:
#time_start = time.time()
sys.stdout.write('Calculating the dipolar time trace... ')
#self.sig = self.dipolar_timetrace(fdd, weights)
self.sig = self.dipolar_timetrace_fast(fdd, weights)
sys.stdout.write('[DONE]\n')
#time_finish = time.time()
#time_elapsed = str(datetime.timedelta(seconds = time_finish - time_start))
#sys.stdout.write('Calculation time: %s\n' % (time_elapsed))
if not (exp_data['t'] == []):
score = rmsd(self.sig, exp_data['sig'], exp_data['t'],
calc_settings['t_min'], calc_settings['t_max'])
sys.stdout.write("RMSD = %f \n" % score)
# Calculate the dipolar spectrum vs theta
if (sim_settings['modes']['spc_vs_theta']):
sys.stdout.write('Calculating the dipolar spectrum vs theta... ')
self.theta_bins = sim_settings['settings']['theta_bins']
self.spc_vs_theta = self.dipolar_spectrum_vs_theta(
fdd, theta, weights)
if not sim_settings['modes']['spc']:
self.spc = self.dipolar_spectrum(fdd, weights)
sys.stdout.write('[DONE]\n')
# Calculate the dipolar spectrum vs xi
if sim_settings['modes']['spc_vs_xi']:
sys.stdout.write('Calculating the dipolar spectrum vs xi... ')
self.xi_bins = sim_settings['settings']['xi_bins']
self.spc_vs_xi = self.dipolar_spectrum_vs_xi(
sim_settings['parameters'], spinA, spinB)
sys.stdout.write('[DONE]\n')
# Calculate the dipolar spectrum vs phi
if sim_settings['modes']['spc_vs_phi']:
sys.stdout.write('Calculating the dipolar spectrum vs phi... ')
self.phi_bins = sim_settings['settings']['phi_bins']
self.spc_vs_phi = self.dipolar_spectrum_vs_phi(
sim_settings['parameters'], spinA, spinB)
sys.stdout.write('[DONE]\n')
# Calculate the dipolar spectrum vs temperature
if (sim_settings['modes']['spc_vs_temp']
and calc_settings['g_selectivity']):
sys.stdout.write(
'Calculating the dipolar spectrum vs temperature... ')
self.temp_bins = sim_settings['settings']['temp_bins']
self.spc_vs_temp, self.g, self.depth_vs_temp = self.dipolar_spectrum_vs_temp(
fdd, weights_xi, spinA, spinB, calc_settings)
sys.stdout.write('[DONE]\n')
sys.stdout.write('The simulation is finished\n\n')