def system(self):
return readsystem.readsystem(self.data)
else:
print('What kind of file is this?!')
exit(1)
base = os.path.splitext(fname)[0]
total_energy = np.array(data_loaded['total_energy'], dtype=float)
histogram = np.array(data_loaded['histogram'])
rel_bins = np.array(data_loaded['rel_bins'])
bin_norm = data_loaded['bin_norm']
max_energy = data_loaded['max_energy']
min_energy = data_loaded['min_energy']
lnw = np.array(data_loaded['lnw'])
lnw -= lnw.max()
lnw -= np.log(np.sum(np.exp(lnw))) # w = w / sum(w) to normalize
system = readsystem.readsystem(data_loaded)
energy_boundaries = [max_energy]
energy_per_rel_bin = 1/bin_norm*(max_energy-min_energy)
for b in rel_bins:
energy_boundaries.append(energy_boundaries[-1] - b*energy_per_rel_bin)
energy_boundaries = np.array(energy_boundaries)
np.savetxt(base+'-energy-boundaries.dat', energy_boundaries)
mean_energy = total_energy/histogram #includes unbounded extremes
np.savetxt(base+'-mean-energy.dat', mean_energy)
np.savetxt(base+'-lnw.dat', lnw) #includes unbounded extremes
with open(base+'-system.dat', 'w') as f:
remaining_entopy = 0
for i in range(1, len(above_count)):
lnw.append(remaining_entopy + np.log(above_count[i] / count[i]))
remaining_entopy = remaining_entopy + np.log(below_count[i] / count[i])
mean_energy.append(above_total[i] / above_count[i])
lnw.append(remaining_entopy)
if replicas[-1]['below_count'] > 0:
mean_energy.append(replicas[-1]['below_total'] /
replicas[-1]['below_count'])
else:
mean_energy.append(np.NaN)
lnw = np.array(lnw)
lnw -= np.log(np.sum(np.exp(lnw))) # w = w / sum(w) to normalize
mean_energy = np.array(mean_energy)
energy_boundaries = []
for i in range(1, len(above_count)):
energy_boundaries.append(replicas[i]['cutoff_energy'])
energy_boundaries = np.array(energy_boundaries)
system = readsystem.readsystem(replicas[0])
np.savetxt(base + '-energy-boundaries.dat', energy_boundaries)
np.savetxt(base + '-mean-energy.dat', mean_energy)
np.savetxt(base + '-lnw.dat', lnw) #includes unbounded extremes
with open(base + '-system.dat', 'w') as f:
yaml.safe_dump(system, f)