def curvature_coupling_loader_membrane(data, **kwargs):
"""
Receive the undulation data and prepare the meshes for the curvature coupling calculation.
"""
#---point heights into "memory"
status('populating memory', tag='load')
midplane_method = kwargs.pop('midplane_method', 'flat')
if kwargs: raise Exception('unprocessed kwargs: %s' % kwargs)
memory = {}
for sn in data['undulations'].keys():
if (sn, 'hqs') not in memory:
dat = data['undulations'][sn]['data']
vecs = dat['vecs']
mesh = dat['mesh']
midplane = mesh.mean(axis=0)
#---assume the average structure is a flat bilayer at the vertical center of the bilayer
if midplane_method == 'flat':
zmeans = midplane.reshape((midplane.shape[0], -1)).mean(axis=1)
midplane = np.array(
[i - zmeans[ii] for ii, i in enumerate(midplane)])
#---assume the average structure is the average height profile of the bilayer
elif midplane_method == 'average':
zmean = midplane.mean(axis=0)
midplane -= zmean
else:
raise Exception('invalid midplane method %s' % midplane_method)
hqs = fft_field(midplane)
memory[(sn, 'hqs')] = hqs
memory[(sn, 'vecs')] = vecs
return memory
def objective(args): """ Fit parameters are defined in sequence for the optimizer. They are: kappa,gamma,vibe,*curvatures-per-dimple. """ kappa,gamma,vibe = args[:3] curvatures = args[3:] composite = self.curvature_sum(cfs,curvatures,method=curvature_sum_method) cqs = cctools.fft_field(composite) termlist = [multipliers(x,y) for x,y in [(hqs,hqs),(hqs,cqs),(cqs,hqs),(cqs,cqs)]] termlist = [np.reshape(np.mean(k,axis=0),-1)[1:] for k in termlist] #---skipping assertion and dropping imaginary termlist = [np.real(k) for k in termlist] hel = (kappa*area*(termlist[0]*q_raw**4+signterm*termlist[1]*q_raw**2 +signterm*termlist[2]*q_raw**2+termlist[3]) +gamma*area*(termlist[0]*q_raw**2)) ratio = hel/((vibe*q_raw+machine_eps)/(np.exp(vibe*q_raw)-1)+machine_eps) return residual(ratio[band])
def objective(args, mode='residual'):
"""
Fit parameters are defined in sequence for the optimizer.
They are: kappa,gamma,vibe,*curvatures-per-dimple.
"""
kappa, gamma, vibe = args[:3]
#---uniform curvatures
if ndrops_uniform != 0:
curvatures = [args[3] for i in range(ndrops_uniform)]
#---one curvature per field
else:
curvatures = args[3:]
composite = self.curvature_sum(cfs,
curvatures,
method=curvature_sum_method)
cqs = cctools.fft_field(composite)
termlist = [
multipliers(x, y)
for x, y in [(hqs, hqs), (hqs, cqs), (cqs, hqs), (cqs,
cqs)]
]
termlist = [
np.reshape(np.mean(k, axis=0), -1)[1:] for k in termlist
]
#---skipping assertion and dropping imaginary
termlist = [np.real(k) for k in termlist]
hel = (
kappa / 2.0 * area *
(termlist[0] * q_raw**4 + signterm * termlist[1] * q_raw**2
+ signterm * termlist[2] * q_raw**2 + termlist[3]) +
gamma * area * (termlist[0] * q_raw**2))
ratio = hel / ((vibe * q_raw + machine_eps) /
(np.exp(vibe * q_raw) - 1) + machine_eps)
if mode == 'residual': return residual(ratio[band])
elif mode == 'ratio': return ratio
else: raise Exception('invalid mode %s' % mode)