psistuff = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=loadsuf,
name=f"{pre}psivsr")
rs = psistuff.r()
psis = psistuff.psi()
observablestuff = ObservableData(scan=scan,
loadsuf=loadsuf,
savesuf=loadsuf,
name=f"{pre}observables")
R = observablestuff.R()
eta = observablestuff.eta()
dband = 2 * np.pi / eta
axarr[0].plot(rs, (dband - np.cos(psis)) / np.cos(psis) * 100,
'-',
color=colors[0])
axarr[0].set_xlabel(r'$r$', fontsize=10)
axarr[0].set_ylabel('molecular strain (\%)', fontsize=10)
axarr[0].legend(frameon=False)
fibrilstrain = FibrilStrain(psistuff, observablestuff, sfile_format='pdf')
rs, thetas = fibrilstrain.mesh_polar(grid_skip=4)
k24 = pair[1]
scan = {}
scan['\\gamma_s'] = gamma
scan['k_{24}'] = k24
scan['\\omega'] = str(omega)
obsfwd = ObservableData(["\\Lambda"],
scan_dir='scanforward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
Lambdas = obsfwd.data[:, 0]
x, y = obsfwd.surfacetwist()[1:], 2 * np.pi / obsfwd.eta()[1:]
ax.plot(x, y, '.', color=colors[js])
ax.plot(x[-1], y[-1], 'rs')
dums = np.linspace(0.05, 0.25, num=150, endpoint=True)
ax.plot(dums, np.cos(dums), '--')
ax.set_xlabel(r"$\psi(R)$", fontsize=10)
ax.set_ylabel(r"$2\pi/\eta$", fontsize=10)
fig.subplots_adjust(left=0.1, right=0.9, bottom=0.15, top=0.95)
fig.savefig(obsfwd.observable_sname("twistvsdband", plot_format="pdf"))
plt.show()
scan['\\Lambda'] = Lambda
scan['k_{24}'] = k24
scan['\\omega'] = omega
obsfwd = ObservableData(["\\gamma_s"],
scan_dir='scanforward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
gammas = obsfwd.data[:, 0]
ysfwd = [
obsfwd.E(),
obsfwd.R(),
obsfwd.eta(),
obsfwd.delta(),
obsfwd.surfacetwist()
]
"""
obsbkwd = ObservableData(["\\gamma_s"],scan_dir='scanbackward',scan=scan,loadsuf=loadsuf,
savesuf=savesuf)
ysbkwd = [obsbkwd.R(),obsbkwd.surfacetwist()]
g_small,g_large,g_eq = find_metastable(obsfwd.R(),obsbkwd.R(),
obsfwd.E(),obsbkwd.E())
print(g_small,g_large,g_eq)
"""
savesuf=savesuf)
if not obsfwd.file_exists:
continue
obsfwd.sort_observables()
obsfwd.remove_duplicates()
Lambdas = obsfwd.data[:,0]
#obsbkwd = ObservableData(["\\Lambda"],scan_dir='scanbackward',scan=scan,loadsuf=loadsuf,
# savesuf=savesuf)
#obsbkwd.sort_observables()
ysfwd = [obsfwd.E(),obsfwd.R(),obsfwd.eta(),obsfwd.delta(),obsfwd.surfacetwist()]
#ysbkwd = [obsbkwd.E(),obsbkwd.R(),obsbkwd.eta(),obsbkwd.delta(),obsbkwd.surfacetwist()]
for i,observable in enumerate(observable_list):
if observable == 'surfacetwist':
ylabel = r'$\psi(R)$'
elif observable == 'eta':
ylabel = r'$2\pi/\eta$'
ysfwd[i] = 2*np.pi/ysfwd[i]
elif observable == 'delta':
ylabel = r'$\delta/\delta_0$'
ysfwd[i] = ysfwd[i]/np.sqrt(2/3)
elif len(observable) > 1:
scan_dir='scanforward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
Lambdas = obsfwd.data[:, 0]
if js == 1:
obsbkwd = ObservableData(["\\Lambda"],
scan_dir='scanbackward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
obsbkwd.sort_observables()
ysbkwd = [obsbkwd.E(), obsbkwd.eta(), obsbkwd.delta()]
ysfwd = [obsfwd.E(), obsfwd.eta(), obsfwd.delta()]
for i, observable in enumerate(observable_list):
if observable == 'surfacetwist':
ylabel = r'$\psi(R)$'
elif observable == 'eta':
ylabel = r'$2\pi/\eta$'
ysfwd[i] = 2 * np.pi / ysfwd[i]
if js == 1:
ysbkwd[i] = 2 * np.pi / ysbkwd[i]
elif observable == 'delta':
ylabel = r'$\delta/\delta_0$'
ysfwd[i] = ysfwd[i] / np.sqrt(2 / 3)
scan_dir='scanforward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
obsbkwd = ObservableData(["\\Lambda"],
scan_dir='scanbackward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
obsbkwd.sort_observables()
observable_list = ['E', 'R', 'eta', 'delta', 'surfacetwist']
ysfwd = [
obsfwd.E(),
obsfwd.R(),
obsfwd.eta(),
obsfwd.delta(),
obsfwd.surfacetwist()
]
ysbkwd = [
obsbkwd.E(),
obsbkwd.R(),
obsbkwd.eta(),
obsbkwd.delta(),
obsbkwd.surfacetwist()
]
for i, observable in enumerate(observable_list):
fig[observable] = plt.figure()
ax[observable] = fig[observable].add_subplot(1, 1, 1)
obsfwd = ObservableData(["strain","averagetwist"],scan_dir=f'scanforward{type}',
scan=scan,loadsuf=loadsuf,savesuf=savesuf)
Req = obsfwd.R()[0]
print(Req)
strains = obsfwd.data[:,0]
stresses = np.gradient(obsfwd.E(),strains)*K22*q*q/1000 # stress in kPa
stresses[0] = 0.0
avgtwist = obsfwd.data[:,1]
minindex = np.argmin(avgtwist)
if type == "no-core":
# incompatibility between the no core and core case so need to do this hack
deltas = obsfwd.eta()
else:
deltas = obsfwd.delta()
ysfwd = [stresses,avgtwist,deltas]
if obsfwd.E()[0] > 1e299:
print("bad calculation at Lambda = ",Lambda)
for j,observable in enumerate(observable_list):
if observable == 'surfacetwist':
ylabel = r'$<\psi>$' + ' (' + r"$\si{\radian}$" + ')'
ax[observable] = fig[observable].add_subplot(1,1,1)
for j,Lambda in enumerate(Lambdas):
scan = {}
scan['\\Lambda']=Lambda
scan['k_{24}']=k24
scan['\\omega']=omega
obsfwd = ObservableData(["\\gamma_s"],scan_dir='scanforward',scan=scan,loadsuf=loadsuf,
savesuf=savesuf)
gammas = obsfwd.data[:,0]
ysfwd = [obsfwd.E(),obsfwd.R(),obsfwd.eta(),
obsfwd.delta(),obsfwd.surfacetwist()]
"""
obsbkwd = ObservableData(["\\gamma_s"],scan_dir='scanbackward',scan=scan,loadsuf=loadsuf,
savesuf=savesuf)
ysbkwd = [obsbkwd.R(),obsbkwd.surfacetwist()]
g_small,g_large,g_eq = find_metastable(obsfwd.R(),obsbkwd.R(),
obsfwd.E(),obsbkwd.E())
print(g_small,g_large,g_eq)
"""
class FibrilStrain(ReadParams):
def __init__(self,scan_dir="",scan={},
loadsuf=["K_{33}","k_{24}","\\Lambda",
"\\omega","\\gamma_s"],
savesuf=["K_{33}","k_{24}","\\Lambda",
"\\omega","\\gamma_s"],
sfile_format="pdf",obsname = "observables",
datfile="data/input.dat",psiname = "psivsr",
psiloadfilepath="data",obsloadfilepath="data",
psisavefilepath="results",obssavefilepath="results"):
ReadParams.__init__(self,datfile=datfile,
scan=scan,loadsuf=loadsuf,savesuf=savesuf)
self.obsdata = ObservableData(scan=scan,loadsuf=loadsuf,savesuf=savesuf,
datfile=datfile,loadfilepath=obsloadfilepath,
savefilepath=obssavefilepath,
scan_dir=scan_dir,name=obsname)
self.psidata = PsiData(scan=scan,loadsuf=loadsuf,savesuf=savesuf,
datfile=datfile,loadfilepath=psiloadfilepath,
savefilepath=obssavefilepath,
scan_dir = scan_dir,name=psiname)
self.scan_dir=scan_dir
self.sfile_format=sfile_format
self.i_R_c = self.find_R_c_index()
return
def find_R_c_index(self):
i = np.argmin(np.abs(self.psidata.r()-self.obsdata.R_c()))
return i
def mesh_polar(self,num_azm=50,grid_skip=1):
azm = np.linspace(0,2*np.pi,num=num_azm)
rs,thetas = np.meshgrid(self.psidata.r()[::grid_skip],
azm)
return rs,thetas
def strain_1d(self,denom='d(r)'):
preferred_dband = np.cos(self.psidata.psi()[self.i_R_c:])
true_dband = 2*np.pi/self.obsdata.eta()
if denom=='d(r)':
dn = preferred_dband
elif denom=='d':
dn = true_dband
else:
raise ValueError(f'setting denominator of the strain equation to '
'"{denom}" is not valid, it must either be "d(r)" '
'(the default value) or "d".')
dums = np.full(self.i_R_c,np.nan)
s0s = (true_dband-preferred_dband)/dn
return np.concatenate((dums,s0s))
def strain_polar(self,r_mesh,denom='d(r)',grid_skip=1):
return np.tile(self.strain_1d(denom=denom)[::grid_skip],
(r_mesh.shape[0],1))
def strain_sname(self,descriptor="polar"):
suffix = self.write_suffix(suffix_type="save")
if self.scan_dir != "":
sname = f"results/_{descriptor}_strain_{self.scan_dir}_{suffix}.{self.sfile_format}"
else:
sname = f"results/_{descriptor}_strain_{suffix}.{self.sfile_format}"
return sname