scan['k_{24}'] = str(k24)
obsfwd = ObservableData(["\\gamma_s"],
scan_dir='scanforward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
obsbkwd = ObservableData(["\\gamma_s"],
scan_dir='scanbackward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
print(k24)
# find all spots where two distinct phases exist (two different radii values)
bool_1 = np.isclose(obsfwd.R(), obsbkwd.R(), rtol=1e-3)
find_j = np.where(bool_1 == False)[0]
if find_j.size > 0: # if two distinct phases exist, then:
# smallest gamma value that they both exist at
jsmall = find_j[0]
# largest gamma value that they both exist at
jlarge = find_j[-1]
# find the point where the fwd E becomes larger than the bkwd E
j = (np.argmin(
np.abs(obsfwd.E()[jsmall:jlarge + 1] -
obsbkwd.E()[jsmall:jlarge + 1])) + len(obsfwd.E()[:jsmall]))
scan['\\omega'] = omega
loadsuf=["K_{33}","k_{24}","\\Lambda","\\omega","\\gamma_s"]
psistuff = PsiData(scan=scan,loadsuf=loadsuf,savesuf=loadsuf)
rs = psistuff.r()/8.0*1000
psis = psistuff.psi()
observablestuff = ObservableData(scan=scan,loadsuf=loadsuf,savesuf=loadsuf)
print(observablestuff.surfacetwist())
R = observablestuff.R()/8.0*1000
fig = plt.figure()
width = 3.487
height = width
fig.set_size_inches(2*width,height)
ax1 = fig.add_subplot(1,2,1)
ax1.plot(rs,psis,'.',label=rf'$\Lambda={Lambda}$')
ax1.set_xlabel(r'$r$' ' ' r'$(\si{\nano\meter})$',fontsize=24)
ax1.set_ylabel(r'$\psi(r)$',fontsize=24)
k24 = k24s[i]
Lambda = Lambdas[i]
q = qs[i]
scan = {}
scan['\\gamma_s']=gamma
scan['k_{24}']=k24
scan['\\omega']=omega
scan['\\Lambda']=Lambda
obsfwd = ObservableData(["strain","averagetwist"],scan_dir='scanforward',
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
ysfwd = [stresses,obsfwd.data[:,1],obsfwd.delta()]
if obsfwd.E()[0] > 1e299:
print("bad calculation at Lambda = ",Lambda)
for j,observable in enumerate(observable_list):
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:
pre = "frustrated"
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)
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)
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]
ysfwd = [obsfwd.R(), obsfwd.surfacetwist()]
if js == 1:
obsbkwd = ObservableData(["\\Lambda"],
scan_dir='scanbackward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
obsbkwd.sort_observables()
ysbkwd = [obsbkwd.R(), obsbkwd.surfacetwist()]
for i, observable in enumerate(observable_list):
if observable == 'surfacetwist':
ylabel = r'$\psi(R)$'
else:
ts = ts[1:]
print(ts)
tcs = np.linspace(0.003,0.2,num=100,endpoint=True)
fig = plt.figure()
fig.set_size_inches(width,height)
ax = fig.add_subplot(1,1,1)
ylabel=observable
Rlin = obsfwd.R(observables_num=7)[1:]
Rfrust = obsbwd.R(observables_num=7)[1:]
ax.plot(ts,Rfrust-Rlin,
'^',color=colors[2],markersize=3)
if observable != "E":
ax.plot(tcs,y_scaling(tcs,0.5,0.25),'--',color='k',lw=1,
label=r'$t^{\frac{1}{2}}$')
#ax.set_xlim(0.002,8)
ax.set_yscale('log')
ax.set_xscale('log')
obsfwd = ObservableData(["\\Lambda"],
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()
gammacoexist = []
k24coexist = []
# load in 2d grid of data in data2d for each observable at the
# specified gamma,k24 pair.
for i,k24 in enumerate(k24s):
scan['k_{24}']=str(k24)
obsfwd = ObservableData(["\\gamma_s"],scan_dir='scanforward',scan=scan,
loadsuf=loadsuf,savesuf=savesuf,datfile='data/inputfwd.dat')
obsbkwd = ObservableData(["\\gamma_s"],scan_dir='scanbackward',scan=scan,
loadsuf=loadsuf,savesuf=savesuf,datfile='data/inputbwd.dat')
bwdlen = len(obsbkwd.R())
print(k24)
# find all spots where two distinct phases exist (two different radii values)
bool_1 = np.isclose(obsfwd.R()[:bwdlen],obsbkwd.R(),rtol=1e-3)
find_j = np.where(bool_1==False)[0]
if find_j.size > 0: # if two distinct phases exist, then:
# smallest gamma value that they both exist at
jsmall = find_j[0]
# largest gamma value that they both exist at
jlarge = find_j[-1]
# find the point where the fwd E becomes larger than the bkwd E
loadsuf=["K_{33}","k_{24}","\\Lambda","\\omega","\\gamma_s"]
psistuff = PsiData(scan=scan,loadsuf=loadsuf,savesuf=loadsuf,
name=f"psivsr{type}")
rs = psistuff.r()*R_units
psis = psistuff.psi()*180/np.pi
observablestuff = ObservableData(scan=scan,loadsuf=loadsuf,savesuf=loadsuf,
name=f"observables{type}")
print(observablestuff.surfacetwist())
R = observablestuff.R()*R_units
fig = plt.figure()
width = 4
height = width
fig.set_size_inches(2*width,height)
ax1 = fig.add_subplot(1,2,1)
ax1.plot(rs,psis,'.',label=rf'$\Lambda={Lambda}$')
ax1.set_xlabel(r'$r$' ' ' r'$(\si{\nano\meter})$',fontsize=24)
ax1.set_ylabel(r'$\psi(r)$' + " (" + r"$^\circ$" + ")",fontsize=24)
ax = {}
q = 24.0 # um^{-1}
K_22 = 6 # pN
for i, observable in enumerate(observable_list):
ax[observable] = fig.add_subplot(3, 1, i + 1)
obsfwd = ObservableData(["strain", "averagetwist"],
scan_dir='scanforward',
scan=scan,
loadsuf=loadsuf,
savesuf=savesuf)
Req = obsfwd.R()[0] / q * 1000 # nm
strains = obsfwd.data[:, 0]
stresses = np.gradient(obsfwd.E(), strains) * K_22 * q * q / 1e3 # in kPa
stresses[0] = 0.0
ysfwd = [stresses, obsfwd.surfacetwist(), obsfwd.delta()]
if obsfwd.E()[0] > 1e299:
print("bad calculation at Lambda = ", Lambda)
for i, observable in enumerate(observable_list):
if observable == 'surfacetwist':
ylabel = r'$\psi(R)$' + ' (' + r'$\si{\radian}$' + ')'
elif observable == "stress":
ylabel = r"$\sigma$" + ' (' + r'$\si{\kilo\pascal}$' + ')'
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)
"""
ax[observable] = fig[observable].add_subplot(1,1,1)
for j,k24 in enumerate(k24s):
scan = {}
scan['\\Lambda']=str(Lambda)
scan['k_{24}']=str(k24)
scan['\\omega']=str(omega)
obsfwd = ObservableData(["\\gamma_s"],scan_dir='scanforward',scan=scan,loadsuf=loadsuf,
savesuf=savesuf)
gammas = obsfwd.data[:,0]
ysfwd = [obsfwd.R(),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)
for i,observable in enumerate(observable_list):