color=colors[js],
marker=mtypes[0],
markeredgewidth=0.5,
markeredgecolor="w")
ax[observable].set_xlabel(r"$\Lambda$", fontsize=10)
for ms, Lambda in enumerate(Lambdalist):
scan['\\Lambda'] = Lambda
psistuff = PsiData(scan=scan,
loadsuf=psi_loadsuf,
savesuf=psi_loadsuf,
name=f"psivsr")
ax["psi(r)"].plot(psistuff.r() / psistuff.r()[-1],
psistuff.psi(),
linestyle=ltypes[0],
label=rf"$\Lambda={Lambda}$",
color=colors[js],
lw=3)
ax["psi(r)"].plot(1.0,
psistuff.psi()[-1],
marker=mtypes[ms],
color=colors[js],
markeredgewidth=0.5,
markeredgecolor="w")
if Lambda == '27':
psistuff = PsiData(scan=scan,
scan = {}
scan['\\gamma_s'] = gamma
scan['k_{24}'] = k24
scan['\\Lambda'] = Lambda
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)
hermitedata = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=loadsuf,
name="hermite-psivsr")
fig = plt.figure()
fig.set_size_inches(width, 3 * height)
ax1 = fig.add_subplot(3, 1, 1)
ax2 = fig.add_subplot(3, 1, 2)
ax3 = fig.add_subplot(3, 1, 3)
ax1.plot(psidata.r(), psidata.psi(), '.', label='actual')
ax1.plot(hermitedata.r(), hermitedata.psi(), '-', label='fit')
ax1.set_ylabel(r'$\psi(r)$')
ax2.plot(psidata.r(), psidata.psiprime(), '.', label='actual')
ax2.plot(hermitedata.r(), hermitedata.psiprime(), '-', label='fit')
ax2.set_ylabel(r'$\frac{d\psi}{dr}$')
ax3.plot(psidata.r(), psidata.rf_fibril(), '.', label='actual')
ax3.plot(hermitedata.r(), hermitedata.rf_fibril(), '-', label='fit')
ax3.legend(frameon=False)
ax3.set_ylabel(r'$r\times f_{\mathrm{fibril}}(r)$')
ax3.set_xlabel(r'$r$')
fig.subplots_adjust(left=0.2)
ax[observable].set_ylabel(ylabel,fontsize = 10)
ax[observable].plot(Lambdas[i_Lambda],ysfwd[i][i_Lambda],color=colors[js],
marker=mtypes[0],markeredgewidth=0.5,markeredgecolor="w")
ax[observable].set_xlabel(r"$\Lambda$",fontsize = 10)
for ms,Lambda in enumerate(Lambdalist):
scan['\\Lambda'] = Lambda
psistuff = PsiData(scan=scan,loadsuf=psi_loadsuf,savesuf=psi_loadsuf,
loadfilepath=loadfilepath,datfile=datfile,
name=f"psivsr")
ax["psi(r)"].plot(psistuff.r()/psistuff.r()[-1],psistuff.psi(),
linestyle=ltypes[0],label=rf"$\Lambda={Lambda}$",
color=colors[js],lw=3)
ax["psi(r)"].plot(1.0,psistuff.psi()[-1],marker=mtypes[ms],
color=colors[js],markeredgewidth=0.5,markeredgecolor="w")
if Lambda == '27':
psistuff = PsiData(scan=scan,loadsuf=psi_loadsuf,savesuf=psi_loadsuf,
loadfilepath=loadfilepath,datfile=datfile,
name=f"frustratedpsivsr")
ax["psi(r)"].plot(psistuff.r()/psistuff.r()[-1],psistuff.psi(),
linestyle=ltypes[1],label=rf"$\Lambda={Lambda}$",
color=colors[js],lw=3)
ax["psi(r)"].plot(1.0,psistuff.psi()[-1],marker=mtypes[ms+1],
scan['\\gamma_s'] = gamma
scan['k_{24}'] = k24
scan['\\Lambda'] = Lambda
scan['\\omega'] = omega
R_units = 1000.0/10.0 # units of nano meters, with q = 10 (um)^{-1}
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)
print("bad calculation at Lambda = ", Lambda)
for i, u in enumerate(strains):
if i == 0:
strain = None
else:
strain = str(u)
psi = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=savesuf,
strain=strain)
ax.plot(psi.r(),
psi.psi(),
'-',
color=colors[i],
label=rf"$\epsilon={u:.3}$")
ax.set_xlabel(r"$r$")
ax.set_ylabel(r"$\psi(r)$")
ax.legend(frameon=False)
fig.subplots_adjust(left=0.2, right=0.8, bottom=0.1, top=0.95, hspace=0.05)
fig.savefig(obsfwd.observable_sname("psivsr-vsstrain", plot_format="pdf"))
plt.show()
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