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)
ax1.legend(frameon=False)
ax2 = fig.add_subplot(1,2,2,projection='polar')
fibrilstrain = FibrilStrain(psistuff,observablestuff,sfile_format='.pdf')
rs,thetas = fibrilstrain.mesh_polar()
rs = rs/8.0*1000
strains = fibrilstrain.strain_polar(rs,denom=denom)
norm = MidpointNormalize(midpoint=0)
im = ax2.contourf(thetas,rs,strains,100,norm=norm,
cmap='bwr')
#clb = fig.colorbar(im,ax=ax2)
#clb.ax.set_title(rf'$\frac{{d-d(r)}}{{{denom}}}$')
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)
strains = fibrilstrain.strain_polar(rs, grid_skip=4)
norm = MidpointNormalize(midpoint=0)
im = axarr[1].contourf(thetas, rs, strains, 100, norm=norm, cmap='bwr')
#clb = fig.colorbar(im,ax=axarr[i+1])
#clb.ax.set_title(rf'$\frac{{d-d(r)}}{{{denom}}}$')
axarr[1].set_xticks([])
axarr[1].set_yticks([])
fig.set_size_inches(width, height)
gs = GridSpec(1, 3, figure=fig, wspace=0.0)
axarr = []
axarr.append(fig.add_subplot(gs[0, 0]))
axarr.append(fig.add_subplot(gs[0, 1:], projection='polar'))
scan = {}
scan['\\gamma_s'] = gamma
scan['k_{24}'] = k24
scan['\\Lambda'] = Lambda
scan['\\omega'] = omega
loadsuf = ["K_{33}", "k_{24}", "\\Lambda", "\\omega", "\\gamma_s"]
fs = FibrilStrain(scan=scan)
axarr[0].plot(fs.psidata.r(), fs.strain_1d() * 100, '-')
print("tension at fibril centre is ", fs.strain_1d()[0] * 100, "%.")
print("tension at the fibril surface is ", fs.strain_1d()[-1] * 100, "%.")
axarr[0].set_xlabel(r'$r$', fontsize=10)
axarr[0].set_ylabel('molecular strain (\%)', fontsize=10)
axarr[0].set_xlim(left=0)
#axarr[0].legend(frameon=False)
rs, thetas = fs.mesh_polar(grid_skip=4)
strains = fs.strain_polar(rs, grid_skip=4) * 100
norm = MidpointNormalize(midpoint=0)
psis = psistuff.psi()
observablestuff = ObservableData(scan=scan,loadsuf=loadsuf,savesuf=loadsuf,
name=f"{type}observables")
R = observablestuff.R()
axarr[0].plot(rs/R,psis,'.',label=rf'{label[i]}')
axarr[0].set_xlabel(r'$r$',fontsize=10)
axarr[0].set_ylabel(r'$\psi(r)$',fontsize=10)
axarr[0].legend(frameon=False)
fibrilstrain = FibrilStrain(psistuff,observablestuff,sfile_format='pdf')
rs,thetas = fibrilstrain.mesh_polar(grid_skip=4)
strains = fibrilstrain.strain_polar(rs,denom=denom,grid_skip=4)
norm = MidpointNormalize(midpoint=0)
im = axarr[i+1].contourf(thetas,rs,strains,100,norm=norm,
cmap='bwr')
#clb = fig.colorbar(im,ax=axarr[i+1])
#clb.ax.set_title(rf'$\frac{{d-d(r)}}{{{denom}}}$')
axarr[i+1].set_xticks([])
name=f"psivsr_{type}",
loadfilepath=loadfilepath,
datfile=datfile,
sfile_format="pdf")
observablestuff = ObservableData(scan=scan,
loadsuf=loadsuf,
savesuf=loadsuf,
name=f"observables_{type}",
loadfilepath=loadfilepath,
datfile=datfile)
R = observablestuff.R()
fibrilstrain = FibrilStrain(psistuff,
observablestuff,
sfile_format='pdf')
rs, thetas = fibrilstrain.mesh_polar(grid_skip=4)
strains = fibrilstrain.strain_polar(rs, grid_skip=4)
strain_percents = strains * 100 # turn into percentage
vmin, vmax = -0.3, 0.1
im = axins[type].contourf(thetas,
rs,
strain_percents,
100,
norm=norm,