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,