if obsfwd.E()[0] > 1e299:
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()
scan['\\omega'] = omega
scan['\\Lambda'] = Lambda
for j, u in enumerate(strains_for[type]):
if j == 0:
strain = None
else:
strain = str(u)
psi = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=savesuf,
strain=strain,
name=names_for[type])
ax[j].plot(psi.r() / q * 1000,
psi.psi(),
'-',
color=colors[i],
label=rf"$\tilde{{\sigma}}=\num{{{stresses[j]:.2e}}}$")
for i, stress in enumerate(stresses):
ax[i].legend(frameon=False)
ax[i].set_ylabel(r'$\psi(\tilde{r})$' + ' (' + r'$\si{\radian}$' + ')')
if (i == 3):
ax[i].set_xlabel(r'$\tilde{r}$' + ' (' + r'$\si{\nano\meter}$' +
loadsuf = ["K_{33}", "k_{24}", "\\Lambda", "\\omega", "\\gamma_s"]
savesuf = ["K_{33}", "k_{24}", "\\Lambda", "\\omega"]
markertypes = ['--', '-.']
for i, gamma in enumerate(gammas):
scan = {}
scan['\\gamma_s'] = gamma
scan['k_{24}'] = k24
scan['\\Lambda'] = Lambda
scan['\\omega'] = omega
psistuff = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=savesuf,
name=f"psivsr",
sfile_format="pdf")
rs = psistuff.r()
psis = psistuff.psi()
print(2 / (rs[-1] * rs[-1]) * simps(rs * psis, rs))
ax1.plot(rs / rs[-1],
psis,
markertypes[i],
label=rf'$\gamma={gamma}$',
lw=2)
ax1.set_xlabel(r'$r/R$', fontsize=10)
scan['\\gamma_s'] = gamma
scan['k_{24}'] = k24
scan['\\Lambda'] = Lambda
scan['\\omega'] = omega
loadsuf = ["K_{33}", "k_{24}", "\\Lambda", "\\omega", "\\gamma_s"]
for i, pre in enumerate(["", "frustrated"]):
if pre == "":
label = "linear"
else:
label = pre
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()
print(R)
eta = observablestuff.eta()
dband = 2 * np.pi / eta
# read in file name info
rp = ReadParams(scan=scan,loadsuf=loadsuf,savesuf=savesuf)
# create a class to do calculations with current parameters in scan.
run = SingleRun(rp,scan_dir=scan_dir,executable=executable,strain=strain)
# run C executable.
run.run_exe()
# move file written by C executable from temporary data path to true data path
run.mv_file(f'observables')
run.mv_file('psivsr',strain=strain)
psistuff = PsiData(scan=scan,loadsuf=loadsuf,savesuf=savesuf,name=f"psivsr",
strain=strain)
rs = psistuff.r()
psis = psistuff.psi()
psiav = simps(integrand(rs,psis),rs)
run.remove_file(fname="psivsr",strain=strain)
# load the final values of E, R, eta, delta, and surface twist.
Ei,Ri,etai,deltai,surftwisti = run.get_all_observables('observables',str2float=True)
if i == 0:
# again, if the strain is zero, then I have just determined the equilibrium
# inverse d band spacing, which I now need to set (and do so below).
types = ['linear', 'frustrated']
axins = {}
axins['linear'] = fig.add_axes([0.25, 0.45, 0.1, 0.1], projection='polar')
axins['frustrated'] = fig.add_axes([0.5, 0.37, 0.25, 0.25],
projection='polar')
for i, type in enumerate(types):
psistuff = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=savesuf,
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,