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
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:
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"]
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
rp = ReadParams(scan=scan, loadsuf=loadsuf, savesuf=savesuf)
# create a class to do calculations with current parameters in scan.
run = SingleRun(rp, 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', newname=newobsname)
run.mv_file('psivsr', newname=newpsiname, strain=strain)
psistuff = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=savesuf,
name=newpsiname,
strain=strain)
rs = psistuff.r()
psis = psistuff.psi()
psiav = simps(integrand(rs, psis), rs)
# load the final values of E, R, eta, delta, and surface twist.
Ei, Ri, etai, deltai, surftwisti = run.get_all_observables(
newobsname, str2float=True)
if i == 0:
# again, if the strain is zero, then I have just determined the equilibrium
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,
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")
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"]
psistuff = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=loadsuf,
name=f"psivsr_frustrated")
rs = psistuff.r()
psis = psistuff.psi()
observablestuff = ObservableData(scan=scan,
loadsuf=loadsuf,
savesuf=loadsuf,
name=f"observables_frustrated")
R = observablestuff.R()
eta = observablestuff.eta()
print("radius is ", R)
axins = inset_axes(ax,
width=width / 3,
height=height / 3,
loc=4,
bbox_to_anchor=(0.1, 0.1, 1, 1),
bbox_transform=ax.transAxes)
types = ['linear', 'frustrated']
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")
rs = psistuff.r() / q
psis = psistuff.psi()
axins.plot(rs, psis, markertypes[i], label=f'{type} twist', lw=2)
print("Radius = ", rs[-1], " nm.")
print("surface twist = ", psis[-1], " rad.")
axins.set_xlabel(r'$\tilde{r}$' + ' (' + r'$\si{\nano\meter}$' + ')',
fontsize=8,
marker=mtypes[1],markeredgewidth=0.5,markeredgecolor="w")
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"$\Lambda={Lambda}$",
gamma = str(0.04)
k24 = str(0.5)
Lambda = str(600.0)
omega = str(20.0)
scan = {}
scan['k_{24}'] = k24
scan['\\gamma_s'] = gamma
scan['\\Lambda'] = Lambda
scan['\\omega'] = omega
loadsuf = ["K_{33}", "k_{24}", "\\Lambda", "\\omega", "\\gamma_s"]
# read in file name info
psidata = PsiData(scan=scan, loadsuf=loadsuf, savesuf=loadsuf)
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)
type = input("specify type (either linear, constant, "
"or no type in which case just press enter):\n")
scan = {}
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}",
sfile_format=".png")
rs = psistuff.r() * R_units
psis = psistuff.psi() * 180 / np.pi
fig = plt.figure()
width = 5
height = width
fig.set_size_inches(width, height)
ax1 = fig.add_subplot(1, 1, 1)
ax1.plot(rs, psis, '.', label=rf'$\Lambda={Lambda}$')
type = input("Now input the type of psi vs r curve (linear, "
"constant, or no type in which case just press enter):\n")
scan = {}
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
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'$\si{\nano\meter}$' +
q = 4 / 1000 # nm^{-1}
scan = {}
scan['\\gamma_s'] = gamma
scan['k_{24}'] = k24
scan['\\Lambda'] = Lambda
scan['\\omega'] = omega
types = ['linear', 'frustrated']
for i, type in enumerate(types):
psistuff = PsiData(scan=scan,
loadsuf=loadsuf,
savesuf=savesuf,
name=f"psivsr_{type}",
sfile_format="pdf")
rs = psistuff.r() / q
psis = psistuff.psi()
ax1.plot(rs, psis, markertypes[i], label=f'{type} tendon', lw=2)
print("Radius = ", rs[-1], " nm.")
print("surface twist = ", psis[-1], " rad.")
ax1.set_xlabel(r'$\tilde{r}$' + ' (' + r'$\si{\nano\meter}$' + ')',
fontsize=10)
ax1.set_ylabel(r'$\psi(\tilde{r})$' + ' (' + r'$\si{\radian}$' + ')',
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()
ax1.plot(rs/rs[-1],psis,markertypes[i],label=rf'$\gamma={gamma}$',lw=2)
ax1.set_xlabel(r'$r/R$',fontsize=10)
ax1.set_ylabel(r'$\psi(r)$',fontsize=10)
ax1.set_xlim(left=0)
ax1.set_ylim(bottom=0)
ax1.legend(frameon=False,fontsize=10)
fig.subplots_adjust(left=0.2,bottom=0.2)
scan['k_{24}'] = str(k24)
scan['\\Lambda'] = str(Lambda)
scan['\\omega'] = str(omega)
scan['K_{33}'] = str(K33)
observablestuff = ObservableData(scan=scan,loadsuf=loadsuf,savesuf=loadsuf,
name=f"observables_frustrated")
delta = observablestuff.delta()
eta = observablestuff.eta()
E0 = observablestuff.E()
print(delta,eta,E0)
psistuff = PsiData(scan=scan,loadsuf=loadsuf,savesuf=savesuf,name=f"psivsr_frustrated",
sfile_format="pdf")
rs = psistuff.r()
psis = psistuff.psi()
psiprimes = psistuff.psiprime()
R0s = np.copy(rs[:len(rs)-10:5])
Es = np.copy(R0s)*0
for i,R0 in enumerate(R0s):
Es[i] = E(R0,rs,psis,psiprimes,delta,eta,K33,k24,Lambda,omega,gamma)
gamma,k24,Lambda,omega = sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4]
denom = sys.argv[5]
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)
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
