def single_E_calc(gamma, scan, scan_dir, fwd_ic, bwd_ic):
loadsuf = ["K_{33}", "k_{24}", "\\Lambda", "\\omega", "\\gamma_s"]
savesuf = ["K_{33}", "k_{24}", "\\Lambda", "\\omega"]
scan['\\gamma_s'] = str(gamma)
ic_dict = {}
if scan_dir == "scanforward":
ic_dict = fwd_ic
elif scan_dir == "scanbackward":
ic_dict = bwd_ic
scan['Rguess'] = str(ic_dict['Rguess0'])
scan['Rupper'] = str(ic_dict['Rupper0'])
scan['Rlower'] = str(ic_dict['Rlower0'])
scan['etaguess'] = str(ic_dict['etaguess0'])
scan['etaupper'] = str(ic_dict['etaupper0'])
scan['etalower'] = str(ic_dict['etalower0'])
scan['deltaguess'] = str(ic_dict['deltaguess0'])
scan['deltaupper'] = str(ic_dict['deltaupper0'])
scan['deltalower'] = str(ic_dict['deltalower0'])
# 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)
# run C executable.
run.run_exe()
# move file written by C executable from temporary data path to true data path
run.mv_file('observables')
# load the final values of E, R, eta, delta, and surface twist.
Ei, Ri, etai, deltai, surftwisti = run.get_all_observables('observables',
str2float=True)
run.concatenate_observables(["\\gamma_s"])
return Ei, Ri, etai, deltai
loadsuf = ["K_{33}", "k_{24}", "\\Lambda", "d_0", "\\omega", "\\gamma_s"]
savesuf = ["K_{33}", "k_{24}", "d_0", "\\omega", "\\gamma_s"]
scan_dir = "scanforward"
# first, load the minimum for delta = 0 case, so you know the upper bound for
# the energy minimum.
scan['\\Lambda'] = '0'
scan['\\omega'] = '0'
rp = ReadParams(scan=scan, loadsuf=loadsuf, savesuf=savesuf)
run = SingleRun(rp)
E0, R0, eta0, delta0, surftwist0 = run.get_all_observables(
'observables_Emin', str2float=True)
scan['\\omega'] = omega
scan['Rguess'] = str(R0)
scan['Rupper'] = str(1.5 * R0)
scan['Rlower'] = str(0.75 * R0)
i = 0
while (i < len(Lambdas)):
Lambda = Lambdas[i]
scan['\\Lambda'] = str(Lambda)
# read in file name info
scan['\\Lambda'] = str(Lambda)
# 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)
# run C executable.
run.run_exe()
# move file written by C executable from temporary data path to true data path
run.mv_file('observables')
# 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 (Ei > 0.1 * FAILED_E):
# if the energy calculation fails, this will be true.
print('hi')
# remove current file with observables for the current Lambda value that are higher than
# the delta = 0 energy.
print(Ei)
run.remove_file("observables")
for j, Lambda in enumerate(Lambdas[i:]):
# write the remaining values of observables as those corresponding to the delta = 0
# case, as non-zero d-band produces a higher energy fibril.
scan['\\Lambda'] = str(Lambda)
def single_E_calc(gamma, scan, loadsuf, savesuf, scan_dir):
scan['\\gamma_s'] = str(gamma)
if scan_dir == "scanforward":
Rguess0 = 0.044
Rlower0 = 0.04
Rupper0 = 0.05
etaguess0 = 6.29
etalower0 = 6.3
etaupper0 = 6.287
deltaguess0 = 0.74
deltalower0 = 0.72
deltaupper0 = 0.8
else:
Rguess0 = 1.5
Rlower0 = 1.0
Rupper0 = 2.0
etaguess0 = 6.4
etalower0 = 6.38
etaupper0 = 6.42
deltaguess0 = 0.815
deltalower0 = 0.813
deltaupper0 = 0.816
scan['Rguess'] = str(Rguess0)
scan['Rupper'] = str(Rupper0)
scan['Rlower'] = str(Rlower0)
scan['etaguess'] = str(etaguess0)
scan['etaupper'] = str(etaupper0)
scan['etalower'] = str(etalower0)
scan['deltaguess'] = str(deltaguess0)
scan['deltaupper'] = str(deltaupper0)
scan['deltalower'] = str(deltalower0)
# 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)
# run C executable.
run.run_exe()
# move file written by C executable from temporary data path to true data path
run.mv_file('observables')
# load the final values of E, R, eta, delta, and surface twist.
Ei, Ri, etai, deltai, surftwisti = run.get_all_observables('observables',
str2float=True)
run.concatenate_observables(["\\gamma_s"])
return Ei, Ri
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
# inverse d band spacing, which I now need to set (and do so below).
eta_eq = etai
R_eq = Ri
# now just adjust my guess for delta
deltaguess = str(deltai)
if np.abs(deltai) < 1e-5:
break
def single_E_calc(gamma,scan,loadsuf,savesuf,scan_dir):
scan['\\gamma_s'] = str(gamma)
k240 = 0.33
k24 = float(scan['k_{24}'])
t = (k24-k240)/k240
if scan_dir == "scanforward":
#Rguess0 = 0.045
#Rupper0 = 0.6
#Rlower0 = 0.4
Rguess0 = lower_Rguess(t)
Rupper0 = Rguess0*1.1
Rlower0 = Rguess0*0.9
etaguess0 = 6.295
etalower0 = 6.29
etaupper0 = 6.3
deltaguess0 = 0.8
deltalower0 = 0.799
deltaupper0 = 0.805
else:
#Rguess0 = 0.7
#Rupper0 = 0.9
#Rlower0 = 0.6
Rguess0 = upper_Rguess(t)
Rupper0 = Rguess0*1.1
Rlower0 = Rguess0*0.9
etaguess0 = 6.34
etalower0 = 6.32
etaupper0 = 6.36
deltaguess0 = 0.813
deltalower0 = 0.808
deltaupper0 = 0.816
scan['Rguess'] = str(Rguess0)
scan['Rupper'] = str(Rupper0)
scan['Rlower'] = str(Rlower0)
scan['etaguess'] = str(etaguess0)
scan['etaupper'] = str(etaupper0)
scan['etalower'] = str(etalower0)
scan['deltaguess'] = str(deltaguess0)
scan['deltaupper'] = str(deltaupper0)
scan['deltalower'] = str(deltalower0)
# 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)
# run C executable.
run.run_exe()
# move file written by C executable from temporary data path to true data path
run.mv_file('observables')
# load the final values of E, R, eta, delta, and surface twist.
Ei,Ri,etai,deltai,surftwisti = run.get_all_observables('observables',str2float=True)
run.concatenate_observables(["\\gamma_s"])
return Ei,Ri