def testdphidrc():
LDCuts = [4., 5., 6.,]
Delta = 1.2
r = np.linspace(0,8., 100)
for LDCut in LDCuts:
coeff, dcoeff = alg.calcCoeff(LDCut = LDCut, Delta = Delta)
dphidrc = dcoeff[0] + dcoeff[1]*r**2. + dcoeff[2]*r**4. + dcoeff[3]*r**6.
plt.figure
plt.plot(r, dphidrc, label = 'LDCUT = %g' % LDCut, linewidth = 3)
plt.legend(); plt.xlabel(r'$r$'); plt.ylabel(r'$\frac{d\phi}{dr_c} (r)$')
def testphi():
LDCut = 6.5
Delta = 1.2
r = np.linspace(LDCut-Delta-0.5, LDCut+2.0, 100)
coeff, dcoeff = alg.calcCoeff(LDCut = LDCut, Delta = Delta)
phi = np.zeros(100)
for n in range(100):
if r[n] <= LDCut - Delta: phi[n] = 1.0
elif r[n] >= LDCut: phi[n] = 0.0
else: phi[n] = coeff[0] + coeff[1]*r[n]**2. + coeff[2]*r[n]**4. + coeff[3]*r[n]**6.
plt.figure
plt.plot(r, phi, linewidth = 3)
plt.xlabel(r'$r$'); plt.ylabel(r'$\phi(r)$')
#various indexing schemes
TrjIter = {'AA': [0, -1, 10], 'CG': [0, -1, 10]}
# compile fortcode
fcompile()
from dSreldrc_fortlib import getdudrc
Trj_AA = pickleTraj(LammpsTraj)
BoxL = Trj_AA.FrameData['BoxL'][0]
#begin looping over different LD cutoffs
for i, LDCut in enumerate(LDCuts):
print '\n\nLDCut = %g\n' % LDCut
#calculate coefficients
(coeff, dcoeff) = alg.calcCoeff(LDCut = LDCut, Delta = 1.2)
#get AA and CG trj
Trj_CG = pickleTraj(base_fmt['cg_trj'] % (fftype, i))
#get Spline Coeffs for CG forcefield
ffield_CG = base_fmt['cg_ff'] % (fftype, i)
paramstring = parse_potential.parseParamString(ffield_CG)
Sys = alg.makeSys(LDCut = LDCuts[i], Delta = Delta, BoxL = BoxL, fftype = fftype, Prefix = 'ldsplinecoeff',
paramstring = paramstring, sample_trajtype = 'CG', eval_trajtype = 'CG', SysData = SysData)
(nknot, spdist, spc0, spc1, spc2, spc3) = alg.getLDSpline(Sys = Sys)
for key in TrjIter.keys():
if TrjIter[key][1] == -1:
if key == 'AA': TrjIter[key][1] = len(Trj_AA)