def lj_template(rij, sigma):
return lennard_jones(rij,
self.eps,
self.m,
self.n,
sigma,
self.rmin(sigma),
shifted=True)
#V = 10.*10.*10.
V = 5.*5.*5.
vL = 4./3.*np.pi*pow(1.,3)
vR = 4./3.*np.pi*pow(1.,3)
Veff = V - nL*vL-vR
c = nL / Veff
sigma = 2. # molecular size (cross section)
D = 2. # relative diffusion coefficient
eps = 1/1.5
m = 12.
n = 6.
sigmaLR = 2.0
rmin = lambda sigma: sigma*pow(m/n, 1./(m-n)) # location of minimum of LJ potential (use for cut-shift point)
rc = rmin(sigmaLR)
LR_pot = lambda r: pot.lennard_jones(r,eps,m,n,sigmaLR,rc,shifted=True)
Rreact = 2.0
Vex = qan.calc_Vex(LR_pot,rc)
Vreact_eff = qan.calc_eff_volume(LR_pot,Rreact)
kdo = 1E-0
##############################################################################################
# Process quasi-reversible simulation data
traj_number = 0
basedir_q = "./db_quasi_reversible_sims/module_weights_L05_S05/boxsize_5_5_5/run_bulk_nL{}_nC{}/trajectory_{}".format(nL,nC,traj_number)
#basedir_q = "./db_quasi_reversible_sims/test_low_memory/boxsize_5_5_5/run_bulk_nL{}_nC{}/trajectory_{}".format(nL,nC,traj_number)