def testSplineCoeff():
import parse_potential as pp
prefix = '/home/cask0/home/tsanyal/c25ld/data/cg_ff/methane/methane_wca_SPLD'
logfile, histfile, sumfile = pp.parseFileNames(prefix)
paramstring = pp.parseParamString(sumfile)
h = pp.parseHist(histfile)['LD']
rho_t = h[0]; rho_m = h[1]
d = alg.makeSysData(isPolymer = False, hasLJ = True)
Sys = alg.makeSys(LDCut = 6.5, SysData = d, Prefix = 'testsys', paramstring = paramstring, fftype = 'wca')
(nknot, spdist, spc0, spc1, spc2, spc3) = alg.getLDSpline(Sys = Sys)
rho = rho_t
dfdrho = np.zeros(len(rho))
frho = np.zeros(len(rho))
for n in range(len(rho)):
x = (rho[n] - min(rho)) * spdist[1]
i = max(min(int(x), nknot-2), 0)
t = max(min(x - float(i), 1.0), 0.0)
frho[n] = spc0[i] + t * (spc1[i] + t*(spc2[i]+t*spc3[i]))
dfdrho[n] = spdist[1] * (spc1[i] + t * (2.*spc2[i]+t*3.*spc3[i]))
fig = plt.figure
ax1 = plt.subplot(211) ; ax2 = plt.subplot(212)
ax1.plot(rho, frho, linewidth = 3, label = r'$f(\rho)$'); ax1.legend()
ax2.plot(rho, dfdrho, linewidth = 3, label = r'$\frac{df}{d\rho}$'); ax2.legend()
N_water = int(sys.argv[5])
LammpsTraj = sys.argv[6]
Prefix = sys.argv[7]
LDCut = float(sys.argv[8])
if len(sys.argv) > 9: checkpt = sys.argv[9]
else: checkpt = 'start'
#MD iteration settings
if isPolymer:
NStep = NStep_polymer
else:
NStep = NStep_methane
#system parameters
SysData = alg.makeSysData(isPolymer = isPolymer, hasLJ = hasLJ, N_mon = N_mon, N_water = N_water)
TempSet = 298.0
Delta = 1.2
#AA traj parameters
Trj, BoxL, mappedatoms = parseTraj(LammpsTraj)
#create the system object
Sys = alg.makeSys(LDCut = LDCut, SysData = SysData, fftype = fftype, BoxL = BoxL, Prefix = Prefix, paramstring = None, Delta = 1.2)
#initialize and energy minimize
sim.system.init.positions.CubicLattice(Sys, Random = 0.1)
sim.system.init.velocities.Canonical(Sys, Temp = TempSet)
Int = Sys.Int
Int.Method = Int.Methods.VVQuench
Int.Run(NStep['Min'])