Esempio n. 1
0
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()
Esempio n. 2
0
	
	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)
	       if key == 'CG': TrjIter[key][1] = len(Trj_CG)
	  
	FrameRange_AA = range(TrjIter['AA'][0], TrjIter['AA'][1], TrjIter['AA'][2])
	FrameRange_CG = range(TrjIter['CG'][0], TrjIter['CG'][1], TrjIter['CG'][2])
	NFrames_AA = len(FrameRange_AA); NFrames_CG = len(FrameRange_CG)
	
	#frame stepping
	####all-atom
	print '---> Calculating AA deriviative...\n'
	EneAA_deriv = 0
	pb = sim.utility.ProgressBar(Text = 'Processing AA frames', Steps = NFrames_AA)