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()
def Restart(checkpt = 'SP'):
if checkpt == 'start':
return
else:
print 'Restarting from after ', checkpt
checkptFile = Prefix + '_%s_sum.txt' % checkpt
paramstring = pp.parseParamString(checkptFile)
Sys.ForceField.SetParamString(paramstring)
Sys.ForceField.Update()
for p in Sys.ForceField: p.FreezeParam()
if checkpt == 'SP':
Pspline.UnfreezeParam()
if checkpt == 'SPLD':
Pspline.SetParam(Knots = 0.)
Plocaldensity.UnfreezeParam()
if not Plj is None: Plj.SetParam(Epsilon = SysData['poly_dict']['LJEpsilon'])
if checkpt == 'LD':
Plocaldensity.UnfreezeParam()
def Restart(checkpt = 'SP'):
#possible options for checkpt are 'start', 'SP' or 'SPLD'
#for 'start', it will run from the start with 0 knot values
#for 'SP' it will run SPLD with previously obtained SP knots
#for 'SPLD' it will run SPLD with previously obtained SPLD knots
if checkpt == 'start':
return
else:
checkptFile = Prefix + '_%s_sum.txt' % checkpt
if os.path.isfile(checkptFile):
paramstring = pp.parseParamString(checkptFile)
Sys.ForceField.SetParamString(paramstring)
Sys.ForceField.Update()
for p in Sys.ForceField: p.FreezeParam()
if checkpt == 'SP':
Pspline.UnfreezeParam()
if checkpt == 'SPLD':
Pspline.UnfreezeParam()
Plocaldensity.UnfreezeParam()
else:
raise IOError('%s not found' % checkptFile)
LDCut = float(sys.argv[9])
#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
#CG forcefield parameters
cg_ff_file = cgffPrefix + '_sum.txt'
paramstring = pp.parseParamString(cg_ff_file)
#boxlength extracted from AA traj
BoxL = pickleTraj(LammpsTraj).FrameData['BoxL']
#create the system object
Sys = alg.makeSys(LDCut = LDCut, SysData = SysData, fftype = fftype, BoxL = BoxL, Prefix = Prefix, paramstring = paramstring, Delta = 1.2)
#initialize system
sim.system.init.positions.CubicLattice(Sys, Random = 0.1)
sim.system.init.velocities.Canonical(Sys, Temp = TempSet)
##different MD steps
Int = Sys.Int
#energy minimization
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)
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
#set up Srel optimizer
Sys.TempSet = TempSet
Opt = sim.srel.OptimizeTrajClass(Sys, Map, Traj = Trj, SaveLoadArgData = True, FilePrefix = Prefix)
sim.srel.optimizetraj.PlotFmt = 'svg'
Opt.MinReweightFrac = 0.2
#lock all potentials in place
def ResetPotentials():
print "Resetting all potentials to base case and freezing."
if not Pspline is None: Pspline.SetParam(Knots = 0.)
if not Plocaldensity is None: Plocaldensity.SetParam(Knots = 0.)
if not Plj is None: Plj.SetParam(Epsilon = 0.)
for ptype in Sys.ForceField:
ptype.FreezeParam()
#srel_minimzation
ResetPotentials()
Opt.Reset()
Opt.FilePrefix = Prefix + '_SPLD'
print "\n\nOptimizing for the case: SPLD"
s = pp.parseParamString('%s_SP_sum.txt' % Prefix)
Sys.ForceField.SetParamString(s)
Pspline.UnfreezeParam()
Plocaldensity.UnfreezeParam()
Sys.ForceField.Update()
print Sys.ForceField.ParamString()
Opt.RunConjugateGradient(StepsEquil = NStep['Equil'], StepsProd = NStep['Prod'], StepsStride = NStep['Freq'])
serial_index = {'AA': (0, poly_dict['N_mon']*poly_dict['N_poly']),
'CG': (0, poly_dict['N_mon']*poly_dict['N_poly'])} #always using a mapped traj
#extract all necessary AA data
Trj_AA = pickleTraj(LammpsTraj)
BoxL = Trj_AA.FrameData['BoxL']
#begin looping over different LD cutoffs
for i, LDCut in enumerate(LDCuts[0:-1]):
print '\n\nLDCUTs = (%g, %g)\n' % (LDCuts[i], LDCuts[i+1])
#extract all necessary CG data
sumfile1 = base_fmt['cg_ff'] % (fftype, i); sumfile2 = base_fmt['cg_ff'] % (fftype, (i+1))
trajfile1 = base_fmt['cg_trj'] % (fftype, i) ; trajfile2 = base_fmt['cg_trj'] % (fftype, (i+1))
ParamString1 = parse_potential.parseParamString(sumfile1); ParamString2 = parse_potential.parseParamString(sumfile2)
Trj_CG_1 = pickleTraj(trajfile1); Trj_CG_2 = pickleTraj(trajfile2)
#create systems with forcefields of LDCuts i and i+1
Sys1 = alg.makeSys(LDCut = LDCuts[i], Delta = Delta, BoxL = BoxL, fftype = fftype, Prefix = 'bennettsys1',
paramstring = ParamString1, sample_trajtype = 'CG', eval_trajtype = 'CG', SysData = SysData)
Sys2 = alg.makeSys(LDCut = LDCuts[i+1], Delta = Delta, BoxL = BoxL, fftype = fftype, Prefix = 'bennettsys2',
paramstring = ParamString2, sample_trajtype = 'CG', eval_trajtype = 'CG', SysData = SysData)
# block average
if not doBlockAvg: NBlocks = 1
for j, b in enumerate(range(NBlocks)):
print '\n======== BLOCK %d ==============\n' % b
block_start_AA = b * int(len(Trj_AA)/NBlocks)
