Python get_edf Examples

Example #1

File: plot-edf-D-ecdec.py Project: gitter-badger/decond

if (args.custom):
    mpl.rcParams['axes.color_cycle'] = color

fitKey = 0

if (args.decond_D is None):
    decond_D = args.decond
else:
    decond_D = args.decond_D

if (args.decond_ecdec is None):
    decond_ecdec = args.decond
else:
    decond_ecdec = args.decond_ecdec

edf, _, eBins = da.get_edf(args.decond)[0:3]
DI, _, _, fit = da.get_diffusion(decond_D)[0:4]
edD, _, _, eBins_edD = da.get_decD(decond_D, da.DecType.energy)[0:4]
edf_edD = da.get_edf(decond_D)[0]
sig_IL, _, eBins_sig = da.get_ec_dec_energy(decond_ecdec)[0:3]

eBins /= da.const.calorie
eBins_edD /= da.const.calorie
eBins_sig /= da.const.calorie
edf *= da.const.angstrom**3 * da.const.calorie
edf_edD *= da.const.angstrom**3 * da.const.calorie
DI /= da.const.angstrom**2 / da.const.pico
edD /= da.const.angstrom**2 / da.const.pico

numPlots = 3

Example #2

File: plot-edf-D-ecdec.py Project: decond/decond

if (args.custom):
    mpl.rcParams['axes.color_cycle'] = color

fitKey = 0

if (args.decond_D is None):
    decond_D = args.decond
else:
    decond_D = args.decond_D

if (args.decond_ecdec is None):
    decond_ecdec = args.decond
else:
    decond_ecdec = args.decond_ecdec

edf, _, eBins = da.get_edf(args.decond)[0:3]
DI, _, _, fit = da.get_diffusion(decond_D)[0:4]
edD, _, _, eBins_edD = da.get_decD(decond_D, da.DecType.energy)[0:4]
edf_edD = da.get_edf(decond_D)[0]
sig_I, _, sig_IL, _, eBins_sig = da.get_ec_dec_energy(decond_ecdec, sep_nonlocal=True, threshold=0)[0:5]

eBins /= da.const.calorie
eBins_edD /= da.const.calorie
eBins_sig /= da.const.calorie
edf *= da.const.angstrom**3 * da.const.calorie
edf_edD *= da.const.angstrom**3 * da.const.calorie
DI /= da.const.angstrom**2 / da.const.pico
edD /= da.const.angstrom**2 / da.const.pico

numPlots = 3

Example #3

    cmap = cm.get_cmap('RdYlBu_r')
    threshold = 0
    cnum = 31

with h5py.File(args.corrData, 'r') as f:
    timeLags = f['timeLags'][...]
    volume = f['volume'][...]
    numMol = f['numMol'][...]
    numIonTypes = numMol.size
    numIonTypePairs = (numIonTypes * (numIonTypes + 1)) // 2
    decgrp = f[da.DecType.energy.value]
    eBins = decgrp['decBins'][...]  # kcal / mol
    edCorr = decgrp['decCorr'][...]  # nm^2 / ps^2
    edCorr *= (da.const.nano / da.const.angstrom)**2  # AA^2 / ps^2

edf = da.get_edf(args.corrData)[0]
edf *= da.const.angstrom**3 * da.const.calorie  # AA^-3 kcal^-1 mol

# validate arguments
if (args.custom):
    assert (len(label) == numIonTypes)
else:
    label = ['{}'.format(i + 1) for i in range(numIonTypes)]

label += ['-'.join(l) for l in it.combinations_with_replacement(label, 2)]

# plot edCorr
rc = {
    'font': {
        'size': 46,
        'family': 'serif',

Example #4

File: plot-edcorr.py Project: decond/decond

    cmap = cm.get_cmap('RdYlBu_r')
    threshold = 0
    cnum = 31

with h5py.File(args.corrData, 'r') as f:
    timeLags = f['timeLags'][...]
    volume = f['volume'][...]
    numMol = f['numMol'][...]
    numIonTypes = numMol.size
    numIonTypePairs = (numIonTypes*(numIonTypes+1)) // 2
    decgrp = f[da.DecType.energy.value]
    eBins = decgrp['decBins'][...]  # kcal / mol
    edCorr = decgrp['decCorr'][...]  # nm^2 / ps^2
    edCorr *= (da.const.nano / da.const.angstrom)**2  # AA^2 / ps^2

edf = da.get_edf(args.corrData)[0]
edf *= da.const.angstrom**3 * da.const.calorie  # AA^-3 kcal^-1 mol

# validate arguments
if (args.custom):
    assert(len(label) == numIonTypes)
else:
    label = ['{}'.format(i+1) for i in range(numIonTypes)]

label += ['-'.join(l) for l in it.combinations_with_replacement(label, 2)]

# plot edCorr
rc = {'font': {'size': 46,
               'family': 'serif',
               'serif': 'Times'},
      'text': {'usetex': True},