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
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
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',
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},