def test_mbar_single_sample():
dataset = pd.read_csv(data[0], sep=" ")
sample = mics.sample(dataset, "beta*E1", "beta*(E2 - E1)", beta=beta)
mixture = mics.mixture([sample], mics.MBAR())
assert mixture.Overlap[0][0] == pytest.approx(1.0)
files = [f'{solute}-in-{solvent}_energy-{i:02d}.csv' for i in states.index]
renamer = lambda x: x.replace('Energy[', 'E').replace('] (kJ/mole)', '')
kT = (kB * T).value_in_unit(unit.kilojoules_per_mole)
mx.verbose = True
samples = mx.pooledsample()
for i, file in zip(states.index, files):
print(f"Reading file {file}")
df = pd.read_csv(file)
df.drop(index=range(15000), inplace=True)
df.rename(renamer, axis='columns', inplace=True)
prev = max(i - 1, 0)
next = min(i + 1, nstates - 1)
samples += mx.sample(df,
f'beta*(E{i}-E0)',
acfun=f'E{next}-E{prev}',
beta=1 / kT,
lambda_vdw=states.lambda_vdw[i],
lambda_coul=states.lambda_coul[i])
samples.histograms().plot(x='potential')
plt.show()
mixture = mx.mixture(samples, engine=mx.MICS(tol=1.0E-11))
# mixture = mx.mixture(samples.subsampling(), engine=mx.MBAR())
f = mixture.free_energies()
kT = (kB * T).value_in_unit(unit.kilocalories_per_mole)
#f['lambda[vdw+coul]'] = f['lambda_vdw'] + f['lambda_coul']
f['delta_g'] = kT * f['f']
f['error(delta_g)'] = kT * f['df']
print(f)
f.plot(x='lambda_vdw', y='delta_g', yerr='error(delta_g)')
mixture.histograms('potential', bins=200).plot(x='potential')
def test_main():
assert mics # use your library here
mics.verbose = True
m = 4
beta = 1.6773985789
data = ["tests/data/log_%d.dat" % (i + 1) for i in range(m)]
samples = mics.pooledsample()
for i in range(m):
dataset = pd.read_csv(data[i], sep=" ")
potential = "beta*E%d" % (i + 1)
autocorr = "beta*(E%d - E%d)" % (min(i + 2, m), max(i, 1))
samples += mics.sample(dataset, potential, autocorr, beta=beta)
def test_read_samples():
for sample in samples:
assert sample.dataset.columns[5] == 'Press'
def test_pooledsample():
neff = [
100.829779921697, 76.82824014457174, 69.63811023389404,
55.179192164637165
]
for i in range(m):
assert samples[i].neff == pytest.approx(neff[i])