def test_dtram_api(self):
"""testing the dTRAM API"""
tramdata = TRAMData(self.inp, b_K_i=self.b_K_i, verbose=True)
dtram_obj = dtram(tramdata, lag=1, maxiter=1, ftol=1.0E-14, verbose=True)
dtram_obj = dtram(tramdata, lag=1, maxiter=100000, ftol=1.0E-14, verbose=True)
maxerr = 1.0E-1
assert_allclose(dtram_obj.f_K, self.f_K, atol=maxerr)
assert_allclose(dtram_obj.f_i, self.f_i, atol=maxerr)
assert_allclose(dtram_obj.pi_i, self.pi_i, atol=maxerr)
assert_allclose(dtram_obj.f_K_i, self.f_K_i, atol=maxerr)
assert_allclose(dtram_obj.pi_K_i, self.pi_K_i, atol=maxerr)
assert_allclose(dtram_obj.estimate_transition_matrices(), self.tmat, atol=maxerr)
def test_dtram_api(self):
"""testing the dTRAM API"""
tramdata = TRAMData(self.inp, b_K_i=self.b_K_i, verbose=True)
dtram_obj = dtram(tramdata,
lag=1,
maxiter=1,
ftol=1.0E-14,
verbose=True)
dtram_obj = dtram(tramdata,
lag=1,
maxiter=100000,
ftol=1.0E-14,
verbose=True)
maxerr = 1.0E-1
assert_allclose(dtram_obj.f_K, self.f_K, atol=maxerr)
assert_allclose(dtram_obj.f_i, self.f_i, atol=maxerr)
assert_allclose(dtram_obj.pi_i, self.pi_i, atol=maxerr)
assert_allclose(dtram_obj.f_K_i, self.f_K_i, atol=maxerr)
assert_allclose(dtram_obj.pi_K_i, self.pi_K_i, atol=maxerr)
assert_allclose(dtram_obj.estimate_transition_matrices(),
self.tmat,
atol=maxerr)
plt.plot(gridpoints, p)
#%%
################################
# OLD code continues...
################################
dtramdata = TRAMData(
sim_data.trajs,
b_K_i=sim_data.gen_harmonic_bias_mtx(gridpoints=sim_data.gridpoints))
try:
dtram_obj = dtram(dtramdata,
lag=opts.lag_time,
maxiter=1,
ftol=opts.f_toler_dtram,
verbose=False)
except pytram.ExpressionError:
raise pytram.ExpressionError, "Input was faulty, ending..."
except pytram.NotConvergedWarning:
pass
#%%
converged = False
nruns = 0
while not converged:
try:
print "Running another 1k steps ..."
T = sim_data.get_reweighted_TransMtx()
p = sim_data.get_reweighted_distribution(T)
plt.plot(gridpoints, p)
#%%
################################
# OLD code continues...
################################
dtramdata = TRAMData( sim_data.trajs,
b_K_i=sim_data.gen_harmonic_bias_mtx(gridpoints=sim_data.gridpoints) )
try:
dtram_obj = dtram(dtramdata, lag=opts.lag_time, maxiter=1,
ftol=opts.f_toler_dtram, verbose=False )
except pytram.ExpressionError:
raise pytram.ExpressionError, "Input was faulty, ending..."
except pytram.NotConvergedWarning:
pass
#%%
converged = False
nruns=0
while not converged:
try:
print "Running another 1k steps ..."
nruns+=1
