def test_get_C_K_ij_lag3():
"""test transition counts at lag time 3"""
trajs = [{
'm': np.array([0, 1, 2, 0], dtype=np.intc),
't': np.zeros(shape=(4, ), dtype=np.intc)
}]
td = TRAMData(trajs)
C_K_ij = np.array([[[1, 0, 0], [0, 0, 0], [0, 0, 0]]], dtype=np.intc)
assert_true(np.all(C_K_ij == td.get_C_K_ij(3)))
def test_Mx_Tx_nMTstates():
seq = np.array(range(20), dtype=np.intc)
trajs = [{'m': seq[:10], 't': seq[:10]}, {'m': seq[10:], 't': seq[10:]}]
td = TRAMData(trajs)
assert_true(np.all((seq - td.T_x) == 0))
assert_true(np.all((seq - td.M_x) == 0))
assert_true(td.n_markov_states == 20)
assert_true(td.n_therm_states == 20)
def test_N_K_i():
trajs = []
for K in xrange(3):
trajs.append({
'm': np.array(range(4), dtype=np.intc),
't': np.ones(shape=(4, ), dtype=np.intc) * K
})
td = TRAMData(trajs)
assert_true(np.all(td.N_K_i == 1))
assert_true(np.all(td.N_K == 4))
assert_true(td.N_K.sum() == 12)
def test_xtram_api(self):
"""testing the xTRAM API"""
tramdata = TRAMData(self.inp, verbose=True)
xtram_obj = xtram(tramdata,
lag=1,
maxiter=1,
ftol=1.0E-13,
verbose=True)
xtram_obj = xtram(tramdata,
lag=1,
maxiter=10000,
ftol=1.0E-13,
verbose=True)
maxerr = 1.0E-1
assert_allclose(xtram_obj.f_K, self.f_K, atol=maxerr)
assert_allclose(xtram_obj.f_i, self.f_i, atol=maxerr)
assert_allclose(xtram_obj.pi_i, self.pi_i, atol=maxerr)
assert_allclose(xtram_obj.f_K_i, self.f_K_i, atol=maxerr)
assert_allclose(xtram_obj.pi_K_i, self.pi_K_i, 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)
def test_get_C_K_ij_lag3():
"""test transition counts at lag time 3"""
trajs = [{'m': np.array([0, 1, 2, 0], dtype=np.intc), 't': np.zeros(shape=(4,), dtype=np.intc)}]
td = TRAMData(trajs)
C_K_ij = np.array([[[1, 0, 0], [0, 0, 0], [0, 0, 0]]], dtype=np.intc)
assert_true(np.all(C_K_ij == td.get_C_K_ij(3)))
plt.show()
#%%
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
#%%
############################################################################
#
# import the data
#
############################################################################
print "#\n################################## IMPORTING DATA ##################################\n#"
reader = Reader(
args.files,
b_K_i_file=args.b_K_i_file,
maxlength=args.maxlength,
skiprows=args.skiprows,
verbose=True
)
tramdata = TRAMData( reader.trajs, b_K_i=reader.b_K_i )
try:
dtram_obj = DTRAM( tramdata.get_C_K_ij( args.lag ), tramdata.b_K_i )
except ExpressionError, e:
print "#\n### ERROR\n#"
print "# Your input was faulty!"
print "# The < %s > object is malformed: %s" % ( e.expression, e.msg )
print "#\n### ABORTING\n\n"
exit( 1 )
print "#\n### SYSTEM INFORMATION\n#"
print "# %25s %24d" % ( "[markov states]", tramdata.n_markov_states )
print "# %25s %24d" % ( "[thermodynamic states]", tramdata.n_therm_states )
############################################################################
############################################################################
#
# import the data
#
############################################################################
print "#\n################################## IMPORTING DATA ##################################\n#"
reader = Reader(
args.files,
kT_file=args.kT_file,
maxlength=args.maxlength,
skiprows=args.skiprows,
verbose=True
)
tramdata = TRAMData( reader.trajs, kT_K=reader.kT_K, kT_target = args.kT_target)
try:
xtram_obj = XTRAM( tramdata.get_C_K_ij( args.lag ), tramdata.u_I_x, tramdata.T_x, tramdata.M_x, tramdata.N_K_i, tramdata.N_K, target = tramdata.kT_target, verbose = args.verbose )
except ExpressionError, e:
print "#\n### ERROR\n#"
print "# Your input was faulty!"
print "# The < %s > object is malformed: %s" % ( e.expression, e.msg )
print "#\n### ABORTING\n\n"
exit( 1 )
print "#\n### SYSTEM INFORMATION\n#"
print "# %25s %24d" % ( "[markov states]", tramdata.n_markov_states )
print "# %25s %24d" % ( "[thermodynamic states]", tramdata.n_therm_states )
############################################################################
print "# %25s %24d" % ("[--lag]", args.lag)
print "# %25s %24d" % ("[--maxiter]", args.maxiter)
print "# %25s %24.5e" % ("[--ftol]", args.ftol)
############################################################################
#
# import the data
#
############################################################################
print "#\n################################## IMPORTING DATA ##################################\n#"
reader = Reader(args.files,
b_K_i_file=args.b_K_i_file,
maxlength=args.maxlength,
skiprows=args.skiprows,
verbose=True)
tramdata = TRAMData(reader.trajs, b_K_i=reader.b_K_i)
try:
dtram_obj = DTRAM(tramdata.get_C_K_ij(args.lag), tramdata.b_K_i)
except ExpressionError, e:
print "#\n### ERROR\n#"
print "# Your input was faulty!"
print "# The < %s > object is malformed: %s" % (e.expression, e.msg)
print "#\n### ABORTING\n\n"
exit(1)
print "#\n### SYSTEM INFORMATION\n#"
print "# %25s %24d" % ("[markov states]", tramdata.n_markov_states)
print "# %25s %24d" % ("[thermodynamic states]", tramdata.n_therm_states)
############################################################################
#
# run the self-consistent-iteration
############################################################################
#
# import the data
#
############################################################################
print(
"#\n################################## IMPORTING DATA ##################################\n#"
)
reader = Reader(args.files,
kT_file=args.kT_file,
maxlength=args.maxlength,
skiprows=args.skiprows,
verbose=True)
tramdata = TRAMData(reader.trajs,
kT_K=reader.kT_K,
kT_target=args.kT_target)
try:
xtram_obj = XTRAM(tramdata.get_C_K_ij(args.lag),
tramdata.u_I_x,
tramdata.T_x,
tramdata.M_x,
tramdata.N_K_i,
target=tramdata.kT_target)
except ExpressionError as e:
print("#\n### ERROR\n#")
print("# Your input was faulty!")
print("# The < %s > object is malformed: %s" % (e.expression, e.msg))
print("#\n### ABORTING\n\n")
exit(1)
print("#\n### SYSTEM INFORMATION\n#")
############################################################################
#
# import the data
#
############################################################################
print "#\n################################## IMPORTING DATA ##################################\n#"
reader = Reader(
args.files,
kT_file=args.kT_file,
maxlength=args.maxlength,
skiprows=args.skiprows,
verbose=True
)
tramdata = TRAMData( reader.trajs, kT_K=reader.kT_K, kT_target = args.kT_target)
try:
xtram_obj = XTRAM( tramdata.get_C_K_ij( args.lag ), tramdata.u_I_x, tramdata.T_x, tramdata.M_x, tramdata.N_K_i, target = tramdata.kT_target )
except ExpressionError, e:
print "#\n### ERROR\n#"
print "# Your input was faulty!"
print "# The < %s > object is malformed: %s" % ( e.expression, e.msg )
print "#\n### ABORTING\n\n"
exit( 1 )
print "#\n### SYSTEM INFORMATION\n#"
print "# %25s %24d" % ( "[markov states]", tramdata.n_markov_states )
print "# %25s %24d" % ( "[thermodynamic states]", tramdata.n_therm_states )
############################################################################