def test_toy_model():
"""test DTRAM with toy model"""
C_K_ij = np.array(
[[[2358, 29, 0], [29, 0, 32], [0, 32, 197518]],
[[16818, 16763, 0], [16763, 0, 16510], [0, 16510, 16635]]],
dtype=np.intc)
b_K_i = np.array([[0.0, 0.0, 0.0], [4.0, 0.0, 8.0]], dtype=np.float64)
dtram = DTRAM(C_K_ij, b_K_i)
assert_raises(NotConvergedWarning,
dtram.sc_iteration,
maxiter=1,
ftol=1.0E-80,
verbose=False)
dtram.sc_iteration(maxiter=200000, ftol=1.0E-15, verbose=True)
pi = np.array([1.82026887e-02, 3.30458960e-04, 9.81466852e-01],
dtype=np.float64)
T = np.array([[9.90504397e-01, 9.49560284e-03, 0.0],
[5.23046803e-01, 0.0, 4.76953197e-01],
[0.0, 1.60589690e-04, 9.99839410e-01]],
dtype=np.float64)
print(pi)
print(dtram.pi_i)
assert_true(np.max(np.abs(dtram.pi_i - pi)) < 1.0E-8)
assert_true(
np.max(np.abs(dtram.estimate_transition_matrix(0) - T)) < 1.0E-8)
def test_three_state_model():
C_K_ij = np.array( [[[2358,29,0],[29,0,32],[0,32,197518]],[[16818,16763,0],[16763,0,16510],[0,16510,16635]]], dtype=np.intc )
gamma_K_j = np.ones( shape=(2,3), dtype=np.float64 )
gamma_K_j[1,0] = np.exp( -4.0 )
gamma_K_j[1,2] = np.exp( -8.0 )
dtram = DTRAM( C_K_ij, gamma_K_j )
assert_raises( NotConvergedWarning, dtram.scf_iteration, maxiter=1, ftol=1.0E-80, verbose=False )
dtram.scf_iteration( maxiter=200000, ftol=1.0E-15, verbose=False )
pi = np.array( [1.82026887e-02,3.30458960e-04,9.81466852e-01], dtype=np.float64 )
T = np.array( [[9.90504397e-01,9.49560284e-03,0.0],[5.23046803e-01,0.0,4.76953197e-01],[0.0,1.60589690e-04,9.99839410e-01]], dtype=np.float64 )
assert_true( np.max( np.abs( dtram.pi_i - pi ) ) < 1.0E-8 )
assert_true( np.max( np.abs( dtram.estimate_transition_matrix()[0,:,:] - T ) ) < 1.0E-8 )
def test_toy_model():
"""test DTRAM with toy model"""
C_K_ij = np.array([
[[2358, 29, 0], [29, 0, 32], [0, 32, 197518]],
[[16818, 16763, 0], [16763, 0, 16510], [0, 16510, 16635]]], dtype=np.intc)
b_K_i = np.array([[0.0, 0.0, 0.0], [4.0, 0.0, 8.0]], dtype=np.float64)
dtram = DTRAM(C_K_ij, b_K_i)
assert_raises(NotConvergedWarning, dtram.sc_iteration, maxiter=1, ftol=1.0E-80, verbose=False)
dtram.sc_iteration(maxiter=200000, ftol=1.0E-15, verbose=True)
pi = np.array([1.82026887e-02, 3.30458960e-04, 9.81466852e-01], dtype=np.float64)
T = np.array([
[9.90504397e-01, 9.49560284e-03, 0.0],
[5.23046803e-01, 0.0, 4.76953197e-01],
[0.0, 1.60589690e-04, 9.99839410e-01]], dtype=np.float64)
print pi
print dtram.pi_i
assert_true(np.max(np.abs(dtram.pi_i - pi)) < 1.0E-8)
assert_true(np.max(np.abs(dtram.estimate_transition_matrix(0) - T)) < 1.0E-8)
############################################################################
#
# 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
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
#
############################################################################
