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_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)))
############################################################################
#
# 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, 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 )
############################################################################
#
# 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
#
############################################################################
# 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#")
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, 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 )
############################################################################
#
# run the self-consistent-iteration
