def test_build_templated_model():
root = new(name="System")
model = new(name="Vs")
root.add(model)
ss = new("SS", name="pout")
Se = new("Se", name="Vs")
zero = new("0", name="0_0")
model.add(ss, Se, zero)
connect(ss, zero)
connect(Se, zero)
file = file_path / "temp.bg"
assert root.name == "System"
with TempFile(file):
save(root, file)
with open(file, 'r') as fs:
temp_data = yaml.load(fs, Loader=yaml.SafeLoader)
assert temp_data["root"] == root.name
assert temp_data["models"].keys() == {"/", "/Vs"}
assert temp_data["models"]["/"]["components"] == ["Vs /Vs"]
assert set(temp_data["models"]["/Vs"]["components"]) == {
"pout base/SS", "Vs base/Se", "0_0 base/0"
}
assert set(temp_data["models"]["/Vs"]["netlist"]) == {"pout 0_0", "Vs 0_0"}
def test_ab_to_c_model():
A = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
B = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
C = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
Re = bgt.new("Re", library="BioChem", value={'r': 1, "R": 1, "T": 1})
Y_AB = bgt.new('1')
Y_C = bgt.new('1')
bg = bgt.new()
bg.add(A, B, Re, Y_AB, C, Y_C)
connect(A, Y_AB)
connect(B, Y_AB)
connect(Y_AB, Re)
connect(Re, Y_C)
connect(Y_C, C)
state_basis, _, _ = bg.basis_vectors
(x_0, dx_0), = (k for k, (v, _) in state_basis.items() if v is A)
(x_1, dx_1), = (k for k, (v, _) in state_basis.items() if v is B)
(x_2, dx_2), = (k for k, (v, _) in state_basis.items() if v is C)
eqns = {
dx_0 + x_0 * x_1 - x_2, dx_1 + x_0 * x_1 - x_2, dx_2 - x_0 * x_1 + x_2
}
relations = set(bg.constitutive_relations)
assert not relations ^ eqns
def test_build_junction_dict():
c = bgt.new("C")
kvl = bgt.new("0")
bg = bgt.new()
bg.add([c, kvl])
connect(kvl, c)
cp, kp = list(c.ports) + list(kvl.ports)
index_map = {cp: 0, kp: 1}
M = adjacency_to_dict(index_map, bg.bonds, offset=1)
assert M[(0, 1)] == 1
assert M[(0, 3)] == -1
assert M[(1, 2)] == 1
assert M[(1, 4)] == 1
def test_failstate(self):
# see issue 110
from BondGraphTools import new, expose, connect
from BondGraphTools.exceptions import InvalidPortException
model = new()
port = new('SS')
model.add(port)
expose(port, label='port_1')
test_model = new()
component = new("0") ## could be anything
test_model.add(component, model)
target_port = (model, 'port_') # typo in port name
with pytest.raises(InvalidPortException):
connect(component, target_port)
def test_connection_feedback(self):
from BondGraphTools import new, connect, add
from BondGraphTools.exceptions import InvalidPortException
model = new()
c1 = new('C')
c2 = new('C')
c3 = new('C')
add(model, c1, c2, c3)
connect(c1, (c2, 0))
with pytest.raises(InvalidPortException) as ex:
connect((c2, 0), c3)
assert "Port is already connected: " in str(ex)
def test_make_a_to_b_inplicit():
A = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
B = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
Re = bgt.new("Re", library="BioChem", value={"R": 1, "T": 1})
a_to_b = bgt.new()
a_to_b.add(A, Re, B)
connect(A, Re)
connect(B, Re)
assert Re.control_vars == ['r']
assert list(a_to_b.state_vars.keys()) == ['x_0', 'x_1']
assert list(a_to_b.control_vars.keys()) == ['u_0']
assert not a_to_b.ports
def test_ported_cap():
model = new()
c = new("C", value=3)
zero = new("0")
ss = new("SS")
model.add(c, zero, ss)
connect(c, zero)
connect(ss, zero)
expose(ss)
assert len(model.ports) == 1
assert model.constitutive_relations == [
sympy.sympify("dx_0 - f_0"),
sympy.sympify("e_0 - x_0/3")
]
def test_ss_exposure():
model = new()
ss = new("SS")
sf = new("Sf", name="Sf")
zero = new("0")
model.add(ss, sf, zero)
connect(sf, zero)
connect(ss, zero)
assert not model.ports
assert set(model.control_vars.values()) == {(sf, 'f'), (ss, 'e'),
(ss, 'f')}
expose(ss, 'pin')
assert model.ports
p, = list(model.ports)
assert p.name is "pin"
assert set(model.control_vars.values()) == {(sf, 'f')}
def test_c_se_sim():
c = new("C", value=1)
se = new("Se")
r = new("R", value=1)
kcl = new("1")
bg = new()
bg.add([c, se, kcl, r])
connect(c, (kcl, kcl.non_inverting))
connect(r, (kcl, kcl.non_inverting))
connect(se, (kcl, kcl.non_inverting))
def u(t, x, dx):
return -np.exp(-t)
assert str(bg.constitutive_relations) == '[dx_0 + u_0 + x_0]'
with pytest.raises(ModelException) as ex:
_ = simulate(
c, timespan=[0, 10], x0=[0]
)
assert "Control variable u_0 must be specified" in ex.args
t, x = simulate(
bg, timespan=[0, 10], x0=[0], control_vars=[u]
)
assert t[0] == 0
assert t[-1] == 10
assert (len(t), 1) == x.shape
assert x[0, 0] == 0
solution = t * np.exp(-t)
res = abs(x - solution)
assert (res < 0.001).all()
def test_ported_cr():
model = bgt.new()
Sf = bgt.new('Sf', name="Sf")
R = bgt.new("R", value=2)
zero = bgt.new("0")
ss = bgt.new("SS")
model.add(Sf, R, zero, ss)
connect(Sf, zero)
connect(R, zero)
connect(ss, zero)
bgt.expose(ss, 'A')
assert len(model.control_vars) == 1
ts, ps, cs = model._build_internal_basis_vectors()
assert len(cs) == 1
assert len(ps) == 7
assert len(ts) == 0
mapping, coords = inverse_coord_maps(ts, ps, cs)
assert len(coords) == 15
coords, mappings, lin_op, nl_op, conttr = model.system_model()
assert nl_op.is_zero_matrix
assert not conttr
assert model.constitutive_relations == [
sympy.sympify('e_0 - 2*f_0 - 2*u_0')
]
def test_c_se_build_ode():
c = new("C", value=1)
se = new("Se")
r = new("R", value=1)
kcl = new("1")
bg = new()
bg.add([c, se, kcl, r])
connect(c, (kcl, kcl.non_inverting))
connect(r, (kcl, kcl.non_inverting))
connect(se, (kcl, kcl.non_inverting))
# "dx_0 - u_0 + x_0"
# so f(x,t) = exp(-t) - x
def u(t, x, dx):
return -np.exp(-t)
residual_func, diff_vars = _bondgraph_to_residuals(bg, control_vars=[u])
r = [0]
residual_func(0, [0], [0], r)
assert r == [-1]
residual_func(0, [0], [2], r)
assert r == [1]
residual_func(0, [2], [0], r)
assert r == [1]
residual_func(0, [0], [1], r)
assert r == [0]
t_test = np.log(4)
residual_func(t_test, [1 / 8], [1 / 8], r)
assert r == [0]
def test_make_a_to_b():
A = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
B = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
Re = bgt.new("Re", library="BioChem", value={"R": 1, "T": 1})
a_to_b = bgt.new()
a_to_b.add(A, Re, B)
connect(A, (Re, 0))
connect(B, (Re, 1))
with pytest.raises(InvalidPortException):
connect(A, Re)
assert Re.control_vars == ['r']
assert list(a_to_b.state_vars.keys()) == ['x_0', 'x_1']
assert list(a_to_b.control_vars.keys()) == ['u_0']
assert not a_to_b.ports
state_basis, _, control_basis = a_to_b.basis_vectors
(x_A, dx_A), = (k for k, (v, _) in state_basis.items() if v is A)
(x_B, dx_B), = (k for k, (v, _) in state_basis.items() if v is B)
(r,) = (k for k, (v, _) in control_basis.items() if v is Re)
solutions = {dx_A + r*x_A - r*x_B, dx_B - r*x_A + r*x_B}
relations = set(a_to_b.constitutive_relations)
assert not solutions ^ relations
def test_ported_series_resistor():
Se = new("Se")
r1 = new("R", value=1)
r2 = new("R", value=2)
kvl = new('1')
ss = new("SS")
model = new()
model.add(Se, r1, r2, kvl, ss)
expose(ss)
connect(Se, kvl.non_inverting)
connect(kvl.inverting, r1)
connect(kvl.inverting, r2)
connect(kvl.inverting, ss)
assert len(model.ports) == 1
assert model.constitutive_relations == [sympy.sympify("e_0 - 3*f_0 - u_0")]
def test_rlc():
c = new("C", value=1)
se = new("Se")
r = new("R", value=1)
l = new("I", value=1)
kvl = new("0")
bg = new()
bg.add([c, se, kvl, r, l])
connect(c, kvl)
connect(r, kvl)
connect(se, kvl)
connect(l, kvl)
_ = simulate(
bg, timespan=[0, 10], x0=[1, 0], control_vars=[1]
)
def test_cv_relations():
c = bgt.new("C", value=1)
se = bgt.new("Se")
r = bgt.new("R", value=1)
kcl = bgt.new("1")
bg = bgt.new()
bg.add([c, se, kcl, r])
connect(c, (kcl, kcl.non_inverting))
connect(r, (kcl, kcl.non_inverting))
connect(se, (kcl, kcl.non_inverting))
assert bg.constitutive_relations == [sympy.sympify("dx_0 + u_0 + x_0")]
def test_a_to_b_model():
A = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
B = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
Re = bgt.new("Re", library="BioChem", value={'r': 1, "R": 1, "T": 1})
Y_A = bgt.new('1')
Y_B = bgt.new('1')
a_to_b = bgt.new()
a_to_b.add(A, Re, B, Y_A, Y_B)
connect(A, Y_A.non_inverting)
connect(B, Y_B.non_inverting)
connect((Re, 0), Y_A.inverting)
connect((Re, 1), Y_B.inverting)
eqns = {sympy.sympify("dx_0 + x_0 -x_1"), sympy.sympify("dx_1 + x_1 -x_0")}
for relation in a_to_b.constitutive_relations:
assert relation in eqns
def test_parallel_crv_relations():
c = bgt.new("C", value=1)
se = bgt.new("Se")
r = bgt.new("R", value=1)
kcl = bgt.new("0")
bg = bgt.new()
bg.add([c, se, kcl, r])
connect(c, kcl)
connect(se, kcl)
connect(r, kcl)
assert bg.constitutive_relations == [sympy.sympify("dx_0 - du_0"),
sympy.sympify("x_0 - u_0")]
def test_cv_subs_state_func():
c = bgt.new("C", value=1)
se = bgt.new("Se")
r = bgt.new("R", value=1)
kcl = bgt.new("1")
bg = bgt.new()
bg.add([c, se, kcl, r])
connect(c, (kcl, kcl.non_inverting))
connect(r, (kcl, kcl.non_inverting))
connect(se, (kcl, kcl.non_inverting))
cv_s = {'u_0': ' -exp(-x_0)'}
subs = [(sympy.Symbol('u_0'), sympy.sympify('-exp(-x_0)'))]
mappings, coords = inverse_coord_maps(*bg.basis_vectors)
assert _generate_cv_substitutions(cv_s, mappings, coords) == subs
def test_zero_junction_relations():
r = bgt.new("R", value=sympy.symbols('r'))
l = bgt.new("I", value=sympy.symbols('l'))
c = bgt.new("C", value=sympy.symbols('c'))
kvl = bgt.new("0", name="kvl")
rlc = bgt.new()
rlc.add([c, l, kvl, r])
connect(r, kvl)
connect(l, kvl)
connect(c, kvl)
rels = kvl.constitutive_relations
assert sympy.sympify("e_1 - e_2") in rels
assert sympy.sympify("e_0 - e_2") in rels
assert sympy.sympify("f_0 + f_1 + f_2") in rels
def test_c_se_sum_switch():
c = new("C", value=1)
se = new("Se")
r = new("R", value=1)
kcl = new("1")
bg = new()
bg.add([c, se, kcl, r])
connect(c, (kcl, kcl.non_inverting))
connect(r, (kcl, kcl.non_inverting))
connect(se, (kcl, kcl.non_inverting))
def bang_bang(t, x, dx):
return 1.5 if x >= 1 else -2.0
t, x = simulate(
bg, timespan=[0, 10], x0=[0], dx0=[1], control_vars=[bang_bang])
assert (x[0, -1] - 1) < 0.001
def test_make_a_to_b():
A = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
B = bgt.new("Ce", library="BioChem", value=[1, 1, 1])
Re = bgt.new("Re", library="BioChem", value={"R": 1, "T": 1})
a_to_b = bgt.new()
a_to_b.add(A, Re, B)
connect(A, (Re, 0))
connect(B, (Re, 1))
with pytest.raises(InvalidPortException):
connect(A, Re)
assert Re.control_vars == ['r']
assert list(a_to_b.state_vars.keys()) == ['x_0', 'x_1']
assert list(a_to_b.control_vars.keys()) == ['u_0']
assert not a_to_b.ports
def test_nlin_se():
rn = Reaction_Network(name="A+B to C", reactions="A+B=C")
system = rn.as_network_model(normalised=True)
for param in system.params:
system.set_param(param, 1)
Ce_A = system / "A"
Ce_B = system / "B"
Ce_C = system / "C"
assert Ce_A is not Ce_B
Y = system / "AB"
bgt.disconnect(Ce_A, Y)
J_A = bgt.new("0", name="Ce_A")
Se_A = bgt.new('Se', value=1, name='e=1')
system.add(J_A),
system.add(Se_A)
connect(J_A, Y)
connect(Ce_A, J_A)
connect(Se_A, J_A)
assert len(system.state_vars) == 3
state_basis, _, _ = system.basis_vectors
(x0, dx0), = (k for k, (v, _) in state_basis.items() if v is Ce_A)
(x1, dx1), = (k for k, (v, _) in state_basis.items() if v is Ce_B)
(x2, dx2), = (k for k, (v, _) in state_basis.items() if v is Ce_C)
E = sympy.S("E")
solutions = {dx1 + E * x1 - x2, dx2 - E * x1 + x2, x0 - E, dx0}
relations = set(system.constitutive_relations)
assert not solutions ^ relations
