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TorkelETorkelE
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use molar units
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‎test/miscellaneous_tests/units.jl

Lines changed: 45 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -11,8 +11,8 @@ using ModelingToolkit: get_iv, get_unit, validate, ValidationError
1111
let
1212
# Creates a `ReactionSystem` programmatically, while designating units.
1313
@variables t [unit=u"s"]
14-
@species A(t) [unit=u"m"] B(t) [unit=u"m"] C(t) [unit=u"m"]
15-
@parameters k1 [unit=u"m/s"] k2 [unit=u"s"^(-1)] k3 [unit=u"m*s"^(-1)]
14+
@species A(t) [unit=u"mol/m^3"] B(t) [unit=u"mol/m^3"] C(t) [unit=u"mol/m^3"]
15+
@parameters k1 [unit=u"mol/(m^3*s)"] k2 [unit=u"s^(-1)"] k3 [unit=u"(m^3)/(s*mol)"]
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rxs = [Reaction(k1, nothing, [A]),
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Reaction(k2, [A], [B]),
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Reaction(k3, [A, B], [B], [1, 1], [2])]
@@ -22,9 +22,9 @@ let
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2323
# Test that all reactions have the correct unit.
2424
for rx in reactions(rs)
25-
@test get_unit(oderatelaw(rx)) == u"m/s"
25+
@test get_unit(oderatelaw(rx)) == u"mol/(s*m^3)"
2626
# we don't currently convert units, so they will be the same as for ODEs
27-
@test get_unit(jumpratelaw(rx)) == u"m/s"
27+
@test get_unit(jumpratelaw(rx)) == u"mol/(s*m^3)"
2828
end
2929

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# Tests that the system can be converted to MTK systems without warnings.
@@ -34,7 +34,7 @@ let
3434
@test_nowarn convert(NonlinearSystem, rs)
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# Tests that creating `Reaction`s with non-matching units yields warnings.
37-
@species B(t) [unit=u"m"] D(t) [unit=u"kg"]
37+
@species B(t) [unit=u"mol"] D(t) [unit=u"kg"]
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bad_rx1 = Reaction(k1, [A], [D])
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bad_rx2 = Reaction(k1, [A], [B, D])
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bad_rx3 = Reaction(k1, [A, D], [B])
@@ -71,14 +71,14 @@ begin
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rs = @reaction_network begin
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@ivs t [unit=u"s"]
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@species begin
74-
A(t), [unit=u"m"]
75-
B(t), [unit=u"m"]
76-
C(t), [unit=u"m"]
74+
A(t), [unit=u"mol/m^3"]
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B(t), [unit=u"mol/m^3"]
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C(t), [unit=u"mol/m^3"]
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end
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@parameters begin
79-
k1, [unit=u"m/s"]
80-
k2, [unit=u"s"^(-1)]
81-
k3, [unit=u"m*s"^(-1)]
79+
k1, [unit=u"mol/(s*m^3)"]
80+
k2, [unit=u"s^(-1)"]
81+
k3, [unit=u"(m^3)/(s*mol)"]
8282
end
8383
k1, 0 --> A
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k2, A --> B
@@ -87,26 +87,26 @@ begin
8787

8888
# Checks that the `ReactionSystem`'s content have the correct units.
8989
@test get_unit(get_iv(rs)) == u"s"
90-
@test all(get_unit.([rs.A, rs.B, rs.C]) .== [u"m", u"m", u"m"])
91-
@test all(get_unit.([rs.k1, rs.k2, rs.k3]) .== [u"m/s", u"s"^(-1), u"m*s"^(-1)])
90+
@test all(get_unit.([rs.A, rs.B, rs.C]) .== [u"mol/m^3", u"mol/m^3", u"mol/m^3"])
91+
@test all(get_unit.([rs.k1, rs.k2, rs.k3]) .== [u"mol/(s*m^3)", u"s^(-1)", u"(m^3)/(s*mol)"])
9292
for rx in reactions(rs)
93-
@test get_unit(oderatelaw(rx)) == u"m/s"
93+
@test get_unit(oderatelaw(rx)) == u"mol/(s*m^3)"
9494
# we don't currently convert units, so they will be the same as for ODEs
95-
@test get_unit(jumpratelaw(rx)) == u"m/s"
95+
@test get_unit(jumpratelaw(rx)) == u"mol/(s*m^3)"
9696
end
9797

9898
# Checks that system declarations with erroneous units yields errors.
9999
@test_logs (:warn, ) match_mode=:any @reaction_network begin
100100
@ivs t [unit=u"1/s"] # Here, t's unit is wrong.
101101
@species begin
102-
A(t), [unit=u"m"]
103-
B(t), [unit=u"m"]
104-
C(t), [unit=u"m"]
102+
A(t), [unit=u"mol/m^3"]
103+
B(t), [unit=u"mol/m^3"]
104+
C(t), [unit=u"mol/m^3"]
105105
end
106106
@parameters begin
107-
k1, [unit=u"m/s"]
108-
k2, [unit=u"s"^(-1)]
109-
k3, [unit=u"m*s"^(-1)]
107+
k1, [unit=u"mol/(s*m^3)"]
108+
k2, [unit=u"s^(-1)"]
109+
k3, [unit=u"(m^3)/(s*mol)"]
110110
end
111111
k1, 0 --> A
112112
k2, A --> B
@@ -115,14 +115,14 @@ begin
115115
@test_logs (:warn, ) match_mode=:any @reaction_network begin
116116
@ivs t [unit=u"s"]
117117
@species begin
118-
A(t), [unit=u"m"]
119-
B(t), [unit=u"m"]
120-
C(t), [unit=u"m"]
118+
A(t), [unit=u"mol/m^3"]
119+
B(t), [unit=u"mol/m^3"]
120+
C(t), [unit=u"mol/m^3"]
121121
end
122122
@parameters begin
123-
k1, [unit=u"m"] # Here, k1's unit is wrong.
124-
k2, [unit=u"s"^(-1)]
125-
k3, [unit=u"m*s"^(-1)]
123+
k1, [unit=u"mol/(m^3)"] # Here, k1's unit is missing "/s".
124+
k2, [unit=u"s^(-1)"]
125+
k3, [unit=u"(m^3)/(s*mol)"]
126126
end
127127
k1, 0 --> A
128128
k2, A --> B
@@ -131,14 +131,14 @@ begin
131131
@test_logs (:warn, ) match_mode=:any @reaction_network begin
132132
@ivs t [unit=u"s"]
133133
@species begin
134-
A(t), [unit=u"m*s"] # Here, A's unit is wrong.
135-
B(t), [unit=u"m"]
136-
C(t), [unit=u"m"]
134+
A(t), [unit=u"mol/(s*m^3)"] # Here, A's unit got an extra "/s".
135+
B(t), [unit=u"mol/m^3"]
136+
C(t), [unit=u"mol/m^3"]
137137
end
138138
@parameters begin
139-
k1, [unit=u"m/s"]
140-
k2, [unit=u"s"^(-1)]
141-
k3, [unit=u"m*s"^(-1)]
139+
k1, [unit=u"mol/(s*m^3)"]
140+
k2, [unit=u"s^(-1)"]
141+
k3, [unit=u"(m^3)/(s*mol)"]
142142
end
143143
k1, 0 --> A
144144
k2, A --> B
@@ -168,20 +168,20 @@ let
168168
@test_nowarn @reaction_network begin
169169
@ivs t [unit=u"s"]
170170
@species begin
171-
X1(t), [unit=u"m"]
172-
Z1(t), [unit=u"m"]
173-
X2(t), [unit=u"m"]
174-
Z2(t), [unit=u"m"]
175-
X3(t), [unit=u"m"]
176-
Y3(t), [unit=u"m"]
177-
Z3(t), [unit=u"m"]
171+
X1(t), [unit=u"mol/m^3"]
172+
Z1(t), [unit=u"mol/m^3"]
173+
X2(t), [unit=u"mol/m^3"]
174+
Z2(t), [unit=u"mol/m^3"]
175+
X3(t), [unit=u"mol/m^3"]
176+
Y3(t), [unit=u"mol/m^3"]
177+
Z3(t), [unit=u"mol/m^3"]
178178
end
179179
@parameters begin
180-
k1, [unit=u"m^(-2)/s"]
181-
v2, [unit=u"m^(-2)/s"]
182-
K2, [unit=u"m"]
183-
v3, [unit=u"m^(-1)/s"]
184-
K3, [unit=u"m"]
180+
k1, [unit=u"(m^6)/(s*mol^2)"]
181+
v2, [unit=u"(m^6)/(s*mol^2)"]
182+
K2, [unit=u"mol/m^3"]
183+
v3, [unit=u"(m^3)/(s*mol)"]
184+
K3, [unit=u"mol/m^3"]
185185
n3
186186
end
187187
k1*X1, 2X1 --> Z1

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