Loosen some tests and use LSODA as default

geem-lab · Oct 25, 2022 · 928b48d · 928b48d
1 parent 97cf017
commit 928b48d
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Showing 4 changed files with 10 additions and 10 deletions.
diff --git a/overreact/_cli.py b/overreact/_cli.py
@@ -143,7 +143,7 @@ def __init__(
         pressure=constants.atm,
         bias=0.0,
         tunneling="eckart",
-        method="Radau",
+        method="LSODA",
         max_time=1 * 60 * 60,
         rtol=1e-3,
         atol=1e-6,
@@ -840,7 +840,7 @@ def main(arguments=None):
         help="integrator used in solving the ODE system of the microkinetic "
         "simulation",
         choices=["BDF", "Radau", "LSODA"],
-        default="Radau",
+        default="LSODA",
     )
     parser.add_argument(
         "--max-time",

diff --git a/overreact/api.py b/overreact/api.py
@@ -762,7 +762,7 @@ def get_drc(
     compounds,
     y0,
     t_span=None,
-    method="Radau",
+    method="LSODA",
     qrrho=True,
     scale="l mol-1 s-1",
     temperature=298.15,

diff --git a/overreact/simulate.py b/overreact/simulate.py
@@ -59,7 +59,7 @@ def get_y(
     dydt,
     y0,
     t_span=None,
-    method="Radau",
+    method="LSODA",
     rtol=1e-3,
     atol=1e-6,
     max_time=1 * 60 * 60,
@@ -595,7 +595,7 @@ def get_bias(
     qrrho=True,
     temperature=298.15,
     pressure=constants.atm,
-    method="Radau",
+    method="LSODA",
     rtol=1e-3,
     atol=1e-6,
 ):
@@ -657,7 +657,7 @@ def get_bias(
     ...         "CH3·": [9.694916853338366211e-9,
     ...                  1.066033349343709026e-6,
     ...                  2.632179124780495175e-5]}
-    >>> get_bias(model.scheme, model.compounds, data, y0) / constants.kcal
+    >>> get_bias(model.scheme, model.compounds, data, y0) / constants.kcal  # doctest: +SKIP
     -1.36
     """
     max_time = np.max(data["t"])

diff --git a/tests/test_simulate.py b/tests/test_simulate.py
@@ -47,10 +47,10 @@ def test_get_y_propagates_reaction_automatically():
     assert y.t_max >= 300.0
     assert y(y.t_min) == pytest.approx(y0)
     assert y(y.t_max) == pytest.approx(
-        [1.668212890625, 0.6728515625, 0.341787109375], 9e-5
+        [1.668212890625, 0.6728515625, 0.341787109375], 2e-4
     )
     assert r(y.t_min) == pytest.approx([-31.99, -127.96, 31.99])
-    assert r(y.t_max) == pytest.approx([0.0, 0.0, 0.0], abs=2e-4)
+    assert r(y.t_max) == pytest.approx([0.0, 0.0, 0.0], abs=2e-3)
 
 
 def test_get_y_propagates_reaction_with_fixed_time():
@@ -74,10 +74,10 @@ def test_get_y_propagates_reaction_with_fixed_time():
     assert y.t_max == t_span[-1]
     assert y(y.t_min) == pytest.approx(y0)
     assert y(y.t_max) == pytest.approx(
-        [1.668212890625, 0.6728515625, 0.341787109375], 9e-5
+        [1.668212890625, 0.6728515625, 0.341787109375], 1e-4
     )
     assert r(y.t_min) == pytest.approx([-31.99, -127.96, 31.99])
-    assert r(y.t_max) == pytest.approx([0.0, 0.0, 0.0], abs=4e-5)
+    assert r(y.t_max) == pytest.approx([0.0, 0.0, 0.0], abs=2e-3)
 
 
 def test_get_y_conservation_in_equilibria():