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195 backward euler python #234

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merged 7 commits into from
Nov 5, 2024
Merged

195 backward euler python #234

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4ee86a2
Updated python wrapper to include Backward Euler options.
davidfillmore Oct 10, 2024
4685448
Added TestAnalyticalBackwardEuler.
davidfillmore Oct 10, 2024
3d42ca7
Added TestAnalyticalStandardBackwardEuler.
davidfillmore Oct 10, 2024
7963fc2
Added multiple grid cell backward Euler tests.
davidfillmore Oct 30, 2024
98d4538
Added places argument with default of 5.
davidfillmore Oct 30, 2024
3c7dd99
Merge branch 'main' into 195-backward-euler-python
dwfncar Oct 30, 2024
9161357
Fixed wrapper.
davidfillmore Oct 31, 2024
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68 changes: 52 additions & 16 deletions python/test/test_analytical.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import random


def TestSingleGridCell(self, solver):
def TestSingleGridCell(self, solver, places=5):
num_grid_cells = 1
time_step = 200.0
temperature = 272.5
Expand Down Expand Up @@ -78,17 +78,17 @@ def TestSingleGridCell(self, solver):
(1.0 + (k1 * np.exp(-k2 * curr_time) - k2 * np.exp(-k1 * curr_time)) / (k2 - k1))

self.assertAlmostEqual(
ordered_concentrations[species_ordering["A"]], A_conc, places=5)
ordered_concentrations[species_ordering["A"]], A_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[species_ordering["B"]], B_conc, places=5)
ordered_concentrations[species_ordering["B"]], B_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[species_ordering["C"]], C_conc, places=5)
ordered_concentrations[species_ordering["C"]], C_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[species_ordering["D"]], D_conc, places=5)
ordered_concentrations[species_ordering["D"]], D_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[species_ordering["E"]], E_conc, places=5)
ordered_concentrations[species_ordering["E"]], E_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[species_ordering["F"]], F_conc, places=5)
ordered_concentrations[species_ordering["F"]], F_conc, places=places)

curr_time += time_step

Expand All @@ -102,7 +102,7 @@ def test_simulation(self):
TestSingleGridCell(self, solver)


class TestAnalyicalStandardRosenbrock(unittest.TestCase):
class TestAnalyticalStandardRosenbrock(unittest.TestCase):
def test_simulation(self):
solver = musica.create_solver(
"configs/analytical",
Expand All @@ -111,7 +111,25 @@ def test_simulation(self):
TestSingleGridCell(self, solver)


def TestMultipleGridCell(self, solver, num_grid_cells):
class TestAnalyticalBackwardEuler(unittest.TestCase):
def test_simulation(self):
solver = musica.create_solver(
"configs/analytical",
musica.micmsolver.backward_euler,
1)
TestSingleGridCell(self, solver, places=2)


class TestAnalyticalStandardBackwardEuler(unittest.TestCase):
def test_simulation(self):
solver = musica.create_solver(
"configs/analytical",
musica.micmsolver.backward_euler_standard_order,
1)
TestSingleGridCell(self, solver, places=2)


def TestMultipleGridCell(self, solver, num_grid_cells, places=5):
time_step = 200.0
temperatures = []
pressures = []
Expand Down Expand Up @@ -221,17 +239,17 @@ def TestMultipleGridCell(self, solver, num_grid_cells):
k1[i] * np.exp(-k2[i] * curr_time) - k2[i] * np.exp(-k1[i] * curr_time)) / (k2[i] - k1[i]))

self.assertAlmostEqual(
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["A"]], A_conc, places=5)
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["A"]], A_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["B"]], B_conc, places=5)
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["B"]], B_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["C"]], C_conc, places=5)
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["C"]], C_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["D"]], D_conc, places=5)
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["D"]], D_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["E"]], E_conc, places=5)
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["E"]], E_conc, places=places)
self.assertAlmostEqual(
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["F"]], F_conc, places=5)
ordered_concentrations[i * len(concentrations.keys()) + species_ordering["F"]], F_conc, places=places)

curr_time += time_step

Expand All @@ -245,7 +263,7 @@ def test_simulation(self):
TestMultipleGridCell(self, solver, 3)


class TestAnalyicalStandardRosenbrockMultipleGridCells(unittest.TestCase):
class TestAnalyticalStandardRosenbrockMultipleGridCells(unittest.TestCase):
def test_simulation(self):
solver = musica.create_solver(
"configs/analytical",
Expand All @@ -254,5 +272,23 @@ def test_simulation(self):
TestMultipleGridCell(self, solver, 3)


class TestAnalyticalBackwardEulerMultipleGridCells(unittest.TestCase):
def test_simulation(self):
solver = musica.create_solver(
"configs/analytical",
musica.micmsolver.backward_euler,
3)
TestMultipleGridCell(self, solver, 3, places=2)


class TestAnalyticalStandardBackwardEulerMultipleGridCells(unittest.TestCase):
def test_simulation(self):
solver = musica.create_solver(
"configs/analytical",
musica.micmsolver.backward_euler_standard_order,
3)
TestMultipleGridCell(self, solver, 3, places=2)


if __name__ == '__main__':
unittest.main()
22 changes: 20 additions & 2 deletions python/wrapper.cpp
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@ PYBIND11_MODULE(musica, m)

py::enum_<musica::MICMSolver>(m, "micmsolver")
.value("rosenbrock", musica::MICMSolver::Rosenbrock)
.value("rosenbrock_standard_order", musica::MICMSolver::RosenbrockStandardOrder);
.value("rosenbrock_standard_order", musica::MICMSolver::RosenbrockStandardOrder)
.value("backward_euler", musica::MICMSolver::BackwardEuler)
.value("backward_euler_standard_order", musica::MICMSolver::BackwardEulerStandardOrder);

m.def(
"create_solver",
Expand Down Expand Up @@ -162,6 +164,14 @@ PYBIND11_MODULE(musica, m)
{
map = micm->rosenbrock_standard_.second.variable_map_;
}
else if (micm->solver_type_ == musica::MICMSolver::BackwardEuler)
{
map = micm->backward_euler_.second.variable_map_;
}
else if (micm->solver_type_ == musica::MICMSolver::BackwardEulerStandardOrder)
{
map = micm->backward_euler_standard_.second.variable_map_;
}

return map;
},
Expand All @@ -182,8 +192,16 @@ PYBIND11_MODULE(musica, m)
{
map = micm->rosenbrock_standard_.second.custom_rate_parameter_map_;
}
else if (micm->solver_type_ == musica::MICMSolver::BackwardEuler)
{
map = micm->backward_euler_.second.custom_rate_parameter_map_;
}
else if (micm->solver_type_ == musica::MICMSolver::BackwardEulerStandardOrder)
{
map = micm->backward_euler_standard_.second.custom_rate_parameter_map_;
}

return map;
},
"Return map of reaction rates");
}
}
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