musica 0.12.2__cp39-cp39-macosx_15_0_x86_64.whl

musica/test/examples/v1/full_configuration/full_configuration.yaml

@@ -0,0 +1,295 @@
+---
+version: 1.0.0
+name: Full Configuration
+species:
+- name: A
+  __absolute tolerance: 1.0e-30
+- name: B
+  tracer type: AEROSOL
+- name: C
+  tracer type: THIRD_BODY
+- name: M
+- name: H2O2
+  HLC(298K) [mol m-3 Pa-1]: 1.011596348
+  HLC exponential factor [K]: 6340
+  diffusion coefficient [m2 s-1]: 1.46e-05
+  N star: 1.74
+  molecular weight [kg mol-1]: 0.0340147
+  density [kg m-3]: 1000
+  __absolute tolerance: 1.0e-10
+- name: ethanol
+  diffusion coefficient [m2 s-1]: 9.5e-06
+  N star: 2.55
+  molecular weight [kg mol-1]: 0.04607
+  __absolute tolerance: 1.0e-20
+- name: ethanol_aq
+  molecular weight [kg mol-1]: 0.04607
+  density [kg m-3]: 1000
+  __absolute tolerance: 1.0e-20
+- name: H2O2_aq
+  molecular weight [kg mol-1]: 0.0340147
+  density [kg m-3]: 1000
+  __absolute tolerance: 1.0e-10
+- name: H2O_aq
+  density [kg m-3]: 1000
+  molecular weight [kg mol-1]: 0.01801
+- name: aerosol stuff
+  molecular weight [kg mol-1]: 0.5
+  density [kg m-3]: 1000
+  __absolute tolerance: 1.0e-20
+- name: more aerosol stuff
+  molecular weight [kg mol-1]: 0.2
+  density [kg m-3]: 1000
+  __absolute tolerance: 1.0e-20
+phases:
+- name: gas
+  species:
+  - A
+  - B
+  - C
+  - ethanol
+- name: aqueous aerosol
+  species:
+  - H2O2_aq
+  - H2O_aq
+  - ethanol_aq
+  - A
+  - B
+  - C
+- name: surface reacting phase
+  species:
+  - aerosol stuff
+  - more aerosol stuff
+- name: cloud
+  species:
+  - B
+  - C
+reactions:
+- type: SIMPOL_PHASE_TRANSFER
+  gas phase: gas
+  gas-phase species: ethanol
+  condensed phase: aqueous aerosol
+  condensed-phase species: ethanol_aq
+  B:
+  - -1970
+  - 2.91
+  - 0.00196
+  - -0.496
+  name: my simpol
+  __irrelevant: "2"
+- type: AQUEOUS_EQUILIBRIUM
+  condensed phase: aqueous aerosol
+  condensed-phase water: H2O_aq
+  A: 0.0114
+  C: 2300
+  k_reverse: 0.32
+  reactants:
+  - species name: A
+    coefficient: 2
+  products:
+  - species name: B
+    coefficient: 1
+  - species name: C
+    coefficient: 1
+  name: my aqueous eq
+  __irrelevant: "2"
+- type: CONDENSED_PHASE_ARRHENIUS
+  condensed phase: aqueous aerosol
+  A: 123.45
+  Ea: 123.45
+  B: 1.3
+  D: 300
+  E: 6.0e-06
+  reactants:
+  - species name: H2O2_aq
+    coefficient: 1
+  - species name: H2O_aq
+    coefficient: 1
+  products:
+  - species name: ethanol_aq
+    coefficient: 1
+  name: my condensed arrhenius
+  __irrelevant: "2"
+- type: CONDENSED_PHASE_ARRHENIUS
+  condensed phase: aqueous aerosol
+  A: 123.45
+  C: 123.45
+  B: 1.3
+  D: 300
+  E: 6.0e-06
+  reactants:
+  - species name: H2O2_aq
+    coefficient: 1
+  - species name: H2O_aq
+    coefficient: 1
+  products:
+  - species name: ethanol_aq
+    coefficient: 1
+  name: my other condensed arrhenius
+- type: CONDENSED_PHASE_PHOTOLYSIS
+  condensed phase: aqueous aerosol
+  reactants:
+  - species name: H2O2_aq
+    coefficient: 1
+  products:
+  - species name: ethanol_aq
+    coefficient: 1
+  scaling factor: 12.3
+  name: condensed photo B
+  __irrelevant: "2"
+- type: EMISSION
+  gas phase: gas
+  products:
+  - species name: B
+    coefficient: 1
+  name: my emission
+  scaling factor: 12.3
+  __irrelevant: "2"
+- type: FIRST_ORDER_LOSS
+  gas phase: gas
+  reactants:
+  - species name: C
+    coefficient: 1
+  name: my first order loss
+  scaling factor: 12.3
+  __irrelevant: "2"
+- type: PHOTOLYSIS
+  gas phase: gas
+  reactants:
+  - species name: B
+    coefficient: 1
+  products:
+  - species name: C
+    coefficient: 1
+  name: photo B
+  scaling factor: 12.3
+  __irrelevant: "2"
+- type: SURFACE
+  gas phase: gas
+  gas-phase species: A
+  reaction probability: 0.02
+  gas-phase products:
+  - species name: B
+    coefficient: 1
+  - species name: C
+    coefficient: 1
+  condensed phase: surface reacting phase
+  name: my surface
+  __irrelevant: "2"
+- type: TROE
+  gas phase: gas
+  reactants:
+  - species name: B
+    coefficient: 1
+  - species name: M
+    coefficient: 1
+  products:
+  - species name: C
+    coefficient: 1
+  k0_A: 1.2e-12
+  k0_B: 167
+  k0_C: 3
+  kinf_A: 136
+  kinf_B: 5
+  kinf_C: 24
+  Fc: 0.9
+  N: 0.8
+  name: my troe
+  __irrelevant: "2"
+- type: TERNARY_CHEMICAL_ACTIVATION
+  gas phase: gas
+  name: my ternary chemical activation
+  reactants:
+  - species name: B
+    coefficient: 1
+  - species name: M
+    coefficient: 1
+  products:
+  - species name: C
+    coefficient: 1
+  k0_A: 32.1
+  k0_B: -2.3
+  k0_C: 102.3
+  kinf_A: 63.4
+  kinf_B: -1.3
+  kinf_C: 908.5
+  Fc: 1.3
+  "N": 32.1
+  __irrelevant: "2"
+- type: BRANCHED_NO_RO2
+  gas phase: gas
+  reactants:
+  - species name: A
+    coefficient: 1
+  alkoxy products:
+  - species name: B
+    coefficient: 1
+  nitrate products:
+  - species name: C
+    coefficient: 1
+  X: 0.00012
+  Y: 167
+  a0: 0.15
+  "n": 9
+  name: my branched
+  __irrelevant: "2"
+- gas phase: gas
+  type: TUNNELING
+  name: "my tunneling"
+  A: 123.45
+  B: 1200
+  C: 100000000
+  reactants:
+  - species name: B
+    coefficient: 1
+  products:
+  - species name: C
+    coefficient: 1
+  __irrelevant: "2"
+- type: WET_DEPOSITION
+  condensed phase: cloud
+  name: rxn cloud
+  scaling factor: 12.3
+  __irrelevant: "2"
+- type: ARRHENIUS
+  gas phase: gas
+  reactants:
+  - species name: B
+    coefficient: 1
+  products:
+  - species name: C
+    coefficient: 1
+  A: 32.1
+  B: -2.3
+  C: 102.3
+  D: 63.4
+  E: -1.3
+  name: my arrhenius
+  __irrelevant: "2"
+- type: ARRHENIUS
+  gas phase: gas
+  reactants:
+  - species name: A
+    coefficient: 1
+  products:
+  - species name: B
+    coefficient: 1.2
+  A: 29.3
+  B: -1.5
+  Ea: 101.2
+  D: 82.6
+  E: -0.98
+  name: my other arrhenius
+- type: USER_DEFINED
+  gas phase: gas
+  reactants:
+  - species name: A
+    coefficient: 1
+  - species name: B
+    coefficient: 1
+  products:
+  - species name: C
+    coefficient: 1.3
+  name: my user defined
+  scaling factor: 12.3
+  __irrelevant: "2"

musica/test/integration/test_analytical.py

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+import pytest
+import numpy as np
+import musica
+import random
+import musica.mechanism_configuration as mc
+from musica.cuda import is_cuda_available
+from musica.constants import GAS_CONSTANT
+
+
+def TestSingleGridCell(solver, state, time_step, places=5):
+    temperature = 272.5
+    pressure = 101253.3
+    air_density = pressure / (GAS_CONSTANT * temperature)
+
+    rate_constants = {
+        "USER.reaction 1": 0.001,
+        "USER.reaction 2": 0.002
+    }
+
+    concentrations = {
+        "A": 0.75,
+        "B": 0,
+        "C": 0.4,
+        "D": 0.8,
+        "E": 0,
+        "F": 0.1
+    }
+    state.set_conditions(temperature, pressure, air_density)
+    state.set_concentrations(concentrations)
+    state.set_user_defined_rate_parameters(rate_constants)
+
+    # test to make sure a second call to set_conditions with an empty dictionary does not change the values
+    state.set_concentrations({})
+    state.set_user_defined_rate_parameters({})
+
+    initial_concentrations = state.get_concentrations()
+    initial_rate_parameters = state.get_user_defined_rate_parameters()
+    initial_temperatures = state.get_conditions()["temperature"]
+    initial_pressures = state.get_conditions()["pressure"]
+    initial_air_density = state.get_conditions()["air_density"]
+    assert np.isclose(initial_concentrations["A"][0], concentrations["A"], atol=1e-13)
+    assert np.isclose(initial_concentrations["B"][0], concentrations["B"], atol=1e-13)
+    assert np.isclose(initial_concentrations["C"][0], concentrations["C"], atol=1e-13)
+    assert np.isclose(initial_concentrations["D"][0], concentrations["D"], atol=1e-13)
+    assert np.isclose(initial_concentrations["E"][0], concentrations["E"], atol=1e-13)
+    assert np.isclose(initial_concentrations["F"][0], concentrations["F"], atol=1e-13)
+    assert np.isclose(initial_rate_parameters["USER.reaction 1"][0], rate_constants["USER.reaction 1"], atol=1e-13)
+    assert np.isclose(initial_rate_parameters["USER.reaction 2"][0], rate_constants["USER.reaction 2"], atol=1e-13)
+    assert np.isclose(initial_temperatures[0], temperature, atol=1e-13)
+    assert np.isclose(initial_pressures[0], pressure, atol=1e-13)
+    assert np.isclose(initial_air_density[0], air_density, atol=1e-13)
+
+    time_step = 1
+    sim_length = 100
+
+    curr_time = time_step
+    initial_A = initial_concentrations["A"][0]
+    initial_C = initial_concentrations["C"][0]
+    initial_D = initial_concentrations["D"][0]
+    initial_F = initial_concentrations["F"][0]
+    # Gets analytical concentrations
+    while curr_time <= sim_length:
+        solver.solve(state, time_step)
+        concentrations = state.get_concentrations()
+        k1 = rate_constants["USER.reaction 1"]
+        k2 = rate_constants["USER.reaction 2"]
+        k3 = 0.004 * np.exp(50.0 / temperature)
+        k4 = 0.012 * np.exp(75.0 / temperature) * \
+            (temperature / 50.0)**(-2) * (1.0 + 1.0e-6 * pressure)
+        A_conc = initial_A * np.exp(-(k3) * curr_time)
+        B_conc = initial_A * (k3 / (k4 - k3)) * \
+            (np.exp(-k3 * curr_time) - np.exp(-k4 * curr_time))
+        C_conc = initial_C + initial_A * \
+            (1.0 + (k3 * np.exp(-k4 * curr_time) - k4 * np.exp(-k3 * curr_time)) / (k4 - k3))
+        D_conc = initial_D * np.exp(-(k1) * curr_time)
+        E_conc = initial_D * (k1 / (k2 - k1)) * \
+            (np.exp(-k1 * curr_time) - np.exp(-k2 * curr_time))
+        F_conc = initial_F + initial_D * \
+            (1.0 + (k1 * np.exp(-k2 * curr_time) - k2 * np.exp(-k1 * curr_time)) / (k2 - k1))
+
+        assert np.isclose(concentrations["A"][0], A_conc, atol=10**-places)
+        assert np.isclose(concentrations["B"][0], B_conc, atol=10**-places)
+        assert np.isclose(concentrations["C"][0], C_conc, atol=10**-places)
+        assert np.isclose(concentrations["D"][0], D_conc, atol=10**-places)
+        assert np.isclose(concentrations["E"][0], E_conc, atol=10**-places)
+        assert np.isclose(concentrations["F"][0], F_conc, atol=10**-places)
+
+        curr_time += time_step
+
+
+def TestMultipleGridCell(solver, state, num_grid_cells, time_step, places=5):
+    concentrations = {
+        "A": [],
+        "B": [],
+        "C": [],
+        "D": [],
+        "E": [],
+        "F": []
+    }
+    rate_constants = {
+        "USER.reaction 1": [],
+        "USER.reaction 2": []
+    }
+    temperatures = []
+    pressures = []
+
+    for i in range(num_grid_cells):
+        temperatures.append(275.0 + random.uniform(-50.0, 50.0))
+        pressures.append(101253.3 + random.uniform(-500.0, 500.0))
+        concentrations["A"].append(0.75 + random.uniform(-0.05, 0.05))
+        concentrations["B"].append(0)
+        concentrations["C"].append(0.4 + random.uniform(-0.05, 0.05))
+        concentrations["D"].append(0.8 + random.uniform(-0.05, 0.05))
+        concentrations["E"].append(0)
+        concentrations["F"].append(0.1 + random.uniform(-0.05, 0.05))
+        rate_constants["USER.reaction 1"].append(
+            0.001 + random.uniform(-0.0001, 0.0001))
+        rate_constants["USER.reaction 2"].append(
+            0.002 + random.uniform(-0.0001, 0.0001))
+
+    state.set_conditions(temperatures, pressures)  # Air density should be calculated in the state
+    state.set_concentrations(concentrations)
+    state.set_user_defined_rate_parameters(rate_constants)
+
+    initial_concentrations = state.get_concentrations()
+    initial_rate_parameters = state.get_user_defined_rate_parameters()
+    initial_temperatures = state.get_conditions()["temperature"]
+    initial_pressures = state.get_conditions()["pressure"]
+    initial_air_density = state.get_conditions()["air_density"]
+
+    for i in range(num_grid_cells):
+        assert np.isclose(initial_concentrations["A"][i], concentrations["A"][i], atol=1e-13)
+        assert np.isclose(initial_concentrations["B"][i], concentrations["B"][i], atol=1e-13)
+        assert np.isclose(initial_concentrations["C"][i], concentrations["C"][i], atol=1e-13)
+        assert np.isclose(initial_concentrations["D"][i], concentrations["D"][i], atol=1e-13)
+        assert np.isclose(initial_concentrations["E"][i], concentrations["E"][i], atol=1e-13)
+        assert np.isclose(initial_concentrations["F"][i], concentrations["F"][i], atol=1e-13)
+        assert np.isclose(
+            initial_rate_parameters["USER.reaction 1"][i],
+            rate_constants["USER.reaction 1"][i],
+            atol=1e-13)
+        assert np.isclose(
+            initial_rate_parameters["USER.reaction 2"][i],
+            rate_constants["USER.reaction 2"][i],
+            atol=1e-13)
+        assert np.isclose(initial_temperatures[i], temperatures[i], atol=1e-13)
+        assert np.isclose(initial_pressures[i], pressures[i], atol=1e-13)
+        assert np.isclose(initial_air_density[i], pressures[i] / (8.31446261815324 * temperatures[i]), atol=1e-13)
+
+    time_step = 1
+    sim_length = 100
+
+    curr_time = time_step
+    initial_A = num_grid_cells * [0.0]
+    initial_C = num_grid_cells * [0.0]
+    initial_D = num_grid_cells * [0.0]
+    initial_F = num_grid_cells * [0.0]
+    for i in range(num_grid_cells):
+        initial_A[i] = initial_concentrations["A"][i]
+        initial_C[i] = initial_concentrations["C"][i]
+        initial_D[i] = initial_concentrations["D"][i]
+        initial_F[i] = initial_concentrations["F"][i]
+
+    k1 = num_grid_cells * [0.0]
+    k2 = num_grid_cells * [0.0]
+    k3 = num_grid_cells * [0.0]
+    k4 = num_grid_cells * [0.0]
+    for i in range(num_grid_cells):
+        k1[i] = rate_constants["USER.reaction 1"][i]
+        k2[i] = rate_constants["USER.reaction 2"][i]
+        k3[i] = 0.004 * np.exp(50.0 / temperatures[i])
+        k4[i] = 0.012 * np.exp(75.0 / temperatures[i]) * \
+            (temperatures[i] / 50.0)**(-2) * (1.0 + 1.0e-6 * pressures[i])
+
+    while curr_time <= sim_length:
+        solver.solve(state, time_step)
+        concentrations = state.get_concentrations()
+
+        for i in range(num_grid_cells):
+            A_conc = initial_A[i] * np.exp(-(k3[i]) * curr_time)
+            B_conc = initial_A[i] * (k3[i] / (k4[i] - k3[i])) * \
+                (np.exp(-k3[i] * curr_time) - np.exp(-k4[i] * curr_time))
+            C_conc = initial_C[i] + initial_A[i] * (1.0 + (
+                k3[i] * np.exp(-k4[i] * curr_time) - k4[i] * np.exp(-k3[i] * curr_time)) / (k4[i] - k3[i]))
+            D_conc = initial_D[i] * np.exp(-(k1[i]) * curr_time)
+            E_conc = initial_D[i] * (k1[i] / (k2[i] - k1[i])) * \
+                (np.exp(-k1[i] * curr_time) - np.exp(-k2[i] * curr_time))
+            F_conc = initial_F[i] + initial_D[i] * (1.0 + (
+                k1[i] * np.exp(-k2[i] * curr_time) - k2[i] * np.exp(-k1[i] * curr_time)) / (k2[i] - k1[i]))
+
+            assert np.isclose(
+                concentrations["A"][i],
+                A_conc,
+                atol=10**-places), f"Grid cell {i} of {num_grid_cells}: A concentration mismatch. Initial A: {initial_concentrations['A'][i]}"
+            assert np.isclose(
+                concentrations["B"][i],
+                B_conc,
+                atol=10**-places), f"Grid cell {i} of {num_grid_cells}: B concentration mismatch. Initial B: {initial_concentrations['B'][i]}"
+            assert np.isclose(
+                concentrations["C"][i],
+                C_conc,
+                atol=10**-places), f"Grid cell {i} of {num_grid_cells}: C concentration mismatch. Initial C: {initial_concentrations['C'][i]}"
+            assert np.isclose(
+                concentrations["D"][i],
+                D_conc,
+                atol=10**-places), f"Grid cell {i} of {num_grid_cells}: D concentration mismatch. Initial D: {initial_concentrations['D'][i]}"
+            assert np.isclose(
+                concentrations["E"][i],
+                E_conc,
+                atol=10**-places), f"Grid cell {i} of {num_grid_cells}: E concentration mismatch. Initial E: {initial_concentrations['E'][i]}"
+            assert np.isclose(
+                concentrations["F"][i],
+                F_conc,
+                atol=10**-places), f"Grid cell {i} of {num_grid_cells}: F concentration mismatch. Initial F: {initial_concentrations['F'][i]}"
+
+        curr_time += time_step
+
+
+def GetMechanism():
+    A = mc.Species(name="A")
+    B = mc.Species(name="B")
+    C = mc.Species(name="C")
+    D = mc.Species(name="D")
+    E = mc.Species(name="E")
+    F = mc.Species(name="F")
+    gas = mc.Phase(name="gas", species=[A, B, C, D, E, F])
+    arr1 = mc.Arrhenius(name="A->B", A=0.004, C=50,
+                        gas_phase=gas, reactants=[A], products=[B])
+    arr2 = mc.Arrhenius(name="B->C", A=0.012, B=-2, C=75, D=50, E=1.0e-6,
+                        gas_phase=gas, reactants=[B], products=[C])
+    user1 = mc.UserDefined(name="reaction 1", gas_phase=gas,
+                           reactants=[D], products=[E])
+    user2 = mc.UserDefined(name="reaction 2", gas_phase=gas,
+                           reactants=[E], products=[F])
+    mechanism = mc.Mechanism(
+        name="analytical test",
+        species=[A, B, C, D, E, F],
+        phases=[gas],
+        reactions=[arr1, arr2, user1, user2],
+    )
+    return mechanism
+
+
+def test_single_grid_cell_standard_rosenbrock():
+    solver = musica.MICM(
+        config_path="configs/v0/analytical",
+        solver_type=musica.SolverType.rosenbrock_standard_order)
+    state = solver.create_state()
+    TestSingleGridCell(solver, state, 200.0, 5)
+
+
+def test_multiple_grid_cells_standard_rosenbrock():
+    for i in range(1, 11):
+        solver = musica.MICM(
+            config_path="configs/v0/analytical",
+            solver_type=musica.SolverType.rosenbrock_standard_order)
+        state = solver.create_state(i)
+        TestMultipleGridCell(solver, state, i, 200.0, 5)
+
+
+def test_cuda_rosenbrock():
+    if is_cuda_available():
+        solver = musica.MICM(
+            config_path="configs/v0/analytical",
+            solver_type=musica.SolverType.cuda_rosenbrock)
+        state = solver.create_state()
+        TestSingleGridCell(solver, state, 200.0, 5)
+    else:
+        pytest.skip("CUDA is not available.")
+
+
+def test_single_grid_cell_backward_euler():
+    solver = musica.MICM(
+        config_path="configs/v0/analytical",
+        solver_type=musica.SolverType.backward_euler_standard_order)
+    state = solver.create_state()
+    TestSingleGridCell(solver, state, 10.0, places=2)
+
+
+def test_multiple_grid_cells_backward_euler():
+    for i in range(1, 11):
+        solver = musica.MICM(
+            config_path="configs/v0/analytical",
+            solver_type=musica.SolverType.backward_euler_standard_order)
+        state = solver.create_state(i)
+        TestMultipleGridCell(solver, state, i, 10.0, places=2)
+
+
+def test_single_grid_cell_rosenbrock():
+    solver = musica.MICM(
+        config_path="configs/v0/analytical",
+        solver_type=musica.SolverType.rosenbrock)
+    state = solver.create_state()
+    TestSingleGridCell(solver, state, 200.0, 5)
+
+
+def test_multiple_grid_cells_rosenbrock():
+    for i in range(1, 11):
+        solver = musica.MICM(
+            config_path="configs/v0/analytical",
+            solver_type=musica.SolverType.rosenbrock)
+        state = solver.create_state(i)
+        TestMultipleGridCell(solver, state, i, 200.0, 5)
+
+
+def test_single_grid_cell_backward_euler_standard_order():
+    solver = musica.MICM(
+        config_path="configs/v0/analytical",
+        solver_type=musica.SolverType.backward_euler_standard_order)
+    state = solver.create_state()
+    TestSingleGridCell(solver, state, 10.0, places=2)
+
+
+def test_multiple_grid_cells_backward_euler_standard_order():
+    for i in range(1, 11):
+        solver = musica.MICM(
+            config_path="configs/v0/analytical",
+            solver_type=musica.SolverType.backward_euler_standard_order)
+        state = solver.create_state(i)
+        TestMultipleGridCell(solver, state, i, 10.0, places=2)
+
+
+if __name__ == '__main__':
+    pytest.main()