musica 0.12.2__cp313-cp313-win_amd64.whl → 0.13.0__cp313-cp313-win_amd64.whl

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

@@ -1,295 +1,196 @@
----
 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
+  - name: A
+    molecular weight [kg mol-1]: 0.02897
+    __absolute tolerance: 1.0e-30
+  - name: B
+    constant concentration [mol m-3]: 1.0e19
+  - name: C
+    constant mixing ratio [mol mol-1]: 1.0e-20
+  - name: M
+    is third body: true
+  - name: H2O2
+    molecular weight [kg mol-1]: 0.0340147
+    __absolute tolerance: 1.0e-10
+  - name: ethanol
+    molecular weight [kg mol-1]: 0.04607
+    __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
+  - name: gas
+    species:
+      - name: A
+        diffusion coefficient [m2 s-1]: 1.0
+      - name: B
+      - name: C
+      - name: ethanol
+      - name: H2O2
 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"
+  - type: EMISSION
+    name: my emission
+    scaling factor: 12.3
+    gas phase: gas
+    products:
+      - species name: B
+        coefficient: 1
+    __irrelevant: 2
+  - type: FIRST_ORDER_LOSS
+    name: my first order loss
+    scaling factor: 12.3
+    gas phase: gas
+    reactants:
+      - species name: C
+        coefficient: 1
+    __irrelevant: 2
+  - type: PHOTOLYSIS
+    name: photo B
+    scaling factor: 12.3
+    gas phase: gas
+    reactants:
+      - species name: B
+        coefficient: 1
+    products:
+      - species name: C
+        coefficient: 1
+    __irrelevant: 2
+  - type: SURFACE
+    name: my surface
+    reaction probability: 2.0e-2
+    gas phase: gas
+    gas-phase species: A
+    gas-phase products:
+      - species name: B
+        coefficient: 1
+      - species name: C
+        coefficient: 1
+    __irrelevant: 2
+  - type: TROE
+    name: my troe
+    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
+    gas phase: gas
+    reactants:
+      - species name: B
+        coefficient: 1
+      - species name: M
+        coefficient: 1
+    products:
+      - species name: C
+        coefficient: 1
+    __irrelevant: 2
+  - type: TERNARY_CHEMICAL_ACTIVATION
+    name: my ternary chemical activation
+    gas phase: gas
+    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
+    reactants:
+      - species name: B
+        coefficient: 1
+      - species name: M
+        coefficient: 1
+    products:
+      - species name: C
+        coefficient: 1
+    __irrelevant: 2
+  - type: BRANCHED_NO_RO2
+    name: my branched
+    X: 1.2e-4
+    Y: 167
+    a0: 0.15
+    n: 9
+    gas phase: gas
+    reactants:
+      - species name: A
+        coefficient: 1
+    alkoxy products:
+      - species name: B
+        coefficient: 1
+    nitrate products:
+      - species name: C
+        coefficient: 1
+    __irrelevant: 2
+  - type: TUNNELING
+    name: my tunneling
+    A: 123.45
+    B: 1200.0
+    C: 1.0e8
+    gas phase: gas
+    reactants:
+      - species name: B
+        coefficient: 1
+    products:
+      - species name: C
+        coefficient: 1
+    __irrelevant: 2
+  - type: ARRHENIUS
+    name: my arrhenius
+    gas phase: gas
+    A: 32.1
+    B: -2.3
+    C: 102.3
+    D: 63.4
+    E: -1.3
+    reactants:
+      - species name: B
+        coefficient: 1
+    products:
+      - species name: C
+        coefficient: 1
+    __irrelevant: 2
+  - type: ARRHENIUS
+    name: my other arrhenius
+    A: 29.3
+    B: -1.5
+    Ea: 101.2
+    D: 82.6
+    E: -0.98
+    gas phase: gas
+    reactants:
+      - species name: A
+        coefficient: 1
+    products:
+      - species name: B
+        coefficient: 1.2
+  - type: USER_DEFINED
+    name: my user defined
+    scaling factor: 12.3
+    gas phase: gas
+    reactants:
+      - species name: A
+        coefficient: 1
+      - species name: B
+        coefficient: 1
+    products:
+      - species name: C
+        coefficient: 1.3
+    __irrelevant: 2
+  - type: TAYLOR_SERIES
+    name: my taylor series
+    A: 12.3
+    B: -1.5
+    C: 1.0e-6
+    D: 340.0
+    E: 0.00032
+    taylor coefficients:
+      - 1.0
+      - 0.1
+      - -0.01
+    gas phase: gas
+    reactants:
+      - species name: B
+        coefficient: 1
+    products:
+      - species name: C
+        coefficient: 1

musica/test/integration/test_chapman.py

@@ -73,8 +73,8 @@ def TestSolve(solver):
 
 
 def GetMechanism():
-    M = mc.Species(tracer_type="THIRD_BODY")
-    O2 = mc.Species(name="O2", tracer_type="CONSTANT")
+    M = mc.Species(is_third_body=True)
+    O2 = mc.Species(name="O2")
     O = mc.Species(name="O", other_properties={
                    "__absolute_tolerance": "1e-12"})
     O1D = mc.Species(name="O1D", other_properties={

musica/test/integration/test_tuvx.py

@@ -18,19 +18,64 @@ def test_full_tuvx(monkeypatch):
     tuvx = musica.TUVX(file)
     assert tuvx is not None
 
-    heating_rates = tuvx.heating_rate_names
-    photolysis_rates = tuvx.photolysis_rate_names
-    rates = tuvx.run()
+    photolysis_rates, heating_rates, dose_rates = tuvx.run()
+
+    assert len(tuvx.heating_rate_names) == 0, "Heating rate names should be empty for this config"
+    assert len(tuvx.photolysis_rate_names) > 0, "No photolysis rate names found"
+    assert len(tuvx.dose_rate_names) > 0, "No dose rate names found"
+    assert len(heating_rates) == 2, "Number of solar zenith angles should be 2 for heating rates"
+    assert len(photolysis_rates) == 2, "Number of solar zenith angles should be 2 for photolysis rates"
+    assert len(dose_rates) == 2, "Number of solar zenith angles should be 2 for dose rates"
+    assert heating_rates.shape[1] == 121, "Number of layers should be 121 for heating rates"
+    assert photolysis_rates.shape[1] == 121, "Number of layers should be 121 for photolysis rates"
+    assert dose_rates.shape[1] == 121, "Number of layers should be 121 for dose rates"
+    assert heating_rates.shape[2] == 0, "Should be no heating rates for this config"
+    assert photolysis_rates.shape[2] == len(tuvx.photolysis_rate_names), "Photolysis rates shape mismatch"
+    assert dose_rates.shape[2] == len(tuvx.dose_rate_names), "Dose rates shape mismatch"
+
+
+def test_fixed_tuvx_from_file(monkeypatch):
+    monkeypatch.chdir("src")
+    file = "test/data/tuvx/fixed/config.json"
+    tuvx = musica.TUVX(config_path=file)
+    assert tuvx is not None
+
+    # Access properties multiple times
+    photolysis_names_1 = tuvx.photolysis_rate_names
+    photolysis_names_2 = tuvx.photolysis_rate_names
+    heating_names_1 = tuvx.heating_rate_names
+    heating_names_2 = tuvx.heating_rate_names
+    dose_names_1 = tuvx.dose_rate_names
+    dose_names_2 = tuvx.dose_rate_names
 
-    assert len(rates) > 0, "No photolysis rates found"
-    assert len(heating_rates) == 0, "Heating rates should be empty for this config"
-    assert len(photolysis_rates) > 0, "No photolysis rates found"
+    # Verify they return the same object (cached)
+    assert photolysis_names_1 is photolysis_names_2
+    assert heating_names_1 is heating_names_2
+    assert dose_names_1 is dose_names_2
+
+    assert len(photolysis_names_1) == 3, "Unexpected number of photolysis rates found"
+    assert len(heating_names_1) == 2, "Unexpected number of heating rates found"
+    assert len(dose_names_1) == 3, "Unexpected number of dose rates found"
+
+    photolysis_rates, heating_rates, dose_rates = tuvx.run()
 
+    assert len(photolysis_rates) == 5, "Unexpected number of solar zenith angles for photolysis rates"
+    assert len(heating_rates) == 5, "Unexpected number of solar zenith angles for heating rates"
+    assert len(dose_rates) == 5, "Unexpected number of solar zenith angles for dose rates"
+    assert photolysis_rates.shape[1] == 4, "Unexpected number of layers for photolysis rates"
+    assert heating_rates.shape[1] == 4, "Unexpected number of layers for heating rates"
+    assert dose_rates.shape[1] == 4, "Unexpected number of layers for dose rates"
+    assert photolysis_rates.shape[2] == len(photolysis_names_1), "Photolysis rates shape mismatch"
+    assert heating_rates.shape[2] == len(heating_names_1), "Heating rates shape mismatch"
+    assert dose_rates.shape[2] == len(dose_names_1), "Dose rates shape mismatch"
 
-def test_fixed_tuvx(monkeypatch):
+
+def test_fixed_tuvx_from_string(monkeypatch):
     monkeypatch.chdir("src")
     file = "test/data/tuvx/fixed/config.json"
-    tuvx = musica.TUVX(file)
+    with open(file, 'r') as f:
+        config_str = f.read()
+    tuvx = musica.TUVX(config_string=config_str)
     assert tuvx is not None
 
     # Access properties multiple times
@@ -38,17 +83,29 @@ def test_fixed_tuvx(monkeypatch):
     photolysis_names_2 = tuvx.photolysis_rate_names
     heating_names_1 = tuvx.heating_rate_names
     heating_names_2 = tuvx.heating_rate_names
+    dose_names_1 = tuvx.dose_rate_names
+    dose_names_2 = tuvx.dose_rate_names
 
     # Verify they return the same object (cached)
     assert photolysis_names_1 is photolysis_names_2
     assert heating_names_1 is heating_names_2
-
-    assert len(heating_names_1) > 0, "No heating rates found"
-    assert len(photolysis_names_1) > 0, "No photolysis rates found"
-
-    # these fail to run due to missing solar zenith angle, but that's not required and these should be able to run
-    # rates = tuvx.run()
-    # print(f"Rates: {rates}")
+    assert dose_names_1 is dose_names_2
+
+    assert len(photolysis_names_1) == 3, "Unexpected number of photolysis rates found"
+    assert len(heating_names_1) == 2, "Unexpected number of heating rates found"
+    assert len(dose_names_1) == 3, "Unexpected number of dose rates found"
+
+    photolysis_rates, heating_rates, dose_rates = tuvx.run()
+
+    assert len(photolysis_rates) == 5, "Unexpected number of solar zenith angles for photolysis rates"
+    assert len(heating_rates) == 5, "Unexpected number of solar zenith angles for heating rates"
+    assert len(dose_rates) == 5, "Unexpected number of solar zenith angles for dose rates"
+    assert photolysis_rates.shape[1] == 4, "Unexpected number of layers for photolysis rates"
+    assert heating_rates.shape[1] == 4, "Unexpected number of layers for heating rates"
+    assert dose_rates.shape[1] == 4, "Unexpected number of layers for dose rates"
+    assert photolysis_rates.shape[2] == len(photolysis_names_1), "Photolysis rates shape mismatch"
+    assert heating_rates.shape[2] == len(heating_names_1), "Heating rates shape mismatch"
+    assert dose_rates.shape[2] == len(dose_names_1), "Dose rates shape mismatch"
 
 
 def test_tuvx_initialization_errors():