PySDM 2.47__tar.gz → 2.49__tar.gz

{PySDM-2.47 → PySDM-2.49}/.appveyor.yml

@@ -4,7 +4,7 @@ branches:
 environment:
   matrix:
   - platform: x86
-  - platform: x64
+#  - platform: x64
   
 build: false
 

{PySDM-2.47 → PySDM-2.49}/.github/workflows/tests+artifacts+pypi.yml

@@ -53,6 +53,7 @@ jobs:
       with:
         fail_ci_if_error: true
         verbose: true
+        token: ${{ secrets.CODECOV_TOKEN }}
 
   pdoc:
     strategy:

{PySDM-2.47 → PySDM-2.49}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.47
+Version: 2.49
 Summary: Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors
@@ -332,14 +332,15 @@ Description: # PySDM
         <summary>Julia (click to expand)</summary>
         
         ```Julia
-        rho_w = pyimport("PySDM.physics.constants_defaults").rho_w
         using Plots; plotlyjs()
         
         for step = 0:1200:3600
             particulator.run(step - particulator.n_steps)
             plot!(
                 radius_bins_edges[1:end-1] / si.um,
-                particulator.products["dv/dlnr"].get()[:] * rho_w / si.g,
+                particulator.formulae.particle_shape_and_density.volume_to_mass(
+                    particulator.products["dv/dlnr"].get()[:]
+                )/ si.g,
                 linetype=:steppost,
                 xaxis=:log,
                 xlabel="particle radius [µm]",
@@ -354,12 +355,12 @@ Description: # PySDM
         <summary>Matlab (click to expand)</summary>
         
         ```Matlab
-        rho_w = py.importlib.import_module('PySDM.physics.constants_defaults').rho_w;
-        
         for step = 0:1200:3600
             particulator.run(int32(step - particulator.n_steps));
             x = radius_bins_edges / si.um;
-            y = particulator.products{"dv/dlnr"}.get() * rho_w / si.g;
+            y = particulator.formulae.particle_shape_and_density.volume_to_mass( ...
+                particulator.products{"dv/dlnr"}.get() ...
+            ) / si.g;
             stairs(...
                 x(1:end-1), ... 
                 double(py.array.array('d',py.numpy.nditer(y))), ...
@@ -378,14 +379,17 @@ Description: # PySDM
         <summary>Python (click to expand)</summary>
         
         ```Python
-        from PySDM.physics.constants_defaults import rho_w
         from matplotlib import pyplot
         
         for step in [0, 1200, 2400, 3600]:
             particulator.run(step - particulator.n_steps)
-            pyplot.step(x=radius_bins_edges[:-1] / si.um,
-                        y=particulator.products['dv/dlnr'].get()[0] * rho_w / si.g,
-                        where='post', label=f"t = {step}s")
+            pyplot.step(
+                x=radius_bins_edges[:-1] / si.um,
+                y=particulator.formulae.particle_shape_and_density.volume_to_mass(
+                    particulator.products['dv/dlnr'].get()[0]
+                ) / si.g,
+                where='post', label=f"t = {step}s"
+            )
         
         pyplot.xscale('log')
         pyplot.xlabel('particle radius [µm]')

{PySDM-2.47 → PySDM-2.49}/PySDM/backends/impl_numba/storage.py

@@ -120,7 +120,7 @@ class Storage(StorageBase):
     @staticmethod
     def _get_empty_data(shape, dtype):
         if dtype in (float, Storage.FLOAT):
-            data = np.full(shape, -1.0, dtype=Storage.FLOAT)
+            data = np.full(shape, np.nan, dtype=Storage.FLOAT)
             dtype = Storage.FLOAT
         elif dtype in (int, Storage.INT):
             data = np.full(shape, -1, dtype=Storage.INT)

{PySDM-2.47 → PySDM-2.49}/PySDM/backends/impl_thrust_rtc/test_helpers/fake_thrust_rtc.py

@@ -145,7 +145,9 @@ class FakeThrustRTC:  # pylint: disable=too-many-public-methods
             dtype = np.bool_
         else:
             raise NotImplementedError(f"Unsupported type {elem_cls}")
-        result = np.empty(size, dtype=dtype)
+        result = np.full(
+            size, np.nan if elem_cls in ("float", "double") else -666, dtype=dtype
+        )
         return FakeThrustRTC.DVVector(result)
 
     @staticmethod

{PySDM-2.47 → PySDM-2.49}/PySDM/dynamics/collisions/breakup_fragmentations/straub2010.py

@@ -79,7 +79,7 @@ class Straub2010Nf(VolumeBasedFragmentationFunction):
         self.arrays["gam"].divide_if_not_zero(self.arrays["tmp"])
 
         for key in ("Nr1", "Nr2", "Nr3", "Nr4", "Nrt"):
-            self.straub_tmp[key] *= 0.0
+            self.straub_tmp[key].fill(0)
 
         self.particulator.backend.straub_fragmentation(
             n_fragment=nf,

{PySDM-2.47 → PySDM-2.49}/PySDM/environments/parcel.py

@@ -71,6 +71,7 @@ class Parcel(Moist):  # pylint: disable=too-many-instance-attributes
         self["z"][:] = params[3]
         self["t"][:] = params[4]
 
+        self._tmp["water_vapour_mixing_ratio"][:] = params[0]
         self.sync_parcel_vars()
         Moist.sync(self)
         self.notify()

{PySDM-2.47 → PySDM-2.49}/PySDM/formulae.py

@@ -83,7 +83,9 @@ class Formulae:  # pylint: disable=too-few-public-methods,too-many-instance-attr
         self.air_dynamic_viscosity = air_dynamic_viscosity
 
         self._components = tuple(
-            i for i in dir(self) if not i.startswith("__") and i != "flatten"
+            i
+            for i in dir(self)
+            if not i.startswith("__") and i not in ("flatten", "get_constant")
         )
 
         constants_defaults = {
@@ -161,6 +163,11 @@ class Formulae:  # pylint: disable=too-few-public-methods,too-many-instance-attr
             functions[attr] = getattr(self, attr)
         return namedtuple("FlattenedFormulae", functions.keys())(**functions)
 
+    def get_constant(self, key: str):
+        """getter-like method for cases where using the `constants` named tuple is not possible
+        (e.g., if calling from a language which does not support named tuples)"""
+        return getattr(self.constants, key)
+
 
 def _formula(func, constants, dimensional_analysis, **kw):
     parameters_keys = tuple(inspect.signature(func).parameters.keys())

{PySDM-2.47 → PySDM-2.49}/PySDM/physics/constants_defaults.py

@@ -38,6 +38,7 @@ Md = (
 )
 
 # https://web.archive.org/web/20200729203147/https://nucleus.iaea.org/rpst/documents/VSMOW_SLAP.pdf
+# heavy-to-light isotope abundance ratios
 VSMOW_R_2H = 155.76 * PPM
 VSMOW_R_3H = 1.85e-11 * PPM
 VSMOW_R_18O = 2005.20 * PPM
@@ -53,19 +54,6 @@ M_16O = 15.99491461957 * si.g / si.mole
 M_17O = 16.99913175651 * si.g / si.mole
 M_18O = 17.99915961287 * si.g / si.mole
 
-Mv = (
-    1
-    - Trivia.mixing_ratio_to_specific_content(
-        VSMOW_R_2H / 2 + VSMOW_R_3H / 2 + VSMOW_R_17O + VSMOW_R_18O
-    )
-) * (
-    (M_1H * 2 + M_16O)
-    + (M_2H + M_1H + M_16O) * VSMOW_R_2H
-    + (M_3H + M_1H + M_16O) * VSMOW_R_3H
-    + (M_1H * 2 + M_17O) * VSMOW_R_17O
-    + (M_1H * 2 + M_18O) * VSMOW_R_18O
-)
-
 R_str = sci.R * si.joule / si.kelvin / si.mole
 N_A = sci.N_A / si.mole
 
@@ -356,6 +344,39 @@ FROESSLING_1938_B = 0.276
 
 
 def compute_derived_values(c: dict):
+    """
+    computes derived quantities such as molar mass ratios, etc.
+
+    water molar mass is computed from from molecular masses and VSMOW isotope abundances
+    (and neglecting molecular binding energies)
+    for discussion, see:
+    - caption of Table 2.1 in [Gat 2010](https://doi.org/10.1142/p027)
+    - [IAPWS Guidelines](http://www.iapws.org/relguide/fundam.pdf)
+    """
+
+    c["Mv"] = (
+        (
+            1
+            - 2 * Trivia.mixing_ratio_to_specific_content(c["VSMOW_R_2H"])
+            - 2 * Trivia.mixing_ratio_to_specific_content(c["VSMOW_R_3H"])
+            - 1 * Trivia.mixing_ratio_to_specific_content(c["VSMOW_R_17O"])
+            - 1 * Trivia.mixing_ratio_to_specific_content(c["VSMOW_R_18O"])
+        )
+        * (c["M_1H"] * 2 + c["M_16O"])
+        + 2
+        * Trivia.mixing_ratio_to_specific_content(c["VSMOW_R_2H"])
+        * (c["M_2H"] + c["M_1H"] + c["M_16O"])
+        + 2
+        * Trivia.mixing_ratio_to_specific_content(c["VSMOW_R_3H"])
+        * (c["M_3H"] + c["M_1H"] + c["M_16O"])
+        + 1
+        * Trivia.mixing_ratio_to_specific_content(c["VSMOW_R_17O"])
+        * (c["M_1H"] * 2 + c["M_17O"])
+        + 1
+        * Trivia.mixing_ratio_to_specific_content(c["VSMOW_R_18O"])
+        * (c["M_1H"] * 2 + c["M_18O"])
+    )
+
     c["eps"] = c["Mv"] / c["Md"]
     c["Rd"] = c["R_str"] / c["Md"]
     c["Rv"] = c["R_str"] / c["Mv"]

PySDM-2.49/PySDM/products/size_spectral/arbitrary_moment.py

@@ -0,0 +1,79 @@
+"""
+factory for arbitrary-moment product classes
+"""
+
+from PySDM.products.impl.moment_product import MomentProduct
+
+
+def make_arbitrary_moment_product(**kwargs):
+    """returns a product class to be instantiated and passed to a builder"""
+    for arg in kwargs:
+        assert arg in (
+            "rank",
+            "attr",
+            "attr_unit",
+            "skip_division_by_m0",
+            "skip_division_by_dv",
+        )
+
+    class ArbitraryMoment(MomentProduct):
+        def __init__(
+            self,
+            name=None,
+            unit=f"({kwargs['attr_unit']})**{kwargs['rank']}"
+            + ("" if kwargs["skip_division_by_dv"] else " / m**3"),
+        ):
+            super().__init__(name=name, unit=unit)
+
+        def _impl(self, **_):
+            self._download_moment_to_buffer(
+                attr=kwargs["attr"],
+                rank=kwargs["rank"],
+                skip_division_by_m0=kwargs["skip_division_by_m0"],
+            )
+            if not kwargs["skip_division_by_dv"]:
+                self.buffer /= self.particulator.mesh.dv
+            return self.buffer
+
+    return ArbitraryMoment
+
+
+ZerothMoment = make_arbitrary_moment_product(
+    rank=0,
+    attr="volume",
+    attr_unit="m^3",
+    skip_division_by_m0=True,
+    skip_division_by_dv=True,
+)
+
+VolumeFirstMoment = make_arbitrary_moment_product(
+    rank=1,
+    attr="volume",
+    attr_unit="m^3",
+    skip_division_by_m0=True,
+    skip_division_by_dv=True,
+)
+
+VolumeSecondMoment = make_arbitrary_moment_product(
+    rank=2,
+    attr="volume",
+    attr_unit="m^3",
+    skip_division_by_m0=True,
+    skip_division_by_dv=True,
+)
+
+RadiusSixthMoment = make_arbitrary_moment_product(
+    rank=6,
+    attr="radius",
+    attr_unit="m",
+    skip_division_by_m0=True,
+    skip_division_by_dv=True,
+)
+
+RadiusFirstMoment = make_arbitrary_moment_product(
+    rank=1,
+    attr="radius",
+    attr_unit="m",
+    skip_division_by_m0=True,
+    skip_division_by_dv=True,
+)

{PySDM-2.47 → PySDM-2.49}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.47
+Version: 2.49
 Summary: Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors
@@ -332,14 +332,15 @@ Description: # PySDM
         <summary>Julia (click to expand)</summary>
         
         ```Julia
-        rho_w = pyimport("PySDM.physics.constants_defaults").rho_w
         using Plots; plotlyjs()
         
         for step = 0:1200:3600
             particulator.run(step - particulator.n_steps)
             plot!(
                 radius_bins_edges[1:end-1] / si.um,
-                particulator.products["dv/dlnr"].get()[:] * rho_w / si.g,
+                particulator.formulae.particle_shape_and_density.volume_to_mass(
+                    particulator.products["dv/dlnr"].get()[:]
+                )/ si.g,
                 linetype=:steppost,
                 xaxis=:log,
                 xlabel="particle radius [µm]",
@@ -354,12 +355,12 @@ Description: # PySDM
         <summary>Matlab (click to expand)</summary>
         
         ```Matlab
-        rho_w = py.importlib.import_module('PySDM.physics.constants_defaults').rho_w;
-        
         for step = 0:1200:3600
             particulator.run(int32(step - particulator.n_steps));
             x = radius_bins_edges / si.um;
-            y = particulator.products{"dv/dlnr"}.get() * rho_w / si.g;
+            y = particulator.formulae.particle_shape_and_density.volume_to_mass( ...
+                particulator.products{"dv/dlnr"}.get() ...
+            ) / si.g;
             stairs(...
                 x(1:end-1), ... 
                 double(py.array.array('d',py.numpy.nditer(y))), ...
@@ -378,14 +379,17 @@ Description: # PySDM
         <summary>Python (click to expand)</summary>
         
         ```Python
-        from PySDM.physics.constants_defaults import rho_w
         from matplotlib import pyplot
         
         for step in [0, 1200, 2400, 3600]:
             particulator.run(step - particulator.n_steps)
-            pyplot.step(x=radius_bins_edges[:-1] / si.um,
-                        y=particulator.products['dv/dlnr'].get()[0] * rho_w / si.g,
-                        where='post', label=f"t = {step}s")
+            pyplot.step(
+                x=radius_bins_edges[:-1] / si.um,
+                y=particulator.formulae.particle_shape_and_density.volume_to_mass(
+                    particulator.products['dv/dlnr'].get()[0]
+                ) / si.g,
+                where='post', label=f"t = {step}s"
+            )
         
         pyplot.xscale('log')
         pyplot.xlabel('particle radius [µm]')

{PySDM-2.47 → PySDM-2.49}/PySDM.egg-info/SOURCES.txt

@@ -800,6 +800,7 @@ tests/unit_tests/physics/test_trivia.py
 tests/unit_tests/physics/test_ventilation_coefficient.py
 tests/unit_tests/products/__init__.py
 tests/unit_tests/products/test_ambient_relative_humidity.py
+tests/unit_tests/products/test_arbitrary_moment.py
 tests/unit_tests/products/test_averaged_terminal_velocity.py
 tests/unit_tests/products/test_collision_rates.py
 tests/unit_tests/products/test_concentration_product.py

{PySDM-2.47 → PySDM-2.49}/PySDM.egg-info/requires.txt

@@ -11,7 +11,7 @@ pyevtk
 matplotlib
 pytest
 pytest-timeout
-PyPartMC==1.1.2
+PyPartMC==1.1.3
 pyrcel
 jupyter-core<5.0.0
 ipywidgets!=8.0.3

{PySDM-2.47 → PySDM-2.49}/README.md

@@ -321,14 +321,15 @@ In the listing below, its usage is interleaved with plotting logic
 <summary>Julia (click to expand)</summary>
 
 ```Julia
-rho_w = pyimport("PySDM.physics.constants_defaults").rho_w
 using Plots; plotlyjs()
 
 for step = 0:1200:3600
     particulator.run(step - particulator.n_steps)
     plot!(
         radius_bins_edges[1:end-1] / si.um,
-        particulator.products["dv/dlnr"].get()[:] * rho_w / si.g,
+        particulator.formulae.particle_shape_and_density.volume_to_mass(
+            particulator.products["dv/dlnr"].get()[:]
+        )/ si.g,
         linetype=:steppost,
         xaxis=:log,
         xlabel="particle radius [µm]",
@@ -343,12 +344,12 @@ savefig("plot.svg")
 <summary>Matlab (click to expand)</summary>
 
 ```Matlab
-rho_w = py.importlib.import_module('PySDM.physics.constants_defaults').rho_w;
-
 for step = 0:1200:3600
     particulator.run(int32(step - particulator.n_steps));
     x = radius_bins_edges / si.um;
-    y = particulator.products{"dv/dlnr"}.get() * rho_w / si.g;
+    y = particulator.formulae.particle_shape_and_density.volume_to_mass( ...
+        particulator.products{"dv/dlnr"}.get() ...
+    ) / si.g;
     stairs(...
         x(1:end-1), ... 
         double(py.array.array('d',py.numpy.nditer(y))), ...
@@ -367,14 +368,17 @@ legend()
 <summary>Python (click to expand)</summary>
 
 ```Python
-from PySDM.physics.constants_defaults import rho_w
 from matplotlib import pyplot
 
 for step in [0, 1200, 2400, 3600]:
     particulator.run(step - particulator.n_steps)
-    pyplot.step(x=radius_bins_edges[:-1] / si.um,
-                y=particulator.products['dv/dlnr'].get()[0] * rho_w / si.g,
-                where='post', label=f"t = {step}s")
+    pyplot.step(
+        x=radius_bins_edges[:-1] / si.um,
+        y=particulator.formulae.particle_shape_and_density.volume_to_mass(
+            particulator.products['dv/dlnr'].get()[0]
+        ) / si.g,
+        where='post', label=f"t = {step}s"
+    )
 
 pyplot.xscale('log')
 pyplot.xlabel('particle radius [µm]')

{PySDM-2.47 → PySDM-2.49}/examples/PySDM_examples/Bieli_et_al_2022/simulation.py

@@ -26,8 +26,14 @@ def make_core(settings, coal_eff):
         adaptive=settings.adaptive,
     )
     builder.add_dynamic(collision)
-    M0 = am.make_arbitrary_moment_product(rank=0, attr="volume", attr_unit="m^3")
-    M1 = am.make_arbitrary_moment_product(rank=1, attr="volume", attr_unit="m^3")
-    M2 = am.make_arbitrary_moment_product(rank=2, attr="volume", attr_unit="m^3")
-    products = (M0(name="M0"), M1(name="M1"), M2(name="M2"))
+    common_args = {
+        "attr": "volume",
+        "attr_unit": "m^3",
+        "skip_division_by_m0": True,
+        "skip_division_by_dv": True,
+    }
+    products = tuple(
+        am.make_arbitrary_moment_product(rank=rank, **common_args)(name=f"M{rank}")
+        for rank in range(3)
+    )
     return builder.build(attributes, products)

{PySDM-2.47 → PySDM-2.49}/examples/PySDM_examples/Jensen_and_Nugent_2017/settings.py

@@ -3,15 +3,19 @@ from PySDM import Formulae
 from PySDM.physics import si
 from PySDM.initialisation.spectra import Lognormal, Sum
 
+INITIAL_RELATIVE_HUMIDITY = 0.8561
+INITIAL_TEMPERATURE = 284.3 * si.K
+INITIAL_PRESSURE = 938.5 * si.hPa
+INITIAL_ALTITUDE = 600 * si.metres
+
 
 @strict
 class Settings:
     def __init__(self, *, aerosol: str, cloud_type: str):
-        # TODO #1266 reuse these values in the Yang et al. '18 example which is based on J&N'16
-        self.p0 = 938.5 * si.hPa
-        self.RH0 = 0.8561
-        self.T0 = 284.3 * si.K
-        self.z0 = 600 * si.m
+        self.p0 = INITIAL_PRESSURE
+        self.RH0 = INITIAL_RELATIVE_HUMIDITY
+        self.T0 = INITIAL_TEMPERATURE
+        self.z0 = INITIAL_ALTITUDE
         self.t_end_of_ascent = 1500 * si.s if cloud_type == "Sc" else None
         self.dt = 1 * si.s  # TODO #1266: not found in the paper yet