Merge pull request open-atmos#489 from slayoo/koehler_refactor

formulae refactors

.github/workflows/julia.yml

@@ -0,0 +1,25 @@
+name: PySDM-readme.jl
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  schedule:
+    - cron: '0 13 * * 4'
+
+jobs:
+  julia:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v1
+      - run: pip install -e .
+      - run: pip install exdown pytest
+      - run: python -c "import exdown; code=exdown.extract('README.md'); f=open('readme.jl', 'w'); f.writelines(block.code for block in code if block.syntax=='Julia'); f.close()"
+      - uses: julia-actions/setup-julia@v1
+      - run: julia readme.jl

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: Build Status
+name: PySDM
 
 defaults:
   run:
@@ -32,9 +32,14 @@ jobs:
       - run: |
           python -We -c "import PySDM"
 
+      # note: this installs PySDM-examples including its dependencies which inclde PySDM itself...
       - run: |
           pip install -r requirements.txt
 
+      # note: ... hence reverting to the currently tested version
+      - run: |
+          pip install -e .
+
       # TODO #184 (https://github.com/numba/numba/issues/6350#issuecomment-728174860)
       - if: matrix.platform == 'ubuntu-latest'
         env: 

.github/workflows/matlab.yml

@@ -0,0 +1,29 @@
+name: PySDM-readme.m
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  schedule:
+    - cron: '0 13 * * 4'
+
+jobs:
+  matlab:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+      - run: pip install -e .
+      - run: pip install exdown pytest
+      - run: python -c "import exdown; code=exdown.extract('README.md'); f=open('readme.m', 'w'); f.writelines(block.code for block in code if block.syntax=='Matlab'); f.close()"
+      - uses: matlab-actions/setup-matlab@v0
+      - uses: matlab-actions/run-command@v0
+        with:
+          command: readme

.github/workflows/python.yml

@@ -0,0 +1,24 @@
+name: PySDM-readme.py
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  schedule:
+    - cron: '0 13 * * 4'
+
+jobs:
+  python:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v1
+      - run: pip install -e .
+      - run: pip install exdown pytest
+      - run: python -c "import exdown; code=exdown.extract('README.md'); f=open('readme.py', 'w'); f.writelines(block.code for block in code if block.syntax=='Python'); f.close()"
+      - run: python readme.py

PySDM/attributes/chemistry/pH.py

@@ -1,5 +1,5 @@
 from PySDM.attributes.impl.intensive_attribute import DerivedAttribute
-from PySDM.dynamics.aqueous_chemistry.support import AQUEOUS_COMPOUNDS
+from PySDM.physics.aqueous_chemistry.support import AQUEOUS_COMPOUNDS
 
 
 class pH(DerivedAttribute):

PySDM/attributes/impl/attribute.py

@@ -12,6 +12,7 @@ def __init__(self, builder, name, dtype=float, size=0):
         self.dtype = dtype
         self.size = size
         self.name = name
+        self.formulae = self.core.formulae
 
     def allocate(self, idx):
         if self.size >= 1:

PySDM/attributes/impl/mapper.py

@@ -7,7 +7,7 @@
 from PySDM.attributes.physics.dry_volume import DryVolume
 from PySDM.attributes.physics.radius import Radius
 from PySDM.attributes.physics.dry_radius import DryRadius
-from PySDM.attributes.physics.terminal_velocity.terminal_velocity import TerminalVelocity
+from PySDM.attributes.physics.terminal_velocity import TerminalVelocity
 from PySDM.attributes.numerics.cell_id import CellID
 from PySDM.attributes.numerics.cell_origin import CellOrigin
 from PySDM.attributes.numerics.position_in_cell import PositionInCell
@@ -17,7 +17,7 @@
 from PySDM.attributes.chemistry.mole_amount import MoleAmount
 from PySDM.attributes.chemistry.concentration import Concentration
 from PySDM.attributes.chemistry.pH import pH
-from PySDM.dynamics.aqueous_chemistry.support import AQUEOUS_COMPOUNDS
+from PySDM.physics.aqueous_chemistry.support import AQUEOUS_COMPOUNDS
 
 attributes = {
     'n': Multiplicities,

PySDM/attributes/physics/critical_volume.py

@@ -3,22 +3,31 @@
 """
 
 from PySDM.attributes.impl.derived_attribute import DerivedAttribute
-from PySDM.physics import formulae as phys
+from PySDM.physics import constants as const
+import numpy as np
 
 
 class CriticalVolume(DerivedAttribute):
     def __init__(self, builder):
         self.cell_id = builder.get_attribute('cell id')
-        self.r_dry = builder.get_attribute('dry radius')
+        self.v_dry = builder.get_attribute('dry volume')
+        self.v_wet = builder.get_attribute('volume')
         self.environment = builder.core.environment
         self.particles = builder.core
-        dependencies = [self.r_dry, self.cell_id]
+        dependencies = [self.v_dry, self.v_wet, self.cell_id]
         super().__init__(builder, name='critical volume', dependencies=dependencies)
 
     def recalculate(self):
         kappa = self.particles.dynamics['Condensation'].kappa
-        r_d = self.r_dry.get().data
+        v_dry = self.v_dry.get().data
+        v_wet = self.v_wet.get().data
         T = self.environment['T'].data
         cell = self.cell_id.get().data
         for i in range(len(self.data)):  # TODO #347 move to backend
-            self.data.data[i] = phys.volume(phys.r_cr(kp=kappa, rd=r_d[i], T=T[cell[i]]))
+            sigma = self.formulae.surface_tension.sigma(T[cell[i]], v_wet[i], v_dry[i])
+            self.data.data[i] = self.formulae.trivia.volume(self.formulae.hygroscopicity.r_cr(
+                kp=kappa,
+                rd3=v_dry[i] / const.pi_4_3,
+                T=T[cell[i]],
+                sgm=sigma
+            ))

PySDM/attributes/physics/dry_radius.py

@@ -3,7 +3,7 @@
 """
 
 from PySDM.attributes.impl.derived_attribute import DerivedAttribute
-from PySDM.physics.formulae import volume
+from PySDM.physics import constants as const
 
 
 class DryRadius(DerivedAttribute):
@@ -14,5 +14,5 @@ def __init__(self, builder):
 
     def recalculate(self):
         self.data.idx = self.volume_dry.data.idx
-        self.data.product(self.volume_dry.get(), 1/volume(1))
+        self.data.product(self.volume_dry.get(), 1/const.pi_4_3)
         self.data **= 1/3

PySDM/attributes/physics/radius.py

@@ -6,7 +6,7 @@
 """
 
 from PySDM.attributes.impl.derived_attribute import DerivedAttribute
-from PySDM.physics.formulae import volume
+from PySDM.physics import constants as const
 
 
 class Radius(DerivedAttribute):
@@ -17,5 +17,5 @@ def __init__(self, builder):
 
     def recalculate(self):
         self.data.idx = self.volume.data.idx
-        self.data.product(self.volume.get(), 1/volume(1))
+        self.data.product(self.volume.get(), 1/const.pi_4_3)
         self.data **= 1/3

PySDM/attributes/physics/terminal_velocity/terminal_velocity.py → PySDM/attributes/physics/terminal_velocity.py

@@ -3,7 +3,7 @@
 """
 
 from PySDM.attributes.impl.derived_attribute import DerivedAttribute
-from .gunn_and_kinzer import Interpolation
+from PySDM.physics.terminal_velocity.gunn_and_kinzer import Interpolation
 
 
 class TerminalVelocity(DerivedAttribute):

PySDM/backends/__init__.py

@@ -39,7 +39,7 @@ def cuda_is_available():
 if cuda_is_available() or cuda.is_available():
     from .thrustRTC.thrustRTC import ThrustRTC
 else:
-    from .thrustRTC.fakeThrustRTC import _flag
+    from .thrustRTC.test_helpers import _flag
 
     _flag.fakeThrustRTC = True
 
@@ -49,9 +49,8 @@ def cuda_is_available():
     ThrustRTC.ENABLE = False
 
     class Random:
-        def __init__(self, size, seed=None):
+        def __init__(self, size, seed):
             self.size = size
-            seed = seed or np.random.randint(0, 2 * 16)
             self.generator = np.random.default_rng(seed)
 
         def __call__(self, storage):