paddle 1.1.1__py3-none-any.whl → 1.1.3__py3-none-any.whl

paddle/__init__.py

@@ -3,8 +3,5 @@ from .write_profile import write_profile
 from .find_init_params import find_init_params
 from .evolve_kinetics import evolve_kinetics
 
-__all__ = ["setup_profile",
-           "write_profile",
-           "find_init_params",
-           "evolve_kinetics"]
-__version__ = "1.1.1"
+__all__ = ["setup_profile", "write_profile", "find_init_params", "evolve_kinetics"]
+__version__ = "1.1.3"

paddle/crm.py

@@ -4,20 +4,20 @@ import time
 import kintera
 import numpy as np
 from snapy import (
-        index,
-        MeshBlockOptions,
-        MeshBlock,
-        OutputOptions,
-        NetcdfOutput,
-        )
+    index,
+    MeshBlockOptions,
+    MeshBlock,
+    OutputOptions,
+    NetcdfOutput,
+)
 from kintera import (
-        ThermoOptions,
-        ThermoX,
-        KineticsOptions,
-        Kinetics,
-        )
+    ThermoOptions,
+    ThermoX,
+    KineticsOptions,
+    Kinetics,
+)
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # input file
     infile = "earth.yaml"
     device = "cpu"
@@ -46,7 +46,7 @@ if __name__ == '__main__':
 
     # set up initial condition
     w = setup_initial_condition(block, thermo_x)
-    print("w = ", w[:,0,0,:])
+    print("w = ", w[:, 0, 0, :])
 
     # integration
     current_time = 0.0
@@ -70,7 +70,7 @@ if __name__ == '__main__':
             block.forward(dt, stage)
 
         # evolve kinetics
-        u[index.icy:] += evolve_kinetics(block, kinet, thermo_x)
+        u[index.icy :] += evolve_kinetics(block, kinet, thermo_x)
 
         current_time += dt
         count += 1

paddle/evolve_kinetics.py

@@ -2,12 +2,14 @@ import torch
 import snapy
 import kintera
 
+
 def evolve_kinetics(
     hydro_w: torch.Tensor,
-    block: snapy.MeshBlock, 
-    kinet: kintera.Kinetics, 
+    block: snapy.MeshBlock,
+    kinet: kintera.Kinetics,
     thermo_x: kintera.ThermoX,
-    dt) -> torch.Tensor:
+    dt,
+) -> torch.Tensor:
     """
     Evolve the chemical kinetics for one time step using implicit method.
 
@@ -26,7 +28,7 @@ def evolve_kinetics(
 
     temp = eos.compute("W->T", (hydro_w,))
     pres = hydro_w[snapy.index.ipr]
-    xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy:],))
+    xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy :],))
     conc = thermo_x.compute("TPX->V", (temp, pres, xfrac))
     cp_vol = thermo_x.compute("TV->cp", (temp, conc))
 

paddle/find_init_params.py

@@ -4,16 +4,18 @@ import numpy as np
 
 from .setup_profile import setup_profile
 
+
 def find_init_params(
-        block: snapy.MeshBlock,
-        param: dict[str, float],
-        *,
-        target_T: float=300.,
-        target_P: float=1.e5, 
-        method: str="moist-adiabat",
-        max_iter: int=50,
-        ftol: float=1.e-2,
-        verbose: bool=True):
+    block: snapy.MeshBlock,
+    param: dict[str, float],
+    *,
+    target_T: float = 300.0,
+    target_P: float = 1.0e5,
+    method: str = "moist-adiabat",
+    max_iter: int = 50,
+    ftol: float = 1.0e-2,
+    verbose: bool = True,
+):
     """Find initial parameters that yield desired T and P
 
     Args:
@@ -44,14 +46,15 @@ def find_init_params(
         temp = eos.compute("W->T", (w,)).squeeze()
 
         # calculate 1D pressure
-        pres = w[snapy.index.ipr,...].squeeze()
+        pres = w[snapy.index.ipr, ...].squeeze()
 
         # temperature function
         t_func = interp1d(
             pres.log().cpu().numpy(),
             temp.log().cpu().numpy(),
             kind="linear",
-            fill_value="extrapolate")
+            fill_value="extrapolate",
+        )
 
         temp1 = np.exp(t_func(np.log(target_P)))
         if verbose:
@@ -69,4 +72,3 @@ def find_init_params(
         count += 1
 
     raise RuntimeError("Failed to converge within the maximum number of iterations.")
-

paddle/setup_profile.py

@@ -4,18 +4,19 @@ import torch
 import snapy
 import kintera
 
+
 def integrate_neutral(
-        thermo_x: kintera.ThermoX,
-        temp: torch.Tensor,
-        pres: torch.Tensor,
-        xfrac: torch.Tensor,
-        grav: float,
-        dz: float,
-        max_iter: int = 100
-        ) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
+    thermo_x: kintera.ThermoX,
+    temp: torch.Tensor,
+    pres: torch.Tensor,
+    xfrac: torch.Tensor,
+    grav: float,
+    dz: float,
+    max_iter: int = 100,
+) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
     """
     A neutral density profile assumes no cloud and:
-        
+
         (1) dP/dz = -rho*g
         (2) d(rho)/dz = ...
 
@@ -68,15 +69,16 @@ def integrate_neutral(
 
     return temp2, pres2, xfrac2
 
+
 def integrate_dry_adiabat(
-        thermo_x: kintera.ThermoX,
-        temp: torch.Tensor,
-        pres: torch.Tensor,
-        xfrac: torch.Tensor,
-        grav: float,
-        dz: float,
-        max_iter: int = 100
-        ) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
+    thermo_x: kintera.ThermoX,
+    temp: torch.Tensor,
+    pres: torch.Tensor,
+    xfrac: torch.Tensor,
+    grav: float,
+    dz: float,
+    max_iter: int = 100,
+) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
     """
     A dry adiabatic profile assumes no cloud and:
 
@@ -84,12 +86,12 @@ def integrate_dry_adiabat(
         (2) dP/dz = -rho*g
 
     In discretized form:
-    
+
         cp_bar = 0.5 * (cp(T_old) + cp(T_new))
         T_new = T_old - g/bar * dz
         rho_bar = 0.5 * (rho_old + rho_new)
         P_new = P_old - rho_bar * g * dz
-        
+
     """
     conc1 = thermo_x.compute("TPX->V", [temp, pres, xfrac])
     cp1 = thermo_x.compute("TV->cp", [temp, conc1]) / conc1.sum(-1)
@@ -136,11 +138,10 @@ def integrate_dry_adiabat(
 
     return temp2, pres2, xfrac2
 
+
 def setup_profile(
-        block: snapy.MeshBlock,
-        param: dict[str, float] = {},
-        method: str = "moist-adiabat"
-        ) -> torch.Tensor:
+    block: snapy.MeshBlock, param: dict[str, float] = {}, method: str = "moist-adiabat"
+) -> torch.Tensor:
     """
     Set up an adiabatic initial condition for the mesh block.
 
@@ -175,16 +176,16 @@ def setup_profile(
         "moist-adiabat",
         "isothermal",
         "pseudo-adiabat",
-        "neutral"
+        "neutral",
     ]
 
     if method not in valid_methods:
         raise ValueError(f"Invalid method '{method}'. Choose from {valid_methods}.")
 
-    Ts = param.get("Ts", 300.)
-    Ps = param.get("Ps", 1.e5)
+    Ts = param.get("Ts", 300.0)
+    Ps = param.get("Ps", 1.0e5)
     grav = param.get("grav", 9.8)
-    Tmin = param.get("Tmin", 0.)
+    Tmin = param.get("Tmin", 0.0)
 
     # get handles to modules
     coord = block.module("hydro.coord")
@@ -204,8 +205,7 @@ def setup_profile(
     ny = len(thermo_y.options.species()) - 1
     nvar = 5 + ny
 
-    w = torch.zeros((nvar, nc3, nc2, nc1),
-                    dtype=x1v.dtype, device=x1v.device)
+    w = torch.zeros((nvar, nc3, nc2, nc1), dtype=x1v.dtype, device=x1v.device)
 
     temp = Ts * torch.ones((nc3, nc2), dtype=w.dtype, device=w.device)
     pres = Ps * torch.ones((nc3, nc2), dtype=w.dtype, device=w.device)
@@ -216,7 +216,7 @@ def setup_profile(
         xfrac[..., index] = param.get(f"x{name}", 0.0)
 
     # dry air mole fraction
-    xfrac[..., 0] = 1. - xfrac[..., 1:].sum(dim=-1)
+    xfrac[..., 0] = 1.0 - xfrac[..., 1:].sum(dim=-1)
 
     # start and end indices for the vertical direction
     # excluding ghost cells
@@ -227,7 +227,7 @@ def setup_profile(
     dz = coord.buffer("dx1f")[ifirst]
 
     # half a grid to cell center
-    thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz / 2.);
+    thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz / 2.0)
 
     # adiabatic extrapolation
     if method == "isothermal":
@@ -245,17 +245,19 @@ def setup_profile(
             xfrac /= xfrac.sum(dim=-1, keepdim=True)
         conc = thermo_x.compute("TPX->V", [temp, pres, xfrac])
 
-        w[snapy.index.ipr, ..., i] = pres;
+        w[snapy.index.ipr, ..., i] = pres
         w[snapy.index.idn, ..., i] = thermo_x.compute("V->D", [conc])
-        w[snapy.index.icy:, ...,i] = thermo_x.compute("X->Y", [xfrac])
+        w[snapy.index.icy :, ..., i] = thermo_x.compute("X->Y", [xfrac])
 
         dz = coord.buffer("dx1f")[i]
         if method.split("-")[0] == "dry":
-            temp, pres, xfrac = integrate_dry_adiabat(thermo_x, temp, pres, xfrac, grav, dz);
+            temp, pres, xfrac = integrate_dry_adiabat(
+                thermo_x, temp, pres, xfrac, grav, dz
+            )
         elif method.split("-")[0] == "neutral":
-            temp, pres, xfrac = integrate_neutral(thermo_x, temp, pres, xfrac, grav, dz);
+            temp, pres, xfrac = integrate_neutral(thermo_x, temp, pres, xfrac, grav, dz)
         else:
-            thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz);
+            thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz)
 
         if torch.any(temp < Tmin):
             i_isothermal = i + 1
@@ -276,5 +278,5 @@ def setup_profile(
         conc = thermo_x.compute("TPX->V", [temp, pres, xfrac])
         w[snapy.index.ipr, ..., i] = pres
         w[snapy.index.idn, ..., i] = thermo_x.compute("V->D", [conc])
-        w[snapy.index.icy:, ..., i] = thermo_x.compute("X->Y", [xfrac])
+        w[snapy.index.icy :, ..., i] = thermo_x.compute("X->Y", [xfrac])
     return w

paddle/write_profile.py

@@ -7,11 +7,12 @@ import torch
 import kintera
 import snapy
 
+
 def write_profile(
     filename: str,
     hydro_w: torch.Tensor,
     block: snapy.MeshBlock,
-    ref_pressure: float = 1.e5,
+    ref_pressure: float = 1.0e5,
     comment: Optional[str] = None,
 ) -> None:
     """
@@ -46,27 +47,28 @@ def write_profile(
         raise ValueError("hydro_w must have shape (N, 1, 1, L).")
 
     # calculate a height grid
-    pres = hydro_w[snapy.index.ipr,...].squeeze() / 1.e5  # Pa -> bar
+    pres = hydro_w[snapy.index.ipr, ...].squeeze() / 1.0e5  # Pa -> bar
     zlev_func = interp1d(
         pres.log().cpu().numpy(),
         coord.buffer("x1v").cpu().numpy(),
         kind="linear",
-        fill_value="extrapolate")
-    zref = zlev_func(np.log(ref_pressure / 1.e5))
-    zlev = (coord.buffer("x1v") - zref) / 1.e3  # m -> km
+        fill_value="extrapolate",
+    )
+    zref = zlev_func(np.log(ref_pressure / 1.0e5))
+    zlev = (coord.buffer("x1v") - zref) / 1.0e3  # m -> km
 
     # calculate temperature
     temp = eos.compute("W->T", (hydro_w,)).squeeze()
 
     # calculate mole fractions
-    xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy:,...],)).squeeze()
+    xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy :, ...],)).squeeze()
 
     # calculate heat capacity
-    conc = thermo_x.compute("TPX->V", (temp, pres * 1.e5, xfrac))
+    conc = thermo_x.compute("TPX->V", (temp, pres * 1.0e5, xfrac))
     cpx = thermo_x.compute("TV->cp", (temp, conc)) / conc.sum(-1)
 
     # calculate entropy
-    ens = thermo_x.compute("TPV->S", (temp, pres * 1.e5, conc)) / conc.sum(-1)
+    ens = thermo_x.compute("TPV->S", (temp, pres * 1.0e5, conc)) / conc.sum(-1)
 
     with open(filename, "w") as f:
         # write comments

{paddle-1.1.1.dist-info → paddle-1.1.3.dist-info}/METADATA

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: paddle
-Version: 1.1.1
+Version: 1.1.3
 Summary: Canoe's utility subroutines
-Project-URL: Homepage, https://github.com/chengcli/paddle
-Project-URL: Repository, https://github.com/chengcli/paddle
-Project-URL: Issues, https://github.com/chengcli/paddle/issues
-Author-email: Cheng Li <chengcli@umich.edu>
+Project-URL: Homepage, https://github.com/elijah-mullens/paddle
+Project-URL: Repository, https://github.com/elijah-mullens/paddle
+Project-URL: Issues, https://github.com/elijah-mullens/paddle/issues
+Author-email: Cheng Li <chengcli@umich.edu>, Elijah Mullens <eem85@cornell.edu>
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research

paddle-1.1.3.dist-info/RECORD

@@ -0,0 +1,10 @@
+paddle/__init__.py,sha256=ET6AzrpqJmUJwj-U9TlCjybszSFCS_EMwAxRYP5ljj8,281
+paddle/crm.py,sha256=HwOLAojR5LBcptqjAC9APEJiWpn8GhxPiAmvvIZ4mTM,1986
+paddle/evolve_kinetics.py,sha256=OWt1-SiLTzaWUCIchwRnBHCjbtcgJIIxrlQ5Lk4iN8c,1541
+paddle/find_init_params.py,sha256=dyRmo-LTwVohbPhSH5LV45jL_XeRmNEcuKPvafBklto,2516
+paddle/setup_profile.py,sha256=MHxRvFyva8CR5_71QSfrLy9ml2rQnW6yy21ZXaVcTGU,8733
+paddle/write_profile.py,sha256=HeBtGaFixGv8DnmJWPiQs-30RsdplSObhMA6ky6eVrg,3908
+paddle-1.1.3.dist-info/METADATA,sha256=7TVy7Gm0xgfNpXc-7pWoXUQ72URw25owBJOyCoxVtd0,1394
+paddle-1.1.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+paddle-1.1.3.dist-info/entry_points.txt,sha256=pDR96GW6ylBZrbFd-tRGthW8qTuYaSLjrEt1LFIEYto,48
+paddle-1.1.3.dist-info/RECORD,,

paddle/data/saturn1d.yaml

@@ -1,88 +0,0 @@
-# Saturn Reference Atmosphere Model
-# 
-# Solar abundances relative to H2, enrichments
-#
-# X_He  = 0.195, 0.6955
-# X_CH4 = 5.50e-04, 9.4
-# X_H2O = 1.026e-03, 10.0
-# X_NH3 = 1.352e-04, 3.0
-# X_H2S = 3.10e-05,  3.0
-#
-# Converted to mole fractions
-#
-# X_H2O = 8.91e-03
-# X_NH3 = 3.52e-04
-# X_H2S = 8.08e-05
-#
-# Dry air composition
-#
-# 0.86838 * H2 + 0.11778 * He + 4.49e-03 * CH4
-# {H: 1.755, He: 0.118, C: 4.49e-03}
-
-reference-state:
-  Tref: 0.
-  Pref: 1.e5
-
-species:
-  - name: dry
-    composition: {H: 1.755, He: 0.118, C: 4.49e-03}
-    cv_R: 2.5
-
-  - name: H2O
-    composition: {H: 2, O: 1}
-    cv_R: 2.5
-    u0_R: 0.
-
-  - name: NH3
-    composition: {H: 2, O: 1}
-    cv_R: 2.5
-    u0_R: 0.
-
-  - name: H2S
-    composition: {H: 2, S: 1}
-    cv_R: 2.5
-    u0_R: 0.
-
-  - name: H2O(l)
-    composition: {H: 2, O: 1}
-    cv_R: 9.0
-    u0_R: -3430.
-
-  - name: NH3(s)
-    composition: {H: 2, O: 1}
-    cv_R: 9.0
-    u0_R: -5520.
-
-  - name: NH4SH(s)
-    composition: {N: 1, H: 5, S: 1}
-    cv_R: 9.0
-    u0_R: -1.2e4
-
-geometry:
-  type: cartesian
-  bounds: {x1min: 0., x1max: 600.e3, x2min: -0.5, x2max: 0.5, x3min: -0.5, x3max: 0.5}
-  cells: {nx1: 200, nx2: 1, nx3: 1, nghost: 0}
-
-dynamics:
-  equation-of-state:
-    type: moist-mixture
-    max-iter: 20
-    ftol: 1.e-6
-
-reactions:
-  - equation: H2O => H2O(l)
-    type: nucleation
-    rate-constant: {formula: h2o_ideal}
-
-  - equation: NH3 => NH3(s)
-    type: nucleation
-    rate-constant: {formula: nh3_ideal}
-
-  - equation: NH3 + H2S <=> NH4SH(s)
-    type: nucleation
-    rate-constant: {formula: nh3_h2s_lewis}
-
-boundary-condition:
-  external:
-    x1-inner: reflecting
-    x1-outer: reflecting

paddle-1.1.1.dist-info/RECORD

@@ -1,11 +0,0 @@
-paddle/__init__.py,sha256=7L9UltY-Uy_Xp_4lc3nhYMinleWBlN4fU-Yztxfw9ko,314
-paddle/crm.py,sha256=LXuvOINJE_d6skKu5wU--LVR2CLnI8N5FP5blatM04s,2034
-paddle/evolve_kinetics.py,sha256=ZuUc8eFDBUVhCFTbft__0vM0mmPolUpys1Nde8_MbwE,1539
-paddle/find_init_params.py,sha256=iEc-NyBlDlGY6k9wfjYqgqU9hMPklp_7YEjvMnEp57M,2525
-paddle/setup_profile.py,sha256=goyafLBjCVJhwe_Kk4GcrCceT-fcBpo_UHwFOqKOiY8,8834
-paddle/write_profile.py,sha256=3PECXsvGzvJvZfKMTdm49nNj61ZCgf488KoCL3ayB_s,3892
-paddle/data/saturn1d.yaml,sha256=07JvsjBGg004TdrhLZOjPZ3m0CYlEhB7fz98Iv1dEGE,1635
-paddle-1.1.1.dist-info/METADATA,sha256=qLhZzHLAxEgfL4aENwcZ8UYK1GamcuW0z1jzt-fy8FE,1340
-paddle-1.1.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-paddle-1.1.1.dist-info/entry_points.txt,sha256=pDR96GW6ylBZrbFd-tRGthW8qTuYaSLjrEt1LFIEYto,48
-paddle-1.1.1.dist-info/RECORD,,