paddle 1.1.4__py3-none-any.whl → 1.1.5__py3-none-any.whl

paddle/__init__.py

@@ -4,4 +4,4 @@ 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__ = "1.1.4"
+__version__ = "1.1.5"

paddle/nc2pt.py

@@ -0,0 +1,39 @@
+#! /usr/bin/env python3
+
+"""
+Read variables in a NetCDF file and write them to jit saved torch tensors.
+Usage: python nc2pt.py input.nc output.pt
+"""
+
+from netCDF4 import Dataset
+import torch
+
+
+def save_tensors(tensor_map: dict[str, torch.Tensor], filename: str):
+    class TensorModule(torch.nn.Module):
+        def __init__(self, tensors):
+            super().__init__()
+            for name, tensor in tensors.items():
+                self.register_buffer(name, tensor)
+
+    module = TensorModule(tensor_map)
+    scripted = torch.jit.script(module)  # Needed for LibTorch compatibility
+    scripted.save(filename)
+
+
+fname = "sod.out0.00019.nc"
+
+nc = Dataset(fname, "r")
+out_fname = "sod.out0.00019.pt"
+
+data = {}
+for varname in nc.variables:
+    var = nc.variables[varname][:]
+    if var.ndim == 4:  # (time, x1, x2, x3) -> (time, x3, x2, x1)
+        data[varname] = torch.tensor(var).permute(0, 3, 2, 1).squeeze()
+    elif var.ndim == 3:  # (x1, x2, x3) -> (x3, x2, x1)
+        data[varname] = torch.tensor(var).permute(2, 1, 0).squeeze()
+    else:
+        data[varname] = torch.tensor(var).squeeze()
+
+save_tensors(data, out_fname)

paddle/pt2nc.py

@@ -0,0 +1,124 @@
+#!/usr/bin/env python3
+"""
+Convert a sequence of PyTorch .pt dumps into a CF‐compliant NetCDF4 file
+with dimensions (time, x, y, z) plus a 'species' axis for mole fractions.
+"""
+
+import os
+import tarfile
+import re
+import torch
+import numpy as np
+from datetime import datetime
+from netCDF4 import Dataset
+
+# ──────────────────────────────── CONFIG ────────────────────────────────
+INPUT_DIR = "."
+OUTPUT_FILE = "thermo_x_xfrac_to_conc.nc"
+# ────────────────────────────────────────────────────────────────────────
+
+# find all .pt files, skip size==0, sort by timestamp
+pt_files = []
+for fn in os.listdir(INPUT_DIR):
+    if not fn.endswith(".pt"):
+        continue
+    full = os.path.join(INPUT_DIR, fn)
+    if os.path.getsize(full) == 0:
+        continue
+    # expect names like thermo_x_xfrac_to_conc_<epoch>.pt
+    m = re.search(r"(\d+)\.pt$", fn)
+    if not m:
+        continue
+    pt_files.append((int(m.group(1)), full))
+
+pt_files.sort(key=lambda x: x[0])
+times_epoch = [ts for ts, _ in pt_files]
+
+# load the first file to infer shapes
+module = torch.jit.load(pt_files[0][1])
+data = {name: param for name, param in module.named_parameters()}
+
+temp0 = data["temp"].numpy()
+pres0 = data["pres"].numpy()
+xfrac0 = data["xfrac"].numpy()
+nx3, nx2, nx1 = temp0.shape
+nspecies = xfrac0.shape[3]
+nt = len(pt_files)
+
+# pre‐allocate arrays in (time, x1, x2, x3) order
+temp_arr = np.empty((nt, nx1, nx2, nx3), dtype=temp0.dtype)
+pres_arr = np.empty((nt, nx1, nx2, nx3), dtype=pres0.dtype)
+xfrac_arr = np.empty((nspecies, nt, nx1, nx2, nx3), dtype=xfrac0.dtype)
+
+# load all timesteps
+for i, (_, path) in enumerate(pt_files):
+    module = torch.jit.load(path)
+    data = {name: param for name, param in module.named_parameters()}
+    t_np = data["temp"].numpy()  # (z, y, x)
+    p_np = data["pres"].numpy()  # (z, y, x)
+    x_np = data["xfrac"].numpy()  # (species, z, y, x)
+
+    # reorder to (x, y, z)
+    temp_arr[i] = t_np.transpose(2, 1, 0)
+    pres_arr[i] = p_np.transpose(2, 1, 0)
+    for j in range(nspecies):
+        xfrac_arr[j, i] = x_np[:, :, :, j].transpose(2, 1, 0)
+
+# create NetCDF4 file
+ds = Dataset(OUTPUT_FILE, "w", format="NETCDF4")
+
+# dimensions
+ds.createDimension("time", nt)
+ds.createDimension("x3", nx3)
+ds.createDimension("x2", nx2)
+ds.createDimension("x1", nx1)
+
+# coordinate variables
+tvar = ds.createVariable("time", "f4", ("time",))
+tvar.units = "seconds since 1970-01-01 00:00:00 UTC"
+tvar.calendar = "gregorian"
+tvar[:] = np.array(times_epoch, dtype="f4")
+
+zvar = ds.createVariable("x1", "f4", ("x1",))
+yvar = ds.createVariable("x2", "f4", ("x2",))
+xvar = ds.createVariable("x3", "f4", ("x3",))
+
+xvar.axis = "X"
+yvar.axis = "Y"
+zvar.axis = "Z"
+
+xvar[:] = np.arange(nx3)
+yvar[:] = np.arange(nx2)
+zvar[:] = np.arange(nx1)
+
+# data variables
+temp_v = ds.createVariable("temp", "f4", ("time", "x1", "x2", "x3"), zlib=True)
+temp_v.units = "K"
+temp_v.long_name = "temperature"
+
+pres_v = ds.createVariable("pres", "f4", ("time", "x1", "x2", "x3"), zlib=True)
+pres_v.units = "Pa"
+pres_v.long_name = "pressure"
+
+xfrac_v = []
+for i in range(nspecies):
+    xfrac_v.append(
+        ds.createVariable(f"xfrac{i}", "f4", ("time", "x1", "x2", "x3"), zlib=True)
+    )
+    xfrac_v[i].units = "1"
+    xfrac_v[i].long_name = "mole fraction of each species"
+
+# write the data
+temp_v[:] = temp_arr
+pres_v[:] = pres_arr
+for i in range(nspecies):
+    xfrac_v[i][:] = xfrac_arr[i]
+
+# global metadata
+ds.title = "Debug fields for thermo_x.xfrac_to_conc"
+ds.institution = "University of Michigan"
+ds.source = "converted from .pt files"
+ds.history = f"Created {datetime.utcnow().isoformat()}Z"
+
+ds.close()
+print(f"Converted file: {OUTPUT_FILE}")

paddle/setup_profile.py

@@ -140,7 +140,10 @@ def integrate_dry_adiabat(
 
 
 def setup_profile(
-    block: snapy.MeshBlock, param: dict[str, float] = {}, method: str = "moist-adiabat"
+    block: snapy.MeshBlock,
+    param: dict[str, float] = {},
+    method: str = "moist-adiabat",
+    verbose: bool = False,
 ) -> torch.Tensor:
     """
     Set up an adiabatic initial condition for the mesh block.
@@ -227,7 +230,7 @@ def setup_profile(
     dz = coord.buffer("dx1f")[ifirst]
 
     # half a grid to cell center
-    thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz / 2.0)
+    thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz / 2.0, verbose=verbose)
 
     # adiabatic extrapolation
     if method == "isothermal":
@@ -257,7 +260,7 @@ def setup_profile(
         elif method.split("-")[0] == "neutral":
             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, verbose=verbose)
 
         if torch.any(temp < Tmin):
             i_isothermal = i + 1

{paddle-1.1.4.dist-info → paddle-1.1.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: paddle
-Version: 1.1.4
+Version: 1.1.5
 Summary: Python Atmospheric Dynamics: Discovery and Learning about Exoplanets. An open-source, user-friendly python frontend of canoe
 Project-URL: Homepage, https://github.com/elijah-mullens/paddle
 Project-URL: Repository, https://github.com/elijah-mullens/paddle
@@ -22,8 +22,8 @@ Classifier: Topic :: Scientific/Engineering :: Astronomy
 Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.9
-Requires-Dist: kintera>=1.0.1
-Requires-Dist: snapy>=0.7.0
+Requires-Dist: kintera>=1.1.5
+Requires-Dist: snapy>=0.8.2
 Requires-Dist: torch<=2.7.1,>=2.7.0
 Provides-Extra: dev
 Requires-Dist: pytest>=7; extra == 'dev'
@@ -31,3 +31,52 @@ Description-Content-Type: text/markdown
 
 # paddle
 Python Atmospheric Dynamics: Discovering and Learning about Exoplanets. An open-source, user-friendly python version of canoe.
+
+## Install docker and docker-compose plugin
+
+
+## Create a python virtual environment
+```bash
+python -m venv pyenv
+```
+
+# Create a docker container
+```bash
+make up
+```
+
+# Terminate a docker container
+```bash
+make down
+```
+
+# Start a docker container
+```bash
+make start
+```
+
+# Build a new docker image (rarely used)
+```bash
+make build
+```
+
+## For Development
+### Cache your github credential
+```bash
+git config credential.helper 'cache --timeout=86400'
+```
+
+### Install paddle package
+```bash
+pip install paddle
+```
+
+### Install pre-commit hook
+```bash
+pip install pre-commit
+```
+
+### Install pre-commit hook
+```bash
+pre-commit install
+```

paddle-1.1.5.dist-info/RECORD

@@ -0,0 +1,13 @@
+paddle/__init__.py,sha256=McGNGlI-ofIhDsJdizgFYpkgJJwWMwg0oidCOPuXbgA,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/nc2pt.py,sha256=LXR0fnUTaOA_uaDsLU4YqdAVFyycB6SvRq12xWhHhLA,1136
+paddle/pt2nc.py,sha256=lLviBm6a2O05RvuPQc8DxV5pGr_VEhlSkrKPV1lQ3yU,3913
+paddle/setup_profile.py,sha256=oJpqPnlq2q1rn_l2flwgbdWwbxbhxx4QOYl4ezWmP-o,8803
+paddle/write_profile.py,sha256=HeBtGaFixGv8DnmJWPiQs-30RsdplSObhMA6ky6eVrg,3908
+paddle-1.1.5.dist-info/METADATA,sha256=e9bgxHKLY-fo1nTgZu2kYrK8toKqXHB4kAmm-Go48II,2197
+paddle-1.1.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+paddle-1.1.5.dist-info/entry_points.txt,sha256=pDR96GW6ylBZrbFd-tRGthW8qTuYaSLjrEt1LFIEYto,48
+paddle-1.1.5.dist-info/licenses/LICENSE,sha256=e6NthgKABUnLRqjuETcBGgsOuA-aJANpNoeXMe9RBso,1071
+paddle-1.1.5.dist-info/RECORD,,

paddle-1.1.4.dist-info/RECORD

@@ -1,11 +0,0 @@
-paddle/__init__.py,sha256=_UwSoQUWYoYGzcqdp5ES7q-Z1Dh-7nqkSOOFAl83BIA,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-1.1.4.dist-info/METADATA,sha256=MPjPtUaGGE4X9a6crnB1ktptBQvsD5n28Nz_mjEJfQY,1558
-paddle-1.1.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-paddle-1.1.4.dist-info/entry_points.txt,sha256=pDR96GW6ylBZrbFd-tRGthW8qTuYaSLjrEt1LFIEYto,48
-paddle-1.1.4.dist-info/licenses/LICENSE,sha256=e6NthgKABUnLRqjuETcBGgsOuA-aJANpNoeXMe9RBso,1071
-paddle-1.1.4.dist-info/RECORD,,