paddle 1.1.8__tar.gz → 1.1.10__tar.gz

{paddle-1.1.8 → paddle-1.1.10}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.8
+current_version = 1.1.10
 commit = True
 tag = True
 

{paddle-1.1.8 → paddle-1.1.10}/.gitignore

@@ -208,3 +208,9 @@ __marimo__/
 
 # docker
 docker-compose.override.yaml
+
+# netcdf outputs
+*.nc
+
+# restart outputs
+*.restart

{paddle-1.1.8 → paddle-1.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: paddle
-Version: 1.1.8
+Version: 1.1.10
 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

paddle-1.1.10/docker-compose.override.yaml.tmp

@@ -0,0 +1,6 @@
+services:
+  dev:
+    volumes:
+      # This is your main working directory
+      # (lhs:rhs, lhs = workspace on physical machine : rhs = virtual machine)
+      - path_to_physical_directory/paddle_docker_workspace:/paddle_docker_workspace

{paddle-1.1.8 → paddle-1.1.10}/docker-compose.yaml

@@ -13,7 +13,7 @@ services:
       - USER_GID=${USER_GID}
     # This is volatile
     # Make sure that you use override.yaml for permanent changes
-    working_dir: /work
+    working_dir: /paddle_docker_workspace
     tty: true
     stdin_open: true
     ports:

{paddle-1.1.8 → paddle-1.1.10}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "paddle"
-version = "1.1.8"
+version = "1.1.10"
 description = "Python Atmospheric Dynamics: Discovery and Learning about Exoplanets. An open-source, user-friendly python frontend of canoe"
 readme = "README.md"
 requires-python = ">=3.9"

{paddle-1.1.8 → paddle-1.1.10}/src/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__ = "1.1.8"
+__version__ = "1.1.10"

paddle-1.1.10/tests/robert.py

@@ -0,0 +1,102 @@
+import torch
+import math
+import time
+from snapy import MeshBlockOptions, MeshBlock
+from snapy import kIDN, kIPR
+
+
+def call_user_output(bvars):
+    hydro_w = bvars["hydro_w"]
+    out = {}
+    temp = hydro_w[kIPR] / (Rd * hydro_w[kIDN])
+    out["temp"] = temp
+    out["theta"] = temp * (p0 / hydro_w[kIPR]).pow(Rd / cp)
+    return out
+
+
+dT = 0.5
+p0 = 1.0e5
+Ts = 303.15
+xc = 500.0
+yc = 0.0
+zc = 260.0
+s = 100.0
+a = 50.0
+grav = 9.8
+Rd = 287.0
+gamma = 1.4
+uniform_bubble = False
+
+# use cuda if available
+if torch.cuda.is_available():
+    device = torch.device("cuda:0")
+else:
+    device = torch.device("cpu")
+
+# set hydrodynamic options
+op = MeshBlockOptions.from_yaml("robert.yaml")
+block = MeshBlock(op)
+block.to(device)
+
+# get handles to modules
+coord = block.module("hydro.coord")
+thermo = block.module("hydro.eos.thermo")
+
+# thermodynamics
+cp = gamma / (gamma - 1.0) * Rd
+
+# set initial condition
+x3v, x2v, x1v = torch.meshgrid(
+    coord.buffer("x3v"), coord.buffer("x2v"), coord.buffer("x1v"), indexing="ij"
+)
+
+# dimensions
+nc3 = coord.buffer("x3v").shape[0]
+nc2 = coord.buffer("x2v").shape[0]
+nc1 = coord.buffer("x1v").shape[0]
+nvar = 5
+
+w = torch.zeros((nvar, nc3, nc2, nc1), device=device)
+
+temp = Ts - grav * x1v / cp
+w[kIPR] = p0 * torch.pow(temp / Ts, cp / Rd)
+
+r = torch.sqrt((x3v - yc) ** 2 + (x2v - xc) ** 2 + (x1v - zc) ** 2)
+temp += torch.where(r <= a, dT * torch.pow(w[kIPR] / p0, Rd / cp), 0.0)
+if not uniform_bubble:
+    temp += torch.where(
+        r > a,
+        dT * torch.exp(-(((r - a) / s) ** 2)) * torch.pow(w[kIPR] / p0, Rd / cp),
+        0.0,
+    )
+w[kIDN] = w[kIPR] / (Rd * temp)
+
+block_vars = {}
+block_vars["hydro_w"] = w
+block_vars = block.initialize(block_vars)
+
+block.set_user_output_func(call_user_output)
+
+# integration
+start_time = time.time()
+current_time = 0.0
+block.make_outputs(block_vars, current_time)
+
+while not block.intg.stop(block.inc_cycle(), current_time):
+    dt = block.max_time_step(block_vars)
+    block.print_cycle_info(block_vars, current_time, dt)
+
+    for stage in range(len(block.intg.stages)):
+        block.forward(block_vars, dt, stage)
+
+    err = block.check_redo(block_vars)
+    if err > 0:
+        continue  # redo current step
+    if err < 0:
+        break  # terminate
+
+    current_time += dt
+    block.make_outputs(block_vars, current_time)
+
+block.finalize(block_vars, current_time)
+print("elapsed time = ", time.time() - start_time)

paddle-1.1.10/tests/robert.yaml

@@ -0,0 +1,64 @@
+reference-state:
+  Tref: 0.
+  Pref: 1.e5
+
+species:
+  - name: dry
+    composition: {O: 0.42, N: 1.56, Ar: 0.01}
+    cv_R: 2.5
+
+geometry:
+  type: cartesian
+  bounds: {x1min: 0., x1max: 1.5e3, x2min: 0., x2max: 1.e3, x3min: -0.5, x3max: 0.5}
+  cells: {nx1: 300, nx2: 200, nx3: 1, nghost: 3}
+
+dynamics:
+  equation-of-state:
+    type: ideal-gas
+    density-floor:  1.e-10
+    pressure-floor: 1.e-10
+    limiter: false
+
+  vertical-projection:
+    type: temperature
+    pressure-margin: 1.e-6
+
+  reconstruct:
+    vertical: {type: weno5, scale: false, shock: true}
+    horizontal: {type: weno5, scale: false, shock: true}
+
+  riemann-solver:
+    type: lmars
+
+boundary-condition:
+  internal:
+    solid-density: 1.e3
+    solid-pressure: 1.9
+    max-iter: 5
+
+  external:
+    x1-inner: reflecting
+    x1-outer: reflecting
+    x2-inner: reflecting
+    x2-outer: reflecting
+    x3-inner: reflecting
+    x3-outer: reflecting
+
+integration:
+  type: rk3
+  cfl: 0.9
+  implicit-scheme: 0
+  nlim: -1
+  tlim: 1080
+  ncycle_out: 10
+
+forcing:
+  const-gravity:
+    grav1: -9.8
+
+outputs:
+  - type: restart
+    dt: 300.
+  - type: netcdf
+    variables: [prim, uov]
+    dt: 30.

paddle-1.1.10/tests/shock.py

@@ -0,0 +1,67 @@
+import torch
+from snapy import MeshBlockOptions, MeshBlock
+from snapy import kIDN, kIPR, kIV1, kIV2, kIV3
+
+# use cuda if available
+if torch.cuda.is_available():
+    device = torch.device("cuda:0")
+else:
+    device = torch.device("cpu")
+
+# set hydrodynamic model
+op = MeshBlockOptions.from_yaml("shock.yaml")
+
+# initialize block
+block = MeshBlock(op)
+block.to(device)
+
+# get handles to modules
+coord = block.hydro.module("coord")
+
+# set initial condition
+x3v, x2v, x1v = torch.meshgrid(
+    coord.buffer("x3v"), coord.buffer("x2v"), coord.buffer("x1v"), indexing="ij"
+)
+
+# dimensions
+nc3 = coord.buffer("x3v").shape[0]
+nc2 = coord.buffer("x2v").shape[0]
+nc1 = coord.buffer("x1v").shape[0]
+nvar = 5
+
+w = torch.zeros((nvar, nc3, nc2, nc1), device=device)
+
+w[kIDN] = torch.where(x1v < 0.0, 1.0, 0.125)
+w[kIPR] = torch.where(x1v < 0.0, 1.0, 0.1)
+w[kIV1] = w[kIV2] = w[kIV3] = 0.0
+
+# internal boundary
+r1 = torch.sqrt(x1v * x1v + x2v * x2v + x3v * x3v)
+solid = torch.where(r1 < 0.1, 1, 0).to(torch.bool)
+
+block_vars = {}
+block_vars["hydro_w"] = w
+block_vars["solid"] = solid
+block_vars = block.initialize(block_vars)
+
+# integration
+current_time = 0.0
+block.make_outputs(block_vars, current_time)
+
+while not block.intg.stop(block.inc_cycle(), current_time):
+    dt = block.max_time_step(block_vars)
+    block.print_cycle_info(block_vars, current_time, dt)
+
+    for stage in range(len(block.intg.stages)):
+        block.forward(block_vars, dt, stage)
+
+    err = block.check_redo(block_vars)
+    if err > 0:
+        continue  # redo current step
+    if err < 0:
+        break  # terminate
+
+    current_time += dt
+    block.make_outputs(block_vars, current_time)
+
+block.finalize(block_vars, current_time)

paddle-1.1.10/tests/shock.yaml

@@ -0,0 +1,60 @@
+reference-state:
+  Tref: 0.
+  Pref: 1.e5
+
+species:
+  - name: dry
+    composition: {O: 0.42, N: 1.56, Ar: 0.01}
+    cv_R: 2.5
+
+geometry:
+  type: cartesian
+  bounds: {x1min: -0.5, x1max: 0.5, x2min: -0.5, x2max: 0.5, x3min: -0.5, x3max: 0.5}
+  cells: {nx1: 256, nx2: 256, nx3: 1, nghost: 3}
+
+dynamics:
+  equation-of-state:
+    type: ideal-gas
+    density-floor:  1.e-10
+    pressure-floor: 1.e-10
+    limiter: false
+
+  vertical-projection:
+    type: none
+    pressure-margin: 1.e-6
+
+  reconstruct:
+    vertical: {type: weno5, scale: false, shock: true}
+    horizontal: {type: weno5, scale: false, shock: true}
+
+  riemann-solver:
+    type: hllc
+
+boundary-condition:
+  internal:
+    solid-density: 1.e3
+    solid-pressure: 1.e9
+    max-iter: 5
+
+  external:
+    x1-inner: outflow
+    x1-outer: outflow
+    x2-inner: outflow
+    x2-outer: outflow
+    x3-inner: outflow
+    x3-outer: outflow
+
+integration:
+  type: rk3
+  cfl: 0.9
+  implicit-scheme: 0
+  nlim: 200
+  tlim: 1.0
+  ncycle_out: 10
+
+outputs:
+  - type: restart
+    dt: 0.1
+  - type: netcdf
+    variables: [prim]
+    dt: 0.01

paddle-1.1.10/tests/straka.py

@@ -0,0 +1,101 @@
+import torch
+import math
+import time
+import kintera
+from snapy import MeshBlockOptions, MeshBlock
+from snapy import kIDN, kIPR
+
+
+def call_user_output(bvars):
+    hydro_w = bvars["hydro_w"]
+    out = {}
+    temp = hydro_w[kIPR] / (Rd * hydro_w[kIDN])
+    out["temp"] = temp
+    out["theta"] = temp * (p0 / hydro_w[kIPR]).pow(Rd / cp)
+    return out
+
+
+p0 = 1.0e5
+Ts = 300.0
+xc = 0.0
+xr = 4.0e3
+zc = 3.0e3
+zr = 2.0e3
+dT = -15.0
+grav = 9.8
+Rd = 287.0
+gamma = 1.4
+K = 75.0
+
+# use cuda if available
+if torch.cuda.is_available():
+    device = torch.device("cuda:0")
+else:
+    device = torch.device("cpu")
+
+# set hydrodynamic options
+op = MeshBlockOptions.from_yaml("straka.yaml")
+
+# initialize block
+block = MeshBlock(op)
+block.to(device)
+
+# get handles to modules
+coord = block.module("hydro.coord")
+thermo = block.module("hydro.eos.thermo")
+eos = block.module("hydro.eos")
+
+# thermodynamics
+Rd = kintera.constants.Rgas / kintera.species_weights()[0]
+cv = kintera.species_cref_R()[0] * Rd
+cp = cv + Rd
+
+# setup a meshgrid for simulation
+x3v, x2v, x1v = torch.meshgrid(
+    coord.buffer("x3v"), coord.buffer("x2v"), coord.buffer("x1v"), indexing="ij"
+)
+
+# dimensions
+nc3 = coord.buffer("x3v").shape[0]
+nc2 = coord.buffer("x2v").shape[0]
+nc1 = coord.buffer("x1v").shape[0]
+nvar = 5
+
+w = torch.zeros((nvar, nc3, nc2, nc1), device=device)
+
+L = torch.sqrt(((x2v - xc) / xr) ** 2 + ((x1v - zc) / zr) ** 2)
+temp = Ts - grav * x1v / cp
+
+w[kIPR] = p0 * torch.pow(temp / Ts, cp / Rd)
+temp += torch.where(L <= 1, dT * (torch.cos(L * math.pi) + 1.0) / 2.0, 0)
+w[kIDN] = w[kIPR] / (Rd * temp)
+
+block_vars = {}
+block_vars["hydro_w"] = w
+block_vars = block.initialize(block_vars)
+
+block.set_user_output_func(call_user_output)
+
+# integration
+start_time = time.time()
+current_time = 0.0
+block.make_outputs(block_vars, current_time)
+
+while not block.intg.stop(block.inc_cycle(), current_time):
+    dt = block.max_time_step(block_vars)
+    block.print_cycle_info(block_vars, current_time, dt)
+
+    for stage in range(len(block.intg.stages)):
+        block.forward(block_vars, dt, stage)
+
+    err = block.check_redo(block_vars)
+    if err > 0:
+        continue  # redo current step
+    if err < 0:
+        break  # terminate
+
+    current_time += dt
+    block.make_outputs(block_vars, current_time)
+
+block.finalize(block_vars, current_time)
+print("elapsed time = ", time.time() - start_time)

paddle-1.1.10/tests/straka.yaml

@@ -0,0 +1,74 @@
+reference-state:
+  Tref: 0.
+  Pref: 1.e5
+
+species:
+  - name: dry
+    composition: {O: 0.42, N: 1.56, Ar: 0.01}
+    cv_R: 2.5
+
+geometry:
+  type: cartesian
+  bounds: {x1min: 0., x1max: 6.4e3, x2min: 0., x2max: 25.6e3, x3min: 0., x3max: 25.6e3}
+  cells: {nx1: 64, nx2: 256, nx3: 1, nghost: 3}
+
+dynamics:
+  equation-of-state:
+    type: ideal-gas
+    density-floor:  1.e-10
+    pressure-floor: 1.e-10
+    limiter: false
+
+  vertical-projection:
+    type: temperature
+    pressure-margin: 1.e-6
+
+  reconstruct:
+    vertical: {type: weno5, scale: false, shock: false}
+    horizontal: {type: weno5, scale: false, shock: false}
+
+  riemann-solver:
+    type: lmars
+
+boundary-condition:
+  internal:
+    solid-density: 1.e3
+    solid-pressure: 1.e9
+    max-iter: 5
+
+  external:
+    x1-inner: reflecting
+    x1-outer: reflecting
+    x2-inner: reflecting
+    x2-outer: reflecting
+    x3-inner: reflecting
+    x3-outer: reflecting
+
+integration:
+  type: rk3
+  cfl: 0.9
+  implicit-scheme: 0
+  nlim: -1
+  tlim: 900
+  ncycle_out: 10
+
+outputs:
+  - type: restart
+    dt: 300.
+  - type: netcdf
+    variables: [prim, uov]
+    dt: 30.
+
+forcing:
+  const-gravity:
+    grav1: -9.8
+
+problem:
+  p0: 1.e5
+  Ts: 300.
+  xc: 0.
+  xr: 4.e3
+  zc: 3.e3
+  zr: 2.e3
+  dT: -15.
+  K: 75.

paddle-1.1.8/docker-compose.override.yaml.tmp

@@ -1,17 +0,0 @@
-services:
-  dev:
-    build:
-      dockerfile: docker/Dockerfile.cuda
-      args:
-        CUDA_VER: "12.9.1"
-    deploy:
-      resources:
-        reservations:
-          devices:
-            # Activate this if your system supports GPU
-            - capabilities: [gpu]
-    volumes:
-      # This is your main working directory
-      - ${HOME}/work:/work
-      # This is where you put your large simulation data
-      - ${HOME}/data/:/data