paddle 1.2.0__tar.gz → 1.2.1__tar.gz

{paddle-1.2.0 → paddle-1.2.1}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.0
+current_version = 1.2.1
 commit = True
 tag = True
 

{paddle-1.2.0 → paddle-1.2.1}/.gitignore

@@ -218,3 +218,6 @@ docker-compose.override.yaml
 # python environment
 .env
 .pyenv
+
+# pt file
+*.pt

{paddle-1.2.0 → paddle-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: paddle
-Version: 1.2.0
+Version: 1.2.1
 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
@@ -23,7 +23,7 @@ Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.9
 Requires-Dist: scipy
-Requires-Dist: snapy>=1.0.3
+Requires-Dist: snapy>=1.1.5
 Requires-Dist: torch<=2.7.1,>=2.7.0
 Provides-Extra: dev
 Requires-Dist: pytest>=7; extra == 'dev'

paddle-1.2.1/example_py_scripts/jupiter_crm.yaml

@@ -0,0 +1,198 @@
+reference-state:
+  Tref: 0.
+  Pref: 1.e5
+
+species:
+  - name: dry
+    composition: {H: 1.5, He: 0.15}
+    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: H2O(l,p)
+    composition: {H: 2, O: 1}
+    cv_R: 9.0
+    u0_R: -3430.
+
+  - name: NH3(s)
+    composition: {N: 1, H: 3}
+    cv_R: 9.0
+    u0_R: -5520.
+
+  - name: NH3(s,p)
+    composition: {N: 1, H: 3}
+    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
+
+  - name: NH4SH(s,p)
+    composition: {N: 1, H: 5, S: 1}
+    cv_R: 9.0
+    u0_R: -1.2e4
+
+geometry:
+  type: cartesian
+
+  bounds:
+    x1min: 0.
+    x1max: 300.e3
+    x2min: 0.
+    x2max: 2400.e3
+    x3min: 0.
+    x3max: 2400.e3
+
+  cells:
+    nx1: 100
+    nx2: 100
+    nx3: 100
+    nghost: 3
+
+distribute:
+  backend: gloo
+  layout: slab
+  nb2: 2
+  nb3: 2
+  verbose: false
+
+dynamics:
+  equation-of-state:
+    type: ideal-moist
+    density-floor:  1.e-10
+    pressure-floor: 1.e-10
+    tracer-floor: 1.e-10
+    limiter: true
+    max-iter: 20
+    ftol: 1.e-6
+
+  vertical-projection:
+    type: temperature
+    pressure-margin: 1.e-6
+
+  reconstruct:
+    vertical: {type: weno5, scale: true, shock: true}
+    horizontal: {type: weno5, scale: true, shock: true}
+
+  riemann-solver:
+    type: hllc
+
+boundary-condition:
+  external:
+    x1-inner: reflecting
+    x1-outer: reflecting
+    x2-inner: reflecting
+    x2-outer: reflecting
+    x3-inner: reflecting
+    x3-outer: reflecting
+
+integration:
+  type: rk3
+  cfl: 0.45
+  implicit-scheme: 1
+  nlim: -1
+  tlim: 100.e5
+  ncycle_out: 1
+
+outputs:
+  - type: restart
+    dt: 1.E5
+  - type: netcdf
+    variables: [prim, uov]
+    dt: 1.E3
+  - type: netcdf
+    variables: [thermo, path]
+    dt: 1.E3
+
+forcing:
+  const-gravity:
+    grav1: -22.
+
+  top-cool:
+    flux: -100.
+    depth: 5
+
+  bot-heat:
+    flux: 100
+    depth: 5
+
+sedimentation:
+  radius:
+    H2O(l,p): 1.0e-10
+    NH3(s,p): 1.0e-10
+    NH4SH(s,p): 1.0e-10
+
+  density:
+    H2O(l,p): 1000.
+    NH3(s,p): 800.
+    NH4SH(s,p): 1500.
+
+  const-vsed:
+    H2O(l,p): -20.0
+    NH3(s,p): -20.0
+    NH4SH(s,p): -20.0
+
+reactions:
+  - equation: H2O => H2O(l)
+    type: nucleation
+    rate-constant: {formula: h2o_ideal}
+
+  - equation: H2O(l) => H2O(l,p)
+    type: coagulation
+    rate-constant: {A: 0.001, b: 0, Ea_R: 0.}
+
+  - equation: H2O(l,p) => H2O
+    type: evaporation
+    rate-constant: {formula: h2o_ideal, diff_c: 0.2e-4, diff_T: 0., diff_P: 0., vm: 18.e-6, diameter: 1.0e-4}
+
+  - equation: NH3 => NH3(s)
+    type: nucleation
+    rate-constant: {formula: nh3_ideal}
+
+  - equation: NH3(s) => NH3(s,p)
+    type: coagulation
+    rate-constant: {A: 0.001, b: 0, Ea_R: 2.}
+
+  - equation: NH3(s,p) => NH3
+    type: evaporation
+    rate-constant: {formula: nh3_ideal, diff_c: 0.2e-4, diff_T: 0., diff_P: 0., vm: 18.e-6, diameter: 1.0e-4}
+
+  - equation: NH3 + H2S <=> NH4SH(s)
+    type: nucleation
+    rate-constant: {formula: nh3_h2s_lewis}
+
+  - equation: NH4SH(s) => NH4SH(s,p)
+    type: coagulation
+    rate-constant: {A: 0.001, b: 0, Ea_R: 0.}
+
+  - equation: NH4SH(s,p) => NH3 + H2S
+    type: evaporation
+    rate-constant: {formula: nh3_h2s_lewis, diff_c: 0.2e-4, diff_T: 0., diff_P: 0., vm: 18.e-6, diameter: 1.0e-4}
+
+problem:
+  Ps: 100.e5
+  Ts: 600.
+  Tmin: 110.
+  xH2O: 3.e-3
+  xNH3: 3.2e-4
+  xH2S: 1.e-5

paddle-1.2.1/example_py_scripts/jupiter_crm_dry.yaml

@@ -0,0 +1,92 @@
+reference-state:
+  Tref: 0.
+  Pref: 1.e5
+
+species:
+  - name: dry
+    composition: {H: 1.5, He: 0.15}
+    cv_R: 2.5
+
+geometry:
+  type: cartesian
+
+  bounds:
+    x1min: 0.
+    x1max: 300.e3
+    x2min: 0.
+    x2max: 2400.e3
+    x3min: 0.
+    x3max: 2400.e3
+
+  cells:
+    nx1: 100
+    nx2: 200
+    nx3: 200
+    nghost: 3
+
+distribute:
+  backend: gloo
+  layout: slab
+  nb2: 2
+  nb3: 2
+  verbose: false
+
+dynamics:
+  equation-of-state:
+    type: ideal-moist
+    density-floor:  1.e-10
+    pressure-floor: 1.e-10
+    tracer-floor: 1.e-10
+    limiter: true
+    max-iter: 10
+    ftol: 1.e-6
+
+  vertical-projection:
+    type: temperature
+    pressure-margin: 1.e-6
+
+  reconstruct:
+    vertical: {type: weno5, scale: true, shock: true}
+    horizontal: {type: weno5, scale: true, shock: true}
+
+  riemann-solver:
+    type: hllc
+
+boundary-condition:
+  external:
+    x1-inner: reflecting
+    x1-outer: reflecting
+    x2-inner: periodic
+    x2-outer: periodic
+    x3-inner: periodic
+    x3-outer: periodic
+
+integration:
+  type: rk3
+  cfl: 0.45
+  implicit-scheme: 1
+  nlim: -1
+  tlim: 100.e5
+  ncycle_out: 1
+
+outputs:
+  - type: restart
+    dt: 10.E5
+  - type: netcdf
+    variables: [prim]
+    dt: 1.E4
+  - type: netcdf
+    variables: [thermo]
+    dt: 1.E4
+
+forcing:
+  const-gravity:
+    grav1: -22.
+
+problem:
+  Ps: 100.e5
+  Ts: 600.
+  Tmin: 110.
+  xH2O: 3.e-3
+  xNH3: 3.2e-4
+  xH2S: 1.e-5

paddle-1.2.1/example_py_scripts/jupiter_gcm.yaml

@@ -0,0 +1,195 @@
+reference-state:
+  Tref: 0.
+  Pref: 1.e5
+
+species:
+  - name: dry
+    composition: {H: 1.5, He: 0.15}
+    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: H2O(l,p)
+    composition: {H: 2, O: 1}
+    cv_R: 9.0
+    u0_R: -3430.
+
+  - name: NH3(s)
+    composition: {N: 1, H: 3}
+    cv_R: 9.0
+    u0_R: -5520.
+
+  - name: NH3(s,p)
+    composition: {N: 1, H: 3}
+    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
+
+  - name: NH4SH(s,p)
+    composition: {N: 1, H: 5, S: 1}
+    cv_R: 9.0
+    u0_R: -1.2e4
+
+geometry:
+  type: gnomonic-equiangle
+
+  bounds:
+    x1min: 69911000
+    x1max: 70211000
+    x2min_pi: -0.25
+    x2max_pi: 0.25
+    x3min_pi: -0.25
+    x3max_pi: 0.25
+
+  cells:
+    nx1: 100
+    nx2: 48
+    nx3: 48
+    nghost: 3
+
+distribute:
+  backend: gloo
+  layout: cubed-sphere
+  nb2: 1
+  nb3: 1
+  verbose: false
+
+dynamics:
+  equation-of-state:
+    type: ideal-moist
+    density-floor:  1.e-10
+    pressure-floor: 1.e-10
+    tracer-floor: 1.e-10
+    limiter: true
+    max-iter: 40
+    ftol: 1.e-6
+
+  vertical-projection:
+    type: temperature
+    pressure-margin: 1.e-6
+
+  reconstruct:
+    vertical: {type: weno5, scale: true, shock: true}
+    horizontal: {type: weno5, scale: true, shock: true}
+
+  riemann-solver:
+    type: hllc
+
+boundary-condition:
+  internal:
+    solid-density: 1.e3
+    solid-pressure: 1.e9
+    max-iter: 5
+
+  external:
+    x1-inner: reflecting
+    x1-outer: reflecting
+    x2-inner: custom
+    x2-outer: custom
+    x3-inner: custom
+    x3-outer: custom
+
+integration:
+  type: rk3
+  cfl: 0.45
+  implicit-scheme: 9
+  nlim: -1
+  tlim: 100.e5
+  ncycle_out: 1
+
+outputs:
+  - type: restart
+    dt: 10.E5
+  - type: netcdf
+    variables: [prim, uov]
+    dt: 1.e4
+  - type: netcdf
+    variables: [thermo]
+    dt: 1.e4
+
+forcing:
+  const-gravity:
+    grav1: -22.
+
+sedimentation:
+  radius:
+    H2O(l,p): 1.0e-10
+    NH3(s,p): 1.0e-10
+    NH4SH(s,p): 1.0e-10
+
+  density:
+    H2O(l,p): 1000.
+    NH3(s,p): 800.
+    NH4SH(s,p): 1500.
+
+  const-vsed:
+    H2O(l,p): -2.0
+    NH3(s,p): -2.0
+    NH4SH(s,p): -2.0
+
+reactions:
+  - equation: H2O => H2O(l)
+    type: nucleation
+    rate-constant: {formula: h2o_ideal}
+
+  - equation: H2O(l) => H2O(l,p)
+    type: coagulation
+    rate-constant: {A: 0.01, b: 0, Ea_R: 0.}
+
+  - equation: H2O(l,p) => H2O
+    type: evaporation
+    rate-constant: {formula: h2o_ideal, diff_c: 0.2e-4, diff_T: 0., diff_P: 0., vm: 18.e-6, diameter: 1.0e-4}
+
+  - equation: NH3 => NH3(s)
+    type: nucleation
+    rate-constant: {formula: nh3_ideal}
+
+  - equation: NH3(s) => NH3(s,p)
+    type: coagulation
+    rate-constant: {A: 0.01, b: 0, Ea_R: 2.}
+
+  - equation: NH3(s,p) => NH3
+    type: evaporation
+    rate-constant: {formula: nh3_ideal, diff_c: 0.2e-4, diff_T: 0., diff_P: 0., vm: 18.e-6, diameter: 1.0e-4}
+
+  - equation: NH3 + H2S <=> NH4SH(s)
+    type: nucleation
+    rate-constant: {formula: nh3_h2s_lewis}
+
+  - equation: NH4SH(s) => NH4SH(s,p)
+    type: coagulation
+    rate-constant: {A: 0.01, b: 0, Ea_R: 0.}
+
+  - equation: NH4SH(s,p) => NH3 + H2S
+    type: evaporation
+    rate-constant: {formula: nh3_h2s_lewis, diff_c: 0.2e-4, diff_T: 0., diff_P: 0., vm: 18.e-6, diameter: 1.0e-4}
+
+problem:
+  Ps: 100.e5
+  Ts: 600.
+  Tmin: 110.
+  xH2O: 3.e-3
+  xNH3: 3.2e-4
+  xH2S: 1.e-5

paddle-1.2.1/example_py_scripts/jupiter_gcm_dry.yaml

@@ -0,0 +1,89 @@
+reference-state:
+  Tref: 0.
+  Pref: 1.e5
+
+species:
+  - name: dry
+    composition: {H: 1.5, He: 0.15}
+    cv_R: 2.5
+
+geometry:
+  type: gnomonic-equiangle
+
+  bounds:
+    x1min: 69911000
+    x1max: 70211000
+    x2min_pi: -0.25
+    x2max_pi: 0.25
+    x3min_pi: -0.25
+    x3max_pi: 0.25
+
+  cells:
+    nx1: 100
+    nx2: 48
+    nx3: 48
+    nghost: 3
+
+distribute:
+  backend: gloo
+  layout: cubed-sphere
+  nb2: 1
+  nb3: 1
+  verbose: false
+
+dynamics:
+  equation-of-state:
+    type: ideal-moist
+    density-floor:  1.e-10
+    pressure-floor: 1.e-10
+    tracer-floor: 1.e-10
+    limiter: true
+    max-iter: 10
+    ftol: 1.e-6
+
+  vertical-projection:
+    type: temperature
+    pressure-margin: 1.e-6
+
+  reconstruct:
+    vertical: {type: weno5, scale: true, shock: true}
+    horizontal: {type: weno5, scale: true, shock: true}
+
+  riemann-solver:
+    type: hllc
+
+boundary-condition:
+  external:
+    x1-inner: reflecting
+    x1-outer: reflecting
+    x2-inner: custom
+    x2-outer: custom
+    x3-inner: custom
+    x3-outer: custom
+
+integration:
+  type: rk3
+  cfl: 0.45
+  implicit-scheme: 9
+  nlim: -1
+  tlim: 100.e5
+  ncycle_out: 1
+
+outputs:
+  - type: restart
+    dt: 10.E5
+  - type: netcdf
+    variables: [prim]
+    dt: 1.e4
+  - type: netcdf
+    variables: [thermo]
+    dt: 1.e4
+
+forcing:
+  const-gravity:
+    grav1: -22.
+
+problem:
+  Ps: 100.e5
+  Ts: 600.
+  Tmin: 110.

{paddle-1.2.0 → paddle-1.2.1}/example_py_scripts/robert.py

@@ -1,6 +1,6 @@
 import torch
 import math
-import time
+import kintera
 from snapy import MeshBlockOptions, MeshBlock
 from snapy import kIDN, kIPR
 
@@ -22,9 +22,6 @@ 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
@@ -39,10 +36,13 @@ block = MeshBlock(op)
 block.to(device)
 
 # get handles to modules
-coord = block.module("hydro.coord")
-thermo = block.module("hydro.eos.thermo")
+coord = block.module("coord")
+eos = block.module("hydro.eos")
+grav = -block.options.hydro().grav().grav1()
 
 # thermodynamics
+gamma = eos.options.gammad()
+Rd = kintera.constants.Rgas / eos.options.weight()
 cp = gamma / (gamma - 1.0) * Rd
 
 # set initial condition
@@ -78,7 +78,6 @@ block_vars, current_time = block.initialize(block_vars)
 block.set_user_output_func(call_user_output)
 
 # integration
-start_time = time.time()
 block.make_outputs(block_vars, current_time)
 
 while not block.intg.stop(block.inc_cycle(), current_time):

{paddle-1.2.0 → paddle-1.2.1}/example_py_scripts/robert.yaml

@@ -15,13 +15,15 @@ geometry:
 distribute:
   backend: gloo
   layout: slab
-  nb2: 1
+  nb2: 4
   nb3: 1
   verbose: false
 
 dynamics:
   equation-of-state:
     type: ideal-gas
+    gammad: 1.4
+    weight: 29.e-3
     density-floor:  1.e-10
     pressure-floor: 1.e-10
     limiter: false