standardised import statements in dycore.physics and dycore.utils #25

tested; runs
ray-chew · Mar 23, 2024 · 6648cc5 · 6648cc5
1 parent 9342503
commit 6648cc5
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Showing 21 changed files with 158 additions and 208 deletions.
diff --git a/docs/source/apis/src.dycore.discretisation.time_update.rst b/docs/source/apis/src.dycore.discretisation.time_update.rst
@@ -13,27 +13,13 @@
 
    .. autosummary::
 
-      colored
       data_init
-      deepcopy
       do
-      euler_backward_non_advective_expl_part
-      euler_backward_non_advective_impl_part
-      euler_forward_non_advective
 
 
 
 
 
-   .. rubric:: Classes
-
-   .. autosummary::
-
-      ElemSpaceDiscr
-      Grid
-      NodeSpaceDiscr
-      read_input
-
 
 
 

diff --git a/docs/source/apis/src.dycore.physics.gas_dynamics.cfl.rst b/docs/source/apis/src.dycore.physics.gas_dynamics.cfl.rst
@@ -0,0 +1,29 @@
+src.dycore.physics.gas\_dynamics.cfl
+====================================
+
+.. automodule:: src.dycore.physics.gas_dynamics.cfl
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      dynamic_timestep
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/source/apis/src.dycore.physics.gas_dynamics.eos.rst b/docs/source/apis/src.dycore.physics.gas_dynamics.eos.rst
@@ -1,4 +1,4 @@
-src.dycore.physics.gas\_dynamics.eos
+src.dycore.physics.gas\_dynamics.eos
 ====================================
 
 .. automodule:: src.dycore.physics.gas_dynamics.eos
@@ -18,7 +18,6 @@
       is_nonhydrostatic
       nonhydrostasy
       rhoe
-      set_ghostcells_p2
       synchronise_variables
 
 

diff --git a/docs/source/apis/src.dycore.physics.gas_dynamics.explicit.rst b/docs/source/apis/src.dycore.physics.gas_dynamics.explicit.rst
@@ -1,4 +1,4 @@
-src.dycore.physics.gas\_dynamics.explicit
+src.dycore.physics.gas\_dynamics.explicit
 =========================================
 
 .. automodule:: src.dycore.physics.gas_dynamics.explicit
@@ -16,9 +16,6 @@
       advect
       advect_rk
       explicit_step_and_flux
-      hll_solver
-      recovery
-      set_explicit_boundary_data
 
 
 

diff --git a/docs/source/apis/src.dycore.physics.gas_dynamics.gas_dynamics.rst b/docs/source/apis/src.dycore.physics.gas_dynamics.gas_dynamics.rst
diff --git a/docs/source/apis/src.dycore.physics.gas_dynamics.recovery.rst b/docs/source/apis/src.dycore.physics.gas_dynamics.recovery.rst
@@ -1,4 +1,4 @@
-src.dycore.physics.gas\_dynamics.recovery
+src.dycore.physics.gas\_dynamics.recovery
 =========================================
 
 .. automodule:: src.dycore.physics.gas_dynamics.recovery
@@ -13,23 +13,15 @@
 
    .. autosummary::
 
+      do
       get_conservatives
       limiters
-      recovery
       slopes
 
 
 
 
 
-   .. rubric:: Classes
-
-   .. autosummary::
-
-      Characters
-      LimiterType
-      States
-
 
 
 

diff --git a/docs/source/apis/src.dycore.physics.gas_dynamics.rst b/docs/source/apis/src.dycore.physics.gas_dynamics.rst
@@ -1,4 +1,4 @@
-src.dycore.physics.gas\_dynamics
+src.dycore.physics.gas\_dynamics
 ================================
 
 .. automodule:: src.dycore.physics.gas_dynamics
@@ -27,9 +27,9 @@ src.dycore.physics.gas\_dynamics
    :toctree:
    :recursive:
 
+   src.dycore.physics.gas_dynamics.cfl
    src.dycore.physics.gas_dynamics.eos
    src.dycore.physics.gas_dynamics.explicit
-   src.dycore.physics.gas_dynamics.gas_dynamics
    src.dycore.physics.gas_dynamics.numerical_flux
    src.dycore.physics.gas_dynamics.recovery
    src.dycore.physics.gas_dynamics.thermodynamic

diff --git a/docs/source/apis/src.dycore.physics.hydrostatics.rst b/docs/source/apis/src.dycore.physics.hydrostatics.rst
@@ -17,8 +17,6 @@
       hydrostatic_initial_pressure
       hydrostatic_state
       loop_over_array
-      set_ghostcells_p2
-      set_ghostnodes_p2
 
 
 

diff --git a/docs/source/apis/src.dycore.physics.low_mach.laplacian.rst b/docs/source/apis/src.dycore.physics.low_mach.laplacian.rst
@@ -13,7 +13,6 @@
 
    .. autosummary::
 
-      jit
       lap2D
       lap2D_5pt
       lap2D_exner
@@ -23,7 +22,6 @@
       lap3D
       lapHS
       lapVS
-      njit
       periodic
       precon_diag_prepare
       stencil_27pt
@@ -38,13 +36,6 @@
 
 
 
-   .. rubric:: Classes
-
-   .. autosummary::
-
-      BdryType
-      prange
-
 
 
 

diff --git a/docs/source/apis/src.dycore.physics.low_mach.mpv.rst b/docs/source/apis/src.dycore.physics.low_mach.mpv.rst
@@ -18,7 +18,6 @@
    .. autosummary::
 
       MPV
-      States
 
 
 

diff --git a/docs/source/apis/src.dycore.physics.low_mach.second_projection.rst b/docs/source/apis/src.dycore.physics.low_mach.second_projection.rst
@@ -13,26 +13,17 @@
 
    .. autosummary::
 
-      bicgstab
       correction_nodes
       divergence_nodes
       euler_backward_non_advective_expl_part
       euler_backward_non_advective_impl_part
       euler_forward_non_advective
       grad_nodes
       grad_nodes_fft
-      jit
       multiply_inverse_coriolis
       operator_coefficients_nodes
-      precon_diag_prepare
       rhs_from_p_old
       scale_wall_node_values
-      set_explicit_boundary_data
-      set_ghostnodes_p2
-      stencil_27pt
-      stencil_9pt_numba_test
-      stencil_hs
-      stencil_vs
 
 
 
@@ -42,9 +33,6 @@
 
    .. autosummary::
 
-      BdryType
-      LinearOperator
-      product
       solver_counter
 
 

diff --git a/src/dycore/physics/gas_dynamics/eos.py b/src/dycore/physics/gas_dynamics/eos.py
@@ -1,6 +1,6 @@
 import numpy as np
 
-from dycore.utils.boundary import set_ghostcells_p2
+import dycore.utils.boundary as bdry
 
 def nonhydrostasy(ud,t,step):
     if step >= 0:
@@ -79,4 +79,4 @@ def synchronise_variables(mpv, Sol, elem, node, ud, th):
         p2bg = np.repeat(p2bg, elem.icx,axis=0)
         mpv.p2_cells = scale_factor * Sol.rhoY**th.gm1 - p2bg
 
-    set_ghostcells_p2(mpv.p2_cells, elem, ud)
+    bdry.set_ghostcells_p2(mpv.p2_cells, elem, ud)
diff --git a/src/dycore/physics/gas_dynamics/explicit.py b/src/dycore/physics/gas_dynamics/explicit.py
@@ -1,7 +1,6 @@
-import numpy as np
-from dycore.utils.boundary import set_explicit_boundary_data
-from dycore.physics.gas_dynamics.recovery import recovery
-from dycore.physics.gas_dynamics.numerical_flux import hll_solver
+import dycore.utils.boundary as bdry
+import dycore.physics.gas_dynamics.recovery as gd_recovery
+import dycore.physics.gas_dynamics.numerical_flux as gd_flux
 
 def advect(Sol, flux, dt, elem, odd, ud, th, mpv, node, label, writer = None):
     """
@@ -70,7 +69,7 @@ def advect(Sol, flux, dt, elem, odd, ud, th, mpv, node, label, writer = None):
 
     # Sol.rhoX += Sol.rho * mpv.HydroState.S0
 
-    set_explicit_boundary_data(Sol, elem, ud, th, mpv)
+    bdry.set_explicit_boundary_data(Sol, elem, ud, th, mpv)
 
 
 
@@ -108,11 +107,11 @@ def explicit_step_and_flux(Sol, flux, lmbda, elem, split_step, stage, ud, th, mp
     :py:class:`management.variable.States`
         `flux` data container.
     """
-    set_explicit_boundary_data(Sol, elem, ud, th, mpv, step=split_step)
+    bdry.set_explicit_boundary_data(Sol, elem, ud, th, mpv, step=split_step)
 
-    Lefts, Rights = recovery(Sol, flux, lmbda, ud, th, elem, split_step, tag)
+    Lefts, Rights = gd_recovery.do(Sol, flux, lmbda, ud, th, elem, split_step, tag)
 
-    # Lefts, Rights, u, Diffs, Ampls, Slopes = recovery(Sol, flux, lmbda, ud, th, elem, split_step, tag)
+    # Lefts, Rights, u, Diffs, Ampls, Slopes = gd_recovery.do(Sol, flux, lmbda, ud, th, elem, split_step, tag)
 
     # if writer is not None:
     #     writer[0].write_all(Sol,mpv,elem,writer[1],th,str(writer[2])+'_split_%i' %split_step)
@@ -146,7 +145,7 @@ def explicit_step_and_flux(Sol, flux, lmbda, elem, split_step, stage, ud, th, mp
     # skipped check_flux_bcs for now; first debug other functions
     # check_flux_bcs(Lefts, Rights, elem, split_step, ud)
 
-    flux = hll_solver(flux,Lefts,Rights,Sol, lmbda, ud, th)
+    flux = gd_flux.hll_solver(flux,Lefts,Rights,Sol, lmbda, ud, th)
 
     ndim = elem.ndim
     left_idx, right_idx = [slice(None)] * ndim, [slice(None)] * ndim
@@ -162,7 +161,7 @@ def explicit_step_and_flux(Sol, flux, lmbda, elem, split_step, stage, ud, th, mp
         Sol.rhoX += lmbda * (flux.rhoX[left_idx] - flux.rhoX[right_idx])
         Sol.rhoY += lmbda * (flux.rhoY[left_idx] - flux.rhoY[right_idx])
 
-    set_explicit_boundary_data(Sol, elem, ud, th, mpv, step=split_step)
+    bdry.set_explicit_boundary_data(Sol, elem, ud, th, mpv, step=split_step)
 
     if tag == 'rk':
         return flux
@@ -234,7 +233,7 @@ def advect_rk(Sol, flux, dt, elem, odd, ud, th, mpv, node, label, writer = None)
             updt = lmbda * (flux[dim].rhoX[left_idx] - flux[dim].rhoX[right_idx])
             setattr(Sol, 'pwchi', updt)
 
-    set_explicit_boundary_data(Sol, elem, ud, th, mpv)
+    bdry.set_explicit_boundary_data(Sol, elem, ud, th, mpv)
 
     # stage = 1
     # for split in range(ndim):

diff --git a/src/dycore/physics/gas_dynamics/numerical_flux.py b/src/dycore/physics/gas_dynamics/numerical_flux.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 import numpy as np
-from scipy import signal
+import scipy as sp
 
 def recompute_advective_fluxes(flux, Sol, *args, **kwargs):
     """
@@ -30,19 +30,19 @@ def recompute_advective_fluxes(flux, Sol, *args, **kwargs):
         kernel_w = np.swapaxes(kernel_u,2,0)
 
         rhoYw = Sol.rhoY * Sol.rhow / Sol.rho
-        flux[2].rhoY[inner_idx] = signal.fftconvolve(rhoYw, kernel_w, mode='valid') / kernel_w.sum()
+        flux[2].rhoY[inner_idx] = sp.signal.fftconvolve(rhoYw, kernel_w, mode='valid') / kernel_w.sum()
     else:
         assert 0, "Unsupported dimension in recompute_advective_flux"
 
     rhoYu = kwargs.get('u',Sol.rhoY * Sol.rhou / Sol.rho)
 
-    flux[0].rhoY[inner_idx] = np.moveaxis(signal.fftconvolve(rhoYu, kernel_u, mode='valid') / kernel_u.sum(), 0, -1)
+    flux[0].rhoY[inner_idx] = np.moveaxis(sp.signal.fftconvolve(rhoYu, kernel_u, mode='valid') / kernel_u.sum(), 0, -1)
 
     rhoYv = kwargs.get('v',Sol.rhoY * Sol.rhov / Sol.rho)
     if ndim == 2:
-        flux[1].rhoY[inner_idx] = signal.fftconvolve(rhoYv, kernel_v, mode='valid') / kernel_v.sum()
+        flux[1].rhoY[inner_idx] = sp.signal.fftconvolve(rhoYv, kernel_v, mode='valid') / kernel_v.sum()
     elif ndim == 3:
-        flux[1].rhoY[inner_idx] = np.moveaxis(signal.fftconvolve(rhoYv, kernel_v, mode='valid') / kernel_v.sum(), -1,0)
+        flux[1].rhoY[inner_idx] = np.moveaxis(sp.signal.fftconvolve(rhoYv, kernel_v, mode='valid') / kernel_v.sum(), -1,0)
     # flux[1].rhoY[...,-1] = 0.
 
 def hll_solver(flux, Lefts, Rights, Sol, lmbda, ud, th):
Original file line number	Diff line number	Diff line change
Expand Up		@@ -18,7 +18,6 @@
		.. autosummary::

		MPV
		States



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