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implement conservative remapping of mixing coefficient in vert_mix module #54

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klindsay28 opened this issue Mar 1, 2021 · 0 comments
Open

implement conservative remapping of mixing coefficient in vert_mix module #54

klindsay28 opened this issue Mar 1, 2021 · 0 comments
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enhancement New feature or request

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@klindsay28
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tracer values tend to jump as bldepth crosses layer interfaces

replacing linear interpolation of piecewise linear mixing coefficients profile with conservative remapping might prevent this
@klindsay28 klindsay28 added the enhancement New feature or request label Mar 1, 2021
klindsay28 added a commit that referenced this issue Mar 4, 2021
@klindsay28
initial steps adding py_driver_2d model
7442993 
based on test_problem

only iage TracerModule implemented
    advection, vert_mix, and horiz_mix processes not vetted with multiple tracers

bldepth variation in time for vert_mix currently turned off
    adaptive time-stepping use many steps when bldepth varies
    perhaps this will improve when #54 is addressed

comp_fcn uses scipy.integrate.solve_ivp to integrate ODEs
    will eventually migrate to PETSc

apply_precond_jacobian not functional yet
    will do this after comp_fcn migration to PETSC

On branch py_driver_2d
Changes to be committed:
	new file:   input/py_driver_2d/model_params.cfg
	new file:   input/py_driver_2d/newton_krylov.cfg
	new file:   input/py_driver_2d/tracer_module_defs.yaml
	new file:   src/py_driver_2d/__init__.py
	new file:   src/py_driver_2d/advection.py
	new file:   src/py_driver_2d/horiz_mix.py
	new file:   src/py_driver_2d/iage.py
	new file:   src/py_driver_2d/model_process.py
	new file:   src/py_driver_2d/model_state.py
	new file:   src/py_driver_2d/setup_solver.py
	new file:   src/py_driver_2d/tracer_module_state.py
	new file:   src/py_driver_2d/vert_mix.py
klindsay28 added a commit that referenced this issue Mar 14, 2021
@klindsay28
merge py_driver_2d (#63)
dbe254e 
* initial steps adding py_driver_2d model

based on test_problem

only iage TracerModule implemented
    advection, vert_mix, and horiz_mix processes not vetted with multiple tracers

bldepth variation in time for vert_mix currently turned off
    adaptive time-stepping use many steps when bldepth varies
    perhaps this will improve when #54 is addressed

comp_fcn uses scipy.integrate.solve_ivp to integrate ODEs
    will eventually migrate to PETSc

apply_precond_jacobian not functional yet
    will do this after comp_fcn migration to PETSC

On branch py_driver_2d
Changes to be committed:
	new file:   input/py_driver_2d/model_params.cfg
	new file:   input/py_driver_2d/newton_krylov.cfg
	new file:   input/py_driver_2d/tracer_module_defs.yaml
	new file:   src/py_driver_2d/__init__.py
	new file:   src/py_driver_2d/advection.py
	new file:   src/py_driver_2d/horiz_mix.py
	new file:   src/py_driver_2d/iage.py
	new file:   src/py_driver_2d/model_process.py
	new file:   src/py_driver_2d/model_state.py
	new file:   src/py_driver_2d/setup_solver.py
	new file:   src/py_driver_2d/tracer_module_state.py
	new file:   src/py_driver_2d/vert_mix.py

* add remap_linear_interpolant method to SpatialAxis class

On branch py_driver_2d
Changes to be committed:
	modified:   src/spatial_axis.py
	modified:   tests/test_spatial_axis.py

* py_driver_2d vert_mix update:
    replace linear interpolation of piecewise linear mixing coefficients profile with conservative remapping
    modest decrease in runtime, due to longer timesteps

    enable bldepth variation in time

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/iage.py
	modified:   src/py_driver_2d/vert_mix.py

* py_driver_2d update: rename dtracer_vals_dt to tracer_tend_vals

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/iage.py
	modified:   src/py_driver_2d/tracer_module_state.py

* py_driver_2d update: add comp_jacobian methods and pass to solve_ivp

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/advection.py
	modified:   src/py_driver_2d/horiz_mix.py
	modified:   src/py_driver_2d/iage.py
	modified:   src/py_driver_2d/model_process.py
	modified:   src/py_driver_2d/model_state.py
	modified:   src/py_driver_2d/tracer_module_state.py
	modified:   src/py_driver_2d/vert_mix.py

* py_driver_2d performance improvements
    use numpy arrays to construct sparse Jacobians, precomputing nnz
    cache Advection and HorizMix Jacobians
    cache remap_linear_interpolant results in VertMix.mixing_coeff

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/advection.py
	modified:   src/py_driver_2d/horiz_mix.py
	modified:   src/py_driver_2d/model_state.py
	modified:   src/py_driver_2d/tracer_module_state.py
	modified:   src/py_driver_2d/vert_mix.py

* py_driver_2d coupled to overall solver

implement apply_precond_jacobian
    precond jacobian is time mean of instantaneous jacobians

fix typo in np.einsum call in TracerModuleState:stats_vars_vals

enable --persist option for py_driver_2d

tighten tolerances in solve_ivp call to 1.0e-6

loosen newton_rel_tol in newton_krylov.cfg to 1.0e-5
    doesn't make sense to be more accurate than solve_ivp tolerances

On branch py_driver_2d
Changes to be committed:
	modified:   input/py_driver_2d/newton_krylov.cfg
	modified:   input/py_driver_2d/tracer_module_defs.yaml
	modified:   src/py_driver_2d/iage.py
	modified:   src/py_driver_2d/model_state.py
	modified:   src/py_driver_2d/tracer_module_state.py
	modified:   src/share.py

* py_driver_2d updates
    adjust vert_mix paramters to increase iage local max
    add more layers in ypos direction

On branch py_driver_2d
Changes to be committed:
	modified:   input/py_driver_2d/model_params.cfg
	modified:   src/py_driver_2d/vert_mix.py

* py_driver_2d: add support for multiple tracers

add 2nd iage tracer with weaker restoring in surface layer

construct jacobian sparsity matrix from jacobian at initial time
    instead of recomputing pattern

On branch py_driver_2d
Changes to be committed:
	modified:   input/py_driver_2d/tracer_module_defs.yaml
	modified:   src/py_driver_2d/advection.py
	modified:   src/py_driver_2d/horiz_mix.py
	modified:   src/py_driver_2d/iage.py
	modified:   src/py_driver_2d/model_process.py
	modified:   src/py_driver_2d/model_state.py
	modified:   src/py_driver_2d/tracer_module_state.py
	modified:   src/py_driver_2d/vert_mix.py
	modified:   src/test_problem/model_state.py

* py_driver_2d: rework apply_precond_jacobian for iage

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/iage.py

* py_driver_2d: add phosphorus tracer module

add {tracer}_depth_ypos_int to history output

rm unused comp_jac_sparsity from class ModelProcess

On branch py_driver_2d
Changes to be committed:
	modified:   input/py_driver_2d/newton_krylov.cfg
	modified:   input/py_driver_2d/tracer_module_defs.yaml
	modified:   src/py_driver_2d/model_process.py
	modified:   src/py_driver_2d/model_state.py
	new file:   src/py_driver_2d/phosphorus.py
	modified:   src/py_driver_2d/tracer_module_state.py

* py_driver_2d: add preformed tracer module

On branch py_driver_2d
Changes to be committed:
	modified:   input/py_driver_2d/model_params.cfg
	modified:   input/py_driver_2d/newton_krylov.cfg
	new file:   input/py_driver_2d/po4_surf.nc
	modified:   input/py_driver_2d/tracer_module_defs.yaml
	new file:   src/py_driver_2d/preformed.py

* py_driver_2d: correct iage restoring rate formula

mv formula to iage.__init__, to avoid it being in more than 1 place

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/iage.py

* update for black: rm trailing comma to satisfy black 20.8b1

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/phosphorus.py

* py_driver_2d: generalize parameter specification for phosphorus tracers

place parameters in dict in phosphorus class

enable specification of parameters in cfg modelinfo

introduce function for evaluation of basic arithmetic operations in a string
    enables phosphorus parameters in cfg file to be expressions

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/phosphorus.py
	modified:   src/utils.py

* py_driver_2d: generalize preformed.gen_surf_restore_fcn and mv to utils

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/preformed.py
	modified:   src/utils.py

* py_driver_2d: modify parameters to increase regenerated po4

On branch py_driver_2d
Changes to be committed:
	modified:   input/py_driver_2d/po4_surf.nc
	modified:   src/py_driver_2d/phosphorus.py
	modified:   src/py_driver_2d/vert_mix.py

* py_driver_2d: refactor __init__ in ModelProcess class and subclasses

On branch py_driver_2d
Changes to be committed:
	modified:   src/py_driver_2d/advection.py
	modified:   src/py_driver_2d/horiz_mix.py
	modified:   src/py_driver_2d/model_process.py
	modified:   src/py_driver_2d/vert_mix.py
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