Feature/doubly_periodic_dycore

[oelbert]

Purpose

Adds infrastructure to the dynamical core to enable doubly-periodic runs, and refactors driver and test infrastructure to be useable with CubedSphere and Tile communicators/partitioners

Remove the sections below which do not apply.

Code changes:

• driver/pace/driver/driver.py: generalized typing CubedSphereCommunicator to Communcator and create correct communicator for doubly periodic runs, added grid type to config
• driver/pace/driver/grid.py: replace CubeSphereCommunicator with Communicator base class for typing
• driver/pace/driver/initialization.py: replace CubeSphereCommunicator with Communicator base class for typing
• driver/pace/driver/state.py: replace CubeSphereCommunicator with Communicator base class for typing
• dsl/pace/dsl/caches/cache_location.py: replace CubeSpherePartitioner with Partitioner base class for typing
• dsl/pace/dsl/dace/dace_config.py: replace CubeSphereCommunicator, CubeSpherePartitioner with Communicator and Partitioner base classes for typing
• dsl/pace/dsl/dace/wrapped_halo_exchange.py: replace CubeSphereCommunicator with Communicator base class for typing
• dsl/pace/dsl/stencil.py replace CubeSphereCommunicator with Communicator base class for typing
• dsl/pace/dsl/stencil_config.py: replace CubeSphereCommunicator, CubeSpherePartitioner with Communicator and Partitioner base classes for typing
• examples/notebooks/functions.py Updated call to GridIndexing.from_sizer_and_communicator()
• examples/notebooks/stencil_definition.ipynb Updated call to GridIndexing.from_sizer_and_communicator()
• fv3core/pace/fv3core/_config.py: update nf_omega for orthogonal grids
• fv3core/pace/fv3core/initialization/dycore_state.py: replace CubeSphereCommunicator with Communicator base class for typing
• fv3core/pace/fv3core/initialization/geos_wrapper.py: updated call signature
• fv3core/pace/fv3core/stencils/a2b_ord4.py: Added handling for grid_type 4
• fv3core/pace/fv3core/stencils/c_sw.py: added handling for grid_type 4
• fv3core/pace/fv3core/stencils/d2a2c_vect.py: added handling for grid_type 4
• fv3core/pace/fv3core/stencils/d_sw.py: added handling for grid_type 4, updated call signatures
• fv3core/pace/fv3core/stencils/delnflux.py fixed precision/rounding issue with nord, may no one ever need to see this code again
• fv3core/pace/fv3core/stencils/divergence_damping.py: Added smagorinsky diffusion for doubly-periodic configs, updated call to a2b_ord4 for grid_type 4
• fv3core/pace/fv3core/stencils/dyn_core.py: updated call signatures and args for doubly-periodic runs
• fv3core/pace/fv3core/stencils/fv_dynamics.py updated call to c2l
• fv3core/pace/fv3core/stencils/fxadv.py: added handling for grid_type 4
• fv3core/pace/fv3core/stencils/nh_p_grad.py: added handling for grid_type 4
• fv3core/pace/fv3core/stencils/tracer_2d_1l.py: replace CubeSphereCommunicator with Communicator base class for typing
• fv3core/pace/fv3core/stencils/updatedzc.py: added handling for grid_type 4
• fv3core/pace/fv3core/stencils/xppm.py: added handling for grid_type 4
• fv3core/pace/fv3core/stencils/xtp_u.py: added handling for grid_type 4
• fv3core/pace/fv3core/stencils/yppm.py: added handling for grid_type 4
• fv3core/pace/fv3core/stencils/ytp_v.py: added handling for grid_type 4
• fv3core/tests/conftest.py: added --dperiodic command line option for doubly periodic test data
• fv3core/tests/mpi/test_doubly_periodic.py: updated call signs
• fv3core/tests/savepoint/translate/translate_a2b_ord4.py: Updated constructor for a2b, but there isn't a good way to test the doubly-periodic config, so we just pass in that case
• fv3core/tests/savepoint/translate/translate_cubedtolatlon.py: update constructor
• fv3core/tests/savepoint/translate/translate_fxadv.py: updated constructor
• fv3core/tests/savepoint/translate/translate_updatedzc.py: updated constructor
• fv3core/tests/savepoint/translate/translate_xtp_u.py: updated constructor
• fv3core/tests/savepoint/translate/translate_ytp_v.py: updated constructor
• physics/tests/conftest.py: added --dperiodic command line option for doubly periodic test data
• stencils/pace/stencils/c2l_ord.py: added handling for grid_type 4 and (re?)added mock echange(?)
• stencils/pace/stencils/fv_update_phys.py: updating call signs, passing grid_type into updates
• stencils/pace/stencils/testing/conftest.py: updating calls, adding dperiodic logic to generate a tile communicator and partitioner instead of a cubedsphere comm and partitioner
• stencils/pace/stencils/testing/test_translate.py: added simple logic to create a tile comm for doubly periodic tests
• stencils/pace/stencils/update_atmos_state.py: changed cubedspherecomm to comm
• stencils/pace/stencils/update_dwind_phys.py: now handling for grid_type 4
• tests/main/fv3core/test_dycore_call.py: updating call signs
• tests/main/physics/test_integration.py: updating call signs
• tests/savepoint/conftest.py: adding dperiodic option for doubly periodic tests
• tests/savepoint/test_checkpoints.py: updating call sign
• util/HISTORY.md: updated with latest additions
• util/pace/util/__init__.py: Partitioner abstract base class is now included in module by default to generalize from just CubedSphere layouts
• util/pace/util/_legacy_restart.py: replace CubeSphereCommunicator with Communicator base class for typing
• util/pace/util/communicator.py: from_layout and size are now abstract methods on all Communicator classes
• util/pace/util/grid/generation.py: replace CubeSphereCommunicator with Communicator base class for typing
• util/pace/util/grid/helper.py: added grid_type to driver grid data
• util/pace/util/partitioner.py: Partitioner is now a useful abstract base class for typing

This got slightly larger than intended, sorry

Checklist

Before submitting this PR, please make sure:

• [x] You have followed the coding standards guidelines established at Code Review Checklist.
• [x] Docstrings and type hints are added to new and updated routines, as appropriate
• [x] All relevant documentation has been updated or added (e.g. README, CONTRIBUTING docs)
• [x] For each public change and fix in pace-util, HISTORY has been updated
• [x] Unit tests are added or updated for non-stencil code changes

Additionally, if this PR contains code authored by new contributors:

• [x] The names of all the new contributors have been added to CONTRIBUTORS.md

[oelbert]

Did you check orchestrated ?

Just checked and DaCe orchestration does work