- domain_decomp_type = 'round_robin'        [Default]
                     = 'graph_partitioning' [New scheme]

- Presently domain_decomp_type is only read from namelist file,
  but not used within ALM

- If lateral_connectivity = .true., the code attempts to read
  grid-to-grid connectivity information from the domain file.

- This grid-to-grid connectivity information for ALM:
   - Follows the convention used by MPAS.
   - Is saved as cellsOnCell data field within the domain netcdf file.
   - dimname(cellsOnCell) = {'nCells','maxEdges'}

- Graph Partitioning (GP) requires PETSc.
- Presently, GP is only implemented for ALM grid with no
  inactive grid cells.

Both, VSFM and framework for lateral subsurface connectivity
require PETSc. Thus, a new subourtine is added that consolidates
the initialization of PETSc.

- The framework requires PETSc.
- It is based of the unstructured grid framework implemented in PFLOTRAN.

- Adds to exchange data for ghost/halo grid cells across
  MPI ranks.
- Adds subroutine to free up memory

- NAG returns an error with the file is empty

Counts up ghost gridcells, landunits, columns, and pfts on
each MPI task

Reads in x/y fields (in meters), if 'xCell'/'yCell' field
are present within the domain netCDF

Adds a check for ghost/halo grid-to-landunit mapping

- Each MPI task can get ghost/halo column level data from it's
  neighbor.
- The subroutine needs to be called outside OpenMP/clump loop

- Memory is allocated for ghost/halo columns for the following
  soil properties:
  - watsat : porosity
  - hksat  : hydraulic conductivity
  - bsw    : Clapp and Hornberger parameter
  - sucsat : minimum soil suction

- Data for the above mentioned soil properties is exchanges among
  MPI tasks

Modified the TGDB01 EOS w.r.t pressure. Pressure is now only accounted in the
computation of density of water when pressure is greater than reference pressure.
In other words, pressure only affects water density under saturated conditions.

The initial infrastructure includes:
 - Setup of column-level lateral connectivity of subsurface mesh for VSFM.
 - For an operator split approach of solving VSFM, adds a subroutine to
   compute the lateral flux.
 - Updates to the 1D VSFM solver to account of lateral flux.

Note:
 - Column level lateral connection are only set between columns of
   istsoil type.
 - Though, VSFM solver can now account for lateral flux, the
   SoilWaterMovementMod() isn't updated at this stage to allow
   lateral transport because mass-balance check needs to be
   updated.

If lateral_connectivity is true, following additional
data are read from land domain file
 - edgesOnCell
 - nEdgesOnCell
 - areaCell
 - dcEdge
 - dvEdge

ALM subsurface mesh now accounts for geometric attributes
read in using MPAS format. These new attributes (distance
between grid cells, distance of edge shared by grid cells,
and area of grid cell) are required when lateral_connectivity
is set as true.

Modifications for the case when flag -DUSE_PETSC_LIB
is not specified.

- In 1D-flow, infiltration is shut off if the top soil layer is
  fully saturated. Thus, the liquid pressure in the soil column
  could only go slightly above atmospheric pressure at max.

- When lateral flows are turned on, seepage face boundary
  condition is needed to allow for exfiltration from the
  soil column.

- When lateral_connectivity = .true., lateral flows between
  soil columns is allowed in the VSFM solver.

- The flux is computed between 'upwind' and 'downwind' control
  volumes.
- Negative values of flux implies, flow occurs from upwind to
  downwind control volume

Following three options are added:

- none               = No lateral flow
- source_sink        = 1D VSFM solution + Lateral flow modeled as source/sink term
- three_dimensional  = 3D VSFM solution (only supported for serial run)

When a solution is unacceptable due to mass balance error threshold,
reduce PETSc SNES tolerance (solution [stol] or relative [rtol])
depending on the reason for the convergance of SNES.

- Renames VSFM subdirectory to MPP (Multi-Physics-Problems), since
  the VSFM approach is planned to be used for other physics scheme.
- Creates subdirectories within MPP top level directory
  - dtypes: For data types
  - vsfm  : For VSFM
  - util  : For utilities
- Updates ALM build script

[BFB]

In order to support future developments, the ALM thermal
model is split into two:
  - For non-urban columns, and
  - For Urban columns

[BFB]

An option to specify PETSc-based thermal model (use_petsc_thermal_model)
is added. Presently, the PETSc-based thermal model is not supported.

- Adds a PETSc based linear solver for the thermal model
  comprising of the following components:
    - Snow,
    - Standing surface water, and
    - Soil

- The PETSc based model uses the same physics formulation as
  the default ALM model.

- DMComposite() from PETSc is used to assembly:
  - Diagonal block matrix: accounts for interactings within a component, and
  - Off-diagonal block matrix: accounts for interactins across compoents.

Removes unnecessary dependency of ALM-MPP on the
following CLM modules:
- clm_time_manager
- column_varcon
- decompMod
- shr_infnan_mod
- shr_kind_mod
- spmdMod
- ColumnType
- EnergyFluxType
- GridcellType
- LandunitType
- SoilHydrologyType
- SoilStateType
- TemperatureType
- WaterstateType

Removes unnecessary dependency of ALM-MPP on the
following CLM modules:
- clm_varcon
- clm_varctl
- clm_varpar
- shr_log_mod

Makes the file names be consistent with module name

Removes unnecessary dependency of ALM-MPP on the
following CLM modules:
- abortutils

Removes unnecessary dependency of ALM-MPP on the
following CLM modules:
- domainLateralMod

Removes few outstanding unnecessary dependency of ALM-MPP on
CLM modules

This refactor removes the hard coded setup of the ALM's
PETSc based thermal model from the MPP (multi-physics-problem)
library. The setup of MPP problem for ALM now occurs in
the biophysics/mpp/driver/alm directory and setup of other
problems for benchmark and verification will occur in
the biophysics/mpp/driver directory.

This refactor removes the hard coded setup of the ALM's
VSFM from the MPP (multi-physics-problem) library.
The setup of MPP problem for ALM now occurs in
the biophysics/mpp/driver/alm directory and setup of other
problems for benchmark and verification will occur in
the biophysics/mpp/driver directory.

- Residual soil mositure can now be specified a non-zero value.
- Connection set of a source-sink or boundary condition can be
  updated.
- Correctly initializes auxvars of a boundary condition.
- Fixes the update value of boundary condition auxvar.

Multiple fixes to ALM's MPP to enable multiple coupled governing
equations.

Adds use_dynamic_linesearch to SoE base type which is set during initialization
step. The dependency of SoE base type on clm_varctl is thus removed.

- Updates the connection_set_type to store type (=horz/vert) for each
  connection within the connection set.
- Fixes mesh setup for lateral connections.

A new runtime option (vsfm_include_seepage_bc) would add
seepage face boundary condition to VSFM formulation if
lateral flow model in on. This seepage face boundary
condition would allow for water to exfiltrate.

- Deletes existing VSFM code from ACME git.
- Adds the VSFM code via git submodule.
- Updates ALM's configure script.

In order to support modifications in VSFM, VSFM initialization by
ALM is updated.

- Updates the hash of ALM-MPP submodule, and
- Minor updates to ALM's initialization of MPP.

- EMI is used to call external physics formulations
  in MPP (i.e. VSFM and PTM).
- EMI uses the same version of PETSc as used by MPP (i.e. PETSc > 3.7.x)

EMI driver for MPP now replaces MPP driver

- Memory allocation of column-level filters in EMI are now changed
  such that they are indexed from 1:num_filter instead of begc:endc.
- During initialization of VSFM, a new column level filter is used
  to unpack data from VSFM into ALM's data structure. This is done
  to avoid overriding column-level data in which VSFM is not active.

The column level mesh attributes (i.e. soil thickness, soil centroid,
and soil layer interface) are needed by PTM for soil and snow layers

Bug fixes based on global ALM simulation with PTM.

xCell and yCell for the land domain are not set by default.
Thus, the output of xCell and yCell resulted in failure when
DEBUG is set to TRUE.