Solver/two phase semi implicit

[bodhinandach]

Describe the PR
This PR is to implement the two-phase one-layer solvers for fully saturated soil simulation. One particle includes both solid phase and liquid phase, which are defined by the corresponding volume fractions (n_s and n_w). The theory of porous media is adopted to set up the governing equations (momentum balance and mass balance). All implementations work coherently with the current MPI and OpenMP parallelization features. Two solvers are presented in this PR: explicit and semi-implicit.

New implementation
TwoPhase Particle

1. New class ParticleTwoPhase derived from Particle, which include all necessary functions for two-phase computation and new variables for two-phase (etc. pore pressure, porosity)
2. New hdf5 structure for ParticleTwoPhase (also includes refactoring of base hdf5 class)

MPMExplicitTwoPhase

1. New class MPMExplicitTwoPhase derived from MPMBase, which includes the main loop for two-phase computation.
2. New input functions in MPMBase to read the new types of input files for two-phase.

MPMSemiImplicitTwoPhase

1. New class MPMSemiImplicitTwoPhase derived from MPMBase, which includes the main loop for two-phase computation.

TwoPhase functions for nodes

1. New functions for the two-phase are implemented in the current Node class directly (see node_multiphase.tcc)

Free surface detection functions in mesh

1. New functions to detect the changing surface are implemented in the Mesh class (see mesh_multiphase.tcc)

Unit tests and benchmarks
All new implementations are validated by corresponding test functions, and the unit-test for two-phase computation is also included. Related 2D and 3D one-dimensional consolidation tests can be found here: cb-geo/mpm-benchmarks#19.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 88.42237% with 648 lines in your changes missing coverage. Please review.

Project coverage is 95.68%. Comparing base (d6ecaab) to head (8a4995c).
Report is 1261 commits behind head on master.

Files with missing lines	Patch %	Lines
include/particles/particle_twophase.tcc	84.18%	112 Missing ⚠️
include/solvers/mpm_semi_implicit_twophase.tcc	68.34%	101 Missing ⚠️
tests/io/write_mesh_particles.cc	49.70%	85 Missing ⚠️
tests/io/write_mesh_particles_unitcell.cc	51.37%	71 Missing ⚠️
include/solvers/mpm_explicit_twophase.tcc	64.52%	55 Missing ⚠️
include/solvers/mpm_semi_implicit_navierstokes.tcc	75.36%	52 Missing ⚠️
include/solvers/mpm_base.tcc	71.90%	34 Missing ⚠️
include/mesh_multiphase.tcc	87.50%	32 Missing ⚠️
...solvers/assembler_eigen_semi_implicit_twophase.tcc	87.44%	27 Missing ⚠️
include/linear_solvers/assembler_base.h	29.41%	24 Missing ⚠️
... and 12 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master       #5      +/-   ##
==========================================
- Coverage   96.77%   95.68%   -1.10%     
==========================================
  Files         130      168      +38     
  Lines       25920    34544    +8624     
==========================================
+ Hits        25083    33050    +7967     
- Misses        837     1494     +657     

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