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Multi-Physics Problem (MPP) library is a standalone library that solves biophysics problems relevant to global land surface models (LSMs).

License: Other

Shell 0.05% CMake 1.74% Makefile 0.10% Python 1.06% Fortran 97.05%

bsd-license land-surface-modeling petsc

mpp's Introduction

MPP

Multi-Physics Problem (MPP) library is a standalone library that solves biophysics problems relevant to global land surface models (LSMs).

Installation

Requirements

Mac
Git
C and Fortran compiler
CMake
PETSc
Message Passing Interface

Installation instructions

Install PETSc

Clone PETSc and check out the supported version.

cd <directory-of-choice>
git clone https://bitbucket.org/petsc/petsc petsc
cd petsc
git checkout v3.16.2

Configure PETSc. (Detailed PETSc installation instructions are available here)

2.1. Set PETSc installation location and architecture

export PETSC_DIR=$PWD
export PETSC_ARCH=<user-defined>

2.2. Set compilers

# Set compilers
export CC=<Parallel-C-compiler>
export CXX=<Parallel-C++-compiler>
export FC=<Parallel-Fortran-compiler>
export MPIEXCE=<Path-to-mpiexec>
export BLAS_DIR=<Path-to-BLAS-dir>

On Mac OS X, one can set BLAS_DIR to /System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate

2.3. Run configure

./configure \
--with-cc=$CC   \
--with-cxx=$CXX \
--with-fc=$FC \
--with-mpiexec=$MPIEXEC \
--with-blas-lapack-lib=$BLAS_DIR

Build PETSc

make PETSC_DIR=$PETSC_DIR PETSC_ARCH=$PETSC_ARCH all

Test PETSc installation

make PETSC_DIR=$PETSC_DIR PETSC_ARCH=$PETSC_ARCH test

Install MPP

Clone MPP repository from github.com.

cd <directory-of-choice>
git clone https://github.com/MPP-LSM/MPP

Configure MPP

cd MPP
make CC=$CC CXX=$CXX FC=$FC config

Build MPP (add SKIP_PETSC_TESTS=yes if building on a node that cannot run tests)

make CC=$CC CXX=$CXX FC=$FC install

Run MPP tests

make CC=$CC CXX=$CXX FC=$FC test

Publication

Bisht, G., Riley, W. J., Hammond, G. E., and Lorenzetti, D. M., Development and evaluation of a variably saturated flow model in the global E3SM Land Model (ELM) version 1.0, Geosci. Model Dev., 11, 4085-4102, https://doi.org/10.5194/gmd-11-4085-2018, 2018

Bisht, G., & Riley, W. J. (2019). Development and verification of a numerical library for solving global terrestrial multi‐physics problems. Journal of Advances in Modeling Earth Systems, 11. https://doi.org/10.1029/2018MS001560

mpp's People

Contributors

Stargazers

Watchers

Forkers

e3sm-project jht1983 anasena gutabeshu

mpp's Issues

Remove duplicate code in VSFMMPPSetSaturationFunctionAuxVarConn

The duplicate code in MultiPhysicsProbVSFM.F90#L1916 and MultiPhysicsProbVSFM.F90#L1999
should be replaced.

Errors on Ubuntu

Encountered following error when testing on Ubuntu:

Compiler error during installation. MPI library was installed via PETSc.
Segmentation fault in thermal_mms test due to uninitialized variable.

Consolidate subroutines in ThermalEnthalpySoilAux

The following subroutines should be consolidated:

ThermalEnthalpySoilAuxSetHeatCap
ThermalEnthalpySoilAuxSetThermalCondWet
ThermalEnthalpySoilAuxSetThermalCondDry
ThermalEnthalpySoilAuxSetThermalAlpha
ThermalEnthalpySoilAuxSetSoilDensity

Account of derivative of thermal conductivity w.r.t. Pressure

Derivative of thermal conductivity at the interface w.r.t. to up/down pressure needs
to be accounted for in the jacobian computation

dtherm_dP_up   = (dist_up*therm_cond_dn/therm_cond_up) * therm_cond_ave_over_dist/(dist_up*therm_cond_dn + dist_dn*therm_cond_up) * dsat_dP_up
dtherm_dP_dn   = (dist_up*therm_cond_up/therm_cond_dn) * therm_cond_ave_over_dist/(dist_up*therm_cond_dn + dist_dn*therm_cond_up) * dsat_dP_dn

Update FETCH-2 SPAC problem

Add following command line options:

Ability to prescribe ET, soil BC, and output filename
Ability to simulate following mesh configurations:
- Mesh for an oak tree with top-soil soil layer as BC,
- Mesh for a pine tree with top-soil soil layer as BC,
- Mesh for an oak and pine tree with top-soil soil layer as BC,

VSFM restart only supports problems with 1 governing equation

Presently, the restart is hardcoded to only support 1 GE (see MultiPhysicsProbVSFM.F90#L674)

Improve code related to setting up of coupling variables

Remove MPPGovEqnSetInternalCouplingVars() and MPPGovEqnSetCouplingVars() as procedures
Rename MPPGovEqnAddCouplingCondition() to MPPGovEqnAddBoundaryCouplingCondition
Rename MPPGovEqnSetCouplingVars() to MPPGovEqnSetBoundaryCouplingVars
Rename MPPGovEqnSetBothCouplingVars() to MPPGovEqnSetCouplingVars()

VSFM pressure_prev is not saved in auxvars

Add support for setting up mesh for common configurations

Add subroutine to set up a mesh for few default configurations so as to avoid code repetition
(e.g. vsfm_sy1991_problem.F90#L267, vsfm_celia1990_problem.F90#L171)

Mesh configuration 1:
- domain extent in x, y, and z direction
- nx, ny, nz
- internal connection type: x-only, y-only, z-only, or in all three directions.
Mesh configuration 2:
- min and max in x, y, and z
- nx, ny, nz
- internal connection type: x-only, y-only, z-only, or in all three directions.

Add new subroutines in MultiPhysicsProbThermal that can set properties individually

Presently MPPThermalSetSoils() is defined as:

  subroutine MPPThermalSetSoils(thermal_mpp, begc, &
                           endc,               &
                           thermal_filter,                 &
                           thermal_lun_type,               &
                           thermal_watsat,                 &
                           thermal_csol,                   &
                           thermal_tkmg,                   &
                           thermal_tkdry                   &
                           )

sets all properties of soils is set at once.

Add new subroutine(s) that:

Set properties one at a time.
Set properties for internal, boundary, and source-sink auxiliary variables.

In MultiPhysicsProbThermal, add the support to set material properties for BC

Presently MPPThermalSetSoils() does not set soil properties for boundary conditions.