Merge v8.1-gsl-merge branch into gsl/develop #14
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ale-reference suite uses the nTiedtke (cu_ntiedtke) and not the tiedtke (cu_tiedtke) parameterization of deep and shallow convection. One motivation of using the cu_ntiedtke option instead of cu_tiedtke is the scale-aware capability of the nTiedtke parameterization, allowing the use of nTiedtke iwth variable-resolution meshes. -> therefore, we decided to rename the package cu_tiedtke_in to cu_ntiedtke_in.
… f_qv, f_qr, and f_qs in module_cu_tiedtke.F and module_cu_ntiedtke.F. Those three variables are not used in the parameterizations. * In ./src/core_atmosphere/physics/mpas_atmphys_driver_convection.F, removed f_qv, f_qr, and f_qs in the calls to cu_tiedtke and cu_ntiedtke.
… f_qv and f_qc in module_cu_kfeta.F. Those two variables are not used in the parameterization. * In ./src/core_atmosphere/physics/mpas_atmphys_driver_convection.F, removed f_qv and f_qc in the call to kf_eta_cps.
…added comments at the top of module.
… f_qv and f_qc in module_ra_cam.F (subroutine camrad). Those two variables are not used in the parameterization. * In ./src/core_atmosphere/physics/mpas_atmphys_driver_radiation_lw(sw).F, removed f_qv and f_qc in the calls to camrad.
…ariable f_qv which is not needed in any of the physics parameterizations.
-> in mpas_atmphys_vars.F, removed the "parameter" definition for f_qc,f_qr,f_qi,
f_qs,f_qg,f_nc,and f_ni. these variables are now simply defined as logicals.
also renamed f_qnc to f_nc, and f_qni to f_ni.
-> in mpas_atmphys_init.F, added subroutine init_physics_flags to initialize f_qc,
f_qr,f_qi,f_qs,f_nc,and f_ni.
-> in mpas_atmphys_driver_pbl.F, changed the call in mynn_bl_driver after renaming
f_qnc to f_nc, and f_qni to f_ni.
By defining the MPAS_USE_MPI_F08 macro at compile time, MPAS can now use the more modern 'mpi_f08' module for MPI. If the MPAS_USE_MPI_F08 macro is not defined, MPAS uses the 'mpi' module as prior to this commit. With the use of the 'mpi_f08' module, certain MPI types are no longer integers in Fortran, but are derived types; e.g., MPI_Comm, MPI_Request, MPI_Datatype, MPI_Info. In some instances, an integer-typed MPI type is still needed for interoperability, and the MPI standard permits this to be done through the 'mpi_val' member of all MPI derived types, e.g., MPI_Comm % mpi_val.
By trying to compile a test program that uses the 'mpi_f08' module, the top-level Makefile can now detect whether the MPI implementation provides an 'mpi_f08' module and, if so, adds a definition of the MPAS_USE_MPI_F08 macro to the CPPFLAGS used in the build.
) This merge enables MPAS to make use of the more modern mpi_f08 module introduced in MPI-3.0. The top-level Makefile now tries to compile a test program that uses mpi_f08, and if that test is successful, the macro MPAS_USE_MPI_F08 is defined in the CPPFLAGS used in the build; otherwise, MPAS will make use of the mpi module as it previously did. With the use of the mpi_f08 module, certain MPI types are no longer integers in Fortran, but are derived types; e.g., MPI_Comm, MPI_Request, MPI_Datatype, and MPI_Info. However, in some instances, an integer-typed MPI type is still needed for interoperability, and the MPI standard permits this to be done through the mpi_val member of all MPI derived types, e.g., MPI_Comm % mpi_val. * framework/mpas_use_mpi_f08: Add logic in top-level Makefile to detect mpi_f08 module availability Allow MPAS to use either of 'mpi_f08' or 'mpi' modules
-> renamed module mpas_atmphys_driver_lsm_shared.F to mpas_atmphys_lsm_shared.F.
-> in mpas_atmphys_driver_lsm.F, now use mpas_atmphys_lsm_shared to call subroutine
correct_tsk_over_seaice. removed subroutine correct_tsk_over_seaice at the bottom
of the module.
-> corrected Makefile accordingly.
…eres The methods previously employed in the mpas_sphere_angle function for computing the side lengths of a spherical triangle were only applicable to unit-radius spheres. This commit generalizes the computation of these side lengths so that the mpas_sphere_angle function can be used to compute spherical angles on spheres of arbitrary radius.
…gh the local variables needed in the calculation of t2m, th2m, and q2 prior to updating all LSM variables (see subroutine lsm_to_MPAS).
…he call to sfcdiags from subroutine driver_lsm to subroutine lsm_to_MPAS. This allows t2m, th2m, and q2 to be correctly computed over seaice points.
This merge updates the calculation of the 2-meter temperature, potential temperature, and specfic humidity over seaice points. In MPAS-v8.0.1, the 2-meter temperature (t2m), potential temperature (th2m), and specific humidity (q2) are computed in subroutine sfcdiags which is called immediately after the call to seaice_noah in subroutine driver_lsm (see mpas_atmphys_driver_lsm.F). This implies that the input variables in subroutine sfcdiags have not yet been weighted by the seaice fraction which in turn impacts the calculation of the 2-meter diagnostics. In order to have t2m, th2m, and q2 to depend on the seaice fraction, this merge moves the correction of local variables as functions of the seaice fraction and calls to subroutine sfcdiags at the top of subroutine lsm_to_MPAS. * NSF-MPAS/lsm_sfcdiags: * In ./src/core_atmosphere/physics/mpas_atmphys_driver_lsm.F, moved the call * In ./src/core_atmosphere/physics/mpas_atmphys_driver_lsm.F, now weigh the * In ./src/core_atmosphere/physics:
…r_seaice.F:
-> mpas_atmphys_driver_seaice.F contains all the sourcecode related to surface
processes over seaice points.
-> in mpas_atmphys_driver_lsm.F, removed all the sourcecode related to surface
processes over seaice points and moved the sourcecode to the seaice driver.
-> changed Makefile accordingly.
…scheme This commit initializes two local variables, mvd_r and mvd_c, in the mp_thompson routine to avoid the potential use of uninitialized memory. Note: Identical changes to those included in this commit have been introduced into newer versions of the Thompson microphysics scheme, and so the changes here can be considered a back-port of fixes.
…v8.0.2 (PR MPAS-Dev#1148) This merge generalizes the mpas_sphere_angle function so that it provides correct results for non-unit-radius spheres. The methods previously employed in the mpas_sphere_angle function for computing the side lengths of a spherical triangle were only applicable to unit-radius spheres. This merge generalizes the computation of these side lengths so that the mpas_sphere_angle function can be used to compute spherical angles on spheres of arbitrary radius. This merge closes Issue MPAS-Dev#1149.
…(PR MPAS-Dev#1152) This merge initializes two local variables, mvd_r and mvd_c, in the mp_thompson routine to avoid the potential use of uninitialized memory. Note: Identical changes to those included in this merge have separately been introduced into newer versions of the Thompson microphysics scheme, and so the changes here can be considered a back-port of these fixes. This merge closes Issue MPAS-Dev#1150.
Since these OpenACC compilation tests don't depend on NetCDF, GPTL, or other libraries, problems can be prevented by removing the linking commands that come from the LIBS variable. For example, the openacc_test rule will fail and the build will abort if a library the compiler expects to link against hasn't built yet.
…corrected the units of the variable dx_p from meters to kilometers (dx_p is used in the Thompson parameterization of the cloud fraction).
This merge fixes a bug when calling the Thompson parameterization of the cloud fraction. The input to the Thompson scheme expects the grid scale to be in units of km, but in the mpas_atmphys_driver_cloudiness module, dx_p was in units of meters. The unit of dx_p has been corrected to be in kilometers. Acknowledgements: Thanks to Brett Wilt for first identifying the bug in the units of dx_p in the call to the Thompson cloud fraction scheme. * mp_thompson_cldfra: * In ./src/core_atmosphere/physics/mpas_atmphys_driver_cloudiness.F, corrected the units of the variable dx_p from meters to kilometers (dx_p is used in the Thompson parameterization of the cloud fraction).
This merge corrects several issues in the MPAS-Atmosphere model, specifically: * Generalize the mpas_sphere_angle function to provide correct results for non-unit-radius spheres. This generalization fixes problems in remapping static fields to the outermost layer of specified-zone cells in limited-area meshes. * Initialize mvd_r and mvd_c before first use in the Thompson microphysics scheme to prevent the potential use of uninitialized memory, which could lead to floating-point exceptions. * Correct the units for the grid scale input field to the Thompson cloud fraction scheme.
…1141) This merge revises the initialization of the flags f_qc, f_qi, f_qr, f_qs, f_qg, f_ni, and f_nc that control which cloud condensate mixing ratios (qc, qr, qi, qs, qg) and cloud number concentrations (nc, ni) are used in the physics parameterizations. Note that the flag f_qv was removed from all physics parameterizations because the mixing ratio qv is always needed. In the original sourcecode, the flags were defined and set to true (or false) manually in mpas_atmphys_vars.F. In the updated sourcecode, the flags are now initialized in subroutine init_physics_flags in mpas_atmphys_init.F. Flags are set to true if the corresponding cloud condensates and number concentrations are actually allocated at run time. This merge also changes the name of the 'cu_tiedtke_in' package to 'cu_ntiedtke_in'. * NSF-MPAS/init_physics_flags: * In ./src/core_atmosphere/physics: * In ./src/core_atmosphere/physics/mpas_atmphys_vars.F, removed the variable f_qv... * In ./src/core_atmosphere/physics/physics_wrf, removed the variables f_qv and f_qc... * In ./src/core_atmosphere/physics/mpas_atmphys_driver_convection.F, added comments... * In ./src/core_atmosphere/physics/physics_wrf, removed the variables f_qv and f_qc... * In ./src/core_atmosphere/physics/physics_wrf, removed the variables f_qv, f_qr, and... * In ./src/core_atmosphere/physics/mpas_atmphys_control.F, the mesoscale-reference suite...
…AS-Dev#1154) This merge removes $(LIBS) from build commands under the 'openacc_test' target in the top-level Makefile. Since these OpenACC compilation tests don't depend on NetCDF, GPTL, or other libraries, problems can be prevented by removing the linking commands that come from the LIBS variable. For example, the openacc_test target will fail if OPENACC=true is specified and if a library the compiler expects to link against hasn't been built yet (e.g., SMIOL). * framework/fix_makefile_openacctest: Remove LIBS from openacc_test in top-level Makefile
…P directives around the loop that calls the seaice driver.
…ted the Copyright at the top of the module.
This merge adds a separate driver to call the parameterization of sea ice. In preparation for the addition of the Noah-MP land surface model (LSM), and because the Noah and Noah-MP LSMs share the same parameterization of sea ice, this merge moves all code related to sea ice that currently sits in the Noah LSM driver to its own driver (mpas_atmphys_driver_seaice.F). The call to the sea ice driver is located in the main driver after the call to the Noah LSM. All outputs are bit-for-bit relative to the original parameterization. * NSF-MPAS/lsm_seaice: * In ./src/core_atmosphere/physics/mpas_atmphys_driver_seaice.F, updated the Copyright... * In ./src/core_atmosphere/physics/mpas_atmphys_driver.F, added OpenMP directives... * In ./src/core_atmosphere/physics, added the file mpas_atmphys_driver_seaice.F:
This merge introduces fixes from MPAS v8.0.2, and it connects the v8.0.2 tag to future commits on 'develop'. * master: In ./src/core_atmosphere/physics/mpas_atmphys_driver_cloudiness.F, corrected the units ... Initialize mvd_r and mvd_c before first use in Thompson microphysics scheme Generalize mpas_sphere_angle function to work for non-unit-radius spheres Update version number to 8.0.2 * master: * In ./src/core_atmosphere/physics/mpas_atmphys_driver_cloudiness.F, corrected the units of the variable dx_p from meters to kilometers (dx_p is used in the Thompson parameterization of the cloud fraction). Initialize mvd_r and mvd_c before first use in Thompson microphysics scheme Generalize mpas_sphere_angle function to work for non-unit-radius spheres Update version number to 8.0.2
This merge updates the MYNN Surface Layer and Planetary Boundary Layer (PBL) schemes. The PBL scheme includes the options needed to run the Eddy Diffusivity Mass Flux (EDMF) parameterizations. * The core of the SFC Layer scheme is located in ./physics_mmm/sf_mynn.F. * The core of the PBL scheme is located in ./physics_mmm/bl_mynn.F and ./physics_mmm/bl_mynn_subroutines.F. * NSF-MPAS/bl_mynn_updated: * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn_subroutines.F, changed all... * In ./src/core_atmosphere/physics/mpas_atmphys_driver_pbl.F, commented out extra... * In ./src/core_atmosphere/physics/physics_mm/bl_mynn.F, removed extra commented... * In ./src/core_atmosphere/physics: * In ./src/core_atmosphere/physics: * In ./src/core_atmosphere/physics: * In ./src/core_atmosphere/physics: * In ./src/core_atmosphere/physics: * In ./src/core_atmosphere/Registry.xml, changed the option config_mynn_topdown... * In ./src/core_atmosphere/physics: * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn_subroutines.F, removed the extra... * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn.F, removed the lines: * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn_subroutines.F, commented out... * In ./src/core_atmosphere/physics, made minor corrections to ./physics_mmm/Makefile... * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn_subroutines.F, removed extra... * In ./src/core_atmosphere/physics, updated the MYNN PBL with the sourcecode available... * In ./src/core_atmosphere/physics/physics_mmm, very minor corrections to mp_radar.F... * In ./src/core_atmosphere/physics, very minor corrections to Makefile, mpas_atmphys_driver_convection.F... * In ./src/core_atmosphere/physics, updated the MYNN surface layer scheme using the...
…itialization of local variable we.
This merge adds code to initialize the 'we' variable in the YSU PBL scheme. Without this initialization, the 'we' variable may be accessed without having been initialized, potentially leading to a floating-point exception.
The `mpas_pool_create_pool` subroutine already allocates the pointer in its arguments. Therefore, calling `allocate` before `mpas_pool_create_pool` actually causes memory leaks.
…Dev#1160) This merge fixes memory leaks due to duplicate allocate calls on pointers in the file structs_and_variables.inc. This file is auto-generated and then included by, e.g., src/core_atmosphere/mpas_atm_core_interface.F at compile time. No functional changes are introduced by this merge. For example, in the auto-generated file src/core_atmosphere/inc/structs_and_variables.inc, there are code snippets similar to the following: subroutine atm_generate_pool_mesh(block, structPool, dimensionPool, packagePool) ! ... (Unrelated lines omitted) ... type(mpas_pool_type), pointer :: newSubPool ! ... (Unrelated lines omitted) ... allocate(newSubPool) call mpas_pool_create_pool(newSubPool) call mpas_pool_add_subpool(structPool, 'mesh', newSubPool) call mpas_pool_add_subpool(block % allStructs, 'mesh', newSubPool) ! ... (Unrelated lines omitted) ... end subroutine atm_generate_pool_mesh The problem is that the mpas_pool_create_pool subroutine already allocates the pointer in its arguments internally. Therefore, calling allocate before mpas_pool_create_pool actually causes memory leaks. The fix adopted in this merge is to simply remove the generation of the 'allocate' calls in the 'structs_and_variables.inc' file for each core.
MPAS Version 8.1.0 This release of MPAS introduces several updates and new capabilities for MPAS-Atmosphere, most notably: * The MYNN Surface Layer and Planetary Boundary Layer (PBL) schemes have been updated. The PBL scheme includes the options needed to run the Eddy Diffusivity Mass Flux (EDMF) scheme. * A separate driver for the parameterization of surface processes over sea-ice points has been added. * The build system now tests for the availability of the modern 'mpi_f08' module in the MPI library. If detected, the 'mpi_f08' module interface to Fortran MPI routines will be used in favor of the older 'mpi' module interface. * The atmosphere core now supports the storage and retrieval of time-invariant fields in a separate I/O stream, offering significant disk space savings, especially in cases where large ensembles or cycled simulations are being run. * The top-level Makefile provides a new 'intel' build target for the Intel oneAPI Fortran, C, and C++ compiler suite. * To support real-data simulations on meshes with grid distances approaching 1 km or less, the init_atmosphere core provides an option, config_30s_supersample_factor, for super-sampling of the 30 arc-second terrestrial fields (terrain, land use, soil category, and MODIS FPAR monthly vegetation fraction). * When compiling, PRECISION=single is now the default, and double-precision builds must be specified with PRECISION=double.
* Updated SOILPARM.TBL and VEGPARM.TBL for RUC LSM. * Add mpas_atmphys_lsm_shared.o to dirver_lsm section * RUC LSM and its 2-m diagnostics stay in the LSM driver. It will provide solutions for land and ice points. Therefore, with RUC LSM, do not do call to dirver_seaice. * Added 2-m variables, will be used for RUC LSM diagnostics. * Removed zero out of frozen and liqid soil water at the first time step. It has been initialized in ruclsminit.
* 3D Reflectivity (#11) * Set initial value of nc for aerosol-aware microphysics * Move call to 3D reflectivity to microphysics * Updated SOILPARM.TBL and VEGPARM.TBL for RUC LSM. * Add mpas_atmphys_lsm_shared.o to dirver_lsm section * RUC LSM and its 2-m diagnostics stay in the LSM driver. It will provide solutions for land and ice points. Therefore, with RUC LSM, do not do call to dirver_seaice. * Added 2-m variables, will be used for RUC LSM diagnostics. * Removed zero out of frozen and liqid soil water at the first time step. It has been initialized in ruclsminit. * Initialize clouds (#12) * Set initial value of nc for aerosol-aware microphysics * Two quick MPAS fixes (#10) * Move call to 3D reflectivity to microphysics * Add flags for Thompson options * Move lookup table functions to utils and add flags to initialization * Clean up microphysics flags for table build and initialization * Add MPAS code for initialization of cloud number concentration * Cleanup (#13) * Set initial value of nc for aerosol-aware microphysics * Two quick MPAS fixes (#10) * Move call to 3D reflectivity to microphysics * Add flags for Thompson options * Move lookup table functions to utils and add flags to initialization * Clean up microphysics flags for table build and initialization * Add option to built hail-aware or non hail-aware lookup tables * Update pointer to microphysics submodule commit * Point to microphysics bugfix * Update src/core_atmosphere/physics/physics_wrf/module_sf_ruclsm.F --------- Co-authored-by: Tanya Smirnova <tanya.smirnova@noaa.gov> Co-authored-by: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
#12) * Updating MYNN-EDMF, cloud-radiation coupling, and surface layer tweaks * Update src/core_atmosphere/Registry.xml fix typo --------- Co-authored-by: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
* "updated GF for MPAS" * "clean the print statements"
jderrico-noaa
requested review from
joeolson42,
haiqinli,
tanyasmirnova,
mdtoyNOAA and
AndersJensen-NOAA
jderrico-noaa
commented
May 9, 2024
tanyasmirnova
approved these changes
May 9, 2024
There was a problem hiding this comment.
@jderrico-noaa Janet, thank you for the commit in RUC LSM. My other comments are not critical, I was just curious. I reviewed carefully the physics part of the merge, and it looks good to me. I will approve this PR.
It's good you made a note of it here so that if issues that might be related to the to the removed variables come up we know where to start looking |
tanyasmirnova
approved these changes
May 9, 2024
AndersJensen-NOAA
approved these changes
May 9, 2024
joeolson42
reviewed
May 10, 2024
joeolson42
reviewed
May 10, 2024
joeolson42
approved these changes
May 10, 2024
AndersJensen-NOAA
pushed a commit
to AndersJensen-NOAA/MPAS-Model
that referenced
this pull request
Sep 12, 2024
re-implementation of the MYNN-EDMF
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
v8.1-gsl-merge branch contains the following PRs:
MPAS v 8.1
Updates for using RUC LSM in 8.1 (Solution #2 for the use of RUC LSM in the MPAS 8.1 #9 )
Update to microphysics for HRRRv5 (Update to Microphysics for HRRRv5 #10 )
Updating MYNN-EDMF, cloud-radiation coupling, and surface layer tweaks ( Updating MYNN-EDMF, cloud-radiation coupling, and surface layer tweaks #12 )
Updated GF for MPAS (updated GF for MPAS #13)