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4.4 ruisdael deposition #101

Merged
merged 32 commits into from
Jun 19, 2024
Merged

4.4 ruisdael deposition #101

merged 32 commits into from
Jun 19, 2024

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CasparJungbacker
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@CasparJungbacker CasparJungbacker commented Jun 6, 2024

This merge introduces:

  • Open boundary conditions
  • Ruisdael deposition routines
  • New land surface model
  • Scalar/tracer manager

@fjansson anything else I forgot?

fjansson and others added 18 commits June 16, 2023 15:46
Land surface model by Bart van Stratum
Emission model by Marco de Bruine
Merged and updated for mixed precision by Fredrik Jansson

The land surface model allows reading in a map of land surface properties.
The emission model allows reading in a map of scalar emission sources.

Squashed commit of the following:

commit 44b5a584861593a63d94c2fea79fc4195dd71e67
Author: Fredrik Jansson <[email protected]>
Date:   Mon Jun 5 12:07:44 2023 +0200

    rebasing Ruisdael emission and LSM on 4.4.1. Fixes for mixed precision.

commit d9f0dba64e9e35080cfe8cdf5502380e50442ee9
Author: Bart van Stratum <[email protected]>
Date:   Wed Sep 8 14:54:23 2021 +0200

    Added CO2 scalar for A-Gs net assimilation, for offline budget checks

commit 378607e40dc127394584b25510abb131f7b62b32
Author: Bart van Stratum <[email protected]>
Date:   Tue Sep 7 09:43:17 2021 +0200

    Added A-Gs option without emission module

commit ec0a375c4f562c7b279efb9e3a83d04b4a483047
Author: Bart van Stratum <[email protected]>
Date:   Tue Sep 7 08:08:14 2021 +0200

    Added CO2 respiration/assimilation to cross-section and time series.

commit 1e3a000292e5067301fee3f578407f0befdcaaa8
Author: Bart van Stratum <[email protected]>
Date:   Mon Sep 6 16:36:23 2021 +0200

    Added A-Gs to the new land surface model

commit 1e64628ba65679857a82c11c5b8d40fa819bcd6b
Author: Bart van Stratum <[email protected]>
Date:   Mon Sep 6 12:05:31 2021 +0200

    Added basic infrastructure for A-Gs and communication with emission module

commit 170eb9f7c182baf436a8ce31568c0922392d1b44
Author: Marco de Bruine <[email protected]>
Date:   Tue Jun 8 16:56:12 2021 +0200

    AG-s <-> emission interface indicators now relative to full list of scalar fields

commit 280e180082b7a02a0cfa0e7c331a0ca19092e307
Author: Marco de Bruine <[email protected]>
Date:   Tue Jun 8 15:53:49 2021 +0200

    Emission <-> AGS interface

commit c1ed132ea2eb221550d37ae7efdb22901a9aef56
Author: Bart van Stratum <[email protected]>
Date:   Fri Nov 6 11:30:33 2020 +0100

    Calculate obukhov length from tile averaged fluxes, instead of
    calculating a tiled mean

commit 314b3f30b3d874f363e65f86ab80e927b1324bc5
Author: Bart van Stratum <[email protected]>
Date:   Tue Nov 3 09:12:35 2020 +0100

    Bugfix harmonic mean calculation (which is currently not used in the
    code..)

commit b852be87c837978c8f1c9443d331d19bcdcb8153
Author: Fredrik Jansson <[email protected]>
Date:   Tue Oct 27 11:25:58 2020 +0100

    update fix for #58 - allow lsmcrossection also for new LSM isurf=11

commit ca74c6d8d42a968e413ace9b567f8468698a2f44
Author: Fredrik Jansson <[email protected]>
Date:   Fri Oct 23 11:03:29 2020 +0200

    emission: remove MPI-parallel .nc read, add better namelist error reporting

commit b2e1b2c0de9b90d81911e42c188048bb443fc0ce
Author: Bart van Stratum <[email protected]>
Date:   Fri Oct 16 10:18:03 2020 +0200

    Added NetCDF file with van Genuchten parameters

commit 06ad4d1eeb5dfbc368d289496d40cbc7862cff54
Author: julietbravo <[email protected]>
Date:   Mon Sep 7 10:31:11 2020 +0200

    Small fix in calculation liq. water fraction, plus added cleanup of
    arrays

commit c7978ffda75a1e23802ebe611485bb3c7819ff67
Author: julietbravo <[email protected]>
Date:   Fri Sep 4 15:02:36 2020 +0200

    Fixed dynamic tile fraction for cases with open water

commit a687c221a3cfcebabf14dc34f00a1b4fc31d7ae7
Author: julietbravo <[email protected]>
Date:   Fri Sep 4 11:33:18 2020 +0200

    Added water tile to time series statistics

commit 3c7651d3846266735c7b404a35e054dd7e4cf97f
Author: julietbravo <[email protected]>
Date:   Thu Jul 30 15:43:29 2020 +0200

    Added additional variables to surface cross-sections

commit e5f807d10c8d2d2c8fdd47dbc5bc4848a25fe3ef
Author: julietbravo <[email protected]>
Date:   Tue Jul 21 14:12:40 2020 +0200

    Modified modlsmcrosssection for new LSM

commit cfb67ebdff01dcb1e9c5caee228685c7a435290e
Author: julietbravo <[email protected]>
Date:   Tue Jul 21 12:45:14 2020 +0200

    Store/load the water tiles for restarts (results = bitwise identical
    now)

commit b66d74a81ca0df84cd2fe00689271f18be9df952
Author: julietbravo <[email protected]>
Date:   Tue Jul 21 09:19:12 2020 +0200

    Fixed some MPI issues in new LSM

commit 600cf7c8baef59aad9a68d7df7c9358225c8f893
Author: julietbravo <[email protected]>
Date:   Mon Jul 20 11:55:18 2020 +0200

    First ~working version with water tile (still has some issues...)

commit 2b150cf1da4cac62c8f075afb4b4b77f399d5c26
Author: julietbravo <[email protected]>
Date:   Tue Jul 7 17:28:34 2020 +0200

    Added option to read the spatial data for heterogeneous land surfaces

commit 5ab96410f234f02dbf62eb70f66b06a7dc27a8a9
Author: julietbravo <[email protected]>
Date:   Tue Jul 7 11:53:21 2020 +0200

    Added restart functionality to new LSM

commit fe7ee50813fb863a9d15d7dc9abc6faf1b01629f
Author: julietbravo <[email protected]>
Date:   Tue Jul 7 11:00:32 2020 +0200

    Added old soil grid definition, different soil interpolation types, plus
    fixed bug in buoyancy calculation

commit 30f7d88376e5e6d2b027088919a981fc372fe893
Author: julietbravo <[email protected]>
Date:   Mon Jul 6 16:29:59 2020 +0200

    Added calculation of liquid water reservoir (plus bugfix ra
    calculation)

commit ccd9203704aa102ef7b6cdb04d8c861dbbf9bbca
Author: julietbravo <[email protected]>
Date:   Mon Jul 6 12:21:21 2020 +0200

    Added root water extraction to soil water budget

commit a08b2a55d642ccc1b6517a5409accfafbd0421bc
Author: julietbravo <[email protected]>
Date:   Mon Jul 6 11:23:16 2020 +0200

    Added bulk (grid point mean) quantities needed for SGS model

commit e2bb8edf036e01f2911fae5b01e13b1323a0effd
Author: julietbravo <[email protected]>
Date:   Mon Jul 6 09:01:42 2020 +0200

    Added calculation of bulk (grid point mean) scalar BCs

commit 8091785397a9d84b67fc4199c4a54c4910c8f53c
Author: julietbravo <[email protected]>
Date:   Fri Jul 3 18:02:56 2020 +0200

    Working surface solver, with fluxes per tile

commit fc4f9c63dd90ca39137ced1a2421a0b9b3153956
Author: julietbravo <[email protected]>
Date:   Thu Jul 2 16:32:56 2020 +0200

    Bugfix calculation canopy resistances

commit 58583106e102f5d984885481b35a70d129ccf933
Author: julietbravo <[email protected]>
Date:   Thu Jul 2 16:30:10 2020 +0200

    Added calculation canopy and soil resistance

commit 7bee52c774053dabf6f991489d11c56ff46d32b5
Author: julietbravo <[email protected]>
Date:   Thu Jul 2 12:13:05 2020 +0200

    Working tiled surface layer solver

commit 1d4ecc26b81c63d685bb7b41aff48479d5921fc3
Author: julietbravo <[email protected]>
Date:   Wed Jul 1 16:25:10 2020 +0200

    Start of tiled surface layer solver

commit 9b97bb6986df8415812ee41f6e69434a65834eb2
Author: julietbravo <[email protected]>
Date:   Wed Jul 1 10:00:08 2020 +0200

    Added calculation hydraulic properties (van Genuchten) and diffusion solver for
    soil moisture

commit 87aafb11966a0dce14a0829f07a73ef8ba7b0ad3
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 16:51:10 2020 +0200

    Added calculation of soil thermal properties, and (explicit) temperature
    diffusion solver

commit b41d465c1d4fb7e6ff0bd509cd2d89662270d868
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 14:39:31 2020 +0200

    Added calculation derived van Genuchten parameters

commit 7f7c4efb71aec947a721ce51259af7a1fc30bc23
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 11:38:47 2020 +0200

    Added minimal set of time series statistics for the new LSM

commit 495aa432ab2d2ea09f4f288bdb74260464fb3cef
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 11:08:45 2020 +0200

    Modified modlsmstat to work with the new LSM

commit 2b9ea85438bb2e5245c8e626e4adad58783df660
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 09:52:26 2020 +0200

    Minor changes new LSM

commit 441e90c58aba0fef028af6293fe11f33996fa334
Author: julietbravo <[email protected]>
Date:   Mon Jun 29 15:45:35 2020 +0200

    Added soil grid and initialisation of soil

commit 8704449727833cc7b71d4db9123697f5f3dfd718
Author: julietbravo <[email protected]>
Date:   Mon Jun 29 13:52:11 2020 +0200

    Added homogeneous initialisation of LSM

commit 9aadb79fac33d87f048eeb33e67a04093bfc81d3
Author: julietbravo <[email protected]>
Date:   Mon Jun 29 12:23:47 2020 +0200

    Added data structures for land-surface tiles

commit ad8a3647b1720baff5a8b9d67a043ad6899306db
Author: julietbravo <[email protected]>
Date:   Mon Jun 15 12:06:48 2020 +0200

    Start at implemention realistic LSM

commit 5aaefd41648409269def3823622773fdd650481a
Author: Fredrik Jansson <[email protected]>
Date:   Thu Oct 15 14:43:57 2020 +0200

    modnudgebounday: use random_number() instead of rand() for better intel/gnu compatibility

commit 93d62083e5ec0859a125f671cf95d0ef70e20714
Author: Marco de Bruine <[email protected]>
Date:   Thu Oct 15 13:43:10 2020 +0200

    Renaming of emission related variables

commit bea90adf8bb8a1ab3ad71d4651e4dab716791a90
Author: Marco de Bruine <[email protected]>
Date:   Tue Sep 15 15:13:54 2020 +0200

    Improved bookkeeping of scalar field numbers and names

commit 76d377c27d744a5448d083f9fd8d3c53c3e7f60e
Author: Marco de Bruine <[email protected]>
Date:   Tue Sep 1 15:05:35 2020 +0200

    Removed temporary forcing at lateral boundaries

commit 1a19cd569de6426996c94e24a1f7a863769a6db5
Author: Marco de Bruine <[email protected]>
Date:   Tue Sep 1 15:02:30 2020 +0200

    Added boundary nudging of scalar fields

commit 9a2bedbf99a65b300640a55b45da5004f5d19b8f
Author: Marco de Bruine <[email protected]>
Date:   Fri Jul 3 14:13:06 2020 +0200

    3D emission and namelist options; emission switch (l_emission) and vertical upper limit to apply emission (kemis)

commit 74bdfad13342e19f26532dbf056ee14ccfb36342
Author: Marco de Bruine <[email protected]>
Date:   Mon Jun 29 16:49:25 2020 +0200

    Typo in modemisdata.f90

commit 19909689ffc946398ab5f769168a46ce562ab11b
Author: Marco de Bruine <[email protected]>
Date:   Mon Jun 29 16:13:57 2020 +0200

    Corrected emission scalar list to work with microphysics, i.e. skip first 2 scalar fields

commit 8733870f68ed4bf2bd4175b6433995952799e87b
Author: Marco de Bruine <[email protected]>
Date:   Mon Jun 29 16:12:01 2020 +0200

    Fixed incorrect NORTH/EAST boundary indices

commit 9df88ce817f20efb04fdfa02b6d041b0bbd754b7
Author: Marco de Bruine <[email protected]>
Date:   Thu Jun 25 11:27:58 2020 +0200

    Add file moddatetime for reading emission files.

commit 080a1359a6454d1ad0e7ade6206d2532927aa025
Author: Marco de Bruine <[email protected]>
Date:   Fri Jun 5 15:17:20 2020 +0200

    Added scaling for model resolution and domain dboundary 'nullifier'

commit 71481ef261a13975e8a1a32ed67fa4da64751a3e
Author: Marco de Bruine <[email protected]>
Date:   Thu Feb 27 15:03:53 2020 +0100

    Realistic surface emissions (WIP)

commit d487543970fa5ef12881b7ac64e071470592d48d
Author: Marco de Bruine <[email protected]>
Date:   Mon Dec 9 15:37:52 2019 +0100

    New emission routines: Reading (parallel netCDF) of 2D surface emission on native grid

commit 578358547ba4a4b0eabaef9b7918bdc0bf7da6bf
Author: Fredrik Jansson <[email protected]>
Date:   Tue Apr 14 15:43:41 2020 +0200

    boundary nudging: add check for tile size being sufficient to contain the nudging domain

commit 66dc2c312e8ef1cec016ac4d6308cb209ce29d95
Author: Fredrik Jansson <[email protected]>
Date:   Fri Apr 10 14:56:32 2020 +0200

    Print warning when unspecified iadv_sv values are set to iadv_mom

commit cb8e7a74b2910edad777181c5f2885b0501f5a38
Author: Fredrik Jansson <[email protected]>
Date:   Tue Apr 7 13:11:48 2020 +0200

    Add boundary nudging by BvS
Open boundary conditions by Frans Liqui Lung
Poisson solver with FFTW and OpenBC from CaNS by Pedro Simões Costa
Merged and updated for mixed precision by Fredrik Jansson

Squashed commit of the following:

commit 9f10ba2
Merge: bec7d8c cc84edf
Author: Fredrik Jansson <[email protected]>
Date:   Wed Dec 14 15:52:02 2022 +0100

    Merge remote-tracking branch 'frans/ruisdael' into ruisdael

commit bec7d8c
Merge: 8d64687 a77d2e7
Author: Fredrik Jansson <[email protected]>
Date:   Tue Dec 13 17:17:00 2022 +0100

    Merge branch 'ruisdael_exner' into ruisdael

commit cc84edf
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 13 11:44:49 2022 +1100

    removed old code to allow for different initial pressure solver

commit 41edb30
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 13 11:36:33 2022 +1100

    adjusted initial convergence correction to be compatible with cosine fourier solver, implemented in modstartup to avoid cross dependency conflict between modpois and modopenboundaries

commit 09498f6
Author: Frans Liqui Lung <[email protected]>
Date:   Sun Oct 2 20:26:12 2022 +0000

    removed print from modsynturb and removed hard set top layer of temperature in modboundary

commit 031b97b
Author: Frans Liqui Lung <[email protected]>
Date:   Thu Sep 15 10:29:21 2022 +0000

    fixed timing issue in modsynturb

commit 8d64687
Author: Fredrik Jansson <[email protected]>
Date:   Thu Nov 17 14:43:12 2022 +0100

    Open boundary conditions and FFTW

    FFTW can be used also with open lateral boundary conditions.
    Pressure solver boundary condition is Neumann on the open boundaries.
    The following modifications are made for the direction(s) with open boundaries:
    * use Discrete Cosine Transform instead of FFT.
      - FFTW_REDFT_10 forward
      - FFTW_REDFT_01 back
    * normalization constant is different, a factor 2 per direction
    * the eigenvalues xrt, yrt are different

    By Pedro Simões Costa and Fredrik Jansson

commit a77d2e7
Author: Fredrik Jansson <[email protected]>
Date:   Fri Sep 16 15:07:13 2022 +0200

    allow multiple planes for crossxz, crossyz and in any MPI tile

commit 98dbc56
Author: Fredrik Jansson <[email protected]>
Date:   Tue Mar 2 11:22:12 2021 +0100

    Added option to disable certain cross-sections (xy, xz, yz)

commit 22174b0
Author: Fredrik Jansson <[email protected]>
Date:   Fri Sep 16 09:37:54 2022 +0200

    add PHYSICS/lconstexner flag, output exnf, exnh to profiles.nc

commit 854ca46
Author: Fredrik Jansson <[email protected]>
Date:   Thu Sep 15 14:44:10 2022 +0200

    try using the initial pressure profile in the exner function

commit 0fd18d2
Merge: f2fe301 41bd220
Author: Fredrik Jansson <[email protected]>
Date:   Mon Aug 8 15:51:58 2022 +0200

    Merge pull request #77 from natalieth/patch-1

    rename randomNumbers

commit f2fe301
Merge: 4b76227 8784487
Author: Fredrik Jansson <[email protected]>
Date:   Mon Aug 8 15:51:29 2022 +0200

    Merge pull request #76 from natalieth/patch-2

    remove comma (typo)

commit 8784487
Author: Natalie Theeuwes <[email protected]>
Date:   Mon Aug 8 15:25:22 2022 +0200

    remove comma (typo)

commit 41bd220
Author: Natalie Theeuwes <[email protected]>
Date:   Mon Aug 8 15:23:19 2022 +0200

    rename randomNumbers

commit 4b76227
Author: Fredrik Jansson <[email protected]>
Date:   Wed Apr 6 20:15:07 2022 +0200

    hypre: switch PFMG-preconditioner to use red-black smoother, faster

commit bf32003
Author: Fredrik Jansson <[email protected]>
Date:   Mon Apr 4 18:33:38 2022 +0200

    add SOLVER namelist variable hypre_logging for setting hypre printing amount

commit 2db7993
Author: Fredrik Jansson <[email protected]>
Date:   Mon Apr 4 18:32:33 2022 +0200

    add alternative name for hypre library for Ubuntu

commit 94f360a
Author: Fredrik Jansson <[email protected]>
Date:   Sat Apr 2 09:11:15 2022 +0200

    hypre singularity-fix: fix off-by-one, move anchor point cose to top of domain

commit 729ce43
Author: Fredrik Jansson <[email protected]>
Date:   Fri Apr 1 16:35:02 2022 +0200

    print wall time of poisson solver, try without modifying neighbors of the special element, zero guess in RK step 1

commit 2f59d56
Author: Fredrik Jansson <[email protected]>
Date:   Tue Mar 29 21:28:30 2022 +0200

    iterative solver: try making the matrix non-singular for better convergence

commit 28717a2
Author: Frans Liqui Lung <[email protected]>
Date:   Mon Mar 7 15:34:02 2022 +1100

    added flag for compatibility periodic simulations

commit 371ec7e
Author: Fredrik Jansson <[email protected]>
Date:   Mon Feb 14 18:25:38 2022 +0100

    hypre: update dummy routine in modnohypre to have same parameters as real routine

commit 4b186a0
Author: Frans Liqui Lung <[email protected]>
Date:   Fri Jan 28 15:40:14 2022 +1100

    finalised extra hypre input for preconditioner

commit 9401ce6
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Jan 11 16:43:16 2022 +1100

    disconnected iterations preconditionar from max iterations total of pressure solver (HYPRE)

commit 7247c00
Author: Frans Liqui Lung <[email protected]>
Date:   Mon Dec 20 17:09:06 2021 +0100

    fixed mistake in initial divergence correction

commit e9c5dd8
Author: Frans Liqui Lung <[email protected]>
Date:   Mon Dec 20 14:11:34 2021 +0100

    added divergence correction for initial field when a heterogneous initialisation is used

commit 55e7fe4
Author: Frans Liqui Lung <[email protected]>
Date:   Mon Dec 20 13:18:01 2021 +0100

    Changed hypre coding to take solver as an input to the hypre subroutines, such that multiple solvers can be created and coexist. This is a preparation to be able to use a different solver to remove any divergence from a heterogneous starting field. Doesn't change anything to the performance/results of the solvers.

commit 3b4aade
Merge: a4289f0 3f42824
Author: Fredrik Jansson <[email protected]>
Date:   Mon Feb 14 18:47:40 2022 +0100

    Merge commit '3f428245ff' into ruisdael

commit 3f42824
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 11:48:44 2021 +0100

    fixed rhointi bug found in modopenboundary during tests

commit 1ae6709
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 09:52:33 2021 +0100

    Adjusted program for openboundaries

commit 73e4926
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 09:37:57 2021 +0100

    fixed bugs found in modstartup during compilation

commit e864a04
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 09:32:28 2021 +0100

    fixed bugs found in advection during compilation

commit c9c9a10
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 09:23:13 2021 +0100

    Adjusted modmpi for openboundaries

commit 4d9fe7f
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 09:20:24 2021 +0100

    fixed bugs found in modopenboundary during compilation

commit 8242f56
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 09:09:56 2021 +0100

    Adjusted modlsm for openboundaries

commit 78de429
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 09:04:31 2021 +0100

    Adjusted modsurface for openboundaries

commit c7a8aae
Author: Frans Liqui Lung <[email protected]>
Date:   Wed Dec 8 08:46:29 2021 +0100

    Adjusted modstartup for openboundaries

commit 356c2af
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 16:46:56 2021 +0100

    Adjusted modglobal for openboundaries

commit b721669
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 16:32:08 2021 +0100

    Adjusted modpois for openboundaries

commit 5b6810b
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 16:25:55 2021 +0100

    Adjusted modgenstat for openboundaries, covariances take non-zero w profile into account

commit 2151204
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 16:18:28 2021 +0100

    Adjusted modforces for openboundaries

commit 24db68a
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 16:16:47 2021 +0100

    Adjusted modsubgrid for openboundaries

commit d250ed8
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 16:14:36 2021 +0100

    Adjusted advection for openboundaries

commit e174ff4
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 16:04:57 2021 +0100

    Adjusted advec_2nd for openboundaries

commit dc2300d
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 15:40:53 2021 +0100

    Adjusted modhypre for openboundaries

commit 6d9b23a
Author: Frans Liqui Lung <[email protected]>
Date:   Tue Dec 7 15:35:30 2021 +0100

    Added modopenboundary.f90 and modsynturb.f90

commit a4289f0
Author: Bart van Stratum <[email protected]>
Date:   Wed Sep 8 14:54:23 2021 +0200

    Added CO2 scalar for A-Gs net assimilation, for offline budget checks

commit 02372b5
Author: Bart van Stratum <[email protected]>
Date:   Tue Sep 7 09:43:17 2021 +0200

    Added A-Gs option without emission module

commit 8c7881f
Author: Bart van Stratum <[email protected]>
Date:   Tue Sep 7 08:08:14 2021 +0200

    Added CO2 respiration/assimilation to cross-section and time series.

commit 4dc4a0b
Author: Bart van Stratum <[email protected]>
Date:   Mon Sep 6 16:36:23 2021 +0200

    Added A-Gs to the new land surface model

commit 3050704
Author: Bart van Stratum <[email protected]>
Date:   Mon Sep 6 12:05:31 2021 +0200

    Added basic infrastructure for A-Gs and communication with emission module

commit bdfa25e
Author: Marco de Bruine <[email protected]>
Date:   Tue Jun 8 16:56:12 2021 +0200

    AG-s <-> emission interface indicators now relative to full list of scalar fields

commit 0424c3c
Author: Marco de Bruine <[email protected]>
Date:   Tue Jun 8 15:53:49 2021 +0200

    Emission <-> AGS interface

commit c05eee0
Merge: d329736 002a862
Author: Fredrik Jansson <[email protected]>
Date:   Mon Nov 9 12:13:43 2020 +0100

    Merge branch 'ruisdael_lsm' into ruisdael

commit 002a862
Author: Bart van Stratum <[email protected]>
Date:   Fri Nov 6 11:30:33 2020 +0100

    Calculate obukhov length from tile averaged fluxes, instead of
    calculating a tiled mean

commit 01a48d8
Author: Bart van Stratum <[email protected]>
Date:   Tue Nov 3 09:12:35 2020 +0100

    Bugfix harmonic mean calculation (which is currently not used in the
    code..)

commit d329736
Author: Fredrik Jansson <[email protected]>
Date:   Tue Oct 27 11:25:58 2020 +0100

    update fix for #58 - allow lsmcrossection also for new LSM isurf=11

commit 8b42f82
Author: Fredrik Jansson <[email protected]>
Date:   Fri Oct 23 11:03:29 2020 +0200

    emission: remove MPI-parallel .nc read, add better namelist error reporting

commit fa1a4b5
Merge: 15a81a3 8230865
Author: Fredrik Jansson <[email protected]>
Date:   Fri Oct 16 15:42:00 2020 +0200

    Merge branch 'ruisdael_lsm' into ruisdael

commit 8230865
Author: Bart van Stratum <[email protected]>
Date:   Fri Oct 16 10:18:03 2020 +0200

    Added NetCDF file with van Genuchten parameters

commit 15a81a3
Merge: 6eddb8f 58f9d33
Author: Fredrik Jansson <[email protected]>
Date:   Thu Oct 15 14:57:17 2020 +0200

    Merge branch 'to4.3_Fredrik' into ruisdael

commit 58f9d33
Author: Fredrik Jansson <[email protected]>
Date:   Thu Oct 15 14:56:53 2020 +0200

    advec_kappa : remove debug write()

commit 6eddb8f
Author: Fredrik Jansson <[email protected]>
Date:   Thu Oct 15 14:43:57 2020 +0200

    modnudgebounday: use random_number() instead of rand() for better intel/gnu compatibility

commit b70f80e
Merge: 796eaae 6b4a3ab
Author: Fredrik Jansson <[email protected]>
Date:   Thu Oct 15 14:04:57 2020 +0200

    Merge branch '4.2_emission' into ruisdael

commit 6b4a3ab
Author: Marco de Bruine <[email protected]>
Date:   Thu Oct 15 13:43:10 2020 +0200

    Renaming of emission related variables

commit 6b199b3
Author: Fredrik Jansson <[email protected]>
Date:   Mon Oct 12 17:01:12 2020 +0200

    advec_kappa: do advection only for the k-range with non-zero input field

commit 85b2be8
Author: Jisk Attema <[email protected]>
Date:   Thu Oct 1 13:57:37 2020 +0200

    Add intent to slabsum arguments

commit 5887bd0
Author: Jisk Attema <[email protected]>
Date:   Tue Sep 29 15:13:12 2020 +0200

    gfortran switches

    when using default-real-8, constants and variables explicitly declared
    as double will become quadruples, which we dont want for DALES.
    quadruple precision could even result in software fallback, which is much
    slower.
    Adding the default-double-8 keeps doubles at double precision.

    Aliging stuff on 64-bit boundaries could help a bit with vectorization.

    Not initializing variables will speed things up when using large arrays

commit 7ebd462
Author: Fredrik Jansson <[email protected]>
Date:   Wed Oct 7 18:59:33 2020 +0200

    fix error in previous fix of #48 - used wrong time array in ls forcing

commit e295c35
Author: Fredrik Jansson <[email protected]>
Date:   Tue Oct 6 10:01:40 2020 +0200

    Update benchmark cases to use the standard kappa scheme 7 instead of the removed experimental one

commit d088437
Author: Fredrik Jansson <[email protected]>
Date:   Tue Oct 6 09:56:14 2020 +0200

    Remove experimental kappa scheme iadv=77
    which is now redundant. The non-uniform grid support has been
    merged into the main kappa scheme.

commit 20b27f8
Author: Fredrik Jansson <[email protected]>
Date:   Tue Oct 6 09:45:00 2020 +0200

    Optimized advec_kappa scheme
    - rlim function inlined and rewritten without division and eps1
    - both branches of if uvw0 > 0 calculated, then selected
      in order to enable vectorization.
    by Jisk Attema and Fredrik Jansson

commit d307f11
Merge: a73ad93 7f86be4
Author: Marco de Bruine <[email protected]>
Date:   Tue Sep 22 10:53:16 2020 +0200

    Merge to4.3 into 4.2_emission

commit a73ad93
Author: Marco de Bruine <[email protected]>
Date:   Tue Sep 22 10:43:18 2020 +0200

    Included all scalar fields in crosssection output (similar to fielddump)

commit 78e6594
Author: Marco de Bruine <[email protected]>
Date:   Tue Sep 15 15:13:54 2020 +0200

    Improved bookkeeping of scalar field numbers and names

commit 7f23960
Merge: 038d2b6 c2db0ee
Author: julietbravo <[email protected]>
Date:   Mon Sep 7 11:05:02 2020 +0200

    Merge branch 'to4.3_lsm' into ruisdael_lsm

commit c2db0ee
Merge: 704d145 7f86be4
Author: julietbravo <[email protected]>
Date:   Mon Sep 7 11:02:57 2020 +0200

    Merge remote-tracking branch 'upstream/to4.3' into to4.3_lsm

commit 704d145
Author: julietbravo <[email protected]>
Date:   Mon Sep 7 10:31:11 2020 +0200

    Small fix in calculation liq. water fraction, plus added cleanup of
    arrays

commit c1eb5a4
Author: julietbravo <[email protected]>
Date:   Fri Sep 4 15:02:36 2020 +0200

    Fixed dynamic tile fraction for cases with open water

commit 4aec697
Author: julietbravo <[email protected]>
Date:   Fri Sep 4 11:33:18 2020 +0200

    Added water tile to time series statistics

commit 13e4129
Author: Marco de Bruine <[email protected]>
Date:   Tue Sep 1 15:05:35 2020 +0200

    Removed temporary forcing at lateral boundaries

commit 36730a8
Author: Marco de Bruine <[email protected]>
Date:   Tue Sep 1 15:02:30 2020 +0200

    Added boundary nudging of scalar fields

commit 0069bf4
Author: julietbravo <[email protected]>
Date:   Thu Jul 30 15:43:29 2020 +0200

    Added additional variables to surface cross-sections

commit 6637916
Author: julietbravo <[email protected]>
Date:   Tue Jul 21 14:12:40 2020 +0200

    Modified modlsmcrosssection for new LSM

commit 45c6b5e
Author: julietbravo <[email protected]>
Date:   Tue Jul 21 12:45:14 2020 +0200

    Store/load the water tiles for restarts (results = bitwise identical
    now)

commit 5925ee2
Author: julietbravo <[email protected]>
Date:   Tue Jul 21 09:19:12 2020 +0200

    Fixed some MPI issues in new LSM

commit 3f8c6ac
Author: julietbravo <[email protected]>
Date:   Mon Jul 20 11:55:18 2020 +0200

    First ~working version with water tile (still has some issues...)

commit e4c0755
Merge: a6ca5f1 f470b41
Author: julietbravo <[email protected]>
Date:   Fri Jul 17 15:39:12 2020 +0200

    Merge remote-tracking branch 'upstream/to4.3' into to4.3_lsm_water

commit a6ca5f1
Author: julietbravo <[email protected]>
Date:   Tue Jul 7 17:28:34 2020 +0200

    Added option to read the spatial data for heterogeneous land surfaces

commit b624922
Author: julietbravo <[email protected]>
Date:   Tue Jul 7 11:53:21 2020 +0200

    Added restart functionality to new LSM

commit cfc205e
Author: julietbravo <[email protected]>
Date:   Tue Jul 7 11:00:32 2020 +0200

    Added old soil grid definition, different soil interpolation types, plus
    fixed bug in buoyancy calculation

commit a2e51fb
Author: julietbravo <[email protected]>
Date:   Mon Jul 6 16:29:59 2020 +0200

    Added calculation of liquid water reservoir (plus bugfix ra
    calculation)

commit 491b393
Author: julietbravo <[email protected]>
Date:   Mon Jul 6 12:21:21 2020 +0200

    Added root water extraction to soil water budget

commit 4891bb5
Author: julietbravo <[email protected]>
Date:   Mon Jul 6 11:23:16 2020 +0200

    Added bulk (grid point mean) quantities needed for SGS model

commit 027b03b
Author: julietbravo <[email protected]>
Date:   Mon Jul 6 09:01:42 2020 +0200

    Added calculation of bulk (grid point mean) scalar BCs

commit a0d4cbf
Author: julietbravo <[email protected]>
Date:   Fri Jul 3 18:02:56 2020 +0200

    Working surface solver, with fluxes per tile

commit 12dd3e3
Author: Marco de Bruine <[email protected]>
Date:   Fri Jul 3 14:13:06 2020 +0200

    3D emission and namelist options; emission switch (l_emission) and vertical upper limit to apply emission (kemis)

commit 3184f6b
Author: julietbravo <[email protected]>
Date:   Thu Jul 2 16:32:56 2020 +0200

    Bugfix calculation canopy resistances

commit 656839f
Author: julietbravo <[email protected]>
Date:   Thu Jul 2 16:30:10 2020 +0200

    Added calculation canopy and soil resistance

commit c56c478
Author: julietbravo <[email protected]>
Date:   Thu Jul 2 12:13:05 2020 +0200

    Working tiled surface layer solver

commit 8def726
Author: julietbravo <[email protected]>
Date:   Wed Jul 1 16:25:10 2020 +0200

    Start of tiled surface layer solver

commit 2b3e826
Author: julietbravo <[email protected]>
Date:   Wed Jul 1 10:00:08 2020 +0200

    Added calculation hydraulic properties (van Genuchten) and diffusion solver for
    soil moisture

commit f215e66
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 16:51:10 2020 +0200

    Added calculation of soil thermal properties, and (explicit) temperature
    diffusion solver

commit 61de721
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 14:39:31 2020 +0200

    Added calculation derived van Genuchten parameters

commit 3261422
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 11:38:47 2020 +0200

    Added minimal set of time series statistics for the new LSM

commit 6b5d8be
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 11:08:45 2020 +0200

    Modified modlsmstat to work with the new LSM

commit 6939641
Author: julietbravo <[email protected]>
Date:   Tue Jun 30 09:52:26 2020 +0200

    Minor changes new LSM

commit 7818aeb
Author: Marco de Bruine <[email protected]>
Date:   Mon Jun 29 16:49:25 2020 +0200

    Typo in modemisdata.f90

commit 0772796
Author: Marco de Bruine <[email protected]>
Date:   Mon Jun 29 16:13:57 2020 +0200

    Corrected emission scalar list to work with microphysics, i.e. skip first 2 scalar fields

commit 1d141d4
Author: Marco de Bruine <[email protected]>
Date:   Mon Jun 29 16:12:01 2020 +0200

    Fixed incorrect NORTH/EAST boundary indices

commit b7dd889
Author: julietbravo <[email protected]>
Date:   Mon Jun 29 15:45:35 2020 +0200

    Added soil grid and initialisation of soil

commit 9e78c3d
Author: julietbravo <[email protected]>
Date:   Mon Jun 29 13:52:11 2020 +0200

    Added homogeneous initialisation of LSM

commit db40554
Author: julietbravo <[email protected]>
Date:   Mon Jun 29 12:23:47 2020 +0200

    Added data structures for land-surface tiles

commit 796eaae
Merge: 7860bb9 e5da4f8
Author: Fredrik Jansson <[email protected]>
Date:   Thu Jun 25 12:01:06 2020 +0200

    Merge remote-tracking branch 'origin/4.2_emission' into ruisdael
    Merge surface emission map code by M de Bruine

commit 7860bb9
Merge: 038d2b6 f0fb85d
Author: Fredrik Jansson <[email protected]>
Date:   Thu Jun 25 11:58:33 2020 +0200

    Merge branch 'to4.3' into ruisdael
    merging for gfortran 10 compatibility

commit e5da4f8
Author: Marco de Bruine <[email protected]>
Date:   Thu Jun 25 11:27:58 2020 +0200

    Add file moddatetime for reading emission files.

commit 5e47c93
Author: julietbravo <[email protected]>
Date:   Mon Jun 15 12:06:48 2020 +0200

    Start at implemention realistic LSM

commit 5cf1aff
Merge: c6c8324 038d2b6
Author: Marco de Bruine <[email protected]>
Date:   Mon Jun 8 11:30:33 2020 +0200

    Merge with ruisdael branch

commit c6c8324
Merge: 1407034 9278ce3
Author: Marco de Bruine <[email protected]>
Date:   Fri Jun 5 16:10:02 2020 +0200

    Merge with master

commit 1407034
Author: Marco de Bruine <[email protected]>
Date:   Fri Jun 5 15:17:20 2020 +0200

    Added scaling for model resolution and domain dboundary 'nullifier'

commit 038d2b6
Merge: 89b4830 1cc8a3c
Author: Fredrik Jansson <[email protected]>
Date:   Wed Jun 3 16:20:56 2020 +0200

    Merge branch 'to4.3' into ruisdael
    for PR #53 - Only set `tauField` when A-gs is enabled

commit baeab65
Author: Marco de Bruine <[email protected]>
Date:   Tue Apr 28 10:38:29 2020 +0200

    Changes in documentation and compiler settings

commit 89b4830
Author: Fredrik Jansson <[email protected]>
Date:   Tue Apr 14 15:43:41 2020 +0200

    boundary nudging: add check for tile size being sufficient to contain the nudging domain

commit 8cd006c
Author: Fredrik Jansson <[email protected]>
Date:   Fri Apr 10 14:56:32 2020 +0200

    Print warning when unspecified iadv_sv values are set to iadv_mom

commit 6e208f5
Author: Fredrik Jansson <[email protected]>
Date:   Tue Apr 7 13:11:48 2020 +0200

    Add boundary nudging by BvS

commit e61fddc
Author: Marco de Bruine <[email protected]>
Date:   Thu Feb 27 15:03:53 2020 +0100

    Realistic surface emissions (WIP)

commit 4b9dec3
Author: Marco de Bruine <[email protected]>
Date:   Mon Dec 9 15:37:52 2019 +0100

    New emission routines: Reading (parallel netCDF) of 2D surface emission on native grid
replacing dot() calls in inner loops of calc_pert(), calc_pert2()
by explicit expressions.
Reordering i,j,k loops (probably minor difference).
By Ruud Janssen and Leon Geers
By Ruud Janssen and Leon Geers
By Ruud Janssen and Leon Geers
Scalar variables or tracers can be accessed by name instead of just index.
By Ruud Janssen and Leon Geers

commit cf15b0b
Author: Leon Geers <[email protected]>
Date:   Thu Aug 3 18:13:50 2023 +0200

    Update tracerdata.inp

    Bugfix: SOx should not be reactive

commit 82daab6
Merge: 10e6c1d c2245b3
Author: Leon Geers <[email protected]>
Date:   Thu Aug 3 11:07:27 2023 +0200

    Merge branch 'ruisdael_tracers' of github.com:dalesteam/dales into ruisdael_tracers

commit 10e6c1d
Author: Leon Geers <[email protected]>
Date:   Thu Aug 3 10:56:36 2023 +0200

    Added SOx as tracer, changed molar mass of NOx to 97% NO and 3% NO2, increased max tracer number in
    modtracers.f90

commit c2245b3
Author: Leon Geers <[email protected]>
Date:   Thu Aug 3 10:56:36 2023 +0200

    Added SOx as tracer, changed molar mass of NOx to 97% NO and 3% NO2

commit 9ca4f0d
Author: Leon Geers <[email protected]>
Date:   Thu Aug 3 10:53:07 2023 +0200

    Update modopenboundary.f90

    Bugfix: line 103 changed 'dxint =' into 'dyint =' (probably copy paste error)

commit 6584821
Author: Ruud Janssen <[email protected]>
Date:   Wed Aug 2 13:00:11 2023 +0200

    Added emission scaling factors

commit 7fd48d4
Author: Leon Geers <[email protected]>
Date:   Wed Aug 2 12:01:09 2023 +0200

    Update moddrydeposition.f90

    mpi_integer was missing (line 77)

commit 4716ada
Merge: eecdf84 4727e00
Author: Gudrun Thorkelsdottir <[email protected]>
Date:   Wed Aug 2 11:09:40 2023 +0200

    Merge of changes to tracer module and addition of deposition compensation point

commit eecdf84
Author: Gudrun Aorkelsdottir <[email protected]>
Date:   Wed Aug 2 11:03:46 2023 +0200

    Added compensation point to the deposition calculations

commit 4727e00
Author: Ruud Janssen <[email protected]>
Date:   Mon Jul 3 17:26:04 2023 +0200

    Unit of tracers changed to mixing ratios consistently

commit edfe255
Author: Ruud Janssen <[email protected]>
Date:   Thu Jun 29 14:40:28 2023 +0200

    Read tracers from file

commit 00d012e
Author: Ruud Janssen <[email protected]>
Date:   Wed Jun 28 15:34:08 2023 +0200

    Added a couple of tracers

commit 7238f74
Author: Ruud Janssen <[email protected]>
Date:   Tue Mar 28 16:04:28 2023 +0200

    Read scalar.inp columns by tracer name

commit 4646fa1
Author: Ruud Janssen <[email protected]>
Date:   Wed Mar 8 15:44:19 2023 +0100

    Removed debugging statement

commit 262ab4a
Author: Ruud Janssen <[email protected]>
Date:   Wed Mar 8 15:41:19 2023 +0100

    Fixed bug that caused negative deposition fluxes

commit c272a49
Author: Ruud Janssen <[email protected]>
Date:   Wed Mar 8 11:41:18 2023 +0100

    Debugged test run with chemistry

commit 881d965
Author: Ruud Janssen <[email protected]>
Date:   Wed Mar 8 11:11:30 2023 +0100

    Added datestamp to fielddump

commit c04147d
Author: Ruud Janssen <[email protected]>
Date:   Tue Mar 7 11:39:12 2023 +0100

    Added check on x- and y-dimension of lsm.inp_xxx.nc

commit a3bb7da
Author: Ruud Janssen <[email protected]>
Date:   Mon Mar 6 14:08:43 2023 +0100

    Solved some merge conflicts

commit c2b8b92
Author: Ruud Janssen <[email protected]>
Date:   Thu Mar 2 18:06:03 2023 +0100

    Minor edit

commit e30ac07
Author: Ruud Janssen <[email protected]>
Date:   Thu Mar 2 17:43:01 2023 +0100

    Implemented tracer_prop in chemistry. First working version. Last commit before moving to ruisdael_deposition2023 branch

commit 19f9d49
Author: Ruud Janssen <[email protected]>
Date:   Thu Feb 23 18:23:22 2023 +0100

    Commented out debugging statements

commit f2027c7
Author: Ruud Janssen <[email protected]>
Date:   Thu Feb 23 16:18:28 2023 +0100

    Minor edits

commit da79823
Author: Ruud Janssen <[email protected]>
Date:   Thu Feb 23 16:14:03 2023 +0100

    Minor edits

commit a5e3f15
Author: Ruud Janssen <[email protected]>
Date:   Thu Feb 23 16:13:22 2023 +0100

    Merged conflicst in b127d20

commit 39b5f15
Author: Ruud Janssen <[email protected]>
Date:   Thu Feb 23 14:57:25 2023 +0100

    Implementation of modtracers in dry deposition, including depcross output

commit 2de3843
Author: Ruud Janssen <[email protected]>
Date:   Thu Feb 23 12:51:47 2023 +0100

    Merged conclifcts in commit c8ca53a

commit 0e81954
Author: Ruud Janssen <[email protected]>
Date:   Thu Feb 23 12:51:27 2023 +0100

    Implementation of modtracers for emissions

commit 40b8aa8
Author: Ruud Janssen <[email protected]>
Date:   Tue Feb 21 16:48:28 2023 +0100

    Implemented lookup for tracer properties

commit 827cbd2
Author: Ruud Janssen <[email protected]>
Date:   Thu Feb 16 18:22:34 2023 +0100

    First commit modtracers.f90. Only contains an init for now.
@CasparJungbacker
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Merging modsurface is a mess, because of the clean-up on dev. Needs some testing, especially the with option ltskininp=.true.

@fjansson
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fjansson commented Jun 7, 2024

@CasparJungbacker for modsurface, there were only small changes introduced in the Ruisdael branch.
I'd say keep the version from dev and add the other stuff by hand.

446679f

  • some calls for the new LSM if that's selected
  • add some pure keywords on functions

0a2259f

  • one open boundaries exchange

01e9def

  • initialize with patterned surface temperature

@CasparJungbacker
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CasparJungbacker commented Jun 10, 2024

Slight problem: looks like the new scalar manager is not backwards compatible. I.e., you have to use a tracerdata.inp file for any run with scalars, even rico.

You can run without tracerdata.inp, but you have to provide some options in the namelist:

&NAMTRACERS
ltracers = .true.
tracernames = 'Nr', 'qr'
/

Bomex seems to run nicely though :-)

@fjansson
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I'm fine with having to add a tracers section to the namoptions file for cases that use the scalars. Then we should just do it for all the sample cases that need it, and mention it in the documentation and release notes. Or did you make it do even more by default if tracers are not specified?

@CasparJungbacker
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I'm fine with having to add a tracers section to the namoptions file for cases that use the scalars. Then we should just do it for all the sample cases that need it, and mention it in the documentation and release notes. Or did you make it do even more by default if tracers are not specified?

Yeah now that I think of it, that might be better. In my latest commit, scalars are named svx if tracernames is left empty. That works for the benchmark rico case, because the columns in scalar.inp are called sv0 and sv1. If they'd have different names, everything crashes again.

@CasparJungbacker
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CasparJungbacker commented Jun 11, 2024

Time series look alright, although we do seem to have a bug in vtke (already fixed). Also the surface temperature flux (wtheta) seems to drift away from 4.4.2 after about 35 hours.

rico

@CasparJungbacker CasparJungbacker marked this pull request as ready for review June 11, 2024 11:01
@fjansson
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the wtheta difference looks a little worrying. Could you add dev to the comparison and perhaps more ensemble members?

@CasparJungbacker
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Now 10 members per ensemble. wtheta has definitely changed.

vtke is also still wrong, but I think that's due to some missing parenthesis.

image

@CasparJungbacker
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Ok, everything looks good now.

image

@fjansson fjansson merged commit 877f094 into dev Jun 19, 2024
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3 participants