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Changelog

Following is a curated changelog of the code. The IDs starts with R represents the svn era id, others are git hash. To find all the changes between tag releases, search for 'Tag'.

Bug fixes and major algorithmic changes

  1. R5178: fix bug of saturate DO in ICM
  2. R5187: incorporated dry bnd treatment from bndry (c/o Jens Wyrwa). However, to get good volume conservation it's best to keep all open flow bnd's wet all the time as before;
  3. R5191: fixed a bug in iwind_form (accidentally re-init'ed after reading);
  4. R5202: fixed a bug on negative ICM tracer concentration - check negative values before sending back to hydro.
  5. R5204: a new option to control behavior of btrack when trajectory hots an open bnd (set vel=0 and exit). Goal is to eventually use this as default;
  6. 64b7181: fixed an efficiency issue and added nc checks in ptrack3 (c/o Marcel Rieker)
  7. 2138e77: Fixed a major bug introduced during reshuffling of _init for PDAF: need to call nodavel before sflux, as uu2,vv20 are needed there.
  8. 5ff2198: revamped AGE module. B.C. now all should use 0. Only 0 and 1 should be used in AGE_hvar_[1:ntr/2].ic, where ntr is @ of age tracers, and the code will 'hold' concentration at 1 at those prisms (level specified in param.nml) that have 1 as i.c. I.C. in AGE_hvar_[ntr/2+1:ntr].ic should =0. Injecting '1' at dry elem's is allowed but results may be harder to interpret.
  9. 6cec698: bug fix for spherical coord in WWM (around dateline);
  10. c46c7bd (Feb 14, 2020): Fei tweaked WENO solver (wrt upwind);
  11. d3adb2c (Feb 14, 2020): changed to bilinear interp for HYCOM hot and nudging scripts (to speed up);
  12. 7506147 (Mar 1, 2020): add limiter for settling vel to avoid char line out of bnd;
  13. 5665418 (Mar 18, 2020): PR from Baptiste mengual for SED3D (sed_frition.F90 merged after the rest).
  14. eb00a00 (Mar 31, 2020): added 12th tracer model (USE_DVD of Klingbeil)
  15. aaf1306 (April 4, 2020): added hybrid ELM transport for efficiency (via branch hybrid_ELM);
  16. 40955ab (April 16, 2020): replaced the fatal error in nadv=2 (aptivity trap) with exit;
  17. e703189 (May 6, 2020): reverted to old simple approach for depositional mass (c/o Baptiste Mengual);
  18. 14e201f (May 7, 2020): switched to ParMETIS v4.0.3;
  19. 33fb37f (Jun 30, 2020): fixed a bug in ielm_transport (Fei Y.);
  20. 55910d1 (July 31, 2020; via branch mem_leak_nc4): reverted the change in schism_io (close/open nc output after/b4 each write, to accommodate PDAF's flexible mode), as this has caused a lot of mem leaking (discovered by Nicole C. when testing ICM).
  21. eaf9093 (Aug 2020): Baptiste M. modified the computation of the bottom shear stress under combined waves and currents in SED3D
  22. 4ac56df (Aug 2020): Paul Ryan and Claire Trenham (CSIRO) fixed some init array issues in hydro and WWM.
  23. 7e9ff0a (Aug 20, 2020): Fei Y fixed a msource bug (init of msource at 0 at elem's not in source_sink.in led to ice rain;
  24. f311026 (Aug. 27, 2020): reverted init of msource to 0 for tracers other than T,S, c/o Nicole Cai. Using ambient values for other tracers can lead to artificial and additional accumulation of nutrients;
  25. 00b6f16 (Nov. 9, 2020): PR #21 from Kijin merged (SED): changed method to compute near bottom vel for \(LSC^2\).
  26. 8083cfa (Nov. 10, 2020): added option for transport solver only (itransport_only)
  27. 6dc44d3 (Dec 14, 2020): Fixed a bug, thanks to Kevin Kartin, on vortex formulism of wave force (missing a factor of area() in \(I_4\));
  28. 28ff9d1 (Dec 16, 2020): added optional self-attraction loading tides. The option shares some constants with tidal potential: freq names and cut-off depth;
  29. b1bcaa0 (April 20, 2021): removed most of goto. Remaining ones: harm.F90, lap.F90, WWM;
  30. 0cec024 (April 21, 2021): bug fix in misc_subs c/o of Fei (inunfl=1: nodeA in final extrap stage may be interface node);
  31. fb30239 (April 22, 2021): bug fix for ellipsoidal earth (tensor frames).
  32. fb79cdc (May 26, 2021): in interpolate_depth_structured2*, added an option to shift 1/2 cell for ll corner (c/o Charles Seaton);
  33. 5e87c24 (June 9, 2021): more changes in interpolate_depth_structured2* to extrap also into right/upper sides.
  34. 843c40f (19 June, 2021): fixed a bug in ptrack3 (pt_in_poly3; c/o Jilian Xiong) that affects quads;

  35. b2cf92b (29 June, 2021): fixed a bug in station outputs in basin scale cases ics=2 (local proj is not accurate if the station is far away from the local frame);

  36. Tag v5.9.0: 657157a (1 July, 2021)

  37. a9f8f6c (8 July, 2021): fixed a bug in iloadtide=1 (index error). Also revamped reading of input files for large core counts.

  38. ab46def (20 July, 2021): merged multi ice model (CICE) from Qian Wang.

  39. 70db927 (11 Aug 2021): bug fixes from Qian Wang on ice matrix (ghost nodes)

  40. 8efc374 (30 Aug 2021): first version of scribe dictated I/O (as an option)
  41. 53689f4 (12 Sept 2021): fixed a bug in weno transport introduced in e794d8c (23 Aug 2021).
  42. c7dd516 (27 Sept 2021): AGE module tweaked (clamped @ i.c. at injection points for both concentrations).
  43. (19 Oct 2021): filtered isolated wet nodes during outputs (should not change other results);
  44. 7455d5d (30 Dec 2021): added a new option nws=-1 (PaHM, Parametric Hurricane Model);
  45. 7455d5d (30 Dec 2021): added Fariall air-sea exchange (USE_BULK_FAIRALL) c/o Jerome Lefevre;
  46. e288f9a (31 Jan 2022): removed the restriction of counter-clockwise orientation in sflux grid;
  47. dde345f (7 April 2022): fixed a bug in sflux, invoked only if nws=2, ihconsv=1, and iwind_form=0: uninit'ed stress values.
  48. 6524e19 (27 April 2022): merged with La Rochelle group on WWM (VOR);
  49. cd0b2a3 (14 Aug 2022): [via Qian_pole_treatment] changed nodalvel() under ics=2; commented out a frame transformation for better vel near poles.
  50. 510874ec (19 Sep 2022): upgraded all nf_ to nf90_ (in sflux)
  51. 24a2723 (27 Sep 2022): PR merge with LRU's modifications for WWM (mostly related to vegetation effects on WWM)
  52. 1828489 (10 Oct 2022): bug fix on msource (mismatch in bcast array dimension)

  53. 87c7611f (21 Oct 2022): PR91 merge from Dr. Jerome Lefevre a) Add GAHM (Generalized Asymmetric Holland Model) in PaHM/parwind.F90 as a second alternative to Holland Model (see details https://wiki.adcirc.org/Generalized_Asymmetric_Holland_Model and https://noaa-ocs-modeling.github.io/PaHM/pahm_manual.pdf); b) Add support for Hurricanes in both South and North Hemisphere (in HM and GAHM models); c) Test using Niran, SW Pacific: (See inside src/Core/PaHM/inputs/ : a track for Cyclone Niran "niran2021-bdeck.dat" and my comparison with HM and GAHM versus a weather model output); d) CAUTION // CAUTION : To switch from HM (1) or GAHM (10), the user still need to change the value of "modelType" in Pahm_Utilities.F90 (line 3210) and recompile schism; e) CAUTION / CAUTION : Unlike in noaa-ocs-modeling.github.io/PaHM, there is not Control File support in SCHISM/PaHM yet.

  54. 6108700 (Feb 24, 2023): Laura L. fixed a bug in wwm_friction

  55. 46767d2 (April 24, 2023): changed hybrid ELM-WENO, by augmenting ELM elem with 1 layer of extra ELM elements to reduce 'shocks' experienced by WENO stencil to help dispersion issue;
  56. 594bf10 (May 9, 2023): deflated global nc and hotstart scribe outputs. However, deflate is not done in combine_hotstart7.f90 as it seems to cause hang in restart;
  57. a6fd5cb (May 15, 2023): revamped nws=4 to allow more variables for 3D. The input needed is 'atmos.nc'.
  58. a832e4fd (Aug 15, 2023): renamed LAP routines and tridag to avoid conflicts with other ESMs.
  59. d31ea846 (Aug 30, 2023): fixed similar bugs on too many open nc handle (c/o Kijin) for 1-way script)
  60. abf37240 (Aug 31, 2023): Ivica J. fixed a bug in FAIRALL option (bulk_psiu should be real*8)
  61. 045962 (Sept 13, 2023): removed goto in lap.F90
  62. 66242aa (Sept 13, 2023): removed goto in harm.F90
  63. 5914ae2 (Mar 26, 2024): fix an init error for diffm* (c/o Ufuk)
  64. ca44ba0 (1 May 2024): fixed bugs in vegetation&marsh module (uninited sav_h0 etc)
  65. cfb58a5 [5 July 2024] replace fatal errors with warning in btrack (no intersecting edges). These are exaordinary exceptions that occur rarely.
    • 2f88fc5 (7 Aug 2024): changed horizontal diffusion method to filter;

Changes in input and output format

The info below can also be found in src/Readme.beta_notes. Most changes are made in param.in (now renamed as param.nml).

  • 2f88fc5 (7 Aug 2024): changed horizontal diffusion method to filter; added an optional parameter niter_hdif, and hdif.gr3 now specifies the filter strength (<=0.2);
  • 44c0c76 (2 Aug 2024): added an optional flag RADFLAG (for wave coupling)
  • c4a5278 (17 July 2024): added Ganthy option for flex vegetation (iveg=2); related optional parameters are: veg_cw and veg_lai;
  • 0fec598 (20 May 2024): added nbins_veg_vert as a mandatory input; veg_vert_z*(1:nbins_veg_vert+1) etc as optional. The latter are required if iveg/=0;
  • 56b88ae (17 May 2024): added station outputs for all tracers (flags in station.in after w);
  • e66f1b3 (3 May 2024): renamed sav_.gr3 as veg_.gr3; also MARSH module now requires iveg/=0;
  • ca44ba0 (1 May 2024): removed isav and replaced it with iveg
  • 4fb6228 (9 Feb 2024): add cmake CPP 'BLD_STANDALONE' to accommodate UFS
  • 9bee0f5 (8 Feb 2024): removed IMPOSE_NET_FLUX and 'meth_sink'
  • d5fb0f1 (3 Jan 2024): merged ZG's stemp branch (sediment-water heat exchange option), with new parameters: stemp_stc, stemp_dz(1:2);
  • 6a079f9 (30 Nov 2023): Fei added i_epsilon2 (to allow spatially variable epsilon2;
  • 376b3a45 (14 Sept, 2023) : removed iflux_out_format (folded it into iflux);

Tag stofs3d-atl.v2.1.0 (identical to v5.11.0): for NOAA STOFS3D Atlantic operational forecast release Tag v5.11.0: (Aug 2022)

  • ae1c210 (14 June 2023): ishapiro=2 now needs shapiro.gr3 (variable coefficients);
  • a6fd5cb (15 May, 2023): revamped nws=4; input is 'atmos'nc'. It needs wind and air pressure at least. If ihconsv/=0, it should also contain 2 heat fluxes ('solar' and 'downwardNetFlux'; the latter is the net surface heat flux). If isconsv/=0, it should also contain 2 salt fluxes: 'prate' and 'evap'.
  • ae67c5e1 (24 April 2023): add USE_NWM_BMI (with if_source/=0) for NWM work;

  • a248ce1d (24 April 2023): replaced nws=3 with USE_ATMOS (together with nws=2);

  • f8e15ee (11 Oct 2022): added lev_tr_source(:)=0 option to allow source injecton to the entire water column;

  • bc113eb2 (30 Sep 2022): added a new flag 'iflux_out_format' to control flux.out format;
  • 24a2723 (27 Sep 2022): [merged PR from LRU] new options related to vegetation effects on WWM. Added iof_wwm(31) as dissipation due to vegetation. Also nws=-3: surface stress formulation from Donelan et al. (1993) based on the wave age;
  • c94b2ca (1 Sep 2022): added 'iof_ugrid' to output UGRID metadata for 3D outputs;
  • a0960ed (25 Aug 2022): added 'iprecip_off_bnd' to optionally turn off precip near land bnd (to avoid some spurious plumes near tropical islands etc);
  • ed26f60 (25 Aug 2022): removed 'impose_net_flux' and replaced it with IMPOSE_NET_FLUX (so this won't be actively supported);

Tag stofs3d-atl.v1.1.0 (identical to v5.10.0): for NOAA STOFS3D Atlantic operational forecast release

Tag v5.10.0: (13 July, 2022)

  • d03830e (16 May 2022): removed the 2 extra lines required in partition.prop (so it's identical to global_to_local.prop now);
  • a71ea69 (12 May 2022): removed ioffline_partition and replaced it with CPP (NO_PARMETIS) to allow build without ParMETIS lib; renamed global_to_local.in as partition.prop;
  • da90a33 (2 May 2022): removed itr_met=1,2;
  • 2165224 (29 April 2022): added optional offline partitioning ioffline_partition to bypass ParMETIS; if on, needs global_to_local.in;
  • 567b612 (28 April 2022): added new WWM outputs and re-ordered after iof_wwm(26); zCoordinate outputs made optional (for performance test);
  • 6524e19 (27 April 2022): a few more WWM related parameters under VOR (turbinjds,alpha,wfwvor_streaming) and new WWM outputs, after merging with lrdev_updates;
  • d44dbdf (1 April, 2022): added an optional threshold inflation ratio for mass conversation for ICM: rinflation_icm
  • 6f367d0 (30 Mar 2022): added optional vertical levels to inject source tracer conventration: lev_tr_source;
  • 7cc7f27 (30 Mar 2022): added an optional threshold depth for mass conversation for ICM: h_massconsv;
  • 1788867 (16 Mar 2022): added optional parameters for S exchange (split from heat exchange): i_hmin_salt_ex,hmin_salt_ex;
  • dcd5356 (31 Jan 2022): removed ramp flags except nramp_elev (use dramp*<=0 to turn off ramp): nramp, nrampbc, nrampwind, nrampwafo,nramp_ss; removed the optional input shapiro_min.gr3;
  • 80f1caa (26 Jan 2022): added 4 parameters in ice.nml: albsn,albsnm, albi,albm
  • d792ed0 (18 Jan 2022): added 2 new ice parameters: ice_atmos_stress_form and cdwin0;
  • b4d2214 (7 Jan 2022): added a new parameter nu_sum_mult to allow sum/product of final relax constants for tracer nudging;
  • f9f0844 (3 Jan 2022): ICE module, added 2 new parameters: lead_closing, Saterm. Also changed ice-wind stress formula;
  • 7455d5d (30 Dec 2021): added a new option nws=-1 (PaHM, Parametric Hurricane Model);
  • 91c91a7 (17 Dec 2021): ICE module, added new parameters: ncyc_fct, depth_ice_fct. Also requires ice_fct.gr3 now;
  • 0e2f90e (17 Dec 2021): added a new parameter in ice.nml mevp_coef and 2 related ones: mevp_alpha[34]
  • 2a7647d (24&29 Nov 2021): added a new parmater loadtide_coef for iloadtide=2,3;
  • a7a0b2b (17 Oct 2021): restored iwindoff;
  • afc7b1a (11 Oct 2021): changed vgrid.in format for ivcor=1 to facilitate parallel read (use change_vgrid.f90 to convert)
  • e9aec89 (1 Oct 2021): added most module outputs; order of flags changed in: ICE, ANALYSIS, SED;
  • 85b585a (1 Sept 2021): add zcor output flag as iof_hydro(25); rest of hydro output flags (iof_hydro) shifted by 1;
  • 8efc374 (30 Aug 2021): first version of scribe dictated I/O (as an option);

  • 1902c1e (16 July 2021): changed hotstart.nc: added nsteps_from_cold and cumsum_eta for DA;

  • Tag v5.9.0: 657157a (1 July, 2021)

  • e281d94 (25 June 2021): added a new option for SAL (Stepanov & Hughes 2004): iloadtide=3;
  • bfb4afc (18 June, 2021): added an optional input shapiro_min.gr3 to be used with ishapiro=2;
  • d07d75d (April 21, 2021): added T,S in required inputs for offline transport (to use hydro only results);
  • b66e554 (April 14, 2021): added ishapiro=2 - Smagorinsky like filter option. In this option, shapiro0 is the coefficient;
  • b43afea (April 2, 2021): changed x,y to double in nc outputs (for newer visIT);
  • 9150d86 (Mar 31, 2021): added a new SAL option (iloadtide=2) using a simple scaling;
  • 084e149 (Feb 25, 2021): Removed parameters: ibtrack_openbnd, iwindoff, dzb_decay (with hardwire); also removed option for negative roughness. Fixed race condition for marsh module.
  • 3576c9c (Jan 24, 2021): added new option for source/sink input: if_source=-1 requires source.nc (which includes elem list inside; allows different time steps and # of records for volume/mass source/sinks. Also, now the source/sink values in .th must be single precision (not double);
  • bcdfce6 (Jan 6, 2021): added main switch for nc output nc_out (useful for other programs to control outputs);
  • 28ff9d1 (Dec 16, 2020): added optional self-attraction loading tides; if iloadtide=1, need amp/phases in loadtide_[FREQ].gr3 (freq's shared with tidal potential);
  • f8ba470 (Dec 3, 2020): Added a new option (meth_sink) to treat net sink: if an elem is dry with a net sink, vsource is reset to 0;
  • f9043e2 (Nov. 12, 2020): merged with LRU branch wwm_lr; removed sav_cd (isav=1 now requires sav_cd.gr3).
    • New parameters related to WWM: fwvor_advxy_stokes,fwvor_advz_stokes, fwvor_advz_stokes, fwvor_breaking, cur_wwm, wafo_obcramp;
    • Changes in WWM .nml: ALPBJ ->B_ALP, BRHD->BRCR.
  • 8083cfa (Nov. 10, 2020): added option for offline transport solver only ('itransport_only');
  • 7e9ff0a (Aug 20, 2020): added two options (selected by i_hmin_airsea_ex) for locally turning off heat/salt exchange.
    • i_hmin_airsea_ex=1: exchange turned off if local grid depth<hmin_airsea_ex;
    • i_hmin_airsea_ex=2: exchange turned off if local water depth<hmin_airsea_ex
    • This replaces the change made by adde1aa (July 8, 2020): added a new parameter hmin_airsea_ex (min total water depth for heat/salt exchange);
  • 2f7bab1 (Jun 28,2020): reorganized ICM process (rates/fluxes) and added output flag in param.nml.
  • 1477780 (May 8, 2020): changed sediment.in to sediment.nml.
    • BEDLOAD_COEFF \(\rightarrow\) bedload_coeff, NEWLAYER_THICK \(\rightarrow\) newlayer_thick, IMETH_BED_EVOL \(\rightarrow\) imeth_bed_evol
    • SAND_SD50 \(\rightarrow\) Sd50, SAND_ERATE \(\rightarrow\) Erate, SED_TYPE \(\rightarrow\) iSedtype, SAND_SRHO \(\rightarrow\) Srho, SAND_WSED \(\rightarrow\) Wsed, SAND_TAU_CE \(\rightarrow\) tau_ce, sed_morph_fac \(\rightarrow\) morph_fac, poro_cst \(\rightarrow\) porosity);