README_PRE_SCHISM

This file combines README files for v3, v2, v1 of SELFE and ELFE, mostly covering
the period before the code entered version control. The versions are separated
by **** markers. The file is included for historical reference

******************* 

Non-hydrostatic SELFE and coupled SELFE and wave model and global SELFE

v3.0a: v2.1c with non-hydrostatic component added.
       (1) changes in hotstart.in: added non-hydrostatic pressure.
       (2) changes in param.in: 
           (a) 'nonhydro' added;
           (b) one more ouput: qnon.63;
       (3) changes in bctides.in: added inu_tr for tracer nudging (only if ntracers/=0).
       (4) fixed bugs carried from v2.1a: 
           (a) check nel_j in quicksearch(); more nudging during abnormal cases;
           (b) in solve_jcg: dimension of sparsem should be 0:(mnei+1) - a mild bug as nne=nnp
               for internal nodes and mnei is achieved usually for internal nodes;

v3.0b: v3.0a with:
       (1) block-Jacobi preconditioner;
       (2) station output option from v3.0c (see below);
       (3) param.in: add station output option (iout_sta; if /=0 need nspool_sta and an input 'station.in').
       (4) bug in misc_subs: nwild declared as real in hgrad_nodes; not corrected until v3.1d.

v3.0c: v3.0b with:
       (1) Makefile cleaned; model source codes are now in different subdirs;
       (2) k2min and psimin changed for k-eps, k-omega and UB closure as suggested in Warner 
           et al. (2005, Ocean Modelling, pp. 87);
       (3) reading of tracer parameters is done for both cold and hot start (eliminated the 
           part inside hotstart section);
       (4) station output is implemented;
       (5) param.in: 
           a) now include all parameters in tracer_param.in if ntracers/=0;
           b) if nonhydro=1, need ihydro_region to indicate if a hydrostatic region needs to
               be specified in hydro_region.gr3 (depth=1 in hydrostatic region);
           c) added station output option (iout_sta; if /=0 need nspool_sta and an input 'station.in');
           d) if USE_HA is turned on in Makefile, 'iharind' is needed to do harmonic analysis;
           e) new option imm=2;
           f) if NAPZD is used, 2 extra output flags: Bbdf.63 and totN.63;
       (6) bctides.in: changed ifltype=0 to zero out vertical advective fluxes for transport
           eqs. (T,S, tarcers) only;
       (7) NAPZD (Spitz model) included; also included a testing model for tracer transport (flag_model=0);
       (8) inunfl=1 implemented;
       (9) new 3D bed deformation model (imm=2) implemented (needs user coding in routine 
           update_bdef()). Haven't updated transport part to ensure conservation!
       (10) simplified maxelev-like  outputs;
       (11) WWM-II coupled in (in progress).
       (12*) posthumous changes (only carried on to v3.1d and beyond): T,S at isolated rewetting; search
             for "new fixes".

v3.0d: v3.0c with:
       (1) in the new 3D bed deformation model (imm=2), impose no-slip bottom condition for vel.
       (2) if WWM is used, the land b.c. part of hgrid.gr3 must have flags for (exterior) land (0) and
           island (1) bnds, and no open bnd is allowed on islands;
       (3) param.in: 
           a) if WWM is used, add a coupling flag (icou_elfe_wwm=0: decoupled so 2 models
                      will run independently); also an output flag 'Hsig.61';

-------------------------------------------------------------------------------------------------------
Spherical coordinates and 2D versions:

v3.1a: v3.0d with lat/lon. (incomplete)
       (1) renamed geometric variables (x,y,z etc);
       (2) removed functions cpp, sums;
       (3) in EcoSim - biology.F90: removed USE elfe_glbl; read_eco_input changed to read_ecoin;
       (4) (su2,sv2) and other variables are in different frames for ics=1 or 2;
       (5) 2D version implemented: 
          a) barotropic and hydrostatic; 
          b) no sediment, eco models or transport eq.
          c) may be coupled to WWM later.
          d) no interpol.gr3 or vgrid.in are needed;
          e) not good for inundation yet (inunfl=0 or 1, especially latter);
       (6) read_param.F90 incorporated into io_subs;
       (5) param.in:
          a) im2d added (1: 2D model);
          b) no long reset zcor.63 output flag;
          c) some parameters no longer matter for 2D model (see sample);
          d) 'Hsig.61' output added if USE_WWM;
          e) ics=2: sphericall coordinate option;

v3.1b: v3.1a with
       (1) implicit Coriolis for 2D model (which destroys symmetry of the elevation matrix);
       (2) param.in: 
          a) add 'theta2' - implicitness factor for Coriolis (2D only);
          b) add 'btrack_noise': a scale to avoid underflow in btrack (for init. nudging);
          c) WWM: output 'WavD.61' added;
       (3) a bug in implicit Coriolis found after 1st beta release;

v3.1c: v3.1b with:
       (1) pframe and eframe changed to ll frame;
       (2) a bug in carea: skip ghost sides;
       (3) post beta release:
          a) bug in dspl_* in elfe_msgp.F90 and also in misc_subs.F90 (index mismatch);
          b) changed eps in quicksearch (bktrk_subs.F90) for lat/lon for robustness; 
             also removed "=" in checking intersection there;

v3.1d: v3.1c with:
       (1) horizontal b.c. enforced in upwind/TVD schemes (transport.F90);
       (2) horizontal b.c. for transport all changed (as I can no longer impose b.c. during outflow);
           impose b.c. only for inflow with a nudging factor;
       (3) bctides.in:
           a) nudging factor needed for all b.c. for T,S, and tracers (except '0'); 
              type -1 & -4 removed (use type 3 or 4);
           b) tracer transport: b.c. -1 replaced by 3 (nudging to i.c.);
       (4) bug fix: inpgb check (minor); check all .gr3 (# of elements and nodes);
       (5) "isolated wet for T,S" carried over from v3.0c.
       (6) for 2D model, changed h_c from 5m to 1.e6m;
       (7) cleaned up code for bound check (arrays) - only carried over to v3.1f and up.
       (8) bug fix in misc_subs: nwild declared as real.
       (9) param.in:
           a) nstep_wwm; new icou_elfe_wwm=2;
       (10) revamped utility/;
       (11) add flag_model=-1 for generic tracer transport for users (carried over only to v3.1j?);

v3.1db: v3.1d (web version) with changes in v3.1ki (to make btrack robust).
v3.1dc: v3.1db with changes in v3.1kj in btrack.
        (1) param.in:
           a) dtb_max[1,2] replaced by dtb_max, dtb_min (max/min dt for all schemes);
           b) btrack_noise removed (hardwired in code);

(goto v3.1g)
v3.1e: v3.1d with (not all new changes carried over):
       (1) momentum conservative scheme (nadv=-1) - incomplete (2D only);
       (2) new inunfl=2 option (momentum conservative wetting); also changed the computation
           near shoreline: (a) ghat1; (b) nodalvel (indvel=1);
       (3) param.in:
           a) new inunfl=2 option;

v3.1f: v3.1d with:
       (1) iterative implicit wet/dry scheme (inunfl=2);

v3.1g: v3.1d with 
       (1) levels1(): different reset of elev. at dry nodes for inunfl=1 (from serial v1.5k10);
       (2) found a bug in 2D momentum eq. (updated eta2 used in layer thickness); 
           inundation results now match 3D;
       (3) indvel=1 and nodavel(): changed to only average wet sides - this improves vel. for wet/dry.
       (4) param.in:
           a) a new parameter izonal5 to turn on Williamson test #5 (zonal flow over 
              an isolated mount)
       (5) a bug in computing flux.dat corrected;
       (6) openMPI compiler option added (from Alberto A.);
       (7) hvis for 2D model added;
       (8) first functional version of WWM;
       (9) for elev. output: -9999 at dry nodes.
       (10) added maxdahv.gr3 output;
       (11) moved init. tracer part to after T,S are initialized (for new EcoSim);
       (12) in sflux_9c: increased relative_weight for "2" to 99;

v3.1gb: intermediate version for testing new WWM.

v3.1h: v3.1g with (auto-tested)
       (1) ICM added;
       (2) hotstart for station outputs should work now;
       (3) bctides.in: tracer b.c. type 1 (input htr_?.th where "?" is tracer #) 
           and 4 (input tr3D.th) added; all types (except for "0") need nudging factor;
       (4) newer sediment model;
       (5) wind stress option for nws>=2 (Pond & Pichard);
       (6) param.in:
           a) a new parameter iwind_form (=-1 with nws>=2 uses old Pond formulation as
              nws=1; =0: use the value calculated from the heat exchange routine if nws>=2);
           b) new WWM output vars.
       (7) WWM from v3.1gb;
       (8) all output variables from WWM available in SELFE;
       (9) h_s>=6m in grid_subs.F90.

(goto v3.1i)
V3.1hb: v3.1h with (unstable yet)
       (1) ELM for WWM;

WWM_New_TMP: newer WWM in waiting;

V3.1i: v3.1h with
       (1) new iupwind_t=2 with a cut-off depth to revert to upwind;
       (2) param.in:
           a) a new parameter h_tvd if iupwind_t=2 (upwind is used if h<h_tvd);
           b) btrack_noise replaced by btrack_nudge (default=1.e-2);
       (3) finished lat/lon part in SELFE for WWM (boundary angles etc);
       (4) abs(ifltype)=4 b.c. works in lat/lon now; uv3D.th use local lat/lon frame;

V3.1ib: V3.1i with
        (1) memory consumption reduced by removing some global arrays in grid_subs.F90;

(goto V3.1j)
V3.1ic: V3.1ib with
        (1) integration ELM (prism based) + kriging;
        (2) param.in:
           a) new pars: kr_co2 (if iupwind_t=0); ibtrack_test (=1 for rotating
              Gausshill test);
           b) removed pars: inter_st

V3.1id: V3.1ic with
        (1) trying kriging transport with large balls;
        (2) param.in:
           a) new parameter for type of drift function in kriging transport:
             'kr_drift' (1: linear; 2: quadratic) - used only if iupwind_t=0;
        (3) temp. stuf: (1) 'new7'; (2) embt(); (3) a bug in constructing kriging ball 
            (ifront changed during iteration);

V3.1ie: V3.1id with
       (1) kriging ELM on node-center control volume (1 CPU for time being);

V3.1j: V3.1ib with
       (1) ELM transport: cubic spline interpolation in the vertical;
       (2) param.in:
          a) ibtrack_test added (=1: rotating Gausshill test with stratified T,S);

V3.1jb: V3.1j with newer WWM.

V3.1jc: V3.1jb with
       (1) bktrk_subs.F90: nudge vertically if hit bottom in quicksearch;

V3.1jd: V3.1jc with
       (1) bktrk_subs.F90: ELM quadratic interpolation - use inverse distance 
           interpolation if zt is below one of 6 (nodes/sides) - only works for ics=1;

V3.1je: V3.1jb with flag_model=-1 option (from v3.1d).
       (1) removed the check for quadratic ELM and pure S zone (carried
         over to v3.1jg)

V3.1jf: V3.1je with (explicit diffusion not stable)
       (1) ELM transport: diffusion included at foot of char. line. 
           (didn't check heat/salt fluxes carefully; diffusion included only if lq=2)

V3.1jg: V3.1je with 
       (1) ELM transport: calculated viscosity/diffusivity at foot of char. line.
       (pending: update upwind parts as well).
       (2) removed the check for quadratic ELM and pure S zone

(goto v3.1kb)
V3.1k: V3.1je with 
       (1) sponge layer for elev. and vel.
       (2) param.in:
          a) 2 new flags (inu_elev and inu_uv); if they=1, need inputs 
             elev_nudge.gr3 or uv_nudge.gr3;
       (3) WWM-II;

V3.1kb: V3.1jg with  [(1-3) from V3.1k]
       (1) sponge layer for elev. and vel.
       (2) param.in:
          a) 2 new flags (inu_elev and inu_uv); if they=1, need inputs
             elev_nudge.gr3 or uv_nudge.gr3;
       (3) WWM-II;
       (4) btracked dfv/dfh now updated for all eqs. (via overwriting after btrack);

V3.1kc: V3.1kb with changes added incrementally. (incomplete)

V3.1kd: V3.1kb without overwriting dfv/dfh after btrack (for closure eqs.).

V3.1ke: V3.1kd with (auto-tested)
        (1) b.c. in ELM transport also nudged like upwind/TVD;
        (2) nudging in T,S=horizontal x vertical now (so vertical relax=1 means
            keep the horizontal relax there);
        (3) param.in:
           a) vnf1,vnf2=1 to keep horizontal relax;

V3.1kf: V3.1ke with (auto-tested)
        (1) interpol.gr3 removed; interpolation in SZ region changed;

V3.1kg: V3.1kf with 
        (1) modified Grant-Madsen wave boundary layer implemented (removed rough());
        (2) param.in:
           a) new parameter iwbl for WBL;
        (3) added tsel after ELM transport;
        (4) sediment: new read_sed_input.F90 (from Jan S.);

(goto v3.1ki)
V3.1kh: V3.1kg with
        (1) impose min. dt for R-K tracking for robustness;
        (2) removed small2;
        (3) param.in:
           a) dtb_max[1,2] replaced by dtb_Euler_min,dtb_RK5_max,dtb_RK5_min;

V3.1ki: V3.1kg with quicksearch underflow changed (from small1 to 0), to 
        make btrack robust 
        a) changes in elfe_glbl: add rmaxvel; in misc_subs.F90: 
           impose rmaxvel for (ufg,vfg); in bktrk_subs.F90: RK5 btrack; quicksearch().

V3.1kj: V3.1ki with (auto-tested)
        (1) RK5 replaced by RK2; revamped btrack to enhance robustness/consistency
            (restalled small1 for underflow);
        (2) min. vel. b4 btrack (in main) excludes wvel;
        (3) param.in:
           a) dtb_max[1,2] replaced by dtb_max, dtb_min (max/min dt for all schemes);
           b) nws=4 option: ascii wind.th (uwind,vwind, pres. at all nodes at each time);
           c) re-organized WWM outputs;
        (4) air_[1,2]_max_window_hours increased to 120 hours;
        (5) put nproc and ntracers into local_to_global_* and changed autocombine_MPI_elfe.pl;

V3.1kk: V3.1kj with (not all changes carried over)
         (1) btrack: nudge vertically if bottom is hit;

Continued into svn/ in Aug 2011.

********
MPI SELFE versions.

v2.0a: from v1.5k2 and Beta1.5 of PELCIRC.
     (1) in levels[0,1]: removed upwindtrack() to simplify the coding;
     (2) changes in param.in: solver parameters; 

V2.0b: v2.0a with:
    (1) nodes/sides exchange includes interface nodes/sides to ensure 
        consistency across processors (for wet/dry);
    (2) binary outputs from each process are v5.0 format and in sub dir outputs/; 
        global-local mapping info
        is in global_to_local.prop; local-global mapping info is in local_to_global*.
    (3) btrack added;
    (4) ST nudging inputs are unformatted (similar to hotstart.in);
    (5) changes in param.in: nscreen replaced by ntracers; added dimensioning parameters
                             for btrack;
    (6) found a bug (carried over from v1.5k2) in itur=3 (xlmax() uses wrong dzz indices).

V2.0c: v2.0b with:
    (1) performance tuned;
    (2) tracers module added;
    (3) Shaprio filter added; geometry check is conditional upon indvel=0;
    (4) TVD added;
    (5) still missing: Kriging; inunfl=1; hvis; test outputs.

V2.0d: v2.0c with:
     (1) rank-specific binary outputs stripped of headers for more efficient combining; 
     (2) the original headers written into local_to_global*;

V2.0e: v2.0d with:
     (1) changes in param.in: added nhot_write after nhot where nhot_write must be multiple of ihfskip;
     (2) EcoSim added.
     (3) a bug: in EcoSim, NBT is same as nbt in btrack() (not fixed yet).

V2.0f.0 (web version): v2.0e with:
     (1) the bug in v2.0e fixed; 
     (2) changes in v1.5k6 (ifltype=-4 etc);
     (3) *3D.th format changed to binary.
     (4) fixed a bug in GOTM (frictional vel.).

V2.0f: V2.0f.0 with:
     (5) timers added; only output maxelev.gr3 if imm/=0.
     (6) performance further tuned.
     (7) horizontal diffusivity added (only for upwind and TVD); ihdif added in param.in.
     (8) in param.in, swap indvel and iwrite and check geometry first for ipre=1. 

V2.0g: updated version of v2.0f. 
     (1) corrected a bug in grid_subs.F90 (mnond and mnlnd for first segment);
     (2) commented out the output of maxelev.gr3.

V2.0gb: V2.0g with
     (1) ifltype=-4: two relaxation constants for incoming and outgoing flow (in param.in).
    
V2.0gc: V2.0gb with horizontal viscosity added.
     (1) islip disabled in param.in (always free slip).

V2.0gd: V2.0gc with
     (1) 2-tier Kriging ELM (in param.in, only kr_co is needed); 
     (2) EcoSim bugs corrected by Marta.

V2.0ge: V2.0gd with P_1^{NC} for velocity (in btrack and viscosity; indvel=1 may be less dissipative
        as it has no filter and btrack interpolation is done using P1_NC).  Still use nodal vel. for Kriging.

V2.0gf: V2.0ge with P_1^{NC} for velocity (in btrack) as an option (indvel=-1 in param.in). Viscosity calculated using P_1.

V2.0gg: V2.0gf with
     (1) add heat and salt transport in ELM (impose hard bounds if ihconsv or isconsv/=0).
     (2) variable albedo and water type (new grid inputs: albedo.gr3 and watertype.gr3).
     (3) fixed a bug in tracers in hotstart.

V2.0gh: V2.0gg with side vel. used for Kriging.

V2.0gi: V2.0gg with changes by Marta (Nov 2008). Added SIRIUS and cpp flag USE_WRAP (for a problem
        relted to ParMetis on sirius).
        (1) fixed a bug in momentum bottom b.c. (horizontal b.c. applied only from higher bottom index).

V2.0gj: V2.0gi with param.in changed to free format and bnd condition (and tides including tidal
        potential) part pushed to bctides.in (first line is date stamp, needed for CORIE processing).
        (1) for icst=2, ts.ic now can have more levels than vgrid.in.

V2.0ha: V2.0gj with new method to calculate baroclinicity.
        (1) changes in param.in: 1) iupwind_s removed (linked to iupwind_t); 2) velmin_btrack (min. vel
                                 for invoking btrack and for abnormal exit in quicksearch) added; 3)
                                 ibcc_mean added (for removal of mean density); 4) mmm (aka bcc_order) removed (use 
                                 trapzoidal rule for vertical integration in baroc. force);
        (2) for icst=2, ts.ic now can have more levels than vgrid.in; fixed bugs in tracer i.c.
        (3) ELM linear interpolation for S,T: vertical interpolation now uses cubic spline; quadratic
            interpolation still uses quadratic in vertical.
        (4) in quicksearch: search surrounding wet elements at start before nudging;
        (5) mean density profile removed when computing baroclinic force. 
        Below are changes made after release:
        (6) a bug in ihdif is fixed;
        (7) a bug in hotstart (ifile) fixed;
        (8) a bug in heat exchange model (attentuation depth) fixed;
        (9) treat soil layer below bottom as black body in heat exchange model so there
            is no need to adjust albedo in shallow water.
        (10) fixed a bug in sparse matrix for Flather b.c.

V2.0hb: V2.0ha with Flather b.c. changed: input eta_mean and vn_mean for each node and level.
        (1) specif.F90 replaced by the one sent by Marta (a bug);
        (2) optinally specify i.c. for elevation (elev.ic, invoked by one parameter in param.in: ic_elev);
V2.0hc: V2.0hb with ELM linear interpolation for S,T using old linear interpolation in vertical. 
         
-----------------------------------------------------------------------------------------------
Coupled SELFE and wave model (incomplete):

V2.1a: V2.0hc coupled to SWAN; SELFE is written as a routine for this purpose.
       (1) the"bug" in (10) of V2.0ha is not a bug; calculate I_3 even for essential b.c.
           segment as it will be sorted out in solver, and to facilitate the checking of 
           matrix symmetry;
       (2) added nudging for tracers; tr_nd only defined at resident nodes for outputs only.

       To avoid dependency on # of processors:
       (1) the starting element in btrack is now 1st wet surrounding element; nudge point
           only initially and in abnormal case in quicksearch(); 
       (2) for quadratic T,S interpolation, upwind stencil is now based on wvel at foot;
       (3) in Euler btrack, commented out "if(idt>1) dtb=dtb+trm";
       (4) in quicksearch: don't search surrounding wet elements at start before nudging;
       (5) changed quicksearch() to enhance robustness (point-in-triangle test and intersection test);
       (6) Bug (3a) found in v3.0a fixed.

V2.1b (the saving in time is not worth it): V2.1a with
       (1) unnecessary exchange_ calls eliminated;

V2.1c: V2.1a with
       (1) cut down exchanges in JCG solver (to prepare for non-hydrostatic);

TODO:
    -- Try to bundle up many arrays? Need to restructure elfe_msgp.
    -- inunfl=1.

    
**********
ELFE (Eulerian-Lagrangian Finite Elements) v1:

V1.1:
----------------------------------------------------------------------------------
elfe1_1a:
elfe1_1b: 1a with all tabs replaced (to clean up debugging messages).
   Is there a bug in ri3? yes.

elfe1_1c: elfe1_1b with: (not successful)
  (1) b.c. revamped (especially for essential b.c.); normal derivatives as unknowns.

elfe1_1[d,e]?: elfe1_1b with various working options.

elfe1_1f1: barotropic solver from 1_1b (i.e., vel. at sides; 5th-order RK btrack); 
  generalized-S coordinates implemented.

elfe1_1f2: elfe1_1f1 with baroclinic parts added. Pre-compute C(s) and C'(s).
elfe1_1f2v: elfe1_1f2 with quadratic interpolation for vel. in btrack. Bad elevation.

elfe1_1f3: elfe1_1f2 with nodal vel. interpolated from its parent triangle in the ball.

elfe1_1f4: elfe1_1f2 with nodal vel. interpolated using power series/LS in the ball.

elfe1_1f5: elfe1_1f4 with power series cut off at 4th order, and quadratic interpolation for vel.

elfe1_1f6: elfe1_1f5 without quadratic interpolation for vel.
 
elfe1_1f7: elfe1_1f6 with interpolation using 1/(1+r). Bad elevation & vel. results.

elfe1_1f8: elfe1_1f5 with quadratic interpolation for vel. for all btrack sub-steps.

elfe1_1f9: elfe1_1f2 with interpolation of vel. using discontinuous element vel. 

elfe1_1f10: elfe1_1f2 with sub-division for wave-continuity eq.

elfe1_1g1: cleaned up version of elfe1_1f10.

elfe1_1g2: elfe1_1g1 with baroclinic part changed (to include surface density).

elfe1_1g3: elfe1_1g2 with S1 revamped to enhance robustness for wet/dry. Added GLS closure.

elfe1_1g4: elfe1_1g3 with minor changes in btrack and GLS.

elfe1_1g5: elfe1_1g4 with baroclinic part changed (cubic spline).

elfe1_1g6: elfe1_1g5 and re-look at BCC in a broader context. Impose a rigid lid for FS.

elfe1_1g7: elfe1_1g5 with bcc calculated from prognostic eq D\rho/Dt=0.

elfe1_1g8: continue from elfe1_1g7; evaluate \int f_bc d\Omega directly.

elfe1_1g9: elfe1_1g5 with hybrid sigma- and z- in BCC.

elfe1_1g10: elfe1_1g9 with pure z, and density de-meaned. 
            (1) A bug found in ASM of GLS model, and changed Ghp=Gh.
            (2) Unconstrain S,T until eqstate; reduce the size of fort.12;
            (3) Impose min. mixing length at the surface layer.
            (4) Hostart works now.

elfe1_1g11: elfe1_1g10 with:
            (1) xlmax=0.4*depth (less constraint for surface layer mixing) 

elfe1_1g12: elfe1_1g11 and:
            (1) Add an option for single btrack;

elfe1_1h1: elfe1_1g12 with:
    (1) Single btrack only;
    (2) hybrid sigma- and z- in BCC (follow g9).
    (3) Fixed a bug in quicksearch (random nudging for some tricky cases).
    (4) ifltype=3, 4 (profile of uv) added.
    (5) changed bottom b.c. for w.

elfe1_1h2: elfe1_1h1 with:
   (1) discontinuous nodal vel.;
   (2) horizontal diffusion added;

elfe1_1h3: elfe1_1h1 with optional Euler btrack. (not tested)

elfe1_1h4: elfe1_1h3 with:
    (1) optional sigma-plane tracking;
    (2) Undo the "bug" in elfe1_1h1 (3), due to some strange problem in CORIE case;

elfe1_1h4b: elfe1_1h4 with output format v4.0.

elfe1_1h5: elfe1_1h4 with
    (1) optional sigma-plane tracking removed
    (2) wetting/drying part revamped
    (3) Fixed a bug in bcc calculation (sigma-method; "+' should be "-" in the y-direction)

elfe1_1h6: elfe1_1h5 with:
    (1) Average S,T as backup for wet/dry
    (2) A "cushion" added for ivcor=2 to prevent sudden shift from S- to sigma
    (3) New output zcor.63 added; new output format v4.0
    (4) Iterative correction for S in the vertical after transport eq.
    (5) Iterative correction for S after btrack

elfe1_1h7: elfe1_1h6 with:
    (1) Blending linear and quadratic for btrack S

elfe1_1h7b: elfe1_1h7 with bounds for S,T enforced differently.

elfe1_1h8: elfe1_1h6 with:
    (1) no (5): Iterative correction for S after btrack; impose bounds after quadratic interpolation
    (2) enforce bounds after transport eqs.

elfe1_1h8b: elfe1_1h8 with diffussion in the excess field calculated by min. vgrid size.

elfe1_1h9: elfe1_1h8b with:
    (1) quadratic interpolation in the vertical in btrack

elfe1_1h9b: elfe1_1h9 with diffussion in the excess field calculated by simple average. 
elfe1_1h9c: elfe1_1h9b with slightly different crietrion for convergence (back to absolute difference only).

elfe1_1h10: elfe1_1h9 with 5-pt smoothing for transport.


----------------------------------------------------------------------------------
V1.2:
----------------------------------------------------------------------------------
elfe1_2a: elfe1_1h9c with:
    (1) obc for S,T nudged;
    (2) Impose max. for Cd for nchi=1,2 (roughness)

elfe1_2b: elfe1_2a with:
    (1) nchi option changed;
    (2) itur=3 changed: input diffmax.gr3 and diffmin.gr3;
    (3) no slip land b.c. option added;
    (4) all .bp inputs replaced by .gr3;
    (5) hotstart format changed

elfe1_2c: elfe1_2b with:
    (1) no-source heat transport implemented (not right if heat exchange is on)
    (2) still depth added (vertical nudging for S,T)
    (3) S,T obc nudged to i.c. (param.in changed)
    (4) general nudging added
    (5) xlfsmin added for surface mixing; 

elfe1_2d: elfe1_2c with:
    (1) still depth replaced by a step function in z;
    (2) clean ups (Cd in UB closure; abnormal cases in qsearch).
    (3) revamped the abnormal case for S-coord. (for h<h_c).
    (4) speeded up rint_lag().
    (5) put mmm (in rint_lag) as a parameter in param.in.
    (6) hybrid lq option added
    (7) heat exchange added (not in 1.2e).

elfe1_2d2: elfe1_2d with heat exchange disabled for T, but Zeng's wind stress enabled when ihconsv=1. 
           This is a compromised version. Do not try to use it for temperature.
elfe1_2d3: elfe1_2d2 with bottom drag part changed (const. Reynolds stress in BL; momen. eq. from 2 to Nz).
elfe1_2d4: elfe1_2d2 with bottom drag part changed (const. Reynolds stress in BL; momen. eq. @ level 2 treated 
           differently from other levels).
elfe1_2d5: elfe1_2d3 with chi=Cd*(u^n**2+v^n**2).
elfe1_2d6: elfe1_2d3 with linear drag formulation (incomplete).
elfe1_2d7: elfe1_2d3 with optional linear drag formulation.
elfe1_2d8: elfe1_2d7 with F.D. for momentum.

elfe1_2e: 1.2d with:
    (0) without heat exchange;
    (1) Conservation of S,T imposed.

elfe1_2g: cleaned-up elfe1_2d7 with changes in baroclincic part consistent with bottom BL.
elfe1_2g2: elfe1_2g with: division for btrack changed for nsub=2.
elfe1_2g3: elfe1_2g2 with:
          (1) ielad added
          (2) optional sub-element linear interpolation for vel. (int_mom)
          (3) horizontal viscosity added 
          (4) Small changes in nchi=1 (Cd no longer reset to 0 after dry).

elfe1_2h: elfe1_2g3 with:
          (1) hhat optionally limited to non-negative;
          (2) Flather 1 obc implemented (not right yet);
          (3) used average total depth to compute river bnd areas;
          (4) 3D t.h. b.c. for eta, vel, S,T implemented (type 4);

elfe1_2h2: elfe1_2h with:
          (1) UB closure revamped;
          (2) depth limit in hvis (sdbt) removed;
          (3) No heat exchange in transport equations;
          (4) ielad=1 changed;
          (5) changes in param.in: delete tempmin line; nadv=1: Euler; =2: R-K (similar for advection
              flag in adv.gr3); 
          (6) added dfv etc. in hotstart.in;

elfe1_2h3: elfe1_2h2 with b.c. for xl changed to xlmin2.
elfe1_2h4: elfe1_2h2 with quadratic interpolation in vertical replaced by linear (i.e., quadratic in horizontal only).
elfe1_2h5: elfe1_2h2 with no ELAD correction, i.e., min. & max enforced directly. This is an experimental version.

elfe1_2i: elfe1_2h5 with:
          (1) mass lumping used in transport and no ELAD correction;
          (2) theta_f unlimited beyond 20;
          (3) optional trapzoidal integration;
          (4) increased # of columns in rrhs and soln (to prepare for ecological model);
          (5) reverse nadv and dtb_max rows, and for nadv=0, input two dtb_max (1 for Euler and
              the other for R-K);

elfe1_2i2: elfe1_2i with sgima-plane leveled above certain vertical level. (experimental; not complete)
elfe1_2i3: elfe1_2i with xlbot limited to 1cm.
elfe1_2i4: elfe1_2i with xlbotmax as a parameter.
elfe1_2i5: elfe1_2i4 with xlfs00 replacing xlfsmin and dz(2)/2 as a parameter.

----------------------------------------------------------------------------------
V1.3: hybrid vertical coordinates
----------------------------------------------------------------------------------
elfe1_3a: elfe1_2i with:
          (1) ivcor=1,3 removed;
          (2) no removal of mean in eqstate;
          (3) changed hotstart.in; mnv removed;
          (4) iback=2 becomes fatal; 
          (5) sub-division in btrack option removed;
          (6) remove elemental mean in baroclinic compuation;
          (7) fixed a bug for nchi=1;

elfe1_3b: elfe1_3a (not upto date) with xlfs00 replacing xlfsmin and dz(2)/2 as a parameter.
elfe1_3c: elfe1_3a with xl limited by min. distance to the 2 walls for non-bnd levels. 
elfe1_3d: elfe1_3a with xl also limited by a maximum (xlmax00) thru'out the domain; 
          changed xlfsmin and xlmax00 to the length without scale 0.4; xl b.c. with full layer
          thickness (instead of 1/2).
elfe1_3e: elfe1_3d with surface b.c. for xl replaced by xlfsmin (not dependent on surface layer thickness).
elfe1_3g: elfe1_3e with xlfs input from xlfs.gr3.
elfe1_3g2: elfe1_3g with S,T limited by saltmin etc. in transport (less restrictive).
elfe1_3g3: elfe1_3g2 with nodalvel evaluated with more strict checks. 

elfe1_3h: elfe1_3g2 with vertical interpolation for S,T, u,v, bcc done in z. 
          (1) Reversed the order of indices for some 2D arrays for cache efficiency. 
          (2) Must compile with sflux_subs7d_zhang or higher.
          (3) Quadratic interpolation is still done in S.
          (4) Fixed a bug in dudn() (for hori. diff.)

elfe1_3i: elfe1_3h with linear interpolation for S,T changed (bottom instead of min. or max).
          (1) Added salt conservation check inside flux check.
elfe1_3i2: elfe1_3i with bcc evaluated in either S or Z plane (quadratic lq_s=2--> S plane bcc).
elfe1_3i3: elfe1_3i with S,T interplation back to v1.3h (this is a confidence-building version).
elfe1_3i4: elfe1_3i with S,T interplation near bottom more carefully done.
elfe1_3i5: elfe1_3i2 with all other vinter() also optionally evaluated in S, except for S,T with lq=1.
elfe1_3i6: elfe1_3i with S,T interplation being a weighted average of max. (min.) and interpolated values,
           based on the relative position of zt. 

elfe1_3j: elfe1_3i5 with Z0 for elevation interpolated in time between beginning and end of a run.

elfe1_3k: elfe1_3i5 with nudging for S, T decoupled (but still shares vertical nudging).
elfe1_3k2: elfe1_3k with bottom xl reverted to v1.2i (half bottom layer thickness).
elfe1_3k3: elfe1_3k with some features of v1.2i restored (for better estuary results):
          (1) restored ss in quicksearch(), and quadratic interpolation part in btrack(). 
              Also linear/quadratic based on lq at the foot not the starting element.

elfe1_3m: elfe1_3k3 with vinter() invoked by interpol=2 (i.e., no longer by lq_s=2).          
elfe1_3m2: elfe1_3m with Z0 varying within a run (new input Z0.th).
elfe1_3m3: elfe1_3m with linear interpolation in S,T also along S-coordinates for interpol=2.
elfe1_3n: elfe1_3m with:
          (1) xlat and ylon pushed into global module (for heat exchange); heat exchange also requires hgrid.ll now;
          (2) this version should be compiled with new heat exchange code (sflux8b or up; use Makefile), 
              which is valid for any region in the world;

elfe1_3n2: elfe1_3n with:
          (1) Changes in bcc calculation for z-layers; impose vel. b.c. for sides below one of its 2 element bottoms.
          (2) added tidal potential. 

elfe1_3p: elfe1_3n2 with tsunami option added. Added one more output: depth-averaged hvel.

----------------------------------------------------------------------------------
V1.4: upwind option for transport
----------------------------------------------------------------------------------
elfe1_4a: elfe1_3p with upwind option.
         (1) added tsel in hotstart.in;
         (2) changed bottom b.c. for w (normal flux= bed deformation rate);
         (3) added heat exchange in upwind option (and nws=3 for conservation check).

elfe1_4b: elfe1_4a with S,T b.c. type 4 (3D.th) imposed only for inflow.
elfe1_4c: elfe1_4a with xlmax calculated from the min. distance from the wall (old way) (in 
          order to cut down mixing; xlmax00 and xlfs0() become obsolete).
elfe1_4c2: elfe1_4c with limit on vel. raised to 5m/s and unlimited for tsunami models. Also fixed a bug in tsunami 
           model (in dp=dp-bdef2).
          (1) removed xlmax00 and xlfs0();
          (2) rename bdef.bp as bdef.gr3.
elfe1_4c3: elfe1_4c2 with:
          (1) 1 new b.c. option iadtype=1 (nudge to a constant vel. for inflow in btrack).
       
elfe1_4d: elfe1_4c with the surface/bottom xlmax reset to xlfs (to prevent xl being too small there).

----------------------------------------------------------------------------------
V1.5: TVD flux limiters option for transport
----------------------------------------------------------------------------------
elfe1_5a: elfe1_4c2 with TVD schemes.
          (1) slightly relaxed the extrema for T,S for ELAD (to include non upwind prisms as well); since
              TVD does not use ELAD, the effects on upwind should be minimal.
elfe1_5b: elfe1_4c2 with explicit upwind for vertical advection and adaptive sub time stepping.
          (1) removed ELAD (ielad inactive)
elfe1_5b2: elfe1_5b with vertical advection being treated implicitly.
elfe1_5c: elfe1_5b2 with fully explicit TVD option.
elfe1_5c2: elfe1_5c with dtb calculated using max. principle form, and eqs. solved with mass conservative form.
elfe1_5c3: elfe1_5c2 with Casulli's definition of upwind ratio as an option (model "C").

elfe1_5d: elfe1_5c3 with option iwindoff.
           (1) fixed a minor bug found by Mike Z.
elfe1_5d2: elfe1_5d with vertical implicit TVD (experimental). Oscillations back.
elfe1_5d3: elfe1_5d with netcdf for atmos. inputs (compiled with sflux*9b and up),
           and evap/precip models added. This is a paralell version of v1.5h.
           (1) add evap.61 and prcp.61 and swap dahv.62 and hvel.64 in param.in.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
elfe1_5e: elfe1_5d with
          (1) discontinuous vel. at nodes; cleaned up some interpolation mode.

elfe1_5e2: elfe1_5e with alternative hvis.
elfe1_5e3: elfe1_5e2 with imposed stress for no-slip bnd, and variable hvis.
elfe1_5e4: elfe1_5e3 with vel. in btrack using averaged values (uu2,vv2).
elfe1_5e5: elfe1_5e4 with Smagorinsky for hvis.
elfe1_5e6: elfe1_5e5 with averaging in upwind S,T.
elfe1_5e7: elfe1_5e5 with (uu2,vv2) computed using old way of elfe1_5d.
elfe1_5e8: elfe1_5e5 with Shapiro filter for u,v.
elfe1_5e9: elfe1_5e8 with Shapiro filter applied to the quad that contains the side center.
elfe1_5e10: elfe1_5e9 with vis_coe=1 for internal sides, =0 for bnd sides.
elfe1_5e11: elfe1_5e9 with vis_coe1 for internal sides, and vis_coe2 for bnd sides (and all nodes).
elfe1_5e12: elfe1_5e11 with variable shapiro.
elfe1_5e14: elfe1_5e11 with interpol restored in btrack and nodalvel (we only) for bottom intrusion. 
           (1) fixed a minor bug found by Mike Z.
           (2) updated kinetic energy calculation for tsunami.
elfe1_5e15: elfe1_5e14 with variable horcon.
           (1) fixed a minor bug found by Mike Z.

elfe1_5g: elfe1_5e15 with boundary mixing length back to similar to
          v1.4d (xlsc.gr3 has the scale factors for the boundary mixing length).

elfe1_5g2: elfe1_5g, with option to turn off baroclinicity in some region.

elfe1_5h: elfe1_5g with netcdf input (sflux*9b and up). 
          (1) add evap/precip module (two more outputs: evap.61 and prcp.61 and swap dahv.62 and hvel.64 in param.in).
          (2) added a flag ihorcon in param.in to bypass hvis calculation if all horcon=0 (horcon.gr3 becomes conditional).
          (3) relaxed the geometry check for side neighborhood if all horcon=0 (then only check geometry for Shapiro filter).
          (4) disabled the bound check in ELM transport (negative T is possible with upwind
              due to heat exchange).


elfe1_5h2: elfe1_5h with nadv=0 option changed so that the depth in adv.gr3 is the nudging factor when between 0 and 1. 
          (1) didn't disable the bound check in ELM transport.

elfe1_5i: elfe1_5h with Kriging in btrack (transport only). From this version on, must compile
          with lapack.
          (1) removed int_mom in param.in;
          (2) disabled the bound check in ELM transport;

elfe1_5i2: elfe1_5i with global Kriging.

elfe1_5i3: elfe1_5i with Kriging ELM for momentum as well (lqk=3: Kriging for S,T and vel.) 
elfe1_5i4: elfe1_5i3 with Kriging ELM for momentum only (removed KELM for S,T; added inter_mom).
           Kriging is not applied (automatically) at bnd nodes/sides as the filter is not applied there.
elfe1_5i5: elfe1_5i4 with KELM for ST as well. Use Shapiro filter for S,T, and calculate ST
           only at sidecenters first.

elfe1_5i6: elfe1_5i4 with wet/dry part revamped for tsunami benchmarking.
           (1) added rmaxvel in param.in;
elfe1_5i7: elfe1_5i6 with some changes in wet/dry part to enhance robustness.
elfe1_5i8: elfe1_5i7 with more changes in wet/dry part (average side vel. and elevation at interface).
elfe1_5i9: elfe1_5i7 with average side vel. only in wet/dry part.
elfe1_5i10: elfe1_5i9 with side vel. in the final extrapolation based on local sides.
elfe1_5i11: elfe1_5i10 with elevation at final extrapolation nodes calculated based on flux.

elfe1_5j1: elfe1_5i11 with itetype (and isatype)=-4 nudged (add tobc and sobc in param.in).
           (1) fixed a bug in tobc and sobc (can vary with open boundary).
           (2) param.in: added ireg_elev for not regulating elevation during wet/dry (because it may 
               contaminate elevations elsewhere e.g. in estuary); this flag should only be turned on
               if resolution and time step is fine enough (e.g., tsunami).
elfe1_5j2: elfe1_5j1 with
           (1) ireg_elev replaced by inunfl (1: resolution fine enough for better inundation algorithm to work).
               If inunfl=0, the old inundation algorithm is used.
elfe1_5j3: elfe1_5j2 with GLS closure from GOTM (itur=4).
           (1) Disabled the node # checks for *3D.th inputs.

elfe1_5j4: elfe1_5j3 with 
           (1) max/min of S,T enforced when isconsv or ihconsv/=0 in upwind/TVD (for ELM, there is no heat/salt budget models).
           (2) added vdiff.63 output.
           (3) fixed a small bug (c/o Ligia) in nchi=1.

elfe1_5k: elfe1_5j4 with
           (1) averaged vel. (from v1.5d) restored as an option (indvel=1, for elevation problems). This
               option does not use Shapiro Filter.

elfe1_5k_sed: elfe1_5k with a simple sediment model adapted from FVCOM (for 2007 summer intern).
            (1) sediment model only works for upwind scheme (iupwind_t/=2 and iupwind_s/=2).
            (2) no b.c. for sedmiment.

elfe1_5k2: elfe1_5k with upwind-TVD transport part mostly as a routine (still not plug-and-play).
           (1) added ntracers in param.in; added tracer conc. in hotstart.in.
           (2) fixed a bug in header() (h_0 should be h0).
           (3) added LAPACK source code (lap.f) so as to bypass the library.
           (4) found a bug in itur=3 (xlmax() uses wrong dzz indices). 
           (5) for nws=2, wind can be overwritten by wind.th (need to uncomment some lines).
           (6) found a bug in P&P closure: su2 and sv2 should be replaced by uu2 and vv2 (not corrected).

elfe1_5k3: elfe1_5k2 with new option ifltype=5 to allow variation along each segment (but depth-averaged).

elfe1_5k4: elfe1_5k2 with 
           (1) vel. at open-bnd nodes (with ifltype=0) calculated by averaging in indvel=0.
           (2) in nodalvel: vertical vel. calcualted using S or Z interpolation based on same
               criterion as hvel.

elfe1_5k5: elfe1_5k2 with
            (1) the bug in P&P closure corrected;
            (2) ifltype=-4 (nudging incoming vel.) added; I_3 is only calculated if iettype==0.

elfe1_5k6: elfe1_5k5 with ifltype=-4 for nudging both incoming and outgoing vel.

elfe1_5k7: elfe1_5k6 with a bug in GOTM (frictional vel.) corrected.
           (1) output maxdahv.gr3 (based on magnitude). 

elfe1_5k8: elfe1_5k7 with input elev.ic for initial elevation.
elfe1_5k9: elfe1_5k8 with 
           (1) new option of 3D deformation for tsunami model (imm=2; needs
               user coding; current default is for 3D displacement from Kelin - in param.in: 
               you need ibdef; a new input bdef3D.gr3 based on Kelin's grid not hgrid.gr3!); 
           (2) no longer reset zcor.63 output flag;
           (3) outputs for max. elev. and dahv with more precision.

Following versions are only in Tsunami_Code/

elfe1_5k10: elfe1_5k9 with eta2 not reset to 0 for init. dry land (inunfl=1).
elfe1_5k11: elfe1_5k10 with changes in deformation stage (imm/=0): (search for "elfe1_5k11")
            (1) initially dry pts will remain dry even during subsidence (init. elev.
                based on ihot=0);


END README