PML_ChangeLog.txt 57.4 KB
Newer Older
1 2
Pierre Cazenave <pica@pml.ac.uk> fvcom-toolbox ChangeLog

3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76
20190220
--------

Minor update.

Thanks to Ricardo Torres and Simon Waldman for their contributions.

README.md
    Updated with the current release details.

doc:
    Updated for the latest release.

fvcom_postproc:
    do_surface_plotMatlabMap
        * Cosmetic changes to the plot.
    show_max_CFL
        * New function to compute the CFL number for a given grid.

fvcom_prepro:
    add_obc_node_list
        * Fix checks for invalid open boundaries.
    add_sponge_nodes_list
        * Code cleanup.
    add_weights_FVCOM_nested_forcing
        * Fix shape of the weights for the nodes.
    change_shallow_bathy
        * New function to adjust bathymetry in the grid.
    find_nesting_region
        * Code cleanup.
    hybrid_coordinate
        * Fix output format for the sigma file.
    interp_POLCOMS2FVCOM
        * Merge the v1 version of this and remove the duplicate.
    make_default_nml
        * Tweak the default number format for bed roughness.
    read_fabm_variables
        * Code cleanup.
    read_sigma
        * Add complete support for generalised and hyperbolic tangent sigma distributions.
    read_sms_mesh
        * Allow a given depth file to override values in the .2dm.
    set_elevtide_tmd
        * Add argument for the location of the TMD data.
    write_FVCOM_river_nml
        * Add argument to supply a vertical distribution as fractional depths (0-1).
    write_FVCOM_tsobcERSEM
        * Code cleanup.

utilities:
    ComputeMatricRx1_nodes
        * New function to calculate the hydrostatic consistency condition.
    Times2Datetime
        * New function to convert FVCOM 'Times' to MATLAB datetime objects.
    concat_by_struct
        * New function to concatenate data contained within a structure.
    mjul2str
        * Make the input always be a double.
    plot_fvcom_field
        * Add quiver plotting option.
    read_FVCOM_river_file
        * New function to read in FVCOM river files.
    read_netCDF_FVCOM
        * Fix loading data with only a single time stamp.
    restrict_spatial_indices
        * New function to eliminate nodes and elements for some given mask.
    sigma_gen
        * Add comment about potential bug (not yet fully investigated).
    sigma_tanh
        * Add option to return the sigma data into the supplied mesh object.
    tubine_area_sigma
        * Add option to plot into subplots.


77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228
20180201
--------

Major update. Added better support for the sediment transport routines in FVCOM. Improved the nesting support.

Thanks to Ricardo Torres, Rory O'Hara Murray and Simon Waldman for their contributions.

README.md
    Updated with the current release details.

doc:
    Updated for the latest release.

examples:
    Add better examples.

fvcom_prepro:
    add_obc_nodes_list
        * Code cleanup.
    add_sponge_nodes_list
        * Code cleanup.
    add_stations_list
        * Code cleanup.
    add_weights_FVCOM_nested_forcing
        * Modifies in place the nested file to add weights for the number of levels suitable for types 3.
    create_nesting_nodes
        * Create a list of the nesting boundary nodes
    estimate_ts
        * Code cleanup.
    find_nesting_region
        * Creates a nesting structure array for direct/indirect or weighted nesting.
    fix_river_nodes
        * Tweak depth optimisation.
    get_HYCOM_forcing
        * Apply scale and offset values correctly.
    get_HYCOM_tsobc
        * Use the new interpo_coarse_to_obc generic function. This is now just a wrapper for that.
    get_NEMO_rivers
        * Add support for passing a set of river positions separately. Can also drop the NEMO Baltic inputs.
    hybrid_coordinates
        * Fix the transition depth optimisation and report the maximum difference between the two sigma level regions.
    interp_POLCOMS2FVCOMv1
        * ?
    interp_coarse_to_obc
        * New function to take coarse regularly gridded model data and interpolate it onto model open boundaries.
    make_default_nml
        * New function to generate a default model namelist struct.
    make_model_nml_generic
        * Create a new model run namelist.
    modify_FVCOM_nested_forcing
        * Modifies nested file to change weights or number of levels and writes a new nested file.
    read_admesh_mesh
        * Read an ADMESH file.
    read_fabm_variables
        * For a given configuration, read the ersem variables required to run the model.
    read_fvcom_bath
        * Code cleanup.
    read_sigma
        * Add support for the hyperbolic tangent function.
    read_sms_mesh
        * Add support for spaces in the header.
    smoothfield
        * Code cleanup.
    smoothfield2
        * Code cleanup.
    write_FVCOM_bath
        * Code cleanup.
    write_FVCOM_bedflag
        * Code cleanup.
    write_FVCOM_elevtide
        * Add ability to pass an array of time strings as well as numeric values.
    write_FVCOM_nested_forcing
        * Add new variables needed by FVCOM4.
    write_FVCOM_restart
        * Enable compression in the netCDF4 file.
    write_FVCOM_river_ERSEM
        * Add missing ERSEM variables (oxygen and alkalinity).
    write_FVCOM_sediment
        * Write forcing files for sediment transport.
    write_FVCOM_sponge
        * Allow for variable sponge coefficient and radius.
    write_FVCOM_tsobcERSEM
        * Removed the reads of the ASCII configuration files (which was very
        slow) and instead extracted the relevant information from the supplied
        mesh object. As such, the requirements for the mesh object have
        changed, so hopefully this won't bite too many people in the behind.
        Also simplified the allocation of the arrays when uniform values are
        given (i.e. when in_salt and in_temp are scalars).
    write_FVCOM_z0
        * Code cleanup.
    write_admesh_mesh
        * Write ADMESH formatted files.
    write_nesting_bdy_file
        * Write nested forcing netCDFs.
    write_model_nml
        * New function to write out a model namelist.

fvcom_postproc:
    do_surface_plotMatlabMap
        * Use the MATLAB mapping toolbox.
    do_vector_plot_MatlabMap
        * Use the MATLAB mapping toolbox.
    do_vector_plot_MatlabMapC
        * Use the MATLAB mapping toolbox.

utilities:
    ST_Dstar
        * Add support for matrices of data.
    ST_erate
        * Code cleanup.
    ST_example
        * Code cleanup.
    ST_phi2d
        * Code cleanup.
    ST_taucr
        * Add support for matrices of data.
    ST_wentworth
        * Code cleanup.
    ST_wset
        * Add support for matrices of data.
    SW_Density
        * Code cleanup.
    Times2Matlab
        * Function to convert from Times strings to MATLAB dates.
    distance_along_BC
        * Calculates the distance from coast along the open boundary nodes.
    distance_to_coast
        * Calculates the distance from the coast in all mesh nodes.
    find_relaxation_boundary
        * Find the elements which fall along the boundary for a nested configuration.
    grid_vert_interp
        * Code cleanup.
    merge_bathymetry
        * This script uses a blending function to combine two bathymetry sources over a common spatial extent.
    mjul2matlab
        * Convert a Modified Julian date to a Matlab Serial Date.
    quiverwcolorbar
        * Generate a quiver plot with arrows colored according to vector magnitude.
    read_netCDF_FVCOM
        * Use Times strings for Times instead of numbers as the latter miss some precision.
    sigma_geo
        * Support even numbers of levels.
    sigma_tanh
        * Fix initialisation of array error and fix an off by one error when generating a sigma distribution.
    turbine_area_sigma
        * Add new argument which is the number of sigma layers in the model.
    write_SMS_2dm
        * Add ability to write depths to the 2dm file.
    zero_to_nan
        * Code cleanup.


229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340
20160811
--------

Fairly major overhaul of the code. Adds a lot of new functionality and tidies
up the code across a large part of the toolbox.

README.md
    * Update the location of functions which still require updating to use
    modern MATLAB netCDF syntax.

doc:
    * Update the documentation for the new release.
    convert_logo.sh
        * Script to convert the logo for the toolbox from PDF to png.

fvcom_prepro:
    add_var_FVCOM_river.m
        * Convert from old netCDF routines to native MATLAB syntax.
    fix_river_nodes.m
        * Add ability to move river nodes to the deepest node within the given
        radius.
    get_HYCOM_forcing.m
        * Add new data sets from the HYCOM server (post-2014).
    get_HYCOM_tsobc.m
        * Add fallback interpolation to inverse distance weighted if the
        triangular interpolation fails.
    get_NEMO_rivers.m
        * New function to read in NEMO formatted river data.
    get_POLCOMS_tsobc.m
        * Fix the parallel pool code syntax.
    hybrid_coordinate.m
        * New function to create a hybrid vertical coordinates file.
    interp_HYCOM2FVCOM.m
        * Clarify help on the shape of the required input data arrays. Update
        the interpolation to extrapolate by removing NaNs from the input data
        and setting the 'nearest' flag on scatteredInterpolant.
    read_fvcom_bath.m
        * Remove loops to speed up reading in the file.
    read_sigma.m
        * Made the sigma distributions be spatially resolved for the UNIFORM,
        GEOMETRIC and GENERALIZED cases. Also removed the UNIFORM distribution
        from the checks on the values of parameters which only belong in the
        GENERALIZED case.
    read_sms_mesh.m
        * Fix behaviour if grid has no open boundaries so we can rely on
        have_strings existing in either case.
    wrf2fvcom.m
        * Add missing global attribute.
    write_FVCOM_TT.m
        * Add support for a variable turbine thrust coefficient.
    write_FVCOM_bath.m
        * Removed loops to speed up writing the file
    write_FVCOM_cor.m
        * Removed loops to speed up writing the file. Remove tabs and clean up
        syntax.
    write_FVCOM_forcing.m
        * Remove stray whitespace.
    write_FVCOM_grid.m
        * Removed loops to speed up writing the file. Minor code tweaks to fix
        MATLAB warnings. Add check that we successfully opened the output file.
    write_FVCOM_groundwater.m
        * Added help which actually refers to this script's function rather
        than the template upon which it was based.
    write_FVCOM_river.m
        * Fix print statement format.
    write_FVCOM_river_ERSEM.m
        * New version to export nutrients alongside the physical parameters for
        FVCOM-ERSEM. Based on write_FVCOM_river.
    write_FVCOM_sponge.m
        * Reconcile the original behaviour (single value at each open boundary)
        and the variable values for each node. Also update the help and general
        formatting of the code.
    write_FVCOM_tsobc.m
        * Removed the reads of the ASCII configuration files (which was very
        slow) and instead extracted the relevant information from the supplied
        mesh object. As such, the requirements for the mesh object have
        changed, so hopefully this won't bite too many people in the behind.
        Also simplified the allocation of the arrays when uniform values are
        given (i.e. when in_salt and in_temp are scalars).
    write_FVCOM_z0.m
        * Added new variable (cbcmin) to support FVCOM version 4. Also tidied
        up the code a bit.

tests:
    fvcom_prepro:
        test_write_FVCOM_tsobc.m
            * Unit test for write_FVCOM_tsobc.
    utilities:
        test_get_POLCOMS_tsobc.m
            * Updated to actually compare the interpolated data rather than just the grid information.
        test_grid2fvcom.m
            * Fix paths to data to load.

utilities:
    grid2fvcom.m
        * Fix the alternative grid handling in the parallel loop. Remove
        commented out code too.
    make_logo.m
        * Make the toolbox logo.
    plot_fvcom_field.m
        * Changed the way fig id is checked, not using 'exist' anymore. Added
        the axis command in.
    read_fvcom_mesh.m
        * Remove loops to speed up reading in the file.
    read_netcdf_vars.m
        * Dimension ids are now added to attributes. Added the ability to
        specify the stride/sample rate.
    read_netcdf_vars_xy.m
        * Function to extract netcdf variables for a number of (x, y)
        locations.


341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391
20160218
--------

Mostly changes to the examples as they were woefully out of date.

README.md
    * Update the list of functions which need to be updated to use MATLAB's
    netCDF routines.

doc:
    Update all the documentation for this release.

examples:
    All examples have been updated to work with the updated tools in the
    toolbox.
    example.m
        * Renamed to example_forcing_setup.m.
    example2.m
        * Renamed to example_smooth_bathy.m.
    example_FVCOM_river.m
        * Updated to work with the toolbox.
    example_FVCOM_tsobc.m
        * Updated to work with the toolbox.
    example_FVCOM_wind_ts_speed.m
        * Updated to work with the toolbox.
    example_init_lag.m
        * Updated to work with the toolbox.
    example_my_project.m
        * Deleted.

fvcom_prepro:
    samples
        * Moved to the examples directory.
    estimate_ts.m
        * Updated the help.
    get_EHYPE_rivers.m
        * Fix exclude behaviour for more than a single river to exclude.
    get_HYCOM_forcing.m
        * Add support for three-hourly data from the HYCOM server.
    set_spectide.m
        * Update the help.
    wrf2fvcom.m
        * Udate the help. Note, this function is unnecessary if you use
        the PML updated version of the FORTRAN code wrf2fvcom in the main
        FVCOM source code (http://gitlab.em.pml.ac.uk/fvcom/uk-fvcom).
    write_FVCOM_bath.m
        * Update the help.
    write_FVCOM_bedflag.m
        * Update to use MATLAB's native netCDF routines.


392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551
20151207
--------

Fairly significant change this time. Added new functions to work with the tidal
turbine parameterisation added to the UK FVCOM code by Rory O'Hara Murray
(Marine Scotland Science). Also added initial support for ECMWF ERA-20C forcing
data. Includes numerous bug fixes and miscellaneous code improvements
(standardising history variables in netCDFs generated with the toolbox, for
example).

README.md
    * Update the list of releases of this toolbox.

doc:
    Update all the documentation for this release.

examples:
    example.m
        * Move existing example scripts into the examples directory to clean up
        the toolbox a bit.
    example2.m
        * Move existing example scripts into the examples directory to clean up
        the toolbox a bit.
    example_FVCOM_river.m
        * Move existing example scripts into the examples directory to clean up
        the toolbox a bit.
    example_FVCOM_tsobc.m
        * Move existing example scripts into the examples directory to clean up
        the toolbox a bit.
    example_FVCOM_wind_ts.m
        * Move existing example scripts into the examples directory to clean up
        the toolbox a bit.
    example_FVCOM_wind_ts_speed.m
        * Move existing example scripts into the examples directory to clean up
        the toolbox a bit.
    example_init_lag.m
        * Move existing example scripts into the examples directory to clean up
        the toolbox a bit.
    example_my_project.m
        * Move existing example scripts into the examples directory to clean up
        the toolbox a bit.
    tidal_turbine_example.m
        * Example script showing how to use Rory O'Hara Murray's tidal turbine
        parameterisation changes in the UK FVCOM code.

fvcom_prepro:
    README.m
        * Add the additional authors to the list of authors.
    add_coriolis.m
        * Fix bug in the variabel to check when setting the Coriolis. The code
        now checks for spherical coordinates rather than checking whether the
        Coriolis has been set. The broken behaviour was a bit recursive.
    estimate_ts.m
        * Set the initial values to infinite rather than ones to make the test
        more robust.
    fix_river_nodes.m
        * New function to check the river nodes assigned to your model are
        valid.
        * Split rivers over multiple nodes if the discharge exceeds
        a user-defined threshold value.
    generate_mjd.m
        * REMOVED (uses the old mexnc netCDF interface).
    get_CFS_forcing.m
        * Updated significantly to download and process the NCEP CFSv2
        reanalysis data. Data are available for use from 1979-2009 (inclusive).
    get_EA_river_climatology.m
        * Add check for whether any rivers have actually been added to prevent
        crashes.
    get_EHYPE_rivers.m
        * Add check for whether any rivers have actually been added to prevent
        crashes.
        * Fix handling of duplicate river nodes.
    get_ERA_forcing.m
        * New function to add and process ECMWF ERA-20C forcing data. Requires
        netCDFs to have been previously downloaded.
    get_HYCOM_forcing.m
        * Add support for the Global Reanalysis data which extends coverage
        back to 1992 (previously limited to 2008 with the Global Analysis
        data). The Global Analysis data is used from 2008 onwards even though
        the reanalysis exists up to 2012.
    get_HYCOM_tsobc.m
        * Remove the old parallel processing bits and replace with the modern
        versions.
        * Also add bounds checking for data downloaded using Python.
    get_NCEP_forcing.m
        * Add support for multi-year downloads.
        * Fix some of the variables to download too.
    init_lag.m
        * Add consistent history variable to the generated netCDF.
    read_sms_mesh.m
        * Populate the alternative coordinate system with zeros rather
        than repeating the values. Also add element centre coordinates for
        cartesian coordinates. This is somewhat redundant given setup_metrics
        does this anyway.
    wrf2fvcom.m
        * Function to convert WRF output to FVCOM formatted netCDFs. Thanks to
        Dmitry Aleynik for his example script upon which this script is based.
    write_FVCOM_TT.m
        * New function to generate a netCDF file containing the tidal turbine
        parameters for FVCOM.
    write_FVCOM_elevtide.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_forcing.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_groundwater.m
        * New function to generate a groundwater forcing file for FVCOM.
    write_FVCOM_heating.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_meanflow.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_nested_forcing.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_obs_TS.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_river.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_river_ERSEM.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_spectide.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_tsobc.m
        * Add consistent history variable to the generated netCDF.
        * Tidy the help too.
    write_FVCOM_tsobcERSEM.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_wind_ts_speed.m
        * Add consistent history variable to the generated netCDF.
    write_FVCOM_z0.m
        * Add consistent history variable to the generated netCDF.
    write_WRF_forcing.m
        * Add consistent history variable to the generated netCDF.

utilities:
    do_ph_change_plot.m
        * Clear out old useless scripts.
    do_ph_change_points_plot.m
        * Clear out old useless scripts.
    do_ph_max_change_plot.m
        * Clear out old useless scripts.
    do_volume.m
        * Clear out old useless scripts.
    do_volume_change.m
        * Clear out old useless scripts.
    do_volume_change2.m
        * Clear out old useless scripts.
    get_BADC_data.m
        * Add optional arguments for username and password for the BADC
        servers.
    grid2fvcom.m
        * Update the parallel processing commands.
        * Add option to enable output on element centres to save memory. The
        default has changed to only be on nodes now. Only u and v data need to
        be output to element centres (e.g. wind, stress).
    qair2rh.m
        * Formatting changes mostly.
    turbine_area_sigma.m
        * Calculate the fraction of the tidal turbine rotor swept area
        occupying each sigma layer.


552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602
20150319
--------

Add support for writing nesting files to force FVCOM. Also bugfix and
streamline existing functions.

examples:
    example_fvcom_inputs.m
        * New example script to generate FVCOM inputs from TPXO tides, NCEP
        surface heat and HYCOM open boundary forcing.

fvcom_prepro:
    add_obc_nodes_list.m
        * Output number of nodes if the verbose flag is set. Minor coding style
        changes.
    add_stations_list.m
        * Add support for exporting the element ID closest to the station of
        interest (as well as the node ID which was already there). Fix some
        formatting issues.
    find_nearest_pt.m
        * Tidy up the code a bit and add extra information to the help.
    get_NCEP_forcing.m
        * Fix off by one error with the air pressure data from NCEP.
    read_fvcom_obc.m
        * Add new function to read in open boundary node IDs from a FVCOM
        casename_obc.dat file.
    read_sms_mesh.m
        * Add spherical coordinates on element centres.
    write_FVCOM_bath.m
        * Minor coding style changes.
    write_FVCOM_nested_forcing.m
        * New function to output nesting data (either interpolated from a
        structured grid/other data source or from a larger FVCOM model) to
        netCDF.
    write_FVCOM_probes.m
        * Fix export of the u and v locations to use the closest element
        instead of the node ID. Using the node ID for the u and v data will
        yield velocity time series miles away from the actual location of
        interest.
    write_FVCOM_restart.m
        * Move variable creation outside of a loop as it doesn't change between
        iterations.

utilities:
    read_netCDF_FVCOM.m
        * Fix verbose output and change indenting here and there. Add a BUGS
        section.
    surrounders.m
        * New function to find the nodes connected to a specified node.


Pierre Cazenave's avatar
Pierre Cazenave committed
603 604 605
20141017
--------

606 607 608 609
Fairly major update to fix a number of bugs and improve functionality. This
includes additional functionality to work with POLCOMS model output (mainly the
input files, configuration files and flat binary outputs). There are also some
new functions to work with FVCOM-ERSEM.
Pierre Cazenave's avatar
Pierre Cazenave committed
610 611 612 613 614 615 616 617 618 619 620

fvcom_prepro:
    get_EA_river_climatology.m
        * Another fix for leap year times.
    get_EHYPE_rivers.m
        * Add option to exclude rivers by name. Add new option to use an
        alternatively formatted input (two column time,flux).
    get_HYCOM_tsobc.m
        * Update interp1 function to use pchip instead of csap as the latter
        will be removed in a future version of MATLAB and the innumerable
        warnings were doing my nut in.
621 622 623 624 625 626 627
    get_POLCOMS_tsobc_gcoms.m
        * Add support for clipping in time.
    get_POLPRED_spectide.m
        * Update help.
    init_lag.m
        * Add new (largely untested) function to create the initial Lagrangian
        netCDF file.
Pierre Cazenave's avatar
Pierre Cazenave committed
628 629 630 631 632 633 634 635 636 637 638 639
    interp_HYCOM2FVCOM.m
        * Fix bug when interpolating velocity data due to incorrectly sized
        preallocated array.
        * Make the way the data to be interpolated onto the element centres
        (i.e. the velocity data), as opposed to the element nodes, more
        understandable.
    read_MetUM_forcing.m
        * Change warning to a simple printed statement.
    read_sigma.m
        * Add the sigma levels for the element centres in additions to the
        element nodes.
    read_sms_mesh.m
640
        * Add Rory as an author.
Pierre Cazenave's avatar
Pierre Cazenave committed
641 642 643
        * Fix bugs when not using bathymetry (i.e. only reading the grid data
        in).
        * Also make a depth array for the element centres.
644 645 646 647 648 649 650 651 652 653 654 655
    write_FVCOM_elevtide.m
        * Add new flags to control which time variables to use. FVCOM reads the
        'Times' variable first if present, then falls back to 'Itime' and
        'Itime2' and finally 'time'.
        * Also reinstate the original version of the calculation of Itime2 as
        the rounding effect was smoothing out the data too much, affecting its
        precision.
        * Update help accordingly.
    write_FVCOM_forcing.m
        * Add new flags to control which time variables to use. FVCOM reads the
        'Times' variable first if present, then falls back to 'Itime' and
        'Itime2' and finally 'time'.
Pierre Cazenave's avatar
Pierre Cazenave committed
656 657 658
    write_FVCOM_restart.m
        * Update the help to better describe how the optional 'out_date'
        argument works.
659 660 661 662 663 664 665 666 667 668 669
    write_FVCOM_river_ERSEM.m
        * Add new function to output river data for FVCOM-ERSEM.
    write_FVCOM_tsobc.m
        * Add new flags to control which time variables to use. FVCOM reads the
        'Times' variable first if present, then falls back to 'Itime' and
        'Itime2' and finally 'time'.
        * Add better check for the size of the input arrays (works with scalars).
    write_FVCOM_tsobcERSEM.m
        * Add new function to output temperature and salinity open boundary
        data for FVCOM-ERSEM.

Pierre Cazenave's avatar
Pierre Cazenave committed
670
utilites:
671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698
    calc_rad.m
        * New function for calculating instantaneous irradiance from a given
        latitude and time.
    calc_scoord.m
        * Calculate POLCOMS s-coordinates.
    distance_to_coast.m
        * Calculate the distance to the model coastline from a given position.
        Requires additional third-party tools (HJB Solver Package - the path to
        this must be edited in the function (not ideal)).
    do_surface_plotMatlabMap.m
        * Add script to plot a surface using the MATLAB mapping toolbox.
    do_surface_plotVel.m
        * Add script to plot a velocity surface using the third-party m_map
        mapping toolbox.
    do_surface_plotVelMatlabMap.m
        * Add script to plot a velocity surface using the MATLAB mapping
        toolbox.
    do_vector_plot_MatlabMap.m
        * Add script to plot velocity vectors with the MATLAB mapping toolbox.
    find_relaxation_boundary.m
        * Add function to find the elements which fall along the boundary.
    get_polcoms_fixed_vars.m
        * Add function to get POLCOMS fixed variables from a flat binary output
        file.
    get_polcoms_timeseriesv1.m
        * Add function to extract time series from POLCOMS outputs.
    greg2julian.m
        * Fix input arguments check.
Pierre Cazenave's avatar
Pierre Cazenave committed
699 700 701 702 703 704
    grid_vert_interp.m
        * Add new argument to allow specifying different coordinates for the
        extrapolation. This allows us to interpolate data which belongs either
        to the element centres or element nodes (defaults to element nodes).
        This is only really important when the model grid falls outside the
        coverage of the supplied data and we're extrapolating data.
705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721
    interpolate_near_coast.m
        * Add new function to interpolate a dataset towards a coastline.
    interpolate_polcoms_timeseries_zet.m
        * Add new function to interpolate POLCOMS surface elevation data
        towards a coastline.
    read_netCDF_FVCOM.m
        * Complete the functionality to be able to slice the data along any
        dimension (siglay, time, node etc.).
        * Fix ability to slice with any combination of space (horizontal and
        vertical) and time.
    read_polcoms_params.m
        * New function to read polcoms parameters.
    read_scoord_param.m
        * New function to read hc, cc, theta and bb from POLCOMS
        scoord_params.dat file
    readzetUBVB.m
        * New function to read POLCOMS output binary files (dailymean).
Pierre Cazenave's avatar
Pierre Cazenave committed
722 723


724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763
20140728
--------

Minor update to fix a number of niggling bugs.

fvcom_prepro:
    add_river_nodes_graphic.m
        * Set the river flag in the Mobj when loading river data.
    add_river_nodes_list.m
        * Set the river flag in the Mobj when loading river data.
    get_EA_river_climatology.m
        * Fix (I think) bug with leap years and climatology across multiple
        years.
    get_EHYPE_rivers.m
        * Add optional arguments to exclude specific rivers (by name). Also add
        new flag to change the assumed format of the input data to be
        "time,flux" rather than the EHYPE-specific raw data format.
    get_FVCOM_rivers.m
        * Set the river flag in the Mobj when loading river data.
    get_HYCOM_tsobc.m
        * Use more stable interpolation (pchip instead of csaps) for the depth
        interpolation of the data for each open boundary node.
    get_POLCOMS_river_discharge.m
        * Set the river flat in the Mobj when loading river data.
    interp_HYCOM2FVCOM.m
        * Add support for the latest syntax for the parallel processing tools
        in MATLAB.
    make_blank_mesh.m
        * Add new flag to the Mobj to indicate whether we have rivers in the
        model.
    write_FVCOM_restart.m
        * Fix the calculation of Itime2 in the restart file (previously always
        set to 0).

utilities:
    grid_vert_interp.m
        * Fix bug in interpolating in the vertical when HYCOM data has only
        a single depth bin.


764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807
20140423
--------

Relatively minor update to bring in some improvements in consistency in the
toolbox (i.e. remove duplicated functions) and fix some bugs in the function to
read the FVCOM outputs (read_netCDF_FVCOM.m).

README.md
    * Flesh out the README with links to the tagged releases as well as a bit
    of history of the toolbox.

fvcom_prepro:
    nodes2elems.m
        * Made the calculation array-based instead of loop-based to increase
        performance.
    smoothfield.m
        * Minor cosmetic changes to the code.
    write_FVCOM_forcing.m
        * Fix a typo.
    read_fvcom_mesh.m [REMOVED]
        * Remove this duplicate function (leave the version in utilities
        instead).

swan_scripts:
    calc_tauw.m
        * Bring in the differences between this version of calc_tauw.m and the
        one in utilities/ (which has been removed).

utilities:
    calc_rad.m
        * New function to calculate theoretical shortwave irradiance based on
        latitude and time of day.
    read_fvcom_mesh.m
        * Bring in the changes from the (now removed) version of this script
        which was in fvcom_prepro.
    read_netCDF_FVCOM.m
        * Fixed a bug where if a 2D array was requested after a 3D array, the
        2D array would cause the function to crash (because it was using a 3D
        index for getVar).
        * Add the global verbose flag and tidy up the help a bit. Change some
        verbose statements to use fprintf instead of disp for better control
        over formatting.


808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901
20140131
--------

Update to include some fixes to the forcing scripts as well as new scripts to
better handle various river data sources.

README.md
    * Add note about the Tidal Model Driver toolbox being an optional
    dependency.

fvcom_prepro:
    get_EA_river_climatology.m
        * New function to use pre-calculated Environment Agency river
        temperature climatology data as input to the FVCOM river
        temperature time series.
    get_EHYPE_rivers.m
        * New function to apply E-HYPE river discharge data to a given model
        domain.
    get_FVCOM_rivers
        * Change the unique call to preserve the order by replacing 'first'
        with 'stable'. This requires a relatively modern MATLAB (post-2011b).
    get_HYCOM_forcing.m
        * Add sea surface height to the list of variables that can be
        downloaded and add the ability to specify particular variables to
        download.
    get_HYCOM_tsobc.m
        * Add support for sea surface height and make the interpolation to the
        boundary nodes less likely to fail when too few HYCOM points are found
        nearby.
    interp_HYCOM2FVCOM.m
        * Fix the identification of the time index in the HYCOM data (use
        hycom.time instead of Mobj.ts_times). Also ignore a field name of 'MT'
        if supplied in varlist.
    read_MetUM_forcing.m
        * Fix the way time is handled. Previously a time variable had to be
        specified in varlist. Now, each data variable's time is returned as an
        array within the MetUM.(variable) struct, giving
        MetUM.(variable).time and MetUM.(variable).data. This means if each
        data variable uses a different time sampling, that can be accounted for
        later (by interpolating to a common time series with interp3, for
        example). Currently the code extracts the first 6 hour's worth of data.
        The assumption there is that the Met Office do 4 runs per day, so
        6 hours of data from each run gives you a day's worth.
    read_sms_map.m
        * Minor cosmetic changes.
    read_sms_mesh.m
        * Minor cosmetic changes.
    write_FVCOM_elevtide.m
        * Simplify the verbose output stuff.
    write_FVCOM_forcing.m
        * Add support for writing all the variables needed for
        a HEATING_CALCULATED model run. This essentially makes
        write_FVCOM_heating redundant, but I'll leave it in as it's a bit
        simpler to understand what's going on there. Also update the way the
        net surface heat flux is calculated (sum long and short, subtract
        latent and sensible). Fix the way the wind variables are handled so
        that both the U10/V10 and uwind_speed/vwind_speed netCDF variables are
        written if only one of data.u10/data.v10 or data.uwnd/data.vwnd is
        given. Change the output of tri' to tri, as tri was being written the
        wrong way around (thanks to Rory O'Hara Murray for spotting that one).
    write_FVCOM_heating.m
        * Clarify the help a bit.
    write_FVCOM_restart.m
        * Make it more obvious when new data is being written in place of
        existing data.
    write_FVCOM_river.m
        * Tidy up the way the times are handled.
    write_FVCOM_river_nml.m
        * Fix the handling of the optional vertical distribution string
        argument.
    write_FVCOM_stations.m
        * Minor cosmetic changes.
    write_WRF_forcing.m
        * Add full suite of variables so that HEATING_CALCULATED can be used
        instead. Fix names of the fields for long and shortwave radiation to
        match the NCEP ones (from n{l,s}wrf to n{l,s}wrs i.e. change last
        letter from f to s).

utilities:
    grid2fvcom.m
        * Check for the presence of the input fields being requested in the
        input struct to avoid finding out that the last field in vars doesn't
        exist in data half way through a time consuming loop. Change the way
        the alternative coordinate arrays are used to accommodate subtleties in
        the parallel code in MATLAB. Also fix some problems which sometimes
        arose when interpolating using the Parallel Computing toolbox (they
        were not reproducible with the serial version, annoyingly).
    read_fvcom_mesh.m
        * Minor cosmetic changes.
    read_netCDF_FVCOM.m
        * Add support for missing Itime and Itime2 values in an output file,
        falling back on the time variable instead.


902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957
20130917
--------

Update to include the ability to use HYCOM and Met Office Unified Model
outputs.

fvcom_prepro:
   calc_sponge_radius.m
      * Fix typo.
   get_FVCOM_rivers.m
      * Use the full set of coastal coordinates when finding the appropriate
      river node.
   get_HYCOM_forcing.m
      * Major update to this function. Now it correctly downloads the relevant
      HYCOM data from the HYCOM OPeNDAP server. Does not work with the third-
      party OPeNDAP toolbox.
   get_HYCOM_tsobc.m
      * New function: interpolates HYCOM data to the boundary nodes for
      temperature and salinity boundary forcing.
   get_MetUM_pp.m
      * Update to build a list of the downloaded files from the BADC server
      Also add new model outputs to the list of files available for download
      (the new files are post-2011 but live in a different directory from the
      pre-2012 data). Also download files in parallel to speed up the process
      (this may be a bad idea so may be removed if that proves to be the
      case).
   get_NCEP_forcing.m
      * Fairly significant change in that this function can now download any
      of the Reanalysis-1, Reanalysis-2 and 20th Century Reanalysis data from
      the NCEP server. Where 4D data are requested, only the surface data is
      returned. I have not tested this with the third-part OPeNDAP toolbox.
   interp_HYCOM2FVCOM.m
      * Use to create spatially varying temperature, salinity, u and v data
      for use in an FVCOM restart file from HYCOM data.
   interp_POLCOMS2FVCOM.m
      * Add inteprolation of the u and v data in the POLCOMS netCDF files.
      Eventually this function will be adjusted to allow the selection of
      only specific variables to be interpolated (as is the case with
      interp_HYCOM2FVCOM).
   read_MetUM_forcing.m
      * New function: reads the specified variables from the netCDF files of
      the converted Met Office Unified Model PP files.
   read_sms_mesh.m
      * Fairly major restructuring to decrease the time it takes to read an
      SMS file by about 50%. This was mainly done to maintain my sanity.
   write_FVCOM_elevtide.m
      * Minor change to the verbose output following the rewritten
      mjulian2greg function.
   write_FVCOM_forcing.m
      * Add support for alternative name for the pressure variable. Also tweak
      the output of the net surface heat flux to only occur when we are
      writing out to a single file.
   write_FVCOM_heating.m
      * Add failsafe functionality when writing the variables to better handle
      NCEP and Met Office data.
   write_FVCOM_restart.m
958
      * Add support for writing out u and v data (on the element centres
959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981
      rather than node positions).
   write_FVCOM_river_nml.m
      * Add support for an optional string to be written out (e.g. 'uniform')
      for the vertical distribution of river discharge to bypass the automated
      string generation.
   write_WRF_forcing.m
      * New function: writes out regularly gridded data in wrf_grid format for
      direct use in FVCOM. The interpolation then occurs within FVCOM rather
      than here, in MATLAB. Thanks to Dmitry Aleynik for his MATLAB function
      which was used as the basis for this function.

utilities:
   grid2fvcom.m
      * Fix a bug in which the position arrays could be written out transposed
      relative to the data arrays (leading to forcing data being in the wrong
      place).
   grid_vert_interp.m
      * Remove any NaN values in the vertical profile to support HYCOM data
      (which have a set of fixed vertical levels).
   pp2nc.m
      * Incorporate changes to better support paths in Windows (in particular
      paths with spaces).
   pp2nc.tcl
982
      * Add (but leave commented out) functions to interpolate the Met Office
983 984
      data onto a geographical grid.
   pp2nc_subset.m
985
      * New function: wrapper function to use convsh to interpolates Met
986 987 988 989 990 991
      Office Unified Model PP files onto a geographical grid (i.e. lat/long).
   subset.tcl
      * New TCL script to interpolate the Met Office Unified Model PP files
      onto a geographical grid.


992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077
20130719
--------

This merges Geoff Cowles' GitHub repository with mine (at least that was the
theory). Hopefully nothing catastrophic has happened.

examples:
    create_files_tutorial.m
        * New directory into which scripts on how to use the tools in the
        toolbox can be placed.

fvcom_prepro:
    add_obc_nodes_list.m
        * Fix open boundary node ordering issues when using unique.
    add_river_nodes_list.m
        * Fix open boundary node ordering issues when using unique.
    calc_sponge_radius.m
        * Fix open boundary node ordering issues when using unique.
    extract_mesoscale.m
        * New script to extract POLCOMS meteorological forcing data.
    get_AMM.m
        * Fix typo.
    get_FVCOM_rivers.m
        * Add Karen to list of authors.
    get_MetUM_pp.m
        * Script to fetch Met Office (UK) operational model (Unified Model)
        forcing files.
    get_NAE2_forcing.m
        * Fix typos.
    get_NCEP_forcing.m
        * Add (optional) support for extracting only particular variables from
        the NCEP Reanalysis 2 OPeNDAP server. Also fix the version check.
    get_POLCOMS_netCDF.m
        * Use a variable rather than getting the name dynamically (makes it
        marginally easier to read).
    get_POLCOMS_tsobc.m
        * Fix some bugs in the way the open boundary node values were stored
        (the order in which they were stored did not match the order of the
        nodes in Casename_obc.dat). Also fix the order of the vertically
        interpolated values so that FVCOM starts at the surface instead of
        mirroring POLCOMS' approach (where the first value is the seabed).
    get_POLCOMS_tsobc_NOCL.m
        * Add NOC Liverpool specific temperature and salinity interpolation
        script.
    interp_POLCOMS2FVCOM.m
        * Fix the vertical ordering of the POLCOMS data. POLCOMS' scalar
        values (temperature, salinity etc.) are stored seabed to surface;
        its depths are stored surface to seabed; FVCOM stores everything
        surface to seabed.
    read_ERA_wind.m
        * Major changes to this function. It is now able to automatically load
        forcing data from a directory hierarchy for a given period.
    read_grid_mesh.m
        * New function to convert .grid format mesh files to mesh objects
        (Mobj).
    write_FVCOM_forcing.m
        * Remove support for pevpr (pevpr is in W/m^{2} from the NCEP
        Reanalysis 2 data; FVCOM wants evaporation in m/s). Update the help
        accordingly.
    write_FVCOM_heating.m
        * New function to write an FVCOM NetCDF heating file (for
        HEATING_CALCULATED).
    write_FVCOM_meanflow_ascii.m
        * Fix the way the open boundary nodes are obtained so their order
        matches the casename_obc.dat file.
    write_FVCOM_restart.m
        * Remove commented out warnings.

tests:
    test_get_POLCOMS_tsobc.m
        * Make minor process on getting this working (still not working).

utilities:
    get_BADC_data
        * Child function for get_MetUM_pp.m to do the actual downloading of
        the pp files.
    grid2fvcom.m
        * Add more elegant case statement rather than using string
        comparisons.
    pp2nc.m
        * Convert Met Office (UK) pp files to a more sensible NetCDF file.
    pp2nc.tcl
        * convsh script to convert from pp to NetCDF format (using with
        pp2nc.m).


1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248
20130521
--------

fvcom_prepro:
    get_FVCOM_rivers.m
        * Function now finds river nodes more intellgently. Also separated out
        the POLCOMS specific code to get_POLCOMS_river_positions.m and
        get_POLCOMS_river_discharge.m) to make the code more reusable if you
        have a different source of river data.
    get_NCEP_forcing.m
        * Expand the help a little.
    get_MetUM_forcing.m
        * New (incomplete) function. As yet unfinished function to download
        forcing data from the Met Office FTP server.
    get_POLCOMS_river_discharge.m
        * New function formerly part of get_FVCOM_rivers.m, but now extracts
        discharges from POLCOMS flow files only.
    get_POLCOMS_river_positions.m
        * New function formerly part of get_FVCOM_rivers.m, but now simply
        finds the coordinates of the rivers in a POLCOMS model grid.
    get_POLCOMS_tsobc.m
        * Open the MATLAB Parallel workers pool to make full use of the
        parallel capability in MATLAB (previously the parfor loop was running
        suboptimally).
    get_POLCOMS_tsobc_gcoms.m
        * New function to be used if the POLCOMS depths are stored in a second
        NetCDF file rather than with the temperature and salinity arrays.
    interp_POLCOMS2FVCOM.m
        * Parallelise the interpolation of the data onto the unstructured
        grid. This requires the Parallel Computing Toolbox (although if it is
        not available, the code still runs, albeit slower!).
    read_sigma.m
        * Updated to include better support for non-uniform sigma coordinates
        (e.g. geometric distributions). See sigma_gen.m, sigma_geo.m and
        sigma_tanh.m for more information.
    read_sms_map.m
        * New function to read an SMS .map file and import the coastline into
        MATLAB.
    mjul2str_noyear.m
        * Deleted this empty function.
    write_FVCOM_forcing.m
        * Fix the evaporation and precipitation arrays being used (should be
        in correct units now).

utilities:
    catstruct.m
        * MATLAB Central function to concatenate two structs.
    grid2fvcom.m
        * Parallelise the code. This requires the Parallel Computing Toolbox,
        but offers significant speed improvements if available.
    grid_vert_interp.m
        * Parallelise the vertical interpolation. As before, this requires the
        Parallel Computing Toolbox.
    sigma_gen.m
    sigma_geo.m
    sigma_tanh.m

tests:
    utilities:
        test_grid2fvcom.m
            * Unit test to ensure changes in grid2fvcom.m do not break its
            functionality (i.e. the modifications don't change the output
            values). This is obviously not valid if grid2fvcom.m is found to
            have a bug!
        test_get_POLCOMS_tsobc.m
            * Unit test to check get_POLCOMS_tsobc.m results don't change
            following changes to the script.
    data:
        * Directory in which data files are kept which are used by the unit
        test scripts.


20130403
--------

fvcom_prepro:
    add_river_nodes_list.m
        * Minor changes to code style.
    add_sponge_nodes_list.m
        * Fix bug which ignores constant sponge radius.
    add_stations_list.m
        * Add message about the outcome if no stations were within the domain.
    add_var_FVCOM_river.m
        * Turn warnings back on.
    example_FVCOM_tsobc.m
        * Add the global NetCDF history variable which includes a reference to
        the FVCOM toolbox.
    example_FVCOM_wind_ts.m
        * Turn warnings back on.
    example_FVCOM_wind_ts_speed.m
        * Turn warnings back on.
    example_init_lag.m
        * Turn warnings back on.
    get_FVCOM_rivers.m
        * Extract positions from the FVCOM-adapted POLCOMS rivers files. The
        POLCOMS positions are too coarse (12km) to be useful for FVCOM. As
        such, this function reads an ASCII file of positions and extracts the
        station's discharge data from the POLCOMS file.
    get_NCEP_forcing.m
        * Adds support for MATLAB's native OPeNDAP tools. Also fixes the
        calculation of net surface heat flux.
    get_POLCOMS_meanflow.m
        * Interpolate mean flow from POLCOMS output at the FVCOM open
        boundaries.
    get_POLCOMS_netCDF.m
        * More code outside the verbose section so it is executed even if
        verbose output is disabled.
    get_POLCOMS_rivers.m
        * Parse the POLCOMS rivers data file.
    get_POLCOMS_tsobc.m
        * Change the vertical interpolation to be scaled within the
        POLCOMS depth range for the current node. The net result is that the
        vertical profiles are squashed or stretched to fit within the FVCOM
        depths. This means the full profile structure is maintained in the
        resulting FVCOM boundary input despite the differing depths at the
        FVCOM boundary node.
    nodes2elems.m
        * Minor changes to coding style.
    read_ERA_wind.m
        * Turn warnings back on.
    read_NCEP_wind.m
        * Turn warnings back on.
    write_FVCOM_bedflag.m
        * Turn warnings back on.
    write_FVCOM_elevtide.m
        * Minor changes to coding style.
    write_FVCOM_forcing.m
        * Export of the surface forcing can now use a precomputed surface heat
        flux rather than having to interpolate the four components only to
        merge them (see write_FVCOM_forcing.m)
    write_FVCOM_meanflow.m
        * Preliminary support for mean flow at the open boundaries. At the
        moment, the mean flow is interpolated from POLCOMS daily mean flow
        values. The necessary tools to write out the FVCOM ASCII mean flow
        files have been created, but I have not yet managed to successfully
        run a model with mean flow. Consider it a work in progress.
    write_FVCOM_meanflow_ascii.m
        * Outputs the results of write_FVCOM_meanflow.m to ASCII for use in
        FVCOM.
    write_FVCOM_obs_TS.m
        * Add the global NetCDF history variable which includes a reference to
        the FVCOM toolbox.
    write_FVCOM_restart.m
        * The routine to replace variables within an FVCOM restart file now
        includes the ability to adjust the times for which the restart file is
        applicable. This is useful if you have a restart file for a model
        domain, but wish to use it for a different time.
    write_FVCOM_river.m
        * The existing river functions have been updated to reflect the
        changes needed in the latest versions of FVCOM (3.1.x). This has also
        been updated to use MATLAB's native NetCDF routines.
    write_FVCOM_river_nml.m
        * New function to write out the name list for the rivers in the model
        domain.
    write_FVCOM_spectide.m
        * Add the global NetCDF history variable which includes a reference to
        the FVCOM toolbox.
    write_FVCOM_sponge.m
        * Fix bug which ignores constant sponge radius.
    write_FVCOM_stations.m
        * Minor change to the error message for the incorrect number of
        arguments.
    write_FVCOM_tsobc.m
        * Add the global NetCDF history variable which includes a reference to
        the FVCOM toolbox. Also enable warnings.
    write_FVCOM_wind_ts_speed.m
        * Add the global NetCDF history variable which includes a reference to
        the FVCOM toolbox. Also enable warnings.
    write_FVCOM_z0.m
        * Add the global NetCDF history variable which includes a reference to
        the FVCOM toolbox. Also enable warnings.
1249

1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273
utilities:
    centroid.m
        * Fix problem with checking the input arguments.
    find_boundary_elements.m
        * New utility to find the element numbers which run along the open
        boundary (needed for the mean flow).
    fix_inside_boundary.m
        * A new function to reorganise open boundary elements to have an edge
        approximately normal to the open boundary has been added
        (fix_inside_boundary.m). The routine is somewhat brute force, and can
        result in invalid unstructured grids. As such, any changes should be
        reviewed in SMS prior to being used in a model run.
    grid2fvcom.m
        * Improve the documentation.
    write_SMS_2dm.m
        * Export unstructured grid data from MATLAB to SMS format.
    write_SMS_cst.m
        * Export open boundary from MATLAB to SMS format.


20130204
--------

fvcom-prepro:
1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424
    add_obc_nodes_graphic.m:
        * Minor fix to make the defined function name match the file name.
    add_obc_nodes_list.m:
        * Add optional new argument to plot a figure of the open boundary
        nodes.
    add_sponge_nodes.m:
        * Minor code cleanup.
    add_sponge_nodes_list.m:
        * New function: For a given list of nodes, apply a given sponge
        coefficient over a specified sponge radius (both given as arguments
        to the function. Follows the same syntax as add_sponge_nodes.m.
    add_stations_list.m:
        * New function: Add a set of stations at which FVCOM will output time
        series. Requires station coordinates and names, and a threshold
        distance beyond which the station is skipped.
    calc_sponge_radius.m:
        * New function: Create sponge layer with variable width radius based on
        the proximity of the closest element or 100km (whichever is smaller).
    estimate_ts.m:
        * Add arguments to the function so that the estimated current velocity
        and tidal range aren't hard-coded in the function.
        * Also add a crude conversion from lat/long distances to UTM (metres)
        using a great circle appoximation.
    example_FVCOM_tsobc.m:
        * Convert the method of writing NetCDF files from third-party toolbox
        to the MATLAB native version.
        * Add arguments to set dynamic file names (rather than hard-coded).
    example_FVCOM_wind_ts_speed.m:
        * Minor code change to calculate the number of elements in an array.
    get_AMM.m:
        * New function: Extract boundary forcing information from NOC
        Operational Tide Surge Model output.
    get_HYCOM_forcing.m:
        * New function: INCOMPLETE! Function to extract boundary forcing
        information from HYCOM model output through OPeNDAP.
    get_NAE2_forcing.m:
        * New function: Get the required parameters from NAE2 MetOffice model
        data to force FVCOM at the surface.
    get_NCEP_forcing.m:
        * New function: Get the required parameters from NCEP through OPeNDAP.
        Requires the air_sea and OPeNDAP toolboxes.
    get_POLCOMS_tsobc.m:
        * New function: Extract temperature and salinity data from the PML
        POLCOMS NetCDF files and interpolate them to the FVCOM open boundary
        nodes.
    get_POLPRED_spectide.m:
        * New function: Extract POLPRED harmonic amplitude and phases for the
        nearest point in the POLPRED grid to the open boundary nodes in the
        FVCOM grid.
    grid2fvcom.m:
        * New function: Interpolate regularly gridded surface forcing data onto
        a given FVCOM grid.
    read_ERA_wind.m:
        * New function: Extract wind data from ERA Interim NetCDF files.
    read_NCEP_wind.m:
        * New function: Read in pairs of NCEP wind vector files and output
        arrays of the required velocity components.
    read_sigma.m:
        * New function: Extract sigma layer and level information from a given
        sigma.dat file.
    read_sms_mesh.m:
        * Add the ability to extract open boundaries from the defined
        nodestrings in the SMS grid file (.2dm).
        * Note: the SMS grid name must be a single word (no spaces). If the
        script fails to load your grid, chances are its name is "Default
        Coverage". If you change it to omit spaces in either the .2dm file or
        the SMS project, this script should work.
    replace_FVCOM_restart_vars.m:
        * New function: For a given FVCOM restart file, replace select variables
        with values from a PML POLCOMS model NetCDF output file. POLCOMS data
        are interpolated first on the FVCOM vertical grid, then the vertically
        interpolated data are interpolated onto the horizontal FVCOM grid.
    set_elevtide.m:
        * New function: Write out timeseries of surface elevations to a NetCDF
        file.
        * Requires the Tide Model Driver MATLAB Toolbox from Oregon State
        University at http://polaris.esr.org/ptm_index.html.
    set_spectide.m:
        * Replace hard-coded variables with arguments to function call.
        * Add support for adding equilibrium amplitudes and beta love numbers.
    write_FVCOM_elevtide.m:
        * New function to accompany set_elevtide.m to output a time series of
        surface elevations.
    write_FVCOM_forcing.m:
        * New function: Write forcing data (u and v winds, heat flux etc.) out
        to NetCDF file(s) depending on specified FVCOM version.
    write_FVCOM_obs_TS.m:
        * Converted to use MATLAB native NetCDF routines.
    write_FVCOM_spectide.m:
        * Replace use of third-party NetCDF library with MATLAB native tools.
        * Add support for writing out equilibrium amplitudes and beta love
        numbers.
    write_FVCOM_sponge.m:
        * Add support for variable width sponge layers (see
        calc_sponge_radius.m).
    write_FVCOM_stations.m:
        * New function: Output list of stations at which FVCOM will output 1D
        time series.
    write_FVCOM_tsobc.m:
        * Create a new function to output temperature and salinity at the open
        boundaries (either spatially uniform or varying (e.g. interpolated from
        POLCOMS using get_POLCOMS_tsobc.m). Based on the example_FVCOM_tsobc.m
        file.
    write_FVCOM_wind_ts_speed.m:
        * Create a new function to output spatially uniform but temporally
        varying wind field. Based on example_FVCOM_wind_ts_speed.m.
    write_FVCOM_z0.m:
        * Add support for MATLAB native NetCDF routines.

fvcom-postproc:
    example_surface_plot.m:
        * Now includes a lot more examples of different types of surface plots
        (e.g. vectors at specific layers).

utilities:
    centroid.m:
        * New function: Calculate the centroid of a given polygon.
    connectivity.m:
        * New function: From Mesh2D toolbox. Read unstructured grid
        connectivity (useful to find grid boundary, for example).
    deg2utm.m:
        * New function: Convert from lat/long to UTM (but automatically
        determine relevant UTM zone). See also wgs2utm (where UTM zone can be
        forced).
    do_residual.m:
        * New function: Calculate the residual vector for a given 2D time
        series.
    do_residual_plot.m:
        * New function: Use the output of do_residual.m to plot residual
        vectors.
    do_transect_plot.m:
        * New function: Pick and plot a transect through model output.
    greg2mjulian.m:
        * Format help to match better with other utilities.
    get_NCEP_year.m:
        * Extract the year from an NCEP Reanalysis file name.
    deg2utm.m:
        * Function to convert from lat/long to UTM.
        * From http://www.mathworks.com/matlabcentral/fileexchange/10915
    show_sigma.m:
        * Made the reading in of the sigma.dat file more resilient (notably to
        comments and blank lines).
    utm2deg.m:
        * Function to convert from UTM to lat/long.
        * From http://www.mathworks.com/matlabcentral/fileexchange/10914
    wgs2utm.m:
        * New function: Convert from lat/long to UTM whilst being able to force
        the UTM zone (allowing for coordinates which spread over several UTM
        zones). See also deg2utm.