GitLab

Bring in the changes from the dev branch into the master branch. These include:

- Support for converting POLCOMS flow, index and grid files into the necessary files to write FVCOM river input files (NetCDF and nml files). The existing river functions have been updated to reflect the changes needed in the latest versions of FVCOM (3.1.x). write_FVCOM_river.m now uses the native MATLAB NetCDF routines to export to NetCDF.
- 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.
- The NCEP surface forcing is now able to use either the MATLAB native support or otherwise (for older versions) the third-party OPeNDAP toolbox (http://www.opendap.org/pub/contributed/source/ml-toolbox/). It is still dependent on the air-sea toolbox (http://woodshole.er.usgs.gov/operations/sea-mat/air_sea-html/index.html). The surface forcing has had the sign convention fixed (see get_NCEP_forcing.m).
- Vertical temperature and salinity profiles from POLCOMS model outputs are scaled to the FVCOM depth rather than truncating. Hopefully this means the full structure of the water column is preserved if POLCOMS and FVCOM differ in their depths (see get_POLCOMS_tsobc.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).
- Some of the older functions have been made more consistent in terms of the coding style (e.g. warnings are now turned on, or not turned off, for all functions). Similarly, the history global variable in any FVCOM NetCDF file now includes the name of the function from which it was generated.
- 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.
- 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.
- Additional tools (write_SMS_2dm.m and write_SMS_cst.m) provide functionality to export data from MATLAB to formats compatible with SMS.

New function to take a CSV file with updated river positions and extract the POLCOMS discharge data at those locations. Nodes which fall outside a model domain are skipped based on a threshold distance. If multiple rivers end up being assigned to the same node, then their discharge values are summed for duration of the time series

Amend the existing script which writes out the NetCDF file needed for the river inputs. This file now writes out multiple rivers with discharges for each. The two new functions (get_POLCOMS_rivers.m and write_FVCOM_river_nml.m) convert a set of POLCOMS river files into arrays in MATLAN which can then be written out with write_FVCOM_river.m. The write_FVCOM_river_nml.m file generates the requisite name list to include multiple rivers in your model

Add warning about the possibility of odd unstructured grids following the use of this function (points outside the model domain(

Add global history variable to the NetCDFs which includes the routine used to generate the file and a reference to the fvcom-toolbox

Add support for specifying a minimum angle between the two element edges adjacent to each node in the open boundary. This means that nodes at the corners of open boundaries or adjacent to land can be more easily eliminated from the analysis

Fix the verbosity of the output when writing the new time data (so it actually works). Also stop writing the new time data if it has already been written once

Add official support for rewriting the time ot the output restart file. This is useful if you want to use a restart file from a model run whose time does not overlap with the new time period

Fix bug whereby the first node ID in each line was being omitted causing errors in the resulting 2dm file, particularly if the node string has only two points

Make the example usage actually vaguely useful and change the mesh name to something more traditional (mesh)

Add support for the surface elevation open boundary node file _elj_obc.dat (which is almost the same as tide_el.dat, but hey ho). Also make the error messages clearer and adjust the formatting statements to match what Dima has in his script

Tool to export a triangulation to an SMS 2dm formatted file. This can then be opened in SMS to check the optimisation performed by fix_inside_boundary and fix any newly introduced poor quality elements

Change the code which identifies nodes just inside the model open boundaries to adjust their positions instead of creating a new array of 'ideal' positions. This means the tool now performs an optimisation on the unstructured grid rather than being a tool which simply provides a set of points which can be used in SMS to try and guide the triangulation (which I discovered does not work)

Function to find points inside an open boundary which are approximately normal to the boundary. This is useful if you want to force the unstructured grid to have elements with a right angle in them along the open boundary

Finish the code to output the mean flow ASCII files and modify the inputs to only require the depth distributed horizontal velocity components (rather than separate arrays of the depth averaged ones. We can calculate depth averaged from the depth distributed values)

Change the interpolation to occur at the boundary nodes to the centroid of the boundary elements (since FVCOM work on velocities at the centre of each element)

1. Do the vertical interpolation of the u and v components separately then at the end calculate the depth averaged velocity as well as the depth averaged u and v components into separate fields in Mobj. This is all necessary for outputting the ASCII files for mean flow and the open boundaries.

2. Make the vertical interpolation scale the POLCOMS-ERSEM depth range to match the current FVCOM node's depth range, thus squeezing or stretching the vertical velocity profiles into the FVCOM depth.

3. Add a commented out section which can be used to plot the vertical profiles to make sure they have interpolated correctly.

1. Remove the totally unnecessary loop iterating through the vertical levels on the vertical interpolation secion. No idea what that was doing there.

2. Change the interpolation of the vertical profiles to scale the POLCOMS depths to the current FVCOM node's depth range. This means the full profile structure is maintained in the interpolated profiles but that it is squashed or stretched to fit the scaled depths. This also means the surface and seabed value are fully captured.

Add support for writing out the boundary element ID file (casename_tide_cell.dat) and the first stab at the velocity components (casename_tide_uv.dat)

Replace the interpolation of a single velocity with the interpolation of the original u and v components and instead calculate the velocity at the end. This means the ASCII files needed for the mean flow can more easily be generated

Add function to find the elements which fall along the open boundaries within the model unstructured grid. This is useful if you plan to use the mean flow tool write_FVCOM_meanflow_ascii) which requires an array of the elements along the open boundary