GitLab

Remove section warning against polygons in the map file. Add a note saying that if polygons have been created in FVCOM, then the effect is that it is a lot easier to handle islands within the domain as SMS has done the hard work of groups different arcs into islands and coastline sections

Fix some remaining FORTRAN code (do loop and float function) to MATLAB. Also add a function description to match the format of the other tools in the toolbox. Also reformat the code to MATLAB standard format (indentation etc.).

Add a function description to match the format of the other tools in the toolbox. Also reformat the code to MATLAB standard format (indentation etc.)

Update the read_sigma function to better deal with geometric distributions. Also clean up the code to read the parameters from the input file (this should be a bit more robust) and add a few checks the input is correct

This function has had the parts of the code which deal with loading the discharge data and river positions farmed out into separate functions (get_POLCOMS_river_positions.m and get_POLCOMS_river_discharge.m). By removing that code from the function, this function can now focus entirely on finding the appropriate river node. The logic whereby nodes assigned multiple rivers have the discharge from those rivers summed remains (which differs from the now-extinct get_POLCOMS_rivers.m function which simply used the first river it came across and omitted any discharges from subsequent rivers)

Remove the original POLCOMS parsing script and replace it instead with two separate functions, one to get the positions and the other to import the discharge rates. The part of the original function responsible for finding suitable nodes and assigning the discharges has been moved into get_FVCOM_rivers.m. The reason for this separation of duties is to make each part more flexible. This approach means I can load my positions from a separate file whilst still using the POLCOMS discharge data. Once I have loaded those data, the function to find the suitable nodes is called separately. If you had an alternative source of data, then the latter function could still be used to find the nodes as all it needs is position information

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