diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..6475c29
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,10 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*~
+*.ini
+*.py#
+*.#*
+*._*
+.DS_Store
+*.ipynb_checkpoints/
diff --git a/README.md b/README.md
index d202570..c583822 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,19 @@
 # sbeach_toolbox
 
-Toolbox to assist in the use of the model SBEACH.
\ No newline at end of file
+Toolbox to assist in the use of the model SBEACH.
+
+Note this code is specifically written to align with (and borrows code from) the XBeach matlab toolbox so as to make the use of both models streamlined.
+
+Written by Joshua Simmons
+
+## Main code
+* `RUN_sbeach_model.m`: this is an example function to call and use the SBEACH toolbox. It provides and
+
+* `SBEACH_GLUE_setup.m` - REMOVE
+* `SBEACH_storm_setup.m` - REMOVE
+
+## Functions
+
+* `fsbeach_setupmodel`: used to construct the data files and config file needed for SBEACH to run in the folder specified
+
+## Example
diff --git a/example/input_data/fielddata/stormdates_narra.mat b/example/input_data/fielddata/stormdates_narra.mat
deleted file mode 100644
index 8009d09..0000000
Binary files a/example/input_data/fielddata/stormdates_narra.mat and /dev/null differ
diff --git a/example/input_data/fielddata/stormdates_other.mat b/example/input_data/fielddata/stormdates_other.mat
deleted file mode 100644
index 3a7a562..0000000
Binary files a/example/input_data/fielddata/stormdates_other.mat and /dev/null differ
diff --git a/example/input_data/fielddata/tide/code/tidedataget.m b/example/input_data/fielddata/tide/code/tidedataget.m
deleted file mode 100644
index fba5416..0000000
--- a/example/input_data/fielddata/tide/code/tidedataget.m
+++ /dev/null
@@ -1,44 +0,0 @@
-% Written by Joshua Simmons 04/01/2016
-% Description: used to tranform offshore to nearshore mike21 using the code
-% OS2NS_MIKE21.m
-
-clear
-clc
-
-%% Settings
-%tide gauge data
-guagedataloc = 'J:\Coastal\Data\Tide\Sydney\Processed\SydTideData.mat';
-
-site = 'Narrabeen'; %embayment of interest
-
-%storm details
-stormdatesloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\stormdates_narra.mat';
-storm = {'2007', '2011', '2014', '2015'};
-
-% save?
-savebool = 1;
-% datasave location
-saveloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\tide\processed\';
-
-%% Code
-%load buoy data,profile data and lookup table
-guagedata = load(guagedataloc);
-
-stormdates = load(stormdatesloc);
-
-% narrow down to date range
-for ii = 1:length(storm)
-    startdate = stormdates.(['storm_' storm{ii}]).startdate;
-    enddate = stormdates.(['storm_' storm{ii}]).enddate;
-    
-    validentries = find(guagedata.SydTideData.time>=startdate & guagedata.SydTideData.time<=enddate);
-    
-    tidedata.tide = guagedata.SydTideData.tide(validentries);
-    tidedata.time = guagedata.SydTideData.time(validentries);
-   
-    if savebool
-        save([saveloc 'tidedata_' lower(site) '_' storm{ii} '.mat'],'tidedata') 
-    end
-    
-    clear tidedata startdate enddate validentries
-end
\ No newline at end of file
diff --git a/example/input_data/fielddata/tide/code/tidedataget_other.m b/example/input_data/fielddata/tide/code/tidedataget_other.m
deleted file mode 100644
index bc645a8..0000000
--- a/example/input_data/fielddata/tide/code/tidedataget_other.m
+++ /dev/null
@@ -1,44 +0,0 @@
-% Written by Joshua Simmons 04/01/2016
-% Description: used to tranform offshore to nearshore mike21 using the code
-% OS2NS_MIKE21.m
-
-clear
-clc
-
-%% Settings
-%tide gauge data
-guagedataloc = 'J:\Coastal\Data\Tide\Sydney\Processed\SydTideData.mat';
-
-site = 'Monavale'; %embayment of interest
-
-%storm details
-stormdatesloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\stormdates_other.mat';
-storm = {'2014', '2015'};
-
-% save?
-savebool = 1;
-% datasave location
-saveloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\tide\processed\';
-
-%% Code
-%load buoy data,profile data and lookup table
-guagedata = load(guagedataloc);
-
-stormdates = load(stormdatesloc);
-
-% narrow down to date range
-for ii = 1:length(storm)
-    startdate = stormdates.(['storm_' storm{ii}]).startdate;
-    enddate = stormdates.(['storm_' storm{ii}]).enddate;
-    
-    validentries = find(guagedata.SydTideData.time>=startdate & guagedata.SydTideData.time<=enddate);
-    
-    tidedata.tide = guagedata.SydTideData.tide(validentries);
-    tidedata.time = guagedata.SydTideData.time(validentries);
-   
-    if savebool
-        save([saveloc 'tidedata_' lower(site) '_' storm{ii} '.mat'],'tidedata') 
-    end
-    
-    clear tidedata startdate enddate validentries
-end
\ No newline at end of file
diff --git a/example/input_data/fielddata/tide/processed/tidedata_narrabeen_2015.mat b/example/input_data/fielddata/tide/processed/tidedata_narrabeen_2015.mat
deleted file mode 100644
index 9e71718..0000000
Binary files a/example/input_data/fielddata/tide/processed/tidedata_narrabeen_2015.mat and /dev/null differ
diff --git a/example/input_data/fielddata/wave/code/fmikeos2ns.m b/example/input_data/fielddata/wave/code/fmikeos2ns.m
deleted file mode 100644
index bf1042f..0000000
--- a/example/input_data/fielddata/wave/code/fmikeos2ns.m
+++ /dev/null
@@ -1,105 +0,0 @@
-function nswaves = fmikeos2ns(oswaves, LookUps, site, contour, location)
-    % Written by Joshua Simmons (WRL) 03/11/2014 
-    % to transform waves from offshore (OS) to nearshore (NS) using MIKE21 model
-    % oswaves - OS wave data - oswaves.Hsig(Significant wave height)/
-    % oswaves.Tp1(Peak period)/oswaves.Wdir(Incident wave direction)
-    % LookUps - MIKE21 wave model output in file "OEH_ARC_PointOutput.mat"
-    % site - embayment of interest - i.e. 'Narrabeen'
-    % contour - 10 or 15 (m) contour for NS output
-    % location - either pure S co-ord (see Mitchell Harley's xyz2spz 
-    % transformation) or location.E and location.N - refers to output 
-    % location for NS waves (gets nearest MIKE21 point)
-    %
-    %V1.1 - updated by Joshua Simmons 21/01/2015 to patch Wamberal/Wanda
-    %error.
-    
-    %find site and contour indices
-    siteidx = getnameidx(LookUps(:,2), site);
-    
-    %apply fix for Wamberal and Wanda
-    % from TM on 21/01/2015: "I've found an error in the .mat file for the
-    % look-up tables; in the pdf I say that all output for all locations runs 
-    % north to south - for Wamberal and Wanda it seems I've output them south to north.
-    % So if you are using output from these two sites, if you haven't realised already, 
-    % alongshore gradients will look inverted."
-    for aa = 1:2; 
-        LookUps{6,1}{aa,1} = flipud(LookUps{6,1}{aa,1}); LookUps{6,1}{aa,1}(:,1) = flipud(LookUps{6,1}{aa,1}(:,1)); 
-        LookUps{7,1}{aa,1} = flipud(LookUps{7,1}{aa,1}); LookUps{7,1}{aa,1}(:,1) = flipud(LookUps{7,1}{aa,1}(:,1));
-    end
-
-    if contour == 10
-        contouridx = 1;
-    elseif contour == 15;
-        contouridx = 2;
-    else
-        error('Contour information not available, select either 10 or 15m contour')
-    end
-    
-    %extract scenarios for easy lookup
-    scenariosidx = getnameidx(LookUps(:,2), 'Offshore Wave Scenarios');
-    scenarios = LookUps{scenariosidx,1};
-    
-    %get nearest location available for output
-    Eouts = LookUps{siteidx,1}{contouridx,1}(:,2);
-    Nouts = LookUps{siteidx,1}{contouridx,1}(:,3);
-    
-    if strcmp(site,'Narrabeen')
-        %compares closes alongshore spacing (s) for log-spiral narrabeen
-        xyz_data.x = cell2mat(Eouts);
-        xyz_data.y = cell2mat(Nouts);
-        xyz_data.z = zeros(size(Eouts));
-        spz = xyz2spz(xyz_data,'NARRA');
-        [~,locationidx] = min(abs(location-spz.s));
-    else
-        %gets nearest output point
-        dists = sqrt((location.E-cell2mat(Eouts)).^2+(location.N-cell2mat(Nouts)).^2);
-        [~,locationidx] = min(abs(dists));
-    end
-    
-    fcount = 1;
-    %loop through oswaves and lookup nswaves
-    for ii = 1:length(oswaves.Hsig)
-        tmpHs = oswaves.Hsig(ii);
-        tmpTp = oswaves.Tp1(ii);
-        tmpWdir = oswaves.Wdir(ii);
-        
-        %find closest scenario match
-        [~,Hsidx] = min(abs(tmpHs-scenarios(:,1)));
-        tmpHsround = scenarios(Hsidx,1);
-        [~,Tpidx] = min(abs(tmpTp-scenarios(:,2)));
-        tmpTpround = scenarios(Tpidx,2);
-        [~,Wdiridx] = min(abs(tmpWdir-scenarios(:,3)));
-        tmpWdirround = scenarios(Wdiridx,3);
-        
-        iter1ind = find(scenarios(:,3) == tmpWdirround);
-        iter2ind = find(scenarios(iter1ind,2) == tmpTpround);
-        iter3ind = find(scenarios(iter1ind(iter2ind),1) == tmpHsround);
-        
-        iter4ind = iter1ind(iter2ind(iter3ind));
-        
-        %now get ns lookup information if available
-        if isempty(iter4ind)
-            %get the closest wave height to scenario chosen
-            [~,iter3ind] = min(abs(tmpHs-scenarios(iter1ind(iter2ind),1)));
-            iter4ind = iter1ind(iter2ind(iter3ind));
-            diffHs = scenarios(iter4ind,1)-tmpHs;
-            disp(['No match found for oswaves(' num2str(ii) ') wave height off by ' num2str(diffHs) 'm']);
-        end
-        
-        nstmp = LookUps{siteidx,1}{contouridx,1}{locationidx,4}(iter4ind,:);
-        %store the values from the lookup table
-        nswaves.Hsig(ii,1) = nstmp(1);
-        nswaves.Hmax(ii,1) = nstmp(2);
-        nswaves.Tp1(ii,1) = nstmp(3);
-        nswaves.T01(ii,1) = nstmp(4);
-        nswaves.Wdir(ii,1) = nstmp(5);
-        nswaves.power(ii,1) = nstmp(6);
-    end
-        try
-            nswaves.date = oswaves.date;
-            nswaves.time = oswaves.time;
-            nswaves.datenums = oswaves.datenums;
-        catch
-            nswaves.datenums = oswaves.datenums;
-        end
-end
\ No newline at end of file
diff --git a/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21.m b/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21.m
deleted file mode 100644
index 5540332..0000000
--- a/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21.m
+++ /dev/null
@@ -1,95 +0,0 @@
-% Written by Joshua Simmons 04/01/2016
-% Description: used to tranform offshore to nearshore mike21 using the code
-% OS2NS_MIKE21.m
-
-clear
-clc
-
-%% Settings
-%buoy data
-buoydataloc = 'J:\Coastal\Data\Wave\Sydney\Processed\SydneyProcessed_CSIROGapFill.mat';
-% the non CSIRO filtered data is the only data available after 2014 so fill
-% from the recent data with gaps.
-backupbuoydata = 'J:\Coastal\Data\Wave\Sydney\Processed\SydneyProcessed.mat';
-
-%location of mike21 runcode
-mike21loc = 'J:\Coastal\Tools\Nearshore Wave Transformations\MIKE21\';
-%location of MALT
-maltloc = 'J:\Coastal\Tools\MALT Logspiral Transformation\';
-%location of profiles for which wave data is required.
-profiledataloc = [437 850 1750 2606 3420]; % s co-ordinate
-
-site = 'Narrabeen'; %embayment of interest
-contour = 10; %m - 10m or 15m contour?
-
-%storm details
-stormdatesloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\stormdates_narra.mat';
-storm = {'2007', '2011', '2014', '2015'};
-
-% save?
-savebool = 1;
-% datasave location
-saveloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\wave\processed\';
-
-%% Code
-% for MIKE21 code and MALT
-addpath(mike21loc);
-addpath(maltloc);
-%load buoy data,profile data and lookup table
-buoydata = load(buoydataloc);
-backupbuoydata = load(backupbuoydata);
-load('OEH_ARC_PointOutput.mat');
-stormdates = load(stormdatesloc);
-
-% narrow down to date range
-for ii = 1:length(storm)
-    startdate = stormdates.(['storm_' storm{ii}]).startdate;
-    enddate = stormdates.(['storm_' storm{ii}]).enddate;
-    
-    validentries = find(buoydata.dates>=startdate & buoydata.dates<=enddate);
-    % if nothing then revert to backup
-    if isempty(validentries) || validentries(end) == length(buoydata.dates)
-        validentries = find(backupbuoydata.dates>=startdate & backupbuoydata.dates<=enddate);
-        oswaves.Hsig = backupbuoydata.Hsig(validentries);
-        oswaves.Tp1 = backupbuoydata.Tp(validentries);
-        oswaves.Wdir = backupbuoydata.Wdir(validentries);
-        oswaves.datenums = backupbuoydata.dates(validentries);        
-    else
-        oswaves.Hsig = buoydata.Hsig(validentries);
-        oswaves.Tp1 = buoydata.Tp(validentries);
-        oswaves.Wdir = buoydata.Wdir(validentries);
-        oswaves.datenums = buoydata.dates(validentries);
-    end
-    
-    fns1 = fieldnames(oswaves);
-    for kk = 1:length(fns1)
-        if any(isnan(oswaves.(fns1{kk})))
-            error('NaN values in wave data')
-        end
-    end
-    
-    tic
-    parfor jj = 1:length(profiledataloc)
-        location = profiledataloc(jj);
-        nswaves = OS2NS_MIKE21(oswaves, LookUps, site, contour, location);
-        
-        % bug fix to ensure no inaccurate wave period estimates
-        nswaves.Tp1 = oswaves.Tp1;
-        
-        tmp(jj) = nswaves;
-    end
-    wavedata.ns.data = tmp;
-    toc
-    
-    wavedata.os = oswaves;
-    
-    wavedata.ns.model = 'MIKE21';
-    wavedata.ns.contour = [num2str(contour) 'm'];
-    wavedata.ns.location = profiledataloc;
-    
-    if savebool
-        save([saveloc 'wavedata_' lower(site) '_' storm{ii} '.mat'],'wavedata') 
-    end
-    
-    clear wavedata oswaves startdate enddate validentries tmp
-end
\ No newline at end of file
diff --git a/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_deewhy.m b/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_deewhy.m
deleted file mode 100644
index 17ca5d3..0000000
--- a/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_deewhy.m
+++ /dev/null
@@ -1,99 +0,0 @@
-% Written by Joshua Simmons 04/01/2016
-% Description: used to tranform offshore to nearshore mike21 using the code
-% OS2NS_MIKE21.m
-
-clear
-clc
-
-%% Settings
-%buoy data
-buoydataloc = 'J:\Coastal\Data\Wave\Sydney\Processed\SydneyProcessed_CSIROGapFill.mat';
-% the non CSIRO filtered data is the only data available after 2014 so fill
-% from the recent data with gaps.
-backupbuoydata = 'J:\Coastal\Data\Wave\Sydney\Processed\SydneyProcessed.mat';
-
-%location of mike21 runcode
-mike21loc = 'J:\Coastal\Tools\Nearshore Wave Transformations\MIKE21\';
-%location of MALT
-maltloc = 'J:\Coastal\Tools\MALT Logspiral Transformation\';
-%location of profiles for which wave data is required.
-% profiledataloc = [6275797.660794820 6275692.739810870 6275536.815570840]; % Northings co-ordinate - Bilgola (at 10m contour)
-% profiledataloc = [6272148.185 6272338.391 6272389.496 6271924.185 6271823.724]; % Northings co-ordinate - Mona Vale (at 10m contour)
-profiledataloc = [6264042.586 6264127.494 6263995.016 6263745.956 6263879.058]; % Northings co-ordinate - Dee Why (at 10m contour)
-profiledataloc2 = [343633.9263 343038.1544 342940.1201 342757.2994 342848.2807]; % Eastings co-ordinate - Dee Why (at 10m contour)
-
-site = 'DeeWhy'; %embayment of interest
-contour = 10; %m - 10m or 15m contour?
-
-%storm details
-stormdatesloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\stormdates_other.mat';
-storm = {'2014', '2015'};
-
-% save?
-savebool = 1;
-% datasave location
-saveloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\wave\processed\';
-
-%% Code
-% for MIKE21 code and MALT
-addpath(mike21loc);
-addpath(maltloc);
-%load buoy data,profile data and lookup table
-buoydata = load(buoydataloc);
-backupbuoydata = load(backupbuoydata);
-load('OEH_ARC_PointOutput.mat');
-stormdates = load(stormdatesloc);
-
-% narrow down to date range
-for ii = 1:length(storm)
-    startdate = stormdates.(['storm_' storm{ii}]).startdate;
-    enddate = stormdates.(['storm_' storm{ii}]).enddate;
-    
-    validentries = find(buoydata.dates>=startdate & buoydata.dates<=enddate);
-    % if nothing then revert to backup
-    if isempty(validentries) || validentries(end) == length(buoydata.dates)
-        validentries = find(backupbuoydata.dates>=startdate & backupbuoydata.dates<=enddate);
-        oswaves.Hsig = backupbuoydata.Hsig(validentries);
-        oswaves.Tp1 = backupbuoydata.Tp(validentries);
-        oswaves.Wdir = backupbuoydata.Wdir(validentries);
-        oswaves.datenums = backupbuoydata.dates(validentries);        
-    else
-        oswaves.Hsig = buoydata.Hsig(validentries);
-        oswaves.Tp1 = buoydata.Tp(validentries);
-        oswaves.Wdir = buoydata.Wdir(validentries);
-        oswaves.datenums = buoydata.dates(validentries);
-    end
-    
-    fns1 = fieldnames(oswaves);
-    for kk = 1:length(fns1)
-        if any(isnan(oswaves.(fns1{kk})))
-            error('NaN values in wave data')
-        end
-    end
-    
-    tic
-    for jj = 1:length(profiledataloc)
-        location.N = profiledataloc(jj);
-        location.E = profiledataloc2(jj);
-        nswaves = fmikeos2ns(oswaves, LookUps, site, contour, location);
-        
-        % bug fix to ensure no inaccurate wave period estimates
-        nswaves.Tp1 = oswaves.Tp1;
-        
-        tmp(jj) = nswaves;
-    end
-    wavedata.ns.data = tmp;
-    toc
-    
-    wavedata.os = oswaves;
-    
-    wavedata.ns.model = 'MIKE21';
-    wavedata.ns.contour = [num2str(contour) 'm'];
-    wavedata.ns.location = profiledataloc;
-    
-    if savebool
-        save([saveloc 'wavedata_' lower(site) '_' storm{ii} '.mat'],'wavedata') 
-    end
-    
-    clear wavedata oswaves startdate enddate validentries tmp
-end
\ No newline at end of file
diff --git a/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_end_effects_check.m b/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_end_effects_check.m
deleted file mode 100644
index 5dae8fa..0000000
--- a/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_end_effects_check.m
+++ /dev/null
@@ -1,105 +0,0 @@
-% Written by Joshua Simmons 04/01/2016
-% Description: used to tranform offshore to nearshore mike21 using the code
-% OS2NS_MIKE21.m
-
-clear
-clc
-
-%% Settings
-%buoy data
-buoydataloc = 'J:\Coastal\Data\Wave\Sydney\Processed\SydneyProcessed_CSIROGapFill.mat';
-% the non CSIRO filtered data is the only data available after 2014 so fill
-% from the recent data with gaps.
-backupbuoydata = 'J:\Coastal\Data\Wave\Sydney\Processed\SydneyProcessed.mat';
-
-%location of mike21 runcode
-mike21loc = 'J:\Coastal\Tools\Nearshore Wave Transformations\MIKE21\';
-%location of MALT
-maltloc = 'J:\Coastal\Tools\MALT Logspiral Transformation\';
-%location of profiles for which wave data is required.
-profiledataloc = [90:20:3870]; % s co-ordinate
-
-site = 'Narrabeen'; %embayment of interest
-contour = 10; %m - 10m or 15m contour?
-
-%storm details
-stormdatesloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\stormdates_narra.mat';
-storm = {'2007', '2011', '2014', '2015'};
-
-% save?
-savebool = 0;
-% datasave location
-saveloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\wave\processed\';
-
-%% Code
-% for MIKE21 code and MALT
-addpath(mike21loc);
-addpath(maltloc);
-%load buoy data,profile data and lookup table
-buoydata = load(buoydataloc);
-backupbuoydata = load(backupbuoydata);
-load('OEH_ARC_PointOutput.mat');
-stormdates = load(stormdatesloc);
-
-% narrow down to date range
-for ii = 1:length(storm)
-    startdate = stormdates.(['storm_' storm{ii}]).startdate;
-    enddate = stormdates.(['storm_' storm{ii}]).enddate;
-    
-    validentries = find(buoydata.dates>=startdate & buoydata.dates<=enddate);
-    % if nothing then revert to backup
-    if isempty(validentries) || validentries(end) == length(buoydata.dates)
-        validentries = find(backupbuoydata.dates>=startdate & backupbuoydata.dates<=enddate);
-        oswaves.Hsig = backupbuoydata.Hsig(validentries);
-        oswaves.Tp1 = backupbuoydata.Tp(validentries);
-        oswaves.Wdir = backupbuoydata.Wdir(validentries);
-        oswaves.datenums = backupbuoydata.dates(validentries);        
-    else
-        oswaves.Hsig = buoydata.Hsig(validentries);
-        oswaves.Tp1 = buoydata.Tp(validentries);
-        oswaves.Wdir = buoydata.Wdir(validentries);
-        oswaves.datenums = buoydata.dates(validentries);
-    end
-    
-    fns1 = fieldnames(oswaves);
-    for kk = 1:length(fns1)
-        if any(isnan(oswaves.(fns1{kk})))
-            error('NaN values in wave data')
-        end
-    end
-    
-    tic
-    parfor jj = 1:length(profiledataloc)
-        location = profiledataloc(jj);
-        nswaves = OS2NS_MIKE21(oswaves, LookUps, site, contour, location);
-        
-        % bug fix to ensure no inaccurate wave period estimates
-        nswaves.Tp1 = oswaves.Tp1;
-        
-%         tmp(jj) = nswaves;
-        Hsig(:,jj) = nswaves.Hsig(:,1);
-        Wdir(:,jj) = nswaves.Wdir(:,1);
-        power(:,jj) = nswaves.power(:,1);
-    end
-    dataout(ii).s = profiledataloc;
-    dataout(ii).Hsig = Hsig;
-    dataout(ii).Wdir = Wdir;
-    dataout(ii).power = power;
-    dataout(ii).osWdir = oswaves.Wdir;
-    dataout(ii).osHsig = oswaves.Hsig;
-%     wavedata.ns.data = tmp;
-    toc
-    
-    wavedata.os = oswaves;
-    
-    wavedata.ns.model = 'MIKE21';
-    wavedata.ns.contour = [num2str(contour) 'm'];
-    wavedata.ns.location = profiledataloc;
-    
-    if savebool
-        save([saveloc 'wavedata_' lower(site) '_' storm{ii} '.mat'],'wavedata') 
-    end
-    
-    clear wavedata oswaves startdate enddate validentries
-    clear power s Hsig Wdir
-end
\ No newline at end of file
diff --git a/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_other.m b/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_other.m
deleted file mode 100644
index f3927e1..0000000
--- a/example/input_data/fielddata/wave/code/run_OS_to_NS_mike21_other.m
+++ /dev/null
@@ -1,99 +0,0 @@
-% Written by Joshua Simmons 04/01/2016
-% Description: used to tranform offshore to nearshore mike21 using the code
-% OS2NS_MIKE21.m
-
-clear
-clc
-
-%% Settings
-%buoy data
-buoydataloc = 'J:\Coastal\Data\Wave\Sydney\Processed\SydneyProcessed_CSIROGapFill.mat';
-% the non CSIRO filtered data is the only data available after 2014 so fill
-% from the recent data with gaps.
-backupbuoydata = 'J:\Coastal\Data\Wave\Sydney\Processed\SydneyProcessed.mat';
-
-%location of mike21 runcode
-mike21loc = 'J:\Coastal\Tools\Nearshore Wave Transformations\MIKE21\';
-%location of MALT
-maltloc = 'J:\Coastal\Tools\MALT Logspiral Transformation\';
-%location of profiles for which wave data is required.
-% profiledataloc = [6275797.660794820 6275692.739810870 6275536.815570840]; % Northings co-ordinate - Bilgola (at 10m contour)
-% profiledataloc = [6272148.185 6272338.391 6272389.496 6271924.185 6271823.724]; % Northings co-ordinate - Mona Vale (at 10m contour)
-profiledataloc = [6264042.586 6264127.494 6263995.016 6263745.956 6263879.058]; % Northings co-ordinate - Dee Why (at 10m contour)
-
-
-
-site = 'DeeWhy'; %embayment of interest
-contour = 10; %m - 10m or 15m contour?
-
-%storm details
-stormdatesloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\stormdates_other.mat';
-storm = {'2014', '2015'};
-
-% save?
-savebool = 1;
-% datasave location
-saveloc = 'D:\7 Erosion Models\a_nb_model_comparison\input_data\fielddata\wave\processed\';
-
-%% Code
-% for MIKE21 code and MALT
-addpath(mike21loc);
-addpath(maltloc);
-%load buoy data,profile data and lookup table
-buoydata = load(buoydataloc);
-backupbuoydata = load(backupbuoydata);
-load('OEH_ARC_PointOutput.mat');
-stormdates = load(stormdatesloc);
-
-% narrow down to date range
-for ii = 1:length(storm)
-    startdate = stormdates.(['storm_' storm{ii}]).startdate;
-    enddate = stormdates.(['storm_' storm{ii}]).enddate;
-    
-    validentries = find(buoydata.dates>=startdate & buoydata.dates<=enddate);
-    % if nothing then revert to backup
-    if isempty(validentries) || validentries(end) == length(buoydata.dates)
-        validentries = find(backupbuoydata.dates>=startdate & backupbuoydata.dates<=enddate);
-        oswaves.Hsig = backupbuoydata.Hsig(validentries);
-        oswaves.Tp1 = backupbuoydata.Tp(validentries);
-        oswaves.Wdir = backupbuoydata.Wdir(validentries);
-        oswaves.datenums = backupbuoydata.dates(validentries);        
-    else
-        oswaves.Hsig = buoydata.Hsig(validentries);
-        oswaves.Tp1 = buoydata.Tp(validentries);
-        oswaves.Wdir = buoydata.Wdir(validentries);
-        oswaves.datenums = buoydata.dates(validentries);
-    end
-    
-    fns1 = fieldnames(oswaves);
-    for kk = 1:length(fns1)
-        if any(isnan(oswaves.(fns1{kk})))
-            error('NaN values in wave data')
-        end
-    end
-    
-    tic
-    for jj = 1:length(profiledataloc)
-        location = profiledataloc(jj);
-        nswaves = OS2NS_MIKE21(oswaves, LookUps, site, contour, location);
-        
-        % bug fix to ensure no inaccurate wave period estimates
-        nswaves.Tp1 = oswaves.Tp1;
-        
-        tmp(jj) = nswaves;
-    end
-    wavedata.ns.data = tmp;
-    toc
-    
-    wavedata.os = oswaves;
-    
-    wavedata.ns.model = 'MIKE21';
-    wavedata.ns.contour = [num2str(contour) 'm'];
-    wavedata.ns.location = profiledataloc;
-    
-    if savebool
-        save([saveloc 'wavedata_' lower(site) '_' storm{ii} '.mat'],'wavedata') 
-    end
-    
-    clear wavedata oswaves startdate enddate validentries tmp
-end
\ No newline at end of file
diff --git a/example/input_data/fielddata/wave/processed/wavedata_narrabeen_2015.mat b/example/input_data/fielddata/wave/processed/wavedata_narrabeen_2015.mat
deleted file mode 100644
index 15b3848..0000000
Binary files a/example/input_data/fielddata/wave/processed/wavedata_narrabeen_2015.mat and /dev/null differ
diff --git a/example/input_data/fielddata/wave/~$2007_survey_to_survey_wave_data.xlsx b/example/input_data/fielddata/wave/~$2007_survey_to_survey_wave_data.xlsx
deleted file mode 100644
index fd0b6a9..0000000
Binary files a/example/input_data/fielddata/wave/~$2007_survey_to_survey_wave_data.xlsx and /dev/null differ
diff --git a/example/input_data/morphology/processed/morphology_narrabeen_2015.mat b/example/input_data/morphology/processed/morphology_narrabeen_2015.mat
deleted file mode 100644
index 235d6a9..0000000
Binary files a/example/input_data/morphology/processed/morphology_narrabeen_2015.mat and /dev/null differ
diff --git a/fsbeach_runsetup.asv b/fsbeach_runsetup.asv
deleted file mode 100644
index 315765d..0000000
--- a/fsbeach_runsetup.asv
+++ /dev/null
@@ -1,6 +0,0 @@
-% SBEACH toolbox
-% Written by Joshua Simmons
-
-function out = fsbeach_runsetup()
-    
-end
\ No newline at end of file
diff --git a/sbeach_exe/final_exe/SBEACH.exe b/sbeach_exe/SBEACH.exe
similarity index 100%
rename from sbeach_exe/final_exe/SBEACH.exe
rename to sbeach_exe/SBEACH.exe
diff --git a/writetofileang.m b/writetofileang.m
index d8323c4..bde5b4d 100644
--- a/writetofileang.m
+++ b/writetofileang.m
@@ -1,5 +1,5 @@
 function writetofileang(angfile, outpath, pfstring)
-    fid = fopen([outpath '\' pfstring '.ANG'],'w');
+    fid = fopen(fullfile(outpath,[pfstring '.ANG']),'w');
     fprintf(fid,'C>         *******************************************************\r\n');
     fprintf(fid,'C>         *   SBEACH wave input file:       %s.ANG              *\r\n',pfstring);
     fprintf(fid,'C>         *******************************************************\r\n');
diff --git a/writetofilecfg.m b/writetofilecfg.m
index 620bda5..31347c7 100644
--- a/writetofilecfg.m
+++ b/writetofilecfg.m
@@ -1,5 +1,5 @@
 function writetofilecfg(OPT, outpath, pfstring)
-    fid = fopen([outpath '\' pfstring '.CFG'],'w');
+    fid = fopen(fullfile(outpath,[pfstring '.CFG']),'w');
     fprintf(fid,'         *******************************************************\r\n');
     fprintf(fid,'         *   SBEACH model configuration file:       %s.CFG   *\r\n',pfstring);
     fprintf(fid,'         *******************************************************\r\n');
diff --git a/writetofileelv.m b/writetofileelv.m
index e03712d..26a8c1b 100644
--- a/writetofileelv.m
+++ b/writetofileelv.m
@@ -1,5 +1,5 @@
 function writetofileelv(elvfile, outpath, pfstring)
-    fid = fopen([outpath '\' pfstring '.ELV'],'w');
+    fid = fopen(fullfile(outpath,[pfstring '.ELV']),'w');
     fprintf(fid,'C>         *******************************************************\r\n');
     fprintf(fid,'C>         *   SBEACH water elevation input file:       %s.ELV   *\r\n',pfstring);
     fprintf(fid,'C>         *******************************************************\r\n');
diff --git a/writetofilehdb.m b/writetofilehdb.m
index 304e1c9..82e0563 100644
--- a/writetofilehdb.m
+++ b/writetofilehdb.m
@@ -1,5 +1,5 @@
 function writetofilehdb(hdbfile, outpath, namestr)
-    fid = fopen([outpath '\' namestr '.HDB'],'w');
+    fid = fopen(fullfile(outpath,[namestr '.HDB']),'w');
     fprintf(fid,'C>         *******************************************************\r\n');
     fprintf(fid,'C>         *    SBEACH hard bottom input file:       %s.HDB  *\r\n',namestr);
     fprintf(fid,'C>         *******************************************************\r\n');
diff --git a/writetofilepri.m b/writetofilepri.m
index 69dff44..9203b06 100644
--- a/writetofilepri.m
+++ b/writetofilepri.m
@@ -1,5 +1,5 @@
 function writetofilepri(prifile, outpath, namestr)
-    fid = fopen([outpath '\' namestr '.PRI'],'w');
+    fid = fopen(fullfile(outpath,[namestr '.PRI']),'w');
     fprintf(fid,'C>         *******************************************************\r\n');
     fprintf(fid,'C>         *    SBEACH initial profile input file:       %s.PRI  *\r\n',namestr);
     fprintf(fid,'C>         *******************************************************\r\n');
diff --git a/writetofileprm.m b/writetofileprm.m
index a5661a2..cfa0d55 100644
--- a/writetofileprm.m
+++ b/writetofileprm.m
@@ -1,5 +1,5 @@
 function writetofileprm(prmfile, outpath, pfstring, rundescription)
-    fid = fopen([outpath pfstring '\' pfstring '_' rundescription '.PRM'],'w');
+    fid = fopen(fullfile(outpath,pfstring, [pfstring '_' rundescription '.PRM']),'w');
     fprintf(fid,'C>         *******************************************************\n');
     fprintf(fid,'C>         *    SBEACH initial profile input file:       %s.PRM  *\n',[pfstring '_' rundescription]);
     fprintf(fid,'C>         *******************************************************\n');
diff --git a/writetofilewav.m b/writetofilewav.m
index f7fe3a1..5368407 100644
--- a/writetofilewav.m
+++ b/writetofilewav.m
@@ -1,5 +1,5 @@
 function writetofilewav(wavfile, outpath, pfstring)
-    fid = fopen([outpath '\' pfstring '.WAV'],'w');
+    fid = fopen(fullfile(outpath,[pfstring '.WAV']),'w');
     fprintf(fid,'C>         *******************************************************\r\n');
     fprintf(fid,'C>         *   SBEACH wave input file:       %s.WAV              *\r\n',pfstring);
     fprintf(fid,'C>         *******************************************************\r\n');