From 9a0c90ca28db1842d3574fbb3d19da118373272d Mon Sep 17 00:00:00 2001
From: Christa van IJzendoorn
 <52737913+christavanijzendoorn@users.noreply.github.com>
Date: Fri, 26 Jul 2024 15:08:31 -0700
Subject: [PATCH] Wave height solve

Change order of calculating runup and reducing the wave height from the significant to the depth-dependent wave height.
---
 aeolis/hydro.py | 43 ++++++++++++++++++++++---------------------
 1 file changed, 22 insertions(+), 21 deletions(-)

diff --git a/aeolis/hydro.py b/aeolis/hydro.py
index e26f30e7..6ac42541 100644
--- a/aeolis/hydro.py
+++ b/aeolis/hydro.py
@@ -118,6 +118,28 @@ def interpolate(s, p, t):
                                         p['wave_file'][:,0],
                                         p['wave_file'][:,2])
 
+            if p['process_runup']:
+                ny = p['ny']
+
+                for iy in range(ny + 1):  # do this computation seperately on every y for now so alongshore variable wave runup can be added in the future
+                
+                    hs = s['Hs'][iy][0]
+                    tp = s['Tp'][iy][0]
+                    wl = s['SWL'][iy][0]
+
+                    eta, sigma_s, R = calc_runup_stockdon(hs, tp, p['beach_slope'])
+                    s['R'][iy][:] = R
+                    s['eta'][iy][:] = eta
+                    s['sigma_s'][iy][:] = sigma_s
+                    
+                    if hasattr(s['runup_mask'], "__len__"):
+                        s['eta'][iy][:] = apply_mask(s['eta'][iy][:], s['runup_mask'][iy][:])
+                        s['R'][iy][:] = apply_mask(s['R'][iy][:], s['runup_mask'][iy][:])
+
+                    s['TWL'][iy][:] = s['SWL'][iy][:]  + s['R'][iy][:]
+                    s['DSWL'][iy][:] = s['SWL'][iy][:] + s['eta'][iy][:]            # Was s['zs'] before
+
+            # Alters wave height based on maximum wave height over depth ratio, gamma default = 0.5
             s['Hs'] = np.minimum(h * p['gamma'], s['Hs'])
 
             # apply complex mask
@@ -136,27 +158,6 @@ def interpolate(s, p, t):
 
     if p['process_runup']:
         ny = p['ny']
-
-        if ('Hs' not in p['external_vars']):
-
-            for iy in range(ny + 1):  # do this computation seperately on every y for now so alongshore variable wave runup can be added in the future
-            
-                hs = s['Hs'][iy][0]
-                tp = s['Tp'][iy][0]
-                wl = s['SWL'][iy][0]
-
-                eta, sigma_s, R = calc_runup_stockdon(hs, tp, p['beach_slope'])
-                s['R'][iy][:] = R
-                s['eta'][iy][:] = eta
-                s['sigma_s'][iy][:] = sigma_s
-                
-                if hasattr(s['runup_mask'], "__len__"):
-                    s['eta'][iy][:] = apply_mask(s['eta'][iy][:], s['runup_mask'][iy][:])
-                    s['R'][iy][:] = apply_mask(s['R'][iy][:], s['runup_mask'][iy][:])
-
-                s['TWL'][iy][:] = s['SWL'][iy][:]  + s['R'][iy][:]
-                s['DSWL'][iy][:] = s['SWL'][iy][:] + s['eta'][iy][:]            # Was s['zs'] before
-
         if ('Hs' in p['external_vars']):
 
             eta, sigma_s, R = calc_runup_stockdon(s['Hs'], s['Tp'], p['beach_slope'])