From 8d034b52c2c9857dec0f6ad408de7b8ec9facfce Mon Sep 17 00:00:00 2001
From: sjdaines <stuart.daines@googlemail.com>
Date: Fri, 20 Dec 2024 20:11:40 +0000
Subject: [PATCH] Sync with PALEOsediment v0.3.3 changes (#30)

This PALEOsediment update refactored ReactionSedimentTransport into four reactions

See
  examples/shelf1D/PALEO_examples_shelf1Dsed_cfg.yaml
---
 examples/Project.toml                         |  2 +
 .../PALEO_examples_shelf1Dsed_cfg.yaml        | 42 +++++++++++++++----
 2 files changed, 35 insertions(+), 9 deletions(-)

diff --git a/examples/Project.toml b/examples/Project.toml
index e76fe62..6405e9b 100644
--- a/examples/Project.toml
+++ b/examples/Project.toml
@@ -25,3 +25,5 @@ ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
 
 [compat]
 PALEOmodel = "0.15.48"
+PALEOsediment = "0.3.3"
+
diff --git a/examples/shelf1D/PALEO_examples_shelf1Dsed_cfg.yaml b/examples/shelf1D/PALEO_examples_shelf1Dsed_cfg.yaml
index 501e031..7aafab3 100644
--- a/examples/shelf1D/PALEO_examples_shelf1Dsed_cfg.yaml
+++ b/examples/shelf1D/PALEO_examples_shelf1Dsed_cfg.yaml
@@ -420,19 +420,43 @@ shelf1D_P_O2_S_CH4_sed:
                 bioratesed:
                     class: ReactionSedimentBioRates
 
-                transportsed:
-                    class: ReactionSedimentTransport
-                    parameters:
-                        L:                             0.15  # 0.15m column with 60 bins
+                # transportsed:
+                #     class: ReactionSedimentTransport
+                #     parameters:
+                #         L:                             0.15  # 0.15m column with 60 bins
+                #         ncellspercol:                  60
+                #         f_grid:                         quadratic
+                #         grid_eta:                       0.075
+                #         zdbl:                           0.04e-2  # diffusive boundary layer at sediment-water interface
+                #     variable_links:
+                #         oceanfloor_temp:  ocean.oceanfloor.temp
+                #         oceanfloor_sal:  ocean.oceanfloor.sal
+                #         oceanfloor_*_conc:  ocean.oceanfloor.*_conc
+
+                gridsed:
+                    class: ReactionSedimentGridn1D
+                    parameters:
+                        L:                             0.15  # 0.15m column
                         ncellspercol:                  60
-                        f_grid:                         quadratic
-                        grid_eta:                       0.075
-                        zdbl:                           0.04e-2  # diffusive boundary layer at sediment-water interface
+                        f_grid:                        quadratic
+                        grid_eta:                      0.075
+                        
+                physsed:
+                    class: ReactionSedimentPhys
+
                     variable_links:
                         oceanfloor_temp:  ocean.oceanfloor.temp
                         oceanfloor_sal:  ocean.oceanfloor.sal
-                        oceanfloor_*_conc:  ocean.oceanfloor.*_conc
-                        
+
+                transportsedsolid:
+                    class: ReactionSedimentTransportSolid
+
+                transportsedsolute:
+                    class: ReactionSedimentTransportSolute
+                    parameters:                        
+                        zdbl:                           0.04e-2  # diffusive boundary layer at sediment-water interface
+                    variable_links:
+                        oceanfloor_*_conc:  ocean.oceanfloor.*_conc    
                        
                 reservoir_O2:
                     class: ReactionReservoirTotal