diff --git a/MOM_input b/MOM_input
index c140eb6..4c8a078 100644
--- a/MOM_input
+++ b/MOM_input
@@ -187,7 +187,7 @@ MINIMUM_DEPTH = 0.5
                                 ! MINIMUM_DEPTH."
 
 ! === module MOM_fixed_initialization ===
-INPUTDIR = "./input/"
+INPUTDIR = "./INPUT/"
                                 ! "The directory in which input files are found."
 
 CHANNEL_CONFIG = global_1deg
diff --git a/README.md b/README.md
index 6dc4401..7296e6d 100644
--- a/README.md
+++ b/README.md
@@ -14,4 +14,4 @@ information.
 
 ## Requirements
 
-This configuration requires payu v1.0.29 or greater to run correctly.
+This configuration requires [Payu](https://github.com/payu-org/payu) > v1.1.3 to run.
diff --git a/datm.streams.xml b/datm.streams.xml
index 039cfb2..8ff9d45 100644
--- a/datm.streams.xml
+++ b/datm.streams.xml
@@ -11,10 +11,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.prsn.1990_1991.nc</file>
+      <file>./INPUT/RYF.prsn.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>prsn  Faxa_prsn</var>
@@ -32,10 +32,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.prra.1990_1991.nc</file>
+      <file>./INPUT/RYF.prra.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>prra  Faxa_prrn</var>
@@ -53,10 +53,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.rlds.1990_1991.nc</file>
+      <file>./INPUT/RYF.rlds.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>rlds  Faxa_lwdn</var>
@@ -75,10 +75,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.rsds.1990_1991.nc</file>
+      <file>./INPUT/RYF.rsds.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>rsds  Faxa_swdn</var>
@@ -97,10 +97,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.huss.1990_1991.nc</file>
+      <file>./INPUT/RYF.huss.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>huss  Sa_shum</var>
@@ -119,10 +119,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.psl.1990_1991.nc</file>
+      <file>./INPUT/RYF.psl.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>psl  Sa_pslv</var>
@@ -141,10 +141,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.tas.1990_1991.nc</file>
+      <file>./INPUT/RYF.tas.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>tas Sa_tbot</var>
@@ -163,10 +163,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.uas.1990_1991.nc</file>
+      <file>./INPUT/RYF.uas.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>uas Sa_u</var>
@@ -185,10 +185,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.vas.1990_1991.nc</file>
+      <file>./INPUT/RYF.vas.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>vas Sa_v</var>
diff --git a/datm_in b/datm_in
index 4507f3e..eda93c2 100644
--- a/datm_in
+++ b/datm_in
@@ -8,8 +8,8 @@
   flds_preso3 = .false.
   flds_wiso = .false.
   iradsw = 1
-  model_maskfile = "./input/access-om2-1deg-nomask-ESMFmesh.nc"
-  model_meshfile = "./input/access-om2-1deg-nomask-ESMFmesh.nc"
+  model_maskfile = "./INPUT/access-om2-1deg-nomask-ESMFmesh.nc"
+  model_meshfile = "./INPUT/access-om2-1deg-nomask-ESMFmesh.nc"
   nx_global = 360
   ny_global = 300
   restfilm = "null"
diff --git a/drof.streams.xml b/drof.streams.xml
index 90c7d9f..74426a8 100644
--- a/drof.streams.xml
+++ b/drof.streams.xml
@@ -11,10 +11,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.friver.1990_1991.nc</file>
+      <file>./INPUT/RYF.friver.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>friver Forr_rofl</var>
@@ -32,10 +32,10 @@
    <year_last>1900</year_last>
    <year_align>1900</year_align>
    <vectors>null</vectors>
-   <meshfile>./input/JRA55do-ESMFmesh.nc</meshfile>
+   <meshfile>./INPUT/JRA55do-ESMFmesh.nc</meshfile>
    <lev_dimname>null</lev_dimname>
    <datafiles>
-      <file>./input/RYF.licalvf.1990_1991.nc</file>
+      <file>./INPUT/RYF.licalvf.1990_1991.nc</file>
    </datafiles>
    <datavars>
       <var>licalvf Forr_rofi</var>
diff --git a/drof_in b/drof_in
index 028d030..5a30ed0 100644
--- a/drof_in
+++ b/drof_in
@@ -1,7 +1,7 @@
 &drof_nml
   datamode = "copyall"
-  model_maskfile = "./input/access-om2-1deg-nomask-ESMFmesh.nc"
-  model_meshfile = "./input/access-om2-1deg-nomask-ESMFmesh.nc"
+  model_maskfile = "./INPUT/access-om2-1deg-nomask-ESMFmesh.nc"
+  model_meshfile = "./INPUT/access-om2-1deg-nomask-ESMFmesh.nc"
   nx_global = 360
   ny_global = 300
   restfilm = "null"
diff --git a/ice_in b/ice_in
index 8e8227f..93b3228 100644
--- a/ice_in
+++ b/ice_in
@@ -17,15 +17,15 @@
   print_global      = .false.
 /
 &grid_nml
-  bathymetry_file = "./input/topog.nc"
+  bathymetry_file = "./INPUT/topog.nc"
   grid_atm = "A"
-  grid_file = "./input/grid.nc"
+  grid_file = "./INPUT/grid.nc"
   grid_format = "nc"
   grid_ice = "B"
   grid_ocn = "A"
   grid_type = "tripole"
   kcatbound = 0
-  kmt_file = "./input/kmt.nc"
+  kmt_file = "./INPUT/kmt.nc"
   nblyr = 1
   ncat = 5
   nfsd = 12
@@ -188,4 +188,4 @@
   f_taubx = 'x' , f_tauby = 'x'
   f_Tref = 'x', f_Qref = 'x'
   f_uocn = 'x' , f_vocn = 'x'
-/
\ No newline at end of file
+/
diff --git a/manifests/input.yaml b/manifests/input.yaml
index fc6d55d..2709d1e 100644
--- a/manifests/input.yaml
+++ b/manifests/input.yaml
@@ -1,128 +1,128 @@
 format: yamanifest
 version: 1.0
 ---
-work/input/JRA55do-ESMFmesh.nc:
+work/INPUT/JRA55do-ESMFmesh.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/share/meshes/share/2024.01.25/JRA55do-ESMFmesh.nc
   hashes:
-    binhash: 100055c7cbb1d91ae5036ce7ba102fe0
+    binhash: 2e3338c0e60e1a635ddb96a6ddf75500
     md5: 1c8481b8c85f59b6cbfc2ed5bc24c77d
-work/input/RYF.friver.1990_1991.nc:
+work/INPUT/RYF.friver.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.friver.1990_1991.nc
   hashes:
-    binhash: df5b6715e020f563acb65673571a565f
+    binhash: abba207de30541a83d25e24b424cfa87
     md5: fa3a55aeb6706a1b422d096f61a772c1
-work/input/RYF.huss.1990_1991.nc:
+work/INPUT/RYF.huss.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.huss.1990_1991.nc
   hashes:
-    binhash: 71d6099511ebc8b43f9b86b325ecf3af
+    binhash: 1d67d219c6f161051dec204a1842a968
     md5: 6032d514fdfdd2b6a84bdef0a4ac3afe
-work/input/RYF.licalvf.1990_1991.nc:
+work/INPUT/RYF.licalvf.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.licalvf.1990_1991.nc
   hashes:
-    binhash: f219ce98f3fcbe6f8ec517740f01aee1
+    binhash: 834da0a081e904fdbc892255d1954062
     md5: 6f927702cbc023cc20d3ddd69695f0a0
-work/input/RYF.prra.1990_1991.nc:
+work/INPUT/RYF.prra.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.prra.1990_1991.nc
   hashes:
-    binhash: 2754bd49fff02bf5330a086310f1c296
+    binhash: 7bc006b83a9891d4f9ef39f4d94ffb05
     md5: ac199086106ec4e41506e6082bccb109
-work/input/RYF.prsn.1990_1991.nc:
+work/INPUT/RYF.prsn.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.prsn.1990_1991.nc
   hashes:
-    binhash: 154a15cde4940309ac5e6fef0d7faba4
+    binhash: a57a154152a830ad1ca820ca9487d5ac
     md5: cd076c877c2c5df61615e04d71ed00e0
-work/input/RYF.psl.1990_1991.nc:
+work/INPUT/RYF.psl.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.psl.1990_1991.nc
   hashes:
-    binhash: 559b1e3183475cfb94a7f013f4acf8ea
+    binhash: 420c371361bb677eb87c01255c6e62b3
     md5: 0dfd94a5c3234fd2016dfdd01e84a170
-work/input/RYF.rhuss.1990_1991.nc:
+work/INPUT/RYF.rhuss.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.rhuss.1990_1991.nc
   hashes:
-    binhash: 1f70c237032f7368e6f2478d2a678c99
+    binhash: fe4460b8d68f94df26adc52fb56a0d6a
     md5: 632519955305cb5c19e286b151439fb5
-work/input/RYF.rlds.1990_1991.nc:
+work/INPUT/RYF.rlds.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.rlds.1990_1991.nc
   hashes:
-    binhash: 9512836673a68507bed403ecd859ba38
+    binhash: 07a7fb6f9d2a3aee4081034f0cfc305a
     md5: 0ea83e107ec883c3f39a12b60ff50d8e
-work/input/RYF.rsds.1990_1991.nc:
+work/INPUT/RYF.rsds.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.rsds.1990_1991.nc
   hashes:
-    binhash: 7ff7cd79ace33fefe2b9a91ea018ea14
+    binhash: 2d6c41b66024e460fcfe0a1668bfe151
     md5: b74bf123f1e4557368a61732cf24f1c2
-work/input/RYF.tas.1990_1991.nc:
+work/INPUT/RYF.tas.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.tas.1990_1991.nc
   hashes:
-    binhash: 8f3c6798cc92a1d0b6573eb44b2a4dd2
+    binhash: 2a7a2f9903346123161b91ed8d5fab52
     md5: 06689885f4f2f726b95a2818ab78a20d
-work/input/RYF.uas.1990_1991.nc:
+work/INPUT/RYF.uas.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.uas.1990_1991.nc
   hashes:
-    binhash: 54ede2172bf85bc861bc64c296a03f8c
+    binhash: bfd4876aac0b31e51a18c7724c84d8b1
     md5: 107bf9480f55597655d2d283b6f6b4ff
-work/input/RYF.vas.1990_1991.nc:
+work/INPUT/RYF.vas.1990_1991.nc:
   fullpath: /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data/RYF.vas.1990_1991.nc
   hashes:
-    binhash: 17224eecb745b6ce72604b41201c1fe7
+    binhash: d15ca562e37e82fb2d31657701f0a560
     md5: 88dc8c70338bbc8f5efc48ed0009a99f
-work/input/access-om2-1deg-ESMFmesh.nc:
+work/INPUT/access-om2-1deg-ESMFmesh.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-ESMFmesh.nc
   hashes:
-    binhash: 5ee42d2f49811906d89c4cdbc618ee99
+    binhash: aa3b7d102b4069d5a5ed9446d857f1a4
     md5: 44e508ac57b244fc357faf5b12933bed
-work/input/access-om2-1deg-nomask-ESMFmesh.nc:
+work/INPUT/access-om2-1deg-nomask-ESMFmesh.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-nomask-ESMFmesh.nc
   hashes:
-    binhash: 07cb65372f403b87b3002134ea2c31eb
+    binhash: 4b1cc45032afeaf93b4894937639f5b9
     md5: 9b7120a42b5cb587492e7c31791eb549
-work/input/grid.nc:
+work/INPUT/grid.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/cice/grids/global.1deg/2024.05.14/grid.nc
   hashes:
-    binhash: 60ac2869d4521fd6441a90b519d9bce0
+    binhash: b347eb0588291c34bb40a24a7bc45173
     md5: 544a40b634c182f3e182da6bcbe8be7b
-work/input/iced.1900-01-01-10800.nc:
+work/INPUT/iced.1900-01-01-10800.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc
   hashes:
-    binhash: a88d7f33c7eef8f6870773f7cc47fc28
+    binhash: 414174d244807698f8c919f763d3d51d
     md5: 87c012d60c58c65bb56caa98779e5e51
-work/input/kmt.nc:
+work/INPUT/kmt.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc
   hashes:
-    binhash: 6fd7a86039ea089fffc371390c14d77a
+    binhash: 670a7fb52cdc440673304d9a775b3dac
     md5: 4dae75252ac93467f10ea26e833e13d2
-work/input/mod_def.ww3:
+work/INPUT/mod_def.ww3:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/ww3/mod_def/global.1deg/2024.04.18/mod_def.ww3
   hashes:
-    binhash: 159d6c5877443faa7e3df3b46551cad8
+    binhash: 73f83a698fa3e4e4f550f52d09bc4705
     md5: 5242d76ab7e3a38e2b1aaccc82c287aa
-work/input/ocean_hgrid.nc:
+work/INPUT/ocean_hgrid.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc
   hashes:
-    binhash: 81c5dd8f8e3c930827a9b4aeef23d06b
+    binhash: 3526d89ffb639455c6a1218f5139d5b2
     md5: 51f58be0f4ea6da2cb438a893f95c689
-work/input/ocean_temp_salt.res.nc:
+work/INPUT/ocean_temp_salt.res.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc
   hashes:
-    binhash: 92bc0a9f9ea8d637267f87be2bd8a913
+    binhash: efb5e5e124648f2d59d4cd56b6e9a023
     md5: c5f7e60b5427a4442f111adc65a2d067
-work/input/ocean_vgrid.nc:
+work/INPUT/ocean_vgrid.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/mom/grids/vertical/global.1deg/2023.07.28/ocean_vgrid.nc
   hashes:
-    binhash: a3cddbc25d8c1cbd84062ba78083201d
+    binhash: ad5bf87f1c69ef3be1061a5c6d1d0411
     md5: a1e0b0b0adc363506ff17a362e83f64a
-work/input/restart.ww3:
+work/INPUT/restart.ww3:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/ww3/initial_conditions/global.1deg/2024.04.18/restart.ww3
   hashes:
-    binhash: 8da6555bf7df572a6f0be0268137292f
+    binhash: 1c4811600847e181e08265d695bc7c22
     md5: e0043b57b4de97a7df82dafa4c7a1a9f
-work/input/salt_sfc_restore.nc:
+work/INPUT/salt_sfc_restore.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc
   hashes:
-    binhash: f2808084d6b7d38ea235244504c5b170
+    binhash: 425ccc4989dc3e1acdecc6ffd7e9a870
     md5: b2bd35c44017597ba99b85fb61ed4d72
-work/input/topog.nc:
+work/INPUT/topog.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om3/share/grids/global.1deg/2020.10.22/topog.nc
   hashes:
-    binhash: efb4a31d2fc409a284775d3bb28d239b
+    binhash: 101cb5069e11e9f3196a5a6804fa0780
     md5: 4e13d88001b646f3cf4f1c3b8db59f91
diff --git a/nuopc.runconfig b/nuopc.runconfig
index 48b2329..15df34a 100644
--- a/nuopc.runconfig
+++ b/nuopc.runconfig
@@ -116,12 +116,12 @@ ALLCOMP_attributes::
      hostname = gadi
      ice_ncat = 5
      mediator_present = true
-     mesh_atm = ./input/access-om2-1deg-nomask-ESMFmesh.nc
+     mesh_atm = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc
      mesh_glc = UNSET
-     mesh_ice = ./input/access-om2-1deg-ESMFmesh.nc
+     mesh_ice = ./INPUT/access-om2-1deg-ESMFmesh.nc
      mesh_lnd = UNSET
-     mesh_mask = ./input/access-om2-1deg-ESMFmesh.nc
-     mesh_ocn = ./input/access-om2-1deg-ESMFmesh.nc
+     mesh_mask = ./INPUT/access-om2-1deg-ESMFmesh.nc
+     mesh_ocn = ./INPUT/access-om2-1deg-ESMFmesh.nc
      model_version = unknown
      ocn2glc_coupling = .false.
      ocn2glc_levels = 1:10:19:26:30:33:35
@@ -330,7 +330,7 @@ OCN_attributes::
 
 ROF_attributes::
      Verbosity = off
-     mesh_rof = ./input/access-om2-1deg-nomask-ESMFmesh.nc
+     mesh_rof = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc
 ::
 
 WAV_attributes::