From 17341585d0049cfc351e5003d19fdf516a86adf7 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Sun, 12 Jul 2026 21:07:33 -0600
Subject: [PATCH 01/28] Initial commit. Checkpoint version 2->3. AB terms
 written in Chebyshev space.

---
 src/IO/Parallel_IO.F90        |  3 ++-
 src/Physics/Checkpointing.F90 | 26 ++++++++++++++++++++------
 2 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/src/IO/Parallel_IO.F90 b/src/IO/Parallel_IO.F90
index 5de1b793a..3fa52b464 100644
--- a/src/IO/Parallel_IO.F90
+++ b/src/IO/Parallel_IO.F90
@@ -180,7 +180,7 @@ Subroutine Initialize_IO_Buffer(self,grid_pars, nvals, mpi_tag, &
                                     averaging_weights, nrec, skip,  &
                                     write_timestamp, averaging_axes, & 
                                     spectral, mode, l_values, cache_spectral, &
-                                    spec_comp, lmax_in, full_cache)
+                                    spec_comp, nr_in, lmax_in, full_cache)
         Implicit None
         Class(io_buffer) :: self
         Integer, Intent(In) :: grid_pars(1:,1:)
@@ -191,6 +191,7 @@ Subroutine Initialize_IO_Buffer(self,grid_pars, nvals, mpi_tag, &
         Logical, Intent(In), Optional :: full_cache, spec_comp
         Integer, Intent(In), Optional :: averaging_axes(3)
         Integer, Intent(In), Optional :: mode
+        Integer, Intent(In), Optional :: nr_in
         Integer, Intent(In), Optional :: lmax_in
         Integer ::  adim(2), in_lmax
         Real*8, Allocatable :: avg_weights(:,:)
diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index 7b127a5d0..4dbec84ae 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -36,10 +36,10 @@ Module Checkpointing
     ! Simple Checkpointing Module
     ! Uses MPI-IO to split writing of files amongst rank zero processes from each row
     Implicit None
-    Type(SphericalBuffer) :: chktmp, chktmp2, bctmp
+    Type(SphericalBuffer) :: chktmp, chktmp2, bctmp,abterms_cheby
     Integer, private :: numfields
     Integer, private :: check_err_off = 100  ! Checkpoint errors report in range 100-200.
-    Integer, private :: checkpoint_version = 2
+    Integer, private :: checkpoint_version = 3
     Integer,private :: checkpoint_tag = 425
     Character*120 :: checkpoint_prefix ='nothing'
     Character*6 :: auto_fmt = '(i2.2)'  ! Format code for quicksaves
@@ -138,6 +138,10 @@ Subroutine Initialize_Checkpointing()
         Call checkpoint_buffer%Init(gpars, mpi_tag=checkpoint_tag, &
                 spectral=.true., cache_spectral = .true., spec_comp = .true.)
         DeAllocate(gpars)
+
+        ! Buffer to hold Adams-Bashforth terms in Chebyshev format
+        nfs(:) = numfields
+        Call abterms_cheby%init(field_count = nfs, config = 'p1a')
     End Subroutine Initialize_Checkpointing
 
     Subroutine Write_Checkpoint(abterms,iteration,dt,new_dt,elapsed_time, input_file)
@@ -152,10 +156,20 @@ Subroutine Write_Checkpoint(abterms,iteration,dt,new_dt,elapsed_time, input_file
         endian_tag=314
         Call chktmp%construct('p1a')
         chktmp%config = 'p1a'
-        !Copy the RHS into chtkmp
-        Call Get_All_RHS(chktmp%p1a)
-        chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms(:,:,:,1:numfields)
-        !Now we want to move from p1a to s2a (rlm space)
+
+        !Copy the RHS (contains state variables at current timestep) into chtkmp
+        Call Get_All_RHS(chktmp%p1a) 
+
+        ! Next, convert the AB terms into chebyshev space and copy them into the buffer
+        Call abterms_cheby%construct('p1a')
+        abterms_cheby%config='p1a'
+        !chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms(:,:,:,1:numfields)
+        ! TRANSFORM ABTERMS CHEBY
+        Call gridcp%to_spectral(abterms,abterms_cheby%p1a)
+        chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms_cheby%p1a(:,:,:,1:numfields)
+        Call abterms_cheby%deconstruct('p1a')
+
+        !Move checkpoint buffer from p1a to s2a (rlm space)
         Call chktmp%reform()
 
         If (ItIsTimeForAQuickSave) Then

From 84ead8b3a8506dee7727bb45d4db7d5a37db47f9 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Mon, 13 Jul 2026 10:52:25 -0600
Subject: [PATCH 02/28] Interpolation from lower resolution now adjusted.

---
 src/Physics/Checkpointing.F90 | 66 ++++++++++++++++++++++++-----------
 1 file changed, 45 insertions(+), 21 deletions(-)

diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index 4dbec84ae..f3435da9c 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -163,8 +163,7 @@ Subroutine Write_Checkpoint(abterms,iteration,dt,new_dt,elapsed_time, input_file
         ! Next, convert the AB terms into chebyshev space and copy them into the buffer
         Call abterms_cheby%construct('p1a')
         abterms_cheby%config='p1a'
-        !chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms(:,:,:,1:numfields)
-        ! TRANSFORM ABTERMS CHEBY
+        !chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms(:,:,:,1:numfields) ! earlier version -- physical space storage
         Call gridcp%to_spectral(abterms,abterms_cheby%p1a)
         chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms_cheby%p1a(:,:,:,1:numfields)
         Call abterms_cheby%deconstruct('p1a')
@@ -577,6 +576,14 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
 
         Call chktmp%reform()    ! move to p1b
 
+        If (version .ge. 2) Then
+            ! For version 2+, the AB terms are stored in Chebyshev space
+            Call abterms_cheby%construct('p1b')
+            abterms_cheby%config='p1b'
+            abterms_cheby%p1b(:,:,:,1:numfields)=chktmp%p1b(:,:,:,numfields+1:numfields*2)
+        Endif
+
+
         If (.not. legacy_format) Then
             ! Load the boundary values array
 
@@ -627,44 +634,55 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                     Call stdout%print(' ')
                 Endif
 
-                If (n_r_old .lt. n_r) Then
+        
+
+                If ((n_r_old .lt. n_r) .and. (version .lt. 2) ) Then
+
+                    ! Prior to version 2, the AB terms were stored in radial-physical space rather
+                    ! than in radial-Chebyshev space.
+                    ! Before proceeding, we need to convert to Chebyshev space.
+                    ! During the read-in process above, old fields were stored in
+                    ! indices 1:n_r_old of first dimension of chktmp%p1b.
 
-                    ! The fields are OK - they are already in chebyshev space
-                    fields(:,:,:,1:numfields) = chktmp%p1b(:,:,:,1:numfields)
 
-                    ! The AB terms are stored in physical space (in radius).
-                    ! They need to be transformed, coefficients copied, and transformed back..
-                    ! First, we need to initialize the old chebyshev grid.
+                    ! (1) Initialize the old Chebyshev grid.
                     Allocate(radius_old(1:n_r_old))
-                    Call cheby_info%Init(radius_old,rmin,rmax)  ! We assume that rmax and rmin do not change
+                    Call cheby_info%Init(radius_old,rmin,rmax)  ! rmax and rmin cannot change
+  
+                    ! (2) Create some buffer space to store the old radial profiles and 
+                    !     the new Chebyshev coefficients.
                     fcount(:,:) = numfields
                     Call chktmp2%init(field_count = fcount, config = 'p1a')
                     Call chktmp2%construct('p1a')
                     chktmp2%p1a(:,:,:,:) = 0.0d0
-                    ! Allocate tempfield1, tempfield2
                     lb = lbound(chktmp%p1b,3)
                     ub = ubound(chktmp%p1b,3)
                     Allocate(tempfield1(1:n_r_old,1:2,lb:ub,1))
                     Allocate(tempfield2(1:n_r_old,1:2,lb:ub,1))
 
+                    ! (3) Convert to the new Chebyshev grid
                     Do i = 1, numfields
                         tempfield1(:,:,:,:) = 0.0d0
                         tempfield2(:,:,:,:) = 0.0d0
+                        ! Subsample smaller-grid fields from larger-grid buffer
                         tempfield1(1:n_r_old,:,:,1) = chktmp%p1b(1:n_r_old,:,:,numfields+i)
-                        call cheby_info%tospec4d(tempfield1,tempfield2)
+                        ! Transform
+                        Call cheby_info%tospec4d(tempfield1,tempfield2)
+
+                        ! Grab Chebyshev coefficients up to old n_max
                         chktmp2%p1a(1:n_r_old,:,:,i) = tempfield2(1:n_r_old,:,:,1)
                     Enddo
                     DeAllocate(tempfield1,tempfield2)
 
 
-                    Call chktmp2%construct('p1b')
+                    !Call chktmp2%construct('p1b')
                     !Normal transform(p1a,p1b)
-                    Call gridcp%From_Spectral(chktmp2%p1a,chktmp2%p1b)
+                    !Call gridcp%From_Spectral(chktmp2%p1a,chktmp2%p1b)
 
-                    abterms(:,:,:,1:numfields) = chktmp2%p1b(:,:,:,1:numfields)
+                    !abterms(:,:,:,1:numfields) = chktmp2%p1b(:,:,:,1:numfields)
                     Call cheby_info%destroy()
-                    Call chktmp2%deconstruct('p1a')
-                    Call chktmp2%deconstruct('p1b')
+                    !Call chktmp2%deconstruct('p1a')
+                    !Call chktmp2%deconstruct('p1b')
                     Deallocate(radius_old)
                 Else ! Rayleigh doesn't currently support degrading radial resolution--exit now
                     If (my_rank .eq. 0) Then
@@ -676,13 +694,19 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                     Stop
                 Endif
 
-            Else
-
-                ! Interpolation is complete, now we just copy into the other arrays
-                fields(:,:,:,1:numfields) = chktmp%p1b(:,:,:,1:numfields)
-                abterms(:,:,:,1:numfields) = chktmp%p1b(:,:,:,numfields+1:numfields*2)
+            Endif
 
+            ! Interpolation is complete, now we just copy into the other arrays
+            fields(:,:,:,1:numfields) = chktmp%p1b(:,:,:,1:numfields)
+            If (version .ge. 2) Then
+                Call gridcp%From_Spectral(abterms_cheby%p1b,abterms)
+                Call abterms_cheby%deconstruct('p1b')
+            Else
+                Call gridcp%From_Spectral(chktmp2%p1a,abterms)
+                Call chktmp2%deconstruct('p1a')
+                !abterms(:,:,:,1:numfields) = chktmp%p1b(:,:,:,numfields+1:numfields*2)
             Endif
+            
             Call chktmp%deconstruct('p1b')
             DeAllocate(old_radius)
 

From 2044e6cc70ed352f90c6192223b21cbdb07f9f9c Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Mon, 13 Jul 2026 14:38:33 -0600
Subject: [PATCH 03/28] Small adjustments to text

---
 src/Physics/Checkpointing.F90 | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index f3435da9c..91d67a78e 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -188,7 +188,6 @@ Subroutine Write_Checkpoint(abterms,iteration,dt,new_dt,elapsed_time, input_file
             checkfile = Trim(my_path)//trim(checkpoint_prefix)//'/'//trim(checkpoint_suffix(i))
             Call checkpoint_buffer%cache_data_spectral(chktmp%s2a,i)
             Call checkpoint_buffer%write_data(filename=checkfile, clear_existing = .true.)
-
         Enddo
 
         Call chktmp%deconstruct('s2a')
@@ -638,8 +637,8 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
 
                 If ((n_r_old .lt. n_r) .and. (version .lt. 2) ) Then
 
-                    ! Prior to version 2, the AB terms were stored in radial-physical space rather
-                    ! than in radial-Chebyshev space.
+                    ! Prior to version 2, the AB terms were stored in radial-physical 
+                    ! space rather than in radial-Chebyshev space.
                     ! Before proceeding, we need to convert to Chebyshev space.
                     ! During the read-in process above, old fields were stored in
                     ! indices 1:n_r_old of first dimension of chktmp%p1b.

From 01e860cf1973ef47e7b488ac2bb8754ea1afcdee Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Tue, 14 Jul 2026 13:36:02 -0600
Subject: [PATCH 04/28] Updates/bug fixes to checkpoints -- tests working

---
 src/Physics/Checkpointing.F90 | 146 ++++++++++++++++------------------
 1 file changed, 68 insertions(+), 78 deletions(-)

diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index 91d67a78e..b6846acc7 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -261,7 +261,7 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
         Real*8, Intent(InOut) :: fields(:,:,:,:), abterms(:,:,:,:)
         Integer :: n_r_old, l_max_old, grid_type_old
         Integer :: i, ierr, mp, lb,ub, ab_offset
-        Integer :: old_pars(7 + nsubmax), fcount(3,2), version
+        Integer :: old_pars(8 + nsubmax), fcount(3,2), version
         Integer :: last_iter, last_auto, endian_tag, funit
         Integer*8 :: found_bytes, expected_bytes, n_r_old_big, l_max_old_big
         Integer :: read_magnetism = 0, read_hydro = 0
@@ -276,7 +276,7 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
         Logical :: legacy_format, fexist
         Integer :: ncheby_old(1:nsubmax)
         Integer :: idom, n_r_loc, n_r_old_loc, irmin, irmax, irmin_old, irmax_old
-        Logical :: first_time_interpolating = .True.
+        Logical :: first_time_interpolating = .True., interpolate=.False.
 
         read_hydro = read_pars(1)
         read_magnetism = read_pars(2)
@@ -373,6 +373,7 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                 If (legacy_format .or. (endian_tag .eq. 314)) Then
                     If (.not. legacy_format) Then
                         Read(funit)version
+                        Write(6,*)'Current Checkpoint Version: ', version
                         Read(funit)n_r_old
                     Else
                         Read(funit)n_r_old
@@ -440,7 +441,8 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
             old_pars(2) = grid_type_old
             old_pars(3) = l_max_old
             old_pars(7) = ierr
-            old_pars(8:8+nsubmax-1) = ncheby_old(1:nsubmax)
+            old_pars(8) = version
+            old_pars(9:9+nsubmax-1) = ncheby_old(1:nsubmax)
             dt_pars(1) = dt
             dt_pars(2) = new_dt
             dt_pars(3) = checkpoint_time
@@ -457,13 +459,14 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
         l_max_old     = old_pars(3)
         checkpoint_iter = old_pars(4)
         last_auto = old_pars(5)
+        version = old_pars(8)
 
         If (old_pars(6) .eq. 2) Then
             under_slash='_'
             legacy_format=.true.
         Endif
 
-        ncheby_old(1:nsubmax) = old_pars(8:8+nsubmax-1)
+        ncheby_old(1:nsubmax) = old_pars(9:9+nsubmax-1)
 
         If (old_pars(7) .ne. 0) Then
             ! Something is wrong with this checkpoint.
@@ -565,6 +568,10 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
             DeAllocate(rinds)
             DeAllocate(gpars)
         Endif
+
+        ! Load the state vector fields and the AB terms.
+        ! During the read-in process below, old fields are stored in
+        ! indices 1:n_r_old of first dimension of chktmp%p1b.
         Do i = 1, numfields*2
             If (read_var(i) .eq. 1) Then
                 checkfile = trim(checkpoint_prefix)//under_slash//trim(checkpoint_suffix(i))
@@ -572,17 +579,8 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                 Call checkpoint_inbuffer%grab_data_spectral(chktmp%s2b,i)
             Endif
         Enddo
-
         Call chktmp%reform()    ! move to p1b
 
-        If (version .ge. 2) Then
-            ! For version 2+, the AB terms are stored in Chebyshev space
-            Call abterms_cheby%construct('p1b')
-            abterms_cheby%config='p1b'
-            abterms_cheby%p1b(:,:,:,1:numfields)=chktmp%p1b(:,:,:,numfields+1:numfields*2)
-        Endif
-
-
         If (.not. legacy_format) Then
             ! Load the boundary values array
 
@@ -608,42 +606,40 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
 
         Endif
 
-        If (ndomains .eq. 1) Then ! Keep everything the same as it was before 
-            ! interpolation in multiple domains was enabled
-
-            ! NOW, if n_r_old and grid_type_old are the same, we can copy chtkmp%p1b into abterms and
-            ! fields.  Otherwise, we need to interpolate onto the current grid
-            ! When we change the checkpointing format, should also store AB terms in cheby-space
-            If  ((n_r_old .ne. n_r) .or. (grid_type_old .ne. grid_type) ) Then
-                ! Interpolate
-                ! We will assume the user kept the same radial domain bounds.
-                ! If they  have not, this will end badly.
-                If (my_rank .eq. 0) Then
-                    Call stdout%print(' ')
-                    Call stdout%print('------ Radial grid has changed.')
-                    Call stdout%print('------ Interpolating onto new grid.')
-                    Write(szstr,'(i13)')grid_type_old
-                    Call stdout%print('------ Old grid_type:     '//TRIM(szstr))
-                    Write(szstr,'(i13)')grid_type
-                    Call stdout%print('------ Current grid_type: '//TRIM(szstr))
-                    Write(szstr,'(i13)')n_r_old
-                    Call stdout%print('------ Old N_R:           '//TRIM(szstr))
-                    Write(szstr,'(i13)')n_r
-                    Call stdout%print('------ Current N_R:       '//TRIM(szstr))
-                    Call stdout%print(' ')
-                Endif
-
-        
-
-                If ((n_r_old .lt. n_r) .and. (version .lt. 2) ) Then
+        If (version .ge. 3) Then
+            ! For version 3+, the AB terms are stored in Chebyshev space
+            Call abterms_cheby%construct('p1b')
+            abterms_cheby%config='p1b'
+            abterms_cheby%p1b = 0d0
+            ub = Min(n_r,n_r_old)
+            abterms_cheby%p1b(1:ub,:,:,1:numfields)=chktmp%p1b(1:ub,:,:,numfields+1:numfields*2)
+            Write(6,*)'In first 3-branch'
+        Endif
 
-                    ! Prior to version 2, the AB terms were stored in radial-physical 
-                    ! space rather than in radial-Chebyshev space.
-                    ! Before proceeding, we need to convert to Chebyshev space.
-                    ! During the read-in process above, old fields were stored in
-                    ! indices 1:n_r_old of first dimension of chktmp%p1b.
 
+        If (ndomains .eq. 1) Then
+            ! Regardless of the checkpoint version or resolution, we can load the state vector
+            ! fields directly from the checkpoint buffer because that portion of the buffer is
+            ! already in the expected Chebyshev format.  
+            ub = Min(n_r,n_r_old)
+            fields = 0d0
+            fields(1:ub,:,:,1:numfields) = chktmp%p1b(1:ub,:,:,1:numfields)
 
+            ! For checkpoint version 3 and later, the AB terms are also stored in
+            ! Chebyshev space, but they need to be in grid space.
+            ! Even if the resolution changes, no further work needs to be done.
+            If (version .ge. 3) Then
+                !Need to convert from Chebyshev space to physical space
+                Call gridcp%From_Spectral(abterms_cheby%p1b,abterms)
+                Call abterms_cheby%deconstruct('p1b')
+            Else
+                ! For checkpoint versions 1 and 2, AB terms were stored in physical space.
+                ! If the grid resolution changed, we need to perform a Chebyshev interpolation.
+                ! If not, we can load directly from the checkpoint buffer.
+                If (n_r_old .eq. n_r) Then
+                    abterms(:,:,:,1:numfields) = chktmp%p1b(:,:,:,numfields+1:numfields*2)
+                Else
+                    Write(6,*)'Inside  interpolation branch'
                     ! (1) Initialize the old Chebyshev grid.
                     Allocate(radius_old(1:n_r_old))
                     Call cheby_info%Init(radius_old,rmin,rmax)  ! rmax and rmin cannot change
@@ -654,7 +650,7 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                     Call chktmp2%init(field_count = fcount, config = 'p1a')
                     Call chktmp2%construct('p1a')
                     chktmp2%p1a(:,:,:,:) = 0.0d0
-                    lb = lbound(chktmp%p1b,3)
+                    lb = lbound(chktmp%p1b,3) ! describes bounds of lm mode index
                     ub = ubound(chktmp%p1b,3)
                     Allocate(tempfield1(1:n_r_old,1:2,lb:ub,1))
                     Allocate(tempfield2(1:n_r_old,1:2,lb:ub,1))
@@ -671,43 +667,37 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                         ! Grab Chebyshev coefficients up to old n_max
                         chktmp2%p1a(1:n_r_old,:,:,i) = tempfield2(1:n_r_old,:,:,1)
                     Enddo
-                    DeAllocate(tempfield1,tempfield2)
-
-
-                    !Call chktmp2%construct('p1b')
-                    !Normal transform(p1a,p1b)
-                    !Call gridcp%From_Spectral(chktmp2%p1a,chktmp2%p1b)
+                    Call gridcp%From_Spectral(chktmp2%p1a,abterms)
 
-                    !abterms(:,:,:,1:numfields) = chktmp2%p1b(:,:,:,1:numfields)
+                    ! clean up
+                    DeAllocate(tempfield1,tempfield2)
                     Call cheby_info%destroy()
-                    !Call chktmp2%deconstruct('p1a')
-                    !Call chktmp2%deconstruct('p1b')
                     Deallocate(radius_old)
-                Else ! Rayleigh doesn't currently support degrading radial resolution--exit now
-                    If (my_rank .eq. 0) Then
-                        Call stdout%print('ERROR: Rayleigh currently does not support degrading radial resolution.')
-                        Call stdout%print('Now exiting')
-                        Call stdout%partial_flush()
-                    Endif
-                    Call pfi%exit()
-                    Stop
-                Endif
+                    Call chktmp2%deconstruct('p1a')
 
-            Endif
+                Endif  ! (n_r_old .eq. n_r)
 
-            ! Interpolation is complete, now we just copy into the other arrays
-            fields(:,:,:,1:numfields) = chktmp%p1b(:,:,:,1:numfields)
-            If (version .ge. 2) Then
-                Call gridcp%From_Spectral(abterms_cheby%p1b,abterms)
-                Call abterms_cheby%deconstruct('p1b')
-            Else
-                Call gridcp%From_Spectral(chktmp2%p1a,abterms)
-                Call chktmp2%deconstruct('p1a')
-                !abterms(:,:,:,1:numfields) = chktmp%p1b(:,:,:,numfields+1:numfields*2)
+            Endif  ! (version .ge. 3)
+
+            ! clean up
+            Call chktmp%deconstruct('p1b') 
+            Deallocate(old_radius)
+
+            ! Finally, print a message if we interpolated
+            If ( (my_rank .eq. 0) .and. (n_r .ne. n_r_old) ) Then
+                Call stdout%print(' ')
+                Call stdout%print('------ Radial grid has changed.')
+                Call stdout%print('------ Interpolating onto new grid.')
+                Write(szstr,'(i13)')grid_type_old
+                Call stdout%print('------ Old grid_type:     '//TRIM(szstr))
+                Write(szstr,'(i13)')grid_type
+                Call stdout%print('------ Current grid_type: '//TRIM(szstr))
+                Write(szstr,'(i13)')n_r_old
+                Call stdout%print('------ Old N_R:           '//TRIM(szstr))
+                Write(szstr,'(i13)')n_r
+                Call stdout%print('------ Current N_R:       '//TRIM(szstr))
+                Call stdout%print(' ')
             Endif
-            
-            Call chktmp%deconstruct('p1b')
-            DeAllocate(old_radius)
 
         Else ! ndomains > 1: we need to loop over domains and (maybe) interpolate
 

From ca398781aeec3dc66a6ebf0890143002b8ef89c5 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Tue, 14 Jul 2026 15:35:01 -0600
Subject: [PATCH 05/28] Adding error messages.

---
 src/Physics/Checkpointing.F90 | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index b6846acc7..86f1b9f0a 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -613,7 +613,6 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
             abterms_cheby%p1b = 0d0
             ub = Min(n_r,n_r_old)
             abterms_cheby%p1b(1:ub,:,:,1:numfields)=chktmp%p1b(1:ub,:,:,numfields+1:numfields*2)
-            Write(6,*)'In first 3-branch'
         Endif
 
 
@@ -636,9 +635,11 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                 ! For checkpoint versions 1 and 2, AB terms were stored in physical space.
                 ! If the grid resolution changed, we need to perform a Chebyshev interpolation.
                 ! If not, we can load directly from the checkpoint buffer.
+                ! Due to the storage convention for versions 1 and 2, interpolation
+                ! can only be carried out if n_r_old < n_r.
                 If (n_r_old .eq. n_r) Then
                     abterms(:,:,:,1:numfields) = chktmp%p1b(:,:,:,numfields+1:numfields*2)
-                Else
+                Else If (n_r_old .lt. n_r) Then
                     Write(6,*)'Inside  interpolation branch'
                     ! (1) Initialize the old Chebyshev grid.
                     Allocate(radius_old(1:n_r_old))
@@ -674,7 +675,16 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                     Call cheby_info%destroy()
                     Deallocate(radius_old)
                     Call chktmp2%deconstruct('p1a')
+                Else
+                    If (my_rank .eq. 0) Then
+                        Call stdout%print('****************** ERROR ******************')
+                        Call stdout%print('ERROR: Rayleigh does not support degrading radial resolution')
+                        Call stdout%print('for checkpoints generated using version 1.3.0 or earlier.')
 
+                        Call stdout%partial_flush()
+                    Endif
+                    Call pfi%exit()
+                    Stop
                 Endif  ! (n_r_old .eq. n_r)
 
             Endif  ! (version .ge. 3)
@@ -697,6 +707,14 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                 Write(szstr,'(i13)')n_r
                 Call stdout%print('------ Current N_R:       '//TRIM(szstr))
                 Call stdout%print(' ')
+                If (n_r_old .gt. n_r) Then
+                Call stdout%print('------ ******************* WARNING *****************************')
+                Call stdout%print('------ Boundary conditions are not formally satisfied by the')
+                Call stdout%print('------ checkpoint save state when N_R is decreased upon restart.')
+                Call stdout%print('------ Drastically degrading the radial resolution may lead')
+                Call stdout%print('------ to unexpected results.')
+                Call stdout%print(' ')
+                Endif
             Endif
 
         Else ! ndomains > 1: we need to loop over domains and (maybe) interpolate

From ae345f327b37ce0d248042b40b69e04b688e611d Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Tue, 14 Jul 2026 16:43:14 -0600
Subject: [PATCH 06/28] Added error condition and message for degrading radial
 resolution using old checkpoint format.

---
 src/Physics/Checkpointing.F90 | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index 86f1b9f0a..5df0e3ba4 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -677,10 +677,18 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
                     Call chktmp2%deconstruct('p1a')
                 Else
                     If (my_rank .eq. 0) Then
-                        Call stdout%print('****************** ERROR ******************')
-                        Call stdout%print('ERROR: Rayleigh does not support degrading radial resolution')
-                        Call stdout%print('for checkpoints generated using version 1.3.0 or earlier.')
-
+                        Call stdout%print(' ')
+                        Call stdout%print('********************************  ERROR   *********************************')
+                        Call stdout%print('------  Rayleigh does not support degrading radial resolution')
+                        Call stdout%print('------  for checkpoints generated using version 1.3.0 or earlier.')
+                        Call stdout%print(' ')
+                        Call stdout%print('------  In order to degrade the radial resolution of this model:')
+                        Call stdout%print('------  (1) Restart from the current checkpoint using this version of')
+                        Call stdout%print('------      Rayleigh and maintain the current radial resolution.')
+                        Call stdout%print('------  (2) Generate a new checkpoint at the current resolution.')
+                        Call stdout%print('------      This checkpoint will be saved using the updated format.')
+                        Call stdout%print('------  (3) Restart using the new checkpoint and desired radial resolution.')
+                        Call stdout%print(' ')
                         Call stdout%partial_flush()
                     Endif
                     Call pfi%exit()

From 34273e74456b003b34caac7373f75f127e3bf991 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Tue, 14 Jul 2026 17:17:20 -0600
Subject: [PATCH 07/28] Removed unused interpolate variable from
 read_checkpoint

---
 src/Physics/Checkpointing.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index 5df0e3ba4..fdde1a4a0 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -276,7 +276,7 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
         Logical :: legacy_format, fexist
         Integer :: ncheby_old(1:nsubmax)
         Integer :: idom, n_r_loc, n_r_old_loc, irmin, irmax, irmin_old, irmax_old
-        Logical :: first_time_interpolating = .True., interpolate=.False.
+        Logical :: first_time_interpolating = .True.
 
         read_hydro = read_pars(1)
         read_magnetism = read_pars(2)

From 7a683950934ec90fbdb76a6b370744e492382f45 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 11:42:22 -0600
Subject: [PATCH 08/28] Updating workflow to also build Rayleigh 1.3 for
 testing

---
 .github/workflows/main.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5164febe2..29dc59458 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -44,6 +44,17 @@ jobs:
         cd "$GITHUB_WORKSPACE"
         make clear_ipynb && git diff --exit-code --name-only
         make doc
+    - name: Build Rayleigh 1.3
+      # Need this for testing checkpoint format compatibility
+      run: |
+        git checkout rayleigh-1.3.0
+        ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
+
+        make fdeps && git diff --exit-code
+        make -j
+        make install 
+        mv ./bin/rayleigh.dbg ./bin/rayleigh.v13       
+        git checkout main
     - name: Build Rayleigh
       # Now build Rayleigh itself
       run: |

From 1c88131ef7273f8c1772df4c54edf428b20e5285 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 11:56:00 -0600
Subject: [PATCH 09/28] updating workflow

---
 .github/workflows/main.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 29dc59458..b7a9638a0 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -47,7 +47,8 @@ jobs:
     - name: Build Rayleigh 1.3
       # Need this for testing checkpoint format compatibility
       run: |
-        git checkout rayleigh-1.3.0
+        git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
+        cd Rayleigh
         ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
 
         make fdeps && git diff --exit-code

From 480ec04983032ff2b1190fc87003caf2fd032c89 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 12:05:06 -0600
Subject: [PATCH 10/28] Another update

---
 .github/workflows/main.yml | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b7a9638a0..081be7935 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -48,16 +48,19 @@ jobs:
       # Need this for testing checkpoint format compatibility
       run: |
         git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
-        cd Rayleigh
+        ls
+        pwd
+        mv Rayleigh Rayleigh_1.3
+        cd Rayleigh_1.3
         ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
 
         make fdeps && git diff --exit-code
         make -j
-        make install 
-        mv ./bin/rayleigh.dbg ./bin/rayleigh.v13       
-        git checkout main
+        make install        
+        cd ..
+        ln -s Rayleigh_1.3/rayleigh.dbg ./bin/rayleigh.v13
     - name: Build Rayleigh
-      # Now build Rayleigh itself
+      # Now build the current Rayleigh
       run: |
         ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
 

From a836a2c7b2b4736c0c378c62b1a121b31f4da4bb Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 12:11:46 -0600
Subject: [PATCH 11/28] Still trying to get 1.3 to build for testing

---
 .github/workflows/main.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 081be7935..873d9809d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -48,12 +48,11 @@ jobs:
       # Need this for testing checkpoint format compatibility
       run: |
         git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
-        ls
-        pwd
         mv Rayleigh Rayleigh_1.3
         cd Rayleigh_1.3
+        ls
+        pwd
         ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
-
         make fdeps && git diff --exit-code
         make -j
         make install        

From 508fd1c9272dc6f77dfc555e529addefbe16db35 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 12:21:16 -0600
Subject: [PATCH 12/28] Debugging workflow

---
 .github/workflows/main.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 873d9809d..395fa421f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -49,13 +49,14 @@ jobs:
       run: |
         git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
         mv Rayleigh Rayleigh_1.3
-        cd Rayleigh_1.3
         ls
-        pwd
-        ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
-        make fdeps && git diff --exit-code
-        make -j
-        make install        
+        pwd        
+        cd Rayleigh_1.3
+
+        #./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
+        #make fdeps && git diff --exit-code
+        #make -j
+        #make install        
         cd ..
         ln -s Rayleigh_1.3/rayleigh.dbg ./bin/rayleigh.v13
     - name: Build Rayleigh

From 46c5b1035fe472e26fee79434b7059e9bf03d65e Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 12:34:42 -0600
Subject: [PATCH 13/28] Still testing workflows

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 395fa421f..d2c248b94 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -58,7 +58,7 @@ jobs:
         #make -j
         #make install        
         cd ..
-        ln -s Rayleigh_1.3/rayleigh.dbg ./bin/rayleigh.v13
+        #ln -s Rayleigh_1.3/rayleigh.dbg ./bin/rayleigh.v13
     - name: Build Rayleigh
       # Now build the current Rayleigh
       run: |

From c93dd3499a304e4dc514753cbe05af86a4beccd3 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 13:14:43 -0600
Subject: [PATCH 14/28] Increased size of abterms_cheby by 1 in last dimension

---
 src/Physics/Checkpointing.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index fdde1a4a0..f37d77884 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -141,6 +141,7 @@ Subroutine Initialize_Checkpointing()
 
         ! Buffer to hold Adams-Bashforth terms in Chebyshev format
         nfs(:) = numfields
+        if (magnetism) nfs(:) = numfields+1 ! magnetic mode has one extra field space used to combined derivatives
         Call abterms_cheby%init(field_count = nfs, config = 'p1a')
     End Subroutine Initialize_Checkpointing
 

From 72a0caa9933ded869aa5054610b61b547ce0dc88 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 13:33:16 -0600
Subject: [PATCH 15/28] Added some additional testing labels to help see
 failing tests better

---
 .github/workflows/main.yml | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d2c248b94..65bae7df5 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -67,12 +67,13 @@ jobs:
         make fdeps && git diff --exit-code
         make -j
         make install
-    - name: Test
+    - name: Chebyshev Test
       run: |
         #Primary test (Chebyshev Mode)
         cd "$GITHUB_WORKSPACE"/tests/c2001_case0
         mpirun -np 4 ../../bin/rayleigh.dbg
-
+    - name: Finite-Difference Test
+      run: |
         # Finite-difference test (uniform grid)
         cd "$GITHUB_WORKSPACE"/tests/c2001_case0_FD_uniform
         mpirun -np 4 ../../bin/rayleigh.dbg
@@ -84,19 +85,23 @@ jobs:
         # J2011 steady mhd test
         # cd "$GITHUB_WORKSPACE"/tests/j2011_steady_mhd_minimal
         # mpirun -np 4 ../../bin/rayleigh.dbg
-
+    - name: Generic Input Tests
+      run: |
         # Generic input test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/generic_input/run_test.sh
-
+    - name: Chi Scalar Tests
+      run: |
         # chi scalar test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/chi_scalar/run_test.sh
-        
+    - name: Custom Reference Test
+      run: |        
         # custom reference state test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/custom_reference/run_test.sh
-
+    - name: Coupled BC Test
+      run: |    
         # coupled bc test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/coupled_bcs/run_test.sh

From 77c19b1f25a1fee5565c404db9c51aaac5f70632 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 14:25:56 -0600
Subject: [PATCH 16/28] Rolling back changes to the main workflow file

---
 .github/workflows/main.yml | 33 ++++++---------------------------
 1 file changed, 6 insertions(+), 27 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 1a96710dd..47e907271 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -44,36 +44,20 @@ jobs:
         cd "$GITHUB_WORKSPACE"
         make clear_ipynb && git diff --exit-code --name-only
         make doc
-    - name: Build Rayleigh 1.3
-      # Need this for testing checkpoint format compatibility
-      run: |
-        git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
-        mv Rayleigh Rayleigh_1.3
-        ls
-        pwd        
-        cd Rayleigh_1.3
-
-        #./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
-        #make fdeps && git diff --exit-code
-        #make -j
-        #make install        
-        cd ..
-        #ln -s Rayleigh_1.3/rayleigh.dbg ./bin/rayleigh.v13
     - name: Build Rayleigh
-      # Now build the current Rayleigh
+      # Now build Rayleigh itself
       run: |
         ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
 
         make fdeps && git diff --exit-code
         make -j
         make install
-    - name: Chebyshev Test
+    - name: Test
       run: |
         #Primary test (Chebyshev Mode)
         cd "$GITHUB_WORKSPACE"/tests/c2001_case0
         mpirun -np 4 ../../bin/rayleigh.dbg
-    - name: Finite-Difference Test
-      run: |
+
         # Finite-difference test (uniform grid)
         cd "$GITHUB_WORKSPACE"/tests/c2001_case0_FD_uniform
         mpirun -np 4 ../../bin/rayleigh.dbg
@@ -85,23 +69,18 @@ jobs:
         # J2011 steady mhd test
         # cd "$GITHUB_WORKSPACE"/tests/j2011_steady_mhd_minimal
         # mpirun -np 4 ../../bin/rayleigh.dbg
-    - name: Generic Input Tests
-      run: |
+
         # Generic input test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/generic_input/run_test.sh
-    - name: Chi Scalar Tests
-      run: |
+
         # chi scalar test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/chi_scalar/run_test.sh
-    - name: Custom Reference Test
-      run: |        
+        
         # custom reference state test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/custom_reference/run_test.sh
-    - name: Coupled BC Test
-      run: |    
 
         # chi custom reference state test
         cd "$GITHUB_WORKSPACE"

From 3e38871580aa9352228b8f810fbd875064c705db Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Thu, 23 Jul 2026 15:06:00 -0600
Subject: [PATCH 17/28] Corrected size of "return-trip" buffers in Fields.F90.
 n_active_scalars and n_passive_scalars were getting double counted

---
 src/Physics/Fields.F90 | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/Physics/Fields.F90 b/src/Physics/Fields.F90
index 72c99c973..730a7f593 100755
--- a/src/Physics/Fields.F90
+++ b/src/Physics/Fields.F90
@@ -452,17 +452,17 @@ Subroutine Initialize_Field_Structure()
 
         ! These following code should pretty much never be modified by the user.
         if (.not. magnetism) then
-            wsfcount(1,2) = n_equations + n_active_scalars + n_passive_scalars
-            wsfcount(2,2) = n_equations + n_active_scalars + n_passive_scalars
-            wsfcount(3,2) = n_equations + n_active_scalars + n_passive_scalars
+            wsfcount(1,2) = n_equations 
+            wsfcount(2,2) = n_equations 
+            wsfcount(3,2) = n_equations 
         else
             emfr     = avar
             emftheta = cvar
             emfphi   = avar+1
             ! seven RHS's (plus scalars) go back for the solve (1 field is differentiated and combined at the end)
-            wsfcount(1,2) = n_equations + 1 + n_active_scalars + n_passive_scalars 
-            wsfcount(2,2) = n_equations + 1 + n_active_scalars + n_passive_scalars 
-            wsfcount(3,2) = n_equations + 1 + n_active_scalars + n_passive_scalars 
+            wsfcount(1,2) = n_equations + 1  
+            wsfcount(2,2) = n_equations + 1 
+            wsfcount(3,2) = n_equations + 1  
         endif
 
 

From 3018a2839e0a73158f9a43ac70adf5a91b82006f Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 13:55:06 -0600
Subject: [PATCH 18/28] Initial draft of checkpoint tests.

---
 .github/workflows/main.yml             | 41 +++++++++---
 tests/checkpoint/compare_check.py      | 58 ++++++++++++++++
 tests/checkpoint/old_format/main_input | 77 +++++++++++++++++++++
 tests/checkpoint/run_test.sh           | 92 ++++++++++++++++++++++++++
 4 files changed, 260 insertions(+), 8 deletions(-)
 create mode 100644 tests/checkpoint/compare_check.py
 create mode 100644 tests/checkpoint/old_format/main_input
 create mode 100644 tests/checkpoint/run_test.sh

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 47e907271..60699ac2a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -52,12 +52,31 @@ jobs:
         make fdeps && git diff --exit-code
         make -j
         make install
-    - name: Test
+    - name: Build Rayleigh v 1.3
+      # Build 1.3 for testing checkpoint compatibility
+      run: |
+      
+        mv Rayleigh Rayleigh_1.3
+        cd Rayleigh_1.3
+        ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
+
+        make fdeps && git diff --exit-code
+        make -j
+        make install
+    - name: Checkpoint Test
+      run: |  
+        # coupled bc test
+        cd "$GITHUB_WORKSPACE"
+        cd ./tests/checkpoint
+        sh ./run_test.sh        
+        
+    - name: Chebyshev Test
       run: |
         #Primary test (Chebyshev Mode)
         cd "$GITHUB_WORKSPACE"/tests/c2001_case0
         mpirun -np 4 ../../bin/rayleigh.dbg
-
+    - name: Finite-difference Test
+      run: |
         # Finite-difference test (uniform grid)
         cd "$GITHUB_WORKSPACE"/tests/c2001_case0_FD_uniform
         mpirun -np 4 ../../bin/rayleigh.dbg
@@ -69,27 +88,33 @@ jobs:
         # J2011 steady mhd test
         # cd "$GITHUB_WORKSPACE"/tests/j2011_steady_mhd_minimal
         # mpirun -np 4 ../../bin/rayleigh.dbg
-
+    - name: Generic Input Test
+      run: |
         # Generic input test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/generic_input/run_test.sh
-
+    - name: Chi Scalar Test
+      run: |
         # chi scalar test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/chi_scalar/run_test.sh
-        
+    - name: Custom Reference Test
+      run: |        
         # custom reference state test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/custom_reference/run_test.sh
-
+    - name: Chi Custom Reference Test
+      run: |    
         # chi custom reference state test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/chi_custom_reference/run_test.sh
-
+    - name: Coupled BC Test
+      run: |  
         # coupled bc test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/coupled_bcs/run_test.sh
-
+    - name: Vforce Diagnostics Test
+      run: |  
         # vforce diagnostics regression test
         cd "$GITHUB_WORKSPACE"
         sh ./tests/vforce_diagnostics/run_test.sh
diff --git a/tests/checkpoint/compare_check.py b/tests/checkpoint/compare_check.py
new file mode 100644
index 000000000..ec83b6832
--- /dev/null
+++ b/tests/checkpoint/compare_check.py
@@ -0,0 +1,58 @@
+from rayleigh_diagnostics import G_Avgs, SPH_Modes
+import numpy as np
+
+def chisq(a1,a2):
+    b = (a1-a2)**2
+    c = np.sum(b)/np.sum(a1*a1)
+    return c**0.5
+
+dirs = ['old_format', 'new_format', 'new_format_same_res', 'new_format_up_res', 'new_format_down_res']
+iters = ['00000100', '00000150', '00000200','00000250']
+tols = [1e-10, 1e-10, 1e-2, 1e-2]
+ndirs = len(dirs)
+for i in range(1,ndirs):
+    #print('=========================')
+    chisqs = []
+    old = dirs[i-1]
+    new = dirs[i]
+    istring = iters[i-1]
+    #print(old,new,istring)
+    
+    sphm_o = SPH_Modes(istring,path=old+'/SPH_Modes/')
+    sphm_n = SPH_Modes(istring,path=new+'/SPH_Modes/')
+    ga_o = G_Avgs(istring,path=old+'/G_Avgs/')
+    ga_n = G_Avgs(istring,path=new+'/G_Avgs/')
+    
+    mx_ref = np.max([sphm_o.vals.real**2,sphm_o.vals.imag**2])**0.5
+    for j, l in enumerate(sphm_o.lvals):
+        for m in range(0,l+1):
+            val_o = sphm_o.vals[m,j,0,0,:]
+            val_n = sphm_n.vals[m,j,0,0,:]
+            c = chisq(val_o.real,val_n.real)
+
+            mx = np.max([val_o.real**2,val_n.imag**2])**0.5
+            chisqs.append(c*mx/mx_ref)
+            
+            if (m > 0):  # m = 0 has no imaginary component
+                c = chisq(val_o.imag,val_n.imag)
+                chisqs.append(c*mx/mx_ref)
+            if ((l == 4000) and (m ==4)):
+                fig,ax = plt.subplots(ncols=2,figsize=(10,5))
+                ax[0].plot(val_o.real)
+                ax[0].plot(val_n.real)
+                ax[1].plot(val_o.imag)
+                ax[1].plot(val_n.imag)
+                plt.show()
+    sph_csq = np.max(chisqs)
+
+    val_o = ga_o.vals[:,0]
+    val_n = ga_n.vals[:,0]
+    ga_csq = chisq(val_o,val_n)
+
+    #print('sph modes: ', sph_csq)
+    #print('G_Avgs: ', ga_csq) 
+    if ( (ga_csq > tols[i-1]) or (sph_csq > tols[i-1]) ):
+        print('Checkpoint Test Error:  Time series do not agree.')
+        exit(1)
+print('Checkpoint Test Passed')
+exit(0)
diff --git a/tests/checkpoint/old_format/main_input b/tests/checkpoint/old_format/main_input
new file mode 100644
index 000000000..66f3d4c8d
--- /dev/null
+++ b/tests/checkpoint/old_format/main_input
@@ -0,0 +1,77 @@
+&problemsize_namelist
+ n_r=48
+ n_theta = 64
+ nprow = 2
+ npcol = 2
+ aspect_ratio = 0.35d0
+ shell_depth = 1.0d0
+/
+&numerical_controls_namelist
+/
+&physical_controls_namelist
+! benchmark_mode = 1
+! benchmark_integration_interval = 100
+! benchmark_report_interval = 5000
+ rotation  = .True.
+ magnetism = .false.
+ viscous_heating = .false.
+ ohmic_heating = .false.
+ advect_reference_state = .false.
+/
+&temporal_controls_namelist
+ max_time_step = 1.0d-4
+ max_iterations = 200
+ checkpoint_interval = 25
+ cflmin = 0.4d0
+ cflmax = 0.6d0
+/
+&io_controls_namelist
+/
+&output_namelist
+
+! New equatorial slices output
+
+sph_mode_ell = 2,4,8, 32
+sph_mode_levels = 1  ! outer boundary
+sph_mode_values = 507 ! radial entropy gradient
+sph_mode_frequency = 10
+sph_mode_nrec = 5
+
+globalavg_values = 401  ! kinetic energy
+globalavg_frequency = 10
+globalavg_nrec = 5
+
+
+full3d_values = 64 ! temperature
+full3d_frequency = 9000000
+/
+
+&Boundary_Conditions_Namelist
+no_slip_boundaries = .true.
+strict_L_Conservation = .false.
+dtdr_bottom = 0.0d0
+T_Top    = 0.0d0
+T_Bottom = 1.0d0
+fix_tvar_top = .true.
+fix_tvar_bottom = .true.
+/
+&Initial_Conditions_Namelist
+init_type=7    ! Benchmark init
+temp_amp = 1.0d-3
+temp_w = 0.01d4
+restart_iter=-1
+conductive_profile=.true.
+/
+&Test_Namelist
+/
+&Reference_Namelist
+Ekman_Number = 1.0d-3
+Rayleigh_Number = 1.0d5
+Prandtl_Number = 1.0d0
+Magnetic_Prandtl_Number = 5.0d0
+reference_type = 1
+heating_type = 0      ! No heating
+gravity_power = 1.0d0  ! g ~ radius
+/
+&Transport_Namelist
+/
diff --git a/tests/checkpoint/run_test.sh b/tests/checkpoint/run_test.sh
new file mode 100644
index 000000000..5fe61e994
--- /dev/null
+++ b/tests/checkpoint/run_test.sh
@@ -0,0 +1,92 @@
+#!/usr/bin/env bash
+
+export RA_ROOT=../../..
+export rayleigh_v13=$RA_ROOT/Rayleigh_1.3/bin/rayleigh.dbg
+export rayleigh_dbg=.$RA_ROOT/bin/rayleigh.dbg
+
+#cd tests/checkpoint
+cp $RA_ROOT/post_processing/rayleigh_diagnostics.py .
+# Generate a checkpoint in the old format using Rayleigh v1.3
+cd old_format
+mpirun -np 4 $rayleigh_v13 -niter 100
+cd ..
+
+# Restart from the old checkpoint format at increased resolution using Rayleigh 1.3.
+lastdir=old_format
+newdir=old_format_up
+
+mkdir $newdir
+mkdir $newdir/Checkpoints
+cp $lastdir/main_input $newdir/.
+cp -r $lastdir/Checkpoints/00000050 $newdir/Checkpoints/.
+
+cd $newdir
+sed -i 's/n_r=48/n_r=64/g' main_input
+sed -i 's/init_type=7/init_type=-1/g' main_input
+sed -i 's/restart_iter=-1/restart_iter=50/g' main_input
+mpirun -np 4 $rayleigh_v13 -niter 100
+cd ..
+
+
+# Restart from the old checkpoint format at same resolution using current Rayleigh.
+lastdir=old_format
+newdir=new_format
+
+mkdir $newdir
+mkdir $newdir/Checkpoints
+cp $lastdir/main_input $newdir/.
+cp -r $lastdir/Checkpoints/00000050 $newdir/Checkpoints/.
+
+cd $newdir
+#sed -i 's/n_r=48/n_r=64/g' main_input
+sed -i 's/init_type=7/init_type=-1/g' main_input
+sed -i 's/restart_iter=-1/restart_iter=50/g' main_input
+mpirun -np 4 $rayleigh_dbg -niter 100
+cd ..
+
+
+# Restart from the new checkpoint format at same resolution.
+lastdir=new_format
+newdir=new_format_same_res
+mkdir $newdir
+mkdir $newdir/Checkpoints
+cp $lastdir/main_input $newdir/.
+cp -r $lastdir/Checkpoints/00000100 $newdir/Checkpoints/.
+
+cd $newdir
+#sed -i 's/n_r=48/n_r=64/g' main_input
+#sed -i 's/init_type=1/init_type=-1/g' main_input
+sed -i 's/restart_iter=50/restart_iter=100/g' main_input
+mpirun -np 4 $rayleigh_dbg -niter 100
+cd ..
+
+# Restart from the new checkpoint format at increased resolution.
+lastdir=new_format_same_res
+newdir=new_format_up_res
+mkdir $newdir
+mkdir $newdir/Checkpoints
+cp $lastdir/main_input $newdir/.
+cp -r $lastdir/Checkpoints/00000150 $newdir/Checkpoints/.
+
+cd $newdir
+sed -i 's/n_r=48/n_r=64/g' main_input
+#sed -i 's/init_type=1/init_type=-1/g' main_input
+sed -i 's/restart_iter=100/restart_iter=150/g' main_input
+mpirun -np 4 $rayleigh_dbg -niter 100
+cd ..
+
+# Restart from the new checkpoint format and degrade resolution.
+lastdir=new_format_up_res
+newdir=new_format_down_res
+mkdir $newdir
+mkdir $newdir/Checkpoints
+cp $lastdir/main_input $newdir/.
+cp -r $lastdir/Checkpoints/00000200 $newdir/Checkpoints/.
+
+cd $newdir
+sed -i 's/n_r=64/n_r=48/g' main_input
+#sed -i 's/init_type=1/init_type=-1/g' main_input
+sed -i 's/restart_iter=150/restart_iter=200/g' main_input
+mpirun -np 4 $rayleigh_dbg -niter 100
+cd ..
+

From 77cd43cfd976bb7999b0dd7788ee10ffec112ddb Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 13:59:45 -0600
Subject: [PATCH 19/28] Added git clone command for building Rayleigh v 1.3.0

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 60699ac2a..0229345e7 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -55,7 +55,7 @@ jobs:
     - name: Build Rayleigh v 1.3
       # Build 1.3 for testing checkpoint compatibility
       run: |
-      
+        git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
         mv Rayleigh Rayleigh_1.3
         cd Rayleigh_1.3
         ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'

From 8df718b8020e2b01b6801fdf1e40e6e81869dfce Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 14:08:00 -0600
Subject: [PATCH 20/28] Fixed path to Rayleigh in run_test.sh Now also calls
 compare_check.py

---
 tests/checkpoint/run_test.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/checkpoint/run_test.sh b/tests/checkpoint/run_test.sh
index 5fe61e994..2a75bf021 100644
--- a/tests/checkpoint/run_test.sh
+++ b/tests/checkpoint/run_test.sh
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-export RA_ROOT=../../..
+export RA_ROOT=../..
 export rayleigh_v13=$RA_ROOT/Rayleigh_1.3/bin/rayleigh.dbg
-export rayleigh_dbg=.$RA_ROOT/bin/rayleigh.dbg
+export rayleigh_dbg=$RA_ROOT/bin/rayleigh.dbg
 
 #cd tests/checkpoint
 cp $RA_ROOT/post_processing/rayleigh_diagnostics.py .
@@ -90,3 +90,4 @@ sed -i 's/restart_iter=150/restart_iter=200/g' main_input
 mpirun -np 4 $rayleigh_dbg -niter 100
 cd ..
 
+python3 compare_check.py

From d90bfab21de5754da57b6d2e9567106dc64e9e21 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 14:14:50 -0600
Subject: [PATCH 21/28] Updated RA_ROOT path

---
 tests/checkpoint/run_test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/checkpoint/run_test.sh b/tests/checkpoint/run_test.sh
index 2a75bf021..f0c6a5fc0 100644
--- a/tests/checkpoint/run_test.sh
+++ b/tests/checkpoint/run_test.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-export RA_ROOT=../..
+export RA_ROOT=../../..
 export rayleigh_v13=$RA_ROOT/Rayleigh_1.3/bin/rayleigh.dbg
 export rayleigh_dbg=$RA_ROOT/bin/rayleigh.dbg
 

From 5d8a039acd62578052374e1b813340df5cf093ad Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 14:23:26 -0600
Subject: [PATCH 22/28] Fixed path to rayleigh_diagnostics.py

---
 tests/checkpoint/run_test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/checkpoint/run_test.sh b/tests/checkpoint/run_test.sh
index f0c6a5fc0..8626bbde5 100644
--- a/tests/checkpoint/run_test.sh
+++ b/tests/checkpoint/run_test.sh
@@ -5,7 +5,7 @@ export rayleigh_v13=$RA_ROOT/Rayleigh_1.3/bin/rayleigh.dbg
 export rayleigh_dbg=$RA_ROOT/bin/rayleigh.dbg
 
 #cd tests/checkpoint
-cp $RA_ROOT/post_processing/rayleigh_diagnostics.py .
+cp ../../post_processing/rayleigh_diagnostics.py .
 # Generate a checkpoint in the old format using Rayleigh v1.3
 cd old_format
 mpirun -np 4 $rayleigh_v13 -niter 100

From bbccb3552fb9e88bf1bab969d3aae7a45ecac772 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 14:32:31 -0600
Subject: [PATCH 23/28] Updated checkpoint test label. Rayleigh 1.3 now
 compiles with -devel flag.

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0229345e7..ff2ede17c 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -58,14 +58,14 @@ jobs:
         git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
         mv Rayleigh Rayleigh_1.3
         cd Rayleigh_1.3
-        ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
+        ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall' -devel
 
         make fdeps && git diff --exit-code
         make -j
         make install
     - name: Checkpoint Test
       run: |  
-        # coupled bc test
+        # Checkpoint Test
         cd "$GITHUB_WORKSPACE"
         cd ./tests/checkpoint
         sh ./run_test.sh        

From 5ec68ef8ad24b07724fd68618965b0a93e18da34 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 14:37:05 -0600
Subject: [PATCH 24/28] Removed devel flag.  Hacked g_csq to force failure.

---
 tests/checkpoint/compare_check.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/checkpoint/compare_check.py b/tests/checkpoint/compare_check.py
index ec83b6832..f3886a080 100644
--- a/tests/checkpoint/compare_check.py
+++ b/tests/checkpoint/compare_check.py
@@ -50,7 +50,8 @@ def chisq(a1,a2):
     ga_csq = chisq(val_o,val_n)
 
     #print('sph modes: ', sph_csq)
-    #print('G_Avgs: ', ga_csq) 
+    #print('G_Avgs: ', ga_csq)
+    ga_csq = 44 
     if ( (ga_csq > tols[i-1]) or (sph_csq > tols[i-1]) ):
         print('Checkpoint Test Error:  Time series do not agree.')
         exit(1)

From 3e4e30a66d871cffdf1ddd2771399db7d72696cc Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 14:44:51 -0600
Subject: [PATCH 25/28] Removing make fdeps from v1.3 build

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index ff2ede17c..7920c01f8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -58,9 +58,9 @@ jobs:
         git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
         mv Rayleigh Rayleigh_1.3
         cd Rayleigh_1.3
-        ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall' -devel
+        ./configure -debian-mkl ${{ matrix.mpi }} --FFLAGS_DBG='-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow -fbacktrace -ffixed-line-length-132 -Wall'
 
-        make fdeps && git diff --exit-code
+        #make fdeps && git diff --exit-code
         make -j
         make install
     - name: Checkpoint Test

From b03239a69b3f9a23d00d67ac712b6fc14eb13601 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Fri, 24 Jul 2026 14:50:54 -0600
Subject: [PATCH 26/28] Removed g_csq hack.  Added label in main.yml

---
 .github/workflows/main.yml        | 1 +
 tests/checkpoint/compare_check.py | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7920c01f8..12f96ce14 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -55,6 +55,7 @@ jobs:
     - name: Build Rayleigh v 1.3
       # Build 1.3 for testing checkpoint compatibility
       run: |
+        # Build Rayleigh v 1.3
         git clone -b rayleigh-1.3.0 https://github.com/geodynamics/Rayleigh.git
         mv Rayleigh Rayleigh_1.3
         cd Rayleigh_1.3
diff --git a/tests/checkpoint/compare_check.py b/tests/checkpoint/compare_check.py
index f3886a080..a9d995aee 100644
--- a/tests/checkpoint/compare_check.py
+++ b/tests/checkpoint/compare_check.py
@@ -51,7 +51,6 @@ def chisq(a1,a2):
 
     #print('sph modes: ', sph_csq)
     #print('G_Avgs: ', ga_csq)
-    ga_csq = 44 
     if ( (ga_csq > tols[i-1]) or (sph_csq > tols[i-1]) ):
         print('Checkpoint Test Error:  Time series do not agree.')
         exit(1)

From 38791f639bf721085729c3838a627e819ac477f3 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Tue, 11 Aug 2026 11:58:50 -0600
Subject: [PATCH 27/28] Added logic to prevent intererence of new checkpoint
 format  with finite-difference mode

---
 src/Physics/Checkpointing.F90 | 36 +++++++++++++++++++++--------------
 1 file changed, 22 insertions(+), 14 deletions(-)

diff --git a/src/Physics/Checkpointing.F90 b/src/Physics/Checkpointing.F90
index 1fdbbef12..2c8e71d4d 100755
--- a/src/Physics/Checkpointing.F90
+++ b/src/Physics/Checkpointing.F90
@@ -174,14 +174,18 @@ Subroutine Write_Checkpoint(abterms,iteration,dt,new_dt,elapsed_time, input_file
         !Copy the RHS (contains state variables at current timestep) into chtkmp
         Call Get_All_RHS(chktmp%p1a) 
 
-        ! Next, convert the AB terms into chebyshev space and copy them into the buffer
-        Call abterms_cheby%construct('p1a')
-        abterms_cheby%config='p1a'
-        !chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms(:,:,:,1:numfields) ! earlier version -- physical space storage
-        Call gridcp%to_spectral(abterms,abterms_cheby%p1a)
-        chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms_cheby%p1a(:,:,:,1:numfields)
-        Call abterms_cheby%deconstruct('p1a')
 
+        If ( (chebyshev) .and. (ndomains .eq. 1) ) Then
+            ! Convert the AB terms into chebyshev space and copy them into the buffer
+            ! For now, if ndomains > 1, we do not perform this conversion
+            Call abterms_cheby%construct('p1a')
+            abterms_cheby%config='p1a'
+            !chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms(:,:,:,1:numfields) ! earlier version -- physical space storage
+            Call gridcp%to_spectral(abterms,abterms_cheby%p1a)
+            chktmp%p1a(:,:,:,numfields+1:numfields*2) = abterms_cheby%p1a(:,:,:,1:numfields)
+            Call abterms_cheby%deconstruct('p1a')
+        Endif
+        
         !Move checkpoint buffer from p1a to s2a (rlm space)
         Call chktmp%reform()
 
@@ -620,7 +624,8 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
 
         Endif
 
-        If (version .ge. 3) Then
+
+        If ( (version .ge. 3) .and. chebyshev ) Then
             ! For version 3+, the AB terms are stored in Chebyshev space
             Call abterms_cheby%construct('p1b')
             abterms_cheby%config='p1b'
@@ -633,15 +638,18 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
         If (ndomains .eq. 1) Then
             ! Regardless of the checkpoint version or resolution, we can load the state vector
             ! fields directly from the checkpoint buffer because that portion of the buffer is
-            ! already in the expected Chebyshev format.  
+            ! already in the expected format.  
             ub = Min(n_r,n_r_old)
             fields = 0d0
             fields(1:ub,:,:,1:numfields) = chktmp%p1b(1:ub,:,:,1:numfields)
 
-            ! For checkpoint version 3 and later, the AB terms are also stored in
-            ! Chebyshev space, but they need to be in grid space.
-            ! Even if the resolution changes, no further work needs to be done.
-            If (version .ge. 3) Then
+            If (.not. chebyshev) Then
+                abterms(:,:,:,1:numfields) = chktmp%p1b(:,:,:,numfields+1:numfields*2)
+
+            Else If (version .ge. 3) Then
+                ! For checkpoint version 3 and later, the AB terms are also stored in
+                ! Chebyshev space, but they need to be in grid space.
+                ! Even if the resolution changes, no further work needs to be done.
                 !Need to convert from Chebyshev space to physical space
                 Call gridcp%From_Spectral(abterms_cheby%p1b,abterms)
                 Call abterms_cheby%deconstruct('p1b')
@@ -740,7 +748,7 @@ Subroutine Read_Checkpoint(fields, abterms,iteration,read_pars)
             Endif
 
         Else ! ndomains > 1: we need to loop over domains and (maybe) interpolate
-
+            ! Note that ndomains > 1 is not possible when running in finite-difference mode.
             ! Loop over the domains to set the Chebyshev coefficients, 
             ! possibly interpolating in radius for each subdomain
             ! The fields are easy, since they are stored in spectral (Chebyshev) space

From ccb120f52f350c603847f429e44e679d367e53f3 Mon Sep 17 00:00:00 2001
From: Nick Featherstone <feathern@gmail.com>
Date: Tue, 11 Aug 2026 12:34:16 -0600
Subject: [PATCH 28/28] Changed init_type to 1 and ell values = 0,4

---
 tests/checkpoint/old_format/main_input | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/checkpoint/old_format/main_input b/tests/checkpoint/old_format/main_input
index 66f3d4c8d..3065b2ee6 100644
--- a/tests/checkpoint/old_format/main_input
+++ b/tests/checkpoint/old_format/main_input
@@ -31,7 +31,7 @@
 
 ! New equatorial slices output
 
-sph_mode_ell = 2,4,8, 32
+sph_mode_ell = 0,4
 sph_mode_levels = 1  ! outer boundary
 sph_mode_values = 507 ! radial entropy gradient
 sph_mode_frequency = 10
@@ -56,7 +56,7 @@ fix_tvar_top = .true.
 fix_tvar_bottom = .true.
 /
 &Initial_Conditions_Namelist
-init_type=7    ! Benchmark init
+init_type=1    ! Benchmark init
 temp_amp = 1.0d-3
 temp_w = 0.01d4
 restart_iter=-1