From a109eceae87e403f3dfe860f2f5ea0ea51bcfb25 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 14:48:54 +0100
Subject: [PATCH 01/28] remove depreciated parameters

---
 runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
index e28b4b068..9f38106fa 100644
--- a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
+++ b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
@@ -10,7 +10,6 @@ force_Er_zero_at_wall = false #true
 Er_constant = 0.0
 T_e = 1.0
 T_wall = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -75,7 +74,6 @@ nstep = 2000
 dt = 0.0005
 nwrite = 200
 nwrite_dfns = 200
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]

From f2332992ff1fca3bbfc61ef8a6248d1e43c62af5 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 15:10:44 +0100
Subject: [PATCH 02/28] Restore krook inputs to MMS input file.

---
 ...D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml
index f45c8828d..1abe96001 100644
--- a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml
+++ b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml
@@ -10,7 +10,6 @@ force_Er_zero_at_wall = false #true
 Er_constant = 0.0
 T_e = 1.0
 T_wall = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -31,8 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-krook_collisions_option = "reference_parameters"
-nuii_krook = 1.0
 z_ngrid = 17
 z_nelement = 16
 z_nelement_local = 16
@@ -71,12 +68,16 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[krook_collisions]
+use_krook = true
+nuii0 = 1.0
+frequency_option = "manual"
+
 [timestepping]
 nstep = 2000
 dt = 0.0005
 nwrite = 200
 nwrite_dfns = 200
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]

From 1b90b49d78cc3dadb55884c44463ece8910d45d1 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 15:11:43 +0100
Subject: [PATCH 03/28] Restore numerical dissipation to MMS test input.

---
 runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
index 9f38106fa..8bf508ee1 100644
--- a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
+++ b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
@@ -86,6 +86,6 @@ split_operators = false
  alpha_switch=1.0
  type="default"
 [ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.1
+vpa_dissipation_coefficient = 0.01
 #z_dissipation_coefficient = 0.1
-r_dissipation_coefficient = 0.0
+#r_dissipation_coefficient = 0.0

From 42d648af9e829bab3ae0e8d424a17c5db189c325 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 15:12:00 +0100
Subject: [PATCH 04/28] Update README with MMS test instructions.

---
 README.md | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/README.md b/README.md
index a0e33b7cf..579793572 100644
--- a/README.md
+++ b/README.md
@@ -393,3 +393,53 @@ so, it skips many cases. To run more comprehensive tests, you can activate the
 To get more output on what tests were successful, an option `--verbose` (or
 `-v`) can be passed in a similar way to `--long` (if any tests fail, the output
 is printed by default).
+
+## Manufactured Solutions Tests
+In addition to the test suite in the `test/` subdirectory, the `moment_kinetics` project
+utilises the method of manufactured solutions to test more complicated models in 1D1V, 
+and 2D2V or 2D3V (for neutral particles). To run these tests we run a normal `moment_kinetics`
+simulation, making use of the manufacted solutions test TOML options. We describe how to use 
+the existing tests below. To set up `moment_kinetics` to use the manufactured solutions features,
+ take the following steps:
+* Install `moment_kinetics` using the instructions above, 
+  using the `plots_post_processing` project and make sure that the `Symbolics` package is installed.
+    ```
+    $ julia -O3 --project
+    julia> ]
+    develop ./moment_kinetics
+    develop ./plots_post_processing/plots_post_processing
+    add Symbolics
+    ```
+    if you will run the tests with MPI, make sure that MPI is also installed at this step.
+* Select an input file representing the desired test. For example, we can pick from the list below.
+* Run the input file using the usual command.
+    ```
+    julia> using moment_kinetics
+    julia> run_moment_kinetics("runs/your_MMS_test_input.toml")
+    ```
+* Use the post processing module to test the error norms for the simulation of interest.
+    ```
+    julia> using plots_post_processing
+    julia> analyze_and_plot_data("runs/your_MMS_test_input")
+    ```
+  This will print out a series of numbers to the terminal which represent the error norms
+  for each field and distribution function compared to the exact analytical solution, at 
+  each time step in the simulation. This error data can be computed for different resolutions.
+
+* Finally, to partially automate this last step when a resolution scan is performed, we provide
+  functions for generating plots of the error data versus resolutions in the file `plot_MMS_sequence.jl`
+  in the `plots_post_processing` project. This can be accessed by using the `run_MMS_test.jl` 
+  script from the command line
+  ```
+  $ julia -O3 --project run_MMS_test.kl
+  ```
+  or by using the underlying functions in the REPL
+  ```
+  import plots_post_processing
+  using plots_post_processing.plot_MMS_sequence
+  run_mms_test()
+  ```
+  Note that currently the lists of files used as input for the plotting functions
+  are hardcoded for the purposes of self-documenting the tests -- these lists could be made
+  input parameters to improve these scripts.
+    

From cf89991c8a07d3063d0ab97cb14d850121e53ed8 Mon Sep 17 00:00:00 2001
From: mrhardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 16:11:53 +0100
Subject: [PATCH 05/28] Update README.md to link to other sections regarding
 setup.

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 579793572..60f5ff93b 100644
--- a/README.md
+++ b/README.md
@@ -401,8 +401,9 @@ and 2D2V or 2D3V (for neutral particles). To run these tests we run a normal `mo
 simulation, making use of the manufacted solutions test TOML options. We describe how to use 
 the existing tests below. To set up `moment_kinetics` to use the manufactured solutions features,
  take the following steps:
-* Install `moment_kinetics` using the instructions above, 
-  using the `plots_post_processing` project and make sure that the `Symbolics` package is installed.
+* Install `moment_kinetics` using the setup instructions above ([Setup](https://github.com/mabarnes/moment_kinetics/tree/mms_bugfixes_and_docs#setup)), 
+  using the `plots_post_processing` project and make sure that the `Symbolics` package is installed, e.g., if following
+  the manual setup instructions ([Manual setup](https://mabarnes.github.io/moment_kinetics/dev/manual_setup/)), these commands would be
     ```
     $ julia -O3 --project
     julia> ]

From 3696e5002172d96e18697c2eece633b743604ba7 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 16:23:50 +0100
Subject: [PATCH 06/28] Initial version of manufactured solutions input
 documentation.

---
 .../manufactured_solution_test_examples.md    | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 docs/src/manufactured_solution_test_examples.md

diff --git a/docs/src/manufactured_solution_test_examples.md b/docs/src/manufactured_solution_test_examples.md
new file mode 100644
index 000000000..f6c681d1a
--- /dev/null
+++ b/docs/src/manufactured_solution_test_examples.md
@@ -0,0 +1,20 @@
+# List of Manufactured Solutions Test TOML inputs
+
+Here we list the existing manufactured solution test inputs.
+
+# 1D1V tests
+
+There are 1D1V tests which complement the check-in testing suite.
+The example input files in this category are as follows:
+
+* 1D1V simulation of kinetic ions (no neutrals) and numerical
+  velocity dissipation.
+```
+runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
+```
+* 1D1V simulation of kinetic ions (no neutrals) and a krook
+  collision operator.
+```
+runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml
+```
+

From 02f26a03c2362ff13b21cae99ad91cd977c9e1b9 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 16:27:30 +0100
Subject: [PATCH 07/28] Link to list of MMS TOML inputs.

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 60f5ff93b..4f0b3fcb8 100644
--- a/README.md
+++ b/README.md
@@ -412,7 +412,8 @@ the existing tests below. To set up `moment_kinetics` to use the manufactured so
     add Symbolics
     ```
     if you will run the tests with MPI, make sure that MPI is also installed at this step.
-* Select an input file representing the desired test. For example, we can pick from the list below.
+* Select an input file representing the desired test. For example, we can pick from the list 
+  [MMS input TOML list](https://mabarnes.github.io/moment_kinetics/dev/manufactured_solution_test_examples/).
 * Run the input file using the usual command.
     ```
     julia> using moment_kinetics

From 81dbaaea4cda3b8865bd847c19314e276577120c Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 16:30:03 +0100
Subject: [PATCH 08/28] Add link in index.md

---
 docs/src/index.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/src/index.md b/docs/src/index.md
index 59b8c7e04..39410aaaf 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -18,6 +18,7 @@ Pages = ["getting_started.md",
          "manual_setup.md",
          "machine_setup_notes.md",
          "parameter_scans.md",
+         "manufactured_solution_test_examples.md",
         ]
 ```
 

From 326bef20a85eb41d5d3e0d47b8f4020b80253afa Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 17:01:18 +0100
Subject: [PATCH 09/28] Add magnetic mirror MMS TOML to documentation list.

---
 .../manufactured_solution_test_examples.md    | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/docs/src/manufactured_solution_test_examples.md b/docs/src/manufactured_solution_test_examples.md
index f6c681d1a..9ebe6340a 100644
--- a/docs/src/manufactured_solution_test_examples.md
+++ b/docs/src/manufactured_solution_test_examples.md
@@ -18,3 +18,40 @@ runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_diss.toml
 runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_16_vperp_1_krook.toml
 ```
 
+# 1D2V tests
+
+* 1D2V simulation of kinetic ions (no neutrals) and a krook
+  collision operator.
+```
+runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml
+```
+* 1D2V simulation of a open field lines in 1D magnetic mirror
+  (no neutrals)
+```
+runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml
+runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml
+runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
+runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
+```
+
+# 2D1V tests
+
+These tests are used to test the spatial advection in simple cases
+with wall boundary conditions.
+
+* 2D1V test of wall boundary conditions and the E x B drift.
+
+# 2D2V tests
+
+These tests are used to test the spatial advection in cases
+with wall boundary conditions or geometrical features where
+two velocity dimensions are necessary.
+
+* 2D2V simulation of a open field lines in 1D magnetic mirror
+  (no neutrals)
+```
+runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml
+runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml
+runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_16_vperp_16_diss.toml
+```
+

From cf8e05215dfb539c7e17cac8395c21558ce3b8a5 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 17:02:13 +0100
Subject: [PATCH 10/28] Update 1D2V Krook operator MMMS test TOML

---
 .../1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml
index 9ec02fede..d9ddc1aeb 100644
--- a/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml
+++ b/runs/1D-wall_MMS_new_nel_r_1_z_16_vpa_8_vperp_8_krook.toml
@@ -10,7 +10,6 @@ force_Er_zero_at_wall = false #true
 Er_constant = 0.0
 T_e = 1.0
 T_wall = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -71,12 +70,16 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[krook_collisions]
+use_krook = true
+nuii0 = 1.0
+frequency_option = "manual"
+
 [timestepping]
 nstep = 2000
 dt = 0.0005
 nwrite = 200
 nwrite_dfns = 200
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]
@@ -88,6 +91,7 @@ split_operators = false
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
+
 [ion_numerical_dissipation]
 vpa_dissipation_coefficient = -1.0
 z_dissipation_coefficient = -1.0

From 6dcedb620ea1e65e1baf55b480457c350d4e3ca9 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Tue, 21 May 2024 17:03:17 +0100
Subject: [PATCH 11/28] Update mirror MMS test input TOML.

---
 ...S_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml | 14 +++++++-------
 ..._ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml | 14 +++++++-------
 ...MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml | 14 +++++++-------
 ..._ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml | 14 +++++++-------
 ...MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml | 14 +++++++-------
 ..._ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml | 14 +++++++-------
 ...ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml | 14 +++++++-------
 ...MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml | 14 +++++++-------
 8 files changed, 56 insertions(+), 56 deletions(-)

diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
index cb8ce6cf2..883a73275 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
@@ -30,13 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 9
 z_nelement = 16
 z_nelement_local = 16
@@ -78,6 +71,13 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[timestepping]
+nstep = 2000
+dt = 0.0005
+nwrite = 200
+nwrite_dfns = 200
+split_operators = false
+
 [manufactured_solns]
  use_for_advance=true
  use_for_init=true
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
index 6d9c31403..50e878cb3 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
@@ -30,13 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 9
 z_nelement = 32
 z_nelement_local = 32
@@ -78,6 +71,13 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[timestepping]
+nstep = 2000
+dt = 0.0005
+nwrite = 200
+nwrite_dfns = 200
+split_operators = false
+
 [manufactured_solns]
  use_for_advance=true
  use_for_init=true
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml
index c0ec6f8f5..1624ca129 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_4_vpa_4_vperp_2_diss.toml
@@ -30,13 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 9
 z_nelement = 4
 z_nelement_local = 4
@@ -78,6 +71,13 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[timestepping]
+nstep = 2000
+dt = 0.0005
+nwrite = 200
+nwrite_dfns = 200
+split_operators = false
+
 [manufactured_solns]
  use_for_advance=true
  use_for_init=true
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml
index dff2bf452..74e3af388 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_64_vpa_64_vperp_32_diss.toml
@@ -30,13 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 9
 z_nelement = 64
 z_nelement_local = 64
@@ -78,6 +71,13 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[timestepping]
+nstep = 2000
+dt = 0.0005
+nwrite = 200
+nwrite_dfns = 200
+split_operators = false
+
 [manufactured_solns]
  use_for_advance=true
  use_for_init=true
diff --git a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml
index a5be20d0d..f4d4956ab 100644
--- a/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml
+++ b/runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_8_vpa_8_vperp_4_diss.toml
@@ -30,13 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 9
 z_nelement = 8
 z_nelement_local = 8
@@ -78,6 +71,13 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[timestepping]
+nstep = 2000
+dt = 0.0005
+nwrite = 200
+nwrite_dfns = 200
+split_operators = false
+
 [manufactured_solns]
  use_for_advance=true
  use_for_init=true
diff --git a/runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml b/runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml
index cf3eb5d19..a4a31ccbb 100644
--- a/runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml
+++ b/runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml
@@ -30,13 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 5
 z_nelement = 16
 z_nelement_local = 16
@@ -78,6 +71,13 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[timestepping]
+nstep = 2000
+dt = 0.0005
+nwrite = 200
+nwrite_dfns = 200
+split_operators = false
+
 [manufactured_solns]
  use_for_advance=true
  use_for_init=true
diff --git a/runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml b/runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml
index 5bd48c14b..01dd1b487 100644
--- a/runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml
+++ b/runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_32_vperp_16_diss.toml
@@ -30,13 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 5
 z_nelement = 32
 z_nelement_local = 32
@@ -78,6 +71,13 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[timestepping]
+nstep = 2000
+dt = 0.0005
+nwrite = 200
+nwrite_dfns = 200
+split_operators = false
+
 [manufactured_solns]
  use_for_advance=true
  use_for_init=true
diff --git a/runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml b/runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml
index d011761cb..f19b91e39 100644
--- a/runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml
+++ b/runs/2D-mirror_MMS_ngrid_5_nel_r_8_z_8_vpa_8_vperp_4_diss.toml
@@ -30,13 +30,6 @@ z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-use_semi_lagrange = false
-n_rk_stages = 4
-split_operators = false
 z_ngrid = 5
 z_nelement = 8
 z_nelement_local = 8
@@ -78,6 +71,13 @@ vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
+[timestepping]
+nstep = 2000
+dt = 0.0005
+nwrite = 200
+nwrite_dfns = 200
+split_operators = false
+
 [manufactured_solns]
  use_for_advance=true
  use_for_init=true

From 80e7f63bcd78c3b21dd7132e05ed46b3e3002651 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 10:30:13 +0100
Subject: [PATCH 12/28] Remove duplicate MMS input TOML for wall boundary case
 that should only differ by retained example by resolution parameters, and can
 thus be easily regenerated.

---
 ...l_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml | 89 -------------------
 ...MS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml | 89 -------------------
 ...l_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml | 89 -------------------
 ...l_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml | 89 -------------------
 4 files changed, 356 deletions(-)
 delete mode 100644 runs/2D-wall_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml
 delete mode 100644 runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml
 delete mode 100644 runs/2D-wall_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml
 delete mode 100644 runs/2D-wall_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml

diff --git a/runs/2D-wall_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml
deleted file mode 100644
index ee1765bf4..000000000
--- a/runs/2D-wall_MMS_nel_r_2_z_2_vpa_16_vperp_1_diss.toml
+++ /dev/null
@@ -1,89 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-force_Er_zero_at_wall = false #true
-Er_constant = 0.0
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 2
-z_nelement_local = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_nelement_local = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 17
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 1
-vperp_nelement = 1
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 17
-vz_nelement = 4
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 17
-vr_nelement = 4
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 17
-vzeta_nelement = 4
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-n_rk_stages = 4
-split_operators = false
-
-[ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.1
-#z_dissipation_coefficient = 0.1
-r_dissipation_coefficient = 0.01
-
-[manufactured_solns]
-use_for_advance = true
-epsilon_offset = 0.1
-use_vpabar_in_mms_dfni = false
diff --git a/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml b/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml
deleted file mode 100644
index 16c5ca77a..000000000
--- a/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss5.toml
+++ /dev/null
@@ -1,89 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-force_Er_zero_at_wall = false #true
-Er_constant = 0.0
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 32
-z_nelement_local = 32
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 32
-r_nelement_local = 32
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 17
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 1
-vperp_nelement = 1
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 17
-vz_nelement = 4
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 17
-vr_nelement = 4
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 17
-vzeta_nelement = 4
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-n_rk_stages = 4
-split_operators = false
-
-[ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.1
-#z_dissipation_coefficient = 0.1
-r_dissipation_coefficient = 0.01
-
-[manufactured_solns]
-use_for_advance = true
-epsilon_offset = 0.1
-use_vpabar_in_mms_dfni = false
diff --git a/runs/2D-wall_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml
deleted file mode 100644
index 2211ef9a6..000000000
--- a/runs/2D-wall_MMS_nel_r_4_z_4_vpa_16_vperp_1_diss.toml
+++ /dev/null
@@ -1,89 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-force_Er_zero_at_wall = false #true
-Er_constant = 0.0
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 4
-z_nelement_local = 4
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 4
-r_nelement_local = 4
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 17
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 1
-vperp_nelement = 1
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 17
-vz_nelement = 4
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 17
-vr_nelement = 4
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 17
-vzeta_nelement = 4
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-n_rk_stages = 4
-split_operators = false
-
-[ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.1
-#z_dissipation_coefficient = 0.1
-r_dissipation_coefficient = 0.01
-
-[manufactured_solns]
-use_for_advance = true
-epsilon_offset = 0.1
-use_vpabar_in_mms_dfni = false
diff --git a/runs/2D-wall_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml
deleted file mode 100644
index 095f8d86e..000000000
--- a/runs/2D-wall_MMS_nel_r_8_z_8_vpa_16_vperp_1_diss.toml
+++ /dev/null
@@ -1,89 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-force_Er_zero_at_wall = false #true
-Er_constant = 0.0
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 8
-z_nelement_local = 8
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 8
-r_nelement_local = 8
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 17
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 1
-vperp_nelement = 1
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 17
-vz_nelement = 4
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 17
-vr_nelement = 4
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 17
-vzeta_nelement = 4
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-n_rk_stages = 4
-split_operators = false
-
-[ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.1
-#z_dissipation_coefficient = 0.1
-r_dissipation_coefficient = 0.01
-
-[manufactured_solns]
-use_for_advance = true
-epsilon_offset = 0.1
-use_vpabar_in_mms_dfni = false

From 783524aed8d87f7ab5c32ad580ef1c333526f778 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 10:30:57 +0100
Subject: [PATCH 13/28] Remove outdated Fokker-Planck input file -- the latest
 example is now hosted in the examples/ directory.

---
 ...3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml | 97 -------------------
 1 file changed, 97 deletions(-)
 delete mode 100644 runs/2V-evolve_ngrid_3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml

diff --git a/runs/2V-evolve_ngrid_3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml b/runs/2V-evolve_ngrid_3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml
deleted file mode 100644
index 543739bed..000000000
--- a/runs/2V-evolve_ngrid_3_nel_r_1_z_1_vpa_6_vperp_3_fkpl_test.toml
+++ /dev/null
@@ -1,97 +0,0 @@
-#use_manufactured_solns_for_init = true
-#use_manufactured_solns_for_advance = false
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-#force_Er_zero_at_wall = false #true
-#Er_constant = 0.0
-#epsilon_offset = 0.1
-#use_vpabar_in_mms_dfni = true
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-Bzed = 1.0
-Bmag = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-constant_ionization_rate = false
-nuii = 1.0
-#nuii_krook = 0.0
-#nuii_pitch = 0.0
-z_ngrid = 1
-z_nelement = 1
-z_nelement_local = 1
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 3
-vpa_nelement = 6
-vpa_L = 6.0
-vpa_bc = "zero"
-#vpa_discretization = "chebyshev_pseudospectral"
-vpa_discretization = "gausslegendre_pseudospectral"
-vperp_ngrid = 3
-vperp_nelement = 3
-vperp_L = 3.0
-#vperp_discretization = "finite_difference"
-#vperp_discretization = "chebyshev_pseudospectral"
-vperp_discretization = "gausslegendre_pseudospectral"
-
-#vz_ngrid = 17
-#vz_nelement = 4
-#vz_L = 12.0
-#vz_bc = "periodic"
-#vz_discretization = "chebyshev_pseudospectral"
-
-#vr_ngrid = 17
-#vr_nelement = 4
-#vr_L = 12.0
-#vr_bc = "periodic"
-#vr_discretization = "chebyshev_pseudospectral"
-
-#vzeta_ngrid = 17
-#vzeta_nelement = 4
-#vzeta_L = 12.0
-#vzeta_bc = "periodic"
-#vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 5000
-dt = 1.0e-2
-nwrite = 5000
-nwrite_dfns = 5000
-n_rk_stages = 4
-split_operators = false
-
-#[ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.0
-#vperp_dissipation_coefficient = 0.0
-#z_dissipation_coefficient = 0.1
-#r_dissipation_coefficient = 0.0

From 0fd79c101a699b000fc8224468a3801bba271409 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 10:32:19 +0100
Subject: [PATCH 14/28] Remove another duplicate MMS input TOML for wall
 boundary case.

---
 ...MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml | 89 -------------------
 1 file changed, 89 deletions(-)
 delete mode 100644 runs/2D-wall_MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml

diff --git a/runs/2D-wall_MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml
deleted file mode 100644
index 3fb456895..000000000
--- a/runs/2D-wall_MMS_nel_r_16_z_16_vpa_16_vperp_1_diss.toml
+++ /dev/null
@@ -1,89 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-force_Er_zero_at_wall = false #true
-Er_constant = 0.0
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 16
-z_nelement_local = 16
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 16
-r_nelement_local = 16
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 17
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 1
-vperp_nelement = 1
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 17
-vz_nelement = 4
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 17
-vr_nelement = 4
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 17
-vzeta_nelement = 4
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-nwrite_dfns = 200
-n_rk_stages = 4
-split_operators = false
-
-[ion_numerical_dissipation]
-#vpa_dissipation_coefficient = 0.1
-#z_dissipation_coefficient = 0.1
-r_dissipation_coefficient = 0.01
-
-[manufactured_solns]
-use_for_advance = true
-epsilon_offset = 0.1
-use_vpabar_in_mms_dfni = false

From 3743703d2432a96d9225882a8d4d7768e5589921 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 10:36:29 +0100
Subject: [PATCH 15/28] Remove duplicate outdated 2D2V CX IZ collisions MMS
 test input TOML.

---
 ...cheb_cxiz_nel_r_2_z_2_vpa_16_vperp_16.toml | 78 -------------------
 ...e_cheb_cxiz_nel_r_2_z_2_vpa_2_vperp_2.toml | 78 -------------------
 ...e_cheb_cxiz_nel_r_2_z_2_vpa_8_vperp_8.toml | 78 -------------------
 3 files changed, 234 deletions(-)
 delete mode 100644 runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_16_vperp_16.toml
 delete mode 100644 runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_2_vperp_2.toml
 delete mode 100644 runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_8_vperp_8.toml

diff --git a/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_16_vperp_16.toml b/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_16_vperp_16.toml
deleted file mode 100644
index 8ad2f5183..000000000
--- a/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_16_vperp_16.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 1.0
-ionization_frequency = 1.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 5
-vperp_nelement = 16
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 5
-vz_nelement = 16
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 5
-vr_nelement = 16
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 5
-vzeta_nelement = 16
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 160
-dt = 0.002
-nwrite = 40
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_2_vperp_2.toml b/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_2_vperp_2.toml
deleted file mode 100644
index 6acb712e9..000000000
--- a/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_2_vperp_2.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 1.0
-ionization_frequency = 1.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 2
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 5
-vperp_nelement = 2
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 5
-vz_nelement = 2
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 5
-vr_nelement = 2
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 5
-vzeta_nelement = 2
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 160
-dt = 0.002
-nwrite = 40
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_8_vperp_8.toml b/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_8_vperp_8.toml
deleted file mode 100644
index 950988d48..000000000
--- a/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_8_vperp_8.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 1.0
-ionization_frequency = 1.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 8
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 5
-vperp_nelement = 8
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 5
-vz_nelement = 8
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 5
-vr_nelement = 8
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 5
-vzeta_nelement = 8
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 160
-dt = 0.002
-nwrite = 40
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true

From 301652fe3452151845330979ebb8c50d44071ebb Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 10:38:29 +0100
Subject: [PATCH 16/28] Update documentation to describe wall-bc MMS test and
 update corresponding input file.

---
 docs/src/manufactured_solution_test_examples.md        |  5 +++++
 .../2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml | 10 +++++++---
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/docs/src/manufactured_solution_test_examples.md b/docs/src/manufactured_solution_test_examples.md
index 9ebe6340a..c6b69edbf 100644
--- a/docs/src/manufactured_solution_test_examples.md
+++ b/docs/src/manufactured_solution_test_examples.md
@@ -40,6 +40,11 @@ These tests are used to test the spatial advection in simple cases
 with wall boundary conditions.
 
 * 2D1V test of wall boundary conditions and the E x B drift.
+  Numerical dissipation in the radial domain is imposed to stabilise
+  an instability that otherwise appears at the grid scale.
+```
+runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml
+```
 
 # 2D2V tests
 
diff --git a/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml b/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml
index 38bc4655a..274fc59e6 100644
--- a/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml
+++ b/runs/2D-wall_MMS_nel_r_32_z_32_vpa_16_vperp_1_diss.toml
@@ -10,7 +10,6 @@ force_Er_zero_at_wall = false #true
 Er_constant = 0.0
 T_e = 1.0
 T_wall = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -71,11 +70,10 @@ vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
 
 [timestepping]
-nstep = 2000
+nstep = 2000 
 dt = 0.0005
 nwrite = 200
 nwrite_dfns = 200
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]
@@ -87,7 +85,13 @@ split_operators = false
  use_vpabar_in_mms_dfni=true
  alpha_switch=1.0
  type="default"
+
 [ion_numerical_dissipation]
 #vpa_dissipation_coefficient = 0.1
 #z_dissipation_coefficient = 0.1
 r_dissipation_coefficient = 0.1
+
+[geometry]
+option="constant-helical"
+pitch=0.5
+rhostar = 1.0

From 230e1e5eb62752dfe432626a33a77ca90206780f Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 10:44:18 +0100
Subject: [PATCH 17/28] Remove duplicate sound-wave (periodic bc) test MMS
 input TOML.

---
 ...on_only_nel_r_12_z_12_vpa_12_vperp_12.toml | 78 -------------------
 ...on_only_nel_r_16_z_16_vpa_16_vperp_16.toml | 78 -------------------
 ...eb_ion_only_nel_r_2_z_2_vpa_2_vperp_2.toml | 78 -------------------
 ...eb_ion_only_nel_r_8_z_8_vpa_8_vperp_8.toml | 78 -------------------
 ...wave_cheb_nel_r_2_z_2_vpa_16_vperp_16.toml | 78 -------------------
 ...d-wave_cheb_nel_r_2_z_2_vpa_2_vperp_2.toml | 78 -------------------
 ...d-wave_cheb_nel_r_2_z_2_vpa_8_vperp_8.toml | 78 -------------------
 7 files changed, 546 deletions(-)
 delete mode 100644 runs/2D-sound-wave_cheb_ion_only_nel_r_12_z_12_vpa_12_vperp_12.toml
 delete mode 100644 runs/2D-sound-wave_cheb_ion_only_nel_r_16_z_16_vpa_16_vperp_16.toml
 delete mode 100644 runs/2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_2_vperp_2.toml
 delete mode 100644 runs/2D-sound-wave_cheb_ion_only_nel_r_8_z_8_vpa_8_vperp_8.toml
 delete mode 100644 runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_16_vperp_16.toml
 delete mode 100644 runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_2_vperp_2.toml
 delete mode 100644 runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_8_vperp_8.toml

diff --git a/runs/2D-sound-wave_cheb_ion_only_nel_r_12_z_12_vpa_12_vperp_12.toml b/runs/2D-sound-wave_cheb_ion_only_nel_r_12_z_12_vpa_12_vperp_12.toml
deleted file mode 100644
index 4c71e51fc..000000000
--- a/runs/2D-sound-wave_cheb_ion_only_nel_r_12_z_12_vpa_12_vperp_12.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 12
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 12
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 12
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 9
-vperp_nelement = 12
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 12
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 12
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 12
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 960
-dt = 0.0003333333333333333
-nwrite = 1280
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb_ion_only_nel_r_16_z_16_vpa_16_vperp_16.toml b/runs/2D-sound-wave_cheb_ion_only_nel_r_16_z_16_vpa_16_vperp_16.toml
deleted file mode 100644
index fcc70e11c..000000000
--- a/runs/2D-sound-wave_cheb_ion_only_nel_r_16_z_16_vpa_16_vperp_16.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 16
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 16
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 9
-vperp_nelement = 16
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 16
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 16
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 16
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 1280
-dt = 0.00025
-nwrite = 1280
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_2_vperp_2.toml b/runs/2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_2_vperp_2.toml
deleted file mode 100644
index 86616d7af..000000000
--- a/runs/2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_2_vperp_2.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 2
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 9
-vperp_nelement = 2
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 2
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 2
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 2
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 160
-dt = 0.002
-nwrite = 160
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb_ion_only_nel_r_8_z_8_vpa_8_vperp_8.toml b/runs/2D-sound-wave_cheb_ion_only_nel_r_8_z_8_vpa_8_vperp_8.toml
deleted file mode 100644
index 5319e6338..000000000
--- a/runs/2D-sound-wave_cheb_ion_only_nel_r_8_z_8_vpa_8_vperp_8.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 8
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 8
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 8
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 9
-vperp_nelement = 8
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 8
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 8
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 8
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 640
-dt = 0.0005
-nwrite = 640
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_16_vperp_16.toml b/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_16_vperp_16.toml
deleted file mode 100644
index 31adc547f..000000000
--- a/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_16_vperp_16.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 5
-vperp_nelement = 16
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 5
-vz_nelement = 16
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 5
-vr_nelement = 16
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 5
-vzeta_nelement = 16
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 160
-dt = 0.002
-nwrite = 40
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_2_vperp_2.toml b/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_2_vperp_2.toml
deleted file mode 100644
index 22c737a0a..000000000
--- a/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_2_vperp_2.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 2
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 9
-vperp_nelement = 2
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 2
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 2
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 2
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 10
-dt = 0.002
-nwrite = 1
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_8_vperp_8.toml b/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_8_vperp_8.toml
deleted file mode 100644
index 8417e702c..000000000
--- a/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_8_vperp_8.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 8
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 5
-vperp_nelement = 8
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 5
-vz_nelement = 8
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 5
-vr_nelement = 8
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 5
-vzeta_nelement = 8
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 160
-dt = 0.002
-nwrite = 40
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true

From e91e7aafb876c2270303b03a0fd95a4682c0a2f4 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 10:47:16 +0100
Subject: [PATCH 18/28] Remove miscellaneous MMS input TOML whose features are
 recored elsewhere.

---
 runs/2D-sound-wave_cheb-manf-Dirichlet.toml   | 56 -------------
 runs/2D-sound-wave_cheb-vperp-manf.toml       | 57 -------------
 runs/2D-sound-wave_cheb-vperp.toml            | 53 ------------
 ...2D-sound-wave_cheb-with-neutrals-manf.toml | 82 -------------------
 ...D-sound-wave_cheb-with-neutrals-small.toml | 75 -----------------
 runs/2D-wall-bc_cheb.toml                     | 72 ----------------
 6 files changed, 395 deletions(-)
 delete mode 100644 runs/2D-sound-wave_cheb-manf-Dirichlet.toml
 delete mode 100644 runs/2D-sound-wave_cheb-vperp-manf.toml
 delete mode 100644 runs/2D-sound-wave_cheb-vperp.toml
 delete mode 100644 runs/2D-sound-wave_cheb-with-neutrals-manf.toml
 delete mode 100644 runs/2D-sound-wave_cheb-with-neutrals-small.toml
 delete mode 100644 runs/2D-wall-bc_cheb.toml

diff --git a/runs/2D-sound-wave_cheb-manf-Dirichlet.toml b/runs/2D-sound-wave_cheb-manf-Dirichlet.toml
deleted file mode 100644
index 7d34bebe8..000000000
--- a/runs/2D-sound-wave_cheb-manf-Dirichlet.toml
+++ /dev/null
@@ -1,56 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-boltzmann_electron_response = true
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.62831853071
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 6
-r_nelement = 2
-r_bc = "Dirichlet"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 8
-vpa_L = 8.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 8
-vperp_L = 8.0
-vperp_discretization = "finite_difference"
-
-[timestepping]
-nstep = 500
-dt = 0.002
-nwrite = 20
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb-vperp-manf.toml b/runs/2D-sound-wave_cheb-vperp-manf.toml
deleted file mode 100644
index 983559017..000000000
--- a/runs/2D-sound-wave_cheb-vperp-manf.toml
+++ /dev/null
@@ -1,57 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-boltzmann_electron_response = true
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.62831853071
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 8
-vpa_L = 8.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 8
-vperp_L = 8.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 500
-dt = 0.002
-nwrite = 20
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb-vperp.toml b/runs/2D-sound-wave_cheb-vperp.toml
deleted file mode 100644
index 3edb4b222..000000000
--- a/runs/2D-sound-wave_cheb-vperp.toml
+++ /dev/null
@@ -1,53 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-boltzmann_electron_response = true
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.62831853071
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 8
-vpa_L = 8.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 8
-vperp_L = 8.0
-vperp_discretization = "finite_difference_vperp"
-
-[timestepping]
-nstep = 1500
-dt = 0.002
-nwrite = 20
-n_rk_stages = 4
-split_operators = false
diff --git a/runs/2D-sound-wave_cheb-with-neutrals-manf.toml b/runs/2D-sound-wave_cheb-with-neutrals-manf.toml
deleted file mode 100644
index b92ca83c1..000000000
--- a/runs/2D-sound-wave_cheb-with-neutrals-manf.toml
+++ /dev/null
@@ -1,82 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-boltzmann_electron_response = true
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 1.0
-ionization_frequency = 1.0
-
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-
-vpa_ngrid = 5
-vpa_nelement = 8
-vpa_L = 8.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-
-vperp_ngrid = 5
-vperp_nelement = 8
-vperp_L = 8.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-gyrophase_ngrid = 5
-gyrophase_nelement = 8
-
-vz_ngrid = 5
-vz_nelement = 8
-vz_L = 8.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 5
-vr_nelement = 8
-vr_L = 8.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 5
-vzeta_nelement = 8
-vzeta_L = 8.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 1375
-dt = 0.002
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-sound-wave_cheb-with-neutrals-small.toml b/runs/2D-sound-wave_cheb-with-neutrals-small.toml
deleted file mode 100644
index d5887a3c3..000000000
--- a/runs/2D-sound-wave_cheb-with-neutrals-small.toml
+++ /dev/null
@@ -1,75 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-boltzmann_electron_response = true
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 1.0
-ionization_frequency = 1.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "periodic"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 2
-vpa_L = 8.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 2
-vperp_L = 8.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 5
-vz_nelement = 2
-vz_L = 8.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 5
-vr_nelement = 2
-vr_L = 8.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 5
-vzeta_nelement = 2
-vzeta_L = 8.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 1375
-dt = 0.002
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall-bc_cheb.toml b/runs/2D-wall-bc_cheb.toml
deleted file mode 100644
index 07faf39be..000000000
--- a/runs/2D-wall-bc_cheb.toml
+++ /dev/null
@@ -1,72 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 0
-#boltzmann_electron_response = true
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-initial_density1 = 1.0
-initial_temperature1 = 1.0
-z_IC_option1 = "gaussian"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-vpa_IC_option1 = "gaussian"
-vpa_IC_density_amplitude1 = 1.0
-vpa_IC_density_phase1 = 0.0
-vpa_IC_upar_amplitude1 = 0.0
-vpa_IC_upar_phase1 = 0.0
-vpa_IC_temperature_amplitude1 = 0.0
-vpa_IC_temperature_phase1 = 0.0
-initial_density2 = 1.0
-initial_temperature2 = 1.0
-z_IC_option2 = "gaussian"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-vpa_IC_option2 = "gaussian"
-vpa_IC_density_amplitude2 = 1.0
-vpa_IC_density_phase2 = 0.0
-vpa_IC_upar_amplitude2 = 0.0
-vpa_IC_upar_phase2 = 0.0
-vpa_IC_temperature_amplitude2 = 0.0
-vpa_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-constant_ionization_rate = false
-z_ngrid = 9
-z_nelement = 3
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 3
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 16
-vpa_nelement = 10
-vpa_L = 8.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 8
-vperp_nelement = 8
-vperp_L = 8.0
-vperp_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 50
-dt = 0.001
-nwrite = 5
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true

From d76ab580d568551c820d48fb0ce141533858ca83 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 10:59:21 +0100
Subject: [PATCH 19/28] Remove duplicate MMS TOML and update the remaining TOML
 for a 1D2V(ions) and 1D3V(neutrals) test with a simple sheath model for
 electrons.

---
 ...ith-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml} |  7 +-
 runs/2D-wall_cheb-with-neutrals-small.toml    | 76 ------------------
 ...th-sheath_nel_r_1_z_2_vpa_12_vperp_12.toml | 77 -------------------
 ...th-sheath_nel_r_1_z_2_vpa_16_vperp_16.toml | 77 -------------------
 ...th-sheath_nel_r_1_z_2_vpa_24_vperp_24.toml | 77 -------------------
 ...with-sheath_nel_r_1_z_2_vpa_2_vperp_2.toml | 77 -------------------
 ...with-sheath_nel_r_1_z_2_vpa_8_vperp_8.toml | 77 -------------------
 runs/2D-wall_cheb-with-neutrals.toml          | 76 ------------------
 8 files changed, 5 insertions(+), 539 deletions(-)
 rename runs/{2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml => 1D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml} (96%)
 delete mode 100644 runs/2D-wall_cheb-with-neutrals-small.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_12_vperp_12.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_16_vperp_16.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_24_vperp_24.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_2_vperp_2.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_8_vperp_8.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals.toml

diff --git a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml b/runs/1D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml
similarity index 96%
rename from runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml
rename to runs/1D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml
index f6f9786b4..763dcf884 100644
--- a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml
+++ b/runs/1D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml
@@ -8,7 +8,6 @@ evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
 T_e = 1.0
 T_wall = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -70,8 +69,12 @@ vzeta_discretization = "chebyshev_pseudospectral"
 nstep = 200
 dt = 0.001
 nwrite = 50
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]
 use_for_advance = true
+
+[geometry]
+option="constant-helical"
+pitch=1.0
+rhostar = 0.0
diff --git a/runs/2D-wall_cheb-with-neutrals-small.toml b/runs/2D-wall_cheb-with-neutrals-small.toml
deleted file mode 100644
index ed213626a..000000000
--- a/runs/2D-wall_cheb-with-neutrals-small.toml
+++ /dev/null
@@ -1,76 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-boltzmann_electron_response = true
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 5
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 5
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 5
-vpa_nelement = 2
-vpa_L = 8.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 5
-vperp_nelement = 2
-vperp_L = 8.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 5
-vz_L = 8.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 5
-vr_L = 8.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 5
-vzeta_L = 8.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 50
-dt = 0.002
-nwrite = 1
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_12_vperp_12.toml b/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_12_vperp_12.toml
deleted file mode 100644
index 9bb859706..000000000
--- a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_12_vperp_12.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-#electron_physics = "boltzmann_electron_response"
-electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 12
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 12
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 12
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 12
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 12
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_16_vperp_16.toml b/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_16_vperp_16.toml
deleted file mode 100644
index 9d6c9a0a2..000000000
--- a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_16_vperp_16.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-#electron_physics = "boltzmann_electron_response"
-electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 16
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 16
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 16
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 16
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_24_vperp_24.toml b/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_24_vperp_24.toml
deleted file mode 100644
index 40265b419..000000000
--- a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_24_vperp_24.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-#electron_physics = "boltzmann_electron_response"
-electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 24
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 24
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 24
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 24
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 24
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_2_vperp_2.toml b/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_2_vperp_2.toml
deleted file mode 100644
index 2fd66d126..000000000
--- a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_2_vperp_2.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-#electron_physics = "boltzmann_electron_response"
-electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 2
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 2
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 2
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 2
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 2
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_8_vperp_8.toml b/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_8_vperp_8.toml
deleted file mode 100644
index 060148f67..000000000
--- a/runs/2D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_8_vperp_8.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-#electron_physics = "boltzmann_electron_response"
-electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 8
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 8
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 8
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 8
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 8
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals.toml b/runs/2D-wall_cheb-with-neutrals.toml
deleted file mode 100644
index cf318cb2e..000000000
--- a/runs/2D-wall_cheb-with-neutrals.toml
+++ /dev/null
@@ -1,76 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-boltzmann_electron_response = true
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 3
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 6
-r_nelement = 3
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 21
-vpa_L = 16.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 11
-vperp_L = 16.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 21
-vz_L = 16.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 11
-vr_L = 16.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 11
-vzeta_L = 16.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 5
-dt = 0.002
-nwrite = 1
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true

From 1ab9b212333156a0b3645eb370da21301da0ba3d Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:04:54 +0100
Subject: [PATCH 20/28] Update 1D2V/1D3V inputs for wall boundary tests with
 neutral species and Boltzmann electrons.

---
 ...h-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml} | 17 ++--
 ...neutrals_nel_r_1_z_12_vpa_12_vperp_12.toml | 77 ------------------
 ...neutrals_nel_r_1_z_16_vpa_16_vperp_16.toml | 80 -------------------
 ...-neutrals_nel_r_1_z_2_vpa_12_vperp_12.toml | 77 ------------------
 ...-neutrals_nel_r_1_z_2_vpa_16_vperp_16.toml | 77 ------------------
 ...-neutrals_nel_r_1_z_2_vpa_24_vperp_24.toml | 77 ------------------
 ...th-neutrals_nel_r_1_z_2_vpa_2_vperp_2.toml | 80 -------------------
 ...th-neutrals_nel_r_1_z_4_vpa_4_vperp_4.toml | 80 -------------------
 ...th-neutrals_nel_r_1_z_8_vpa_8_vperp_8.toml | 80 -------------------
 9 files changed, 10 insertions(+), 635 deletions(-)
 rename runs/{2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_8_vperp_8.toml => 1D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml} (91%)
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_12_vpa_12_vperp_12.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_16_vpa_16_vperp_16.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_12_vperp_12.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_16_vperp_16.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_24_vperp_24.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_2_vperp_2.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_4_vpa_4_vperp_4.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_8_vpa_8_vperp_8.toml

diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_8_vperp_8.toml b/runs/1D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml
similarity index 91%
rename from runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_8_vperp_8.toml
rename to runs/1D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml
index 5b666c5f5..faec93898 100644
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_8_vperp_8.toml
+++ b/runs/1D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml
@@ -8,7 +8,6 @@ evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
 T_e = 1.0
 T_wall = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -38,30 +37,30 @@ r_nelement = 1
 r_bc = "periodic"
 r_discretization = "chebyshev_pseudospectral"
 vpa_ngrid = 6
-vpa_nelement = 8
+vpa_nelement = 4
 vpa_L = 12.0
 vpa_bc = "periodic"
 vpa_discretization = "chebyshev_pseudospectral"
 vperp_ngrid = 6
-vperp_nelement = 8
+vperp_nelement = 4
 vperp_L = 6.0
 #vperp_discretization = "finite_difference"
 vperp_discretization = "chebyshev_pseudospectral"
 
 vz_ngrid = 6
-vz_nelement = 8
+vz_nelement = 4
 vz_L = 12.0
 vz_bc = "periodic"
 vz_discretization = "chebyshev_pseudospectral"
 
 vr_ngrid = 6
-vr_nelement = 8
+vr_nelement = 4
 vr_L = 12.0
 vr_bc = "periodic"
 vr_discretization = "chebyshev_pseudospectral"
 
 vzeta_ngrid = 6
-vzeta_nelement = 8
+vzeta_nelement = 4
 vzeta_L = 12.0
 vzeta_bc = "periodic"
 vzeta_discretization = "chebyshev_pseudospectral"
@@ -70,8 +69,12 @@ vzeta_discretization = "chebyshev_pseudospectral"
 nstep = 200
 dt = 0.001
 nwrite = 50
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]
 use_for_advance = true
+
+[geometry]
+option="constant-helical"
+pitch=1.0
+rhostar=0.0
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_12_vpa_12_vperp_12.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_12_vpa_12_vperp_12.toml
deleted file mode 100644
index ff950dc04..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_12_vpa_12_vperp_12.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 12
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 12
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 12
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 12
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 12
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 12
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 30
-dt = 0.001
-nwrite = 30
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_16_vpa_16_vperp_16.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_16_vpa_16_vperp_16.toml
deleted file mode 100644
index 5e65f7667..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_16_vpa_16_vperp_16.toml
+++ /dev/null
@@ -1,80 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-Er_constant = 0.5
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 16
-z_nelement_local = 1
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 16
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 16
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 16
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 16
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 8000
-dt = 0.000125
-nwrite = 800
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_12_vperp_12.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_12_vperp_12.toml
deleted file mode 100644
index bca3cf3e4..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_12_vperp_12.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 12
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 12
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 12
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 12
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 12
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_16_vperp_16.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_16_vperp_16.toml
deleted file mode 100644
index 6c96b00a1..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_16_vperp_16.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 16
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 16
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 16
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 16
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_24_vperp_24.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_24_vperp_24.toml
deleted file mode 100644
index 36acdc822..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_24_vperp_24.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 24
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 24
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 24
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 24
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 24
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_2_vperp_2.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_2_vperp_2.toml
deleted file mode 100644
index 69d538075..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_2_vperp_2.toml
+++ /dev/null
@@ -1,80 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-Er_constant = 0.5
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 2
-z_nelement_local = 1
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 2
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 2
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 2
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 2
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 2
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 1000
-dt = 0.001
-nwrite = 100
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_4_vpa_4_vperp_4.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_4_vpa_4_vperp_4.toml
deleted file mode 100644
index 331f29348..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_4_vpa_4_vperp_4.toml
+++ /dev/null
@@ -1,80 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-Er_constant = 0.5
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 4
-z_nelement_local = 1
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 4
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 4
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 4
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 4
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 4
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 2000
-dt = 0.0005
-nwrite = 200
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_8_vpa_8_vperp_8.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_8_vpa_8_vperp_8.toml
deleted file mode 100644
index aadca516b..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_8_vpa_8_vperp_8.toml
+++ /dev/null
@@ -1,80 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-Er_constant = 0.5
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 8
-z_nelement_local = 1
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_nelement_local = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 8
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 8
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 8
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 8
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 8
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 4000
-dt = 0.00025
-nwrite = 400
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true

From 1a1d19e46746ac797c074ad6080d1c4dcc339932 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:12:37 +0100
Subject: [PATCH 21/28] Remove duplicate input TOML and update a representative
 input TOML for a 2D2V/2D3V simulation with Boltzmann electrons, ions and
 neutrals and wall boundary condions.

---
 ...eutrals_nel_r_16_z_16_vpa_16_vperp_16.toml | 77 ------------------
 ...th-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml | 77 ------------------
 ...-neutrals_nel_r_2_z_2_vpa_12_vperp_12.toml | 78 -------------------
 ...-neutrals_nel_r_2_z_2_vpa_16_vperp_16.toml | 78 -------------------
 ...th-neutrals_nel_r_2_z_2_vpa_2_vperp_2.toml | 77 ------------------
 ...th-neutrals_nel_r_2_z_2_vpa_4_vperp_4.toml |  9 ++-
 ...th-neutrals_nel_r_2_z_2_vpa_8_vperp_8.toml | 78 -------------------
 ...th-neutrals_nel_r_4_z_4_vpa_4_vperp_4.toml | 77 ------------------
 ...th-neutrals_nel_r_6_z_6_vpa_6_vperp_6.toml | 77 ------------------
 ...th-neutrals_nel_r_8_z_8_vpa_8_vperp_8.toml | 77 ------------------
 10 files changed, 5 insertions(+), 700 deletions(-)
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_16_z_16_vpa_16_vperp_16.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_12_vperp_12.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_16_vperp_16.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_2_vperp_2.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_8_vperp_8.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_4_z_4_vpa_4_vperp_4.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_6_z_6_vpa_6_vperp_6.toml
 delete mode 100644 runs/2D-wall_cheb-with-neutrals_nel_r_8_z_8_vpa_8_vperp_8.toml

diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_16_z_16_vpa_16_vperp_16.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_16_z_16_vpa_16_vperp_16.toml
deleted file mode 100644
index 29bc9f548..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_16_z_16_vpa_16_vperp_16.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 16
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 16
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 16
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 16
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 16
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 16
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 240
-dt = 0.000125
-nwrite = 240
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml
deleted file mode 100644
index d05b70ef9..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 1
-r_nelement = 1
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 4
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 4
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 4
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 4
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 4
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_12_vperp_12.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_12_vperp_12.toml
deleted file mode 100644
index 6a531f156..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_12_vperp_12.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 6
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 12
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 12
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 12
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 12
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 12
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_16_vperp_16.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_16_vperp_16.toml
deleted file mode 100644
index d8fbcba42..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_16_vperp_16.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 6
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 16
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 16
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 16
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 16
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 16
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_2_vperp_2.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_2_vperp_2.toml
deleted file mode 100644
index e1b13e79b..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_2_vperp_2.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 2
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 2
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 2
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 2
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 2
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 30
-dt = 0.001
-nwrite = 30 
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_4_vperp_4.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_4_vperp_4.toml
index f06da8dcd..a8ae905fb 100644
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_4_vperp_4.toml
+++ b/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_4_vperp_4.toml
@@ -7,9 +7,6 @@ evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
 T_e = 1.0
 T_wall = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -71,8 +68,12 @@ vzeta_discretization = "chebyshev_pseudospectral"
 nstep = 200
 dt = 0.001
 nwrite = 50
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]
 use_for_advance = true
+
+[geometry]
+option="constant-helical"
+pitch=0.5
+rhostar=1.0
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_8_vperp_8.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_8_vperp_8.toml
deleted file mode 100644
index ba617c52a..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_8_vperp_8.toml
+++ /dev/null
@@ -1,78 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 6
-z_nelement = 2
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 6
-r_nelement = 2
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 6
-vpa_nelement = 8
-vpa_L = 12.0
-vpa_bc = "periodic"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 6
-vperp_nelement = 8
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 6
-vz_nelement = 8
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 6
-vr_nelement = 8
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 6
-vzeta_nelement = 8
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 200
-dt = 0.001
-nwrite = 50
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_4_z_4_vpa_4_vperp_4.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_4_z_4_vpa_4_vperp_4.toml
deleted file mode 100644
index 47a354798..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_4_z_4_vpa_4_vperp_4.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 4
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 4
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 4
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 4
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 4
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 4
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 4
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 60
-dt = 0.0005
-nwrite = 60
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_6_z_6_vpa_6_vperp_6.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_6_z_6_vpa_6_vperp_6.toml
deleted file mode 100644
index 19cb1221e..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_6_z_6_vpa_6_vperp_6.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 6
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 6
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 6
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 6
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 6
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 6
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 6
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 90
-dt = 0.0003333333333333333
-nwrite = 90
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true
diff --git a/runs/2D-wall_cheb-with-neutrals_nel_r_8_z_8_vpa_8_vperp_8.toml b/runs/2D-wall_cheb-with-neutrals_nel_r_8_z_8_vpa_8_vperp_8.toml
deleted file mode 100644
index add58f910..000000000
--- a/runs/2D-wall_cheb-with-neutrals_nel_r_8_z_8_vpa_8_vperp_8.toml
+++ /dev/null
@@ -1,77 +0,0 @@
-n_ion_species = 1
-n_neutral_species = 1
-electron_physics = "boltzmann_electron_response"
-#electron_physics = "boltzmann_electron_response_with_simple_sheath"
-evolve_moments_density = false
-evolve_moments_parallel_flow = false
-evolve_moments_parallel_pressure = false
-evolve_moments_conservation = false
-T_e = 1.0
-T_wall = 1.0
-rhostar = 1.0
-initial_density1 = 0.5
-initial_temperature1 = 1.0
-initial_density2 = 0.5
-initial_temperature2 = 1.0
-z_IC_option1 = "sinusoid"
-z_IC_density_amplitude1 = 0.001
-z_IC_density_phase1 = 0.0
-z_IC_upar_amplitude1 = 0.0
-z_IC_upar_phase1 = 0.0
-z_IC_temperature_amplitude1 = 0.0
-z_IC_temperature_phase1 = 0.0
-z_IC_option2 = "sinusoid"
-z_IC_density_amplitude2 = 0.001
-z_IC_density_phase2 = 0.0
-z_IC_upar_amplitude2 = 0.0
-z_IC_upar_phase2 = 0.0
-z_IC_temperature_amplitude2 = 0.0
-z_IC_temperature_phase2 = 0.0
-charge_exchange_frequency = 0.0
-ionization_frequency = 0.0
-z_ngrid = 9
-z_nelement = 8
-z_bc = "wall"
-z_discretization = "chebyshev_pseudospectral"
-r_ngrid = 9
-r_nelement = 8
-r_bc = "periodic"
-r_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 9
-vpa_nelement = 8
-vpa_L = 12.0
-vpa_bc = "zero"
-vpa_discretization = "chebyshev_pseudospectral"
-vperp_ngrid = 9
-vperp_nelement = 8
-vperp_L = 6.0
-#vperp_discretization = "finite_difference"
-vperp_discretization = "chebyshev_pseudospectral"
-
-vz_ngrid = 9
-vz_nelement = 8
-vz_L = 12.0
-vz_bc = "periodic"
-vz_discretization = "chebyshev_pseudospectral"
-
-vr_ngrid = 9
-vr_nelement = 8
-vr_L = 12.0
-vr_bc = "periodic"
-vr_discretization = "chebyshev_pseudospectral"
-
-vzeta_ngrid = 9
-vzeta_nelement = 8
-vzeta_L = 12.0
-vzeta_bc = "periodic"
-vzeta_discretization = "chebyshev_pseudospectral"
-
-[timestepping]
-nstep = 120
-dt = 0.00025
-nwrite = 120
-n_rk_stages = 4
-split_operators = false
-
-[manufactured_solns]
-use_for_advance = true

From b7ece68cee38f57c9ad07bcc5963fb0c7089cb05 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:30:33 +0100
Subject: [PATCH 22/28] Reduce resolution in example TOML input for 2D2V test
 involving only ions and periodic BC.

---
 ...ve_cheb_ion_only_nel_r_2_z_2_vpa_4_vperp_4.toml} | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)
 rename runs/{2D-sound-wave_cheb_ion_only_nel_r_4_z_4_vpa_4_vperp_4.toml => 2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_4_vperp_4.toml} (95%)

diff --git a/runs/2D-sound-wave_cheb_ion_only_nel_r_4_z_4_vpa_4_vperp_4.toml b/runs/2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_4_vperp_4.toml
similarity index 95%
rename from runs/2D-sound-wave_cheb_ion_only_nel_r_4_z_4_vpa_4_vperp_4.toml
rename to runs/2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_4_vperp_4.toml
index ef26afc7e..7cd239b48 100644
--- a/runs/2D-sound-wave_cheb_ion_only_nel_r_4_z_4_vpa_4_vperp_4.toml
+++ b/runs/2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_4_vperp_4.toml
@@ -6,9 +6,6 @@ evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
 T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -30,11 +27,11 @@ z_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
 z_ngrid = 9
-z_nelement = 4
+z_nelement = 2
 z_bc = "periodic"
 z_discretization = "chebyshev_pseudospectral"
 r_ngrid = 9
-r_nelement = 4
+r_nelement = 2
 r_bc = "periodic"
 r_discretization = "chebyshev_pseudospectral"
 vpa_ngrid = 9
@@ -71,8 +68,12 @@ vzeta_discretization = "chebyshev_pseudospectral"
 nstep = 320
 dt = 0.001
 nwrite = 320
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]
 use_for_advance = true
+
+[geometry]
+option="constant-helical"
+pitch=0.5
+rhostar = 1.0

From 280ebb46b98295cbdab1862583aa1cf9c28bcab1 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:31:12 +0100
Subject: [PATCH 23/28] Update example TOML input for 2D tests with neutrals
 and wall boundary conditions.

---
 ...D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_4_vperp_4.toml | 9 +++++----
 runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_4_vperp_4.toml   | 9 +++++----
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_4_vperp_4.toml b/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_4_vperp_4.toml
index c18763222..d7702a536 100644
--- a/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_4_vperp_4.toml
+++ b/runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_4_vperp_4.toml
@@ -6,9 +6,6 @@ evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
 T_e = 1.0
-Bzed = 0.5
-Bmag = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -71,8 +68,12 @@ vzeta_discretization = "chebyshev_pseudospectral"
 nstep = 160
 dt = 0.002
 nwrite = 40
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]
 use_for_advance = true
+
+[geometry]
+option="constant-helical"
+pitch=0.5
+rhostar = 1.0
diff --git a/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_4_vperp_4.toml b/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_4_vperp_4.toml
index 808db6f3e..2b86fd507 100644
--- a/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_4_vperp_4.toml
+++ b/runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_4_vperp_4.toml
@@ -6,9 +6,6 @@ evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
 T_e = 1.0
-Bzed = 0.5 
-Bmag = 1.0
-rhostar = 1.0
 initial_density1 = 0.5
 initial_temperature1 = 1.0
 initial_density2 = 0.5
@@ -71,8 +68,12 @@ vzeta_discretization = "chebyshev_pseudospectral"
 nstep = 160
 dt = 0.002
 nwrite = 40
-n_rk_stages = 4
 split_operators = false
 
 [manufactured_solns]
 use_for_advance = true
+
+[geometry]
+option="constant-helical"
+pitch=0.5
+rhostar = 1.0

From 0e88e7830a38901bc492f011000bca3ab32e020d Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:33:09 +0100
Subject: [PATCH 24/28] Update list of MMS test input TOML.

---
 .../manufactured_solution_test_examples.md    | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/docs/src/manufactured_solution_test_examples.md b/docs/src/manufactured_solution_test_examples.md
index c6b69edbf..79fb5e49f 100644
--- a/docs/src/manufactured_solution_test_examples.md
+++ b/docs/src/manufactured_solution_test_examples.md
@@ -34,6 +34,20 @@ runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_16_vpa_16_vperp_8_diss.toml
 runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
 ```
 
+# 1D2V/1D3V test (with neutrals)
+
+* A test with ions and neutral species and wall boundary conditions, 
+  using the Boltzmann electron response to model the electron species.
+```
+runs/1D-wall_cheb-with-neutrals_nel_r_1_z_2_vpa_4_vperp_4.toml
+```
+
+* A test with neutral species and wall boundary conditions, using a simple
+  sheath model for electrons based on the Boltzmann electron response.
+```
+runs/1D-wall_cheb-with-neutrals-with-sheath_nel_r_1_z_2_vpa_4_vperp_4.toml
+```
+
 # 2D1V tests
 
 These tests are used to test the spatial advection in simple cases
@@ -52,6 +66,12 @@ These tests are used to test the spatial advection in cases
 with wall boundary conditions or geometrical features where
 two velocity dimensions are necessary.
 
+* 2D2V simulation with periodic boundary conditions, 
+  Boltzmann electrons and ions
+```
+runs/2D-sound-wave_cheb_ion_only_nel_r_2_z_2_vpa_4_vperp_4.toml
+```
+
 * 2D2V simulation of a open field lines in 1D magnetic mirror
   (no neutrals)
 ```
@@ -60,3 +80,26 @@ runs/2D-mirror_MMS_ngrid_5_nel_r_16_z_16_vpa_16_vperp_8_diss.toml
 runs/2D-mirror_MMS_ngrid_5_nel_r_32_z_32_vpa_16_vperp_16_diss.toml
 ```
 
+# 2D2V/2D3V tests
+
+These tests include a two-dimensional domain, ions, and neutrals 
+(which have three velocity dimensions).
+
+* 2D2V/2D3V simulation on a domain with wall boundaries, with
+  helical geometry, Boltzmann electrons, neutrals, and ions.
+```
+runs/2D-wall_cheb-with-neutrals_nel_r_2_z_2_vpa_4_vperp_4.toml
+```
+
+* 2D2V/2D3V simulation on a periodic domain, with
+  helical geometry, Boltzmann electrons, neutrals, and ions.
+```
+runs/2D-sound-wave_cheb_nel_r_2_z_2_vpa_4_vperp_4.toml
+```
+
+* 2D2V/2D3V simulation on a periodic domain, with
+  model charge exchange and ionisation collisions,
+  helical geometry, Boltzmann electrons, neutrals, and ions.
+```
+runs/2D-sound-wave_cheb_cxiz_nel_r_2_z_2_vpa_4_vperp_4.toml
+```

From b3ee23c3c0a183d8b07220a8932cb1d05ab1b262 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:34:03 +0100
Subject: [PATCH 25/28] Catch minor bug in jpari function argument list.

---
 moment_kinetics/ext/manufactured_solns_ext.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/moment_kinetics/ext/manufactured_solns_ext.jl b/moment_kinetics/ext/manufactured_solns_ext.jl
index de6d4e44b..0707af732 100644
--- a/moment_kinetics/ext/manufactured_solns_ext.jl
+++ b/moment_kinetics/ext/manufactured_solns_ext.jl
@@ -412,7 +412,7 @@ using IfElse
         # get N_e factor for boltzmann response
         if composition.electron_physics == boltzmann_electron_response_with_simple_sheath && nr == 1 
             # so 1D MMS test with 3V neutrals where ion current can be calculated prior to knowing Er
-            jpari_into_LHS_wall = jpari_into_LHS_wall_sym(Lr, Lz, r_bc, z_bc,
+            jpari_into_LHS_wall = jpari_into_LHS_wall_sym(Lr, Lz, r_bc, z_bc, composition,
                                                           manufactured_solns_input)
             N_e = -2.0*sqrt(pi*composition.me_over_mi)*exp(-composition.phi_wall/composition.T_e)*jpari_into_LHS_wall
         elseif composition.electron_physics == boltzmann_electron_response_with_simple_sheath && nr > 1 

From bef5c4d43a59c87b302fda8347caf02716daae8b Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:43:27 +0100
Subject: [PATCH 26/28] Add some further explanation for how to use the input
 files.

---
 docs/src/manufactured_solution_test_examples.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/src/manufactured_solution_test_examples.md b/docs/src/manufactured_solution_test_examples.md
index 79fb5e49f..1fb33d28b 100644
--- a/docs/src/manufactured_solution_test_examples.md
+++ b/docs/src/manufactured_solution_test_examples.md
@@ -1,6 +1,12 @@
 # List of Manufactured Solutions Test TOML inputs
 
 Here we list the existing manufactured solution test inputs.
+These inputs are examples only, and in most cases we only
+keep the lowest resolution examples. The user should copy
+these inputs and make a series of TOML with increasing resolutions
+to generate a series of simulations on which the numerical errors
+can be tested and compared to the expected scaling of the 
+numerical method employed.
 
 # 1D1V tests
 

From 1ab022522f5bf17815e2e5061b8bd7e18f3ea339 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:56:47 +0100
Subject: [PATCH 27/28] 1D2V/1D3V periodic boundary test case with neutrals.

---
 ...-wave_cheb_nel_r_1_z_2_vpa_4_vperp_4.toml} | 78 +++++++++++--------
 1 file changed, 44 insertions(+), 34 deletions(-)
 rename runs/{periodic-bc-with-neutrals.toml => 1D-sound-wave_cheb_nel_r_1_z_2_vpa_4_vperp_4.toml} (55%)

diff --git a/runs/periodic-bc-with-neutrals.toml b/runs/1D-sound-wave_cheb_nel_r_1_z_2_vpa_4_vperp_4.toml
similarity index 55%
rename from runs/periodic-bc-with-neutrals.toml
rename to runs/1D-sound-wave_cheb_nel_r_1_z_2_vpa_4_vperp_4.toml
index 2c5792fdf..e8127a7ad 100644
--- a/runs/periodic-bc-with-neutrals.toml
+++ b/runs/1D-sound-wave_cheb_nel_r_1_z_2_vpa_4_vperp_4.toml
@@ -1,69 +1,79 @@
 n_ion_species = 1
 n_neutral_species = 1
-#boltzmann_electron_response = true
 electron_physics = "boltzmann_electron_response"
 evolve_moments_density = false
 evolve_moments_parallel_flow = false
 evolve_moments_parallel_pressure = false
 evolve_moments_conservation = false
 T_e = 1.0
-T_wall = 1.0
-initial_density1 = 1.0
+initial_density1 = 0.5
 initial_temperature1 = 1.0
-z_IC_option1 = "gaussian"
+initial_density2 = 0.5
+initial_temperature2 = 1.0
+z_IC_option1 = "sinusoid"
 z_IC_density_amplitude1 = 0.001
 z_IC_density_phase1 = 0.0
 z_IC_upar_amplitude1 = 0.0
 z_IC_upar_phase1 = 0.0
 z_IC_temperature_amplitude1 = 0.0
 z_IC_temperature_phase1 = 0.0
-vpa_IC_option1 = "gaussian"
-vpa_IC_density_amplitude1 = 1.0
-vpa_IC_density_phase1 = 0.0
-vpa_IC_upar_amplitude1 = 0.0
-vpa_IC_upar_phase1 = 0.0
-vpa_IC_temperature_amplitude1 = 0.0
-vpa_IC_temperature_phase1 = 0.0
-initial_density2 = 1.0
-initial_temperature2 = 1.0
-z_IC_option2 = "gaussian"
+z_IC_option2 = "sinusoid"
 z_IC_density_amplitude2 = 0.001
 z_IC_density_phase2 = 0.0
 z_IC_upar_amplitude2 = 0.0
 z_IC_upar_phase2 = 0.0
 z_IC_temperature_amplitude2 = 0.0
 z_IC_temperature_phase2 = 0.0
-vpa_IC_option2 = "gaussian"
-vpa_IC_density_amplitude2 = 1.0
-vpa_IC_density_phase2 = 0.0
-vpa_IC_upar_amplitude2 = 0.0
-vpa_IC_upar_phase2 = 0.0
-vpa_IC_temperature_amplitude2 = 0.0
-vpa_IC_temperature_phase2 = 0.0
 charge_exchange_frequency = 0.0
 ionization_frequency = 0.0
-constant_ionization_rate = false
-z_ngrid = 20
-z_nelement = 10
+z_ngrid = 5
+z_nelement = 2
 z_bc = "periodic"
 z_discretization = "chebyshev_pseudospectral"
-vpa_ngrid = 20
-vpa_nelement = 10
-vpa_L = 8.0
+r_ngrid = 1
+r_nelement = 1
+r_bc = "periodic"
+r_discretization = "chebyshev_pseudospectral"
+vpa_ngrid = 5
+vpa_nelement = 4
+vpa_L = 12.0
 vpa_bc = "periodic"
 vpa_discretization = "chebyshev_pseudospectral"
-vz_ngrid = 20
-vz_nelement = 10
-vz_L = 8.0
+
+vperp_ngrid = 5
+vperp_nelement = 4
+vperp_L = 6.0
+#vperp_discretization = "finite_difference"
+vperp_discretization = "chebyshev_pseudospectral"
+
+vz_ngrid = 5
+vz_nelement = 4
+vz_L = 12.0
 vz_bc = "periodic"
 vz_discretization = "chebyshev_pseudospectral"
 
+vr_ngrid = 5
+vr_nelement = 4
+vr_L = 12.0
+vr_bc = "periodic"
+vr_discretization = "chebyshev_pseudospectral"
+
+vzeta_ngrid = 5
+vzeta_nelement = 4
+vzeta_L = 12.0
+vzeta_bc = "periodic"
+vzeta_discretization = "chebyshev_pseudospectral"
+
 [timestepping]
-nstep = 50
-dt = 0.001
-nwrite = 1
-n_rk_stages = 4
+nstep = 160
+dt = 0.002
+nwrite = 40
 split_operators = false
 
 [manufactured_solns]
 use_for_advance = true
+
+[geometry]
+option="constant-helical"
+pitch=1.0
+rhostar = 0.0

From 9056f4ee45b0f4ba5d0db741cd7806fe688f97e7 Mon Sep 17 00:00:00 2001
From: Michael Hardman <michael.hardman@physics.ox.ac.uk>
Date: Wed, 22 May 2024 11:58:32 +0100
Subject: [PATCH 28/28] Include 1D periodic BC case with neutrals in
 documentation.

---
 docs/src/manufactured_solution_test_examples.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/src/manufactured_solution_test_examples.md b/docs/src/manufactured_solution_test_examples.md
index 1fb33d28b..6b680ca16 100644
--- a/docs/src/manufactured_solution_test_examples.md
+++ b/docs/src/manufactured_solution_test_examples.md
@@ -42,6 +42,12 @@ runs/1D-mirror_MMS_ngrid_9_nel_r_1_z_32_vpa_32_vperp_16_diss.toml
 
 # 1D2V/1D3V test (with neutrals)
 
+* A test with periodic boundary conditions in 1D, Boltzmann
+  electrons, neutrals, and ions.
+```
+runs/1D-sound-wave_cheb_nel_r_1_z_2_vpa_4_vperp_4.toml
+```
+
 * A test with ions and neutral species and wall boundary conditions, 
   using the Boltzmann electron response to model the electron species.
 ```