diff --git a/.github/workflows/check_pyrokinetics.yml b/.github/workflows/check_pyrokinetics.yml
new file mode 100644
index 0000000000..45b45276f5
--- /dev/null
+++ b/.github/workflows/check_pyrokinetics.yml
@@ -0,0 +1,62 @@
+# Run these tests automatically on Github on every push and pull request.
+name: Check Pyrokinetics
+on: [push, pull_request]
+
+# We always run in a bash shell
+defaults:
+  run:
+    shell: bash
+
+# First build stella, and then perform pyrokinetics tests
+jobs:
+
+#-----------------------------------------------------------------------
+#                              Quick build                              
+#-----------------------------------------------------------------------
+
+  # Build stella to perform pyrokinetics tests
+  pyrokinetics-tests: 
+    name: Check Pyrokinetics
+    runs-on: ubuntu-22.04
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+      STELLA_SYSTEM: gnu_ubuntu
+
+    steps:
+
+      # Check-out repository under $GITHUB_WORKSPACE
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          sudo apt update
+          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
+          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
+
+      # Build stella executable
+      - name: Build stella
+        run: |
+          git submodule update --init --recursive
+          make -j 12
+          chmod +x stella
+          
+      # Install dependencies
+      - name: Install dependencies and python virtual environment
+        run: |
+          sudo apt update
+          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
+          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
+          pip3 install --upgrade pip
+          pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
+          pip3 install EXTERNALS/pyrokinetics/.
+          sed -i 's/nproc = 16/nproc = 1/g' AUTOMATIC_TESTS/config.ini
+          
+      # Perform pyrokinetics tests
+      - name: Pyrokinetics tests
+        run: make pyrokinetics-tests
+
+
+
diff --git a/.github/workflows/check_stella.yml b/.github/workflows/check_stella.yml
index 26b0102598..583085eb5c 100644
--- a/.github/workflows/check_stella.yml
+++ b/.github/workflows/check_stella.yml
@@ -22,10 +22,11 @@ jobs:
       MPIRUN: mpiexec -np
     
     # Run the same set-up multiple times
+    # Note that macos-12 has been deprecated on GitHub in 2025 
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-12, macos-13, macos-14, ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
+        os: [macos-13, macos-14, ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
         compiler: [Make, CMake]
     
     # Operating system
@@ -45,10 +46,10 @@ jobs:
             echo "FFTW_LIB_DIR=/usr/local/Cellar/fftw/3.3.10_1/lib/" >> $GITHUB_ENV
             echo "Set FFTW_INC_DIR = /usr/local/include/" 
             echo "FFTW_INC_DIR=/usr/local/include/" >> $GITHUB_ENV
-            echo "Set NETCDF_LIB_DIR = /usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1/lib/"
-            echo "NETCDF_LIB_DIR=/usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1/lib/" >> $GITHUB_ENV
-            echo "Set NETCDF_INC_DIR = /usr/local/Cellar/netcdf-fortran/4.6.1/include/"
-            echo "NETCDF_INC_DIR=/usr/local/Cellar/netcdf-fortran/4.6.1/include/" >> $GITHUB_ENV 
+            echo "Set NETCDF_LIB_DIR = /usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1_1/lib/"
+            echo "NETCDF_LIB_DIR=/usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1_1/lib/" >> $GITHUB_ENV
+            echo "Set NETCDF_INC_DIR = /usr/local/Cellar/netcdf-fortran/4.6.1_1/include/"
+            echo "NETCDF_INC_DIR=/usr/local/Cellar/netcdf-fortran/4.6.1_1/include/" >> $GITHUB_ENV
           elif [ ${{ matrix.os }} == 'macos-14' ]; then 
             echo "Set STELLA_SYSTEM = macos"
             echo "STELLA_SYSTEM=macos" >> $GITHUB_ENV 
@@ -56,10 +57,10 @@ jobs:
             echo "FFTW_LIB_DIR=/opt/homebrew/Cellar/fftw/3.3.10_1/lib/" >> $GITHUB_ENV
             echo "Set FFTW_INC_DIR = /opt/homebrew/include/" 
             echo "FFTW_INC_DIR=/opt/homebrew/include/" >> $GITHUB_ENV
-            echo "Set NETCDF_LIB_DIR = /opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1/lib/"
-            echo "NETCDF_LIB_DIR=/opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1/lib/" >> $GITHUB_ENV
-            echo "Set NETCDF_INC_DIR = /opt/homebrew/Cellar/netcdf-fortran/4.6.1/include/"
-            echo "NETCDF_INC_DIR=/opt/homebrew/Cellar/netcdf-fortran/4.6.1/include/" >> $GITHUB_ENV 
+            echo "Set NETCDF_LIB_DIR = /opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1_1/lib/"
+            echo "NETCDF_LIB_DIR=/opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1_1/lib/" >> $GITHUB_ENV
+            echo "Set NETCDF_INC_DIR = /opt/homebrew/Cellar/netcdf-fortran/4.6.1_1/include/"
+            echo "NETCDF_INC_DIR=/opt/homebrew/Cellar/netcdf-fortran/4.6.1_1/include/" >> $GITHUB_ENV
           elif ${{ contains(matrix.os, 'ubuntu') }}; then  
             echo "Set STELLA_SYSTEM = gnu_ubuntu"
             echo "STELLA_SYSTEM=gnu_ubuntu" >> $GITHUB_ENV
@@ -87,6 +88,22 @@ jobs:
       # Check-out repository under $GITHUB_WORKSPACE
       - name: Check-out repository
         uses: actions/checkout@v4 
+
+      # Print system information
+      - name: System information
+        run: |
+          if ${{ contains(matrix.os, 'macos') }}; then  
+            echo " "; echo "System information:"; echo "$(system_profiler SPHardwareDataType | sed 's/^/  /')"
+            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
+            echo " "; echo "Clang version:"; echo "$(clang --version | sed 's/^/  /')"
+            make numerical-tests-system
+          elif ${{ contains(matrix.os, 'ubuntu') }}; then  
+            echo " "; echo "System information:"; echo "$(cat /etc/*release | sed 's/^/  /')"
+            echo " "; echo "Number of cores:"; echo "$(lscpu | egrep 'Model name|Socket|Thread|NUMA|CPU\(s\)' | sed 's/^/  /')"
+            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
+            echo " "; echo "Netcdf version:"; echo "$(nf-config --all | sed 's/^/  /')"
+            make numerical-tests-system
+          fi
           
       # Build stella executable
       - name: Build stella
@@ -114,31 +131,29 @@ jobs:
              cmake . -B COMPILATION/build_cmake
              cmake --build COMPILATION/build_cmake -j 4
           fi
-
-      # Print system information
-      - name: System information
-        run: |
-          if ${{ contains(matrix.os, 'macos') }}; then  
-            echo " "; echo "System information:"; echo "$(system_profiler SPHardwareDataType | sed 's/^/  /')"
-            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
-            echo " "; echo "Clang version:"; echo "$(clang --version | sed 's/^/  /')"
-            make numerical-tests-system
-          elif ${{ contains(matrix.os, 'ubuntu') }}; then  
-            echo " "; echo "System information:"; echo "$(cat /etc/*release | sed 's/^/  /')"
-            echo " "; echo "Number of cores:"; echo "$(lscpu | egrep 'Model name|Socket|Thread|NUMA|CPU\(s\)' | sed 's/^/  /')"
-            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
-            echo " "; echo "Netcdf version:"; echo "$(nf-config --all | sed 's/^/  /')"
-            make numerical-tests-system
-          fi
           
       # Check $GITHUB_WORKSPACE
       - name: Check Github Workspace
+        if: success() || failure()
         run: | 
           echo " "; echo "Running directory:"; echo "  $(pwd)"
           echo " "; echo "Files in directory:"; echo "$(ls -la | sed 's/^/  /')"
           
+      # Location of packages
+      - name: Location of packages
+        if: success() || failure()
+        run: |
+          if [ ${{ matrix.compiler }} == 'CMake' ]; then 
+             echo " "; echo "--------- DIRECTORIES OF PACKAGES ----------"
+             cat COMPILATION/build_cmake/CMakeCache.txt
+          fi
+          if [ ${{ matrix.compiler }} == 'Make' ]; then 
+             echo " "; echo "Check the CMake compilation for the location of the packages." 
+          fi
+          
       # Install python environment
       - name: Install python virtual environment
+        if: success() || failure()
         run: |
           if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then 
             python3 -m venv AUTOMATIC_TESTS/venv
@@ -187,7 +202,7 @@ jobs:
           if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
           make numerical-tests-6
           
-      - name: Python tests 7 - Electromagnetic effects"
+      - name: Python tests 7 - Electromagnetic effects
         if: success() || failure() 
         run: |
           if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
@@ -225,7 +240,7 @@ jobs:
           git submodule update --init --recursive
           make -j 12
           
-          # Stella is bugged when compiling without the falg debug = on
+          # Stella is bugged when compiling without the flag debug = on
           # So the python tests will break when compiling with CMake
           #cmake . -B COMPILATION/build_cmake
           #cmake --build COMPILATION/build_cmake -j 4
diff --git a/.gitignore b/.gitignore
index 3a395c987e..a5c8f864f4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -38,6 +38,8 @@ system_fortran.f90
 
 # Stellapy
 !stellapy/data/stella
+*.pickle
+stellapy_figures/
 
 # Fortran tests
 automated-fortran-tests
@@ -76,6 +78,9 @@ share/python-wheels/
 *.egg
 MANIFEST
 
+# External modules
+EXTERNALS/pyrokinetics/src/pyrokinetics/_version.py
+
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.
diff --git a/.gitmodules b/.gitmodules
index 1dccd2ef3a..f64d447cbf 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -7,3 +7,6 @@
 [submodule "externals/neasyf"]
 	path = EXTERNALS/neasyf
 	url = https://github.com/PlasmaFAIR/neasy-f.git
+[submodule "EXTERNALS/pyrokinetics"]
+	path = EXTERNALS/pyrokinetics
+	url = https://github.com/pyro-kinetics/pyrokinetics
diff --git a/AUTOMATIC_TESTS/Makefile b/AUTOMATIC_TESTS/Makefile
index bbfba59808..3183154daa 100644
--- a/AUTOMATIC_TESTS/Makefile
+++ b/AUTOMATIC_TESTS/Makefile
@@ -53,6 +53,11 @@ numerical-tests-system:
 test-tools: check-tests-dependencies $(PROJECT_DIR)/stella
 	@echo "Running: test stella tools"
 	@python3 -m pytest -v -rF -W ignore::DeprecationWarning $(TEST_DIR)/test_tools/
+
+# Run the automated stella tests (the -r flag shows the full stella output and -rf shows extra info about the failed outputs)
+pyrokinetics-tests: check-tests-dependencies $(PROJECT_DIR)/stella
+	@echo "Running: automated stella tests for pyrokinetics"
+	@python3 -m pytest -v -rF -W ignore::DeprecationWarning $(TEST_DIR)/pyrokinetics_tests/
 	
 # Run the automated stella tests (the -r flag shows the full stella output)
 # -rA shows all outputs, -rf shows only failed outputs 
diff --git a/AUTOMATIC_TESTS/check_automated_stella_tests_requirements.py b/AUTOMATIC_TESTS/check_automated_stella_tests_requirements.py
index a706954ec2..e733dcb91f 100644
--- a/AUTOMATIC_TESTS/check_automated_stella_tests_requirements.py
+++ b/AUTOMATIC_TESTS/check_automated_stella_tests_requirements.py
@@ -14,7 +14,10 @@
 for line in contents:
     if line.startswith("#"):
         continue
+    if line.replace(' ','').replace('\n','').replace('\t','')=='':
+        continue
     module = line.split("=")[0]
+    if 'pyrokinetics' in line: module = 'pyrokinetics'
     requirements.append(module.replace(">", "").replace("~", "").replace("\n", ""))
 
 failed_modules = []
@@ -33,6 +36,7 @@
             Run:
                 make create-test-virtualenv
                 source AUTOMATIC_TESTS/venv/bin/activate
+                pip install EXTERNALS/pyrokinetics/.
             to install and activate test dependencies
             """
         )
diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/empty.in b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/empty.in
new file mode 100644
index 0000000000..db80510203
--- /dev/null
+++ b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/empty.in
@@ -0,0 +1,38 @@
+
+! Smallest possible input file that runs without errors
+! and that runs fast, hence we set (nkx,nky,nzed,nmu,nvpa)
+
+&parameters_numerical
+  nstep=10
+/
+&stella_diagnostics_knobs
+  nwrite = 1
+/
+&species_parameters_1 
+/
+&kt_grids_knobs
+  grid_option='range'
+/
+&kt_grids_range_parameters
+  naky = 10
+  aky_min = 0.1
+  aky_max = 1.0
+  nakx = 1
+  akx_min = 0.0
+  akx_max = 0.0
+/
+&zgrid_parameters 
+  nzed = 8
+/
+&vpamu_grids_parameters
+  nmu = 4 
+  nvgrid = 6 
+/
+&millergeo_parameters
+  rhoc = 0.5
+  shat = 0.796
+  qinp = 1.4
+  rmaj = 2.77778
+  rgeo = 2.77778
+  kappa = 1.0
+/ 
diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC.in b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC.in
new file mode 100644
index 0000000000..16f623608d
--- /dev/null
+++ b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC.in
@@ -0,0 +1,97 @@
+ 
+! Simple linear example using CBC
+
+&parameters_physics
+  adiabatic_option = 'iphi00=2'
+  full_flux_surface = .false.
+  include_apar = .false.
+  nonlinear = .false.
+  vnew_ref = 0.01
+/
+&parameters_numerical
+  delt = 0.05 
+  nstep = 10
+  print_extra_info_to_terminal = .false.
+/
+&stella_diagnostics_knobs
+  nsave = 10
+  nwrite = 1
+  save_for_restart = .false.
+  write_all = .true.
+/
+&species_knobs
+  nspec = 2
+  species_option = 'stella'
+/
+&species_parameters_1
+  dens = 1.0
+  fprim = 1.0
+  mass = 1.0
+  temp = 1.0
+  tprim = 3.0
+  type = 'ion'
+  z = 1.0
+/
+&species_parameters_2
+  dens = 1.0
+  fprim = 1.0
+  mass = 0.0005446
+  temp = 1.0
+  tprim = 3.0
+  type = 'electron'
+  z = -1.0
+/
+&kt_grids_knobs
+  grid_option='range'
+/
+&kt_grids_range_parameters
+  naky = 10
+  aky_min = 0.1
+  aky_max = 1.0
+  nakx = 1
+  akx_min = 0.0
+  akx_max = 0.0
+/
+&zgrid_parameters
+  boundary_option = 'zero'
+  nperiod = 1
+  nzed = 8
+/
+&vpamu_grids_parameters
+  nmu = 4 
+  nvgrid = 6 
+/
+&init_g_knobs
+  ginit_option = 'noise'
+  phiinit = 0.01
+/
+&dissipation
+  hyper_dissipation = .true.
+/
+&geo_knobs
+  geo_option = 'miller'
+/
+&time_advance_knobs 
+  explicit_option = 'rk2'
+/
+&layouts_knobs
+  vms_layout = 'vms'
+  xyzs_layout = 'yxzs'
+/
+&millergeo_parameters
+  nzed_local = 128
+  rhoc = 0.5
+  shat = 0.796
+  qinp = 1.4
+  rmaj = 2.77778
+  rgeo = 2.77778
+  shift = 0.0
+  kappa = 1.0
+  kapprim = 0.0
+  tri = 0.0
+  triprim = 0.0
+  betaprim = 0.0
+  d2qdr2 = 0.0
+  d2psidr2 = 0.0
+  betadbprim = 0.0
+/ 
diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC_old.in b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC_old.in
new file mode 100644
index 0000000000..746c5e468e
--- /dev/null
+++ b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC_old.in
@@ -0,0 +1,96 @@
+ 
+! Simple linear example using CBC
+
+&physics_flags
+  adiabatic_option = 'iphi00=2'
+  full_flux_surface = .false.
+  include_apar = .false.
+  nonlinear = .false.
+/
+&species_knobs
+  nspec = 2
+  species_option = 'stella'
+/
+&species_parameters_1
+  dens = 1.0
+  fprim = 1.0
+  mass = 1.0
+  temp = 1.0
+  tprim = 3.0
+  type = 'ion'
+  z = 1.0
+/
+&species_parameters_2
+  dens = 1.0
+  fprim = 1.0
+  mass = 0.0005446
+  temp = 1.0
+  tprim = 3.0
+  type = 'electron'
+  z = -1.0
+/
+&kt_grids_knobs
+  grid_option='range'
+/
+&kt_grids_range_parameters
+  naky = 10
+  aky_min = 0.1
+  aky_max = 1.0
+  nakx = 1
+  akx_min = 0.0
+  akx_max = 0.0
+/
+&zgrid_parameters
+  boundary_option = 'zero'
+  nperiod = 1
+  nzed = 8
+/
+&vpamu_grids_parameters
+  nmu = 4 
+  nvgrid = 6 
+/
+&knobs
+  delt = 0.05 
+  nstep = 1000
+  print_extra_info_to_terminal = .false.  
+/
+&stella_diagnostics_knobs
+  nsave = 100
+  nwrite = 10
+  save_for_restart = .false.
+  write_all = .true.
+/
+&init_g_knobs
+  ginit_option = 'noise'
+  phiinit = 0.01
+/
+&dissipation
+  hyper_dissipation = .true.
+/
+&geo_knobs
+  geo_option = 'miller'
+/
+&time_advance_knobs 
+  explicit_option = 'rk2'
+/
+&layouts_knobs
+  vms_layout = 'vms'
+  xyzs_layout = 'yxzs'
+/
+&millergeo_parameters
+  nzed_local = 128
+  rhoc = 0.5
+  shat = 0.796
+  qinp = 1.4
+  rmaj = 2.77778
+  rgeo = 2.77778
+  shift = 0.0
+  kappa = 1.0
+  kapprim = 0.0
+  tri = 0.0
+  triprim = 0.0
+  betaprim = 0.0
+  d2qdr2 = 0.0
+  d2psidr2 = 0.0
+  betadbprim = 0.0
+/ 
diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC_quick.in b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC_quick.in
new file mode 100644
index 0000000000..7f0ee39249
--- /dev/null
+++ b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC_quick.in
@@ -0,0 +1,96 @@
+ 
+! Simple linear example using CBC
+
+&physics_flags
+  adiabatic_option = 'iphi00=2'
+  full_flux_surface = .false.
+  include_apar = .false.
+  nonlinear = .false.
+/
+&species_knobs
+  nspec = 2
+  species_option = 'stella'
+/
+&species_parameters_1
+  dens = 1.0
+  fprim = 1.0
+  mass = 1.0
+  temp = 1.0
+  tprim = 3.0
+  type = 'ion'
+  z = 1.0
+/
+&species_parameters_2
+  dens = 1.0
+  fprim = 1.0
+  mass = 0.0005446
+  temp = 1.0
+  tprim = 3.0
+  type = 'electron'
+  z = -1.0
+/
+&kt_grids_knobs
+  grid_option='range'
+/
+&kt_grids_range_parameters
+  naky = 10
+  aky_min = 0.1
+  aky_max = 1.0
+  nakx = 1
+  akx_min = 0.0
+  akx_max = 0.0
+/
+&zgrid_parameters
+  boundary_option = 'zero'
+  nperiod = 1
+  nzed = 8
+/
+&vpamu_grids_parameters
+  nmu = 4 
+  nvgrid = 6 
+/
+&knobs
+  delt = 0.05 
+  nstep = 10
+  print_extra_info_to_terminal = .false.  
+/
+&stella_diagnostics_knobs
+  nsave = 10
+  nwrite = 1
+  save_for_restart = .false.
+  write_all = .true.
+/
+&init_g_knobs
+  ginit_option = 'noise'
+  phiinit = 0.01
+/
+&dissipation
+  hyper_dissipation = .true.
+/
+&geo_knobs
+  geo_option = 'miller'
+/
+&time_advance_knobs 
+  explicit_option = 'rk2'
+/
+&layouts_knobs
+  vms_layout = 'vms'
+  xyzs_layout = 'yxzs'
+/
+&millergeo_parameters
+  nzed_local = 128
+  rhoc = 0.5
+  shat = 0.796
+  qinp = 1.4
+  rmaj = 2.77778
+  rgeo = 2.77778
+  shift = 0.0
+  kappa = 1.0
+  kapprim = 0.0
+  tri = 0.0
+  triprim = 0.0
+  betaprim = 0.0
+  d2qdr2 = 0.0
+  d2psidr2 = 0.0
+  betadbprim = 0.0
+/ 
diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1a_whether_stella_runs.py b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1a_whether_stella_runs.py
new file mode 100755
index 0000000000..4fbb2508df
--- /dev/null
+++ b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1a_whether_stella_runs.py
@@ -0,0 +1,131 @@
+################################################################################
+#              Check whether pyrokinetics can plot stella output               #
+################################################################################
+
+# Python modules
+import os, sys
+import pathlib 
+import numpy as np
+import xarray as xr  
+
+# Package to run stella 
+module_path = str(pathlib.Path(__file__).parent.parent.parent / 'run_local_stella_simulation.py')
+with open(module_path, 'r') as file: exec(file.read())
+
+# Global variables  
+input_filename = 'miller_linear_CBC.in'  
+local_stella_run_directory = 'Not/Run/Yet'
+
+#-------------------------------------------------------------------------------
+#                         Run local stella simulation                          #
+#-------------------------------------------------------------------------------
+def test_whether_we_can_run_a_local_stella_simulation(tmp_path):
+    '''Run a local stella simulation in a temporary folder <tmp_path>.'''  
+    
+    # Save the temporary folder <tmp_path> as a global variable so the
+    # other tests can access the output files from the local stella run.
+    global local_stella_run_directory
+    local_stella_run_directory = tmp_path
+    
+    # Run stella inside of <tmp_path> based on <input_filename>
+    run_local_stella_simulation(input_filename, tmp_path)
+    print('\n  -->  Successfully ran a local stella simulation.')
+    return 
+    
+#-------------------------------------------------------------------------------
+#                    Check whether output files are present                    #
+#-------------------------------------------------------------------------------
+def test_whether_all_output_files_are_gerenated_when_running_stella(error=False):  
+    '''To ensure that stella ran correctly, check that all output files are generated.'''
+    
+    # Gather the output files generated during the local stella run inside <tmp_path>
+    local_files = os.listdir(local_stella_run_directory)
+    
+    # Create a list of the output files we expect when stella has been run
+    stem = input_filename.replace('.in','')
+    expected_files = ['in', 'out.nc', 'geometry', 'fluxes', 'omega', 'out', 'final_fields', 'species.input', 'error']
+    expected_files = [stem+'.'+extension for extension in expected_files]
+    
+    # Check whether all these output files are present
+    for expected_file in expected_files:
+        if not (expected_file in local_files):
+            print(f'ERROR: The "{expected_file}" output file was not generated when running stella.'); error = True
+            
+    # The <pytest> module will check whether all <assert> statements are true,
+    # if it runs into a statement which is false, the test will be labeled as
+    # "Failed" and the string in the second argument of the <assert> statement 
+    # will be printed to the command prompt as "AssertionError: <error message>"
+    assert (not error), f'Some output files were not generated when running stella.'
+    
+    # The test will stop as soon as an <assert> error was triggered, hence we
+    # will only reach this final line of code if the test ran successfully
+    print(f'  -->  All the expected files (.in, .geometry, .out.nc, .fluxes, .omega, ...) are generated.')
+    return 
+        
+#-------------------------------------------------------------------------------
+#         Check whether all quantities are present in the netcdf file          #
+#-------------------------------------------------------------------------------
+def test_whether_correct_quantities_are_present_in_netcdf_file(error=False):
+    '''Check whether the correct quantities are present in the netcdf output file.''' 
+    
+    # Find the netcdf output file which was generated during our local stella run
+    local_netcdf_file = local_stella_run_directory / input_filename.replace('.in', '.out.nc')
+    
+    # Open the netcdf file
+    with xr.open_dataset(local_netcdf_file) as local_netcdf:
+    
+        # Check whether all the dimensions are present in the netcdf file
+        expected_keys = ['kx', 'ky', 'tube', 'zed', 'alpha', 'vpa', 'mu', 'species', 't', 'char10', 'char200', 'ri']  
+        for key in expected_keys:
+            if (key not in local_netcdf): print(f'ERROR: The quantity {key} could not be found in the netcdf file.'); error = True
+        if not error: print(f'  -->  The netcdf file contains the following dimensions: {expected_keys}.')  
+    
+        # Check whether all the species information is present in the netcdf file
+        expected_keys = ['charge', 'mass', 'dens', 'temp', 'tprim', 'fprim', 'vnew', 'type_of_species'] 
+        for key in expected_keys:
+            if (key not in local_netcdf): print(f'ERROR: The quantity {key} could not be found in the netcdf file.'); error = True
+        if not error: print(f'  -->  The netcdf file contains the following species information: {expected_keys}.')
+         
+        # Check whether all the geometry data is present in the netcdf file
+        expected_keys = ['bmag', 'b_dot_grad_z', 'gradpar', 'gbdrift', 'gbdrift0', 'cvdrift', 'cvdrift0', 'kperp2', \
+            'gds2', 'gds21', 'gds22', 'grho', 'jacob', 'djacdrho', 'beta', 'q', 'shat', 'd2qdr2', 'drhodpsi', 'd2psidr2', 'jtwist'] 
+        for key in expected_keys:
+            if (key not in local_netcdf): print(f'ERROR: The quantity {key} could not be found in the netcdf file.'); error = True
+        if not error: print(f'  -->  The netcdf file contains the following geometry data: {expected_keys}.')
+        
+        # Check whether all the diagnostics data is present in the netcdf file
+        dist_extensions = ['_vs_vpamus', '_vs_zvpas', '_vs_zmus', '_vs_zvpamus']
+        expected_keys = ['t', 'omega', 'phi2', 'apar2', 'bpar2', 'omega']; new_keys = True
+        expected_keys += [i+j for i in ['pflux', 'qflux', 'vflux'] for j in ['_vs_s', '_vs_kxkyzs']]
+        expected_keys += [i+j for i in ['g2', 'h2', 'f2', 'g2nozonal', 'h2nozonal', 'f2nozonal'] for j in dist_extensions]
+        expected_keys += ['g2_vs_zkykxs', 'h2_vs_zkykxs', 'f2_vs_zkykxs']
+        for key in expected_keys:
+            if (key not in local_netcdf): 
+                print(f'ERROR: The quantity {key} could not be found in the netcdf file.'); new_keys = False
+            
+        # Try old stella names
+        if new_keys==False:
+            print('--------------------------------------------------')
+            print(' The new stella keys werent found, try old keys.')
+            print('--------------------------------------------------')
+            expected_keys = ['t', 'omega', 'phi2', 'apar2', 'bpar2', 'pflx', 'vflx', 'phi_vs_t', 'phi2_vs_kxky', \
+               'pflx_vs_kxky', 'vflx_vs_kxky', 'qflx_vs_kxky', 'pflux_x', 'vflux_x', 'qflux_x', \
+               'dens_x', 'upar_x', 'temp_x', 'pflx_kxky', 'vflx_kxky', 'qflx_kxky', 'gvmus', 'gzvs']  
+            for key in expected_keys:
+               if (key not in local_netcdf): 
+                   print(f'ERROR: The quantity {key} could not be found in the netcdf file.'); error = True
+                       
+        if not error: print(f'  -->  The netcdf file contains the following diagnostics data: {expected_keys}.')
+            
+        # The <pytest> module will check whether all <assert> statements are true,
+        # if it runs into a statement which is false, the test will be labeled as
+        # "Failed" and the string in the second argument of the <assert> statement 
+        # will be printed to the command prompt as "AssertionError: <error message>"
+        assert (not error), f'Some quantities were not found in the netcdf file.' 
+        
+        # The test will stop as soon as an <assert> error was triggered, hence we
+        # will only reach this final line of code if the test ran successfully
+        print(f'  -->  The netcdf file contains all the expected data.')
+        
+    return 
+     
diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1b_whether_pyrokinetics_loads.py b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1b_whether_pyrokinetics_loads.py
new file mode 100755
index 0000000000..5262d76077
--- /dev/null
+++ b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1b_whether_pyrokinetics_loads.py
@@ -0,0 +1,40 @@
+################################################################################
+#              Check whether pyrokinetics can plot stella output               #
+################################################################################
+
+# Python modules
+import os, sys
+import pathlib 
+import numpy as np
+import xarray as xr  
+
+# Package to run stella 
+module_path = str(pathlib.Path(__file__).parent.parent.parent / 'run_local_stella_simulation.py')
+with open(module_path, 'r') as file: exec(file.read())
+
+# Pyrokinetics package
+from pyrokinetics import Pyro
+
+# Global variables  
+input_filename = 'miller_linear_CBC.in'  
+local_stella_run_directory = 'Not/Run/Yet'
+
+#-------------------------------------------------------------------------------
+#                         Run local stella simulation                          #
+#-------------------------------------------------------------------------------
+def test_whether_we_can_load_pyrokinetics(tmp_path):
+    '''Run a local stella simulation in a temporary folder <tmp_path>.'''  
+    
+    # Save the temporary folder <tmp_path> as a global variable so the
+    # other tests can access the output files from the local stella run.
+    global local_stella_run_directory
+    local_stella_run_directory = tmp_path
+    
+    # Run stella inside of <tmp_path> based on <input_filename>
+    run_local_stella_simulation(input_filename, tmp_path) 
+    
+    # Load the pyro data
+    local_input_file = local_stella_run_directory / input_filename
+    pyro = Pyro(gk_file=local_input_file, gk_code="STELLA")
+    print('\n  -->  Successfully loaded pyrokinetics.')
+    return
diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1c_whether_pyrokinetics_loads_for_empty_input.py b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1c_whether_pyrokinetics_loads_for_empty_input.py
new file mode 100755
index 0000000000..af8f211742
--- /dev/null
+++ b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/test_1c_whether_pyrokinetics_loads_for_empty_input.py
@@ -0,0 +1,41 @@
+################################################################################
+#              Check whether pyrokinetics can plot stella output               #
+################################################################################
+
+# Python modules
+import os, sys
+import pathlib 
+import numpy as np
+import xarray as xr  
+
+# Package to run stella 
+module_path = str(pathlib.Path(__file__).parent.parent.parent / 'run_local_stella_simulation.py')
+with open(module_path, 'r') as file: exec(file.read())
+
+# Pyrokinetics package
+from pyrokinetics import Pyro
+
+# Global variables  
+input_filename = 'empty.in'  
+local_stella_run_directory = 'Not/Run/Yet'
+
+#-------------------------------------------------------------------------------
+#                         Run local stella simulation                          #
+#-------------------------------------------------------------------------------
+def TODO_test_whether_we_can_load_pyrokinetics(tmp_path):
+    '''Run a local stella simulation in a temporary folder <tmp_path>.'''  
+    
+    # Save the temporary folder <tmp_path> as a global variable so the
+    # other tests can access the output files from the local stella run.
+    global local_stella_run_directory
+    local_stella_run_directory = tmp_path
+    
+    # Run stella inside of <tmp_path> based on <input_filename>
+    run_local_stella_simulation(input_filename, tmp_path) 
+    
+    # Load the pyro data
+    local_input_file = local_stella_run_directory / input_filename
+    pyro = Pyro(gk_file=local_input_file, gk_code="STELLA")
+    print('\n  -->  Successfully loaded pyrokinetics.')
+    return 
+
diff --git a/COMPILATION/CMakeLists.txt b/COMPILATION/CMakeLists.txt
index a9ca6fa89a..dc586e6217 100644
--- a/COMPILATION/CMakeLists.txt
+++ b/COMPILATION/CMakeLists.txt
@@ -8,7 +8,10 @@ project(stella
   VERSION 0.3
   LANGUAGES Fortran)
 
-set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/COMPILATION/cmake" ${CMAKE_MODULE_PATH})
+# Cmake files
+set(CMAKE_MODULE_PATH
+"${CMAKE_SOURCE_DIR}/COMPILATION/cmake" 
+${CMAKE_MODULE_PATH})
 
 # Sets default build type to RelWithDebInfo
 include(BuildType)
@@ -42,7 +45,7 @@ option(STELLA_UPDATE_GIT_SUBMODULES "Check submodules are up-to-date during buil
 
 # Sources that don't need preprocessing
 set(STELLA_SOURCES_f90
-  ../EXTERNALS/utils/define.inc
+  ../STELLA_CODE/utils/define.inc
   ../STELLA_CODE/calculations/calculations_kxky.f90
   ../STELLA_CODE/calculations/dist_redistribute.f90
   ../STELLA_CODE/calculations/finite_differences.f90
@@ -157,7 +160,7 @@ add_executable(stella
 target_link_libraries(stella PRIVATE libstella)
 
 # The include.inc file is located in EXTERNALS/utils/
-include_directories("${CMAKE_SOURCE_DIR}/EXTERNALS/utils")
+include_directories("${CMAKE_SOURCE_DIR}/STELLA_CODE/utils")
 
 # When target `stella` is built, a symlink will be created
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
@@ -269,6 +272,14 @@ target_compile_definitions(libstella PRIVATE
   $<$<Fortran_COMPILER_ID:Intel>:FCOMPILER=_INTEL_>
   $<$<Fortran_COMPILER_ID:Cray>:FCOMPILER=_CRAY_>
   )
+  
+
+# Find hdf5 packages (their CMake file needs the C language)
+# These lines are only needed for Mac systems on Github since January 2025
+# For some reason CMake could not find the hdf5 libraries anymore after a Github update
+ENABLE_LANGUAGE(C)
+find_package(HDF5 REQUIRED)
+target_link_libraries(libstella PUBLIC ${HDF5_LIBRARIES}) 
 
 ############################################################
 # Add some extra flags for Debug configs
@@ -289,7 +300,7 @@ target_compile_options(libstella PRIVATE
 # Internal libraries: <stella_utils> and <mini_libstell>
 ############################################################
 
-add_subdirectory(../EXTERNALS/utils ${CMAKE_CURRENT_BINARY_DIR}/EXTERNALS/utils)
+add_subdirectory(../STELLA_CODE/utils ${CMAKE_CURRENT_BINARY_DIR}/STELLA_CODE/utils)
 add_subdirectory(../EXTERNALS/mini_libstell ${CMAKE_CURRENT_BINARY_DIR}/EXTERNALS/mini_libstell)
 target_link_libraries(libstella PUBLIC mini_libstell stella_utils)
 
diff --git a/COMPILATION/LoadModules/README.md b/COMPILATION/LoadModules/README.md
new file mode 100644
index 0000000000..442fb38a67
--- /dev/null
+++ b/COMPILATION/LoadModules/README.md
@@ -0,0 +1,60 @@
+# stella compilation: Load modules
+
+## Download stella
+
+First, download stella from the GitHub repository:
+>> git clone https://github.com/stellaGK/stella.git
+>> git submodule update --init --recursive
+
+## Load the system dependent modules
+
+Each system has its own modules installed, therefore a load_modules.SYSTEM file
+has been written for each specific system. Source the load_modules.SYSTEM file:
+
+>> source COMPILATION/LoadModules/load_modules.marenostrum
+>> source COMPILATION/LoadModules/load_modules.xula
+
+## Compile with CMake
+
+>> cmake . -B COMPILATION/build_cmake
+>> cmake --build COMPILATION/build_cmake
+
+
+-- Found MPI_Fortran: /mnt/lustre/home/spack/spack/opt/spack/linux-rocky8-icelake/oneapi-2023.1.0/intel-oneapi-mpi-2021.9.0-alz6lstmpi2dfpkk3trayc2xqpj54hi6/lib/libmpifort.so (found version "3.1") 
+
+
+
+
+# Set-up system dependent modules
+
+## Module availability
+
+To check the available modules:
+>> module avail intel
+>> module avail mpi
+>> module avail netcdf
+>> module avail hdf5
+
+## Module location 
+
+To check the location of a loaded module:
+>> module show intel
+>> module show mpi
+>> module show netcdf
+>> module show hdf5
+
+## Local directory without GitHub link
+
+If the stella directory is not linked to GitHub, the git_version library will
+most likely refuse to compile, to resolve this issue do:
+>> git init
+
+
+## Check if the correct modules are loaded with CMake
+
+When setting up the modules, it is the easiest to use CMake to check the compilation.
+>> cmake . -B COMPILATION/build_cmake
+
+
+
+
diff --git a/COMPILATION/LoadModules/load_modules.dirac b/COMPILATION/LoadModules/load_modules.dirac
new file mode 100755
index 0000000000..9a81b0b0b5
--- /dev/null
+++ b/COMPILATION/LoadModules/load_modules.dirac
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+# Unload the preloaded modules
+module purge
+
+# Load dirac modules needed for stella 
+module load intel/mkl/2020.2;\
+module load intel/impi/2020.2/intel;\
+module load openblas/0.2.15;\
+module load netlib-scalapack-2.0.2-intel-17.0.4-wwvkcj6;\
+module load szip-2.1.1-gcc-5.4.0-6vkwvdj;\
+module load zlib/1.2.11;\
+module load hdf5-1.10.4-intel-17.0.4-swn7n43;\
+module load netcdf-4.4.1.1-intel-17.0.4-zysrbqw;\
+module load netcdf-fortran-4.4.4-intel-17.0.4-cesnirf;\
+module load fftw-3.3.6-pl2-intel-17.0.4-qssvkuw;\
+
+export STELLA_SYSTEM="dirac"
+export MAKEFLAGS="-IMakefiles"
diff --git a/COMPILATION/LoadModules/load_modules.marconi b/COMPILATION/LoadModules/load_modules.marconi
new file mode 100755
index 0000000000..36839d7cb3
--- /dev/null
+++ b/COMPILATION/LoadModules/load_modules.marconi
@@ -0,0 +1,27 @@
+#!/bin/sh
+
+# Unload the preloaded modules
+module purge
+
+# Load Marconi modules needed for stella 
+module load env-skl
+module load intel/pe-xe-2018--binary 
+module load intelmpi/2018--binary
+module load szip/2.1--gnu--6.1.0
+module load zlib/1.2.8--gnu--6.1.0
+module load hdf5/1.10.4--intel--pe-xe-2018--binary
+module load netcdf/4.6.1--intel--pe-xe-2018--binary
+module load netcdff/4.4.4--intel--pe-xe-2018--binary
+module load fftw/3.3.7--intelmpi--2018--binary 
+module load mkl/2018--binary 
+module load scalapack
+module load blas  
+module load git
+
+# Set some directories for the make file of Marconi
+export NETCDF_LIB_DIR=/cineca/prod/opt/libraries/netcdff/4.4.4/intel--pe-xe-2018--binary/lib
+export NETCDF_INC_DIR=/cineca/prod/opt/libraries/netcdff/4.4.4/intel--pe-xe-2018--binary/include
+export FFTW_LIB_DIR=$FFTW_DIR/lib
+export FFTW_INC_DIR=$FFTW_INC
+export STELLA_SYSTEM="marconi"
+export MAKEFLAGS="-IMakefiles"
diff --git a/COMPILATION/LoadModules/load_modules.marenostrum b/COMPILATION/LoadModules/load_modules.marenostrum
new file mode 100755
index 0000000000..78b2041c20
--- /dev/null
+++ b/COMPILATION/LoadModules/load_modules.marenostrum
@@ -0,0 +1,33 @@
+#!/bin/sh
+
+# Unload the preloaded modules
+module purge
+
+# Load Marenostrum modules needed for stella (option 1)
+module load oneapi 
+module load ucx/1.15.0 
+module load fftw/3.3.10 
+module load hdf5/1.14.1-2 
+module load pnetcdf/1.12.3 
+module load netcdf/2023-06-14 
+module load lapack/3.11-gcc 
+module load petsc/3.20.5
+
+# Load Marenostrum modules needed for stella (option 2)
+#module load openmpi/4.1.5-gcc 
+#module load hdf5/1.14.1-2-gcc-openmpi 
+#module load pnetcdf/1.12.3-gcc-openmpi 
+#module load netcdf/c-4.9.2_fortran-4.6.1_cxx4-4.3.1_hdf5-1.14.1-2_pnetcdf-1.12.3-gcc-openmpi 
+#module load gcc/13.2.0  
+#module load fftw/3.3.10-gcc-ompi 
+#module load hdf5/1.14.1-2-gcc-openmpi 
+#module load intel-advisor/2023.2.0
+#module load cmake
+
+# Set some directories for the make file of marenostrum
+export NETCDF_INC_DIR=$NETCDF_INC
+export NETCDF_LIB_DIR=$NETCDF_LIB
+export FFTW_INC_DIR=-I$FFTW_INCL
+export FFTW_LIB_DIR=$FFTW_DIR/lib
+export STELLA_SYSTEM="marenostrum"
+export MAKEFLAGS="-IMakefiles"
diff --git a/COMPILATION/LoadModules/load_modules.stellar b/COMPILATION/LoadModules/load_modules.stellar
new file mode 100755
index 0000000000..b1ae4292ad
--- /dev/null
+++ b/COMPILATION/LoadModules/load_modules.stellar
@@ -0,0 +1,18 @@
+#!/bin/sh
+
+# Unload the preloaded modules
+module purge
+
+# Load stellar modules needed for stella
+module load intel/2021.1.2
+module load openmpi/intel-2021.1/4.1.2
+module load fftw/intel-2021.1/openmpi-4.1.0/3.3.9
+module load hdf5/intel-2021.1/openmpi-4.1.0/1.10.6
+module load netcdf/intel-2021.1/hdf5-1.10.6/openmpi-4.1.0/4.7.4
+module load anaconda3/2020.11
+module load scalapack/openmpi-4.1.0/2.0.2
+module load cudatoolkit/11.4
+module load gsl/2.6
+
+export STELLA_SYSTEM="stellar"
+export MAKEFLAGS="-IMakefiles"
diff --git a/COMPILATION/LoadModules/load_modules.xula b/COMPILATION/LoadModules/load_modules.xula
new file mode 100755
index 0000000000..a29deb4881
--- /dev/null
+++ b/COMPILATION/LoadModules/load_modules.xula
@@ -0,0 +1,37 @@
+# Clean modules
+module purge
+
+# Set environment variables
+export STELLA_SYSTEM='xula'
+export MAKEFLAGS=-IMakefiles
+
+# Load Xula modules
+module load gcc-8.5.0-gcc-8.5.0-okhf4dl
+module load openmpi-4.1.5-gcc-8.5.0-wc244g5
+module load fftw-3.3.10-gcc-8.5.0-gyw6vjk 
+module load hdf5-1.14.1-2-gcc-8.5.0-nmh7bhg
+module load netcdf-c-4.9.2-gcc-8.5.0-tm5mqc4
+module load netcdf-fortran-4.6.0-gcc-8.5.0-5t42x57
+module load parallel-netcdf-1.12.3-gcc-8.5.0-jjzb3pe
+module load netlib-scalapack-2.2.0-gcc-8.5.0-jpwc63q
+module load netlib-lapack-3.11.0-gcc-8.5.0-af4h4co
+
+# Compile stella with CMake
+module load cmake-3.26.3-gcc-9.4.0-6t6wfdo
+
+# Numerical tests need python
+module load python-3.10.10-gcc-8.5.0-ze5tho3
+module load py-pip-23.0-gcc-8.5.0-myj46az
+
+# Check loaded modules
+echo "   "
+echo "GCC version:"
+gcc --version
+echo "Python version:"
+python --version
+echo "   "
+
+# Set some directories for the make file of xula
+export NETCDF_HOME=/mnt/lustre/home/spack/spack/opt/spack/linux-rocky8-icelake/gcc-8.5.0/netcdf-c-4.9.2-tm5mqc44n3zsrs4sildwyrv2ynjxfnlh/
+export FFT_HOME=/mnt/lustre/home/spack/spack/opt/spack/linux-rocky8-icelake/gcc-8.5.0/fftw-3.3.10-gyw6vjk5lqaocgtvd42czbeai4qdiecq/
+export LAPACK_HOME=/mnt/lustre/home/spack/spack/opt/spack/linux-rocky8-icelake/gcc-8.5.0/netlib-lapack-3.11.0-af4h4cocidqmbtafrjzzqwky3wjlswmm/
diff --git a/COMPILATION/Makefile.compilerflags b/COMPILATION/Makefile.compilerflags
index 29e27bebc7..4e1f93ad09 100644
--- a/COMPILATION/Makefile.compilerflags
+++ b/COMPILATION/Makefile.compilerflags
@@ -10,7 +10,7 @@
 # The "?=" sets a variable if it does not already have a value. 
 ####################################################################
 
-DEBUG ?= in                # Turns on debug mode (bin) 
+DEBUG ?=                   # Turns on debug mode (bin) 
 TEST ?=                    # Turns on test mode (bin) 
 OPT ?= on                  # Optimization (on, aggressive, undefined)
 STATIC ?=                  # Prevents linking with shared libraries (bin)
@@ -25,37 +25,42 @@ USE_SFINCS ?=              # Link to sfincs library at compilation
 USE_LAPACK ?= on           # Use LAPACK, needed for test particle collisions
 HAS_ISO_C_BINDING ?= on    # Does the compiler support the iso_c_binding features of Fortran? (needed for local parallel LU decomposition) 
 
-# Which FFT library to use (fftw,fftw3,mkl_fftw,undefined)
+# Which FFT library to use (fftw, fftw3, mkl_fftw, undefined)
 # We can't have any spaces behind 'fftw3' so we can't put the comment behind it
 USE_FFT ?= fftw3
 
+# The compiler either uses the "-J" flag or the "-module" flag to 
+# denote the directory where the *.mod files can be found
+MODULE_FLAG = -J 
+
 # The following variables can be set in platform-dependent Makefile's
 # For example, inside stella/Makefiles/Makefile.marconi
+MAKE      = make
+CPP       = cpp
+CPPFLAGS  = -P -traditional
+FC	       = f90
+MPIFC    ?= mpif90
+H5FC     ?= h5fc
+H5FC_par ?= h5pfc
+F90FLAGS  =
+F90OPTFLAGS =
+CC        = cc
+MPICC    ?= mpicc
+H5CC     ?= h5cc
+H5CC_par ?= h5pcc
+CFLAGS    =
+COPTFLAGS =
+LD        = $(FC)
+LDFLAGS   = $(F90FLAGS)
+ARCH      = ar
+ARCHFLAGS = cr
+RANLIB    = ranlib
+AWK       = awk
+PERL      = perl
+FORD     ?= ford
 
-MAKE		 = make
-CPP		     = cpp
-CPPFLAGS	 = -P -traditional
-FC	         = f90
-MPIFC       ?= mpif90
-H5FC		?= h5fc
-H5FC_par	?= h5pfc
-F90FLAGS	 =
-F90OPTFLAGS	 =
-CC		     = cc
-MPICC		?= mpicc
-H5CC		?= h5cc
-H5CC_par	?= h5pcc
-CFLAGS		 =
-COPTFLAGS 	 =
-LD 		     = $(FC)
-LDFLAGS 	 = $(F90FLAGS)
-ARCH 		 = ar
-ARCHFLAGS 	 = cr
-RANLIB		 = ranlib
-AWK 		 = awk
-PERL		 = perl
-FORD       	?= ford
-
+# The following variables can be set in platform-dependent Makefile's
+# For example, inside stella/Makefiles/Makefile.marconi
 MPI_INC ?=
 MPI_LIB ?=
 FFT_INC ?=
@@ -71,6 +76,8 @@ SFINCS_INC ?=
 PETSC_LIB ?=
 PETSC_INC ?=
 LIBSTELL_LIB ?=
+LAPACK_LIB ?=
+LAPACK_INC ?=
 
 ####################################################################
 #                        PLATFORM DEPENDENCE                       #
@@ -164,11 +171,13 @@ endif
 ifdef USE_NETCDF
 	ifeq ($(NETCDF_LIB),)
 		NETCDF_LIB = -lnetcdf
-    endif
+	endif
 	CPPFLAGS += -DNETCDF
 endif
 ifdef USE_LAPACK
-    LAPACK_LIB ?= -llapack
+	ifeq ($(LAPACK_LIB),)
+		LAPACK_LIB = -llapack
+	endif
 	CPPFLAGS += -DLAPACK
 endif
 ifdef USE_HDF5
@@ -244,7 +253,8 @@ export NETCDF_LIB
 export COMPILATION_DIR
 export FC 
 
-# Export some variable, so they become available to compile the utils scripts
+# Export some variables, so they become available to the other make files
+export MODULE_FLAG
 export INC_FLAGS
 export CPPFLAGS
 export CPP
diff --git a/COMPILATION/Makefile.externals b/COMPILATION/Makefile.externals
index 76384d6820..4650510cb1 100644
--- a/COMPILATION/Makefile.externals
+++ b/COMPILATION/Makefile.externals
@@ -73,9 +73,9 @@
 # Define the directories where the external libraries are located 
 # Export UTILS_DIR and MINILIBSTELL_DIR because they're used in their make files
 export MINILIBSTELL_DIR := $(EXTERNALS_DIR)/mini_libstell
-export UTILS_DIR := $(EXTERNALS_DIR)/utils
 export GIT_VERSION_DIR := $(EXTERNALS_DIR)/git_version/src
 export NEASYF_DIR := $(EXTERNALS_DIR)/neasyf/src
+export UTILS_DIR := $(STELLA_DIR)/utils
 
 # Check directories
 .PHONY: print-directories-externals
diff --git a/COMPILATION/Makefile.externals.git_version b/COMPILATION/Makefile.externals.git_version
index e4866be941..8b6f01333f 100644
--- a/COMPILATION/Makefile.externals.git_version
+++ b/COMPILATION/Makefile.externals.git_version
@@ -22,7 +22,16 @@ $(GIT_VERSION_DIR)/git_version.f90:
 	@echo "  "
 
 # Now that we made sure that the submodule exists, include its makefile
+GIR_PROJECT := $(shell if [ -d $(PROJECT_DIR)/.git ]; then echo "ok"; fi)
+ifeq ($(GIR_PROJECT),)
+$(info   )
+$(info WARNING: The .git folder does not exist.)
+$(info To use the latest external projects, please link the code to Github.)
+$(info   )
+endif
+ifeq ($(GIR_PROJECT),ok)
 sinclude $(GIT_VERSION_DIR)/../Makefile
+endif
 
 # The fortdep script doesn't know about Fortran submodules,
 # so we need to write the dependencies ourselves:
@@ -37,10 +46,10 @@ $(FPP)/git_version_impl.f90: $(GIT_VERSION_DIR)/git_version_impl.F90 | $(GIT_VER
 # Create *.o files from *.f90 files using the Fortran f90 (FC) compiler 
 $(OBJ)/git_version.o: $(GIT_VERSION_DIR)/git_version.f90 
 	@echo "   (git) *.f90 to *.o: $(notdir $<)" 
-	@$(FC) $(F90FLAGS) $(INC_FLAGS) -I $(MOD) -J $(MOD) -o $@ -c $<
+	@$(FC) $(F90FLAGS) $(INC_FLAGS) -I $(MOD) $(MODULE_FLAG) $(MOD) -o $@ -c $<
 $(OBJ)/git_version_impl.o: $(FPP)/git_version_impl.f90 
 	@echo "   (git) *.f90 to *.o: $(notdir $<)" 
-	@$(FC) $(F90FLAGS) $(INC_FLAGS) -I $(MOD) -J $(MOD) -o $@ -c $<
+	@$(FC) $(F90FLAGS) $(INC_FLAGS) -I $(MOD) $(MODULE_FLAG) $(MOD) -o $@ -c $<
 
 # Extra commands so we can compile mini_libstell separately through
 # >> make mini_libstell_clean; make mini_libstell
diff --git a/COMPILATION/Makefile.externals.neasyf b/COMPILATION/Makefile.externals.neasyf
index 853a33cb9e..886b94feea 100644
--- a/COMPILATION/Makefile.externals.neasyf
+++ b/COMPILATION/Makefile.externals.neasyf
@@ -14,7 +14,7 @@ $(NEASYF_DIR)/neasyf.f90:
 # Create *.o files from *.f90 files using the Fortran f90 (FC) compiler 
 $(OBJ)/neasyf.o: $(NEASYF_DIR)/neasyf.f90 
 	@echo "   (neasyf) *.f90 to *.o: $(notdir $<)" 
-	@$(FC) $(F90FLAGS) $(INC_FLAGS) -I $(MOD) -J $(MOD) -o $@ -c $<
+	@$(FC) $(F90FLAGS) $(INC_FLAGS) -I $(MOD) $(MODULE_FLAG) $(MOD) -o $@ -c $<
 
 # If make is killed or interrupted during the execution of their recipes, 
 # the targets in ".PRECIOUS" are not deleted.
diff --git a/COMPILATION/Makefile.stella b/COMPILATION/Makefile.stella
index f78ea69616..f0333db289 100644
--- a/COMPILATION/Makefile.stella
+++ b/COMPILATION/Makefile.stella
@@ -232,7 +232,7 @@ setup-stella: ensure-that-all-f90-files-exist
 
 # The -I $(MOD) flag makes sure that the compiler looks for the *.mod files in the $(MOD) directory
 # The -J $(MOD) flag makes sure that the compiler writes the *.mod files to the $(MOD) directory
-MOD_FLAGS_STELLA := -I $(MOD) -I $(UTILS_MOD) -I $(MINILIBSTELL_MOD) -J $(MOD)
+MOD_FLAGS_STELLA := -I $(MOD) -I $(UTILS_MOD) -I $(MINILIBSTELL_MOD) $(MODULE_FLAG) $(MOD)
  
 # Build object files '*.o' from '*.f90' files using the Fortran f90 compiler
 $(OBJ)/%.o: $(STELLA_DIR)/%.f90 $(external_modules) | $(OBJ) $(MOD)
@@ -242,7 +242,7 @@ $(OBJ)/%.o: $(FPP)/%.f90 $(external_modules) | $(OBJ) $(MOD)
 	@echo "   (stella) *.f90 to *.o: $(notdir $<)" 
 	@$(FC) $(F90FLAGS) $(INC_FLAGS) $(MOD_FLAGS_STELLA) -o $@ -c $< 
 	
-$(OBJ)/%.o: $(CALCULATIONS)/%.f90 $(external_modules) | $(OBJ)  $(MOD)
+$(OBJ)/%.o: $(CALCULATIONS)/%.f90 $(external_modules) | $(OBJ) $(MOD)
 	@echo "   (stella) *.f90 to *.o: $(notdir $<)" 
 	@$(FC) $(F90FLAGS) $(INC_FLAGS) $(MOD_FLAGS_STELLA) -o $@ -c $< 
 $(OBJ)/%.o: $(DIAGNOSTICS)/%.f90 $(external_modules) | $(OBJ) $(MOD)
diff --git a/COMPILATION/Makefiles/Compilers/Makefile.gcc b/COMPILATION/Makefiles/Compilers/Makefile.gcc
new file mode 100644
index 0000000000..bcfbf0c245
--- /dev/null
+++ b/COMPILATION/Makefiles/Compilers/Makefile.gcc
@@ -0,0 +1,3 @@
+# Compiler: GNU gfortran/gcc
+
+include $(COMPILATION_DIR)/Makefiles/Compilers/Makefile.gnu-gfortran
diff --git a/COMPILATION/Makefiles/Makefile.marenostrum b/COMPILATION/Makefiles/Makefile.marenostrum
new file mode 100644
index 0000000000..0f7f94fbef
--- /dev/null
+++ b/COMPILATION/Makefiles/Makefile.marenostrum
@@ -0,0 +1,60 @@
+# Host: mn4
+
+$(warning Processing Makefile.marenostrum)
+helplocal:
+                # GK_SYSTEM = mn4
+                # You are using  Makefile.mn4 to build gs2 executables on bsc.
+
+define STANDARD_SYSTEM_CONFIGURATION
+
+export MAKEFLAGS='-j -IMakefiles';\
+export TESTEXEC='mpirun -N 48 -n 48';
+endef
+
+COMPILER=intel
+
+USE_FFT = fftw3
+USE_NETCDF = on
+
+# This line disables the automated checking
+# of the intel version which is slow
+DBLESIZEOPT = -double-size 128
+
+include $(COMPILATION_DIR)/Makefiles/Compilers/Makefile.$(COMPILER)
+
+FC=mpiifort
+CC=icc
+MPIFC=mpiifort
+MPICC=mpiicc
+
+ifeq ($(USE_FFT),fftw3)
+        FFT_INC = $(FFTW_ROOT)/include
+        FFT_DIR = $(FFTW_ROOT)
+        FFT_LIB = -lfftw3 $(FFTW_LDFLAGS) #-lfftw3_mpi
+        CPPFLAGS   += -I $(FFT_INC)
+endif
+
+USE_HDF5=
+
+PETSC_INC=$(PETSC_DIR)/include
+
+#Note the module system sets some env vars for us
+#unfortunately some clash with values we use
+ifdef USE_NETCDF
+  NETCDF_DIR=$(NETCDF)
+  NETCDF_INC= -I $(NETCDF_ROOT)/include/
+  NETCDF_LIB= -L $(NETCDF_ROOT)/lib/ -lnetcdff -L$(NETCDF_HOME)/lib/ -lnetcdf
+endif
+
+#MPI_INC=-I$(MPI_ROOT)/include64/
+#MPI_LIB=-lmpi
+
+$(warning USE_NETCDF=$(USE_NETCDF))
+
+# The compiler either uses the "-J" flag or the "-module" flag to 
+# denote the directory where the *.mod files can be found
+MODULE_FLAG = -module
+
+# Without this the mini_linstell gets issues with the netcdf routines (cdf_inquire)
+F90FLAGS = -DNETCDF
+
diff --git a/COMPILATION/Makefiles/Makefile.stellar b/COMPILATION/Makefiles/Makefile.stellar
new file mode 100644
index 0000000000..60bb06875a
--- /dev/null
+++ b/COMPILATION/Makefiles/Makefile.stellar
@@ -0,0 +1,17 @@
+
+USE_HDF5 = on
+F90FLAGS = -DNETCDF
+
+COMPILER = intel
+include $(COMPILATION_DIR)/Makefiles/Compilers/Makefile.$(COMPILER)
+
+FFT_INC    = -I/usr/local/fftw/intel-2021.1/openmpi-4.1.0/3.3.9/include
+FFT_LIB    = -L/usr/local/fftw/intel-2021.1/openmpi-4.1.0/3.3.9/lib64 -lfftw3
+NETCDF_INC = -I/usr/local/netcdf/intel-2021.1/hdf5-1.10.6/openmpi-4.1.0/4.7.4/include
+NETCDF_LIB = -L/usr/local/netcdf/intel-2021.1/hdf5-1.10.6/openmpi-4.1.0/4.7.4/lib64 -lnetcdf -lnetcdff
+HDF5_INC   = -I/usr/local/hdf5/intel-2021.1/openmpi-4.1.0/1.10.6/include
+HDF5_LIB   = -L/usr/local/hdf5/intel-2021.1/openmpi-4.1.0/1.10.6/lib64
+
+# The compiler either uses the "-J" flag or the "-module" flag to 
+# denote the directory where the *.mod files can be found
+MODULE_FLAG = -module
diff --git a/COMPILATION/Makefiles/Makefile.xula b/COMPILATION/Makefiles/Makefile.xula
index 1d7cd544a2..66f022613e 100644
--- a/COMPILATION/Makefiles/Makefile.xula
+++ b/COMPILATION/Makefiles/Makefile.xula
@@ -1,54 +1,44 @@
-# Host: Marconi
+# Host: Xula
 
 helplocal:
-		# GK_SYSTEM = marconi
-		# You are using  Makefile.marconi to build gs2 executables on MARCONI.
-
-COMPILER=intel
-CHIP=skylake
+    # STELLA_SYSTEM = xula
+    # You are using  Makefile.xula to build the stella executables on xula.
 
+# Toggle options
 USE_FFT = fftw3
 USE_NETCDF = on
 
-# This line disables the automated checking
-# of the intel version which is slow
+# This line disables the automated checking of the intel version which is slow
 DBLESIZEOPT = -double-size 128
 
+# Use the GCC or GNU GFortran compiler
+COMPILER=gnu-gfortran
 include $(COMPILATION_DIR)/Makefiles/Compilers/Makefile.$(COMPILER)
 
-FC=ifort
-CC=icc
-
-MPIFC=mpifort
-MPICC=mpiicc
-MPIFC=mpif90
-MPI_HOME=/mnt/lustre/ohpc/admin/spack/0.12.1/opt/spack/linux-centos7-x86_64/intel-19.0.5.281/openmpi-3.1.3-xnwkw7bcmpsrdymg77auoyudr2pr3mu5
-MPI_INC=-I$(MPI_HOME)/include/	MPI_LIB=-L$(MPI_HOME)/lib/
-
-ifeq ($(USE_FFT),fftw3)	
-     	FFT_DIR=/mnt/lustre/ohpc/admin/spack/0.12.1/opt/spack/linux-centos7-x86_64/intel-19.0.5.281/fftw-3.3.8-ymonpurwnnwrjsw3zw4kh5d7brp2sbn6
-	FFT_INC = -I$(FFT_DIR)/include/
-	FFT_LIB = -lfftw3 -lfftw3_mpi -L$(FFT_DIR)/lib/
-        CPPFLAGS += -I$(FFT_INC)
-endif	
-
-USE_HDF5=
+# The NETCDF_HOME, FFT_HOME and LAPACK_HOME variables are set in the load_modules.xula file
+# Here we tell the compiler where the libraries can be found
+LAPACK_DIR=$(LAPACK_HOME)
+LAPACK_INC= -I$(LAPACK_DIR)/include/
+LAPACK_LIB= -L$(LAPACK_DIR)/lib64/ -llapack
+
+ifeq ($(USE_FFT),fftw3)
+  FFT_DIR=$(FFT_HOME)
+  FFT_INC = -I$(FFT_DIR)/include/
+  FFT_LIB = -lfftw3 -lfftw3_mpi -L$(FFT_DIR)/lib/
+  CPPFLAGS += -I$(FFT_INC)
+endif
 
-#Note the module system sets some env vars for us
-#unfortunately some clash with values we use
 ifdef USE_NETCDF
   NETCDF_DIR=$(NETCDF_HOME)
   NETCDF_INC= -I$(NETCDF_DIR)/include/
-  NETCDF_LIB= -L$(NETCDF_DIR)/lib/ -lnetcdff -L$(NETCDF_DIR)lib/ -lnetcdf
+  NETCDF_LIB= -L$(NETCDF_DIR)/lib/ -L$(NETCDF_DIR)/lib64/ -lnetcdf -lnetcdff
 endif
 
 ifdef USE_SFINCS
-      SFINCS_LIB = -L$(SFINCS_DIR) -lsfincs
-      SFINCS_INC = -I$(SFINCS_DIR)
-
-      PETSC_INC = -I$(PETSC_HOME)/include -I$(LAPACK_HOME)/include -I$(MKL_HOME)/include
-      PETSC_LIB = -L$(PETSC_HOME)/lib -lpetsc -L$(LAPACK_HOME)/lib -llapack -L$(MKL_HOME)/lib/intel64 -lmkl_intel_lp64
-
-      HDF5_INC = -I$(HDF5_HOME)/include
-      HDF5_LIB = -L$(HDF5_HOME)/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5 -lhdf5_hl
+  SFINCS_LIB = -L$(SFINCS_DIR) -lsfincs
+  SFINCS_INC = -I$(SFINCS_DIR)
+  PETSC_INC = -I$(PETSC_HOME)/include -I$(LAPACK_HOME)/include -I$(MKL_HOME)/include
+  PETSC_LIB = -L$(PETSC_HOME)/lib -lpetsc -L$(LAPACK_HOME)/lib -llapack -L$(MKL_HOME)/lib/intel64 -lmkl_intel_lp64
+  HDF5_INC = -I$(HDF5_HOME)/include
+  HDF5_LIB = -L$(HDF5_HOME)/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5 -lhdf5_hl
 endif
diff --git a/DOCUMENTATION/example_output/input.dimensions b/DOCUMENTATION/example_output/input.dimensions
new file mode 100644
index 0000000000..cff3e5ba2e
Binary files /dev/null and b/DOCUMENTATION/example_output/input.dimensions differ
diff --git a/DOCUMENTATION/example_output/input.dt1.fluxes_vs_t b/DOCUMENTATION/example_output/input.dt1.fluxes_vs_t
new file mode 100644
index 0000000000..041bae384a
--- /dev/null
+++ b/DOCUMENTATION/example_output/input.dt1.fluxes_vs_t
@@ -0,0 +1,3001 @@
+      #time            pflux (s=0)        pflux (s=1)        vflux (s=0)        vflux (s=1)        qflux (s=0)        qflux (s=1)        
+  0.00000000e+00     8.62160000e-19     1.66990000e-20     0.00000000e+00     0.00000000e+00    -5.00410000e-19     8.34490000e-19
+  1.00000000e+00    -1.91750000e-06    -1.91750000e-06     0.00000000e+00     0.00000000e+00    -1.90430000e-05    -5.74370000e-06
+  2.00000000e+00     1.15600000e-07     1.15600000e-07     0.00000000e+00     0.00000000e+00    -1.16780000e-05    -1.20690000e-06
+  3.00000000e+00     5.36840000e-07     5.36840000e-07     0.00000000e+00     0.00000000e+00    -4.43960000e-06     2.25120000e-07
+  4.00000000e+00     2.68240000e-07     2.68240000e-07     0.00000000e+00     0.00000000e+00    -1.98960000e-06     1.82400000e-07
+  5.00000000e+00     1.06940000e-07     1.06940000e-07     0.00000000e+00     0.00000000e+00    -8.23130000e-07     1.17330000e-07
+  6.00000000e+00     4.03230000e-08     4.03230000e-08     0.00000000e+00     0.00000000e+00    -3.48060000e-07     6.88370000e-08
+  7.00000000e+00     2.80740000e-08     2.80740000e-08     0.00000000e+00     0.00000000e+00    -2.03740000e-07     6.07540000e-08
+  8.00000000e+00     3.06520000e-09     3.06520000e-09     0.00000000e+00     0.00000000e+00    -5.12440000e-08     1.88690000e-08
+  9.00000000e+00     6.10650000e-09     6.10650000e-09     0.00000000e+00     0.00000000e+00    -3.15130000e-08     1.78840000e-08
+  1.00000000e+01     2.00670000e-09     2.00670000e-09     0.00000000e+00     0.00000000e+00    -9.30150000e-09     7.84450000e-09
+  1.10000000e+01     1.06400000e-09     1.06400000e-09     0.00000000e+00     0.00000000e+00    -2.50760000e-09     4.37610000e-09
+  1.20000000e+01    -2.16270000e-10    -2.16270000e-10     0.00000000e+00     0.00000000e+00    -3.53130000e-10     1.26350000e-09
+  1.30000000e+01    -2.98570000e-10    -2.98570000e-10     0.00000000e+00     0.00000000e+00     5.21680000e-09     4.64280000e-10
+  1.40000000e+01     9.04160000e-10     9.04160000e-10     0.00000000e+00     0.00000000e+00     2.88910000e-09     1.95650000e-09
+  1.50000000e+01     1.17930000e-09     1.17930000e-09     0.00000000e+00     0.00000000e+00     3.42660000e-09     2.17410000e-09
+  1.60000000e+01     9.92800000e-10     9.92800000e-10     0.00000000e+00     0.00000000e+00     5.53470000e-09     1.72060000e-09
+  1.70000000e+01     5.92500000e-10     5.92500000e-10     0.00000000e+00     0.00000000e+00     5.55920000e-09     1.03520000e-09
+  1.80000000e+01     2.57560000e-10     2.57560000e-10     0.00000000e+00     0.00000000e+00     6.75750000e-09     4.51860000e-10
+  1.90000000e+01     2.14010000e-10     2.14010000e-10     0.00000000e+00     0.00000000e+00     7.36010000e-09     3.42620000e-10
+  2.00000000e+01     3.08510000e-10     3.08510000e-10     0.00000000e+00     0.00000000e+00     8.19980000e-09     4.45940000e-10
+  2.10000000e+01     3.58290000e-10     3.58290000e-10     0.00000000e+00     0.00000000e+00     8.89560000e-09     4.95510000e-10
+  2.20000000e+01     3.53350000e-10     3.53350000e-10     0.00000000e+00     0.00000000e+00     9.65020000e-09     4.68930000e-10
+  2.30000000e+01     3.24410000e-10     3.24410000e-10     0.00000000e+00     0.00000000e+00     1.07200000e-08     4.04980000e-10
+  2.40000000e+01     3.19720000e-10     3.19720000e-10     0.00000000e+00     0.00000000e+00     1.22000000e-08     3.71530000e-10
+  2.50000000e+01     3.48620000e-10     3.48620000e-10     0.00000000e+00     0.00000000e+00     1.36710000e-08     3.88630000e-10
+  2.60000000e+01     3.86260000e-10     3.86260000e-10     0.00000000e+00     0.00000000e+00     1.56410000e-08     4.08810000e-10
+  2.70000000e+01     4.31950000e-10     4.31950000e-10     0.00000000e+00     0.00000000e+00     1.78270000e-08     4.38000000e-10
+  2.80000000e+01     4.74960000e-10     4.74960000e-10     0.00000000e+00     0.00000000e+00     2.05610000e-08     4.54650000e-10
+  2.90000000e+01     5.18950000e-10     5.18950000e-10     0.00000000e+00     0.00000000e+00     2.37640000e-08     4.65330000e-10
+  3.00000000e+01     5.57690000e-10     5.57690000e-10     0.00000000e+00     0.00000000e+00     2.79210000e-08     4.51070000e-10
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+  2.91230000e+03     2.10400000e-01     2.10400000e-01     0.00000000e+00     0.00000000e+00     9.58850000e+00     2.22740000e-01
+  2.91300000e+03     2.05130000e-01     2.05130000e-01     0.00000000e+00     0.00000000e+00     9.58690000e+00     2.20750000e-01
+  2.91400000e+03     2.07000000e-01     2.07000000e-01     0.00000000e+00     0.00000000e+00     9.53230000e+00     2.23430000e-01
+  2.91510000e+03     2.09680000e-01     2.09680000e-01     0.00000000e+00     0.00000000e+00     9.50120000e+00     2.23580000e-01
+  2.91610000e+03     2.07860000e-01     2.07860000e-01     0.00000000e+00     0.00000000e+00     9.49370000e+00     2.21330000e-01
+  2.91720000e+03     2.04820000e-01     2.04820000e-01     0.00000000e+00     0.00000000e+00     9.43040000e+00     2.18580000e-01
+  2.91820000e+03     1.95230000e-01     1.95230000e-01     0.00000000e+00     0.00000000e+00     9.36960000e+00     2.06810000e-01
+  2.91900000e+03     1.97470000e-01     1.97470000e-01     0.00000000e+00     0.00000000e+00     9.36340000e+00     2.14280000e-01
+  2.92000000e+03     1.96130000e-01     1.96130000e-01     0.00000000e+00     0.00000000e+00     9.32790000e+00     2.12470000e-01
+  2.92110000e+03     2.03010000e-01     2.03010000e-01     0.00000000e+00     0.00000000e+00     9.28250000e+00     2.21690000e-01
+  2.92210000e+03     1.92540000e-01     1.92540000e-01     0.00000000e+00     0.00000000e+00     9.25670000e+00     2.07540000e-01
+  2.92320000e+03     1.98730000e-01     1.98730000e-01     0.00000000e+00     0.00000000e+00     9.19730000e+00     2.17420000e-01
+  2.92420000e+03     1.93540000e-01     1.93540000e-01     0.00000000e+00     0.00000000e+00     9.18270000e+00     2.08700000e-01
+  2.92530000e+03     2.06590000e-01     2.06590000e-01     0.00000000e+00     0.00000000e+00     9.18900000e+00     2.31430000e-01
+  2.92600000e+03     2.02480000e-01     2.02480000e-01     0.00000000e+00     0.00000000e+00     9.19330000e+00     2.25210000e-01
+  2.92700000e+03     1.99470000e-01     1.99470000e-01     0.00000000e+00     0.00000000e+00     9.18020000e+00     2.18890000e-01
+  2.92810000e+03     1.88900000e-01     1.88900000e-01     0.00000000e+00     0.00000000e+00     9.15110000e+00     2.04290000e-01
+  2.92910000e+03     1.94270000e-01     1.94270000e-01     0.00000000e+00     0.00000000e+00     9.21290000e+00     2.09610000e-01
+  2.93020000e+03     2.04840000e-01     2.04840000e-01     0.00000000e+00     0.00000000e+00     9.18700000e+00     2.26620000e-01
+  2.93130000e+03     2.06480000e-01     2.06480000e-01     0.00000000e+00     0.00000000e+00     9.12230000e+00     2.31690000e-01
+  2.93200000e+03     2.01400000e-01     2.01400000e-01     0.00000000e+00     0.00000000e+00     9.11660000e+00     2.24170000e-01
+  2.93300000e+03     1.99940000e-01     1.99940000e-01     0.00000000e+00     0.00000000e+00     9.10620000e+00     2.19810000e-01
+  2.93410000e+03     1.98650000e-01     1.98650000e-01     0.00000000e+00     0.00000000e+00     9.12330000e+00     2.17620000e-01
+  2.93510000e+03     1.99170000e-01     1.99170000e-01     0.00000000e+00     0.00000000e+00     9.16830000e+00     2.19440000e-01
+  2.93620000e+03     2.06570000e-01     2.06570000e-01     0.00000000e+00     0.00000000e+00     9.15770000e+00     2.24110000e-01
+  2.93720000e+03     1.93560000e-01     1.93560000e-01     0.00000000e+00     0.00000000e+00     9.08310000e+00     2.10180000e-01
+  2.93830000e+03     1.96360000e-01     1.96360000e-01     0.00000000e+00     0.00000000e+00     9.07880000e+00     2.13860000e-01
+  2.93900000e+03     1.95000000e-01     1.95000000e-01     0.00000000e+00     0.00000000e+00     9.11370000e+00     2.09860000e-01
+  2.94000000e+03     2.02290000e-01     2.02290000e-01     0.00000000e+00     0.00000000e+00     9.08610000e+00     2.22010000e-01
+  2.94110000e+03     2.00910000e-01     2.00910000e-01     0.00000000e+00     0.00000000e+00     9.09030000e+00     2.20170000e-01
+  2.94220000e+03     1.98450000e-01     1.98450000e-01     0.00000000e+00     0.00000000e+00     9.07890000e+00     2.11580000e-01
+  2.94320000e+03     1.94290000e-01     1.94290000e-01     0.00000000e+00     0.00000000e+00     9.06320000e+00     2.10800000e-01
+  2.94430000e+03     1.98020000e-01     1.98020000e-01     0.00000000e+00     0.00000000e+00     9.03700000e+00     2.14530000e-01
+  2.94500000e+03     1.95840000e-01     1.95840000e-01     0.00000000e+00     0.00000000e+00     9.02260000e+00     2.11190000e-01
+  2.94600000e+03     1.92120000e-01     1.92120000e-01     0.00000000e+00     0.00000000e+00     8.98660000e+00     2.09120000e-01
+  2.94710000e+03     1.96000000e-01     1.96000000e-01     0.00000000e+00     0.00000000e+00     8.96250000e+00     2.12990000e-01
+  2.94810000e+03     1.88660000e-01     1.88660000e-01     0.00000000e+00     0.00000000e+00     8.92810000e+00     2.03290000e-01
+  2.94920000e+03     1.89270000e-01     1.89270000e-01     0.00000000e+00     0.00000000e+00     8.97970000e+00     2.01960000e-01
+  2.95020000e+03     1.89640000e-01     1.89640000e-01     0.00000000e+00     0.00000000e+00     8.97240000e+00     2.08810000e-01
+  2.95130000e+03     1.87450000e-01     1.87450000e-01     0.00000000e+00     0.00000000e+00     8.94100000e+00     2.01700000e-01
+  2.95200000e+03     1.94390000e-01     1.94390000e-01     0.00000000e+00     0.00000000e+00     8.95920000e+00     2.12090000e-01
+  2.95300000e+03     1.92580000e-01     1.92580000e-01     0.00000000e+00     0.00000000e+00     8.95000000e+00     2.06890000e-01
+  2.95410000e+03     1.92730000e-01     1.92730000e-01     0.00000000e+00     0.00000000e+00     8.98190000e+00     2.06370000e-01
+  2.95520000e+03     1.90430000e-01     1.90430000e-01     0.00000000e+00     0.00000000e+00     8.97270000e+00     2.05950000e-01
+  2.95620000e+03     1.94830000e-01     1.94830000e-01     0.00000000e+00     0.00000000e+00     8.96240000e+00     2.09780000e-01
+  2.95730000e+03     1.91300000e-01     1.91300000e-01     0.00000000e+00     0.00000000e+00     8.94380000e+00     2.06090000e-01
+  2.95800000e+03     1.87130000e-01     1.87130000e-01     0.00000000e+00     0.00000000e+00     8.94160000e+00     2.02840000e-01
+  2.95900000e+03     1.89810000e-01     1.89810000e-01     0.00000000e+00     0.00000000e+00     8.97260000e+00     2.02860000e-01
+  2.96010000e+03     1.98820000e-01     1.98820000e-01     0.00000000e+00     0.00000000e+00     9.04070000e+00     2.12630000e-01
+  2.96110000e+03     2.03790000e-01     2.03790000e-01     0.00000000e+00     0.00000000e+00     9.08020000e+00     2.20410000e-01
+  2.96220000e+03     1.98510000e-01     1.98510000e-01     0.00000000e+00     0.00000000e+00     9.09140000e+00     2.15410000e-01
+  2.96320000e+03     2.01840000e-01     2.01840000e-01     0.00000000e+00     0.00000000e+00     9.10090000e+00     2.20160000e-01
+  2.96430000e+03     2.00090000e-01     2.00090000e-01     0.00000000e+00     0.00000000e+00     9.15400000e+00     2.17500000e-01
+  2.96500000e+03     1.96200000e-01     1.96200000e-01     0.00000000e+00     0.00000000e+00     9.22280000e+00     2.10160000e-01
+  2.96610000e+03     1.96670000e-01     1.96670000e-01     0.00000000e+00     0.00000000e+00     9.27560000e+00     2.06710000e-01
+  2.96710000e+03     2.01670000e-01     2.01670000e-01     0.00000000e+00     0.00000000e+00     9.30830000e+00     2.16080000e-01
+  2.96820000e+03     2.05740000e-01     2.05740000e-01     0.00000000e+00     0.00000000e+00     9.33840000e+00     2.23590000e-01
+  2.96920000e+03     2.05330000e-01     2.05330000e-01     0.00000000e+00     0.00000000e+00     9.35900000e+00     2.23690000e-01
+  2.97030000e+03     2.04830000e-01     2.04830000e-01     0.00000000e+00     0.00000000e+00     9.38840000e+00     2.16150000e-01
+  2.97100000e+03     2.04080000e-01     2.04080000e-01     0.00000000e+00     0.00000000e+00     9.39630000e+00     2.14120000e-01
+  2.97200000e+03     1.98930000e-01     1.98930000e-01     0.00000000e+00     0.00000000e+00     9.42100000e+00     2.08630000e-01
+  2.97310000e+03     2.05790000e-01     2.05790000e-01     0.00000000e+00     0.00000000e+00     9.44590000e+00     2.16340000e-01
+  2.97410000e+03     2.03040000e-01     2.03040000e-01     0.00000000e+00     0.00000000e+00     9.43590000e+00     2.15520000e-01
+  2.97520000e+03     2.03000000e-01     2.03000000e-01     0.00000000e+00     0.00000000e+00     9.41720000e+00     2.16450000e-01
+  2.97620000e+03     2.00890000e-01     2.00890000e-01     0.00000000e+00     0.00000000e+00     9.41160000e+00     2.14310000e-01
+  2.97700000e+03     2.03980000e-01     2.03980000e-01     0.00000000e+00     0.00000000e+00     9.39130000e+00     2.18920000e-01
+  2.97800000e+03     2.02620000e-01     2.02620000e-01     0.00000000e+00     0.00000000e+00     9.37330000e+00     2.16010000e-01
+  2.97910000e+03     2.10590000e-01     2.10590000e-01     0.00000000e+00     0.00000000e+00     9.40590000e+00     2.23860000e-01
+  2.98010000e+03     2.12550000e-01     2.12550000e-01     0.00000000e+00     0.00000000e+00     9.45540000e+00     2.29330000e-01
+  2.98120000e+03     2.13500000e-01     2.13500000e-01     0.00000000e+00     0.00000000e+00     9.45160000e+00     2.32200000e-01
+  2.98220000e+03     2.10170000e-01     2.10170000e-01     0.00000000e+00     0.00000000e+00     9.41380000e+00     2.28580000e-01
+  2.98330000e+03     2.11570000e-01     2.11570000e-01     0.00000000e+00     0.00000000e+00     9.39840000e+00     2.29210000e-01
+  2.98400000e+03     2.06720000e-01     2.06720000e-01     0.00000000e+00     0.00000000e+00     9.43500000e+00     2.22430000e-01
+  2.98500000e+03     2.06890000e-01     2.06890000e-01     0.00000000e+00     0.00000000e+00     9.42350000e+00     2.20690000e-01
+  2.98610000e+03     2.09380000e-01     2.09380000e-01     0.00000000e+00     0.00000000e+00     9.40320000e+00     2.23480000e-01
+  2.98710000e+03     2.09720000e-01     2.09720000e-01     0.00000000e+00     0.00000000e+00     9.41770000e+00     2.23110000e-01
+  2.98820000e+03     2.06250000e-01     2.06250000e-01     0.00000000e+00     0.00000000e+00     9.39560000e+00     2.19170000e-01
+  2.98930000e+03     2.03920000e-01     2.03920000e-01     0.00000000e+00     0.00000000e+00     9.40330000e+00     2.17450000e-01
+  2.99000000e+03     2.14520000e-01     2.14520000e-01     0.00000000e+00     0.00000000e+00     9.44250000e+00     2.29680000e-01
+  2.99100000e+03     2.11170000e-01     2.11170000e-01     0.00000000e+00     0.00000000e+00     9.47790000e+00     2.23160000e-01
+  2.99210000e+03     2.00750000e-01     2.00750000e-01     0.00000000e+00     0.00000000e+00     9.50090000e+00     2.15320000e-01
+  2.99310000e+03     2.10810000e-01     2.10810000e-01     0.00000000e+00     0.00000000e+00     9.51600000e+00     2.25110000e-01
+  2.99420000e+03     2.07140000e-01     2.07140000e-01     0.00000000e+00     0.00000000e+00     9.52750000e+00     2.18720000e-01
+  2.99520000e+03     2.21340000e-01     2.21340000e-01     0.00000000e+00     0.00000000e+00     9.51000000e+00     2.41450000e-01
+  2.99630000e+03     2.18100000e-01     2.18100000e-01     0.00000000e+00     0.00000000e+00     9.53630000e+00     2.37850000e-01
+  2.99700000e+03     2.13130000e-01     2.13130000e-01     0.00000000e+00     0.00000000e+00     9.57260000e+00     2.30100000e-01
+  2.99800000e+03     2.17420000e-01     2.17420000e-01     0.00000000e+00     0.00000000e+00     9.59850000e+00     2.38050000e-01
+  2.99910000e+03     2.09210000e-01     2.09210000e-01     0.00000000e+00     0.00000000e+00     9.57060000e+00     2.26110000e-01
diff --git a/DOCUMENTATION/example_output/input.geo b/DOCUMENTATION/example_output/input.geo
new file mode 100644
index 0000000000..09cca5910d
Binary files /dev/null and b/DOCUMENTATION/example_output/input.geo differ
diff --git a/DOCUMENTATION/example_output/input.in b/DOCUMENTATION/example_output/input.in
new file mode 100644
index 0000000000..66cf7e7954
--- /dev/null
+++ b/DOCUMENTATION/example_output/input.in
@@ -0,0 +1,11 @@
+&physics_flags
+  nonlinear = .true.
+/
+&species_knobs
+  nspec = 2
+/
+&vmec_parameters
+  torflux = 0.49
+  vmec_filename = 'wout_w7xr003.nc'
+/
+
diff --git a/DOCUMENTATION/example_output/input.out.nc.t200-3000 b/DOCUMENTATION/example_output/input.out.nc.t200-3000
new file mode 100644
index 0000000000..c47bc04fc5
Binary files /dev/null and b/DOCUMENTATION/example_output/input.out.nc.t200-3000 differ
diff --git a/EXTERNALS/mini_libstell/makefile b/EXTERNALS/mini_libstell/makefile
index 6257fcb9db..59b1da5775 100644
--- a/EXTERNALS/mini_libstell/makefile
+++ b/EXTERNALS/mini_libstell/makefile
@@ -72,7 +72,7 @@ $(BUILD)/mini_libstell.a: $(libstell_objects) | $(OBJ)
 	
 # The -J $(MOD) flag makes sure that the compiler writes the *.mod files to the $(MOD) directory
 # The -I $(MOD) flag makes sure that the compiler looks for the *.mod files in the $(MOD) directory
-MOD_FLAGS_MINI := -I $(MOD) -J $(MOD)
+MOD_FLAGS_MINI := -I $(MOD) $(MODULE_FLAG) $(MOD)
 
 # Pattern rules to compile the scripts
 # For the preprocessed files *.F, we need to give the "NETCDF" option through the -D flag
diff --git a/EXTERNALS/pyrokinetics b/EXTERNALS/pyrokinetics
new file mode 160000
index 0000000000..70c7d32da2
--- /dev/null
+++ b/EXTERNALS/pyrokinetics
@@ -0,0 +1 @@
+Subproject commit 70c7d32da2d114f1df79ad7f5002f5d830c50112
diff --git a/POST_PROCESSING/stellapy/data/geometry/get_RZBFromCosineAndSineTransformVMEC.py b/POST_PROCESSING/stellapy/data/geometry/get_RZBFromCosineAndSineTransformVMEC.py
new file mode 100644
index 0000000000..d9ede933a7
--- /dev/null
+++ b/POST_PROCESSING/stellapy/data/geometry/get_RZBFromCosineAndSineTransformVMEC.py
@@ -0,0 +1,585 @@
+
+#!/usr/bin/python3   
+import sys, os
+import pathlib
+import numpy as np
+import pickle
+import netCDF4 as nc4   
+from stellapy.utils.decorators.exit_program import exit_program
+
+# Stellapy package
+sys.path.append(os.path.abspath(pathlib.Path(os.environ.get('STELLAPY')).parent)+os.path.sep)   
+from stellapy.data.geometry.get_interpolationWeights import get_interpolationWeightsOnHalfGrid
+from stellapy.data.geometry.get_interpolationWeights import get_interpolationWeightsOnFullGrid
+from stellapy.data.geometry.calculate_gridDivisionsAndSize import calculate_iota 
+from stellapy.utils.files.ensure_dir import ensure_dir
+
+#===============================================================================
+#                             Get (R,Z,B) from VMEC                            #
+#===============================================================================
+    
+def get_RZBFromCosineAndSineTransformVMEC(wout_path, svalue, quantity, ntheta=50, nzeta=50):
+    
+    # Read from pickle 
+    pickle_path = pathlib.Path(wout_path).parent/'Pickles'; ensure_dir(pickle_path)
+    pickle_path = pickle_path / (pathlib.Path(wout_path).stem+f"_{svalue:.2f}_{quantity}_{nzeta}_{ntheta}.pickle")
+    if (os.path.isfile(pickle_path)):  
+        file = open(pickle_path, 'rb');  
+        DATA = pickle.load(file); file.close()  
+        return DATA.R, DATA.Z, DATA.Q, DATA.zeta, DATA.theta, DATA.nfp
+    
+    # Reac the VMEC file
+    xm, xn, xm_nyq, xn_nyq, _, _, ns, nfp, rmnc, zmns, lmns, bmnc, gmnc, _ = read_vmecdata(wout_path)
+
+    # Create a (zeta,theta) grid in cylindrical coordinates with (<ntheta>,<nzeta>) points   
+    # In stellarators these coordinates are usually denoted by (u,v)
+    theta = np.linspace(0, 2*np.pi, num=ntheta)       # u 
+    zeta  = np.linspace(0, 2*np.pi/nfp, num=nzeta)    # v
+    
+    # Copy the toroidal and poloidal mode numbers to ease the notation
+    # Note that in stella we put int(n)/nfp below, however, this is already included above in <zeta> 
+    m_nyq = np.array([ int(m) for m in xm_nyq ])
+    n_nyq = np.array([ int(n) for n in xn_nyq ])
+    m = np.array([ int(m) for m in xm ])
+    n = np.array([ int(n) for n in xn ])
+       
+    # Get the interpolation weights, for when svalue lies between two flux surfaces   
+    surfaces_indexes, surfaces_weights = get_interpolationWeightsOnHalfGrid(ns, svalue)
+
+    # Initiate the (R,Z) coordinates and the quantity Q
+    R = np.zeros((ntheta, nzeta))
+    Z = np.zeros((ntheta, nzeta))
+    Q = np.zeros((ntheta, nzeta))
+    
+    # Select the chosen quantity
+    if quantity=="B": qmnc = bmnc;      qmns = [None]
+    if quantity=="J": qmnc = gmnc;      qmns = [None]
+    if quantity=="L": qmnc = [None];    qmns = lmns
+    
+    # Consine and Sine Fourier transforms 
+    for interpolation in [0,1]:
+        for itheta in range(len(theta)):
+            for izeta in range(len(zeta)):
+    
+                # When svalue denotes a flux surface between two flux surfaces
+                # that are given by vmec, we need to interpolate the values
+                weight = surfaces_weights[interpolation]
+                isurf  = surfaces_indexes[interpolation]
+    
+                # Get the <imn> angles versus (m,n)
+                angle = m * theta[itheta] - n * zeta[izeta]
+                angle_nyq = m_nyq * theta[itheta] - n_nyq * zeta[izeta]
+    
+                # Get the cosinus and sinus of these angles
+                cos_angle = np.cos(angle); cos_angle_nyq = np.cos(angle_nyq)
+                sin_angle = np.sin(angle); sin_angle_nyq = np.sin(angle_nyq)
+    
+                # Calculate the (R,Z) coordinates by adding each (m,n) contribution 
+                R[itheta, izeta] += np.sum(rmnc[isurf,:]*cos_angle[:]*weight)
+                Z[itheta, izeta] += np.sum(zmns[isurf,:]*sin_angle[:]*weight)
+    
+                # Calculate the quantities Q (qmnc), L (lmns) or J (bmnc) from the (m_nyq, n_nyq) contributions
+                if np.all(qmnc[0]!=None): Q[itheta, izeta] += np.sum(qmnc[isurf,:]*cos_angle_nyq[:]*weight)
+                if np.all(qmns[0]!=None): Q[itheta, izeta] += np.sum(qmns[isurf,:]*sin_angle_nyq[:]*weight)
+                
+    # Save the data as a pickle
+    DATA = DATAOBJECT_RZQ(R, Z, Q, zeta, theta, nfp) 
+    file = open(pickle_path,  "wb"); 
+    pickle.dump(DATA , file); 
+    file.close()      
+    return R, Z, Q, zeta, theta, nfp
+
+#--------------------------
+class DATAOBJECT_RZQ:
+    def __init__(self, R, Z, Q, zeta, theta, nfp):
+        self.R = R 
+        self.Z = Z 
+        self.Q = Q 
+        self.zeta = zeta 
+        self.theta = theta 
+        self.nfp = nfp 
+        return
+    
+#-----------------------------
+def get_RZBKappaFromCosineAndSineTransformVMEC(wout_path, svalue, ntheta=50, nzeta=50):
+    
+    # Read from pickle  
+    pickle_path = pathlib.Path(wout_path).parent/'Pickles'; ensure_dir(pickle_path)
+    pickle_path = pickle_path / (pathlib.Path(wout_path).stem+f"_{svalue:.2f}_kappa_{nzeta}_{ntheta}.pickle")
+    if (os.path.isfile(pickle_path)):  
+        file = open(pickle_path, 'rb');  
+        DATA = pickle.load(file); file.close()   
+        vmec_data = {'xm' : DATA.xm, 'xn' : DATA.xn, 'mnmax' : DATA.mnmax, 'lmns' : DATA.lmns}
+        vmec_data['surfaces_indexes'] = DATA.surfaces_indexes; vmec_data['surfaces_weights'] = DATA.surfaces_weights
+        return DATA, vmec_data
+    
+    # Reac the VMEC file
+    xm, xn, xm_nyq, xn_nyq, mnmax, mnmax_nyq, ns, nfp, rmnc, zmns, lmns, bmnc, gmnc, iotas = read_vmecdata(wout_path)
+    dataset = nc4.Dataset(wout_path, mode='r') 
+    bsupumnc = dataset.variables['bsupumnc'][:].data 
+    bsupvmnc = dataset.variables['bsupvmnc'][:].data 
+    bsubumnc = dataset.variables['bsubumnc'][:].data
+    bsubvmnc = dataset.variables['bsubvmnc'][:].data
+    bsubsmns = dataset.variables['bsubsmns'][:].data
+    Aminor = dataset.variables['Aminor_p'][:].data 
+    isigng = dataset.variables['signgs'][:].data
+    phi = dataset.variables['phi'][:].data   
+    iotaf = dataset.variables['iotaf'][:].data
+    iota = calculate_iota(svalue, ns, iotas)  
+    edge_toroidal_flux_over_2pi = phi[ns-1] / (2*np.pi)*isigng 
+    
+    # Create a (zeta,theta) grid in cylindrical coordinates with (<ntheta>,<nzeta>) points   
+    # In stellarators these coordinates are usually denoted by (u,v) 
+    theta = np.linspace(0, 2*np.pi, num=ntheta)     # u 
+    zeta  = np.linspace(0, 2*np.pi/nfp, num=nzeta)  # v
+    
+    # Copy the toroidal and poloidal mode numbers to ease the notation
+    # Note that in stella we put int(n)/nfp below, however, this is already included above in <zeta> 
+    m_nyq = np.array([ int(m) for m in xm_nyq ])
+    n_nyq = np.array([ int(n) for n in xn_nyq ])
+    m = np.array([ int(m) for m in xm ])
+    n = np.array([ int(n) for n in xn ])
+       
+    # Get the interpolation weights, for when svalue lies between two flux surfaces   
+    surfaces_indexes, surfaces_weights = get_interpolationWeightsOnHalfGrid(ns, svalue)
+    surfaces_indexes_fullgrid, surfaces_weights_fullgrid = get_interpolationWeightsOnFullGrid(ns, svalue)
+    
+    # Initiate quentities versus r 
+    d_R_d_s_mnc = np.zeros((ns, mnmax)) 
+    d_Z_d_s_mns = np.zeros((ns, mnmax)) 
+    d_Lambda_d_s_mns = np.zeros((ns, mnmax)) 
+    d_B_d_s_mnc = np.zeros((ns, mnmax_nyq)) 
+    
+    # Initiate the coordinates
+    Z = np.zeros((ntheta, nzeta)) 
+    R = np.zeros((ntheta, nzeta)) 
+    d_R_d_s = np.zeros((ntheta, nzeta)) 
+    d_R_d_zeta = np.zeros((ntheta, nzeta)) 
+    d_R_d_theta = np.zeros((ntheta, nzeta)) 
+    d_Z_d_s = np.zeros((ntheta, nzeta)) 
+    d_Z_d_zeta = np.zeros((ntheta, nzeta)) 
+    d_Z_d_theta = np.zeros((ntheta, nzeta)) 
+    d_Lambda_d_s = np.zeros((ntheta, nzeta)) 
+    d_Lambda_d_zeta = np.zeros((ntheta, nzeta)) 
+    d_Lambda_d_theta = np.zeros((ntheta, nzeta)) 
+    
+    # Initiate the quantities
+    B = np.zeros((ntheta, nzeta)) 
+    sqrt_g = np.zeros((ntheta, nzeta)) 
+    d_B_d_s = np.zeros((ntheta, nzeta)) 
+    d_B_d_zeta = np.zeros((ntheta, nzeta)) 
+    d_B_d_theta = np.zeros((ntheta, nzeta)) 
+    B_sup_theta = np.zeros((ntheta, nzeta)) 
+    B_sup_zeta = np.zeros((ntheta, nzeta)) 
+    B_sub_s = np.zeros((ntheta, nzeta)) 
+    B_sub_theta = np.zeros((ntheta, nzeta)) 
+    B_sub_zeta = np.zeros((ntheta, nzeta)) 
+    B_cross_grad_B_dot_grad_alpha = np.zeros((ntheta, nzeta)) 
+    B_cross_grad_B_dot_grad_alpha_noshear = np.zeros((ntheta, nzeta)) 
+    
+    # Step along s=rho**2
+    normalized_toroidal_flux_full_grid = [ (i-1)/[ns-1] for i in np.arange(1,ns+1,1) ] 
+    ds = normalized_toroidal_flux_full_grid[1] - normalized_toroidal_flux_full_grid[0]
+    
+    # Consine and Sine Fourier transforms 
+    for interpolation in [0,1]:
+        for itheta in range(len(theta)):
+            for izeta in range(len(zeta)):  
+                
+                # When svalue denotes a flux surface between two flux surfaces
+                # that are given by vmec, we need to interpolate the values
+                weight = surfaces_weights[interpolation]
+                isurf  = surfaces_indexes[interpolation]
+                weight_fullgrid = surfaces_weights_fullgrid[interpolation] 
+                isurff_fullgrid  = surfaces_indexes_fullgrid[interpolation]
+                        
+                # Get the <imn> angles versus (m,n)
+                angle = m * theta[itheta] - n * zeta[izeta]
+                angle_nyq = m_nyq * theta[itheta] - n_nyq * zeta[izeta]
+                
+                # Get the cosinus and sinus of these angles
+                cos_angle = np.cos(angle); cos_angle_nyq = np.cos(angle_nyq)
+                sin_angle = np.sin(angle); sin_angle_nyq = np.sin(angle_nyq)  
+            
+                # Get the derivative of rmns; zmns and lmns with respect to s 
+                # B and Lambda are on the half mesh, so their radial derivatives are on the full mesh.
+                # R and Z are on the full mesh, so their radial derivatives are on the half mesh.
+                d_R_d_s_mnc[1:ns,:] = (rmnc[1:ns,:] - rmnc[0:ns-1,:]) / ds
+                d_Z_d_s_mns[1:ns,:] = (zmns[1:ns,:] - zmns[0:ns-1,:]) / ds
+                d_Lambda_d_s_mns[1:ns-1,:] = (lmns[2:ns,:] - lmns[1:ns-1,:]) / ds 
+                d_R_d_s_mnc[0] = 0; d_Z_d_s_mns[0] = 0
+                d_Lambda_d_s_mns[0] = d_Lambda_d_s_mns[1]
+                d_Lambda_d_s_mns[ns-1] = d_Lambda_d_s_mns[ns-2]  
+                
+                # Get the coordinate grids
+                Z[itheta, izeta] += np.sum(zmns[isurff_fullgrid,:]*sin_angle[:])*weight_fullgrid
+                R[itheta, izeta] += np.sum(rmnc[isurff_fullgrid,:]*cos_angle[:])*weight_fullgrid
+                d_R_d_theta[itheta, izeta] += -np.sum(m[:]*rmnc[isurff_fullgrid,:]*sin_angle[:])*weight_fullgrid 
+                d_R_d_zeta[itheta, izeta] += np.sum(n[:]*rmnc[isurff_fullgrid,:]*sin_angle[:])*weight_fullgrid 
+                d_Z_d_theta[itheta, izeta] += np.sum(m[:]*zmns[isurff_fullgrid,:]*cos_angle[:])*weight_fullgrid
+                d_Z_d_zeta[itheta, izeta] += -np.sum(n[:]*zmns[isurff_fullgrid,:]*cos_angle[:])*weight_fullgrid
+                d_Lambda_d_theta[itheta, izeta] += np.sum(m[:]*lmns[isurf,:]*cos_angle[:])*weight
+                d_Lambda_d_zeta[itheta, izeta] += -np.sum(n[:]*lmns[isurf,:]*cos_angle[:])*weight       
+                  
+                # Radial derivatives, since R is on the full mesh, its radial derivative is on the half mesh.
+                d_R_d_s[itheta, izeta] += np.sum(d_R_d_s_mnc[isurf]*cos_angle[:])*weight
+                d_Z_d_s[itheta, izeta] += np.sum(d_Z_d_s_mns[isurf]*sin_angle[:])*weight
+                d_Lambda_d_s[itheta, izeta] += np.sum(d_Lambda_d_s_mns[isurff_fullgrid]*sin_angle[:])*weight_fullgrid
+            
+                # Get the derivative of bmnc with respect to s and do a simplistic extrapolation at the endpoints (mn_nyq)
+                d_B_d_s_mnc[1:ns-1,:] = (bmnc[2:ns,:] - bmnc[1:ns-1,:]) / ds
+                d_B_d_s_mnc[0,:] = d_B_d_s_mnc[1,:]; d_B_d_s_mnc[ns-1,:] = d_B_d_s_mnc[ns-2,:]
+                
+                # Calculate magnetic quantities (derivatives to <s> are clacluated on the full grid
+                B[itheta, izeta] += np.sum(bmnc[isurf,:]*cos_angle_nyq[:]*weight)
+                sqrt_g[itheta, izeta] += np.sum(gmnc[isurf,:]*cos_angle_nyq[:]*weight)
+                
+                d_B_d_s[itheta, izeta] += np.sum(d_B_d_s_mnc[isurff_fullgrid,:]*cos_angle_nyq[:]*weight_fullgrid) # d_B_d_s_mnc??
+                d_B_d_theta[itheta, izeta] += -np.sum(m_nyq[:]*bmnc[isurf,:]*sin_angle_nyq[:]*weight)
+                d_B_d_zeta[itheta, izeta] += np.sum(n_nyq[:]*bmnc[isurf,:]*sin_angle_nyq[:]*weight) # n -> n*nfp???
+                
+                B_sup_theta[itheta, izeta] += np.sum(bsupumnc[isurf,:]*cos_angle_nyq[:]*weight)
+                B_sup_zeta[itheta, izeta] += np.sum(bsupvmnc[isurf,:]*cos_angle_nyq[:]*weight)
+                
+                B_sub_s[itheta, izeta] += np.sum(bsubsmns[isurff_fullgrid,:]*sin_angle_nyq[:]*weight_fullgrid)
+                B_sub_theta[itheta, izeta] += np.sum(bsubumnc[isurf,:]*cos_angle_nyq[:]*weight)
+                B_sub_zeta[itheta, izeta] += np.sum(bsubvmnc[isurf,:]*cos_angle_nyq[:]*weight)
+                
+    # Normalize B
+    L_reference = a = Aminor
+    B_reference = Bref = 2*abs(edge_toroidal_flux_over_2pi) / (L_reference*L_reference)
+    sign_torflux = np.sign(edge_toroidal_flux_over_2pi)
+    bmag = B/B_reference 
+    
+    # Calculate the shear
+    d_iota_d_s_on_half_grid = np.zeros(ns)
+    d_iota_d_s_on_half_grid[1:ns-1] = (iotaf[1:ns-1] - iotaf[0:ns-2]) / ds
+    d_iota_d_s = d_iota_d_s_on_half_grid[surfaces_indexes[0]]*surfaces_weights[0] 
+    d_iota_d_s += d_iota_d_s_on_half_grid[surfaces_indexes[1]]*surfaces_weights[1]
+    shat = (-2*svalue / iota)*d_iota_d_s
+    
+    # We need cos(tzeta) and sin(zeta) to transform (R) to (X,Y) as a function of (theta, zeta)
+    cos_angle = (np.cos(zeta))[np.newaxis,:]
+    sin_angle = (np.sin(zeta))[np.newaxis,:]
+    
+    # X = R*cos(ζ); dX/dζ = (dR/dζ)*cos(ζ) - R*sin(ζ); dX/dθ = dR/dθ*cos(ζ)
+    d_X_d_s = d_R_d_s*cos_angle
+    d_X_d_zeta = d_R_d_zeta*cos_angle - R*sin_angle
+    d_X_d_theta = d_R_d_theta*cos_angle
+    
+    # Y = R*sin(ζ); dY/dζ = (dR/dζ)*sin(ζ) + R*cos(ζ); dY/dθ = dR/dθ*sin(ζ)
+    d_Y_d_s = d_R_d_s*sin_angle
+    d_Y_d_zeta = d_R_d_zeta*sin_angle + R*cos_angle
+    d_Y_d_theta = d_R_d_theta*sin_angle
+    
+    # Use the dual relations to get the Cartesian components of ∇s, ∇θ, and ∇ζ
+    #     ∇s = 1/sqrt(g) (e_θ x e_ζ) = 1/sqrt(g) ((dX/dθ)e_X + (dY/dθ)e_Y + (dZ/dθ)e_Z) x ((dX/dζ)e_X + (dY/dζ)e_Y + (dZ/dζ)e_Z)
+    #     ∇s . e_X = 1/sqrt(g) ( dY/dθ * dZ/dζ - dZ/dθ * dY/dζ ) 
+    #     ∇s . e_Y = 1/sqrt(g) ( dZ/dθ * dX/dζ - dX/dθ * dZ/dζ )
+    #     ∇s . e_Z = 1/sqrt(g) ( dX/dθ * dY/dζ - dY/dθ * dX/dζ ) 
+    grad_s_X = (d_Y_d_theta * d_Z_d_zeta - d_Z_d_theta * d_Y_d_zeta) / sqrt_g
+    grad_s_Y = (d_Z_d_theta * d_X_d_zeta - d_X_d_theta * d_Z_d_zeta) / sqrt_g
+    grad_s_Z = (d_X_d_theta * d_Y_d_zeta - d_Y_d_theta * d_X_d_zeta) / sqrt_g
+    grad_zeta_X = (d_Y_d_s * d_Z_d_theta - d_Z_d_s * d_Y_d_theta) / sqrt_g
+    grad_zeta_Y = (d_Z_d_s * d_X_d_theta - d_X_d_s * d_Z_d_theta) / sqrt_g
+    grad_zeta_Z = (d_X_d_s * d_Y_d_theta - d_Y_d_s * d_X_d_theta) / sqrt_g
+    grad_theta_X = (d_Y_d_zeta * d_Z_d_s - d_Z_d_zeta * d_Y_d_s) / sqrt_g
+    grad_theta_Y = (d_Z_d_zeta * d_X_d_s - d_X_d_zeta * d_Z_d_s) / sqrt_g
+    grad_theta_Z = (d_X_d_zeta * d_Y_d_s - d_Y_d_zeta * d_X_d_s) / sqrt_g
+    
+    # In VMEC s = psi_t/psi_{t,LCFS} so psi_t = s*psi_{t,LCFS}
+    # ∇psi_t = (dpsi_t/ds) * ∇s + 0*∇θ + 0*∇ζ = d(psi_{t,LCFS}*s)/ds * ∇s = psi_{t,LCFS} * ∇s 
+    grad_psit_X = grad_s_X * edge_toroidal_flux_over_2pi
+    grad_psit_Y = grad_s_Y * edge_toroidal_flux_over_2pi
+    grad_psit_Z = grad_s_Z * edge_toroidal_flux_over_2pi
+    
+    # ∇alpha = ∇(theta_pest - iota*zeta) = ∇(theta + Lambda - iota*zeta)
+    #        = (dλ/ds - ζ (diota/ds) ∇s + (1 + dλ/dθ) ∇θ + (dλ/dζ - iota) ∇ζ
+    # First add the part the final two terms in ∇alpha = (dλ/ds - ζ (diota/ds) ∇s + (1 + dλ/dθ) ∇θ + (dλ/dζ - iota) ∇ζ
+    grad_alpha_X = (1 + d_Lambda_d_theta) * grad_theta_X + (-iota + d_Lambda_d_zeta) * grad_zeta_X
+    grad_alpha_Y = (1 + d_Lambda_d_theta) * grad_theta_Y + (-iota + d_Lambda_d_zeta) * grad_zeta_Y
+    grad_alpha_Z = (1 + d_Lambda_d_theta) * grad_theta_Z + (-iota + d_Lambda_d_zeta) * grad_zeta_Z
+    
+    # Then add the part which depends on zeta, assuming alpha = theta_pest - iota*zeta
+    grad_alpha_X += (d_Lambda_d_s - zeta[np.newaxis,:]*d_iota_d_s)*grad_s_X
+    grad_alpha_Y += (d_Lambda_d_s - zeta[np.newaxis,:]*d_iota_d_s)*grad_s_Y
+    grad_alpha_Z += (d_Lambda_d_s - zeta[np.newaxis,:]*d_iota_d_s)*grad_s_Z
+    
+    # Only the secular term, and without the secular term 
+    grad_alpha_X_shearingpart = -zeta[np.newaxis,:]*d_iota_d_s*grad_s_X
+    grad_alpha_Y_shearingpart = -zeta[np.newaxis,:]*d_iota_d_s*grad_s_Y
+    grad_alpha_Z_shearingpart = -zeta[np.newaxis,:]*d_iota_d_s*grad_s_Z
+    grad_alpha_X_noshear = grad_alpha_X - grad_alpha_X_shearingpart
+    grad_alpha_Y_noshear = grad_alpha_Y - grad_alpha_Y_shearingpart
+    grad_alpha_Z_noshear = grad_alpha_Z - grad_alpha_Z_shearingpart
+    
+    # <grad_alpha_grad_alpha> = (a^2) ∇α . ∇α
+    # <grad_alpha_grad_psit> = (1/Bref) ∇α . ∇ψt 
+    # <grad_psit_grad_psit> = (1/(a^2*Bref^2)) ∇ψt . ∇ψt 
+    grad_alpha_grad_alpha = (a*a) * (grad_alpha_X * grad_alpha_X + grad_alpha_Y * grad_alpha_Y + grad_alpha_Z * grad_alpha_Z) 
+    grad_alpha_grad_psit = (1./Bref) * (grad_alpha_X * grad_psit_X + grad_alpha_Y * grad_psit_Y + grad_alpha_Z * grad_psit_Z)   
+    grad_psit_grad_psit = 1/(a*a*Bref*Bref) * (grad_psit_X * grad_psit_X + grad_psit_Y * grad_psit_Y + grad_psit_Z * grad_psit_Z) 
+    
+    # Without shear 
+    grad_alpha_grad_alpha_noshear = (a*a) * (grad_alpha_X_noshear * grad_alpha_X_noshear + grad_alpha_Y_noshear * grad_alpha_Y_noshear + grad_alpha_Z_noshear * grad_alpha_Z_noshear) 
+    grad_alpha_grad_psit_noshear = (1./Bref) * (grad_alpha_X_noshear * grad_psit_X + grad_alpha_Y_noshear * grad_psit_Y + grad_alpha_Z_noshear * grad_psit_Z)   
+
+    # <B_cross_grad_B_dot_grad_psit> = B x ∇B . ∇ψt = psi_{t,LCFS}/sqrt(g) (- dB/dθ B_zeta + dB/dζ B_theta)  
+    B_cross_grad_B_dot_grad_psit = edge_toroidal_flux_over_2pi / sqrt_g * (B_sub_theta * d_B_d_zeta - B_sub_zeta * d_B_d_theta)
+    
+    # We neglect shear in the calculation of <B_cross_grad_B_dot_grad_alpha>
+    # By setting <d_iota_d_s> = 0 or making sure (zeta-zeta_center)=0 at each point
+    # So that we have a rectangular cross-section at each point 
+    B_cross_grad_B_dot_grad_alpha[:,:] = 0 \
+        + (B_sub_s[:,:]*d_B_d_theta[:,:]*(d_Lambda_d_zeta[:,:] - iota) \
+        + B_sub_theta[:,:]*d_B_d_zeta[:,:]*(d_Lambda_d_s[:,:] - zeta[:]*d_iota_d_s) \
+        + B_sub_zeta[:,:]*d_B_d_s[:,:]*(1 + d_Lambda_d_theta[:,:]) \
+        - B_sub_zeta[:,:]*d_B_d_theta[:,:]*(d_Lambda_d_s[:,:] - zeta[:]*d_iota_d_s) \
+        - B_sub_theta[:,:]*d_B_d_s[:,:]*(d_Lambda_d_zeta[:,:] - iota) \
+        - B_sub_s[:,:]*d_B_d_zeta[:,:]*(1 + d_Lambda_d_theta[:,:])) / sqrt_g[:,:] 
+    B_cross_grad_B_dot_grad_alpha_shearingpart = \
+        + (B_sub_theta[:,:]*d_B_d_zeta[:,:]*(-d_iota_d_s) \
+        - B_sub_zeta[:,:]*d_B_d_theta[:,:]*(-d_iota_d_s)) / sqrt_g[:,:] 
+    B_cross_grad_B_dot_grad_alpha_noshear[:,:] = 0 \
+        + (B_sub_s[:,:]*d_B_d_theta[:,:]*(d_Lambda_d_zeta[:,:] - iota) \
+        + B_sub_theta[:,:]*d_B_d_zeta[:,:]*(d_Lambda_d_s[:,:]) \
+        + B_sub_zeta[:,:]*d_B_d_s[:,:]*(1 + d_Lambda_d_theta[:,:]) \
+        - B_sub_zeta[:,:]*d_B_d_theta[:,:]*(d_Lambda_d_s[:,:]) \
+        - B_sub_theta[:,:]*d_B_d_s[:,:]*(d_Lambda_d_zeta[:,:] - iota) \
+        - B_sub_s[:,:]*d_B_d_zeta[:,:]*(1 + d_Lambda_d_theta[:,:])) / sqrt_g[:,:] 
+        
+    # Calculate grad B (could be wrong!)
+    # ∇B = (dB/ds) ∇s + (dB/dtheta) ∇theta + (dB/dzeta) ∇zeta
+    gradB_X = d_B_d_s*grad_s_X + d_B_d_theta*grad_theta_X + d_B_d_zeta*grad_zeta_X 
+    gradB_Y = d_B_d_s*grad_s_Y + d_B_d_theta*grad_theta_Y + d_B_d_zeta*grad_zeta_Y 
+    gradB_Z = d_B_d_s*grad_s_Y + d_B_d_theta*grad_theta_Z + d_B_d_zeta*grad_zeta_Z 
+        
+    # Collect the vmec data needed for <pest_to_vmec>
+    vmec_data = {'xm' : xm, 'xn' : xn, 'mnmax' : mnmax, 'lmns' : lmns}
+    vmec_data['surfaces_indexes'] = surfaces_indexes; vmec_data['surfaces_weights'] = surfaces_weights
+    
+    # Save the data as a pickle
+    DATA = DATAOBJECT_KAPPA(zeta, theta, nfp, iota, xm, xn, mnmax, lmns, surfaces_indexes, surfaces_weights, 
+        d_R_d_s_mnc, d_Z_d_s_mns, d_Lambda_d_s_mns, d_B_d_s_mnc, Z, R, B, d_R_d_s, d_R_d_zeta, d_R_d_theta, 
+        d_Z_d_s, d_Z_d_zeta, d_Z_d_theta, d_Lambda_d_s, d_Lambda_d_zeta, d_Lambda_d_theta, sqrt_g, 
+        d_B_d_s, d_B_d_zeta, d_B_d_theta, B_sup_theta, B_sup_zeta, B_sub_s, B_sub_theta, 
+        B_sub_zeta, B_cross_grad_B_dot_grad_alpha, ns, normalized_toroidal_flux_full_grid, ds, 
+        B_cross_grad_B_dot_grad_alpha_noshear, B_cross_grad_B_dot_grad_alpha_shearingpart, 
+        grad_alpha_grad_alpha, grad_alpha_grad_psit, grad_psit_grad_psit, B_cross_grad_B_dot_grad_psit,
+        grad_alpha_grad_alpha_noshear, grad_alpha_grad_psit_noshear, shat, sign_torflux, 
+        L_reference, B_reference, bmag)
+    file = open(pickle_path,  "wb"); 
+    pickle.dump(DATA , file); 
+    file.close()      
+    
+    # Return the curvature and the coordinates
+    return DATA, vmec_data
+
+#--------------------------
+class DATAOBJECT_KAPPA:
+    def __init__(self, zeta, theta, nfp, iota, xm, xn, mnmax, lmns, surfaces_indexes, surfaces_weights, 
+        d_R_d_s_mnc, d_Z_d_s_mns, d_Lambda_d_s_mns, d_B_d_s_mnc, Z, R, B, d_R_d_s, d_R_d_zeta, d_R_d_theta, 
+        d_Z_d_s, d_Z_d_zeta, d_Z_d_theta, d_Lambda_d_s, d_Lambda_d_zeta, d_Lambda_d_theta, sqrt_g, 
+        d_B_d_s, d_B_d_zeta, d_B_d_theta, B_sup_theta, B_sup_zeta, B_sub_s, B_sub_theta, 
+        B_sub_zeta, B_cross_grad_B_dot_grad_alpha, ns, normalized_toroidal_flux_full_grid, ds, 
+        B_cross_grad_B_dot_grad_alpha_noshear, B_cross_grad_B_dot_grad_alpha_shearingpart, 
+        grad_alpha_grad_alpha, grad_alpha_grad_psit, grad_psit_grad_psit, B_cross_grad_B_dot_grad_psit,
+        grad_alpha_grad_alpha_noshear, grad_alpha_grad_psit_noshear, shat, sign_torflux,
+        L_reference, B_reference, bmag):
+        self.R = R; self.Z = Z; self.B = B; self.sqrt_g = sqrt_g 
+        self.zeta = zeta; self.theta = theta; self.ds = ds; self.ns = ns 
+        self.nfp = nfp; self.iota = iota; self.shat = shat; self.sign_torflux = sign_torflux
+        self.xm = xm; self.xn = xn; self.mnmax = mnmax 
+        self.lmns = lmns; self.surfaces_indexes = surfaces_indexes; self.surfaces_weights = surfaces_weights 
+        self.d_R_d_s_mnc = d_R_d_s_mnc; self.d_Z_d_s_mns = d_Z_d_s_mns; self.d_B_d_s_mnc = d_B_d_s_mnc;  self.d_Lambda_d_s_mns = d_Lambda_d_s_mns 
+        self.d_R_d_s = d_R_d_s; self.d_Z_d_s = d_Z_d_s; self.d_Lambda_d_s = d_Lambda_d_s 
+        self.d_R_d_zeta = d_R_d_zeta; self.d_Z_d_zeta = d_Z_d_zeta; self.d_Lambda_d_zeta = d_Lambda_d_zeta 
+        self.d_R_d_theta = d_R_d_theta; self.d_Z_d_theta = d_Z_d_theta; self.d_Lambda_d_theta = d_Lambda_d_theta 
+        self.d_B_d_s = d_B_d_s; self.B_sub_s = B_sub_s; self.B_sub_zeta = B_sub_zeta  
+        self.d_B_d_zeta = d_B_d_zeta; self.B_sup_zeta = B_sup_zeta 
+        self.d_B_d_theta = d_B_d_theta; self.B_sup_theta = B_sup_theta; self.B_sub_theta = B_sub_theta 
+        self.B_cross_grad_B_dot_grad_alpha = B_cross_grad_B_dot_grad_alpha 
+        self.normalized_toroidal_flux_full_grid = normalized_toroidal_flux_full_grid  
+        self.B_cross_grad_B_dot_grad_alpha_noshear = B_cross_grad_B_dot_grad_alpha_noshear
+        self.B_cross_grad_B_dot_grad_alpha_shearingpart = B_cross_grad_B_dot_grad_alpha_shearingpart
+        self.grad_alpha_grad_alpha = grad_alpha_grad_alpha; self.grad_alpha_grad_psit = grad_alpha_grad_psit
+        self.grad_psit_grad_psit = grad_psit_grad_psit; self.B_cross_grad_B_dot_grad_psit = B_cross_grad_B_dot_grad_psit
+        self.grad_alpha_grad_alpha_noshear = grad_alpha_grad_alpha_noshear; self.grad_alpha_grad_psit_noshear = grad_alpha_grad_psit_noshear
+        self.L_reference = L_reference; self.B_reference = B_reference; self.bmag = bmag
+        return
+
+#-------------------------------------
+def get_CosineAndSineTransformOfRZQ_forFieldLine(wout_path, svalue, quantity, nzeta=50, toroidal_turns=1, alpha0=0):
+    
+    # Reac the VMEC file
+    xm, xn, xm_nyq, xn_nyq, mnmax, mnmax_nyq, ns, nfp, rmnc, zmns, lmns, bmnc, gmnc, iotas = read_vmecdata(wout_path) 
+    
+    # Select the quantity
+    if quantity=='B': qmnc = bmnc; qmns = [None]
+    elif quantity=='lambda': qmnc = gmnc; qmns = [None]
+    else: exit_program('No other options are implemented.', get_CosineAndSineTransformOfRZQ_forFieldLine, sys._getframe().f_lineno)
+        
+    # Needed quantities
+    iota = calculate_iota(svalue, ns, iotas) 
+    
+    # Get the pest theta and initiate the vmec theta    
+    poloidal_turns = toroidal_turns*iota
+    theta_pest = np.linspace(-poloidal_turns*np.pi, poloidal_turns*np.pi, nzeta)
+    theta_vmec = np.empty((nzeta))
+                                 
+    # The zeta array is calculted from alpha0 = theta_pest - iota * zeta
+    zeta = np.array([(x-alpha0)/iota for x in theta_pest]) 
+    
+    # Copy the toroidal and poloidal mode numbers to ease the notation
+    m_nyq = np.array([ int(m) for m in xm_nyq ])
+    n_nyq = np.array([ int(n) for n in xn_nyq ])
+    m = np.array([ int(m) for m in xm ])
+    n = np.array([ int(n) for n in xn ])
+       
+    # Get the interpolation weights, for when svalue lies between two flux surfaces   
+    surfaces_indexes, surfaces_weights = get_interpolationWeightsOnHalfGrid(ns, svalue)
+    
+    # Initiate the (R,Z) coordinates and the quantity Q
+    R_mn = np.zeros((nzeta, mnmax))
+    Z_mn = np.zeros((nzeta, mnmax))
+    Q_mn = np.zeros((nzeta, mnmax_nyq))
+        
+    # Collect the vmec data needed for <pest_to_vmec>
+    vmec_data = {'xm' : xm, 'xn' : xn, 'mnmax' : mnmax, 'lmns' : lmns}
+    vmec_data['surfaces_indexes'] = surfaces_indexes; vmec_data['surfaces_weights'] = surfaces_weights
+    
+    # Consine and Sine Fourier transforms 
+    for interpolation in [0,1]:
+        for izeta in range(len(zeta)):
+            
+            # Calculate the theta angle for vmec
+            theta_vmec[izeta] = pest_to_vmec(theta_pest[izeta], zeta[izeta], vmec_data)
+            
+            # When svalue denotes a flux surface between two flux surfaces
+            # that are given by vmec, we need to interpolate the values
+            weight = surfaces_weights[interpolation]
+            isurf  = surfaces_indexes[interpolation]
+            
+            # Get the angle 
+            angle = m * theta_vmec[izeta] - n * zeta[izeta] 
+            angle_nyq = m_nyq * theta_vmec[izeta] - n_nyq * zeta[izeta]
+            
+            # Get the cosinus and sinus
+            cos_angle = np.cos(angle); cos_angle_nyq = np.cos(angle_nyq)
+            sin_angle = np.sin(angle); sin_angle_nyq = np.sin(angle_nyq)  
+            
+            # Calculate the (R,Z) coordinates  
+            R_mn[izeta, :] += rmnc[isurf,:]*cos_angle*weight
+            Z_mn[izeta, :] += zmns[isurf,:]*sin_angle*weight 
+            
+            # Calculate the quantity Q
+            if np.all(qmnc[0]!=None): Q_mn[izeta, :] += qmnc[isurf,:]*cos_angle_nyq*weight
+            if np.all(qmns[0]!=None): Q_mn[izeta, :] += qmns[isurf,:]*sin_angle_nyq*weight 
+                
+    # Sum away the (m,n) modes
+    R = np.sum(R_mn[:, :], axis=1)
+    Z = np.sum(Z_mn[:, :], axis=1)
+    Q = np.sum(Q_mn[:, :], axis=1) 
+    
+    # Return R(zeta,theta); Z(zeta, theta) and Q(zeta, theta)
+    return R, Z, Q, zeta, theta_pest, nfp
+
+#--------------------------  
+def read_vmecdata(wout_path):
+
+    # Read the netcdf file
+    dataset = nc4.Dataset(wout_path, mode='r')
+  
+    # Poloidal and toroidal mode numbers
+    # For most VMECs
+    xm = dataset.variables['xm'][:]             # Poloidal mode numbers  xm(mn_mode)   
+    xn = dataset.variables['xn'][:]             # Toroidal mode numbers  xn(mn_mode)  
+    xm_nyq = dataset.variables['xm_nyq'][:]     # Poloidal mode numbers (Nyquist) xm_nyq(mn_mode_nyq)
+    xn_nyq = dataset.variables['xn_nyq'][:]     # Toroidal mode numbers (Nyquist) xn_nyq(mn_mode_nyq) 
+    
+    # Dimensions
+    ns  = int(dataset.variables['ns'][:])               
+    nfp = int(dataset.variables['nfp'][:]) 
+    mnmax = int(dataset.variables['mnmax'][:])  
+    mnmax_nyq = int(dataset.variables['mnmax_nyq'][:]) 
+     
+    # Read rmnc, zmns and bmnc versus (radius,mn_mode)
+    rmnc = dataset.variables['rmnc'][:]     # cosmn component of cylindrical R, full mesh  
+    zmns = dataset.variables['zmns'][:]     # sinmn component of cylindrical Z, full mesh 
+    bmnc = dataset.variables['bmnc'][:]     # cosmn component of mod-B, half mesh   
+    lmns = dataset.variables['lmns'][:]     # cosmn component of lambda, half mesh   
+    gmnc = dataset.variables['gmnc'][:]     # cosmn component of jacobian, half mesh   
+    
+    # Rotational transform 
+    iotas = dataset.variables['iotas'][:]
+    
+    # Stellarator-asymmetric terms 
+    lasym = dataset.variables['lasym__logical__'][:]
+    if lasym: print('ABORT: <lasym> is not implemented yet.'); sys.exit()
+    
+    # Check grid sizes
+    print(f'  xm: {np.shape(xm)}') 
+    print(f'  xn: {np.shape(xn)}') 
+    print(f'  xm_nyq: {np.shape(xm_nyq)}') 
+    print(f'  xn_nyq: {np.shape(xn_nyq)}') 
+    print(f'  rmnc: {np.shape(rmnc)}') 
+    print(f'  zmns: {np.shape(zmns)}') 
+    print(f'  lmns: {np.shape(lmns)}')
+    print(f'  bmnc: {np.shape(bmnc)}') 
+    print(f'  gmnc: {np.shape(gmnc)}'); print()
+    return xm, xn, xm_nyq, xn_nyq, mnmax, mnmax_nyq, ns, nfp, rmnc, zmns, lmns, bmnc, gmnc, iotas
+
+#--------------------------
+def pest_to_vmec(theta_pest=0.8, zeta0=0.0, vmec_data=None):
+    from scipy.optimize import fsolve 
+    x_roots = fsolve(lambda x: fzero_residual(x, theta_pest, zeta0, vmec_data), x0=theta_pest)
+    return x_roots
+ 
+#--------------------------  
+def fzero_residual(x, theta_pest_target=0.0, zeta0=0.0, vmec_data=None):
+    ''' Note that lmns and lmnc use the non-Nyquist xm, xn, and mnmax.
+    Also note that lmns and lmnc are on the HALF grid.
+    residual = (theta_pest based on theta_vmec_try) - theta_pest_target = theta_vmec_try + Lambda - theta_pest_target
+    The variable x plays the role of theta_vmec_try. '''
+   
+    # The data needed from the vmec file
+    xm = vmec_data['xm']  
+    xn = vmec_data['xn']      
+    mnmax = vmec_data['mnmax']   
+    lmns = vmec_data['lmns']     
+    surfaces_indexes = vmec_data['surfaces_indexes']
+    surfaces_weights = vmec_data['surfaces_weights']
+    
+    # x = theta_vmec_try in Matt's VMEC_2_GS2 interface
+    fzero_residual = x - theta_pest_target
+    
+    # Iterate over the modes
+    for imn in range(mnmax):
+        
+        # Get the angle 
+        sin_angle = np.sin(xm[imn]*x - xn[imn]*zeta0)
+        
+        # Interpolate the calculation between the flux surfaces
+        for interpolation in [0,1]:
+            
+            # When svalue denotes a flux surface between two flux surfaces
+            # that are given by vmec, we need to interpolate the values
+            weight = surfaces_weights[interpolation]
+            isurf  = surfaces_indexes[interpolation]
+            
+            # Calculate fzero_residual
+            fzero_residual = fzero_residual + lmns[isurf, imn]*sin_angle*weight
+
+    return fzero_residual
+ 
+#===============================================================================
+#                                   TEST CODE                                  #
+#===============================================================================
+
+if __name__ == "__main__":   
+    wout_path = pathlib.Path('/home/hanne/CIEMAT/RESEARCH/MagneticEquilibria/VmecFiles/wout_asdex.nc')
+    wout_path = pathlib.Path('/home/hanne/CIEMAT/RESEARCH/MagneticEquilibria/VmecFiles/wout_tok_cbc_2T.nc')
+    wout_path = pathlib.Path('/home/hanne/CIEMAT/RESEARCH/MagneticEquilibria/VmecFiles/wout_w7xr003.nc')
+    wout_path = pathlib.Path('/home/hanne/CIEMAT/RESEARCH/MagneticEquilibria/VmecFiles/wout_aug_vacuum.nc')
+    _, _, Q, zeta, theta, nfp = get_RZBFromCosineAndSineTransformVMEC(wout_path, svalue=0.7, quantity='B', ntheta=20, nzeta=20)
+    
\ No newline at end of file
diff --git a/POST_PROCESSING/stellapy/data/geometry/get_interpolationWeights.py b/POST_PROCESSING/stellapy/data/geometry/get_interpolationWeights.py
new file mode 100644
index 0000000000..74fb0959ab
--- /dev/null
+++ b/POST_PROCESSING/stellapy/data/geometry/get_interpolationWeights.py
@@ -0,0 +1,20 @@
+ 
+from stellapy.data.geometry.calculate_geometricQuantitiesVMEC import vmec 
+    
+def get_interpolationWeightsOnHalfGrid(ns, svalue):
+    """" Get the interpolation weights, for when svalue lies between two flux surfaces. """
+    VMEC = vmec(verbose=False)  
+    VMEC.alpha0 = 0
+    VMEC.normalized_toroidal_flux_used = svalue
+    VMEC.calculate_normalizedToroidalFluxOnFullAndHalfGrids(ns)
+    VMEC.calculate_interpolationWeights(ns)  
+    return VMEC.radial_index_half, VMEC.radial_weight_half 
+
+def get_interpolationWeightsOnFullGrid(ns, svalue):
+    """" Get the interpolation weights, for when svalue lies between two flux surfaces. """
+    VMEC = vmec(verbose=False)  
+    VMEC.alpha0 = 0
+    VMEC.normalized_toroidal_flux_used = svalue
+    VMEC.calculate_normalizedToroidalFluxOnFullAndHalfGrids(ns)
+    VMEC.calculate_interpolationWeights(ns)  
+    return VMEC.radial_index_full, VMEC.radial_weight_full
\ No newline at end of file
diff --git a/POST_PROCESSING/stellapy/plot/geometry/plot_fluxSurfacein3D.py b/POST_PROCESSING/stellapy/plot/geometry/plot_fluxSurfacein3D.py
new file mode 100644
index 0000000000..0bc63a4557
--- /dev/null
+++ b/POST_PROCESSING/stellapy/plot/geometry/plot_fluxSurfacein3D.py
@@ -0,0 +1,135 @@
+"""
+
+Plot B(X,Y,Z).
+
+Hanne Thienpondt 
+25/02/2025
+
+"""
+
+#!/usr/bin/python3   
+from PIL import Image
+import os, sys 
+import pathlib
+import numpy as np 
+import matplotlib
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D #@UnusedImport 
+
+# Stellapy package
+sys.path.append(os.path.abspath(pathlib.Path(os.environ.get('STELLAPY')).parent)+os.path.sep)   
+from stellapy.data.geometry.get_RZBFromCosineAndSineTransformVMEC import get_RZBFromCosineAndSineTransformVMEC 
+from stellapy.data.geometry.get_RZBFromCosineAndSineTransformVMEC import get_CosineAndSineTransformOfRZQ_forFieldLine
+from stellapy.utils.files.ensure_dir import ensure_dir 
+    
+def plot_fluxSurfacein3D(wout_path, svalue=None, rho=0.7, ntheta=50, nzeta=50, quantity="B", \
+        set_title=False, colorbar=False, show=True, force_limits=False, vmin=0, vmax=0, plot_field_line=False): 
+     
+    # Check the quantity: B, jacobian or lambda
+    if quantity not in ["B", "J", "L"]: return 
+     
+    # Radial position
+    if svalue==None: svalue = rho*rho
+     
+    # Read R(zeta,theta); Z(zeta, theta) and Q(zeta, theta) from the VMEC netcdf file
+    R, Z, Q, zeta, _, nfp = get_RZBFromCosineAndSineTransformVMEC(wout_path, svalue, quantity, ntheta, nzeta)
+    
+    # Create the figure
+    fig = plt.figure(figsize=(18, 9))
+    ax = fig.add_subplot(projection='3d')  
+    ax.set_rasterization_zorder(-10)
+    
+    # Iterate over the field periods
+    for i in range(nfp+1):
+     
+        # Transform (R,Z) to (X,Y) 
+        X = R*np.cos(zeta+i*2*np.pi/nfp)
+        Y = R*np.sin(zeta+i*2*np.pi/nfp)
+        
+        # Plot
+        ax, m = plot3D(ax, X, Y, Z, Q) 
+        
+        # Remember limits
+        if not force_limits:
+            vmin = np.min([vmin,np.min(X)])
+            vmax = np.max([vmax,np.max(X)])
+      
+    # Plot the field line   
+    if plot_field_line:   
+        R, Z, Q, zeta, theta_pest, nfp = get_CosineAndSineTransformOfRZQ_forFieldLine(wout_path, svalue, quantity, nzeta=50, toroidal_turns=1, alpha0=0)
+        X = R*np.cos(zeta+i*2*np.pi/nfp)
+        Y = R*np.sin(zeta+i*2*np.pi/nfp)
+        ax.plot(X, Y, Z, color='red', lw=10) 
+        
+    # Set limits
+    ax.set_xlim([vmin, vmax])
+    ax.set_ylim([vmin, vmax])    
+    ax.set_zlim3d([vmin, vmax])
+       
+    # Set title
+    if set_title:
+        if quantity=="B": ax.set_title('Magnetic field strength')
+        if quantity=="L": ax.set_title('Lambda')
+        if quantity=="J": ax.set_title('Jacobian')
+       
+    # Intial viewing angle
+    view = "narrow"; angle=5
+    if view=="top": ax.view_init(90,angle)
+    if view=="bottom": ax.view_init(270,angle)
+    if view=="side": ax.view_init(0,angle)
+    if view=="both": ax.view_init(45,angle)
+    if view=="narrow": ax.view_init(15,angle)
+       
+    # Show figure 
+    ax.set_box_aspect((np.ptp([vmin, vmax]), np.ptp([vmin, vmax]), np.ptp([vmin, vmax])))  
+    if colorbar: fig.colorbar(m)
+    ax.set_axis_off()
+    if show: plt.show()
+    return fig, ax
+
+#---------------------
+def plot3D(ax,x,y,z,f):
+      
+    # fourth dimention - colormap
+    # create colormap ccording to x-value (can use any 50x50 array)
+    color_dimension = f # change to desired fourth dimension
+    minn, maxx = color_dimension.min(), color_dimension.max()
+    norm = matplotlib.colors.Normalize(minn, maxx)
+    m = plt.cm.ScalarMappable(norm=norm, cmap='jet')
+    m.set_array([])
+    fcolors = m.to_rgba(color_dimension)
+    
+    # plot 
+    ax.plot_surface(x,y,z, rstride=1, cstride=1, facecolors=fcolors, vmin=minn, vmax=maxx, shade=False)
+    ax.set_xlabel('X [m]')
+    ax.set_ylabel('Y [m]')
+    ax.set_zlabel('Z [m]')  
+    return ax, m
+
+
+#-------------------------------------------------------------------------------
+#                        Run as the main script
+#-------------------------------------------------------------------------------
+if __name__ == "__main__":
+
+    # VMEC file
+    stella_folder = os.path.abspath(pathlib.Path(os.environ.get('STELLAPY')).parent.parent)
+    figure_folder = stella_folder / pathlib.Path("stellapy_figures"); ensure_dir(figure_folder)
+    vmec = stella_folder / pathlib.Path("DOCUMENTATION/VMEC_equilibria/wout_w7x_standardConfig.nc"); device = 'W7X'
+    vmec = stella_folder / pathlib.Path("DOCUMENTATION/VMEC_equilibria/wout_161s1.nc"); device = 'NCSX'
+    
+    # Radial location
+    rho = 0.8
+    
+    # Resolution
+    n = 50
+    dpi = 500
+            
+    # Plot the last closed flux surface     
+    fig, ax = plot_fluxSurfacein3D(vmec, rho=rho, ntheta=n, nzeta=n, quantity="B", show=False)
+     
+    # Save the figure as eps 
+    name = figure_folder/("rho"+str(int(rho*100))+"_n"+str(n)+"_"+device+".png")
+    fig.savefig(name, format='png', dpi=dpi)
+    print("Saved 3D flux surface for "+vmec.name)  
+                
diff --git a/POST_PROCESSING/stellapy/plot/nonlinear/quantity_vs_xy.py b/POST_PROCESSING/stellapy/plot/nonlinear/quantity_vs_xy.py
index 6f9cab1fa1..cc9805bf0e 100755
--- a/POST_PROCESSING/stellapy/plot/nonlinear/quantity_vs_xy.py
+++ b/POST_PROCESSING/stellapy/plot/nonlinear/quantity_vs_xy.py
@@ -1,4 +1,12 @@
- 
+"""
+
+Plot potential(x,y).
+
+Hanne Thienpondt 
+25/02/2025
+
+"""
+
 #!/usr/bin/python3  
 import copy
 import sys, os
@@ -20,6 +28,7 @@
 from stellapy.plot.utils.surface.get_colorMap import get_colorMap
 from stellapy.utils.decorators.exit_program import exit_program
 from stellapy.simulations.Research import create_research
+from stellapy.utils.files.ensure_dir import ensure_dir 
 from stellapy.plot.utils.labels import standardLabels
 from stellapy.utils.commandprompt.bash import Bash 
 
@@ -28,7 +37,7 @@
 #===============================================================================
 
 def plot_quantity_vs_xy(folder, z_quantity="phi", specie=None, tstart=None, tend=None, z=None, 
-        remove_zonal_modes=True, log=False, crange=None, ordersOfMagnitude=2, interpolation_step=20): 
+        remove_zonal_modes=True, log=False, crange=None, ordersOfMagnitude=2, interpolation_step=20, show=True): 
     
     # Create <simulations> based on the given <folder>
     research = create_research(folders=folder) 
@@ -57,8 +66,8 @@ def plot_quantity_vs_xy(folder, z_quantity="phi", specie=None, tstart=None, tend
                     
     # Show the figure 
     mpl.rcParams["savefig.directory"] = folder
-    plt.show()
-    return
+    if show: plt.show()
+    return fig
 
 #---------------------------------------- 
 def subplot_quantity_vs_xy(ax, simulation, z_quantity, specie, t_range=None, z=None, interpolation_step=None,
@@ -260,14 +269,20 @@ def get_fourierSpaceDataFromSaturatedFiles(simulation, z_quantity, specie, z):
     plot_quantity_vs_xy(**bash.get_arguments())   
 
 ################################################################################
-#                                  DEBUG MODE                                  #
+#                               STELLAPY EXAMPLE                               #
 ################################################################################
     
-if __name__ == "__main__":
-    import pathlib
-    folder = pathlib.Path("/home/hanne/CIEMAT/RUNS/test_CBC2/biggrid")
-    plot_quantity_vs_xy(folder, z=0, tstart=310)
-    sys.exit()
+if __name__ == "__main__":    
+    
+    # Example output file
+    stella_folder = os.path.abspath(pathlib.Path(os.environ.get('STELLAPY')).parent.parent)
+    figure_folder = stella_folder / pathlib.Path("stellapy_figures"); ensure_dir(figure_folder)
+    data_folder = stella_folder / pathlib.Path("DOCUMENTATION/example_output")
+
+    # Plot potential(x,y)
+    fig = plot_quantity_vs_xy(data_folder, z_quantity='phi', show=False)
+    fig.savefig(figure_folder / "potential_vs_xy.png", format='png', dpi=500)
+    print("Saved potential(x,y)")  
      
      
 
diff --git a/STELLA_CODE/diagnostics/diagnostics_potential.f90 b/STELLA_CODE/diagnostics/diagnostics_potential.f90
index 7bbeeac246..98e5fca244 100644
--- a/STELLA_CODE/diagnostics/diagnostics_potential.f90
+++ b/STELLA_CODE/diagnostics/diagnostics_potential.f90
@@ -54,7 +54,9 @@ subroutine write_potential_to_netcdf_file(istep, nout, timer, write_to_netcdf_fi
       use stella_io, only: write_phi2_nc
       use stella_io, only: write_apar2_nc
       use stella_io, only: write_bpar2_nc
-      use stella_io, only: write_phi_nc 
+      use stella_io, only: write_phi_nc
+      use stella_io, only: write_apar_nc
+      use stella_io, only: write_bpar_nc
       use stella_io, only: write_kspectra_nc
       use stella_time, only: code_dt, code_time
 
@@ -64,7 +66,11 @@ subroutine write_potential_to_netcdf_file(istep, nout, timer, write_to_netcdf_fi
       
       ! Input file
       use parameters_diagnostics, only: write_phi_vs_kxkyz
+      use parameters_diagnostics, only: write_apar_vs_kxkyz
+      use parameters_diagnostics, only: write_bpar_vs_kxkyz
       use parameters_diagnostics, only: write_phi2_vs_kxky
+      use parameters_diagnostics, only: write_apar2_vs_kxky
+      use parameters_diagnostics, only: write_bpar2_vs_kxky
 
       implicit none 
 
@@ -103,10 +109,18 @@ subroutine write_potential_to_netcdf_file(istep, nout, timer, write_to_netcdf_fi
          call volume_average(apar_vs_kykxzt, apar2) 
          call volume_average(bpar_vs_kykxzt, bpar2)
          call write_potential_to_ascii_file(istep, phi2, apar2, bpar2) 
-         if (include_apar) then 
-            write (*, '(A2,I7,A2,ES12.4,A2,ES12.4,A2,ES12.4,A2,ES12.4)') " ", istep, " ", code_time, " ", code_dt, " ", phi2, " ", apar2
+         if (include_apar .and. include_bpar) then 
+            write (*, '(A2,I7,A2,ES12.4,A2,ES12.4,A2,ES12.4,A2,ES12.4,A2,ES12.4)') &
+            " ", istep, " ", code_time, " ", code_dt, " ", phi2, " ", apar2, " ", bpar2
+         else if (include_apar) then 
+            write (*, '(A2,I7,A2,ES12.4,A2,ES12.4,A2,ES12.4,A2,ES12.4)') &
+            " ", istep, " ", code_time, " ", code_dt, " ", phi2, " ", apar2
+         else if (include_bpar) then 
+            write (*, '(A2,I7,A2,ES12.4,A2,ES12.4,A2,ES12.4,A2,ES12.4)') &
+            " ", istep, " ", code_time, " ", code_dt, " ", phi2, " ", bpar2
          else
-            write (*, '(A2,I7,A2,ES12.4,A2,ES12.4,A2,ES12.4)') " ", istep, " ", code_time, " ", code_dt, " ", phi2
+            write (*, '(A2,I7,A2,ES12.4,A2,ES12.4,A2,ES12.4)') &
+            " ", istep, " ", code_time, " ", code_dt, " ", phi2
          end if
       end if
 
@@ -123,39 +137,40 @@ subroutine write_potential_to_netcdf_file(istep, nout, timer, write_to_netcdf_fi
          call write_apar2_nc(nout, apar2)
          call write_bpar2_nc(nout, bpar2)
 
-         ! Write phi(t,ky,kx,z,tube) to the netcdf file
+         ! Write phi(t,ky,kx,z,tube), apar(t,ky,kx,z,tube) and bpar(t,ky,kx,z,tube) to the netcdf file
          if (write_phi_vs_kxkyz) then
             if (debug) write (*, *) 'diagnostics::diagnostics_stella::write_phi_nc'
             call write_phi_nc(nout, phi_vs_kykxzt)
          end if
+         if (write_apar_vs_kxkyz .and. include_apar) then
+            if (debug) write (*, *) 'diagnostics::diagnostics_stella::write_apar_nc'
+            call write_apar_nc(nout, apar_vs_kykxzt)
+         end if
+         if (write_bpar_vs_kxkyz .and. include_bpar) then
+            if (debug) write (*, *) 'diagnostics::diagnostics_stella::write_bpar_nc'
+            call write_bpar_nc(nout, bpar_vs_kykxzt)
+         end if
 
          ! Write phi2(t,ky,kx) to the netcdf file
          if (write_phi2_vs_kxky) then
-            if (debug) write (*, *) 'diagnostics::diagnostics_stella::write_kspectra_nc'
-            
-            ! For phi2
+            if (debug) write (*, *) 'diagnostics::diagnostics_stella::write_kspectra_nc' 
             allocate (phi2_vs_kxky(naky, nakx)) 
             call fieldline_average(real(phi_vs_kykxzt * conjg(phi_vs_kykxzt)), phi2_vs_kxky)
             call write_kspectra_nc(nout, phi2_vs_kxky, "phi2_vs_kxky", "electrostatic potential")
             deallocate (phi2_vs_kxky)
-            
-            ! For apar
-            if (include_apar) then
-               allocate (apar2_vs_kxky(naky, nakx))
-               call fieldline_average(real(apar_vs_kykxzt * conjg(apar_vs_kykxzt)), apar2_vs_kxky)
-               call write_kspectra_nc(nout, apar2_vs_kxky, "apar2_vs_kxky", "parallel vector potential")
-               deallocate (apar2_vs_kxky)
-            end if
-            
-            ! For bpar
-            if (include_bpar) then
-               allocate (bpar2_vs_kxky(naky, nakx))
-               call fieldline_average(real(bpar_vs_kykxzt * conjg(bpar_vs_kykxzt)), bpar2_vs_kxky)
-               call write_kspectra_nc(nout, bpar2_vs_kxky, "bpar2_vs_kxky", "parallel magnetic field fluctuation")
-               deallocate (bpar2_vs_kxky)
-            end if
-            
          end if
+         if (write_apar2_vs_kxky .and. include_apar) then 
+            allocate (apar2_vs_kxky(naky, nakx))
+            call fieldline_average(real(apar_vs_kykxzt * conjg(apar_vs_kykxzt)), apar2_vs_kxky)
+            call write_kspectra_nc(nout, apar2_vs_kxky, "apar2_vs_kxky", "parallel vector potential")
+            deallocate (apar2_vs_kxky)
+         end if 
+         if (write_bpar2_vs_kxky .and. include_bpar) then
+            allocate (bpar2_vs_kxky(naky, nakx))
+            call fieldline_average(real(bpar_vs_kykxzt * conjg(bpar_vs_kykxzt)), bpar2_vs_kxky)
+            call write_kspectra_nc(nout, bpar2_vs_kxky, "bpar2_vs_kxky", "parallel magnetic field fluctuation")
+            deallocate (bpar2_vs_kxky)
+         end if 
          
       end if
       
diff --git a/STELLA_CODE/grids/zgrid.f90 b/STELLA_CODE/grids/zgrid.f90
index bca11e55b0..cd1c3dcbbb 100644
--- a/STELLA_CODE/grids/zgrid.f90
+++ b/STELLA_CODE/grids/zgrid.f90
@@ -88,24 +88,32 @@ subroutine read_parameters
                                                       text_option('periodic', boundary_option_self_periodic), &
                                                       text_option('linked', boundary_option_linked), &
                                                       text_option('stellarator', boundary_option_linked_stellarator)/)
-                                                      
+      
+      ! Variables in the <zgrid_parameters> namelist
       namelist /zgrid_parameters/ nzed, nperiod, ntubes, &
          shat_zero, boundary_option, zed_equal_arc, &
          grad_x_grad_y_zero, dkx_over_dky
 
+      ! Load the default values of the variables
       call set_default_parameters()
+      
+      ! Load the values set in the input file
       in_file = input_unit_exist("zgrid_parameters", exist)
       if (exist) read (unit=in_file, nml=zgrid_parameters)
-
       ierr = error_unit()
+      
+      ! Change the text of <boundary_option> to an integer 
+      ! Note that boundary_option may be changed to self-periodic later,
+      ! if magnetic shear or nabla x cdot nabla y is smaller than shat_zero or grad_x_grad_y_zero
       call get_option_value &
          (boundary_option, boundaryopts, boundary_option_switch, &
           ierr, "boundary_option in dist_fn_knobs")
+          
+      ! Make sure <nzed> is an even integer, otherwise the potential explodes
+      if (MOD(nzed,2) .eq. 1) nzed = nzed + 1
 
-      ! note that boundary_option may be changed to self-periodic later
-      ! if magnetic shear or nabla x \cdot nabla y is smaller than shat_zero or grad_x_grad_y_zero
-      ! cannot do this here as these quantities have yet to be input
-
+      ! <nzed> specifies the grid points left and right of z=0 in a single segment
+      ! whereas <nzgrid> is the total number of grid points
       nzgrid = nzed / 2 + (nperiod - 1) * nzed
 
       ! force use of equal arc grid to ensure gradpar alpha-independent
@@ -122,16 +130,19 @@ subroutine set_default_parameters()
       nperiod = 1
       ntubes = 1
       boundary_option = 'default'
+      
       ! if zed_equal_arc = T, then zed is chosen to be arc length
       ! if zed_equal_arc = F, then zed is poloidal (axisymmetric)
       ! or zeta (toroidal) angle
       zed_equal_arc = .false.
-      ! set minimum shat value below which we assume
-      ! periodic BC
+      
+      ! set minimum shat value below which we assume periodic BC
       shat_zero = 1.e-5
+      
       ! set the minimum nabla x . nabla value at the end of the FT which we assume
       ! periodic BC instead of the stellarator symmetric ones
       grad_x_grad_y_zero = 1.e-5
+      
       ! set the ratio between dkx and dky, assuming jtwist = 1.
       ! if it is < 0, the code will just use the nfield_periods in the input file
       dkx_over_dky = -1
diff --git a/STELLA_CODE/gyrokinetic_terms/response_matrix.fpp b/STELLA_CODE/gyrokinetic_terms/response_matrix.fpp
index 1ab662f6ae..52a6781c8f 100644
--- a/STELLA_CODE/gyrokinetic_terms/response_matrix.fpp
+++ b/STELLA_CODE/gyrokinetic_terms/response_matrix.fpp
@@ -125,6 +125,7 @@ contains
 
    end subroutine setup_response_matrix_file_io
 
+#ifdef ISO_C_BINDING
    subroutine setup_shared_memory_window
 
       use mpi
@@ -168,6 +169,7 @@ contains
       end if
 
    end subroutine setup_shared_memory_window
+#endif
 
    subroutine construct_response_matrix
 
diff --git a/STELLA_CODE/parameters/parameters_diagnostics.f90 b/STELLA_CODE/parameters/parameters_diagnostics.f90
index c8b265c348..b7f9cb4ab3 100644
--- a/STELLA_CODE/parameters/parameters_diagnostics.f90
+++ b/STELLA_CODE/parameters/parameters_diagnostics.f90
@@ -19,7 +19,11 @@ module parameters_diagnostics
 
    ! Write potential in <diagnostics_potential>
    public :: write_phi_vs_kxkyz
+   public :: write_apar_vs_kxkyz
+   public :: write_bpar_vs_kxkyz
    public :: write_phi2_vs_kxky
+   public :: write_apar2_vs_kxky
+   public :: write_bpar2_vs_kxky
 
    ! Write omega in <diagnostics_omega>
    public :: write_omega_vs_kxky
@@ -62,7 +66,11 @@ module parameters_diagnostics
 
    ! Write potential in <diagnostics_potential>
    logical :: write_phi_vs_kxkyz
+   logical :: write_apar_vs_kxkyz
+   logical :: write_bpar_vs_kxkyz
    logical :: write_phi2_vs_kxky
+   logical :: write_apar2_vs_kxky
+   logical :: write_bpar2_vs_kxky
 
    ! Write omega in <diagnostics_omega>
    logical :: write_omega_vs_kxky
@@ -216,6 +224,124 @@ subroutine read_diagnostics_knobs
       
    contains 
    
+      !**********************************************************************
+      !                        SET DEFAULT PARAMETERS                       !
+      !********************************************************************** 
+      ! Write the time traces by default, while we will not write any higher 
+      ! dimensional data by default to have a small netCDF file.
+      !********************************************************************** 
+      subroutine set_default_parameters
+
+         use parameters_physics, only: radial_variation
+         use parameters_physics, only: nonlinear
+
+         implicit none
+         
+         ! Track code 
+         if (debug) write (*, *) 'read_diagnostics_parameters::set_default_parameters'
+
+         ! Write data to the ascii files at every <nwrite> time steps.
+         ! Write data to the netcdf file every <nwrite*nc_mult> time steps.
+         nwrite = 50 
+         nc_mult = 1
+
+         ! Save gvmu(vpa, nmu, i[s,kx,ky,z]) at every <nsave> time steps so that we can restart the simulation.
+         ! From <gvmu> we can calculate <phi> through quasi-neutrality, so <gvmu> is all that we need to save.
+         save_for_restart = .false.
+         nsave = -1
+         
+         ! Togggle all write statements together 
+         write_all = .false.
+         
+         !------------------------------
+         !          Potential          !
+         !------------------------------ 
+         
+         ! Write phi2(t), apar2(t), bpar2(t), phi(kx,ky,z), phi2(kx,ky)
+         write_phi2_vs_time = .true.
+         write_apar2_vs_time = .true.
+         write_bpar2_vs_time = .true. 
+         write_phi_vs_kxkyz = .false.
+         write_apar_vs_kxkyz = .false.
+         write_bpar_vs_kxkyz = .false.
+         write_phi2_vs_kxky = .false.
+         write_apar2_vs_kxky = .false.
+         write_bpar2_vs_kxky = .false.
+          
+         !------------------------------
+         !    Distribution function    !
+         !------------------------------ 
+         
+         ! Write the distribution functions g, h and f 
+         ! Note that these arrays are very large 
+         write_g2_vs_vpamus = .false.
+         write_g2_vs_zvpas = .false.
+         write_g2_vs_zmus = .false.
+         write_g2_vs_kxkyzs = .false.
+         write_g2_vs_zvpamus = .false.
+         write_distribution_g = .true.
+         write_distribution_h = .false.
+         write_distribution_f = .false. 
+         
+         !------------------------------
+         !            Omega            !
+         !------------------------------ 
+         
+         ! For linear simulations write omega by default 
+         write_omega_vs_kxky = .not. nonlinear
+         
+         ! We calculate running averages for omega over <navg> time points
+         write_omega_avg_vs_kxky = .false.
+         navg = 50
+
+         ! Stop linear simulations when gamma is constant (careful since we won't catch jumpers!)
+         ! It will check the growth rate gamma over <navg> time steps, hence we need 
+         ! <omega_vs_kykx> over the last <navg> time steps, written by <write_omega_avg_vs_kxky>
+         autostop = .false.
+                  
+         !------------------------------
+         !           Fluxes            !
+         !------------------------------ 
+         
+         ! Write the particle flux, heat flux and momentum flux
+         write_fluxes_vs_time = .true. 
+         write_fluxes_kxkyz = .false.   
+         write_fluxes_kxky = .false.   
+
+         ! Flux definition with an extra factor 1/<nabla rho> in front.
+         ! Toggle to include or not include the factor 1/<∇̃ρ>_ψ in the flux definition
+         flux_norm = .true.
+         
+         !------------------------------
+         !           Moments           !
+         !------------------------------ 
+         
+         ! Write the density, temperature and upar
+         write_moments = .false.
+         
+         !------------------------------
+         !      Radial variation       !
+         !------------------------------ 
+         
+         ! If <radial_variation> = True, automatically write the corresponding data
+         write_radial_fluxes = radial_variation
+         write_radial_moments = radial_variation
+         
+         !------------------------------
+         !   Backwards compatibility   !
+         !------------------------------ 
+         
+         ! Backwards compatibility, these flags have been removed
+         write_phi_vs_time = .false.
+         write_apar_vs_time = .false.
+         write_bpar_vs_time = .false.
+         write_gvmus = .false.
+         write_gzvs = .false. 
+         write_kspectra = .false.   
+         write_omega = .false.
+
+      end subroutine set_default_parameters 
+   
       !**********************************************************************
       !                           READ INPUT FILE                           !
       !**********************************************************************
@@ -239,10 +365,15 @@ subroutine read_input_file
          ! and mp_abort if <stella_diagnostics_knobs> is in the input file
          namelist /diagnostics/ nwrite, navg, nsave, autostop, save_for_restart, flux_norm, nc_mult, &
             write_phi2_vs_time, write_apar2_vs_time, write_bpar2_vs_time, write_fluxes_vs_time, &
-            write_phi_vs_kxkyz, write_g2_vs_vpamus, write_g2_vs_zvpas, write_g2_vs_zmus, &
+            write_phi_vs_kxkyz, write_apar_vs_kxkyz, write_bpar_vs_kxkyz, &
+            write_g2_vs_vpamus, write_g2_vs_zvpas, write_g2_vs_zmus, &
             write_g2_vs_kxkyzs, write_g2_vs_zvpamus, write_distribution_g, write_distribution_h, write_distribution_f, &
-            write_omega_vs_kxky, write_omega_avg_vs_kxky, write_phi2_vs_kxky, write_moments, write_radial_fluxes, &
-            write_radial_moments, write_fluxes_kxkyz, write_fluxes_kxky, write_all, flux_norm, nc_mult
+            write_phi2_vs_kxky, write_apar2_vs_kxky, write_bpar2_vs_kxky, &
+            write_omega_vs_kxky, write_omega_avg_vs_kxky, write_moments, write_radial_fluxes, &
+            write_radial_moments, write_fluxes_kxkyz, write_fluxes_kxky, write_all, flux_norm, nc_mult, &
+            ! Backwards compatibility for old stella code
+            write_omega, write_phi_vs_time, write_apar_vs_time, write_bpar_vs_time, &
+            write_kspectra, write_gvmus, write_gzvs
             
          !-------------------------------------------------------------------
          
@@ -271,7 +402,11 @@ subroutine read_input_file
             write_omega_vs_kxky = .true.
             write_omega_avg_vs_kxky = .true.
             write_phi_vs_kxkyz = .true.
+            write_apar_vs_kxkyz = .true.
+            write_bpar_vs_kxkyz = .true.
             write_phi2_vs_kxky = .true.
+            write_apar2_vs_kxky = .true.
+            write_bpar2_vs_kxky = .true.
             write_moments = .true.
             write_fluxes_kxkyz = .true.
             write_fluxes_kxky = .true.
@@ -318,9 +453,13 @@ subroutine broadcast_parameters
          call broadcast(write_all)
          call broadcast(write_omega_vs_kxky)
          call broadcast(write_omega_avg_vs_kxky)
+         call broadcast(write_phi_vs_kxkyz)
+         call broadcast(write_apar_vs_kxkyz)
+         call broadcast(write_bpar_vs_kxkyz)
          call broadcast(write_phi2_vs_kxky)
+         call broadcast(write_apar2_vs_kxky)
+         call broadcast(write_bpar2_vs_kxky)
          call broadcast(write_moments)
-         call broadcast(write_phi_vs_kxkyz)
          call broadcast(write_g2_vs_vpamus)
          call broadcast(write_g2_vs_zvpas)
          call broadcast(write_g2_vs_zmus)
diff --git a/STELLA_CODE/stella.f90 b/STELLA_CODE/stella.f90
index 1fa1e9bf32..9ee1d7ea5c 100644
--- a/STELLA_CODE/stella.f90
+++ b/STELLA_CODE/stella.f90
@@ -511,7 +511,7 @@ subroutine print_header
 
       use mp, only: proc0
       use parameters_numerical, only: print_extra_info_to_terminal
-      use parameters_physics, only: include_apar
+      use parameters_physics, only: include_apar, include_bpar
       implicit none
       
       ! Only print the header on the first processor
@@ -523,10 +523,18 @@ subroutine print_header
          write (*, '(A)') "                OVERVIEW OF THE SIMULATION"
          write (*, '(A)') "############################################################"
       end if
-      if (include_apar) then
+      if (include_apar .and. include_bpar) then
+         write (*, '(A)') " "
+         write (*, '(A)') "    istep       time          dt          |phi|^2       |apar|^2      |bpar|^2"
+         write (*, '(A)') "--------------------------------------------------------------------------------"
+      else if (include_apar) then
          write (*, '(A)') " "
          write (*, '(A)') "    istep       time          dt          |phi|^2       |apar|^2"
          write (*, '(A)') "--------------------------------------------------------------------"
+      else if (include_bpar) then
+         write (*, '(A)') " "
+         write (*, '(A)') "    istep       time          dt          |phi|^2       |bpar|^2"
+         write (*, '(A)') "--------------------------------------------------------------------"
       else
          write (*, '(A)') " "
          write (*, '(A)') "    istep       time          dt          |phi|^2  "
diff --git a/EXTERNALS/utils/CMakeLists.txt b/STELLA_CODE/utils/CMakeLists.txt
similarity index 100%
rename from EXTERNALS/utils/CMakeLists.txt
rename to STELLA_CODE/utils/CMakeLists.txt
diff --git a/EXTERNALS/utils/command_line.fpp b/STELLA_CODE/utils/command_line.fpp
similarity index 100%
rename from EXTERNALS/utils/command_line.fpp
rename to STELLA_CODE/utils/command_line.fpp
diff --git a/EXTERNALS/utils/constants.fpp b/STELLA_CODE/utils/constants.fpp
similarity index 100%
rename from EXTERNALS/utils/constants.fpp
rename to STELLA_CODE/utils/constants.fpp
diff --git a/EXTERNALS/utils/convert.f90 b/STELLA_CODE/utils/convert.f90
similarity index 100%
rename from EXTERNALS/utils/convert.f90
rename to STELLA_CODE/utils/convert.f90
diff --git a/EXTERNALS/utils/define.inc b/STELLA_CODE/utils/define.inc
similarity index 100%
rename from EXTERNALS/utils/define.inc
rename to STELLA_CODE/utils/define.inc
diff --git a/EXTERNALS/utils/fft_work.f90 b/STELLA_CODE/utils/fft_work.f90
similarity index 100%
rename from EXTERNALS/utils/fft_work.f90
rename to STELLA_CODE/utils/fft_work.f90
diff --git a/EXTERNALS/utils/file_utils.fpp b/STELLA_CODE/utils/file_utils.fpp
similarity index 100%
rename from EXTERNALS/utils/file_utils.fpp
rename to STELLA_CODE/utils/file_utils.fpp
diff --git a/EXTERNALS/utils/gauss_quad.f90 b/STELLA_CODE/utils/gauss_quad.f90
similarity index 100%
rename from EXTERNALS/utils/gauss_quad.f90
rename to STELLA_CODE/utils/gauss_quad.f90
diff --git a/EXTERNALS/utils/job_manage.fpp b/STELLA_CODE/utils/job_manage.fpp
similarity index 100%
rename from EXTERNALS/utils/job_manage.fpp
rename to STELLA_CODE/utils/job_manage.fpp
diff --git a/EXTERNALS/utils/linear_solve.f90 b/STELLA_CODE/utils/linear_solve.f90
similarity index 100%
rename from EXTERNALS/utils/linear_solve.f90
rename to STELLA_CODE/utils/linear_solve.f90
diff --git a/EXTERNALS/utils/makefile b/STELLA_CODE/utils/makefile
similarity index 97%
rename from EXTERNALS/utils/makefile
rename to STELLA_CODE/utils/makefile
index 8c7e56d500..c19b61197c 100644
--- a/EXTERNALS/utils/makefile
+++ b/STELLA_CODE/utils/makefile
@@ -71,7 +71,7 @@ $(BUILD)/utils.a: $(utils_objects) | $(OBJ)
 	
 # The -J $(MOD) flag makes sure that the compiler writes the *.mod files to the $(MOD) directory
 # The -I $(MOD) flag makes sure that the compiler looks for the *.mod files in the $(MOD) directory
-MOD_FLAGS_UTILS := -I$(MOD) -J$(MOD)
+MOD_FLAGS_UTILS := -I $(MOD) $(MODULE_FLAG) $(MOD)
 
 # Pattern rules to compile the scripts
 # Create *.o files from *.f90 files using the $(FC) compiler 
diff --git a/EXTERNALS/utils/mp.fpp b/STELLA_CODE/utils/mp.fpp
similarity index 100%
rename from EXTERNALS/utils/mp.fpp
rename to STELLA_CODE/utils/mp.fpp
diff --git a/EXTERNALS/utils/mp_lu_decomposition.fpp b/STELLA_CODE/utils/mp_lu_decomposition.fpp
similarity index 100%
rename from EXTERNALS/utils/mp_lu_decomposition.fpp
rename to STELLA_CODE/utils/mp_lu_decomposition.fpp
diff --git a/EXTERNALS/utils/mt19937.f90 b/STELLA_CODE/utils/mt19937.f90
similarity index 100%
rename from EXTERNALS/utils/mt19937.f90
rename to STELLA_CODE/utils/mt19937.f90
diff --git a/EXTERNALS/utils/netcdf_utils.fpp b/STELLA_CODE/utils/netcdf_utils.fpp
similarity index 100%
rename from EXTERNALS/utils/netcdf_utils.fpp
rename to STELLA_CODE/utils/netcdf_utils.fpp
diff --git a/EXTERNALS/utils/ran.fpp b/STELLA_CODE/utils/ran.fpp
similarity index 100%
rename from EXTERNALS/utils/ran.fpp
rename to STELLA_CODE/utils/ran.fpp
diff --git a/EXTERNALS/utils/redistribute.f90 b/STELLA_CODE/utils/redistribute.f90
similarity index 100%
rename from EXTERNALS/utils/redistribute.f90
rename to STELLA_CODE/utils/redistribute.f90
diff --git a/EXTERNALS/utils/spfunc.fpp b/STELLA_CODE/utils/spfunc.fpp
similarity index 100%
rename from EXTERNALS/utils/spfunc.fpp
rename to STELLA_CODE/utils/spfunc.fpp
diff --git a/EXTERNALS/utils/spl.f90 b/STELLA_CODE/utils/spl.f90
similarity index 100%
rename from EXTERNALS/utils/spl.f90
rename to STELLA_CODE/utils/spl.f90
diff --git a/EXTERNALS/utils/system_fortran.fpp b/STELLA_CODE/utils/system_fortran.fpp
similarity index 100%
rename from EXTERNALS/utils/system_fortran.fpp
rename to STELLA_CODE/utils/system_fortran.fpp
diff --git a/EXTERNALS/utils/text_options.f90 b/STELLA_CODE/utils/text_options.f90
similarity index 100%
rename from EXTERNALS/utils/text_options.f90
rename to STELLA_CODE/utils/text_options.f90