Docs: fix broken links in Examples section

EZoni · Sep 10, 2024 · 9d35f6e · 9d35f6e
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Showing 21 changed files with 17 additions and 17 deletions.
diff --git a/Docs/source/developers/particles.rst b/Docs/source/developers/particles.rst
@@ -160,7 +160,7 @@ Attribute name      ``int``/``real``  Description                        Default
                                       when they were created.
 ==================  ================  =================================  ==============
 
-A Python example that adds runtime options can be found in :download:`Examples/Tests/particle_data_python <../../../Examples/Tests/particle_data_python/PICMI_inputs_prev_pos_2d.py>`
+A Python example that adds runtime options can be found in :download:`Examples/Tests/particle_data_python <../../../Examples/Tests/particle_data_python/inputs_test_2d_prev_positions_picmi.py>`
 
 .. note::
 

diff --git a/Docs/source/usage/examples.rst b/Docs/source/usage/examples.rst
@@ -43,7 +43,7 @@ Particle Accelerator & Beam Physics
    :maxdepth: 1
 
    examples/gaussian_beam/README.rst
-   examples/beam-beam_collision/README.rst
+   examples/beam_beam_collision/README.rst
 
 
 High Energy Astrophysical Plasma Physics
@@ -101,7 +101,7 @@ examples below were generated at that time.
 .. toctree::
    :maxdepth: 1
 
-   examples/ohm_solver_EM_modes/README.rst
+   examples/ohm_solver_em_modes/README.rst
    examples/ohm_solver_ion_beam_instability/README.rst
    examples/ohm_solver_ion_Landau_damping/README.rst
 
@@ -127,11 +127,11 @@ Manipulating fields via Python
 
 An example of using Python to access the simulation charge density, solve the Poisson equation (using ``superLU``) and write the resulting electrostatic potential back to the simulation is given in the input file below. This example uses the ``fields.py`` module included in the ``pywarpx`` library.
 
-* :download:`Direct Poisson solver example <../../../Examples/Physics_applications/capacitive_discharge/PICMI_inputs_2d.py>`
+* :download:`Direct Poisson solver example <../../../Examples/Physics_applications/capacitive_discharge/inputs_test_2d_background_mcc_picmi.py>`
 
 An example of initializing the fields by accessing their data through Python, advancing the simulation for a chosen number of time steps, and plotting the fields again through Python. The simulation runs with 128 regular cells, 8 guard cells, and 10 PML cells, in each direction. Moreover, it uses div(E) and div(B) cleaning both in the regular grid and in the PML and initializes all available electromagnetic fields (E,B,F,G) identically.
 
-* :download:`Unit pulse with PML <../../../Examples/Tests/python_wrappers/PICMI_inputs_2d.py>`
+* :download:`Unit pulse with PML <../../../Examples/Tests/python_wrappers/inputs_test_2d_python_wrappers_picmi.py>`
 
 
 Many Further Examples, Demos and Tests

diff --git a/Docs/source/usage/examples/beam-beam_collision b/Docs/source/usage/examples/beam-beam_collision
diff --git a/Docs/source/usage/examples/beam_beam_collision b/Docs/source/usage/examples/beam_beam_collision
@@ -0,0 +1 @@
+../../../../Examples/Physics_applications/beam_beam_collision/
diff --git a/Docs/source/usage/examples/ohm_solver_EM_modes b/Docs/source/usage/examples/ohm_solver_EM_modes
diff --git a/Docs/source/usage/examples/ohm_solver_em_modes b/Docs/source/usage/examples/ohm_solver_em_modes
@@ -0,0 +1 @@
+../../../../Examples/Tests/ohm_solver_em_modes/
diff --git a/Docs/source/usage/pwfa.rst b/Docs/source/usage/pwfa.rst
@@ -5,7 +5,7 @@ In-Depth: PWFA
 
 As described in the :doc:`../theory/intro`, one of the key applications of the WarpX exascale computing platform is in modelling future, compact and economic plasma-based accelerators.
 In this section we describe the simulation setup of a realistic *electron beam driven plasma wakefield accelerator* (PWFA) configuration.
-For illustration purposes the setup can be explored with **WarpX** using the example input file :download:`PWFA <../../../Examples/Physics_applications/plasma_acceleration/inputs_2d_boost>`.
+For illustration purposes the setup can be explored with **WarpX** using the example input file :download:`PWFA <../../../Examples/Physics_applications/plasma_acceleration/inputs_test_2d_plasma_acceleration_boosted>`.
 
 The simulation setup consists of 4 particle species: drive beam (driver), witness beam (beam), plasma electrons (plasma_e), and plasma ions (plasma_p).
 The species physical parameters are summarized in the following table.

diff --git a/...s_applications/beam_beam_collision/README → ...plications/beam_beam_collision/README.rst b/...s_applications/beam_beam_collision/README → ...plications/beam_beam_collision/README.rst
diff --git a/..._applications/capacitive_discharge/README → ...lications/capacitive_discharge/README.rst b/..._applications/capacitive_discharge/README → ...lications/capacitive_discharge/README.rst
@@ -22,17 +22,17 @@ The implementation has been tested against the benchmark results from :cite:t:`e
 Run
 ---
 
-The 1D PICMI input file can be used to reproduce the results from Turner et al. for a given case, ``N`` from 1 to 4, by executing ``python3 PICMI_inputs_1d.py -n N``, e.g.,
+The 1D PICMI input file can be used to reproduce the results from Turner et al. for a given case, ``N`` from 1 to 4, by executing ``python3 inputs_base_1d_picmi.py -n N``, e.g.,
 
 .. code-block:: bash
 
-   python3 PICMI_inputs_1d.py -n 1
+   python3 inputs_base_1d_picmi.py -n 1
 
 For `MPI-parallel <https://www.mpi-forum.org>`__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system.
 
-.. literalinclude:: PICMI_inputs_1d.py
+.. literalinclude:: inputs_base_1d_picmi.py
    :language: python3
-   :caption: You can copy this file from ``Examples/Physics_applications/capacitive_discharge/PICMI_inputs_1d.py``.
+   :caption: You can copy this file from ``Examples/Physics_applications/capacitive_discharge/inputs_base_1d_picmi.py``.
 
 
 Analyze

diff --git a/Examples/Physics_applications/capacitive_discharge/analysis_2d.py b/Examples/Physics_applications/capacitive_discharge/analysis_2d.py
@@ -2,7 +2,7 @@
 
 # Copyright 2021 Modern Electron
 
-# This script checks that the PICMI_inputs_2d.py run more-or-less matches the
+# This script checks that the inputs_test_2d_background_mcc_picmi.py run more-or-less matches the
 # results from the non-PICMI run. The PICMI run is using an external Poisson
 # solver that directly solves the Poisson equation using matrix inversion
 # rather than the iterative approach from the MLMG solver.

diff --git a/...cs_applications/laser_acceleration/README → ...pplications/laser_acceleration/README.rst b/...cs_applications/laser_acceleration/README → ...pplications/laser_acceleration/README.rst
diff --git a/...les/Physics_applications/laser_ion/README → ...Physics_applications/laser_ion/README.rst b/...les/Physics_applications/laser_ion/README → ...Physics_applications/laser_ion/README.rst
diff --git a/...s_applications/plasma_acceleration/README → ...plications/plasma_acceleration/README.rst b/...s_applications/plasma_acceleration/README → ...plications/plasma_acceleration/README.rst
diff --git a/...Physics_applications/plasma_mirror/README → ...ics_applications/plasma_mirror/README.rst b/...Physics_applications/plasma_mirror/README → ...ics_applications/plasma_mirror/README.rst
diff --git a/...hysics_applications/uniform_plasma/README → ...cs_applications/uniform_plasma/README.rst b/...hysics_applications/uniform_plasma/README → ...cs_applications/uniform_plasma/README.rst
diff --git a/Examples/Tests/gaussian_beam/README → Examples/Tests/gaussian_beam/README.rst b/Examples/Tests/gaussian_beam/README → Examples/Tests/gaussian_beam/README.rst
diff --git a/Examples/Tests/langmuir/README → Examples/Tests/langmuir/README.rst b/Examples/Tests/langmuir/README → Examples/Tests/langmuir/README.rst
diff --git a/Examples/Tests/ohm_solver_em_modes/README → ...ples/Tests/ohm_solver_em_modes/README.rst b/Examples/Tests/ohm_solver_em_modes/README → ...ples/Tests/ohm_solver_em_modes/README.rst
diff --git a/...ests/ohm_solver_ion_Landau_damping/README → .../ohm_solver_ion_Landau_damping/README.rst b/...ests/ohm_solver_ion_Landau_damping/README → .../ohm_solver_ion_Landau_damping/README.rst
diff --git a/...ts/ohm_solver_ion_beam_instability/README → ...hm_solver_ion_beam_instability/README.rst b/...ts/ohm_solver_ion_beam_instability/README → ...hm_solver_ion_beam_instability/README.rst
diff --git a/...s/ohm_solver_magnetic_reconnection/README → ...m_solver_magnetic_reconnection/README.rst b/...s/ohm_solver_magnetic_reconnection/README → ...m_solver_magnetic_reconnection/README.rst
@@ -12,19 +12,19 @@ Run
 
 The following **Python** script configures and launches the simulation.
 
-.. dropdown:: Script ``PICMI_inputs.py``
+.. dropdown:: Script ``inputs_test_2d_ohm_solver_magnetic_reconnection_picmi.py``
 
-   .. literalinclude:: PICMI_inputs.py
+   .. literalinclude:: inputs_test_2d_ohm_solver_magnetic_reconnection_picmi.py
       :language: python3
-      :caption: You can copy this file from ``Examples/Tests/ohm_solver_magnetic_reconnection/PICMI_inputs.py``.
+      :caption: You can copy this file from ``Examples/Tests/ohm_solver_magnetic_reconnection/inputs_test_2d_ohm_solver_magnetic_reconnection_picmi.py``.
 
 Running the full simulation should take about 4 hours if executed on 1 V100 GPU.
 For `MPI-parallel <https://www.mpi-forum.org>`__ runs, prefix these lines with
 ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system.
 
    .. code-block:: bash
 
-      python3 PICMI_inputs.py
+      python3 inputs_test_2d_ohm_solver_magnetic_reconnection_picmi.py
 
 Analyze
 -------