From 375709b28461355da8158fdcbb1801bedc788229 Mon Sep 17 00:00:00 2001 From: Edoardo Zoni Date: Mon, 9 Sep 2024 17:06:21 -0700 Subject: [PATCH 1/2] Docs: fix broken links in Examples section --- Docs/source/developers/particles.rst | 2 +- Docs/source/usage/examples.rst | 8 ++-- .../source/usage/examples/beam-beam_collision | 1 - .../source/usage/examples/beam_beam_collision | 1 + .../source/usage/examples/ohm_solver_EM_modes | 1 - .../source/usage/examples/ohm_solver_em_modes | 1 + Docs/source/usage/pwfa.rst | 2 +- .../{README => README.rst} | 0 .../{README => README.rst} | 8 ++-- .../capacitive_discharge/analysis_2d.py | 2 +- .../laser_acceleration/{README => README.rst} | 24 +++++----- .../laser_ion/{README => README.rst} | 12 ++--- .../{README => README.rst} | 16 +++---- .../plasma_mirror/{README => README.rst} | 0 .../spacecraft_charging/analysis.py | 2 +- .../uniform_plasma/{README => README.rst} | 0 .../inputs_test_2d_collision_xz_picmi.py | 4 +- .../gaussian_beam/{README => README.rst} | 8 ++-- .../Tests/langmuir/{README => README.rst} | 44 +++++++++---------- ..._test_3d_load_external_field_grid_picmi.py | 2 +- ...t_3d_load_external_field_particle_picmi.py | 2 +- .../{README => README.rst} | 18 ++++---- .../{README => README.rst} | 8 ++-- .../{README => README.rst} | 10 ++--- .../{README => README.rst} | 8 ++-- .../particle_boundary_interaction/analysis.py | 2 +- .../Tests/pass_mpi_communicator/analysis.py | 2 +- .../inputs_test_2d_pass_mpi_comm_picmi.py | 4 +- .../Tests/point_of_contact_eb/analysis.py | 2 +- 29 files changed, 97 insertions(+), 97 deletions(-) delete mode 120000 Docs/source/usage/examples/beam-beam_collision create mode 120000 Docs/source/usage/examples/beam_beam_collision delete mode 120000 Docs/source/usage/examples/ohm_solver_EM_modes create mode 120000 Docs/source/usage/examples/ohm_solver_em_modes rename Examples/Physics_applications/beam_beam_collision/{README => README.rst} (100%) rename Examples/Physics_applications/capacitive_discharge/{README => README.rst} (91%) rename Examples/Physics_applications/laser_acceleration/{README => README.rst} (79%) rename Examples/Physics_applications/laser_ion/{README => README.rst} (93%) rename Examples/Physics_applications/plasma_acceleration/{README => README.rst} (76%) rename Examples/Physics_applications/plasma_mirror/{README => README.rst} (100%) rename Examples/Physics_applications/uniform_plasma/{README => README.rst} (100%) rename Examples/Tests/gaussian_beam/{README => README.rst} (75%) rename Examples/Tests/langmuir/{README => README.rst} (74%) rename Examples/Tests/ohm_solver_em_modes/{README => README.rst} (85%) rename Examples/Tests/ohm_solver_ion_Landau_damping/{README => README.rst} (84%) rename Examples/Tests/ohm_solver_ion_beam_instability/{README => README.rst} (86%) rename Examples/Tests/ohm_solver_magnetic_reconnection/{README => README.rst} (80%) diff --git a/Docs/source/developers/particles.rst b/Docs/source/developers/particles.rst index 53a0090b5c9..37260d1ed64 100644 --- 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 index 0492372b4e6..244fbda6f75 100644 --- 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 deleted file mode 120000 index 8c6ac6b30b1..00000000000 --- a/Docs/source/usage/examples/beam-beam_collision +++ /dev/null @@ -1 +0,0 @@ -../../../../Examples/Physics_applications/beam-beam_collision \ No newline at end of file diff --git a/Docs/source/usage/examples/beam_beam_collision b/Docs/source/usage/examples/beam_beam_collision new file mode 120000 index 00000000000..2f46224fd8b --- /dev/null +++ b/Docs/source/usage/examples/beam_beam_collision @@ -0,0 +1 @@ +../../../../Examples/Physics_applications/beam_beam_collision/ \ No newline at end of file diff --git a/Docs/source/usage/examples/ohm_solver_EM_modes b/Docs/source/usage/examples/ohm_solver_EM_modes deleted file mode 120000 index 485be7241ae..00000000000 --- a/Docs/source/usage/examples/ohm_solver_EM_modes +++ /dev/null @@ -1 +0,0 @@ -../../../../Examples/Tests/ohm_solver_EM_modes \ No newline at end of file diff --git a/Docs/source/usage/examples/ohm_solver_em_modes b/Docs/source/usage/examples/ohm_solver_em_modes new file mode 120000 index 00000000000..03214170a1f --- /dev/null +++ b/Docs/source/usage/examples/ohm_solver_em_modes @@ -0,0 +1 @@ +../../../../Examples/Tests/ohm_solver_em_modes/ \ No newline at end of file diff --git a/Docs/source/usage/pwfa.rst b/Docs/source/usage/pwfa.rst index 5119184089c..1d3481b5589 100644 --- 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/Examples/Physics_applications/beam_beam_collision/README b/Examples/Physics_applications/beam_beam_collision/README.rst similarity index 100% rename from Examples/Physics_applications/beam_beam_collision/README rename to Examples/Physics_applications/beam_beam_collision/README.rst diff --git a/Examples/Physics_applications/capacitive_discharge/README b/Examples/Physics_applications/capacitive_discharge/README.rst similarity index 91% rename from Examples/Physics_applications/capacitive_discharge/README rename to Examples/Physics_applications/capacitive_discharge/README.rst index 708b4528cd5..13b6b3010b3 100644 --- a/Examples/Physics_applications/capacitive_discharge/README +++ b/Examples/Physics_applications/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 `__ 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 index e9782fabe23..f52f69f4bf4 100755 --- 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/Examples/Physics_applications/laser_acceleration/README b/Examples/Physics_applications/laser_acceleration/README.rst similarity index 79% rename from Examples/Physics_applications/laser_acceleration/README rename to Examples/Physics_applications/laser_acceleration/README.rst index 0ba3b5382f2..66de28de7a7 100644 --- a/Examples/Physics_applications/laser_acceleration/README +++ b/Examples/Physics_applications/laser_acceleration/README.rst @@ -24,43 +24,43 @@ For `MPI-parallel `__ runs, prefix these lines with ` This example can be run **either** as: - * **Python** script: ``python3 PICMI_inputs_3d.py`` or - * WarpX **executable** using an input file: ``warpx.3d inputs_3d max_step=400`` + * **Python** script: ``python3 inputs_test_3d_laser_acceleration_picmi.py`` or + * WarpX **executable** using an input file: ``warpx.3d inputs_test_3d_laser_acceleration max_step=400`` .. tab-set:: .. tab-item:: Python: Script - .. literalinclude:: PICMI_inputs_3d.py + .. literalinclude:: inputs_test_3d_laser_acceleration_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py``. + :caption: You can copy this file from ``Examples/Physics_applications/laser_acceleration/inputs_test_3d_laser_acceleration_picmi.py``. .. tab-item:: Executable: Input File - .. literalinclude:: inputs_3d + .. literalinclude:: inputs_test_3d_laser_acceleration :language: ini - :caption: You can copy this file from ``Examples/Physics_applications/laser_acceleration/inputs_3d``. + :caption: You can copy this file from ``Examples/Physics_applications/laser_acceleration/inputs_test_3d_laser_acceleration``. .. tab-item:: RZ This example can be run **either** as: - * **Python** script: ``python3 PICMI_inputs_rz.py`` or - * WarpX **executable** using an input file: ``warpx.rz inputs_3d max_step=400`` + * **Python** script: ``python3 inputs_test_rz_laser_acceleration_picmi.py`` or + * WarpX **executable** using an input file: ``warpx.rz inputs_test_rz_laser_acceleration max_step=400`` .. tab-set:: .. tab-item:: Python: Script - .. literalinclude:: PICMI_inputs_rz.py + .. literalinclude:: inputs_test_rz_laser_acceleration_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py``. + :caption: You can copy this file from ``Examples/Physics_applications/laser_acceleration/inputs_test_rz_laser_acceleration_picmi.py``. .. tab-item:: Executable: Input File - .. literalinclude:: inputs_rz + .. literalinclude:: inputs_test_rz_laser_acceleration :language: ini - :caption: You can copy this file from ``Examples/Physics_applications/laser_acceleration/inputs_rz``. + :caption: You can copy this file from ``Examples/Physics_applications/laser_acceleration/inputs_test_rz_laser_acceleration``. Analyze ------- diff --git a/Examples/Physics_applications/laser_ion/README b/Examples/Physics_applications/laser_ion/README.rst similarity index 93% rename from Examples/Physics_applications/laser_ion/README rename to Examples/Physics_applications/laser_ion/README.rst index 29862a30518..e55cf6889d4 100644 --- a/Examples/Physics_applications/laser_ion/README +++ b/Examples/Physics_applications/laser_ion/README.rst @@ -21,8 +21,8 @@ Run This example can be run **either** as: -* **Python** script: ``mpiexec -n 2 python3 PICMI_inputs_2d.py`` or -* WarpX **executable** using an input file: ``mpiexec -n 2 warpx.2d inputs_2d`` +* **Python** script: ``mpiexec -n 2 python3 inputs_test_2d_laser_ion_acc_picmi.py`` or +* WarpX **executable** using an input file: ``mpiexec -n 2 warpx.2d inputs_test_2d_laser_ion_acc`` .. tip:: @@ -35,16 +35,16 @@ This example can be run **either** as: .. tab-item:: Python: Script - .. literalinclude:: PICMI_inputs_2d.py + .. literalinclude:: inputs_test_2d_laser_ion_acc_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Physics_applications/laser_ion/PICMI_inputs_2d.py``. + :caption: You can copy this file from ``Examples/Physics_applications/laser_ion/inputs_test_2d_laser_ion_acc_picmi.py``. .. tab-item:: Executable: Input File - .. literalinclude:: inputs_2d + .. literalinclude:: inputs_test_2d_laser_ion_acc :language: ini - :caption: You can copy this file from ``Examples/Physics_applications/laser_ion/inputs_2d``. + :caption: You can copy this file from ``Examples/Physics_applications/laser_ion/inputs_test_2d_laser_ion_acc``. Analyze ------- diff --git a/Examples/Physics_applications/plasma_acceleration/README b/Examples/Physics_applications/plasma_acceleration/README.rst similarity index 76% rename from Examples/Physics_applications/plasma_acceleration/README rename to Examples/Physics_applications/plasma_acceleration/README.rst index d5775e93aa8..0c1b1819cab 100644 --- a/Examples/Physics_applications/plasma_acceleration/README +++ b/Examples/Physics_applications/plasma_acceleration/README.rst @@ -16,7 +16,7 @@ In the Beam, Plasma & Accelerator Simulation Toolkit (BLAST), `HiPACE++ `__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system. @@ -35,17 +35,17 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. note:: - TODO: This input file should use the boosted frame method, like the ``inputs_3d_boost`` file. + TODO: This input file should use the boosted frame method, like the ``inputs_test_3d_plasma_acceleration_boosted`` file. - .. literalinclude:: PICMI_inputs_plasma_acceleration.py + .. literalinclude:: inputs_test_3d_plasma_acceleration_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration.py``. + :caption: You can copy this file from ``Examples/Physics_applications/plasma_acceleration/inputs_test_3d_plasma_acceleration_picmi.py``. .. tab-item:: Executable: Input File - .. literalinclude:: inputs_3d_boost + .. literalinclude:: inputs_test_3d_plasma_acceleration_boosted :language: ini - :caption: You can copy this file from ``Examples/Physics_applications/plasma_acceleration/inputs_3d_boost``. + :caption: You can copy this file from ``Examples/Physics_applications/plasma_acceleration/inputs_test_3d_plasma_acceleration_boosted``. Analyze ------- diff --git a/Examples/Physics_applications/plasma_mirror/README b/Examples/Physics_applications/plasma_mirror/README.rst similarity index 100% rename from Examples/Physics_applications/plasma_mirror/README rename to Examples/Physics_applications/plasma_mirror/README.rst diff --git a/Examples/Physics_applications/spacecraft_charging/analysis.py b/Examples/Physics_applications/spacecraft_charging/analysis.py index 6528a3bde65..8819c435fb7 100755 --- a/Examples/Physics_applications/spacecraft_charging/analysis.py +++ b/Examples/Physics_applications/spacecraft_charging/analysis.py @@ -6,7 +6,7 @@ thermal plasma. The potential on the spacecraft decreases over the time to reach an equilibrium floating potential. -An input Python file PICMI_inputs_rz.py is used. +An input Python file inputs_test_rz_spacecraft_charging_picmi.py is used. The test will check the curve fitting parameters v0 and tau defined by the following exponential function: phi(t)=v0(1-exp(-t/tau)) diff --git a/Examples/Physics_applications/uniform_plasma/README b/Examples/Physics_applications/uniform_plasma/README.rst similarity index 100% rename from Examples/Physics_applications/uniform_plasma/README rename to Examples/Physics_applications/uniform_plasma/README.rst diff --git a/Examples/Tests/collision/inputs_test_2d_collision_xz_picmi.py b/Examples/Tests/collision/inputs_test_2d_collision_xz_picmi.py index f1b3e8d3b28..7bc83a1e801 100755 --- a/Examples/Tests/collision/inputs_test_2d_collision_xz_picmi.py +++ b/Examples/Tests/collision/inputs_test_2d_collision_xz_picmi.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 # # --- Input file for binary Coulomb collision testing. This input script -# --- runs the same test as inputs_2d but via Python, therefore the input +# --- runs the same test as inputs_test_2d_collision_xz but via Python, therefore the input # --- values where directly copied from inputs_2d. from pywarpx import picmi @@ -142,5 +142,5 @@ ##### SIMULATION EXECUTION ###### ################################# -# sim.write_input_file('PICMI_inputs_2d') +# sim.write_input_file('inputs_test_2d_collision_xz') sim.step(max_steps) diff --git a/Examples/Tests/gaussian_beam/README b/Examples/Tests/gaussian_beam/README.rst similarity index 75% rename from Examples/Tests/gaussian_beam/README rename to Examples/Tests/gaussian_beam/README.rst index bfca2bb2398..e3baf9842c2 100644 --- a/Examples/Tests/gaussian_beam/README +++ b/Examples/Tests/gaussian_beam/README.rst @@ -11,7 +11,7 @@ Run This example can be run **either** as: -* **Python** script: ``python3 PICMI_inputs_gaussian_beam.py`` or +* **Python** script: ``python3 inputs_test_3d_gaussian_beam_picmi.py`` or * WarpX **executable** using an input file: (*TODO*) For `MPI-parallel `__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system. @@ -20,15 +20,15 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. tab-item:: Python: Script - .. literalinclude:: PICMI_inputs_gaussian_beam.py + .. literalinclude:: inputs_test_3d_gaussian_beam_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Tests/gaussian_beam/PICMI_inputs_gaussian_beam.py``. + :caption: You can copy this file from ``Examples/Tests/gaussian_beam/inputs_test_3d_gaussian_beam_picmi.py``. .. tab-item:: Executable: Input File .. note:: - TODO: This input file should be created following the ``PICMI_inputs_gaussian_beam.py`` file. + TODO: This input file should be created following the ``inputs_test_3d_gaussian_beam_picmi.py`` file. Analyze diff --git a/Examples/Tests/langmuir/README b/Examples/Tests/langmuir/README.rst similarity index 74% rename from Examples/Tests/langmuir/README rename to Examples/Tests/langmuir/README.rst index 60c0018744c..4748f428dc1 100644 --- a/Examples/Tests/langmuir/README +++ b/Examples/Tests/langmuir/README.rst @@ -23,19 +23,19 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. tab-item:: Python: Script - This example can be run as a **Python** script: ``python3 PICMI_inputs_3d.py``. + This example can be run as a **Python** script: ``python3 inputs_test_3d_langmuir_multi_picmi.py``. - .. literalinclude:: PICMI_inputs_3d.py + .. literalinclude:: inputs_test_3d_langmuir_multi_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Tests/langmuir/PICMI_inputs_3d.py``. + :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_test_3d_langmuir_multi_picmi.py``. .. tab-item:: Executable: Input File - This example can be run as WarpX **executable** using an input file: ``warpx.3d inputs_3d`` + This example can be run as WarpX **executable** using an input file: ``warpx.3d inputs_test_3d_langmuir_multi`` - .. literalinclude:: inputs_3d + .. literalinclude:: inputs_test_3d_langmuir_multi :language: ini - :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_3d``. + :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_test_3d_langmuir_multi``. .. tab-item:: 2D @@ -43,19 +43,19 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. tab-item:: Python: Script - This example can be run as a **Python** script: ``python3 PICMI_inputs_2d.py``. + This example can be run as a **Python** script: ``python3 inputs_test_2d_langmuir_multi_picmi.py``. - .. literalinclude:: PICMI_inputs_2d.py + .. literalinclude:: inputs_test_2d_langmuir_multi_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Tests/langmuir/PICMI_inputs_2d.py``. + :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_test_2d_langmuir_multi_picmi.py``. .. tab-item:: Executable: Input File - This example can be run as WarpX **executable** using an input file: ``warpx.2d inputs_2d`` + This example can be run as WarpX **executable** using an input file: ``warpx.2d inputs_test_2d_langmuir_multi`` - .. literalinclude:: inputs_2d + .. literalinclude:: inputs_test_2d_langmuir_multi :language: ini - :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_2d``. + :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_test_2d_langmuir_multi``. .. tab-item:: RZ @@ -64,19 +64,19 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. tab-item:: Python: Script - This example can be run as a **Python** script: ``python3 PICMI_inputs_rz.py``. + This example can be run as a **Python** script: ``python3 inputs_test_rz_langmuir_multi_picmi.py``. - .. literalinclude:: PICMI_inputs_rz.py + .. literalinclude:: inputs_test_rz_langmuir_multi_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Tests/langmuir/PICMI_inputs_rz.py``. + :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_test_rz_langmuir_multi_picmi.py``. .. tab-item:: Executable: Input File - This example can be run as WarpX **executable** using an input file: ``warpx.rz inputs_rz`` + This example can be run as WarpX **executable** using an input file: ``warpx.rz inputs_test_rz_langmuir_multi`` - .. literalinclude:: inputs_rz + .. literalinclude:: inputs_test_rz_langmuir_multi :language: ini - :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_rz``. + :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_test_rz_langmuir_multi``. .. tab-item:: 1D @@ -87,15 +87,15 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. note:: - TODO: This input file should be created, like the ``inputs_1d`` file. + TODO: This input file should be created, like the ``inputs_test_1d_langmuir_multi`` file. .. tab-item:: Executable: Input File - This example can be run as WarpX **executable** using an input file: ``warpx.1d inputs_1d`` + This example can be run as WarpX **executable** using an input file: ``warpx.1d inputs_test_1d_langmuir_multi`` - .. literalinclude:: inputs_1d + .. literalinclude:: inputs_test_1d_langmuir_multi :language: ini - :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_1d``. + :caption: You can copy this file from ``Examples/Tests/langmuir/inputs_test_1d_langmuir_multi``. Analyze diff --git a/Examples/Tests/load_external_field/inputs_test_3d_load_external_field_grid_picmi.py b/Examples/Tests/load_external_field/inputs_test_3d_load_external_field_grid_picmi.py index 231552d088e..ee24fb667cf 100644 --- a/Examples/Tests/load_external_field/inputs_test_3d_load_external_field_grid_picmi.py +++ b/Examples/Tests/load_external_field/inputs_test_3d_load_external_field_grid_picmi.py @@ -134,5 +134,5 @@ ##### SIMULATION EXECUTION ###### ################################# -# sim.write_input_file('PICMI_inputs_3d') +# sim.write_input_file('inputs_test_3d_load_external_field_grid') sim.step(max_steps) diff --git a/Examples/Tests/load_external_field/inputs_test_3d_load_external_field_particle_picmi.py b/Examples/Tests/load_external_field/inputs_test_3d_load_external_field_particle_picmi.py index c2ec6c1a5b7..75977a01729 100644 --- a/Examples/Tests/load_external_field/inputs_test_3d_load_external_field_particle_picmi.py +++ b/Examples/Tests/load_external_field/inputs_test_3d_load_external_field_particle_picmi.py @@ -134,5 +134,5 @@ ##### SIMULATION EXECUTION ###### ################################# -# sim.write_input_file('PICMI_inputs_3d') +# sim.write_input_file('inputs_test_3d_load_external_field_particle') sim.step(max_steps) diff --git a/Examples/Tests/ohm_solver_em_modes/README b/Examples/Tests/ohm_solver_em_modes/README.rst similarity index 85% rename from Examples/Tests/ohm_solver_em_modes/README rename to Examples/Tests/ohm_solver_em_modes/README.rst index 034ee5815f0..24d95d2bcb8 100644 --- a/Examples/Tests/ohm_solver_em_modes/README +++ b/Examples/Tests/ohm_solver_em_modes/README.rst @@ -13,11 +13,11 @@ Run The same input script can be used for 1d, 2d or 3d Cartesian simulations as well as replicating either the parallel propagating or ion-Bernstein modes as indicated below. -.. dropdown:: Script ``PICMI_inputs.py`` +.. dropdown:: Script ``inputs_test_1d_ohm_solver_em_modes_picmi.py`` - .. literalinclude:: PICMI_inputs.py + .. literalinclude:: inputs_test_1d_ohm_solver_em_modes_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Tests/ohm_solver_EM_modes/PICMI_inputs.py``. + :caption: You can copy this file from ``Examples/Tests/ohm_solver_EM_modes/inputs_test_1d_ohm_solver_em_modes_picmi.py``. For `MPI-parallel `__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system. @@ -29,7 +29,7 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. code-block:: bash - python3 PICMI_inputs.py -dim {1/2/3} --bdir z + python3 inputs_test_1d_ohm_solver_em_modes_picmi.py -dim {1/2/3} --bdir z .. tab-item:: Perpendicular propagating waves @@ -37,7 +37,7 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. code-block:: bash - python3 PICMI_inputs.py -dim {1/2/3} --bdir {x/y} + python3 inputs_test_1d_ohm_solver_em_modes_picmi.py -dim {1/2/3} --bdir {x/y} Analyze ------- @@ -82,17 +82,17 @@ Run The following script initializes a thermal plasma in a metallic cylinder with periodic boundaries at the cylinder ends. -.. dropdown:: Script ``PICMI_inputs_rz.py`` +.. dropdown:: Script ``inputs_test_rz_ohm_solver_em_modes_picmi.py`` - .. literalinclude:: PICMI_inputs_rz.py + .. literalinclude:: inputs_test_rz_ohm_solver_em_modes_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Tests/ohm_solver_EM_modes/PICMI_inputs_rz.py``. + :caption: You can copy this file from ``Examples/Tests/ohm_solver_EM_modes/inputs_test_rz_ohm_solver_em_modes_picmi.py``. The example can be executed using: .. code-block:: bash - python3 PICMI_inputs_rz.py + python3 inputs_test_rz_ohm_solver_em_modes_picmi.py Analyze ------- diff --git a/Examples/Tests/ohm_solver_ion_Landau_damping/README b/Examples/Tests/ohm_solver_ion_Landau_damping/README.rst similarity index 84% rename from Examples/Tests/ohm_solver_ion_Landau_damping/README rename to Examples/Tests/ohm_solver_ion_Landau_damping/README.rst index dd4f94b4edf..d54f4e16aa6 100644 --- a/Examples/Tests/ohm_solver_ion_Landau_damping/README +++ b/Examples/Tests/ohm_solver_ion_Landau_damping/README.rst @@ -14,17 +14,17 @@ Run The same input script can be used for 1d, 2d or 3d simulations and to sweep different temperature ratios. -.. dropdown:: Script ``PICMI_inputs.py`` +.. dropdown:: Script ``inputs_test_2d_ohm_solver_landau_damping_picmi.py`` - .. literalinclude:: PICMI_inputs.py + .. literalinclude:: inputs_test_2d_ohm_solver_landau_damping_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Tests/ohm_solver_ion_Landau_damping/PICMI_inputs.py``. + :caption: You can copy this file from ``Examples/Tests/ohm_solver_ion_Landau_damping/inputs_test_2d_ohm_solver_landau_damping_picmi.py``. For `MPI-parallel `__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system. .. code-block:: bash - python3 PICMI_inputs.py -dim {1/2/3} --temp_ratio {value} + python3 inputs_test_2d_ohm_solver_landau_damping_picmi.py -dim {1/2/3} --temp_ratio {value} Analyze ------- diff --git a/Examples/Tests/ohm_solver_ion_beam_instability/README b/Examples/Tests/ohm_solver_ion_beam_instability/README.rst similarity index 86% rename from Examples/Tests/ohm_solver_ion_beam_instability/README rename to Examples/Tests/ohm_solver_ion_beam_instability/README.rst index 59469cf4aa9..49b5f1ac0a0 100644 --- a/Examples/Tests/ohm_solver_ion_beam_instability/README +++ b/Examples/Tests/ohm_solver_ion_beam_instability/README.rst @@ -13,11 +13,11 @@ Run The same input script can be used for 1d, 2d or 3d simulations as well as replicating either the resonant or non-resonant condition as indicated below. -.. dropdown:: Script ``PICMI_inputs.py`` +.. dropdown:: Script ``inputs_test_1d_ohm_solver_ion_beam_picmi.py`` - .. literalinclude:: PICMI_inputs.py + .. literalinclude:: inputs_test_1d_ohm_solver_ion_beam_picmi.py :language: python3 - :caption: You can copy this file from ``Examples/Tests/ohm_solver_ion_beam_instability/PICMI_inputs.py``. + :caption: You can copy this file from ``Examples/Tests/ohm_solver_ion_beam_instability/inputs_test_1d_ohm_solver_ion_beam_picmi.py``. For `MPI-parallel `__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system. @@ -29,7 +29,7 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. code-block:: bash - python3 PICMI_inputs.py -dim {1/2/3} --resonant + python3 inputs_test_1d_ohm_solver_ion_beam_picmi.py -dim {1/2/3} --resonant .. tab-item:: Non-resonant case @@ -37,7 +37,7 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. code-block:: bash - python3 PICMI_inputs.py -dim {1/2/3} + python3 inputs_test_1d_ohm_solver_ion_beam_picmi.py -dim {1/2/3} Analyze ------- diff --git a/Examples/Tests/ohm_solver_magnetic_reconnection/README b/Examples/Tests/ohm_solver_magnetic_reconnection/README.rst similarity index 80% rename from Examples/Tests/ohm_solver_magnetic_reconnection/README rename to Examples/Tests/ohm_solver_magnetic_reconnection/README.rst index 943b5bd0248..5181a6381d8 100644 --- a/Examples/Tests/ohm_solver_magnetic_reconnection/README +++ b/Examples/Tests/ohm_solver_magnetic_reconnection/README.rst @@ -12,11 +12,11 @@ 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 `__ runs, prefix these lines with @@ -24,7 +24,7 @@ For `MPI-parallel `__ runs, prefix these lines with .. code-block:: bash - python3 PICMI_inputs.py + python3 inputs_test_2d_ohm_solver_magnetic_reconnection_picmi.py Analyze ------- diff --git a/Examples/Tests/particle_boundary_interaction/analysis.py b/Examples/Tests/particle_boundary_interaction/analysis.py index b80cf4b52aa..3b9d2f12b84 100755 --- a/Examples/Tests/particle_boundary_interaction/analysis.py +++ b/Examples/Tests/particle_boundary_interaction/analysis.py @@ -5,7 +5,7 @@ The sphere is centered on O and has a radius of 0.2 (EB) The electron is initially at: (0,0,-0.25) and moves with a velocity: (0.5e10,0,1.0e10) with a time step of 1e-11. -An input file PICMI_inputs_rz.py is used. +An input file inputs_test_rz_particle_boundary_interaction_picmi.py is used. """ import os diff --git a/Examples/Tests/pass_mpi_communicator/analysis.py b/Examples/Tests/pass_mpi_communicator/analysis.py index af55346e1f5..041687c4775 100755 --- a/Examples/Tests/pass_mpi_communicator/analysis.py +++ b/Examples/Tests/pass_mpi_communicator/analysis.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 # This is a script that analyses the simulation results from -# the script `PICMI_inputs_2d`. +# the script `inputs_test_2d_pass_mpi_comm_picmi.py`. import sys diff --git a/Examples/Tests/pass_mpi_communicator/inputs_test_2d_pass_mpi_comm_picmi.py b/Examples/Tests/pass_mpi_communicator/inputs_test_2d_pass_mpi_comm_picmi.py index 200cea7be0f..c87a7a0045c 100755 --- a/Examples/Tests/pass_mpi_communicator/inputs_test_2d_pass_mpi_comm_picmi.py +++ b/Examples/Tests/pass_mpi_communicator/inputs_test_2d_pass_mpi_comm_picmi.py @@ -126,7 +126,7 @@ # simulation run ########################## -# TODO: Enable in pyAMReX, then enable lines in PICMI_inputs_2d.py again +# TODO: Enable in pyAMReX, then enable lines in inputs_test_2d_pass_mpi_comm_picmi.py again # https://github.com/AMReX-Codes/pyamrex/issues/163 # sim.step(max_steps, mpi_comm=new_comm) @@ -141,7 +141,7 @@ # If any of these tests fail, the terminal will print that the # program crashed. -# TODO: Enable in pyAMReX, then enable lines in PICMI_inputs_2d.py again +# TODO: Enable in pyAMReX, then enable lines in inputs_test_2d_pass_mpi_comm_picmi.py again # https://github.com/AMReX-Codes/pyamrex/issues/163 # comm_world_size = comm_world.size # new_comm_size = new_comm.size diff --git a/Examples/Tests/point_of_contact_eb/analysis.py b/Examples/Tests/point_of_contact_eb/analysis.py index 9fb097f99d4..3f42aa6eeca 100755 --- a/Examples/Tests/point_of_contact_eb/analysis.py +++ b/Examples/Tests/point_of_contact_eb/analysis.py @@ -5,7 +5,7 @@ It compares the numerical results with the analytical solutions. The sphere is centered on O and has a radius of 0.2 (EB) The electron is initially at: (-0.25,0,0) and moves with a normalized momentum: (1,0.5,0) -An input file PICMI_inputs_3d.py is used. +An input file inputs_test_3d_point_of_contact_eb is used. """ import os From 9230b1a56d7b9d5e35aba87aeb57b24c4f78f9ad Mon Sep 17 00:00:00 2001 From: Remi Lehe Date: Mon, 9 Sep 2024 19:22:27 -0700 Subject: [PATCH 2/2] Fix a few more paths --- .../beam_beam_collision/README.rst | 4 ++-- .../plasma_mirror/README.rst | 4 ++-- .../uniform_plasma/README.rst | 16 ++++++++-------- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/Examples/Physics_applications/beam_beam_collision/README.rst b/Examples/Physics_applications/beam_beam_collision/README.rst index 559a81277db..4f89365c8f0 100644 --- a/Examples/Physics_applications/beam_beam_collision/README.rst +++ b/Examples/Physics_applications/beam_beam_collision/README.rst @@ -24,9 +24,9 @@ The PICMI input file is not available for this example yet. For `MPI-parallel `__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system. -.. literalinclude:: inputs +.. literalinclude:: inputs_test_3d_beam_beam_collision :language: ini - :caption: You can copy this file from ``Examples/Physics_applications/beam-beam_collision/inputs``. + :caption: You can copy this file from ``Examples/Physics_applications/beam-beam_collision/inputs_test_3d_beam_beam_collision``. Visualize diff --git a/Examples/Physics_applications/plasma_mirror/README.rst b/Examples/Physics_applications/plasma_mirror/README.rst index 8741db09699..56f1da7db46 100644 --- a/Examples/Physics_applications/plasma_mirror/README.rst +++ b/Examples/Physics_applications/plasma_mirror/README.rst @@ -33,9 +33,9 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. tab-item:: Executable: Input File - .. literalinclude:: inputs_2d + .. literalinclude:: inputs_test_2d_plasma_mirror :language: ini - :caption: You can copy this file from ``Examples/Physics_applications/plasma_mirror/inputs_2d``. + :caption: You can copy this file from ``Examples/Physics_applications/plasma_mirror/inputs_test_2d_plasma_mirror``. Analyze diff --git a/Examples/Physics_applications/uniform_plasma/README.rst b/Examples/Physics_applications/uniform_plasma/README.rst index 50d132712c6..04a0fb4555c 100644 --- a/Examples/Physics_applications/uniform_plasma/README.rst +++ b/Examples/Physics_applications/uniform_plasma/README.rst @@ -21,15 +21,15 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. note:: - TODO: This input file should be created following the ``inputs_3d`` file. + TODO: This input file should be created following the ``inputs_test_3d_uniform_plasma`` file. .. tab-item:: Executable: Input File - This example can be run **either** as WarpX **executable** using an input file: ``warpx.3d inputs_3d`` + This example can be run **either** as WarpX **executable** using an input file: ``warpx.3d inputs_test_3d_uniform_plasma`` - .. literalinclude:: inputs_3d + .. literalinclude:: inputs_test_3d_uniform_plasma :language: ini - :caption: You can copy this file from ``usage/examples/lwfa/inputs_3d``. + :caption: You can copy this file from ``usage/examples/lwfa/inputs_test_3d_uniform_plasma``. .. tab-item:: 2D @@ -39,15 +39,15 @@ For `MPI-parallel `__ runs, prefix these lines with ` .. note:: - TODO: This input file should be created following the ``inputs_2d`` file. + TODO: This input file should be created following the ``inputs_test_2d_uniform_plasma`` file. .. tab-item:: Executable: Input File - This example can be run **either** as WarpX **executable** using an input file: ``warpx.2d inputs_2d`` + This example can be run **either** as WarpX **executable** using an input file: ``warpx.2d inputs_test_2d_uniform_plasma`` - .. literalinclude:: inputs_2d + .. literalinclude:: inputs_test_2d_uniform_plasma :language: ini - :caption: You can copy this file from ``usage/examples/lwfa/inputs_2d``. + :caption: You can copy this file from ``usage/examples/lwfa/inputs_test_2d_uniform_plasma``. Analyze -------