add laser wakefield example

ComputationalRadiationPhysics · Aug 3, 2024 · cfe0bf5 · cfe0bf5
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diff --git a/docs/source/usage/picmi/intro.rst b/docs/source/usage/picmi/intro.rst
@@ -48,16 +48,25 @@ After you have installed the dependencies you must include the PIConGPU PICMI im
 .. note::
    Above, we used ``$PICSRC`` as a short hand for the path to picongpu's source code directory, provided from your shell environment if a pre-configured profile is used.
 
-After you have installed all PICMI dependencies, simply create a user script, see :ref:`here <example_PICMI_setup>`, and generate a picongpu setup, see :ref:`generating a PIConGPU setup with PICMI <generating_setups_with_PICMI>`.
+After you have installed all PICMI dependencies, simply create a user script, see the :ref:`warm plasma <example_PICMI_setup_warm_plasma>` and :ref:`laser wakefield <example_PICMI_setup_lwfa>` examples, and generate a picongpu setup, see :ref:`generating a PIConGPU setup with PICMI <generating_setups_with_PICMI>`.
 
 Example User Script for a warm plasma setup:
 --------------------------------------
-.. _example_PICMI_setup:
+.. _example_PICMI_setup_warm_plasma:
 
 .. literalinclude:: ../../../../share/picongpu/pypicongpu/examples/warm_plasma/main.py
    :language: python
 
-Creates a directory ``generated_input``, where you can run ``pic-build`` and subsequently ``tbg``.
+Creates a directory ``warm_plasma``, where you can run ``pic-build`` and subsequently ``tbg``.
+
+Example User Script for a laser wakefield setup:
+--------------------------------------
+.. _example_PICMI_setup_lwfa:
+
+.. literalinclude:: ../../../../share/picongpu/pypicongpu/examples/laser_wakefield/main.py
+   :language: python
+
+Creates a directory ``LWFA``, where you can run ``pic-build`` and subsequently ``tbg``.
 
 Generation of PIConGPU setups with PICMI
 ----------------------------------------
@@ -188,24 +197,17 @@ Parameters/Methods prefixed with ``picongpu_`` are PIConGPU-exclusive.
 
     If neither is set a warning is printed prompting for either of the options above.
 
-- **Interaction**
-  Configuration of the PIC-algorithm extensions, example of use as follows:
-
-  .. code:: python
+Ionization:
+^^^^^^^^^^^
+The PIConGPU PICMI interface currently supports the configuration of ionization only through a picongpu specific PICMI extension, not the in the PICMI standard defined interface, due to the lack of standardization of ionization algorithm names in the PICMI standard.
 
-    from picongpu import picmi
-    from picongpu.interaction.ionization.fieldionization import ADK, ADKVariant
-    from picongpu.interaction import Interaction
+Use the **Interaction** interface
 
-    e = picmi.Species(name="e", particle_type="electron")
-    nitrogen = picmi.Species(name="nitrogen", particle_type="N", charge_state=2)
 
-    ADK_ionization = ADK(ADK_variant = ADKVariant.LinearPolarization, ion_species = nitrogen, ionization_electron_species=e)
-    interaction = Interaction(ground_state_ionizaion_model_list=[ADK_Ionization])
+- **Interaction**
+  picongpu specific configuration of PIC-algorithm extensions.
 
-    sim = picmi.simulation(picongpu_interaction=interaction)
-    sim.add_species(e, ...)
-    sim.add_species(nitrogen, ...)
+    - ``__init__(ground_state_ionizaion_model_list= <list of ionization models>)``
 
 Output
 ^^^^^^

diff --git a/share/picongpu/pypicongpu/examples/laser_wakefield/.gitignore b/share/picongpu/pypicongpu/examples/laser_wakefield/.gitignore
@@ -0,0 +1 @@
+LWFA
diff --git a/share/picongpu/pypicongpu/examples/laser_wakefield/main.py b/share/picongpu/pypicongpu/examples/laser_wakefield/main.py
@@ -0,0 +1,202 @@
+"""
+This file is part of PIConGPU.
+Copyright 2024 PIConGPU contributors
+Authors: Masoud Afshari, Brian Edward Marre
+License: GPLv3+
+"""
+
+from picongpu import picmi
+from picongpu import pypicongpu
+import numpy as np
+
+"""
+@file PICMI user script reproducing the PIConGPU LWFA example
+
+This Python script is example PICMI user script reproducing the LaserWakefield example setup, based on 8.cfg.
+"""
+
+
+# generation modifiers
+ENABLE_IONS = True
+ENABLE_IONIZATION = True
+ADD_CUSTOM_INPUT = True
+OUTPUT_DIRECTORY_PATH = "LWFA"
+
+numberCells = np.array([192, 2048, 192])
+cellSize = np.array([0.1772e-6, 0.4430e-7, 0.1772e-6])  # unit: meter)
+
+# Define the simulation grid based on grid.param
+grid = picmi.Cartesian3DGrid(
+    picongpu_n_gpus=[2, 4, 1],
+    number_of_cells=numberCells.tolist(),
+    lower_bound=[0, 0, 0],
+    upper_bound=(numberCells * cellSize).tolist(),
+    lower_boundary_conditions=["open", "open", "open"],
+    upper_boundary_conditions=["open", "open", "open"],
+)
+
+gaussianProfile = picmi.distribution.GaussianDistribution(
+    density=1.0e25,
+    center_front=8.0e-5,
+    sigma_front=8.0e-5,
+    center_rear=10.0e-5,
+    sigma_rear=8.0e-5,
+    factor=-1.0,
+    power=4.0,
+    vacuum_cells_front=50,
+)
+
+# for particle type see https://github.com/openPMD/openPMD-standard/blob/upcoming-2.0.0/EXT_SpeciesType.md
+electrons = picmi.Species(particle_type="electron", name="electron", initial_distribution=gaussianProfile)
+
+hydrogen_ionization = picmi.Species(
+    particle_type="H", name="hydrogen", charge_state=0, initial_distribution=gaussianProfile
+)
+
+hydrogen_fully_ionized = picmi.Species(
+    particle_type="H", name="hydrogen", picongpu_fixed_charge=True, initial_distribution=gaussianProfile
+)
+
+solver = picmi.ElectromagneticSolver(
+    grid=grid,
+    method="Yee",
+)
+
+laser = picmi.GaussianLaser(
+    wavelength=0.8e-6,
+    waist=5.0e-6 / 1.17741,
+    duration=5.0e-15,
+    propagation_direction=[0.0, 1.0, 0.0],
+    polarization_direction=[1.0, 0.0, 0.0],
+    focal_position=[float(numberCells[0] * cellSize[0] / 2.0), 4.62e-5, float(numberCells[2] * cellSize[2] / 2.0)],
+    centroid_position=[float(numberCells[0] * cellSize[0] / 2.0), 0.0, float(numberCells[2] * cellSize[2] / 2.0)],
+    picongpu_polarization_type=pypicongpu.laser.GaussianLaser.PolarizationType.CIRCULAR,
+    a0=8.0,
+    picongpu_phase=0.0,
+)
+
+randomLayout = picmi.PseudoRandomLayout(n_macroparticles_per_cell=2)
+
+# Initialize particles  based on speciesInitialization.param
+# simulation schema : https://github.com/BrianMarre/picongpu/blob/2ddcdab4c1aca70e1fc0ba02dbda8bd5e29d98eb/share/picongpu/pypicongpu/schema/simulation.Simulation.json
+
+if not ENABLE_IONIZATION:
+    hydrogen = hydrogen_fully_ionized
+    interaction = None
+else:
+    hydrogen = hydrogen_ionization
+    adk_ionization_model = picmi.ADK(
+        ADK_variant=picmi.ADKVariant.CircularPolarization,
+        ion_species=hydrogen_ionization,
+        ionization_electron_species=electrons,
+        ionization_current=None,
+    )
+
+    bsi_effectiveZ_ionization_model = picmi.BSI(
+        BSI_extensions=[picmi.BSIExtension.EffectiveZ],
+        ion_species=hydrogen_ionization,
+        ionization_electron_species=electrons,
+        ionization_current=None,
+    )
+
+    interaction = picmi.Interaction(
+        ground_state_ionization_model_list=[adk_ionization_model, bsi_effectiveZ_ionization_model]
+    )
+
+sim = picmi.Simulation(
+    solver=solver,
+    max_steps=4000,
+    time_step_size=1.39e-16,
+    picongpu_moving_window_move_point=0.9,
+    picongpu_interaction=interaction,
+)
+
+sim.add_species(electrons, layout=randomLayout)
+
+if ENABLE_IONS:
+    sim.add_species(hydrogen, layout=randomLayout)
+
+sim.add_laser(laser, None)
+
+# additional non standardized custom user input
+# only active if custom templates are used
+
+# for generating setup with custom input see standard implementation,
+#  see https://picongpu.readthedocs.io/en/latest/usage/picmi/custom_template.html
+if ADD_CUSTOM_INPUT:
+    min_weight_input = pypicongpu.customuserinput.CustomUserInput()
+    min_weight_input.addToCustomInput({"minimum_weight": 10.0}, "minimum_weight")
+    sim.picongpu_add_custom_user_input(min_weight_input)
+
+    output_configuration = pypicongpu.customuserinput.CustomUserInput()
+    output_configuration.addToCustomInput(
+        {
+            "png_plugin_data_list": "['Ex', 'Ey', 'Ez', 'Bx', 'By', 'Bz', 'Jx', 'Jy', 'Jz']",
+            "png_plugin_SCALE_IMAGE": 1.0,
+            "png_plugin_SCALE_TO_CELLSIZE": True,
+            "png_plugin_WHITE_BOX_PER_GPU": False,
+            "png_plugin_EM_FIELD_SCALE_CHANNEL1": 7,
+            "png_plugin_EM_FIELD_SCALE_CHANNEL2": -1,
+            "png_plugin_EM_FIELD_SCALE_CHANNEL3": -1,
+            "png_plugin_CUSTOM_NORMALIZATION_SI": "5.0e12 / constants.c, 5.0e12, 15.0",
+            "png_plugin_PRE_PARTICLE_DENS_OPACITY": 0.25,
+            "png_plugin_PRE_CHANNEL1_OPACITY": 1.0,
+            "png_plugin_PRE_CHANNEL2_OPACITY": 1.0,
+            "png_plugin_PRE_CHANNEL3_OPACITY": 1.0,
+            "png_plugin_preParticleDensCol": "colorScales::grayInv",
+            "png_plugin_preChannel1Col": "colorScales::green",
+            "png_plugin_preChannel2Col": "colorScales::none",
+            "png_plugin_preChannel3Col": "colorScales::none",
+            "png_plugin_preChannel1": "field_E.x() * field_E.x();",
+            "png_plugin_preChannel2": "field_E.y()",
+            "png_plugin_preChannel3": "-1.0_X * field_E.y()",
+            "png_plugin_period": 100,
+            "png_plugin_axis": "yx",
+            "png_plugin_slicePoint": 0.5,
+            "png_plugin_species_name": "electron",
+            "png_plugin_folder_name": "pngElectronsYX",
+        },
+        "png plugin configuration",
+    )
+
+    output_configuration.addToCustomInput(
+        {
+            "energy_histogram_species_name": "electron",
+            "energy_histogram_period": 100,
+            "energy_histogram_bin_count": 1024,
+            "energy_histogram_min_energy": 0.0,
+            "energy_histogram_maxEnergy": 1000.0,
+            "energy_histogram_filter": "all",
+        },
+        "energy histogram plugin configuration",
+    )
+
+    output_configuration.addToCustomInput(
+        {
+            "phase_space_species_name": "electron",
+            "phase_space_period": 100,
+            "phase_space_space": "y",
+            "phase_space_momentum": "py",
+            "phase_space_min": -1.0,
+            "phase_space_max": 1.0,
+            "phase_space_filter": "all",
+        },
+        "phase space plugin configuration",
+    )
+
+    output_configuration.addToCustomInput(
+        {"opnePMD_period": 100, "opnePMD_file": "simData", "opnePMD_extension": "bp"}, "openPMD plugin configuration"
+    )
+
+    output_configuration.addToCustomInput(
+        {"checkpoint_period": 100, "checkpoint_backend": "openPMD", "checkpoint_restart_backend": "openPMD"},
+        "checkpoint configuration",
+    )
+
+    output_configuration.addToCustomInput(
+        {"macro_particle_count_period": 100, "macro_particle_count_species_name": "electron"},
+        "macro particle count plugin configuration",
+    )
+    sim.picongpu_add_custom_user_input(output_configuration)
+
+sim.write_input_file(OUTPUT_DIRECTORY_PATH)
diff --git a/share/picongpu/pypicongpu/examples/warm_plasma/.gitignore b/share/picongpu/pypicongpu/examples/warm_plasma/.gitignore
@@ -1 +1 @@
-generated_input
+warm_plasma
diff --git a/share/picongpu/pypicongpu/examples/warm_plasma/main.py b/share/picongpu/pypicongpu/examples/warm_plasma/main.py
@@ -1,5 +1,14 @@
+"""
+This file is part of PIConGPU.
+Copyright 2021-2024 PIConGPU contributors
+Authors: Hannes Troepgen
+License: GPLv3+
+"""
+
 from picongpu import picmi
 
+OUTPUT_DIRECTORY_PATH = "warm_plasma"
+
 boundary_conditions = ["periodic", "periodic", "periodic"]
 grid = picmi.Cartesian3DGrid(
     # note: [x] * 3 == [x, x, x]
@@ -36,4 +45,4 @@
 layout = picmi.PseudoRandomLayout(n_macroparticles_per_cell=25)
 sim.add_species(electron, layout)
 
-sim.write_input_file("generated_input")
+sim.write_input_file(OUTPUT_DIRECTORY_PATH)