BeamMonitor: Enable Filtering by Cycle (Turn) (#713)

* Elements: Pass Cycle, Filter openPMD * Examples: Update Programmable Signature For cycle argument * Documentation * Add Example * Update Docstrings Co-authored-by: Chad Mitchell <[email protected]> * Rename `cycle_intervals` -> `period_sample_intervals` * Update `Marker` * Rename: `cycle` -> `period` --------- Co-authored-by: Chad Mitchell <[email protected]>
ECP-WarpX · Oct 9, 2024 · dfe9b28 · dfe9b28
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diff --git a/docs/source/usage/examples.rst b/docs/source/usage/examples.rst
@@ -70,6 +70,16 @@ Beam Distributions
 
    examples/distgen/README
 
+
+Channels & Rings
+----------------
+
+.. toctree::
+   :maxdepth: 1
+
+   examples/fodo_channel/README.rst
+
+
 Lattice Design & Optimization
 -----------------------------
 

diff --git a/docs/source/usage/parameters.rst b/docs/source/usage/parameters.rst
@@ -449,6 +449,11 @@ Lattice Elements
                 openPMD `iteration encoding <https://openpmd-api.readthedocs.io/en/0.14.0/usage/concepts.html#iteration-and-series>`__: (v)ariable based, (f)ile based, (g)roup based (default)
                 variable based is an `experimental feature with ADIOS2 <https://openpmd-api.readthedocs.io/en/0.14.0/backends/adios2.html#experimental-new-adios2-schema>`__.
 
+            * ``<element_name>.period_sample_intervals`` (``int``, default value: ``1``)
+
+                for periodic lattice, only output every Nth period (turn).
+                By default, diagnostics are returned every cycle.
+
             * ``<element_name>.nonlinear_lens_invariants`` (``boolean``, default value: ``false``)
 
                 Compute and output the invariants H and I within the nonlinear magnetic insert element (see: ``nonlinear_lens``).

diff --git a/docs/source/usage/python.rst b/docs/source/usage/python.rst
@@ -632,7 +632,7 @@ This module provides elements for the accelerator lattice.
    :param rotation: rotation error in the transverse plane [degrees]
    :param name: an optional name for the element
 
-.. py:class:: impactx.elements.BeamMonitor(name, backend="default", encoding="g")
+.. py:class:: impactx.elements.BeamMonitor(name, backend="default", encoding="g", period_sample_intervals=1)
 
    A beam monitor, writing all beam particles at fixed ``s`` to openPMD files.
 
@@ -649,6 +649,7 @@ This module provides elements for the accelerator lattice.
    :param name: name of the series
    :param backend: I/O backend, e.g., ``bp``, ``h5``, ``json``
    :param encoding: openPMD iteration encoding: (v)ariable based, (f)ile based, (g)roup based (default)
+   :param period_sample_intervals: for periodic lattice, only output every Nth period (turn)
 
    .. py:property:: name
 

diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
@@ -219,6 +219,23 @@ add_impactx_test(FODO.py.MPI
     examples/fodo/plot_fodo.py
 )
 
+# FODO Channel ################################################################
+#
+add_impactx_test(FODO_channel
+        examples/fodo_channel/input_fodo.in
+        OFF  # ImpactX MPI-parallel
+        examples/fodo_channel/analysis_fodo.py
+        examples/fodo_channel/plot_fodo.py
+)
+add_impactx_test(FODO_channel.py
+        examples/fodo_channel/run_fodo.py
+        OFF  # ImpactX MPI-parallel
+        examples/fodo_channel/analysis_fodo.py
+        examples/fodo_channel/plot_fodo.py
+)
+label_impactx_test(FODO_channel slow)
+label_impactx_test(FODO_channel.py slow)
+
 # Chicane #####################################################################
 #
 add_impactx_test(chicane

diff --git a/examples/fodo_channel/README.rst b/examples/fodo_channel/README.rst
@@ -0,0 +1,74 @@
+.. _examples-fodo-channel:
+
+FODO Channel
+============
+
+A 300m channel of 100 stable FODO cells (3m each) with a zero-current phase advance of 67.8 degrees.
+
+The matched Twiss parameters at entry are:
+
+* :math:`\beta_\mathrm{x} = 2.82161941` m
+* :math:`\alpha_\mathrm{x} = -1.59050035`
+* :math:`\beta_\mathrm{y} = 2.82161941` m
+* :math:`\alpha_\mathrm{y} = 1.59050035`
+
+We use a 2 GeV electron beam with initial unnormalized rms emittance of 2 nm.
+
+The second moments of the particle distribution after the FODO cell should coincide with the second moments of the particle distribution before the FODO cell, to within the level expected due to noise due to statistical sampling.
+
+In this test, the initial and final values of :math:`\lambda_x`, :math:`\lambda_y`, :math:`\lambda_t`, :math:`\epsilon_x`, :math:`\epsilon_y`, and :math:`\epsilon_t` must agree with nominal values.
+This test also demonstrates the ``period_sample_intervals`` capability of our beam monitor diagnostics, only creating output every 10th FODO cell
+
+
+Run
+---
+
+This example can be run **either** as:
+
+* **Python** script: ``python3 run_fodo.py`` or
+* ImpactX **executable** using an input file: ``impactx input_fodo.in``
+
+For `MPI-parallel <https://www.mpi-forum.org>`__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system.
+
+.. tab-set::
+
+   .. tab-item:: Python: Script
+
+       .. literalinclude:: run_fodo.py
+          :language: python3
+          :caption: You can copy this file from ``examples/fodo/run_fodo.py``.
+
+   .. tab-item:: Executable: Input File
+
+       .. literalinclude:: input_fodo.in
+          :language: ini
+          :caption: You can copy this file from ``examples/fodo/input_fodo.in``.
+
+
+Analyze
+-------
+
+We run the following script to analyze correctness:
+
+.. dropdown:: Script ``analysis_fodo.py``
+
+   .. literalinclude:: analysis_fodo.py
+      :language: python3
+      :caption: You can copy this file from ``examples/fodo/analysis_fodo.py``.
+
+
+Visualize
+---------
+
+You can run the following script to visualize the beam evolution over time:
+
+.. dropdown:: Script ``plot_fodo.py``
+
+   .. literalinclude:: plot_fodo.py
+      :language: python3
+      :caption: You can copy this file from ``examples/fodo/plot_fodo.py``.
+
+.. figure:: https://gist.githubusercontent.com/ax3l/8ae7dcb9e07c361e002fa56d6b16cb16/raw/cc952670bb946cd7a62282bc7aa3f03f3d5faa16/fodo_channel.png
+   :alt: preserved emittance in the FODO channel.
+
+   FODO transverse emittance evolution (preserved)
diff --git a/examples/fodo_channel/analysis_fodo.py b/examples/fodo_channel/analysis_fodo.py
@@ -0,0 +1,105 @@
+#!/usr/bin/env python3
+#
+# Copyright 2022-2023 ImpactX contributors
+# Authors: Axel Huebl, Chad Mitchell
+# License: BSD-3-Clause-LBNL
+#
+
+
+import numpy as np
+import openpmd_api as io
+from scipy.stats import moment
+
+
+def get_moments(beam):
+    """Calculate standard deviations of beam position & momenta
+    and emittance values
+
+    Returns
+    -------
+    sigx, sigy, sigt, emittance_x, emittance_y, emittance_t
+    """
+    sigx = moment(beam["position_x"], moment=2) ** 0.5  # variance -> std dev.
+    sigpx = moment(beam["momentum_x"], moment=2) ** 0.5
+    sigy = moment(beam["position_y"], moment=2) ** 0.5
+    sigpy = moment(beam["momentum_y"], moment=2) ** 0.5
+    sigt = moment(beam["position_t"], moment=2) ** 0.5
+    sigpt = moment(beam["momentum_t"], moment=2) ** 0.5
+
+    epstrms = beam.cov(ddof=0)
+    emittance_x = (sigx**2 * sigpx**2 - epstrms["position_x"]["momentum_x"] ** 2) ** 0.5
+    emittance_y = (sigy**2 * sigpy**2 - epstrms["position_y"]["momentum_y"] ** 2) ** 0.5
+    emittance_t = (sigt**2 * sigpt**2 - epstrms["position_t"]["momentum_t"] ** 2) ** 0.5
+
+    return (sigx, sigy, sigt, emittance_x, emittance_y, emittance_t)
+
+
+# initial/final beam
+series = io.Series("diags/openPMD/monitor.h5", io.Access.read_only)
+last_step = list(series.iterations)[-1]
+initial = series.iterations[1].particles["beam"].to_df()
+final = series.iterations[last_step].particles["beam"].to_df()
+
+# compare number of particles
+num_particles = 10000
+assert num_particles == len(initial)
+assert num_particles == len(final)
+
+# compare beamline length: 300m
+assert np.isclose(
+    300.0, series.iterations[last_step].particles["beam"].get_attribute("z_ref")
+)
+# compare beam monitor outputs: 10 (every 10th FODO element + 1)
+assert len(series.iterations) == 11
+
+print("Initial Beam:")
+sigx, sigy, sigt, emittance_x, emittance_y, emittance_t = get_moments(initial)
+print(f"  sigx={sigx:e} sigy={sigy:e} sigt={sigt:e}")
+print(
+    f"  emittance_x={emittance_x:e} emittance_y={emittance_y:e} emittance_t={emittance_t:e}"
+)
+
+atol = 0.0  # ignored
+rtol = 2.2 * num_particles**-0.5  # from random sampling of a smooth distribution
+print(f"  rtol={rtol} (ignored: atol~={atol})")
+
+assert np.allclose(
+    [sigx, sigy, sigt, emittance_x, emittance_y, emittance_t],
+    [
+        7.5451170454175073e-005,
+        7.5441588239210947e-005,
+        9.9775878164077539e-004,
+        1.9959540393751392e-009,
+        2.0175015289132990e-009,
+        2.0013820193294972e-006,
+    ],
+    rtol=rtol,
+    atol=atol,
+)
+
+
+print("")
+print("Final Beam:")
+sigx, sigy, sigt, emittance_x, emittance_y, emittance_t = get_moments(final)
+print(f"  sigx={sigx:e} sigy={sigy:e} sigt={sigt:e}")
+print(
+    f"  emittance_x={emittance_x:e} emittance_y={emittance_y:e} emittance_t={emittance_t:e}"
+)
+
+atol = 0.0  # ignored
+rtol = 2.2 * num_particles**-0.5  # from random sampling of a smooth distribution
+print(f"  rtol={rtol} (ignored: atol~={atol})")
+
+assert np.allclose(
+    [sigx, sigy, sigt, emittance_x, emittance_y, emittance_t],
+    [
+        7.4790118496224206e-005,
+        7.5357525169680140e-005,
+        9.9775879288128088e-004,
+        1.9959539836392703e-009,
+        2.0175014668882125e-009,
+        2.0013820380883801e-006,
+    ],
+    rtol=rtol,
+    atol=atol,
+)
diff --git a/examples/fodo_channel/input_fodo.in b/examples/fodo_channel/input_fodo.in
@@ -0,0 +1,60 @@
+###############################################################################
+# Particle Beam(s)
+###############################################################################
+beam.npart = 10000
+beam.units = static
+beam.kin_energy = 2.0e3
+beam.charge = 1.0e-9
+beam.particle = electron
+beam.distribution = waterbag_from_twiss
+beam.alphaX = -1.5905003499999992
+beam.alphaY = 1.5905003499999992
+beam.alphaT = 0.0
+beam.betaX = 2.8216194100262637
+beam.betaY = 2.8216194100262637
+beam.betaT = 0.5
+beam.emittX = 2e-09
+beam.emittY = 2e-09
+beam.emittT = 2e-06
+
+
+###############################################################################
+# Beamline: lattice elements and segments
+###############################################################################
+lattice.elements = monitor drift1 quad1 drift2 quad2 drift3
+lattice.nslice = 5
+lattice.periods = 101  # FODO channel of 101 periods
+
+monitor.type = beam_monitor
+monitor.period_sample_intervals = 10
+monitor.backend = h5
+
+drift1.type = drift
+drift1.ds = 0.25
+
+quad1.type = quad
+quad1.ds = 1.0
+quad1.k = 1.0
+
+drift2.type = drift
+drift2.ds = 0.5
+
+quad2.type = quad
+quad2.ds = 1.0
+quad2.k = -1.0
+
+drift3.type = drift
+drift3.ds = 0.25
+
+
+###############################################################################
+# Algorithms
+###############################################################################
+algo.particle_shape = 2
+algo.space_charge = false
+
+
+###############################################################################
+# Diagnostics
+###############################################################################
+diag.slice_step_diagnostics = false