Rename cycle_intervals -> period_sample_intervals

docs/source/usage/parameters.rst

@@ -449,9 +449,9 @@ 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>.cycle_intervals`` (``int``, default value: ``1``)
+            * ``<element_name>.period_sample_intervals`` (``int``, default value: ``1``)
 
-                For periodic lattice, only output every N cycles (turns).
+                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``)

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", cycle_intervals=1)
+.. 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.
 
@@ -649,7 +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 cycle_intervals: for periodic lattice, only output every N cycles (turns)
+   :param period_sample_intervals: for periodic lattice, only output every Nth period (turn)
 
    .. py:property:: name
 

examples/fodo_channel/README.rst

@@ -17,7 +17,7 @@ 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 ``cycle_intervals`` capability of our beam monitor diagnostics, only creating output every 10th FODO cell
+This test also demonstrates the ``period_sample_intervals`` capability of our beam monitor diagnostics, only creating output every 10th FODO cell
 
 
 Run

examples/fodo_channel/input_fodo.in

@@ -26,7 +26,7 @@ lattice.nslice = 5
 lattice.periods = 101  # FODO channel of 101 periods
 
 monitor.type = beam_monitor
-monitor.cycle_intervals = 10
+monitor.period_sample_intervals = 10
 monitor.backend = h5
 
 drift1.type = drift

examples/fodo_channel/run_fodo.py

@@ -46,7 +46,7 @@
 sim.add_particles(bunch_charge_C, distr, npart)
 
 # add beam diagnostics
-monitor = elements.BeamMonitor("monitor", backend="h5", cycle_intervals=10)
+monitor = elements.BeamMonitor("monitor", backend="h5", period_sample_intervals=10)
 
 # design the accelerator lattice)
 ns = 5  # number of slices per ds in the element

src/ImpactX.cpp

@@ -181,10 +181,10 @@ namespace impactx {
         }
 
         // periods through the lattice
-        int periods = 1;
-        amrex::ParmParse("lattice").queryAdd("periods", periods);
+        int num_periods = 1;
+        amrex::ParmParse("lattice").queryAdd("periods", num_periods);
 
-        for (int cycle=0; cycle < periods; ++cycle) {
+        for (int period=0; period < num_periods; ++period) {
             // loop over all beamline elements
             for (auto &element_variant: m_lattice) {
                 // update element edge of the reference particle
@@ -263,7 +263,7 @@ namespace impactx {
                     // assuming that the distribution did not change
 
                     // push all particles with external maps
-                    Push(*amr_data->m_particle_container, element_variant, step, cycle);
+                    Push(*amr_data->m_particle_container, element_variant, step, period);
 
                     // move "lost" particles to another particle container
                     collect_lost_particles(*amr_data->m_particle_container);

src/initialization/InitElement.cpp

@@ -395,8 +395,8 @@ namespace detail
             pp_element.queryAdd("backend", openpmd_backend);
             std::string openpmd_encoding{"g"};
             pp_element.queryAdd("encoding", openpmd_encoding);
-            int cycle_intervals = 1;
-            pp_element.queryAdd("cycle_intervals", cycle_intervals);
+            int period_sample_intervals = 1;
+            pp_element.queryAdd("period_sample_intervals", period_sample_intervals);
 
             // optional: add and calculate additional particle properties
             // property: nonlinear lens invariants
@@ -414,7 +414,7 @@ namespace detail
                 pp_element.queryAdd("cn", cn);
             }
 
-            m_lattice.emplace_back(diagnostics::BeamMonitor(openpmd_name, openpmd_backend, openpmd_encoding, cycle_intervals));
+            m_lattice.emplace_back(diagnostics::BeamMonitor(openpmd_name, openpmd_backend, openpmd_encoding, period_sample_intervals));
         } else if (element_type == "line")
         {
             // Parse the lattice elements for the sub-lattice in the line

src/particles/elements/diagnostics/openPMD.H

@@ -76,9 +76,9 @@ namespace detail
          * @param series_name name of the data series, usually the element name
          * @param backend file format backend for openPMD, e.g., "bp" or "h5"
          * @param encoding openPMD iteration encoding: "v"ariable based, "f"ile based, "g"roup based (default)
-         * @param cycle_intervals for periodic lattice, only output every N cycles (turns)
+         * @param period_sample_intervals for periodic lattice, only output every Nth period (turn)
          */
-        BeamMonitor (std::string series_name, std::string backend="default", std::string encoding="g", int cycle_intervals=1);
+        BeamMonitor (std::string series_name, std::string backend="default", std::string encoding="g", int period_sample_intervals=1);
 
         BeamMonitor (BeamMonitor const & other) = default;
         BeamMonitor (BeamMonitor && other) = default;
@@ -159,7 +159,7 @@ namespace detail
 
         int m_file_min_digits = 6; //! minimum number of digits to iteration number in file name
 
-        int m_cycle_intervals = 1; //! only output every N cycles (turns) of periodic lattices
+        int m_period_sample_intervals = 1; //! only output every N cycles (turns) of periodic lattices
 
         /** This rank's offset in the MPI-global particle array, by level
          *

src/particles/elements/diagnostics/openPMD.cpp

@@ -154,8 +154,8 @@ namespace detail
 #endif // ImpactX_USE_OPENPMD
     }
 
-    BeamMonitor::BeamMonitor (std::string series_name, std::string backend, std::string encoding, int cycle_intervals) :
-        m_series_name(std::move(series_name)), m_OpenPMDFileType(std::move(backend)), m_cycle_intervals(cycle_intervals)
+    BeamMonitor::BeamMonitor (std::string series_name, std::string backend, std::string encoding, int period_sample_intervals) :
+        m_series_name(std::move(series_name)), m_OpenPMDFileType(std::move(backend)), m_period_sample_intervals(period_sample_intervals)
     {
 #ifdef ImpactX_USE_OPENPMD
         // pick first available backend if default is chosen
@@ -181,7 +181,7 @@ namespace detail
 
         amrex::ParmParse pp_diag("diag");
         // turn filter
-        pp_diag.queryAdd("cycle_intervals", m_cycle_intervals);
+        pp_diag.queryAdd("period_sample_intervals", m_period_sample_intervals);
         // legacy options from other diagnostics
         pp_diag.queryAdd("file_min_digits", m_file_min_digits);
 
@@ -318,7 +318,7 @@ namespace detail
     )
     {
         // filter out this turn?
-        if (cycle % m_cycle_intervals != 0)
+        if (cycle % m_period_sample_intervals != 0)
             return;
 
 #ifdef ImpactX_USE_OPENPMD

src/python/elements.cpp

@@ -218,7 +218,7 @@ void init_elements(py::module& m)
              py::arg("name"),
              py::arg("backend") = "default",
              py::arg("encoding") = "g",
-             py::arg("cycle_intervals") = 1,
+             py::arg("period_sample_intervals") = 1,
              "This element writes the particle beam out to openPMD data."
         )
         .def_property_readonly("name",