Add reduced_diags general input (#5479)

dpgrote · pre-commit-ci[bot] · web-flow · commit 9e5346e350ce · 2024-12-04T21:08:26.000Z
This PR adds the `reduced_diags` input parameter group that allows
setting of parameters common to all reduced diagnostics. For example
'reduced_diags.intervals` can be set once rather than having to set it
for each individual reduced diagnostic.

---------

Co-authored-by: pre-commit-ci[bot] &lt;66853113+pre-commit-ci[bot]@users.noreply.github.com&gt;
diff --git a/Docs/source/usage/parameters.rst b/Docs/source/usage/parameters.rst
@@ -3589,22 +3589,27 @@ This shifts analysis from post-processing to runtime calculation of reduction op
     * ``Timestep``
         This type outputs the simulation's physical timestep (in seconds) at each mesh refinement level.
 
-* ``<reduced_diags_name>.intervals`` (`string`)
+* ``reduced_diags.intervals`` (`string`)
     Using the `Intervals Parser`_ syntax, this string defines the timesteps at which reduced
-    diagnostics are written to file.
+    diagnostics are written to the file.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.intervals``.
 
-* ``<reduced_diags_name>.path`` (`string`) optional (default `./diags/reducedfiles/`)
-    The path that the output file will be stored.
+* ``reduced_diags.path`` (`string`) optional (default `./diags/reducedfiles/`)
+    The path where the output file will be stored.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.path``.
 
-* ``<reduced_diags_name>.extension`` (`string`) optional (default `txt`)
-    The extension of the output file.
+* ``reduced_diags.extension`` (`string`) optional (default `txt`)
+    The extension of the output file (the suffix).
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.extension``.
 
-* ``<reduced_diags_name>.separator`` (`string`) optional (default a `whitespace`)
+* ``reduced_diags.separator`` (`string`) optional (default a `whitespace`)
     The separator between row values in the output file.
     The default separator is a whitespace.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.separator``.
 
-* ``<reduced_diags_name>.precision`` (`integer`) optional (default `14`)
+* ``reduced_diags.precision`` (`integer`) optional (default `14`)
     The precision used when writing out the data to the text files.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.precision``.
 
 Lookup tables and other settings for QED modules
 ------------------------------------------------
diff --git a/Examples/Physics_applications/laser_ion/inputs_test_2d_laser_ion_acc_picmi.py b/Examples/Physics_applications/laser_ion/inputs_test_2d_laser_ion_acc_picmi.py
@@ -196,7 +196,6 @@
 histuH_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histuH",
-    period=100,
     species=hydrogen,
     bin_number=1000,
     bin_min=0.0,
@@ -208,7 +207,6 @@
 histue_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histue",
-    period=100,
     species=electrons,
     bin_number=1000,
     bin_min=0.0,
@@ -222,7 +220,6 @@
 histuzAll_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histuzAll",
-    period=100,
     species=hydrogen,
     bin_number=1000,
     bin_min=-0.474,
@@ -233,7 +230,6 @@
 field_probe_z_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_Z",
-    period=100,
     integrate=0,
     probe_geometry="Line",
     x_probe=0.0,
@@ -246,7 +242,6 @@
 field_probe_scat_point_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_ScatPoint",
-    period=1,
     integrate=0,
     probe_geometry="Point",
     x_probe=0.0,
@@ -256,7 +251,6 @@
 field_probe_scat_line_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_ScatLine",
-    period=100,
     integrate=1,
     probe_geometry="Line",
     x_probe=-2.5e-6,
@@ -267,7 +261,8 @@
 )
 
 load_balance_costs_rdiag = picmi.ReducedDiagnostic(
-    diag_type="LoadBalanceCosts", name="LBC", period=100
+    diag_type="LoadBalanceCosts",
+    name="LBC",
 )
 
 # Set up simulation
@@ -278,6 +273,7 @@
     particle_shape="cubic",
     warpx_numprocs=[1, 2],  # deactivate `numprocs` for dynamic load balancing
     warpx_use_filter=1,
+    warpx_reduced_diags_intervals=100,
     warpx_load_balance_intervals=100,
     warpx_load_balance_costs_update="heuristic",
 )
diff --git a/Examples/Tests/implicit/inputs_test_1d_semi_implicit_picard b/Examples/Tests/implicit/inputs_test_1d_semi_implicit_picard
@@ -85,7 +85,6 @@ diag1.electrons.variables = z w ux uy uz
 diag1.protons.variables = z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1
diff --git a/Examples/Tests/implicit/inputs_test_1d_theta_implicit_picard b/Examples/Tests/implicit/inputs_test_1d_theta_implicit_picard
@@ -85,7 +85,6 @@ diag1.electrons.variables = z w ux uy uz
 diag1.protons.variables = z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1
diff --git a/Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb b/Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb
@@ -109,7 +109,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1
diff --git a/Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb_filtered b/Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb_filtered
@@ -109,7 +109,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1
diff --git a/Examples/Tests/implicit/inputs_test_2d_theta_implicit_strang_psatd b/Examples/Tests/implicit/inputs_test_2d_theta_implicit_strang_psatd
@@ -92,7 +92,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1
diff --git a/Python/pywarpx/picmi.py b/Python/pywarpx/picmi.py
@@ -2770,6 +2770,21 @@ class Simulation(picmistandard.PICMI_Simulation):
 
     warpx_used_inputs_file: string, optional
         The name of the text file that the used input parameters is written to,
+
+    warpx_reduced_diags_path: string, optional
+        Sets the default path for reduced diagnostic output files
+
+    warpx_reduced_diags_extension: string, optional
+        Sets the default extension for reduced diagnostic output files
+
+    warpx_reduced_diags_intervals: string, optional
+        Sets the default intervals for reduced diagnostic output files
+
+    warpx_reduced_diags_separator: string, optional
+        Sets the default separator for reduced diagnostic output files
+
+    warpx_reduced_diags_precision: integer, optional
+        Sets the default precision for reduced diagnostic output files
     """
 
     # Set the C++ WarpX interface (see _libwarpx.LibWarpX) as an extension to
@@ -2836,6 +2851,12 @@ def init(self, kw):
         self.checkpoint_signals = kw.pop("warpx_checkpoint_signals", None)
         self.numprocs = kw.pop("warpx_numprocs", None)
 
+        self.reduced_diags_path = kw.pop("warpx_reduced_diags_path", None)
+        self.reduced_diags_extension = kw.pop("warpx_reduced_diags_extension", None)
+        self.reduced_diags_intervals = kw.pop("warpx_reduced_diags_intervals", None)
+        self.reduced_diags_separator = kw.pop("warpx_reduced_diags_separator", None)
+        self.reduced_diags_precision = kw.pop("warpx_reduced_diags_precision", None)
+
         self.inputs_initialized = False
         self.warpx_initialized = False
 
@@ -2902,6 +2923,13 @@ def initialize_inputs(self):
 
         pywarpx.warpx.numprocs = self.numprocs
 
+        reduced_diags = pywarpx.warpx.get_bucket("reduced_diags")
+        reduced_diags.path = self.reduced_diags_path
+        reduced_diags.extension = self.reduced_diags_extension
+        reduced_diags.intervals = self.reduced_diags_intervals
+        reduced_diags.separator = self.reduced_diags_separator
+        reduced_diags.precision = self.reduced_diags_precision
+
         particle_shape = self.particle_shape
         for s in self.species:
             if s.particle_shape is not None:
@@ -3943,7 +3971,7 @@ def __init__(
         self,
         diag_type,
         name=None,
-        period=1,
+        period=None,
         path=None,
         extension=None,
         separator=None,
diff --git a/Source/Diagnostics/ReducedDiags/ReducedDiags.cpp b/Source/Diagnostics/ReducedDiags/ReducedDiags.cpp
@@ -28,12 +28,15 @@ m_rd_name{rd_name}
 {
     BackwardCompatibility();
 
+    const ParmParse pp_rd("reduced_diags");
     const ParmParse pp_rd_name(m_rd_name);
 
     // read path
+    pp_rd.query("path", m_path);
     pp_rd_name.query("path", m_path);
 
     // read extension
+    pp_rd.query("extension", m_extension);
     pp_rd_name.query("extension", m_extension);
 
     // check if it is a restart run
@@ -61,13 +64,16 @@ m_rd_name{rd_name}
 
     // read reduced diags intervals
     std::vector<std::string> intervals_string_vec = {"1"};
-    pp_rd_name.getarr("intervals", intervals_string_vec);
+    pp_rd.queryarr("intervals", intervals_string_vec);
+    pp_rd_name.queryarr("intervals", intervals_string_vec);
     m_intervals = utils::parser::IntervalsParser(intervals_string_vec);
 
     // read separator
+    pp_rd.query("separator", m_sep);
     pp_rd_name.query("separator", m_sep);
 
     // precision of data in the output file
+    utils::parser::queryWithParser(pp_rd, "precision", m_precision);
     utils::parser::queryWithParser(pp_rd_name, "precision", m_precision);
 }
 // end constructor
