From 7d51f86d1d0338703cc8bb3acd0bccf3503a2210 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Mon, 6 May 2024 08:25:25 -0700
Subject: [PATCH 1/6] Diagnostics: Warn w/o Positions

If a user specifies `<diag_name>.<species_name>.variables`
without including particle position arguments we now warn.
---
 Docs/source/usage/parameters.rst               |  5 +++--
 .../Diagnostics/ParticleDiag/ParticleDiag.cpp  | 18 ++++++++++++++++--
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/Docs/source/usage/parameters.rst b/Docs/source/usage/parameters.rst
index 5f97730e880..40c16a06df5 100644
--- a/Docs/source/usage/parameters.rst
+++ b/Docs/source/usage/parameters.rst
@@ -2689,10 +2689,11 @@ In-situ capabilities can be used by turning on Sensei or Ascent (provided they a
 
 * ``<diag_name>.<species_name>.variables`` (list of `strings` separated by spaces, optional)
     List of particle quantities to write to output.
-    Choices are ``w`` for the particle weight and ``ux`` ``uy`` ``uz`` for the particle momenta.
+    Choices are ``x``, ``y``, ``z`` for the particle positions (3D and RZ), ``x`` & ``z`` in 2D, ``z`` in 1D,
+    ``w`` for the particle weight and ``ux``, ``uy``, ``uz`` for the particle momenta.
     When using the lab-frame electrostatic solver, ``phi`` (electrostatic potential, on the macroparticles) is also available.
     By default, all particle quantities (except ``phi``) are written.
-    If ``<diag_name>.<species_name>.variables = none``, no particle data are written, except for particle positions, which are always included.
+    If ``<diag_name>.<species_name>.variables = none``, no particle data are written.
 
 * ``<diag_name>.<species_name>.random_fraction`` (`float`) optional
     If provided ``<diag_name>.<species_name>.random_fraction = a``, only `a` fraction of the particle data of this species will be dumped randomly in diag ``<diag_name>``, i.e. if `rand() < a`, this particle will be dumped, where `rand()` denotes a random number generator.
diff --git a/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp b/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
index 7ed64ccf8ec..17f739dbda0 100644
--- a/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
+++ b/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
@@ -6,6 +6,8 @@
 #include "Utils/TextMsg.H"
 #include "WarpX.H"
 
+#include <ablastr/warn_manager/WarnManager.H>
+
 #include <AMReX_ParmParse.H>
 
 #include <map>
@@ -13,7 +15,7 @@
 
 using namespace amrex;
 
-ParticleDiag::ParticleDiag(
+ParticleDiag::ParticleDiag (
     const std::string& diag_name, const std::string& name,
     WarpXParticleContainer* pc, PinnedMemoryParticleContainer* pinned_pc):
     m_diag_name(diag_name), m_name(name), m_pc(pc), m_pinned_pc(pinned_pc)
@@ -28,10 +30,11 @@ ParticleDiag::ParticleDiag(
     amrex::Vector<std::string> variables;
     const int variables_specified = pp_diag_name_species_name.queryarr("variables", variables);
 
-    if (variables_specified){
+    if (variables_specified) {
         // If only specific variables have been specified, fill m_plot_flags with zero and only set
         // requested variables to one
         std::fill(m_plot_flags.begin(), m_plot_flags.end(), 0);
+        bool contains_positions = false;
         if (variables[0] != "none"){
             const std::map<std::string, int> existing_variable_names = pc->getParticleComps();
             for (const auto& var : variables){
@@ -47,9 +50,20 @@ ParticleDiag::ParticleDiag(
                         "variables argument '" + var
                         +"' is not an existing attribute for this species");
                     m_plot_flags[existing_variable_names.at(var)] = 1;
+
+                    if (var == "x" || var == "y" || var == "z")
+                        contains_positions = true;
                 }
             }
         }
+
+        if (!contains_positions) {
+            ablastr::warn_manager::WMRecordWarning(
+                "Diagnostics",
+                diag_name + "." + name + ".variables contains no particle positions!",
+                ablastr::warn_manager::WarnPriority::high
+            );
+        }
     }
 
 #ifdef WARPX_DIM_RZ

From cc28d203b4aa832c02a76fdb3d619d58781f442f Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Mon, 6 May 2024 08:40:38 -0700
Subject: [PATCH 2/6] openPMD: Skip 0-positions for deselected comps

---
 Source/Diagnostics/WarpXOpenPMD.H   |  6 ++-
 Source/Diagnostics/WarpXOpenPMD.cpp | 67 +++++++++++++++--------------
 2 files changed, 40 insertions(+), 33 deletions(-)

diff --git a/Source/Diagnostics/WarpXOpenPMD.H b/Source/Diagnostics/WarpXOpenPMD.H
index 12aa46de058..99d6e0682ab 100644
--- a/Source/Diagnostics/WarpXOpenPMD.H
+++ b/Source/Diagnostics/WarpXOpenPMD.H
@@ -218,11 +218,13 @@ private:
   /** This function sets up the entries for storing the particle positions and global IDs
   *
   * @param[in] currSpecies Corresponding openPMD species
+  * @param[in] positionComponents user-selected components of the particle position
   * @param[in] np          Number of particles
   * @param[in] isBTD       Is this a back-transformed diagnostics output?
   */
   void SetupPos (
         openPMD::ParticleSpecies& currSpecies,
+        std::vector<std::string> const & positionComponents,
         const unsigned long long& np,
         bool isBTD = false);
 
@@ -231,12 +233,14 @@ private:
    * Sets the entries for storing particle position offset, constant records (charge, mass) and ED-PIC attributes.
    *
    * @param[in] currSpecies Corresponding openPMD species
+   * @param[in] positionComponents user-selected components of the particle position
    * @param[in] np          Number of particles
    * @param[in] charge      Charge of the particles (note: fix for ions)
    * @param[in] mass        Mass of the particles
    */
   void SetConstParticleRecordsEDPIC (
         openPMD::ParticleSpecies& currSpecies,
+        std::vector<std::string> const & positionComponents,
         const unsigned long long& np,
         amrex::ParticleReal charge,
         amrex::ParticleReal mass);
@@ -284,8 +288,8 @@ private:
    * @param[in] name species name
    * @param[in] iteration timestep
    * @param[in] write_real_comp The real attribute ids, from WarpX
-   * @param[in] real_comp_names The real attribute names, from WarpX
    * @param[in] write_int_comp The int attribute ids, from WarpX
+   * @param[in] real_comp_names The real attribute names, from WarpX
    * @param[in] int_comp_names The int attribute names, from WarpX
    * @param[in] charge         Charge of the particles (note: fix for ions)
    * @param[in] mass           Mass of the particles
diff --git a/Source/Diagnostics/WarpXOpenPMD.cpp b/Source/Diagnostics/WarpXOpenPMD.cpp
index 965eb82b31e..848b6818865 100644
--- a/Source/Diagnostics/WarpXOpenPMD.cpp
+++ b/Source/Diagnostics/WarpXOpenPMD.cpp
@@ -213,32 +213,29 @@ namespace detail
         return make_pair(record_name, component_name);
     }
 
-    /** Return the component labels for particle positions
+    /** Return the user-selected components for particle positions
+     *
+     * @param[in] write_real_comp The real attribute ids, from WarpX
+     * @param[in] real_comp_names The real attribute names, from WarpX
      */
     inline std::vector< std::string >
-    getParticlePositionComponentLabels (bool ignore_dims=false)
+    getParticlePositionComponentLabels (
+        amrex::Vector<int> const & write_real_comp,
+        amrex::Vector<std::string> const & real_comp_names)
     {
-        using vs = std::vector< std::string >;
-        auto positionComponents = vs{"x", "y", "z"};
-        if (!ignore_dims) {
-#if defined(WARPX_DIM_1D_Z)
-            positionComponents = vs{"z"};
-#elif defined(WARPX_DIM_XZ)
-            positionComponents = vs{"x", "z"};
-#elif defined(WARPX_DIM_RZ)
-            // note: although we internally store particle positions
-            //       for AMReX in r,z and a theta attribute, we
-            //       actually need them for algorithms (e.g. push)
-            //       and I/O in Cartesian.
-            //       Other attributes like momentum are consequently
-            //       stored in x,y,z internally.
-            positionComponents = vs{"x", "y", "z"};
-#elif defined(WARPX_DIM_3D)
-            positionComponents = vs{"x", "y", "z"};
-#else
-#   error Unknown WarpX dimensionality.
-#endif
+        std::vector< std::string > positionComponents;
+
+        int idx = 0;
+        for (auto const & comp : real_comp_names ) {
+            if (write_real_comp[idx]) {
+                if (comp == "position_x" || comp == "position_y" || comp == "position_z") {
+                    std::string const last_letter{comp.back()};
+                    positionComponents.push_back(last_letter);
+                }
+            }
+            idx++;
         }
+
         return positionComponents;
     }
 
@@ -705,16 +702,18 @@ WarpXOpenPMDPlot::DumpToFile (ParticleContainer* pc,
         doParticleSetup = is_first_flush_with_particles || is_last_flush_and_never_particles;
     }
 
+    auto const positionComponents = detail::getParticlePositionComponentLabels(write_real_comp, real_comp_names);
+
     // this setup stage also implicitly calls "makeEmpty" if needed (i.e., is_last_flush_and_never_particles)
     //   for BTD, we call this multiple times as we may resize in subsequent dumps if number of particles in the buffer > 0
     if (doParticleSetup || is_resizing_flush) {
-        SetupPos(currSpecies, NewParticleVectorSize, isBTD);
+        SetupPos(currSpecies, positionComponents, NewParticleVectorSize, isBTD);
         SetupRealProperties(pc, currSpecies, write_real_comp, real_comp_names, write_int_comp, int_comp_names,
                             NewParticleVectorSize, isBTD);
     }
 
     if (is_last_flush_to_step) {
-        SetConstParticleRecordsEDPIC(currSpecies, NewParticleVectorSize, charge, mass);
+        SetConstParticleRecordsEDPIC(currSpecies, positionComponents, NewParticleVectorSize, charge, mass);
     }
 
     // open files from all processors, in case some will not contribute below
@@ -978,6 +977,7 @@ WarpXOpenPMDPlot::SaveRealProperty (ParticleIter& pti,
 void
 WarpXOpenPMDPlot::SetupPos (
     openPMD::ParticleSpecies& currSpecies,
+    std::vector<std::string> const & positionComponents,
     const unsigned long long& np,
     bool const isBTD)
 {
@@ -986,7 +986,6 @@ WarpXOpenPMDPlot::SetupPos (
     auto realType = openPMD::Dataset(openPMD::determineDatatype<amrex::ParticleReal>(), {np}, options);
     auto idType = openPMD::Dataset(openPMD::determineDatatype< uint64_t >(), {np}, options);
 
-    auto const positionComponents = detail::getParticlePositionComponentLabels();
     for( auto const& comp : positionComponents ) {
         currSpecies["position"][comp].resetDataset( realType );
     }
@@ -998,6 +997,7 @@ WarpXOpenPMDPlot::SetupPos (
 void
 WarpXOpenPMDPlot::SetConstParticleRecordsEDPIC (
         openPMD::ParticleSpecies& currSpecies,
+        std::vector<std::string> const & positionComponents,
         const unsigned long long& np,
         amrex::ParticleReal const charge,
         amrex::ParticleReal const mass)
@@ -1006,7 +1006,6 @@ WarpXOpenPMDPlot::SetConstParticleRecordsEDPIC (
     const auto *const scalar = openPMD::RecordComponent::SCALAR;
 
     // define record shape to be number of particles
-    auto const positionComponents = detail::getParticlePositionComponentLabels(true);
     for( auto const& comp : positionComponents ) {
         currSpecies["positionOffset"][comp].resetDataset( realType );
     }
@@ -1037,16 +1036,20 @@ WarpXOpenPMDPlot::SetConstParticleRecordsEDPIC (
 #endif
 
     // meta data
-    currSpecies["position"].setUnitDimension( detail::getUnitDimension("position") );
-    currSpecies["positionOffset"].setUnitDimension( detail::getUnitDimension("positionOffset") );
+    if (!positionComponents.empty()) {
+        currSpecies["position"].setUnitDimension( detail::getUnitDimension("position") );
+        currSpecies["positionOffset"].setUnitDimension( detail::getUnitDimension("positionOffset") );
+    }
     currSpecies["charge"].setUnitDimension( detail::getUnitDimension("charge") );
     currSpecies["mass"].setUnitDimension( detail::getUnitDimension("mass") );
 
     // meta data for ED-PIC extension
-    currSpecies["position"].setAttribute( "macroWeighted", 0u );
-    currSpecies["position"].setAttribute( "weightingPower", 0.0 );
-    currSpecies["positionOffset"].setAttribute( "macroWeighted", 0u );
-    currSpecies["positionOffset"].setAttribute( "weightingPower", 0.0 );
+    if (!positionComponents.empty()) {
+        currSpecies["position"].setAttribute( "macroWeighted", 0u );
+        currSpecies["position"].setAttribute( "weightingPower", 0.0 );
+        currSpecies["positionOffset"].setAttribute( "macroWeighted", 0u );
+        currSpecies["positionOffset"].setAttribute( "weightingPower", 0.0 );
+    }
     currSpecies["id"].setAttribute( "macroWeighted", 0u );
     currSpecies["id"].setAttribute( "weightingPower", 0.0 );
     currSpecies["charge"].setAttribute( "macroWeighted", 0u );

From e848d8c51fb7bae4da6d8171b3144826da933f4b Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 7 May 2024 16:17:40 -0700
Subject: [PATCH 3/6] Clang-Tidy: Braces

---
 Source/Diagnostics/ParticleDiag/ParticleDiag.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp b/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
index 17f739dbda0..140122b5573 100644
--- a/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
+++ b/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
@@ -51,8 +51,9 @@ ParticleDiag::ParticleDiag (
                         +"' is not an existing attribute for this species");
                     m_plot_flags[existing_variable_names.at(var)] = 1;
 
-                    if (var == "x" || var == "y" || var == "z")
+                    if (var == "x" || var == "y" || var == "z") {
                         contains_positions = true;
+                    }
                 }
             }
         }

From 20758253722300a270f527f63c40a0b3d3a50b09 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 7 May 2024 18:16:25 -0700
Subject: [PATCH 4/6] Update Examples

---
 .../laser_acceleration/inputs_rz              |  4 +-
 .../uniform_plasma/inputs_3d                  |  2 +-
 Examples/Tests/Implicit/inputs_1d             |  4 +-
 .../Tests/Implicit/inputs_1d_semiimplicit     |  4 +-
 Examples/Tests/Implicit/inputs_vandb_2d       |  4 +-
 Examples/Tests/electrostatic_sphere/inputs_rz |  2 +-
 Examples/Tests/langmuir/inputs_3d             |  4 +-
 Examples/Tests/photon_pusher/inputs_3d        | 32 +++++++--------
 Examples/Tests/plasma_lens/inputs_3d          |  2 +-
 Examples/Tests/plasma_lens/inputs_boosted_3d  |  2 +-
 Examples/Tests/plasma_lens/inputs_lattice_3d  |  2 +-
 Examples/Tests/plasma_lens/inputs_short_3d    |  2 +-
 Examples/Tests/qed/breit_wheeler/inputs_2d    | 28 ++++++-------
 Examples/Tests/qed/breit_wheeler/inputs_3d    | 28 ++++++-------
 .../Tests/qed/quantum_synchrotron/inputs_2d   | 18 ++++-----
 .../Tests/qed/quantum_synchrotron/inputs_3d   | 18 ++++-----
 Regression/WarpX-tests.ini                    | 40 +++++++++----------
 17 files changed, 98 insertions(+), 98 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/inputs_rz b/Examples/Physics_applications/laser_acceleration/inputs_rz
index 7365523b574..b61ed6f83ec 100644
--- a/Examples/Physics_applications/laser_acceleration/inputs_rz
+++ b/Examples/Physics_applications/laser_acceleration/inputs_rz
@@ -89,5 +89,5 @@ diagnostics.diags_names = diag1
 diag1.intervals = 10
 diag1.diag_type = Full
 diag1.fields_to_plot = Er Et Ez Br Bt Bz jr jt jz rho
-diag1.electrons.variables = w ux uy uz orig_x orig_z
-diag1.beam.variables = w ux uy uz
+diag1.electrons.variables = x y z w ux uy uz orig_x orig_z
+diag1.beam.variables = x y z w ux uy uz
diff --git a/Examples/Physics_applications/uniform_plasma/inputs_3d b/Examples/Physics_applications/uniform_plasma/inputs_3d
index b0275f6eed6..83310088176 100644
--- a/Examples/Physics_applications/uniform_plasma/inputs_3d
+++ b/Examples/Physics_applications/uniform_plasma/inputs_3d
@@ -45,7 +45,7 @@ electrons.uz_th  = 0.01 # uth the std of the (unitless) momentum
 diagnostics.diags_names = diag1 chk
 diag1.intervals = 4
 diag1.diag_type = Full
-diag1.electrons.variables = ux uy uz w
+diag1.electrons.variables = x y z ux uy uz w
 diag1.fields_to_plot = Bx By Bz Ex Ey Ez jx jy jz rho
 
 chk.intervals = 6
diff --git a/Examples/Tests/Implicit/inputs_1d b/Examples/Tests/Implicit/inputs_1d
index 50d28a2db75..465d9dd6965 100644
--- a/Examples/Tests/Implicit/inputs_1d
+++ b/Examples/Tests/Implicit/inputs_1d
@@ -71,8 +71,8 @@ diagnostics.diags_names = diag1
 diag1.intervals = 100
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho divE
-diag1.electrons.variables = w ux uy uz
-diag1.protons.variables = w ux uy uz
+diag1.electrons.variables = z w ux uy uz
+diag1.protons.variables = z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
 particle_energy.type = ParticleEnergy
diff --git a/Examples/Tests/Implicit/inputs_1d_semiimplicit b/Examples/Tests/Implicit/inputs_1d_semiimplicit
index 2271a0bb1bc..4008a559588 100644
--- a/Examples/Tests/Implicit/inputs_1d_semiimplicit
+++ b/Examples/Tests/Implicit/inputs_1d_semiimplicit
@@ -71,8 +71,8 @@ diagnostics.diags_names = diag1
 diag1.intervals = 100
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho divE
-diag1.electrons.variables = w ux uy uz
-diag1.protons.variables = w ux uy uz
+diag1.electrons.variables = z w ux uy uz
+diag1.protons.variables = z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
 particle_energy.type = ParticleEnergy
diff --git a/Examples/Tests/Implicit/inputs_vandb_2d b/Examples/Tests/Implicit/inputs_vandb_2d
index 2dc57323efe..33ce964710a 100644
--- a/Examples/Tests/Implicit/inputs_vandb_2d
+++ b/Examples/Tests/Implicit/inputs_vandb_2d
@@ -82,8 +82,8 @@ diagnostics.diags_names = diag1
 diag1.intervals = 20
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho divE
-diag1.electrons.variables = w ux uy uz
-diag1.protons.variables = w ux uy uz
+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
 particle_energy.type = ParticleEnergy
diff --git a/Examples/Tests/electrostatic_sphere/inputs_rz b/Examples/Tests/electrostatic_sphere/inputs_rz
index 26d8b0c7afc..2b6151e6d8c 100644
--- a/Examples/Tests/electrostatic_sphere/inputs_rz
+++ b/Examples/Tests/electrostatic_sphere/inputs_rz
@@ -39,5 +39,5 @@ diag1.fields_to_plot = Er Et Ez rho
 diag2.intervals = 30
 diag2.diag_type = Full
 diag2.fields_to_plot = none
-diag2.electron.variables = ux uy uz w phi
+diag2.electron.variables = x y z ux uy uz w phi
 diag2.format = openpmd
diff --git a/Examples/Tests/langmuir/inputs_3d b/Examples/Tests/langmuir/inputs_3d
index 432b4788171..604ed9bc514 100644
--- a/Examples/Tests/langmuir/inputs_3d
+++ b/Examples/Tests/langmuir/inputs_3d
@@ -93,5 +93,5 @@ diagnostics.diags_names = diag1
 diag1.intervals = max_step
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz part_per_cell rho
-diag1.electrons.variables = w ux
-diag1.positrons.variables = uz
+diag1.electrons.variables = x y z w ux
+diag1.positrons.variables = x y z uz
diff --git a/Examples/Tests/photon_pusher/inputs_3d b/Examples/Tests/photon_pusher/inputs_3d
index e2c75981e0e..3977a187e1b 100644
--- a/Examples/Tests/photon_pusher/inputs_3d
+++ b/Examples/Tests/photon_pusher/inputs_3d
@@ -140,19 +140,19 @@ p_dn_10.single_particle_weight = 1.0
 diagnostics.diags_names = diag1
 diag1.intervals = 50
 diag1.diag_type = Full
-diag1.p_xp_1.variables = ux uy uz
-diag1.p_xn_1.variables = ux uy uz
-diag1.p_yp_1.variables = ux uy uz
-diag1.p_yn_1.variables = ux uy uz
-diag1.p_zp_1.variables = ux uy uz
-diag1.p_zn_1.variables = ux uy uz
-diag1.p_dp_1.variables = ux uy uz
-diag1.p_dn_1.variables = ux uy uz
-diag1.p_xp_10.variables = ux uy uz
-diag1.p_xn_10.variables = ux uy uz
-diag1.p_yp_10.variables = ux uy uz
-diag1.p_yn_10.variables = ux uy uz
-diag1.p_zp_10.variables = ux uy uz
-diag1.p_zn_10.variables = ux uy uz
-diag1.p_dp_10.variables = ux uy uz
-diag1.p_dn_10.variables = ux uy uz
+diag1.p_xp_1.variables = x y z ux uy uz
+diag1.p_xn_1.variables = x y z ux uy uz
+diag1.p_yp_1.variables = x y z ux uy uz
+diag1.p_yn_1.variables = x y z ux uy uz
+diag1.p_zp_1.variables = x y z ux uy uz
+diag1.p_zn_1.variables = x y z ux uy uz
+diag1.p_dp_1.variables = x y z ux uy uz
+diag1.p_dn_1.variables = x y z ux uy uz
+diag1.p_xp_10.variables = x y z ux uy uz
+diag1.p_xn_10.variables = x y z ux uy uz
+diag1.p_yp_10.variables = x y z ux uy uz
+diag1.p_yn_10.variables = x y z ux uy uz
+diag1.p_zp_10.variables = x y z ux uy uz
+diag1.p_zn_10.variables = x y z ux uy uz
+diag1.p_dp_10.variables = x y z ux uy uz
+diag1.p_dn_10.variables = x y z ux uy uz
diff --git a/Examples/Tests/plasma_lens/inputs_3d b/Examples/Tests/plasma_lens/inputs_3d
index 7763013adb1..a87c1eb7f44 100644
--- a/Examples/Tests/plasma_lens/inputs_3d
+++ b/Examples/Tests/plasma_lens/inputs_3d
@@ -48,4 +48,4 @@ particles.repeated_plasma_lens_strengths_B = 0.0 0.0 0.0 0.0
 diagnostics.diags_names = diag1
 diag1.intervals = 84
 diag1.diag_type = Full
-diag1.electrons.variables = ux uy uz
+diag1.electrons.variables = x y z ux uy uz
diff --git a/Examples/Tests/plasma_lens/inputs_boosted_3d b/Examples/Tests/plasma_lens/inputs_boosted_3d
index ecdf3b3baec..fa18ac439c4 100644
--- a/Examples/Tests/plasma_lens/inputs_boosted_3d
+++ b/Examples/Tests/plasma_lens/inputs_boosted_3d
@@ -50,4 +50,4 @@ particles.repeated_plasma_lens_strengths_B = 0.0 0.0 0.0 0.0
 diagnostics.diags_names = diag1
 diag1.intervals = 84
 diag1.diag_type = Full
-diag1.electrons.variables = ux uy uz
+diag1.electrons.variables = x y z ux uy uz
diff --git a/Examples/Tests/plasma_lens/inputs_lattice_3d b/Examples/Tests/plasma_lens/inputs_lattice_3d
index a41ca8baee9..94e57de8290 100644
--- a/Examples/Tests/plasma_lens/inputs_lattice_3d
+++ b/Examples/Tests/plasma_lens/inputs_lattice_3d
@@ -70,4 +70,4 @@ plasmalens4.dEdx = 200000.
 diagnostics.diags_names = diag1
 diag1.intervals = 84
 diag1.diag_type = Full
-diag1.electrons.variables = ux uy uz
+diag1.electrons.variables = x y z ux uy uz
diff --git a/Examples/Tests/plasma_lens/inputs_short_3d b/Examples/Tests/plasma_lens/inputs_short_3d
index 8fa111df3c9..5c91ab26498 100644
--- a/Examples/Tests/plasma_lens/inputs_short_3d
+++ b/Examples/Tests/plasma_lens/inputs_short_3d
@@ -52,4 +52,4 @@ particles.repeated_plasma_lens_strengths_B = 0.0 0.0 0.0 0.0
 diagnostics.diags_names = diag1
 diag1.intervals = 1 #84
 diag1.diag_type = Full
-diag1.electrons.variables = ux uy uz
+diag1.electrons.variables = x y z ux uy uz
diff --git a/Examples/Tests/qed/breit_wheeler/inputs_2d b/Examples/Tests/qed/breit_wheeler/inputs_2d
index 7f507dd08d7..857b3243ac6 100644
--- a/Examples/Tests/qed/breit_wheeler/inputs_2d
+++ b/Examples/Tests/qed/breit_wheeler/inputs_2d
@@ -201,19 +201,19 @@ diagnostics.diags_names = diag1
 diag1.intervals = 2
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex
-diag1.p1.variables = ux uy uz w opticalDepthBW
-diag1.p2.variables = ux uy uz w opticalDepthBW
-diag1.p3.variables = ux uy uz w opticalDepthBW
-diag1.p4.variables = ux uy uz w opticalDepthBW
-
-diag1.ele1.variables = ux uy uz w opticalDepthQSR
-diag1.ele2.variables = ux uy uz w opticalDepthQSR
-diag1.ele3.variables = ux uy uz w opticalDepthQSR
-diag1.ele4.variables = ux uy uz w opticalDepthQSR
-
-diag1.pos1.variables = ux uy uz w opticalDepthQSR
-diag1.pos2.variables = ux uy uz w opticalDepthQSR
-diag1.pos3.variables = ux uy uz w opticalDepthQSR
-diag1.pos4.variables = ux uy uz w opticalDepthQSR
+diag1.p1.variables = x z ux uy uz w opticalDepthBW
+diag1.p2.variables = x z ux uy uz w opticalDepthBW
+diag1.p3.variables = x z ux uy uz w opticalDepthBW
+diag1.p4.variables = x z ux uy uz w opticalDepthBW
+
+diag1.ele1.variables = x z ux uy uz w opticalDepthQSR
+diag1.ele2.variables = x z ux uy uz w opticalDepthQSR
+diag1.ele3.variables = x z ux uy uz w opticalDepthQSR
+diag1.ele4.variables = x z ux uy uz w opticalDepthQSR
+
+diag1.pos1.variables = x z ux uy uz w opticalDepthQSR
+diag1.pos2.variables = x z ux uy uz w opticalDepthQSR
+diag1.pos3.variables = x z ux uy uz w opticalDepthQSR
+diag1.pos4.variables = x z ux uy uz w opticalDepthQSR
 
 diag1.format = plotfile
diff --git a/Examples/Tests/qed/breit_wheeler/inputs_3d b/Examples/Tests/qed/breit_wheeler/inputs_3d
index 2749a60b888..b79dfd9c030 100644
--- a/Examples/Tests/qed/breit_wheeler/inputs_3d
+++ b/Examples/Tests/qed/breit_wheeler/inputs_3d
@@ -201,19 +201,19 @@ diagnostics.diags_names = diag1
 diag1.intervals = 2
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex
-diag1.p1.variables = ux uy uz w opticalDepthBW
-diag1.p2.variables = ux uy uz w opticalDepthBW
-diag1.p3.variables = ux uy uz w opticalDepthBW
-diag1.p4.variables = ux uy uz w opticalDepthBW
-
-diag1.ele1.variables = ux uy uz w opticalDepthQSR
-diag1.ele2.variables = ux uy uz w opticalDepthQSR
-diag1.ele3.variables = ux uy uz w opticalDepthQSR
-diag1.ele4.variables = ux uy uz w opticalDepthQSR
-
-diag1.pos1.variables = ux uy uz w opticalDepthQSR
-diag1.pos2.variables = ux uy uz w opticalDepthQSR
-diag1.pos3.variables = ux uy uz w opticalDepthQSR
-diag1.pos4.variables = ux uy uz w opticalDepthQSR
+diag1.p1.variables = x y z ux uy uz w opticalDepthBW
+diag1.p2.variables = x y z ux uy uz w opticalDepthBW
+diag1.p3.variables = x y z ux uy uz w opticalDepthBW
+diag1.p4.variables = x y z ux uy uz w opticalDepthBW
+
+diag1.ele1.variables = x y z ux uy uz w opticalDepthQSR
+diag1.ele2.variables = x y z ux uy uz w opticalDepthQSR
+diag1.ele3.variables = x y z ux uy uz w opticalDepthQSR
+diag1.ele4.variables = x y z ux uy uz w opticalDepthQSR
+
+diag1.pos1.variables = x y z ux uy uz w opticalDepthQSR
+diag1.pos2.variables = x y z ux uy uz w opticalDepthQSR
+diag1.pos3.variables = x y z ux uy uz w opticalDepthQSR
+diag1.pos4.variables = x y z ux uy uz w opticalDepthQSR
 
 diag1.format = plotfile
diff --git a/Examples/Tests/qed/quantum_synchrotron/inputs_2d b/Examples/Tests/qed/quantum_synchrotron/inputs_2d
index 2fc00231280..2ac2c782ccd 100644
--- a/Examples/Tests/qed/quantum_synchrotron/inputs_2d
+++ b/Examples/Tests/qed/quantum_synchrotron/inputs_2d
@@ -178,12 +178,12 @@ diagnostics.diags_names = diag1
 diag1.intervals = 2
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex
-diag1.p1.variables = ux uy uz w opticalDepthQSR
-diag1.p2.variables = ux uy uz w opticalDepthQSR
-diag1.p3.variables = ux uy uz w opticalDepthQSR
-diag1.p4.variables = ux uy uz w opticalDepthQSR
-
-diag1.qsp_1.variables = ux uy uz w opticalDepthBW
-diag1.qsp_2.variables = ux uy uz w opticalDepthBW
-diag1.qsp_3.variables = ux uy uz w opticalDepthBW
-diag1.qsp_4.variables = ux uy uz w opticalDepthBW
+diag1.p1.variables = x z ux uy uz w opticalDepthQSR
+diag1.p2.variables = x z ux uy uz w opticalDepthQSR
+diag1.p3.variables = x z ux uy uz w opticalDepthQSR
+diag1.p4.variables = x z ux uy uz w opticalDepthQSR
+
+diag1.qsp_1.variables = x z ux uy uz w opticalDepthBW
+diag1.qsp_2.variables = x z ux uy uz w opticalDepthBW
+diag1.qsp_3.variables = x z ux uy uz w opticalDepthBW
+diag1.qsp_4.variables = x z ux uy uz w opticalDepthBW
diff --git a/Examples/Tests/qed/quantum_synchrotron/inputs_3d b/Examples/Tests/qed/quantum_synchrotron/inputs_3d
index 9bc963f7e94..429666ef938 100644
--- a/Examples/Tests/qed/quantum_synchrotron/inputs_3d
+++ b/Examples/Tests/qed/quantum_synchrotron/inputs_3d
@@ -178,12 +178,12 @@ diagnostics.diags_names = diag1
 diag1.intervals = 2
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex
-diag1.p1.variables = ux uy uz w opticalDepthQSR
-diag1.p2.variables = ux uy uz w opticalDepthQSR
-diag1.p3.variables = ux uy uz w opticalDepthQSR
-diag1.p4.variables = ux uy uz w opticalDepthQSR
-
-diag1.qsp_1.variables = ux uy uz w opticalDepthBW
-diag1.qsp_2.variables = ux uy uz w opticalDepthBW
-diag1.qsp_3.variables = ux uy uz w opticalDepthBW
-diag1.qsp_4.variables = ux uy uz w opticalDepthBW
+diag1.p1.variables = x y z ux uy uz w opticalDepthQSR
+diag1.p2.variables = x y z ux uy uz w opticalDepthQSR
+diag1.p3.variables = x y z ux uy uz w opticalDepthQSR
+diag1.p4.variables = x y z ux uy uz w opticalDepthQSR
+
+diag1.qsp_1.variables = x y z ux uy uz w opticalDepthBW
+diag1.qsp_2.variables = x y z ux uy uz w opticalDepthBW
+diag1.qsp_3.variables = x y z ux uy uz w opticalDepthBW
+diag1.qsp_4.variables = x y z ux uy uz w opticalDepthBW
diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index f8859ef7df5..861a1325c1b 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -554,7 +554,7 @@ analysisRoutine = Examples/Tests/electrostatic_sphere_eb/analysis_rz.py
 [ElectrostaticSphereLabFrame]
 buildDir = .
 inputFile = Examples/Tests/electrostatic_sphere/inputs_3d
-runtime_params = warpx.do_electrostatic=labframe diag2.electron.variables=ux uy uz w phi
+runtime_params = warpx.do_electrostatic=labframe diag2.electron.variables=x y z ux uy uz w phi
 dim = 3
 addToCompileString =
 cmakeSetupOpts = -DWarpX_DIMS=3
@@ -1189,7 +1189,7 @@ analysisOutputImage = langmuir_fluid_multi_analysis.png
 [Langmuir_multi_1d]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_1d
-runtime_params = algo.current_deposition=esirkepov diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz
+runtime_params = algo.current_deposition=esirkepov diag1.electrons.variables=z w ux uy uz diag1.positrons.variables=z w ux uy uz
 dim = 1
 addToCompileString = USE_OPENPMD=TRUE QED=FALSE
 cmakeSetupOpts = -DWarpX_DIMS=1 -DWarpX_OPENPMD=ON -DWarpX_QED=OFF
@@ -1208,7 +1208,7 @@ analysisOutputImage = langmuir_multi_1d_analysis.png
 [Langmuir_multi_2d_MR]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver = ckc  warpx.use_filter = 1  amr.max_level = 1  amr.ref_ratio = 4  warpx.fine_tag_lo = -10.e-6 -10.e-6  warpx.fine_tag_hi = 10.e-6 10.e-6  diag1.electrons.variables = w ux uy uz  diag1.positrons.variables = w ux uy uz
+runtime_params = algo.maxwell_solver = ckc  warpx.use_filter = 1  amr.max_level = 1  amr.ref_ratio = 4  warpx.fine_tag_lo = -10.e-6 -10.e-6  warpx.fine_tag_hi = 10.e-6 10.e-6  diag1.electrons.variables = x z w ux uy uz  diag1.positrons.variables = x z w ux uy uz
 dim = 2
 addToCompileString =
 cmakeSetupOpts = -DWarpX_DIMS=2
@@ -1227,7 +1227,7 @@ analysisOutputImage = Langmuir_multi_2d_MR.png
 [Langmuir_multi_2d_MR_anisotropic]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver = ckc  warpx.use_filter = 1  amr.max_level = 1 amr.ref_ratio_vect = 4 2 warpx.fine_tag_lo = -10.e-6 -10.e-6  warpx.fine_tag_hi = 10.e-6 10.e-6  diag1.electrons.variables = w ux uy uz  diag1.positrons.variables = w ux uy uz
+runtime_params = algo.maxwell_solver = ckc  warpx.use_filter = 1  amr.max_level = 1 amr.ref_ratio_vect = 4 2 warpx.fine_tag_lo = -10.e-6 -10.e-6  warpx.fine_tag_hi = 10.e-6 10.e-6  diag1.electrons.variables = x z w ux uy uz  diag1.positrons.variables = x z w ux uy uz
 dim = 2
 addToCompileString =
 cmakeSetupOpts = -DWarpX_DIMS=2
@@ -1246,7 +1246,7 @@ analysisOutputImage = Langmuir_multi_2d_MR.png
 [Langmuir_multi_2d_MR_momentum_conserving]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=ckc warpx.use_filter=1 amr.max_level=1 amr.ref_ratio=4 warpx.fine_tag_lo=-10.e-6 -10.e-6 warpx.fine_tag_hi=10.e-6 10.e-6 algo.field_gathering=momentum-conserving diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz
+runtime_params = algo.maxwell_solver=ckc warpx.use_filter=1 amr.max_level=1 amr.ref_ratio=4 warpx.fine_tag_lo=-10.e-6 -10.e-6 warpx.fine_tag_hi=10.e-6 10.e-6 algo.field_gathering=momentum-conserving diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz
 dim = 2
 addToCompileString =
 cmakeSetupOpts = -DWarpX_DIMS=2
@@ -1265,7 +1265,7 @@ analysisOutputImage = Langmuir_multi_2d_MR_momentum_conserving.png
 [Langmuir_multi_2d_MR_psatd]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver = psatd  warpx.use_filter = 1  amr.max_level = 1  amr.ref_ratio = 4  warpx.fine_tag_lo = -10.e-6 -10.e-6  warpx.fine_tag_hi = 10.e-6 10.e-6  diag1.electrons.variables = w ux uy uz  diag1.positrons.variables = w ux uy uz psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
+runtime_params = algo.maxwell_solver = psatd  warpx.use_filter = 1  amr.max_level = 1  amr.ref_ratio = 4  warpx.fine_tag_lo = -10.e-6 -10.e-6  warpx.fine_tag_hi = 10.e-6 10.e-6  diag1.electrons.variables = x z w ux uy uz  diag1.positrons.variables = x z w ux uy uz psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1284,7 +1284,7 @@ analysisOutputImage = Langmuir_multi_2d_MR_psatd.png
 [Langmuir_multi_2d_nodal]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = warpx.grid_type=collocated algo.current_deposition=direct diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz
+runtime_params = warpx.grid_type=collocated algo.current_deposition=direct diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz
 dim = 2
 addToCompileString =
 cmakeSetupOpts = -DWarpX_DIMS=2
@@ -1303,7 +1303,7 @@ analysisOutputImage = langmuir_multi_2d_analysis.png
 [Langmuir_multi_2d_psatd]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=psatd diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz diag1.fields_to_plot=Ex Ey Ez jx jy jz part_per_cell warpx.cfl = 0.7071067811865475 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
+runtime_params = algo.maxwell_solver=psatd diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz diag1.fields_to_plot=Ex Ey Ez jx jy jz part_per_cell warpx.cfl = 0.7071067811865475 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1322,7 +1322,7 @@ analysisOutputImage = langmuir_multi_2d_analysis.png
 [Langmuir_multi_2d_psatd_current_correction]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 algo.current_deposition=esirkepov psatd.periodic_single_box_fft=1 psatd.current_correction=1 diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz diag1.fields_to_plot =Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475
+runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 algo.current_deposition=esirkepov psatd.periodic_single_box_fft=1 psatd.current_correction=1 diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz diag1.fields_to_plot =Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1341,7 +1341,7 @@ analysisOutputImage = langmuir_multi_2d_analysis.png
 [Langmuir_multi_2d_psatd_current_correction_nodal]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 algo.current_deposition=direct psatd.periodic_single_box_fft=1 psatd.current_correction=1 warpx.grid_type=collocated diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz diag1.fields_to_plot =Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475
+runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 algo.current_deposition=direct psatd.periodic_single_box_fft=1 psatd.current_correction=1 warpx.grid_type=collocated diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz diag1.fields_to_plot =Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1360,7 +1360,7 @@ analysisOutputImage = langmuir_multi_2d_analysis.png
 [Langmuir_multi_2d_psatd_momentum_conserving]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=psatd algo.field_gathering=momentum-conserving diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz diag1.fields_to_plot=Ex Ey Ez jx jy jz part_per_cell warpx.cfl = 0.7071067811865475 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
+runtime_params = algo.maxwell_solver=psatd algo.field_gathering=momentum-conserving diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz diag1.fields_to_plot=Ex Ey Ez jx jy jz part_per_cell warpx.cfl = 0.7071067811865475 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1417,7 +1417,7 @@ analysisOutputImage = Langmuir_multi_2d_psatd_multiJ_nodal.png
 [Langmuir_multi_2d_psatd_nodal]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=psatd warpx.grid_type=collocated algo.current_deposition=direct diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz diag1.fields_to_plot=Ex Ey Ez jx jy jz part_per_cell warpx.cfl = 0.7071067811865475 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
+runtime_params = algo.maxwell_solver=psatd warpx.grid_type=collocated algo.current_deposition=direct diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz diag1.fields_to_plot=Ex Ey Ez jx jy jz part_per_cell warpx.cfl = 0.7071067811865475 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1436,7 +1436,7 @@ analysisOutputImage = langmuir_multi_2d_analysis.png
 [Langmuir_multi_2d_psatd_Vay_deposition]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 algo.current_deposition=vay diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz diag1.fields_to_plot = Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475
+runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 algo.current_deposition=vay diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz diag1.fields_to_plot = Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1455,7 +1455,7 @@ analysisOutputImage = langmuir_multi_2d_analysis.png
 [Langmuir_multi_2d_psatd_Vay_deposition_particle_shape_4]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 algo.current_deposition=vay diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz diag1.fields_to_plot = Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475 algo.particle_shape=4
+runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 algo.current_deposition=vay diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz diag1.fields_to_plot = Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475 algo.particle_shape=4
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1474,7 +1474,7 @@ analysisOutputImage = langmuir_multi_2d_analysis.png
 [Langmuir_multi_2d_psatd_Vay_deposition_nodal]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_2d
-runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 warpx.grid_type=collocated algo.current_deposition=vay diag1.electrons.variables=w ux uy uz diag1.positrons.variables=w ux uy uz diag1.fields_to_plot = Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475
+runtime_params = algo.maxwell_solver=psatd amr.max_grid_size=128 warpx.grid_type=collocated algo.current_deposition=vay diag1.electrons.variables=x z w ux uy uz diag1.positrons.variables=x z w ux uy uz diag1.fields_to_plot = Ex Ey Ez jx jy jz part_per_cell rho divE warpx.cfl = 0.7071067811865475
 dim = 2
 addToCompileString = USE_PSATD=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
@@ -1492,7 +1492,7 @@ analysisOutputImage = langmuir_multi_2d_analysis.png
 
 [Langmuir_multi_nodal]
 buildDir = .
-inputFile = Examples/Tests/langmuir/inputs_3d
+inputFile =
 runtime_params = warpx.grid_type=collocated algo.current_deposition=direct
 dim = 3
 addToCompileString =
@@ -1721,7 +1721,7 @@ analysisOutputImage = langmuir_multi_analysis.png
 [Langmuir_multi_rz]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_rz
-runtime_params = diag1.electrons.variables=w ux uy uz diag1.ions.variables=w ux uy uz diag1.dump_rz_modes=0
+runtime_params = diag1.electrons.variables=x y z w ux uy uz diag1.ions.variables=x y z w ux uy uz diag1.dump_rz_modes=0
 dim = 2
 addToCompileString = USE_RZ=TRUE
 cmakeSetupOpts = -DWarpX_DIMS=RZ
@@ -1741,7 +1741,7 @@ aux1File = Regression/PostProcessingUtils/post_processing_utils.py
 [Langmuir_multi_rz_psatd]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_rz
-runtime_params = algo.maxwell_solver=psatd diag1.electrons.variables=w ux uy uz diag1.ions.variables=w ux uy uz diag1.dump_rz_modes=0 algo.current_deposition=direct warpx.do_dive_cleaning=0 psatd.update_with_rho=1 electrons.random_theta=0 ions.random_theta=0 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
+runtime_params = algo.maxwell_solver=psatd diag1.electrons.variables=x y z w ux uy uz diag1.ions.variables=x y z w ux uy uz diag1.dump_rz_modes=0 algo.current_deposition=direct warpx.do_dive_cleaning=0 psatd.update_with_rho=1 electrons.random_theta=0 ions.random_theta=0 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium
 dim = 2
 addToCompileString = USE_RZ=TRUE USE_PSATD=TRUE BLAS_LIB=-lblas LAPACK_LIB=-llapack
 cmakeSetupOpts = -DWarpX_DIMS=RZ -DWarpX_PSATD=ON
@@ -1761,7 +1761,7 @@ aux1File = Regression/PostProcessingUtils/post_processing_utils.py
 [Langmuir_multi_rz_psatd_current_correction]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_rz
-runtime_params = algo.maxwell_solver=psatd diag1.electrons.variables=w ux uy uz diag1.ions.variables=w ux uy uz diag1.dump_rz_modes=0 algo.current_deposition=direct warpx.do_dive_cleaning=0 amr.max_grid_size=128 psatd.periodic_single_box_fft=1 psatd.current_correction=1 diag1.fields_to_plot=jr jz Er Ez Bt rho divE electrons.random_theta=0 ions.random_theta=0
+runtime_params = algo.maxwell_solver=psatd diag1.electrons.variables=x y z w ux uy uz diag1.ions.variables=x y z w ux uy uz diag1.dump_rz_modes=0 algo.current_deposition=direct warpx.do_dive_cleaning=0 amr.max_grid_size=128 psatd.periodic_single_box_fft=1 psatd.current_correction=1 diag1.fields_to_plot=jr jz Er Ez Bt rho divE electrons.random_theta=0 ions.random_theta=0
 dim = 2
 addToCompileString = USE_RZ=TRUE USE_PSATD=TRUE BLAS_LIB=-lblas LAPACK_LIB=-llapack
 cmakeSetupOpts = -DWarpX_DIMS=RZ -DWarpX_PSATD=ON
@@ -1781,7 +1781,7 @@ aux1File = Regression/PostProcessingUtils/post_processing_utils.py
 [Langmuir_multi_rz_psatd_multiJ]
 buildDir = .
 inputFile = Examples/Tests/langmuir/inputs_rz
-runtime_params = amr.max_grid_size=32 algo.maxwell_solver=psatd diag1.electrons.variables=w ux uy uz diag1.ions.variables=w ux uy uz diag1.dump_rz_modes=0 algo.current_deposition=direct warpx.do_dive_cleaning=0 psatd.update_with_rho=1 warpx.n_rz_azimuthal_modes=2 electrons.random_theta=0 electrons.num_particles_per_cell_each_dim=2 4 2 ions.random_theta=0 ions.num_particles_per_cell_each_dim=2 4 2 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium warpx.do_multi_J=1 warpx.do_multi_J_n_depositions=4 warpx.use_filter=1
+runtime_params = amr.max_grid_size=32 algo.maxwell_solver=psatd diag1.electrons.variables=x y z w ux uy uz diag1.ions.variables=x y z w ux uy uz diag1.dump_rz_modes=0 algo.current_deposition=direct warpx.do_dive_cleaning=0 psatd.update_with_rho=1 warpx.n_rz_azimuthal_modes=2 electrons.random_theta=0 electrons.num_particles_per_cell_each_dim=2 4 2 ions.random_theta=0 ions.num_particles_per_cell_each_dim=2 4 2 psatd.current_correction=0 warpx.abort_on_warning_threshold=medium warpx.do_multi_J=1 warpx.do_multi_J_n_depositions=4 warpx.use_filter=1
 dim = 2
 addToCompileString = USE_RZ=TRUE USE_PSATD=TRUE BLAS_LIB=-lblas LAPACK_LIB=-llapack
 cmakeSetupOpts = -DWarpX_DIMS=RZ -DWarpX_PSATD=ON

From c734171d65468b7ff06bafb6ebfa8e9804c88de7 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 7 May 2024 21:54:16 -0700
Subject: [PATCH 5/6] RZ: x,y,z

---
 Source/Diagnostics/ParticleDiag/ParticleDiag.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp b/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
index 140122b5573..1a64ae20f0e 100644
--- a/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
+++ b/Source/Diagnostics/ParticleDiag/ParticleDiag.cpp
@@ -36,7 +36,11 @@ ParticleDiag::ParticleDiag (
         std::fill(m_plot_flags.begin(), m_plot_flags.end(), 0);
         bool contains_positions = false;
         if (variables[0] != "none"){
-            const std::map<std::string, int> existing_variable_names = pc->getParticleComps();
+            std::map<std::string, int> existing_variable_names = pc->getParticleComps();
+#ifdef WARPX_DIM_RZ
+            // we reconstruct to Cartesian x,y,z for RZ particle output
+            existing_variable_names["y"] = PIdx::theta;
+#endif
             for (const auto& var : variables){
                 if (var == "phi") {
                     // User requests phi on particle. This is *not* part of the variables that

From b670db87303f771486f64678b58f85f44cb881d3 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Thu, 9 May 2024 00:45:37 -0700
Subject: [PATCH 6/6] Fix: openPMD Low-D position/positionOffset

Continue to write defaults for coarse and fine
position of omitted dimensions to zero.
---
 Source/Diagnostics/WarpXOpenPMD.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/Source/Diagnostics/WarpXOpenPMD.cpp b/Source/Diagnostics/WarpXOpenPMD.cpp
index 848b6818865..45d5dc1cdee 100644
--- a/Source/Diagnostics/WarpXOpenPMD.cpp
+++ b/Source/Diagnostics/WarpXOpenPMD.cpp
@@ -1014,9 +1014,12 @@ WarpXOpenPMDPlot::SetConstParticleRecordsEDPIC (
 #if defined(WARPX_DIM_1D_Z)
     currSpecies["position"]["x"].resetDataset( realType );
     currSpecies["position"]["y"].resetDataset( realType );
+    currSpecies["positionOffset"]["x"].resetDataset( realType );
+    currSpecies["positionOffset"]["y"].resetDataset( realType );
 #endif
 #if defined(WARPX_DIM_XZ)
     currSpecies["position"]["y"].resetDataset( realType );
+    currSpecies["positionOffset"]["y"].resetDataset( realType );
 #endif
 
     // make constant
@@ -1030,9 +1033,12 @@ WarpXOpenPMDPlot::SetConstParticleRecordsEDPIC (
 #if defined(WARPX_DIM_1D_Z)
     currSpecies["position"]["x"].makeConstant( 0._prt );
     currSpecies["position"]["y"].makeConstant( 0._prt );
+    currSpecies["positionOffset"]["x"].makeConstant( 0._prt );
+    currSpecies["positionOffset"]["y"].makeConstant( 0._prt );
 #endif
 #if defined(WARPX_DIM_XZ)
     currSpecies["position"]["y"].makeConstant( 0._prt );
+    currSpecies["positionOffset"]["y"].makeConstant( 0._prt );
 #endif
 
     // meta data