Diagnostics: Fix Position Selection (#4914)

* Diagnostics: Warn w/o Positions

If a user specifies `<diag_name>.<species_name>.variables`
without including particle position arguments we now warn.

* openPMD: Skip 0-positions for deselected comps

* Clang-Tidy: Braces

* Update Examples

* RZ: x,y,z

* Fix: openPMD Low-D position/positionOffset

Continue to write defaults for coarse and fine
position of omitted dimensions to zero.

Author: ax3l

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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