Merge upstream with added cleanup (#52)

* CI: Add Missing Python Analysis for EB Test (ECP-WarpX#2147)

* CI: Add Missing Python Analysis for EB Test

* Use 1 MPI Process for Azure

* a few _rt (ECP-WarpX#2146)

* PSATD: div Cleaning Implemented only with psatd.J_linear_in_time=1 (ECP-WarpX#2142)

* BTD: Don't Flush If Written (ECP-WarpX#2148)

Written BTD buffers for lab snapshot data are reset to zero size
(count). When we do the final write of all partly filled buffers
in `FilterComputePackFlushLastTimestep`, we should not write such
already completed backtransformed lab snapshots again.

* openPMD: `groupBased` Option Missing (ECP-WarpX#2149)

The `groupBased` iteration encoding (input: `g`) was not parsed.

* Remove predefined constants from example input files (ECP-WarpX#2153)

* BTD_ReducedSliceDiag: BTD Plotfiles (ECP-WarpX#2152)

By accident, the 2nd test did not use plotfile output.

* Allow extra particle attributes (besides ux, uy, uz and w) to be set at particle creation in AddNParticles() (ECP-WarpX#2115)

* exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index

* added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation

* added function to get index of a particle component given the PID name

* changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id

* changed warpx_addRealComp to accept a species name as input and only add the new component for that species

* added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime

* changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index

* updated test according to PR ECP-WarpX#2119 changes

* removed unneeded BL_ASSERT(nattr == 1) statement

* fixed bug in add_particles to correctly determine the number of extra attributes

* fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species

* use isinstance(attr, ndarray) rather than type(attr) is np.ndarray

* generalize_runtime_comps_io

* fix OpenPMD

* fix OpenPMD

* fix plot flags in WritePlotFile

* fix offset and comment

* changed extra pid test to not use an underscore in the pid name

* switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays

* License update in test file

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* fix typo

* added a test with unique_particles=False

* Apply suggestions from code review

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* updated docstring and comments

Co-authored-by: atmyers <atmyers2@gmail.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Add predefined density profile to parameters documentation (ECP-WarpX#2155)

* Release 21.08 (ECP-WarpX#2158)

* AMReX/PICSAR: 21.08
* WarpX: 21.08

* initialize guard cells for macroscopic properties (ECP-WarpX#2159)

* openPMD: Style Cleaning (Dec/Def) (ECP-WarpX#2160)

In our code base, definitions and declarations of functions need a
space after their name. This makes them easy to search for.

Ref.:
  https://warpx.readthedocs.io/en/21.08/developers/contributing.html#style-and-conventions

* openPMD: Use Steps if != BTD (ECP-WarpX#2157)

* openPMD: Use Steps if != BTD

For all but back-transformed diagnostics, we can use efficient,
temporally sequentially increasing writes to iteration numbers
for iterations.

This allows us to give a guarantee to HPC I/O libraries on how
to arrange data, e.g., we can use ADIOS2 BeginStep() and
EndStep().

This enables paths to:
- streaming workflows, such as ADIOS2 SST or SSC, where we stage data
  over the network instead of using files
  https://openpmd-api.readthedocs.io/en/0.14.0/usage/streaming.html

This mitigates:
- host-side memory aggregation for ADIOS2 with openPMD `groupBased`
  iteration encoding
  https://openpmd-api.readthedocs.io/en/0.14.0/backends/adios2.html#memory-usage

* openPMD: Open Iterations Explicitly

Explicitly open iterations. Usually, file-open operations are delayed
until the first load/storeChunk operation is flush-ed. In parallel
contexts where we might want to do only particle writes from a few
ranks but no field wries in the future, this will avoid that we run
into hangs from the non-collective nature of the first flush.

The Streaming API (i.e., Series::writeIterations()) will call this
method implicitly as well, but back-transformed diags (particles)
might still need this.

* openPMD: 0.13.0+

Needed for streaming API and collective open.

* openPMD: Missing Include (ECP-WarpX#2162)

Fix compile issue on Conda-Forge (Windows with Clang).

* PEC Analysis: Remove Unused Imports (ECP-WarpX#2165)

Fix a LGTM warning on unused imports in our PEC analysis scripts.

* BinaryCollision: use more general particle data structure (ECP-WarpX#2137)

* Added B field to plasma lens (ECP-WarpX#2163)

* Added B field to plasma lens

* Fix B field and updated CI test to include the B field

* Updated benchmark

* Fixed bug where specifying write_dir for particle diagnostic did not work (ECP-WarpX#2167)

* Add particle weight as an explicit argument for _libwarpx.py::add_particles() (ECP-WarpX#2161)

* added particle weight as an explicit argument for _libwarpx.py::add_particles()

* changes requested during code review

* RZ PSATD: Time Averaging for Multi-J Algorithm (ECP-WarpX#2141)

* RZ PSATD: Time Averaging for Multi-J Algorithm

* Fix Wrong Signs in Bm

* Use Time Averaging in CI Test, Update Benchmark

* Minor Fix

* Shift parsing of physical/mathematical constants from hard-coding to table lookup (ECP-WarpX#2128)

* Shift parsing of physical/mathematical constants from hard-coding to table lookup
* Make constants map local and static for now, until there's a reason for it to be accessible/modifiable
* Accept rewording
* Accept rewording

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Moved some routines to .cpp file (ECP-WarpX#2168)

* In add_particles, used None for input parameter values (ECP-WarpX#2169)

* More cleanup of particle boundaries (ECP-WarpX#2171)

* Moved some routines to .cpp file

* Moved more stuff to a header file

* make parameter less prone to numerical issues in single precision (ECP-WarpX#2173)

* ES Solver: Fix SP Build (ECP-WarpX#2174)

Fix HIP:
```
/home/runner/work/WarpX/WarpX/Source/FieldSolver/ElectrostaticSolver.cpp:434:9: error: non-constant-expression cannot be narrowed from type 'double' to 'float' in initializer list [-Wc++11-narrowing]
        1.-beta[0]*beta[0], 1.-beta[1]*beta[1], 1.-beta[2]*beta[2])});
        ^~~~~~~~~~~~~~~~~~
/home/runner/work/WarpX/WarpX/build_sp/_deps/fetchedamrex-src/Src/Base/AMReX_SPACE.H:151:31: note: expanded from macro 'AMREX_D_DECL'
                              ^
/home/runner/work/WarpX/WarpX/Source/FieldSolver/ElectrostaticSolver.cpp:434:9: note: insert an explicit cast to silence this issue
        1.-beta[0]*beta[0], 1.-beta[1]*beta[1], 1.-beta[2]*beta[2])});
        ^~~~~~~~~~~~~~~~~~
```

* EB: RZ Warnings (ECP-WarpX#2176)

Not an implementation yet, just adding aborts and silencing warnings.

* fix typo (ECP-WarpX#2175)

* Fix: Performance Tests (Boundary) (ECP-WarpX#2178)

The performance tests were aborting since we changed the boundary
condition inputs last month. This fixes it.

* CI: Cover Performance Tests (ECP-WarpX#2179)

* CI: Cover Performance Tests

Make sure their syntax stays up-to-date.

* Performance Test in CI: Fake Output

Add "fake" output so we do not have unused variables when the tests
are run.

* reverted (or fixed) various unneccesary changes between ME fork and upstream/development

Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: MaxThevenet <maxence.thevenet@desy.de>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
Co-authored-by: atmyers <atmyers2@gmail.com>
Co-authored-by: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: David Grote <grote1@llnl.gov>
Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com>
Co-authored-by: Phil Miller <unmobile+gh@gmail.com>
Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr>

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.15.0)
-project(WarpX VERSION 21.07)
+project(WarpX VERSION 21.08)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 
@@ -57,7 +57,7 @@ option(WarpX_MPI           "Multi-node support (message-passing)"       ON)
 option(WarpX_OPENPMD       "openPMD I/O (HDF5, ADIOS)"                  OFF)
 option(WarpX_PSATD         "spectral solver support"                    OFF)
 option(WarpX_QED           "QED support (requires PICSAR)"                    ON)
-option(WarpX_QED_TABLE_GEN "QED table generation (requires PICSAR and Boost)"   OFF)
+option(WarpX_QED_TABLE_GEN "QED table generation (requires PICSAR and Boost)" OFF)
 # TODO: sensei, legacy hdf5?
 
 set(WarpX_DIMS_VALUES 2 3 RZ)

Docs/source/conf.py

@@ -66,9 +66,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'21.07'
+version = u'21.08'
 # The full version, including alpha/beta/rc tags.
-release = u'21.07'
+release = u'21.08'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/source/developers/gnumake/openpmd.rst

@@ -9,7 +9,7 @@ therefore we recommend to use `spack <https://
 spack.io>`__ in order to facilitate the installation.
 
 More specifically, we recommend that you try installing the
-`openPMD-api library 0.12.0a or newer <https://openpmd-api.readthedocs.io/en/0.12.0-alpha/>`_
+`openPMD-api library 0.13.0 or newer <https://openpmd-api.readthedocs.io/en/0.13.0/>`_
 using spack (first section below). If this fails, a back-up solution
 is to install parallel HDF5 with spack, and then install the openPMD-api
 library from source.

Docs/source/install/dependencies.rst

@@ -20,7 +20,7 @@ Optional dependencies include:
 - `FFTW3 <http://www.fftw.org>`_: for spectral solver (PSATD) support
 - `BLAS++ <https://bitbucket.org/icl/blaspp>`_ and `LAPACK++ <https://bitbucket.org/icl/lapackpp>`_: for spectral solver (PSATD) support in RZ geometry
 - `Boost 1.66.0+ <https://www.boost.org/>`__: for QED lookup tables generation support
-- `openPMD-api 0.12.0+ <https://github.com/openPMD/openPMD-api>`__: we automatically download and compile a copy of openPMD-api for openPMD I/O support
+- `openPMD-api 0.13.0+ <https://github.com/openPMD/openPMD-api>`__: we automatically download and compile a copy of openPMD-api for openPMD I/O support
 
   - see `optional I/O backends <https://github.com/openPMD/openPMD-api#dependencies>`__
 - `CCache <https://ccache.dev>`__: to speed up rebuilds (needs 3.7.9+ for CUDA)

Docs/source/usage/parameters.rst

@@ -604,6 +604,10 @@ Particle initialization
       and ``<species_name>.xmax`` (and same in all directions). This requires additional
       parameter ``<species_name>.density``. i.e., the plasma density in :math:`m^{-3}`.
 
+    * ``predefined``: Predefined density profile.
+      This requires additional parameters ``<species_name>.predefined_profile_name`` and ``<species_name>.predefined_profile_params``.
+      Currently, only a parabolic channel density profile is implemented.
+
     * ``parse_density_function``: the density is given by a function in the input file.
       It requires additional argument ``<species_name>.density_function(x,y,z)``, which is a
       mathematical expression for the density of the species, e.g.
@@ -701,7 +705,7 @@ Particle initialization
       ``vzbar`` until it reaches ``zinject_plane``.
 
 * ``species_name.predefined_profile_name`` (`string`)
-    Only read of ``<species_name>.electrons.profile`` is `predefined`.
+    Only read if ``<species_name>.profile`` is ``predefined``.
 
     * If ``parabolic_channel``, the plasma profile is a parabolic profile with
       cosine-like ramps at the beginning and the end of the profile.

Examples/Tests/PEC/analysis_pec.py

@@ -20,7 +20,6 @@
 import yt
 yt.funcs.mylog.setLevel(50)
 import numpy as np
-from scipy.constants import e, m_e, epsilon_0, c
 sys.path.insert(1, '../../../../warpx/Regression/Checksum/')
 import checksumAPI
 

Examples/Tests/PEC/analysis_pec_mr.py

@@ -20,7 +20,6 @@
 import yt
 yt.funcs.mylog.setLevel(50)
 import numpy as np
-from scipy.constants import e, m_e, epsilon_0, c
 sys.path.insert(1, '../../../../warpx/Regression/Checksum/')
 import checksumAPI
 

Examples/Tests/PerformanceTests/automated_test_1_uniform_rest_32ppc

@@ -0,0 +1 @@
+../../../Tools/PerformanceTests/automated_test_1_uniform_rest_32ppc

Examples/Tests/PerformanceTests/automated_test_2_uniform_rest_1ppc

@@ -0,0 +1 @@
+../../../Tools/PerformanceTests/automated_test_2_uniform_rest_1ppc

Examples/Tests/PerformanceTests/automated_test_3_uniform_drift_4ppc

@@ -0,0 +1 @@
+../../../Tools/PerformanceTests/automated_test_3_uniform_drift_4ppc

Examples/Tests/PerformanceTests/automated_test_4_labdiags_2ppc

@@ -0,0 +1 @@
+../../../Tools/PerformanceTests/automated_test_4_labdiags_2ppc

Examples/Tests/PerformanceTests/automated_test_5_loadimbalance

@@ -0,0 +1 @@
+../../../Tools/PerformanceTests/automated_test_5_loadimbalance

Examples/Tests/PerformanceTests/automated_test_6_output_2ppc

@@ -0,0 +1 @@
+../../../Tools/PerformanceTests/automated_test_6_output_2ppc

Examples/Tests/multi_J/inputs_rz

@@ -39,7 +39,7 @@ warpx.do_divb_cleaning = 1
 warpx.do_multi_J = 1
 warpx.do_multi_J_n_depositions = 2
 psatd.J_linear_in_time = 1
-psatd.do_time_averaging = 0
+psatd.do_time_averaging = 1
 
 # PSATD
 psatd.update_with_rho = 1

Examples/Tests/plasma_lens/analysis.py

@@ -53,10 +53,13 @@ def applylens(x0, vx0, vz0, lens_length, lens_strength):
     vx1 = -w*A*np.sin(w*t + phi)
     return x1, vx1
 
+vel_z = eval(ds.parameters.get('my_constants.vel_z'))
+
 plasma_lens_period = float(ds.parameters.get('particles.repeated_plasma_lens_period'))
 plasma_lens_starts = [float(x) for x in ds.parameters.get('particles.repeated_plasma_lens_starts').split()]
 plasma_lens_lengths = [float(x) for x in ds.parameters.get('particles.repeated_plasma_lens_lengths').split()]
-plasma_lens_strengths = [eval(x) for x in ds.parameters.get('particles.repeated_plasma_lens_strengths').split()]
+plasma_lens_strengths_E = [eval(x) for x in ds.parameters.get('particles.repeated_plasma_lens_strengths_E').split()]
+plasma_lens_strengths_B = [eval(x) for x in ds.parameters.get('particles.repeated_plasma_lens_strengths_B').split()]
 
 clight = c
 
@@ -81,8 +84,9 @@ def applylens(x0, vx0, vz0, lens_length, lens_strength):
     tt = tt + dt
     xx = xx + dt*ux
     yy = yy + dt*uy
-    xx, ux = applylens(xx, ux, uz, plasma_lens_lengths[i], plasma_lens_strengths[i])
-    yy, uy = applylens(yy, uy, uz, plasma_lens_lengths[i], plasma_lens_strengths[i])
+    lens_strength = plasma_lens_strengths_E[i] + plasma_lens_strengths_B[i]*vel_z
+    xx, ux = applylens(xx, ux, uz, plasma_lens_lengths[i], lens_strength)
+    yy, uy = applylens(yy, uy, uz, plasma_lens_lengths[i], lens_strength)
     dt = plasma_lens_lengths[i]/uz
     tt = tt + dt
     zz = z_lens + plasma_lens_lengths[i]
@@ -92,10 +96,10 @@ def applylens(x0, vx0, vz0, lens_length, lens_strength):
 xx = xx + dt0*ux
 yy = yy + dt1*uy
 
-assert abs(xx - xx_sim) < 0.011, Exception('error in x particle position')
-assert abs(yy - yy_sim) < 0.011, Exception('error in y particle position')
-assert abs(ux - ux_sim) < 70., Exception('error in x particle velocity')
-assert abs(uy - uy_sim) < 70., Exception('error in y particle velocity')
+assert abs(np.abs((xx - xx_sim)/xx)) < 0.003, Exception('error in x particle position')
+assert abs(np.abs((yy - yy_sim)/yy)) < 0.003, Exception('error in y particle position')
+assert abs(np.abs((ux - ux_sim)/ux)) < 5.e-5, Exception('error in x particle velocity')
+assert abs(np.abs((uy - uy_sim)/uy)) < 5.e-5, Exception('error in y particle velocity')
 
 test_name = os.path.split(os.getcwd())[1]
 checksumAPI.evaluate_checksum(test_name, filename)

Examples/Tests/plasma_lens/inputs_3d

@@ -17,31 +17,35 @@ boundary.particle_lo = absorbing absorbing absorbing
 boundary.particle_hi = absorbing absorbing absorbing
 
 warpx.do_pml = 0
-warpx.const_dt = 1.e-6
+warpx.const_dt = 1.e-7
 warpx.do_electrostatic = labframe
 
 # Algorithms
 algo.particle_shape = 1
 
+my_constants.vel_z = 0.2e6
+
 # particles
 particles.species_names = electrons
 
 electrons.charge = -q_e
 electrons.mass = m_e
 electrons.injection_style = "MultipleParticles"
-electrons.multiple_particles_pos_x = 0.5 0.
-electrons.multiple_particles_pos_y = 0. 0.4
+electrons.multiple_particles_pos_x = 0.05 0.
+electrons.multiple_particles_pos_y = 0. 0.04
 electrons.multiple_particles_pos_z = 0.05 0.05
 electrons.multiple_particles_vel_x = 0. 0.
 electrons.multiple_particles_vel_y = 0. 0.
-electrons.multiple_particles_vel_z = 0.02e6/clight 0.02e6/clight
+electrons.multiple_particles_vel_z = vel_z/clight vel_z/clight
 electrons.multiple_particles_weight = 1. 1.
 
 particles.E_ext_particle_init_style = repeated_plasma_lens
+particles.B_ext_particle_init_style = repeated_plasma_lens
 particles.repeated_plasma_lens_period = 0.5
 particles.repeated_plasma_lens_starts = 0.1 0.11 0.12 0.13
 particles.repeated_plasma_lens_lengths = 0.1 0.11 0.12 0.13
-particles.repeated_plasma_lens_strengths = 0.07 0.06 0.06 0.03
+particles.repeated_plasma_lens_strengths_E = 0.06 0.08 0.06 0.02
+particles.repeated_plasma_lens_strengths_B = 0.08/vel_z 0.04/vel_z 0.06/vel_z 0.04/vel_z
 
 # Diagnostics
 diagnostics.diags_names = diag1

LICENSE.txt

@@ -1,4 +1,4 @@
-WarpX v21.07 Copyright (c) 2018-2021, The Regents of the University of California, through Lawrence Berkeley National Laboratory, and Lawrence Livermore National Security, LLC, for the operation of Lawrence Livermore National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
+WarpX v21.08 Copyright (c) 2018-2021, The Regents of the University of California, through Lawrence Berkeley National Laboratory, and Lawrence Livermore National Security, LLC, for the operation of Lawrence Livermore National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
 
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Python/pywarpx/_libwarpx.py

@@ -179,11 +179,9 @@ def _array1d_from_pointer(pointer, dtype, size):
 libwarpx.warpx_getChargeDensityCP.restype = _LP_LP_c_real
 libwarpx.warpx_getChargeDensityCPLoVects.restype = _LP_c_int
 libwarpx.warpx_getChargeDensityFP.restype = _LP_LP_c_real
-libwarpx.warpx_getGatheredChargeDensityFP.restype = _LP_LP_c_real
 libwarpx.warpx_getChargeDensityFPLoVects.restype = _LP_c_int
-libwarpx.warpx_getPhiFP.restype = _LP_LP_c_real
+libwarpx.warpx_getGatheredChargeDensityFP.restype = _LP_LP_c_real
 libwarpx.warpx_getGatheredPhiFP.restype = _LP_LP_c_real
-libwarpx.warpx_setPhiGridFP.restype = None
 libwarpx.warpx_getPointerFullPhiFP.restype = _LP_LP_c_real
 
 libwarpx.warpx_getEx_nodal_flag.restype = _LP_c_int
@@ -376,7 +374,7 @@ def getCellSize(direction, level=0):
 #
 #    libwarpx.warpx_ComputePMLFactors(lev, dt)
 
-def add_particles(species_name, x=0., y=0., z=0., ux=0., uy=0., uz=0.,
+def add_particles(species_name, x=None, y=None, z=None, ux=None, uy=None, uz=None, w=None,
                   unique_particles=True, **kwargs):
     '''
 
@@ -388,11 +386,12 @@ def add_particles(species_name, x=0., y=0., z=0., ux=0., uy=0., uz=0.,
     species_name     : the species to add the particle to
     x, y, z          : arrays or scalars of the particle positions (default = 0.)
     ux, uy, uz       : arrays or scalars of the particle momenta (default = 0.)
+    w                : array or scalar of particle weights (default = 0.)
     unique_particles : whether the particles are unique or duplicated on
                        several processes. (default = True)
-    kwargs           : dictionary containing an entry for the particle weights
-                       (with keyword 'w') and all the extra particle attribute
-                       arrays. If an attribute is not given it will be set to 0.
+    kwargs           : dictionary containing an entry for all the extra particle
+                       attribute arrays. If an attribute is not given it will be
+                       set to 0.
 
     '''
 
@@ -403,48 +402,69 @@ def add_particles(species_name, x=0., y=0., z=0., ux=0., uy=0., uz=0.,
     lenux = np.size(ux)
     lenuy = np.size(uy)
     lenuz = np.size(uz)
-
-    if (lenx == 0 or leny == 0 or lenz == 0 or lenux == 0 or
-        lenuy == 0 or lenuz == 0):
-        return
-
-    maxlen = max(lenx, leny, lenz, lenux, lenuy, lenuz)
-    assert lenx==maxlen or lenx==1, "Length of x doesn't match len of others"
-    assert leny==maxlen or leny==1, "Length of y doesn't match len of others"
-    assert lenz==maxlen or lenz==1, "Length of z doesn't match len of others"
-    assert lenux==maxlen or lenux==1, "Length of ux doesn't match len of others"
-    assert lenuy==maxlen or lenuy==1, "Length of uy doesn't match len of others"
-    assert lenuz==maxlen or lenuz==1, "Length of uz doesn't match len of others"
+    lenw = np.size(w)
+
+    # --- Find the max length of the parameters supplied
+    maxlen = 0
+    if x is not None:
+        maxlen = max(maxlen, lenx)
+    if y is not None:
+        maxlen = max(maxlen, leny)
+    if z is not None:
+        maxlen = max(maxlen, lenz)
+    if ux is not None:
+        maxlen = max(maxlen, lenux)
+    if uy is not None:
+        maxlen = max(maxlen, lenuy)
+    if uz is not None:
+        maxlen = max(maxlen, lenuz)
+    if w is not None:
+        maxlen = max(maxlen, lenw)
+
+    # --- Make sure that the lengths of the input parameters are consistent
+    assert x is None or lenx==maxlen or lenx==1, "Length of x doesn't match len of others"
+    assert y is None or leny==maxlen or leny==1, "Length of y doesn't match len of others"
+    assert z is None or lenz==maxlen or lenz==1, "Length of z doesn't match len of others"
+    assert ux is None or lenux==maxlen or lenux==1, "Length of ux doesn't match len of others"
+    assert uy is None or lenuy==maxlen or lenuy==1, "Length of uy doesn't match len of others"
+    assert uz is None or lenuz==maxlen or lenuz==1, "Length of uz doesn't match len of others"
+    assert w is None or lenw==maxlen or lenw==1, "Length of w doesn't match len of others"
     for key, val in kwargs.items():
         assert np.size(val)==1 or len(val)==maxlen, f"Length of {key} doesn't match len of others"
 
+    # --- If the length of the input is zero, then quietly return
+    # --- This is not an error - it just means that no particles are to be injected.
+    if maxlen == 0:
+        return
+
+    # --- Broadcast scalars into appropriate length arrays
+    # --- If the parameter was not supplied, use the default value
     if lenx == 1:
-        x = np.array(x)*np.ones(maxlen)
+        x = np.full(maxlen, (x or 0.), float)
     if leny == 1:
-        y = np.array(y)*np.ones(maxlen)
+        y = np.full(maxlen, (y or 0.), float)
     if lenz == 1:
-        z = np.array(z)*np.ones(maxlen)
+        z = np.full(maxlen, (z or 0.), float)
     if lenux == 1:
-        ux = np.array(ux)*np.ones(maxlen)
+        ux = np.full(maxlen, (ux or 0.), float)
     if lenuy == 1:
-        uy = np.array(uy)*np.ones(maxlen)
+        uy = np.full(maxlen, (uy or 0.), float)
     if lenuz == 1:
-        uz = np.array(uz)*np.ones(maxlen,'d')
-
+        uz = np.full(maxlen, (uz or 0.), float)
+    if lenw == 1:
+        w = np.full(maxlen, (w or 0.), float)
     for key, val in kwargs.items():
         if np.size(val) == 1:
-            kwargs[key] = np.array(val)*np.ones(maxlen)
+            kwargs[key] = np.full(maxlen, val, float)
 
     # --- The -3 is because the comps include the velocites
     nattr = get_nattr_species(species_name) - 3
     attr = np.zeros((maxlen, nattr))
+    attr[:,0] = w
 
     for key, vals in kwargs.items():
-        if key == 'w':
-            attr[:,0] = vals
-        else:
-            # --- The -3 is because components 1 to 3 are velocities
-            attr[:,get_particle_comp_index(species_name, key)-3] = vals
+        # --- The -3 is because components 1 to 3 are velocities
+        attr[:,get_particle_comp_index(species_name, key)-3] = vals
 
     libwarpx.warpx_addNParticles(
         ctypes.c_char_p(species_name.encode('utf-8')), x.size,
@@ -1258,32 +1278,6 @@ def get_mesh_charge_density_fp(level, include_ghosts=True):
     return _get_mesh_field_list(libwarpx.warpx_getChargeDensityFP, level, None, include_ghosts)
 
 
-def get_mesh_phi_fp(level, include_ghosts=True):
-    '''
-
-    This returns a list of numpy arrays containing the mesh electrostatic
-    potential data on each grid for this process. This version returns the
-    density on the fine patch for the given level.
-
-    The data for the numpy arrays are not copied, but share the underlying
-    memory buffer with WarpX. The numpy arrays are fully writeable.
-
-    Parameters
-    ----------
-
-        level          : the AMR level to get the data for
-        include_ghosts : whether to include ghost zones or not
-
-    Returns
-    -------
-
-        A List of numpy arrays.
-
-    '''
-
-    return _get_mesh_field_list(libwarpx.warpx_getPhiFP, level, None, include_ghosts)
-
-
 def get_pointer_full_phi_fp(level):
     """This returns the full phi grid multifab from warpx"""
     return _get_mesh_field_list(libwarpx.warpx_getPointerFullPhiFP, level, None, True)

Python/pywarpx/picmi.py

@@ -33,7 +33,6 @@ class constants:
     m_p = 1.67262192369e-27
     hbar = 1.054571817e-34
     kb = 1.380649e-23
-    torr_SI = 133.322368421
 
 picmistandard.register_constants(constants)
 

Python/setup.py

@@ -54,7 +54,7 @@
     package_data = {}
 
 setup(name = 'pywarpx',
-      version = '21.07',
+      version = '21.08',
       packages = ['pywarpx'],
       package_dir = {'pywarpx': 'pywarpx'},
       description = """Wrapper of WarpX""",