Field probe line detector (#2513)

* FieldProbe using Particle

Update FieldProbe.cpp

Update FieldProbeParticleContainer.H

Updates FieldProbe and FieldProbeParticleContainer

* Make <diag>.integrate optional

The param parser query keeps te default value if no entry is found.

* Fixed number particle needed for AddNParticles

* Removing unnecessary type definition

* Added Doxygen-style comments to FieldProbe.cpp
Corrected Poynting calculation by implementing vacuum permeability

* Added Doxygen comments

* Implement virtual function ReducedDiags::AllocData() + comments

* InitData implemented

* Fixed Doxygen commenting.

* Now uses WarpX physics constant for vaccuum permeability

* forgotton comments to MultiReducedDiags

* Update Source/Diagnostics/ReducedDiags/FieldProbe.H

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.H

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.H

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.H

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update FieldProbe.H

* Update FieldProbe.cpp

* Update Source/Diagnostics/ReducedDiags/ReducedDiags.H

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

* Update Source/Diagnostics/ReducedDiags/MultiReducedDiags.H

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

* Update Source/Diagnostics/ReducedDiags/MultiReducedDiags.H

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update FieldProbeParticleContainer.H

* Update Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.H

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

* Update FieldProbeParticleContainer.cpp

* Update FieldProbe.cpp

* Update FieldProbe.H

* Update Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.H

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

* Update Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.H

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

* Update FieldProbeParticleContainer.cpp

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/ReducedDiags.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Changed enumerated class to struct w/ enumeration. Can remove "static_cast<int>"

* FieldProbeParticleContainer::iterator implemented

* Cleaned up output += operator, fixed output comments

* style fix

* Replaces Tabs with 4 spaces

* Defined modes and interp order to avoid GPU compilation errors

* 1 more tab fix

* EoL white spaces

* fixed a typoX

* Explicitly capturing "this" in parallel for to combat error saying "error #3223-D: Implicit capture of 'this' in extended lambda expression"

* removed unncessacesy double define

* moved output out of ParallelFor. temp variable for integrate

* Parse integrate, integrate all time steps, output setup for integrate and regular

* Fixed integrate bug.

* ammend header. integreate variable name change.

* Integrate values in input file

* updates to timing for integrate

* Update Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.cpp

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

* whitespace

* Update Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.cpp

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

* Update Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.cpp

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

* Functionality to create 2D line of particles. Input included. No output yet

* ammend compiler errors

* Apply suggestions from code review - Style

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

* Update reduce_diag_names

* 2D array setup- not complete

* field_probe_integrate change

* review amends

* Apply suggestions from code review - Style

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

* Vectors + AddNParticles

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

* Update FieldProbe.cpp

* Update FieldProbe.H

* bug fix and inputs

* reintroduce raw_fields functionality

* docs update and correction

* whitespaces

* Fix GPU Compile (raw_fields)

* changed f_probe to m_probe apropriately

* Typos

Co-authored-by: David Grote <dpgrote@lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Better name for ParticleVal

* used map for observables and units

* Apply suggestions from code review

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

* Simplified output. Fixed double integration error

* Update FieldProbe.H

Removed unneeded variable

* comments and fixed rawFields

* white spaces

* Apply suggestions from code review

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

* Update FieldProbe.H

* Guard on write

* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp

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

* Fix Syntax Error in Write

* Fix Init: Only 1 Particle (MPI)

Only one MPI rank adds a particle, which we done distribute
into the right rank.

* Fix MPI Deadlock: No Early Return

We just want to skip the write to `m_data`, not the rest
of the logic.

* Vector storage, Add N particle, debugging

* Fix Probe in Domain Logic

General global check, not only on a single rank.

* comments

* Container: Add `const_iterator`

* Fix MPI Comms

* Cleaning

* Remove PrintAll Leftover

* 1-D Output vector

* Reduced Diags: Support LoadBalance

* Cleaning of "Definitions ()"

* Updating inputs for testing Line

* data type specification

* IO

* Update inputs

* Update inputs

* error in header. Send to IO CPU

* Apply suggestions from code review

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

* moved rank communication out of tile loop

* change m_data_vector. IO particle count

* Fixed input for rename. Gather particle number

* Apply suggestions from code review

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

* Gather

* Changed data output method to pushing values on vector
MPI Gather and Gatherv for data
Tell Evolve to run Load Balance
Tell InitData to run Load Balance
Define output method by printing valid particles

NOTE! Needs cleaning, commenting, removing some debugging tools

* Apply suggestions from code review

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

* Suggestions from review

* defensive programming on if / if else
added comments throughout
removed temporary debugging lines

* Documentation for line detector option

* Whitespaces

* MPI_Gather -> amrex::ParallelDescriptor::Gather

* ParallelDiscriptor, vectors at the end, no more 1990's malloc for capacity allocation

* whitespaces

* output optimized for CSV

* Python notebook for reference

* Input file for current test on CORI

* 2D plane functionality

* Regression test

* Delete DoubleSlit_2021_11_17.ipynb

* Whitespace fix

* pandas

* Error set to 2.5%, fixed source

* style

* zenodo orcid

* Apply suggestions from code review

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

* Review changes and swapped MPI direct call for Amrex::ParallelDescriptor

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update WarpX-tests.ini

Fix Regression Test

* Update WarpX-tests.ini

Open PMD in cmakeSetupOpts

* Update dependencies.rst

* Update analysis_field_probe.py

* Update WarpX-tests.ini

* Analysis Script: Executable

```
chmod a+x scriptname.py
```

and use explicitly `python3`

* openPMD: optional for this test

* Inputs: add `geometry.dims = 2`

* Remove: diag1.write_species = 0

- segfaults for plotfiles (bug?)
- not needed, since we have no particles anyway

* Fix: typo in analysis

* test requirements: pandas

* Fix: Types

* as string: `<red_diag>.probe_geometry`

change this to a string, which is more user-friendly

* Python Script: Simplify + Style

* C++: Clean Up

* Azure: Run `apt update`

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: David Grote <dpgrote@lbl.gov>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

1 files changed, 1 insertions, 2 deletions

diff --git a/Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.cpp b/Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.cpp
index c72362b6b..111e97e96 100644
--- a/Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.cpp
+++ b/Source/Diagnostics/ReducedDiags/FieldProbeParticleContainer.cpp
@@ -108,8 +108,7 @@ FieldProbeParticleContainer::AddNParticles (int lev,
 #elif defined(WARPX_DIM_XZ) || defined(WARPX_DIM_RZ)
         amrex::ignore_unused(y) ;
         p.pos(0) = x[i];
-        p.pos(1) = 0;
-        p.pos(2) = z[i];
+        p.pos(1) = z[i];
 #endif
         // write position, cpu id, and particle id to particle
         pinned_tile.push_back(p);