Particle Buffer for Backtransformed Diagnostics #1898

RevathiJambunathan · 2021-04-19T20:43:43Z

This PR implements the capability to transform particle-data from boosted-frame to lab-frame and visualize it using plotfiles and openpmd format using the new BTD interface.

Please note that the output below is not in SI to compare with old BTD. However, the code has been fixed to only output SI units similar to FullDiagnostics.
Also an Abort is added in the code when adios backend is used with openpmd format to write particles in lab-frame. A corresponding Issue is generated #2448

Below is the 2D input file that was used to verify the simulations using the customized output from old BTD with that from new BTD using plotfile and openpmd format.
inputs_2d_boost_testBTD.txt

Output from old-BTD for 2nd snapshot

Output from new-BTD with plotfile format

Output from new BTD with openpmd format :
I was unable to plot particles and fields in the same slice using openpmd-viewer , but they are plotted separately here

I compared the mean(uz) from old BTD and new BTD (plotfile) and found that both outputs agree exactly.
for completeness : mean(uz) for the driver particles in WarpX units from old and new BTD = 59605413002956.99

Source/Diagnostics/WarpXOpenPMD.cpp

Source/Diagnostics/WarpXOpenPMD.H

Source/Diagnostics/WarpXOpenPMD.cpp

ax3l · 2021-10-18T22:57:49Z

ADIOS2 backend issue will we approached in openPMD/openPMD-api#1126

We will add an assert for now.

RevathiJambunathan · 2021-10-25T18:06:33Z

a9e84d5 This commit add the Abort.
When test for adios (bp) backend with write_species = 0, I had to restructure some of the code to ensure that only fields output works. So the commit include that as well.

This commit add this in the documentation.
8137d3e. Also added documentation mentioning how to use BackTransformed option. This was necessary to explain the abort.

…article container

…Data common to both are initialized separately

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

Add Prabhat's suggestion Co-authored-by: Prabhat Kumar <[email protected]>

…ntum_z is 3.68e-3 and the current tolerance is 2.5e-3

RevathiJambunathan · 2022-01-06T21:52:40Z

Examples/Physics_applications/capacitive_discharge/analysis.py

@@ -15,5 +15,5 @@

 my_check = checksumAPI.evaluate_checksum(
    'background_mcc', 'Python_background_mcc_plt00050',
-    do_particles=True, rtol=2.5e-3
+    do_particles=True, rtol=3.7e-3


@roelof-groenewald I changed this temporarily to 3.7e-3 as that was the relative difference for particle_momentum_z for electrons. All other quantities in the checksum are within this tolerance. Was 2.5e-3 chosen specifically or was this driven by the maximum difference in the checksum?
This PR changes when time get updated, and as a result, background_mcc benchmarks are updated since the potential hi uses the updated time

That sounds fine. The 2.5e-3 tolerance was not intelligently chosen, but by the needed tolerance for the test to pass so increasing it to 3.7e-3 is fine.

Thanks a lot!

ax3l

We have a couple of known issues:

openPMD: ADIOS2 particle resize/output seems to be not working yet
plotfiles: reading back pure particle output does not work yet

but we can address them in follow-ups.

ax3l · 2022-03-17T18:58:01Z

Source/Diagnostics/WarpXOpenPMD.cpp

+  m_doParticleSetUp = false;
+  if (counter.GetTotalNumParticles() > 0 and ParticleFlushOffset == 0) {
+      // This will trigger meta-data flush for particles the first-time non-zero number of particles are flushed.
+      m_doParticleSetUp = true;
+  }


Improvements incoming via #2980 (related to #2900)

ax3l mentioned this pull request Jun 11, 2021

Conductor shapes and particle scraping #1901

Closed

ax3l requested review from ax3l and atmyers June 28, 2021 21:14

ax3l added the component: diagnostics all types of outputs label Jun 28, 2021

RevathiJambunathan force-pushed the AddParticlesForBTD branch from 79948f7 to 5e02f5f Compare July 26, 2021 19:04

RevathiJambunathan force-pushed the AddParticlesForBTD branch from 4203c13 to 3ee1df9 Compare August 24, 2021 00:52

RevathiJambunathan force-pushed the AddParticlesForBTD branch 3 times, most recently from 93c5c5c to 8c6ffe0 Compare September 13, 2021 21:57

RevathiJambunathan marked this pull request as ready for review September 20, 2021 20:48

RevathiJambunathan force-pushed the AddParticlesForBTD branch 2 times, most recently from e32554c to 877945e Compare September 21, 2021 17:57

RevathiJambunathan force-pushed the AddParticlesForBTD branch from 877945e to 9e87d3c Compare October 1, 2021 19:08

RevathiJambunathan force-pushed the AddParticlesForBTD branch from a9e4ef4 to 0db228f Compare October 12, 2021 00:56

ax3l self-assigned this Oct 12, 2021

RevathiJambunathan force-pushed the AddParticlesForBTD branch 3 times, most recently from f95521b to 911bf14 Compare October 18, 2021 19:06

ax3l reviewed Oct 18, 2021

View reviewed changes

Source/Diagnostics/WarpXOpenPMD.cpp Outdated Show resolved Hide resolved

ax3l reviewed Oct 18, 2021

View reviewed changes

Source/Diagnostics/WarpXOpenPMD.H Outdated Show resolved Hide resolved

ax3l reviewed Oct 18, 2021

View reviewed changes

Source/Diagnostics/WarpXOpenPMD.H Outdated Show resolved Hide resolved

ax3l reviewed Oct 18, 2021

View reviewed changes

Source/Diagnostics/WarpXOpenPMD.cpp Outdated Show resolved Hide resolved

ax3l mentioned this pull request Oct 18, 2021

[WIP] ADIOS2: Fix Parallel Resize openPMD/openPMD-api#1126

Open

2 tasks

RevathiJambunathan mentioned this pull request Oct 18, 2021

ADIOS2 backend does not work with particle buffers for BTD for >1 mpi simulation #2448

Open

RevathiJambunathan linked an issue Oct 21, 2021 that may be closed by this pull request

Support for particle visualization in BTD with plotfiles/openpmd #2472

Closed

RevathiJambunathan force-pushed the AddParticlesForBTD branch from 1a82f80 to 8137d3e Compare October 25, 2021 18:04

RevathiJambunathan force-pushed the AddParticlesForBTD branch 2 times, most recently from 7dc3abf to 87cff7e Compare October 29, 2021 19:04

RevathiJambunathan and others added 16 commits January 4, 2022 20:20

variable name change for clarity

1b5959e

if num particles in tmp array is 0, return

aaa727a

Use new BTD inputs to set up BTD for particles in the corresponding p…

8f82d77

…article container

unused var

49f7fd3

fix logic error

70229e9

speciesID undefined

0ae5ce1

separate particle and field buffer calls and initialization for BTD. …

62a6c20

…Data common to both are initialized separately

rename variable so it does not ghost existing varname

e140b1e

add more comments

41aebd7

Assert that fields are on

fb849cd

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

c3ac1c2

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

redundant function definition

87bce0a

unused variable

68dc68b

unused variable zp

37ace97

1D 2D 3D definition

6d82387

fix else

2e7cf66

RevathiJambunathan force-pushed the AddParticlesForBTD branch from 0774f1c to 2e7cf66 Compare January 5, 2022 04:21

RevathiJambunathan and others added 4 commits January 4, 2022 20:24

Apply suggestions from code review

7e0da5c

Add Prabhat's suggestion Co-authored-by: Prabhat Kumar <[email protected]>

missing semicolon and ignore xp yp for 1D

380b176

resetting benchmarks for boosted sims and mcc sim

a251387

temporarily changing tolerance since the relative difference for mome…

707f8e3

…ntum_z is 3.68e-3 and the current tolerance is 2.5e-3

RevathiJambunathan commented Jan 6, 2022

View reviewed changes

ax3l approved these changes Jan 7, 2022

View reviewed changes

ax3l merged commit b673c59 into ECP-WarpX:development Jan 7, 2022

ax3l mentioned this pull request Jan 12, 2022

Plotfiles: diag1.write_species = 0 segfaults #2738

Open

ax3l mentioned this pull request Mar 17, 2022

openPMD: Handle Zero Particles Well #2980

Merged

4 tasks

ax3l reviewed Mar 17, 2022

View reviewed changes

ax3l mentioned this pull request Mar 17, 2022

Particle openPMD IO issues when species not present in the first dump #2900

Closed

ax3l added the component: boosted frame boosted frame components & logic label Mar 21, 2022

ax3l mentioned this pull request Jan 31, 2023

ADIOS2: Fix BTD Particle Resize w/ Empty Ranks #3657

Merged

7 tasks

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Particle Buffer for Backtransformed Diagnostics #1898

Particle Buffer for Backtransformed Diagnostics #1898

RevathiJambunathan commented Apr 19, 2021 •

edited

Loading

ax3l commented Oct 18, 2021 •

edited

Loading

RevathiJambunathan commented Oct 25, 2021 •

edited

Loading

RevathiJambunathan Jan 6, 2022 •

edited

Loading

roelof-groenewald Jan 6, 2022

RevathiJambunathan Jan 6, 2022

ax3l left a comment

ax3l Mar 17, 2022 •

edited

Loading

Particle Buffer for Backtransformed Diagnostics #1898

Particle Buffer for Backtransformed Diagnostics #1898

Conversation

RevathiJambunathan commented Apr 19, 2021 • edited Loading

ax3l commented Oct 18, 2021 • edited Loading

RevathiJambunathan commented Oct 25, 2021 • edited Loading

RevathiJambunathan Jan 6, 2022 • edited Loading

Choose a reason for hiding this comment

roelof-groenewald Jan 6, 2022

Choose a reason for hiding this comment

RevathiJambunathan Jan 6, 2022

Choose a reason for hiding this comment

ax3l left a comment

Choose a reason for hiding this comment

ax3l Mar 17, 2022 • edited Loading

Choose a reason for hiding this comment

RevathiJambunathan commented Apr 19, 2021 •

edited

Loading

ax3l commented Oct 18, 2021 •

edited

Loading

RevathiJambunathan commented Oct 25, 2021 •

edited

Loading

RevathiJambunathan Jan 6, 2022 •

edited

Loading

ax3l Mar 17, 2022 •

edited

Loading