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Fix openPMD Meta-Data #349

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Merged
ax3l merged 4 commits into from
Apr 25, 2023
Merged

Fix openPMD Meta-Data #349

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ba83cf3
CI: Add openPMD-validator
ax3l Apr 24, 2023
a50c702
openPMD: Add 0-valued positionOffset
ax3l Apr 24, 2023
a4ef5e9
openPMD positionOffset: Reference Particle
ax3l Apr 24, 2023
03769f2
CI: Update Windows Powershell
ax3l Apr 25, 2023
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2 changes: 2 additions & 0 deletions .github/workflows/dependencies/gcc-openmpi.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -26,3 +26,5 @@ python3 -m pip install -U pip setuptools wheel
python3 -m pip install -U cmake pytest
python3 -m pip install -r requirements_mpi.txt
python3 -m pip install -r examples/requirements.txt

python3 -m pip install -U openPMD-validator
2 changes: 2 additions & 0 deletions .github/workflows/dependencies/gcc.sh
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Expand Up @@ -24,3 +24,5 @@ sudo apt-get install -y \
python3 -m pip install -U pip setuptools wheel
python3 -m pip install -U cmake pytest
python3 -m pip install -r examples/requirements.txt

python3 -m pip install -U openPMD-validator
4 changes: 4 additions & 0 deletions .github/workflows/macos.yml
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Expand Up @@ -54,6 +54,7 @@ jobs:
python3 -m pip install --upgrade pytest
python3 -m pip install -r requirements_mpi.txt
python3 -m pip install -r examples/requirements.txt
python3 -m pip install --upgrade openPMD-validator
set -e
- name: CCache Cache
uses: actions/cache@v3
Expand Down Expand Up @@ -93,3 +94,6 @@ jobs:
{ cat Backtrace.0.0; exit 1; }
impactx.MPI.OMP.DP.OPMD examples/fodo/input_fodo.in algo.particle_shape = 3 || \
{ cat Backtrace.0.0; exit 1; }

- name: validate created openPMD files
run: find build -name *.h5 | xargs -n1 -I{} openPMD_check_h5 -i {}
6 changes: 6 additions & 0 deletions .github/workflows/ubuntu.yml
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Expand Up @@ -66,6 +66,9 @@ jobs:

python3 examples/fodo/run_fodo.py

- name: validate created openPMD files
run: find build -name *.h5 | xargs -n1 -I{} openPMD_check_h5 -i {}

build_gcc_python:
name: GCC w/o MPI w/ Python
runs-on: ubuntu-20.04
Expand Down Expand Up @@ -125,3 +128,6 @@ jobs:
cmake --build build --target pip_install

python3 examples/fodo/run_fodo.py

- name: validate created openPMD files
run: find build -name *.h5 | xargs -n1 -I{} openPMD_check_h5 -i {}
5 changes: 5 additions & 0 deletions .github/workflows/windows.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ jobs:
python3 -m pip install -U pip setuptools wheel pytest
python3 -m pip install -r requirements.txt
python3 -m pip install -r examples/requirements.txt
python3 -m pip install -U openPMD-validator
- name: Build
run: |
$env:HDF5_DIR = "C:/Program Files/HDF_Group/HDF5/1.12.2/cmake/"
Expand Down Expand Up @@ -137,6 +138,7 @@ jobs:
python3 -m pip install -U pip setuptools wheel pytest
python3 -m pip install -r requirements.txt
python3 -m pip install -r examples/requirements.txt
python3 -m pip install -U openPMD-validator
- name: Build
shell: cmd
run: |
Expand Down Expand Up @@ -175,3 +177,6 @@ jobs:
# if errorlevel 1 exit 1
# cmake --build build --target pip_install
# if errorlevel 1 exit 1

- name: validate created openPMD files
run: find build -name *.h5 | xargs -n1 -I{} openPMD_check_h5 -i {}
4 changes: 3 additions & 1 deletion src/particles/elements/diagnostics/openPMD.H
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Expand Up @@ -83,11 +83,13 @@ namespace detail

/** Prepare entering the element before starting push logic.
*
* @param[in] pc particle container.
* @param[in] pc particle container
* @param[in] ref_part reference particle
* @param[in] step global step for diagnostics
*/
void prepare (
PinnedContainer & pc,
RefPart const & ref_part,
int step
);

Expand Down
16 changes: 15 additions & 1 deletion src/particles/elements/diagnostics/openPMD.cpp
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Expand Up @@ -211,6 +211,7 @@ namespace detail

void BeamMonitor::prepare (
PinnedContainer & pc,
RefPart const & ref_part,
int step
) {
#ifdef ImpactX_USE_OPENPMD
Expand Down Expand Up @@ -253,6 +254,17 @@ namespace detail
getComponentRecord(component_name).resetDataset(d_fl);
}
}

// openPMD coarse position
{
beam["positionOffset"]["x"].resetDataset(d_fl);
beam["positionOffset"]["x"].makeConstant(ref_part.x);
beam["positionOffset"]["y"].resetDataset(d_fl);
beam["positionOffset"]["y"].makeConstant(ref_part.y);
beam["positionOffset"]["ct"].resetDataset(d_fl);
beam["positionOffset"]["ct"].makeConstant(ref_part.t);
Comment on lines +264 to +265
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@ax3l ax3l Apr 24, 2023 •
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@cemitch99 here for positionOffset and in position, do we want to output s+delta s instead of ct + c*dt?

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@cemitch99 cemitch99 Apr 24, 2023

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Not sure I follow what the intended output is here. I understand that by "ct" you mean "ref_part.t", but what is meant by "dt"? Does this represent one or more particle values of the "t" coordinate?

In general, I would say that "s" is qualitatively different from the other variables like ct. It is an independent variable, it is associated only with the reference particle, and the other (beam particle) values are given as functions of "s".

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@ax3l ax3l Apr 24, 2023

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Thanks, ah yes I was confused for a second... So per particle, splitting the longitudinal position (for a fixed s) into ref_part.t (should we call this ref_part.ct?) and position.ct makes sense...

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@cemitch99 cemitch99 Apr 25, 2023

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Yes, that's true.

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@ax3l ax3l Apr 25, 2023

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Ok, will do in #350

}

// AoS: Int
beam["id"][scalar].resetDataset(d_ui);

Expand Down Expand Up @@ -298,7 +310,7 @@ namespace detail
*/

// prepare element access
this->prepare(pinned_pc, step);
this->prepare(pinned_pc, ref_part, step);

// loop over refinement levels
int const nLevel = pinned_pc.finestLevel();
Expand All @@ -320,6 +332,8 @@ namespace detail
auto series = std::any_cast<io::Series>(m_series);
io::WriteIterations iterations = series.writeIterations();
io::Iteration iteration = iterations[m_step];

// close iteration
iteration.close();
}

Expand Down