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Merge pull request #3261 from ComputationalRadiationPhysics/release-0…
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….5.0

Release 0.5.0
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@PrometheusPi
PrometheusPi authored Jun 3, 2020
2 parents d340812 + b49a6f5 commit 454a28e
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20 changes: 10 additions & 10 deletions .travis.yml
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Expand Up @@ -6,7 +6,7 @@ cache:
apt: true
directories:
- $HOME/.cache/spack
- $HOME/.cache/cmake-3.10.0
- $HOME/.cache/cmake-3.11.4
pip: true

addons:
Expand Down Expand Up @@ -37,31 +37,31 @@ install:
mkdir -p $SPACK_ROOT &&
git clone --depth 50 https://github.com/spack/spack.git $SPACK_ROOT &&
echo -e "config:""\n build_jobs:"" 2" > $SPACK_ROOT/etc/spack/config.yaml &&
echo -e "packages:""\n cmake:""\n version:"" [3.10.0]""\n paths:""\n cmake@3.10.0:"" /home/travis/.cache/cmake-3.10.0""\n buildable:"" False" > $SPACK_ROOT/etc/spack/packages.yaml;
echo -e "packages:""\n cmake:""\n version:"" [3.11.4]""\n paths:""\n cmake@3.11.4:"" /home/travis/.cache/cmake-3.11.4""\n buildable:"" False" > $SPACK_ROOT/etc/spack/packages.yaml;
fi
- spack compiler add
# required dependencies - CMake 3.10.0
# required dependencies - CMake 3.11.4
- if [ "$TRAVIS_OS_NAME" == "linux" ]; then
if [ ! -f $HOME/.cache/cmake-3.10.0/bin/cmake ]; then
wget -O cmake.sh https://cmake.org/files/v3.10/cmake-3.10.0-Linux-x86_64.sh &&
sh cmake.sh --skip-license --exclude-subdir --prefix=$HOME/.cache/cmake-3.10.0 &&
if [ ! -f $HOME/.cache/cmake-3.11.4/bin/cmake ]; then
wget -O cmake.sh https://cmake.org/files/v3.11/cmake-3.11.4-Linux-x86_64.sh &&
sh cmake.sh --skip-license --exclude-subdir --prefix=$HOME/.cache/cmake-3.11.4 &&
rm cmake.sh;
fi;
elif [ "$TRAVIS_OS_NAME" == "osx" ]; then
if [ ! -d /Applications/CMake.app/Contents/ ]; then
curl -L -s -o cmake.dmg https://cmake.org/files/v3.10/cmake-3.10.0-Darwin-x86_64.dmg &&
curl -L -s -o cmake.dmg https://cmake.org/files/v3.11/cmake-3.11.4-Darwin-x86_64.dmg &&
yes | hdiutil mount cmake.dmg &&
sudo cp -R "/Volumes/cmake-3.10.0-Darwin-x86_64/CMake.app" /Applications &&
sudo cp -R "/Volumes/cmake-3.11.4-Darwin-x86_64/CMake.app" /Applications &&
hdiutil detach /dev/disk1s1 &&
rm cmake.dmg;
fi;
fi
- travis_wait spack install
cmake
$COMPILERSPEC
# required dependencies - Boost 1.62.0
# required dependencies - Boost 1.65.1
- travis_wait spack install
boost@1.62.0~date_time~graph~iostreams~locale~log~random~thread~timer~wave
boost@1.65.1~date_time~graph~iostreams~locale~log~random~thread~timer~wave
$COMPILERSPEC
- spack clean -a
- source /etc/profile &&
Expand Down
12 changes: 9 additions & 3 deletions .zenodo.json
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Expand Up @@ -111,10 +111,16 @@
"id": "GPL-3.0"
},
"references": [
"M. Vranic et al. (2015). Classical radiation reaction in particle-in-cell simulations. DOI:10.1016/j.cpc.2016.04.002",
"A. Gonoskov et al. (2015). Extended particle-in-cell schemes for physics in ultrastrong laser fields: Review and developments. DOI:10.1103/PhysRevE.92.023305",
"L. V. Keldysh (1965). Ionization in the field of a strong electromagnetic wave.",
"D. Bauer and P. Mulser (1999). Exact field ionization rates in the barrier-suppression regime from numerical time-dependent Schr\u00f6dinger-equation calculations. DOI:10.1103/PhysRevA.59.569",
"A. Huebl et al. (2015). openPMD 1.0.0 - A meta data standard for particle and mesh based data. DOI:10.5281/zenodo.33624"
"R. Pausch et al. (2014). How to test and verify radiation diagnostics simulations within particle-in-cell frameworks. DOI:10.1016/j.nima.2013.10.073",
"A. Huebl (2014). Injection Control for Electrons in Laser-Driven Plasma Wakes on the Femtosecond Time Scale. DOI:10.5281/zenodo.15924",
"A. Gonoskov et al. (2015). Extended particle-in-cell schemes for physics in ultrastrong laser fields: Review and developments. DOI:10.1103/PhysRevE.92.023305",
"A. Huebl et al. (2015). openPMD: A meta data standard for particle and mesh based data. DOI:10.5281/zenodo.591699",
"M. Vranic et al. (2016). Classical radiation reaction in particle-in-cell simulations. DOI:10.1016/j.cpc.2016.04.002",
"A. Matthes et al. (2016). In situ, steerable, hardware-independent and data-structure agnostic visualization with ISAAC. DOI:10.14529/jsfi160403",
"A. Huebl et al. (2017). On the Scalability of Data Reduction Techniques in Current and Upcoming HPC Systems from an Application Perspective. DOI:10.1007/978-3-319-67630-2_2",
"R. Pausch et al. (2018). Quantitatively consistent computation of coherent and incoherent radiation in particle-in-cell codes - a general form factor formalism for macro-particles. DOI:10.1016/j.nima.2018.02.020",
"A. Huebl (2019). PIConGPU: Predictive Simulations of Laser-Particle Accelerators with Manycore Hardware. DOI:10.5281/zenodo.3266820"
]
}
284 changes: 283 additions & 1 deletion CHANGELOG.md
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@@ -1,6 +1,288 @@
Changelog
=========

0.5.0
-----

**Date:** 2020-06-03

Perfectly Matched Layer (PML) and Bug Fixes

This release adds a new field absorber for the Yee solver, convolutional
perfectly matched layer (PML). Compared to the still supported exponential
dampling absorber, PML provides better absorption rate and much less spurious
reflections.

We added new plugins for computing emittance and transition radiation, particle
rendering with the ISAAC plugin, Python tools for reading and visualizing output
of a few plugins.

The release also adds a few quality-of-life features, including a new memory
calculator, better command-line experience with new options and bashcompletion,
improved error handling, cleanup of the example setups, and extensions to
documentation.

Thanks to Igor Andriyash, Sergei Bastrakov, Xeinia Bastrakova, Andrei Berceanu,
Finn-Ole Carstens, Alexander Debus, Jian Fuh Ong, Marco Garten, Axel Huebl,
Sophie Rudat (Koßagk), Anton Lebedev, Felix Meyer, Pawel Ordyna, Richard Pausch,
Franz Pöschel, Adam Simpson, Sebastian Starke, Klaus Steiniger, René Widera
for contributions to this release!

### Changes to "0.4.0"

**User Input Changes:**
- Particle pusher acceleration #2731
- stop moving window after N steps #2792
- Remove unused ABSORBER_FADE_IN_STEPS from .param files in examples #2942
- add namespace "radiation" around code related to radiation plugin #3004
- Add a runtime parameter for window move point #3022
- Ionization: add silicon to pre-defines #3078
- Make dependency between boundElectrons and atomicNumbers more explicit #3076
- openPMD: use particle id naming #3165
- Docs: update `species.param` #2793 #2795

**New Features:**
- PIC:
- Particle pusher acceleration #2731
- Stop moving window after N steps #2792
- Auto domain adjustment #2840
- Add a wrapper around main() to catch and report exceptions #2962
- Absorber perfectly matched layer PML #2950 #2967
- Make dependency between boundElectrons and atomicNumbers more explicit #3076
- PMacc:
- `ExchangeTypeNames` Verify Parameter for Access #2926
- Name directions in species buffer warnings #2925
- Add an implementation of exp for pmacc vectors #2956
- SimulationFieldHelper: getter method to access cell description #2986
- plugins:
- PhaseSpaceData: allow multiple iterations #2754
- Python MPL Visualizer: plot for several simulations #2762
- Emittance Plugin #2588
- DataReader: Emittance & PlotMPL: Emittance, SliceEmittance, EnergyWaterfall #2737
- Isaac: updated for particle rendering #2940
- Resource Monitor Plugin: Warnings #3013
- Transition radiation plugin #3003
- Add output and python module doc for radiation plugin #3052
- Add reference to thesis for emittance plugin doc #3101
- Plugins: ADIOS & PhaseSpace Wterminate #2817
- Calorimeter Plugin: Document File Suffix #2800
- Fix returning a stringstream by value #3251
- tools:
- Support alpaka accelerator `threads` #2701
- Add getter for omega and n to python module #2776
- Python Tools: Incorporate sim_time into readers and visualizers #2779
- Add PIConGPU memory calculator #2806
- Python visualizers as jupyter widgets #2691
- pic-configure: add `--force/-f` option #2901
- Correct target thickness in memory calculator #2873
- CMake: Warning in 3.14+ Cache List #3008
- Add an option to account for PML in the memory calculator #3029
- Update profile hemera-hzdr: CMake version #3059
- Travis CI: OSX sed Support #3073
- CMake: mark cuda 10.2 as tested #3118
- Avoid bash completion file path repetition #3136
- Bashcompletion #3069
- Jupyter widgets output capture #3149
- Docs: Add ionization prediction plot #2870
- pic-edit: clean cmake file cache if new param added #2904
- CMake: Honor _ROOT Env Hints #2891
- Slurm: Link stdout live #2839

**Bug Fixes:**
- PIC:
- fix EveryNthCellImpl #2768
- Split `ParserGridDistribution` into `hpp/cpp` file #2899
- Add missing inline qualifiers potentially causing multiple definitions #3006
- fix wrong used method prefix #3114
- fix wrong constructor call #3117
- Fix calculation of omega_p for logging #3163
- Fix laser bug in case focus position is at the init plane #2922
- Fix binomial current interpolation #2838
- Fix particle creation if density zero #2831
- Avoid two slides #2774
- Fix warning: comparison of unsigned integer #2987
- PMacc:
- Typo fix in Send/receive buffer warning #2924
- Explicitly specify template argument for std::forward #2902
- Fix signed int overflow in particle migration between supercells #2989
- Boost 1.67.0+ Template Aliases #2908
- Fix multiple definitions of PMacc identifiers and aliases #3036
- Fix a compilation issue with ForEach lookup #2985
- plugins:
- Fix misspelled words in plugin documentation #2705
- Fix particle merging #2753
- OpenMPI: Use ROMIO for IO #2857
- Radiation Plugin: fix bool conditions for hdf5 output #3021
- CMake Modules: Update ADIOS FindModule #3116
- ADIOS Particle Writer: Fix timeOffset #3120
- openPMD: use particle id naming #3165
- Include int16 and uint16 types as traits for ADIOS #2929
- Fix observation direction of transition radiation plugin #3091
- Fix doc transition radiation plugin #3089
- Fix doc rad plugin units and factors #3113
- Fix wrong underline in TransRad plugin doc #3102
- Fix docs for radiation in 2D #2772
- Fix radiation plugin misleading filename #3019
- tools:
- Update cuda_memtest: NVML Noise #2785
- Dockerfile: No SSH Deamon & Keys, Fix Flex Build #2970
- Fix hemera k80_restart.tpl #2938
- Templates/profile for hemera k20 queue #2935
- Splash2txt Build: Update deps #2914
- splash2txt: fix file name trimming #2913
- Fix compile splash2txt #2912
- Docker CUDA Image: Hwloc Default #2906
- Fix Python EnergyHistogramData: skip of first iteration #2799
- Spack: Fix Compiler Docs #2997
- Singularity: Workaround Chmod Issue, No UCX #3017
- Fix examples particle filters #3065
- Fix CUDA device selection #3084
- Fix 8.cfg for Bremsstrahlung example #3097
- Fix taurus profile #3152
- Fix a typo in density ratio value of the KHI example #3162
- Fix GCC constexpr lambda bug #3188
- CFL Static Assert: new grid.param #2804
- Fix missing exponent in fieldIonization.rst #2790
- Spack: Improve Bootstrap #2773
- Fix python requirements: remove sys and getopt #3172

**Misc:**
- refactoring:
- PIC:
- Eliminate M_PI (again) #2833
- Fix MappingDesc name hiding #2835
- More fixes for MSVC capturing constexpr in lambdas #2834
- Core Particles: C++11 Using for Typedef #2859
- Remove unused getCommTag() in FieldE, FieldB, FieldJ #2947
- Add a using declaration for Difference type to yee::Curl #2955
- Separate the code processing currents from MySimulation #2964
- Add DataConnector::consume(), which shares and consumes the input #2951
- Move picongpu/simulationControl to picongpu/simulation/control #2971
- Separate the code processing particles from MySimulation #2974
- Refactor cell types #2972
- Rename `compileTime` into `meta` #2983
- Move fields/FieldManipulator to fields/absorber/ExponentialDamping #2995
- Add picongpu::particles::manipulate() as a high-level interface to particle manipulation #2993
- `particles::forEach` #2991
- Refactor and modernize implementation of fields #3005
- Modernize ArgsParser::ArgsErrorCode #3023
- Allow constructor for density free formular functor #3024
- Reduce PML memory consumption #3122
- Bremsstrahlung: use more constexpr #3176
- Pass mapping description by value instead of pointer from simulation stages #3014
- Add missing inline specifiers for functions defined in header files #3051
- Remove ZigZag current deposition #2837
- Fix style issues with particlePusherAcceleration #2781
- PMacc:
- Supercell particle counter #2637
- ForEachIdx::operator(): Use Universal Reference #2881
- Remove duplicated definition of `BOOST_MPL_LIMIT_VECTOR_SIZE` #2883
- Cleanup `pmacc/types.hpp` #2927
- Add pmacc::memory::makeUnique similar to std::make_unique #2949
- PMacc Vector: C++11 Using #2957
- Remove pmacc::forward and pmacc::RefWrapper #2963
- Add const getters to ParticleBox #2941
- Remove unused pmacc::traits::GetEmptyDefaultConstructibleType #2976
- Remove pmacc::traits::IsSameType which is no longer used #2979
- Remove template parameter for initialization method of Pointer and FramePointer #2977
- Remove pmacc::expressions which is no longer used #2978
- Remove unused pmacc::IDataSorter #3030
- Change PMACC_C_STRING to produce a static constexpr member #3050
- Refactor internals of pmacc::traits::GetUniqueTypeId #3049
- rename "counterParticles" to "numParticles" #3062
- Make pmacc::DataSpace conversions explicit #3124
- plugins:
- Small update for python visualizers #2882
- Add namespace "radiation" around code related to radiation plugin #3004
- Remove unused includes of pthread #3040
- SpeciesEligibleForSolver for radiation plugin #3061
- ADIOS: Avoid unsafe temporary strings #2946
- tools:
- Update cuda_memtest: CMake CUDA_ROOT Env #2892
- Update hemera tpl after SLURM update #3123
- Add pillow as dependency #3180
- Params: remove `boost::vector<>` usage #2769
- Use _X syntax in OnceIonized manipulator #2745
- Add missing const to some GridController getters #3154
- documentation:
- Containers: Update 0.4.0 #2750
- Merge 0.4.0 Changelog #2748
- Update Readme & License: People #2749
- Add .zenodo.json #2747
- Fix species.param docu (in all examples too) #2795
- Fix species.param example doc and grammar #2793
- Further improve wording in docs #2710
- MemoryCalculator: fix example output for documentation #2822
- Manual: Plugin & Particle Sections, Map #2820
- System: D.A.V.I.D.E #2821
- License Header: Update 2019 #2845
- Docs: Memory per Device Spelling #2868
- CMake 3.11.0+ #2959
- CUDA 9.0+, GCC 5.1+, Boost 1.65.1+ #2961
- CMake: CUDA 9.0+ #2965
- Docs: Update Sphinx #2969
- CMake: CUDA 9.2-10.1, Boost <= 1.70.0 #2975
- Badge: Commits Since Release & Good First #2980
- Update info on maintainers in README.md #2984
- Fix grammar in all `.profile.example` #2930
- Docs: Dr.s #3009
- Fix old file name in radiation doc #3018
- System: ARIS #3039
- fix typo in getNode and getDevice #3046
- Window move point clean up #3045
- Docs: Cori's KNL Nodes (NERSC) #3043
- Fix various sphinx issues not related to doxygen #3056
- Extend the particle merger plugin documentation #3057
- Fix docs using outdated ManipulateDeriveSpecies #3068
- Adjust cores per gpu on taurus after multicore update #3071
- Docs: create conda env for building docs #3074
- Docs: add missing checkpoint options #3080
- Remove titan ornl setup and doc #3086
- Summit: Profile & Templates #3007
- Update URL to ADIOS #3099
- License Header: Update 2020 #3138
- Add PhD thesis reference in radiation plugin #3151
- Spack: w/o Modules by Default #3182
- Add a brief description of simulation output to basics #3183
- Fix a typo in exchange communication tag status output #3141
- Add a link to PoGit to the docs #3115
- fix optional install instructions in the Summit profile #3094
- Update the form factor documentation #3083
- Docs: Add New References #3072
- Add information about submit.cfg and submit.tpl files to docs. #3070
- Fix style (underline length) in profile.rst #2936
- Profiles: Section Title Length #2934
- Contributor name typo in LICENSE.md #2880
- Update modules and memory in gpu_picongpu.profile #2923
- Add k80_picongpu.profile and k80.tpl #2919
- Update taurus-tud profiles for the `ml` partition #2903
- Hypnos: CMake 3.13.4 #2887
- Docs: Install Blosc #2829
- Docs: Source Intro Details #2828
- Taurus Profile: Project #2819
- Doc: Add System Links #2818
- remove grep file redirect #2788
- Correct jupyter widget example #3191
- fix typo: `UNIT_LENGHT` to `UNIT_LENGTH` #3194
- Change link to CRP group @ HZDR #2814
- Examples: Unify .cfg #2826
- Remove unused ABSORBER_FADE_IN_STEPS from .param files in examples #2942
- Field absorber test example #2948
- Singularity: Avoid Dotfiles in Home #2981
- Boost: No std::auto_ptr #3012
- Add YeePML to comments for field solver selection #3042
- Add a runtime parameter for window move point #3022
- Ionization: add silicon to pre-defines #3078
- Add 1.cfg to Bremsstrahlung example #3098
- Fix cmake flags for MSVS #3126
- Fix missing override flags #3156
- Fix warning #222-D: floating-point operation result is out of range #3170
- Update alpaka to 0.4.0 and cupla to 0.2.0 #3175
- Slurm update taurus: workdir to chdir #3181
- Adjust profiles for taurus-tud #2990
- Update mallocMC to 2.3.1crp #2893
- Change imread import from scipy.misc to imageio #3192

0.4.3
-----

Expand Down Expand Up @@ -35,7 +317,7 @@ Klaus Steiniger, and René Widera for contributions to this release!
- Add system links #2818
- Taurus:
- add project #2819
- add Power9 V100 nodes #2856
- add Power9 V100 nodes #2856
- add D.A.V.I.D.E (CINECA) #2821
- add JURECA (JSC) #2869
- add JUWELS (JSC) #2874
Expand Down
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