add new example

CHANGELOG.md

@@ -1,6 +1,133 @@
 Change Log / Release Log for PIConGPU
 ================================================================
 
+0.1.0
+-----
+**Date:** 2015-05-21
+
+This is version `0.1.0` of PIConGPU, a *pre-beta* version.
+
+Initial field ionization support was added, including the first model for BSI.
+The code-base was substantially hardened, fixing several minor and major
+issues. Especially, several restart related issues, an issue with 2D3V zigzack
+current calculation and a memory issue with Jetson TK1 boards were fixed.
+A work-around for a critical CUDA 6.5 compiler bug was applied to all affected
+parts of the code.
+
+### Changes to "Open Beta RC6"
+
+**.param file changes:**
+ See full syntax for each file at
+ https://github.com/ComputationalRadiationPhysics/picongpu/tree/0.1.0/src/picongpu/include/simulation_defines/param
+ - `componentsConfig.param` & `gasConfig.param` fix typo `gasHomogeneous` #577
+ - `physicalConstants.param`: new variable `GAMMA_THRESH` #669
+ - `speciesAttributes.param`: new identifier `boundElectrons` and
+   new aliases `ionizer`, `atomicNumbers`
+ - `ionizationEnergies.param`, `ionizerConfig.param`: added
+
+**.unitless file changes:**
+ See full syntax for each file at
+ https://github.com/ComputationalRadiationPhysics/picongpu/tree/0.1.0/src/picongpu/include/simulation_defines/unitless
+ - `gasConfig.unitless`: typo in `gasHomogeneous` #577
+ - `speciesAttributes.unitless`: new unit for `boundElectrons` identifier
+ - `speciesDefinition.unitless`: new traits `GetCharge`, `GetMass`,
+   `GetChargeState` and added `ionizers`
+ - `ionizerConfig.unitless`: added
+
+**New Features:**
+ - initial support for field ionization:
+   - basic framework and BSI #595
+   - attribute (constant flag) for proton and neutron number #687 #731
+   - attribute `boundElectrons` #706
+ - tools:
+   - python scripts:
+     - new reader for `SliceFieldPrinter` plugin #578
+     - new analyzer tool for numerical heating #672 #692
+   - `cuda_memtest`:
+     - 32bit host system support (Jetson TK1) #583
+     - works without `nvidia-smi`, `grep` or `gawk` - optional with NVML for
+       GPU serial number detection (Jetson TK1) #626
+   - `splash2txt`:
+     - removed build option `S2T_RELEASE` and uses `CMAKE_BUILD_TYPE` #591
+   - `tbg`:
+     - allows for defaults for `-s`, `-t`, `-c` via env vars #613 #622
+   - 3D live visualization: `server` tool that collects `clients` and
+     simulations was published #641
+ - new/updated particle traits and attributes:
+   - `getCharge`, `getMass` #596
+   - attributes are now automatically initialized to their generic
+     defaults #607 #615
+ - libPMacc:
+   - machine-dependent `UInt` vector class is now split in explicit
+     `UInt32` and `UInt64` classes #665
+   - nvidia random number generators (RNG) refactored #711
+ - plugins:
+   - background fields do now affect plugins/outputs #600
+   - `Radiation` uses/requires HDF5 output #419 #610 #628 #646 #716
+   - `SliceFieldPrinter` supports `FieldJ`, output in one file,
+     updated command-line syntax #548
+   - `CountParticles`, `EnergyFields`, `EnergyParticles` support restarts
+     without overwriting their previous output #636 #703
+
+**Bug Fixes:**
+ - CUDA 6.5: `int(bool)` casts were broken (affects plugins
+   `BinEnergyParticles`, `PhaseSpace` and might had an effect on methods of the
+   basic PIC cycle) #570 #651 #656 #657 #678 #680
+ - the ZigZag current solver was broken for 2D3V if non-zero
+   momentum-components in z direction were used (e.g. warm plasmas or
+   purely transversal KHI) #823
+ - host-device-shared memory (SoC) support was broken (Jetson TK1) #633
+ - boost 1.56.0+ support via `Resolve<T>` trait #588 #593 #594
+ - potential race condition in field update and pusher #604
+ - using `--gridDist` could cause a segfault when adding additional arguments,
+   e.g., in 2D3V setups #638
+ - `MessageHeader` (used in `png` and 2D live visualization) leaked memory #683
+ - restarts with HDF5:
+   - static load-balancing via `--gridDist` in y-direction was broken #639
+   - parallel setups with particle-empty GPUs hung with HDF5 #609 #611 #642
+   - 2D3V field reads were broken (each field's z-component was not initialized
+     with the checkpointed values again, e.g., `B_z`) #688 #689
+   - loading more than 4 billion global particles was potentially broken #721
+ - plugins:
+   - `Visualization` (png & 2D live sim) memory bug in double precision runs #621
+   - `ADIOS`
+     - storing more than 4 billion particles was broken #666
+     - default of `adios.aggregators` was broken (now = MPI_Size) #662
+     - parallel setups with particle-empty GPUs did hang #661
+   - `HDF5`/`ADIOS` output of grid-mapped particle energy for non-relativistic
+     particles was zero #669
+ - libPMacc:
+   - CMake: path detection could fail #796 #808
+   - `DeviceBuffer<*,DIM3>::getPointer()` was broken (does not affect
+     PIConGPU) #647
+   - empty super-cell memory foot print reduced #648
+   - `float2int` return type should be int #623
+   - CUDA 7:
+     - cuSTL prefixed templates with `_` are not allowed; usage of static dim
+       member #630
+     - explicit call to `template`-ed `operator()` to avoid waring #750
+     - `EnvironmentController` caused a warning about `extendend friend syntax` #644
+   - multi-GPU nodes might fail to start up when not using `default` compute
+     mode with CUDA 7 drivers #643
+
+**Misc:**
+ - HDF5 support requires libSplash 1.2.4+ #642 #715
+ - various code clean-up for MSVC #563 #564 #566 #624 #625
+ - plugins:
+   - removed `LineSliceFields` #590
+   - `png` plugin write speedup ~2.3x by increasing file size about 12% #698
+ - updated contribution guidelines, install, cfg examples #601 #598 #617 #620
+   #673 #700 #714
+ - updated module examples and cfg files for:
+   - lawrencium (LBL) #612
+   - titan (ORNL) #618
+   - hypnos (HZDR) #670
+ - an `Empty` example was added, which defaults to the setup given by
+   all `.param` files in default mode (a standard PIC cycle without lasers nor
+   particles), see `src/picongpu/include/simulation_defines/` #634
+ - some source files had wrong file permissions #668
+
+
 Open Beta RC6
 -------------
 **Date:** 2014-11-25

README.md

@@ -112,6 +112,9 @@ codes. See the [user guide](https://github.com/ComputationalRadiationPhysics/pic
 our [getting started video](http://www.youtube.com/watch?v=7ybsD8G4Rsk) and
 [contact](http://www.hzdr.de/db/Cms?pNid=132&pOid=30354) us!
 
+Please sign up on our **PIConGPU-Users** mailing list:
+[Subscribe (Feed)](https://cg.hzdr.de/Lists/picongpu-users/List.html)
+
 **Upgrades:** Every time we update the *master* branch, we publish a new release
 of PIConGPU. Before you pull the changes in, please read our [ChangeLog](CHANGELOG.md)!
 You may have to update some of your simulation `.param` files by hand
@@ -141,10 +144,9 @@ Active Team
 - Axel Huebl*
 - Maximilian Knespel
 - Richard Pausch*
-- Felix Schmitt*
-- Conrad Schumann
+- Stefan Tietze
 - Rene Widera*
-- Benjamin Worpitz
+- Benjamin Worpitz*
 
 ### Participants, Former Members and Thanks
 
@@ -156,8 +158,10 @@ The PIConGPU Team expresses its thanks to:
 - Anton Helm
 - Wolfgang Hoehnig
 - Dr. Remi Lehe
+- Felix Schmitt(*)
 - Benjamin Schneider
 - Joseph Schuchart
+- Conrad Schumann
 - Klaus Steiniger
 
 Kudos to everyone who helped!

doc/TBG_macros.cfg

@@ -23,8 +23,8 @@
 ## To see all flags available for your PIConGPU binary, run
 ## picongpu --help. The avalable flags depend on your configuration flags.
 ##
-## Flags that target a specific species e.g. electrons (--png_e) or ions
-## (--png_i) must only be used if the respective species is activated (configure flags).
+## Flags that target a specific species e.g. electrons (--e_png) or ions
+## (--i_png) must only be used if the respective species is activated (configure flags).
 ##
 ## If not stated otherwise, variables/flags must not be used more than once!
 ################################################################################
@@ -83,88 +83,73 @@ TBG_periodic="--periodic 1 0 1"
 # Enables moving window (sliding) in your simulation
 TBG_movingWindow="-m"
 
+################################################################################
+## Placeholder for multi data plugins:
+##  
+## placeholders must be substituted with the real data name
+##
+## <species> = species name e.g. e (electrons), i (ions)
+## <field>  = field names e.g. FieldE, FieldB, FieldJ
+################################################################################
 
 # The following flags are available for the radiation plugin.
 # For a full description, see the plugins section in the online wiki.
-#--radiation_e.period 	Radiation is calculated every .period steps. Currently 0 or 1
-#--radiation_e.dump 	Period, after which the calculated radiation data should be dumped to the file system
-#--radiation_e.lastRadiation 	If set to 1, the spectra summed between the last and the current dump-time-step are stored
-#--radiation_e.folderLastRad 	Folder in which the summed spectra are stored
-#--radiation_e.totalRadiation 	Set to 1 to store spectra summed from simulation start till current time step
-#--radiation_e.folderTotalRad 	Folder in which total radiation spectra are stored
-#--radiation_e.start 	Time step to start calculating the radition
-#--radiation_e.end 	Time step to stop calculating the radiation
-#--radiation_e.omegaList 	If spectrum frequencies are taken from a file, this gives the path to this list
-#--radiation_e.radPerGPU 	If set to 1, each GPU stores its own spectra without summing the entire simulation area
-#--radiation_e.folderRadPerGPU 	Folder where the GPU specific spectras are stored
-TBG_radiation="--radiation_e.period 1 --radiation_e.dump 2 --radiation_e.totalRadiation 1 \
-               --radiation_e.lastRadiation 0 --radiation_e.start 2800 --radiation_e.end 3000"
+#--<species>_radiation.period 	Radiation is calculated every .period steps. Currently 0 or 1
+#--<species>_radiation.dump 	Period, after which the calculated radiation data should be dumped to the file system
+#--<species>_radiation.lastRadiation 	If flag is set, the spectra summed between the last and the current dump-time-step are stored
+#--<species>_radiation.folderLastRad 	Folder in which the summed spectra are stored
+#--<species>_radiation.totalRadiation 	If flag is set, store spectra summed from simulation start till current time step
+#--<species>_radiation.folderTotalRad 	Folder in which total radiation spectra are stored
+#--<species>_radiation.start 	Time step to start calculating the radition
+#--<species>_radiation.end 	Time step to stop calculating the radiation
+#--<species>_radiation.omegaList 	If spectrum frequencies are taken from a file, this gives the path to this list
+#--<species>_radiation.radPerGPU 	If flag is set, each GPU stores its own spectra without summing the entire simulation area
+#--<species>_radiation.folderRadPerGPU 	Folder where the GPU specific spectras are stored
+#--e_<species>_radiation.compression    If flag is set, the hdf5 output will be compressed.
+TBG_radiation="--<species>_radiation.period 1 --<species>_radiation.dump 2 --<species>_radiation.totalRadiation \
+               --<species>_radiation.lastRadiation --<species>_radiation.start 2800 --<species>_radiation.end 3000"
 
 
 # Create 2D images in PNG format every .period steps.
-# Images can be created for the following particle species:
-# - Electrons (--png_e)
-# - Ions      (--png_i)
 # The slice plane is defined using .axis [yx,yz] and .slicePoint (offset from origin
 # as a float within [0.0,1.0].
 # The output folder can be set with .folder.
 # Can be used more than once to print different images, e.g. for YZ and YX planes.
-TBG_E_pngYZ="--png_e.period 10 --png_e.axis yz --png_e.slicePoint 0.5 --png_e.folder pngElectronsYZ"
-TBG_E_pngYX="--png_e.period 10 --png_e.axis yx --png_e.slicePoint 0.5 --png_e.folder pngElectronsYX"
-TBG_I_pngYZ="--png_i.period 10 --png_i.axis yz --png_i.slicePoint 0.5 --png_i.folder pngIonsYZ"
-TBG_I_pngYX="--png_i.period 10 --png_i.axis yx --png_i.slicePoint 0.5 --png_i.folder pngIonsYX"
+TBG_<species>_pngYZ="--<species>_png.period 10 --<species>_png.axis yz --<species>_png.slicePoint 0.5 --<species>_png.folder pngElectronsYZ"
+TBG_<species>_pngYX="--<species>_png.period 10 --<species>_png.axis yx --<species>_png.slicePoint 0.5 --<species>_png.folder pngElectronsYX"
 
 
 # Notification period of position plugin (single-particle debugging)
-TBG_E_pos_dbg="--pos_e.period 1"
+TBG_<species>_pos_dbg="--<species>_position.period 1"
 
 
-# Create a particle-energy histogram [in keV] every .period steps for:
-# - Electrons (--bin_e)
-# - Ions      (--bin_i)
-TBG_eBin="--bin_e.period 500 --bin_e.binCount 1024 --bin_e.minEnergy 0 --bin_e.maxEnergy 500000"
-TBG_iBin="--bin_i.period 500 --bin_i.binCount 1024 --bin_i.minEnergy 0 --bin_i.maxEnergy 500000"
+# Create a particle-energy histogram [in keV] per species for every .period steps
+TBG_<species>_Histogram="--<species>_energyHistogram.period 500 --<species>_energyHistogram.binCount 1024 \
+                       --<species>_energyHistogram.minEnergy 0 --<species>_energyHistogram.maxEnergy 500000"
 
 
 # Calculate a 2D phase space
 # - requires parallel libSplash for HDF5 output
 # - momentum range in m_e c
-TBG_ePSxpx="--ps_e.period 10 --ps_e.space x --ps_e.momentum px --ps_e.min -1.0 --ps_e.max 1.0"
-TBG_ePSxpz="--ps_e.period 10 --ps_e.space x --ps_e.momentum pz --ps_e.min -1.0 --ps_e.max 1.0"
-TBG_ePSypx="--ps_e.period 10 --ps_e.space y --ps_e.momentum px --ps_e.min -1.0 --ps_e.max 1.0"
-TBG_ePSypy="--ps_e.period 10 --ps_e.space y --ps_e.momentum py --ps_e.min -1.0 --ps_e.max 1.0"
-TBG_ePSypz="--ps_e.period 10 --ps_e.space y --ps_e.momentum pz --ps_e.min -1.0 --ps_e.max 1.0"
-
-
-# Binary density output for slides every .period steps over axis .axis [yx,yz]
-# at offset .slicePoint [0.0,1.0] from origin to folder .folder.
-# Possible for:
-# - Electrons (--binDensity_e)
-# - Ions      (--binDensity_i)
-TBG_E_binaryDensity="--binDensity_e.period 100 --binDensity_e.axis yx \
-                   --binDensity_e.slicePoint 0.5 --binDensity_e.folder densityElectrons"
-TBG_I_binaryDensity="--binDensity_i.period 100 --binDensity_i.axis yx \
-                   --binDensity_i.slicePoint 0.5 --binDensity_i.folder densityIons"
+TBG_<species>_PSxpx="--<species>_phaseSpace.period 10 --<species>_phaseSpace.space x --<species>_phaseSpace.momentum px --<species>_phaseSpace.min -1.0 --<species>_phaseSpace.max 1.0"
+TBG_<species>_PSxpz="--<species>_phaseSpace.period 10 --<species>_phaseSpace.space x --<species>_phaseSpace.momentum pz --<species>_phaseSpace.min -1.0 --<species>_phaseSpace.max 1.0"
+TBG_<species>_ePSypx="--<species>_phaseSpace.period 10 --<species>_phaseSpace.space y --<species>_phaseSpace.momentum px --<species>_phaseSpace.min -1.0 --<species>_phaseSpace.max 1.0"
+TBG_<species>_PSypy="--<species>_phaseSpace.period 10 --<species>_phaseSpace.space y --<species>_phaseSpace.momentum py --<species>_phaseSpace.min -1.0 --<species>_phaseSpace.max 1.0"
+TBG_<species>_PSypz="--<species>_phaseSpace.period 10 --<species>_phaseSpace.space y --<species>_phaseSpace.momentum pz --<species>_phaseSpace.min -1.0 --<species>_phaseSpace.max 1.0"
 
 
 # Sum up total energy every .period steps for
-# - Electrons (--energy_e)
-# - Ions      (--energy_i)
-# - Fields    (--energy_fields)
-TBG_sumEnergy="--energy_fields.period 10 --energy_e.period 10 --energy_i.period 10"
+# - species   (--<species>_energy)
+# - fields    (--fields_energy)
+TBG_sumEnergy="--fields_energy.period 10 --<species>_energy.period 10"
 
 
-# Count the number of macro particles every .period steps for
-# - Electrons (--elec_cnt)
-# - Ions      (--ions_cnt)
-TBG_macroCount="--elec_cnt.period 100 --ions_cnt.period 100"
+# Count the number of macro particles per species for every .period steps
+TBG_macroCount="--<species>_macroParticlesCount.period 100"
 
 
-# Count makro particles per super cell
-#   (creates HDF5 output via libSplash)
-# - Electrons (--countPerSuperCell_e)
-# - Ions      (--countPerSuperCell_i)
-TBG_countPerSuper="--countPerSuperCell_e.period 100 --countPerSuperCell_i.period 100"
+# Count makro particles of a species per super cell
+TBG_countPerSuper="--<species>_macroParticlesPerSuperCell.period 100 --<species>_macroParticlesPerSuperCell.period 100"
 
 # Dump simulation data (fields and particles) to HDF5 files using libSplash.
 # Data is dumped every .period steps to the fileset .file.
@@ -191,10 +176,10 @@ TBG_restart="--restart"
 #   --restart-directory /path/to/simOutput/checkpoints
 
 # Connect to a live-view server (start the server in advance)
-TBG_liveViewYX="--live_e.period 1 --live_e.slicePoint 0.5 --live_e.ip 10.0.2.254 \
-                --live_e.port 2020 --live_e.axis yx"
-TBG_liveViewYZ="--live_e.period 1 --live_e.slicePoint 0.5 --live_e.ip 10.0.2.254 \
-                --live_e.port 2021 --live_e.axis yz"
+TBG_liveViewYX="--<species>_liveView.period 1 --<species>_liveView.slicePoint 0.5 --<species>_liveView.ip 10.0.2.254 \
+                --<species>_liveView.port 2020 --<species>_liveView.axis yx"
+TBG_liveViewYZ="--<species>_liveView.period 1 --<species>_liveView.slicePoint 0.5 --<species>_liveView.ip 10.0.2.254 \
+                --<species>_liveView.port 2021 --<species>_liveView.axis yz"
 
 
 ################################################################################

examples/Bunch/cmakeFlags

@@ -30,7 +30,8 @@
 #   - increase by 1, no gaps
 
 flags[0]="-DCUDA_ARCH=sm_35"
-
+flags[1]="-DCUDA_ARCH=sm_35 -DPARAM_OVERWRITES:LIST=-DPARAM_INCLUDE_FIELDBACKGROUND=true"
+flags[2]="-DCUDA_ARCH=sm_35 -DPARAM_OVERWRITES:LIST=-DPARAM_INCLUDE_FIELDBACKGROUND=true;-DPARAM_DIMENSION=DIM2"
 
 ################################################################################
 # execution

examples/Bunch/include/simulation_defines/param/componentsConfig.param

@@ -1,5 +1,5 @@
 /**
- * Copyright 2013-2014 Axel Huebl, Anton Helm, Richard Pausch
+ * Copyright 2013-2015 Axel Huebl, Anton Helm, Richard Pausch
  *
  * This file is part of PIConGPU.
  *
@@ -36,6 +36,7 @@ namespace simulation_starter = defaultPIConGPU;
  *                            in 'x' direction
  *  - laserWavepacket       : wavepacket (Gaussian in time and space, not focusing)
  *  - laserPlaneWave        : a plane wave
+ *  - laserPolynom          : a polynomial laser envelope
  */
 namespace laserProfile = laserPlaneWave;