Merge pull request #2789 from ComputationalRadiationPhysics/release-0…

….4.1 Release 0.4.1
ComputationalRadiationPhysics · Nov 6, 2018 · f6f8ebd · f6f8ebd
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diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,120 @@
+{
+    "creators": [
+      {
+        "affiliation": "HZDR, TU Dresden",
+        "name": "Huebl, Axel",
+        "orcid": "0000-0003-1943-7141"
+      },
+      {
+        "affiliation": "HZDR",
+        "name": "Widera, René",
+        "orcid": "0000-0003-1642-0459"
+      },
+      {
+        "affiliation": "LogMeIn, Inc.",
+        "name": "Worpitz, Benjamin"
+      },
+      {
+        "affiliation": "HZDR, TU Dresden",
+        "name": "Pausch, Richard",
+        "orcid": "0000-0001-7990-9564"
+      },
+      {
+        "affiliation": "HZDR, TU Dresden",
+        "name": "Burau, Heiko"
+      },
+      {
+        "affiliation": "HZDR, TU Dresden",
+        "name": "Garten, Marco",
+        "orcid": "0000-0001-6994-2475"
+      },
+      {
+        "affiliation": "HZDR",
+        "name": "Starke, Sebastian"
+      },
+      {
+        "affiliation": "HZDR, TU Dresden",
+        "name": "Grund, Alexander",
+        "orcid": "0000-0002-7196-8452"
+      },
+      {
+        "affiliation": "HZDR",
+        "name": "Debus, Alexander",
+        "orcid": "0000-0002-3844-3697"
+      },
+      {
+        "affiliation": "HZDR, TU Dresden",
+        "name": "Matthes, Alexander",
+        "orcid": "0000-0002-6702-2015"
+      },
+      {
+        "affiliation": "HZDR",
+        "name": "Bastrakov, Sergei",
+        "orcid": "0000-0003-3396-6154"
+      },
+      {
+        "affiliation": "HZDR",
+        "name": "Steiniger, Klaus",
+        "orcid": "0000-0001-8965-1149"
+      },
+      {
+        "affiliation": "HZDR",
+        "name": "Göthel, Ilja"
+      },
+      {
+        "affiliation": "HZDR, TU Dresden",
+        "name": "Rudat, Sophie"
+      },
+      {
+        "affiliation": "HZDR",
+        "name": "Kelling, Jeffrey",
+        "orcid": "0000-0003-1761-2591"
+      },
+      {
+        "affiliation": "HZDR",
+        "name": "Bussmann, Michael",
+        "orcid": "0000-0002-8258-3881"
+      }
+    ],
+    "grants": [
+      {
+        "acronym": "EUCALL",
+        "code": "654220",
+        "funder": {
+          "acronyms": [
+            "EC"
+          ],
+          "doi": "10.13039/501100000780",
+          "links": {
+            "self": "https://zenodo.org/api/funders/10.13039/501100000780"
+          },
+          "name": "European Commission"
+        },
+        "links": {
+          "self": "https://zenodo.org/api/grants/10.13039/501100000780::654220"
+        },
+        "program": "H2020",
+        "title": "European Cluster of Advanced Laser Light Sources"
+      }
+    ],
+    "keywords": [
+      "PIConGPU",
+      "CUDA",
+      "OpenMP",
+      "manycore",
+      "Plasma Physics",
+      "GPU"
+    ],
+    "language": "eng",
+    "access_right": "open",
+    "license": {
+      "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"
+    ]
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,46 @@
 Changelog
 =========
 
+0.4.1
+-----
+**Date:** 2018-11-06
+
+Minor Bugs and Example Updates
+
+This release fixes minor bugs found after the 0.4.0 release.
+Some examples were slightly outdated in syntax, the new "probe particle"
+`EveryNthCell` initialization functor was broken when not used with equal
+spacing per dimension. In some rare cases, sliding could occur twice in
+moving window simulations.
+
+Thanks to Axel Huebl, René Widera, Richard Pausch and Andrei Berceanu for
+contributions to this release!
+
+### Changes to "0.4.1"
+
+**Bug Fixes:**
+- PIConGPU:
+  - avoid sliding twice in some corner-cases #2774
+  - EveryNthCell: broken if not used with same spacing #2768
+  - broken compile with particle merging #2753
+- Examples:
+  - fix outdated derive species #2756
+  - remove current deposition in bunch example #2758
+  - fix 2D case of single electron init (via density) #2766
+- Tools:
+  - Python Regex: r Literals #2767
+  - `cuda_memtest`: avoid noisy output if NVML is not found #2785
+
+**Misc:**
+- `.param` files: refactor `boost::vector<>` usage #2769
+- Docs:
+  - Spack: Improve Bootstrap #2773
+  - Fix docs for radiation in 2D #2772
+  - Containers: Update 0.4.0 #2750
+  - Update Readme & License: People #2749
+  - Add `.zenodo.json` #2747
+
+
 0.4.0
 -----
 **Date:** 2018-10-19

diff --git a/LICENSE.md b/LICENSE.md
@@ -1,13 +1,15 @@
- PIConGPU - Licenses
-================================================================================
-
-**Copyright 2009-2017** Florian Berninger, Heiko Burau, Michael Bussmann,
-                        Alexander Debus, Robert Dietrich, Carlchristian Eckert,
-                        Wen Fu, Marco Garten, Anton Helm, Wolfgang Hoehnig,
-                        Axel Huebl, Maximilian Knespel, Remi Lehe,
-                        Richard Pausch, Felix Schmitt, Conrad Schumann,
-                        Benjamin Schneider, Joseph Schuchart, Klaus Steiniger,
-                        Rene Widera, Benjamin Worpitz
+PIConGPU - Licenses
+===============================================================================
+
+**Copyright 2009-2018** (in alphabetical order)
+
+Sergei Bastrakov, Florian Berninger, Heiko Burau, Michael Bussmann,
+Alexander Debus, Robert Dietrich, Carlchristian Eckert, Wen Fu, Marco Garten,
+Ilja Goethel, Alexander Grund, Sebastian Hahn, Anton Helm, Wolfgang Hoehnig,
+Axel Huebl, Jeffrey Kelling, Maximilian Knespel, Remi Lehe, Alexander Matthes,
+Richard Pausch, Rophie Rudat, Felix Schmitt, Conrad Schumann,
+Benjamin Schneider, Joseph Schuchart, Sebastian Starke, Klaus Steiniger,
+Rene Widera, Benjamin Worpitz
 
 See [active team](README.md#active-team).
 

diff --git a/README.md b/README.md
@@ -200,7 +200,7 @@ Active Team
 ### Scientific Supervision
 
 - Dr. Michael Bussmann
-- Dr.-Ing. Guido Juckeland
+- Axel Huebl
 
 ### Maintainers* and core developers
 
@@ -210,18 +210,20 @@ Active Team
 - Axel Huebl*
 - Alexander Matthes
 - Richard Pausch*
+- Sophie Rudat
 - Sebastian Starke
+- Dr. Klaus Steiniger
 - Rene Widera*
 
 ### Former Members, Contributions and Thanks
 
 The PIConGPU Team expresses its gratitude to:
 
 Florian Berninger, Heiko Burau, Robert Dietrich, Carlchristian Eckert,
-Wen Fu, Ph.D., Alexander Grund, Anton Helm, Wolfgang Hoehnig, Maximilian
-Knespel, Dr. Remi Lehe, Felix Schmitt, Benjamin Schneider, Joseph Schuchart,
-Conrad Schumann, Klaus Steiniger, Stefan Tietze, Marija Vranic, Ph.D.,
-Benjamin Worpitz, Erik Zenker, Alexander Matthes
+Wen Fu, Ph.D., Alexander Grund, Sebastian Hahn, Anton Helm, Wolfgang Hoehnig,
+Dr.-Ing. Guido Juckeland, Jeffrey Kelling, Maximilian Knespel, Dr. Remi Lehe,
+Felix Schmitt, Benjamin Schneider, Joseph Schuchart, Conrad Schumann,
+Stefan Tietze, Marija Vranic, Ph.D., Benjamin Worpitz, and Erik Zenker.
 
 Kudos to everyone, mentioned or unmentioned, who contributed further in any
 way!

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -105,9 +105,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.4.0'
+version = u'0.4.1'
 # The full version, including alpha/beta/rc tags.
-release = u'0.4.0'
+release = u'0.4.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/source/install/instructions/spack.rst b/docs/source/install/instructions/spack.rst
@@ -24,14 +24,14 @@ First `install spack <http://spack.readthedocs.io/en/latest/getting_started.html
    # get spack
    git clone https://github.com/spack/spack.git $HOME/src/spack
 
+   # build spack's dependencies via spack :)
+   $HOME/src/spack/bin/spack bootstrap
+
    # activate the spack environment
    source $HOME/src/spack/share/spack/setup-env.sh
 
-   # build spack's dependencies via spack :)
-   spack bootstrap
-
    # install a supported compiler
-   spack compiler list | grep [email protected] | spack install [email protected] && spack load [email protected] && spack compiler add
+   spack compiler list | grep [email protected] 1>/dev/null && spack install [email protected] && spack load [email protected] && spack compiler add
 
    # add the PIConGPU repository
    git clone https://github.com/ComputationalRadiationPhysics/spack-repo.git $HOME/src/spack-repo

diff --git a/docs/source/models/field_ionization_comparison_c_ii_ionization.py b/docs/source/models/field_ionization_comparison_c_ii_ionization.py
@@ -77,27 +77,27 @@ def ADK_rate_simple(Z, E_i, F):
     p_H = plt.plot(fields, H, label="ADK H")
 
     p_Csimple = plt.plot(fields, Csimple,
-                         label="ADK C  $ \quad Z = 2\mathrm{+}$")
+                         label=r"ADK C  $ \quad Z = 2\mathrm{+}$")
     p_Ceff = plt.plot(fields, Ceff,
-                      label="ADK C (eff) $ \quad Z = 3.136 = Z_\mathrm{eff}$")
+                      label=r"ADK C (eff) $ \quad Z = 3.136 = Z_\mathrm{eff}$")
     plt.vlines(E_H**2./(4*1), ymin, ymax,
                colors="{}".format(p_H[0].get_color()),
-               label="$F_\mathrm{BSI}$ H", linestyles="--")
+               label=r"$F_\mathrm{BSI}$ H", linestyles="--")
 
     plt.vlines(E_C[1]**2. / (4*2), ymin, ymax,
                colors="{}".format(p_Csimple[0].get_color()),
-               label="$F_\mathrm{BSI}$ C", linestyles="--")
+               label=r"$F_\mathrm{BSI}$ C", linestyles="--")
     plt.vlines(E_C[1]**2. / (4*3.136), ymin, ymax,
                colors="{}".format(p_Ceff[0].get_color()),
-               label="$F_\mathrm{BSI}$ C (eff)", linestyles="--")
+               label=r"$F_\mathrm{BSI}$ C (eff)", linestyles="--")
 
     plt.title("Comparison of ADK ionization rates for\nCarbon-II and Hydrogen")
     plt.ylim([ymin, ymax])
     plt.xlim([1e-2, 1e1])
     plt.yscale("log")
     plt.xscale("log")
-    plt.ylabel("ionization rate $\Gamma$ [s$^{-1}$]")
-    plt.xlabel("field strength $F$ [AU = 5.1422$\cdot 10^{11}$ V/m]")
+    plt.ylabel(r"ionization rate $\Gamma$ [s$^{-1}$]")
+    plt.xlabel(r"field strength $F$ [AU = 5.1422$\cdot 10^{11}$ V/m]")
     plt.legend(loc="best")
 
     plt.show()
diff --git a/docs/source/models/field_ionization_effective_potentials.py b/docs/source/models/field_ionization_effective_potentials.py
@@ -78,16 +78,16 @@ def V_eff(x, Z_eff, F):
     plt.hlines(-E_CII, xmin, xmax)
 
     # add the legend and format the plot
-    plt.title("Effective atomic potentials of Carbon-II and Hydrogen in\n"
-              "homogeneous electric field $F_\mathrm{BSI}$ (C-II)")
+    plt.title(r"Effective atomic potentials of Carbon-II and Hydrogen in\n"
+              r"homogeneous electric field $F_\mathrm{BSI}$ (C-II)")
     plt.legend(loc="best")
     plt.text(xmin+1, -E_H+.05, r"$E_\mathrm{i}$ H")
     plt.text(xmin+1, -E_CII+.05, r"$E_\mathrm{i}$ C-II (Z_eff)")
     plt.text(xmin+1, -2.1, r"$V_\mathrm{eff} = -\frac{Z}{|x|} + Fx$")
     plt.text(xmin+1, -2.6, r"$\mathrm{\ with\ } F = F_\mathrm{BSI}$(C-II)")
     plt.xlim([-10., 10.])
     plt.ylim([-3., 1.])
-    plt.ylabel("$V_\mathrm{eff}$ [AU = Rydberg]")
-    plt.xlabel("$x$ [AU = Bohr radii]")
+    plt.ylabel(r"$V_\mathrm{eff}$ [AU = Rydberg]")
+    plt.xlabel(r"$x$ [AU = Bohr radii]")
 
     plt.show()
diff --git a/docs/source/usage/plugins/adios.rst b/docs/source/usage/plugins/adios.rst
@@ -22,7 +22,7 @@ One can e.g. disable the output of particles by setting:
    /* output all species */
    using FileOutputParticles = VectorAllSpecies;
    /* disable */
-   using FileOutputParticles = bmpl::vector0< >;
+   using FileOutputParticles = MakeSeq_t< >;
 
 .cfg file
 ^^^^^^^^^

diff --git a/docs/source/usage/plugins/hdf5.rst b/docs/source/usage/plugins/hdf5.rst
@@ -38,7 +38,7 @@ One can e.g. disable the output of particles by setting:
    /* output all species */
    using FileOutputParticles = VectorAllSpecies;
    /* disable */
-   using FileOutputParticles = bmpl::vector0< >;
+   using FileOutputParticles = MakeSeq_t< >;
 
 .cfg file
 ^^^^^^^^^

diff --git a/docs/source/usage/plugins/radiation.rst b/docs/source/usage/plugins/radiation.rst
@@ -326,8 +326,6 @@ Tool                           Description
 Known Issues
 ^^^^^^^^^^^^
 
-Currently, the radiation plugin does not support 2D simulations. 
-This should be fixed with `issue #289 <https://github.com/ComputationalRadiationPhysics/picongpu/issues/289>`_ .
 The plugin supports multiple radiation species but spectra (frequencies and observation directions) are the same for all species. 
 
 

diff --git a/docs/source/usage/workflows/probeParticles.rst b/docs/source/usage/workflows/probeParticles.rst
@@ -20,7 +20,7 @@ Workflow
 
 .. code-block:: cpp
 
-    using ParticleFlagsProbes = bmpl::vector<
+    using ParticleFlagsProbes = MakeSeq_t<
         particlePusher< particles::pusher::Probe >,
         shape< UsedParticleShape >,
         interpolation< UsedField2Particle >
@@ -84,7 +84,7 @@ and add it to ``VectorAllSpecies``:
 
 .. code-block:: cpp
 
-   using InitPipeline = mpl::vector<
+   using InitPipeline = bmpl::vector<
        // ... ,
        CreateDensity<
            densityProfiles::ProbeEveryFourthCell,

diff --git a/docs/source/usage/workflows/quasiNeutrality.rst b/docs/source/usage/workflows/quasiNeutrality.rst
@@ -15,7 +15,7 @@ For fully ionized ions, just use ``ManipulateDeriveSpecies`` in :ref:`speciesIni
 
 .. code-block:: cpp
 
-   using InitPipeline = mpl::vector<
+   using InitPipeline = bmpl::vector<
        /* density profile from density.param and
         *     start position from particle.param */
        CreateDensity<
@@ -72,7 +72,7 @@ Then again in :ref:`speciesInitialization.param <usage-params-core>` set your in
 
 .. code-block:: cpp
 
-   using InitPipeline = mpl::vector<
+   using InitPipeline = bmpl::vector<
        /* density profile from density.param and
         *     start position from particle.param */
        CreateDensity<

diff --git a/include/picongpu/param/fileOutput.param b/include/picongpu/param/fileOutput.param
@@ -111,7 +111,7 @@ namespace picongpu
     /** FileOutputParticles: Groups all Species that shall be dumped **********
      *
      * hint: to disable particle output set to
-     *   using FileOutputParticles = bmpl::vector0< >;
+     *   using FileOutputParticles = MakeSeq_t< >;
      */
     using FileOutputParticles = VectorAllSpecies;