From c4332a38becaea3b48f48dd15c8844aebd1b8b48 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Sat, 20 Jul 2019 18:49:45 +0200
Subject: [PATCH 01/11] Fix new issue with Mayavi dependencies

---
 src/python/espressomd/visualization.pyx | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/python/espressomd/visualization.pyx b/src/python/espressomd/visualization.pyx
index 5947d81d258..db417c0a31a 100644
--- a/src/python/espressomd/visualization.pyx
+++ b/src/python/espressomd/visualization.pyx
@@ -6,12 +6,16 @@ try:
         from .visualization_mayavi import mayaviLive
     else:
         raise ImportError("Cannot connect to X server")
-except ImportError as e:
-    class mayaviLive(object):
-        deferred_ImportError = e
+except BaseException as e:
+    if isinstance(e, ImportError) or isinstance(e, RuntimeError) and \
+            e.args[0] == 'No pyface.toolkits plugin could be loaded for wx':
+        class mayaviLive(object):
+            deferred_ImportError = e
 
-        def __init__(self, *args, **kwargs):
-            raise self.deferred_ImportError
+            def __init__(self, *args, **kwargs):
+                raise self.deferred_ImportError
+    else:
+        raise e
 
 try:
     from .visualization_opengl import openGLLive

From 028ad7981bdb61f5ea2b5886d30c8609d48cfee2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Sat, 20 Jul 2019 18:52:13 +0200
Subject: [PATCH 02/11] Update tutorials kernel to Python3

Python2 is not supported anymore. Tutorials now start with the
Python3 kernel.
---
 doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb  | 10 +++++-----
 .../02-charged_system/02-charged_system-1.ipynb        | 10 +++++-----
 .../02-charged_system/02-charged_system-2.ipynb        | 10 +++++-----
 .../04-lattice_boltzmann_part1.ipynb                   | 10 +++++-----
 .../04-lattice_boltzmann_part2.ipynb                   | 10 +++++-----
 .../04-lattice_boltzmann_part3.ipynb                   | 10 +++++-----
 .../04-lattice_boltzmann_part4.ipynb                   | 10 +++++-----
 .../05-raspberry_electrophoresis.ipynb                 | 10 +++++-----
 doc/tutorials/08-visualization/08-visualization.ipynb  | 10 +++++-----
 doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb  | 10 +++++-----
 doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb  | 10 +++++-----
 doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb  | 10 +++++-----
 12 files changed, 60 insertions(+), 60 deletions(-)

diff --git a/doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb b/doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb
index 940b5fb2db7..c92c3f7cf47 100644
--- a/doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb
+++ b/doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb
@@ -598,21 +598,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15rc1"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/02-charged_system/02-charged_system-1.ipynb b/doc/tutorials/02-charged_system/02-charged_system-1.ipynb
index d3a3354ba26..61f6d856831 100644
--- a/doc/tutorials/02-charged_system/02-charged_system-1.ipynb
+++ b/doc/tutorials/02-charged_system/02-charged_system-1.ipynb
@@ -461,21 +461,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.14"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/02-charged_system/02-charged_system-2.ipynb b/doc/tutorials/02-charged_system/02-charged_system-2.ipynb
index 2afb32949a7..fed6d5a19cb 100644
--- a/doc/tutorials/02-charged_system/02-charged_system-2.ipynb
+++ b/doc/tutorials/02-charged_system/02-charged_system-2.ipynb
@@ -471,21 +471,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.14"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part1.ipynb b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part1.ipynb
index f7e8775ca0f..8528d0a2251 100644
--- a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part1.ipynb
+++ b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part1.ipynb
@@ -521,21 +521,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
index d8e68103332..9a152884286 100644
--- a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
+++ b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
@@ -192,21 +192,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part3.ipynb b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part3.ipynb
index 9273fab2eab..4d57a7f67b4 100644
--- a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part3.ipynb
+++ b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part3.ipynb
@@ -187,21 +187,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part4.ipynb b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part4.ipynb
index 431b546bc41..59bb2ae11b8 100644
--- a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part4.ipynb
+++ b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part4.ipynb
@@ -124,21 +124,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb b/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb
index ba32ec538b0..ac1c46563cd 100644
--- a/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb
+++ b/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb
@@ -615,21 +615,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/08-visualization/08-visualization.ipynb b/doc/tutorials/08-visualization/08-visualization.ipynb
index f217b0f45ef..afdd9c25d3a 100644
--- a/doc/tutorials/08-visualization/08-visualization.ipynb
+++ b/doc/tutorials/08-visualization/08-visualization.ipynb
@@ -384,21 +384,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15rc1"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
index a4ec29660d3..c95205b8230 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
@@ -820,21 +820,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15rc1"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
index 259875c8d57..23689af8240 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
@@ -852,21 +852,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15rc1"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
index 2f4922eaa59..c310b248b70 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
@@ -680,21 +680,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15rc1"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

From 48e9682246c4930530f3e4efe9f5504cb375605f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Sat, 20 Jul 2019 18:54:26 +0200
Subject: [PATCH 03/11] Fix matplotlib plotting in notebook mode

Having the matplotlib import statement in the same cell as plt.show()
causes the matplotlib object to be returned instead of being drawn in
the notebook. The user has to run the cell again to get the plot drawn.
---
 .../02-charged_system/02-charged_system-2.ipynb       | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/doc/tutorials/02-charged_system/02-charged_system-2.ipynb b/doc/tutorials/02-charged_system/02-charged_system-2.ipynb
index fed6d5a19cb..3c897e5a2fd 100644
--- a/doc/tutorials/02-charged_system/02-charged_system-2.ipynb
+++ b/doc/tutorials/02-charged_system/02-charged_system-2.ipynb
@@ -425,8 +425,15 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "plt.ion()\n",
-    "\n",
+    "plt.ion()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "plt.figure(figsize=(10, 6), dpi=80)\n",
     "plt.plot(z_values, z_dens_na, label='Na')\n",
     "plt.plot(z_values, z_dens_cl, label='Cl')\n",

From dc7e9824b4422b140e39a004d1d743effdd535fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Sat, 20 Jul 2019 19:02:57 +0200
Subject: [PATCH 04/11] Move main() definition

---
 .../scripts/nacl_units_vis.py                 | 159 +++++++++---------
 1 file changed, 81 insertions(+), 78 deletions(-)

diff --git a/doc/tutorials/02-charged_system/scripts/nacl_units_vis.py b/doc/tutorials/02-charged_system/scripts/nacl_units_vis.py
index e207dc30d8b..665dfb1333f 100644
--- a/doc/tutorials/02-charged_system/scripts/nacl_units_vis.py
+++ b/doc/tutorials/02-charged_system/scripts/nacl_units_vis.py
@@ -67,88 +67,91 @@ def decreaseTemp():
     'g', visualization_opengl.KeyboardFireEvent.Hold, decreaseTemp))
 
 
-def main():
+print("\n--->Setup system")
+
+# System parameters
+n_ppside = 10
+n_part = int(n_ppside**3)
+n_ionpairs = n_part / 2
+density = 1.5736
+time_step = 0.001823
+temp = 298.0
+gamma = 20.0
+#l_bjerrum = 0.885^2 * e^2/(4*pi*epsilon_0*k_B*T)
+l_bjerrum = 130878.0 / temp
+
+num_steps_equilibration = 30
+
+# Particle parameters
+types = {"Cl": 0, "Na": 1}
+numbers = {"Cl": n_ionpairs, "Na": n_ionpairs}
+charges = {"Cl": -1.0, "Na": 1.0}
+lj_sigmas = {"Cl": 3.85, "Na": 2.52}
+lj_epsilons = {"Cl": 192.45, "Na": 17.44}
+
+lj_cuts = {"Cl": 3.0 * lj_sigmas["Cl"],
+           "Na": 3.0 * lj_sigmas["Na"]}
+
+masses = {"Cl": 35.453, "Na": 22.99}
+
+# Setup System
+box_l = (n_ionpairs * sum(masses.values()) / density)**(1. / 3.)
+system.box_l = [box_l, box_l, box_l]
+system.periodicity = [1, 1, 1]
+system.time_step = time_step
+system.cell_system.skin = 0.3
+system.thermostat.set_langevin(kT=temp, gamma=gamma, seed=42)
+
+# Place particles on a face-centered cubic lattice
+q = 1
+l = box_l / n_ppside
+for i in range(n_ppside):
+    for j in range(n_ppside):
+        for k in range(n_ppside):
+            p = numpy.array([i, j, k]) * l
+            if q < 0:
+                system.part.add(id=len(
+                    system.part), type=types["Cl"], pos=p, q=charges["Cl"], mass=masses["Cl"])
+            else:
+                system.part.add(id=len(
+                    system.part), type=types["Na"], pos=p, q=charges["Na"], mass=masses["Na"])
 
-    print("\n--->Setup system")
-
-    # System parameters
-    n_ppside = 10
-    n_part = int(n_ppside**3)
-    n_ionpairs = n_part / 2
-    density = 1.5736
-    time_step = 0.001823
-    temp = 298.0
-    gamma = 20.0
-    #l_bjerrum = 0.885^2 * e^2/(4*pi*epsilon_0*k_B*T)
-    l_bjerrum = 130878.0 / temp
-
-    num_steps_equilibration = 30
-
-    # Particle parameters
-    types = {"Cl": 0, "Na": 1}
-    numbers = {"Cl": n_ionpairs, "Na": n_ionpairs}
-    charges = {"Cl": -1.0, "Na": 1.0}
-    lj_sigmas = {"Cl": 3.85, "Na": 2.52}
-    lj_epsilons = {"Cl": 192.45, "Na": 17.44}
-
-    lj_cuts = {"Cl": 3.0 * lj_sigmas["Cl"],
-               "Na": 3.0 * lj_sigmas["Na"]}
-
-    masses = {"Cl": 35.453, "Na": 22.99}
-
-    # Setup System
-    box_l = (n_ionpairs * sum(masses.values()) / density)**(1. / 3.)
-    system.box_l = [box_l, box_l, box_l]
-    system.periodicity = [1, 1, 1]
-    system.time_step = time_step
-    system.cell_system.skin = 0.3
-    system.thermostat.set_langevin(kT=temp, gamma=gamma, seed=42)
-
-    # Place particles on a face-centered cubic lattice
-    q = 1
-    l = box_l / n_ppside
-    for i in range(n_ppside):
-        for j in range(n_ppside):
-            for k in range(n_ppside):
-                p = numpy.array([i, j, k]) * l
-                if q < 0:
-                    system.part.add(id=len(
-                        system.part), type=types["Cl"], pos=p, q=charges["Cl"], mass=masses["Cl"])
-                else:
-                    system.part.add(id=len(
-                        system.part), type=types["Na"], pos=p, q=charges["Na"], mass=masses["Na"])
-
-                q *= -1
             q *= -1
         q *= -1
+    q *= -1
+
+
+def combination_rule_epsilon(rule, eps1, eps2):
+    if rule == "Lorentz":
+        return (eps1 * eps2)**0.5
+    else:
+        return ValueError("No combination rule defined")
+
+
+def combination_rule_sigma(rule, sig1, sig2):
+    if rule == "Berthelot":
+        return (sig1 + sig2) * 0.5
+    else:
+        return ValueError("No combination rule defined")
+
+# Lennard-Jones interactions parameters
+for s in [["Cl", "Na"], ["Cl", "Cl"], ["Na", "Na"]]:
+    lj_sig = combination_rule_sigma(
+        "Berthelot", lj_sigmas[s[0]], lj_sigmas[s[1]])
+    lj_cut = combination_rule_sigma(
+        "Berthelot", lj_cuts[s[0]], lj_cuts[s[1]])
+    lj_eps = combination_rule_epsilon(
+        "Lorentz", lj_epsilons[s[0]], lj_epsilons[s[1]])
+
+    system.non_bonded_inter[types[s[0]], types[s[1]]].lennard_jones.set_params(
+        epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, shift="auto")
 
-    def combination_rule_epsilon(rule, eps1, eps2):
-        if rule == "Lorentz":
-            return (eps1 * eps2)**0.5
-        else:
-            return ValueError("No combination rule defined")
-
-    def combination_rule_sigma(rule, sig1, sig2):
-        if rule == "Berthelot":
-            return (sig1 + sig2) * 0.5
-        else:
-            return ValueError("No combination rule defined")
-
-    # Lennard-Jones interactions parameters
-    for s in [["Cl", "Na"], ["Cl", "Cl"], ["Na", "Na"]]:
-        lj_sig = combination_rule_sigma(
-            "Berthelot", lj_sigmas[s[0]], lj_sigmas[s[1]])
-        lj_cut = combination_rule_sigma(
-            "Berthelot", lj_cuts[s[0]], lj_cuts[s[1]])
-        lj_eps = combination_rule_epsilon(
-            "Lorentz", lj_epsilons[s[0]], lj_epsilons[s[1]])
-
-        system.non_bonded_inter[types[s[0]], types[s[1]]].lennard_jones.set_params(
-            epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, shift="auto")
-
-    print("\n--->Tuning Electrostatics")
-    p3m = electrostatics.P3M(prefactor=l_bjerrum, accuracy=1e-2)
-    system.actors.add(p3m)
+print("\n--->Tuning Electrostatics")
+p3m = electrostatics.P3M(prefactor=l_bjerrum, accuracy=1e-2)
+system.actors.add(p3m)
+
+
+def main():
 
     print("\n--->Temperature Equilibration")
     system.time = 0.0

From 67033d4199d3c762ca6c3cb641a15200205f7bc1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Mon, 22 Jul 2019 11:32:31 +0200
Subject: [PATCH 05/11] Fix matplotlib plotting in notebook mode

Same as 48e9682246c.
---
 doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb |  1 -
 doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb | 10 +++++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
index c95205b8230..b96d7e1633a 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
@@ -785,7 +785,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import matplotlib.pyplot as plt\n",
     "plt.figure(figsize=(10,10))\n",
     "plt.grid()\n",
     "plt.xticks(range(0,20))\n",
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
index 23689af8240..ed899c4ccb7 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
@@ -248,7 +248,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "plt.figure(figsize=(10,10))\n",
     "plt.xlim(0, box_size)\n",
     "plt.ylim(0, box_size)\n",

From c719778a76ab89dea9bcbe39e508ad8ae0d66851 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Mon, 22 Jul 2019 11:34:49 +0200
Subject: [PATCH 06/11] Fix base64 encoding error in Python3

---
 doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb | 6 ++++--
 doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb | 6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
index b96d7e1633a..07012da5bf4 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
@@ -612,6 +612,7 @@
     "import matplotlib.pyplot as plt\n",
     "import matplotlib.animation as animation\n",
     "from tempfile import NamedTemporaryFile\n",
+    "import base64\n",
     "\n",
     "VIDEO_TAG = \"\"\"<video controls>\n",
     " <source src=\"data:video/x-m4v;base64,{0}\" type=\"video/mp4\">\n",
@@ -622,8 +623,9 @@
     "    if not hasattr(anim, '_encoded_video'):\n",
     "        with NamedTemporaryFile(suffix='.mp4') as f:\n",
     "            anim.save(f.name, fps=20, extra_args=['-vcodec', 'libx264'])\n",
-    "            video = open(f.name, \"rb\").read()\n",
-    "        anim._encoded_video = video.encode(\"base64\")\n",
+    "            with open(f.name, \"rb\") as g:\n",
+    "                video = g.read()\n",
+    "        anim._encoded_video = base64.b64encode(video).decode('ascii')\n",
     "        plt.close(anim._fig)\n",
     "    return VIDEO_TAG.format(anim._encoded_video)\n",
     "\n",
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
index ed899c4ccb7..1ea928f213d 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
@@ -289,6 +289,7 @@
     "import matplotlib.pyplot as plt\n",
     "import matplotlib.animation as animation\n",
     "from tempfile import NamedTemporaryFile\n",
+    "import base64\n",
     "\n",
     "VIDEO_TAG = \"\"\"<video controls>\n",
     " <source src=\"data:video/x-m4v;base64,{0}\" type=\"video/mp4\">\n",
@@ -299,8 +300,9 @@
     "    if not hasattr(anim, '_encoded_video'):\n",
     "        with NamedTemporaryFile(suffix='.mp4') as f:\n",
     "            anim.save(f.name, fps=20, extra_args=['-vcodec', 'libx264'])\n",
-    "            video = open(f.name, \"rb\").read()\n",
-    "        anim._encoded_video = video.encode(\"base64\")\n",
+    "            with open(f.name, \"rb\") as g:\n",
+    "                video = g.read()\n",
+    "        anim._encoded_video = base64.b64encode(video).decode('ascii')\n",
     "        plt.close(anim._fig)\n",
     "    return VIDEO_TAG.format(anim._encoded_video)\n",
     "\n",

From 105f1835942830507960b2f85865d60e0aa989b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Mon, 22 Jul 2019 11:51:22 +0200
Subject: [PATCH 07/11] Use carriage return when updating progress bars

---
 .../11-ferrofluid/11-ferrofluid_part1.ipynb   | 12 +++---
 .../11-ferrofluid/11-ferrofluid_part2.ipynb   | 38 ++++++++++---------
 .../11-ferrofluid/11-ferrofluid_part3.ipynb   | 27 ++++++-------
 3 files changed, 40 insertions(+), 37 deletions(-)

diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
index 07012da5bf4..e8d0942c34c 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
@@ -513,9 +513,9 @@
     "equil_steps = 1000\n",
     "for i in range(equil_rounds):\n",
     "  system.integrator.run(equil_steps)\n",
-    "  print(\"Dipolar energy: %.2f\" % system.analysis.energy()[\"dipolar\"])\n",
-    "  print(\"progress: {:6.2f} %\".format((float(i)+1)/equil_rounds * 100))\n",
-    "print(\"Equilibration done\")"
+    "  print(\"progress: {:3.0f}%, dipolar energy: {:9.2f}\".format(\n",
+    "        (i + 1) * 100. / equil_rounds, system.analysis.energy()[\"dipolar\"]), end=\"\\r\")\n",
+    "print(\"\\nEquilibration done\")"
    ]
   },
   {
@@ -653,7 +653,7 @@
     "    xdata, ydata = system.part[:].pos_folded[:,0], system.part[:].pos_folded[:,1]\n",
     "    ax.figure.canvas.draw()\n",
     "    part.set_data(xdata, ydata)\n",
-    "    print(\"progress: {} %\".format((float(i)+1)/loops * 100))\n",
+    "    print(\"progress: {:3.0f}%\".format((i + 1) * 100. / loops), end=\"\\r\")\n",
     "    return part,"
    ]
   },
@@ -711,7 +711,7 @@
     "    for c in cs.clusters:\n",
     "        cluster_sizes.append(c[1].size())\n",
     "    system.integrator.run(100)\n",
-    "    print(\"progress: {} %\".format((float(i)+1)/loops * 100))"
+    "    print(\"progress: {:3.0f}%\".format((float(i)+1)/loops * 100), end=\"\\r\")"
    ]
   },
   {
@@ -734,7 +734,7 @@
     "plt.xlabel('x-position', fontsize=20)\n",
     "plt.ylabel('y-position', fontsize=20)\n",
     "plt.plot(system.part[:].pos_folded[:,0], system.part[:].pos_folded[:,1], 'o')\n",
-    "plt.show()\n"
+    "plt.show()"
    ]
   },
   {
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
index 1ea928f213d..880e06258ec 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part2.ipynb
@@ -230,9 +230,9 @@
     "equil_steps = 200\n",
     "for i in range(equil_rounds):\n",
     "  system.integrator.run(equil_steps)\n",
-    "  print(\"Dipolar energy: %.2f\" % system.analysis.energy()[\"dipolar\"])\n",
-    "  print(\"progress: {:6.2f} %\".format((float(i)+1)/equil_rounds * 100))\n",
-    "print(\"Equilibration done\")"
+    "  print(\"progress: {:3.0f}%, dipolar energy: {:9.2f}\".format(\n",
+    "        (i + 1) * 100. / equil_rounds, system.analysis.energy()[\"dipolar\"]), end=\"\\r\")\n",
+    "print(\"\\nEquilibration done\")"
    ]
   },
   {
@@ -323,7 +323,7 @@
     "    xdata, ydata = system.part[:].pos_folded[:,0], system.part[:].pos_folded[:,1]\n",
     "    ax.figure.canvas.draw()\n",
     "    part.set_data(xdata, ydata)\n",
-    "    print(\"progress: {} %\".format((float(i)+1)/100 * 100))\n",
+    "    print(\"progress: {:3.0f}%\".format(i + 1), end=\"\\r\")\n",
     "    return part,"
    ]
   },
@@ -582,15 +582,15 @@
     "    print(\"Set magnetic field constraint...\")\n",
     "    H_constraint = espressomd.constraints.HomogeneousMagneticField(H=H_field)\n",
     "    system.constraints.add(H_constraint)\n",
-    "    print(\"done\")\n",
+    "    print(\"done\\n\")\n",
     "    \n",
     "    # Equilibration\n",
     "    print(\"Equilibration...\")\n",
     "    for i in range(equil_rounds):\n",
     "        system.integrator.run(equil_steps)\n",
-    "        print(\"Dipolar energy: %.2f\" % system.analysis.energy()[\"dipolar\"])\n",
-    "        print(\"progress: {:6.2f} %\".format((float(i)+1)/equil_rounds * 100))\n",
-    "    print(\"Equlilibration done \\n\")\n",
+    "        print(\"progress: {:3.0f}%, dipolar energy: {:9.2f}\".format(\n",
+    "              (i+1)*100./equil_rounds, system.analysis.energy()[\"dipolar\"]), end=\"\\r\")\n",
+    "    print(\"\\nEqulilibration done\\n\")\n",
     "    \n",
     "    # Sampling\n",
     "    print(\"Sampling...\")\n",
@@ -598,13 +598,14 @@
     "    for i in range(loops):\n",
     "        system.integrator.run(20)\n",
     "        magn_temp += dipm_tot.calculate()[2]\n",
-    "        print(\"progress: {:6.2f} %\".format((float(i)+1)/loops * 100))\n",
+    "        print(\"progress: {:3.0f}%\".format((i+1)*100./loops), end=\"\\r\")\n",
+    "    print(\"\\n\")\n",
     "    \n",
     "    # save average magnetization\n",
     "    magnetization_perp.append(magn_temp / loops)\n",
-    "    print(\"Sampling for alpha = {} done \\n\".format(alpha))\n",
+    "    print(\"Sampling for alpha = {} done\\n\".format(alpha))\n",
     "    print(\"magnetizations = {}\".format(magnetization_perp))\n",
-    "    print(\"total progress: {:6.2f} %\\n\".format((float(alphas.index(alpha))+1)/len(alphas) * 100))\n",
+    "    print(\"total progress: {:5.1f}%\\n\".format((alphas.index(alpha)+1)*100./len(alphas)))\n",
     "    \n",
     "    # remove constraint\n",
     "    system.constraints.clear()\n",
@@ -642,15 +643,15 @@
     "    print(\"Set magnetic field constraint...\")\n",
     "    H_constraint = espressomd.constraints.HomogeneousMagneticField(H=H_field)\n",
     "    system.constraints.add(H_constraint)\n",
-    "    print(\"done\")\n",
+    "    print(\"done\\n\")\n",
     "    \n",
     "    # Equilibration\n",
     "    print(\"Equilibration...\")\n",
     "    for i in range(equil_rounds):\n",
     "        system.integrator.run(equil_steps)\n",
-    "        print(\"Dipolar energy: %.2f\" % system.analysis.energy()[\"dipolar\"])\n",
-    "        print(\"progress: {:6.2f} %\".format((float(i)+1)/equil_rounds * 100))\n",
-    "    print(\"Equlilibration done \\n\")\n",
+    "        print(\"progress: {:3.0f}%, dipolar energy: {:9.2f}\".format(\n",
+    "              (i+1)*100./equil_rounds, system.analysis.energy()[\"dipolar\"]), end=\"\\r\")\n",
+    "    print(\"\\nEqulilibration done\\n\")\n",
     "    \n",
     "    # Sampling\n",
     "    print(\"Sampling...\")\n",
@@ -658,13 +659,14 @@
     "    for i in range(loops):\n",
     "        system.integrator.run(20)\n",
     "        magn_temp += dipm_tot.calculate()[0]\n",
-    "        print(\"progress: {:6.2f} %\".format((float(i)+1)/loops * 100))\n",
+    "        print(\"progress: {:3.0f}%\".format((i+1)*100./loops), end=\"\\r\")\n",
+    "    print(\"\\n\")\n",
     "    \n",
     "    # save average magnetization\n",
     "    magnetization_para.append(magn_temp / loops)\n",
-    "    print(\"Sampling for alpha = {} done \\n\".format(alpha))\n",
+    "    print(\"Sampling for alpha = {} done\\n\".format(alpha))\n",
     "    print(\"magnetizations = {}\".format(magnetization_para))\n",
-    "    print(\"total progress: {:6.2f} %\\n\".format((float(alphas.index(alpha))+1)/len(alphas) * 100))\n",
+    "    print(\"total progress: {:5.1f}%\\n\".format((alphas.index(alpha)+1)*100./len(alphas)))\n",
     "    \n",
     "    # remove constraint\n",
     "    system.constraints.clear()\n",
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
index c310b248b70..dadbc17b89a 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
@@ -257,9 +257,9 @@
     "equil_steps = 1000\n",
     "for i in range(equil_rounds):\n",
     "  system.integrator.run(equil_steps)\n",
-    "  print(\"Dipolar energy: %.2f\" % system.analysis.energy()[\"dipolar\"])\n",
-    "  print(\"progress: {:6.2f} %\".format((float(i)+1)/equil_rounds * 100))\n",
-    "print(\"Equilibration done\")"
+    "  print(\"progress: {:3.0f}%, dipolar energy: {:9.2f}\".format(\n",
+    "        (i + 1) * 100. / equil_rounds, system.analysis.energy()[\"dipolar\"]), end=\"\\r\")\n",
+    "print(\"\\nEquilibration done\")"
    ]
   },
   {
@@ -330,12 +330,12 @@
     "    \n",
     "    # print progress only every 10th cycle\n",
     "    if (i+1)%10 == 0:\n",
-    "        print(\"progress: {:6.2f} %\".format((float(i)+1)/loops * 100))\n",
-    "    \n",
+    "        print(\"progress: {:3.0f}%\".format((i+1)*100./loops), end=\"\\r\")\n",
+    "print(\"\\nSampling done\")\n",
+    "\n",
     "# calculate average first and second moment of total dipole moment\n",
     "dipm_tot = dipm_tot_sum / loops\n",
-    "dipm_tot_2 = dipm_tot_2_sum / loops\n",
-    "print(\"Sampling done\")"
+    "dipm_tot_2 = dipm_tot_2_sum / loops"
    ]
   },
   {
@@ -529,15 +529,15 @@
     "    print(\"Set magnetic field constraint...\")\n",
     "    H_constraint = espressomd.constraints.HomogeneousMagneticField(H=H_field)\n",
     "    system.constraints.add(H_constraint)\n",
-    "    print(\"done\")\n",
+    "    print(\"done\\n\")\n",
     "    \n",
     "    # Equilibration\n",
     "    print(\"Equilibration...\")\n",
     "    for i in range(equil_rounds):\n",
     "        system.integrator.run(equil_steps)\n",
-    "        print(\"Dipolar energy: %.2f\" % system.analysis.energy()[\"dipolar\"])\n",
-    "        print(\"progress: {:6.2f} %\".format((float(i)+1)/10 * 100))\n",
-    "    print(\"Equlilibration done \\n\")\n",
+    "        print(\"progress: {:3.0f}%, dipolar energy: {:9.2f}\".format(\n",
+    "              (i+1)*100./equil_rounds, system.analysis.energy()[\"dipolar\"]), end=\"\\r\")\n",
+    "    print(\"\\nEqulilibration done\\n\")\n",
     "    \n",
     "    # Sampling\n",
     "    print(\"Sampling...\")\n",
@@ -545,13 +545,14 @@
     "    for i in range(loops_m):\n",
     "        system.integrator.run(20)\n",
     "        magn_temp += dipm_tot_calc.calculate()[0]\n",
-    "        print(\"progress: {:6.2f} %\".format((float(i)+1)/loops_m * 100))\n",
+    "        print(\"progress: {:3.0f}%\".format((i+1)*100./loops_m), end=\"\\r\")\n",
+    "    print(\"\\n\")\n",
     "    \n",
     "    # save average magnetization\n",
     "    magnetization.append(magn_temp / loops_m)\n",
     "    print(\"Sampling for alpha = {} done \\n\".format(alpha))\n",
     "    print(\"magnetizations = {}\".format(magnetization))\n",
-    "    print(\"total progress: {:6.2f} %\\n\".format((float(alphas.index(alpha))+1)/len(alphas) * 100))\n",
+    "    print(\"total progress: {:5.1f}%\\n\".format((alphas.index(alpha)+1)*100./len(alphas)))\n",
     "    \n",
     "    # remove constraint\n",
     "    system.constraints.clear()\n",

From 343f79d3c664316b5080868a13d4655a8cf6f2cf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Tue, 23 Jul 2019 20:42:37 +0200
Subject: [PATCH 08/11] Docs: fix file extension

---
 doc/sphinx/visualization.rst                   | 4 ++--
 src/python/espressomd/visualization_opengl.pyx | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/sphinx/visualization.rst b/doc/sphinx/visualization.rst
index 63d6880d862..bab3acc9fd9 100644
--- a/doc/sphinx/visualization.rst
+++ b/doc/sphinx/visualization.rst
@@ -175,10 +175,10 @@ screenshots without blocking the simulation script::
 
     for i in range(100):
         system.integrator.run(1)
-        visualizer.screenshot('screenshot_{}.jpg'.format(i))
+        visualizer.screenshot('screenshot_{}.png'.format(i))
 
     # You may consider creating a video with ffmpeg:
-    # ffmpeg -f image2 -framerate 30 -i 'screenshot_%d.jpg' output.mp4
+    # ffmpeg -f image2 -framerate 30 -i 'screenshot_%d.png' output.mp4
 
 It is also possible to create a snapshot during online visualization.
 Simply press the *enter* key to create a snapshot of the current window,
diff --git a/src/python/espressomd/visualization_opengl.pyx b/src/python/espressomd/visualization_opengl.pyx
index 4dfccb04688..be17e80b89b 100644
--- a/src/python/espressomd/visualization_opengl.pyx
+++ b/src/python/espressomd/visualization_opengl.pyx
@@ -495,7 +495,7 @@ class openGLLive(object):
 
     def screenshot(self, path):
         """Renders the current state into an image file at ``path`` with
-        dimensions of ``specs['window_size']``."""
+        dimensions of ``specs['window_size']`` in PNG format."""
 
         # ON FIRST CALL: INIT AND CREATE BUFFERS
         if not self.screenshot_initialized:
@@ -536,7 +536,7 @@ class openGLLive(object):
         OpenGL.GL.glLoadMatrixf(self.camera.modelview)
         self._draw_system()
 
-        # READ THE PIXES
+        # READ THE PIXELS
         OpenGL.GL.glReadBuffer(OpenGL.GL.GL_COLOR_ATTACHMENT0)
         data = OpenGL.GL.glReadPixels(
             0, 0, self.specs['window_size'][0], self.specs['window_size'][1], OpenGL.GL.GL_RGB, OpenGL.GL.GL_FLOAT)

From 7f62174e6b83833a1fe795dba10ea2207d8e9666 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Tue, 23 Jul 2019 20:49:54 +0200
Subject: [PATCH 09/11] Docs: use safer ffmpeg command

---
 doc/sphinx/visualization.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/sphinx/visualization.rst b/doc/sphinx/visualization.rst
index bab3acc9fd9..6655698b6bc 100644
--- a/doc/sphinx/visualization.rst
+++ b/doc/sphinx/visualization.rst
@@ -175,10 +175,10 @@ screenshots without blocking the simulation script::
 
     for i in range(100):
         system.integrator.run(1)
-        visualizer.screenshot('screenshot_{}.png'.format(i))
+        visualizer.screenshot('screenshot_{:0>5}.png'.format(i))
 
     # You may consider creating a video with ffmpeg:
-    # ffmpeg -f image2 -framerate 30 -i 'screenshot_%d.png' output.mp4
+    # ffmpeg -f image2 -framerate 30 -i 'screenshot_%05d.png' output.mp4
 
 It is also possible to create a snapshot during online visualization.
 Simply press the *enter* key to create a snapshot of the current window,

From 46f2271c25dfb62e77c5bb91f63b89b7d7b8050c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Wed, 24 Jul 2019 17:48:29 +0200
Subject: [PATCH 10/11] Remove Python2-specific workarounds

---
 .../04-lattice_boltzmann_part1.ipynb             |  7 ++-----
 .../04-lattice_boltzmann_part2.ipynb             |  6 ++----
 .../04-lattice_boltzmann_part3.ipynb             |  6 ++----
 .../11-ferrofluid/11-ferrofluid_part1.ipynb      | 16 ----------------
 4 files changed, 6 insertions(+), 29 deletions(-)

diff --git a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part1.ipynb b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part1.ipynb
index 8528d0a2251..e5a130a2af7 100644
--- a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part1.ipynb
+++ b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part1.ipynb
@@ -54,8 +54,7 @@
     "\n",
     "### Notes on the **ESPResSo** version you will need\n",
     "\n",
-    "With version 3.1 **ESPResSo** offers GPU support for LB. We recommend however\n",
-    "version 3.3, which has more features. We absolutely recommend using the GPU code,\n",
+    "**ESPResSo** offers both CPU and GPU support for LB. We recommend using the GPU code,\n",
     "as it is much (100x) faster than the CPU code.\n",
     "\n",
     "For the tutorial you will have to compile in the following features: \n",
@@ -381,7 +380,6 @@
     "espressomd.assert_features(['CUDA', 'LB_BOUNDARIES_GPU'])\n",
     "from espressomd import System, lb, lbboundaries, shapes\n",
     "import numpy as np\n",
-    "import sys\n",
     "\n",
     "# System setup\n",
     "system = System(box_l=[1.0, 1.0, 1.0])  # The box_l is specified below.\n",
@@ -453,8 +451,7 @@
     "for i in range(10):\n",
     "    system.integrator.run(400)\n",
     "    lbf.print_vtk_velocity(\"fluid%04i.vtk\" % i)\n",
-    "    sys.stdout.write(\"\\rloop: %02i\" % i)\n",
-    "    sys.stdout.flush()\n",
+    "    print(\"\\rloop: %02i\" % (i+1), end=\"\")\n",
     "\n",
     "\n",
     "print(\"\\nIntegration finished.\")\n",
diff --git a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
index 9a152884286..d1b5a346f46 100644
--- a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
+++ b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
@@ -94,7 +94,6 @@
     "from espressomd.accumulators import Correlator\n",
     "\n",
     "import numpy as np\n",
-    "import sys\n",
     "\n",
     "# Constants\n",
     "loops = 40000\n",
@@ -138,10 +137,9 @@
     "    system.integrator.run(steps)\n",
     "\n",
     "    if i % 1e2 == 0:\n",
-    "        sys.stdout.write(\"\\rSampling: {:.0f}%\".format(i * 100. / loops))\n",
-    "        sys.stdout.flush()\n",
+    "        print(\"\\rSampling: {:.0f}%\".format(i * 100. / loops), end=\"\")\n",
     "\n",
-    "sys.stdout.write(\"\\rSampling finished.\\n\")\n",
+    "print(\"\\rSampling finished.\")\n",
     "\n",
     "c.finalize()\n",
     "corrdata = c.result()\n",
diff --git a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part3.ipynb b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part3.ipynb
index 4d57a7f67b4..9f84d699646 100644
--- a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part3.ipynb
+++ b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part3.ipynb
@@ -66,7 +66,6 @@
     "\n",
     "from numpy import savetxt, zeros\n",
     "import numpy as np\n",
-    "import sys\n",
     "\n",
     "# Setup constant\n",
     "time_step = 0.01\n",
@@ -144,10 +143,9 @@
     "for i in range(loops):\n",
     "    system.integrator.run(step_per_loop)\n",
     "    system.analysis.append()\n",
-    "    sys.stdout.write(\"\\rSampling: {:.0f}%\".format(i * 100. / loops))\n",
-    "    sys.stdout.flush()\n",
+    "    print(\"\\rSampling: {:.0f}%\".format(i * 100. / loops), end=\"\")\n",
     "\n",
-    "sys.stdout.write(\"\\rSampling finished.\\n\")\n",
+    "print(\"\\rSampling finished.\")\n",
     "\n",
     "c.finalize()\n",
     "corrdata = c.result()\n",
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
index e8d0942c34c..76f88aa95bd 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
@@ -206,22 +206,6 @@
     "## Python Version"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "If you are using python 2 issue the following command to activate the python 3 print syntax"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from __future__ import print_function"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

From a1ab0936c43abd4e34baca3c62db7dcc9c50c74d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Wed, 24 Jul 2019 17:49:43 +0200
Subject: [PATCH 11/11] Fix typos

---
 .../04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb | 4 ++--
 doc/tutorials/04-lattice_boltzmann/scripts/part4_plot.py  | 2 +-
 .../05-raspberry_electrophoresis.ipynb                    | 2 +-
 doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb     | 8 ++++----
 doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb     | 2 +-
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
index d1b5a346f46..981f2999e17 100644
--- a/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
+++ b/doc/tutorials/04-lattice_boltzmann/04-lattice_boltzmann_part2.ipynb
@@ -78,7 +78,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Our first step is to investigate the diffusion of a single particle that is coupled to an LB fluid by the point coupling method. Start with an friction coefficient of 1.0:"
+    "Our first step is to investigate the diffusion of a single particle that is coupled to an LB fluid by the point coupling method. Start with a friction coefficient of 1.0:"
    ]
   },
   {
@@ -124,7 +124,7 @@
     "# Equilibrate\n",
     "print(\"Equilibrating the system.\")\n",
     "system.integrator.run(1000)\n",
-    "print(\"Equlibration finished.\")\n",
+    "print(\"Equilibration finished.\")\n",
     "\n",
     "# Setup observable correlator\n",
     "pos = ParticlePositions(ids=(0,))\n",
diff --git a/doc/tutorials/04-lattice_boltzmann/scripts/part4_plot.py b/doc/tutorials/04-lattice_boltzmann/scripts/part4_plot.py
index 5376653345d..e4dbbf21a36 100644
--- a/doc/tutorials/04-lattice_boltzmann/scripts/part4_plot.py
+++ b/doc/tutorials/04-lattice_boltzmann/scripts/part4_plot.py
@@ -37,6 +37,6 @@
 plt.plot(pos, ana, label='analytical')
 plt.plot(pos, scaling * sim, '+', label='simulated')
 plt.xlabel('$x$-axis ($\AA$)', fontsize=20)
-plt.ylabel('LB fluid velocity $u_y(x)$ ($\AA/s)$', fontsize=20)
+plt.ylabel('LB fluid velocity $u_y(x)$ ($\AA/s$)', fontsize=20)
 plt.legend(fontsize=20)
 plt.show()
diff --git a/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb b/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb
index ac1c46563cd..61d8e43c436 100644
--- a/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb
+++ b/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb
@@ -19,7 +19,7 @@
     "resemble a raspberry as can be seen in Fig. 1. After covering the construction of a raspberry colloid, we then\n",
     "briefly discuss the inclusion of hydrodynamic interactions via a lattice-Boltzmann fluid. Finally we will cover\n",
     "including ions via the restrictive primitive model (hard sphere ions) and the addition of an electric field\n",
-    "to measure the electrokinetic properties. this script will run a raspberry electrophoresis simulation and write the time and position of the colloid out to a file named <tt>posVsTime.dat</tt> in the same directory.\n",
+    "to measure the electrokinetic properties. This script will run a raspberry electrophoresis simulation and write the time and position of the colloid out to a file named <tt>posVsTime.dat</tt> in the same directory.\n",
     "A sample set of data is included in the file <tt>posVsTime_sample.dat</tt>."
    ]
   },
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
index 76f88aa95bd..9dcdeaa992a 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part1.ipynb
@@ -217,7 +217,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For interessting ferrofluid systems, where the fraction of ferromagnetic particles in the liquid carrier and their dipole moment are not vanishingly small, the ferromagnetic particles form clusters of different shapes and sizes. If the fraction and/or dipole moments are big enought the clusters can interconnect with each other and form a whole space occuping network.\n",
+    "For interesting ferrofluid systems, where the fraction of ferromagnetic particles in the liquid carrier and their dipole moment are not vanishingly small, the ferromagnetic particles form clusters of different shapes and sizes. If the fraction and/or dipole moments are big enough the clusters can interconnect with each other and form a whole space occupying network.\n",
     "In this part we want to investigate the number of clusters as well as their shape and size in our simulated monolayer ferrofluid system. It should be noted that a monolayer is a quasi three dimensional system (q2D), i.e. two dimensional for the positions and three dimensional for the orientation of the dipole moments."
    ]
   },
@@ -414,7 +414,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now we choose the steeptes descent integrator to remove possible overlaps of the particles. Therefore we integrate until the energy of the whole system is lower than $5 k_BT$."
+    "Now we choose the steepest descent integrator to remove possible overlaps of the particles. Therefore we integrate until the energy of the whole system is lower than $5 k_BT$."
    ]
   },
   {
@@ -452,7 +452,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To calculate the dipole-dipole interaction we use the Dipolar P3M method (see Ref. <a href='#[1]'>[1]</a>) which is based on the Ewald summation. At default the boundary conditions of the system are set to conducting which means the dielectric constant is set to infinity for the surrounding medium. As we want to simulate a two dimensional system we additionally use the dipolar layer correction (DLC) (see Ref. <a href='#[2]'>[2]</a>). As we add <tt>DipolarP3M</tt> to our system as an actor, a tuning function is started automatically which tries to find the optimal parameters for Dipolar P3M and prints them to the screen. The last line of the output is the value of the tuned skin."
+    "To calculate the dipole-dipole interaction we use the Dipolar P3M method (see Ref. <a href='#[1]'>[1]</a>) which is based on the Ewald summation. By default the boundary conditions of the system are set to conducting which means the dielectric constant is set to infinity for the surrounding medium. As we want to simulate a two dimensional system we additionally use the dipolar layer correction (DLC) (see Ref. <a href='#[2]'>[2]</a>). As we add <tt>DipolarP3M</tt> to our system as an actor, a tuning function is started automatically which tries to find the optimal parameters for Dipolar P3M and prints them to the screen. The last line of the output is the value of the tuned skin."
    ]
   },
   {
@@ -506,7 +506,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As we are interested in the clustersizes and the number of clusters we now set up the cluster analysis with the distance criterion that a particle is added to a cluster if the nearest neigbors of it are closer than $1.3\\cdot\\sigma_{lj}$."
+    "As we are interested in the cluster sizes and the number of clusters we now set up the cluster analysis with the distance criterion that a particle is added to a cluster if the nearest neigbors of it are closer than $1.3\\cdot\\sigma_{lj}$."
    ]
   },
   {
diff --git a/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb b/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
index dadbc17b89a..b6b1cbe74a4 100644
--- a/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
+++ b/doc/tutorials/11-ferrofluid/11-ferrofluid_part3.ipynb
@@ -85,7 +85,7 @@
     "    \\chi = \\frac{\\beta\\mu_0}{V} \\left \\lbrack \\frac{1}{Z_c}\\sum_{\\alpha} \\mu_{\\alpha}^2~ e^{ -\\beta E_{\\alpha}(H=0) + \\beta\\mu_0\\mu_{\\boldsymbol{H},\\alpha}H } - \\frac{1}{Z_c}\\sum_{\\alpha} \\mu_{\\alpha}~ e^{ -\\beta E_{\\alpha}(H=0) + \\beta\\mu_0\\mu_{\\boldsymbol{H},\\alpha}H }~~ \\frac{1}{Z_c}\\sum_{\\alpha'}\\mu_{\\alpha'}~ e^{ -\\beta E_{\\alpha'}(H=0) + \\beta\\mu_0\\mu_{\\boldsymbol{H},\\alpha}H }\\right \\rbrack = \\frac{\\beta\\mu_0}{V} \\left \\lbrack \\langle \\mu_{\\boldsymbol{H}}^2 \\rangle - \\langle \\mu_{\\boldsymbol{H}} \\rangle^2 \\right \\rbrack = \\frac{\\beta\\mu_0}{V} \\left(\\Delta \\mu_{\\boldsymbol{H}}\\right)^2\n",
     "\\end{equation}\n",
     "\n",
-    "At zero external magentic field ($H = 0$) there is no distinct direction for the system, so we can take the fluctuations $\\Delta \\mu$ in all directions and divide it by the dimension. Thus we can use more data points of our simulation for the average and get a more precise estimator for the susceptibility. Thus finally the fluctuation formula for the initial susceptibility in three dimensions reads\n",
+    "At zero external magnetic field ($H = 0$) there is no distinct direction for the system, so we can take the fluctuations $\\Delta \\mu$ in all directions and divide it by the dimension. Thus we can use more data points of our simulation for the average and get a more precise estimator for the susceptibility. Thus finally the fluctuation formula for the initial susceptibility in three dimensions reads\n",
     "\n",
     "\\begin{equation}\n",
     "    \\chi_{init} = \\frac{\\beta\\mu_0}{3V} \\left \\lbrack \\langle \\boldsymbol{\\mu}^2 \\rangle - \\langle \\boldsymbol{\\mu} \\rangle^2 \\right \\rbrack = \\frac{V\\beta\\mu_0}{3} \\left \\lbrack \\langle \\boldsymbol{M}^2 \\rangle - \\langle \\boldsymbol{M} \\rangle^2 \\right \\rbrack\n",