Merge branch 'python' into tutorial_04_summer_school_2020

espressomd · Oct 8, 2020 · 446fd10 · 446fd10
2 parents 8469df0 + b724921
commit 446fd10
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diff --git a/doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb b/doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb
diff --git a/doc/tutorials/02-charged_system/02-charged_system-1.ipynb b/doc/tutorials/02-charged_system/02-charged_system-1.ipynb
@@ -33,6 +33,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import espressomd\n",
+    "espressomd.assert_features(['WCA', 'ELECTROSTATICS'])\n",
+    "\n",
     "from espressomd import System, interactions, electrostatics, observables, accumulators\n",
     "\n",
     "import numpy as np\n",
@@ -146,14 +149,14 @@
     "* Implement a function to place the rod particles along the $x_3$ axis in the middle of the simulation box and the ions randomly distributed \n",
     "* Use the signature ``setup_rod_and_counterions(system, ion_valency, counterion_type, rod_charge_dens, N_rod_beads, rod_type) ``\n",
     "* Determine the number of counterions from the condition of neutrality for the whole system (the rod should be positive, the counterions negative)\n",
-    "* Assign the rod particles and cointerions their correct ``type``\n",
+    "* Assign the rod particles and counterions their correct ``type``\n",
     "* Give the counterions a charge ``q`` according to their ``ion_valency``\n",
-    "* Give the rod particles a charge such that the ``rod_charge_dens`` is uniformely distributed along the ``N_rod_beads`` individual particles\n",
+    "* Give the rod particles a charge such that the ``rod_charge_dens`` is uniformly distributed along the ``N_rod_beads`` individual particles\n",
     "* Fix the rod particles in space so they do not get moved if forces act upon them\n",
     "* Return the newly created counterion particles\n",
     "\n",
     "**Hints:**\n",
-    "* Look into [Eespresso particle properties](http://espressomd.org/html/doc/espressomd.html?#module-espressomd.particle_data) to find the keywords to set charges and fix particles\n",
+    "* Look into [espresso particle properties](http://espressomd.org/html/doc/espressomd.html?#module-espressomd.particle_data) to find the keywords to set charges and to fix particles\n",
     "* use np.random.random() to generate the counterion positions"
    ]
   },
@@ -278,7 +281,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Before we can start the simulation, we need to remove the overlap between particles to avoid large forces which would crash the simulation. For this, we use the steepest descent integrator with a relative convergence criterium for forces and energies."
+    "Before we can start the simulation, we need to remove the overlap between particles to avoid large forces which would crash the simulation. For this, we use the steepest descent integrator with a relative convergence criterion for forces and energies."
    ]
   },
   {
@@ -715,7 +718,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For multivalent counterions, the manning parameter $\\xi$ has to be multiplied by the valency $\\nu$. The result depends only on the product of ``rod_charge_dens`` and ``ion_velancy``, so we only need one curve"
+    "For multivalent counterions, the manning parameter $\\xi$ has to be multiplied by the valency $\\nu$. The result depends only on the product of ``rod_charge_dens`` and ``ion_valency``, so we only need one curve"
    ]
   },
   {

diff --git a/doc/tutorials/02-charged_system/CMakeLists.txt b/doc/tutorials/02-charged_system/CMakeLists.txt
@@ -14,10 +14,8 @@ configure_tutorial_target(
   scripts/nacl_units.py
   scripts/nacl_units_vis.py)
 
-nb_export(
-  TARGET tutorial_02 SUFFIX "1" FILE "02-charged_system-1.ipynb" HTML_RUN
-  VAR_SUBST
-  "num_steps_equilibration=200;num_configs=100;integ_steps_per_config=250")
+nb_export(TARGET tutorial_02 SUFFIX "1" FILE "02-charged_system-1.ipynb"
+          HTML_RUN)
 nb_export(
   TARGET tutorial_02 SUFFIX "2" FILE "02-charged_system-2.ipynb" HTML_RUN
   VAR_SUBST