Update docs 4.1

NEWS

@@ -124,13 +124,13 @@ Interface changes
   number generation. For the following individual methods a random
   number seed has to be passed using the keyword argument ``seed``:
 
-   * [Langevin thermostat](http://espressomd.org/html/doc/espressomd.html?#espressomd.thermostat.Thermostat.set_langevin)
-   * [DPD thermostat](http://espressomd.org/html/doc/espressomd.html?#espressomd.thermostat.Thermostat.set_dpd)
-   * [LB Thermostat](http://espressomd.org/html/doc/espressomd.html?#espressomd.thermostat.Thermostat.set_lb)
-   * [Thermalized bond](http://espressomd.org/html/doc/espressomd.html?#espressomd.interactions.ThermalizedBond)
-   * [Wang-Landau reaction ensemble](http://espressomd.org/html/doc/espressomd.html?#module-espressomd.reaction_ensemble)
-   * [Constant pH ensemble](http://espressomd.org/html/doc/espressomd.html?#espressomd.reaction_ensemble.ConstantpHEnsemble)
-   * [Widom insertion method](http://espressomd.org/html/doc/espressomd.html?#espressomd.reaction_ensemble.WidomInsertion)
+   * [Langevin thermostat](http://espressomd.org/html/doc4.1.0/espressomd.html?#espressomd.thermostat.Thermostat.set_langevin)
+   * [DPD thermostat](http://espressomd.org/html/doc4.1.0/espressomd.html?#espressomd.thermostat.Thermostat.set_dpd)
+   * [LB Thermostat](http://espressomd.org/html/doc4.1.0/espressomd.html?#espressomd.thermostat.Thermostat.set_lb)
+   * [Thermalized bond](http://espressomd.org/html/doc4.1.0/espressomd.html?#espressomd.interactions.ThermalizedBond)
+   * [Wang-Landau reaction ensemble](http://espressomd.org/html/doc4.1.0/espressomd.html?#module-espressomd.reaction_ensemble)
+   * [Constant pH ensemble](http://espressomd.org/html/doc4.1.0/espressomd.html?#espressomd.reaction_ensemble.ConstantpHEnsemble)
+   * [Widom insertion method](http://espressomd.org/html/doc4.1.0/espressomd.html?#espressomd.reaction_ensemble.WidomInsertion)
 
 * Changes in the lattice-Boltzmann (LB) interface:
 
@@ -143,13 +143,13 @@ Interface changes
      parameter of the LB thermostat.
 
   For more detailed information on how to set up a LB fluid and
-  thermostat, please see http://espressomd.org/html/doc/lb.html.
+  thermostat, please see http://espressomd.org/html/doc4.1.0/lb.html.
 
 * The method for polymer creation has been replaced. Now
   ``espressomd.polymer.positions()`` can be used to obtain particle
   positions for one or more polymer chains. Based on these positions,
   polymers can be created. For an example please see
-  http://espressomd.org/html/doc/particles.html#setting-up-polymer-chains.
+  http://espressomd.org/html/doc4.1.0/particles.html#setting-up-polymer-chains.
 
 
 Changed and removed functionality
@@ -368,7 +368,7 @@ Physics related corrections:
     module did not get assigned a random velocity. This was not a problem if you were looking at observables
     which do not depend on velocity.
 
-  * Particles which were created in the Reaction Ensemble module were assigned a random velocity which was not distributed according to the Maxwell-Boltzmann distribution. This was not a problem if you were looking at observables which do not depend on velocity. If you looked at velocity dependent observables but used a thermostat for thermalization before taking a sample you are also fine.  (#2377).
+  * Particles which were created in the Reaction Ensemble module were assigned a random velocity which was not distributed according to the Maxwell-Boltzmann distribution. This was not a problem if you were looking at observables which do not depend on velocity. If you looked at velocity-dependent observables but used a thermostat for thermalization before taking a sample you are also fine.  (#2377).
 
   * Under some conditions, the torque on self-propelled particles
     in a lattice-Boltzmann fluid was incorrect due to a sign error in the

doc/sphinx/analysis.rst

@@ -394,16 +394,16 @@ The instantaneous pressure is calculated (if there are no electrostatic interact
 by the volume averaged, direction averaged instantaneous virial pressure
 
 .. math::
-     p = \frac{2E_{kinetic}}{Vf} + \frac{\sum_{j>i} {F_{ij}r_{ij}}}{3V}
+     p = \frac{2E_{\text{kinetic}}}{Vf} + \frac{\sum_{j>i} {F_{ij}r_{ij}}}{3V}
      :label: eqptens
 
 where :math:`f=3` is the number of translational degrees of freedom of
 each particle, :math:`V` is the volume of the system,
-:math:`E_{kinetic}` is the kinetic energy, :math:`F_{ij}` the force
+:math:`E_{\text{kinetic}}` is the kinetic energy, :math:`F_{ij}` the force
 between particles i and j, and :math:`r_{ij}` is the distance between
 them. The kinetic energy divided by the degrees of freedom is
 
-.. math:: \frac{2E_{kinetic}}{f} = \frac{1}{3}\sum_{i} {m_{i}v_{i}^{2}}.
+.. math:: \frac{2E_{\text{kinetic}}}{f} = \frac{1}{3}\sum_{i} {m_{i}v_{i}^{2}}.
 
 Note that Equation :eq:`eqptens` can only be applied to pair potentials and
 central forces. Description of how contributions from other interactions

doc/sphinx/installation.rst

@@ -63,9 +63,9 @@ Cython
     At least version 0.23 is required.
 
 
-.. _Installing Requirements on Ubuntu Linux:
+.. _Installing requirements on Ubuntu Linux:
 
-Installing Requirements on Ubuntu Linux
+Installing requirements on Ubuntu Linux
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 To make |es| run on 18.04 LTS, its dependencies can be installed with:
@@ -117,9 +117,24 @@ ROCm SDK to make use of GPU computation:
 
 After installing the ROCm SDK, please reboot your computer.
 
-.. _Installing Requirements on Mac OS X:
 
-Installing Requirements on Mac OS X
+.. _Installing requirements on other Linux distributions:
+
+Installing requirements on other Linux distributions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Please refer to the following Dockerfiles to find the minimum set of packages
+required to compile |es| on other Linux distributions:
+
+* `CentOS 7 <https://github.com/espressomd/docker/blob/master/docker/centos-python3/Dockerfile-7>`_
+* `Fedora 30 <https://github.com/espressomd/docker/blob/master/docker/centos-python3/Dockerfile-next>`_
+* `Debian 10 <https://github.com/espressomd/docker/blob/master/docker/debian-python3/Dockerfile-10>`_
+* `OpenSUSE Leap 15.1 <https://github.com/espressomd/docker/blob/master/docker/opensuse/Dockerfile-15.1>`_
+
+
+.. _Installing requirements on Mac OS X:
+
+Installing requirements on Mac OS X
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Preparation
@@ -172,9 +187,9 @@ If you want to install Homebrew, use the following commands.
     sudo xcodebuild -license accept
     /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
 
-Installing Packages using MacPorts
+Installing packages using MacPorts
 """"""""""""""""""""""""""""""""""
-    
+
 Run the following commands:
 
 .. code-block:: bash
@@ -191,7 +206,7 @@ Run the following commands:
     sudo port select --set mpi openmpi-mp
 
 
-Installing Packages using Homebrew
+Installing packages using Homebrew
 """"""""""""""""""""""""""""""""""
 
 .. code-block:: bash
@@ -312,7 +327,7 @@ different configuration headers:
   .. code-block:: c++
 
     #define ELECTROSTATICS
-    #define LENNARD-JONES
+    #define LENNARD_JONES
 
 *  :file:`$builddir2/myconfig.hpp`:
 

doc/sphinx/lb.rst

@@ -288,7 +288,7 @@ Electrohydrodynamics
         .. note::
            This needs the feature ``LB_ELECTROHYDRODYNAMICS``.
 
-If the feature is activated, the Lattice Boltzmann Code can be
+If the feature is activated, the lattice-Boltzmann code can be
 used to implicitly model surrounding salt ions in an external electric
 field by having the charged particles create flow.
 

doc/sphinx/running.rst

@@ -77,9 +77,9 @@ would like to recompute the forces, despite the fact that they are
 already correctly calculated. To this aim, the option ``recalc_forces`` can be used to
 enforce force recalculation.
 
-.. _Isotropic NPT thermostat integrator:
+.. _Isotropic NPT integrator:
 
-Isotropic NPT thermostat
+Isotropic NPT integrator
 ------------------------
 
 :py:func:`~espressomd.integrate.Integrator.set_isotropic_npt`
@@ -90,16 +90,16 @@ discussed here and only a brief summary is given in :ref:`Thermostats`.
 To activate the NPT integrator, use :py:func:`~espressomd.integrate.Integrator.set_isotropic_npt`
 with parameters:
 
-    * ``ext_pressure``:  (float) The external pressure as float variable.
-    * ``piston``:        (float) The mass of the applied piston as float variable.
-    * ``direction``:     [int, int, int] Flags to enable/disable box dimensions to be subject to fluctuations. By default, all directions are enabled.
+    * ``ext_pressure``: The external pressure
+    * ``piston``: The mass of the applied piston
+    * ``direction``: Flags to enable/disable box dimensions to be subject to fluctuations. By default, all directions are enabled.
 
 Additionally, a NPT thermostat has to be set by :py:func:`~espressomd.thermostat.Thermostat.set_npt()`
 with parameters:
 
-    * ``kT``:     (float) Thermal energy of the heat bath
-    * ``gamma0``: (float) Friction coefficient of the bath
-    * ``gammav``: (float) Artificial friction coefficient for the volume fluctuations.
+    * ``kT``: Thermal energy of the heat bath
+    * ``gamma0``: Friction coefficient of the bath
+    * ``gammav``: Artificial friction coefficient for the volume fluctuations.
 
 A code snippet would look like::
 
@@ -129,7 +129,7 @@ where
 Here :math:`\mathcal{P}` is the instantaneous pressure, :math:`d` the dimension of the system (number of flags set by ``direction``), :math:`f_{ij}` the short range interaction force between particles :math:`i` and :math:`j` and :math:`x_{ij}= x_j - x_i`.
 
 In addition to this deterministic force, a friction :math:`-\frac{\gamma^V}{Q}\Pi(t)` and noise :math:`\sqrt{k_B T \gamma^V} \eta(t)` are added for the box
-volume dynamics and the particle dynamics. . This introduces three new parameters:
+volume dynamics and the particle dynamics. This introduces three new parameters:
 The friction coefficient for the box :math:`\gamma^V` (parameter ``gammav``), the friction coefficient of the particles :math:`\gamma^0` (parameter ``gamma0``) and the thermal energy :math:`k_BT` (parameter ``kT``).
 For a discussion of these terms and their discretisation, see :ref:`Langevin thermostat`, which uses the same approach, but only for particles.
 As a result of box geometry changes, the particle positions and velocities have to be rescaled 
@@ -172,7 +172,7 @@ Notes:
 
 * The NPT algorithm is only tested for all 3 directions enabled for scaling. Usage of ``direction`` is considered an experimental feature.
 * In step 4, only those coordinates are scaled for which ``direction`` is set.
-* The for the instantaneous pressure the same limitations of applicability hold as described in :ref:`Pressure`.
+* For the instantaneous pressure, the same limitations of applicability hold as described in :ref:`Pressure`.
 * The particle forces :math:`F` include interactions as well as a friction and noise term analogous to the terms in the :ref:`Langevin thermostat`.
 * The particle forces are only calculated in step 5 and then reused in step 1 of the next iteration. See :ref:`Velocity Verlet Algorithm` for the implications of that.
 

doc/sphinx/system_setup.rst

@@ -280,7 +280,7 @@ at temperature :math:`T` and satisfies
 In the |es| implementation of the Langevin thermostat,
 the additional terms only enter in the force calculation.
 This reduces the accuracy of the Velocity Verlet integrator
-by one order in :math:`dt` because forces are now velocity dependent.
+by one order in :math:`dt` because forces are now velocity-dependent.
 
 The random process :math:`\eta(t)` is discretized by drawing an uncorrelated random number
 :math:`\overline{\eta}` for each component of all the particle forces. 
@@ -380,7 +380,7 @@ The friction coefficients and cutoff are controlled via the
 see there.
 
 The friction (dissipative) and noise (random) term are coupled via the
-fluctuation- dissipation theorem. The friction term is a function of the
+fluctuation-dissipation theorem. The friction term is a function of the
 relative velocity of particle pairs. The DPD thermostat is better for
 dynamics than the Langevin thermostat, since it mimics hydrodynamics in
 the system.
@@ -412,17 +412,7 @@ Isotropic NPT thermostat
 This feature allows to simulate an (on average) homogeneous and isotropic system in the NPT ensemble.
 In order to use this feature, ``NPT`` has to be defined in the :file:`myconfig.hpp`.
 Activate the NPT thermostat with the command :py:func:`~espressomd.thermostat.Thermostat.set_npt`
-and set the following parameters:
-
-    * ``kT``:     (float) Thermal energy of the heat bath
-    * ``gamma0``: (float) Friction coefficient of the bath
-    * ``gammav``: (float) Artificial friction coefficient for the volume fluctuations.
-
-Also, setup the integrator for the NPT ensemble with :py:func:`~espressomd.integrate.Integrator.set_isotropic_npt`
-and the parameters:
-
-    * ``ext_pressure``:  (float) The external pressure.
-    * ``piston``:        (float) The mass of the applied piston.
+and setup the integrator for the NPT ensemble with :py:func:`~espressomd.integrate.Integrator.set_isotropic_npt`.
 
 For example::
 
@@ -432,7 +422,7 @@ For example::
     system.thermostat.set_npt(kT=1.0, gamma0=1.0, gammav=1.0)
     system.integrator.set_isotropic_npt(ext_pressure=1.0, piston=1.0)
 
-For an explanation of the algorithm involved, see :ref:`Isotropic NPT thermostat`
+For an explanation of the algorithm involved, see :ref:`Isotropic NPT integrator`.
 
 Be aware that this feature is neither properly examined for all systems
 nor is it maintained regularly. If you use it and notice strange

src/python/espressomd/integrate.pyx

@@ -144,7 +144,9 @@ cdef class Integrator:
         piston : :obj:`float`
             The mass of the applied piston.
         direction : (3,) array_like of :obj:`int`, optional
-            Set the box geometry for non-cubic boxes.
+            Select which dimensions are allowed to fluctuate by assigning
+            them to ``1``. In the special case where all dimensions are set
+            to ``0`` (default), they are all set to ``1`` in the core.
         cubic_box : :obj:`bool`, optional
             If this optional parameter is true, a cubic box is assumed.
 

src/python/espressomd/thermostat.pyx

@@ -424,7 +424,6 @@ cdef class Thermostat:
                 Friction coefficient of the bath
             gammav : :obj:`float`
                 Artificial friction coefficient for the volume fluctuations.
-                Mass of the artificial piston.
 
             """