Merge branch 'python' into lb_force_density

.gitlab-ci.yml

@@ -123,16 +123,6 @@ no_rotation:
     - docker
     - linux
 
-nocheckmaxset:
-  <<: *global_job_definition
-  stage: build
-  script:
-    - export with_cuda=false myconfig=nocheck-maxset make_check=false
-    - bash maintainer/CI/build_cmake.sh
-  tags:
-    - docker
-    - linux
-
 ### Builds with different Distributions
 
 #debian:8 removed: similar to ubuntu:1404

doc/sphinx/installation.rst

@@ -405,8 +405,6 @@ General features
 
 -  ``COMFIXED`` Allows to fix the center of mass of all particles of a certain type.
 
--  ``MOLFORCES`` (EXPERIMENTAL)
-
 -  ``BOND_CONSTRAINT`` Turns on the RATTLE integrator which allows for fixed lengths bonds
    between particles.
 
@@ -537,48 +535,12 @@ Some of the short-range interactions have additional features:
 Debug messages
 ^^^^^^^^^^^^^^
 
-Finally, there are a number of flags for debugging. The most important
-one are
+Finally, there is a flag for debugging:
 
 -  ``ADDITIONAL_CHECKS`` Enables numerous additional checks which can detect inconsistencies
    especially in the cell systems. These checks are however too slow to
    be enabled in production runs.
 
-The following flags control the debug output of various sections of
-|es|. You will however understand the output very often only by
-looking directly at the code.
-
--  ``COMM_DEBUG`` Output from the asynchronous communication code.
-
--  ``EVENT_DEBUG`` Notifications for event calls, i.e. the ``on_...`` functions in
-   ``initialize.c``. Useful if some module does not correctly respond to
-   changes of e.g. global variables.
-
--  ``CELL_DEBUG`` Cellsystem output.
-
--  ``GHOST_DEBUG`` Cellsystem output specific to the handling of ghost cells and the
-   ghost cell communication.
-
--  ``HALO_DEBUG``
-
--  ``P3M_DEBUG``
-
--  ``THERMO_DEBUG`` Output from the thermostats.
-
--  ``VIRTUAL_SITES_DEBUG``
-
--  ``ASYNC_BARRIER`` Introduce a barrier after each asynchronous command completion. Helps
-   in the detection of mismatching communication.
-
--  ``FORCE_CORE`` Causes |es| to try to provoke a core dump when exiting unexpectedly.
-
--  ``MPI_CORE`` Causes |es| to try this even with MPI errors.
-
--  ``CUDA_DEBUG``
-
--  ``H5MD_DEBUG``
-
-
 
 
 Features marked as experimental

doc/sphinx/introduction.rst

@@ -299,6 +299,7 @@ Currently, the following tutorials are available:
 * :file:`08-visualization`: Using the online visualizers of |es|.
 * :file:`10-reaction_ensemble`: Modelling chemical reactions by means of the reaction ensemble.
 * :file:`11-ferrofluid`: Modelling a colloidal suspension of magnetic particles.
+* :file:`12-constant_pH`: Modelling an acid dissociation curve using the constant pH method
 
 .. _Sample scripts:
 

doc/sphinx/particles.rst

@@ -510,11 +510,6 @@ Please note that the velocity attribute of the virtual particles does not carry
     The behavior of virtual sites can be fine-tuned with the following
     switches in :file:`myconfig.hpp`.
 
-    - ``VIRTUAL_SITES_NO_VELOCITY`` specifies that the velocity of virtual sites is not computed
-
-    - ``VIRTUAL_SITES_THERMOSTAT`` specifies that the Langevin thermostat should also act on virtual
-       sites
-
     - ``THERMOSTAT_IGNORE_NON_VIRTUAL`` specifies that the thermostat does not act on non-virtual particles
 
 .. _Particle number counting feature:
@@ -529,16 +524,13 @@ Particle number counting feature
 
 
 
-Knowing the number of particles of a certain type in simulations in the grand canonical ensemble,
-or other purposes, when particles of certain types are created and
-deleted frequently is often of interest. Particle ids can be stored in a map for each
-individual type and so random ids of particles of a certain type can be
-drawn.  ::
+Knowing the number of particles of a certain type in simulations where particle numbers can fluctuate is of interest.
+Particle ids can be stored in a map for each
+individual type::
 
     import espressomd
     system = espressomd.System()
     system.setup_type_map([_type])
-    system.find_particle(_type)
     system.number_of_particles(_type)
 
 If you want to keep track of particle ids of a certain type you have to
@@ -547,9 +539,7 @@ initialize the method by calling  ::
     system.setup_type_map([_type])
 
 After that will keep track of particle ids of that type. Keeping track of particles of a given type is not enabled by default since it requires memory.
-When using the
-keyword ``find_particle`` and a particle type, the command will return a randomly
-chosen particle id, for a particle of the given type. The keyword
+The keyword
 ``number_of_particles`` as argument will return the number of
 particles which have the given type. For counting the number of particles of a given type you could also use :meth:`espressomd.particle_data.ParticleList.select` ::
 
@@ -558,7 +548,7 @@ particles which have the given type. For counting the number of particles of a g
     ...
     number_of_particles = len(system.part.select(type=type))
 
-However calling ``select(type=type)`` results in looping over all particles. Therefore calling ``select()`` is slow compared to using :meth:`espressomd.system.System.number_of_particles` which directly can return the number of particles with that type.
+However calling ``select(type=type)`` results in looping over all particles which is slow. In contrast, :meth:`espressomd.system.System.number_of_particles` directly can return the number of particles with that type.
 
 .. _Self-propelled swimmers:
 

doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb

@@ -522,13 +522,13 @@
     "_uncorrelated_ samples:\n",
     "\n",
     "\\begin{equation}\n",
-    "    SE      = \\sqrt{\\frac{\\sigma}{N}},\n",
+    "    SE      = \\sqrt{\\frac{\\sigma^2}{N}},\n",
     "\\end{equation}\n",
     "\n",
-    "where $\\sigma$ is the standard deviation\n",
+    "where $\\sigma^2$ is the variance\n",
     "\n",
     "\\begin{equation}\n",
-    "    \\sigma  = \\left\\langle x^2 - \\langle x\\rangle^2 \\right\\rangle\n",
+    "    \\sigma^2  = \\left\\langle x^2 - \\langle x\\rangle^2 \\right\\rangle\n",
     "\\end{equation}"
    ]
   },

doc/tutorials/10-reaction_ensemble/10-reaction_ensemble.tex

@@ -92,7 +92,7 @@ \subsection{Constant pH method}
 In the constant pH method, the acceptance probability for a reaction is
 
 \begin{equation} 
-P_{\text{acc}} = \text{min}\left\lbrace  1, e^{\beta \Delta E_\text{pot} \pm \ln{10} (\text{pH - pK}_\text{a})}\right\rbrace \text{,}
+P_{\text{acc}} = \text{min}\left\lbrace  1, e^{\beta \Delta E_\text{pot} \pm \ln_{10} (\text{pH - pK}_\text{a})}\right\rbrace \text{,}
 \end{equation}
 and the acceptance probability of a reaction is $P_\text{acc}=\frac{N_\text{HA}}{N0}$ for a dissociation and $P_\text{acc}=\frac{N_\text{A}}{N0}$ for an association reaction \cite{landsgesell2017simulation}. Here $\Delta E_\text{pot}$ is the potential energy change due to the reaction, while $\text{pH - p}K_\text{a}$ is an input parameter composed by two terms, pH and -p$K_\text{a}$, that represent, respectively, the concentration of \ce{H+} ions in the solution and the logarithm in base 10 of the thermodynamic dissociation constant for HA when the system is approximated as a dilute solution ($\gamma_i \approx 1$):
 \begin{equation}