Update manual for runtime steps (#275)

* Update topology.md

* Update running.md

docs/_docs/running.md

@@ -129,9 +129,16 @@ faunus -v 5 -i in.json 2>> error.log
 
 ## Parallelization
 
+By default, Monte Carlo moves and energy evaluations run in _serial_ and are
+not sped up by OpenMP/MPI as described below. Pragmas for non-bonded interactions
+can relatively easily be added, but this currently requires source modifications.
+We are working to make this user-controllable and in the meantime consider using
+an [embarrassingly parallel](https://en.wikipedia.org/wiki/Embarrassingly_parallel)
+scheme via different random seeds (provided that your system equilibrates quickly).
+
 ### OpenMP
 
-Several routines in Faunus can run in parallel using multiple threads. The only prerequisite is that Faunus was
+Some routines in Faunus can run in parallel using multiple threads. The only prerequisite is that Faunus was
 compiled with OpenMP support (which is default). The number of threads is controlled with an environment variable.
 The following example demonstrates how to run Faunus using 4 threads:  
 

docs/_docs/topology.md

@@ -31,6 +31,8 @@ random:              # seed for pseudo random number generator
 Below is a list of possible geometries, specified by `type`, for the simulation container,
 indicating if and in which directions periodic boundary conditions (PBC) are applied.
 Origin ($0,0,0$) is always placed in the geometric _center_ of the simulation container.
+Particles are always kept inside the simulation container with an external
+potential that is zero if inside; infinity if outside.
 
 `geometry` | PBC      | Required keywords
 ---------- | -------- | --------------------------------------
@@ -41,6 +43,15 @@ Origin ($0,0,0$) is always placed in the geometric _center_ of the simulation co
 `cylinder` | $z$      | `radius`, `length` (along _z_)
 `sphere`   | none     | `radius`
 
+### Simulation Steps
+
+The variables `macro` and `micro` are positive integers and their product
+defines the total number simulations steps.
+In each step a random Monte Carlo move is drawn from a weighted distribution.
+For each `macro` step, all analysis methods are, if befitting, instructed to
+flush buffered data to disk and may also trigger terminal output.
+For this reason `macro` is typically set lower than `micro`.
+
 ## Atom Properties
 
 Atoms are the smallest possible particle entities with properties defined below.