Add Drude blurb

docs-source/usersguide/application.rst

@@ -1068,13 +1068,18 @@ temperature control with a velocity scaling algorithm that produces more
 accurate transport properties :cite:`Basconi2013`.  This velocity scaling
 results from propagating a chain of extra variables, which slightly reduces the
 computational efficiency with respect to :code:`LangevinMiddleIntegrator`.  The
-integrator is minimally created by specifying only the timestep::
-
-    integrator = NoseHooverIntegrator(0.004*picoseconds)
-
-However, many optional settings may be tuned as described XXXXXXXX.  Note that
-for this integrator, the velocities are offset by half a time step from the
-positions.
+thermostated integrator is minimally created similarly to the
+:code:`LangevinMiddleIntegrator` example above::
+
+    NoseHooverIntegrator integrator(300*kelvin, 25/picosecond, 0.004*picoseconds);
+
+The first argument specifies the target temperature.  The second specifies the
+frequency of interaction with the heat bath: a lower value interacts minimally,
+yielding the microcanonical ensemble in the limit of a zero frequency, while a
+larger frequency will perturb the system greater, keeping it closer to the
+target temperature.  The third argument is the integration timestep that, like
+the other arguments, must be specified with units.  Note that for this
+integrator, the velocities are offset by half a time step from the positions.
 
 Leapfrog Verlet Integrator
 --------------------------

docs-source/usersguide/library.rst

@@ -3634,7 +3634,7 @@ the Drude particle and the spring constant *k* by
 A damped interaction\ :cite:`Thole1981` is used between dipoles that are
 bonded to each other.
 
-The equations of motion can be integrated with two different methods:
+The equations of motion can be integrated with three different methods:
 
 #. In the Self Consistent Field (SCF) method, the ordinary particles are first
    updated as usual.  A local energy minimization is then performed to select new
@@ -3649,3 +3649,9 @@ The equations of motion can be integrated with two different methods:
    temperature, while using a much lower temperature for their relative internal
    motion.  In practice, this produces dipole moments very close to those from the
    SCF solution while being much faster to compute.
+#. The Nosé-Hoover dual thermostat method.  In this approach the motion of
+   non-Drude sites and center of mass motion of Drude pairs are thermostated to
+   the target temperature with one thermostat.  Another thermostat is used to keep
+   relative motion of Drude pairs to a different, typically much lower,
+   temperature to maintain separation of nuclear and electronic degrees of
+   freedom.

docs-source/usersguide/references.bib

@@ -49,7 +49,7 @@
   issue = {7},
   pages = {2887-2899},
   year = {2013},
-  doi= {https://doi.org/10.1021/ct400109a}
+  doi= {10.1021/ct400109a}
 }
 
 @article{Berendsen1987