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tsoc
openmm
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4603c429
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4603c429
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Jun 15, 2020
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Andy Simmonett
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Clean up application.rst blurb
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docs-source/usersguide/application.rst
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@@ -1081,41 +1081,9 @@ 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.
More verbose invocation is possible::
NoseHooverIntegrator integrator(300*kelvin, 25/picosecond,
0.004*picoseconds, 3, 3, 7);
where the extra arguments are the chain length, number of multi-timesteps and
number of Yoshida-Suzuki points, as described in section
:ref:`nosehoover-integrators-theory`.
This integrator supports partitioning of the system into an arbitrary number of
subsystems, where each can be coupled to a different heat bath. As an example::
NoseHooverIntegrator integrator(0.004*picoseconds)
integrator.addSubsystemThermostat(thermostatedParticles, thermostatedPairs,
centerOfMassTemperature, centerOfMassCollisionFrequency,
relativeTemperature, relativeCollisionFrequency,
chainLength, numMTS, numYoshidaSuzuki)
Here the first argument to :code:`addSubsystemThermostat` is a list of the
particles to be controlled by that thermostat, which will be thermostated to
the :code:`centerOfMassTemperature`. The :code:`thermostatedPairs` is a list
of pairs whose center of mass motion will be thermostated to
:code:`centerOfMassTemperature`, while the relative motion of each pair will be
thermostated to :code:`relativeTemperature`. It is possible for one of
:code:`thermostatedAtoms` or :code:`thermostatedPairs` to be empty. The final
three arguments have the same default values as the simple constructor
described above. Making multiple calls to :code:`addSubsystemThermostat` with
different lists of atoms and pairs permits the creation of differently
thermostated subsystems: note that because some platforms can reorder similar
molecules, all molecules of a given type must be controled by the same
thermostat. This more advanced syntax allows the setup of Drude oscillator
simulations, but a more convenient form is provided through the
:code:`DrudeNoseHooverIntegrator` class, described in :ref:`drude-plugin`.
Note that for this integrator, the velocities are offset by half a time step
from the positions.
This integrator supports lots of other options, including the ability to couple
different parts of the system to thermostats at different temperatures. See the
API documentation for details.
Leapfrog Verlet Integrator
--------------------------
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