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These examples show how new force field terms are implemented. The
HarmonicOscillator example implements a harmonic potential that ties
an individual atom to a specific point in space. The ElectricField example
implements an external electric field that acts on all charges.
Three implementations are provided for each example, one in Python,
one in C and one in Cython. The Python and Cython examples require
Python 2.2 (or later), Cython 0.123 (or later), and MMTK 2.5.7 (or
later). The C examples require Python 1.5.2 (or later) and MMTK 2.0
(or later).
The Python versions are the easiest to write, test, and understand,
but they are also by far the slowest. For simple energy calculations
like in these two exemples, a Python version may be sufficient. In
most cases, a Cython or C implementation will be necessary, but a
Python version can be very useful in designing, testing, and debugging
an equivalent Cython or C implementation.
Cython is a compiled version of Python that permits adding C type
declarations for gaining speed. If all variables have C type
declarations, then Cython code is as fast as hand-written C
code. However, as the examples show, Cython code is much more compact,
mostly because Cython handles the bookkeeping behind Python extension
types automatically. I expect Cython to become the tool of choice
for writing C extensions in the future, so I do recommend everyone
to have a look at it.
For more information about Cython, and for downloading it, see
http://www.cython.org/.
As the examples make clear, a force field term always consists of two
parts: the force field term itself, always implemented in Python, and
a corresponding energy evaluator term, implemented in Python, C, or
Cython. The energy evaluator part is what is called for each energy
evaluation. The force field part is only executed once, to prepare the
parameters. For efficiency reasons, as much work as possible should
therefore be done in the force field part.
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