#Doxygen equations pdf
#Doxygen equations code

That documentation will be best viewed after formatting by Doxygen, which employs other tools like LaTeX and Markdown for beautification. In addition, we need developers to provide good local documentation for our mathematical algorithms in the form of Doxygen comments. The Drake notation is designed to facilitate comparison between the typeset and coded math in order to verify correct implementation. We need to translate that mathematics into code, where there is much less typographical flexibility. That literature can provide clear, concise, and unambiguous documentation of the equations and algorithms we are using, but employs typeset mathematics to do so.

#Doxygen equations code

Where possible, we refer to published literature to supplement our code documentation. However, much of this can be useful to users of the Drake API also so it is included in the external documentation. Some comments are specifically targeted to those developers, and formatting compromises have been made so that the information in this section is (mostly) readable from the source code used to generate it (for example, ASCII drawings instead of image files, simple Markdown tables rather than fancy-but-unreadable html ones). Much of the information here is most useful for programmers who are writing or reading Drake multibody code. In this section we provide general documentation about our terminology, notation, and abstraction choices in a form that can be referenced from code documentation.

We need a shared, unambiguous notation in code that can employ programmers' awesome pattern-matching skills to make errors visible.

Coded algorithms should be comparable equation-by-equation against the typeset literature sources from which they are derived.

Disciplined notation is essential to prevent coordinate frame errors.

You can't reason properly about spatial algorithms if you treat translation and rotation separately.

In Drake we use terminology, notation, and abstractions that have been designed specifically to reduce the possibility of errors, based on these observations: This will also have the benefit of carrying over automatically to PyOpenMM docstrings automatically!Translating from the mathematics of multibody mechanics to correct code is a difficult process and requires careful discipline to ensure that the resulting code is correct. Where K is the spring constant, r is the interatomic distance, and r0 is the equilibrium length of the bond. * a bond has been added, you can modify its force field parameters by calling setBondParameters(). To use it, create a HarmonicBondForce object then call addBond() once for each bond. * This class implements an interaction between pairs of particles that varies harmonically with the distance

#Doxygen equations pdf

The Theory Guide PDF does have this documented, but to provide absolute security, it would be useful to document the equations relevant to the parameters for each function in the OpenMM header file doxygen documentation as well.

LJ sigma vs radius, harmonic spring constants off by a factor of 2).

Add text version of equation describing parameters to OpenMM doxygen headersĬhris Bruns reminded us today that PyOpenMM's 'simtk.unit' feature won't save us from using the wrong meaning for the parameter (e.g.