Import('env')

env.IMPModuleDoc(env.IMPModuleGetDocs(),
                 authors=["Daniel Russel", "Dina Schneidman"],
                 brief="MODULENAME provides benchmarks of a variety of aspects of \\imp",
                 publications=env.StandardPublications(),
                 license=env.StandardLicense(),
                 overview="""The benchmarks are run daily on
flute.ucsf.edu.  The results are displayed normalized against the
fastest runtime in each set (with a few exceptions, noted below).
Each benchmark is shown first in a "fast" build and second in a
"release" build with checks disabled to give an idea of the speed
comparison. The benchmark source codes can be found in the bin
directory of the benchmark module.

A simple Brownian dynamics simulation with the specified number of
particles
\\image html "benchmark/doc/bdfast.png"
\\image html "benchmark/doc/bdrelease.png"

A simple test modifying the particles and (for the 'score' entries)
evaluating a simple, incremental, score.
\\image html "benchmark/doc/changingfast.png"
\\image html "benchmark/doc/changingrelease.png"

The various IMP::core::ClosePairFinder implementations are benchmarked
on random sets of particles. The benchmarks for the quadratic one are listed as
taking 10x less time than they did.
\\image html "benchmark/doc/cpffast.png"
\\image html "benchmark/doc/cpfrelease.png"


A benchmark of the various close pairs finders in the context of
a simulation. The benchmarks for the quadratic one are listed as
taking 10x less time than they did.
\\image html "benchmark/doc/colfast.png"
\\image html "benchmark/doc/colrelease.png"

A special close pair finder is provided for rigid bodies, name
IMP::core::RigidClosePairsFinder. Here it is compared against
using all the member particles.
\\image html "benchmark/doc/rigidfast.png"
\\image html "benchmark/doc/rigidrelease.png"


There are several ways of doing connectivity restraints in \imp:
IMP::misc::ConnectedPairContainer and IMP::core::ConnectivityRestraint.
They are benchmarked here.
\\image html "benchmark/doc/connectivityfast.png"
\\image html "benchmark/doc/connectivityrelease.png"

The next benchmark looks at evaluating restraints on various sorts
of containers, namely IMP::core::ListSingletonContainer and
IMP::core::SingletonContainerSet.
\\image html "benchmark/doc/containerfast.png"
\\image html "benchmark/doc/containerrelease.png"

When peforming lots of operations on a set of cartesian coordinates
and is faster to copy them into a IMP::algebra::Vector3Ds than
to access them in the IMP::core::XYZ decorator each time. This
benchmark gives an idea of the speed tradeoffs involved.
\\image html "benchmark/doc/xyzfast.png"
\\image html "benchmark/doc/xyzrelease.png"


""")