Guillaume Fraux

Wrap Chemharp to Julia, and use it for IO

11

I should wrap [Chemharp](https://github.com/Luthaf/Chemharp) to Julia, and use it to replace the Trajectories module. I can wrap the C interface or the C++ interface here. I should have a look...

Add commons potentials

2

This is a meta-issue about potentials, the code would need a lot of them : #### Short range - [ ] Morse potential #### Biochem potentials - [ ] CHARMM...

The coverage is only 55% today, this should be improved up to 90% at least.

Another meta-issue about thermostating and barostating the system. There are two ways to do this : ### Enforcing the parameters after the integration This can be done by modifying the...

Use a lookup in a table to save time in potential computations ?

6

See this gist : https://gist.github.com/Luthaf/a30fae741ed9f937a97b The output on my machine : ``` Relative difference: 0.0030037844682750453 Direct computing elapsed time: 1.238753331 seconds (320000000 bytes allocated, 10.19% gc time) Table lookup elapsed...

Since `info` and `warn` now uses an `io` first parameter, this can be done easily.

To speedup the computation. See http://en.wikipedia.org/wiki/Verlet_list. This would have to be implemented as a `ForceComputer` subtype.

We should check for positive temperature and other parameters when creating a new Thermostat (as subtype of `Control`).

Long-range interactions

1

Meta-issue about long-range potentials computations. As far as I know, there are two main ways to do this : - [ ] Ewalds summation - [ ] PPPM base computations

Having input files with a nice syntax would be great. The [YAML](http://www.wikiwand.com/en/YAML) format seems to be a good format for this, and there is already a [Julia parser](https://github.com/dcjones/YAML.jl). This can...