lumol
lumol copied to clipboard
lumol-org
Universal extensible molecular simulation engine
This issue is to discuss the possibility of adding path integral methods to the already existing classical MD / MC framework. Quantum-classical isomorphism enables mapping of the thermodynamics of a...
Currently, the center of mass computation does not check if all particles of a molecule are adjacent, or if some particles are wrapped into the simulation cell. If a molecule...
As discussed in #213, this might be useful in conjunction with binary formats without topology information. For example, one can write both the trajectory in a binary format and the...
We currently manually format the elapsed time manually in the output log: https://github.com/lumol-org/lumol/blob/0f6efbd38b0bf132af2f912c0b233e5a8829bf02/src/bin/lumol.rs#L66-L87 This code could be replaced by using the [humantime](https://github.com/tailhook/humantime) crate instead.
Because we use TOML as format for the input, the user can add keys that are not used by the input system now: ```toml [input] version = 1 [global] cutoff...
More usefull potentials should be added. I know about theses: - [x] Morse potential - [x] Buckingham potential - [ ] Cosine series Are there any others?
Follow-up of https://github.com/lumol-org/lumol/pull/130#issuecomment-290916546. We have three propositions: 1. Rename `Array2` to `UnsafeArray2` and `Array3` to `UnsafeArray3`, but keep the indexing 'safe'. 2. Remove the unchecked access with `Index`, and use...
There are various free energy methods that utilize scaling of intermolecular interactions. For example one can compute the chemical potential by inserting an additional particle/molecule into the system. This insertion...
Universe properties (`Forces`, `KineticEnergy`, ...) can be expensive to compute. It would be nice to cache them. But there are two difficult things in CS: naming and cache invalidation. Because...
If the simulation crashes, or to restart a simulation for more steps, a restart file is needed. It should be some private binary format, but with compatibility between multiple versions...