CODEWITHSUNDEEP
c++
arc_lupus
arc_lupus

Reputation: 4114

Memory saving system for molecule calculations

I am currently working on a MD simulation. It stores the molecule positions in a vector. For each time step, that vector is stored for display in a second vector, resulting in

std::vector<std::vector<molecule> > data;

The size of data is time steps*<number of molecules>*sizeof(molecule), where sizeof(molecule) is (already reduced) 3*sizeof(double), as the position vector. Still I get memory problems for larger amounts of time steps and number of molecules.

Thus, is there an additional possibility to decrease the amount of data? My current workflow is that I calculate all molecules first, store them, and then render them by using the data of each molecule for each step, the rendering is done with Irrlicht. (Maybe later with blender).

Upvotes: 1

Views: 52

Answers (2)

user1196549
user1196549

Reputation:

If the trajectories are smooth, you can consider to compress data by storing only for every Nth step and restoring the intermediate positions by interpolation.

If the time step is small, linear interpolation can do. Top quality can be provided by cubic splines. Anyway, the computation of the spline coefficients is a global operation that you can only perform in the end and that required extra storage (!), and you might prefer Cardinal splines, which can be built locally, from four consecutive positions.

enter image description here

Upvotes: 3

Pete Kirkham
Pete Kirkham

Reputation: 49321

You could gain a factor of 2 improvement by storing the positions in single precision rather than double - it will be sufficient for rendering, if not for the simulation.

But ultimately you will need to store the results in a file and render offline.

Upvotes: 0

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