Declare external Resources in mdp / tpr files. - Redmine #2901
Unify data representation not present in the .tpr files and include
information about this data in pre-processing steps (currently via
.mdp-files).
To avoid transform experimental data or very large and complex data
input to tpr-format would ultimately turn tpr files to a wrapper file
format for all sorts of input data sources we use during simulations.
Currently essential dyanmics uses an external data file that is provided as an command line option to mdrun; in the future, all code that relies on external experimental data for driving simulations will rely on this, e.g. cryo-EM fitting, WAXS/SAXS module, secondary structure driven simulations as well as contact driven md.
Instead of the current design, we would rather like to store handles to the data sources in the tpr file format.
These data sources should be
- labelled
- have a specified type
- handle to the raw data
- include a source sanity check, if possible
Related to #2282, #2590
(from redmine: issue id 2901, created on 2019-03-21 by cblau, closed on 2019-12-28)
- Relations:
- relates #3374 (closed)
- Changesets:
- Revision 75a273b0 on 2019-04-05T15:21:10Z:
densityfitting - MDModule declaration
Declaring the infrastructure for running molecular dynamics simulations with
addional forces that are derived from densities.
Adds a IForceProvider for density fitting simulation that is set up with
its DensityFittingParameters that are in turn built from DensityFittingOptions.
refs #2282 #2901
Change-Id: I0732a78747582a6e23bba1e141d73c4cda421011