The MDANSE Workflow

Here we describe a typical computational workflow for most users which goes through three main stages (1) trajectory conversion, (2) analysis calculation and (3) results plotting.

1. Trajectory conversion

To load a trajectory into MDANSE and run an analysis calculation the trajectory must be in the MDANSE trajectory format, saved as a HDF file.

Most likely your trajectory is in whatever format was output by your preferred Molecular Dynamics simulation software, and you need to convert it first. Once you have converted your trajectory to the MDANSE HDF format, you can use it as input for all kinds of analysis. See also trajectory-converters

2a. Analysis parameters

Most analysis jobs offered by MDANSE allow a number of different parameters which can be adjusted. We describe some of the more common parameters found in MDANSE below.

Frames

It is not necessary to use all the time frames of your MD simulation. You can decide to limit the range of simulation time, and reduce the number of the frames taken in that range by increasing the step between them. Only the frames you selected will be passed to the analysis job. See also param-frames.

Atom selection

Just as it is not necessary to include all the time frames in the analysis, it is also possible to select only a subset of all the atoms present in the trajectory. Once you have defined a selection, you can decide to run an analysis job on the selected atoms, and ignore the rest. This is useful if you are trying to determine which atoms contribute to a specific feature in your results. See also param-atom-selection.

Resolution

The resolution is enabled only for the analysis types which calculate an energy spectrum. This is normally applied to calculations involving Fourier transform of a correlation function. The resolution is applied by multiplying the time-dependent function with a window function before applying the Fourier transform. The details are given in the section Instrument resolution.

Weighting

The partial (usually by element) properties calculated can be combined using the weights chosen by the user, as described in the section Weights. Please remember that the MDANSE_GUI normally recommends the weighting scheme appropriate to the type of analysis performed.

Output files

All the output arrays created in the analysis are written to the filesystem in the format chosen by the user. (If you intend to continue visualising the results within the MDANSE_GUI, you will need to use the HDF5 format. If, however, you were planning to process the results further using other software, then you will need to pick the ASCII output. See also Output files)

2b. Analysis results

The analysis jobs are run in steps, iterating over each part of the trajectory.

The iterations over steps will produce partial results. This is where the specific equations described in the documentation of an analysis type are applied. The partial results will be combined into the final result.

The partial properties are calculated, typically per atom type, or per pair of atom types and are combined into the total result.

3. Plotting

If the HDF5 format was chosen for the analysis job output file, the file can then be opened in the MDANSE_GUI and plotted. As the MDANSE_GUI plotting is built on the matplotlib library many options found in the matplotlib are available in MDANSE_GUI. Additionally as the analysis calculations store unit information with results, MDANSE_GUI allows users to interactively switch between different units.