Getting Started#

Installation#

The Viscosity step is installed with the rest of SEAMM by seamm-manager. To add it to an existing installation:

seamm-manager install viscosity-step

See the SEAMM installation documentation for more.

An example#

The viscosity of water at 298 K, analyzing one production run:

  1. Forcefield, choosing a water model, then Packmol to fill a cubic cell with a few hundred water molecules at the experimental density.

  2. LAMMPS, with these sub-steps:

    • Initialization, Minimization and Velocities;

    • NPT dynamics for about 100 ps to equilibrate the density;

    • NVT dynamics for the production run, a few nanoseconds, with Sample the pressure tensor set to every 5 fs on its trajectory tab, and the centres of mass of the molecules sampled every 1 ps if the diffusivity is wanted too.

  3. Viscosity, with MD to analyze set to “the last MD run”. The run is divided into 5 blocks to estimate the errors.

  4. Optionally Diffusivity, also analyzing the last MD run, which uses this viscosity for its finite-size correction.

If the pressure tensor is not sampled often enough, the flowchart is refused when it is checked or submitted, with a message saying what to change.

That should be enough to get started. For more detail about the functionality in this plug-in, see the User Guide.