SOMD basics

SOMD is an ab-initio molecular dynamics (AIMD) package designed for the SIESTA DFT code. The SOMD code provides some useful subroutines (potential calculator interfaces, integrators, barostats, etc.) to perform standard Born-Oppenheimer molecular dynamics (BOMD) simulations. Thus, SOMD itself should be regarded as a library, just like the OpenMM package. And you should write proper python scripts to assemble the provided subroutines into meaningful simulation protocols.

Module structures

The SOMD code contains four main submodules: constants, core, potentials and apps.

• The constants module contains physical constants and default values of SOMD.
• The core module contains core components of SOMD, e.g., the internal representation of an atomic system, the integrators, etc.
• The potentials module contains interfaces to various potential calculators.
• The apps module contains some useful applications, e.g., the trajectory writers, system data loggers, pre-defined simulation protocols, etc. (Note that the barostats are regarded as applications as well, because the first-order barostats implemented in SOMD behave like other post-integration-step applications.)

somd
├── constants  <-- Physical constants and default values.
├── core       <-- Core components.
│   ├── systems         <-- Representations of the simulated systems.
│   ├── groups          <-- Atom groups.
│   ├── integrators     <-- Integrators to propagate the systems.
│   └── potential_base  <-- Base class of all potential calculator interfaces.
├── potentials <-- Potential calculator interfaces.
│   ├── SIESTA          <-- SIESTA wrapper.
│   ├── DFTD3           <-- DFTD3 wrapper.
│   ├── DFTD4           <-- DFTD4 wrapper.
│   ├── NEP             <-- NEP_CPU wrapper.
│   ├── PLUMED          <-- PLUMED wrapper.
│   ...
├── apps       <-- Useful applications based on the SOMD core.
│   ├── barostats       <-- Barostats.
│   ├── trajectories    <-- Trajectory writers.
│   ├── loggers         <-- System data loggers.
│   ├── simulations     <-- Wrapper class of the simulation processes.
│   ├── active_learning <-- Wrapper class of the active learning processes.
│   ...