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system.md

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Set up the simulated system.

Tile now, simulated systems in SOMD are represented by the somd.core.systems.MDSYSTEM class. You could initialize a system containing ten atoms by:

>>> system = somd.core.systems.MDSYSTEM(10)

You may also assign a label for your system during the initialization:

>>> system = somd.core.systems.MDSYSTEM(10, label='SYSTEM')

The generated system object contains information about a typical atomic system, e.g., the atomic positions (system.positions), the atomic velocities (system.velocities) and the cell vectors (system.box). You could execute the import somd; help(somd.core.systems.MDSYSTEM) command in a python REPL to view a full list of valid attributes.

Specifically, the somd.core.systems module provides two useful methods to initialize the simulated systems from files:

  • The create_system_from_poscar method could perform system initialization using the POSCAR files. For example: 
    >>> system = somd.core.systems.create_system_from_poscar('H2O.POSCAR')
  • The create_system_from_pdb method could perform system initialization using the PDB files. For example: 
    >>> system = somd.core.systems.create_system_from_pdb('H2O.pdb')

Both method reads atomic types, atomic positions and simulation box data from corresponding files, then initializes a MDSYSTEM instance based on the read data.