Performing Simulations

Whether we want to perform a molecular dynamics, energy minimization, or any other kind of simulation one needs define the system of interest, prior to execution. In other words inital conditions of the problem must be given. In addition, the force field (inter-atomistic potential) namely, the governing equations of the problem, needs to be given as well.

mapp.md.atoms container class
mapp.dmd.atoms container class

class mapp.md.atoms and mapp.dmd.atoms are containers for such information, they store the configuration of the system (per atom quantities such as position inside the unitcell, and etc.) and force field kind and relevant parameters

Defining Initial Value

One of the common ways to give present a system configuration is using a file. There are some static methods provided in both containers that can be utilised to present construct containers from a file. These static method names start with import_

MD

mapp.md.atoms.import_cfg(cfg_file) Imports cfg file to mapp.md.atoms.

DMD

mapp.dmd.atoms.import_cfg(N,cfg_file) Imports cfg file to mapp.dmd.atoms.

Defining Governing Equations

explain defining forcefield

MD

mapp.md.atoms.ff_lj(...) Lennard-Jones potential
mapp.md.atoms.ff_fs(...) Finnis-Sinclair EAM
mapp.md.atoms.ff_eam_funcfl(...) Tabulated EAM force field given by FuncFL file/s
mapp.md.atoms.ff_eam_setfl(setfl_file) Tabulated EAM force field given by a single SetFL file
mapp.md.atoms.ff_eam_fs(fs_file) Tabulated Finnis-Sinclair EAM

DMD

mapp.dmd.atoms.ff_eam_funcfl(...) Tabulated EAM force field given by FuncFL file/s
mapp.dmd.atoms.ff_eam_setfl(...) Tabulated EAM force field given by a single SetFL file
mapp.dmd.atoms.ff_eam_fs(...) Tabulated Finnis-Sinclair EAM