mapp4py.md.atoms

class mapp4py.md.atoms

container class

Attributes
B

(symm<double[dim][dim]>) unitcell matrix inverse (\mathbf{H}^{-1})

H

(symm<double[dim][dim]>) unitcell matrix

S_pe

(double) potential energy stress

comm_coords

(int[dim]) communication coordinates

comm_dims

(int[dim]) communication dimensions

comm_rank

(int) communication rank

comm_size

(int) communication size

elems

(dict{int:string}) elements dictionary

hP

(double) Planck constant

kB

(double) Boltzmann constant

natms

(int) number of atoms

pe

(double) potential energy

skin

(double) size of skin

step

(int) step number

vol

(double) unitcell volume

Methods

add_elem(elem,mass)

Add a new element to the system

autogrid()

Autogrids the simualtion box

cell_change(N)

Replicates the box in each dimension according to the given values by the vector

create_temp(temp,seed)

Create a random velcity field

do(func)

acts a given function on every atom

ff_eam_fs(fs_file)

Tabulated Finnis-Sinclair EAM

ff_eam_funcfl(funcfl_files,elems=None)

Tabulated EAM force field given by FuncFL file/s

ff_eam_setfl(setfl_file)

Tabulated EAM force field given by a single SetFL file

ff_fs(…)

Finnis-Sinclair EAM

ff_lj(eps,sigma,r_c,shift=False,elems=None)

Lennard-Jones potential

import_cfg(cfg_file)

Imports cfg file to mapp4py.md.atoms.

mul(N)

Replicates the box in each dimension according to the given values by the vector

strain(E)

Strain the system (NEED MORE EXPLANATION TBCMPLTD)

bct_polarity

ff_eam_func