mapp4py.dmd.atoms

class mapp4py.dmd.atoms

container class

Attributes
B

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

H

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

S_fe

(double) stress

ave_comp

(double[nelems]) average mu per element

ave_mu

(double[nelems]) average mu per element

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

ext_mu

(double[nelems]) external mu per element

fe

(double) free energy

hP

(double) Planck constant

kB

(double) Boltzmann constant

natms

(int) number of atoms

pe

(double) free energy

s

(double) free energy

skin

(double) size of skin

step

(int) step number

temp

(double) temperature

vol

(double) unitcell volume

Methods

autogrid()

Autogrids the simualtion box

do(func)

acts a given function on every atom

ff_eam_fs(fs_file,r_crd,C,elems=None)

Tabulated Finnis-Sinclair EAM

ff_eam_funcfl(funcfl_files,r_crd,C,elems=None)

Tabulated EAM force field given by FuncFL file/s

ff_eam_setfl(setfl_file,r_crd,C,elems=None)

Tabulated EAM force field given by a single SetFL file

import_cfg(N,cfg_file)

Imports cfg file to mapp4py.dmd.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)