Merge branch 'lebedeva2' of https://github.com/zbych127/lammps into collected-post-stable-patches

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

:line

pair_style lebedeva command :h3

[Syntax:]

pair_style hybrid/overlay lebedeva cutoff :pre

[Examples:]

pair_style hybrid/overlay lebedeva 20.0

pair_coeff * * none

pair_coeff 1 2 lebedeva  CC.Lebedeva   C C :pre

pair_style hybrid/overlay rebo lebedeva 14.0

pair_coeff * * rebo                 CH.airebo  C C

pair_coeff 1 2 lebedeva  CC.Lebedeva      C C :pre

[Description:]

The {lebedeva} style computes the Lebedeva interaction

potential as described in "(Lebedeva et al.)"_#Leb01. An important simplification is made,

which is to take all normals along the z-axis.

:c,image(Eqs/pair_lebedeva.png)

It is important to have a sufficiently large cutoff to ensure smooth forces.

Energies are shifted so that they go continuously to zero at the cutoff assuming

that the exponential part of {Vij} (first term) decays sufficiently fast.

This shift is achieved by the last term in the equation for {Vij} above.

The parameter file (e.g. CC.Lebedeva), is intended for use with metal

"units"_units.html, with energies in meV. An additional parameter, {S},

is available to facilitate scaling of energies.

This potential must be used in combination with hybrid/overlay.

Other interactions can be set to zero using pair_style {none}.

[Restrictions:]

This fix is part of the USER-MISC package.  It is only enabled if

LAMMPS was built with that package.  See the "Build

package"_Build_package.html doc page for more info.

[Related commands:]

"pair_coeff"_pair_coeff.html

"pair_none"_pair_none.html

"pair_style hybrid/overlay"_pair_hybrid.html

[Default:] none

:line

:link(Leb01)

[(Lebedeva et al.)] I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)

Ideal graphene structure in YZ plane created with create_graphen.pl

2 atoms

2 atom types

	0.0 20 xlo xhi

	0.0 20 ylo yhi

	0.0 5 zlo zhi

Atoms

 1 1 10 10 0.0 

 2 2 0 0 3.35

# After running LAMMPS with this input script a number of dump files is created. 

# To extract the data from there I used grep script:

# grep '^2 ' *cfg > LammpsResult.dat

# After that after removing some text from LammpsResult.dat,

# the data can be viewed by lebedeva00.plot

#

# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland

# Email: softquake@gmail.com

# ---------- Start simulation --------------------- 

clear

units metal 

dimension 3 

boundary f f f 

atom_style atomic 

# ========================== Create Atomistic Structure ===========================

region whole block 0 20 0 20 0 10

create_box 2 whole 

read_data 2particles.dat add append

region graphite block INF INF INF INF 0 10 units box

group graphite type 1 2

group graphene1 type 1

group graphene2 type 2

pair_style hybrid/overlay lebedeva 20

pair_coeff * * none

pair_coeff 1 2 lebedeva CC.Lebedeva C C

mass 1 12.01 # Carbon

mass 2 12.01 # Carbon

neighbor 0.3 bin 

neigh_modify delay 1 check yes 

compute              peratom all pe/atom

dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz

dump_modify 1 pad 3

thermo 10 

thermo_style custom step pe press temp

thermo_modify lost ignore

label STEP_LOOP

variable MYSTEP loop 0 400 pad # in degrees

variable DELTA_STEP equal 0.05

displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0

run 1

next MYSTEP

jump SELF STEP_LOOP

print "all done"

# Lebedeva Potential. Original values from Lebedeva. May be played with ;)

#

# Cite as: Irina V. Lebedeva, Andrey A. Knizhnik, Andrey M. Popov, Yurii E. Lozovik, Boris V. Potapkin, 

# Modeling of graphene-based NEMS

# Physica E 44 (6), 949 (2012)

# https://doi.org/10.1016/j.physe.2011.07.018

#

# Parameters must be in this order as here, otherwise their values may be changed. 

# The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C

#      A       B           C       z0     alpha   D1      D2       lambda1   lambda2     S

# These are values according to Levedeva et al

#C  C   10.510  11.6523.34  35.883  3.34   4.16   -0.86232 0.10049  0.48703   0.46445     1.0

# These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162

C  C   14.558  21.204  1.8  3.198   4.16   -0.862 0.10049  0.6   0.4     1.0