Merge pull request #1843 from oywg11/new-ILP-parameters

   * :doc:`wall/region <fix_wall_region>`

   * :doc:`wall/region/ees <fix_wall_ees>`

   * :doc:`wall/srd <fix_wall_srd>`

   *

   *

   *

   *

   *

.. note::

   Two new sets of parameters of ILP for two-dimensional hexagonal

   Materials are presented in :ref:`(Ouyang) <Ouyang>`.  These parameters provide

   a good description in both short- and long-range interaction regimes.

   Four new sets of parameters of ILP for 2D layered Materials with bilayer and 

   bulk configurations are presented in :ref:`(Ouyang1) <Ouyang1>` and :ref:`(Ouyang2) <Ouyang2>`, respectively.

   These parameters provide a good description in both short- and long-range interaction regimes.

   While the old ILP parameters published in :ref:`(Leven2) <Leven2>` and

   :ref:`(Maaravi) <Maaravi2>` are only suitable for long-range interaction

   regime. This feature is essential for simulations in high pressure

   regime (i.e., the interlayer distance is smaller than the equilibrium

   distance). The benchmark tests and comparison of these parameters can

   be found in :ref:`(Ouyang) <Ouyang>`.

   be found in :ref:`(Ouyang1) <Ouyang1>` and :ref:`(Ouyang2) <Ouyang2>`.

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

Other interactions can be set to zero using pair\_style *none*\ .

**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).

.. _Ouyang:

.. _Ouyang1:

**(Ouyang)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

.. _Ouyang2:

**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).

.. _lws: http://lammps.sandia.gov

   Two new sets of parameters of KC potential for hydrocarbons, CH.KC

   (without the taper function) and CH\_taper.KC (with the taper function)

   are presented in :ref:`(Ouyang) <Ouyang1>`.  The energy for the KC potential

   are presented in :ref:`(Ouyang1) <Ouyang3>`.  The energy for the KC potential

   with the taper function goes continuously to zero at the cutoff.  The

   parameters in both CH.KC and CH\_taper.KC provide a good description in

   both short- and long-range interaction regimes. While the original

   suitable for long-range interaction regime.  This feature is essential

   for simulations in high pressure regime (i.e., the interlayer distance

   is smaller than the equilibrium distance).  The benchmark tests and

   comparison of these parameters can be found in :ref:`(Ouyang) <Ouyang1>`.

   comparison of these parameters can be found in :ref:`(Ouyang1) <Ouyang3>` and :ref:`(Ouyang2) <Ouyang4>`.

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

Other interactions can be set to zero using pair\_style *none*\ .

**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

.. _Ouyang1:

.. _Ouyang3:

**(Ouyang)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

.. _Ouyang4:

**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).

.. _lws: http://lammps.sandia.gov

"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 ilp/graphene/hbn command :h3

[Syntax:]

pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre

cutoff = global cutoff (distance units)

tap_flag = 0/1 to turn off/on the taper function :ul

[Examples:]

pair_style  hybrid/overlay ilp/graphene/hbn 16.0 1

pair_coeff  * * ilp/graphene/hbn  BNCH.ILP B N C :pre

pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0

pair_coeff  * * rebo              CH.rebo     NULL NULL C

pair_coeff  * * tersoff           BNC.tersoff B    N    NULL

pair_coeff  * * ilp/graphene/hbn  BNCH.ILP    B    N    C

pair_coeff  1 1 coul/shield 0.70

pair_coeff  1 2 coul/shield 0.695

pair_coeff  2 2 coul/shield 0.69 :pre

[Description:]

The {ilp/graphene/hbn} style computes the registry-dependent interlayer

potential (ILP) potential as described in "(Leven1)"_#Leven1,

"(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2.

The normals are calculated in the way as described

in "(Kolmogorov)"_#Kolmogorov2.

:c,image(Eqs/pair_ilp_graphene_hbn.jpg)

Where Tap(r_ij) is the taper function which provides a continuous

cutoff (up to third derivative) for interatomic separations larger than

r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above

equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2.

It is important to include all the pairs to build the neighbor list for

calculating the normals.

NOTE: This potential (ILP) is intended for interlayer interactions between two

different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.

To perform a realistic simulation, this potential must be used in combination with

intralayer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.

To keep the intralayer properties unaffected, the interlayer interaction

within the same layers should be avoided. Hence, each atom has to have a layer

identifier such that atoms residing on the same layer interact via the

appropriate intralayer potential and atoms residing on different layers

interact via the ILP. Here, the molecule id is chosen as the layer identifier,

thus a data file with the "full" atom style is required to use this potential.

The parameter file (e.g. BNCH.ILP), is intended for use with {metal}

"units"_units.html, with energies in meV. Two additional parameters,

{S}, and {rcut} are included in the parameter file. {S} is designed to

facilitate scaling of energies. {rcut} is designed to build the neighbor

list for calculating the normals for each atom pair.

NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),

are fitted with taper function by setting the cutoff equal to 16.0

Angstrom.  Using different cutoff or taper function should be careful.

The parameters for atoms pairs between Boron and Nitrogen are fitted with

a screened Coulomb interaction "coul/shield"_pair_coul_shield.html. Therefore,

to simulated the properties of h-BN correctly, this potential must be used in

combination with the pair style "coul/shield"_pair_coul_shield.html.

NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal

Materials are presented in "(Ouyang)"_#Ouyang.  These parameters provide

a good description in both short- and long-range interaction regimes.

While the old ILP parameters published in "(Leven2)"_#Leven2 and

"(Maaravi)"_#Maaravi2 are only suitable for long-range interaction

regime. This feature is essential for simulations in high pressure

regime (i.e., the interlayer distance is smaller than the equilibrium

distance).  The benchmark tests and comparison of these parameters can

be found in "(Ouyang)"_#Ouyang.

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

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

This pair style tallies a breakdown of the total interlayer potential

energy into sub-categories, which can be accessed via the "compute

pair"_compute_pair.html command as a vector of values of length 2.

The 2 values correspond to the following sub-categories:

{E_vdW} = vdW (attractive) energy

{E_Rep} = Repulsive energy :ol

To print these quantities to the log file (with descriptive column

headings) the following commands could be included in an input script:

compute 0 all pair ilp/graphene/hbn

variable Evdw  equal c_0\[1\]

variable Erep  equal c_0\[2\]

thermo_style custom step temp epair v_Erep v_Evdw :pre

:line

[Mixing, shift, table, tail correction, restart, rRESPA info]:

This pair style does not support the pair_modify mix, shift, table, and

tail options.

This pair style does not write their information to binary restart

files, since it is stored in potential files. Thus, you need to

re-specify the pair_style and pair_coeff commands in an input script

that reads a restart file.

[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.

This pair potential requires the newton setting to be {on} for pair

interactions.

The BNCH.ILP potential file provided with LAMMPS (see the potentials

directory) are parameterized for {metal} units.  You can use this

potential with any LAMMPS units, but you would need to create your

BNCH.ILP potential file with coefficients listed in the appropriate

units, if your simulation does not use {metal} units.

[Related commands:]

"pair_coeff"_pair_coeff.html,

"pair_none"_pair_none.html,

"pair_style hybrid/overlay"_pair_hybrid.html,

"pair_style drip"_pair_drip.html,

"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,

"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,

"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,

"pair_style pair_coul_shield"_pair_coul_shield.html.

[Default:] tap_flag = 1

:line

:link(Leven1)

[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).

:link(Leven2)

[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).

:link(Maaravi2)

[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

:link(Kolmogorov2)

[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).

:link(Ouyang)

[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

"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 kolmogorov/crespi/full command :h3

[Syntax:]

pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre

cutoff = global cutoff (distance units)

tap_flag = 0/1 to turn off/on the taper function :ul

[Examples:]

pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0

pair_coeff * * none

pair_coeff * * kolmogorov/crespi/full  CH.KC   C C :pre

pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1

pair_coeff * * rebo                    CH.rebo      C H

pair_coeff * * kolmogorov/crespi/full  CH_taper.KC  C H :pre

[Description:]

The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi (KC)

interaction potential as described in "(Kolmogorov)"_#Kolmogorov1.

No simplification is made,

:c,image(Eqs/pair_kolmogorov_crespi_full.jpg)

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

forces and to include all the pairs to build the neighbor list for

calculating the normals.  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. This is essential only

when the tapper function is turned off. The formula of taper function

can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.

NOTE: This potential (ILP) is intended for interlayer interactions between two

different layers of graphene. To perform a realistic simulation, this potential

must be used in combination with intralayer potential, such as

"AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.

To keep the intralayer properties unaffected, the interlayer interaction

within the same layers should be avoided. Hence, each atom has to have a layer

identifier such that atoms residing on the same layer interact via the

appropriate intralayer potential and atoms residing on different layers

interact via the ILP. Here, the molecule id is chosen as the layer identifier,

thus a data file with the "full" atom style is required to use this potential.

The parameter file (e.g. CH.KC), is intended for use with {metal}

"units"_units.html, with energies in meV. Two additional parameters, {S},

and {rcut} are included in the parameter file. {S} is designed to

facilitate scaling of energies. {rcut} is designed to build the neighbor

list for calculating the normals for each atom pair.

NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC

(without the taper function) and CH_taper.KC (with the taper function)

are presented in "(Ouyang)"_#Ouyang1.  The energy for the KC potential

with the taper function goes continuously to zero at the cutoff.  The

parameters in both CH.KC and CH_taper.KC provide a good description in

both short- and long-range interaction regimes. While the original

parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 are only

suitable for long-range interaction regime.  This feature is essential

for simulations in high pressure regime (i.e., the interlayer distance

is smaller than the equilibrium distance).  The benchmark tests and

comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.

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

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

This pair style tallies a breakdown of the total interlayer potential

energy into sub-categories, which can be accessed via the "compute

pair"_compute_pair.html command as a vector of values of length 2.

The 2 values correspond to the following sub-categories:

{E_vdW} = vdW (attractive) energy

{E_Rep} = Repulsive energy :ol

To print these quantities to the log file (with descriptive column

headings) the following commands could be included in an input script:

compute 0 all pair kolmogorov/crespi/full

variable Evdw  equal c_0\[1\]

variable Erep  equal c_0\[2\]

thermo_style custom step temp epair v_Erep v_Evdw :pre

:line

[Mixing, shift, table, tail correction, restart, rRESPA info]:

This pair style does not support the pair_modify mix, shift, table,

and tail options.

This pair style does not write their information to binary restart

files, since it is stored in potential files. Thus, you need to

re-specify the pair_style and pair_coeff commands in an input script

that reads a restart file.

[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.

This pair potential requires the newton setting to be {on} for pair

interactions.

The CH.KC potential file provided with LAMMPS (see the potentials

folder) are parameterized for metal units.  You can use this potential

with any LAMMPS units, but you would need to create your own custom

CC.KC potential file with all coefficients converted to the appropriate

units.

[Related commands:]

"pair_coeff"_pair_coeff.html,

"pair_none"_pair_none.html,

"pair_style hybrid/overlay"_pair_hybrid.html,

"pair_style drip"_pair_drip.html,

"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,

"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,

"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.

[Default:] tap_flag = 0

:line

:link(Kolmogorov1)

[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

:link(Ouyang1)

[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).