Updated documentation and source

section for more info on packages.

NOTE: In the "Angles" section of the data file, the atom ID 'j'

corresponding to the dipole to restrain must come before the atom ID

of the reference atom 'i'. A third atom ID 'k' must also be provided,

although 'k' is just a 'dummy' atom which can be any atom; it may be

useful to choose a convention (e.g., 'k'='i') and adhere to it.  For

example, if ID=1 for the dipolar atom to restrain, and ID=2 for the

reference atom, the corresponding line in the "Angles" section of the

data file would read: X X 1 2 2

defining the direction of the dipole vector to restrain must come

before the atom ID of the reference atom 'i'. A third atom ID 'k' must

also be provided to comply with the requirement of a valid angle

definition. This atom ID k should be chosen to be that of an atom

bonded to atom 'i' to avoid errors with "lost angle atoms" when running

in parallel. Since the LAMMPS code checks for valid angle definitions,

cannot use the same atom ID of either 'i' or 'j' (this was allowed

and recommended with older LAMMPS versions).

The "newton" command for intramolecular interactions must be "on"

(which is the default).

(which is the default except when using some accelerator packages).

This angle style should not be used with SHAKE.

:link(Tranchida2)

[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,

arXiv preprint arXiv:1801.10233, (2018).

Journal of Computational Physics, (2018).

:link(Tranchida1)

[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,

arXiv preprint arXiv:1801.10233, (2018).

Journal of Computational Physics, (2018).

[Syntax:]

pair_style atm args = cutoff :pre

pair_style atm cutoff :pre

cutoff = global cutoff for 3-body interactions (distance units) :ul

[Examples:]

pair_style hybrid/overlay lj/cut 6.5 atm 2.5

pair_coeff * * lj/cut 1.0 1.0

pair_coeff	* * atm * 0.072 :pre

pair_coeff 1 1 atm 1 0.064

pair_coeff 1 1 atm 2 0.080

pair_coeff 1 2 atm 2 0.100

pair_coeff 2 2 atm 2 0.125 :pre

[Description:]

:c,image(Eqs/pair_atm.jpg)

where r12, r23 and r31 are the distances between the atoms,

gamma1 is included by the sides r12 and r31

with similar definitions for gamma2 and gamma3,

nu is the three-body interaction strength (energy times distance^9 units).

where nu is the three-body interaction strength,

and the distances between pairs of atoms r12, r23 and r31

and the angles gamma1, gamma2 and gamma3

are shown at the diagram:

:c,image(JPG/pair_atm_dia.jpg)

There is no \"central\" atom, the interaction is symmetric with respect

to permutation of atom types.

The {atm} potential is typically used in combination with a two-body

potential using the "pair_style hybrid/overlay"_pair_hybrid.html

command as in the example above.

The potential is calculated if all three atoms are in the

"neighbor list"_neighbor.html

and the distances between atoms satisfy r12 r23 r31 > cutoff^3.

The following coefficients must be defined for each pair of atoms

types via the "pair_coeff"_pair_coeff.html command as in the examples

above, or in the restart files read by the

"read_restart"_read_restart.html commands:

K - the type of the third atom

nu (energy/distance^9 units) :ul

For a single-atom type simulation, only a single entry is required, eg

pair_coeff 1 1 1 nu :pre

where all three atoms are of type 1.

For a two-atom type simulation, more pair_coeff commands can be used.

ATM interaction is symmetric with respect to permutation of atoms,

it is necessary to provide pair_coeff command for one permutation.

For example, the command

pair_coeff 1 1 2 nu :pre

The {atm} is typically used in compination with some two-body potential

using "hybrid/overlay"_pair_hybrid.html style as in an example above.

also implies

The calculations are not undertaken if the distances between atoms satisfy

r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined

tolerance tol is not used.

pair_coeff 1 2 1 nu

pair_coeff 2 1 1 nu :pre

The Axilrod-Teller-Muto potential file must contain entries for all the

elements listed in the pair_coeff command.  It can also contain

entries for additional elements not being used in a particular

simulation; LAMMPS ignores those entries.

Thus, to specify all ATM interactions between two atom types (eg 1 and 2)

it is sufficient to provide four pair_coeff commands, eg:

For a single-element simulation, only a single entry is required

(e.g. 1 1 1).  For a two-element simulation, the file must contain 4

entries (eg. 1 1 1, 1 1 2, 1 2 2, 2 2 2), that

specify ATM parameters for all combinations of the two elements

interacting in three-body configurations.  Thus for 3 elements, 10

entries would be required, etc.

pair_coeff 1 1 1 nu1

pair_coeff 1 1 2 nu2

pair_coeff 1 2 2 nu3

pair_coeff 2 2 2 nu4 :pre

For 3 atom types, 10 pair_coeff commands

(eg 111, 112, 113, 122, 123, 133, 222, 223, 233, 333)

will describe all possible ATM interactions, etc.

It is not necessary to provide the pair_coeff commands for interactions

of all combinations of atom types: if some combination is not defined then

there is no ATM interaction for this combination and all its permutations.

--------------------

[Steve:]

I think a better syntax for the pair coeff command might be this:

pair_coeff I J v1 v2 ... vN

when 1,2,...N are the number of atom types defined.

Then there be one pair_coeff command for each type pair,

the same syntax as all other potentials in LAMMPS use.

[Sergey:]

The reason for my original pair_coeff command syntax is that

I would like to reserve further arguments for possible extension of

ATM potential in LAMMPS to further terms in the multipole expansion of

many-body dispersion interaction.

For example, the next term would be dipole-dipole-quadrupole, it may be

activated if the next argument of pair_coeff is present

without breaking backward compatibility.

Also, the command you propose

(i) will not account that the value of nu for different permutations

of atom types is the same, and

(ii) will make the numbering of atom types messy since there is

no requirement to supply the values of nu for all triplets.

--------------------

:line

[Shift, table, tail correction, rRESPA info]:

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

This pair styles do not support the "pair_modify"_pair_modify.html

mix, shift, table, and tail options.

This pair style does not support the "pair_modify"_pair_modify.html

shift, table, and tail options.

This pair style writes its information to "binary restart

files"_restart.html, so pair_style and pair_coeff commands do not need

to be specified in an input script that reads a restart file.

This pair style can only be used via the {pair} keyword of the

"run_style respa"_run_style.html command.  It does not support the

[Restrictions:]

This pair style is part of the MANYBODY package.  It is only enabled

if LAMMPS was built with that package.  See

the "Making LAMMPS"_Section_start.html#start_3 section for more info.

if LAMMPS was built with that package.  See the "Making

LAMMPS"_Section_start.html#start_3 section for more info.

[Related commands:]

:link(Axilrod)

[(Axilrod)]

Axilrod and Teller, J Chem Phys, 11, 299 (1943);

Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).

Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).