mods to Sergey's files

<HTML>

<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> 

</CENTER>

<HR>

<H3>pair_style atm command 

</H3>

<P><B>Syntax:</B>

</P>

<PRE>pair_style atm args = cutoff 

</PRE>

<P><B>Examples:</B>

</P>

<PRE>pair_style 2.5

pair_coeff * * * 0.072 

</PRE>

<PRE>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>

<P><B>Description:</B>

</P>

<P>The <I>atm</I> style computes a 3-body <A HREF = "#Axilrod">Axilrod-Teller-Muto</A>

potential for the energy E of a system of atoms as

</P>

<CENTER><IMG SRC = "Eqs/pair_atm.jpg">

</CENTER>

<P>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).

</P>

<P>The <I>atm</I> is typically used in compination with some two-body potential

using <A HREF = "pair_hybrid.html">hybrid/overlay</A> style as in an example above.

</P>

<P>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.

</P>

<P>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.

</P>

<P>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.

</P>

<HR>

<P><B>Shift, table, tail correction, rRESPA info</B>:

</P>

<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>

shift, table, and tail options.

</P>

<P>This pair style can only be used via the <I>pair</I> keyword of the

<A HREF = "run_style.html">run_style respa</A> command.  It does not support the

<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.

</P>

<HR>

<P><B>Restrictions:</B>

</P>

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

if LAMMPS was built with that package.  See

the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.

</P>

<P><B>Related commands:</B>

</P>

<P><A HREF = "pair_coeff.html">pair_coeff</A>

</P>

<P><B>Default:</B> none

</P>

<HR>

<A NAME = "Axilrod"></A>

<P><B>(Axilrod)</B>

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

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

</P>

</HTML>

[Syntax:]

pair_style atm args = cutoff :pre

pair_style atm cutoff :pre

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

[Examples:]

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

gamma1 is the angle ???, gamma2 is the angle ???, gamma3 is the angle

???, and nu is the three-body interaction strength.

A diagram of the 3 atoms might help here.

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

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

The rest of this section needs some work to make things more clear.

You need to explain exactly how the cutoff is used.

I don't think this is true:

The calculations are not undertaken if the distances between atoms satisfy

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

r12 r23 r31 > cutoff^3. 

If r12 > cutoff+skin, then that pair of atoms is not in

the neighbor list, regardless of what r23 and r31 are,

so how can it be computed?

What does this line mean?

Virtual cutoff distance based on a user defined

tolerance tol is not used.

You must explain exactly what the user needs to put

in the input script to model single element and multi-element

systems.

You refer to an ATM potential file, but I don't think there is

such a thing.  There is no code in pair_atm.cpp that reads

a file.  Isn't it all pair_coeff commands?  In LAMMPS lingo,

potential files are the files in the potentials dir.

There is no such thing for ATM, right?

What is the geometry of i,j,k interactions - you don't explain it.

Which one is the central atom?

You say all the K values for a particular I,J must be specified.

I don't see where the code checks for this.

This is the way to word the explation of the per-pair values required:

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:

?? explain what K is and what are the allowed values

nu (energy/distance^9 units) :ul

Again: what file are you talking about?

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

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

entries would be required, etc.

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.

Note that you refer to "elements", but the pair coeff command

knows nothing about elements.  Only atom types.  There

could be 10 atom types that all map to the same chemical

element.

: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, Butsuri, Gakkwaishi 17, 629 (1943).

accelerate: use of all the various accelerator packages

airebo:   polyethylene with AIREBO potential

atm:      Axilrod-Teller-Muto potential

balance:  dynamic load balancing, 2d system

body:     body particles, 2d system

cmap:     CMAP 5-body contributions to CHARMM force field

# Axilrod-Teller-Muto potential example

variable	x index 1

variable	y index 1

variable	z index 1

fix		1 all nvt temp 1.033 1.033 0.05

timestep        0.002

thermo		1

thermo		5

run 		50

run 		25

LAMMPS (29 Jun 2018)

# Axilrod-Teller-Muto potential example

variable	x index 1

variable	y index 1

variable	z index 1

variable	xx equal 10*$x

variable	xx equal 10*1

variable	yy equal 10*$y

variable	yy equal 10*1

variable	zz equal 10*$z

variable	zz equal 10*1

units		lj

atom_style	atomic

lattice		fcc 0.65

Lattice spacing in x,y,z = 1.83252 1.83252 1.83252

region		box block 0 ${xx} 0 ${yy} 0 ${zz}

region		box block 0 10 0 ${yy} 0 ${zz}

region		box block 0 10 0 10 0 ${zz}

region		box block 0 10 0 10 0 10

create_box	1 box

Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)

  1 by 1 by 1 MPI processor grid

create_atoms	1 box

Created 4000 atoms

  Time spent = 0.00120211 secs

pair_style	hybrid/overlay lj/cut 4.5 atm 2.5

pair_coeff	* * lj/cut 1.0 1.0

pair_coeff	* * atm * 0.072

mass		* 1.0

velocity	all create 1.033 12345678 loop geom

fix		1 all nvt temp 1.033 1.033 0.05

timestep        0.002

thermo		5

run 		25

Neighbor list info ...

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 4.8

  ghost atom cutoff = 4.8

  binsize = 2.4, bins = 8 8 8

  2 neighbor lists, perpetual/occasional/extra = 2 0 0

  (1) pair lj/cut, perpetual, half/full from (2)

      attributes: half, newton on

      pair build: halffull/newton

      stencil: none

      bin: none

  (2) pair atm, perpetual

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0        1.033   -4.5929584            0   -3.0438458   -3.6506231 

       5    1.0335109   -4.5924034            0   -3.0425247   -3.6376817 

      10    1.0347484   -4.5941952            0   -3.0424606   -3.6032204 

      15    1.0357954   -4.5962409            0   -3.0429363   -3.5421887 

      20    1.0350606    -4.595891            0   -3.0436883   -3.4478779 

      25    1.0301813   -4.5896962            0   -3.0448107   -3.3111695 

Loop time of 34.5602 on 1 procs for 25 steps with 4000 atoms

Performance: 124.999 tau/day, 0.723 timesteps/s

100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

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

Pair    | 34.556     | 34.556     | 34.556     |   0.0 | 99.99

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0.001323   | 0.001323   | 0.001323   |   0.0 |  0.00

Output  | 0.00018287 | 0.00018287 | 0.00018287 |   0.0 |  0.00

Modify  | 0.0016184  | 0.0016184  | 0.0016184  |   0.0 |  0.00

Other   |            | 0.0006311  |            |       |  0.00

Nlocal:    4000 ave 4000 max 4000 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    10895 ave 10895 max 10895 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    640000 ave 640000 max 640000 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs:  1.28e+06 ave 1.28e+06 max 1.28e+06 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1280000

Ave neighs/atom = 320

Neighbor list builds = 0

Dangerous builds = 0

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:36