mods to Sergey's files
This commit is contained in:
Steven J. Plimpton
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doc/src/pair_atm.html
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91
doc/src/pair_atm.html
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<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>pair_style atm command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style atm args = cutoff
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style 2.5
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pair_coeff * * * 0.072
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</PRE>
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<PRE>pair_style hybrid/overlay lj/cut 6.5 atm 2.5
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pair_coeff * * lj/cut 1.0 1.0
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pair_coeff * * atm * 0.072
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>atm</I> style computes a 3-body <A HREF = "#Axilrod">Axilrod-Teller-Muto</A>
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potential for the energy E of a system of atoms as
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</P>
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<CENTER><IMG SRC = "Eqs/pair_atm.jpg">
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</CENTER>
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<P>where r12, r23 and r31 are the distances between the atoms,
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gamma1 is included by the sides r12 and r31
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with similar definitions for gamma2 and gamma3,
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nu is the three-body interaction strength (energy times distance^9 units).
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</P>
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<P>The <I>atm</I> is typically used in compination with some two-body potential
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using <A HREF = "pair_hybrid.html">hybrid/overlay</A> style as in an example above.
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</P>
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<P>The calculations are not undertaken if the distances between atoms satisfy
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r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined
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tolerance tol is not used.
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</P>
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<P>The Axilrod-Teller-Muto potential file must contain entries for all the
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elements listed in the pair_coeff command. It can also contain
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entries for additional elements not being used in a particular
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simulation; LAMMPS ignores those entries.
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</P>
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<P>For a single-element simulation, only a single entry is required
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(e.g. 1 1 1). For a two-element simulation, the file must contain 4
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entries (eg. 1 1 1, 1 1 2, 1 2 2, 2 2 2), that
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specify ATM parameters for all combinations of the two elements
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interacting in three-body configurations. Thus for 3 elements, 10
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entries would be required, etc.
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</P>
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<HR>
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<P><B>Shift, table, tail correction, rRESPA info</B>:
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</P>
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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shift, table, and tail options.
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</P>
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<P>This pair style can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. It does not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This pair style is part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package. See
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the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Axilrod"></A>
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<P><B>(Axilrod)</B>
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Axilrod and Teller, J Chem Phys, 11, 299 (1943);
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Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).
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</P>
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</HTML>
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@ -10,16 +10,18 @@ pair_style atm command :h3
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[Syntax:]
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pair_style atm args = cutoff :pre
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pair_style atm cutoff :pre
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cutoff = global cutoff for 3-body interactions (distance units) :ul
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[Examples:]
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pair_style 2.5
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pair_coeff * * * 0.072 :pre
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pair_style hybrid/overlay lj/cut 6.5 atm 2.5
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pair_coeff * * lj/cut 1.0 1.0
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pair_coeff * * atm * 0.072 :pre
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pair_style hybrid/overlay lj/cut 6.5 atm 2.5
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pair_coeff * * lj/cut 1.0 1.0
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pair_coeff * * atm * 0.072 :pre
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[Description:]
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@ -28,18 +30,60 @@ potential for the energy E of a system of atoms as
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:c,image(Eqs/pair_atm.jpg)
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where r12, r23 and r31 are the distances between the atoms,
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gamma1 is included by the sides r12 and r31
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with similar definitions for gamma2 and gamma3,
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nu is the three-body interaction strength (energy times distance^9 units).
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where r12, r23 and r31 are the distances between pairs of atoms,
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gamma1 is the angle ???, gamma2 is the angle ???, gamma3 is the angle
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???, and nu is the three-body interaction strength.
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A diagram of the 3 atoms might help here.
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The {atm} is typically used in compination with some two-body potential
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using "hybrid/overlay"_pair_hybrid.html style as in an example above.
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The {atm} potential is typically used in combination with a two-body
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potential using the "pair_style hybrid/overlay"_pair_hybrid.html
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command as in the example above.
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--------------------
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The rest of this section needs some work to make things more clear.
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You need to explain exactly how the cutoff is used.
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I don't think this is true:
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The calculations are not undertaken if the distances between atoms satisfy
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r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined
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r12 r23 r31 > cutoff^3.
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If r12 > cutoff+skin, then that pair of atoms is not in
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the neighbor list, regardless of what r23 and r31 are,
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so how can it be computed?
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What does this line mean?
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Virtual cutoff distance based on a user defined
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tolerance tol is not used.
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You must explain exactly what the user needs to put
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in the input script to model single element and multi-element
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systems.
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You refer to an ATM potential file, but I don't think there is
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such a thing. There is no code in pair_atm.cpp that reads
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a file. Isn't it all pair_coeff commands? In LAMMPS lingo,
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potential files are the files in the potentials dir.
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There is no such thing for ATM, right?
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What is the geometry of i,j,k interactions - you don't explain it.
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Which one is the central atom?
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You say all the K values for a particular I,J must be specified.
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I don't see where the code checks for this.
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This is the way to word the explation of the per-pair values required:
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The following coefficients must be defined for each pair of atoms
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types via the "pair_coeff"_pair_coeff.html command as in the examples
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above, or in the restart files read by the
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"read_restart"_read_restart.html commands:
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?? explain what K is and what are the allowed values
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nu (energy/distance^9 units) :ul
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Again: what file are you talking about?
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The Axilrod-Teller-Muto potential file must contain entries for all the
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elements listed in the pair_coeff command. It can also contain
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entries for additional elements not being used in a particular
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@ -52,12 +96,29 @@ specify ATM parameters for all combinations of the two elements
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interacting in three-body configurations. Thus for 3 elements, 10
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entries would be required, etc.
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I think a better syntax for the pair coeff command might be this:
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pair_coeff I J v1 v2 ... vN
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when 1,2,...N are the number of atom types defined.
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Then there be one pair_coeff command for each type pair,
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the same syntax as all other potentials in LAMMPS use.
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Note that you refer to "elements", but the pair coeff command
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knows nothing about elements. Only atom types. There
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could be 10 atom types that all map to the same chemical
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element.
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:line
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[Shift, table, tail correction, rRESPA info]:
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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This pair style does not support the "pair_modify"_pair_modify.html
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shift, table, and tail options.
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This pair styles do not support the "pair_modify"_pair_modify.html
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mix, shift, table, and tail options.
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This pair style writes its information to "binary restart
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files"_restart.html, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.
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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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@ -68,8 +129,8 @@ This pair style can only be used via the {pair} keyword of the
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[Restrictions:]
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This pair style is part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package. See
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the "Making LAMMPS"_Section_start.html#start_3 section for more info.
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if LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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@ -82,4 +143,4 @@ the "Making LAMMPS"_Section_start.html#start_3 section for more info.
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:link(Axilrod)
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[(Axilrod)]
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Axilrod and Teller, J Chem Phys, 11, 299 (1943);
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Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).
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Muto, Nippon, Sugaku, Butsuri, Gakkwaishi 17, 629 (1943).
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