mods to Sergey's files
This commit is contained in:
Steven J. Plimpton
91
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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@ -10,7 +10,9 @@ pair_style atm command :h3
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[Syntax:]
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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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[Examples:]
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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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: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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where r12, r23 and r31 are the distances between pairs of atoms,
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gamma1 is included by the sides r12 and r31
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gamma1 is the angle ???, gamma2 is the angle ???, gamma3 is the angle
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with similar definitions for gamma2 and gamma3,
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???, and nu is the three-body interaction strength.
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nu is the three-body interaction strength (energy times distance^9 units).
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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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The {atm} potential is typically used in combination with a two-body
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using "hybrid/overlay"_pair_hybrid.html style as in an example above.
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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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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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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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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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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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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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interacting in three-body configurations. Thus for 3 elements, 10
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entries would be required, etc.
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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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: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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This pair styles do not support the "pair_modify"_pair_modify.html
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shift, table, and tail options.
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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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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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"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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[Restrictions:]
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This pair style is part of the MANYBODY package. It is only enabled
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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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if LAMMPS was built with that package. See the "Making
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the "Making LAMMPS"_Section_start.html#start_3 section for more info.
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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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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:link(Axilrod)
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[(Axilrod)]
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[(Axilrod)]
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Axilrod and Teller, J Chem Phys, 11, 299 (1943);
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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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@ -59,6 +59,7 @@ sub-directories:
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accelerate: use of all the various accelerator packages
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accelerate: use of all the various accelerator packages
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airebo: polyethylene with AIREBO potential
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airebo: polyethylene with AIREBO potential
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atm: Axilrod-Teller-Muto potential
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balance: dynamic load balancing, 2d system
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balance: dynamic load balancing, 2d system
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body: body particles, 2d system
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body: body particles, 2d system
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cmap: CMAP 5-body contributions to CHARMM force field
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cmap: CMAP 5-body contributions to CHARMM force field
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@ -1,3 +1,5 @@
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# Axilrod-Teller-Muto potential example
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variable x index 1
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variable x index 1
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variable y index 1
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variable y index 1
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variable z index 1
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variable z index 1
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@ -24,6 +26,6 @@ velocity all create 1.033 12345678 loop geom
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fix 1 all nvt temp 1.033 1.033 0.05
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fix 1 all nvt temp 1.033 1.033 0.05
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timestep 0.002
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timestep 0.002
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thermo 1
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thermo 5
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run 50
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run 25
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100
examples/atm/log.9Jul18.atm.g++.1
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100
examples/atm/log.9Jul18.atm.g++.1
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@ -0,0 +1,100 @@
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LAMMPS (29 Jun 2018)
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# Axilrod-Teller-Muto potential example
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 10*$x
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variable xx equal 10*1
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variable yy equal 10*$y
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variable yy equal 10*1
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variable zz equal 10*$z
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variable zz equal 10*1
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units lj
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atom_style atomic
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lattice fcc 0.65
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Lattice spacing in x,y,z = 1.83252 1.83252 1.83252
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 10 0 ${yy} 0 ${zz}
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region box block 0 10 0 10 0 ${zz}
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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Time spent = 0.00120211 secs
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pair_style hybrid/overlay lj/cut 4.5 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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mass * 1.0
|
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velocity all create 1.033 12345678 loop geom
|
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fix 1 all nvt temp 1.033 1.033 0.05
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timestep 0.002
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thermo 5
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run 25
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
|
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max neighbors/atom: 2000, page size: 100000
|
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|
master list distance cutoff = 4.8
|
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ghost atom cutoff = 4.8
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|
binsize = 2.4, bins = 8 8 8
|
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
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|
(1) pair lj/cut, perpetual, half/full from (2)
|
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attributes: half, newton on
|
||||||
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pair build: halffull/newton
|
||||||
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stencil: none
|
||||||
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bin: none
|
||||||
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(2) pair atm, perpetual
|
||||||
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attributes: full, newton on
|
||||||
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pair build: full/bin/atomonly
|
||||||
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stencil: full/bin/3d
|
||||||
|
bin: standard
|
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Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
|
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Step Temp E_pair E_mol TotEng Press
|
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0 1.033 -4.5929584 0 -3.0438458 -3.6506231
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||||||
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5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817
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||||||
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10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204
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||||||
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15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887
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||||||
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20 1.0350606 -4.595891 0 -3.0436883 -3.4478779
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||||||
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25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695
|
||||||
|
Loop time of 34.5602 on 1 procs for 25 steps with 4000 atoms
|
||||||
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|
||||||
|
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
|
||||||
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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
|
||||||
100
examples/atm/log.9Jul18.atm.g++.4
Normal file
100
examples/atm/log.9Jul18.atm.g++.4
Normal file
@ -0,0 +1,100 @@
|
|||||||
|
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 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4000 atoms
|
||||||
|
Time spent = 0.000735998 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) = 5.532 | 5.532 | 5.532 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 10.061 on 4 procs for 25 steps with 4000 atoms
|
||||||
|
|
||||||
|
Performance: 429.382 tau/day, 2.485 timesteps/s
|
||||||
|
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 9.8393 | 9.9439 | 10.008 | 2.0 | 98.84
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.052154 | 0.11613 | 0.22077 | 18.7 | 1.15
|
||||||
|
Output | 7.2241e-05 | 8.2552e-05 | 0.00011158 | 0.0 | 0.00
|
||||||
|
Modify | 0.00053763 | 0.00055265 | 0.00056624 | 0.0 | 0.01
|
||||||
|
Other | | 0.0002971 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 1000 ave 1000 max 1000 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 5835 ave 5835 max 5835 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 160000 ave 160000 max 160000 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 320000 ave 320000 max 320000 min
|
||||||
|
Histogram: 4 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: 0:00:10
|
||||||
@ -49,8 +49,8 @@ PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
|
|||||||
if (lmp->citeme) lmp->citeme->add(cite_atm_package);
|
if (lmp->citeme) lmp->citeme->add(cite_atm_package);
|
||||||
|
|
||||||
single_enable = 0;
|
single_enable = 0;
|
||||||
restartinfo = 0;
|
//restartinfo = 1; // it does save restart info, correct?
|
||||||
one_coeff = 1;
|
//one_coeff = 0; // it does not only use * *, correct?
|
||||||
manybody_flag = 1;
|
manybody_flag = 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -229,7 +229,9 @@ void PairATM::write_restart(FILE *fp)
|
|||||||
for (i = 1; i <= atom->ntypes; i++) {
|
for (i = 1; i <= atom->ntypes; i++) {
|
||||||
for (j = i; j <= atom->ntypes; j++) {
|
for (j = i; j <= atom->ntypes; j++) {
|
||||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||||
if (setflag[i][j]) for (k = i; k <= atom->ntypes; k++) fwrite(&nu[i][j][k],sizeof(double),1,fp);
|
if (setflag[i][j])
|
||||||
|
for (k = i; k <= atom->ntypes; k++)
|
||||||
|
fwrite(&nu[i][j][k],sizeof(double),1,fp);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -11,10 +11,6 @@
|
|||||||
See the README file in the top-level LAMMPS directory.
|
See the README file in the top-level LAMMPS directory.
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
Contributing author: Sergey Lishchuk
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#ifdef PAIR_CLASS
|
#ifdef PAIR_CLASS
|
||||||
|
|
||||||
PairStyle(atm,PairATM)
|
PairStyle(atm,PairATM)
|
||||||
@ -46,9 +42,9 @@ class PairATM : public Pair {
|
|||||||
double cut_global, cut_sixth;
|
double cut_global, cut_sixth;
|
||||||
double ***nu;
|
double ***nu;
|
||||||
|
|
||||||
protected:
|
void allocate();
|
||||||
virtual void allocate();
|
void interaction_ddd(double, double, double, double, double, double *,
|
||||||
void interaction_ddd(double, double, double, double, double, double *, double *, double *, double *, double *, int, double &);
|
double *, double *, double *, double *, int, double &);
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
Reference in New Issue
Block a user