mirror of https://github.com/lammps/lammps.git
more changes to ATM source and doc file
This commit is contained in:
Steven J. Plimpton
parent
eeaf907227
commit
d4385ade15
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@ -582,7 +582,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
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"dt/reset"_fix_dt_reset.html,
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"efield"_fix_efield.html,
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"ehex"_fix_ehex.html,
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"enforce2d"_fix_enforce2d.html,
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"enforce2d (k)"_fix_enforce2d.html,
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"evaporate"_fix_evaporate.html,
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"external"_fix_external.html,
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"freeze"_fix_freeze.html,
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@ -929,6 +929,7 @@ KOKKOS, o = USER-OMP, t = OPT.
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"adp (o)"_pair_adp.html,
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"airebo (oi)"_pair_airebo.html,
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"airebo/morse (oi)"_pair_airebo.html,
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"atm"_pair_atm.html,
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"beck (go)"_pair_beck.html,
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"body"_pair_body.html,
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"bop"_pair_bop.html,
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@ -16,7 +16,7 @@ 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_style atm 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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@ -33,106 +33,92 @@ 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 nu is the three-body interaction strength,
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and the distances between pairs of atoms r12, r23 and r31
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and the angles gamma1, gamma2 and gamma3
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are shown at the diagram:
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where nu is the three-body interaction strength. The distances
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between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2,
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gamma3 are as shown in this diagram:
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:c,image(JPG/pair_atm_dia.jpg)
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There is no \"central\" atom, the interaction is symmetric with respect
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to permutation of atom types.
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Note that for the interaction between a triplet of atoms I,J,K, there
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is no "central" atom. The interaction is symmetric with respect to
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permutation of the three atoms. In fact, it is computed 3 times by
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the code with each of I,J,K being atom 1. Thus the nu value must be
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the same for all those permutations of the atom types of I,J,K as
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discussed below.
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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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The potential is calculated if all three atoms are in the
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"neighbor list"_neighbor.html
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and the distances between atoms satisfy r12 r23 r31 > cutoff^3.
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The potential for a triplet of atom is calculated only if all 3
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distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
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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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K - the type of the third atom
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nu (energy/distance^9 units) :ul
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K = atom type of the third atom (1 to Ntypes)
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nu = prefactor (energy/distance^9 units) :ul
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For a single-atom type simulation, only a single entry is required, eg
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K can be specified in one of two ways. An explicit numeric value can
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be used, as in the 2nd example above. J <= K is required. LAMMPS
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sets the coefficients for the other 5 symmetric interactions to the
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same values. E.g. if I = 1, J = 2, K = 3, then these 6 values are set
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to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321. This
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enforces the symmetry discussed above.
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pair_coeff 1 1 1 nu :pre
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A wildcard asterisk can be used for K to set the coefficients for
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multiple triplets of atom types. This takes the form "*" or "*n" or
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"n*" or "m*n". If N = the number of atom types, then an asterisk with
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no numeric values means all types from 1 to N. A leading asterisk
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means all types from 1 to n (inclusive). A trailing asterisk means
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all types from n to N (inclusive). A middle asterisk means all types
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from m to n (inclusive). Note that only type triplets with J <= K are
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considered; if asterisks imply type triplets where K < J, they are
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ignored.
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where all three atoms are of type 1.
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For a two-atom type simulation, more pair_coeff commands can be used.
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ATM interaction is symmetric with respect to permutation of atoms,
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it is necessary to provide pair_coeff command for one permutation.
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For example, the command
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Note that a pair_coeff command can override a previous setting for the
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same I,J,K triplet. For example, these commands set nu for all I,J.K
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triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet:
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pair_coeff 1 1 2 nu :pre
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pair_coeff * * * 0.25
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pair_coeff 2 3 4 0.1 :pre
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also implies
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Note that for a simulation with a single atom type, only a single
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entry is required, e.g.
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pair_coeff 1 2 1 nu
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pair_coeff 2 1 1 nu :pre
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pair_coeff 1 1 1 0.25 :per
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Thus, to specify all ATM interactions between two atom types (eg 1 and 2)
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it is sufficient to provide four pair_coeff commands, eg:
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For a simulation with two atom types, four pair_coeff commands will
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specify all possible nu values:
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pair_coeff 1 1 1 nu1
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pair_coeff 1 1 2 nu2
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pair_coeff 1 2 2 nu3
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pair_coeff 2 2 2 nu4 :pre
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For 3 atom types, 10 pair_coeff commands
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(eg 111, 112, 113, 122, 123, 133, 222, 223, 233, 333)
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will describe all possible ATM interactions, etc.
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It is not necessary to provide the pair_coeff commands for interactions
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of all combinations of atom types: if some combination is not defined then
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there is no ATM interaction for this combination and all its permutations.
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For a simulation with three atom types, ten pair_coeff commands will
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specify all possible nu values:
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--------------------
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pair_coeff 1 1 1 nu1
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pair_coeff 1 1 2 nu2
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pair_coeff 1 1 3 nu3
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pair_coeff 1 2 2 nu4
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pair_coeff 1 2 3 nu5
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pair_coeff 1 3 3 nu6
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pair_coeff 2 2 2 nu7
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pair_coeff 2 2 3 nu8
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pair_coeff 2 3 3 nu9
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pair_coeff 3 3 3 nu10 :pre
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[Steve:]
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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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[Sergey:]
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The reason for my original pair_coeff command syntax is that
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I would like to reserve further arguments for possible extension of
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ATM potential in LAMMPS to further terms in the multipole expansion of
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many-body dispersion interaction.
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For example, the next term would be dipole-dipole-quadrupole, it may be
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activated if the next argument of pair_coeff is present
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without breaking backward compatibility.
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Also, the command you propose
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(i) will not account that the value of nu for different permutations
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of atom types is the same, and
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(ii) will make the numbering of atom types messy since there is
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no requirement to supply the values of nu for all triplets.
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--------------------
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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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By default the nu value for all triplets is set to 0.0. Thus it is
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not required to provide pair_coeff commands that enumerate triplet
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interactions for all K types. If some I,J,K combination is not
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speficied, then there will be no 3-body ATM interactions for that
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combination and all its permutations. However, as with all pair
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styles, it is required to specify a pair_coeff command for all I,J
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combinations, else an error will result.
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:line
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@ -103,6 +103,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
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"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
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"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
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"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
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"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential
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"pair_style beck"_pair_beck.html - Beck potential
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"pair_style body"_pair_body.html - interactions between body particles
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"pair_style bop"_pair_bop.html - BOP potential of Pettifor
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@ -26,7 +26,7 @@ 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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Time spent = 0.00125098 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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@ -60,26 +60,26 @@ Neighbor list info ...
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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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5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817
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10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204
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15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887
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20 1.0350606 -4.595891 0 -3.0436883 -3.4478779
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25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695
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Loop time of 34.5602 on 1 procs for 25 steps with 4000 atoms
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0 1.033 -4.733482 0 -3.1843694 -3.924644
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5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065
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10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962
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15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106
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20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572
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25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651
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Loop time of 27.841 on 1 procs for 25 steps with 4000 atoms
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Performance: 124.999 tau/day, 0.723 timesteps/s
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Performance: 155.167 tau/day, 0.898 timesteps/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 34.556 | 34.556 | 34.556 | 0.0 | 99.99
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Pair | 27.837 | 27.837 | 27.837 | 0.0 | 99.99
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.001323 | 0.001323 | 0.001323 | 0.0 | 0.00
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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
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Other | | 0.0006311 | | | 0.00
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Comm | 0.0015321 | 0.0015321 | 0.0015321 | 0.0 | 0.01
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Output | 0.00016594 | 0.00016594 | 0.00016594 | 0.0 | 0.00
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Modify | 0.001785 | 0.001785 | 0.001785 | 0.0 | 0.01
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Other | | 0.0006731 | | | 0.00
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -97,4 +97,4 @@ Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:36
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Total wall time: 0:00:29
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@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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Time spent = 0.000735998 secs
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Time spent = 0.000769138 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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@ -60,26 +60,26 @@ Neighbor list info ...
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 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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5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817
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10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204
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15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887
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20 1.0350606 -4.595891 0 -3.0436883 -3.4478779
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25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695
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Loop time of 10.061 on 4 procs for 25 steps with 4000 atoms
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0 1.033 -4.733482 0 -3.1843694 -3.924644
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5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065
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10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962
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15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106
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20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572
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25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651
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Loop time of 7.22029 on 4 procs for 25 steps with 4000 atoms
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Performance: 429.382 tau/day, 2.485 timesteps/s
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Performance: 598.314 tau/day, 3.462 timesteps/s
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100.0% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 9.8393 | 9.9439 | 10.008 | 2.0 | 98.84
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Pair | 7.1346 | 7.1684 | 7.1863 | 0.8 | 99.28
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.052154 | 0.11613 | 0.22077 | 18.7 | 1.15
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Output | 7.2241e-05 | 8.2552e-05 | 0.00011158 | 0.0 | 0.00
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Modify | 0.00053763 | 0.00055265 | 0.00056624 | 0.0 | 0.01
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Other | | 0.0002971 | | | 0.00
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Comm | 0.032945 | 0.0509 | 0.084664 | 9.1 | 0.70
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Output | 0.00010133 | 0.00011051 | 0.00013804 | 0.0 | 0.00
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Modify | 0.00059557 | 0.00060683 | 0.00061274 | 0.0 | 0.01
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Other | | 0.000318 | | | 0.00
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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@ -97,4 +97,4 @@ Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:10
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Total wall time: 0:00:07
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@ -61,10 +61,12 @@ PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
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PairATM::~PairATM()
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{
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if (copymode) return;
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if (allocated) {
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memory->destroy(nu);
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(nu);
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}
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}
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@ -89,6 +91,8 @@ void PairATM::compute(int eflag, int vflag)
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double **f = atom->f;
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int *type = atom->type;
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double cutoffsq = cut_global*cut_global;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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@ -127,10 +131,11 @@ void PairATM::compute(int eflag, int vflag)
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rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
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r6 = rij2*rik2*rjk2;
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if (r6 > cut_sixth) continue;
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if (r6 > cutoffsq) continue;
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nu_local = nu[type[i]][type[j]][type[k]];
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if (nu_local == 0.0) continue;
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interaction_ddd(nu_local,
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r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
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@ -152,32 +157,50 @@ void PairATM::compute(int eflag, int vflag)
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ---------------------------------------------------------------------- */
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void PairATM::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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memory->create(nu,n+1,n+1,n+1,"pair:nu");
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// initialize all nu values to 0.0
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for (int i = 1; i <= n; i++)
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for (int j = 1; j <= n; j++)
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for (int k = 1; k <= n; k++)
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nu[i][j][k] = 0.0;
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}
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/* ----------------------------------------------------------------------
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reads the input script line with arguments you define
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global settings
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------------------------------------------------------------------------- */
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void PairATM::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal pair_style command");
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cut_global = force->numeric(FLERR,arg[0]);
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}
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/* ----------------------------------------------------------------------
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set coefficients for one i,j,k type triplet
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set coefficients for one I,J,K type triplet
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------------------------------------------------------------------------- */
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void PairATM::coeff(int narg, char **arg)
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||||
{
|
||||
if (narg != 4)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int n = atom->ntypes;
|
||||
for (int i = 0; i <= n; i++)
|
||||
for (int j = 0; j <= n; j++)
|
||||
for (int k = 0; k <= n; k++)
|
||||
nu[i][j][k] = 0.0;
|
||||
|
||||
int ilo,ihi,jlo,jhi,klo,khi;
|
||||
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
|
||||
|
|
@ -185,16 +208,11 @@ void PairATM::coeff(int narg, char **arg)
|
|||
|
||||
double nu_one = force->numeric(FLERR,arg[3]);
|
||||
|
||||
cut_sixth = cut_global*cut_global;
|
||||
cut_sixth = cut_sixth*cut_sixth*cut_sixth;
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j<=jhi; j++) {
|
||||
for (int k = MAX(klo,j); k<=khi; k++) {
|
||||
nu[i][j][k] = nu[i][k][j] =
|
||||
nu[j][i][k] = nu[j][k][i] =
|
||||
nu[k][i][j] = nu[k][j][i] = nu_one;
|
||||
nu[i][j][k] = nu_one;
|
||||
count++;
|
||||
}
|
||||
setflag[i][j] = 1;
|
||||
|
|
@ -211,18 +229,28 @@ void PairATM::coeff(int narg, char **arg)
|
|||
void PairATM::init_style()
|
||||
{
|
||||
// need a full neighbor list
|
||||
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
perform initialization for one i,j type pair
|
||||
init for one i,j type pair and corresponding j,i
|
||||
also for all k type permutations
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairATM::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
// set all 6 symmetric permutations of I,J,K types to same nu value
|
||||
|
||||
int ntypes = atom->ntypes;
|
||||
for (int k = j; k <= ntypes; k++)
|
||||
nu[i][k][j] = nu[j][i][k] = nu[j][k][i] = nu[k][i][j] = nu[k][j][i] =
|
||||
nu[i][j][k];
|
||||
|
||||
return cut_global;
|
||||
}
|
||||
|
||||
|
|
@ -239,7 +267,7 @@ void PairATM::write_restart(FILE *fp)
|
|||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j])
|
||||
for (k = i; k <= atom->ntypes; k++)
|
||||
for (k = j; k <= atom->ntypes; k++)
|
||||
fwrite(&nu[i][j][k],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
|
|
@ -260,7 +288,7 @@ void PairATM::read_restart(FILE *fp)
|
|||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||
if (setflag[i][j]) for (k = i; k <= atom->ntypes; k++) {
|
||||
if (setflag[i][j]) for (k = j; k <= atom->ntypes; k++) {
|
||||
if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp);
|
||||
MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
|
@ -288,25 +316,14 @@ void PairATM::read_restart_settings(FILE *fp)
|
|||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairATM::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
memory->create(nu,n+1,n+1,n+1,"pair:a");
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Axilrod-Teller-Muto (dipole-dipole-dipole) potential
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairATM::interaction_ddd(double nu,
|
||||
double r6, double rij2, double rik2, double rjk2,
|
||||
double *rij, double *rik, double *rjk,
|
||||
double *fj, double *fk, int eflag, double &eng)
|
||||
double r6, double rij2, double rik2, double rjk2,
|
||||
double *rij, double *rik, double *rjk,
|
||||
double *fj, double *fk, int eflag, double &eng)
|
||||
{
|
||||
double r5inv,rri,rrj,rrk,rrr;
|
||||
r5inv = nu / (r6*r6*sqrt(r6));
|
||||
|
|
@ -314,14 +331,14 @@ void PairATM::interaction_ddd(double nu,
|
|||
rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2];
|
||||
rrk = rjk[0]*rik[0] + rjk[1]*rik[1] + rjk[2]*rik[2];
|
||||
rrr = 5.0*rri*rrj*rrk;
|
||||
for (int i=0; i<3; i++) {
|
||||
fj[i] = rrj*(rrk - rri)*rik[i]
|
||||
- (rrk*rri - rjk2*rik2 + rrr/rij2)*rij[i]
|
||||
+ (rrk*rri - rik2*rij2 + rrr/rjk2)*rjk[i];
|
||||
for (int i = 0; i < 3; i++) {
|
||||
fj[i] = rrj*(rrk - rri)*rik[i] -
|
||||
(rrk*rri - rjk2*rik2 + rrr/rij2) * rij[i] +
|
||||
(rrk*rri - rik2*rij2 + rrr/rjk2) * rjk[i];
|
||||
fj[i] *= 3.0*r5inv;
|
||||
fk[i] = rrk*(rri + rrj)*rij[i]
|
||||
+ (rri*rrj + rik2*rij2 - rrr/rjk2)*rjk[i]
|
||||
+ (rri*rrj + rij2*rjk2 - rrr/rik2)*rik[i];
|
||||
fk[i] = rrk*(rri + rrj)*rij[i] +
|
||||
(rri*rrj + rik2*rij2 - rrr/rjk2) * rjk[i] +
|
||||
(rri*rrj + rij2*rjk2 - rrr/rik2) * rik[i];
|
||||
fk[i] *= 3.0*r5inv;
|
||||
}
|
||||
if (eflag) eng = (r6 - 0.6*rrr)*r5inv;
|
||||
|
|
|
|||
Loading…
Reference in New Issue