Updated documentation and source
This commit is contained in:
Sergey Lishchuk
@ -21,10 +21,14 @@ 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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<<<<<<< HEAD
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pair_coeff 1 1 atm 1 0.064
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pair_coeff 1 1 atm 2 0.080
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pair_coeff 1 2 atm 2 0.100
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pair_coeff 2 2 atm 2 0.125 :pre
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=======
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pair_coeff * * atm * 0.072 :pre
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>>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
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[Description:]
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@ -33,6 +37,7 @@ 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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<<<<<<< HEAD
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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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@ -42,11 +47,18 @@ are shown at the diagram:
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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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=======
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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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>>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
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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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<<<<<<< HEAD
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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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@ -78,6 +90,57 @@ pair_coeff 2 1 1 nu :pre
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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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=======
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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 > 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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simulation; LAMMPS ignores those entries.
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>>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
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pair_coeff 1 1 1 nu1
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pair_coeff 1 1 2 nu2
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@ -121,6 +184,19 @@ 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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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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@ -155,4 +231,8 @@ 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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<<<<<<< HEAD
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Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).
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=======
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Muto, Nippon, Sugaku, Butsuri, Gakkwaishi 17, 629 (1943).
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>>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
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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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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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body: body particles, 2d system
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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 y 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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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
Normal file
100
examples/atm/log.9Jul18.atm.g++.1
Normal file
@ -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
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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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Performance: 124.999 tau/day, 0.723 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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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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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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Nghost: 10895 ave 10895 max 10895 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 640000 ave 640000 max 640000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 1.28e+06 ave 1.28e+06 max 1.28e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1280000
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Ave neighs/atom = 320
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Neighbor list builds = 0
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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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100
examples/atm/log.9Jul18.atm.g++.4
Normal file
100
examples/atm/log.9Jul18.atm.g++.4
Normal file
@ -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 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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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
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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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Performance: 429.382 tau/day, 2.485 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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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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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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Nghost: 5835 ave 5835 max 5835 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 160000 ave 160000 max 160000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 320000 ave 320000 max 320000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1280000
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Ave neighs/atom = 320
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Neighbor list builds = 0
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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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@ -49,8 +49,13 @@ PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
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if (lmp->citeme) lmp->citeme->add(cite_atm_package);
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single_enable = 0;
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<<<<<<< HEAD
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restartinfo = 1;
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one_coeff = 0;
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=======
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//restartinfo = 1; // it does save restart info, correct?
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//one_coeff = 0; // it does not only use * *, correct?
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>>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
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manybody_flag = 1;
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}
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@ -129,9 +134,13 @@ void PairATM::compute(int eflag, int vflag)
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r6 = rij2*rik2*rjk2;
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if (r6 > cut_sixth) continue;
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<<<<<<< HEAD
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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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=======
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interaction_ddd(nu[type[i]][type[j]][type[k]],
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>>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
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r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
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f[i][0] -= fj[0] + fk[0];
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Reference in New Issue
Block a user