pair_style hybrid command¶
Accelerator Variants: hybrid/kk
pair_style hybrid/overlay command¶
Accelerator Variants: hybrid/overlay/kk
pair_style hybrid style1 args style2 args ... pair_style hybrid/overlay style1 args style2 args ...
style1,style2 = list of one or more pair styles and their arguments
pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0 pair_coeff 1*2 1*2 eam niu3 pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0 pair_coeff 1*2 3 lj/cut 0.5 1.2 pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0 pair_coeff * * lj/cut 1.0 1.0 pair_coeff * * coul/long
The hybrid and hybrid/overlay styles enable the use of multiple pair styles in one simulation. With the hybrid style, exactly one pair style is assigned to each pair of atom types. With the hybrid/overlay style, one or more pair styles can be assigned to each pair of atom types. The assignment of pair styles to type pairs is made via the pair_coeff command.
Here are two examples of hybrid simulations. The hybrid style could be used for a simulation of a metal droplet on a LJ surface. The metal atoms interact with each other via an eam potential, the surface atoms interact with each other via a lj/cut potential, and the metal/surface interaction is also computed via a lj/cut potential. The hybrid/overlay style could be used as in the second example above, where multiple potentials are superposed in an additive fashion to compute the interaction between atoms. In this example, using lj/cut and coul/long together gives the same result as if the lj/cut/coul/long potential were used by itself. In this case, it would be more efficient to use the single combined potential, but in general any combination of pair potentials can be used together in to produce an interaction that is not encoded in any single pair_style file, e.g. adding Coulombic forces between granular particles.
All pair styles that will be used are listed as “sub-styles” following the hybrid or hybrid/overlay keyword, in any order. Each sub-style’s name is followed by its usual arguments, as illustrated in the example above. See the doc pages of individual pair styles for a listing and explanation of the appropriate arguments.
Note that an individual pair style can be used multiple times as a sub-style. For efficiency this should only be done if your model requires it. E.g. if you have different regions of Si and C atoms and wish to use a Tersoff potential for pure Si for one set of atoms, and a Tersoff potential for pure C for the other set (presumably with some third potential for Si-C interactions), then the sub-style tersoff could be listed twice. But if you just want to use a Lennard-Jones or other pairwise potential for several different atom type pairs in your model, then you should just list the sub-style once and use the pair_coeff command to assign parameters for the different type pairs.
There is one exception to this option to list an individual pair style multiple times: GPU-enabled pair styles in the GPU package. This is because the GPU package currently assumes that only one instance of a pair style is being used.
In the pair_coeff commands, the name of a pair style must be added after the I,J type specification, with the remaining coefficients being those appropriate to that style. If the pair style is used multiple times in the pair_style command, then an additional numeric argument must also be specified which is a number from 1 to M where M is the number of times the sub-style was listed in the pair style command. The extra number indicates which instance of the sub-style these coefficients apply to.
For example, consider a simulation with 3 atom types: types 1 and 2 are Ni atoms, type 3 are LJ atoms with charges. The following commands would set up a hybrid simulation:
pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0 pair_coeff * * eam/alloy nialhjea Ni Ni NULL pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0 pair_coeff 1*2 3 lj/cut 0.8 1.3
As an example of using the same pair style multiple times, consider a simulation with 2 atom types. Type 1 is Si, type 2 is C. The following commands would model the Si atoms with Tersoff, the C atoms with Tersoff, and the cross-interactions with Lennard-Jones:
pair_style hybrid lj/cut 2.5 tersoff tersoff pair_coeff * * tersoff 1 Si.tersoff Si NULL pair_coeff * * tersoff 2 C.tersoff NULL C pair_coeff 1 2 lj/cut 1.0 1.5
If pair coefficients are specified in the data file read via the read_data command, then the same rule applies. E.g. “eam/alloy” or “lj/cut” must be added after the atom type, for each line in the “Pair Coeffs” section, e.g.
Pair Coeffs 1 lj/cut/coul/cut 1.0 1.0 ...
Note that the pair_coeff command for some potentials such as pair_style eam/alloy includes a mapping specification of elements to all atom types, which in the hybrid case, can include atom types not assigned to the eam/alloy potential. The NULL keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO, etc), to denote an atom type that will be assigned to a different sub-style.
For the hybrid style, each atom type pair I,J is assigned to exactly one sub-style. Just as with a simulation using a single pair style, if you specify the same atom type pair in a second pair_coeff command, the previous assignment will be overwritten.
For the hybrid/overlay style, each atom type pair I,J can be assigned to one or more sub-styles. If you specify the same atom type pair in a second pair_coeff command with a new sub-style, then the second sub-style is added to the list of potentials that will be calculated for two interacting atoms of those types. If you specify the same atom type pair in a second pair_coeff command with a sub-style that has already been defined for that pair of atoms, then the new pair coefficients simply override the previous ones, as in the normal usage of the pair_coeff command. E.g. these two sets of commands are the same:
pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 pair_coeff 2 2 1.5 0.8 pair_style hybrid/overlay lj/cut 2.5 pair_coeff * * lj/cut 1.0 1.0 pair_coeff 2 2 lj/cut 1.5 0.8
Coefficients must be defined for each pair of atoms types via the pair_coeff command as described above, or in the data file or restart files read by the read_data or read_restart commands, or by mixing as described below.
For both the hybrid and hybrid/overlay styles, every atom type pair I,J (where I <= J) must be assigned to at least one sub-style via the pair_coeff command as in the examples above, or in the data file read by the read_data, or by mixing as described below.
If you want there to be no interactions between a particular pair of atom types, you have 3 choices. You can assign the type pair to some sub-style and use the neigh_modify exclude type command. You can assign it to some sub-style and set the coefficients so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ potential). Or, for hybrid and hybrid/overlay simulations, you can use this form of the pair_coeff command in your input script:
pair_coeff 2 3 none
or this form in the “Pair Coeffs” section of the data file:
If an assignment to none is made in a simulation with the hybrid/overlay pair style, it wipes out all previous assignments of that atom type pair to sub-styles.
Note that you may need to use an atom_style hybrid command in your input script, if atoms in the simulation will need attributes from several atom styles, due to using multiple pair potentials.
Different force fields (e.g. CHARMM vs AMBER) may have different rules for applying weightings that change the strength of pairwise interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 neighbors in the molecular bond topology, as normally set by the special_bonds command. Different weights can be assigned to different pair hybrid sub-styles via the pair_modify special command. This allows multiple force fields to be used in a model of a hybrid system, however, there is no consistent approach to determine parameters automatically for the interactions between the two force fields, this is only recommended when particles described by the different force fields do not mix.
Here is an example for mixing CHARMM and AMBER: The global amber setting sets the 1-4 interactions to non-zero scaling factors and then overrides them with 0.0 only for CHARMM:
special_bonds amber pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
The this input achieves the same effect:
special_bonds 0.0 0.0 0.1 pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5 pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333 pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
Here is an example for mixing Tersoff with OPLS/AA based on a data file that defines bonds for all atoms where for the Tersoff part of the system the force constants for the bonded interactions have been set to 0. Note the global settings are effectively lj/coul 0.0 0.0 0.5 as required for OPLS/AA:
special_bonds lj/coul 1e-20 1e-20 0.5 pair_hybrid tersoff lj/cut/coul/long 12.0 pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
For use with the various compute */tally computes, the pair_modify compute/tally command can be used to selectively turn off processing of the compute tally styles, for example, if those pair styles (e.g. many-body styles) do not support this feature.
See the pair_modify doc page for details on the specific syntax, requirements and restrictions.
The potential energy contribution to the overall system due to an individual sub-style can be accessed and output via the compute pair command.
Several of the potentials defined via the pair_style command in LAMMPS are really many-body potentials, such as Tersoff, AIREBO, MEAM, ReaxFF, etc. The way to think about using these potentials in a hybrid setting is as follows.
A subset of atom types is assigned to the many-body potential with a single pair_coeff command, using “* *” to include all types and the NULL keywords described above to exclude specific types not assigned to that potential. If types 1,3,4 were assigned in that way (but not type 2), this means that all many-body interactions between all atoms of types 1,3,4 will be computed by that potential. Pair_style hybrid allows interactions between type pairs 2-2, 1-2, 2-3, 2-4 to be specified for computation by other pair styles. You could even add a second interaction for 1-1 to be computed by another pair style, assuming pair_style hybrid/overlay is used.
But you should not, as a general rule, attempt to exclude the many-body interactions for some subset of the type pairs within the set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That is not conceptually well-defined for many-body interactions, since the potential will typically calculate energies and foces for small groups of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to find the additional atoms in the group. It is typically non-physical to think of excluding an interaction between a particular pair of atoms when the potential computes 3-body or 4-body interactions.
However, you can still use the pair_coeff none setting or the neigh_modify exclude command to exclude certain type pairs from the neighbor list that will be passed to a many-body sub-style. This will alter the calculations made by a many-body potential, since it builds its list of 3-body, 4-body, etc interactions from the pair list. You will need to think carefully as to whether it produces a physically meaningful result for your model.
For example, imagine you have two atom types in your model, type 1 for atoms in one surface, and type 2 for atoms in the other, and you wish to use a Tersoff potential to compute interactions within each surface, but not between surfaces. Then either of these two command sequences would implement that model:
pair_style hybrid tersoff pair_coeff * * tersoff SiC.tersoff C C pair_coeff 1 2 none pair_style tersoff pair_coeff * * SiC.tersoff C C neigh_modify exclude type 1 2
Either way, only neighbor lists with 1-1 or 2-2 interactions would be passed to the Tersoff potential, which means it would compute no 3-body interactions containing both type 1 and 2 atoms.
Here is another example, using hybrid/overlay, to use 2 many-body potentials together, in an overlapping manner. Imagine you have CNT (C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C interactions, and AIREBO for C/C interactions. Si atoms are type 1; C atoms are type 2. Something like this will work:
pair_style hybrid/overlay tersoff airebo 3.0 pair_coeff * * tersoff SiC.tersoff.custom Si C pair_coeff * * airebo CH.airebo NULL C
Note that to prevent the Tersoff potential from computing C/C interactions, you would need to modify the SiC.tersoff file to turn off C/C interaction, i.e. by setting the appropriate coefficients to 0.0.
Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Speed packages doc page.
Since the hybrid and hybrid/overlay styles delegate computation to the individual sub-styles, the suffix versions of the hybrid and hybrid/overlay styles are used to propagate the corresponding suffix to all sub-styles, if those versions exist. Otherwise the non-accelerated version will be used.
The individual accelerated sub-styles are part of the GPU, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package doc page for more info.
You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
See the Speed packages doc page for more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info¶
Any pair potential settings made via the pair_modify command are passed along to all sub-styles of the hybrid potential.
For atom type pairs I,J and I != J, if the sub-style assigned to I,I and J,J is the same, and if the sub-style allows for mixing, then the coefficients for I,J can be mixed. This means you do not have to specify a pair_coeff command for I,J since the I,J type pair will be assigned automatically to the sub-style defined for both I,I and J,J and its coefficients generated by the mixing rule used by that sub-style. For the hybrid/overlay style, there is an additional requirement that both the I,I and J,J pairs are assigned to a single sub-style. See the “pair_modify” command for details of mixing rules. See the See the doc page for the sub-style to see if allows for mixing.
The hybrid pair styles supports the pair_modify shift, table, and tail options for an I,J pair interaction, if the associated sub-style supports it.
For the hybrid pair styles, the list of sub-styles and their respective settings are written to binary restart files, so a pair_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart file. Thus, pair_coeff commands need to be re-specified in the restart input script.
These pair styles support the use of the inner, middle, and outer keywords of the run_style respa command, if their sub-styles do.
When using a long-range Coulombic solver (via the kspace_style command) with a hybrid pair_style, one or more sub-styles will be of the “long” variety, e.g. lj/cut/coul/long or buck/coul/long. You must insure that the short-range Coulombic cutoff used by each of these long pair styles is the same or else LAMMPS will generate an error.