For simulations without pairwise interactions (see "pair_style none" -command), and just bonded interactions, you still need to set the -neighbor skin distance. Pairwise neighbor lists will not be formed -but the skin distance also determines which atoms are communicated -from nearby processors, so it should be slightly large enough that all -bond, angle, etc atoms are acquired. -
The style value selects what algorithm is used to build the list. The bin style creates the list by binning which is an operation that scales linearly with N/P, the number of atoms per processor where N = @@ -71,7 +64,24 @@ the pairwise list and the number of times neighbor lists were built are printed to the screen and log file. See this section for details.
-Restrictions: none +
Restrictions: +
+For simulations without pairwise interactions (see "pair_style none" +command), but that include bonded interactions, you still need to set +the neighbor skin distance. Pairwise neighbor lists will not be +formed, but the pair cutoff (0.0 in this case) plus the skin distance +is the range at which atoms are communicated from nearby processors. +This needs to be large enough that atoms in the same bond, angle, etc +as an atom owned by a processor are acquired. What distance is +appropriate depends on the newton bond setting. For +newton bond off, the distance needs to be the furthest distance +between any two atoms in the bond, angle, etc. E.g. the distance +between the 1-4 atoms in a dihedral. For newton bond on, the distance +is between the central atom in the bond, angle, etc and any other +atom. E.g. the distance between the 2-4 atoms in a dihedral. +
+The same logic applies to systems that include bonded interactions and +a pairwise cutoff shorter than the distances just described.
Related commands:
diff --git a/doc/neighbor.txt b/doc/neighbor.txt index 937793022e..9a04488d4c 100644 --- a/doc/neighbor.txt +++ b/doc/neighbor.txt @@ -30,13 +30,6 @@ need to be built, but more pairs must be checked for possible force interactions every timestep. The default value for {skin} depends on the choice of units for the simulation (see below). -For simulations without pairwise interactions (see "pair_style none" -command), and just bonded interactions, you still need to set the -neighbor skin distance. Pairwise neighbor lists will not be formed -but the skin distance also determines which atoms are communicated -from nearby processors, so it should be slightly large enough that all -bond, angle, etc atoms are acquired. - The {style} value selects what algorithm is used to build the list. The {bin} style creates the list by binning which is an operation that scales linearly with N/P, the number of atoms per processor where N = @@ -68,7 +61,24 @@ the pairwise list and the number of times neighbor lists were built are printed to the screen and log file. See "this section"_Section_start.html#2_7 for details. -[Restrictions:] none +[Restrictions:] + +For simulations without pairwise interactions (see "pair_style none" +command), but that include bonded interactions, you still need to set +the neighbor skin distance. Pairwise neighbor lists will not be +formed, but the pair cutoff (0.0 in this case) plus the skin distance +is the range at which atoms are communicated from nearby processors. +This needs to be large enough that atoms in the same bond, angle, etc +as an atom owned by a processor are acquired. What distance is +appropriate depends on the "newton bond"_newton.html setting. For +newton bond off, the distance needs to be the furthest distance +between any two atoms in the bond, angle, etc. E.g. the distance +between the 1-4 atoms in a dihedral. For newton bond on, the distance +is between the central atom in the bond, angle, etc and any other +atom. E.g. the distance between the 2-4 atoms in a dihedral. + +The same logic applies to systems that include bonded interactions and +a pairwise cutoff shorter than the distances just described. [Related commands:] diff --git a/doc/set.html b/doc/set.html index 1c439ad155..ac034cd732 100644 --- a/doc/set.html +++ b/doc/set.html @@ -13,7 +13,7 @@Syntax:
-set style ID keyword value ... +set style ID keyword values ...
type value = atom type @@ -45,6 +45,8 @@ diameter value = particle diameter (distance units) density value = particle density (mass/distance^3 units) volume value = particle volume (distance^3 units) + image nx ny nz + nx,ny,nz = which periodic image of the simulation box the atom is in bond value = bond type for all bonds between selected atoms angle value = angle type for all angles between selected atoms dihedral value = dihedral type for all dihedrals between selected atoms @@ -150,6 +152,28 @@ combined with its density determines their mass.Keyword volume sets the effective size of all selected particles.
+Keyword image sets which image of the simulation box the atom is +considered to be in. It is only applied to periodic dimensions. An +image of 0 means it is inside the box as defined. A value of 2 means +add 2 box lengths to get the true value. A value of -1 means subtract +1 box length to get the true value. LAMMPS updates these flags as +atoms cross periodic boundaries during the simulation. The flags can +be output with atom snapshots via the dump command. If a +value of NULL is specified for any of nx,ny,nz, then the current image +value for that dimension is unchanged. +
+This command can be useful after a system has been equilibrated and +atoms have diffused one or more box lengths in various directions. +This command can then reset the image values for atoms so that they +are effectively inside the simulation box, e.g if a diffusion +coefficient is about to be measured via the fix msd +command. Care should be taken not to reset the image flags of two +atoms in a bond to the same value if the bond straddles a periodic +boundary (rather they should be different by +/- 1). This will not +affect the dynamics of a simulation, but may mess up analysis of the +trajectories if a LAMMPS diagnostic or your own analysis relies on the +image flags to unwrap a molecule which straddles the periodic box. +
For the diameter and density and volume keywords, the atom style being used must support the use of those parameters. For example, granular particles store a diameter and diff --git a/doc/set.txt b/doc/set.txt index 9ecc601dca..fe8800ba8c 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -10,7 +10,7 @@ set command :h3 [Syntax:] -set style ID keyword value ... :pre +set style ID keyword values ... :pre style = {atom} or {group} or {region} :ulb,l ID = atom ID or group ID or region ID :l @@ -18,7 +18,7 @@ one or more keyword/value pairs may be appended :l keyword = {type} or {type/fraction} or {mol} or \ {x} or {y} or {z} or {vx} or {vy} or {vz} or \ {charge} or {dipole} or {dipole/random} or {quat/random} or \ - {diameter} or {density} or {volume} or + {diameter} or {density} or {volume} or {image} or {bond} or {angle} or {dihedral} or {improper} :l {type} value = atom type {type/fraction} values = type fraction seed @@ -41,6 +41,8 @@ keyword = {type} or {type/fraction} or {mol} or \ {diameter} value = particle diameter (distance units) {density} value = particle density (mass/distance^3 units) {volume} value = particle volume (distance^3 units) + {image} nx ny nz + nx,ny,nz = which periodic image of the simulation box the atom is in {bond} value = bond type for all bonds between selected atoms {angle} value = angle type for all angles between selected atoms {dihedral} value = dihedral type for all dihedrals between selected atoms @@ -145,6 +147,28 @@ combined with its density determines their mass. Keyword {volume} sets the effective size of all selected particles. +Keyword {image} sets which image of the simulation box the atom is +considered to be in. It is only applied to periodic dimensions. An +image of 0 means it is inside the box as defined. A value of 2 means +add 2 box lengths to get the true value. A value of -1 means subtract +1 box length to get the true value. LAMMPS updates these flags as +atoms cross periodic boundaries during the simulation. The flags can +be output with atom snapshots via the "dump"_dump.html command. If a +value of NULL is specified for any of nx,ny,nz, then the current image +value for that dimension is unchanged. + +This command can be useful after a system has been equilibrated and +atoms have diffused one or more box lengths in various directions. +This command can then reset the image values for atoms so that they +are effectively inside the simulation box, e.g if a diffusion +coefficient is about to be measured via the "fix msd"_fix_msd.html +command. Care should be taken not to reset the image flags of two +atoms in a bond to the same value if the bond straddles a periodic +boundary (rather they should be different by +/- 1). This will not +affect the dynamics of a simulation, but may mess up analysis of the +trajectories if a LAMMPS diagnostic or your own analysis relies on the +image flags to unwrap a molecule which straddles the periodic box. + For the {diameter} and {density} and {volume} keywords, the "atom style"_atom_style.html being used must support the use of those parameters. For example, granular particles store a diameter and