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26
doc/src/dump.txt
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@ -491,17 +491,21 @@ There are several options for outputting atom coordinates. The {x},
appropriate distance "units"_units.html (Angstroms, sigma, etc). Use appropriate distance "units"_units.html (Angstroms, sigma, etc). Use
{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size, {xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
so that each value is 0.0 to 1.0. If the simulation box is triclinic so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. Use (tilted), then all atom coords will still be between 0.0 and 1.0.
{xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the image I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
flags for each atom. Unwrapped means that if the atom has passed thru the non-orthogonal vectors of the simulation box edges, as discussed
a periodic boundary one or more times, the value is printed for what in "Section howto 6.12"_Section_howto.html#howto_12.
the coordinate would be if it had not been wrapped back into the
periodic box. Note that using {xu}, {yu}, {zu} means that the Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
coordinate values may be far outside the box bounds printed with the image flags for each atom. Unwrapped means that if the atom has
snapshot. Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, passed thru a periodic boundary one or more times, the value is
except that the unwrapped coordinates are scaled by the box size. Atoms printed for what the coordinate would be if it had not been wrapped
that have passed through a periodic boundary will have the corresponding back into the periodic box. Note that using {xu}, {yu}, {zu} means
cooordinate increased or decreased by 1.0. that the coordinate values may be far outside the box bounds printed
with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using
{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
the box size. Atoms that have passed through a periodic boundary will
have the corresponding cooordinate increased or decreased by 1.0.
The image flags can be printed directly using the {ix}, {iy}, {iz} The image flags can be printed directly using the {ix}, {iy}, {iz}
attributes. For periodic dimensions, they specify which image of the attributes. For periodic dimensions, they specify which image of the

72
doc/src/pair_dpd_conservative.txt
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@ -1,72 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style dpd/conservative command :h3
[Syntax:]
pair_style dpd/conservative cutoff :pre
cutoff = global cutoff for DPD interactions (distance units) :ul
[Examples:]
pair_style dpd/conservative 2.5
pair_coeff * * 3.0 2.5
pair_coeff 1 1 3.0 :pre
[Description:]
Style {dpd/conservative} computes the conservative force for
dissipative particle dynamics (DPD). The conservative force on atom I
due to atom J is given by
:c,image(Eqs/pair_dpd_conservative.jpg)
where the weighting factor, omega_ij, varies between 0 and 1, and is
chosen to have the following functional form:
:c,image(Eqs/pair_dpd_omega.jpg)
where Rij is a unit vector in the direction Ri - Rj, and Rc is the
cutoff. Note that alternative definitions of the weighting function
exist, but would have to be implemented as a separate pair style
command.
Style {dpd/conservative} differs from the other dpd styles in that the
dissipative and random forces are not computed within the pair style.
For style {dpd/conservative}, the pairwise energy is due only to the
conservative force term Fc, and is shifted to be zero at the cutoff
distance Rc. The pairwise virial is calculated using only the
conservative term.
Style {dpd/conservative} requires the following coefficients to be
defined for each pair of atoms types via the
"pair_coeff"_pair_coeff.html command as in the examples above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
A (force units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global DPD
cutoff is used.
:line
[Restrictions:]
The pair style {dpd/conservative} is only available if LAMMPS is built
with the USER-DPD package.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_dpd"_pair_dpd.html
[Default:] none