forked from lijiext/lammps
210 lines
8.0 KiB
Plaintext
210 lines
8.0 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style dpd command :h3
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pair_style dpd/gpu command :h3
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pair_style dpd/omp command :h3
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pair_style dpd/tstat command :h3
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pair_style dpd/tstat/gpu command :h3
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pair_style dpd/tstat/omp command :h3
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[Syntax:]
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pair_style dpd T cutoff seed
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pair_style dpd/tstat Tstart Tstop cutoff seed :pre
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T = temperature (temperature units)
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Tstart,Tstop = desired temperature at start/end of run (temperature units)
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cutoff = global cutoff for DPD interactions (distance units)
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seed = random # seed (positive integer) :ul
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[Examples:]
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pair_style dpd 1.0 2.5 34387
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pair_coeff * * 3.0 1.0
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pair_coeff 1 1 3.0 1.0 1.0 :pre
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pair_style dpd/tstat 1.0 1.0 2.5 34387
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pair_coeff * * 1.0
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pair_coeff 1 1 1.0 1.0 :pre
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[Description:]
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Style {dpd} computes a force field for dissipative particle dynamics
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(DPD) following the exposition in "(Groot)"_#Groot.
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Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions,
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which is equivalent to the non-conservative portion of the DPD force
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field. This pair-wise thermostat can be used in conjunction with any
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"pair style"_pair_style.html, and in leiu of per-particle thermostats
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like "fix langevin"_fix_langevin.html or ensemble thermostats like
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Nose Hoover as implemented by "fix nvt"_fix_nh.html. To use
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{dpd/stat} as a thermostat for another pair style, use the "pair_style
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hybrid/overlay"_pair_hybrid.html command to compute both the desired
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pair interaction and the thermostat for each pair of particles.
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For style {dpd}, the force on atom I due to atom J is given as a sum
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of 3 terms
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:c,image(Eqs/pair_dpd.jpg)
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where Fc is a conservative force, Fd is a dissipative force, and Fr is
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a random force. Rij is a unit vector in the direction Ri - Rj, Vij is
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the vector difference in velocities of the two atoms = Vi - Vj, alpha
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is a Gaussian random number with zero mean and unit variance, dt is
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the timestep size, and w(r) is a weighting factor that varies between
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0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma),
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where Kb is the Boltzmann constant and T is the temperature parameter
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in the pair_style command.
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For style {dpd/tstat}, the force on atom I due to atom J is the same
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as the above equation, except that the conservative Fc term is
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dropped. Also, during the run, T is set each timestep to a ramped
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value from Tstart to Tstop.
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For style {dpd}, the pairwise energy associated with style {dpd} is
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only due to the conservative force term Fc, and is shifted to be zero
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at the cutoff distance Rc. The pairwise virial is calculated using
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all 3 terms. For style {dpd/tstat} there is no pairwise energy, but
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the last two terms of the formula make a contribution to the virial.
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For style {dpd}, the following coefficients must be defined for each
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pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
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the examples above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands:
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A (force units)
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gamma (force/velocity units)
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cutoff (distance units) :ul
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The last coefficient is optional. If not specified, the global DPD
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cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
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where T is the temperature set by the "pair_style"_pair_style.html
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command so it does not need to be specified.
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For style {dpd/tstat}, the coefficiencts defined for each pair of
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atoms types via the "pair_coeff"_pair_coeff.html command is the same,
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except that A is not included.
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The GPU-accelerated versions of these styles are implemented based on
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the work of "(Afshar)"_#Afshar and "(Phillips)"_#Phillips.
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NOTE: If you are modeling DPD polymer chains, you may want to use the
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"pair_style srp"_pair_srp.html command in conjuction with these pair
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styles. It is a soft segmental repulsive potential (SRP) that can
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prevent DPD polymer chains from crossing each other.
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NOTE: The virial calculation for pressure when using this pair style
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includes all the components of force listed above, including the
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random force.
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:line
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Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in "Section_accelerate"_Section_accelerate.html
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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These pair styles do not support mixing. Thus, coefficients for all
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I,J pairs must be specified explicitly.
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These pair styles do not support the "pair_modify"_pair_modify.html
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shift option for the energy of the pair interaction. Note that as
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discussed above, the energy due to the conservative Fc term is already
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shifted to be 0.0 at the cutoff distance Rc.
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The "pair_modify"_pair_modify.html table option is not relevant
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for these pair styles.
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These pair style do not support the "pair_modify"_pair_modify.html
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tail option for adding long-range tail corrections to energy and
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pressure.
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These pair styles writes their information to "binary restart
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files"_restart.html, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file. Note
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that the user-specified random number seed is stored in the restart
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file, so when a simulation is restarted, each processor will
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re-initialize its random number generator the same way it did
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initially. This means the random forces will be random, but will not
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be the same as they would have been if the original simulation had
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continued past the restart time.
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These pair styles can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. They do not support the
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{inner}, {middle}, {outer} keywords.
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The {dpd/tstat} style can ramp its target temperature over multiple
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runs, using the {start} and {stop} keywords of the "run"_run.html
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command. See the "run"_run.html command for details of how to do
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this.
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:line
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[Restrictions:]
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The default frequency for rebuilding neighbor lists is every 10 steps
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(see the "neigh_modify"_neigh_modify.html command). This may be too
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infrequent for style {dpd} simulations since particles move rapidly
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and can overlap by large amounts. If this setting yields a non-zero
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number of "dangerous" reneighborings (printed at the end of a
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simulation), you should experiment with forcing reneighboring more
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often and see if system energies/trajectories change.
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These pair styles requires you to use the "comm_modify vel
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yes"_comm_modify.html command so that velocites are stored by ghost
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atoms.
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These pair styles will not restart exactly when using the
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"read_restart"_read_restart.html command, though they should provide
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statistically similar results. This is because the forces they
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compute depend on atom velocities. See the
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"read_restart"_read_restart.html command for more details.
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[Related commands:]
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"pair_coeff"_pair_coeff.html, "fix nvt"_fix_nh.html, "fix
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langevin"_fix_langevin.html, "pair_style srp"_pair_srp.html
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[Default:] none
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:line
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:link(Groot)
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[(Groot)] Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
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:link(Afshar)
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[(Afshar)] Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys
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Comm, 184, 1119-1128 (2013).
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:link(Phillips)
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[(Phillips)] C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput
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Phys Comm, 230, 7191-7201 (2011).
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