249 lines
8.4 KiB
ReStructuredText
249 lines
8.4 KiB
ReStructuredText
.. index:: pair\_style dpd
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pair\_style dpd command
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=======================
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pair\_style dpd/gpu command
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===========================
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pair\_style dpd/intel command
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=============================
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pair\_style dpd/omp command
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===========================
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pair\_style dpd/tstat command
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=============================
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pair\_style dpd/tstat/gpu command
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=================================
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pair\_style dpd/tstat/omp command
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=================================
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Syntax
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""""""
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.. parsed-literal::
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pair_style dpd T cutoff seed
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pair_style dpd/tstat Tstart Tstop cutoff seed
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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)
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Examples
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""""""""
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.. parsed-literal::
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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
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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
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Description
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"""""""""""
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Style *dpd* computes a force field for dissipative particle dynamics
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(DPD) following the exposition in :ref:`(Groot) <Groot1>`.
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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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:doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
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like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
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Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`. To use
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*dpd/tstat* as a thermostat for another pair style, use the :doc:`pair\_style hybrid/overlay <pair_hybrid>` 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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.. image:: Eqs/pair_dpd.jpg
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:align: center
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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 :doc:`pair\_coeff <pair_coeff>` 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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:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
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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)
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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 :doc:`pair\_style <pair_style>`
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command so it does not need to be specified.
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For style *dpd/tstat*\ , the coefficients defined for each pair of
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atoms types via the :doc:`pair\_coeff <pair_coeff>` 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 :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`.
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.. note::
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If you are modeling DPD polymer chains, you may want to use the
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:doc:`pair\_style srp <pair_srp>` command in conjunction 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::
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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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----------
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Styles with a *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 on the :doc:`Speed packages <Speed_packages>` doc
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page. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page 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 :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
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:doc:`suffix <suffix>` command in your input script.
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See the :doc:`Speed packages <Speed_packages>` doc page for more
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instructions on how to use the accelerated styles effectively.
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----------
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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 :doc:`pair\_modify <pair_modify>`
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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 :doc:`pair\_modify <pair_modify>` table option is not relevant
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for these pair styles.
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These pair style do not support the :doc:`pair\_modify <pair_modify>`
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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 :doc:`binary restart files <restart>`, 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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:doc:`run\_style respa <run_style>` 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 :doc:`run <run>`
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command. See the :doc:`run <run>` command for details of how to do
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this.
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----------
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Restrictions
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""""""""""""
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The default frequency for rebuilding neighbor lists is every 10 steps
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(see the :doc:`neigh\_modify <neigh_modify>` 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 :doc:`comm\_modify vel yes <comm_modify>` command so that velocities 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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:doc:`read\_restart <read_restart>` 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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:doc:`read\_restart <read_restart>` command for more details.
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Related commands
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""""""""""""""""
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:doc:`pair\_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`pair\_style srp <pair_srp>`
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**Default:** none
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----------
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.. _Groot1:
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**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
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.. _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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.. _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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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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