.. index:: compute dpd

compute dpd command

===================

Syntax

""""""

.. parsed-literal::

   compute ID group-ID dpd

* ID, group-ID are documented in :doc:`compute <compute>` command

* dpd = style name of this compute command

Examples

""""""""

.. parsed-literal::

   compute 1 all dpd

Description

"""""""""""

Define a computation that accumulates the total internal conductive

energy (U_cond), the total internal mechanical energy (U_mech), the

total internal energy (U) and the *harmonic* average of the internal

temperature (dpdTheta) for the entire system of particles.  See the

:doc:`compute dpd/atom <compute_dpd_atom>` command if you want

per-particle internal energies and internal temperatures.

The system internal properties are computed according to the following

relations:

.. image:: Eqs/compute_dpd.jpg

   :align: center

where N is the number of particles in the system

----------

**Output info:**

This compute calculates a global vector of length 5 (U_cond, U_mech,

U, dpdTheta, N_particles), which can be accessed by indices 1-5.  See

:ref:`this section <howto_15>` for an overview of LAMMPS

output options.

The vector values will be in energy and temperature :doc:`units <units>`.

Restrictions

""""""""""""

The compute *dpd* is only available if LAMMPS is built with the

USER-DPD package and requires the :doc:`atom_style dpd <atom_style>`.

Related commands

""""""""""""""""

:doc:`compute dpd/atom <compute_dpd_atom>`,

:doc:`thermo_style <thermo_style>`

**Default:** none

----------

.. _Larentzos:

**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and

W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative

Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

Laboratory, Aberdeen Proving Ground, MD (2014).

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Section_commands.html#comm

.. index:: compute dpd/atom

compute dpd/atom command

========================

Syntax

""""""

.. parsed-literal::

   compute ID group-ID dpd/atom

* ID, group-ID are documented in :doc:`compute <compute>` command

* dpd/atom = style name of this compute command

Examples

""""""""

compute 1 all dpd/atom

Description

"""""""""""

Define a computation that accesses the per-particle internal

conductive energy (u_cond), internal mechanical energy (u_mech) and

internal temperatures (dpdTheta) for each particle in a group.  See

the :doc:`compute dpd <compute_dpd>` command if you want the total

internal conductive energy, the total internal mechanical energy, and

average internal temperature of the entire system or group of dpd

particles.

**Output info:**

This compute calculates a per-particle array with 3 columns (u_cond,

u_mech, dpdTheta), which can be accessed by indices 1-3 by any command

that uses per-particle values from a compute as input.  See

:ref:`Section_howto15 <howto_15>` for an overview of

LAMMPS output options.

The per-particle array values will be in energy (u_cond, u_mech) and

temperature (dpdTheta) :doc:`units <units>`.

Restrictions

""""""""""""

The compute *dpd/atom* is only available if LAMMPS is built with the

USER-DPD package.

Related commands

""""""""""""""""

:doc:`dump custom <dump>`, :doc:`compute dpd <compute_dpd>`

**Default:** none

----------

.. _Larentzos:

**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and

W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative

Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

Laboratory, Aberdeen Proving Ground, MD (2014).

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Section_commands.html#comm

.. index:: fix eos/cv

fix eos/cv command

==================

Syntax

""""""

.. parsed-literal::

   fix ID group-ID eos/cv cv

* ID, group-ID are documented in :doc:`fix <fix>` command

* eos/cv = style name of this fix command

* cv = constant-volume heat capacity (energy/temperature units)

Examples

""""""""

.. parsed-literal::

   fix 1 all eos/cv 0.01

Description

"""""""""""

Fix *eos/cv* applies a mesoparticle equation of state to relate the

particle internal energy (u_i) to the particle internal temperature

(dpdTheta_i).  The *eos/cv* mesoparticle equation of state requires

the constant-volume heat capacity, and is defined as follows:

.. image:: Eqs/fix_eos-cv.jpg

   :align: center

where Cv is the constant-volume heat capacity, u_cond is the internal

conductive energy, and u_mech is the internal mechanical energy.  Note

that alternative definitions of the mesoparticle equation of state are

possible.

----------

Restrictions

""""""""""""

The fix *eos/cv* is only available if LAMMPS is built with the

USER-DPD package.

Related commands

""""""""""""""""

:doc:`fix shardlow <fix_shardlow>`, :doc:`pair dpd/fdt <pair_dpd_fdt>`

**Default:** none

----------

.. _Larentzos:

**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and

W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative

Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

Laboratory, Aberdeen Proving Ground, MD (2014).

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Section_commands.html#comm

.. index:: fix eos/table

fix eos/table command

=====================

Syntax

""""""

.. parsed-literal::

   fix ID group-ID eos/table style file N keyword

* ID, group-ID are documented in :doc:`fix <fix>` command

* eos/table = style name of this fix command

* style = *linear* = method of interpolation

* file = filename containing the tabulated equation of state

* N = use N values in *linear* tables

* keyword = name of table keyword correponding to table file

Examples

""""""""

.. parsed-literal::

   fix 1 all eos/table linear eos.table 100000 KEYWORD

Description

"""""""""""

Fix *eos/table* applies a tabulated mesoparticle equation of state to

relate the particle internal energy (u_i) to the particle internal

temperature (dpdTheta_i).

Fix *eos/table* creates interpolation tables of length *N* from

internal energy values listed in a file as a function of internal

temperature.

The interpolation tables are created by fitting cubic splines to the

file values and interpolating energy values at each of *N* internal

temperatures, and vice-versa.  During a simulation, these tables are

used to interpolate internal energy or temperature values as needed.

The interpolation is done with the *linear* style.

For the *linear* style, the internal temperature is used to find 2

surrounding table values from which an internal energy is computed by

linear interpolation, and vice-versa.

The filename specifies a file containing tabulated internal

temperature and internal energy values.  The keyword specifies a

section of the file.  The format of this file is described below.

----------

The format of a tabulated file is as follows (without the

parenthesized comments):

.. parsed-literal::

   # EOS TABLE                (one or more comment or blank lines)

.. parsed-literal::

   KEYWORD                    (keyword is first text on line)

   N 500                      (N  parameter)

                              (blank)

   1   1.00 0.000             (index, internal temperature, internal energy)

   2   1.02 0.001

   ...

   500 10.0 0.500

A section begins with a non-blank line whose 1st character is not a

"#"; blank lines or lines starting with "#" can be used as comments

between sections.  The first line begins with a keyword which

identifies the section.  The line can contain additional text, but the

initial text must match the argument specified in the fix command.

The next line lists the number of table entries.  The parameter "N" is

required and its value is the number of table entries that follow.

Note that this may be different than the *N* specified in the :doc:`fix eos/table <fix_style>` command.  Let Ntable = *N* in the fix

command, and Nfile = "N" in the tabulated file.  What LAMMPS does is a

preliminary interpolation by creating splines using the Nfile

tabulated values as nodal points.  It uses these to interpolate as

needed to generate energy and temperature values at Ntable different

points.  The resulting tables of length Ntable are then used as

described above, when computing energy and temperature relationships.

This means that if you want the interpolation tables of length Ntable

to match exactly what is in the tabulated file (with effectively no

preliminary interpolation), you should set Ntable = Nfile.

Following a blank line, the next N lines list the tabulated values.

On each line, the 1st value is the index from 1 to N, the 2nd value is

the internal temperature (in temperature units), the 3rd value is the

internal energy (in energy units).

Note that the internal temperature and internal energy values must 

increase from one line to the next.

Note that one file can contain many sections, each with a tabulated

potential.  LAMMPS reads the file section by section until it finds

one that matches the specified keyword.

----------

Restrictions

""""""""""""

The fix *eos/table* is only available if LAMMPS is built with the 

USER-DPD package.

The equation of state must be a monotonically increasing function.

An exit error will occur if the internal temperature or internal

energies are not within the table cutoffs.

Related commands

""""""""""""""""

:doc:`fix shardlow <fix_shardlow>`, :doc:`pair dpd/fdt <dpd_fdt>`

**Default:** none

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Section_commands.html#comm

.. index:: fix shardlow

fix shardlow command

====================

Syntax

""""""

.. parsed-literal::

   fix ID group-ID shardlow

* ID, group-ID are documented in :doc:`fix <fix>` command

* shardlow = style name of this fix command

Examples

""""""""

.. parsed-literal::

   fix 1 all shardlow

Description

"""""""""""

Specifies that the Shardlow splitting algorithm (SSA) is to be used to

integrate the DPD equations of motion.  The SSA splits the integration

into a stochastic and deterministic integration step.  The fix

*shardlow* performs the stochastic integration step and must be used

in conjunction with a deterministic integrator (e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nph>`).  The stochastic

integration of the dissipative and random forces is performed prior to

the deterministic integration of the conservative force. Further

details regarding the method are provided in :ref:`(Lisal) <Lisal>` and

:ref:`(Larentzos) <Larentzos>`.

The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt <pair_style>` or :doc:`pair_style dpd/fdt/energy <pair_style>` command to properly initialize the

fluctuation-dissipation theorem parameter(s) sigma (and kappa, if

necessary).

Note that numerous variants of DPD can be specified by choosing an

appropriate combination of the integrator and :doc:`pair_style dpd/fdt <pair_style>` command.  DPD under isothermal conditions can

be specified by using fix *shardlow*, fix *nve* and pair_style

*dpd/fdt*.  DPD under isoenergetic conditions can be specified by

using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*.  DPD

under isobaric conditions can be specified by using fix shardlow, fix

*nph* and pair_style *dpd/fdt*.  DPD under isoenthalpic conditions can

be specified by using fix shardlow, fix *nph* and pair_style

*dpd/fdt/energy*.  Examples of each DPD variant are provided in the

examples/USER/dpd directory.

----------

Restrictions

""""""""""""

This fix is only available if LAMMPS is built with the USER-DPD

package.  See the :ref:`Making LAMMPS <start_3>` section

for more info.

This fix is currently limited to orthogonal simulation cell

geometries.

This fix must be used with an additional fix that specifies time

integration, e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`.

The Shardlow splitting algorithm requires the sizes of the sub-domain

lengths to be larger than twice the cutoff+skin.  Generally, the

domain decomposition is dependant on the number of processors

requested.

Related commands

""""""""""""""""

:doc:`pair_style dpd/fdt <pair_dpd_fdt>`, :doc:`fix eos/cv <fix_eos_cv>`

**Default:** none

----------

.. _Lisal:

**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative

particle dynamics as isothermal, isobaric, isoenergetic, and

isoenthalpic conditions using Shardlow-like splitting algorithms.",

J. Chem. Phys., 135, 204105 (2011).

.. _Larentzos:

**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and

W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic

Dissipative Particle Dynamics Using Shardlow-Like Splitting

Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014).

.. _Larentzos:

**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and

W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative

Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

Laboratory, Aberdeen Proving Ground, MD (2014).

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Section_commands.html#comm