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48
doc/_sources/atom_style.txt
View File

@ -10,10 +10,10 @@ Syntax
atom_style style args
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *tri* or *template* or *hybrid*
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *tri* or *template* or *hybrid*
.. parsed-literal::
args = none for any style except *body* and *hybrid*
args = none for any style except the following
*body* args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
@ -48,6 +48,12 @@ used before a simulation is setup via a :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
command.
.. note::
Many of the atom styles discussed here are only enabled if
LAMMPS was built with a specific package, as listed below in the
Restrictions section.
Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style *bond*, angular
terms cannot be used or added later to the model. It is OK to use a
@ -78,6 +84,8 @@ quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *dipole* | charge and dipole moment | system with dipolar particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dpd* | internal temperature and internal energies | DPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *electron* | charge and spin and eradius | electronic force field |
+--------------+-----------------------------------------------------+--------------------------------------+
| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles |
@ -147,6 +155,10 @@ position, which is represented by the eradius = electron size.
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *dpd* style is for dissipative particle dynamics (DPD) particles
which store the particle internal temperature (dpdTheta), internal
conductive energy (uCond) and internal mechanical energy (uMech).
The *meso* style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).
@ -272,16 +284,30 @@ Restrictions
This command cannot be used after the simulation box is defined by a
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command.
Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the :ref:`Making LAMMPS <start_3>` section for more info.
The *angle*, *bond*, *full*, *molecular*, and *template* styles are
part of the MOLECULE package. The *line* and *tri* styles are part
of the ASPHERE pacakge. The *body* style is part of the BODY package.
The *dipole* style is part of the DIPOLE package. The *peri* style is
part of the PERI package for Peridynamics. The *electron* style is
part of the USER-EFF package for :doc:`electronic force fields <pair_eff>`. The *meso* style is part of the USER-SPH
package for smoothed particle hydrodyanmics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS. The
*wavepacket* style is part of the USER-AWPMD package for the
:doc:`antisymmetrized wave packet MD method <pair_awpmd>`. They are
only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
part of the MOLECULE package.
The *line* and *tri* styles are part of the ASPHERE pacakge.
The *body* style is part of the BODY package.
The *dipole* style is part of the DIPOLE package.
The *peri* style is part of the PERI package for Peridynamics.
The *electron* style is part of the USER-EFF package for :doc:`electronic force fields <pair_eff>`.
The *dpd* style is part of the USER-DPD package for dissipative
particle dynamics (DPD).
The *meso* style is part of the USER-SPH package for smoothed particle
hydrodyanmics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *wavepacket* style is part of the USER-AWPMD package for the
:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
Related commands
""""""""""""""""

45
doc/_sources/read_data.txt
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@ -582,6 +582,8 @@ of analysis.
+------------+---------------------------------------------------------------------------+
| dipole | atom-ID atom-type q x y z mux muy muz |
+------------+---------------------------------------------------------------------------+
| dpd | atom-ID atom-type theta x y z |
+------------+---------------------------------------------------------------------------+
| electron | atom-ID atom-type q spin eradius x y z |
+------------+---------------------------------------------------------------------------+
| ellipsoid | atom-ID atom-type ellipsoidflag density x y z |
@ -596,7 +598,7 @@ of analysis.
+------------+---------------------------------------------------------------------------+
| peri | atom-ID atom-type volume density x y z |
+------------+---------------------------------------------------------------------------+
| smd | atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z |
| smd | atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z |
+------------+---------------------------------------------------------------------------+
| sphere | atom-ID atom-type diameter density x y z |
+------------+---------------------------------------------------------------------------+
@ -609,33 +611,34 @@ of analysis.
| hybrid | atom-ID atom-type x y z sub-style1 sub-style2 ... |
+------------+---------------------------------------------------------------------------+
The keywords have these meanings:
The per-atom values have these meanings and units, listed alphabetically:
* atom-ID = integer ID of atom
* molecule-ID = integer ID of molecule the atom belongs to
* atom-type = type of atom (1-Ntype)
* q = charge on atom (charge units)
* diameter = diameter of spherical atom (distance units)
* ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
* lineflag = 1 for line segment particles, 0 for point particles
* triangleflag = 1 for triangular particles, 0 for point particles
* bodyflag = 1 for body particles, 0 for point particles
* template-index = which molecule within the molecule template the atom is part of
* template-atom = which atom within a template molecule the atom is
* density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
* mass = mass of particle (mass units)
* volume = volume of particle (distance^3 units)
* x,y,z = coordinates of atom
* mux,muy,muz = components of dipole moment of atom (dipole units)
* rho = density (need units) for SPH particles
* e = energy (need units) for SPH particles
* contact-radius = ??? (distance units)
* cs_re,cs_im = real/imaginary parts of wavepacket coefficients
* cv = heat capacity (need units) for SPH particles
* spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
* density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
* diameter = diameter of spherical atom (distance units)
* e = energy (need units) for SPH particles
* ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
* eradius = electron radius (or fixed-core radius)
* etag = integer ID of electron that each wavepacket belongs to
* cs_re,cs_im = real/imaginary parts of wavepacket coefficients
* kernel_radius = ??? (distance units)
* contact_radius = ??? (distance units)
* kernel-radius = ??? (distance units)
* lineflag = 1 for line segment particles, 0 for point or spherical particles
* mass = mass of particle (mass units)
* molecule-ID = integer ID of molecule the atom belongs to
* mux,muy,muz = components of dipole moment of atom (dipole units)
* q = charge on atom (charge units)
* rho = density (need units) for SPH particles
* spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
* template-atom = which atom within a template molecule the atom is
* template-index = which molecule within the molecule template the atom is part of
* theta = internal temperature of a DPD particle
* triangleflag = 1 for triangular particles, 0 for point or sperhical particles
* volume = volume of Peridynamic particle (distance^3 units)
* x,y,z = coordinates of atom (distance units)
The units for these quantities depend on the unit style; see the
:doc:`units <units>` command for details.

6
doc/_sources/set.txt
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@ -13,7 +13,7 @@ Syntax
* style = *atom* or *type* or *mol* or *group* or *region*
* ID = atom ID range or type range or mol ID range or group ID or region ID
* one or more keyword/value pairs may be appended
* keyword = *type* or *type/fraction* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *meso/e* or *meso/cv* or *meso/rho* or *smd/contact/radius* or *smd/mass/density* or *i_name* or *d_name*
* keyword = *type* or *type/fraction* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *meso/e* or *meso/cv* or *meso/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or *i_name* or *d_name*
.. parsed-literal::
*type* value = atom type
@ -83,6 +83,7 @@ Syntax
value can be an atom-style variable (see below)
*smd/mass/density* = set particle mass based on volume by providing a mass density
value can be an atom-style variable (see below)
*dpd/theta* value = internal temperature of DPD particles (temperature units)
*i_name* value = value for custom integer vector with name
*d_name* value = value for custom floating-point vector with name
@ -382,6 +383,9 @@ other. Note that the SPH smoothing kernel diameter used for computing
long range, nonlocal interactions, is set using the *diameter*
keyword.
Keyword *dpd/theta* sets the internal temperature of a DPD particle
as defined by the USER-DPD package.
Keywords *i_name* and *d_name* refer to custom integer and
floating-point properties that have been added to each atom via the
:doc:`fix property/atom <fix_property_atom>` command. When that command

64
doc/atom_style.html
View File

@ -132,10 +132,10 @@
</pre></div>
</div>
<ul class="simple">
<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>dpd</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
</ul>
<pre class="literal-block">
args = none for any style except <em>body</em> and <em>hybrid</em>
args = none for any style except the following
<em>body</em> args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
@ -168,6 +168,12 @@ what attributes are associated with the atoms. This command must be
used before a simulation is setup via a <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or <a class="reference internal" href="create_box.html"><em>create_box</em></a>
command.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Many of the atom styles discussed here are only enabled if
LAMMPS was built with a specific package, as listed below in the
Restrictions section.</p>
</div>
<p>Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style <em>bond</em>, angular
terms cannot be used or added later to the model. It is OK to use a
@ -213,51 +219,55 @@ quantities.</p>
<td>charge and dipole moment</td>
<td>system with dipolar particles</td>
</tr>
<tr class="row-odd"><td><em>electron</em></td>
<tr class="row-odd"><td><em>dpd</em></td>
<td>internal temperature and internal energies</td>
<td>DPD particles</td>
</tr>
<tr class="row-even"><td><em>electron</em></td>
<td>charge and spin and eradius</td>
<td>electronic force field</td>
</tr>
<tr class="row-even"><td><em>ellipsoid</em></td>
<tr class="row-odd"><td><em>ellipsoid</em></td>
<td>shape, quaternion, angular momentum</td>
<td>aspherical particles</td>
</tr>
<tr class="row-odd"><td><em>full</em></td>
<tr class="row-even"><td><em>full</em></td>
<td>molecular + charge</td>
<td>bio-molecules</td>
</tr>
<tr class="row-even"><td><em>line</em></td>
<tr class="row-odd"><td><em>line</em></td>
<td>end points, angular velocity</td>
<td>rigid bodies</td>
</tr>
<tr class="row-odd"><td><em>meso</em></td>
<tr class="row-even"><td><em>meso</em></td>
<td>rho, e, cv</td>
<td>SPH particles</td>
</tr>
<tr class="row-even"><td><em>molecular</em></td>
<tr class="row-odd"><td><em>molecular</em></td>
<td>bonds, angles, dihedrals, impropers</td>
<td>uncharged molecules</td>
</tr>
<tr class="row-odd"><td><em>peri</em></td>
<tr class="row-even"><td><em>peri</em></td>
<td>mass, volume</td>
<td>mesocopic Peridynamic models</td>
</tr>
<tr class="row-even"><td><em>smd</em></td>
<tr class="row-odd"><td><em>smd</em></td>
<td>volume, kernel diameter, contact radius, mass</td>
<td>solid and fluid SPH particles</td>
</tr>
<tr class="row-odd"><td><em>sphere</em></td>
<tr class="row-even"><td><em>sphere</em></td>
<td>diameter, mass, angular velocity</td>
<td>granular models</td>
</tr>
<tr class="row-even"><td><em>template</em></td>
<tr class="row-odd"><td><em>template</em></td>
<td>template index, template atom</td>
<td>small molecules with fixed topology</td>
</tr>
<tr class="row-odd"><td><em>tri</em></td>
<tr class="row-even"><td><em>tri</em></td>
<td>corner points, angular momentum</td>
<td>rigid bodies</td>
</tr>
<tr class="row-even"><td><em>wavepacket</em></td>
<tr class="row-odd"><td><em>wavepacket</em></td>
<td>charge, spin, eradius, etag, cs_re, cs_im</td>
<td>AWPMD</td>
</tr>
@ -300,6 +310,9 @@ Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.</p>
<p>For the <em>peri</em> style, the particles are spherical and each stores a
per-particle mass and volume.</p>
<p>The <em>dpd</em> style is for dissipative particle dynamics (DPD) particles
which store the particle internal temperature (dpdTheta), internal
conductive energy (uCond) and internal mechanical energy (uMech).</p>
<p>The <em>meso</em> style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).</p>
@ -399,16 +412,21 @@ more instructions on how to use the accelerated styles effectively.</p>
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command cannot be used after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="create_box.html"><em>create_box</em></a> command.</p>
<p>Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The <em>angle</em>, <em>bond</em>, <em>full</em>, <em>molecular</em>, and <em>template</em> styles are
part of the MOLECULE package. The <em>line</em> and <em>tri</em> styles are part
of the ASPHERE pacakge. The <em>body</em> style is part of the BODY package.
The <em>dipole</em> style is part of the DIPOLE package. The <em>peri</em> style is
part of the PERI package for Peridynamics. The <em>electron</em> style is
part of the USER-EFF package for <a class="reference internal" href="pair_eff.html"><em>electronic force fields</em></a>. The <em>meso</em> style is part of the USER-SPH
package for smoothed particle hydrodyanmics (SPH). See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in LAMMPS. The
<em>wavepacket</em> style is part of the USER-AWPMD package for the
<a class="reference internal" href="pair_awpmd.html"><em>antisymmetrized wave packet MD method</em></a>. They are
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
part of the MOLECULE package.</p>
<p>The <em>line</em> and <em>tri</em> styles are part of the ASPHERE pacakge.</p>
<p>The <em>body</em> style is part of the BODY package.</p>
<p>The <em>dipole</em> style is part of the DIPOLE package.</p>
<p>The <em>peri</em> style is part of the PERI package for Peridynamics.</p>
<p>The <em>electron</em> style is part of the USER-EFF package for <a class="reference internal" href="pair_eff.html"><em>electronic force fields</em></a>.</p>
<p>The <em>dpd</em> style is part of the USER-DPD package for dissipative
particle dynamics (DPD).</p>
<p>The <em>meso</em> style is part of the USER-SPH package for smoothed particle
hydrodyanmics (SPH). See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in LAMMPS.</p>
<p>The <em>wavepacket</em> style is part of the USER-AWPMD package for the
<a class="reference internal" href="pair_awpmd.html"><em>antisymmetrized wave packet MD method</em></a>.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>

245
doc/compute_dpd.html Normal file
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@ -0,0 +1,245 @@
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<div class="section" id="compute-dpd-command">
<span id="index-0"></span><h1>compute dpd command<a class="headerlink" href="#compute-dpd-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID dpd
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>dpd = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all dpd
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>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 <em>harmonic</em> average of the internal
temperature (dpdTheta) for the entire system of particles. See the
<a class="reference internal" href="compute_dpd_atom.html"><em>compute dpd/atom</em></a> command if you want
per-particle internal energies and internal temperatures.</p>
<p>The system internal properties are computed according to the following
relations:</p>
<img alt="Eqs/compute_dpd.jpg" class="align-center" src="Eqs/compute_dpd.jpg" />
<p>where N is the number of particles in the system</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>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
<a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS
output options.</p>
<p>The vector values will be in energy and temperature <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The compute <em>dpd</em> is only available if LAMMPS is built with the
USER-DPD package and requires the <a class="reference internal" href="atom_style.html"><em>atom_style dpd</em></a>.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_dpd_atom.html"><em>compute dpd/atom</em></a>,
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="larentzos"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and
W.D. Mattson, &#8220;LAMMPS Implementation of Constant Energy Dissipative
Particle Dynamics (DPD-E)&#8221;, ARL-TR-6863, U.S. Army Research
Laboratory, Aberdeen Proving Ground, MD (2014).</p>
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<div class="section" id="compute-dpd-atom-command">
<span id="index-0"></span><h1>compute dpd/atom command<a class="headerlink" href="#compute-dpd-atom-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID dpd/atom
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>dpd/atom = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>compute 1 all dpd/atom</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>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 <a class="reference internal" href="compute_dpd.html"><em>compute dpd</em></a> 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.</p>
<p><strong>Output info:</strong></p>
<p>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
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-particle array values will be in energy (u_cond, u_mech) and
temperature (dpdTheta) <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The compute <em>dpd/atom</em> is only available if LAMMPS is built with the
USER-DPD package.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="dump.html"><em>dump custom</em></a>, <a class="reference internal" href="compute_dpd.html"><em>compute dpd</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="larentzos"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and
W.D. Mattson, &#8220;LAMMPS Implementation of Constant Energy Dissipative
Particle Dynamics (DPD-E)&#8221;, ARL-TR-6863, U.S. Army Research
Laboratory, Aberdeen Proving Ground, MD (2014).</p>
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<div class="section" id="compute-temp-body-command">
<span id="index-0"></span><h1>compute temp/body command<a class="headerlink" href="#compute-temp-body-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID temp/body keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>temp/body = style name of this compute command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>bias</em> or <em>dof</em></li>
</ul>
<pre class="literal-block">
<em>bias</em> value = bias-ID
bias-ID = ID of a temperature compute that removes a velocity bias
<em>dof</em> value = <em>all</em> or <em>rotate</em>
all = compute temperature of translational and rotational degrees of freedom
rotate = compute temperature of just rotational degrees of freedom
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all temp/body
compute myTemp mobile temp/body bias tempCOM
compute myTemp mobile temp/body dof rotate
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates the temperature of a group of
body particles, including a contribution from both their
translational and rotational kinetic energy. This differs from the
usual <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a> command, which assumes point
particles with only translational kinetic energy.</p>
<p>Only body particles can be included in the group. For 3d particles,
each has 6 degrees of freedom (3 translational, 3 rotational). For 2d
body particles, each has 3 degrees of freedom (2 translational, 1
rotational).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This choice for degrees of freedom (dof) assumes that all body
particles in your model will freely rotate, sampling all their
rotational dof. It is possible to use a combination of interaction
potentials and fixes that induce no torque or otherwise constrain some
of all of your particles so that this is not the case. Then there are
less dof and you should use the <a class="reference internal" href="compute_modify.html"><em>compute_modify extra</em></a> command to adjust the dof accordingly.</p>
</div>
<p>The translational kinetic energy is computed the same as is described
by the <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a> command. The rotational
kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
for the aspherical particle and w is its angular velocity, which is
computed from its angular momentum.</p>
<p>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute. The formula for the components of the
tensor is the same as the above formula, except that v^2 and w^2 are
replaced by vx*vy and wx*wy for the xy component, and the appropriate
elements of the inertia tensor are used. The 6 components of the
vector are ordered xx, yy, zz, xy, xz, yz.</p>
<p>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <em>dynamic</em> option of the
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command if this is not the case.</p>
<p>This compute subtracts out translational degrees-of-freedom due to
fixes that constrain molecular motion, such as <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> and <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a>. This means the
temperature of groups of atoms that include these constraints will be
computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the <em>extra</em> option of the
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command.</p>
<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span>this howto section</span></a> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.</p>
<hr class="docutils" />
<p>The keyword/value option pairs are used in the following ways.</p>
<p>For the <em>bias</em> keyword, <em>bias-ID</em> refers to the ID of a temperature
compute that removes a &#8220;bias&#8221; velocity from each atom. This allows
compute temp/sphere to compute its thermal temperature after the
translational kinetic energy components have been altered in a
prescribed way, e.g. to remove a flow velocity profile. Thermostats
that use this compute will work with this bias term. See the doc
pages for individual computes that calculate a temperature and the doc
pages for fixes that perform thermostatting for more details.</p>
<p>For the <em>dof</em> keyword, a setting of <em>all</em> calculates a temperature
that includes both translational and rotational degrees of freedom. A
setting of <em>rotate</em> calculates a temperature that includes only
rotational degrees of freedom.</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The scalar value calculated by this compute is &#8220;intensive&#8221;. The
vector values are &#8220;extensive&#8221;.</p>
<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><em>units</em></a>. The
vector values will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the BODY package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This compute requires that atoms store angular momementum and a
quaternion as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
command.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_temp.html"><em>compute temp</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="fix-eos-cv-command">
<span id="index-0"></span><h1>fix eos/cv command<a class="headerlink" href="#fix-eos-cv-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID eos/cv cv
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>eos/cv = style name of this fix command</li>
<li>cv = constant-volume heat capacity (energy/temperature units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix 1 all eos/cv 0.01
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Fix <em>eos/cv</em> applies a mesoparticle equation of state to relate the
particle internal energy (u_i) to the particle internal temperature
(dpdTheta_i). The <em>eos/cv</em> mesoparticle equation of state requires
the constant-volume heat capacity, and is defined as follows:</p>
<img alt="Eqs/fix_eos-cv.jpg" class="align-center" src="Eqs/fix_eos-cv.jpg" />
<p>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.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The fix <em>eos/cv</em> is only available if LAMMPS is built with the
USER-DPD package.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a>, <a class="reference internal" href="pair_dpd_fdt.html"><em>pair dpd/fdt</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="larentzos"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and
W.D. Mattson, &#8220;LAMMPS Implementation of Constant Energy Dissipative
Particle Dynamics (DPD-E)&#8221;, ARL-TR-6863, U.S. Army Research
Laboratory, Aberdeen Proving Ground, MD (2014).</p>
</div>
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"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
fix eos/cv command :h3
[Syntax:]
fix ID group-ID eos/cv cv :pre
ID, group-ID are documented in "fix"_fix.html command
eos/cv = style name of this fix command
cv = constant-volume heat capacity (energy/temperature units) :ul
[Examples:]
fix 1 all eos/cv 0.01 :pre
[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:
:c,image(Eqs/fix_eos-cv.jpg)
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.
:line
[Restrictions:]
The fix {eos/cv} is only available if LAMMPS is built with the
USER-DPD package.
[Related commands:]
"fix shardlow"_fix_shardlow.html, "pair dpd/fdt"_pair_dpd_fdt.html
[Default:] none
:line
:link(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).

288
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<div class="section" id="fix-eos-table-command">
<span id="index-0"></span><h1>fix eos/table command<a class="headerlink" href="#fix-eos-table-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID eos/table style file N keyword
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>eos/table = style name of this fix command</li>
<li>style = <em>linear</em> = method of interpolation</li>
<li>file = filename containing the tabulated equation of state</li>
<li>N = use N values in <em>linear</em> tables</li>
<li>keyword = name of table keyword correponding to table file</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix 1 all eos/table linear eos.table 100000 KEYWORD
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Fix <em>eos/table</em> applies a tabulated mesoparticle equation of state to
relate the particle internal energy (u_i) to the particle internal
temperature (dpdTheta_i).</p>
<p>Fix <em>eos/table</em> creates interpolation tables of length <em>N</em> from
internal energy values listed in a file as a function of internal
temperature.</p>
<p>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy values at each of <em>N</em> 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 <em>linear</em> style.</p>
<p>For the <em>linear</em> 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.</p>
<p>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.</p>
<hr class="docutils" />
<p>The format of a tabulated file is as follows (without the
parenthesized comments):</p>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># EOS TABLE (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>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
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; 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.</p>
<p>The next line lists the number of table entries. The parameter &#8220;N&#8221; is
required and its value is the number of table entries that follow.
Note that this may be different than the <em>N</em> specified in the <code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">eos/table</span></code> command. Let Ntable = <em>N</em> in the fix
command, and Nfile = &#8220;N&#8221; 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.</p>
<p>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).</p>
<p>Note that the internal temperature and internal energy values must
increase from one line to the next.</p>
<p>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.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The fix <em>eos/table</em> is only available if LAMMPS is built with the
USER-DPD package.</p>
<p>The equation of state must be a monotonically increasing function.</p>
<p>An exit error will occur if the internal temperature or internal
energies are not within the table cutoffs.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a>, <code class="xref doc docutils literal"><span class="pre">pair</span> <span class="pre">dpd/fdt</span></code></p>
<p><strong>Default:</strong> none</p>
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113
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@ -0,0 +1,113 @@
"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
fix eos/table command :h3
[Syntax:]
fix ID group-ID eos/table style file N keyword :pre
ID, group-ID are documented in "fix"_fix.html 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 :ul
[Examples:]
fix 1 all eos/table linear eos.table 100000 KEYWORD :pre
[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.
:line
The format of a tabulated file is as follows (without the
parenthesized comments):
# EOS TABLE (one or more comment or blank lines) :pre
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 :pre
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 "fix
eos/table"_fix_style.html 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.
:line
[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:]
"fix shardlow"_fix_shardlow.html, "pair dpd/fdt"_dpd_fdt.html
[Default:] none

36
doc/genindex.html
View File

@ -416,6 +416,14 @@
</dt>
<dt><a href="compute_dpd.html#index-0">compute dpd</a>
</dt>
<dt><a href="compute_dpd_atom.html#index-0">compute dpd/atom</a>
</dt>
<dt><a href="compute_erotate_asphere.html#index-0">compute erotate/asphere</a>
</dt>
@ -543,12 +551,12 @@
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
</dt>
@ -1018,6 +1026,14 @@
</dt>
<dt><a href="fix_eos_cv.html#index-0">fix eos/cv</a>
</dt>
<dt><a href="fix_eos_table.html#index-0">fix eos/table</a>
</dt>
<dt><a href="fix_evaporate.html#index-0">fix evaporate</a>
</dt>
@ -1312,6 +1328,10 @@
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<dt><a href="fix_shardlow.html#index-0">fix shardlow</a>
</dt>
<dt><a href="fix_smd.html#index-0">fix smd</a>
</dt>
@ -1724,6 +1744,14 @@
</dt>
<dt><a href="pair_dpd_conservative.html#index-0">pair_style dpd/conservative</a>
</dt>
<dt><a href="pair_dpd_fdt.html#index-0">pair_style dpd/fdt</a>
</dt>
<dt><a href="pair_dsmc.html#index-0">pair_style dsmc</a>
</dt>
@ -1827,12 +1855,12 @@
<dt><a href="pair_lj_sf.html#index-0">pair_style lj/sf</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
</dt>

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<div class="section" id="pair-style-body-rounded-polygon-command">
<span id="index-0"></span><h1>pair_style body/rounded/polygon command<a class="headerlink" href="#pair-style-body-rounded-polygon-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style body/rounded/polygon cutoff_global cutoff_inner delta_ua c_n
</pre></div>
</div>
<ul class="simple">
<li>cutoff_global = global cutoff for COM interactions (distance units)</li>
<li>cutoff_inner = cutoff for vertex-vertex and vertex-edge interactions (distance units)</li>
<li>delta_ua = characteristic contact length (distance units)</li>
<li>c_n = normal friction coefficient (energy time/distance^2)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style body/rounded/polygon 6.0 0.5 0.5 0.1
pair_coeff 1 1 1.0 100.0 12.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>body/rounded/polygon</em> implements the pairwise body/body
interactions between 2D convex polygons, as described
in <a class="reference internal" href="#fraige"><span>Fraige</span></a>. This pair style is designed for use with
the &#8220;rounded/polygon&#8221; body style, which is specified as
an argument to the &#8220;atom-style body/rounded/polygon&#8221; command.
See the <a class="reference internal" href="body.html"><em>body</em></a> doc page for more details about the body
styles LAMMPS supports.</p>
<p>The &#8220;rounded/polygon&#8221; style treats a body particle as a discrete
element model (DEM) polygon composed of N vertices.
The coordinates of a body particle are its center-of-mass (COM).
The initial position of the vertices are specified the data file.
The current implementation follows the multiple contact points model as
described in <a class="reference internal" href="#fraige"><span>Fraige</span></a>, but neglects and the contact history
the tangential contact forces for now.</p>
<p>The parameters <em>delta_ua</em> and <em>c_n</em> are the characteristic contact length
and the normal friction coefficient, respectively. See Eqs. (1) and (5)
in <a class="reference internal" href="#fraige"><span>Fraige</span></a> for more details.</p>
<p>For style <em>body/rounded/polygon</em>, the following coefficients
must be defined for each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
command as in the examples above:</p>
<ul class="simple">
<li>sigma = vertex rounded diameter (distance units)</li>
<li>k_n = normal repulsion strength (energy/distance^2)</li>
<li>k_na = normal attraction strength (energy/distance^2)</li>
<li>cutoff = cutoff for COM interactions (distance units)</li>
</ul>
<p>The last parameter is optional. If not specified, the global
cutoff specified in the pair_style command is used.</p>
<p>Note that the current implementation assumes that the edge length
of the polygons (L) should be at least twice greater than
the vertex rounded radius (sigma) so as to distinguish vertex-vertex from
vertex-edge contacts.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Because this pair style requires the body velocities to compute
the friction component of the forces, users should specify
<em>comm_modify vel yes</em> in the input script with this pair style.</p>
</div>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of this pair style can be mixed. The
default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for
details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the BODY package. It is only enabled if LAMMPS
was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Defining particles to be bodies so they participate in body/body or
body/particle interactions requires the use of the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a> command.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<p id="fraige"><strong>(Fraige)</strong> F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
Particuology, 6, 455 (2008).</p>
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<div class="section" id="pair-style-dpd-conservative-command">
<span id="index-0"></span><h1>pair_style dpd/conservative command<a class="headerlink" href="#pair-style-dpd-conservative-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style dpd/conservative cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for DPD interactions (distance units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style dpd/conservative 2.5
pair_coeff * * 3.0 2.5
pair_coeff 1 1 3.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>dpd/conservative</em> computes the conservative force for
dissipative particle dynamics (DPD). The conservative force on atom I
due to atom J is given by</p>
<img alt="Eqs/pair_dpd_conservative.jpg" class="align-center" src="Eqs/pair_dpd_conservative.jpg" />
<p>where the weighting factor, omega_ij, varies between 0 and 1, and is
chosen to have the following functional form:</p>
<img alt="Eqs/pair_dpd_omega.jpg" class="align-center" src="Eqs/pair_dpd_omega.jpg" />
<p>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.</p>
<p>Style <em>dpd/conservative</em> differs from the other dpd styles in that the
dissipative and random forces are not computed within the pair style.</p>
<p>For style <em>dpd/conservative</em>, 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.</p>
<p>Style <em>dpd/conservative</em> requires the following coefficients to be
defined for each pair of atoms types via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The pair style <em>dpd/conservative</em> is only available if LAMMPS is built
with the USER-DPD package.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="pair_dpd.html"><em>pair_dpd</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-dpd-fdt-command">
<span id="index-0"></span><h1>pair_style dpd/fdt command<a class="headerlink" href="#pair-style-dpd-fdt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-dpd-fdt-energy-command">
<h1>pair_style dpd/fdt/energy command<a class="headerlink" href="#pair-style-dpd-fdt-energy-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style style args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>dpd/fdt</em> or <em>dpd/fdt/energy</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>dpd/fdt</em> args = T cutoff seed
T = temperature (temperature units)
cutoff = global cutoff for DPD interactions (distance units)
seed = random # seed (positive integer)
<em>dpd/fdt/energy</em> args = cutoff seed
cutoff = global cutoff for DPD interactions (distance units)
seed = random # seed (positive integer)
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style dpd/fdt 300.0 2.5 34387
pair_coeff * * 3.0 1.0 2.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style dpd/fdt/energy 2.5 34387
pair_coeff * * 3.0 1.0 0.1 2.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> set the fluctuation-dissipation
theorem parameters and compute the conservative force for dissipative
particle dynamics (DPD). The conservative force on atom I due to atom
J is given by</p>
<img alt="Eqs/pair_dpd_conservative.jpg" class="align-center" src="Eqs/pair_dpd_conservative.jpg" />
<p>where the weighting factor, omega_ij, varies between 0 and 1, and is
chosen to have the following functional form:</p>
<img alt="Eqs/pair_dpd_omega.jpg" class="align-center" src="Eqs/pair_dpd_omega.jpg" />
<p>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.</p>
<p>These pair style differ from the other dpd styles in that the
dissipative and random forces are not computed within the pair style.
This style can be combined with the <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a>
to perform the stochastic integration of the dissipative and random
forces through the Shardlow splitting algorithm approach.</p>
<p>The pairwise energy associated with styles <em>dpd/fdt</em> and
<em>dpd/fdt/energy</em> is only due 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.</p>
<p>For style <em>dpd/fdt</em>, the fluctuation-dissipation theorem defines gamma
to be set equal to sigma*sigma/(2 T), where T is the set point
temperature specified as a pair style parameter in the above examples.
This style can be combined with <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a> to
perform DPD simulations under isothermal and isobaric conditions (see
<a class="reference internal" href="#lisal"><span>(Lisal)</span></a>). The following coefficients must be defined for
each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
as in the examples above, or in the data file or restart files read by
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>sigma (force*time^(1/2) units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used.</p>
<p>For style <em>dpd/fdt/energy</em>, the fluctuation-dissipation theorem
defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where
dpdTheta is the average internal temperature for the pair.
Furthermore, the fluctuation-dissipation defines alpha*alpha to be set
equal to 2*kB*kappa, where kappa is the mesoparticle thermal
conductivity parameter. This style can be combined with <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a> to perform DPD simulations under
isoenergetic and isoenthalpic conditions (see <a class="reference internal" href="#lisal"><span>(Lisal)</span></a>). The
following coefficients must be defined for each pair of atoms types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>sigma (force*time^(1/2) units)</li>
<li>kappa (1/time units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used.</p>
<p>For style <em>dpd/fdt/energy</em>, the particle internal temperature is
related to the particle internal energy through a mesoparticle
equation of state. Thus, an an additional <a class="reference internal" href="fix.html"><em>fix eos</em></a> must be
specified.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>Pair styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> are only available if
LAMMPS is built with the USER-DPD package.</p>
<p>Pair styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> require use of the
<code class="xref doc docutils literal"><span class="pre">communicate</span> <span class="pre">vel</span> <span class="pre">yes</span></code> option so that velocites are
stored by ghost atoms.</p>
<p>Pair style <em>dpd/fdt/energy</em> requires <a class="reference internal" href="atom_style.html"><em>atom_style dpd</em></a>
to be used in order to properly account for the particle internal
energies and temperatures.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="lisal"><strong>(Lisal)</strong> M. Lisal, J.K. Brennan, J. Bonet Avalos, &#8220;Dissipative
particle dynamics as isothermal, isobaric, isoenergetic, and
isoenthalpic conditions using Shardlow-like splitting algorithms.&#8221;,
J. Chem. Phys., 135, 204105 (2011).</p>
</div>
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@ -631,74 +631,78 @@ of analysis.</p>
<tr class="row-even"><td>dipole</td>
<td>atom-ID atom-type q x y z mux muy muz</td>
</tr>
<tr class="row-odd"><td>electron</td>
<tr class="row-odd"><td>dpd</td>
<td>atom-ID atom-type theta x y z</td>
</tr>
<tr class="row-even"><td>electron</td>
<td>atom-ID atom-type q spin eradius x y z</td>
</tr>
<tr class="row-even"><td>ellipsoid</td>
<tr class="row-odd"><td>ellipsoid</td>
<td>atom-ID atom-type ellipsoidflag density x y z</td>
</tr>
<tr class="row-odd"><td>full</td>
<tr class="row-even"><td>full</td>
<td>atom-ID molecule-ID atom-type q x y z</td>
</tr>
<tr class="row-even"><td>line</td>
<tr class="row-odd"><td>line</td>
<td>atom-ID molecule-ID atom-type lineflag density x y z</td>
</tr>
<tr class="row-odd"><td>meso</td>
<tr class="row-even"><td>meso</td>
<td>atom-ID atom-type rho e cv x y z</td>
</tr>
<tr class="row-even"><td>molecular</td>
<tr class="row-odd"><td>molecular</td>
<td>atom-ID molecule-ID atom-type x y z</td>
</tr>
<tr class="row-odd"><td>peri</td>
<tr class="row-even"><td>peri</td>
<td>atom-ID atom-type volume density x y z</td>
</tr>
<tr class="row-even"><td>smd</td>
<td>atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z</td>
<tr class="row-odd"><td>smd</td>
<td>atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z</td>
</tr>
<tr class="row-odd"><td>sphere</td>
<tr class="row-even"><td>sphere</td>
<td>atom-ID atom-type diameter density x y z</td>
</tr>
<tr class="row-even"><td>template</td>
<tr class="row-odd"><td>template</td>
<td>atom-ID molecule-ID template-index template-atom atom-type x y z</td>
</tr>
<tr class="row-odd"><td>tri</td>
<tr class="row-even"><td>tri</td>
<td>atom-ID molecule-ID atom-type triangleflag density x y z</td>
</tr>
<tr class="row-even"><td>wavepacket</td>
<tr class="row-odd"><td>wavepacket</td>
<td>atom-ID atom-type charge spin eradius etag cs_re cs_im x y z</td>
</tr>
<tr class="row-odd"><td>hybrid</td>
<tr class="row-even"><td>hybrid</td>
<td>atom-ID atom-type x y z sub-style1 sub-style2 ...</td>
</tr>
</tbody>
</table>
<p>The keywords have these meanings:</p>
<p>The per-atom values have these meanings and units, listed alphabetically:</p>
<ul class="simple">
<li>atom-ID = integer ID of atom</li>
<li>molecule-ID = integer ID of molecule the atom belongs to</li>
<li>atom-type = type of atom (1-Ntype)</li>
<li>q = charge on atom (charge units)</li>
<li>diameter = diameter of spherical atom (distance units)</li>
<li>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles</li>
<li>lineflag = 1 for line segment particles, 0 for point particles</li>
<li>triangleflag = 1 for triangular particles, 0 for point particles</li>
<li>bodyflag = 1 for body particles, 0 for point particles</li>
<li>template-index = which molecule within the molecule template the atom is part of</li>
<li>template-atom = which atom within a template molecule the atom is</li>
<li>density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)</li>
<li>mass = mass of particle (mass units)</li>
<li>volume = volume of particle (distance^3 units)</li>
<li>x,y,z = coordinates of atom</li>
<li>mux,muy,muz = components of dipole moment of atom (dipole units)</li>
<li>rho = density (need units) for SPH particles</li>
<li>e = energy (need units) for SPH particles</li>
<li>contact-radius = ??? (distance units)</li>
<li>cs_re,cs_im = real/imaginary parts of wavepacket coefficients</li>
<li>cv = heat capacity (need units) for SPH particles</li>
<li>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)</li>
<li>density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)</li>
<li>diameter = diameter of spherical atom (distance units)</li>
<li>e = energy (need units) for SPH particles</li>
<li>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles</li>
<li>eradius = electron radius (or fixed-core radius)</li>
<li>etag = integer ID of electron that each wavepacket belongs to</li>
<li>cs_re,cs_im = real/imaginary parts of wavepacket coefficients</li>
<li>kernel_radius = ??? (distance units)</li>
<li>contact_radius = ??? (distance units)</li>
<li>kernel-radius = ??? (distance units)</li>
<li>lineflag = 1 for line segment particles, 0 for point or spherical particles</li>
<li>mass = mass of particle (mass units)</li>
<li>molecule-ID = integer ID of molecule the atom belongs to</li>
<li>mux,muy,muz = components of dipole moment of atom (dipole units)</li>
<li>q = charge on atom (charge units)</li>
<li>rho = density (need units) for SPH particles</li>
<li>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)</li>
<li>template-atom = which atom within a template molecule the atom is</li>
<li>template-index = which molecule within the molecule template the atom is part of</li>
<li>theta = internal temperature of a DPD particle</li>
<li>triangleflag = 1 for triangular particles, 0 for point or sperhical particles</li>
<li>volume = volume of Peridynamic particle (distance^3 units)</li>
<li>x,y,z = coordinates of atom (distance units)</li>
</ul>
<p>The units for these quantities depend on the unit style; see the
<a class="reference internal" href="units.html"><em>units</em></a> command for details.</p>

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@ -135,7 +135,7 @@
<li>style = <em>atom</em> or <em>type</em> or <em>mol</em> or <em>group</em> or <em>region</em></li>
<li>ID = atom ID range or type range or mol ID range or group ID or region ID</li>
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or <em>length</em> or <em>tri</em> or <em>theta</em> or <em>theta/random</em> or <em>angmom</em> or <em>omega</em> or <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>meso/e</em> or <em>meso/cv</em> or <em>meso/rho</em> or <em>smd/contact/radius</em> or <em>smd/mass/density</em> or <em>i_name</em> or <em>d_name</em></li>
<li>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or <em>length</em> or <em>tri</em> or <em>theta</em> or <em>theta/random</em> or <em>angmom</em> or <em>omega</em> or <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>meso/e</em> or <em>meso/cv</em> or <em>meso/rho</em> or <em>smd/contact/radius</em> or <em>smd/mass/density</em> or <em>dpd/theta</em> or <em>i_name</em> or <em>d_name</em></li>
</ul>
<pre class="literal-block">
<em>type</em> value = atom type
@ -205,6 +205,7 @@
value can be an atom-style variable (see below)
<em>smd/mass/density</em> = set particle mass based on volume by providing a mass density
value can be an atom-style variable (see below)
<em>dpd/theta</em> value = internal temperature of DPD particles (temperature units)
<em>i_name</em> value = value for custom integer vector with name
<em>d_name</em> value = value for custom floating-point vector with name
</pre>
@ -462,6 +463,8 @@ prevent different individual physical bodies from penetrating each
other. Note that the SPH smoothing kernel diameter used for computing
long range, nonlocal interactions, is set using the <em>diameter</em>
keyword.</p>
<p>Keyword <em>dpd/theta</em> sets the internal temperature of a DPD particle
as defined by the USER-DPD package.</p>
<p>Keywords <em>i_name</em> and <em>d_name</em> refer to custom integer and
floating-point properties that have been added to each atom via the
<a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command. When that command