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7
doc/html/_sources/compute_dpd.txt
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@ -55,8 +55,11 @@ 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>`.
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
This command also requires use of the :doc:`atom_style dpd <atom_style>`
command.
Related commands
""""""""""""""""

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doc/html/_sources/compute_dpd_atom.txt
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@ -46,8 +46,11 @@ Restrictions
""""""""""""
The compute *dpd/atom* is only available if LAMMPS is built with the
USER-DPD package.
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
This command also requires use of the :doc:`atom_style dpd <atom_style>`
command.
Related commands
""""""""""""""""

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doc/html/_sources/fix.txt
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@ -186,6 +186,7 @@ of :ref:`this page <cmd_5>`.
* :doc:`drag <fix_drag>` - drag atoms towards a defined coordinate
* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
* :doc:`efield <fix_efield>` - impose electric field on system
* :doc:`ehex <fix_ehex>` - ehanced heat exchange algorithm
* :doc:`enforce2d <fix_enforce2d>` - zero out z-dimension velocity and force
* :doc:`evaporate <fix_evaporate>` - remove atoms from simulation periodically
* :doc:`external <fix_external>` - callback to an external driver program

79
doc/html/_sources/fix_ehex.txt
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@ -71,69 +71,33 @@ hundred (LJ and SPC/E water) with little computational overhead.
In both algorithms (non-translational) kinetic energy is constantly
swapped between regions (reservoirs) to impose a heat flux onto the
system. The equations of motion are therefore modified if a particle
*i* is located inside a reservoir
.. image:: Eqs/fix_ehex01.jpg
:align: center
where
.. image:: Eqs/fix_ehex02.jpg
:align: center
We use
.. image:: Eqs/fix_ehex03.jpg
:align: center
to label those parts of the simulation box which are not
thermostatted.) The input parameter *region-ID* of this fix
corresponds to *k*\ . The energy swap is modelled by introducing an
:math:`i` is located inside a reservoir :math:`\Gamma_\ *k*\` where :math:`k>0`. We
use :math:`\Gamma_\ *0*\` to label those parts of the simulation box which
are not thermostatted.) The input parameter *region-ID* of this fix
corresponds to :math:`k`. The energy swap is modelled by introducing an
additional thermostatting force to the equations of motion, such that
the time evolution of coordinates and momenta of particle *i* becomes
:ref:`(Wirnsberger) <Wirnsberger>`
the time evolution of coordinates and momenta of particle :math:`i`
becomes :ref:`(Wirnsberger) <Wirnsberger>`
.. image:: Eqs/fix_ehex04.jpg
.. image:: src/Eqs/fix_ehex_eom.jpg
:align: center
The thermostatting force is given by
.. image:: Eqs/fix_ehex05.jpg
.. image:: src/Eqs/fix_ehex_f.jpg
:align: center
where
.. image:: Eqs/fix_ehex06.jpg
:align: center
is the mass and
.. image:: Eqs/fix_ehex07.jpg
:align: center
maps the particle position to the respective reservoir. The quantity
.. image:: Eqs/fix_ehex08.jpg
:align: center
corresponds to the input parameter *F*\ , which is the energy flux into
the reservoir. Furthermore,
.. image:: Eqs/fix_ehex09.jpg
:align: center
and
.. image:: Eqs/fix_ehex10.jpg
:align: center
denote the non-translational kinetic
energy and the centre of mass velocity of that reservoir. The
thermostatting force does not affect the centre of mass velocities of
the individual reservoirs and the entire simulation box. A derivation
of the equations and details on the numerical implementation with
velocity Verlet in LAMMPS can be found in reference
"(Wirnsberger)"#_Wirnsberger.
where :math:`m_i` is the mass and :math:`k(\mathbf r_i)` maps the particle
position to the respective reservoir. The quantity
:math:`F_*\Gamma_*k(\mathbf r_i)**` corresponds to the input parameter
*F*\ , which is the energy flux into the reservoir. Furthermore,
:math:`K_*\Gamma_*k(\mathbf r_i)**` and :math:`v_*\Gamma_*k(\mathbf r_i)**`
denote the non-translational kinetic energy and the centre of mass
velocity of that reservoir. The thermostatting force does not affect
the centre of mass velocities of the individual reservoirs and the
entire simulation box. A derivation of the equations and details on
the numerical implementation with velocity Verlet in LAMMPS can be
found in reference "(Wirnsberger)"#_Wirnsberger.
.. note::
@ -193,7 +157,7 @@ constraints will be satisfied.
bond distances, which goes to zero with order three in the
timestep. For example, in a simulation of SPC/E water with a timestep
of 2 fs the maximum relative error in the bond distances was found to
be on the order of :c,image(Eqs/fix_ehex07.jpg) for relatively large
be on the order of :math:`10^\ *-7*\` for relatively large
temperature gradients. A higher precision can be achieved by
decreasing the timestep.
@ -220,8 +184,7 @@ was built with that package. See the :ref:`Making LAMMPS <start_3>` section for
Related commands
""""""""""""""""
:doc:`fix heat <fix_heat>`, :doc:`fix thermal/conductivity <fix_thermal_conductivity>`,
:doc:`compute temp <compute_temp>`, :doc:`compute temp/region <compute_temp_region>`
:doc:`fix heat <fix_heat>`, :doc:`fix thermal/conductivity <fix_thermal_conductivity>`, :doc:`compute temp <compute_temp>`, :doc:`compute temp/region <compute_temp_region>`
**Default:** none

6
doc/html/compute_dpd.html
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@ -164,8 +164,10 @@ output options.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</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"><span class="doc">atom_style dpd</span></a>.</p>
<p>This command is part of the USER-DPD 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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
command.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

6
doc/html/compute_dpd_atom.html
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@ -162,8 +162,10 @@ and temperature (dpdTheta) <a class="reference internal" href="units.html"><span
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The compute <em>dpd/atom</em> is only available if LAMMPS is built with the
USER-DPD package.</p>
<p>This command is part of the USER-DPD 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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
command.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

1
doc/html/fix.html
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@ -292,6 +292,7 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span class=
<li><a class="reference internal" href="fix_drag.html"><span class="doc">drag</span></a> - drag atoms towards a defined coordinate</li>
<li><a class="reference internal" href="fix_dt_reset.html"><span class="doc">dt/reset</span></a> - reset the timestep based on velocity, forces</li>
<li><a class="reference internal" href="fix_efield.html"><span class="doc">efield</span></a> - impose electric field on system</li>
<li><a class="reference internal" href="fix_ehex.html"><span class="doc">ehex</span></a> - ehanced heat exchange algorithm</li>
<li><a class="reference internal" href="fix_enforce2d.html"><span class="doc">enforce2d</span></a> - zero out z-dimension velocity and force</li>
<li><a class="reference internal" href="fix_evaporate.html"><span class="doc">evaporate</span></a> - remove atoms from simulation periodically</li>
<li><a class="reference internal" href="fix_external.html"><span class="doc">external</span></a> - callback to an external driver program</li>

55
doc/html/fix_ehex.html
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@ -187,39 +187,27 @@ hundred (LJ and SPC/E water) with little computational overhead.</p>
<p>In both algorithms (non-translational) kinetic energy is constantly
swapped between regions (reservoirs) to impose a heat flux onto the
system. The equations of motion are therefore modified if a particle
<em>i</em> is located inside a reservoir</p>
<img alt="Eqs/fix_ehex01.jpg" class="align-center" src="Eqs/fix_ehex01.jpg" />
<p>where</p>
<img alt="Eqs/fix_ehex02.jpg" class="align-center" src="Eqs/fix_ehex02.jpg" />
<p>We use</p>
<img alt="Eqs/fix_ehex03.jpg" class="align-center" src="Eqs/fix_ehex03.jpg" />
<p>to label those parts of the simulation box which are not
thermostatted.) The input parameter <em>region-ID</em> of this fix
corresponds to <em>k</em>. The energy swap is modelled by introducing an
<span class="math">\(i\)</span> is located inside a reservoir <span class="math">\(\Gamma_\ *k*\` where :math:`k&gt;0\)</span>. We
use <span class="math">\(\Gamma_\ *0*\` to label those parts of the simulation box which
are not thermostatted.) The input parameter *region-ID* of this fix
corresponds to :math:`k\)</span>. The energy swap is modelled by introducing an
additional thermostatting force to the equations of motion, such that
the time evolution of coordinates and momenta of particle <em>i</em> becomes
<a class="reference internal" href="#wirnsberger"><span class="std std-ref">(Wirnsberger)</span></a></p>
<img alt="Eqs/fix_ehex04.jpg" class="align-center" src="Eqs/fix_ehex04.jpg" />
the time evolution of coordinates and momenta of particle <span class="math">\(i\)</span>
becomes <a class="reference internal" href="#wirnsberger"><span class="std std-ref">(Wirnsberger)</span></a></p>
<img alt="src/Eqs/fix_ehex_eom.jpg" class="align-center" src="src/Eqs/fix_ehex_eom.jpg" />
<p>The thermostatting force is given by</p>
<img alt="Eqs/fix_ehex05.jpg" class="align-center" src="Eqs/fix_ehex05.jpg" />
<p>where</p>
<img alt="Eqs/fix_ehex06.jpg" class="align-center" src="Eqs/fix_ehex06.jpg" />
<p>is the mass and</p>
<img alt="Eqs/fix_ehex07.jpg" class="align-center" src="Eqs/fix_ehex07.jpg" />
<p>maps the particle position to the respective reservoir. The quantity</p>
<img alt="Eqs/fix_ehex08.jpg" class="align-center" src="Eqs/fix_ehex08.jpg" />
<p>corresponds to the input parameter <em>F</em>, which is the energy flux into
the reservoir. Furthermore,</p>
<img alt="Eqs/fix_ehex09.jpg" class="align-center" src="Eqs/fix_ehex09.jpg" />
<p>and</p>
<img alt="Eqs/fix_ehex10.jpg" class="align-center" src="Eqs/fix_ehex10.jpg" />
<p>denote the non-translational kinetic
energy and the centre of mass velocity of that reservoir. The
thermostatting force does not affect the centre of mass velocities of
the individual reservoirs and the entire simulation box. A derivation
of the equations and details on the numerical implementation with
velocity Verlet in LAMMPS can be found in reference
&#8220;(Wirnsberger)&#8221;#_Wirnsberger.</p>
<img alt="src/Eqs/fix_ehex_f.jpg" class="align-center" src="src/Eqs/fix_ehex_f.jpg" />
<p>where <span class="math">\(m_i\)</span> is the mass and <span class="math">\(k(\mathbf r_i)\)</span> maps the particle
position to the respective reservoir. The quantity
<span class="math">\(F_*\Gamma_*k(\mathbf r_i)**\)</span> corresponds to the input parameter
<em>F</em>, which is the energy flux into the reservoir. Furthermore,
<span class="math">\(K_*\Gamma_*k(\mathbf r_i)**\)</span> and <span class="math">\(v_*\Gamma_*k(\mathbf r_i)**\)</span>
denote the non-translational kinetic energy and the centre of mass
velocity of that reservoir. The thermostatting force does not affect
the centre of mass velocities of the individual reservoirs and the
entire simulation box. A derivation of the equations and details on
the numerical implementation with velocity Verlet in LAMMPS can be
found in reference &#8220;(Wirnsberger)&#8221;#_Wirnsberger.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This fix only integrates the thermostatting force and must be
@ -270,7 +258,7 @@ implementation of the eHEX algorithm introduces a small error in the
bond distances, which goes to zero with order three in the
timestep. For example, in a simulation of SPC/E water with a timestep
of 2 fs the maximum relative error in the bond distances was found to
be on the order of :c,image(Eqs/fix_ehex07.jpg) for relatively large
be on the order of :math:<a href="#id1"><span class="problematic" id="id2">`</span></a>10^<em>-7</em>` for relatively large
temperature gradients. A higher precision can be achieved by
decreasing the timestep.</p>
</div>
@ -290,8 +278,7 @@ was built with that package. See the <a class="reference internal" href="Sectio
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a>, <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a>,
<a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>, <a class="reference internal" href="compute_temp_region.html"><span class="doc">compute temp/region</span></a></p>
<p><a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a>, <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a>, <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>, <a class="reference internal" href="compute_temp_region.html"><span class="doc">compute temp/region</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).</p>

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