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doc/html/Section_accelerate.html
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@ -346,7 +346,7 @@ Lennard-Jones <a class="reference internal" href="pair_lj.html"><span class="doc
<p>To see what accelerate styles are currently available, see
<a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section_commands 5</span></a> of the manual. The
doc pages for individual commands (e.g. <a class="reference internal" href="pair_lj.html"><span class="doc">pair lj/cut</span></a> or
<span class="xref doc">fix nve</span>) also list any accelerated variants available
<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) also list any accelerated variants available
for that style.</p>
<p>To use an accelerator package in LAMMPS, and one or more of the styles
it provides, follow these general steps. Details vary from package to

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@ -679,7 +679,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="fix_npt_asphere.html"><span class="doc">npt/asphere (o)</span></a></td>
<td><a class="reference internal" href="fix_npt_body.html"><span class="doc">npt/body</span></a></td>
<td><a class="reference internal" href="fix_npt_sphere.html"><span class="doc">npt/sphere (o)</span></a></td>
<td><span class="xref doc">nve (ckio)</span></td>
<td><a class="reference internal" href="fix_nve.html"><span class="doc">nve (ckio)</span></a></td>
<td><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">nve/asphere (i)</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_nve_asphere_noforce.html"><span class="doc">nve/asphere/noforce</span></a></td>

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@ -1749,7 +1749,7 @@ do NOT perform time integration updates. Thus they should be used in
conjunction with a constant NVE integration fix such as these:</p>
</div>
<ul class="simple">
<li><span class="xref doc">fix nve</span></li>
<li><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a></li>
<li><a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a></li>
<li><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></li>
</ul>
@ -1816,7 +1816,7 @@ or read in via the <a class="reference internal" href="read_data.html"><span cla
they do not move at all, move together as a group at constant velocity
or in response to a net force acting on them, move in a prescribed
fashion (e.g. rotate around a point), etc. Note that if a time
integration fix like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>
integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>
is not used with the group that contains wall particles, their
positions and velocities will not be updated.</p>
<ul class="simple">

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doc/html/Section_packages.html
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@ -2329,7 +2329,7 @@ classical limits in the simulation.</p>
<p>See these two doc pages to get started:</p>
<p><a class="reference internal" href="fix_qtb.html"><span class="doc">fix qtb</span></a> provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
<p><a class="reference internal" href="fix_qbmsst.html"><span class="doc">fix qbmsst</span></a> enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.</p>

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doc/html/_sources/fix_nve.txt Normal file
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@ -0,0 +1,93 @@
.. index:: fix nve
fix nve command
===============
fix nve/cuda command
====================
fix nve/intel command
=====================
fix nve/kk command
==================
fix nve/omp command
===================
Syntax
""""""
.. parsed-literal::
fix ID group-ID nve
* ID, group-ID are documented in :doc:`fix <fix>` command
* nve = style name of this fix command
Examples
""""""""
.. parsed-literal::
fix 1 all nve
Description
"""""""""""
Perform constant NVE integration to update position and velocity for
atoms in the group each timestep. V is volume; E is energy. This
creates a system trajectory consistent with the microcanonical
ensemble.
----------
Styles with a *cuda*\ , *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See :doc:`Section_accelerate <Section_accelerate>` of the manual for
more instructions on how to use the accelerated styles effectively.
----------
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :ref:`output commands <howto_15>`. No parameter of this fix can
be used with the *start/stop* keywords of the :doc:`run <run>` command.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm

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doc/html/atom_modify.html
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@ -210,7 +210,7 @@ over the smaller set of atoms. Otherwise the reordering required by
this option will be a net slow-down. The <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify include</span></a> and <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify group</span></a>
commands are two examples of commands that require this setting to
work efficiently. Several <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, most notably time
integration fixes like <span class="xref doc">fix nve</span>, also take advantage of
integration fixes like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, also take advantage of
this setting if the group they operate on is the group specified by
this command. Note that specifying &#8220;all&#8221; as the group-ID effectively
turns off the <em>first</em> option.</p>

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doc/html/fix.html
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@ -166,7 +166,7 @@ underscores.</p>
<p class="last">The <a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a> command is the only way to turn off a
fix; simply specifying a new fix with a similar style will not turn
off the first one. This is especially important to realize for
integration fixes. For example, using a <span class="xref doc">fix nve</span>
integration fixes. For example, using a <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>
command for a second run after using a <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command
for the first run, will not cancel out the NVT time integration
invoked by the &#8220;fix nvt&#8221; command. Thus two time integrators would be
@ -318,7 +318,7 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span class=
<li><a class="reference internal" href="fix_npt_asphere.html"><span class="doc">npt/asphere</span></a> - NPT for aspherical particles</li>
<li><a class="reference internal" href="fix_nve_body.html"><span class="doc">npt/body</span></a> - NPT for body particles</li>
<li><a class="reference internal" href="fix_npt_sphere.html"><span class="doc">npt/sphere</span></a> - NPT for spherical particles</li>
<li><span class="xref doc">nve</span> - constant NVE time integration</li>
<li><a class="reference internal" href="fix_nve.html"><span class="doc">nve</span></a> - constant NVE time integration</li>
<li><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">nve/asphere</span></a> - NVE for aspherical particles</li>
<li><a class="reference internal" href="fix_nve_asphere_noforce.html"><span class="doc">nve/asphere/noforce</span></a> - NVE for aspherical particles without forces&#8221;</li>
<li><a class="reference internal" href="fix_nve_body.html"><span class="doc">nve/body</span></a> - NVE for body particles</li>

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doc/html/fix_drude_transform.html
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@ -208,7 +208,7 @@ atoms will simply not be transformed.</p>
<hr class="docutils" />
<p>This fix does NOT perform time integration. It only transform masses,
coordinates, velocities and forces. Thus you must use separate time
integration fixes, like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> to actually update the velocities and positions of
integration fixes, like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> to actually update the velocities and positions of
atoms. In order to thermalize the reduced degrees of freedom at
different temperatures, two Nose-Hoover thermostats must be defined,
acting on two distinct groups.</p>

2
doc/html/fix_gld.html
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@ -173,7 +173,7 @@ to be a Prony series.</p>
<p class="last">While this fix bears many similarities to <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, it has one significant
difference. Namely, <a class="reference internal" href="#"><span class="doc">fix gld</span></a> performs time integration,
whereas <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> does NOT. To this end, the
specification of another fix to perform time integration, such as <span class="xref doc">fix nve</span>, is NOT necessary.</p>
specification of another fix to perform time integration, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, is NOT necessary.</p>
</div>
<p>With this fix active, the force on the <em>j</em>th atom is given as</p>
<img alt="_images/fix_gld1.jpg" class="align-center" src="_images/fix_gld1.jpg" />

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doc/html/fix_gle.html
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@ -164,7 +164,7 @@ vibrational modes in the system to inexpensive (approximate)
modelling of nuclear quantum effects. Contrary to
<a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this fix performs both
thermostatting and evolution of the Hamiltonian equations of motion, so it
should not be used together with <span class="xref doc">fix nve</span> &#8211; at least not
should not be used together with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> &#8211; at least not
on the same atom groups.</p>
<p>Each degree of freedom in the thermostatted group is supplemented
with Ns additional degrees of freedom s, and the equations of motion

2
doc/html/fix_heat.html
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@ -209,7 +209,7 @@ energy change is 0.0 or use <a class="reference internal" href="fix_viscous.html
energy from the system.</p>
<p>This fix does not change the coordinates of its atoms; it only scales
their velocities. Thus you must still use an integration fix
(e.g. <span class="xref doc">fix nve</span>) on the affected atoms. This fix should
(e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) on the affected atoms. This fix should
not normally be used on atoms that have their temperature controlled
by another fix - e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> fix.</p>
</div>

2
doc/html/fix_ipi.html
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@ -193,7 +193,7 @@ environment.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a></p>
<hr class="docutils" />
<p id="ipicpc"><strong>(IPI-CPC)</strong> Ceriotti, More and Manolopoulos, Comp Phys Comm, 185,
1019-1026 (2014).</p>

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doc/html/fix_langevin.html
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@ -177,7 +177,7 @@
<h2>Description</h2>
<p>Apply a Langevin thermostat as described in <a class="reference internal" href="fix_langevin_eff.html#schneider"><span class="std std-ref">(Schneider)</span></a>
to a group of atoms which models an interaction with a background
implicit solvent. Used with <span class="xref doc">fix nve</span>, this command
implicit solvent. Used with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, this command
performs Brownian dynamics (BD), since the total force on each atom
will have the form:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">F</span> <span class="o">=</span> <span class="n">Fc</span> <span class="o">+</span> <span class="n">Ff</span> <span class="o">+</span> <span class="n">Fr</span>
@ -218,7 +218,7 @@ thermostatting takes place; see the description below.</p>
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies forces to effect
thermostatting. Thus you must use a separate time integration fix,
like <span class="xref doc">fix nve</span> to actually update the velocities and
like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the velocities and
positions of atoms using the modified forces. Likewise, this fix
should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> commands.</p>

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@ -209,7 +209,7 @@ from them before thermostating takes place; see the description below.</p>
<p class="last">Like the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command, this fix does
NOT perform time integration. It only modifies forces to effect
thermostating. Thus you must use a separate time integration fix, like
<span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
velocities and positions of atoms using the modified forces.
Likewise, this fix should not normally be used on atoms that also have
their temperature controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> commands.</p>

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@ -175,14 +175,14 @@ whose movement can influence nearby atoms.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The atoms affected by this fix should not normally be time
integrated by other fixes (e.g. <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>), since that will change their positions and
integrated by other fixes (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>), since that will change their positions and
velocities twice.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">As atoms move due to this fix, they will pass thru periodic
boundaries and be remapped to the other side of the simulation box,
just as they would during normal time integration (e.g. via the <span class="xref doc">fix nve</span> command). It is up to you to decide whether
just as they would during normal time integration (e.g. via the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command). It is up to you to decide whether
periodic boundaries are appropriate with the kind of atom motion you
are prescribing with this fix.</p>
</div>
@ -211,7 +211,7 @@ specified, <em>V</em> is the specified velocity vector with components
specified. This style also sets the velocity of each atom to V =
(Vx,Vy,Vz). If any of the velocity components is specified as NULL,
then the position and velocity of that component is time integrated
the same as the <span class="xref doc">fix nve</span> command would perform, using
the same as the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command would perform, using
the corresponding force component on the atom.</p>
<p>Note that the <em>linear</em> style is identical to using the <em>variable</em>
style with an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> that uses the
@ -234,7 +234,7 @@ elapsed since the fix was specified. This style also sets the
velocity of each atom to the time derivative of this expression. If
any of the amplitude components is specified as NULL, then the
position and velocity of that component is time integrated the same as
the <span class="xref doc">fix nve</span> command would perform, using the
the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command would perform, using the
corresponding force component on the atom.</p>
<p>Note that the <em>wiggle</em> style is identical to using the <em>variable</em>
style with <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> that use the
@ -282,7 +282,7 @@ atom.</p>
<p>Any of the 6 variables can be specified as NULL. If both the
displacement and velocity variables for a particular x,y,z component
are specified as NULL, then the position and velocity of that
component is time integrated the same as the <span class="xref doc">fix nve</span>
component is time integrated the same as the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>
command would perform, using the corresponding force component on the
atom. If only the velocity variable for a component is specified as
NULL, then the displacement variable will be used to set the position
@ -337,7 +337,7 @@ position and velocity of atoms on the outermost rRESPA level.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a></p>
<p><strong>Default:</strong> none</p>
<p>The option default is units = lattice.</p>
</div>

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doc/html/fix_nh.html
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@ -325,7 +325,7 @@ be used with care, since it can be unphysical to dilate some atoms and
not others, because it can introduce large, instantaneous
displacements between a pair of atoms (one dilated, one not) that are
far from the dilation origin. Also note that for atoms not in the fix
group, a separate time integration fix like <span class="xref doc">fix nve</span> or
group, a separate time integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or
<a class="reference internal" href="#"><span class="doc">fix nvt</span></a> can be used on them, independent of whether they
are dilated or not.</p>
<hr class="docutils" />
@ -494,7 +494,7 @@ become inefficient due to the highly skewed simulation box.</p>
<p class="last">Unlike the <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a> command
which performs thermostatting but NO time integration, these fixes
perform thermostatting/barostatting AND time integration. Thus you
should not use any other time integration fix, such as <span class="xref doc">fix nve</span> on atoms to which this fix is applied. Likewise,
should not use any other time integration fix, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> on atoms to which this fix is applied. Likewise,
fix nvt and fix npt should not normally be used on atoms that also
have their temperature controlled by another fix - e.g. by <a class="reference internal" href="#"><span class="doc">fix langevin</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>
commands.</p>
@ -706,7 +706,7 @@ over time or the atom count becomes very small.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>,
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>,
<a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a></p>
</div>
<div class="section" id="default">

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@ -221,7 +221,7 @@ the simulation. These can be overridden using the fix_modify keywords <em>e0</em
<p class="last">Unlike the <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a> command
which performs thermostatting but NO time integration, this fix
performs thermostatting/barostatting AND time integration. Thus you
should not use any other time integration fix, such as <span class="xref doc">fix nve</span> on atoms to which this fix is applied. Likewise,
should not use any other time integration fix, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> on atoms to which this fix is applied. Likewise,
this fix should not be used on atoms that have their temperature
controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix langevin</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> commands.</p>
</div>

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@ -0,0 +1,263 @@
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<div class="section" id="fix-nve-command">
<span id="index-0"></span><h1>fix nve command</h1>
</div>
<div class="section" id="fix-nve-cuda-command">
<h1>fix nve/cuda command</h1>
</div>
<div class="section" id="fix-nve-intel-command">
<h1>fix nve/intel command</h1>
</div>
<div class="section" id="fix-nve-kk-command">
<h1>fix nve/kk command</h1>
</div>
<div class="section" id="fix-nve-omp-command">
<h1>fix nve/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">nve</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>nve = style name of this fix command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Perform constant NVE integration to update position and velocity for
atoms in the group each timestep. V is volume; E is energy. This
creates a system trajectory consistent with the microcanonical
ensemble.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. 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>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
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4
doc/html/fix_nve_asphere.html
View File

@ -151,7 +151,7 @@
orientation, and angular velocity for aspherical particles in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.</p>
<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@ -192,7 +192,7 @@ shape attribute.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

4
doc/html/fix_nve_body.html
View File

@ -149,7 +149,7 @@ orientation, and angular velocity for body particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
consistent with the microcanonical ensemble. See <a class="reference internal" href="Section_howto.html#howto-14"><span class="std std-ref">Section_howto 14</span></a> of the manual and the <a class="reference internal" href="body.html"><span class="doc">body</span></a>
doc page for more details on using body particles.</p>
<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@ -172,7 +172,7 @@ point particles.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

4
doc/html/fix_nve_eff.html
View File

@ -147,7 +147,7 @@
<p>Perform constant NVE integration to update position and velocity for
nuclei and electrons in the group for the <a class="reference internal" href="pair_eff.html"><span class="doc">electron force field</span></a> model. V is volume; E is energy. This creates a
system trajectory consistent with the microcanonical ensemble.</p>
<p>The operation of this fix is exactly like that described by the <span class="xref doc">fix nve</span> command, except that the radius and radial velocity
<p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, except that the radius and radial velocity
of electrons are also updated.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@ -165,7 +165,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix nvt/eff</span></a>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix npt/eff</span></a></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix nvt/eff</span></a>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix npt/eff</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

4
doc/html/fix_nve_limit.html
View File

@ -164,7 +164,7 @@ missed on successive timesteps as atoms move. See the
for details.</p>
<p>Note that if a velocity reset occurs the integrator will not conserve
energy. On steps where no velocity resets occur, this integrator is
exactly like the <span class="xref doc">fix nve</span> command. Since forces are
exactly like the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command. Since forces are
unaltered, pressures computed by thermodynamic output will still be
very large for overlapped configurations.</p>
<div class="admonition note">
@ -202,7 +202,7 @@ the <a class="reference internal" href="run.html"><span class="doc">run</span></
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_noforce.html"><span class="doc">fix nve/noforce</span></a>,
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_noforce.html"><span class="doc">fix nve/noforce</span></a>,
<a class="reference internal" href="pair_soft.html"><span class="doc">pair_style soft</span></a></p>
<p><strong>Default:</strong> none</p>
</div>

4
doc/html/fix_nve_line.html
View File

@ -150,7 +150,7 @@ group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble. See
<a class="reference internal" href="Section_howto.html"><span class="doc">Section_howto 14</span></a> of the manual for an overview of
using line segment particles.</p>
<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@ -170,7 +170,7 @@ 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><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

2
doc/html/fix_nve_noforce.html
View File

@ -171,7 +171,7 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

4
doc/html/fix_nve_sphere.html
View File

@ -158,7 +158,7 @@
angular velocity for finite-size spherical particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
consistent with the microcanonical ensemble.</p>
<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
<p>If the <em>update</em> keyword is used with the <em>dipole</em> value, then the
orientation of the dipole moment of each particle is also updated
@ -203,7 +203,7 @@ be point particles.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

4
doc/html/fix_nve_tri.html
View File

@ -150,7 +150,7 @@ group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble. See
<a class="reference internal" href="Section_howto.html"><span class="doc">Section_howto 14</span></a> of the manual for an overview of
using triangular particles.</p>
<p>This fix differs from the <span class="xref doc">fix nve</span> command, which
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@ -170,7 +170,7 @@ 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><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

2
doc/html/fix_nvt_sllod.html
View File

@ -267,7 +267,7 @@ equilibration.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>, <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a></p>
</div>
<div class="section" id="default">

4
doc/html/fix_press_berendsen.html
View File

@ -175,7 +175,7 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
commands which perform Nose/Hoover barostatting AND time integration,
this fix does NOT perform time integration. It only modifies the box
size and atom coordinates to effect barostatting. Thus you must use a
separate time integration fix, like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> to actually update the positions and velocities of
separate time integration fix, like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> to actually update the positions and velocities of
atoms. This fix can be used in conjunction with thermostatting fixes
to control the temperature, such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> or <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a>.</p>
</div>
@ -316,7 +316,7 @@ various <a class="reference internal" href="Section_howto.html#howto-15"><span c
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a>,
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a>,
<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a></p>
</div>
<div class="section" id="default">

6
doc/html/fix_qtb.html
View File

@ -158,7 +158,7 @@
<h2>Description</h2>
<p>This command performs the quantum thermal bath scheme proposed by
<a class="reference internal" href="#dammak"><span class="std std-ref">(Dammak)</span></a> to include self-consistent quantum nuclear effects,
when used in conjunction with the <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> commands.</p>
when used in conjunction with the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> commands.</p>
<p>Classical molecular dynamics simulation does not include any quantum
nuclear effect. Quantum treatment of the vibrational modes will
introduce zero point energy into the system, alter the energy power
@ -241,7 +241,7 @@ Mbytes.</p>
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies forces to a colored
thermostat. Thus you must use a separate time integration fix, like
<span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
velocities and positions of atoms (as shown in the
examples). Likewise, this fix should not normally be used with other
fixes or commands that also specify system temperatures , e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> and <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>.</p>
@ -263,7 +263,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href="
<hr class="docutils" />
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, <a class="reference internal" href="fix_qbmsst.html"><span class="doc">fix qbmsst</span></a></p>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, <a class="reference internal" href="fix_qbmsst.html"><span class="doc">fix qbmsst</span></a></p>
</div>
<hr class="docutils" />
<div class="section" id="default">

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@ -187,7 +187,7 @@ velocities with zero aggregate linear and/or angular momentum.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This fix performs its operations at the same point in the
timestep as other time integration fixes, such as <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, or <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>.
timestep as other time integration fixes, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, or <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>.
Thus fix recenter should normally be the last such fix specified in
the input script, since the adjustments it makes to atom coordinates
should come after the changes made by time integration. LAMMPS will

10
doc/html/fix_rigid.html
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@ -288,10 +288,10 @@ differences may accumulate to produce divergent trajectories.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">You should not update the atoms in rigid bodies via other
time-integration fixes (e.g. <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>), or you will be integrating
time-integration fixes (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>), or you will be integrating
their motion more than once each timestep. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> should be used for the non-rigid particles.</p>
time integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> should be used for the non-rigid particles.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
@ -303,7 +303,7 @@ your time integration fix. E.g. use &#8220;fix 1 mobile nve&#8221; instead of
move. You can move atoms with a constant velocity by assigning them
an initial velocity (via the <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> command),
setting the force on them to 0.0 (via the <a class="reference internal" href="fix_setforce.html"><span class="doc">fix setforce</span></a> command), and integrating them as usual
(e.g. via the <span class="xref doc">fix nve</span> command).</p>
(e.g. via the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command).</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
@ -685,10 +685,10 @@ also accounted for by this fix.</p>
<hr class="docutils" />
<p>If your simlulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, and <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
rigid fixes can be used in tandem with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, and <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
<p>If you wish to perform NVE dynamics (no thermostatting or
barostatting), use fix rigid or fix rigid/nve to integrate the rigid
bodies, and <span class="xref doc">fix nve</span> to integrate the non-rigid
bodies, and <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to integrate the non-rigid
particles.</p>
<p>If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use fix rigid/nvt for the rigid bodies, and any

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@ -148,7 +148,7 @@
integrate the DPD equations of motion. The SSA splits the integration
into a stochastic and deterministic integration step. The fix
<em>shardlow</em> performs the stochastic integration step and must be used
in conjunction with a deterministic integrator (e.g. <span class="xref doc">fix nve</span> or <span class="xref doc">fix nph</span>). The stochastic
in conjunction with a deterministic integrator (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <span class="xref doc">fix nph</span>). 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 <a class="reference internal" href="pair_dpd_fdt.html#lisal"><span class="std std-ref">(Lisal)</span></a> and
@ -176,7 +176,7 @@ for more info.</p>
<p>This fix is currently limited to orthogonal simulation cell
geometries.</p>
<p>This fix must be used with an additional fix that specifies time
integration, e.g. <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
integration, e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
<p>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

4
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@ -184,7 +184,7 @@ time. Thus it is easy to specify a time-dependent temperature.</p>
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies velocities to effect
thermostatting. Thus you must use a separate time integration fix,
like <span class="xref doc">fix nve</span> to actually update the positions of atoms
like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the positions of atoms
using the modified velocities. Likewise, this fix should not normally
be used on atoms that also have their temperature controlled by
another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> commands.</p>
@ -270,7 +270,7 @@ over time or the atom count becomes very small.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>, <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>,
<a class="reference internal" href="fix_press_berendsen.html"><span class="doc">fix press/berendsen</span></a></p>
<p><strong>Default:</strong> none</p>

4
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@ -199,7 +199,7 @@ time. Thus it is easy to specify a time-dependent temperature.</p>
Nose/Hoover thermostatting AND time integration, these fixes do NOT
perform time integration. They only modify velocities to effect
thermostatting. Thus you must use a separate time integration fix,
like <span class="xref doc">fix nve</span> to actually update the positions of atoms
like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the positions of atoms
using the modified velocities. Likewise, these fixes should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> commands.</p>
@ -269,7 +269,7 @@ over time or the atom count becomes very small.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>, <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>,
<a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a></p>
<p><strong>Default:</strong> none</p>

2
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@ -193,7 +193,7 @@ value.</p>
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies velocities to effect
thermostatting. Thus you must use a separate time integration fix,
like <span class="xref doc">fix nve</span> to actually update the positions of atoms
like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the positions of atoms
using the modified velocities. Likewise, this fix should not normally
be used on atoms that also have their temperature controlled by
another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> commands.</p>

2
doc/html/fix_tfmc.html
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@ -192,7 +192,7 @@ Carlo algorithm and thus strictly speaking does not perform time
integration, it is similar in the sense that it uses the forces on all
atoms in order to update their positions. Therefore, it is implemented
as a time integration fix, and no other fixes of this type (such as
<span class="xref doc">fix nve</span>) should be used at the same time. Because
<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) should be used at the same time. Because
velocities do not play a role in this kind of Monte Carlo simulations,
instantaneous temperatures as calculated by <a class="reference internal" href="compute_temp.html"><span class="doc">temperature computes</span></a> or <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> have no meaning: the only relevant
temperature is the sampling temperature <em>Temp</em>. Similarly, performing

2
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@ -273,7 +273,7 @@ the electronic subsystem. The ordering of the Nx*Ny*Nz columns is
with the z index varing fastest, y the next fastest, and x the
slowest.</p>
<p>These fixes do not change the coordinates of their atoms; they only
scales their velocities. Thus a time integration fix (e.g. <span class="xref doc">fix nve</span>) should still be used to time integrate the affected
scales their velocities. Thus a time integration fix (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) should still be used to time integrate the affected
atoms. The fixes should not normally be used on atoms that have their
temperature controlled by another fix - e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or
<a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>.</p>

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@ -169,7 +169,7 @@ specified group and drive the system with an effective infinite-mass
piston capable of driving shock waves.</p>
<p>A momentum mirror technique is used, which means that if an atom (or
the wall) moves such that an atom is outside the wall on a timestep by
a distance delta (e.g. due to <span class="xref doc">fix nve</span>), then it is put
a distance delta (e.g. due to <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>), then it is put
back inside the face by the same delta, and the velocity relative to
the moving wall is flipped in z. For instance, a stationary particle
hit with a piston wall with velocity vz, will end the timestep with a

4
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@ -173,10 +173,10 @@
<p>Bound the simulation with one or more walls which reflect particles
in the specified group when they attempt to move thru them.</p>
<p>Reflection means that if an atom moves outside the wall on a timestep
by a distance delta (e.g. due to <span class="xref doc">fix nve</span>), then it is
by a distance delta (e.g. due to <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>), then it is
put back inside the face by the same delta, and the sign of the
corresponding component of its velocity is flipped.</p>
<p>When used in conjunction with <span class="xref doc">fix nve</span> and <a class="reference internal" href="run_style.html"><span class="doc">run_style verlet</span></a>, the resultant time-integration algorithm is
<p>When used in conjunction with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> and <a class="reference internal" href="run_style.html"><span class="doc">run_style verlet</span></a>, the resultant time-integration algorithm is
equivalent to the primitive splitting algorithm (PSA) described by
<a class="reference internal" href="#bond"><span class="std std-ref">Bond</span></a>. Because each reflection event divides
the corresponding timestep asymmetrically, energy conservation is only

4
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@ -1206,6 +1206,10 @@
</dt>
<dt><a href="fix_nve.html#index-0">fix nve</a>
</dt>
<dt><a href="fix_nve_asphere.html#index-0">fix nve/asphere</a>
</dt>

2
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@ -250,7 +250,7 @@ simulation.</p>
include and perform all the usual operations of an input script that
uses the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. There are a few exceptions and
points to consider, as discussed here.</p>
<p>Fixes that perform time integration, such as <span class="xref doc">fix nve</span> or
<p>Fixes that perform time integration, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or
<a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> are not invoked, since no time integration is
performed. Fixes that perturb or constrain the forces on atoms will
be invoked, just as they would during a normal run. Examples are <a class="reference internal" href="fix_indent.html"><span class="doc">fix indent</span></a> and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>. So you

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