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<div class="section" id="fix-npt-sphere-command">
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<span id="index-0"></span><h1>fix npt/sphere command<a class="headerlink" href="#fix-npt-sphere-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="fix-npt-sphere-omp-command">
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<h1>fix npt/sphere/omp command<a class="headerlink" href="#fix-npt-sphere-omp-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID npt/sphere keyword value ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>npt/sphere = style name of this fix command</li>
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<li>additional thermostat and barostat related keyword/value pairs from the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> command can be appended</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
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fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
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fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
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fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Perform constant NPT integration to update position, velocity, and
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angular velocity each timestep for finite-sizex spherical particles in
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the group using a Nose/Hoover temperature thermostat and Nose/Hoover
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pressure barostat. P is pressure; T is temperature. This creates a
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system trajectory consistent with the isothermal-isobaric ensemble.</p>
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<p>This fix differs from the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> command, which
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assumes point particles and only updates their position and velocity.</p>
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<p>The thermostat is applied to both the translational and rotational
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degrees of freedom for the spherical particles, assuming a compute is
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used which calculates a temperature that includes the rotational
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degrees of freedom (see below). The translational degrees of freedom
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can also have a bias velocity removed from them before thermostatting
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takes place; see the description below.</p>
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<p>Additional parameters affecting the thermostat and barostat are
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specified by keywords and values documented with the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> command. See, for example, discussion of the <em>temp</em>,
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<em>iso</em>, <em>aniso</em>, and <em>dilate</em> keywords.</p>
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<p>The particles in the fix group are the only ones whose velocities and
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positions are updated by the velocity/position update portion of the
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NPT integration.</p>
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<p>Regardless of what particles are in the fix group, a global pressure is
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computed for all particles. Similarly, when the size of the simulation
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box is changed, all particles are re-scaled to new positions, unless the
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keyword <em>dilate</em> is specified with a value of <em>partial</em>, in which case
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only the particles in the fix group are re-scaled. The latter can be
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useful for leaving the coordinates of particles in a solid substrate
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unchanged and controlling the pressure of a surrounding fluid.</p>
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<hr class="docutils" />
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<p>This fix computes a temperature and pressure each timestep. To do
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this, the fix creates its own computes of style “temp/sphere” and
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“pressure”, as if these commands had been issued:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute fix-ID_temp all temp/sphere
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compute fix-ID_press all pressure fix-ID_temp
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</pre></div>
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</div>
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<p>See the <a class="reference internal" href="compute_temp_sphere.html"><em>compute temp/sphere</em></a> and <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a> commands for details. Note that the
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IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
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+ underscore + “press”, and the group for the new computes is “all”
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since pressure is computed for the entire system.</p>
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<p>Note that these are NOT the computes used by thermodynamic output (see
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the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command) with ID = <em>thermo_temp</em>
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and <em>thermo_press</em>. This means you can change the attributes of this
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fix’s temperature or pressure via the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command or print this temperature
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or pressure during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command using the appropriate compute-ID.
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It also means that changing attributes of <em>thermo_temp</em> or
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<em>thermo_press</em> will have no effect on this fix.</p>
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<p>Like other fixes that perform thermostatting, this fix can be used
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with <a class="reference internal" href="compute.html"><em>compute commands</em></a> that calculate a temperature
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after removing a “bias” from the atom velocities. E.g. removing the
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center-of-mass velocity from a group of atoms or only calculating
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temperature on the x-component of velocity or only calculating
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temperature for atoms in a geometric region. This is not done by
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default, but only if the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual <a class="reference internal" href="compute.html"><em>compute commands</em></a> to determine which ones include a bias. In
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this case, the thermostat works in the following manner: the current
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temperature is calculated taking the bias into account, bias is
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removed from each atom, thermostatting is performed on the remaining
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thermal degrees of freedom, and the bias is added back in.</p>
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<hr class="docutils" />
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<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
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.</p>
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<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
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<p>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
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use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
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more instructions on how to use the accelerated styles effectively.</p>
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</div>
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>This fix writes the state of the Nose/Hoover thermostat and barostat
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to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. See the
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<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>temp</em> and <em>press</em> options are
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supported by this fix. You can use them to assign a
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<a class="reference internal" href="compute.html"><em>compute</em></a> you have defined to this fix which will be used
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in its thermostatting or barostatting procedure. If you do this, note
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that the kinetic energy derived from the compute temperature should be
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consistent with the virial term computed using all atoms for the
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pressure. LAMMPS will warn you if you choose to compute temperature
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on a subset of atoms.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option is supported by this
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fix to add the energy change induced by Nose/Hoover thermostatting and
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barostatting to the system’s potential energy as part of
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<a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>.</p>
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<p>This fix computes the same global scalar and global vector of
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quantities as does the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> command.</p>
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<p>This fix can ramp its target temperature and pressure over multiple
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runs, using the <em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a>
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command. See the <a class="reference internal" href="run.html"><em>run</em></a> command for details of how to do
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this.</p>
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<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>This fix requires that atoms store torque and angular velocity (omega)
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and a radius as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a>
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command.</p>
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<p>All particles in the group must be finite-size spheres. They cannot
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be point particles.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>, <a class="reference internal" href="fix_nve_sphere.html"><em>fix nve_sphere</em></a>, <a class="reference internal" href="fix_nvt_sphere.html"><em>fix nvt_sphere</em></a>, <a class="reference internal" href="fix_npt_asphere.html"><em>fix npt_asphere</em></a>, <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a></p>
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<p><strong>Default:</strong> none</p>
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